Sample records for em structure based

  1. Lipid environment of membrane proteins in cryo-EM based structural analysis. (United States)

    Mio, Kazuhiro; Sato, Chikara


    Cryoelectron microscopy (cryo-EM) in association with a single particle analysis method (SPA) is now a promising tool to determine the structures of proteins and their macromolecular complexes. The development of direct electron detection cameras and image processing technologies has allowed the structures of many important proteins to be solved at near-atomic resolution or, in some cases, at atomic resolution, by overcoming difficulties in crystallization or low yield of protein production. In the case of membrane-integrated proteins, the proteins were traditionally solubilized and stabilized with various kind of detergents. However, the density of detergent micelles diminished the contrast of membrane proteins in cryo-EM studies and made it difficult to obtain high-resolution structures. To improve the resolution of membrane protein structures in cryo-EM studies, major improvements have been made both in sample preparation techniques and in hardware and software developments. The focus of our review is on improvements which have been made in the various techniques for sample preparation for cryo-EM studies, with a specific interest placed on techniques for mimicking the lipid environment of membrane proteins.

  2. The <em>Chlamydiales> Pangenome Revisited: Structural Stability and Functional Coherence

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    Fotis E. Psomopoulos


    Full Text Available The entire publicly available set of 37 genome sequences from the bacterial order <em>Chlamydiales> has been subjected to comparative analysis in order to reveal the salient features of this pangenome and its evolutionary history. Over 2,000 protein families are detected across multiple species, with a distribution consistent to other studied pangenomes. Of these, there are 180 protein families with multiple members, 312 families with exactly 37 members corresponding to core genes, 428 families with peripheral genes with varying taxonomic distribution and finally 1,125 smaller families. The fact that, even for smaller genomes of <em>Chlamydiales>, core genes represent over a quarter of the average protein complement, signifies a certain degree of structural stability, given the wide range of phylogenetic relationships within the group. In addition, the propagation of a corpus of manually curated annotations within the discovered core families reveals key functional properties, reflecting a coherent repertoire of cellular capabilities for <em>Chlamydiales>. We further investigate over 2,000 genes without homologs in the pangenome and discover two new protein sequence domains. Our results, supported by the genome-based phylogeny for this group, are fully consistent with previous analyses and current knowledge, and point to future research directions towards a better understanding of the structural and functional properties of <em>Chlamydiales>.

  3. High Performance Computing of Complex Electromagnetic Algorithms Based on GPU/CPU Heterogeneous Platform and Its Applications to EM Scattering and Multilayered Medium Structure

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    Zhe Song


    Full Text Available The fast and accurate numerical analysis for large-scale objects and complex structures is essential to electromagnetic simulation and design. Comparing to the exploration in EM algorithms from mathematical point of view, the computer programming realization is coordinately significant while keeping up with the development of hardware architectures. Unlike the previous parallel algorithms or those implemented by means of parallel programming on multicore CPU with OpenMP or on a cluster of computers with MPI, the new type of large-scale parallel processor based on graphics processing unit (GPU has shown impressive ability in various scenarios of supercomputing, while its application in computational electromagnetics is especially expected. This paper introduces our recent work on high performance computing based on GPU/CPU heterogeneous platform and its application to EM scattering problems and planar multilayered medium structure, including a novel realization of OpenMP-CUDA-MLFMM, a developed ACA method and a deeply optimized CG-FFT method. With fruitful numerical examples and their obvious enhancement in efficiencies, it is convincing to keep on deeply investigating and understanding the computer hardware and their operating mechanism in the future.

  4. Structural Analysis of Hypothetical Proteins from <em>Helicobacter pyloriem>: An Approach to Estimate Functions of Unknown or Hypothetical Proteins

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    Bong-Jin Lee


    Full Text Available <em>Helicobacter pylori em>(>H. pyloriem> have a unique ability to survive in extreme acidic environments and to colonize the gastric mucosa. It can cause diverse gastric diseases such as peptic ulcers, chronic gastritis, mucosa-associated lymphoid tissue (MALT lymphoma, gastric cancer, <em>etc>. Based on genomic research of <em>H. pyloriem>, over 1600 genes have been functionally identified so far. However, <em>H. pyloriem> possess some genes that are uncharacterized since: (i the gene sequences are quite new; (ii the function of genes have not been characterized in any other bacterial systems; and (iii sometimes, the protein that is classified into a known protein based on the sequence homology shows some functional ambiguity, which raises questions about the function of the protein produced in <em>H. pyloriem>. Thus, there are still a lot of genes to be biologically or biochemically characterized to understand the whole picture of gene functions in the bacteria. In this regard, knowledge on the 3D structure of a protein, especially unknown or hypothetical protein, is frequently useful to elucidate the structure-function relationship of the uncharacterized gene product. That is, a structural comparison with known proteins provides valuable information to help predict the cellular functions of hypothetical proteins. Here, we show the 3D structures of some hypothetical proteins determined by NMR spectroscopy and X-ray crystallography as a part of the structural genomics of <em>H. pyloriem>. In addition, we show some successful approaches of elucidating the function of unknown proteins based on their structural information.

  5. Cryo-EM structures of tau filaments from Alzheimer's disease. (United States)

    Fitzpatrick, Anthony W P; Falcon, Benjamin; He, Shaoda; Murzin, Alexey G; Murshudov, Garib; Garringer, Holly J; Crowther, R Anthony; Ghetti, Bernardino; Goedert, Michel; Scheres, Sjors H W


    Alzheimer's disease is the most common neurodegenerative disease, and there are no mechanism-based therapies. The disease is defined by the presence of abundant neurofibrillary lesions and neuritic plaques in the cerebral cortex. Neurofibrillary lesions comprise paired helical and straight tau filaments, whereas tau filaments with different morphologies characterize other neurodegenerative diseases. No high-resolution structures of tau filaments are available. Here we present cryo-electron microscopy (cryo-EM) maps at 3.4-3.5 Å resolution and corresponding atomic models of paired helical and straight filaments from the brain of an individual with Alzheimer's disease. Filament cores are made of two identical protofilaments comprising residues 306-378 of tau protein, which adopt a combined cross-β/β-helix structure and define the seed for tau aggregation. Paired helical and straight filaments differ in their inter-protofilament packing, showing that they are ultrastructural polymorphs. These findings demonstrate that cryo-EM allows atomic characterization of amyloid filaments from patient-derived material, and pave the way for investigation of a range of neurodegenerative diseases.

  6. Structure of the E. coli ribosome-EF-Tu complex at EM. (United States)

    Fischer, Niels; Neumann, Piotr; Konevega, Andrey L; Bock, Lars V; Ficner, Ralf; Rodnina, Marina V; Stark, Holger


    Single particle electron cryomicroscopy (cryo-EM) has recently made significant progress in high-resolution structure determination of macromolecular complexes due to improvements in electron microscopic instrumentation and computational image analysis. However, cryo-EM structures can be highly non-uniform in local resolution and all structures available to date have been limited to resolutions above 3 Å. Here we present the cryo-EM structure of the 70S ribosome from Escherichia coli in complex with elongation factor Tu, aminoacyl-tRNA and the antibiotic kirromycin at 2.65-2.9 Å resolution using spherical aberration (Cs)-corrected cryo-EM. Overall, the cryo-EM reconstruction at 2.9 Å resolution is comparable to the best-resolved X-ray structure of the E. coli 70S ribosome (2.8 Å), but provides more detailed information (2.65 Å) at the functionally important ribosomal core. The cryo-EM map elucidates for the first time the structure of all 35 rRNA modifications in the bacterial ribosome, explaining their roles in fine-tuning ribosome structure and function and modulating the action of antibiotics. We also obtained atomic models for flexible parts of the ribosome such as ribosomal proteins L9 and L31. The refined cryo-EM-based model presents the currently most complete high-resolution structure of the E. coli ribosome, which demonstrates the power of cryo-EM in structure determination of large and dynamic macromolecular complexes.

  7. Accelerated cryo-EM structure determination with parallelisation using GPUs in RELION-2. (United States)

    Kimanius, Dari; Forsberg, Björn O; Scheres, Sjors Hw; Lindahl, Erik


    By reaching near-atomic resolution for a wide range of specimens, single-particle cryo-EM structure determination is transforming structural biology. However, the necessary calculations come at large computational costs, which has introduced a bottleneck that is currently limiting throughput and the development of new methods. Here, we present an implementation of the RELION image processing software that uses graphics processors (GPUs) to address the most computationally intensive steps of its cryo-EM structure determination workflow. Both image classification and high-resolution refinement have been accelerated more than an order-of-magnitude, and template-based particle selection has been accelerated well over two orders-of-magnitude on desktop hardware. Memory requirements on GPUs have been reduced to fit widely available hardware, and we show that the use of single precision arithmetic does not adversely affect results. This enables high-resolution cryo-EM structure determination in a matter of days on a single workstation.

  8. Refinement of Atomic Structures Against cryo-EM Maps. (United States)

    Murshudov, G N


    This review describes some of the methods for atomic structure refinement (fitting) against medium/high-resolution single-particle cryo-EM reconstructed maps. Some of the tools developed for macromolecular X-ray crystal structure analysis, especially those encapsulating prior chemical and structural information can be transferred directly for fitting into cryo-EM maps. However, despite the similarities, there are significant differences between data produced by these two techniques; therefore, different likelihood functions linking the data and model must be used in cryo-EM and crystallographic refinement. Although tools described in this review are mostly designed for medium/high-resolution maps, if maps have sufficiently good quality, then these tools can also be used at moderately low resolution, as shown in one example. In addition, the use of several popular crystallographic methods is strongly discouraged in cryo-EM refinement, such as 2Fo-Fc maps, solvent flattening, and feature-enhanced maps (FEMs) for visualization and model (re)building. Two problems in the cryo-EM field are overclaiming resolution and severe map oversharpening. Both of these should be avoided; if data of higher resolution than the signal are used, then overfitting of model parameters into the noise is unavoidable, and if maps are oversharpened, then at least parts of the maps might become very noisy and ultimately uninterpretable. Both of these may result in suboptimal and even misleading atomic models. © 2016 Elsevier Inc. All rights reserved.

  9. Focused classification and refinement in high-resolution cryo-EM structural analysis of ribosome complexes. (United States)

    von Loeffelholz, Ottilie; Natchiar, S Kundhavai; Djabeur, Nadia; Myasnikov, Alexander G; Kratzat, Hanna; Ménétret, Jean-François; Hazemann, Isabelle; Klaholz, Bruno P


    Cryo electron microscopy (cryo-EM) historically has had a strong impact on the structural and mechanistic analysis of protein synthesis by the prokaryotic and eukaryotic ribosomes. Vice versa, studying ribosomes has helped moving forwards many methodological aspects in single particle cryo-EM, at the level of automated data collection and image processing including advanced techniques for particle sorting to address structural and compositional heterogeneity. Here we review some of the latest ribosome structures, where cryo-EM allowed gaining unprecedented insights based on 3D structure sorting with focused classification and refinement methods helping to reach local resolution levels better than 3Å. Such high-resolution features now enable the analysis of drug interactions with RNA and protein side-chains including even the visualization of chemical modifications of the ribosomal RNA. These advances represent a major breakthrough in structural biology and show the strong potential of cryo-EM beyond the ribosome field including for structure-based drug design. Copyright © 2017 Elsevier Ltd. All rights reserved.

  10. Unravelling the structures of biological macromolecules by cryo-EM (United States)

    Fernandez-Leiro, Rafael; Scheres, Sjors H.W.


    Preface Understanding how proteins and other biological macromolecules perform their complicated tasks in the living cell is often aided by knowledge of their three-dimensional structures. Because many tasks involve the cleavage or formation of chemical bonds, structural characterisation at the atomic level is most useful. Recent developments in electron microscopy of frozen hydrated samples (cryo-EM) have provided unprecedented opportunities for the structural characterization of biological macromolecules. This is resulting in a wave of new information about biological processes that were impossible to characterize with previously existing techniques in structural biology. PMID:27629640

  11. Structural Composites With Tuned EM Chirality (United States)


    First  copper  wires  braided  with   Kevlar  and  nylon  to  form  conductive  coils  are   woven   among   structural... fiber   to   create   a   fabric.   This   yielded   a   composite   with   all   coils   possessing   the   same

  12. Model-based local density sharpening of cryo-EM maps (United States)

    Jakobi, Arjen J; Wilmanns, Matthias


    Atomic models based on high-resolution density maps are the ultimate result of the cryo-EM structure determination process. Here, we introduce a general procedure for local sharpening of cryo-EM density maps based on prior knowledge of an atomic reference structure. The procedure optimizes contrast of cryo-EM densities by amplitude scaling against the radially averaged local falloff estimated from a windowed reference model. By testing the procedure using six cryo-EM structures of TRPV1, β-galactosidase, γ-secretase, ribosome-EF-Tu complex, 20S proteasome and RNA polymerase III, we illustrate how local sharpening can increase interpretability of density maps in particular in cases of resolution variation and facilitates model building and atomic model refinement. PMID:29058676

  13. Model-based local density sharpening of cryo-EM maps. (United States)

    Jakobi, Arjen J; Wilmanns, Matthias; Sachse, Carsten


    Atomic models based on high-resolution density maps are the ultimate result of the cryo-EM structure determination process. Here, we introduce a general procedure for local sharpening of cryo-EM density maps based on prior knowledge of an atomic reference structure. The procedure optimizes contrast of cryo-EM densities by amplitude scaling against the radially averaged local falloff estimated from a windowed reference model. By testing the procedure using six cryo-EM structures of TRPV1, β-galactosidase, γ-secretase, ribosome-EF-Tu complex, 20S proteasome and RNA polymerase III, we illustrate how local sharpening can increase interpretability of density maps in particular in cases of resolution variation and facilitates model building and atomic model refinement.


    Directory of Open Access Journals (Sweden)

    Maria José da Silva Feitosa


    Full Text Available Nos últimos anos intensificaram-se os estudos referentes às bases do comprometimento organizacional, contempladas no modelo Meyer e Allen. Nessa perfectiva, o presente estudo objetiva verificar as bases afetiva, normativa e instrumental em duas empresas de consultoria. Para tanto, foi realizada uma pesquisa descritiva, de abordagem quantitativa. Os resultados apontam que a base afetiva se destacou em ambas as empresas, tanto em uma análise por gênero, quanto em uma perspectiva geral. Esse resultado pode estar relacionado à possibilidade de que os estudantes que ingressam em empresas juniores se entusiasmem com a oportunidade de aplicar seus conhecimentos e se comprometam de forma afetiva com a organização. No entanto, para testar essa relação sugere-se a realização de novos estudos.

  15. Structural Analysis of Plate Based Tensegrity Structures

    DEFF Research Database (Denmark)

    Hald, Frederik; Kirkegaard, Poul Henning; Damkilde, Lars


    Plate tensegrity structures combine tension cables with a cross laminated timber plate and can then form e.g. a roof structure. The topology of plate tensegrity structures is investigated through a parametric investigation. Plate tensegrity structures are investigated, and a method...... for determination of the structures pre-stresses is used. A parametric investigation is performed to determine a more optimized form of the plate based tensegrity structure. Conclusions of the use of plate based tensegrity in civil engineering and further research areas are discussed....

  16. Iterative Molecular Dynamics-Rosetta Membrane Protein Structure Refinement Guided by Cryo-EM Densities. (United States)

    Leelananda, Sumudu P; Lindert, Steffen


    Knowing atomistic details of proteins is essential not only for the understanding of protein function but also for the development of drugs. Experimental methods such as X-ray crystallography, NMR, and cryo-electron microscopy (cryo-EM) are the preferred forms of protein structure determination and have achieved great success over the most recent decades. Computational methods may be an alternative when experimental techniques fail. However, computational methods are severely limited when it comes to predicting larger macromolecule structures with little sequence similarity to known structures. The incorporation of experimental restraints in computational methods is becoming increasingly important to more reliably predict protein structure. One such experimental input used in structure prediction and refinement is cryo-EM densities. Recent advances in cryo-EM have arguably revolutionized the field of structural biology. Our previously developed cryo-EM-guided Rosetta-MD protocol has shown great promise in the refinement of soluble protein structures. In this study, we extended cryo-EM density-guided iterative Rosetta-MD to membrane proteins. We also improved the methodology in general by picking models based on a combination of their score and fit-to-density during the Rosetta model selection. By doing so, we have been able to pick models superior to those with the previous selection based on Rosetta score only and we have been able to further improve our previously refined models of soluble proteins. The method was tested with five membrane spanning protein structures. By applying density-guided Rosetta-MD iteratively we were able to refine the predicted structures of these membrane proteins to atomic resolutions. We also showed that the resolution of the density maps determines the improvement and quality of the refined models. By incorporating high-resolution density maps (∼4 Å), we were able to more significantly improve the quality of the models than when

  17. Stochastic EM-based TFBS motif discovery with MITSU. (United States)

    Kilpatrick, Alastair M; Ward, Bruce; Aitken, Stuart


    The Expectation-Maximization (EM) algorithm has been successfully applied to the problem of transcription factor binding site (TFBS) motif discovery and underlies the most widely used motif discovery algorithms. In the wider field of probabilistic modelling, the stochastic EM (sEM) algorithm has been used to overcome some of the limitations of the EM algorithm; however, the application of sEM to motif discovery has not been fully explored. We present MITSU (Motif discovery by ITerative Sampling and Updating), a novel algorithm for motif discovery, which combines sEM with an improved approximation to the likelihood function, which is unconstrained with regard to the distribution of motif occurrences within the input dataset. The algorithm is evaluated quantitatively on realistic synthetic data and several collections of characterized prokaryotic TFBS motifs and shown to outperform EM and an alternative sEM-based algorithm, particularly in terms of site-level positive predictive value. Java executable available for download at, supported on Linux/OS X. © The Author 2014. Published by Oxford University Press.

  18. <em>Salmonella> source attribution based on microbial subtyping

    DEFF Research Database (Denmark)

    Barco, Lisa; Barrucci, Federica; Olsen, John Elmerdahl


    source attribution models have been implemented by using serotyping and phage-typing data. Molecular-based methods may prove to be similarly valuable in the future, as already demonstrated for other food-borne pathogens like Campylobacter. This review assesses the state of the art concerning Salmonella...... source attribution through microbial subtyping approach. It summarizes the available microbial subtyping attribution models and discusses the use of conventional phenotypic typing methods, as well as of the most commonly applied molecular typing methods in the European Union (EU) laboratories...

  19. A fragment based method for modeling of protein segments into cryo-EM density maps. (United States)

    Ismer, Jochen; Rose, Alexander S; Tiemann, Johanna K S; Hildebrand, Peter W


    Single-particle analysis of electron cryo-microscopy (cryo-EM) is a key technology for elucidation of macromolecular structures. Recent technical advances in hardware and software developments significantly enhanced the resolution of cryo-EM density maps and broadened the applicability and the circle of users. To facilitate modeling of macromolecules into cryo-EM density maps, fast and easy to use methods for modeling are now demanded. Here we investigated and benchmarked the suitability of a classical and well established fragment-based approach for modeling of segments into cryo-EM density maps (termed FragFit). FragFit uses a hierarchical strategy to select fragments from a pre-calculated set of billions of fragments derived from structures deposited in the Protein Data Bank, based on sequence similarly, fit of stem atoms and fit to a cryo-EM density map. The user only has to specify the sequence of the segment and the number of the N- and C-terminal stem-residues in the protein. Using a representative data set of protein structures, we show that protein segments can be accurately modeled into cryo-EM density maps of different resolution by FragFit. Prediction quality depends on segment length, the type of secondary structure of the segment and local quality of the map. Fast and automated calculation of FragFit renders it applicable for implementation of interactive web-applications e.g. to model missing segments, flexible protein parts or hinge-regions into cryo-EM density maps.

  20. Antibody-based affinity cryo-EM grid. (United States)

    Yu, Guimei; Li, Kunpeng; Jiang, Wen


    The Affinity Grid technique combines sample purification and cryo-Electron Microscopy (cryo-EM) grid preparation into a single step. Several types of affinity surfaces, including functionalized lipids monolayers, streptavidin 2D crystals, and covalently functionalized carbon surfaces have been reported. More recently, we presented a new affinity cryo-EM approach, cryo-SPIEM, which applies the traditional Solid Phase Immune Electron Microscopy (SPIEM) technique to cryo-EM. This approach significantly simplifies the preparation of affinity grids and directly works with native macromolecular complexes without need of target modifications. With wide availability of high affinity and high specificity antibodies, the antibody-based affinity grid would enable cryo-EM studies of the native samples directly from cell cultures, targets of low abundance, and unstable or short-lived intermediate states. Copyright © 2016 Elsevier Inc. All rights reserved.

  1. Reliability based structural design

    NARCIS (Netherlands)

    Vrouwenvelder, A.C.W.M.


    According to ISO 2394, structures shall be designed, constructed and maintained in such a way that they are suited for their use during the design working life in an economic way. To fulfil this requirement one needs insight into the risk and reliability under expected and non-expected actions. A

  2. Solution NMR Structure of Hypothetical Protein CV_2116 Encoded by a Viral Prophage Element in <em>Chromobacterium violaceumem>

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    Yunhuang Yang


    Full Text Available CV_2116 is a small hypothetical protein of 82 amino acids from the Gram-negative coccobacillus <em>Chromobacterium violaceumem>. A PSI-BLAST search using the CV_2116 sequence as a query identified only one hit (E = 2e−07 corresponding to a hypothetical protein OR16_04617 from <em>Cupriavidus basilensisem> OR16, which failed to provide insight into the function of CV_2116. The <em>CV_2116em> gene was cloned into the p15TvLic expression plasmid, transformed into <em>E. coliem>, and 13C- and 15N-labeled NMR samples of CV_2116 were overexpressed in <em>E. coliem> and purified for structure determination using NMR spectroscopy. The resulting high-quality solution NMR structure of CV_2116 revealed a novel α + β fold containing two anti-parallel β -sheets in the <em>N>-terminal two-thirds of the protein and one α-helix in the <em>C>-terminal third of the protein. CV_2116 does not belong to any known protein sequence family and a Dali search indicated that no similar structures exist in the protein data bank. Although no function of CV_2116 could be derived from either sequence or structural similarity searches, the neighboring genes of <em>CV_2116em> encode various proteins annotated as similar to bacteriophage tail assembly proteins. Interestingly, <em>C. violaceumem> exhibits an extensive network of bacteriophage tail-like structures that likely result from lateral gene transfer by incorporation of viral DNA into its genome (prophages due to bacteriophage infection. Indeed, <em>C. violaceumem> has been shown to contain four prophage elements and <em>CV_2116em> resides in the fourth of these elements. Analysis of the putative operon in which CV_2116 resides indicates that CV_2116 might be a component of the bacteriophage tail-like assembly that occurs in <em>C. violaceumem>.

  3. Gene Sequence Based Clustering Assists in Dereplication of <em>Pseudoalteromonas luteoviolaceaem> Strains with Identical Inhibitory Activity and Antibiotic Production

    Directory of Open Access Journals (Sweden)

    Lone Gram


    Full Text Available Some microbial species are chemically homogenous, and the same secondary metabolites are found in all strains. In contrast, we previously found that five strains of <em>P. luteoviolacea em>were closely related by 16S rRNA gene sequence but produced two different antibiotic profiles. The purpose of the present study was to determine whether such bioactivity differences could be linked to genotypes allowing methods from phylogenetic analysis to aid in selection of strains for biodiscovery. Thirteen <em>P. luteoviolacea em>strains divided into three chemotypes based on production of known antibiotics and four antibacterial profiles based on inhibition assays against <em>Vibrio anguillarum em>and <em>Staphylococcus aureusem>. To determine whether chemotype and inhibition profile are reflected by phylogenetic clustering we sequenced 16S rRNA, <em>gyrB em>and <em>recA em>genes. Clustering based on 16S rRNA gene sequences alone showed little correlation to chemotypes and inhibition profiles, while clustering based on concatenated 16S rRNA, <em>gyrB,> em>and <em>recA em>gene sequences resulted in three clusters, two of which uniformly consisted of strains of identical chemotype and inhibition profile. A major time sink in natural products discovery is the effort spent rediscovering known compounds, and this study indicates that phylogeny clustering of bioactive species has the potential to be a useful dereplication tool in biodiscovery efforts.

  4. Single-particle cryo-EM using alignment by classification (ABC: the structure of Lumbricus terrestris haemoglobin

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    Pavel Afanasyev


    Full Text Available Single-particle cryogenic electron microscopy (cryo-EM can now yield near-atomic resolution structures of biological complexes. However, the reference-based alignment algorithms commonly used in cryo-EM suffer from reference bias, limiting their applicability (also known as the `Einstein from random noise' problem. Low-dose cryo-EM therefore requires robust and objective approaches to reveal the structural information contained in the extremely noisy data, especially when dealing with small structures. A reference-free pipeline is presented for obtaining near-atomic resolution three-dimensional reconstructions from heterogeneous (`four-dimensional' cryo-EM data sets. The methodologies integrated in this pipeline include a posteriori camera correction, movie-based full-data-set contrast transfer function determination, movie-alignment algorithms, (Fourier-space multivariate statistical data compression and unsupervised classification, `random-startup' three-dimensional reconstructions, four-dimensional structural refinements and Fourier shell correlation criteria for evaluating anisotropic resolution. The procedures exclusively use information emerging from the data set itself, without external `starting models'. Euler-angle assignments are performed by angular reconstitution rather than by the inherently slower projection-matching approaches. The comprehensive `ABC-4D' pipeline is based on the two-dimensional reference-free `alignment by classification' (ABC approach, where similar images in similar orientations are grouped by unsupervised classification. Some fundamental differences between X-ray crystallography versus single-particle cryo-EM data collection and data processing are discussed. The structure of the giant haemoglobin from Lumbricus terrestris at a global resolution of ∼3.8 Å is presented as an example of the use of the ABC-4D procedure.

  5. Single-particle cryo-EM using alignment by classification (ABC): the structure of Lumbricus terrestris haemoglobin. (United States)

    Afanasyev, Pavel; Seer-Linnemayr, Charlotte; Ravelli, Raimond B G; Matadeen, Rishi; De Carlo, Sacha; Alewijnse, Bart; Portugal, Rodrigo V; Pannu, Navraj S; Schatz, Michael; van Heel, Marin


    Single-particle cryogenic electron microscopy (cryo-EM) can now yield near-atomic resolution structures of biological complexes. However, the reference-based alignment algorithms commonly used in cryo-EM suffer from reference bias, limiting their applicability (also known as the 'Einstein from random noise' problem). Low-dose cryo-EM therefore requires robust and objective approaches to reveal the structural information contained in the extremely noisy data, especially when dealing with small structures. A reference-free pipeline is presented for obtaining near-atomic resolution three-dimensional reconstructions from heterogeneous ('four-dimensional') cryo-EM data sets. The methodologies integrated in this pipeline include a posteriori camera correction, movie-based full-data-set contrast transfer function determination, movie-alignment algorithms, (Fourier-space) multivariate statistical data compression and unsupervised classification, 'random-startup' three-dimensional reconstructions, four-dimensional structural refinements and Fourier shell correlation criteria for evaluating anisotropic resolution. The procedures exclusively use information emerging from the data set itself, without external 'starting models'. Euler-angle assignments are performed by angular reconstitution rather than by the inherently slower projection-matching approaches. The comprehensive 'ABC-4D' pipeline is based on the two-dimensional reference-free 'alignment by classification' (ABC) approach, where similar images in similar orientations are grouped by unsupervised classification. Some fundamental differences between X-ray crystallography versus single-particle cryo-EM data collection and data processing are discussed. The structure of the giant haemoglobin from Lumbricus terrestris at a global resolution of ∼3.8 Å is presented as an example of the use of the ABC-4D procedure.

  6. Net Energy, CO2 Emission and Land-Based Cost-Benefit Analyses of <em>Jatropha> em>Biodiesel: A Case Study of the Panzhihua Region of Sichuan Province in China

    Directory of Open Access Journals (Sweden)

    Xiangzheng Deng


    Full Text Available Bioenergy is currently regarded as a renewable energy source with a high growth potential. Forest-based biodiesel, with the significant advantage of not competing with grain production on cultivated land, has been considered as a promising substitute for diesel fuel by many countries, including China. Consequently, extracting biodiesel from <em>Jatropha> curcasem> has become a growing industry. However, many key issues related to the development of this industry are still not fully resolved and the prospects for this industry are complicated. The aim of this paper is to evaluate the net energy, CO2 emission, and cost efficiency of <em>Jatropha> biodiesel as a substitute fuel in China to help resolve some of the key issues by studying data from this region of China that is well suited to growing <em>Jatropha>. Our results show that: (1 <em>Jatropha> biodiesel is preferable for global warming mitigation over diesel fuel in terms of the carbon sink during <em>Jatropha> tree growth. (2 The net energy yield of <em>Jatropha> biodiesel is much lower than that of fossil fuel, induced by the high energy consumption during <em>Jatropha> plantation establishment and the conversion from seed oil to diesel fuel step. Therefore, the energy efficiencies of the production of <em>Jatropha> and its conversion to biodiesel need to be improved. (3 Due to current low profit and high risk in the study area, farmers have little incentive to continue or increase <em>Jatropha> production. (4 It is necessary to provide more subsidies and preferential policies for <em>Jatropha> plantations if this industry is to grow. It is also necessary for local government to set realistic objectives and make rational plans to choose proper sites for <em>Jatropha> biodiesel development and the work reported here should assist that effort. Future research focused on breading high-yield varieties, development of efficient field

  7. Cryo-EM structure of haemoglobin at 3.2 Å determined with the Volta phase plate (United States)

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


    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.

  8. A structural dynamic factor model for the effects of monetary policy estimated by the EM algorithm

    DEFF Research Database (Denmark)

    Bork, Lasse

    This paper applies the maximum likelihood based EM algorithm to a large-dimensional factor analysis of US monetary policy. Specifically, economy-wide effects of shocks to the US federal funds rate are estimated in a structural dynamic factor model in which 100+ US macroeconomic and financial time...... as opposed to the orthogonal factors resulting from the popular principal component approach to structural factor models. Correlated factors are economically more sensible and important for a richer monetary policy transmission mechanism. Secondly, I consider both static factor loadings as well as dynamic...... series are driven by the joint dynamics of the federal funds rate and a few correlated dynamic factors. This paper contains a number of methodological contributions to the existing literature on data-rich monetary policy analysis. Firstly, the identification scheme allows for correlated factor dynamics...

  9. Plasma-based accelerator structures

    Energy Technology Data Exchange (ETDEWEB)

    Schroeder, Carl B. [Univ. of California, Berkeley, CA (United States)


    Plasma-based accelerators have the ability to sustain extremely large accelerating gradients, with possible high-energy physics applications. This dissertation further develops the theory of plasma-based accelerators by addressing three topics: the performance of a hollow plasma channel as an accelerating structure, the generation of ultrashort electron bunches, and the propagation of laser pulses is underdense plasmas.

  10. Cryo-EM studies of the structure and dynamics of vacuolar-type ATPases. (United States)

    Mazhab-Jafari, Mohammad T; Rubinstein, John L


    Electron cryomicroscopy (cryo-EM) has significantly advanced our understanding of molecular structure in biology. Recent innovations in both hardware and software have made cryo-EM a viable alternative for targets that are not amenable to x-ray crystallography or nuclear magnetic resonance (NMR) spectroscopy. Cryo-EM has even become the method of choice in some situations where x-ray crystallography and NMR spectroscopy are possible but where cryo-EM can determine structures at higher resolution or with less time or effort. Rotary adenosine triphosphatases (ATPases) are crucial to the maintenance of cellular homeostasis. These enzymes couple the synthesis or hydrolysis of adenosine triphosphate to the use or production of a transmembrane electrochemical ion gradient, respectively. However, the membrane-embedded nature and conformational heterogeneity of intact rotary ATPases have prevented their high-resolution structural analysis to date. Recent application of cryo-EM methods to the different types of rotary ATPase has led to sudden advances in understanding the structure and function of these enzymes, revealing significant conformational heterogeneity and characteristic transmembrane α helices that are highly tilted with respect to the membrane. In this Review, we will discuss what has been learned recently about rotary ATPase structure and function, with a particular focus on the vacuolar-type ATPases.

  11. Cryo EM structure of intact rotary H+-ATPase/synthase from Thermus thermophilus. (United States)

    Nakanishi, Atsuko; Kishikawa, Jun-Ichi; Tamakoshi, Masatada; Mitsuoka, Kaoru; Yokoyama, Ken


    Proton translocating rotary ATPases couple ATP hydrolysis/synthesis, which occurs in the soluble domain, with proton flow through the membrane domain via a rotation of the common central rotor complex against the surrounding peripheral stator apparatus. Here, we present a large data set of single particle cryo-electron micrograph images of the V/A type H+-rotary ATPase from the bacterium Thermus thermophilus, enabling the identification of three rotational states based on the orientation of the rotor subunit. Using masked refinement and classification with signal subtractions, we obtain homogeneous reconstructions for the whole complexes and soluble V1 domains. These reconstructions are of higher resolution than any EM map of intact rotary ATPase reported previously, providing a detailed molecular basis for how the rotary ATPase maintains structural integrity of the peripheral stator apparatus, and confirming the existence of a clear proton translocation path from both sides of the membrane.

  12. Reliability Based Ship Structural Design

    DEFF Research Database (Denmark)

    Dogliani, M.; Østergaard, C.; Parmentier, G.


    This paper deals with the development of different methods that allow the reliability-based design of ship structures to be transferred from the area of research to the systematic application in current design. It summarises the achievements of a three-year collaborative research project dealing...... with developments of models of load effects and of structural collapse adopted in reliability formulations which aim at calibrating partial safety factors for ship structural design. New probabilistic models of still-water load effects are developed both for tankers and for containerships. New results are presented...... of non-linear wave induced load effects and the corresponding long-term formulations. Methods to combine linear and non-linear components of wave induced load effects have been developed and checked by alternative methods.These improved models were used for the reliability assessment of the primary hull...

  13. CryoEM structures of two spliceosomal complexes: starter and dessert at the spliceosome feast. (United States)

    Nguyen, Thi Hoang Duong; Galej, Wojciech P; Fica, Sebastian M; Lin, Pei-Chun; Newman, Andrew J; Nagai, Kiyoshi


    The spliceosome is formed on pre-mRNA substrates from five small nuclear ribonucleoprotein particles (U1, U2, U4/U6 and U5 snRNPs), and numerous non-snRNP factors. Saccharomyces cerevisiae U4/U6.U5 tri-snRNP comprises U5 snRNA, U4/U6 snRNA duplex and approximately 30 proteins and represents a substantial part of the spliceosome before activation. Schizosaccharomyces pombe U2.U6.U5 spliceosomal complex is a post-catalytic intron lariat spliceosome containing U2 and U5 snRNPs, NTC (nineteen complex), NTC-related proteins (NTR), U6 snRNA, and an RNA intron lariat. Two recent papers describe near-complete atomic structures of these complexes based on cryoEM single-particle analysis. The U4/U6.U5 tri-snRNP structure provides crucial insight into the activation mechanism of the spliceosome. The U2.U6.U5 complex reveals the striking architecture of NTC and NTR and important features of the group II intron-like catalytic RNA core remaining after spliced mRNA is released. These two structures greatly advance our understanding of the mechanism of pre-mRNA splicing. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

  14. The potential of cryo-electron microscopy for structure-based drug design. (United States)

    Boland, Andreas; Chang, Leifu; Barford, David


    Structure-based drug design plays a central role in therapeutic development. Until recently, protein crystallography and NMR have dominated experimental approaches to obtain structural information of biological molecules. However, in recent years rapid technical developments in single particle cryo-electron microscopy (cryo-EM) have enabled the determination to near-atomic resolution of macromolecules ranging from large multi-subunit molecular machines to proteins as small as 64 kDa. These advances have revolutionized structural biology by hugely expanding both the range of macromolecules whose structures can be determined, and by providing a description of macromolecular dynamics. Cryo-EM is now poised to similarly transform the discipline of structure-based drug discovery. This article reviews the potential of cryo-EM for drug discovery with reference to protein ligand complex structures determined using this technique. © 2017 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society.

  15. Higher-order structure of the 30-nm chromatin fiber revealed by cryo-EM. (United States)

    Zhu, Ping; Li, Guohong


    Genomic DNA is hierarchically packaged into chromatin in eukaryotes. As a central-level chromatin structure between nucleosomal arrays and higher order organizations, 30 nm chromatin fiber, and its dynamics play a crucial role in regulating DNA accessibility for gene transcription. However, despite extensive efforts over three decades, the higher-order structure of the 30 nm chromatin fiber remains unresolved and controversial. We have recently reconstituted the 30 nm chromatin fibers from 12 nucleosomal arrays in vitro in the presence of linker histone H1, and determined their cryo-EM structures at resolution of 11 Å (Song et al., Science 344, 376-380). Here, we briefly reviewed the higher-order structure studies of chromatin fibers, mainly focusing on the insights from the cryo-EM structures we recently solved. © 2016 IUBMB Life, 68(11):873-878, 2016. © 2016 International Union of Biochemistry and Molecular Biology.

  16. Structure of <em>Salmonella typhimuriumem> OMP Synthase in a Complete Substrate Complex

    DEFF Research Database (Denmark)

    Grubmeyer, Charles; Hansen, Michael Riis; Fedorov, Alexander A.


    Dimeric Salmonella typhimurium orotate phosphoribosyltransferase (OMP synthase, EC, a key enzyme in de novo pyrimidine nucleotide synthesis, has been cocrystallized in a complete substrate E·MgPRPP·orotate complex and the structure determined to 2.2 Å resolution. This structure resem...


    Directory of Open Access Journals (Sweden)

    Gilson Iannini


    Full Text Available

    O principal objetivo deste trabalho é discutir o sentido do recurso de Lacan ao paradigma estrutural. A presente investigação enfatiza a função desse recurso no que tange as relações entre psicanálise e história das ciências. Freud, ao buscar estabelecer a identidade epistemológica da psicanálise precisou escolher entre <em>Naturwissenschaften em>e <em>Geisteswissenschaften. em>Sua opção pelo modelo das ciências naturais implica certo desconforto epistemológico entre modelo e objeto. O recurso lacaniano à estrutura é uma estratégia de criar um novo espaço para a psicanálise no âmbito das ciências. A influência dos trabalhos de Koyré é determinante. Apenas uma ciência estruturalista poderia formular uma concepção não-psicologicista e não naturalista de sujeito. Isso se mostra particularmente no que concerne à categoria de causa.    

    The main aim of this paper is to discuss the meaning of Lacan's uses of the structural paradigm. The investigation will emphasize the function of this use in terms of relations between psychoanalysis and history of sciences. Freud, in order to establish the epistemological identity for psychoanalyses was impelled to choose between <em>Naturwissenschaften em>or <em>Geisteswissenschaften. em>By assuming<em> em>the natural sciences model Freud has created what one can call a certain epistemological discomfort: model and object seems not to fit each other. The influence of Koyre's work is here remarkable. Lacan's uses of structural paradigm may be seemed as a strategy to create a new space for psychoanalysis in science. Only a structuralist science could formulate a conception of the subject that is nor naturalistic, nor psychological. This is showed particularly in what concerns the category of cause.    

  18. Program structure-based blocking (United States)

    Bertolli, Carlo; Eichenberger, Alexandre E.; O'Brien, John K.; Sura, Zehra N.


    Embodiments relate to program structure-based blocking. An aspect includes receiving source code corresponding to a computer program by a compiler of a computer system. Another aspect includes determining a prefetching section in the source code by a marking module of the compiler. Yet another aspect includes performing, by a blocking module of the compiler, blocking of instructions located in the prefetching section into instruction blocks, such that the instruction blocks of the prefetching section only contain instructions that are located in the prefetching section.

  19. High-resolution cryo-EM proteasome structures in drug development. (United States)

    Morris, Edward P; da Fonseca, Paula C A


    With the recent advances in biological structural electron microscopy (EM), protein structures can now be obtained by cryo-EM and single-particle analysis at resolutions that used to be achievable only by crystallographic or NMR methods. We have explored their application to study protein-ligand interactions using the human 20S proteasome, a well established target for cancer therapy that is also being investigated as a target for an increasing range of other medical conditions. The map of a ligand-bound human 20S proteasome served as a proof of principle that cryo-EM is emerging as a realistic approach for more general structural studies of protein-ligand interactions, with the potential benefits of extending such studies to complexes that are unfavourable to other methods and allowing structure determination under conditions that are closer to physiological, preserving ligand specificity towards closely related binding sites. Subsequently, the cryo-EM structure of the Plasmodium falciparum 20S proteasome, with a new prototype specific inhibitor bound, revealed the molecular basis for the ligand specificity towards the parasite complex, which provides a framework to guide the development of highly needed new-generation antimalarials. Here, the cryo-EM analysis of the ligand-bound human and P. falciparum 20S proteasomes is reviewed, and a complete description of the methods used for structure determination is provided, including the strategy to overcome the bias orientation of the human 20S proteasome on electron-microscope grids and details of the icr3d software used for three-dimensional reconstruction.

  20. RBI - Risk Based Inspection: new concept applied to management of FPSOs (Floating, Production and Storage Offshore) structural integrity; IBR-Inspecao baseada em risco: um novo conceito aplicado a gestao da integridade estrutural de FPSOs

    Energy Technology Data Exchange (ETDEWEB)

    Farias, Bruno de; Figueiredo, Eduardo; Luiz, Marcio [PETROBRAS S.A., Rio de Janeiro, RJ (Brazil); Meurer, Gustavo; Duarte, Romulo; Belligotti, Rufo; Krzonkalla, Viviane [ABS Consulting, Rio de Janeiro, RJ (Brazil)


    Due to the difficulties of adapting the plan of inspection, typical of oil tankers, the units of the FPSO, began to occur large periods of unavailability of the cargo tanks. Also, with the expansion of the fleet, began to notice a difficulty in meeting the plan of inspection of the FPSO's hull. To improve the management of structural integrity of its FPSO's, PETROBRAS aims to ABS Consulting with the development and implementation of Risk-Based Inspection, known as RBI. This concept is applicable to various branches of industry. The companies began their implementation of oil by refineries. The development application for a ship's hull is recent and PETROBRAS is one of the first companies to implement the IBR for monitoring of the FPSO hull. (author)

  1. Automated structure refinement of macromolecular assemblies from cryo-EM maps using Rosetta. (United States)

    Wang, Ray Yu-Ruei; Song, Yifan; Barad, Benjamin A; Cheng, Yifan; Fraser, James S; DiMaio, Frank


    Cryo-EM has revealed the structures of many challenging yet exciting macromolecular assemblies at near-atomic resolution (3-4.5Å), providing biological phenomena with molecular descriptions. However, at these resolutions, accurately positioning individual atoms remains challenging and error-prone. Manually refining thousands of amino acids - typical in a macromolecular assembly - is tedious and time-consuming. We present an automated method that can improve the atomic details in models that are manually built in near-atomic-resolution cryo-EM maps. Applying the method to three systems recently solved by cryo-EM, we are able to improve model geometry while maintaining the fit-to-density. Backbone placement errors are automatically detected and corrected, and the refinement shows a large radius of convergence. The results demonstrate that the method is amenable to structures with symmetry, of very large size, and containing RNA as well as covalently bound ligands. The method should streamline the cryo-EM structure determination process, providing accurate and unbiased atomic structure interpretation of such maps.

  2. Expectation maximization algorithm based haplotype relative risk (EM-HRR): test of linkage disequilibrium using incomplete case-parents trios. (United States)

    Guo, Chao-Yu; DeStefano, Anita L; Lunetta, Kathryn L; Dupuis, Josée; Cupples, L Adrienne


    The Haplotype Relative Risk (HRR) was first proposed [Falk et al., Ann Hum Genet 1987] to test for Linkage Disequilibrium (LD) between a marker and a putative disease locus using case-parent trios. Spurious association does not appear in such family-based studies under population admixture. In this paper, we extend the HRR to accommodate incomplete trios via the Expectation-Maximization (EM) algorithm [Dempster et al., J R Stat Soc Ser B, 1977]. In addition to triads and dyads (parent-offspring pair), the EM-HRR easily incorporates individuals with no parental genotype information available, which is excluded from the one parent Transmission/Disequilibrium Test (1-TDT) [Sun et al., Am J Epidemiol 1999]. Due to the data structure of EM-HRR, transmitted alleles are always available regardless of the number of missing parental genotypes. As a result of having a larger sample size, computer simulations reveal that the EM-HRR is more powerful in detecting LD than the 1-TDT in a population under Hardy-Weinberg Equilibirum (HWE). If admixture is not extreme, the EM-HRR remains more powerful. When a large degree of admixture exists, the EM-HRR performs better the 1-TDT when the association is strong, though not as well when the association is weak. We illustrate the proposed method with an application to the Framingham Heart Study. Copyright (c) 2005 S. Karger AG, Basel.

  3. Structure of <em>Escherichia coliem> Hfq bound to polyriboadenylate RNA

    DEFF Research Database (Denmark)

    Link, Todd M; Valentin-Hansen, Poul; Brennan, Richard G


    studies. Indeed, Hfq bound to the oligoribonucleotides (AGG)(8), (AGC)(8), and the shorter (A-R-N)(4) sequence, AACAACAAGAAG, with nanomolar affinities. The abundance of (A-R-N)(4) and (A-R-N)(5) triplet repeats in the E. coli genome suggests additional RNA targets for Hfq. Further, the structure provides...

  4. <em>C*->algebras of homoclinic and heteroclinic structure in expansive dynamics

    DEFF Research Database (Denmark)

    Thomsen, Klaus

    , and the constructions of Ruelle and Putnam for Smale spaces. The general setup is used to analyze the structure of the -algebras arising from the homoclinic and heteroclinic equivalence relations in expansive dynamical systems; in particular expansive group endomorphisms and automorphisms, and generalized 1-solenoids...

  5. Volta phase plate data collection facilitates image processing and cryo-EM structure determination. (United States)

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


    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.

  6. EM absorption reduction in wireless mobile antenna using printed paper-based metamaterial (United States)

    Alam, Touhidul; Islam, Mohammad Tariqul; Kibria, Salehin; Cho, Mengu; Faruque, Mohammad Rashed Iqbal


    This paper presents a printed negative index metamaterial for electromagnetic (EM) absorption reduction in portable wireless antenna. The perceptible novelty exhibited in this paper is that EM absorption reduction toward the human head with paper-based metamaterial attachment. This research has been performed using human head phantom integrated in the commercially available CST Microwave Studio software package. The EM absorption has been reduced by 13.2 and 6% at 900 and 1800 MHz, respectively.

  7. Structural and Catalytic Differences between Two FADH2-Dependent Monooxygenases: 2,4,5-TCP 4-Monooxygenase (TftD from <em>Burkholderia em>cepacia> AC1100 and 2,4,6-TCP 4-Monooxygenase (TcpA from <em>Cupriavidus em>necator> JMP134

    Directory of Open Access Journals (Sweden)

    ChulHee Kang


    Full Text Available 2,4,5-TCP 4-monooxygenase (TftD and 2,4,6-TCP 4-monooxygenase (TcpA have been discovered in the biodegradation of 2,4,5-trichlorophenol (2,4,5-TCP and 2,4,6-trichlorophenol (2,4,6-TCP. TcpA and TftD belong to the reduced flavin adenine dinucleotide (FADH2-dependent monooxygenases and both use 2,4,6-TCP as a substrate; however, the two enzymes produce different end products. TftD catalyzes a typical monooxygenase reaction, while TcpA catalyzes a typical monooxygenase reaction followed by a hydrolytic dechlorination. We have previously reported the 3D structure of TftD and confirmed the catalytic residue, His289. Here we have determined the crystal structure of TcpA and investigated the apparent differences in specificity and catalysis between these two closely related monooxygenases through structural comparison. Our computational docking results suggest that Ala293 in TcpA (Ile292 in TftD is possibly responsible for the differences in substrate specificity between the two monooxygenases. We have also identified that Arg101 in TcpA could provide inductive effects/charge stabilization during hydrolytic dechlorination. The collective information provides a fundamental understanding of the catalytic reaction mechanism and the parameters for substrate specificity. The information may provide guidance for designing bioremediation strategies for polychlorophenols, a major group of environmental pollutants.

  8. Accelerated EM-based clustering of large data sets

    NARCIS (Netherlands)

    Verbeek, J.J.; Nunnink, J.R.J.; Vlassis, N.


    Motivated by the poor performance (linear complexity) of the EM algorithm in clustering large data sets, and inspired by the successful accelerated versions of related algorithms like k-means, we derive an accelerated variant of the EM algorithm for Gaussian mixtures that: (1) offers speedups that

  9. High-Resolution Macromolecular Structure Determination by MicroED, a cryo-EM Method (United States)

    Rodriguez, J.A.; Gonen, T.


    Microelectron diffraction (MicroED) is a new cryo-electron microscopy (cryo-EM) method capable of determining macromolecular structures at atomic resolution from vanishingly small 3D crystals. MicroED promises to solve atomic resolution structures from even the tiniest of crystals, less than a few hundred nanometers thick. MicroED complements frontier advances in crystallography and represents part of the rebirth of cryo-EM that is making macromolecular structure determination more accessible for all. Here we review the concept and practice of MicroED, for both the electron microscopist and crystallographer. Where other reviews have addressed specific details of the technique (Hattne et al., 2015; Shi et al., 2016; Shi, Nannenga, Iadanza, & Gonen, 2013), we aim to provide context and highlight important features that should be considered when performing a MicroED experiment. PMID:27572734

  10. Cryo-EM structure of a novel calicivirus, Tulane virus.

    Directory of Open Access Journals (Sweden)

    Guimei Yu

    Full Text Available Tulane virus (TV is a newly isolated cultivatable calicivirus that infects juvenile rhesus macaques. Here we report a 6.3 Å resolution cryo-electron microscopy structure of the TV virion. The TV virion is about 400 Å in diameter and consists of a T = 3 icosahedral protein capsid enclosing the RNA genome. 180 copies of the major capsid protein VP1 (∼57 KDa are organized into two types of dimers A/B and C/C and form a thin, smooth shell studded with 90 dimeric protrusions. The overall capsid organization and the capsid protein fold of TV closely resemble that of other caliciviruses, especially of human Norwalk virus, the prototype human norovirus. These close structural similarities support TV as an attractive surrogate for the non-cultivatable human noroviruses. The most distinctive feature of TV is that its C/C dimers are in a highly flexible conformation with significantly reduced interactions between the shell (S domain and the protruding (P domain of VP1. A comparative structural analysis indicated that the P domains of TV C/C dimers were much more flexible than those of other caliciviruses. These observations, combined with previous studies on other caliciviruses, led us to hypothesize that the enhanced flexibility of C/C dimer P domains are likely required for efficient calicivirus-host cell interactions and the consequent uncoating and genome release. Residues in the S-P1 hinge between the S and P domain may play a critical role in the flexibility of P domains of C/C dimers.

  11. Cryo-EM structure of haemoglobin at 3.2 Å determined with the Volta phase plate (United States)

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


    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

  12. Structure and optics of the eyes of the box jellyfish <em>Chiropsella bronzieem>

    DEFF Research Database (Denmark)

    O’Connor, Megan; Garm, Anders Lydik; Nilsson, Dan-E.


    Cubomedusae have a total of 24 eyes of four morphologically different types. Two of these eye types are camera-type eyes (upper and lower lens-eye), while the other two eye types are simpler pigment pit eyes (pit and slit eye). Here, we give a description of the visual system of the box jellyfish...... those in the previously investigated species Tripedalia cystophora. In the lower lens-eye of C. bronzie, blur circles subtend 20 and 52° for closed and open pupil, respectively, effectively removing all but the coarsest structures of the image. Histology reveals that the retina of the lower lens......-eye, in addition to pigmented photoreceptors, also contains long pigment-cells, with both dark and white pigment, where the dark pigment migrates on light/dark adaptation. Unlike the upper lens-eye lens of T.cystophora, the same eye in C.bronzie did not display any significant optical power....

  13. EM-Fold: De novo atomic-detail protein structure determination from medium resolution density maps (United States)

    Lindert, Steffen; Alexander, Nathan; Wötzel, Nils; Karakaş, Mert; Stewart, Phoebe L.; Meiler, Jens


    Electron density maps of membrane proteins or large macromolecular complexes are frequently only determined at medium resolution between 4 Å and 10 Å, either by cryo-electron microscopy (cryoEM) or X-ray crystallography. In these density maps the general arrangement of secondary structure elements is revealed while their directionality and connectivity remain elusive. We demonstrate that the topology of proteins with up to 250 amino acids can be determined from such density maps when combined with a computational protein folding protocol. Furthermore, we accurately reconstruct atomic detail in loop regions and amino acid side chains not visible in the experimental data. The EM-Fold algorithm assembles the secondary structure elements de novo before atomic detail is added using Rosetta. In a benchmark of 27 proteins the protocol consistently and reproducibly achieves models with RMSD values smaller than 3 Å. PMID:22405005

  14. Reliability-based optimization of engineering structures

    DEFF Research Database (Denmark)

    Sørensen, John Dalsgaard


    The theoretical basis for reliability-based structural optimization within the framework of Bayesian statistical decision theory is briefly described. Reliability-based cost benefit problems are formulated and exemplitied with structural optimization. The basic reliability-based optimization......-assessment and a reliability-based decision problem for offshore wind turbines....

  15. Grouped fuzzy SVM with EM-based partition of sample space for clustered microcalcification detection. (United States)

    Wang, Huiya; Feng, Jun; Wang, Hongyu


    Detection of clustered microcalcification (MC) from mammograms plays essential roles in computer-aided diagnosis for early stage breast cancer. To tackle problems associated with the diversity of data structures of MC lesions and the variability of normal breast tissues, multi-pattern sample space learning is required. In this paper, a novel grouped fuzzy Support Vector Machine (SVM) algorithm with sample space partition based on Expectation-Maximization (EM) (called G-FSVM) is proposed for clustered MC detection. The diversified pattern of training data is partitioned into several groups based on EM algorithm. Then a series of fuzzy SVM are integrated for classification with each group of samples from the MC lesions and normal breast tissues. From DDSM database, a total of 1,064 suspicious regions are selected from 239 mammography, and the measurement of Accuracy, True Positive Rate (TPR), False Positive Rate (FPR) and EVL = TPR* 1-FPR are 0.82, 0.78, 0.14 and 0.72, respectively. The proposed method incorporates the merits of fuzzy SVM and multi-pattern sample space learning, decomposing the MC detection problem into serial simple two-class classification. Experimental results from synthetic data and DDSM database demonstrate that our integrated classification framework reduces the false positive rate significantly while maintaining the true positive rate.

  16. The apo structure of sucrose hydrolase from <em>Xanthomonas campestrisem> pv. <em>campestris em>shows an open active-site groove

    DEFF Research Database (Denmark)

    Champion, Elise; Remaud-Simeon, Magali; Skov, Lars Kobberøe


    are reported. Sucrose hydrolysis catalyzed by the enzyme follows Michaelis-Menten kinetics, with a K(m) of 60.7 mM and a k(cat) of 21.7 s(-1). The structure of the enzyme was solved at a resolution of 1.9 A in the resting state with an empty active site. This represents the first apo structure from subfamily 4...

  17. Cryo-EM structure of a 3D DNA-origami object (United States)

    Bai, Xiao-chen; Martin, Thomas G.; Scheres, Sjors H. W.; Dietz, Hendrik


    A key goal for nanotechnology is to design synthetic objects that may ultimately achieve functionalities known today only from natural macromolecular complexes. Molecular self-assembly with DNA has shown potential for creating user-defined 3D scaffolds, but the level of attainable positional accuracy has been unclear. Here we report the cryo-EM structure and a full pseudoatomic model of a discrete DNA object that is almost twice the size of a prokaryotic ribosome. The structure provides a variety of stable, previously undescribed DNA topologies for future use in nanotechnology and experimental evidence that discrete 3D DNA scaffolds allow the positioning of user-defined structural motifs with an accuracy that is similar to that observed in natural macromolecules. Thereby, our results indicate an attractive route to fabricate nanoscale devices that achieve complex functionalities by DNA-templated design steered by structural feedback. PMID:23169645

  18. The Complete Mitochondrial Genome of the Pink Stem Borer, <em>Sesamia inferensem>, in Comparison with Four Other Noctuid Moths

    Directory of Open Access Journals (Sweden)

    Yu-Zhou Du


    Full Text Available The complete 15,413-bp mitochondrial genome (mitogenome of <em>Sesamia inferensem> (Walker (Lepidoptera: Noctuidae was sequenced and compared with those of four other noctuid moths. All of the mitogenomes analyzed displayed similar characteristics with respect to gene content, genome organization, nucleotide comparison, and codon usages. Twelve-one protein-coding genes (PCGs utilized the standard ATN, but the <em>cox1 em>gene used CGA as the initiation codon; <em>cox1em>, <em>cox2em>, and <em>nad4em> genes had the truncated termination codon T in the <em>S. inferens em>mitogenome. All of the tRNA genes had typical cloverleaf secondary structures except for <em>trnS1(AGNem>, in which the dihydrouridine (DHU arm did not form a stable stem-loop structure. Both the secondary structures of <em>rrnL> and <em>rrnS> genes inferred from the <em>S. inferens em>mitogenome closely resembled those of other noctuid moths. In the A+T-rich region, the conserved motif “ATAGA” followed by a long T-stretch was observed in all noctuid moths, but other specific tandem-repeat elements were more variable. Additionally, the <em>S. inferens em>mitogenome contained a potential stem-loop structure, a duplicated 17-bp repeat element, a decuplicated segment, and a microsatellite “(AT7”, without a poly-A element upstream of the<em> trnM em>in the A+T-rich region. Finally, the phylogenetic relationships were reconstructed based on amino acid sequences of mitochondrial 13 PCGs, which support the traditional morphologically based view of relationships within the Noctuidae.

  19. High-resolution modeling of protein structures based on flexible fitting of low-resolution structural data. (United States)

    Zheng, Wenjun; Tekpinar, Mustafa


    To circumvent the difficulty of directly solving high-resolution biomolecular structures, low-resolution structural data from Cryo-electron microscopy (EM) and small angle solution X-ray scattering (SAXS) are increasingly used to explore multiple conformational states of biomolecular assemblies. One promising venue to obtain high-resolution structural models from low-resolution data is via data-constrained flexible fitting. To this end, we have developed a new method based on a coarse-grained Cα-only protein representation, and a modified form of the elastic network model (ENM) that allows large-scale conformational changes while maintaining the integrity of local structures including pseudo-bonds and secondary structures. Our method minimizes a pseudo-energy which linearly combines various terms of the modified ENM energy with an EM/SAXS-fitting score and a collision energy that penalizes steric collisions. Unlike some previous flexible fitting efforts using the lowest few normal modes, our method effectively utilizes all normal modes so that both global and local structural changes can be fully modeled with accuracy. This method is also highly efficient in computing time. We have demonstrated our method using adenylate kinase as a test case which undergoes a large open-to-close conformational change. The EM-fitting method is available at a web server (, and the SAXS-fitting method is available as a pre-compiled executable upon request. © 2014 Elsevier Inc. All rights reserved.

  20. EM-Based Optimization Exploiting Partial Space Mapping and Exact Sensitivities

    DEFF Research Database (Denmark)

    Bandler, J. W.; Mohamed, A. S.; Bakr, M. H.


    We present a family of robust techniques for exploiting sensitivities in EM-based circuit optimization through Space Mapping (SM). We utilize derivative Information for parameter extractions and mapping updates. We exploit a Partial Space Mapping (PSM) concept where a reduced set of parameters is...... is sufficient for parameter extraction optimization. Upfront gradients of both EM (fine) model and coarse surrogates can initialize possible mapping approximations. Illustrations include a two-section 10:1 impedance transformer and a microstrip bandstop filter....

  1. Motion Structural Optimization Strategy for Rhombic Element Based Foldable Structure

    Directory of Open Access Journals (Sweden)

    Seung Hyun Jeong


    Full Text Available This research presents a new systematical design approach of foldable structure composed of several rhombic elements by applying genetic algorithm. As structural shapes represented by a foldable structure can be easily and dramatically morphed by manipulating rotational directions and angle of joints, the foldable structure has been used for various elementary structural members and engineering mechanisms. However a systematic design approach determining detail rotational angle and directions of unit cells for arbitrary shaped target areas has not been proposed yet. This research contributes to it by developing a new structural optimization method determining optimal angle and rotation directions to cover arbitrary shaped target areas of interest with aggregated rhombic elements. To achieve this purpose, we present an optimization formulation minimizing the sum of distances between each reference joint of an arbitrary shaped target area and its closest outer joints of foldable structure. To find out the outer joint set of a given foldable structure, an efficient geometric analysis method based on Delaunay triangulation is also developed and implemented. To show the validity and limitations of the present approach, several foldable structure design problems for two-dimensional arbitrary shaped target areas are solved with the present optimization procedure.

  2. Using a SMALP platform to determine a sub-nm single particle cryo-EM membrane protein structure. (United States)

    Parmar, Mayuriben; Rawson, Shaun; Scarff, Charlotte A; Goldman, Adrian; Dafforn, Timothy R; Muench, Stephen P; Postis, Vincent L G


    The field of membrane protein structural biology has been revolutionized over the last few years with a number of high profile structures being solved using cryo-EM including Piezo, Ryanodine receptor, TRPV1 and the Glutamate receptor. Further developments in the EM field hold the promise of even greater progress in terms of greater resolution, which for membrane proteins is still typically within the 4-7Å range. One advantage of a cryo-EM approach is the ability to study membrane proteins in more "native" like environments for example proteoliposomes, amphipols and nanodiscs. Recently, styrene maleic acid co-polymers (SMA) have been used to extract membrane proteins surrounded by native lipids (SMALPs) maintaining a more natural environment. We report here the structure of the Escherichia coli multidrug efflux transporter AcrB in a SMALP scaffold to sub-nm resolution, with the resulting map being consistent with high resolution crystal structures and other EM derived maps. However, both the C-terminal helix (TM12) and TM7 are poorly defined in the map. These helices are at the exterior of the helical bundle and form the greater interaction with the native lipids and SMA polymer and may represent a more dynamic region of the protein. This work shows the promise of using an SMA approach for single particle cryo-EM studies to provide sub-nm structures. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

  3. Reliability based Design of Coastal Structures

    DEFF Research Database (Denmark)

    Burcharth, H. F.


    Conventional design practice for coastal structures is deterministic in nature and is based on the concept of a design load which should not exceed the resistance (carrying capacity) of the structure. The design load is usually defined on a probabilistic basis as a characteristic value of the loa...

  4. Orientation selectivity based structure for texture classification (United States)

    Wu, Jinjian; Lin, Weisi; Shi, Guangming; Zhang, Yazhong; Lu, Liu


    Local structure, e.g., local binary pattern (LBP), is widely used in texture classification. However, LBP is too sensitive to disturbance. In this paper, we introduce a novel structure for texture classification. Researches on cognitive neuroscience indicate that the primary visual cortex presents remarkable orientation selectivity for visual information extraction. Inspired by this, we investigate the orientation similarities among neighbor pixels, and propose an orientation selectivity based pattern for local structure description. Experimental results on texture classification demonstrate that the proposed structure descriptor is quite robust to disturbance.

  5. Orthonormal bases for  <em>α>-modulation spaces

    DEFF Research Database (Denmark)

    Nielsen, Morten


    We construct an orthonormal basis for the family of bi-variate α-modulation spaces. The construction is based on local trigonometric bases, and the basis elements are closely related to so-called brushlets. As an application, we show that m-term nonlinear approximation with the representing system...

  6. Estratégia e estrutura: em busca do alinhamento organizacional em um clube social esportivo Strategy and structure: the quest for organizational alignment in a social sports club

    Directory of Open Access Journals (Sweden)

    Augusto de Toledo Cruz Junior


    Full Text Available A literatura descreve tipologias de formas organizações, que podem ser divididas em organização baseada em trabalho e organização baseada em conhecimento. A forma de representação mais utilizada é o organograma. Contudo, esta forma de representação não consegue ilustrar adequadamente a dinâmica de funcionamento da organização, sobretudo em organizações em que o conhecimento e a experiência são os ativos-chave. Com o objetivo de investigar o processo de alinhamento entre estratégia e estrutura, a abordagem metodológica adotada foi a pesquisa-ação. A pesquisa foi realizada ao longo de 6 meses, no período dos anos 2003 e 2004, em um clube situado na cidade de São Paulo. Participaram da pesquisa um grupo de 12 gerentes, 10 supervisores, 9 coordenadores e 5 dos principais diretores. Este artigo mostra como um clube de atividades sociais, culturais e esportivas projetou sua estrutura organizacional alinhada à formação de competências e às suas dinâmicas de funcionamento, para operar com características de uma organização baseada em conhecimento. A nova forma de representação da estrutura organizacional, denominada organigraph, ajudou o clube a explicitar a estratégia emergente, para operar em um mercado competitivo turbulento e implementá-la como regra simples a ser seguida por todos. Além disto, é apresentado um modelo de avaliação do desempenho derivado de um organigraph.The academic and practical literature describes organizational typologies that can be classified according to two main categories: job-based and knowledge-based organizations. The organizational structure is most commonly represented or described by the organizational chart. However, this form of representation fails to adequately depict the organization's work dynamics, above all in companies whose key assets are knowledge and experience. To investigate the alignment between strategy and structure, the methodological approach adopted here

  7. Cryo-EM structure of isomeric molluscan hemocyanin triggered by viral infection.

    Directory of Open Access Journals (Sweden)

    Hongtao Zhu

    Full Text Available Hemocyanins (Hcs of arthropods and mollusks function not only as oxygen transporters, but also as phenoloxidases (POs. In invertebrates, PO is an important component in the innate immune cascade, where it functions as the initiator of melanin synthesis, a pigment involved in encapsulating and killing of pathogenic microbes. Although structures of Hc from several species of invertebrates have been reported, the structural basis for how PO activity is triggered by structural changes of Hc in vivo remains poorly understood. Here, we report a 6.8 Å cryo-electron microscopy (cryo-EM structure of the isomeric form of hemocyanin, which was isolated from Abalone Shriveling syndrome-associated Virus (AbSV infected abalone (Halitotis diversicolor, and build a pseudoatomic model of isomeric H. diversicolor hemocyanin 1 (HdH1. Our results show that, compared with native form of HdH1, the architecture of isomeric HdH1 turns into a more relaxed form. The interactions between certain functional units (FUs present in the native form of Hc either decreased or were totally abolished in the isomeric form of Hc. As a result of that, native state Hc switches to its isomeric form, enabling it to play its role in innate immune responses against invading pathogens.

  8. Primed for Discovery: Atomic-Resolution Cryo-EM Structure of a Reovirus Entry Intermediate

    Directory of Open Access Journals (Sweden)

    Shane D. Trask


    Full Text Available A recently solved structure of the aquareovirus virion (Zhang, X; Jin, L.; Fang, Q; Hui, W.H.; Zhou Z.H. 3.3 Å Cryo-EM Structure of a Nonenveloped Virus Reveals a Priming Mechanism for Cell Entry. Cell 2010, 141, 472-482 [1] provides new insights into the order of entry events, as well as confirming and refining several aspects of the entry mechanism, for aquareovirus and the related orthoreovirus. In particular, the structure provides evidence of a defined order for the progressive proteolytic cleavages of myristoylated penetration protein VP5 that prime the virion for membrane penetration. These observations reinforce the concept that, much like enveloped viruses, nonenveloped virions often undergo priming events that lead to a meta-stable state, preparing the virus for membrane penetration under the appropriate circumstances. In addition, this and other recent studies highlight the increasing power of electron cryomicroscopy to analyze large, geometrically regular structures, such as icosahedral viruses, at atomic resolution.

  9. Homogeneous 1-based structures and interpretability in random structures


    Koponen, Vera


    Let $V$ be a finite relational vocabulary in which no symbol has arity greater than 2. Let $M$ be countable $V$-structure which is homogeneous, simple and 1-based. The first main result says that if $M$ is, in addition, primitive, then it is strongly interpretable in a random structure. The second main result, which generalizes the first, implies (without the assumption on primitivity) that if $M$ is "coordinatized" by a set with SU-rank 1 and there is no definable (without parameters) nontri...

  10. Diffusion-based EM algorithm for distributed estimation of Gaussian mixtures in wireless sensor networks. (United States)

    Weng, Yang; Xiao, Wendong; Xie, Lihua


    Distributed estimation of Gaussian mixtures has many applications in wireless sensor network (WSN), and its energy-efficient solution is still challenging. This paper presents a novel diffusion-based EM algorithm for this problem. A diffusion strategy is introduced for acquiring the global statistics in EM algorithm in which each sensor node only needs to communicate its local statistics to its neighboring nodes at each iteration. This improves the existing consensus-based distributed EM algorithm which may need much more communication overhead for consensus, especially in large scale networks. The robustness and scalability of the proposed approach can be achieved by distributed processing in the networks. In addition, we show that the proposed approach can be considered as a stochastic approximation method to find the maximum likelihood estimation for Gaussian mixtures. Simulation results show the efficiency of this approach.

  11. Specific PCR-based detection of <em>Alternaria helianthiem>

    DEFF Research Database (Denmark)

    Udayashankar, A.C.; Nayaka, S. Chandra; Archana, B.


    Alternaria helianthi is an important seed-borne pathogenic fungus responsible for blight disease in sunflower. The current detection methods, which are based on culture and morphological identification, are time-consuming, laborious and are not always reliable. A PCR-based diagnostic method...... tested. The detection limit of the PCR method was of 10 pg from template DNA. The primers could also detect the pathogen in infected sunflower seed. This species-specific PCR method provides a quick, simple, powerful and reliable alternative to conventional methods in the detection and identification...

  12. Risk-Based Assessment of Structural Robustness

    Directory of Open Access Journals (Sweden)

    Oana-Mihaela Ioniţă


    Full Text Available Providing safety of structures is one of the main aims of design. In traditional design it is achieved by designing structural components against specified limit states. However, as showed the Ronan Point collapse in UK in 1968, when a gas explosion in one of flats on the 18-th floor of the residential building caused the failure of an entire section of the building, this approach is not sufficient. The approach does not exclude the risk of local damage to a structure due to accidental events that can occur during service life of the structure. While probability of occurrence of such events for ordinary structures is low, and, therefore, they are not considered explicitly in design, their effect on structural safety becomes significant if the structure is not robust, that is when some local damage can trigger a chain reaction of failures causing collapse of the whole structure or of a major part of it, the so called progressive collapse. The purpose of this paper is to outline the basic premises for the utilization of risk assessment in evaluating the robustness of structures. In the following the robustness assessment is understood as a process of decision making based on risks.

  13. Value-based <em>Q(s,S) em>policy for joint replenishments

    DEFF Research Database (Denmark)

    Johansen, Søren Glud; Thorstenson, Anders

    We improve the previously proposed Q(s, S) policy for the stochastic joint replenishment problem. In our value-based Q(s, S) policy, item inventories are reviewed after each demand instant when the total demand since the last replenishment is close to Q. At each such review instance a new...

  14. Reliability-Based Optimization in Structural Engineering

    DEFF Research Database (Denmark)

    Enevoldsen, I.; Sørensen, John Dalsgaard


    In this paper reliability-based optimization problems in structural engineering are formulated on the basis of the classical decision theory. Several formulations are presented: Reliability-based optimal design of structural systems with component or systems reliability constraints, reliability......-based optimal inspection planning and reliability-based experiment planning. It is explained how these optimization problems can be solved by application of similar techniques. The reliability estimation is limited to first order reliability methods (FORM) for both component and systems reliability evaluation....... The solution strategies applying first order non-linear optimization algorithms are described in detail with special attention to sensitivity analysis and stability of the optimization process. Furthermore, several practical aspects are treated as: Development of the reliability-based optimization model...

  15. Structure-based barcoding of proteins. (United States)

    Metri, Rahul; Jerath, Gaurav; Kailas, Govind; Gacche, Nitin; Pal, Adityabarna; Ramakrishnan, Vibin


    A reduced representation in the format of a barcode has been developed to provide an overview of the topological nature of a given protein structure from 3D coordinate file. The molecular structure of a protein coordinate file from Protein Data Bank is first expressed in terms of an alpha-numero code and further converted to a barcode image. The barcode representation can be used to compare and contrast different proteins based on their structure. The utility of this method has been exemplified by comparing structural barcodes of proteins that belong to same fold family, and across different folds. In addition to this, we have attempted to provide an illustration to (i) the structural changes often seen in a given protein molecule upon interaction with ligands and (ii) Modifications in overall topology of a given protein during evolution. The program is fully downloadable from the website © 2013 The Protein Society.

  16. Abstract Generation based on Rhetorical Structure Extraction

    CERN Document Server

    Ono, K; Ono, Kenji; Sumita, Kazuo


    We have developed an automatic abstract generation system for Japanese expository writings based on rhetorical structure extraction. The system first extracts the rhetorical structure, the compound of the rhetorical relations between sentences, and then cuts out less important parts in the extracted structure to generate an abstract of the desired length. Evaluation of the generated abstract showed that it contains at maximum 74\\% of the most important sentences of the original text. The system is now utilized as a text browser for a prototypical interactive document retrieval system.

  17. Phylogeny of <em>Orchidantha> (Lowiaceae) and the Zingiberales Based on Six DNA Regions

    DEFF Research Database (Denmark)

    Johansen, Louise Buchholt


    Very little is known about the small, tropical, monogeneric monocotyledon family Lowiaceae within the order Zingiberales. The phylogenetic position of Lowiaceae within Zingiberales is unclear, as are relationships within its single genus Orchidantha, which includes at least 16 species. This paper...... presents a phylogenetic analysis of Zingiberales based on 613 parsimony informative characters of the plastid matK gene, the trnL-trnF region, the rps16 intron, and a conservative part of the nuclear ribosomal ITS region (part of the 18S, 5.8S, and 26S rDNA). The resulting single most parsimonious tree...... indicates that Lowiaceae is sister to all the remaining families of Zingiberales. An analysis of the family (14 species) based on a data set consisting of six plastid and nuclear DNA regions, includes the first use of a cam intron for estimating phylogeny. The results suggest that the nuclear calmodulin...

  18. EM-based optimization exploiting partial space mapping and exact sensitivities

    DEFF Research Database (Denmark)

    Bandler, John W.; Mohamed, Achmed S.; Bakr, Mohamed H.


    We present a family of robust techniques for exploiting sensitivities in electromagnetic (EM)-based circuit optimization through space mapping (SM) technology. We utilize derivative information for parameter extractions and mapping updates. We exploit a partial SM (PSM) concept, where a reduced set...... of parameters is sufficient for parameter extraction optimization. It reflects the idea of tuning and execution time is reduced. Upfront gradients of both EM (fine) model and coarse surrogates can initialize possible mapping approximations. We introduce several effective approaches for updating the mapping...

  19. Prevalência de transtornos ansiosos e algumas comorbidades em idosos: um estudo de base populacional


    Mayara B. Machado; Zuleide Maria Ignácio; Luciano K. Jornada; Gislaine Z. Réus; Helena M. Abelaira; Camila O. Arent; Mágada T. Schwalm; Renan A. Ceretta; Luciane B. Ceretta; João Quevedo


    RESUMO Objetivo Avaliar a prevalência de transtornos ansiosos e fatores associados em uma amostra populacional de idosos do Sul de Santa Catarina. Métodos Estudo transversal com base em dados populacionais, que avaliou 1.021 indivíduos idosos entre 60 e 79 anos. Foram realizadas entrevistas domiciliares para aferição de variáveis sobre transtornos ansiosos, por meio do questionário MINI, dados sociodemográficos, hipertensão arterial sistêmica (HAS), infarto agudo do miocárdio (IAM) e dosa...

  20. Risco de suicídio em jovens com transtornos de ansiedade: estudo de base populacional


    Moisés Ederson da Silva Rodrigues; Tatiane Brito da Silveira; Karen Jansen; Ana Laura Sica Cruzeiro; Liliane Ores; Ricardo Tavares Pinheiro; Ricardo Azevedo da Silva; Elaine Tomasi; Luciano Dias de Mattos Souza


    Este estudo teve por objetivo verificar a relação entre a presença de transtornos de ansiedade e risco de suicídio em jovens. Em delineamento transversal de base populacional, os jovens respondiam a um questionário sobre questões sociodemográficas, comportamentais e de saúde. Avaliou-se o bem-estar psicológico através da Escala de Faces de Andrews e consumo de substâncias foi efetuado pelo Teste de Triagem do Envolvimento com Álcool, Cigarro e Outras Substâncias, (Alcohol, Smoking and Substan...

  1. Cultivo de orquídea em substratos à base de casca de café


    Adriane Marinho de Assis; Lilian Keiko Unemoto; Lilian Yukari Yamamoto; Alessandro Borini Lone; Gilberto Rostirolla Batista de Souza; Ricardo Tadeu de Faria; Sérgio Ruffo Roberto; Lúcia Sadayo Assari Takahashi


    A utilização de resíduos agrícolas como substrato é uma alternativa promissora no cultivo de orquídeas, reduzindo os custos e o acúmulo desses materiais no ambiente. O objetivo do trabalho foi avaliar o desenvolvimento de orquídea híbrida (C. forbesii x C. labiata) x C. labiata em substratos à base de casca de café. O delineamento experimental utilizado foi o inteiramente casualizado, com seis tratamentos (xaxim desfibrado; casca de café; casca de café + coco em pó; casca de café + fibra de c...

  2. Cultivo de Oncidium baueri Lindley (Orchidaceae) em substratos a base de coco


    Assis,Adriane Marinho de; Faria,Ricardo Tadeu de; Unemoto,Lilian Keiko; Colombo,Larissa Abgariani


    Entre os substratos utilizados no cultivo de orquídeas, a fibra de coco vem se destacando como promissor substituto do xaxim, material utilizado por muitos produtores e colecionadores de orquídeas, porém ameaçado de extinção. Objetivou-se, neste trabalho, foi avaliar a eficiência de substratos à base de coco, no cultivo da orquídea Oncidium baueri. As mudas foram cultivadas em vasos de polipropileno, permanecendo em viveiro com 50% de luminosidade. Os tratamentos constituíram-se de xaxim desf...

  3. Controlling for <em>false negativesem> in agent-based models

    DEFF Research Database (Denmark)

    Secchi, Davide; Seri, Raffaello


    This article is concerned with the study of statistical power in agent-based modeling (ABM). After an overview of classic statistics theory on how to interpret Type-II error (whose occurrence is also referred to as a false negative) and power, the manuscript presents a study on ABM simulation art...... of simulation runs to reach an appropriate level of power. The study concludes with the importance for organizational behavior scholars to perform their models in an attempt to reach a power of 0.95 or higher at the 0.01 significance level....

  4. 3.5Å cryoEM structure of hepatitis B virus core assembled from full-length core protein.

    Directory of Open Access Journals (Sweden)

    Xuekui Yu

    Full Text Available The capsid shell of infectious hepatitis B virus (HBV is composed of 240 copies of a single protein called HBV core antigen (HBc. An atomic model of a core assembled from truncated HBc was determined previously by X-ray crystallography. In an attempt to obtain atomic structural information of HBV core in a near native, non-crystalline environment, we reconstructed a 3.5Å-resolution structure of a recombinant core assembled from full-length HBc by cryo electron microscopy (cryoEM and derived an atomic model. The structure shows that the 240 molecules of full-length HBc form a core with two layers. The outer layer, composed of the N-terminal assembly domain, is similar to the crystal structure of the truncated HBc, but has three differences. First, unlike the crystal structure, our cryoEM structure shows no disulfide bond between the Cys61 residues of the two subunits within the dimer building block, indicating such bond is not required for core formation. Second, our cryoEM structure reveals up to four more residues in the linker region (amino acids 140-149. Third, the loops in the cryoEM structures containing this linker region in subunits B and C are oriented differently (~30° and ~90° from their counterparts in the crystal structure. The inner layer, composed of the C-terminal arginine-rich domain (ARD and the ARD-bound RNAs, is partially-ordered and connected with the outer layer through linkers positioned around the two-fold axes. Weak densities emanate from the rims of positively charged channels through the icosahedral three-fold and local three-fold axes. We attribute these densities to the exposed portions of some ARDs, thus explaining ARD's accessibility by proteases and antibodies. Our data supports a role of ARD in mediating communication between inside and outside of the core during HBV maturation and envelopment.

  5. 3.5Å cryoEM Structure of Hepatitis B Virus Core Assembled from Full-Length Core Protein (United States)

    Yu, Xuekui; Jin, Lei; Jih, Jonathan; Shih, Chiaho; Hong Zhou, Z.


    The capsid shell of infectious hepatitis B virus (HBV) is composed of 240 copies of a single protein called HBV core antigen (HBc). An atomic model of a core assembled from truncated HBc was determined previously by X-ray crystallography. In an attempt to obtain atomic structural information of HBV core in a near native, non-crystalline environment, we reconstructed a 3.5Å-resolution structure of a recombinant core assembled from full-length HBc by cryo electron microscopy (cryoEM) and derived an atomic model. The structure shows that the 240 molecules of full-length HBc form a core with two layers. The outer layer, composed of the N-terminal assembly domain, is similar to the crystal structure of the truncated HBc, but has three differences. First, unlike the crystal structure, our cryoEM structure shows no disulfide bond between the Cys61 residues of the two subunits within the dimer building block, indicating such bond is not required for core formation. Second, our cryoEM structure reveals up to four more residues in the linker region (amino acids 140-149). Third, the loops in the cryoEM structures containing this linker region in subunits B and C are oriented differently (~30° and ~90°) from their counterparts in the crystal structure. The inner layer, composed of the C-terminal arginine-rich domain (ARD) and the ARD-bound RNAs, is partially-ordered and connected with the outer layer through linkers positioned around the two-fold axes. Weak densities emanate from the rims of positively charged channels through the icosahedral three-fold and local three-fold axes. We attribute these densities to the exposed portions of some ARDs, thus explaining ARD’s accessibility by proteases and antibodies. Our data supports a role of ARD in mediating communication between inside and outside of the core during HBV maturation and envelopment. PMID:24039702

  6. Psicoterapia baseada em evidências em crianças e adolescentes Evidence-based psychotherapies for children and adolescents

    Directory of Open Access Journals (Sweden)

    Gabriel Ferreira Pheula


    Full Text Available CONTEXTO: O termo tratamentos baseados em evidências refere-se a intervenções que possuem evidência de eficácia em pesquisas empíricas. Tratamentos psicológicos baseados em evidências têm sido identificados como um objetivo principal nos Estados Unidos, e, atualmente, há uma clara orientação em direção à sua indicação para os transtornos psiquiátricos mais prevalentes. OBJETIVO: Revisar a efetividade de intervenções psicossociais para as principais formas clínicas dos transtornos mentais na infância e adolescência, e os desafios para a pesquisa em tratamentos baseados em evidência. MÉTODOS: Revisão bibliográfica do banco de dados Medline, de 1985 a 2005, e revisão de artigos encontrados em capítulos de livros e artigos de revisão. RESULTADOS: Psicoterapias com suporte empírico em depressão, ansiedade, transtornos do comportamento disruptivo e transtorno de déficit de atenção/hiperatividade. CONCLUSÃO: Houve um progresso importante na pesquisa em psicoterapia na infância e adolescência, que se reflete na quantidade de estudos e na identificação de tratamentos baseados em evidências. O desafio atual engloba a generalização de tais achados para a prática clínica.BACKGROUND: Evidence-based treatments refer to interventions that have empirical research on their behalf. Evidence-based psychological therapy have been identified as a national goal in United States, and there is now clear guidance regarding referral for major mental health conditions. OBJECTIVE: Review the effectiveness of psychosocial interventions for all major forms of mental health problems in childhood and adolescence, and the challenges to research Evidence-Based treatments. METHODS: Computerized search of Medline database from 1985 to 2005 and review bibliographies of book chapters and review articles. RESULTS: We present empirically based psychological treatments for depression, anxiety, disruptive behavior disorder, attention deficit

  7. Estudo experimental comparativo entre diferentes curativos à base de prata em queimaduras de 2º. grau em ratos

    Directory of Open Access Journals (Sweden)

    Decio Luis Portella


    Full Text Available Introdução: Milhares de pessoas são vítimas de queimaduras todos os anos, sendo a etiologia por escaldo a mais frequente. Muitas dessas vítimas apresentam queimaduras de pequena extensão corpórea e espessura parcial superficial, sendo tratadas de forma ambulatorial ou mesmo não procurando atendimento médico especializado. Em todo o mundo, a utilização de curativos à base de prata tornou-se rotineira e comum, beirando o uso indiscriminado. Diversos são os curativos que apresentam a prata como agente principal. Este trabalho avaliou queimaduras por escaldo, de pequena extensão e espessura parcial em ratos. Material e Métodos: Utilizou-se 45 ratos Wistar divididos em cinco grupos e, após queimadura por escaldo, foram tratados com soro fisiológico, sulfadiazina de prata, carboximetilcelulose com prata (Aquacel®, espuma de polietileno associada à prata (Mepilex® e prata nanocristalina (Actcoat®. Os ratos foram sacrificados nos dias 1o , 2o , 4o , 6o , 9o , 12o , 18o , 21o , 24o. e a área queimada foi enviada para análise histopatológica, sem o conhecimento de qual curativo foi utilizado. Os critérios de avaliação foram: epitelização; extensão da área cicatrizada; infiltrado inflamatório crônico; neoformação vascular; proliferação fibroblástica, fibras elásticas e colágeno jovem. Para cada critério avaliado, foi atribuído uma nota conforme a sua maior intensidade na lâmina histológica. Resultados: A análise estatística mostrou significância para neoformação vascular (p<0,043, infiltrado inflamatório (p<0.004 e fibras elásticas (p<0,001. Apesar da diferença estatisticamente significante para neoformação vascular entre os grupos, não foi possível identificar qual grupo difere dos demais. A presença de infiltrado inflamatório foi maior nos ratos tratados com sulfadiazina de prata e com Actcoat® que nos ratos tratados com Mepilex® (p = 0,035 e p = 0,019 respectivamente. As fibras elásticas foram

  8. Electronic structure of Fe-based superconductors

    Indian Academy of Sciences (India)

    Abstract. Fe-based superconductors have drawn much attention during the last decade due to the presence of superconductivity in materials containing the magnetic element, Fe, and the coexistence of superconductivity and magnetism. Extensive study of the electronic structure of these systems suggested the dominant ...

  9. Electronic structure of Fe-based superconductors

    Indian Academy of Sciences (India)


    May 29, 2015 ... Fe-based superconductors have drawn much attention during the last decade due to the presence of superconductivity in materials containing the magnetic element, Fe, and the coexistence of superconductivity and magnetism. Extensive study of the electronic structure of these systems suggested the ...

  10. Narrative Structure in Inquiry-Based Learning (United States)

    Kinsey, L. Christine; Moore, Teresa E.


    Our goal with this paper is three-fold. We want to increase awareness of inquiry-based learning by presenting the strategy we use to develop and implement lessons and activities. We describe our approach to structuring lessons in mathematics in a way that engages the students by using language and constructs with which they are familiar from other…

  11. Vibrational Based Inspection of Civil Engineering Structures

    DEFF Research Database (Denmark)

    Rytter, Anders

    and Structural Engineering at the University of Aalborg since the beginning of 1992. Both projects have been supported by the Danish Technical Research Council. Further, the first mentioned project was supported by the Danish Energy Agency. Their financial support is gratefully acknowledged.......The thesis has been written in relation to two different research projects. Firstly, an offshore test programme, Integrated Experimental/Numerical Analysis of the Dynamic behavior of offshore structures, which was performed at the department of Building Technology and Structural Engineering...... at the University of Aalborg from 1988 to 1991. Secondly, a research project, In-Field Vibration Based Inspection of Civil Engineering Structures, which has been performed as a pilot project by the Consulting Engineers Rambøll, Hannemann and Højlund in cooperation with the department of Building Technology...

  12. Ultrastructure and LSU rDNA-based phylogeny of <em>Peridinium lomnickiiem> and description of <em>Chimonodinium> gen. nov. (Dinophyceae)

    DEFF Research Database (Denmark)

    Craveiro, Sandra C.; Calado, António J.; Daugbjerg, Niels


    Several populations of Peridinium lomnickii were examined by SEM and serial section TEM. Comparison with typical Peridinium, Peridiniopsis, Palatinus and Scrippsiella species revealed significant structural differences, congruent with phylogenetic hypotheses derived from partial LSU rDNA sequences....... Chimonodinium gen. nov. is described as a new genus of peridinioids, characterized by the Kofoidian plate formula Po, cp, x, 4', 3a, 7'', 6c, 5s, 5''', 2'''', the absence of pyrenoids, the presence of a microtubular basket with four or five overlapping rows of microtubules associated with a small peduncle...

  13. Yellow fluorescent protein phiYFPv (Phialidium): structure and structure-based mutagenesis

    Energy Technology Data Exchange (ETDEWEB)

    Pletneva, Nadya V.; Pletnev, Vladimir Z., E-mail:; Souslova, Ekaterina; Chudakov, Dmitry M. [Russian Academy of Sciences, Moscow (Russian Federation); Lukyanov, Sergey [Russian Academy of Sciences, Moscow (Russian Federation); Nizhny Novgorod State Medical Academy, Nizhny Novgorod (Russian Federation); Martynov, Vladimir I.; Arhipova, Svetlena; Artemyev, Igor [Russian Academy of Sciences, Moscow (Russian Federation); Wlodawer, Alexander [National Cancer Institute, Frederick, MD 21702 (United States); Dauter, Zbigniew [National Cancer Institute, Argonne, IL 60439 (United States); Pletnev, Sergei [National Cancer Institute, Argonne, IL 60439 (United States); SAIC-Frederick, 9700 South Cass Avenue, Argonne, IL 60439 (United States); Russian Academy of Sciences, Moscow (Russian Federation)


    The yellow fluorescent protein phiYFPv with improved folding has been developed from the spectrally identical wild-type phiYFP found in the marine jellyfish Phialidium. The yellow fluorescent protein phiYFPv (λ{sub em}{sup max} ≃ 537 nm) with improved folding has been developed from the spectrally identical wild-type phiYFP found in the marine jellyfish Phialidium. The latter fluorescent protein is one of only two known cases of naturally occurring proteins that exhibit emission spectra in the yellow–orange range (535–555 nm). Here, the crystal structure of phiYFPv has been determined at 2.05 Å resolution. The ‘yellow’ chromophore formed from the sequence triad Thr65-Tyr66-Gly67 adopts the bicyclic structure typical of fluorophores emitting in the green spectral range. It was demonstrated that perfect antiparallel π-stacking of chromophore Tyr66 and the proximal Tyr203, as well as Val205, facing the chromophore phenolic ring are chiefly responsible for the observed yellow emission of phiYFPv at 537 nm. Structure-based site-directed mutagenesis has been used to identify the key functional residues in the chromophore environment. The obtained results have been utilized to improve the properties of phiYFPv and its homologous monomeric biomarker tagYFP.

  14. Segmentation of neuronal structures using SARSA (λ)-based boundary amendment with reinforced gradient-descent curve shape fitting. (United States)

    Zhu, Fei; Liu, Quan; Fu, Yuchen; Shen, Bairong


    The segmentation of structures in electron microscopy (EM) images is very important for neurobiological research. The low resolution neuronal EM images contain noise and generally few features are available for segmentation, therefore application of the conventional approaches to identify the neuron structure from EM images is not successful. We therefore present a multi-scale fused structure boundary detection algorithm in this study. In the algorithm, we generate an EM image Gaussian pyramid first, then at each level of the pyramid, we utilize Laplacian of Gaussian function (LoG) to attain structure boundary, we finally assemble the detected boundaries by using fusion algorithm to attain a combined neuron structure image. Since the obtained neuron structures usually have gaps, we put forward a reinforcement learning-based boundary amendment method to connect the gaps in the detected boundaries. We use a SARSA (λ)-based curve traveling and amendment approach derived from reinforcement learning to repair the incomplete curves. Using this algorithm, a moving point starts from one end of the incomplete curve and walks through the image where the decisions are supervised by the approximated curve model, with the aim of minimizing the connection cost until the gap is closed. Our approach provided stable and efficient structure segmentation. The test results using 30 EM images from ISBI 2012 indicated that both of our approaches, i.e., with or without boundary amendment, performed better than six conventional boundary detection approaches. In particular, after amendment, the Rand error and warping error, which are the most important performance measurements during structure segmentation, were reduced to very low values. The comparison with the benchmark method of ISBI 2012 and the recent developed methods also indicates that our method performs better for the accurate identification of substructures in EM images and therefore useful for the identification of imaging

  15. Prevalência de transtornos ansiosos e algumas comorbidades em idosos: um estudo de base populacional

    Directory of Open Access Journals (Sweden)

    Mayara B. Machado


    Full Text Available RESUMO Objetivo Avaliar a prevalência de transtornos ansiosos e fatores associados em uma amostra populacional de idosos do Sul de Santa Catarina. Métodos Estudo transversal com base em dados populacionais, que avaliou 1.021 indivíduos idosos entre 60 e 79 anos. Foram realizadas entrevistas domiciliares para aferição de variáveis sobre transtornos ansiosos, por meio do questionário MINI, dados sociodemográficos, hipertensão arterial sistêmica (HAS, infarto agudo do miocárdio (IAM e dosagem de colesterol. Resultados As prevalências entre os transtornos ansiosos foram de 22,0% para o transtorno de ansiedade generalizada (TAG; 14,8% para fobia social (FS; 10,5% para transtorno do pânico (TP; e 8,5% para o transtorno obsessivo-compulsivo (TOC. Além disso, 40,5% dos indivíduos apresentaram pelo menos um transtorno de ansiedade. A distribuição dos transtornos foi semelhante nos dois gêneros; TAG foi mais prevalente nos indivíduos de menor escolaridade; TOC foi mais presente em indivíduos casados ou em união estável. Em relação às variáveis clínicas, HAS foi associada à presença de TOC; FS foi associada com IAM; TOC e FS foram associados com HDL > 40 mg/dL. Conclusão Os dados demonstram que os quadros de ansiedade são muito frequentes em idosos da comunidade, se sobrepõem de forma significativa e estão associados a algumas variáveis clínicas cardiovasculares.

  16. Metacognição em Grupos de Problem-based Learning (PBL

    Directory of Open Access Journals (Sweden)

    Adriana Vargas


    Full Text Available Aprendizagem em grupo é um processo que envolve a mobilização de funções cognitivas e desenvolve competências necessárias no decorrer da vida. A Problem-based Learning (PBL, uma proposta de aprendizagem em grupo, enfatiza o desenvolvimento cognitivo e pode potencializar a metacognição. Objetivou-se responder as questões: 1 a PBL é uma metodologia que envolve o desenvolvimento da metacognição? 2 pode-se relacionar os estudos da metacognição no contexto grupal à PBL? Realizou-se o estado do conhecimento do tema, entre 2010 a 2015, contendo os termos metacognition e Problem-based Learning, no portal de periódicos da CAPES. Oito pesquisas foram selecionadas por descreverem evidências empíricas da metacognição em grupos de PBL. A PBL pode ser aplicada aos estudos de aprendizagem em grupo e metacognição, por mobilizar conhecimentos, a tomada de consciência e o autocontrole.

  17. Intelligent-based Structural Damage Detection Model (United States)

    Lee, Eric Wai Ming; Yu, Kin Fung


    This paper presents the application of a novel Artificial Neural Network (ANN) model for the diagnosis of structural damage. The ANN model, denoted as the GRNNFA, is a hybrid model combining the General Regression Neural Network Model (GRNN) and the Fuzzy ART (FA) model. It not only retains the important features of the GRNN and FA models (i.e. fast and stable network training and incremental growth of network structure) but also facilitates the removal of the noise embedded in the training samples. Structural damage alters the stiffness distribution of the structure and so as to change the natural frequencies and mode shapes of the system. The measured modal parameter changes due to a particular damage are treated as patterns for that damage. The proposed GRNNFA model was trained to learn those patterns in order to detect the possible damage location of the structure. Simulated data is employed to verify and illustrate the procedures of the proposed ANN-based damage diagnosis methodology. The results of this study have demonstrated the feasibility of applying the GRNNFA model to structural damage diagnosis even when the training samples were noise contaminated.

  18. Two-Component Systems of <em>Mycobacterium tuberculosisem>—Structure-Based Approaches

    DEFF Research Database (Denmark)

    Tucker, Paul; Nowak, Elzbieta; Morth, Jens Preben


    Mycobacterium tuberculosis contains few two‐component systems compared to many other bacteria, possibly because it has more serine/threonine signaling pathways. Even so, these two‐component systems appear to play an important role in early intracellular survival of the pathogen as well as in aspe...

  19. Microtermolides A and B from termite-associated <em>Streptomyces> sp. and structural revision of vinylamycin

    DEFF Research Database (Denmark)

    Carr, Gavin; Poulsen, Michael; Klassen, Jonathan L.


    Microtermolides A (1) and B (2) were isolated from a Streptomyces sp. strain associated with fungus-growing termites. The structures of 1 and 2 were determined by 1D- and 2D-NMR spectroscopy and high-resolution mass spectrometry. Structural elucidation of 1 led to the re-examination of the struct......Microtermolides A (1) and B (2) were isolated from a Streptomyces sp. strain associated with fungus-growing termites. The structures of 1 and 2 were determined by 1D- and 2D-NMR spectroscopy and high-resolution mass spectrometry. Structural elucidation of 1 led to the re...

  20. Reliability Based Optimization of Structural Systems

    DEFF Research Database (Denmark)

    Sørensen, John Dalsgaard


    The optimization problem to design structural systems such that the reliability is satisfactory during the whole lifetime of the structure is considered in this paper. Some of the quantities modelling the loads and the strength of the structure are modelled as random variables. The reliability....... For these optimization problems it is described how a sensitivity analysis can be performed. Next, new optimization procedures to solve the optimization problems are presented. Two of these procedures solve the system reliability based optimization problem sequentially using quasi-analytical derivatives. Finally...... is estimated using first. order reliability methods ( FORM ). The design problem is formulated as the optimization problem to minimize a given cost function such that the reliability of the single elements satisfies given requirements or such that the systems reliability satisfies a given requirement...

  1. In Situ Data Processing With Workflow-based Embedded Cyberinfrastructure (emCI) (United States)

    Mehta, G.; Silva, F.; Graham, E. A.; Vahi, K.; Deelman, E.; Rundel, P.


    field. Scientists can also create embedded workflows for data analysis and sensor retasking, allowing for much faster response to events in the field as well as disconnected operation from the emCI portal. Workflows executed at the emCI portal can include heavier computations, and combine data from multiple sensors by performing data analysis on data from multiple sources. The emCI portal also supports workflows for data transfers, visualization, and the automatic monitoring of the embedded infrastructure. We have prototyped the emCI toolkit in a project that uses automated digital cameras and weather stations for observing climate change based on plant phenology observations. In this application, embedded workflows are being used to coordinate the field data collection, reduce and analyze image data in the field, and retask cameras based on embedded triggers. We are currently in the process of moving our deployment from prototype to production stage at the Stunt Ranch UC Reserve in the Santa Monica Mountains.

  2. Cramer-Rao lower bound optimization of an EM-CCD-based scintillation gamma camera. (United States)

    Korevaar, Marc A N; Goorden, Marlies C; Beekman, Freek J


    Scintillation gamma cameras based on low-noise electron multiplication (EM-)CCDs can reach high spatial resolutions. For further improvement of these gamma cameras, more insight is needed into how various parameters that characterize these devices influence their performance. Here, we use the Cramer-Rao lower bound (CRLB) to investigate the sensitivity of the energy and spatial resolution of an EM-CCD-based gamma camera to several parameters. The gamma camera setup consists of a 3 mm thick CsI(Tl) scintillator optically coupled by a fiber optic plate to the E2V CCD97 EM-CCD. For this setup, the position and energy of incoming gamma photons are determined with a maximum-likelihood detection algorithm. To serve as the basis for the CRLB calculations, accurate models for the depth-dependent scintillation light distribution are derived and combined with a previously validated statistical response model for the EM-CCD. The sensitivity of the lower bounds for energy and spatial resolution to the EM gain and the depth-of-interaction (DOI) are calculated and compared to experimentally obtained values. Furthermore, calculations of the influence of the number of detected optical photons and noise sources in the image area on the energy and spatial resolution are presented. Trends predicted by CRLB calculations agree with experiments, although experimental values for spatial and energy resolution are typically a factor of 1.5 above the calculated lower bounds. Calculations and experiments both show that an intermediate EM gain setting results in the best possible spatial or energy resolution and that the spatial resolution of the gamma camera degrades rapidly as a function of the DOI. Furthermore, calculations suggest that a large improvement in gamma camera performance is achieved by an increase in the number of detected photons or a reduction of noise in the image area. A large noise reduction, as is possible with a new generation of EM-CCD electronics, may improve the

  3. 3D reconstruction of synapses with deep learning based on EM Images (United States)

    Xiao, Chi; Rao, Qiang; Zhang, Dandan; Chen, Xi; Han, Hua; Xie, Qiwei


    Recently, due to the rapid development of electron microscope (EM) with its high resolution, stacks delivered by EM can be used to analyze a variety of components that are critical to understand brain function. Since synaptic study is essential in neurobiology and can be analyzed by EM stacks, the automated routines for reconstruction of synapses based on EM Images can become a very useful tool for analyzing large volumes of brain tissue and providing the ability to understand the mechanism of brain. In this article, we propose a novel automated method to realize 3D reconstruction of synapses for Automated Tapecollecting Ultra Microtome Scanning Electron Microscopy (ATUM-SEM) with deep learning. Being different from other reconstruction algorithms, which employ classifier to segment synaptic clefts directly. We utilize deep learning method and segmentation algorithm to obtain synaptic clefts as well as promote the accuracy of reconstruction. The proposed method contains five parts: (1) using modified Moving Least Square (MLS) deformation algorithm and Scale Invariant Feature Transform (SIFT) features to register adjacent sections, (2) adopting Faster Region Convolutional Neural Networks (Faster R-CNN) algorithm to detect synapses, (3) utilizing screening method which takes context cues of synapses into consideration to reduce the false positive rate, (4) combining a practical morphology algorithm with a suitable fitting function to segment synaptic clefts and optimize the shape of them, (5) applying the plugin in FIJI to show the final 3D visualization of synapses. Experimental results on ATUM-SEM images demonstrate the effectiveness of our proposed method.

  4. Navigating 3D electron microscopy maps with EM-SURFER. (United States)

    Esquivel-Rodríguez, Juan; Xiong, Yi; Han, Xusi; Guang, Shuomeng; Christoffer, Charles; Kihara, Daisuke


    The Electron Microscopy DataBank (EMDB) is growing rapidly, accumulating biological structural data obtained mainly by electron microscopy and tomography, which are emerging techniques for determining large biomolecular complex and subcellular structures. Together with the Protein Data Bank (PDB), EMDB is becoming a fundamental resource of the tertiary structures of biological macromolecules. To take full advantage of this indispensable resource, the ability to search the database by structural similarity is essential. However, unlike high-resolution structures stored in PDB, methods for comparing low-resolution electron microscopy (EM) density maps in EMDB are not well established. We developed a computational method for efficiently searching low-resolution EM maps. The method uses a compact fingerprint representation of EM maps based on the 3D Zernike descriptor, which is derived from a mathematical series expansion for EM maps that are considered as 3D functions. The method is implemented in a web server named EM-SURFER, which allows users to search against the entire EMDB in real-time. EM-SURFER compares the global shapes of EM maps. Examples of search results from different types of query structures are discussed. We developed EM-SURFER, which retrieves structurally relevant matches for query EM maps from EMDB within seconds. The unique capability of EM-SURFER to detect 3D shape similarity of low-resolution EM maps should prove invaluable in structural biology.

  5. Variabilidade genética em batata-doce com base em marcadores isoenzimáticos

    Directory of Open Access Journals (Sweden)

    Oliveira Antonio Carlos B. de


    Full Text Available A variabilidade genética de 55 clones de batata-doce, compreendendo cultivares comerciais e acessos obtidos de coletas, foi avaliada por meio de padrões isoenzimáticos, utilizando-se técnicas de análise multivariada. Cultivou-se uma planta por vaso, com 2 litros de capacidade, preenchido com terra, esterco e areia lavada na proporção de 3:2:1, com três repetições. As coletas das folhas e raízes novas para análises iniciaram-se aos 45 dias após o plantio. Foram utilizados, para folhas, os sistemas enzimáticos: GOT, alfaEST, betaEST, PGI, PGM e IDH e, para as raízes: PRX, alfaEST, betaEST, PGI, PGM e IDH. A combinação dos diferentes padrões enzimáticos e tecidos analisados possibilitou a discriminação individual de 32 dos 55 clones analisados. Os 23 clones restantes foram incluídos em sete grupos distintos, com base nos fenótipos isoenzimáticos exibidos. Os clones, dentro de cada um desses grupos, foram considerados materiais de mesmo genótipo, devido, também, às suas características morfológicas semelhantes. A aEST de raízes foi o sistema que apresentou maior número de bandas polimórficas, proporcionando a discriminação individual de 32 clones. O método de agrupamento de Tocher reuniu os 39 clones em nove grupos e, a análise pelo método das médias das distâncias, revelou a formação de onze grupos de similaridade. O clone 46 formou um grupo individual pelo método de Tocher e foi o mais divergente pelo método das médias das distâncias. Por apresentar boas características comerciais e produtivas, seria um dos clones eleitos para se iniciar programas de cruzamentos.

  6. Guidelines for the integration of EMS based in ISO 14001 with Cleaner Production

    Directory of Open Access Journals (Sweden)

    José Augusto de Oliveira


    Full Text Available Abstract This study aims to propose guidelines for the integration of the Environmental Management System (EMS based on ISO 14001 with the Cleaner Production (CP. For this, a systematic review was applied and five case studies have been carried out in industrial companies with considerable environmental performance. Located in the state of São Paulo, the researched companies have got CP projects to ensure environmental and economic gains and shown prominent compatibilities with the EMS based on ISO 14001. The proposed guidelines were performed in three parts: the planning stage, the integration stage and the stage of evaluation and analysis. The main compatibilities include dissemination of the environmental culture, synergy between some specific requirements of the standard and the CP, as the general requirements, legal requirements, environmental policy, training, qualification and monitoring. The guidelines can increase operational efficiency and strategic environmental management in enterprises.

  7. Ego-motion based on EM for bionic navigation (United States)

    Yue, Xiaofeng; Wang, L. J.; Liu, J. G.


    Researches have proved that flying insects such as bees can achieve efficient and robust flight control, and biologists have explored some biomimetic principles regarding how they control flight. Based on those basic studies and principles acquired from the flying insects, this paper proposes a different solution of recovering ego-motion for low level navigation. Firstly, a new type of entropy flow is provided to calculate the motion parameters. Secondly, EKF, which has been used for navigation for some years to correct accumulated error, and estimation-Maximization, which is always used to estimate parameters, are put together to determine the ego-motion estimation of aerial vehicles. Numerical simulation on MATLAB has proved that this navigation system provides more accurate position and smaller mean absolute error than pure optical flow navigation. This paper has done pioneering work in bionic mechanism to space navigation.

  8. Bioinspired twisted composites based on Bouligand structures (United States)

    Pinto, F.; Iervolino, O.; Scarselli, G.; Ginzburg, D.; Meo, M.


    The coupling between structural support and protection makes biological systems an important source of inspiration for the development of advanced smart composite structures. In particular, some particular material configurations can be implemented into traditional composites in order to improve their impact resistance and the out-of-plane properties, which represents one of the major weakness of commercial carbon fibres reinforced polymers (CFRP) structures. Based on this premise, a three-dimensional twisted arrangement shown in a vast multitude of biological systems (such as the armoured cuticles of Scarabei, the scales of Arapaima Gigas and the smashing club of Odontodactylus Scyllarus) has been replicated to develop an improved structural material characterised by a high level of in-plane isotropy and a higher interfacial strength generated by the smooth stiffness transition between each layer of fibrils. Indeed, due to their intrinsic layered nature, interlaminar stresses are one of the major causes of failure of traditional CFRP and are generated by the mismatch of the elastic properties between plies in a traditional laminate. Since the energy required to open a crack or a delamination between two adjacent plies is due to the difference between their orientations, the gradual angle variation obtained by mimicking the Bouligand Structures could improve energy absorption and the residual properties of carbon laminates when they are subjected to low velocity impact event. Two different bioinspired laminates were manufactured following a double helicoidal approach and a rotational one and were subjected to a complete test campaign including low velocity impact loading and compared to a traditional quasi-isotropic panel. Fractography analysis via X-Ray tomography was used to understand the mechanical behaviour of the different laminates and the residual properties were evaluated via Compression After Impact (CAI) tests. Results confirmed that the biological

  9. Structure-Based Design of Ricin Inhibitors

    Directory of Open Access Journals (Sweden)

    Jon D. Robertus


    Full Text Available Ricin is a potent cytotoxin easily purified in large quantities. It presents a significant public health concern due to its potential use as a bioterrorism agent. For this reason, extensive efforts have been underway to develop antidotes against this deadly poison. The catalytic A subunit of the heterodimeric toxin has been biochemically and structurally well characterized, and is an attractive target for structure-based drug design. Aided by computer docking simulations, several ricin toxin A chain (RTA inhibitors have been identified; the most promising leads belonging to the pterin family. Development of these lead compounds into potent drug candidates is a challenging prospect for numerous reasons, including poor solubility of pterins, the large and highly polar secondary binding pocket of RTA, as well as the enzyme’s near perfect catalytic efficiency and tight binding affinity for its natural substrate, the eukaryotic ribosome. To date, the most potent RTA inhibitors developed using this approach are only modest inhibitors with apparent IC50 values in the 10−4 M range, leaving significant room for improvement. This review highlights the variety of techniques routinely employed in structure-based drug design projects, as well as the challenges faced in the design of RTA inhibitors.

  10. A Memory-Based Approach to Two-Player Texas Hold'em (United States)

    Rubin, Jonathan; Watson, Ian

    A Case-Based Reasoning system, nicknamed SARTRE, that uses a memory-based approach to play two-player, limit Texas Hold'em is introduced. SARTRE records hand histories from strong players and attempts to re-use this information to handle novel situations. SARTRE'S case features and their representations are described, followed by the results obtained when challenging a world-class computerised opponent. Our experimental methodology attempts to address how well SARTRE'S performance can approximate the performance of the expert player, who SARTRE originally derived the experience-base from.

  11. Structure-based inhibitors of tau aggregation (United States)

    Seidler, P. M.; Boyer, D. R.; Rodriguez, J. A.; Sawaya, M. R.; Cascio, D.; Murray, K.; Gonen, T.; Eisenberg, D. S.


    Aggregated tau protein is associated with over 20 neurological disorders, which include Alzheimer's disease. Previous work has shown that tau's sequence segments VQIINK and VQIVYK drive its aggregation, but inhibitors based on the structure of the VQIVYK segment only partially inhibit full-length tau aggregation and are ineffective at inhibiting seeding by full-length fibrils. Here we show that the VQIINK segment is the more powerful driver of tau aggregation. Two structures of this segment determined by the cryo-electron microscopy method micro-electron diffraction explain its dominant influence on tau aggregation. Of practical significance, the structures lead to the design of inhibitors that not only inhibit tau aggregation but also inhibit the ability of exogenous full-length tau fibrils to seed intracellular tau in HEK293 biosensor cells into amyloid. We also raise the possibility that the two VQIINK structures represent amyloid polymorphs of tau that may account for a subset of prion-like strains of tau.

  12. Mapeamento da base de conhecimento fundamentado em arquétipos: contribuição à informática em saúde.


    Marcia Narumi Shiraishi Kondo


    Esta tese apresenta um modelo de representação de conhecimento fundamentado em arquétipos para o mapeamento da base de conhecimento que separa a informação e o conhecimento. De um lado, a informação representada por uma estrutura de dados comum com o mínimo de semânticas e, do outro, o conhecimento especificado por arquétipos que representam os conceitos formais hierarquizados em matrizes. Os arquétipos permitem a integração de dados existentes e de sistemas não estruturados do ponto de vista...

  13. Cryo-EM structure of the bacteriophage T4 portal protein assembly at near-atomic resolution. (United States)

    Sun, Lei; Zhang, Xinzheng; Gao, Song; Rao, Prashant A; Padilla-Sanchez, Victor; Chen, Zhenguo; Sun, Siyang; Xiang, Ye; Subramaniam, Sriram; Rao, Venigalla B; Rossmann, Michael G


    The structure and assembly of bacteriophage T4 has been extensively studied. However, the detailed structure of the portal protein remained unknown. Here we report the structure of the bacteriophage T4 portal assembly, gene product 20 (gp20), determined by cryo-electron microscopy (cryo-EM) to 3.6 Å resolution. In addition, analysis of a 10 Å resolution cryo-EM map of an empty prolate T4 head shows how the dodecameric portal assembly interacts with the capsid protein gp23 at the special pentameric vertex. The gp20 structure also verifies that the portal assembly is required for initiating head assembly, for attachment of the packaging motor, and for participation in DNA packaging. Comparison of the Myoviridae T4 portal structure with the known portal structures of φ29, SPP1 and P22, representing Podo- and Siphoviridae, shows that the portal structure probably dates back to a time when self-replicating microorganisms were being established on Earth.

  14. Network repair based on community structure (United States)

    Wang, Tianyu; Zhang, Jun; Sun, Xiaoqian; Wandelt, Sebastian


    Real-world complex systems are often fragile under disruptions. Accordingly, research on network repair has been studied intensively. Recently proposed efficient strategies for network disruption, based on collective influence, call for more research on efficient network repair strategies. Existing strategies are often designed to repair networks with local information only. However, the absence of global information impedes the creation of efficient repairs. Motivated by this limitation, we propose a concept of community-level repair, which leverages the community structure of the network during the repair process. Moreover, we devise a general framework of network repair, with in total six instances. Evaluations on real-world and random networks show the effectiveness and efficiency of the community-level repair approaches, compared to local and random repairs. Our study contributes to a better understanding of repair processes, and reveals that exploitation of the community structure improves the repair process on a disrupted network significantly.

  15. Structure-activity studies: in vitro antileishmanial and antimalarial activities of anthraquinones from <em>Morinda lucidaem>

    DEFF Research Database (Denmark)

    Sittie, A A; Lemmich, E; Olsen, C E


    Anthraquinones have been isolated by bioassay-guided fractionation from Morinda lucida. Structure-activity studies show that an aldehyde group at C-2 and a phenolic hydroxy group at C-3 enhance the activity of the anthraquinones against the growth of Plasmodium falciparum and promastigotes...

  16. Structural, electronic, and hyperfine properties of pure and Ta-doped <em>m>-ZrO2

    DEFF Research Database (Denmark)

    Taylor, M.A.; Alonso, R.E.; Errico, L.A.


    A combination of experiments and ab initio quantum-mechanical calculations has been applied to examine electronic, structural, and hyperfine interactions in pure and Ta-doped zirconium dioxide in its monoclinic phase (m-ZrO2). From the theoretical point of view, the full-potential linear augmente...

  17. Holistic corpus-based dialectology Dialetologia holística baseada em corpus

    Directory of Open Access Journals (Sweden)

    Benedikt Szmrecsanyi


    Full Text Available This paper is concerned with sketching future directions for corpus-based dialectology. We advocate a holistic approach to the study of geographically conditioned linguistic variability, and we present a suitable methodology, 'corpusbased dialectometry', in exactly this spirit. Specifically, we argue that in order to live up to the potential of the corpus-based method, practitioners need to (i abandon their exclusive focus on individual linguistic features in favor of the study of feature aggregates, (ii draw on computationally advanced multivariate analysis techniques (such as multidimensional scaling, cluster analysis, and principal component analysis, and (iii aid interpretation of empirical results by marshalling state-of-the-art data visualization techniques. To exemplify this line of analysis, we present a case study which explores joint frequency variability of 57 morphosyntax features in 34 dialects all over Great Britain.Este artigo debruça-se sobre o esboço propositivo de futuras direções para a dialetologia baseada em corpus. Defendemos uma abordagem holística para o estudo da variabilidade linguística geograficamente condicionada, e apresentamos uma metodologia adequada para tal - a dialetometria baseada em corpus. Mais especificamente, defendemos que para que se obtenham todos os resultados esperados da metodologia de corpus, pesquisadores devem: (i abandonar seu foco exclusivo em traços linguísticos individuais em favor do estudo dos agregados de traços, (ii amparar-se em métodos computacionais avançados de técnicas de análise multivariada (tais como escalagem multidimensional, análise de clusters, e análise de componente principal, e (iii auxiliar a interpretação de resultados empíricos através da utilização do estado da arte em técnicas de visualização. A fim de exemplificarmos essa linha de análise, apresentamos um estudo de caso que explora a variabilidade da frequência agregada de 57 tra

  18. <em>α>-Glucosidase Inhibitory Constituents from <em>Acanthopanax senticosusem> Harm Leaves

    Directory of Open Access Journals (Sweden)

    Hai-Xue Kuang


    Full Text Available A new triterpene glycoside, 3-<em>O-[(α>-L-rhamnopyranosyl(1→2]-[<em>β>-D-glucuronopyranosyl-6-<em>O>-methyl ester]-olean-12-ene-28-olic acid (1 and a new indole alkaloid, 5-methoxy-2-oxoindolin-3-acetic acid methyl ester (5 were isolated from the leaves of <em>Acanthopanax senticosusem> Harms along with six known compounds. The structures of the new compounds were determined by means of 2D-NMR experiments and chemical methods. All the isolated compounds were evaluated for their glycosidase inhibition activities and compound 6 showed significant <em>α>-glucosidase inhibition activity.

  19. A Study of Wind Turbine Comprehensive Operational Assessment Model Based on EM-PCA Algorithm (United States)

    Zhou, Minqiang; Xu, Bin; Zhan, Yangyan; Ren, Danyuan; Liu, Dexing


    To assess wind turbine performance accurately and provide theoretical basis for wind farm management, a hybrid assessment model based on Entropy Method and Principle Component Analysis (EM-PCA) was established, which took most factors of operational performance into consideration and reach to a comprehensive result. To verify the model, six wind turbines were chosen as the research objects, the ranking obtained by the method proposed in the paper were 4#>6#>1#>5#>2#>3#, which are completely in conformity with the theoretical ranking, which indicates that the reliability and effectiveness of the EM-PCA method are high. The method could give guidance for processing unit state comparison among different units and launching wind farm operational assessment.

  20. Crescimento de mudas de Eucalyptus camaldulensis em substratos à base de casca de arroz carbonizada

    Directory of Open Access Journals (Sweden)

    Dagma Kratz


    Full Text Available RESUMO Com base na importância do substrato na produção de mudas florestais, objetivou-se, com este trabalho, avaliar a viabilidade técnica de 13 substratos, preparados com misturas de substrato comercial à base de casca de pinus e vermiculita (SC, casca de arroz carbonizada com diferentes granulometrias [maior que 2 mm (CAC1, CAC com granulometria entre 1 - 2 mm (CAC2, CAC com granulometria entre 0,5 - 1 mm (CAC3, CAC com granulometria menor que 0,5 mm (CAC4], fibra de coco (FC e vermiculita média (VM, na produção de mudas de Eucalyptus camaldulensis, e a correlação de suas propriedades físicas e químicas com seu crescimento. Foram utilizados tubetes de 55 cm³. As mudas permaneceram 60 dias em estufa de vidro e 30 dias a pleno sol. Foram avaliadas a altura, diâmetro de colo, fitomassas secas aérea e radicial, facilidade de retirada do tubete, agregação das raízes ao substrato e relação entre altura e diâmetro de colo. Concluiu-se que o substrato formado por CAC pura, em diferentes granulometrias e em mistura com os outros componentes, é viável tecnicamente para a produção de mudas de Eucalyptus camaldulensis, embora aquele formado pela mistura de 50% de CAC e VM tenha resultado em maior crescimento das mudas. As propriedades dos substratos, densidade aparente, pH e capacidade de troca catiônica são importantes na produção de mudas, pois apresentaram correlações significativas com as variáveis biométricas.

  1. Direct imaging electron microscopy (EM) methods in modern structural biology: overview and comparison with X-ray crystallography and single-particle cryo-EM reconstruction in the studies of large macromolecules. (United States)

    Miyaguchi, Katsuyuki


    Determining the structure of macromolecules is important for understanding their function. The fine structure of large macromolecules is currently studied primarily by X-ray crystallography and single-particle cryo-electron microscopy (EM) reconstruction. Before the development of these techniques, macromolecular structure was often examined by negative-staining, rotary-shadowing and freeze-etching EM, which are categorised here as 'direct imaging EM methods'. In this review, the results are summarised by each of the above techniques and compared with respect to four macromolecules: the ryanodine receptor, cadherin, rhodopsin and the ribosome-translocon complex (RTC). The results of structural analysis of the ryanodine receptor and cadherin are consistent between each technique. The results obtained for rhodopsin vary to some extent within each technique and between the different techniques. Finally, the results for RTC are inconsistent between direct imaging EM and other analytical techniques, especially with respect to the space within RTC, the reasons for which are discussed. Then, the role of direct imaging EM methods in modern structural biology is discussed. Direct imaging methods should support and verify the results obtained by other analytical methods capable of solving three-dimensional molecular architecture, and they should still be used as a primary tool for studying macromolecule structure in vivo. © 2014 Société Française des Microscopies and Société de Biologie Cellulaire de France. Published by John Wiley & Sons Ltd.

  2. Rapid Development of Microsatellite Markers with 454 Pyrosequencing in a Vulnerable Fish<em>,> the Mottled Skate<em>, Raja em>pulchra>

    Directory of Open Access Journals (Sweden)

    Jung-Ha Kang


    Full Text Available The mottled skate, <em>Raja pulchraem>, is an economically valuable fish. However, due to a severe population decline, it is listed as a vulnerable species by the International Union for Conservation of Nature. To analyze its genetic structure and diversity, microsatellite markers were developed using 454 pyrosequencing. A total of 17,033 reads containing dinucleotide microsatellite repeat units (mean, 487 base pairs were identified from 453,549 reads. Among 32 loci containing more than nine repeat units, 20 primer sets (62% produced strong PCR products, of which 14 were polymorphic. In an analysis of 60 individuals from two <em>R. pulchra em>populations, the number of alleles per locus ranged from 1–10, and the mean allelic richness was 4.7. No linkage disequilibrium was found between any pair of loci, indicating that the markers were independent. The Hardy–Weinberg equilibrium test showed significant deviation in two of the 28 single-loci after sequential Bonferroni’s correction. Using 11 primer sets, cross-species amplification was demonstrated in nine related species from four families within two classes. Among the 11 loci amplified from three other <em>Rajidae> family species; three loci were polymorphic. A monomorphic locus was amplified in all three <em>Rajidae> family species and the <em>Dasyatidae> family. Two <em>Rajidae> polymorphic loci amplified monomorphic target DNAs in four species belonging to the Carcharhiniformes class, and another was polymorphic in two Carcharhiniformes species.

  3. Synthesis of a 2,2'-Bipyridyl Functionalized Oligovinylene-Phenylene Using Heck and Horner-Wadsworth-Emmons Reactions and X-ray Crystal Structure of <em>E>-(4-(4-Bromostyrylphenyl(methylsulfane

    Directory of Open Access Journals (Sweden)

    Orsolya Karácsony


    Full Text Available The synthesis of a new 2,2'-bipyridyl functionalized oligovinylenephenylene (OVP-5 containing a methyl protected thiol using Heck coupling and the Horner-Wadsworth-Emmons reaction and is described. A key step involving a diisopropylcarbodiimide promoted dehydration of a stable b-hydroxyphosphonate intermediate was identified. The structure of precursor <em>E>-(4-(4-bromostyrylphenyl(methylsulfane (1 was determined using X-ray crystallography.

  4. Damage Assessment of Aerospace Structural Components by Impedance Based Health Monitoring (United States)

    Gyekenyesi, Andrew L.; Martin, Richard E.; Sawicki, Jerzy T.; Baaklini, George Y.


    This paper addresses recent efforts at the NASA Glenn Research Center at Lewis Field relating to the set-up and assessment of electro-mechanical (E/M) impedance based structural health monitoring. The overall aim is the application of the impedance based technique to aeronautic and space based structural components. As initial steps, a laboratory was created, software written, and experiments conducted on aluminum plates in undamaged and damaged states. A simulated crack, in the form of a narrow notch at various locations, was analyzed using piezoelectric-ceramic (PZT: lead, zirconate, titarate) patches as impedance measuring transducers. Descriptions of the impedance quantifying hardware and software are provided as well as experimental results. In summary, an impedance based health monitoring system was assembled and tested. The preliminary data showed that the impedance based technique was successful in recognizing the damage state of notched aluminum plates.

  5. Genome-wide discovery and verification of novel structured RNAs in <em>Plasmodium falciparumem>

    DEFF Research Database (Denmark)

    Mourier, Tobias; Carret, Celine; Kyes, Sue


    We undertook a genome-wide search for novel noncoding RNAs (ncRNA) in the malaria parasite Plasmodium falciparum. We used the RNAz program to predict structures in the noncoding regions of the P. falciparum 3D7 genome that were conserved with at least one of seven other Plasmodium spp. genome...... chimp malaria parasite P. reichenowi. The high confirmation rate within a single parasite life cycle stage suggests that many more of the predictions may be expressed in other stages of the organism's life cycle....

  6. Importance of structure and density of macroalgae communities (<em>Fucus serratusem>) for photosynthetic production and light utilisation

    DEFF Research Database (Denmark)

    Binzer, Thomas; Sand-Jensen, Kaj


    Determination of photosynthetic production in plant communities is essential for evaluating plant growth rates and carbon fluxes in ecosystems, but it cannot easily be derived from the photosynthetic response of individual leaves or thalli, which has been the focus of virtually all previous aquatic...... day-night cycle is attained at an LAI of 5 to 6. Maximum gross production was about 3-fold lower in F. serratus communities than in terrestrial communities in forests, grasslands and crops. Manipulating F. serratus communities to a more vertical structure increased light penetration and gross...

  7. Assessing the accuracy of template-based structure prediction metaservers by comparison with structural genomics structures. (United States)

    Gront, Dominik; Grabowski, Marek; Zimmerman, Matthew D; Raynor, John; Tkaczuk, Karolina L; Minor, Wladek


    The explosion of the size of the universe of known protein sequences has stimulated two complementary approaches to structural mapping of these sequences: theoretical structure prediction and experimental determination by structural genomics (SG). In this work, we assess the accuracy of structure prediction by two automated template-based structure prediction metaservers ( and by measuring the structural similarity of the predicted models to corresponding experimental models determined a posteriori. Of 199 targets chosen from SG programs, the metaservers predicted the structures of about a fourth of them "correctly." (In this case, "correct" was defined as placing more than 70 % of the alpha carbon atoms in the model within 2 Å of the experimentally determined positions.) Almost all of the targets that could be modeled to this accuracy were those with an available template in the Protein Data Bank (PDB) with more than 25 % sequence identity. The majority of those SG targets with lower sequence identity to structures in the PDB were not predicted by the metaservers with this accuracy. We also compared metaserver results to CASP8 results, finding that the models obtained by participants in the CASP competition were significantly better than those produced by the metaservers.

  8. Inatividade física em idosos não institucionalizados: estudo de base populacional

    Directory of Open Access Journals (Sweden)

    Bruno Morbeck de Queiroz


    Full Text Available O objetivo deste estudo é descrever a prevalência de inatividade física e analisar os fatores sociodemográficos, de estilo de vida e condições de saúde associados em idosos do Nordeste brasileiro. Estudo descritivo e de associação, baseado em dados secundários originados de uma pesquisa epidemiológica de base populacional envolvendo 316 idosos. O nível de atividade física foi avaliado por meio do International Physical Activity Questionnaire. As variáveis explanatórias foram: sexo, grupo etário, arranjo familiar, sabe ler e escrever, trabalho remunerado ou voluntário, tabagismo, sintomatologia depressiva, pressão arterial elevada, hiperglicemia em jejum e capacidade funcional. A prevalência da inatividade física foi de 46,5. Os resultados da análise múltipla indicaram que a inatividade física foi positivamente associada ao grupo etário ≥ 80 anos (RP = 2,37, a falta de ocupação (RP = 4,86 e a dependência nas atividades instrumentais de vida diária (RP = 1,47 e nas atividades básicas de vida diária (RP = 1,60. A inatividade física foi altamente prevalente na população estudada, tornando-se imprescindível a discussão de programas que incentivem e possibilite maior adesão à prática da atividade física, tendo em vista o combate a inatividade física e os fatores de risco decorrentes deste comportamento.

  9. Cryptic speciation in the recently discovered American cycliophoran <em>Symbion americanusem>; genetic structure and population expansion

    DEFF Research Database (Denmark)

    Baker, J.M.; Funch, Peter; Giribet, G.


      Symbion americanus was recently described as the second species in the phylum Cycliophora, living commensally on the American commercial lobster Homarus americanus. A previous genetic analysis of American and European populations of cycliophorans suggested that haplotype divergence in S....... americanus was much greater than in its European counterpart S. pandora. This study examined the population structure and demographics of 169 individuals thought to belong to S. americanus collected from lobsters over 13 North American localities (Nova Scotia, Canada to Maryland, USA) between October 2003...... and January 2006. Cytochrome c oxidase subunit I sequence data clearly suggested the presence of three cryptic lineages in a species complex, often co-occurring in the same lobster specimens. One of these lineages, named the "G" lineage, was represented by very few individuals and therefore was excluded from...

  10. Varying-energy CT imaging method based on EM-TV (United States)

    Chen, Ping; Han, Yan


    For complicated structural components with wide x-ray attenuation ranges, conventional fixed-energy computed tomography (CT) imaging cannot obtain all the structural information. This limitation results in a shortage of CT information because the effective thickness of the components along the direction of x-ray penetration exceeds the limit of the dynamic range of the x-ray imaging system. To address this problem, a varying-energy x-ray CT imaging method is proposed. In this new method, the tube voltage is adjusted several times with the fixed lesser interval. Next, the fusion of grey consistency and logarithm demodulation are applied to obtain full and lower noise projection with a high dynamic range (HDR). In addition, for the noise suppression problem of the analytical method, EM-TV (expectation maximization-total Jvariation) iteration reconstruction is used. In the process of iteration, the reconstruction result obtained at one x-ray energy is used as the initial condition of the next iteration. An accompanying experiment demonstrates that this EM-TV reconstruction can also extend the dynamic range of x-ray imaging systems and provide a higher reconstruction quality relative to the fusion reconstruction method.

  11. Allometric and Isometric variations in the Italian <em>Apodemus sylvaticusem> and <em>Apodemus flavicollisem> with respect to the conditions of allopatry and sympatry / Variazioni allometriche e isometriche in <em>Apodemus sylvaticusem> e <em>Apodemus flavicollisem> italiani, rispetto alle condizioni di allopatria e simpatria

    Directory of Open Access Journals (Sweden)

    Giovanni Amori


    thickness and positively linked to skull length is allometric. The intraspecific comparison perhaps reflects a gradient of skull length, whereas the interspecific one a difference in size and thickness between <em>A. sylvaticusem> and <em>A. flavicollisem> skull. On the other hand it appears, from Filippucci et al. (1984 that the importance of genetical factors is highly dependent on the particular character examined and on the species under study. In such a manner, results which are ecologically rather similar could be obtained with different processes. Conversely, the isometry and allopatry of characters seems to depend on different ways from the taxonomical, evolutive and ecologica1 context taken into account. Namely, some characters seem to be more subject to the competitive pressure, others to the genera1 structural model of the species. On the other hand, it is not sure that competition can explain all the observed phenomena, some of which may have a multiple base. More research is needed in order to elucidate such casual aspects of observed phenomena. Riassunto Su <em>Apodemus sylvaticusem> dell'Italia insulare e su <em>A. sylvaticusem> ed <em>Apodemus flavicollisem> dell'Italia peninsulare sono stati studiati alcuni caratteri cranici, evidenziandone l'isometria o l'allometria. Su detti caratteri sono stati verificati e discussi i modelli eco1ogici: variazione di nicchia, spostamento dei caratteri, convergenza fenotipica e parallelismo di caratteri in condizione di simpatria e/o allopatria.

  12. Lagrangian based methods for coherent structure detection

    Energy Technology Data Exchange (ETDEWEB)

    Allshouse, Michael R., E-mail: [Center for Nonlinear Dynamics and Department of Physics, University of Texas at Austin, Austin, Texas 78712 (United States); Peacock, Thomas, E-mail: [Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 (United States)


    There has been a proliferation in the development of Lagrangian analytical methods for detecting coherent structures in fluid flow transport, yielding a variety of qualitatively different approaches. We present a review of four approaches and demonstrate the utility of these methods via their application to the same sample analytic model, the canonical double-gyre flow, highlighting the pros and cons of each approach. Two of the methods, the geometric and probabilistic approaches, are well established and require velocity field data over the time interval of interest to identify particularly important material lines and surfaces, and influential regions, respectively. The other two approaches, implementing tools from cluster and braid theory, seek coherent structures based on limited trajectory data, attempting to partition the flow transport into distinct regions. All four of these approaches share the common trait that they are objective methods, meaning that their results do not depend on the frame of reference used. For each method, we also present a number of example applications ranging from blood flow and chemical reactions to ocean and atmospheric flows.

  13. Structure Based Antibody-Like Peptidomimetics

    Directory of Open Access Journals (Sweden)

    Mark I. Greene


    Full Text Available Biologics such as monoclonal antibodies (mAb and soluble receptors represent new classes of therapeutic agents for treatment of several diseases. High affinity and high specificity biologics can be utilized for variety of clinical purposes. Monoclonal antibodies have been used as diagnostic agents when coupled with radionuclide, immune modulatory agents or in the treatment of cancers. Among other limitations of using large molecules for therapy the actual cost of biologics has become an issue. There is an effort among chemists and biologists to reduce the size of biologics which includes monoclonal antibodies and receptors without a reduction of biological efficacy. Single chain antibody, camel antibodies, Fv fragments are examples of this type of deconstructive process. Small high-affinity peptides have been identified using phage screening. Our laboratory used a structure-based approach to develop small-size peptidomimetics from the three-dimensional structure of proteins with immunoglobulin folds as exemplified by CD4 and antibodies. Peptides derived either from the receptor or their cognate ligand mimics the functions of the parental macromolecule. These constrained peptides not only provide a platform for developing small molecule drugs, but also provide insight into the atomic features of protein-protein interactions. A general overview of the reduction of monoclonal antibodies to small exocyclic peptide and its prospects as a useful diagnostic and as a drug in the treatment of cancer are discussed.

  14. An EM algorithm based on an internal list for estimating haplotype distributions of rare variants from pooled genotype data. (United States)

    Kuk, Anthony Y C; Li, Xiang; Xu, Jinfeng


    Pooling is a cost effective way to collect data for genetic association studies, particularly for rare genetic variants. It is of interest to estimate the haplotype frequencies, which contain more information than single locus statistics. By viewing the pooled genotype data as incomplete data, the expectation-maximization (EM) algorithm is the natural algorithm to use, but it is computationally intensive. A recent proposal to reduce the computational burden is to make use of database information to form a list of frequently occurring haplotypes, and to restrict the haplotypes to come from this list only in implementing the EM algorithm. There is, however, the danger of using an incorrect list, and there may not be enough database information to form a list externally in some applications. We investigate the possibility of creating an internal list from the data at hand. One way to form such a list is to collapse the observed total minor allele frequencies to "zero" or "at least one", which is shown to have the desirable effect of amplifying the haplotype frequencies. To improve coverage, we propose ways to add and remove haplotypes from the list, and a benchmarking method to determine the frequency threshold for removing haplotypes. Simulation results show that the EM estimates based on a suitably augmented and trimmed collapsed data list (ATCDL) perform satisfactorily. In two scenarios involving 25 and 32 loci respectively, the EM-ATCDL estimates outperform the EM estimates based on other lists as well as the collapsed data maximum likelihood estimates. The proposed augmented and trimmed CD list is a useful list for the EM algorithm to base upon in estimating the haplotype distributions of rare variants. It can handle more markers and larger pool size than existing methods, and the resulting EM-ATCDL estimates are more efficient than the EM estimates based on other lists.

  15. Structure-Based Algorithms for Microvessel Classification

    KAUST Repository

    Smith, Amy F.


    © 2014 The Authors. Microcirculation published by John Wiley & Sons Ltd. Objective: Recent developments in high-resolution imaging techniques have enabled digital reconstruction of three-dimensional sections of microvascular networks down to the capillary scale. To better interpret these large data sets, our goal is to distinguish branching trees of arterioles and venules from capillaries. Methods: Two novel algorithms are presented for classifying vessels in microvascular anatomical data sets without requiring flow information. The algorithms are compared with a classification based on observed flow directions (considered the gold standard), and with an existing resistance-based method that relies only on structural data. Results: The first algorithm, developed for networks with one arteriolar and one venular tree, performs well in identifying arterioles and venules and is robust to parameter changes, but incorrectly labels a significant number of capillaries as arterioles or venules. The second algorithm, developed for networks with multiple inlets and outlets, correctly identifies more arterioles and venules, but is more sensitive to parameter changes. Conclusions: The algorithms presented here can be used to classify microvessels in large microvascular data sets lacking flow information. This provides a basis for analyzing the distinct geometrical properties and modelling the functional behavior of arterioles, capillaries, and venules.

  16. Sistema Jargão : um sistema para analise de base de dados em linguagem natural


    Ivan Rizzo Guilherme


    Resumo: Neste trabalho são apresentados os aspectos teóricos e a implementação de um sistema computacional,denominado de Jargão, para a tarefa da análise de Base de Dados em Linguagem Natural. O sistema utiliza os conceitos de um novo modelo de neurônio, formalizado através dos conceitos de linguagem nebulosa, que suporta o processamento da linguagem natural. Este modelo de neurônio é utilizado na construção de redes neurais estruturadas hierarquicamente que permitem representar os complexos ...

  17. Genetic diversity and population structure of the endangered marsupial <em>Sarcophilus harrisii em>(Tasmanian devil)

    DEFF Research Database (Denmark)

    Miller, Webb; Hayes, Vanessa M.; Ratan, Aakrosh


    The Tasmanian devil (Sarcophilus harrisii) is threatened with extinction because of a contagious cancer known as Devil Facial Tumor Disease. The inability to mount an immune response and to reject these tumors might be caused by a lack of genetic diversity within a dwindling population. Here we...... report a whole-genome analysis of two animals originating from extreme northwest and southeast Tasmania, the maximal geographic spread, together with the genome from a tumor taken from one of them. A 3.3-Gb de novo assembly of the sequence data from two complementary next-generation sequencing platforms...... that the observed low genetic diversity in today's population preceded the Devil Facial Tumor Disease disease outbreak by at least 100 y. Using a genetically characterized breeding stock based on the genome sequence will enable preservation of the extant genetic diversity in future Tasmanian devil populations....

  18. The Effect of Ambulance Staffing Models in a Metropolitan, Fire-Based EMS System. (United States)

    Cortez, Eric J; Panchal, Ashish R; Davis, James E; Keseg, David P


    Introduction The staffing of ambulances with different levels of Emergency Medical Service (EMS) providers is a difficult decision with evidence being mixed on the benefit of each model. Hypothesis/Problem The objective of this study was to describe a pilot program evaluating alternative staffing on two ambulances utilizing the paramedic-basic (PB) model (staffed with one paramedic and one emergency medical technician[EMT]). This was a retrospective study conducted from September 17, 2013 through December 31, 2013. The PB ambulances were compared to geographically matched ambulances staffed with paramedic-paramedic (PP ambulances). One PP and one PB ambulance were based at Station A; one PP and one PB ambulance were based at Station B. The primary outcome was total on-scene time. Secondary outcomes included time-to-electrocardiogram (EKG), time-to-intravenous (IV) line insertion, IV-line success rate, and percentage of protocol violations. Inclusion criteria were all patients requesting prehospital services that were attended to by these teams. Patients were excluded if they were not attended to by the study ambulance vehicles. Descriptive statistics were reported as medians and interquartile ranges (IQR). Proportions were reported with 95% confidence intervals (CI). The Mann-Whitley U test was used for significance testing (Pfire-based EMS system. Prehosp Disaster Med. 2017;32(2):175-179.

  19. Structure-based characterization of multiprotein complexes. (United States)

    Wiederstein, Markus; Gruber, Markus; Frank, Karl; Melo, Francisco; Sippl, Manfred J


    Multiprotein complexes govern virtually all cellular processes. Their 3D structures provide important clues to their biological roles, especially through structural correlations among protein molecules and complexes. The detection of such correlations generally requires comprehensive searches in databases of known protein structures by means of appropriate structure-matching techniques. Here, we present a high-speed structure search engine capable of instantly matching large protein oligomers against the complete and up-to-date database of biologically functional assemblies of protein molecules. We use this tool to reveal unseen structural correlations on the level of protein quaternary structure and demonstrate its general usefulness for efficiently exploring complex structural relationships among known protein assemblies. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

  20. Study of methane solubility in oil base used in oil base drilling fluid; Estudo da solubilidade de metano em base oleo utilizada em fluido de perfuracao base oleo

    Energy Technology Data Exchange (ETDEWEB)

    Silva, Carolina Teixeira da; Mariolani, Jose Ricardo Lenzi [Universidade Estadual de Campinas, SP (Brazil); Ribeiro, Paulo Roberto; Lomba, Rosana Fatima Teixeira; Bonet, Euclides Jose


    During drilling a well, it is necessary to prevent and control high pressurized zones because while drilling on those zones, could occur a kick if the formation pressure were higher then downhole pressure, allowing the entering of undesirables fluids from the formation to the wellbore. If the well is not controlled this kick could became a blowout, generating damages to the environment, to the equipment and the human life. When drilling using oil-based mud, the concern related to the well control would be higher due the gas solubility in the mud, which could make it hard to detect the kick, especially in deep and ultra deep waters. In this work we have studied the interaction between methane and organic liquids used in drilling fluids, and the measurement and analysis of the thermodynamic properties of those gas liquid mixtures. There have been measured parameters like the oil formation volume factor (FVF{sub o}), bubble pressure, solubility (Rs) and the density of the saturated liquid in function of methane mole fraction and temperature. The results have shown that the gas solubility, at downhole conditions and during kick circulation, is a factor very important to the safety during well drilling in deep and ultra deep waters. (author)

  1. Adaptive Baseline Enhances EM-Based Policy Search: Validation in a View-Based Positioning Task of a Smartphone Balancer (United States)

    Wang, Jiexin; Uchibe, Eiji; Doya, Kenji


    EM-based policy search methods estimate a lower bound of the expected return from the histories of episodes and iteratively update the policy parameters using the maximum of a lower bound of expected return, which makes gradient calculation and learning rate tuning unnecessary. Previous algorithms like Policy learning by Weighting Exploration with the Returns, Fitness Expectation Maximization, and EM-based Policy Hyperparameter Exploration implemented the mechanisms to discard useless low-return episodes either implicitly or using a fixed baseline determined by the experimenter. In this paper, we propose an adaptive baseline method to discard worse samples from the reward history and examine different baselines, including the mean, and multiples of SDs from the mean. The simulation results of benchmark tasks of pendulum swing up and cart-pole balancing, and standing up and balancing of a two-wheeled smartphone robot showed improved performances. We further implemented the adaptive baseline with mean in our two-wheeled smartphone robot hardware to test its performance in the standing up and balancing task, and a view-based approaching task. Our results showed that with adaptive baseline, the method outperformed the previous algorithms and achieved faster, and more precise behaviors at a higher successful rate. PMID:28167910

  2. Adaptive Baseline Enhances EM-Based Policy Search: Validation in a View-Based Positioning Task of a Smartphone Balancer. (United States)

    Wang, Jiexin; Uchibe, Eiji; Doya, Kenji


    EM-based policy search methods estimate a lower bound of the expected return from the histories of episodes and iteratively update the policy parameters using the maximum of a lower bound of expected return, which makes gradient calculation and learning rate tuning unnecessary. Previous algorithms like Policy learning by Weighting Exploration with the Returns, Fitness Expectation Maximization, and EM-based Policy Hyperparameter Exploration implemented the mechanisms to discard useless low-return episodes either implicitly or using a fixed baseline determined by the experimenter. In this paper, we propose an adaptive baseline method to discard worse samples from the reward history and examine different baselines, including the mean, and multiples of SDs from the mean. The simulation results of benchmark tasks of pendulum swing up and cart-pole balancing, and standing up and balancing of a two-wheeled smartphone robot showed improved performances. We further implemented the adaptive baseline with mean in our two-wheeled smartphone robot hardware to test its performance in the standing up and balancing task, and a view-based approaching task. Our results showed that with adaptive baseline, the method outperformed the previous algorithms and achieved faster, and more precise behaviors at a higher successful rate.

  3. Reliability-Based Optimization of Structural Elements

    DEFF Research Database (Denmark)

    Sørensen, John Dalsgaard

    In this paper structural elements from an optimization point of view are considered, i.e. only the geometry of a structural element is optimized. Reliability modelling of the structural element is discussed both from an element point of view and from a system point of view. The optimization...

  4. Combined SAXS/EM Based Models of the S. elongatus Post-Translational Circadian Oscillator and its Interactions with the Output His-Kinase SasA

    Energy Technology Data Exchange (ETDEWEB)

    Pattanayek, Rekha; Williams, Dewight R.; Rossi, Gian; Weigand, Steven; Mori, Tetsuya; Johnson, Carl H.; Stewart, Phoebe L.; Egli, Martin (Vanderbilt); (NWU)


    The circadian clock in the cyanobacterium Synechococcus elongatus is composed of a post-translational oscillator (PTO) that can be reconstituted in vitro from three different proteins in the presence of ATP and a transcription-translation feedback loop (TTFL). The homo-hexameric KaiC kinase, phosphatase and ATPase alternates between hypo- and hyper-phosphorylated states over the 24-h cycle, with KaiA enhancing phosphorylation, and KaiB antagonizing KaiA and promoting KaiC subunit exchange. SasA is a His kinase that relays output signals from the PTO formed by the three Kai proteins to the TTFL. Although the crystal structures for all three Kai proteins are known, atomic resolution structures of Kai and Kai/SasA protein complexes have remained elusive. Here, we present models of the KaiAC and KaiBC complexes derived from solution small angle X-ray scattering (SAXS), which are consistent with previous EM based models. We also present a combined SAXS/EM model of the KaiC/SasA complex, which has two N-terminal SasA sensory domains occupying positions on the C-terminal KaiC ring reminiscent of the orientations adopted by KaiB dimers. Using EM we demonstrate that KaiB and SasA compete for similar binding sites on KaiC. We also propose an EM based model of the ternary KaiABC complex that is consistent with the sequestering of KaiA by KaiB on KaiC during the PTO dephosphorylation phase. This work provides the first 3D-catalogue of protein-protein interactions in the KaiABC PTO and the output pathway mediated by SasA.

  5. Combined SAXS/EM based models of the S. elongatus post-translational circadian oscillator and its interactions with the output His-kinase SasA.

    Directory of Open Access Journals (Sweden)

    Rekha Pattanayek

    Full Text Available The circadian clock in the cyanobacterium Synechococcus elongatus is composed of a post-translational oscillator (PTO that can be reconstituted in vitro from three different proteins in the presence of ATP and a transcription-translation feedback loop (TTFL. The homo-hexameric KaiC kinase, phosphatase and ATPase alternates between hypo- and hyper-phosphorylated states over the 24-h cycle, with KaiA enhancing phosphorylation, and KaiB antagonizing KaiA and promoting KaiC subunit exchange. SasA is a His kinase that relays output signals from the PTO formed by the three Kai proteins to the TTFL. Although the crystal structures for all three Kai proteins are known, atomic resolution structures of Kai and Kai/SasA protein complexes have remained elusive. Here, we present models of the KaiAC and KaiBC complexes derived from solution small angle X-ray scattering (SAXS, which are consistent with previous EM based models. We also present a combined SAXS/EM model of the KaiC/SasA complex, which has two N-terminal SasA sensory domains occupying positions on the C-terminal KaiC ring reminiscent of the orientations adopted by KaiB dimers. Using EM we demonstrate that KaiB and SasA compete for similar binding sites on KaiC. We also propose an EM based model of the ternary KaiABC complex that is consistent with the sequestering of KaiA by KaiB on KaiC during the PTO dephosphorylation phase. This work provides the first 3D-catalogue of protein-protein interactions in the KaiABC PTO and the output pathway mediated by SasA.

  6. PRISM-EM: template interface-based modelling of multi-protein complexes guided by cryo-electron microscopy density maps. (United States)

    Kuzu, Guray; Keskin, Ozlem; Nussinov, Ruth; Gursoy, Attila


    The structures of protein assemblies are important for elucidating cellular processes at the molecular level. Three-dimensional electron microscopy (3DEM) is a powerful method to identify the structures of assemblies, especially those that are challenging to study by crystallography. Here, a new approach, PRISM-EM, is reported to computationally generate plausible structural models using a procedure that combines crystallographic structures and density maps obtained from 3DEM. The predictions are validated against seven available structurally different crystallographic complexes. The models display mean deviations in the backbone of EM was further tested on different benchmark sets; the accuracy was evaluated with respect to the structure of the complex, and the correlation with EM density maps and interface predictions were evaluated and compared with those obtained using other methods. PRISM-EM was then used to predict the structure of the ternary complex of the HIV-1 envelope glycoprotein trimer, the ligand CD4 and the neutralizing protein m36.

  7. Floating structures (based on water activities)


    Rodionovskaya Inna Serafi movna; Kocheryaev Stanislav Alexandrovich; Shakhova Marina Evgenevna


    The article briefly describes the types of structures that are widely spread worldwide, and many well-known projects that remain unimplemented. Particular attention is driven to the main features of floating structures and areas of their application. Despite the advances of the present-day technology, floating structures are only used in the travel industry and low-rise construction. The authors consider a substantial though yet unexplored potential of rivers, seas and lakes, a...

  8. Modal Based Fatigue Monitoring of Steel Structures

    DEFF Research Database (Denmark)

    Graugaard-Jensen, J.; Brincker, Rune; Hjelm, H. P.


    In this paper it is shown how the accumulated fatigue in steel structures can be estimated with high accuracy by continuously measuring the accelerations in a few points of the structure. First step is to obtain a good estimate of the mode shapes by performing a natural input modal analysis. The so...... by applying the mode shapes of the calibrated Finite Element model and strains are obtained using the shape functions for the actual elements. The technique has been applied on a model frame structure in the laboratory and on a wind loaded lattice pylon structure. In both cases the estimated stresses has been...

  9. A Limited Structural Modification Results in a Significantly More Efficacious Diazachrysene-Based Filovirus Inhibitor

    Directory of Open Access Journals (Sweden)

    Rekha G. Panchal


    Full Text Available Ebola (EBOV and Marburg (MARV filoviruses are highly infectious pathogens causing deadly hemorrhagic fever in humans and non-human primates. Promising vaccine candidates providing immunity against filoviruses have been reported. However, the sporadic nature and swift progression of filovirus disease underlines the need for the development of small molecule therapeutics providing immediate antiviral effects. Herein we describe a brief structural exploration of two previously reported diazachrysene (DAAC-based EBOV inhibitors. Specifically, three analogs were prepared to examine how slight substituent modifications would affect inhibitory efficacy and inhibitor-mediated toxicity during not only EBOV, but also MARV cellular infection. Of the three analogs, one was highly efficacious, providing IC50 values of 0.696 µM ± 0.13 µM and 2.76 µM ± 0.21 µM against EBOV and MARV infection, respectively, with little or no associated cellular toxicity. Overall, the structure-activity and structure-toxicity results from this study provide a framework for the future development of DAAC-based filovirus inhibitors that will be both active and non-toxic <em>in vivoem>.

  10. Structure based alignment and clustering of proteins (STRALCP) (United States)

    Zemla, Adam T.; Zhou, Carol E.; Smith, Jason R.; Lam, Marisa W.


    Disclosed are computational methods of clustering a set of protein structures based on local and pair-wise global similarity values. Pair-wise local and global similarity values are generated based on pair-wise structural alignments for each protein in the set of protein structures. Initially, the protein structures are clustered based on pair-wise local similarity values. The protein structures are then clustered based on pair-wise global similarity values. For each given cluster both a representative structure and spans of conserved residues are identified. The representative protein structure is used to assign newly-solved protein structures to a group. The spans are used to characterize conservation and assign a "structural footprint" to the cluster.

  11. Synthesis, Antigenicity Against Human Sera and Structure-Activity Relationships of Carbohydrate Moieties from <em>Toxocara> larvae and Their Analogues

    Directory of Open Access Journals (Sweden)

    Takashi Tsuchiya


    Full Text Available Stereocontrolled syntheses of biotin-labeled oligosaccharide portions containing the Galβ1-3GalNAc core of the TES-glycoprotein antigen obtained from larvae of the parasite <em>Toxocara> and their analogues have been accomplished. Trisaccharides Fuc2Meα1-2Gal4Meβ1-3GalNAcα1-OR (A, Fucα1-2Gal4Meβ1-3GalNAcα1-OR (B, Fuc2Meα1-2Galβ1-3GalNAcα1-OR (C, Fucα1-2Galβ1-3GalNAcα1-OR (D and a disaccharide Fuc2Meα1-2Gal4Meβ1-OR (E (R = biotinylated probe were synthesized by block synthesis using 5-(methoxycarbonylpentyl-2,3,4,6-tetra-<em>O>-acetyl-β-D-galactopyranosyl-(1®3-2-azide-4-<em>O>-benzyl-2-deoxy-α-D-galactopyranoside as a common glycosyl acceptor. We examined the antigenicity of these five oligosaccharides by enzyme linked immunosorbent assay (ELISA. Our results demonstrate that the <em>O>-methyl groups in these oligosaccharides are important for their antigenicity and the biotinylated oligosaccharides A, B, C and E have high serodiagnostic potential to detect infections caused by <em>Toxocara> larvae.

  12. [Research on remote sensing monitoring of soil salinization based on measured hyperspectral and EM38 data]. (United States)

    Yao, Yuan; Ding, Jian-Li; Kelimul, Ardak; Zhang, Fang; Lei, Lei


    In the present study, the delta oasis between the Weigan River and the Kuqa River was selected as our study area. Firstly, the measured hyperspectral data related to different soil salinization extent was combined with electromagnetic induction instrument (EM38) in order to establish a soil salinization monitoring model; Secondly, by using the scaling transformation method, the model was adopted to calibrate the soil salinity index calculated from Landsat-TM images. Thirdly, the calibrated Landsat-TM images were used for the retrieval of regional soil salinity, and the retrieved data was verified based on the measured data. We found that at wavelengths of 456, 533, 686 and 1 373 nm, the interpretated data of EM38 were highly correlated with soil spectral reflectance (obtained via first order differentiation transformation of the spectra). Additionally, the soil salinity index model constructed from the combination of 456, 686 and 1 373 nm waveband was the best model among the different saliniza tion monitoring models. The authors' conclusion is that with R2 = 0.799 3 (p salinity information at regional scale by combining the electromagnetic and multispectral data performed better than those monitoring models with only salinity index extracted from multispectral remote sensing method (R2 = 0.587 4, p salinization.

  13. Bases do pensamento fenomenológico e existencial em William James

    Directory of Open Access Journals (Sweden)

    Ana Maria Lopez Calvo de Feijoo

    Full Text Available Neste artigo, temos por objetivo investigar os fundamentos e as bases do pensamento fenomenológico e existencial advindos da Psicologia de William James no que diz respeito à noção de consciência, método e prática clínica. Para tanto, analisamos algumas obras de James e dividimos as suas propostas em três momentos distintos: pragmatismo, funcionalismo e empirismo. Por meio das elaborações em cada um desses momentos, tentamos esclarecer os pontos de encontro e os pontos de desencontro com os pensamentos fenomenológico e existencial. Concluímos que o ponto de encontro diz respeito à tentativa de não objetivação da consciência. Quanto ao desencontro, consideramos que James ainda toma a consciência como objeto da Psicologia e que a fenomenologia e as perspectivas existenciais se afastam da ideia de objeto, uma vez que não consideram a consciência contraposta ao mundo. Outro desencontro apresenta-se na acentuada divergência entre James e o pensamento fenomenológico e existencial no que se refere ao método e à prática bem como aos objetivos da clínica.

  14. Comparison of EM-based and level set partial volume segmentations of MR brain images (United States)

    Tagare, Hemant D.; Chen, Yunmei; Fulbright, Robert K.


    EM and level set algorithms are competing methods for segmenting MRI brain images. This paper presents a fair comparison of the two techniques using the Montreal Neurological Institute's software phantom. There are many flavors of level set algorithms for segmentation into multiple regions (multi-phase algorithms, multi-layer algorithms). The specific algorithm evaluated by us is a variant of the multi-layer level set algorithm. It uses a single level set function for segmenting the image into multiple classes and can be run to completion without restarting. The EM-based algorithm is standard. Both algorithms have the capacity to model a variable number of partial volume classes as well as image inhomogeneity (bias field). Our evaluation consists of systematically changing the number of partial volume classes, additive image noise, and regularization parameters. The results suggest that the performances of both algorithms are comparable across noise, number of partial volume classes, and regularization. The segmentation errors of both algorithms are around 5 - 10% for cerebrospinal fluid, gray and white matter. The level set algorithm appears to have a slight advantage for gray matter segmentation. This may be beneficial in studying certain brain diseases (Multiple Sclerosis or Alzheimer's disease) where small changes in gray matter volume are significant.

  15. O Mestrado do Programa de Pós-graduação em Epidemiologia da UFPel baseado em consórcio de pesquisa: uma experiência inovadora UFPel's epidemiology MSc program based on research consortium: an innovative experience

    Directory of Open Access Journals (Sweden)

    Aluísio J. D. Barros


    Full Text Available O Programa de Pós-graduação em Epidemiologia da UFPel realizou um intenso trabalho de auto-avaliação para resolver problemas identificados com seu curso de mestrado. O resultado foi a introdução de uma estrutura curricular baseada em dois pilares. De um lado, disciplinas de cunho teórico, fornecendo a base da formação do mestrando; de outro, disciplinas de cunho prático, onde os alunos trabalham coletivamente a construção de seu projeto de pesquisa, passando pela escolha de um tema, revisão da literatura, definição de objetivos e da metodologia. Esse esforço conjunto culmina na realização de um trabalho de campo único, na forma de um estudo transversal de base populacional, em que todos os mestrandos participam de maneira integral, obtendo dados para sua dissertação. Essa estratégia tem garantido a formação de mestres em epidemiologia com forte base teórica e com experiência de preparação e condução de um trabalho de campo. Além disso, tem sido possível manter um tempo de titulação abaixo de 24 meses. Cerca de 80% dos egressos têm publicado pelo menos um artigo baseado em seu mestrado. Destas publicações, quase 90% têm se dado em periódicos classificados como Internacional-A no Qualis da Capes.The postgraduate program in epidemiology of the Federal University of Pelotas, Brazil, went through an intense self-assessment process to solve problems related to its Master's course. The result was the introduction of a curricular structure based on two pillars. The first one: theoretical courses to offer students the bases of epidemiology. The other, practical training in which students work in groups to design their research projects, from the choice of a research question, to literature review, definition of objectives and methods. This joint effort leads to shared fieldwork, a cross-sectional population-based study, where all students have full participation and get data for their dissertations. This strategy

  16. Comparison of sequence-based and structure-based phylogenetic ...

    Indian Academy of Sciences (India)


    The extent of divergence in the three-dimensional (3-D) structures of homologous proteins in a family is related to the extent of similarity in their amino acid sequences. (Lesk and Chothia 1980). It is well known that the 3-D structures and structural features of homologous proteins are conserved better than their amino acid ...

  17. Distributed Prognostics Based on Structural Model Decomposition (United States)

    National Aeronautics and Space Administration — Within systems health management, prognostics focuses on predicting the remaining useful life of a system. In the model-based prognostics paradigm, physics-based...

  18. Emergency Medical Service (EMS) Stations (United States)

    Kansas Data Access and Support Center — EMS Locations in Kansas The EMS stations dataset consists of any location where emergency medical services (EMS) personnel are stationed or based out of, or where...

  19. The EM Method in a Probabilistic Wavelet-Based MRI Denoising

    Directory of Open Access Journals (Sweden)

    Marcos Martin-Fernandez


    Full Text Available Human body heat emission and others external causes can interfere in magnetic resonance image acquisition and produce noise. In this kind of images, the noise, when no signal is present, is Rayleigh distributed and its wavelet coefficients can be approximately modeled by a Gaussian distribution. Noiseless magnetic resonance images can be modeled by a Laplacian distribution in the wavelet domain. This paper proposes a new magnetic resonance image denoising method to solve this fact. This method performs shrinkage of wavelet coefficients based on the conditioned probability of being noise or detail. The parameters involved in this filtering approach are calculated by means of the expectation maximization (EM method, which avoids the need to use an estimator of noise variance. The efficiency of the proposed filter is studied and compared with other important filtering techniques, such as Nowak’s, Donoho-Johnstone’s, Awate-Whitaker’s, and nonlocal means filters, in different 2D and 3D images.

  20. Modelo de oposições múltiplas modificado: abordagem baseada em traços distintivos Modified multiple oppositions' model: approach based on distinctive features

    Directory of Open Access Journals (Sweden)

    Karina Carlesso Pagliarin


    Full Text Available O objetivo deste trabalho foi propor uma abordagem com enfoque em traços distintivos para o Modelo de Oposições Múltiplas e testar sua aplicação em um sujeito falante do Português Brasileiro. O Modelo foi aplicado em um sujeito do sexo masculino, com desvio fonológico moderado-severo e idade de seis anos e meio. Após avaliação fonológica, procedeu-se à seleção dos sons-alvo. Considerou-se o sistema fonológico inicial, bem como os traços distintivos alterados ([+voz], [+soante], [+aproximante], [coronal/±anterior], [-contínuo]. Os traços com maior número de alterações eram [+voz, +soante, +aproximante], justificando a escolha dos seguintes sons-alvo para tratamento: /r/ x /l/ x // x // x /z/, em onset medial.Tendo como base a aplicação desse modelo em falantes do inglês, percebeu-se a necessidade de introduzir alguns procedimentos, como: a escolha dos sons-alvo a partir dos traços distintivos alterados e a estrutura da sessão terapêutica. Ao final, o sujeito foi reavaliado a fim de verificar as aquisições no sistema fonológico. Após dez sessões de fonoterapia,o sujeito adquiriu os fonemas /l, , , z/, generalizando-os para outras posições na palavra (/Z/ e /l/ em onset inicial. Verificou-se, também, a ocorrência de generalização para a mesma classe e para outras classes de sons (/b/, /d/, /g/, /v/. No entanto, o fonema /r/ não foi adquirido. Esta proposta mostrou-se efetiva, pois o sujeito apresentou melhora em seu sistema fonológico com poucas sessões terapêuticas. Pôde-se observar que o Modelo de Oposições Múltiplas, utilizando a abordagem com base em traços distintivos é eficaz, pois favoreceu diversas mudanças fonológicas.The aim of this study was to propose an approach based on distinctive features for the Multiple Oppositions Model, and to test its application on a Brazilian Portuguese speaker. The model was used with a male subject with moderate-severe phonological disorder and six years

  1. Combinatorics of RNA Secondary Structures with Base Triples. (United States)

    Müller, Robert; Nebel, Markus E


    The structure of RNA has been the subject of intense research over the last decades due to its importance for the correct functioning of RNA molecules in biological processes. Hence, a large number of models for RNA folding and corresponding algorithms for structure prediction have been developed. However, previous models often only consider base pairs, although every base is capable of up to three edge-to-edge interactions with other bases. Recently, Höner zu Siederdissen et al. presented an extended model of RNA secondary structure, including base triples together with a folding algorithm-the first thermodynamics-based algorithm that allows the prediction of secondary structures with base triples. In this article, we investigate the search space processed by this new algorithm, that is, the combinatorics of extended RNA secondary structures with base triples. We present generalized definitions for structural motifs like hairpins, stems, bulges, or interior loops occurring in structures with base triples. Furthermore, we prove precise asymptotic results for the number of different structures (size of search space) and expectations for various parameters associated with structural motifs (typical shape of folding). Our analysis shows that the asymptotic number of secondary structures of size n increases exponentially to [Formula: see text] compared to the classic model by Stein and Waterman for which [Formula: see text] structures exist. A comparison with the classic model reveals large deviations in the expected structural appearance, too. The inclusion of base triples constitutes a significant refinement of the combinatorial model of RNA secondary structure, which, by our findings, is quantitatively characterized. Our results are of special theoretical interest, because a closer look at the numbers involved suggests that extended RNA secondary structures constitute a new combinatorial class not bijective with any other combinatorial objects studied so far.

  2. Lipid Nanodiscs as a Tool for High-Resolution Structure Determination of Membrane Proteins by Single-Particle Cryo-EM. (United States)

    Efremov, Rouslan G; Gatsogiannis, Christos; Raunser, Stefan


    The "resolution revolution" in electron cryomicroscopy (cryo-EM) profoundly changed structural biology of membrane proteins. Near-atomic structures of medium size to large membrane protein complexes can now be determined without crystallization. This significantly accelerates structure determination and also the visualization of small bound ligands. There is an additional advantage: the structure of membrane proteins can now be studied in their native or nearly native lipid bilayer environment. A popular lipid bilayer mimetic are lipid nanodiscs, which have been thoroughly characterized and successfully utilized in multiple applications. Here, we provide a guide for using lipid nanodiscs as a tool for single-particle cryo-EM of membrane proteins. We discuss general methodological aspects and specific challenges of protein reconstitution into lipid nanodiscs and high-resolution structure determination of the nanodisc-embedded complexes. Furthermore, we describe in detail case studies of two successful applications of nanodiscs in cryo-EM, namely, the structure determination of the rabbit ryanodine receptor, RyR1, and the pore-forming TcdA1 toxin subunit from Photorhabdus luminescens. We discuss cryo-EM-specific hurdles concerning sample homogeneity, distribution of reconstituted particles in vitreous ice, and solutions to overcome them. © 2017 Elsevier Inc. All rights reserved.

  3. Expression of Selected <em>Ginkgo em>>biloba em>Heat Shock Protein Genes After Cold Treatment Could Be Induced by Other Abiotic Stress

    Directory of Open Access Journals (Sweden)

    Feng Xu


    Full Text Available Heat shock proteins (HSPs play various stress-protective roles in plants. In this study, three <em>HSP> genes were isolated from a suppression subtractive hybridization (SSH cDNA library of <em>Ginkgo bilobaem> leaves treated with cold stress. Based on the molecular weight, the three genes were designated <em>GbHSP16.8em>, <em>GbHSP17em> and <em>GbHSP70em>. The full length of the three genes were predicted to encode three polypeptide chains containing 149 amino acids (Aa, 152 Aa, and 657 Aa, and their corresponding molecular weights were predicted as follows: 16.67 kDa, 17.39 kDa, and 71.81 kDa respectively. The three genes exhibited distinctive expression patterns in different organs or development stages. <em>GbHSP16.8em> and <em>GbHSP70em> showed high expression levels in leaves and a low level in gynoecia, <em>GbHSP17em> showed a higher transcription in stamens and lower level in fruit. This result indicates that <em>GbHSP16.8em> and <em>GbHSP70 em>may play important roles in <em>Ginkgo> leaf development and photosynthesis, and <em>GbHSP17em> may play a positive role in pollen maturation. All three <em>GbHSPs> were up-regulated under cold stress, whereas extreme heat stress only caused up-regulation of <em>GbHSP70em>, UV-B treatment resulted in up-regulation of <em>GbHSP16.8em> and <em>GbHSP17em>, wounding treatment resulted in up-regulation of <em>GbHSP16.8em> and <em>GbHSP70em>, and abscisic acid (ABA treatment caused up-regulation of <em>GbHSP70em> primarily.

  4. Structuring AHP-based maintenance policy selection

    NARCIS (Netherlands)

    Goossens, Adriaan; Basten, Robertus Johannes Ida; Hummel, J. Marjan; van der Wegen, Leonardus L.M.


    We aim to structure the maintenance policy selection process for ships, using the Analytic Hierarchy Process (AHP). Maintenance is an important contributor to reach the intended life-time of capital technical assets, and it is gaining increasing interest and relevance. A maintenance policy is a

  5. Risk based design of civil structures

    NARCIS (Netherlands)

    Van Gelder, P.; Roos, A.; Vrijling, H.


    The Art and Science of Model Building: A Bayesian Approach, by Prof. A. Der Kiureghian; The talk will describe a Bayesian approach to developing models, with special emphasis on limit-state models for reinforced concrete structures. The formulation can incorporate all kinds of information

  6. Comparison of sequence-based and structure-based phylogenetic ...

    Indian Academy of Sciences (India)


    Dec 12, 2006 ... Using a dataset of 108 protein domain families of known structures with at least 10 members per family we present a comparison of extent of structural and sequence dissimilarities among pairs of proteins which are inputs into the construction of phylogenetic trees. We find that correlation between the ...

  7. Structural dynamics of ribosome subunit association studied by mixing-spraying time-resolved cryo-EM (United States)

    Chen, Bo; Kaledhonkar, Sandip; Sun, Ming; Shen, Bingxin; Lu, Zonghuan; Barnard, David; Lu, Toh-Ming; Gonzalez, Ruben L.; Frank, Joachim


    Ribosomal subunit association is a key checkpoint in translation initiation, but its structural dynamics are poorly understood. Here, we used a recently developed mixing-spraying, time-resolved, cryogenic electron microscopy (cryo-EM) method to study ribosomal subunit association in the sub-second time range. We have improved this method and increased the cryo-EM data yield by tenfold. Pre-equilibrium states of the association reaction were captured by reacting the mixture of ribosomal subunits for 60 ms and 140 ms. We also identified three distinct ribosome conformations in the associated ribosomes. The observed proportions of these conformations are the same in these two time points, suggesting that ribosomes equilibrate among the three conformations within less than 60 ms upon formation. Our results demonstrate that the mixing-spraying method can capture multiple states of macromolecules during a sub-second reaction. Other fast processes, such as translation initiation, decoding and ribosome recycling, are amenable to study with this method. PMID:26004440

  8. Mapping Porosity Structure Offshore Torrey Pines State Natural Reserve and Del Mar, California Using a Surface Towed EM System (United States)

    Martin, Thomas Patrick

    Controlled source electromagnetic methods have been used in exploration of the offshore environment for over 50 years to map the resistivity structure of the earth. Developments in both instrumentation and computational power have lead to many advancements that have led to discoveries and insights about the subsurface. One of these advancements has been the development of towed EM acquisition systems. One system the Marine EM Lab at Scripps Institution of Oceanography has developed is a shallow water system, named Porpoise, can be used in water depths as shallow as 5m. In May of 2014, a one day field test of this new shallow water acquisition system took place offshore of Del Mar and Torrey Pines State Natural Reserve, California. The data from this field test corresponds with previous interpretations of paleochannels directly offshore modern day San Dieguito and Soledad Valley river outflows. With resistivity data, it is possible to indirectly map porosity in the near surface and to map geological features. The data dense and economical operation of the Porpoise acquisition system can be used to map resistivity and indirectly porosity in a variety of shallow water marine environments. This field test proves the viability and limitations of the Porpoise system.

  9. Sandwich Structure Based On Corrugated-Core: A Review

    Directory of Open Access Journals (Sweden)

    Zaid N. Z. M.


    Full Text Available Sandwich structures are commonly based on polymeric foam and honeycomb core material, for use in lightweight applications such as fuselage in aero plane, hull in marine construction and others. A review of sandwich structure based on corrugated-core is proposed and presented in this paper. Firstly, this paper aims to provide a means of comparing available sandwich structure in industries. Secondly, this paper aims to provide sandwich structure with corrugated-core for future research development efforts in field of sandwich construction. This paper starts with introduction of composite material such as sandwich structure, the advantages of sandwich structure was shown. After that these papers provide the structure of sandwich structure which includes the two faces and the cores. Furthermore, sandwich structure with different cores, which is honeycomb, foam core and corrugated core are discussed. At the end, the paper discussed more on corrugated-core for future research development.

  10. Cryo-EM structure of Hepatitis C virus IRES bound to the human ribosome at 3.9-Å resolution (United States)

    Quade, Nick; Boehringer, Daniel; Leibundgut, Marc; van den Heuvel, Joop; Ban, Nenad


    Hepatitis C virus (HCV), a widespread human pathogen, is dependent on a highly structured 5'-untranslated region of its mRNA, referred to as internal ribosome entry site (IRES), for the translation of all of its proteins. The HCV IRES initiates translation by directly binding to the small ribosomal subunit (40S), circumventing the need for many eukaryotic translation initiation factors required for mRNA scanning. Here we present the cryo-EM structure of the human 40S ribosomal subunit in complex with the HCV IRES at 3.9 Å resolution, determined by focused refinement of an 80S ribosome-HCV IRES complex. The structure reveals the molecular details of the interactions between the IRES and the 40S, showing that expansion segment 7 (ES7) of the 18S rRNA acts as a central anchor point for the HCV IRES. The structural data rationalizes previous biochemical and genetic evidence regarding the initiation mechanism of the HCV and other related IRESs.

  11. Photonic structures based on hybrid nanocomposites (United States)

    Husaini, Saima

    In this thesis, photonic structures embedded with two types of nanomaterials, (i) quantum dots and (ii) metal nanoparticles are studied. Both of these exhibit optical and electronic properties different from their bulk counterpart due to their nanoscale physical structure. By integrating these nanomaterials into photonic structures, in which the electromagnetic field can be confined and controlled via modification of geometry and composition, we can enhance their linear and nonlinear optical properties to realize functional photonic structures. Before embedding quantum dots into photonic structures, we study the effect of various host matrices and fabrication techniques on the optical properties of the colloidal quantum dots. The two host matrices of interest are SU8 and PMMA. It is shown that the emission properties of the quantum dots are significantly altered in these host matrices (especially SU8) and this is attributed to a high rate of nonradiative quenching of the dots. Furthermore, the effects of fabrication techniques on the optical properties of quantum dots are also investigated. Finally a microdisk resonator embedded with quantum dots is fabricated using soft lithography and luminescence from the quantum dots in the disk is observed. We investigate the absorption and effective index properties of silver nanocomposite films. It is shown that by varying the fill factor of the metal nanoparticles and fabrication parameters such as heating time, we can manipulate the optical properties of the metal nanocomposite. Optimizing these parameters, a silver nanocomposite film with a 7% fill factor is prepared. A one-dimensional photonic crystal consisting of alternating layers of the silver nanocomposite and a polymer (Polymethyl methacrylate) is fabricated using spin coating and its linear and nonlinear optical properties are investigated. Using reflectivity measurements we demonstrate that the one-dimensional silver-nanocomposite-dielectric photonic crystal


    Energy Technology Data Exchange (ETDEWEB)

    Fox, K.; Choi, A.; Marra, J.; Billings, A.


    Collaborative work between the Savannah River National Laboratory (SRNL) and SIA Radon in Russia was divided among three tasks for calendar year 2010. The first task focused on the study of simplified high level waste glass compositions with the objective of identifying the compositional drivers that lead to crystallization and poor chemical durability. The second task focused on detailed characterization of more complex waste glass compositions with unexpectedly poor chemical durabilities. The third task focused on determining the structure of select high level waste glasses made with varying frit compositions in order to improve models under development for predicting the melt rate of the Defense Waste Processing Facility (DWPF) glasses. The majority of these tasks were carried out at SIA Radon. Selection and fabrication of the glass compositions, along with chemical composition measurements and evaluations of durability were carried out at SRNL and are described in this report. SIA Radon provided three summary reports based on the outcome of the three tasks. These reports are included as appendices to this document. Briefly, the result of characterization of the Task 1 glasses may indicate that glass compositions where iron is predominantly tetrahedrally coordinated have more of a tendency to crystallize nepheline or nepheline-like phases. For the Task 2 glasses, the results suggested that the relatively low fraction of tetrahedrally coordinated boron and the relatively low concentrations of Al{sub 2}O{sub 3} available to form [BO{sub 4/2}]{sup -}Me{sup +} and [AlO{sub 4/2}]{sup -}Me{sup +} tetrahedral units are not sufficient to consume all of the alkali ions, and thus these alkali ions are easily leached from the glasses. All of the twelve Task 3 glass compositions were determined to be mainly amorphous, with some minor spinel phases. Several key structural units such as metasilicate chains and rings were identified, which confirms the current modeling

  13. CSTutor: A Sketch-Based Tool for Visualizing Data Structures (United States)

    Buchanan, Sarah; Laviola, Joseph J., Jr.


    We present CSTutor, a sketch-based interface designed to help students understand data structures, specifically Linked Lists, Binary Search Trees, AVL Trees, and Heaps. CSTutor creates an environment that seamlessly combines a user's sketched diagram and code. In each of these data structure modes, the user can naturally sketch a data structure on…

  14. BPS: a database of RNA base-pair structures. (United States)

    Xin, Yurong; Olson, Wilma K


    The BPS ( is a database of RNA base-pair structures, higher-order base interactions and isosteric pairs (base pairs with similar shape). The main functions of the BPS are to find and annotate the structural and chemical features of the Watson-Crick and non-Watson-Crick (noncanonical) base pairs in high-resolution RNA structures, and to provide a user-friendly interface to browse and search for the base pairs. The current database contains 91,265 bp and 3386 higher-order base interactions from 426 RNA crystal structures and 61,819 bp that fall into one of 17 different isosteric classes. The base-pair data can be accessed by searches of base-pair patterns, structure identifiers (IDs) and structural types. The BPS also includes an Atlas with representative images of the various base pairs, higher-order base interactions and isosteric pairs and links to statistical information about these groups of structures.

  15. Kinematic Structures Description of Bionic Hand Based on VF Set (United States)

    Liu, Xiancan; Bai, Pengying; Luo, Min; Gao, Meng; Zhan, Qiang


    This paper presents a method for describing kinematic structure of bionic hand based on VF (virtual finger) set. At first, a 20 DOFs (degrees of freedom) human hand kinematic model is built, which is expressed by five fingers’ kinematic chains consisting of kinematic pairs and symbols that represent geometric relationships of kinematic pairs’ axes. Based on the concept of VF, the hand fingers are divided into two types: VFAA having adduction/abduction motion and VFFE having flexion/extension motion. The concept of VF set comprising VFAAs and VFFEs is defined, human hand and six basic grasp postures are described by VF set. Then, the structures corresponding VFAA and VFFE are given according to active and passive forms of finger joints, and VFFE Structure-Base comprising 20 conventional structures is built. Based on VF set and the structures of VFAA and VFFE, VF sets and kinematic structures of several classic bionic hands are given.

  16. Structure-based bayesian sparse reconstruction

    KAUST Repository

    Quadeer, Ahmed Abdul


    Sparse signal reconstruction algorithms have attracted research attention due to their wide applications in various fields. In this paper, we present a simple Bayesian approach that utilizes the sparsity constraint and a priori statistical information (Gaussian or otherwise) to obtain near optimal estimates. In addition, we make use of the rich structure of the sensing matrix encountered in many signal processing applications to develop a fast sparse recovery algorithm. The computational complexity of the proposed algorithm is very low compared with the widely used convex relaxation methods as well as greedy matching pursuit techniques, especially at high sparsity. © 1991-2012 IEEE.

  17. Structural Bases of Postresuscitative Heart Failure

    Directory of Open Access Journals (Sweden)

    V. T. Dolgikh


    Full Text Available An experiment on 106 non-inbred male albino rats undergone 4-minute clinical death from acute blood loss has revealed that the first three days after resuscitation are marked by a concomitance of vascular disorders and cardiomyocytic dystrophic changes, the leading role being played by sludge, stasis, thrombosis, increased vascular permeability, perivascular edema, and hemorrhages. Cardiomyocytic destruction (various contractures, block-like myofibrillolysis, myocytoly-sis is a structural basis of postresuscitative heart failure. Three days later the heart displayed concomitant processes of recovery and damage. Three types of cardiac morphological changes have been identified in relation to the ratio of these processes.

  18. Benefits of Risk Based Inspection Planning for Offshore Structures

    DEFF Research Database (Denmark)

    Straub, D.M.; Goyet, J.; Sørensen, John Dalsgaard


    The economical benefits of applying risk-based inspection planning (RBI) for offshore structures subject to fatigue are evaluated based on experiences from past industrial projects. To this end, the factors influencing the cost of inspection, repair and failure of structures are discussed......, the financial benefit of RBI is assessed....

  19. Base pairing in RNA structures: A computational analysis of ...

    Indian Academy of Sciences (India)

    The base pairing patterns in RNA structures are more versatile and completely different as compared to DNA. We present here results of ab-initio studies of structures and interaction energies of eight selected RNA base pairs reported in literature. Interaction energies, including BSSE correction, of hydrogen added crystal ...

  20. [Structuralization of digestive endoscopy report based on NLP]. (United States)

    Kong, Xiao-feng; Li, Ying; Li, Hao-min; Lu, Xu-dong


    This paper presents a method based on NLP to realize structuralization of digestive endoscopy reports. The method is taking advantage of existing NLP's processing technologies and introducing minimal standard terminology (MST) to transform a narrative gastroscopy report into the structuralization report based on MST, whose accuracy rate is 92.3%.

  1. Global stability-based design optimization of truss structures using ...

    Indian Academy of Sciences (India)

    Home; Journals; Sadhana; Volume 38; Issue 1. Global stability-based design optimization of truss structures using multiple objectives. Tugrul Talaslioglu ... Furthermore, a pure pareto-ranking based multi-objective optimization model is employed for the design optimization of the truss structure with multiple objectives.

  2. Gas inflow in oil base fluids; Influxo de gas em fluidos a base de oleo

    Energy Technology Data Exchange (ETDEWEB)

    Lazaro, Welmar [PETROBRAS, Rio de Janeiro (Brazil). Dept. de Perfuracao. Div. de Fluidos de Perfuracao; Boas, Mario Barbosa V. [PETROBRAS, Rio de Janeiro (Brazil). Centro de Pesquisas. Div. de Explotacao


    One of the major problems related to the use of oil base fluids is the dissolution of the natural gas in the fluid. This paper attempts initially at making a bibliographical review of all that was written on the subject of drilling fluids up to now. It also mentions some theoretical aspects regarding the process of gas dissolution in diesel oils, in order to produce an understanding of how the dissolution mechanism is processed. For a same increase in measured volume on the surface, the amount of gas incorporated into the fluid is significantly larger if the gas is dissolved in the oil phase than if it is emulsified in the fluid, as occurs when the fluid is water base. A rig team used to working with water-base fluids may be surprised with the fact that an increase of 20 bbl of fluid on the surface of a 5000 m well can mean the incorporation of about 1800 m{sup 3} of gas, if the fluid is oil-base and all the gas is in solution instead of the incorporation of 900 m{sup 3} if the fluid is water base. This paper has the goal of warning drilling engineers and technicians about this problem, as well as presenting charts and equations that allow for a more realistic evaluation of the amount of gas incorporated into oil fluids. (author) 16 refs., 7 figs., 2 tabs.

  3. Redução de fósforo em dietas para frangos com base em valores de equivalência da fitase

    Directory of Open Access Journals (Sweden)

    Luciana de Paula Naves


    Full Text Available O objetivo deste trabalho foi avaliar o uso de valores de equivalência da fitase como base para redução de fósforo disponível (P-disp em dietas para frangos. Foram avaliados dez planos nutricionais com seis repetições de 15 aves cada uma. Avaliaram-se: desempenho, teor de cinzas na tíbia e custo da ração. De 1 a 7 e de 36 a 42 dias de idade, as aves receberam dieta basal; de 8 a 21 dias, dieta sem fitase contendo 3,9 g kg-1 de P-disp e quatro dietas com fitase contendo de 1,1 a 2,5 g kg-1 de P-disp; e de 22 a 35 dias, dieta sem fitase contendo 3,4 g kg-1 de P-disp mais dieta com fitase contendo 1,6 g kg-1 de P-disp. O melhor plano nutricional foi composto pelas dietas: 4,7 g kg-1 de P-disp sem fitase (1 a 7 dias; 2,0 g kg-1 de P-disp suplementada com fitase (8 a 21 dias; 3,4 g kg-1 de P-disp em ração sem fitase (22 a 35 dias; e 3,0 g kg-1 de P-disp em ração sem fitase (36 a 42 dias. A redução do P-disp ocorre no período de 8 a 21 dias de idade e corresponde a 2,0 g kg-1 de ração suplementada com fitase.

  4. Low Diversity Bacterial Community and the Trapping Activity of Metabolites from Cultivable Bacteria Species in the Female Reproductive System of the Oriental Fruit Fly, <em>Bactrocera dorsalisem> Hendel (Diptera: Tephritidae

    Directory of Open Access Journals (Sweden)

    Hongyu Zhang


    Full Text Available Our goal was to identify the bacteria inhabiting the reproductive system of the female oriental fruit fly, <em>Bactrocera dorsalisem> (Hendel, and evaluate the chemotaxis of <em>B>. <em>dorsalis> to the metabolites produced by the bacteria. Based on 16S rRNA-based polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE, 18 operational taxonomic units (OTUs were assigned to the five bacterial classes <em>Betaproteobacteria>, <em>Alphaproteobacteria>, <em>Gammaproteobacteria>, <em>Bacilli> and <em>Actinobacteria>. Nine OTUs were assigned to <em>Gammaproteobacteria>, which was the most highly represented class. <em>Enterobacteriaceae> constituted the dominant family, and within this family, three genera and five species were identified, including <em>Enterobacter sakazakiiem>, <em>Klebsiella> <em>oxytoca>, <em>Klebsiella> <em>pneumoniae,> Raoultellaem> <em>terrigena em>and <em>Enterobacter> <em>amnigenus>. In this set, the first two species were the dominant components, and the latter three species were the minor ones. Finally, we found that the metabolites produced by <em>R.> terrigenaem>, <em>K. oxytocaem> and <em>K.> pneumoniae em>were attractive to the <em>B.> dorsalisem> adults, and in field studies, <em>B.> dorsalisem> adults were most attracted to <em>K.> oxytocaem>. Collectively, our results suggest that the female reproductive system plays an important role in the transfer of enterobacteria from the gut to fruit. Our data may prompt the development of a female-targeted population control strategy for this fly.

  5. Image-Based Chemical Structure Determination. (United States)

    Ofner, Johannes; Brenner, Florian; Wieland, Karin; Eitenberger, Elisabeth; Kirschner, Johannes; Eisenmenger-Sittner, Christoph; Török, Szilvia; Döme, Balazs; Konegger, Thomas; Kasper-Giebl, Anne; Hutter, Herbert; Friedbacher, Gernot; Lendl, Bernhard; Lohninger, Hans


    Chemical imaging is a powerful tool for understanding the chemical composition and nature of heterogeneous samples. Recent developments in elemental, vibrational, and mass-spectrometric chemical imaging with high spatial resolution (50-200 nm) and reasonable timescale (a few hours) are capable of providing complementary chemical information about various samples. However, a single technique is insufficient to provide a comprehensive understanding of chemically complex materials. For bulk samples, the combination of different analytical methods and the application of statistical methods for extracting correlated information across different techniques is a well-established and powerful concept. However, combined multivariate analytics of chemical images obtained via different imaging techniques is still in its infancy, hampered by a lack of analytical methodologies for data fusion and analysis. This study demonstrates the application of multivariate statistics to chemical images taken from the same sample via various methods to assist in chemical structure determination.

  6. Image structure-based saliency detection (United States)

    Hong, Jing; Chen, Yufei; Liu, Xianhui; Zhao, Weidong; Jia, Ning; Zhou, Qiangqiang


    We consider image intrinsic structure in two aspects: foreground saliency computation and background saliency calculation. On the one hand, a segmented image is represented as a weighted undirected graph, and we calculate the foreground saliency by choosing some superpixels as ranking queries, where we apply a robust background measure to select those for accuracy. On the other hand, we compute the posterior probabilities to measure the background saliency and in terms of the probability, we construct a probability tree via multimerging on superpixels, and then apply the optimization strategy to the background saliency. We evaluate our proposed algorithm on two benchmark datasets and our algorithm yields the competitive results when compared with nine state-of-the-art algorithms in terms of five evaluation metrics.

  7. Psicanálise baseada em evidências? Evidence-based psychoanalysis?

    Directory of Open Access Journals (Sweden)

    Liana Albernaz de Melo Bastos


    Full Text Available A partir da discussão sobre a eficácia da psicanálise, a autora considera necessário o diálogo com as neurociências e a psicofarmacologia. Aponta como o critério de eficácia, entendido pela medicina baseada em evidências, apaga a dimensão da narratividade e, conseqüentemente, da subjetividade. Apresenta uma vinheta de um atendimento emergencial no Hospital Universitário Clementino Fraga Filho como possibilidade de se manter a escuta psicanalítica no atendimento psiquiátrico.Based on the discussion concerning the efficacy of psychoanalysis, the author considers the need to engage in dialogue with the neurosciences and psychopharmacology. She indicates how the criterion of efficacy, as defined by evidence-based medicine, erases the dimension of the narrative and consequently that of subjectivity. She presents as a vignette an emergency case at the Clementino Fraga Filho University Hospital in Rio de Janeiro, illustrating the possibility of maintaining psychoanalytic listening in psychiatric treatment.

  8. GIO-EMS and International Collaboration in Satellite based Emergency Mapping (United States)

    Kucera, Jan; Lemoine, Guido; Broglia, Marco


    During the last decade, satellite based emergency mapping has developed into a mature operational stage. The European Union's GMES Initial Operations - Emergency Management Service (GIO-EMS), is operational since April 2012. It's set up differs from other mechanisms (for example from the International Charter "Space and Major Disasters"), as it extends fast satellite tasking and delivery with the value adding map production as a single service, which is available, free of charge, to the authorized users of the service. Maps and vector datasets with standard characteristics and formats ranging from post-disaster damage assessment to recovery and disaster prevention are covered by this initiative. Main users of the service are European civil protection authorities and international organizations active in humanitarian aid. All non-sensitive outputs of the service are accessible to the public. The European Commission's in-house science service Joint Research Centre (JRC) is the technical and administrative supervisor of the GIO-EMS. The EC's DG ECHO Monitoring and Information Centre acts as the service's focal point and DG ENTR is responsible for overall service governance. GIO-EMS also aims to contribute to the synergy with similar existing mechanisms at national and international level. The usage of satellite data for emergency mapping has increased during the last years and this trend is expected to continue because of easier accessibility to suitable satellite and other relevant data in the near future. Furthermore, the data and analyses coming from volunteer emergency mapping communities are expected to further enrich the content of such cartographic products. In the case of major disasters the parallel activity of more providers is likely to generate non-optimal use of resources, e.g. unnecessary duplication; whereas coordination may lead to reduced time needed to cover the disaster area. Furthermore the abundant number of geospatial products of different

  9. Applications of NMR to structure-based drug design in structural genomics. (United States)

    Powers, Robert


    Structural genomics is poised to have a tremendous impact on traditional structure-based drug design programs. As a result, there is a growing need to obtain rapid structural information in a reliable form that is amenable to rational drug design. In this manner, NMR has been expanding and evolving its role in aiding the design process. A variety of NMR methodologies that cover a range of inherent resolution are described in the context of structure-based drug design in the era of structural genomics.

  10. Structural Acoustic Physics Based Modeling of Curved Composite Shells (United States)


    NUWC-NPT Technical Report 12,236 19 September 2017 Structural Acoustic Physics -Based Modeling of Curved Composite Shells Rachel E. Hesse...SUBTITLE Structural Acoustic Physics -Based Modeling of Curved Composite Shells 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM was to use physics -based modeling (PBM) to investigate wave propagations through curved shells that are subjected to acoustic excitation. An

  11. Maximality-Based Structural Operational Semantics for Petri Nets (United States)

    Saīdouni, Djamel Eddine; Belala, Nabil; Bouneb, Messaouda


    The goal of this work is to exploit an implementable model, namely the maximality-based labeled transition system, which permits to express true-concurrency in a natural way without splitting actions on their start and end events. One can do this by giving a maximality-based structural operational semantics for the model of Place/Transition Petri nets in terms of maximality-based labeled transition systems structures.


    Directory of Open Access Journals (Sweden)

    Lais Barreto Franco


    Full Text Available Com esse trabalho se objetivou, através de componentes principais e regressão múltipla, estimar a produtividade de café com base em nutrientes foliares. A pesquisa foi desenvolvida em uma área cultivada com café arábica - Coffea arabica L.. Construiu-se uma grade irregular com 100 pontos amostrais. Para a realização da análise foliar, foram amostradas folhas do terceiro e quarto pares do ramo produtivo. A produção foi avaliada em julho de 2008 e convertida em produtividade. Os valores encontrados foram submetidos a uma análise de componentes principais (PCA. Com a finalidade de encontrar um modelo para a produtividade, foram ajustados modelos de regressão linear múltipla utilizando as componentes principais geradas. A análise geoestatística foi utilizada para quantificar o grau de dependência espacial. Comprovada a dependência, construiu-se mapas temáticos. A estimativa de produtividade a partir de modelos de regressão múltipla utilizando as componentes principais retornou valores semelhantes aos observados para os dados reais. Essa ferramenta é eficiente para estimar a produtividade com base nas componentes geradas à partir dos nutrientes foliares.

  13. Earnings with Condition Based Maintenance; Ganhos com manutencao preditiva baseada em dados de processo em tempo real

    Energy Technology Data Exchange (ETDEWEB)

    Barabas, Elizabeth [Softbrasil Automacao, Sao Paulo, SP (Brazil)


    Keeping active in perfect functioning is essential for any company. Today, the maintenance has been performed in most of the stops for maintenance. In a modern industrial environment, where the systems provide data and process information in real time, it is possible bring the performance of the plant to a optimized level, through the maintenance based on condition of equipment. This work described the earnings with CBM (Condition Based Maintenance)

  14. Selective upregulation of a single distinctly structured <em>var> gene in chondroitin sulphate A-adhering <em>Plasmodium falciparumem> involved in pregnancy-associated malaria

    DEFF Research Database (Denmark)

    Salanti, Ali; Staalsoe, Trine; Lavstsen, Thomas


    after selection for adhesion to CSA in vitro. The gene belongs to a highly conserved and common var gene subfamily (var2csa). The var2csa genes are structurally distinct from all other var genes in the parasite genome in lacking both CIDR and DBL-gamma domains. These domains have previously been...

  15. Engenharia de Avaliações com Base em Modelos Gamlss


    de Araújo Florencio, Lutemberg


    A determinação técnica do valor de um bem imóvel (casas, terrenos, entre outros) é de extrema importância para a tomada de decisão em diversos segmentos da sociedade e em muitos órgãos governamentais e privados. Cabe à Engenharia de Avaliações, enquanto ciência do valor, coletar, tratar e analisar dados e estimar modelos que expliquem, de maneira satisfatória, a variabilidade observada nos preços, no mercado em que se estuda. Entretanto, não-normalidade, heteroscedasticidade e ...

  16. X-ray and EM structures of a natively glycosylated HIV-1 envelope trimer. (United States)

    Gristick, Harry B; Wang, Haoqing; Bjorkman, Pamela J


    The structural and biochemical characterization of broadly neutralizing anti-HIV-1 antibodies (bNAbs) has been essential in guiding the design of potential vaccines to prevent infection by HIV-1. While these studies have revealed critical mechanisms by which bNAbs recognize and/or accommodate N-glycans on the trimeric envelope glycoprotein (Env), they have been limited to the visualization of high-mannose glycan forms only, since heterogeneity introduced from the presence of complex glycans makes it difficult to obtain high-resolution structures. 3.5 and 3.9 Å resolution crystal structures of the HIV-1 Env trimer with fully processed and native glycosylation were solved, revealing a glycan shield of high-mannose and complex-type N-glycans that were used to define the complete epitopes of two bNAbs. Here, the refinement of the N-glycans in the crystal structures is discussed and comparisons are made with glycan densities in glycosylated Env structures derived by single-particle cryo-electron microscopy.

  17. Genetic distances in soybean based on RAPD markers Distâncias genéticas em soja com base em marcadores RAPD

    Directory of Open Access Journals (Sweden)



    Full Text Available Four methods were applied to determine pairwise genetic distances among five soybean genotypes which are potential genitors for a mapping population. Additionally, individual plants from the most divergent pair of genotypes were evaluated by the RAPD technique to determine their degree of homozygosity. Genetic distances based on RAPD data were calculated by the modified Rogers' distance, and also by the following arithmetical complements of similarity: simple match, Nei and Li, and Gower. These genetic distances were similar, presenting a correlation coefficient ranging from 0.99 to 1.00. In all four methods lines UFV 91-717 and Ichigowase were the most divergent ones (4.53 to 21.43%. DNA samples from five plants from each of the two most divergent genotypes were amplified with 28 different primers. Among the amplified products, only five were polymorphic in each group (2.10%, demonstrating their high intragroup degree of homozygosity. These homozygosity were maintained when DNA samples from 12 plants from each of the two most divergent genotypes were amplified. These parameters were extremely useful for the confirmation of the chosen pair of genitors to generate a mapping population.Aplicaram-se quatro métodos para determinar as distâncias genéticas entre cinco cultivares de soja, que são genitores potenciais para uma população de mapeamento genético. Adicionalmente, o grau de homozigose do par de genótipos mais divergente foi avaliado por meio da técnica de RAPD. Calcularam-se as distâncias genéticas fundadas em dados obtidos pela técnica de RAPD pela distância modificada de Rogers e pelos seguintes complementos aritméticos de similaridade: distância simples; Nei e Li, e Gower. As distâncias genéticas foram similares, apresentando valores de coeficiente de correlação de 0,99 a 1,00. Nos quatro métodos, as linhagens UFV 91-717 e Ichigowase foram as mais divergentes (4,53 to 21,43%. Amostras de DNA de cinco plantas de cada

  18. EMS in Viracept--initial ('traditional') assessment of risk to patients based on linear dose response relations. (United States)

    Gocke, Elmar; Müller, Lutz; Pfister, Thomas


    Prior to having performed in depth toxicological, genotoxicological and DMPK studies on ethyl methanesulfonate (EMS) providing solid evidence for a thresholded dose response relationship, we had prepared and shared with regulatory authorities a preliminary risk estimate based on standard linear dose-effect projections. We estimated that maximal lifetime cancer risk was in the order of 10(-3) (for lifetime ingestion of the maximally contaminated tablets) or 10(-4) for the exposure lasting for 3 months. This estimate was based on a lifetime cancer study with methyl methanesulfonate (MMS; as insufficient data were available for EMS) in rodents and default linear back extrapolation. Analogous estimates were made specifically for breast cancer based on short term tumorigenicity studies with EMS in rats, for the induction of heritable mutations based on specific locus and dominant lethal tests in mice and for the induction of birth defects based on teratogenicity studies in mice. We concluded that even under worst case assumptions of linear dose relations the chance of experiencing these adverse effects would be very small, comprising at most a minute additional burden among the background incidence of the patients.

  19. Modeling Protein Structures Based on Density Maps at Intermediate Resolutions (United States)

    Ma, Jianpeng

    Structural biology is now in a special era in which increasingly more complex biomolecules are being studied. For many of them, only low- or intermediateresolution density maps (6-10 Å) can be obtained by, for instance, electron cryomicroscopy (cryo-EM) (Bottcher et al., 1997; Conway et al., 1997; DeRosier and Harrison, 1997; Kuhn et al., 2002; Li et al., 2002; Mancini et al., 2000; Zhang et al., 2000; Zhou et al., 2000, 2001a,b). In certain cases, analysis in terms of intermediateresolution density maps is also inevitable in X-ray crystallography as exemplified in the lengthy process of structural determination of the 50S ribosomal subunit that incremented from 9 Å, 5 Å, to 2.4 Å (Ban et al., 1998, 1999, 2000). As a common feature in all these cases, it is usually impossible, with conventional methods, to construct reasonably accurate atomic models from density maps. However, for the purpose of structural analysis, it would still be very helpful if one can build some kind of pseudo-atomic models from the density maps because this will not only facilitate the structural determination to higher resolutions, but also assist further biochemical studies and functional interpretation. For example, significant insights into the architecture and organization of proteins can often be learned if one can roughly locate the major secondary structural elements such as α-helices and β-sheets. This rationale is supported by the fact that the knowledge of protein folds can be obtained primarily from the spatial arrangement of the secondary structural elements independent of the sequence identity of the proteins, as different sequences can have the same fold.

  20. em arquitetura e urbanismo

    Directory of Open Access Journals (Sweden)

    Ana Maria Sala Minucci Martins


    Full Text Available Está sendo desenvolvido projeto de pesquisa denominado Geometria Fractal e suas Aplicações em Arquitetura e Urbanismo, com o fito de estudar e desenvolver ferramentas analíticas e propositivas para serem aplicadas em arquitetura e urbanismo, com base em conceitos provenientes da geometria fractal.

  1. Structural Health Monitoring Based on Combined Structural Global and Local Frequencies

    Directory of Open Access Journals (Sweden)

    Jilin Hou


    Full Text Available This paper presents a parameter estimation method for Structural Health Monitoring based on the combined measured structural global frequencies and structural local frequencies. First, the global test is experimented to obtain the low order modes which can reflect the global information of the structure. Secondly, the mass is added on the member of structure to increase the local dynamic characteristic and to make the member have local primary frequency, which belongs to structural local frequency and is sensitive to local parameters. Then the parameters of the structure can be optimized accurately using the combined structural global frequencies and structural local frequencies. The effectiveness and accuracy of the proposed method are verified by the experiment of a space truss.

  2. Combining cryo-electron microscopy (cryo-EM) and cross-linking mass spectrometry (CX-MS) for structural elucidation of large protein assemblies. (United States)

    Schmidt, Carla; Urlaub, Henning


    Determining the structures of, and gaining insight into, the function of large protein complexes at the molecular or atomic level has become a key part of modern structural biology. Electron cryo-microscopy (cryo-EM) can solve structures of highly dynamic macromolecular complexes that are not feasible with other structural techniques like X-ray of crystallized proteins (protein complexes) or nuclear magnetic resonance (NMR) spectroscopy of proteins (protein complexes) in solution. To resolve the regions that are less well defined in cryo-EM images, cross-linking coupled with mass spectrometry (CX-MS) provides valuable information on the proximity between amino-acid residues as distance constraints for homology or de novo modelling. The CX-MS strategy involves covalent linkage, with chemical cross-linkers, of residues close to each other in three-dimensional space and identifying these connections by mass spectrometry. In this article, we summarise the advances of CX-MS and its integration with cryo-EM for structural reconstruction. We further evaluate a number of important examples of structure determination that followed this combinatorial strategy. Copyright © 2017 Elsevier Ltd. All rights reserved.

  3. Cryo-EM Structure of a KCNQ1/CaM Complex Reveals Insights into Congenital Long QT Syndrome. (United States)

    Sun, Ji; MacKinnon, Roderick


    KCNQ1 is the pore-forming subunit of cardiac slow-delayed rectifier potassium (I Ks ) channels. Mutations in the kcnq1 gene are the leading cause of congenital long QT syndrome (LQTS). Here, we present the cryoelectron microscopy (cryo-EM) structure of a KCNQ1/calmodulin (CaM) complex. The conformation corresponds to an "uncoupled," PIP 2 -free state of KCNQ1, with activated voltage sensors and a closed pore. Unique structural features within the S4-S5 linker permit uncoupling of the voltage sensor from the pore in the absence of PIP 2 . CaM contacts the KCNQ1 voltage sensor through a specific interface involving a residue on CaM that is mutated in a form of inherited LQTS. Using an electrophysiological assay, we find that this mutation on CaM shifts the KCNQ1 voltage-activation curve. This study describes one physiological form of KCNQ1, depolarized voltage sensors with a closed pore in the absence of PIP 2 , and reveals a regulatory interaction between CaM and KCNQ1 that may explain CaM-mediated LQTS. Copyright © 2017 Elsevier Inc. All rights reserved.

  4. Thematic clustering of text documents using an EM-based approach

    Directory of Open Access Journals (Sweden)

    Kim Sun


    Full Text Available Abstract Clustering textual contents is an important step in mining useful information on the web or other text-based resources. The common task in text clustering is to handle text in a multi-dimensional space, and to partition documents into groups, where each group contains documents that are similar to each other. However, this strategy lacks a comprehensive view for humans in general since it cannot explain the main subject of each cluster. Utilizing semantic information can solve this problem, but it needs a well-defined ontology or pre-labeled gold standard set. In this paper, we present a thematic clustering algorithm for text documents. Given text, subject terms are extracted and used for clustering documents in a probabilistic framework. An EM approach is used to ensure documents are assigned to correct subjects, hence it converges to a locally optimal solution. The proposed method is distinctive because its results are sufficiently explanatory for human understanding as well as efficient for clustering performance. The experimental results show that the proposed method provides a competitive performance compared to other state-of-the-art approaches. We also show that the extracted themes from the MEDLINE® dataset represent the subjects of clusters reasonably well.

  5. Agentes de saúde em comunidades urbanas Community-based health workers in urban areas

    Directory of Open Access Journals (Sweden)

    João Cláudio L. Fernandes


    Full Text Available A utilização de agentes comunitários nos programas de atenção primária à saúde é uma experiência amplamente difundida, principalmente nos países do Terceiro Mundo. É importante, entretanto, discriminar o perfil de atuação destes agentes em função da área onde atuam, principalmente no que diz respeito às diferenças entre o meio rural e o urbano. A simples substituição de profissionais de medicina, odontologia, psicologia etc, por agentes comunitários pode significar uma abordagem limitada do conceito de atenção primária, levando ao desenvolvimento de modelos assistenciais distintos, determinados em função da classe social a que se dirigem. Neste artigo, é apontada a necessidade de formação de recursos humanos de nível superior para a atenção primária à saúde, buscando-se também identificar o lugar dos agentes comunitários nesta área, sua especificidade técnica, bem como alguns obstáculos percebidos neste campo profissional.The employment of community-based health workers (CHWs in primary health care projects is a widespread experience, mainly in Third World countries. However, it is important to differentiate between the rural and urban profiles of these professionals. The replacement of medical/odontological/psychological professionals by CHWs alone may represent a limited approach to primary health care problems, leading to the development of different health care patterns, depending on the social class they are addressed. This paper points to need for the qualification of high-level health personnel also trying to identify the location of CHWs in this field, their technical specificity, as well as some difficulties observed in this practice.

  6. Evaluating population and community structure against climate and land-use determinants to improve the conservation of the rare <em>Narcissus pseudonarcissusem> subsp. <em>nobilis>


    Vaz, Ana Sofia; Silva, Duarte; Alves, Paulo; Vicente, Joana Raquel; Barreto Caldas, Francisco; Pradinho Honrado, João; Lomba, Angela


    Climate and land-use changes are among the most relevant determinants of future persistence of rare plant species in rural landscapes. We analysed the structure of populations of a rare plant, Narcissus pseudonarcissus subsp. nobilis, and of their respective plant communities against several environmental variables (climate-, topography-, land-use-, and soil-related) in order to identify the pressures that may directly or indirectly affect the persistence of the rare species. Overall, local l...

  7. Constituents from <em>Vigna em>vexillata> and Their Anti-Inflammatory Activity

    Directory of Open Access Journals (Sweden)

    Guo-Feng Chen


    Full Text Available The seeds of <em>Vigna em>genus are important food resources and there have already been many reports regarding their bioactivities. In our preliminary bioassay, the chloroform layer of methanol extracts of<em> V. vexillata em>demonstrated significant anti-inflammatory bioactivity. Therefore, the present research is aimed to purify and identify the anti-inflammatory principles of <em>V. vexillataem>. One new sterol (1 and two new isoflavones (2,3 were reported from the natural sources for the first time and their chemical structures were determined by the spectroscopic and mass spectrometric analyses. In addition, 37 known compounds were identified by comparison of their physical and spectroscopic data with those reported in the literature. Among the isolates, daidzein (23, abscisic acid (25, and quercetin (40 displayed the most significant inhibition of superoxide anion generation and elastase release.

  8. <em>Serpula lacrymansem>, The Dry Rot Fungus and Tolerance Towards Copper-Based Wood Preservatives

    DEFF Research Database (Denmark)

    Hastrup, Anne Christine Steenkjær; Jensen, Bo; Clausen, Carol


    Serpula lacrymans (Wulfen : Fries) Schröter, the dry rot fungus, is considered the most (Wulfen : Fries) Schröterthe dry rot fungus, is considered the most economically important wood decay fungus in temperate regions of the world i.e. northern Europe, Japan and Australia. Previously copper based...

  9. Molecular phylogeny of <em>Edraianthus em>(Grassy Bells; Campanulaceae) based on non-coding plastid DNA sequences

    DEFF Research Database (Denmark)

    Stefanovic, Sasa; Lakusic, Dmitar; Kuzmina, Maria


    divided into three sections: E. sect. Edraianthus, E. sect. Uniflori, and E. sect. Spathulati. We present here the first phylogenetic study of Edraianthus based on multiple plastid DNA sequences (trnL-F region and rbcL-atpB spacer) derived from a wide taxonomic sampling and geographic range. While...

  10. The cryo-EM structure of hibernating 100S ribosome dimer from pathogenic Staphylococcus aureus. (United States)

    Matzov, Donna; Aibara, Shintaro; Basu, Arnab; Zimmerman, Ella; Bashan, Anat; Yap, Mee-Ngan F; Amunts, Alexey; Yonath, Ada E


    Formation of 100S ribosome dimer is generally associated with translation suppression in bacteria. Trans-acting factors ribosome modulation factor (RMF) and hibernating promoting factor (HPF) were shown to directly mediate this process in E. coli. Gram-positive S. aureus lacks an RMF homolog and the structural basis for its 100S formation was not known. Here we report the cryo-electron microscopy structure of the native 100S ribosome from S. aureus, revealing the molecular mechanism of its formation. The structure is distinct from previously reported analogs and relies on the HPF C-terminal extension forming the binding platform for the interactions between both of the small ribosomal subunits. The 100S dimer is formed through interactions between rRNA h26, h40, and protein uS2, involving conformational changes of the head as well as surface regions that could potentially prevent RNA polymerase from docking to the ribosome.Under conditions of nutrient limitation, bacterial ribosomes undergo dimerization, forming a 100S complex that is translationally inactive. Here the authors present the structural basis for formation of the 100S complexes in Gram-positive bacteria, shedding light on the mechanism of translation suppression by the ribosome-silencing factors.

  11. Measurement and Structural Model Class Separation in Mixture CFA: ML/EM versus MCMC (United States)

    Depaoli, Sarah


    Parameter recovery was assessed within mixture confirmatory factor analysis across multiple estimator conditions under different simulated levels of mixture class separation. Mixture class separation was defined in the measurement model (through factor loadings) and the structural model (through factor variances). Maximum likelihood (ML) via the…

  12. Plasmonic effects in unidimensional structures and graphene-based nanostructures


    Dias, Eduardo José Machado Correia Brioso


    Dissertação de mestrado em Física (área de especialização em Física Fundamental) O presente trabalho tem como objectivo discutir efeitos plasmónicos em nanoestruturas baseadas em grafeno. São estudadas, em primeiro lugar, uma cunha infinita (dieléctrica ou metálica) e uma superfície ranhurada perfeitamente condutora. Ambos os casos são estudados com e sem um revestimento de grafeno, de modo a comparar ambos os resultados e discutir a influência do mesmo nas respectivas propried...

  13. Gerenciamento de custos em pequenas empresas prestadoras de serviço utilizando o activity based costing (abc

    Directory of Open Access Journals (Sweden)

    Nara Medianeira Stefano Mestre


    Full Text Available Esse estudo teve como objetivo principal propor uma sistemática de gerenciamento de custos fundamentada em custos Activity-Based Costing (ABC para as pequenas empresas prestadoras de serviços para melhor gerenciar seus custos. Definida uma sistemática, aplicou-se, parcialmente, em uma organização que tem como foco prestar assistência e consultoria em informática, para a atividade “entrega do produto (implantação de sistema.” Para melhor elaborar os direcionadores de custos (cost drivers e calcular o custo do serviço, houve a necessidade de esse conhecer e presenciar os processos, atividades e os recursos envolvidos. Portanto, a proposta baseada no método ABC é aplicável em pequenas empresas prestadoras de serviços pelo fato de originar uma investigação de custos mais precisa e, com isso, proporcionar informações para a tomada de decisões.

  14. Active Sensing Based Bolted Structure Health Monitoring Using Piezoceramic Transducers


    Wang, R.L.; Gu, H.; SONG, G.


    Bolted structures are commonly used in civil infrastructure. It is important to perform bolt inspection regularly to ensure the safety of structures. Traditional bolt inspection methods are time-consuming; moreover, bulky instruments are needed in these methods. In this paper, a piezoceramic based active sensing approach is developed to perform the health monitoring of bolted structures. Surface-bonded piezoceramic patches are used as health monitoring transducers. Wavelet packet analysis is ...

  15. Graph-based linear scaling electronic structure theory. (United States)

    Niklasson, Anders M N; Mniszewski, Susan M; Negre, Christian F A; Cawkwell, Marc J; Swart, Pieter J; Mohd-Yusof, Jamal; Germann, Timothy C; Wall, Michael E; Bock, Nicolas; Rubensson, Emanuel H; Djidjev, Hristo


    We show how graph theory can be combined with quantum theory to calculate the electronic structure of large complex systems. The graph formalism is general and applicable to a broad range of electronic structure methods and materials, including challenging systems such as biomolecules. The methodology combines well-controlled accuracy, low computational cost, and natural low-communication parallelism. This combination addresses substantial shortcomings of linear scaling electronic structure theory, in particular with respect to quantum-based molecular dynamics simulations.

  16. Provenance graph query method based on double layer index structure (United States)

    Cai, Qing Qiu; Cui, Hong Gang; Tang, Hao


    Order to solve the problem that the efficiency of the existing source map is low and the resource occupancy rate is high, considering the relationship between the origin information and the data itself and the internal structure of the origin information, a method of provenance graph query based on double layer index structure is proposed. Firstly, we propose a two layer index structure based on the global index of the dictionary table and the local index based on the bitmap. The global index is used to query the server nodes stored in the source map. The local index is used to query the global index. Finally, based on the double-level index structure, a method of starting map query is designed. The experimental results show that the proposed method not only improves the efficiency of query and reduces the waste of memory resources.

  17. Vibration Based Methods For Damage Detection In Structures

    Directory of Open Access Journals (Sweden)

    Manoach E.


    Full Text Available Vibration based damage detection methods are among the most popular and promising approaches for health monitoring of structures. In this work a critical review of different methods for damage detection methods of structures is presented. The theoretical bases of the most popular methods based on the changes in the modal properties of the structures are deduced. The review includes the modal displacements, the mode shape slopes, the modal curvatures and the strain energy methods. The efficiency of all these methods is compared by using a finite element analysis of intact and damaged beams. The methods are tested experimentally by using a scanning laser vibrometer to measure the modal properties of specially prepared composite beams with defects. All this methods are compared with the damage detection method based on the analysis of the Poincaré maps of the motion of the structures. Conclusions concerning the advantages and the applicability of the considered methods are deduced.

  18. Sensitivity based reduced approaches for structural reliability analysis

    Indian Academy of Sciences (India)

    captured by a safety-factor based approach due to the intricate nonlinear relationships between the system parameters and the natural frequencies. For these reasons a scientific and systematic approach is required to predict the probability of failure of a structure at the design stage. Probabilistic structural reliability analysis ...

  19. Extended structures of two coordination polymers based on 1, 10 ...

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Chemical Sciences; Volume 128; Issue 3. Extended structures of two coordination polymers based on 1,10-phenanthroline derivatives:Preparation, structural characterization and properties. Yan-Ju Huang Ya-Ru Pan Gang Du Yi-Xin Cao. Regular Articles Volume 128 Issue 3 March 2016 pp 459- ...

  20. Creation of the cathodoluminescence structures based on thin film technology

    Directory of Open Access Journals (Sweden)

    Tzyrkunov Yu. A.


    Full Text Available Technologiсal route and technological processes for the batch production of thin film cathodoluminescence structures for the high resolution displays were chosen. Cathodoluminescence structures with luminance of glow up to 1000 cd/m2 based on film 6 – 8 mkm thickness were experimentally created and investigated.

  1. Active metamaterial on the base of integral NEMS-structures


    Khartov, S.


    The conception of integrated nanoelectromechanical systems (NEMS) formation method is considered. The method is based on original combination of self-organizing and self-aligning processes. The functionality of proposed NEMS-structures and possible applications of nanomaterial which constituted by two-dimensional array of such structures are discussed. The results of experiments directed to proposed NEMS-technology realization are led.

  2. Probability based high temperature engineering creep and structural fire resistance

    CERN Document Server

    Razdolsky, Leo


    This volume on structural fire resistance is for aerospace, structural, and fire prevention engineers; architects, and educators. It bridges the gap between prescriptive- and performance-based methods and simplifies very complex and comprehensive computer analyses to the point that the structural fire resistance and high temperature creep deformations will have a simple, approximate analytical expression that can be used in structural analysis and design. The book emphasizes methods of the theory of engineering creep (stress-strain diagrams) and mathematical operations quite distinct from those of solid mechanics absent high-temperature creep deformations, in particular the classical theory of elasticity and structural engineering. Dr. Razdolsky’s previous books focused on methods of computing the ultimate structural design load to the different fire scenarios. The current work is devoted to the computing of the estimated ultimate resistance of the structure taking into account the effect of high temperatur...

  3. RNA structural motif recognition based on least-squares distance. (United States)

    Shen, Ying; Wong, Hau-San; Zhang, Shaohong; Zhang, Lin


    RNA structural motifs are recurrent structural elements occurring in RNA molecules. RNA structural motif recognition aims to find RNA substructures that are similar to a query motif, and it is important for RNA structure analysis and RNA function prediction. In view of this, we propose a new method known as RNA Structural Motif Recognition based on Least-Squares distance (LS-RSMR) to effectively recognize RNA structural motifs. A test set consisting of five types of RNA structural motifs occurring in Escherichia coli ribosomal RNA is compiled by us. Experiments are conducted for recognizing these five types of motifs. The experimental results fully reveal the superiority of the proposed LS-RSMR compared with four other state-of-the-art methods.

  4. Discrete Discriminant analysis based on tree-structured graphical models

    DEFF Research Database (Denmark)

    Perez de la Cruz, Gonzalo; Eslava, Guillermina

    The purpose of this paper is to illustrate the potential use of discriminant analysis based on tree{structured graphical models for discrete variables. This is done by comparing its empirical performance using estimated error rates for real and simulated data. The results show that discriminant...... analysis based on tree{structured graphical models is a simple nonlinear method competitive with, and sometimes superior to, other well{known linear methods like those assuming mutual independence between variables and linear logistic regression....

  5. Near-Atomic Resolution Structure Determination of a Cypovirus Capsid and Polymerase Complex Using Cryo-EM at 200kV. (United States)

    Li, Xiaowu; Zhou, Niyun; Chen, Wenyuan; Zhu, Bin; Wang, Xurong; Xu, Bin; Wang, Jiawei; Liu, Hongrong; Cheng, Lingpeng


    Single-particle cryo-electron microscopy (cryo-EM) allows the high-resolution structural determination of biological assemblies in a near-native environment. However, all high-resolution (better than 3.5Å) cryo-EM structures reported to date were obtained by using 300kV transmission electron microscopes (TEMs). We report here the structures of a cypovirus capsid of 750-Å diameter at 3.3-Å resolution and of RNA-dependent RNA polymerase (RdRp) complexes within the capsid at 3.9-Å resolution using a 200-kV TEM. The newly resolved structure revealed conformational changes of two subdomains in the RdRp. These conformational changes, which were involved in RdRp's switch from non-transcribing to transcribing mode, suggest that the RdRp may facilitate the unwinding of genomic double-stranded RNA. The possibility of 3-Å resolution structural determinations for biological assemblies of relatively small sizes using cryo-EM at 200kV was discussed. Copyright © 2016 Elsevier Ltd. All rights reserved.

  6. Preliminary data on the density and structure of a fallow deer (<em>Cervus damaem> population in the Foreste Casentinesi M. Falterona and Campigna National Park

    Directory of Open Access Journals (Sweden)

    Luciano Cicognani


    Full Text Available Abstract In a sample area covering 1200 ha located in the northern part of the Foreste Casentinesi National Park a survey was conducted in 1996 and 1997 on the Fallow deer (<em>Cervus damaem> population. The survey was conducted during the rutting period. The censusing method is an adaptation of the Lincoln Index estimation where the capture, marking and recapture process was replaced by individual observations in "lekking areas". Since the stay of the bucks in a territory is not uniform, due to the high level of variability of the reproductive strategies, the mixing of the bucks improves the reliability of the method. The estimate of the total population was 189, the sex ratio was 1:1 and the yearlings/adults ratio was 1:2.2.

  7. A conversão do conhecimento em uma universidade federal com base em Nonaka e Takeuchi


    Begnini, Sergio


    Este estudo tem como foco o estudo sobre a conversão do conhecimento na área administrativa de uma universidade federal, com base no modelo SECI de Nonaka e Takeuchi.  O objetivo principal é analisar como o conhecimento, no âmbito da gestão administrativa, é criado e difundido, na Universidade Federal da Fronteira Sul, sob o ponto de vista de seus dirigentes, na perspectiva do modelo SECI de Nonaka e Takeuchi. Trata-se de um estudo com abordagem quantitativa e com procedimentos metodológicos ...

  8. The latent structure of secure base script knowledge. (United States)

    Waters, Theodore E A; Fraley, R Chris; Groh, Ashley M; Steele, Ryan D; Vaughn, Brian E; Bost, Kelly K; Veríssimo, Manuela; Coppola, Gabrielle; Roisman, Glenn I


    There is increasing evidence that attachment representations abstracted from childhood experiences with primary caregivers are organized as a cognitive script describing secure base use and support (i.e., the secure base script). To date, however, the latent structure of secure base script knowledge has gone unexamined-this despite that such basic information about the factor structure and distributional properties of these individual differences has important conceptual implications for our understanding of how representations of early experience are organized and generalized, as well as methodological significance in relation to maximizing statistical power and precision. In this study, we report factor and taxometric analyses that examined the latent structure of secure base script knowledge in 2 large samples. Results suggested that variation in secure base script knowledge-as measured by both the adolescent (N = 674) and adult (N = 714) versions of the Attachment Script Assessment-is generalized across relationships and continuously distributed. (c) 2015 APA, all rights reserved).

  9. Interactive Reliability-Based Optimization of Structural Systems

    DEFF Research Database (Denmark)

    Pedersen, Claus

    In order to introduce the basic concepts within the field of reliability-based structural optimization problems, this chapter is devoted to a brief outline of the basic theories. Therefore, this chapter is of a more formal nature and used as a basis for the remaining parts of the thesis. In section...... 2.2 a general non-linear optimization problem and corresponding terminology are presented whereupon optimality conditions and the standard form of an iterative optimization algorithm are outlined. Subsequently, the special properties and characteristics concerning structural optimization problems...... the reliability-based structural optimization (RBSO) problem is formulated and described....

  10. Neighboring Structure Visualization on a Grid-based Layout. (United States)

    Marcou, G; Horvath, D; Varnek, A


    Here, we describe an algorithm to visualize chemical structures on a grid-based layout in such a way that similar structures are neighboring. It is based on structure reordering with the help of the Hilbert Schmidt Independence Criterion, representing an empirical estimate of the Hilbert-Schmidt norm of the cross-covariance operator. The method can be applied to any layout of bi- or three-dimensional shape. The approach is demonstrated on a set of dopamine D5 ligands visualized on squared, disk and spherical layouts. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. Data base on avian mortality on man-made structures

    Energy Technology Data Exchange (ETDEWEB)

    Dailey, N. S.


    A computerized data base concerning avian mortality on man-made structures is available for searching at the Ecological Sciences Information Center of the Information Center Complex, Information Division, Oak Ridge National Laboratory. This data base, which contains entries from the available literature, provides information on avian mortality from either collision into or electrocution on man-made structures. Primary emphasis has been placed on avian collision with obstacles such as television and radio towers, airport ceilometers, transmission lines, and cooling towers. Other structures included in the studies are fences, glass walls and windows, lighthouses, telegraph and telephone wires, buildings, monuments, smokestacks, and water towers.

  12. Structure of 2,4-Diaminopyrimidine - Theobromine Alternate Base Pairs (United States)

    Gengeliczki, Zsolt; Callahan, Michael P.; Kabelac, Martin; Rijs, Anouk M.; deVries, Mattanjah S.


    We report the structure of clusters of 2,4-diaminopyrimidine with 3,7-dimethylxanthine (theobromine) in the gas phase determined by IR-UV double resonance spectroscopy in both the near-IR and mid-IR regions in combination with ab initio computations. These clusters represent potential alternate nucleobase pairs, geometrically equivalent to guanine-cytosine. We have found the four lowest energy structures, which include the Watson-Crick base pairing motif. This Watson-Crick structure has not been observed by resonant two-photon ionization (R2PI) in the gas phase for the canonical DNA base pairs.

  13. Strengthening of Concrete Structures with cement based bonded composites

    DEFF Research Database (Denmark)

    Täljsten, Björn; Blanksvärd, Thomas


    Due to demands on higher loads, degradation, re-construction etc. there is a constant need for repair or strengthening of existing concrete structures. Many varying methods exist to strengthen concrete structures, one such commonly used technique utilizes surface epoxy bonded FRPs (Fibre Reinforced...... with improved working environment and better compatibility to the base concrete structure. This study gives an overview of different cement based systems, all with very promising results for structural upgrading. Studied parameters are structural retrofit for bending, shear and confinement. It is concluded...... that the use of carbon FRPs provides the highest strengthening effect and that the fibres should be imbedded into a matrix for enhanced utilisation of inherent strain capacity...

  14. Finite Element Based HWB Centerbody Structural Optimization and Weight Prediction (United States)

    Gern, Frank H.


    This paper describes a scalable structural model suitable for Hybrid Wing Body (HWB) centerbody analysis and optimization. The geometry of the centerbody and primary wing structure is based on a Vehicle Sketch Pad (VSP) surface model of the aircraft and a FLOPS compatible parameterization of the centerbody. Structural analysis, optimization, and weight calculation are based on a Nastran finite element model of the primary HWB structural components, featuring centerbody, mid section, and outboard wing. Different centerbody designs like single bay or multi-bay options are analyzed and weight calculations are compared to current FLOPS results. For proper structural sizing and weight estimation, internal pressure and maneuver flight loads are applied. Results are presented for aerodynamic loads, deformations, and centerbody weight.

  15. Structural differences between yeast and mammalian microtubules revealed by cryo-EM

    Energy Technology Data Exchange (ETDEWEB)

    Howes, Stuart C. [Univ. of California, Berkeley, CA (United States). Biophysics Graduate Group; Geyer, Elisabeth A. [Univ. of Texas Southwestern Medical Center, Dallas, TX (United States). Dept. of Biophysics; Univ. of Texas Southwestern Medical Center, Dallas, TX (United States). Dept. of Biochemistry; LaFrance, Benjamin [Univ. of California, Berkeley, CA (United States). Molecular and Cell Biology Graduate Program; Zhang, Rui [Univ. of California, Berkeley, CA (United States). Howard Hughes Medical Inst.; Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Molecular Biophysics and Integrated Bioimaging Division; Kellogg, Elizabeth H. [Univ. of California, Berkeley, CA (United States). Howard Hughes Medical Inst.; Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Molecular Biophysics and Integrated Bioimaging Division; Westermann, Stefan [Univ. of Duisburg-Essen, Essen (Germany). Dept. of Molecular Genetics, Center for Medical Biotechnology; Rice, Luke M. [Univ. of Texas Southwestern Medical Center, Dallas, TX (United States). Dept. of Biophysics; Univ. of Texas Southwestern Medical Center, Dallas, TX (United States). Dept. of Biochemistry; Nogales, Eva [Univ. of California, Berkeley, CA (United States). Howard Hughes Medical Inst.; Univ. of California, Berkeley, CA (United States). Dept. of Molecular Biology and California Inst. for Quantitative Biosciences; Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Molecular Biophysics and Integrated Bioimaging Division


    Microtubules are polymers of αβ-tubulin heterodimers essential for all eukaryotes. Despite sequence conservation, there are significant structural differences between microtubules assembled in vitro from mammalian or budding yeast tubulin. Yeast MTs were not observed to undergo compaction at the interdimer interface as seen for mammalian microtubules upon GTP hydrolysis. Lack of compaction might reflect slower GTP hydrolysis or a different degree of allosteric coupling in the lattice. The microtubule plus end–tracking protein Bim1 binds yeast microtubules both between αβ-tubulin heterodimers, as seen for other organisms, and within tubulin dimers, but binds mammalian tubulin only at interdimer contacts. At the concentrations used in cryo-electron microscopy, Bim1 causes the compaction of yeast microtubules and induces their rapid disassembly. In conclusion, our studies demonstrate structural differences between yeast and mammalian microtubules that likely underlie their differing polymerization dynamics. These differences may reflect adaptations to the demands of different cell size or range of physiological growth temperatures.

  16. Avaliação de espermatozoides caprinos congelados em meio à base de água de coco em pó (ACP-101® ou TRIS

    Directory of Open Access Journals (Sweden)

    R.V. Oliveira


    Full Text Available Compararam-se as características cinéticas e morfológicas de espermatozoides caprinos congelados nos meios à base de ACP-101® e TRIS. Os diluentes utilizados foram: ACP-101® (+ 2,5% gema ovo + 7% glicerol e TRIS (+ 20% gema ovo + 6,8% glicerol. Quarenta e oito ejaculados de quatro bodes foram coletados, avaliados, divididos em duas alíquotas e diluídos nos meios ACP-101® e TRIS, respectivamente, posteriormente congelados e, após 30 dias, descongelados. A avaliação da motilidade espermática por computador foi realizada aos 5, 60 e 120 minutos pós-descongelação. As características de motilidade espermática analisadas foram: motilidade total (MT (% e progressiva (MP (%, velocidades média do trajeto do espermatozoide (VAP (µm/s e linear (VSL (µm/s e população de espermatozoides rápidos (ER (%. As avaliações de morfologia espermática quantificaram a porcentagem de espermatozoides normais (N e as alterações da cabeça (AC, da peça intermediária (API e do flagelo (AF, aos cinco e 120 minutos pós-descongelação. O diluente TRIS apresentou resultados cinéticos mais elevados que o ACP-101® aos 60 e 120 minutos pós-descongelação. As AC aos 120 minutos pós-descongelação foram mais altas nos espermatozoides congelados em ACP-101®. Conclui-se que o diluente TRIS promoveu maior viabilidade in vitro dos espermatozoides caprinos pós-descongelação.

  17. Cryo-EM structure of Mcm2-7 double hexamer on DNA suggests a lagging-strand DNA extrusion model (United States)

    Noguchi, Yasunori; Yuan, Zuanning; Bai, Lin; Schneider, Sarah; Zhao, Gongpu; Li, Huilin


    During replication initiation, the core component of the helicase—the Mcm2-7 hexamer—is loaded on origin DNA as a double hexamer (DH). The two ring-shaped hexamers are staggered, leading to a kinked axial channel. How the origin DNA interacts with the axial channel is not understood, but the interaction could provide key insights into Mcm2-7 function and regulation. Here, we report the cryo-EM structure of the Mcm2-7 DH on dsDNA and show that the DNA is zigzagged inside the central channel. Several of the Mcm subunit DNA-binding loops, such as the oligosaccharide–oligonucleotide loops, helix 2 insertion loops, and presensor 1 (PS1) loops, are well defined, and many of them interact extensively with the DNA. The PS1 loops of Mcm 3, 4, 6, and 7, but not 2 and 5, engage the lagging strand with an approximate step size of one base per subunit. Staggered coupling of the two opposing hexamers positions the DNA right in front of the two Mcm2–Mcm5 gates, with each strand being pressed against one gate. The architecture suggests that lagging-strand extrusion initiates in the middle of the DH that is composed of the zinc finger domains of both hexamers. To convert the Mcm2-7 DH structure into the Mcm2-7 hexamer structure found in the active helicase, the N-tier ring of the Mcm2-7 hexamer in the DH-dsDNA needs to tilt and shift laterally. We suggest that these N-tier ring movements cause the DNA strand separation and lagging-strand extrusion. PMID:29078375

  18. Structure-Based Rational Design of Adenosine Receptor Ligands. (United States)

    Gutiérrez-de-Terán, Hugo; Sallander, Jessica; Sotelo, Eddy


    The family of adenosine receptors (ARs) is focus of several medicinal chemistry programs aimed to find new potent and selective drugs. Each receptor subtype has been proposed as a relevant drug target in the treatment of, e.g., cardiovascular or inflammatory diseases, asthma or Parkinson's disease. Until recently, most of these efforts have been dominated by ligand-based or empirical approaches. However, the latest advances in G protein-coupled receptor (GPCR) crystallography allowed for a thorough structural characterization of the A2AAR subtype, which has been crystalized with a number of agonists and antagonists. Consequently, the ligand discovery of AR ligands has been enriched with a number of structure-based approaches. These include the generation of higher-confident homology models for the remaining AR subtypes, virtual screening identification of novel chemotypes, structure-based lead-optimization programs, rationalization of selectivity profiles, or the structural characterization of novel binding sites that enable the design of novel allosteric modulators. Computational methodologies have importantly contributed to the success of these structure-based approaches, and the recent advances in the field are also analyzed in this review. We conclude that the design of adenosine receptor ligands has improved dramatically with the consideration of structure- based approaches, which is paving the way to a better understanding of the biology and pharmacological modulation of this relevant family of receptors.

  19. Divergência genética em germoplasma de aveias silvestres com base em caracteres multicategóricos e quantitativos

    Directory of Open Access Journals (Sweden)

    Simone Meredith Scheffer-Basso


    Full Text Available As aveias silvestres são importantes fontes de genes para programas de melhoramento e sua caracterização é fundamental para a efetiva conservação e uso. Por isso, o objetivo deste estudo foi avaliar a divergência genética em uma coleção de 71 subamostras de aveias silvestres, do Banco de Germoplasma da Embrapa Trigo, com base em caracteres multicategóricos e quantitativos. Procederam-se às análises de variância, para os caracteres quantitativos, e multivariada, para ambos os tipos de caracteres. Os métodos de agrupamento UPGMA, a partir da distância euclidiana média (caracteres multicategóricos, e de ligação completa, com base na distância de Mahalanobis (caracteres quantitativos, foram os mais adequados para ilustrar a relação entre as subamostras. A pilosidade da base dos grãos foi o caractere com maior contribuição relativa para divergência genética (32,16% e a menor contribuição foi da pilosidade do nó superior (0,081%. As subamostras divergiram quanto a vinte caracteres: pilosidade da bainha da folha inferior, bordas da lâmina imediatamente abaixo da folha bandeira, nó superior, face externa do lema e base do grão; posição da folha bandeira e das ramificações na panícula; frequência de plantas com folha bandeira recurvada; intensidade da pilosidade do nó superior e da cerosidade do lema; orientação das ramificações na panícula; comprimento dos pelos basais do grão, ráquila, panícula, glumas e planta; cor do lema, tipo de arista, número de grãos por espigueta e ciclo. O germoplasma apresenta elevada variabilidade genética e genes de interesse para o melhoramento de aveias.

  20. Prevention of post weaning diarrhoea by a <em>Saccharomyces cerevisiaeem>-derived product based on whole yeast

    DEFF Research Database (Denmark)

    Jensen, K. H.; Damgaard, B. M.; Andresen, Lars Ole


    The aim of this study was to examine whether yeast derivate (YD) based on whole brewery yeast added to the creep feed of suckling and newly weaned piglets or to the creep feed of the piglets and the sow's diet prevented post weaning diarrhoea (PWD) or affected performance. Thirty sows...... and their litters were randomly allocated to three treatment groups: PSP (1.5 g/kg of YD to the sows’ feed from 1 wk before expected farrowing to weaning; 3 g/kg or 2 g/kg of YD added to the piglets’ creep feed from 2 wk of age until 2 wk post weaning (PW) and from wk 2 to 5 PW, respectively); PP (YD added...... to the piglets’ creep feed as in PSP); or C (control, no YD added). At weaning (4 wk of age) 2 individually housed piglets from all litters were subjected to either experimental Escherichia coli (E. coli) challenge or placebo treatment on d 1 to 3 PW, whereas performance was measured on 3 group-housed piglets...

  1. General enumeration of RNA secondary structures based on new ...

    African Journals Online (AJOL)

    Crick base pairs between AU and GC. Based on the new representation, this paper also computes the number of various types of constrained secondary structures taking the minimum stack length 1 and minimum size m for each bonding loop as ...

  2. Dynamic fracture modeling in shell structures based on XFEM

    NARCIS (Netherlands)

    Larsson, R.; Mediavilla, J.; Fagerström, M.


    Through-the-thickness crack propagation in thin-walled structures is dealt with in this paper. The formulation is based on the cohesive zone concept applied to a kinematically consistent shell model enhanced with an XFEM-based discontinuous kinematical representation. The resulting formulation

  3. Design and manufacturing of bio-based sandwich structures

    CSIR Research Space (South Africa)

    John, Maya J


    Full Text Available The aim of this chapter is to discuss the design and manufacturing of bio-based sandwich structures. As the economic advantages of weight reduction have become mandatory for many advanced industries, bio-based sandwich panels have emerged...

  4. Bruxismo do sono: possibilidades terapêuticas baseadas em evidências Sleep bruxism: therapeutic possibilities based in evidences

    Directory of Open Access Journals (Sweden)

    Eduardo Machado


    Full Text Available INTRODUÇÃO: o bruxismo do sono (BS é uma desordem de movimentos estereotipados e periódicos, associados ao ranger e/ou apertar de dentes durante o sono, decorrentes da contração rítmica dos músculos mastigatórios. Essa condição não é uma doença, porém quando exacerbada pode ocasionar desequilíbrio e alteração das estruturas orofaciais. Dessa forma, surge a necessidade de se obter terapêuticas efetivas e seguras para o controle e o manejo do paciente bruxômano. As alternativas de tratamento variam desde terapêuticas orodentais e farmacológicas até técnicas comportamentais-cognitivas. OBJETIVOS: através de uma revisão sistemática da literatura, tendo como bases de pesquisa a Medline, Cochrane, Embase, Pubmed, Lilacs e BBO, no período compreendido entre 1990 e 2008, e com enfoque em estudos clínicos randomizados e quasi-randomizados, revisões sistemáticas e meta-análises, esse trabalho teve como objetivo analisar e discutir métodos de tratamento para o BS. RESULTADOS: pela análise da literatura verifica-se que existe uma grande quantidade de opções terapêuticas para o BS, porém muitas das terapias não têm suporte científico que as sustente. Assim, a escolha terapêutica deve ser pautada em evidências científicas e no bom senso clínico, objetivando uma melhora na qualidade de vida do paciente bruxômano.INTRODUCTION: Sleep bruxism (SB is defined as a stereotyped and periodic movement disorder, characterized by tooth grinding and/or clenching occurring during sleep, associated with rhythmic masticatory muscle activity. This condition isn't a disease, but when exacerbated may cause an unbalance and changing of orofacial structures. Thus, it is necessary to obtain effective and safe treatments for the control and management of the bruxist patient. The treatment alternatives ranges from oral devices to pharmacological and cognitive-behavioral techniques. OBJECTIVES: This study, through a systematic literature

  5. Otimização de layouts industriais com base em busca tabu

    Directory of Open Access Journals (Sweden)

    Martins Valdair Candido


    Full Text Available Este artigo aborda uma solução computacional para o problema de layout industrial considerando hard-constraints não tratadas em trabalhos anteriores. O problema é solucionado em duas etapas. Na primeira, uma solução inicial baseada em heurística construtiva é gerada e na segunda, por intermédio da aplicação da meta-heurística busca tabu, a solução inicial é melhorada. Como contribuição, apresenta-se a ferramenta computacional denominada Ambiente Visual para Otimização de Layout Industrial (AVOLI, a fim de gerar layouts viáveis e eficientes capazes de tratar problemas de grande porte sujeitos a um conjunto de restrições realistas.

  6. Natural Products from Antarctic Colonial Ascidians of the Genera <em>Aplidium> and <em>Synoicum>: Variability and Defensive Role

    Directory of Open Access Journals (Sweden)

    Conxita Avila


    Full Text Available Ascidians have developed multiple defensive strategies mostly related to physical, nutritional or chemical properties of the tunic. One of such is chemical defense based on secondary metabolites. We analyzed a series of colonial Antarctic ascidians from deep-water collections belonging to the genera <em>Aplidium> and <em>Synoicum> to evaluate the incidence of organic deterrents and their variability. The ether fractions from 15 samples including specimens of the species <em>A.> <em>falklandicum>, <em>A.> <em>fuegiense>, <em>A.> <em>meridianum>, <em>A.> <em>millari> and <em>S.> <em>adareanum> were subjected to feeding assays towards two relevant sympatric predators: the starfish <em>Odontaster> <em>validus>, and the amphipod <em>Cheirimedon> <em>femoratus>. All samples revealed repellency. Nonetheless, some colonies concentrated defensive chemicals in internal body-regions rather than in the tunic. Four ascidian-derived meroterpenoids, rossinones B and the three derivatives 2,3-epoxy-rossinone B, 3-epi-rossinone B, 5,6-epoxy-rossinone B, and the indole alkaloids meridianins A–G, along with other minoritary meridianin compounds were isolated from several samples. Some purified metabolites were tested in feeding assays exhibiting potent unpalatabilities, thus revealing their role in predation avoidance. Ascidian extracts and purified compound-fractions were further assessed in antibacterial tests against a marine Antarctic bacterium. Only the meridianins showed inhibition activity, demonstrating a multifunctional defensive role. According to their occurrence in nature and within our colonial specimens, the possible origin of both types of metabolites is discussed.

  7. Towards Fully Automated Structure-Based Function Prediction In Structural Genomics: A Case Study (United States)

    Watson, James D.; Sanderson, Steve; Ezersky, Alexandra; Savchenko, Alexei; Edwards, Aled; Orengo, Christine; Joachimiak, Andrzej; Laskowski, Roman A.; Thornton, Janet M.


    Summary As the global Structural Genomics projects have picked up pace the number of structures annotated in the Protein Data Bank as “hypothetical protein” or “unknown function” has grown significantly. A major challenge now involves the development of computational methods to accurately and automatically assign functions to these proteins. As part of the Midwest Center for Structural Genomics (MCSG) we have developed a fully automated functional analysis server, ProFunc, which performs a battery of analyses on a submitted structure. The analyses combine a number of sequence-based and structure-based methods to identify functional clues. After the first stage of the Protein Structure Initiative (PSI) we review the success of the pipeline and the importance of structure-based function prediction. As a dataset we have chosen all structures solved by the MCSG during the 5 years of the first PSI. Our analysis suggests that two of the structure-based methods are particularly successful and provide examples of local similarity difficult to identify using current sequence methods. No one method is successful in all cases so through the use of a number of complementary sequence and structural approaches, the ProFunc server increases the chance that at least one method will find a significant hit that can help elucidate function. Manual assessment of the results is a time-consuming process and subject to individual interpretation and human error. We present a method based on the Gene Ontology schema using GO-slims that can allow the automated assessment of hits with a success rate approaching that of expert manual assessment. PMID:17316683

  8. Desnutrição e obesidade infantis em duas coortes de base populacional no Sul do Brasil: tendências e diferenciais

    Directory of Open Access Journals (Sweden)

    Cora L. Post

    Full Text Available Prevalências de déficits antropométricos e de obesidade foram medidas em duas coortes de nascimento de base populacional na cidade de Pelotas, Rio Grande do Sul, em 1982 e 1993, quando as crianças tinham cerca de um ano de idade. Identificados todos os nascimentos hospitalares em cada ano, cerca de 20% das crianças foram visitadas e submetidas a exame antropométrico, totalizando 1.449 crianças em 1982 e 1.359 em 1993. Houve 20% de perdas em 1982 e 7% em 1993. Em onze anos, a prevalência de déficit de peso/idade (< -2 desvios-padrão da refe-rência NCHS caiu de 5,4% para 3,8%, a de peso/comprimento reduziu-se de 1,3% para 0,8%, enquanto que a de comprimento/idade aumentou discretamente (5,3% para 6,1%. A obesidade cresceu de 4,0% para 6,7%. Em 1993 houve um ganho ponderal médio maior, aos 12 meses, do que em 1982, já que o peso ao nascer permaneceu inalterado. Crianças de mais baixa renda apresentam prevalências de cerca de 10% de déficits de peso/idade e comprimento/idade, enquanto que nas categorias de renda superior estes déficits são de 3% ou menos. Os progressos em alguns indicadores, portanto, não lograram eliminar diferenciais sociais. Por outro lado, a obesidade apresentou uma tendência crescente com o nível de renda familiar.

  9. Sintomatologia depressiva em adolescentes iniciais: estudo de base populacional Depressive symptomatology in early adolescents: population-based study

    Directory of Open Access Journals (Sweden)

    Luciano Dias de Mattos Souza


    Full Text Available OBJETIVO: Verificar a prevalência de sintomatologia depressiva em adolescentes entre 11 e 15 anos em Pelotas, RS, e identificar seus fatores associados. MÉTODOS: Estudo transversal de base populacional com amostra representativa de adolescentes da zona urbana da cidade de Pelotas, RS. Dos 448 setores censitários existentes no município, 79 foram aleatoriamente sorteados. Os jovens entre 11 e 15 anos localizados nestes setores foram convidados a responder o questionário auto-aplicado que continha perguntas sobre: idade, sexo, vida escolar, religião, atividades físicas, entretenimento, tabaco, consumo de álcool, uso de outras drogas, relacionamentos sexuais e conduta. Além disso, a sintomatologia depressiva dos adolescentes foi avaliada por meio da escala Children's Depression Inventory (CDI, também presente no instrumento de pesquisa. Para a análise dos dados foi utilizada a regressão logística ajustada ao modelo hierárquico. RESULTADOS: A prevalência de depressão foi de 2,1%. Após a regressão logística ajustada ao modelo hierárquico, estiveram significativamente associados à depressão: baixa condição socioeconômica, histórico de fracasso acadêmico, ausência de prática religiosa, abuso de álcool nos últimos 30 dias e indicativo de transtorno de conduta. CONCLUSÃO: É evidenciada a necessidade de programas preventivos e integrados de política na adolescência para depressão e comportamentos de risco à saúde.AIM: Verify the prevalence of depressive symptomatology in adolescents aged between 11 and 15 in Pelotas, RS, and identify its associated factors. METHODS: A cross-sectional base-populational study with a representative sample of adolescents of urban area of Pelotas, RS. Among the 448 census tracts in the urban area of Pelotas, 79 were randomly selected. Youths between 11 and 15 years answered a confidential self-report questionnaire on issues such as: age, gender, school life, religion, physical activities

  10. A produção sobre controle aversivo no Brasil com base em publicações


    Garcia, Maria Christina Leme Cezário


    Na análise do comportamento o domínio do controle aversivo revela-se controverso, seja com relação às modalidades a serem inclusas no tema, seja, mais especificamente, com relação à definição de punição, uma das modalidades mais clássicas abordadas sob este rótulo. Esta pesquisa teve por objetivo caracterizar o estudo do controle aversivo no Brasil com base em artigos publicados em revistas nacionais, incluindo, nesta caracterização, a definição de punição presente nesses estudos. Os artigos ...

  11. Hidratação e equilíbrio ácido-base em pacientes cirúrgicos


    Moriya,Takachi; Martins,Antonio Carlos Pereira; Cherri,Jesualdo; Piccinato,Carlos Eli; Okano,Nelson; Carneiro,João José; Iwakura,Ricardo


    Estudou-se a influência da hidratação em 30 pacientes submetidos a cirurgia de pequeno e grande porte. Os pacientes foram divididos em grupos de 5 conforme o porte cirúrgico e o tipo de hidratação: restrição hídrica, segundo o balanço diário e sobrecarga hidrossalina. As alterações mais relevantes do equilíbrio ácido base foram: pré-operatório - alcalose respiratória; pós-operatório imediato - acidose respiratória; 1º, 2º e 3º dias de pós-operatório - alcalose respiratória, metabólica ou mist...

  12. XML Structural Join Based on Extended Region Coding (United States)

    Yang, YANG; Hai-ge, LI

    XML has become a standard technology in exchange of a wide variety of data on web and internet for its structure, label, portability and expansibility. To efficiently query XML documents has been the primary urgent task. At the present time, most of XML index and query are based on encoding the XML document tree, so all kinds of XML encoding schemes are proposed, and region coding is the mainstream coding and used most commonly, such as Dietz coding, Li-Moon coding, Zhang coding, Wan coding, etc. The paper proposes an extended region coding based on region coding. Preorder XML document tree, and take preorder numerical orders of a node's all descendants as the region. When carrying out structural join, if preorder numerical order of a node is in this region, structural relation can be ensured. So this extended region coding can help effectively judge structural relation and the XML document tree needn't be traversed. Furthermore, the better structural join algorithms of XML path queries have received considerable attention recently, and some researchers have proposed some fine algorithms to solve the problem. Stack-Tree-Desc algorithm is one of these fine algorithms, it need separately scan ancestor list and descendant list one time to decide ancestor/descendant structural relation, but some unneeded join nodes still be scanned. For this reason, if some element nodes of ancestor list and descendant list which don't need participate in structural join can be jumped, the query efficiency is enhanced. Therefore, based on Stack-Tree-Desc algorithm an improved algorithm which introduces index structure to avoid scanning unwanted nodes, so ordered scanning is unnecessary, the consuming time of query shortens accordingly. And this improved algorithm can quickly judge structural relation based on extended region coding presented in this paper. Experiment is conducted to test the effectiveness of the extended region coding and the Indexed Stack-Tree-Desc algorithm

  13. Vibration-based localisation of structural deterioration in frame-like civil engineering structures

    DEFF Research Database (Denmark)

    Ulriksen, Martin Dalgaard; Damkilde, Lars


    to other structural systems, for instance, wind turbines—can provide reliable damage localisation in frame-like structures. The performance of the method, which is based on statistical interrogation of changes in a surrogate of the transfer matrix, is tested in a Monte Carlo setting with a numerical steel......With the existing trend of minimising material use in typical frame-like civil engineering structures, such as buildings, bridges, and offshore platforms, these structures will typically be subjected to substantial wind induced vibrations. Besides being a source of disturbance for the occupants...... frame model subjected to white noise excitation....

  14. Extracellular vesicles: a platform for the structure determination of membrane proteins by Cryo-EM. (United States)

    Zeev-Ben-Mordehai, Tzviya; Vasishtan, Daven; Siebert, C Alistair; Whittle, Cathy; Grünewald, Kay


    Membrane protein-enriched extracellular vesicles (MPEEVs) provide a platform for studying intact membrane proteins natively anchored with the correct topology in genuine biological membranes. This approach circumvents the need to conduct tedious detergent screens for solubilization, purification, and reconstitution required in classical membrane protein studies. We have applied this method to three integral type I membrane proteins, namely the Caenorhabditis elegans cell-cell fusion proteins AFF-1 and EFF-1 and the glycoprotein B (gB) from Herpes simplex virus type 1 (HSV1). Electron cryotomography followed by subvolume averaging allowed the 3D reconstruction of EFF-1 and HSV1 gB in the membrane as well as an analysis of the spatial distribution and interprotein interactions on the membrane. MPEEVs have many applications beyond structural/functional investigations, such as facilitating the raising of antibodies, for protein-protein interaction assays or for diagnostics use, as biomarkers, and possibly therapeutics. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

  15. Cryo-EM structure of Saccharomyces cerevisiae target of rapamycin complex 2. (United States)

    Karuppasamy, Manikandan; Kusmider, Beata; Oliveira, Taiana M; Gaubitz, Christl; Prouteau, Manoel; Loewith, Robbie; Schaffitzel, Christiane


    The target of rapamycin (TOR) kinase assembles into two distinct multiprotein complexes, conserved across eukaryote evolution. In contrast to TOR complex 1 (TORC1), TORC2 kinase activity is not inhibited by the macrolide rapamycin. Here, we present the structure of Saccharomyces cerevisiae TORC2 determined by electron cryo-microscopy. TORC2 contains six subunits assembling into a 1.4 MDa rhombohedron. Tor2 and Lst8 form the common core of both TOR complexes. Avo3/Rictor is unique to TORC2, but interacts with the same HEAT repeats of Tor2 that are engaged by Kog1/Raptor in mammalian TORC1, explaining the mutual exclusivity of these two proteins. Density, which we conclude is Avo3, occludes the FKBP12-rapamycin-binding site of Tor2's FRB domain rendering TORC2 rapamycin insensitive and recessing the kinase active site. Although mobile, Avo1/hSin1 further restricts access to the active site as its conserved-region-in-the-middle (CRIM) domain is positioned along an edge of the TORC2 active-site-cleft, consistent with a role for CRIM in substrate recruitment.

  16. International EMS Systems

    DEFF Research Database (Denmark)

    Langhelle, Audun; Lossius, Hans Morten; Silfvast, Tom


    is the only country that has emergency medicine (EM) as a recognised speciality but there is a need for more fully trained specialists in EM; (4) Norway: the ordinary ground ambulance is pointed out as the weakest link in the EM chain and a health reform demands extensive co-operation between the new health...... enterprises to re-establish a nation-wide air ambulance service; (5) Sweden: to create evidence based medicine standards for treatment in emergency medicine, a better integration of all part of the chain of survival, a formalised education in EM and a nation wide physician staffed helicopter EMS (HEMS) cover....

  17. Structure-based druggability assessment of the mammalian structural proteome with inclusion of light protein flexibility.

    Directory of Open Access Journals (Sweden)

    Kathryn A Loving


    Full Text Available Advances reported over the last few years and the increasing availability of protein crystal structure data have greatly improved structure-based druggability approaches. However, in practice, nearly all druggability estimation methods are applied to protein crystal structures as rigid proteins, with protein flexibility often not directly addressed. The inclusion of protein flexibility is important in correctly identifying the druggability of pockets that would be missed by methods based solely on the rigid crystal structure. These include cryptic pockets and flexible pockets often found at protein-protein interaction interfaces. Here, we apply an approach that uses protein modeling in concert with druggability estimation to account for light protein backbone movement and protein side-chain flexibility in protein binding sites. We assess the advantages and limitations of this approach on widely-used protein druggability sets. Applying the approach to all mammalian protein crystal structures in the PDB results in identification of 69 proteins with potential druggable cryptic pockets.

  18. Structure-based druggability assessment of the mammalian structural proteome with inclusion of light protein flexibility. (United States)

    Loving, Kathryn A; Lin, Andy; Cheng, Alan C


    Advances reported over the last few years and the increasing availability of protein crystal structure data have greatly improved structure-based druggability approaches. However, in practice, nearly all druggability estimation methods are applied to protein crystal structures as rigid proteins, with protein flexibility often not directly addressed. The inclusion of protein flexibility is important in correctly identifying the druggability of pockets that would be missed by methods based solely on the rigid crystal structure. These include cryptic pockets and flexible pockets often found at protein-protein interaction interfaces. Here, we apply an approach that uses protein modeling in concert with druggability estimation to account for light protein backbone movement and protein side-chain flexibility in protein binding sites. We assess the advantages and limitations of this approach on widely-used protein druggability sets. Applying the approach to all mammalian protein crystal structures in the PDB results in identification of 69 proteins with potential druggable cryptic pockets.

  19. O olhar da comunidade sobre o arranjo socioprodutivo de turismo de base comunitária em Morretes (PR)


    Zamignan, Gabriela


    Resumo: Atualmente, diante da concorrência imposta pelo mercado globalizado, pequenas comunidades rurais buscam por novas formas de organização e desenvolvimento territorial, como acontece com a experiência do Arranjo Socioprodutivo de Base Comunitária nas comunidades da Região Sudoeste da Microbacia do Rio Sagrado, em Morretes, Litoral do Paraná. Nesta experiência, enquanto o arranjo socioprodutivo e político de base comunitária (APL.Com) oportuniza modos de produção artesanais, o Turismo Co...

  20. Ensemble-based prediction of RNA secondary structures. (United States)

    Aghaeepour, Nima; Hoos, Holger H


    Accurate structure prediction methods play an important role for the understanding of RNA function. Energy-based, pseudoknot-free secondary structure prediction is one of the most widely used and versatile approaches, and improved methods for this task have received much attention over the past five years. Despite the impressive progress that as been achieved in this area, existing evaluations of the prediction accuracy achieved by various algorithms do not provide a comprehensive, statistically sound assessment. Furthermore, while there is increasing evidence that no prediction algorithm consistently outperforms all others, no work has been done to exploit the complementary strengths of multiple approaches. In this work, we present two contributions to the area of RNA secondary structure prediction. Firstly, we use state-of-the-art, resampling-based statistical methods together with a previously published and increasingly widely used dataset of high-quality RNA structures to conduct a comprehensive evaluation of existing RNA secondary structure prediction procedures. The results from this evaluation clarify the performance relationship between ten well-known existing energy-based pseudoknot-free RNA secondary structure prediction methods and clearly demonstrate the progress that has been achieved in recent years. Secondly, we introduce AveRNA, a generic and powerful method for combining a set of existing secondary structure prediction procedures into an ensemble-based method that achieves significantly higher prediction accuracies than obtained from any of its component procedures. Our new, ensemble-based method, AveRNA, improves the state of the art for energy-based, pseudoknot-free RNA secondary structure prediction by exploiting the complementary strengths of multiple existing prediction procedures, as demonstrated using a state-of-the-art statistical resampling approach. In addition, AveRNA allows an intuitive and effective control of the trade-off between

  1. Self-assembly of boron-based supramolecular structures


    Christinat, Nicolas


    This work describes the synthesis and characterization of boronic acid-based supramolecular structures. Macrocycles, dendritic structures, polymers, rotaxanes, and cages were assembled using four types of reversible reactions. The key point of the strategy is the parallel utilization of two –or more– of these reactions. Initially, aryl and alkylboronic acids were condensed with dihydroxypyridine ligands to give tetrameric or pentameric macrocycles, in which four or five boronate esters are co...

  2. Textile structures from hyaluronan based core-shell fibers (United States)

    Pitucha, T.; Lipenska, K.; Kubickova, J.; Zapotocky, V.; Velebny, V.


    Core-shell fibers based on the combination of soluble and insoluble types of hyaluronan were successfully created using wet-spinning method. High swelling of the fibers in synergy with tight textile structures were employed to ensure release of the dissolved fiber core through local cracks in the fiber shell. Thanks to the biocompatibility and resorbability of hyaluronan, the braided or knitted textile structures made from these fibers have a potential to be employed as a drug carrier in medical applications.

  3. Space mapping interpolating surrogates for highly optimized EM-based design of microwave devices

    DEFF Research Database (Denmark)

    Bandler, John; Cheng, Qingsha; Dakroury, Sameh


    the surrogate with the fine model locally. Accuracy and convergence properties are demonstrated using a seven-section capacitively-loaded impedance transformer. A highly optimized six-section H-plane waveguide filter design emerges after only four HFSS EM simulations, excluding necessary Jacobian estimations...

  4. Stability of cassava flour-based food bars Estabilidade de alimento em barra à base de farinha de mandioca

    Directory of Open Access Journals (Sweden)

    Erica Caroline da Silva


    Full Text Available The consumption of Brazilian cassava has been reduced due to a lack of adjustment to the modern lifestyle. To reverse this trend, new products could be developed specifically targeted to high-value niche markets. Cereal bars stand out as fast food high in nutritional value. A bar formula mimicking cereal bars was prepared using a mixture of Brazilian cassava flour, hydrogenated vegetable fat, dried bananas, ground cashew nuts, and glucose syrup. After being pressed, the bars were dried for 1 hour at 65 °C, packaged in films, and stored under ambient conditions. Its stability was continuously monitored for 210 days in order to ensure its safety and enable its introduction to the market. Texture loss was observed in the packed bars after 90 days of storage, but the sensory characteristics allowed the testers to perceive this tendency after only 30 days of storage. However, chemical, physical, and microbial analyses confirmed that the bars were safe for consumption for 180 days. The results showed that a 45 g cassava flour-based bar enriched with nuts and dried fruits can meet 6% of the recommended daily fiber intake with a caloric value between that of the common cereal bar and that of an energy bar. Adapting the formula with ingredients (fruits, nuts from different regions of Brazil may add value to this traditional product as a fast food.A farinha de mandioca apresenta redução de consumo por não se adequar ao estilo de vida moderno. Para inverter esta tendência, novos produtos poderão ser desenvolvidos e direcionados a mercados valorizados. As barras de cereais destacam-se como fast food de bom perfil nutricional. Uma fórmula foi usada para mimetizar as barras de cereais, usando uma mistura de farinha de mandioca, gordura vegetal, bananas secas, castanha de caju e xarope de glicose. As barras prensadas foram secas por 1 hora a 65 °C, embaladas em filmes e armazenadas em condição ambiente. A estabilidade do produto foi acompanhada

  5. Impedance-based structural health monitoring (Conference Presentation) (United States)

    Park, Gyuhae; Inman, Daniel J.


    This paper presents an overview of impedance-based structural health monitoring, which has been pioneered by Inman and his research group. The basic principle behind this technique is to apply high frequency structural excitations (typically greater than 30 kHz) through the surface-bonded piezoelectric transducers, and measure the impedance of structures by monitoring the current and voltage applied to the piezoelectric transducers. Changes in impedance indicate changes in the structure, which in turn can indicate that damage has occurred. For the last two decades, extensive research works have been performed to various applications, including mechanical, aerospace and civil structural components. The technique has been also extended to piezoelectric sensor diagnostics, concrete cure monitoring, and biomedical applications. This paper presents the summary of how this technique has been evolved with the significant contribution by Inman.

  6. A prática clínica baseada em evidências: parte II - buscando as evidências em fontes de informação Evidence based clinical practice: part II - searching evidence databases

    Directory of Open Access Journals (Sweden)

    Wanderley Marques Bernardo


    Full Text Available A busca da resposta a uma questão clínica bem construída pode ser realizada em inúmeras fontes de informação científica. Na dependência de onde obtemos a informação, a decisão clínica não será sustentada pelas melhores evidências disponíveis na atualidade, expondo o paciente a um risco desnecessário. A busca pode ser realizada em bases primárias, que disponibilizam os trabalhos originais, cabendo ao leitor o ônus de selecionar e analisar criticamente a validade de seus resultados. A busca pode também ser realizada em bases secundárias, que economizam o tempo do leitor na seleção metodológica e avaliação crítica. Entre as bases primárias, recomendamos o Medline e o SciELO, onde a busca pode ter início com a utilização das palavras-chaves, obtidas na construção da pergunta estruturada segundo o acrônimo P.I.C.O., em seguida, organizadas com a adição dos booleanos AND, OR ou NOT. Entre as bases secundárias que acrescem qualidade científica na seleção das evidências apresentadas, algumas fornecem respostas fundamentadas em trabalhos inviduais, como o ACP Journal Club, o Evidence Based Medicine e o InfoPoems, outras abordam questões clínicas organizadas em forma de livro, como o Clinical Evidence e o UpToDate. A Cochrane Review apresenta evidências de boa qualidade a partir de revisões sistemáticas de ensaios clínicos preferencialmente aleatorizados. A obtenção de estudos que respondem a uma questão clínica faz parte do atendimento que procura integrar a melhor evidência científica às necessidades de atendimento do paciente. Para tanto, conta com recursos tecnológicos, como os PDAs, Palmtops e Notebooks, cada vez mais adaptados para trazer a última informação divulgada pela Internet que auxilia na tomada de decisão clínica à beira do leito.The inadequacy of most of traditional sources for medical information, like textbook and review article, do not sustained the clinical decision based on

  7. Smartphone based hemispherical photography for canopy structure measurement (United States)

    Wan, Xuefen; Cui, Jian; Jiang, Xueqin; Zhang, Jingwen; Yang, Yi; Zheng, Tao


    The canopy is the most direct and active interface layer of the interaction between plant and environment, and has important influence on energy exchange, biodiversity, ecosystem matter and climate change. The measurement about canopy structure of plant is an important foundation to analyze the pattern, process and operation mechanism of forest ecosystem. Through the study of canopy structure of plant, solar radiation, ambient wind speed, air temperature and humidity, soil evaporation, soil temperature and other forest environmental climate characteristics can be evaluated. Because of its accuracy and effectiveness, canopy structure measurement based on hemispherical photography has been widely studied. However, the traditional method of canopy structure hemispherical photogrammetry based on SLR camera and fisheye lens. This method is expensive and difficult to be used in some low-cost occasions. In recent years, smartphone technology has been developing rapidly. The smartphone not only has excellent image acquisition ability, but also has the considerable computational processing ability. In addition, the gyroscope and positioning function on the smartphone will also help to measure the structure of the canopy. In this paper, we present a smartphone based hemispherical photography system. The system consists of smart phones, low-cost fisheye lenses and PMMA adapters. We designed an Android based App to obtain the canopy hemisphere images through low-cost fisheye lenses and provide horizontal collimation information. In addition, the App will add the acquisition location tag obtained by GPS and auxiliary positioning method in hemisphere image information after the canopy structure hemisphere image acquisition. The system was tested in the urban forest after it was completed. The test results show that the smartphone based hemispherical photography system can effectively collect the high-resolution canopy structure image of the plant.

  8. Hard and soft acids and bases: structure and process. (United States)

    Reed, James L


    Under investigation is the structure and process that gives rise to hard-soft behavior in simple anionic atomic bases. That for simple atomic bases the chemical hardness is expected to be the only extrinsic component of acid-base strength, has been substantiated in the current study. A thermochemically based operational scale of chemical hardness was used to identify the structure within anionic atomic bases that is responsible for chemical hardness. The base's responding electrons have been identified as the structure, and the relaxation that occurs during charge transfer has been identified as the process giving rise to hard-soft behavior. This is in contrast the commonly accepted explanations that attribute hard-soft behavior to varying degrees of electrostatic and covalent contributions to the acid-base interaction. The ability of the atomic ion's responding electrons to cause hard-soft behavior has been assessed by examining the correlation of the estimated relaxation energies of the responding electrons with the operational chemical hardness. It has been demonstrated that the responding electrons are able to give rise to hard-soft behavior in simple anionic bases.

  9. Estrutura da pastagem e padrões de desfolhação em capim-mombaça em diferentes alturas do dossel forrageiro Sward structure and defoliation patterns in mombaçagrass according to different canopy heights

    Directory of Open Access Journals (Sweden)

    Ana Luisa Palhano


    Full Text Available Com o objetivo de avaliar o padrão de desfolhação em pastagens de capim-mombaça (Panicum maximum, Jacq., novilhas leiteiras da raça HPB foram submetidas, em testes de pastejo, a cinco alturas de dossel (60, 80, 100, 120 e 140 cm, em um delineamento completamente casualizado, com duas repetições. Caracterizou-se a estrutura do dossel por meio de: altura; oferta de forragem, massa de forragem e de lâminas foliares; densidade volumétrica da forragem, de colmos mais bainhas e de lâminas foliares; densidade populacional de perfilhos; número e comprimento de lâminas foliares expandidas e em expansão. Com o aumento da altura do dossel, observou-se redução linear (Y= 0,369606 + 0,001555 x, R² = 0,5560, P = 0,008 na probabilidade de desfolhação das plantas, como resultado da maior massa de forragem. Com o incremento em altura do dossel, notadamente à altura de 85 cm, os animais passaram a ingerir maior proporção de lâminas foliares expandidas à medida que as mesmas apresentaram-se mais acessíveis, apesar da maior preferência por lâminas foliares em expansão. A intensidade de desfolhação das folhas expandidas diminuiu linearmente (Y= 80,866791 – 0,370979 x, R² = 0,6076, P = 0,004, refletindo o aumento em seu comprimento (Y= -104,311106 + 2,877570 x – 0,012035 x², R² = 0,9271, P = 0,002 e também a maior resistência à apreensão, imposta pela idade das folhas. Com o aumento em altura do dossel, o padrão de desfolhação foi alterado, de maneira que os animais passaram a executar um pastejo mais periférico nas touceiras e com acesso reduzido às folhas em expansão, de melhor valor nutritivo.To evaluate the pattern of defoliation in a Mombaça (Panicum maximum grass pasture, experimental paddocks were grazed by Holstein heifers to maintain canopy height of: 60, 80, 100, 120 and 140 cm height. The experimental design was completely randomized, with two replications. The assessed sward structures were: canopy height

  10. Symmetric metamaterials based on flower-shaped structure

    Energy Technology Data Exchange (ETDEWEB)

    Tuong, P.V. [Department of Physics, Quantum Photonic Science Research Center and Research Institute for Nature Sciences, Hanyang University, Seoul 133-791 (Korea, Republic of); Institute of Material Sciences, Vietnam Academy of Science and Technology, Hanoi (Viet Nam); Park, J.W. [Department of Physics, Quantum Photonic Science Research Center and Research Institute for Nature Sciences, Hanyang University, Seoul 133-791 (Korea, Republic of); Rhee, J.Y. [Sungkyunkwan University, Suwon (Korea, Republic of); Kim, K.W. [Sunmoon University, Asan (Korea, Republic of); Cheong, H. [Sogang University, Seoul (Korea, Republic of); Jang, W.H. [Electromagnetic Wave Institute, Korea Radio Promotion Association, Seoul (Korea, Republic of); Lee, Y.P., E-mail: [Department of Physics, Quantum Photonic Science Research Center and Research Institute for Nature Sciences, Hanyang University, Seoul 133-791 (Korea, Republic of)


    We proposed new models of metamaterials (MMs) based on a flower-shaped structure (FSS), whose “meta-atoms” consist of two flower-shaped metallic parts separated by a dielectric layer. Like the non-symmetric MMs based on cut-wire-pairs or electric ring resonators, the symmetrical FSS demonstrates the negative permeability at GHz frequencies. Employing the results, we designed a symmetric negative-refractive-index MM [a symmetric combined structure (SCS)], which is composed of FSSs and cross continuous wires. The MM properties of the FSS and the SCS are presented numerically and experimentally. - Highlights: • A new designed of sub-wavelength metamaterial, flower-shaped structure was proposed. • Flower-shaped meta-atom illustrated effective negative permeability. • Based on the meta-atom, negative refractive index was conventionally gained. • Negative refractive index was demonstrated with symmetric properties for electromagnetic wave. • Dimensional parameters were studied under normal electromagnetic wave.

  11. Serial section scanning electron microscopy (S3EM on silicon wafers for ultra-structural volume imaging of cells and tissues.

    Directory of Open Access Journals (Sweden)

    Heinz Horstmann

    Full Text Available High resolution, three-dimensional (3D representations of cellular ultrastructure are essential for structure function studies in all areas of cell biology. While limited subcellular volumes have been routinely examined using serial section transmission electron microscopy (ssTEM, complete ultrastructural reconstructions of large volumes, entire cells or even tissue are difficult to achieve using ssTEM. Here, we introduce a novel approach combining serial sectioning of tissue with scanning electron microscopy (SEM using a conductive silicon wafer as a support. Ribbons containing hundreds of 35 nm thick sections can be generated and imaged on the wafer at a lateral pixel resolution of 3.7 nm by recording the backscattered electrons with the in-lens detector of the SEM. The resulting electron micrographs are qualitatively comparable to those obtained by conventional TEM. S(3EM images of the same region of interest in consecutive sections can be used for 3D reconstructions of large structures. We demonstrate the potential of this approach by reconstructing a 31.7 µm(3 volume of a calyx of Held presynaptic terminal. The approach introduced here, Serial Section SEM (S(3EM, for the first time provides the possibility to obtain 3D ultrastructure of large volumes with high resolution and to selectively and repetitively home in on structures of interest. S(3EM accelerates process duration, is amenable to full automation and can be implemented with standard instrumentation.

  12. Optical-based smart structures for tamper-indicating applications

    Energy Technology Data Exchange (ETDEWEB)

    Sliva, P.; Anheier, N.C.; Simmons, K.L.; Undem, H.A.


    This report is a compilation of several related projects performed from 1991 through 1996 concerning the design, construction, and application of optical-based smart structure to tamper-indicating and sensing secure containers. Due to several influences, the projects were carried through to varying degrees of completion. Cancellation of the overall project at the client level motivated the authors to gather all of the technology and ideas about smart structures developed during these several projects, whether completed or just conceptualized, into one document. Although each section individually discusses a specific project, the overall document is written chronologically with each successive section showing how increased smart structure complexity was integrated into the container.

  13. A Sign-Based Phrase Structure Grammar for Turkish

    CERN Document Server

    Sehitoglu, O T


    This study analyses Turkish syntax from an informational point of view. Sign based linguistic representation and principles of HPSG (Head-driven Phrase Structure Grammar) theory are adapted to Turkish. The basic informational elements are nested and inherently sorted feature structures called signs. In the implementation, logic programming tool ALE (Attribute Logic Engine) which is primarily designed for implementing HPSG grammars is used. A type and structure hierarchy of Turkish language is designed. Syntactic phenomena such a s subcategorization, relative clauses, constituent order variation, adjuncts, nomina l predicates and complement-modifier relations in Turkish are analyzed. A parser is designed and implemented in ALE.

  14. Tunable reflecting terahertz filter based on chirped metamaterial structure. (United States)

    Yang, Jing; Gong, Cheng; Sun, Lu; Chen, Ping; Lin, Lie; Liu, Weiwei


    Tunable reflecting terahertz bandstop filter based on chirped metamaterial structure is demonstrated by numerical simulation. In the metamaterial, the metal bars are concatenated to silicon bars with different lengths. By varying the conductivity of the silicon bars, the reflectivity, central frequency and bandwidth of the metamaterial could be tuned. Light illumination could be introduced to change the conductivity of the silicon bars. Numerical simulations also show that the chirped metamaterial structure is insensitive to the incident angle and polarization-dependent. The proposed chirped metamaterial structure can be operated as a tunable bandstop filter whose modulation depth, bandwidth, shape factor and center frequency can be controlled by light pumping.

  15. Method for Real-Time Model Based Structural Anomaly Detection (United States)

    Smith, Timothy A. (Inventor); Urnes, James M., Sr. (Inventor); Reichenbach, Eric Y. (Inventor)


    A system and methods for real-time model based vehicle structural anomaly detection are disclosed. A real-time measurement corresponding to a location on a vehicle structure during an operation of the vehicle is received, and the real-time measurement is compared to expected operation data for the location to provide a modeling error signal. A statistical significance of the modeling error signal to provide an error significance is calculated, and a persistence of the error significance is determined. A structural anomaly is indicated, if the persistence exceeds a persistence threshold value.

  16. Integrated Reliability-Based Optimal Design of Structures

    DEFF Research Database (Denmark)

    Sørensen, John Dalsgaard; Thoft-Christensen, Palle


    the reliability decreases with time it is often necessary to design an inspection and repair programme. For example the reliability of offshore steel structures decreases with time due to corrosion and development of fatigue cracks. Until now most inspection and repair strategies are based on experience rather......In conventional optimal design of structural systems the weight or the initial cost of the structure is usually used as objective function. Further, the constraints require that the stresses and/or strains at some critical points have to be less than some given values. Finally, all variables...

  17. Structural Design Methodology Based on Concepts of Uncertainty (United States)

    Lin, K. Y.; Du, Jiaji; Rusk, David


    In this report, an approach to damage-tolerant aircraft structural design is proposed based on the concept of an equivalent "Level of Safety" that incorporates past service experience in the design of new structures. The discrete "Level of Safety" for a single inspection event is defined as the compliment of the probability that a single flaw size larger than the critical flaw size for residual strength of the structure exists, and that the flaw will not be detected. The cumulative "Level of Safety" for the entire structure is the product of the discrete "Level of Safety" values for each flaw of each damage type present at each location in the structure. Based on the definition of "Level of Safety", a design procedure was identified and demonstrated on a composite sandwich panel for various damage types, with results showing the sensitivity of the structural sizing parameters to the relative safety of the design. The "Level of Safety" approach has broad potential application to damage-tolerant aircraft structural design with uncertainty.

  18. Distance matrix-based approach to protein structure prediction. (United States)

    Kloczkowski, Andrzej; Jernigan, Robert L; Wu, Zhijun; Song, Guang; Yang, Lei; Kolinski, Andrzej; Pokarowski, Piotr


    Much structural information is encoded in the internal distances; a distance matrix-based approach can be used to predict protein structure and dynamics, and for structural refinement. Our approach is based on the square distance matrix D = [r(ij)(2)] containing all square distances between residues in proteins. This distance matrix contains more information than the contact matrix C, that has elements of either 0 or 1 depending on whether the distance r (ij) is greater or less than a cutoff value r (cutoff). We have performed spectral decomposition of the distance matrices D = sigma lambda(k)V(k)V(kT), in terms of eigenvalues lambda kappa and the corresponding eigenvectors v kappa and found that it contains at most five nonzero terms. A dominant eigenvector is proportional to r (2)--the square distance of points from the center of mass, with the next three being the principal components of the system of points. By predicting r (2) from the sequence we can approximate a distance matrix of a protein with an expected RMSD value of about 7.3 A, and by combining it with the prediction of the first principal component we can improve this approximation to 4.0 A. We can also explain the role of hydrophobic interactions for the protein structure, because r is highly correlated with the hydrophobic profile of the sequence. Moreover, r is highly correlated with several sequence profiles which are useful in protein structure prediction, such as contact number, the residue-wise contact order (RWCO) or mean square fluctuations (i.e. crystallographic temperature factors). We have also shown that the next three components are related to spatial directionality of the secondary structure elements, and they may be also predicted from the sequence, improving overall structure prediction. We have also shown that the large number of available HIV-1 protease structures provides a remarkable sampling of conformations, which can be viewed as direct structural information about the

  19. Determinação em linha de gramatura de silicone à base de água, em processo de fabricação de protetor de papéis auto-adesivos por interferometria infravermelha.


    Fortunato Resende Guimarães


    O objetivo deste trabalho é desenvolver e testar uma técnica de medição de gramatura de silicone para o processo de fabricação de protetores de papéis para papéis auto-adesivos, de modo a contribuir com a viabilidade da aplicação de emulsão de silicone à base d'água em substituição ao silicone à base de solvente. A técnica usada foi a Espectroscopia por Infravermelho próximo. As técnicas que utilizam o infravermelho próximo já têm sido usadas em análises em linha por mais de 25 anos. Os resul...

  20. Reliability-Based Structural Optimization of Wave Energy Converters

    DEFF Research Database (Denmark)

    Ambühl, Simon; Kramer, Morten; Sørensen, John Dalsgaard


    More and more wave energy converter (WEC) concepts are reaching prototype level. Once the prototype level is reached, the next step in order to further decrease the levelized cost of energy (LCOE) is optimizing the overall system with a focus on structural and maintenance (inspection) costs......, as well as on the harvested power from the waves. The target of a fully-developed WEC technology is not maximizing its power output, but minimizing the resulting LCOE. This paper presents a methodology to optimize the structural design of WECs based on a reliability-based optimization problem...

  1. Structure-Based Search for New Inhibitors of Cholinesterases

    Directory of Open Access Journals (Sweden)

    Barbara Malawska


    Full Text Available Cholinesterases are important biological targets responsible for regulation of cholinergic transmission, and their inhibitors are used for the treatment of Alzheimer’s disease. To design new cholinesterase inhibitors, of different structure-based design strategies was followed, including the modification of compounds from a previously developed library and a fragment-based design approach. This led to the selection of heterodimeric structures as potential inhibitors. Synthesis and biological evaluation of selected candidates confirmed that the designed compounds were acetylcholinesterase inhibitors with IC50 values in the mid-nanomolar to low micromolar range, and some of them were also butyrylcholinesterase inhibitors.

  2. Multifunctional Material Structures Based on Laser-Etched Carbon Nanotube Arrays

    Directory of Open Access Journals (Sweden)

    Aline Emplit


    Full Text Available High-power electronics in the transportation and aerospace sectors need size and weight reduction. Multifunctional and multistructured materials are currently being developed to couple electromagnetic (EM and thermal properties, i.e., shielding against electromagnetic impulsions, and thermal management across the thermal interface material (TIM. In this work, we investigate laser-machined patterned carbon nanotube (CNT micro-brushes as an alternative to metallic structures for driving simultaneously EM and heat propagation. The thermal and electromagnetic response of the CNT array is expected to be sensitive to the micro-structured pattern etched in the CNT brush.

  3. Protein 3D Structure and Electron Microscopy Map Retrieval Using 3D-SURFER2.0 and EM-SURFER. (United States)

    Han, Xusi; Wei, Qing; Kihara, Daisuke


    With the rapid growth in the number of solved protein structures stored in the Protein Data Bank (PDB) and the Electron Microscopy Data Bank (EMDB), it is essential to develop tools to perform real-time structure similarity searches against the entire structure database. Since conventional structure alignment methods need to sample different orientations of proteins in the three-dimensional space, they are time consuming and unsuitable for rapid, real-time database searches. To this end, we have developed 3D-SURFER and EM-SURFER, which utilize 3D Zernike descriptors (3DZD) to conduct high-throughput protein structure comparison, visualization, and analysis. Taking an atomic structure or an electron microscopy map of a protein or a protein complex as input, the 3DZD of a query protein is computed and compared with the 3DZD of all other proteins in PDB or EMDB. In addition, local geometrical characteristics of a query protein can be analyzed using VisGrid and LIGSITE CSC in 3D-SURFER. This article describes how to use 3D-SURFER and EM-SURFER to carry out protein surface shape similarity searches, local geometric feature analysis, and interpretation of the search results. © 2017 by John Wiley & Sons, Inc. Copyright © 2017 John Wiley & Sons, Inc.

  4. Variabilidade em população base de pimenteiras ornamentais (Capsicum annuum L.

    Directory of Open Access Journals (Sweden)

    João José da Silva Neto


    Full Text Available O objetivo deste trabalho foi caracterizar progênies de uma população base de pimenteiras (Capsicum annuum L.. Foram utilizadas 54 plantas de uma geração F2 de pimenteiras ornamentais, para se avaliarem os seguintes caracteres morfoagronômicos: altura da planta (AP, diâmetro da copa (DDC, altura da primeira bifurcação (APB, diâmetro do caule (DCL, comprimento da folha (CFL, largura da folha (LFL, comprimento da corola (CDC, comprimento de antera (CANT, comprimento do estilete (CES e largura da pétala (LAP. O delineamento experimental foi inteiramente casualizado, com três repetições. Os dados foram submetidos à Análise de Variância, com posterior agrupamento das médias para o teste de Scott-Knott (p<0,01. Com exceção do CANT, verificaram-se diferenças significativas para os demais descritores, pelo Teste F. O DCL foi o descritor com maior herdabilidade (99,49%, seguido de DDC (96,14% e APB (94,05%. O caractere DCL apresentou maior variabilidade entre as plantas, formando 13 classes, seguido de DDC, com oito e APB, com seis classes. Quando se utilizaram as técnicas multivariadas, foi possível agrupar as 54 plantas em oito grupos, sendo o grupo 1 o que reuniu maior número de plantas (35. A característica que mais contribuiu para a divergência genética foi o diâmetro do caule (68,97%, seguida pelo diâmetro da copa (9,22%, altura da primeira bifurcação (6,76% e altura da planta (4,58%. Já as características de flor foram as que menos contribuíram para a variabilidade (10,47%. Houve variabilidade entre as plantas estudadas, sendo possível praticar seleção dentro dessa família, dando continuidade ao Programa de Melhoramento de Pimenteiras.

  5. Is EM dead? (United States)

    Knott, Graham; Genoud, Christel


    Since electron microscopy (EM) first appeared in the 1930s, it has held centre stage as the primary tool for the exploration of biological structure. Yet, with the recent developments of light microscopy techniques that overcome the limitations imposed by the diffraction boundary, the question arises as to whether the importance of EM in on the wane. This Commentary describes some of the pioneering studies that have shaped our understanding of cell structure. These include the development of cryo-EM techniques that have given researchers the ability to capture images of native structures and at the molecular level. It also describes how a number of recent developments significantly increase the ability of EM to visualise biological systems across a range of length scales, and in 3D, ensuring that EM will remain at the forefront of biology research for the foreseeable future.

  6. A protein structural classes prediction method based on predicted secondary structure and PSI-BLAST profile. (United States)

    Ding, Shuyan; Li, Yan; Shi, Zhuoxing; Yan, Shoujiang


    Knowledge of protein secondary structural classes plays an important role in understanding protein folding patterns. In this paper, 25 features based on position-specific scoring matrices are selected to reflect evolutionary information. In combination with other 11 rational features based on predicted protein secondary structure sequences proposed by the previous researchers, a 36-dimensional representation feature vector is presented to predict protein secondary structural classes for low-similarity sequences. ASTRALtraining dataset is used to train and design our method, other three low-similarity datasets ASTRALtest, 25PDB and 1189 are used to test the proposed method. Comparisons with other methods show that our method is effective to predict protein secondary structural classes. Stand alone version of the proposed method (PSSS-PSSM) is written in MATLAB language and it can be downloaded from Copyright © 2013 Elsevier Masson SAS. All rights reserved.

  7. Stochastic collocation-based finite element of structural nonlinear dynamics with application in composite structures

    Directory of Open Access Journals (Sweden)

    Sepahvand K.


    Full Text Available Stochastic analysis of structures having nonlinearity by means of sampling methods leads to expensive cost in term of computational time. In contrast, non-sampling methods based on the spectral representation of uncertainty are very efficient with comparable accurate results. In this pa- per, the application of spectral methods to nonlinear dynamics of structures with random parameters is investigated. The impact of the parameter randomness on structural responses has been consid- ered. To this end, uncertain parameters and the structure responses are represented using the gPC expansions with unknown deterministic coefficients and random orthogonal polynomial basis. The deterministic finite element model of the structure is used as black-box and it is executed on a set of random collocation points. As the sample structure responses are estimated, a nonlinear optimization process is employed to calculate the unknown coefficients. The method has this main advantage that can be used for complicated nonlinear structural dynamic problems for which the deterministic FEM model has been already developed. Furthermore, it is very time efficient in comparison with sampling methods, as MC simulations. The application of the method is applied to the nonlinear transient analysis of composite beam structures including uncertain quadratic random damping. The results show that the proposed method can capture the large range of uncertainty in input parameters as well as in structural dynamic responses while it is too time-efficient.

  8. Structural parameter study on polymer-based ultrasonic motor (United States)

    Wu, Jiang; Mizuno, Yosuke; Nakamura, Kentaro


    Our previous study has shown that traveling-wave rotary ultrasonic motors using polymer-based vibrators can work in the same way as conventional motors with metal-based vibrators. It is feasible to enhance the performance, particularly output torques, of polymer-based motors by adjusting several key dimensions of their vibrators. In this study, poly phenylene sulfide, a functional polymer exhibiting low attenuation at ultrasonic frequency, is selected as the vibrating body, which is activated with a piezoelectric ceramic element bonded on its back surface. The optimal thicknesses of the polymer-based motors are higher than those of metal-based motors. When the same voltages were applied, the maximum torques and output powers available with the polymer-based motors were lower than the values of the metal-based motors with the same structures. The reasons for the lower torque were explained on the basis of vibration modes. First, the force factors of the polymer-based vibrators are lower than those of metal-based vibrators owing to the great difference in the mechanical constants between polymers and piezoelectric ceramics. Subsequently, though the force factors of polymer-based vibrators can be slightly enhanced by increasing their thicknesses, the unavoidable radial vibrations become higher and cause undesirable friction loss, which reduces the output torques. Though the polymer-based motors have rotation speeds comparable to those of metal-based motors, their output power are lower due to the low electromechanical coupling factors of the polymer-based vibrators.

  9. Strain Concentration at Structural Discontinuities and Its Prediction Based on Characteristics of Compliance Change in Structures (United States)

    Kasahara, Naoto

    Elevated temperature structural design codes pay attention to strain concentration at structural discontinuities due to creep and plasticity, since it causes an increase in creep-fatigue damage of materials. One of the difficulties in predicting strain concentration is its dependence on the magnitude of loading, the constitutive equations, and the duration of loading. In this study, the author investigated the fundamental mechanism of strain concentration and its main factors. The results revealed that strain concentration is caused by strain redistribution between elastic and inelastic regions, which can be quantified by the characteristics of structural compliance. The characteristics of structural compliance are controlled by elastic region in structures and are insensitive to constitutive equations. It means that inelastic analysis can be easily applied to obtain compliance characteristics. By utilizing this fact, a simplified inelastic analysis method was proposed based on the characteristics of compliance change for the prediction of strain concentration.

  10. Structure and properties of triolein-based polyurethane networks. (United States)

    Zlatanić, Alisa; Petrović, Zoran S; Dusek, Karel


    Polyurethane networks based on vegetable oils have very heterogeneous composition, and it is difficult to find a close correlation between their structure and properties. To establish benchmark structure-properties relationships, we have prepared model polyurethane networks based on triolein and 4,4'-diphenylmethane diisocyanate (MDI). Cross-linking in the middle of fatty acid chains leaves significant parts of the triglyceride as dangling chains. To examine their effect on properties, we have synthesized another polyurethane network using triolein without dangling chains (removed by metathesis). The structure of polyols was studied in detail since it affects the structure of polyurethane networks. The network structure was analyzed from swelling and mechanical measurements and by applying network and rubber elasticity theories. The cross-linking density in both networks was found to be close to theoretical. The triolein-based model network displayed modulus (around 6 MPa), tensile strength (8.7 MPa), and elongation at break (136%), characteristic of hard rubbers. Glass transition temperatures of the networks from triolein and its metathesis analogue were 25 and 31.5 degrees C, respectively.

  11. Density-Based and Transport-Based Core-Periphery Structures in Networks

    CERN Document Server

    Lee, Sang Hoon; Porter, Mason A


    Networks often possess mesoscale structures, and studying them can yield insights into both structure and function. It is most common to study community structure, but numerous other types of mesoscale structures also exist. In this paper, we examine core-periphery structures based on both density and transportation. In such structures, core network components are well-connected both among themselves and to peripheral components, which are not well-connected to anything. We examine core-periphery structures in a wide range of examples of transportation, social, and financial networks---including road networks in large urban areas, a rabbit warren, a dolphin social network, a European interbank network, and a migration network between counties in the United States. We illustrate that a recently developed transport-based notion of node coreness is very useful for characterizing transportation networks. We also generalize this notion to examine core versus peripheral edges, and we show that this new diagnostic i...

  12. Parâmetros genéticos e diversidade em progênies de Macaúba com base em características morfológicas e fisiológicas

    Directory of Open Access Journals (Sweden)

    Gisele Pereira Domiciano


    Full Text Available A obtenção de estimativas confiáveis de parâmetros genéticos, incluindo dados relacionados à variabilidade das populações sob melhoramento, é essencial para se elucidar a estrutura genética das populações e para se inferir sobre sua variabilidade genética e seu potencial de melhoramento. Nesse sentido, este trabalho teve por objetivo estimar parâmetros genéticos e a diversidade em progênies de Macaúba com base em características morfológicas e fisiológicas. Para o estudo, foram avaliadas características morfológicas e fisiológicas em 15 progênies de macaúba, em delineamento em blocos ao acaso com 5 repetições e 3 plantas por parcela, no espaçamento de 5x5m. Não houve variabilidade para a maioria das características fisiológicas no conjunto de progênies avaliadas. Porém, verificou-se variabilidade genética para os caracteres morfológicos avaliados. As famílias de macaúba agruparam-se em três grupos distintos quanto à diversidade genética, sendo a família CPAC-03 a mais divergente em relação às demais. A eficiência no uso da água e o comprimento de raquis foram as características que mais contribuíram para a dissimilaridade das famílias de macaúba.

  13. Biomedical application of hierarchically built structures based on metal oxides (United States)

    Korovin, M. S.; Fomenko, A. N.


    Nowadays, the use of hierarchically built structures in biology and medicine arouses much interest. The aim of this work is to review and summarize the available literature data about hierarchically organized structures in biomedical application. Nanoparticles can serve as an example of such structures. Medicine holds a special place among various application methods of similar systems. Special attention is paid to inorganic nanoparticles based on different metal oxides and hydroxides, such as iron, zinc, copper, and aluminum. Our investigations show that low-dimensional nanostructures based on aluminum oxides and hydroxides have an inhibitory effect on tumor cells and possess an antimicrobial activity. At the same time, it is obvious that the large-scale use of nanoparticles by humans needs to thoroughly study their properties. Special attention should be paid to the study of nanoparticle interaction with living biological objects. The numerous data show that there is no clear understanding of interaction mechanisms between nanoparticles and various cell types.

  14. Reliability based Robustness of Timber Structures through NDT Data Updating

    DEFF Research Database (Denmark)

    Sousa, Hélder S.; Sørensen, John Dalsgaard; Kirkegaard, Poul Henning


    This work presents a framework for reliability-based assessment of timber structures / members using data gathered from non-destructive test results. These results are used for modeling an update of the mechanical characteristics of timber, using Bayesian methods. Results gathered from ultrasound...

  15. Three decades of structure- and property-based molecular design

    DEFF Research Database (Denmark)

    Müller, Klaus


    -oriented medicinal chemistry. The exploration of oxetane is given as an example. For the sake of brevity, this account cannot detail all further developments that have taken place in each individual area of structure- and property-based drug discovery and it can only hint at important developments in other...

  16. A new structural reliability index based on uncertainty theory

    Directory of Open Access Journals (Sweden)

    Pidong WANG


    Full Text Available The classical probabilistic reliability theory and fuzzy reliability theory cannot directly measure the uncertainty of structural reliability with uncertain variables, i.e., subjective random and fuzzy variables. In order to simultaneously satisfy the duality of randomness and subadditivity of fuzziness in the reliability problem, a new quantification method for the reliability of structures is presented based on uncertainty theory, and an uncertainty-theory-based perspective of classical Cornell reliability index is explored. In this paper, by introducing the uncertainty theory, we adopt the uncertain measure to quantify the reliability of structures for the subjective probability or fuzzy variables, instead of probabilistic and possibilistic measures. We utilize uncertain variables to uniformly represent the subjective random and fuzzy parameters, based on which we derive solutions to analyze the uncertainty reliability of structures with uncertainty distributions. Moreover, we propose the Cornell uncertainty reliability index based on the uncertain expected value and variance. Experimental results on three numerical applications demonstrate the validity of the proposed method.

  17. Electronic structure of Fe- vs. Ru-based dye molecules

    DEFF Research Database (Denmark)

    Johnson, Phillip S.; Cook, Peter L.; Zegkinoglou, Ioannis


    In order to explore whether Ru can be replaced by inexpensive Fe in dye molecules for solar cells, the differences in the electronic structure of Fe- and Ru-based dyes are investigated by X-ray absorption spectroscopy and first-principles calculations. Molecules with the metal in a sixfold...

  18. Structural mapping based on potential field and remote sensing data ...

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Earth System Science; Volume 126; Issue 6. Structural mapping based on potential field and remote sensing data, South Rewa Gondwana Basin, India. Swarnapriya Chowdari Bijendra Singh B Nageswara Rao Niraj Kumar A P Singh D V Chandrasekhar. Volume 126 Issue 6 August 2017 Article ...

  19. An Algorithm for Term Conflation Based on Tree Structures. (United States)

    Diaz, Irene; Morato, Jorge; Llorens, Juan


    Presents a new stemming algorithm based on tree structures that improves relevance in information retrieval by conflation, grouping similar words into a single term. Highlights include the normalization process used in automatic thesaurus construction; theoretical aspects; the normalization algorithm; and experiments with English and Spanish. (LRW)

  20. Factor Structure of the TOEFL Internet-Based Test (United States)

    Sawaki, Yasuyo; Stricker, Lawrence J.; Oranje, Andreas H.


    This construct validation study investigated the factor structure of the Test of English as a Foreign Language[TM] Internet-based test (TOEFL[R] iBT). An item-level confirmatory factor analysis was conducted for a test form completed by participants in a field study. A higher-order factor model was identified, with a higher-order general factor…

  1. A new entropy based method for computing software structural complexity

    CERN Document Server

    Roca, J L


    In this paper a new methodology for the evaluation of software structural complexity is described. It is based on the entropy evaluation of the random uniform response function associated with the so called software characteristic function SCF. The behavior of the SCF with the different software structures and their relationship with the number of inherent errors is investigated. It is also investigated how the entropy concept can be used to evaluate the complexity of a software structure considering the SCF as a canonical representation of the graph associated with the control flow diagram. The functions, parameters and algorithms that allow to carry out this evaluation are also introduced. After this analytic phase follows the experimental phase, verifying the consistency of the proposed metric and their boundary conditions. The conclusion is that the degree of software structural complexity can be measured as the entropy of the random uniform response function of the SCF. That entropy is in direct relation...

  2. A fingerprint based metric for measuring similarities of crystalline structures. (United States)

    Zhu, Li; Amsler, Maximilian; Fuhrer, Tobias; Schaefer, Bastian; Faraji, Somayeh; Rostami, Samare; Ghasemi, S Alireza; Sadeghi, Ali; Grauzinyte, Migle; Wolverton, Chris; Goedecker, Stefan


    Measuring similarities/dissimilarities between atomic structures is important for the exploration of potential energy landscapes. However, the cell vectors together with the coordinates of the atoms, which are generally used to describe periodic systems, are quantities not directly suitable as fingerprints to distinguish structures. Based on a characterization of the local environment of all atoms in a cell, we introduce crystal fingerprints that can be calculated easily and define configurational distances between crystalline structures that satisfy the mathematical properties of a metric. This distance between two configurations is a measure of their similarity/dissimilarity and it allows in particular to distinguish structures. The new method can be a useful tool within various energy landscape exploration schemes, such as minima hopping, random search, swarm intelligence algorithms, and high-throughput screenings.

  3. A fingerprint based metric for measuring similarities of crystalline structures

    Energy Technology Data Exchange (ETDEWEB)

    Zhu, Li; Fuhrer, Tobias; Schaefer, Bastian; Grauzinyte, Migle; Goedecker, Stefan, E-mail: [Department of Physics, Universität Basel, Klingelbergstr. 82, 4056 Basel (Switzerland); Amsler, Maximilian [Department of Physics, Universität Basel, Klingelbergstr. 82, 4056 Basel (Switzerland); Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208 (United States); Faraji, Somayeh; Rostami, Samare; Ghasemi, S. Alireza [Institute for Advanced Studies in Basic Sciences, P.O. Box 45195-1159, Zanjan (Iran, Islamic Republic of); Sadeghi, Ali [Physics Department, Shahid Beheshti University, G. C., Evin, 19839 Tehran (Iran, Islamic Republic of); Wolverton, Chris [Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208 (United States)


    Measuring similarities/dissimilarities between atomic structures is important for the exploration of potential energy landscapes. However, the cell vectors together with the coordinates of the atoms, which are generally used to describe periodic systems, are quantities not directly suitable as fingerprints to distinguish structures. Based on a characterization of the local environment of all atoms in a cell, we introduce crystal fingerprints that can be calculated easily and define configurational distances between crystalline structures that satisfy the mathematical properties of a metric. This distance between two configurations is a measure of their similarity/dissimilarity and it allows in particular to distinguish structures. The new method can be a useful tool within various energy landscape exploration schemes, such as minima hopping, random search, swarm intelligence algorithms, and high-throughput screenings.

  4. A fingerprint based metric for measuring similarities of crystalline structures (United States)

    Zhu, Li; Amsler, Maximilian; Fuhrer, Tobias; Schaefer, Bastian; Faraji, Somayeh; Rostami, Samare; Ghasemi, S. Alireza; Sadeghi, Ali; Grauzinyte, Migle; Wolverton, Chris; Goedecker, Stefan


    Measuring similarities/dissimilarities between atomic structures is important for the exploration of potential energy landscapes. However, the cell vectors together with the coordinates of the atoms, which are generally used to describe periodic systems, are quantities not directly suitable as fingerprints to distinguish structures. Based on a characterization of the local environment of all atoms in a cell, we introduce crystal fingerprints that can be calculated easily and define configurational distances between crystalline structures that satisfy the mathematical properties of a metric. This distance between two configurations is a measure of their similarity/dissimilarity and it allows in particular to distinguish structures. The new method can be a useful tool within various energy landscape exploration schemes, such as minima hopping, random search, swarm intelligence algorithms, and high-throughput screenings.

  5. Modern earthquake engineering offshore and land-based structures

    CERN Document Server

    Jia, Junbo


    This book addresses applications of earthquake engineering for both offshore and land-based structures. It is self-contained as a reference work and covers a wide range of topics, including topics related to engineering seismology, geotechnical earthquake engineering, structural engineering, as well as special contents dedicated to design philosophy, determination of ground motions, shock waves, tsunamis, earthquake damage, seismic response of offshore and arctic structures, spatial varied ground motions, simplified and advanced seismic analysis methods, sudden subsidence of offshore platforms, tank liquid impacts during earthquakes, seismic resistance of non-structural elements, and various types of mitigation measures, etc. The target readership includes professionals in offshore and civil engineering, officials and regulators, as well as researchers and students in this field.

  6. Self-diagnosis of smart structures based on dynamical properties (United States)

    Fritzen, C.-P.; Kraemer, P.


    When we talk about "smart structures" we can think about different properties and capabilities which make a structure "intelligent" in a certain sense. Originally, the expression "smart" was used in the context that a structure can react and adapt to certain environmental conditions, such as change of shape, compensation of deformations, active vibration damping, etc. Over the last year, the expression "smart" has been extended to the field of structural health monitoring (SHM), where sensor networks, actuators and computational capabilities are used to enable a structure to perform a self-diagnosis with the goal that this structure can release early warnings about a critical health state, locate and classify damage or even to forecast the remaining life-time. This paper intends to give an overview and point out recent developments of vibration-based methods for SHM. All these methods have in common that a structural change due to a damage results in a more or less significant change of the dynamic behavior. For the diagnosis an inverse problem has to be solved. We discuss the use of modal information as well as the direct use of forced and ambient vibrations in the time and frequency domain. Examples from civil and aerospace engineering as well as off-shore wind energy plants show the applicability of these methods.

  7. Statistical Pattern-Based Assessment of Structural Health Monitoring Data

    Directory of Open Access Journals (Sweden)

    Mohammad S. Islam


    Full Text Available In structural health monitoring (SHM, various sensors are installed at critical locations of a structure. The signals from sensors are either continuously or periodically analyzed to determine the state and performance of the structure. An objective comparison of the sensor data at different time ranges is essential for assessing the structural condition or excessive load experienced by the structure which leads to potential damage in the structure. The objectives of the current study are to establish a relationship between the data from various sensors to estimate the reliability of the data and potential damage using the statistical pattern matching techniques. In order to achieve these goals, new methodologies based on statistical pattern recognition techniques have been developed. The proposed methodologies have been developed and validated using sensor data obtained from an instrumented bridge and road test data from heavy vehicles. The application of statistical pattern matching techniques are relatively new in SHM data interpretation and current research demonstrates that it has high potential in assessing structural conditions, especially when the data are noisy and susceptible to environmental disturbances.

  8. Hidratação e equilíbrio ácido-base em pacientes cirúrgicos Hydration and acid-base balance in surgical patients


    Takachi Moriya; Antonio Carlos Pereira Martins; Jesualdo Cherri; Carlos Eli Piccinato; Nelson Okano; João José Carneiro; Ricardo Iwakura


    Estudou-se a influência da hidratação em 30 pacientes submetidos a cirurgia de pequeno e grande porte. Os pacientes foram divididos em grupos de 5 conforme o porte cirúrgico e o tipo de hidratação: restrição hídrica, segundo o balanço diário e sobrecarga hidrossalina. As alterações mais relevantes do equilíbrio ácido base foram: pré-operatório - alcalose respiratória; pós-operatório imediato - acidose respiratória; 1º, 2º e 3º dias de pós-operatório - alcalose respiratória, metabólica ou mist...

  9. Relações alométricas para estimativa da fitomassa aérea em pupunheira Peach palm biomass estimates based on allometric relationships

    Directory of Open Access Journals (Sweden)

    Fernando Vinicio A. Vega


    Full Text Available A estimativa da fitomassa aérea da pupunheira (Bactris gasipaes Kunth por meio de relações alométricas tem aplicação teórica e prática, sendo essencial em estudos de fisiologia de crescimento, bem como para identificar respostas e predizer a produção. No presente trabalho foram avaliadas diferentes equações buscando o melhor ajuste alométrico representativo da fitomassa da pupunheira cultivada para a produção de palmito. Foram utilizadas palmeiras inermes, da raça Putumayo, em diferentes estádios de desenvolvimento, cultivadas em Ubatuba (SP no espaçamento de 2 x 1 m. Selecionaram-se 117 plantas, com alturas entre 0,22 e 5,04 m e diâmetros entre 2,23 e 27,06 cm. Medidas diretas, relacionadas ao crescimento, foram realizadas antes do corte. Em seguida as plantas foram separadas em diferentes partes estruturais, sendo medidas, pesadas e secas, obtendo-se a massa da matéria seca. Os dados foram submetidos à análise de regressão e ajuste de equações, tendo como variáveis independentes os caracteres facilmente mensuráveis e não destrutivos. A fitomassa da pupunheira pode ser estimada de forma precisa a partir de equações simples, valendo-se de relações alométricas. A altura da haste principal, medida do solo até a inserção da folha +1, foi o caráter preditório indireto ideal para estimar a fitomassa de pupunheiras em cultivo comercial. Identificou-se também que, do estádio de implantação ao início de colheita de palmito, a contribuição dos perfilhos para a fitomassa aérea total é pequena e pode ser desprezada.Biomass estimates based on allometric relationships have theoretical and practical application. These data are useful tools in growth analysis experiments and yield prediction. Several equations were studied to define the best allometric fit to peach palm grown for heart-of-palm purpose. Spineless peach palms (Bactris gasipaes Kunth, from Putumayo landrace, were utilized. The experiment, in a 2 x 1

  10. Qualidade dos resumos estruturados apresentados em congresso médico Quality of the structured abstracts presented at a congress

    Directory of Open Access Journals (Sweden)

    Edilson F. dos Santos


    Full Text Available OBJETIVO: Avaliar e comparar a qualidade dos resumos apresentados em congresso médico (anais do XIV Congresso da Sociedade Brasileira de Infectologia, Novembro de 2005. A hipótese testada foi de que trabalhos de melhor qualidade são escolhidos para apresentação oral. MÉTODOS: Todos os 63 resumos apresentados oralmente e uma amostra aleatória simples (n=63 dos 664 expostos como pôster. A qualidade foi aferida por intermédio de questionário estruturado, constituído por 33 critérios, organizados em oito categorias: objetivo, delineamento, local, participantes, intervenção, medida das variáveis, resultados e conclusão. O questionário foi aplicado de maneira não cega por um dos pesquisadores. O escore final podia variar entre 0 (péssimo e 1 (excelente. RESULTADOS: Os resumos publicados nos anais do congresso obtiveram avaliação apenas regular na aferição da qualidade. Os escores médios de qualidade foram 0,60 e 0,62, respectivamente, para os resumos apresentados oralmente e como pôsteres (diferença não significativa; p=0,086. Os critérios que mais comprometeram a qualidade pertencem às categorias participantes, medida das variáveis, local e conclusão. CONCLUSÃO: A hipótese testada, de melhor qualidade dos resumos selecionados para apresentação oral, não foi confirmada. Recomenda-se aos organizadores de congressos a utilização de critérios objetivos de qualidade para selecionar a forma de exposição dos trabalhos nesse tipo de evento científico e mesmo melhorar a sua qualidade.OBJECTIVE: To assess and compare quality of abstracts presented at a medical congress (XIV Congresso da Sociedade Brasileira de Infectologia, November, 2005. The hypothesis is that material of better quality is chosen for oral presentation. METHODS: All the 63 abstracts selected for oral presentation were compared with a random sample (n=63 of the 664 abstracts registered as poster presentations. Quality was measured by a structured

  11. Dissimilarity-based classification of anatomical tree structures

    DEFF Research Database (Denmark)

    Sørensen, Lauge Emil Borch Laurs; Lo, Pechin Chien Pau; Dirksen, Asger


    A novel method for classification of abnormality in anatomical tree structures is presented. A tree is classified based on direct comparisons with other trees in a dissimilarity-based classification scheme. The pair-wise dissimilarity measure between two trees is based on a linear assignment...... between the branch feature vectors representing those trees. Hereby, localized information in the branches is collectively used in classification and variations in feature values across the tree are taken into account. An approximate anatomical correspondence between matched branches can be achieved...

  12. Jogo da Minoria: um modelo baseado em agentes aplicado ao mercado financeiro Minority Game: an agent-based model applied to financial market

    Directory of Open Access Journals (Sweden)

    Antonio Fernando Crepaldi


    Full Text Available Nos últimos anos houve uma contribuição significativa dos físicos para a construção de um tipo de modelo baseado em agentes que busca reproduzir, em simulação computacional, o comportamento do mercado financeiro. Esse modelo, chamado Jogo da Minoria consiste de um grupo de agentes que vão ao mercado comprar ou vender ativos. Eles tomam decisões com base em estratégias e, por meio delas, os agentes estabelecem um intrincado jogo de competição e coordenação pela distribuição da riqueza. O modelo tem demonstrado resultados bastante ricos e surpreendentes, tanto na dinâmica do sistema como na capacidade de reproduzir características estatísticas e comportamentais do mercado financeiro. Neste artigo, são apresentadas a estrutura e a dinâmica do Jogo da Minoria, bem como as contribuições recentes relacionadas ao Jogo da Minoria denominado de Grande Canônico, que é um modelo mais bem ajustado às características do mercado financeiro e reproduz as regularidades estatísticas do preço dos ativos chamadas fatos estilizados.Over the past ten years physicists have made a significant contribution to the building of an agent-based model to reproduce the behavior of financial markets using computer simulation. This model, called the Minority Game, consists of a group of agents that buy or sell assets. They make decisions based on strategies, and through them the agents establish an intricate game of competition and coordination resulting in the distribution of wealth. The model has shown outstanding surprising results concerning both the dynamics of the system and the ability to reproduce statistical and behavior characteristics of the financial market. In this study, the structure and dynamics of the Minority Game and the recent contributions related to the Grand Canonical Minority game, a model which is better adapted to the characteristics of the financial market and reproduce the statistical regularities of asset prices (called

  13. Development of multifunctional fluoroelastomers based on nanocomposites; Desenvolvimento de elastomeros fluorados multifuncionais baseados em nanocompositos

    Energy Technology Data Exchange (ETDEWEB)

    Zen, Heloisa Augusto


    The fluoropolymers are known for their great mechanical properties, high thermal stability and resistance to aggressive chemical environment, and because of those properties they are widely used in industries, such as automobile, petroleum, chemistry, manufacturing, among others. To improve the thermal properties and gases barrier of the polymeric matrix, the incorporation of nanoparticle is used, this process permits the polymer to maintain their own characteristics and acquire new properties of nanoparticle. Because of those properties, the structural and morphological modification of fluoropolymers are very hard to be obtained through traditional techniques, in order to surmount this difficulty, the ionizing radiation is a well-known and effective method to modify fluoropolymers structures. In this thesis a nanocomposite polymeric based on fluoroelastomer (FKM) was developed and incorporated with four different configurations of nanoparticles: clay Cloisite 15A, POSS 1159, POSS 1160 and POSS 1163. After the nanocomposites films were obtained, a radiation induced grafting process was carried out, followed by sulfonation in order to obtain a ionic exchanged membrane. The effect of nanoparticle incorporation and the ionizing radiation onto films were characterized by X-ray diffraction, thermal and mechanical analysis, scanning electron microscopy and swelling; and the membranes were evaluated by degree of grafting, ionic exchange capacity and swelling. After the films were characterized, the crosslinking effect was observed to be predominant for the nanocomposites irradiated before the vulcanization, whereas the degradation was the predominant effect in the nanocomposites irradiated after vulcanization. (author)

  14. Warning system based on theoretical-experimental study of dispersion of soluble pollutants in rivers Sistema de alerta com base em estudo teórico-experimental de dispersão de poluentes solúveis em rios

    Directory of Open Access Journals (Sweden)

    Celso B. de M. Ribeiro


    Full Text Available Information about capacity of transport and dispersion of soluble pollutants in natural streams are important in the management of water resources, especially in planning preventive measures to minimize the problems caused by accidental or intentional waste, in public health and economic activities that depend on the use of water. Considering this importance, this study aimed to develop a warning system for rivers, based on experimental techniques using tracers and analytical equations of one-dimensional transport of soluble pollutants conservative, to subsidizing the decision-making in the management of water resources. The system was development in JAVA programming language and MySQL database can predict the travel time of pollutants clouds from a point of eviction and graphically displays the temporal distribution of concentrations of passage clouds, in a particular location, downstream from the point of its launch.Informações sobre a capacidade de transporte e dispersão de poluentes solúveis em cursos de água naturais são importantes no gerenciamento dos recursos hídricos, principalmente no planejamento preventivo de medidas que visem a minimizar problemas à saúde pública e às atividades econômicas que dependem do uso da água, ocasionados por despejos acidentais ou intencionais. Considerando tal importância, este trabalho teve como objetivo desenvolver um sistema de alerta para rios, com base em resultados experimentais, utilizando técnicas de traçadores e equações analíticas de transporte unidimensional de poluentes solúveis conservativos, visando a subsidiar a tomada de decisão no gerenciamento dos recursos hídricos. O sistema desenvolvido em linguagem de programação JAVA e banco de dados MySQL permite prever o tempo de percurso da nuvem de poluentes a partir de um ponto de despejo de um poluente e apresenta, graficamente, a distribuição temporal de concentrações da passagem da nuvem, em um determinado local,

  15. Blind Test of Physics-Based Prediction of Protein Structures (United States)

    Shell, M. Scott; Ozkan, S. Banu; Voelz, Vincent; Wu, Guohong Albert; Dill, Ken A.


    We report here a multiprotein blind test of a computer method to predict native protein structures based solely on an all-atom physics-based force field. We use the AMBER 96 potential function with an implicit (GB/SA) model of solvation, combined with replica-exchange molecular-dynamics simulations. Coarse conformational sampling is performed using the zipping and assembly method (ZAM), an approach that is designed to mimic the putative physical routes of protein folding. ZAM was applied to the folding of six proteins, from 76 to 112 monomers in length, in CASP7, a community-wide blind test of protein structure prediction. Because these predictions have about the same level of accuracy as typical bioinformatics methods, and do not utilize information from databases of known native structures, this work opens up the possibility of predicting the structures of membrane proteins, synthetic peptides, or other foldable polymers, for which there is little prior knowledge of native structures. This approach may also be useful for predicting physical protein folding routes, non-native conformations, and other physical properties from amino acid sequences. PMID:19186130

  16. Electronic and chemical properties of graphene-based structures:

    DEFF Research Database (Denmark)

    Vanin, Marco

    In the present thesis several aspects of graphene-based structures have been investigated using density functional theory calculations to solve the electronic structure problem. A review of the implementation of a localized basis-set within the projector augmented wave method - the way of describ......In the present thesis several aspects of graphene-based structures have been investigated using density functional theory calculations to solve the electronic structure problem. A review of the implementation of a localized basis-set within the projector augmented wave method - the way...... of describing the core electrons employed - is also presented. The investigation of the binding of graphene on metallic model surfaces is presented comparing the results from traditional exchange and correlation functionals to the results obtained with a new type of non-local functional, which includes van der...... are easier to remove and therefore only zigzag edges are left. Finally, functionalized graphene has been investigated as catalyst for the electrochemical reduction of CO2 to chemical fuels and comparisons are made with traditional transition-metal surfaces. The investigated porphyrin-like structures...

  17. Image quality assessment based on textural structure and normalized noise (United States)

    Zhang, Chun-e.; Qiu, Zhengding


    Traditional image quality assessments are mostly based on error analysis and the errors only stem from the absolute differences of pixel values or transform coefficients between the two compared images. With consideration of Human Vision System this paper proposes a quality assessment based on textural structure and normalized noise, SNPSNR. The time-frequency property of wavelet transform is utilized to represent images' textural structure and then the structural noise is figured as the difference between wavelet transform coefficients emphasized by textural structure. The noises on each level, i.e., each channel, are weighted by HVS. Due to the energy distribution property of wavelet transform, the noise quantity difference on each transform level is quite large and is not proportional to the influence caused by them. We normalize the structural noise on different levels by normalizing the coefficients on each level. SNPSNR computation adopting the PSNR form and the result data are fitted with Differential Mean Opinion Scores (DMOS) using logistic function. SNPSNR gains better performance when compared with MSSIM, HVSNR and PSNR.

  18. Structure Learning for Deep Neural Networks Based on Multiobjective Optimization. (United States)

    Liu, Jia; Gong, Maoguo; Miao, Qiguang; Wang, Xiaogang; Li, Hao


    This paper focuses on the connecting structure of deep neural networks and proposes a layerwise structure learning method based on multiobjective optimization. A model with better generalization can be obtained by reducing the connecting parameters in deep networks. The aim is to find the optimal structure with high representation ability and better generalization for each layer. Then, the visible data are modeled with respect to structure based on the products of experts. In order to mitigate the difficulty of estimating the denominator in PoE, the denominator is simplified and taken as another objective, i.e., the connecting sparsity. Moreover, for the consideration of the contradictory nature between the representation ability and the network connecting sparsity, the multiobjective model is established. An improved multiobjective evolutionary algorithm is used to solve this model. Two tricks are designed to decrease the computational cost according to the properties of input data. The experiments on single-layer level, hierarchical level, and application level demonstrate the effectiveness of the proposed algorithm, and the learned structures can improve the performance of deep neural networks.

  19. Blind test of physics-based prediction of protein structures. (United States)

    Shell, M Scott; Ozkan, S Banu; Voelz, Vincent; Wu, Guohong Albert; Dill, Ken A


    We report here a multiprotein blind test of a computer method to predict native protein structures based solely on an all-atom physics-based force field. We use the AMBER 96 potential function with an implicit (GB/SA) model of solvation, combined with replica-exchange molecular-dynamics simulations. Coarse conformational sampling is performed using the zipping and assembly method (ZAM), an approach that is designed to mimic the putative physical routes of protein folding. ZAM was applied to the folding of six proteins, from 76 to 112 monomers in length, in CASP7, a community-wide blind test of protein structure prediction. Because these predictions have about the same level of accuracy as typical bioinformatics methods, and do not utilize information from databases of known native structures, this work opens up the possibility of predicting the structures of membrane proteins, synthetic peptides, or other foldable polymers, for which there is little prior knowledge of native structures. This approach may also be useful for predicting physical protein folding routes, non-native conformations, and other physical properties from amino acid sequences.

  20. Single-Walled Carbon-Nanotubes-Based Organic Memory Structures

    Directory of Open Access Journals (Sweden)

    Sundes Fakher


    Full Text Available The electrical behaviour of organic memory structures, based on single-walled carbon-nanotubes (SWCNTs, metal–insulator–semiconductor (MIS and thin film transistor (TFT structures, using poly(methyl methacrylate (PMMA as the gate dielectric, are reported. The drain and source electrodes were fabricated by evaporating 50 nm gold, and the gate electrode was made from 50 nm-evaporated aluminium on a clean glass substrate. Thin films of SWCNTs, embedded within the insulating layer, were used as the floating gate. SWCNTs-based memory devices exhibited clear hysteresis in their electrical characteristics (capacitance–voltage (C–V for MIS structures, as well as output and transfer characteristics for transistors. Both structures were shown to produce reliable and large memory windows by virtue of high capacity and reduced charge leakage. The hysteresis in the output and transfer characteristics, the shifts in the threshold voltage of the transfer characteristics, and the flat-band voltage shift in the MIS structures were attributed to the charging and discharging of the SWCNTs floating gate. Under an appropriate gate bias (1 s pulses, the floating gate is charged and discharged, resulting in significant threshold voltage shifts. Pulses as low as 1 V resulted in clear write and erase states.

  1. Valence band electronic structure of Pd based ternary chalcogenide superconductors

    Energy Technology Data Exchange (ETDEWEB)

    Lohani, H. [Institute of Physics, Sachivalaya Marg, Bhubaneswar 751005 (India); Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400085 (India); Mishra, P. [Institute of Physics, Sachivalaya Marg, Bhubaneswar 751005 (India); Goyal, R.; Awana, V.P.S. [National Physical Laboratory(CSIR), Dr. K. S. Krishnan Road, New Delhi 110012 (India); Sekhar, B.R., E-mail: [Institute of Physics, Sachivalaya Marg, Bhubaneswar 751005 (India); Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400085 (India)


    Highlights: • VB Photoemission study and DFT calculations on Pd based ternary superconductors are presented. • Nb{sub 2}Pd{sub 0.95}S{sub 5} shows a temperature dependent pseudogap. • VB spectral features of ternary superconductors are correlated to their structural geometry. - Abstract: We present a comparative study of the valence band electronic structure of Pd based ternary chalcogenide superconductors Nb{sub 2}Pd{sub 0.95}S{sub 5}, Ta{sub 2}Pd{sub 0.97}S{sub 6} and Ta{sub 2}Pd{sub 0.97}Te{sub 6} using experimental photoemission spectroscopy and density functional based theoretical calculations. We observe a qualitatively similarity between valence band (VB) spectra of Nb{sub 2}Pd{sub 0.95}S{sub 5} and Ta{sub 2}Pd{sub 0.97}S{sub 6}. Further, we find a pseudogap feature in Nb{sub 2}Pd{sub 0.95}S{sub 5} at low temperature, unlike other two compounds. We have correlated the structural geometry with the differences in VB spectra of these compounds. The different atomic packing in these compounds could vary the strength of inter-orbital hybridization among various atoms which leads to difference in their electronic structure as clearly observed in our DOS calculations.

  2. Adhesives Based on Furan Resin for Structural Laminated Timber

    Directory of Open Access Journals (Sweden)

    Octavia ZELENIUC


    Full Text Available In wood laminated products manufacturing thephenol-based adhesives are especially used. Recentlyother adhesives such as polyurethanes were promotedon the market for structural applications withremarkable properties. Structural adhesives have tofulfil the requirements according to their uses, underwet or dry conditions as adhesive type I and type IIrespectively. Criteria for evaluating structuraladhesives, includes delamination resistance, shearstrength of bond and percent of wood failure. Thisstudy has the objective to evaluate the bondingperformance of furan based resin and its suitability forstructural purposes. There are some investigationsabout the possibility of incorporating the furan resin intowood adhesive formulations but their industrialexploitation is still modest. Three experimentaladhesive compositions based on furan and ureaformaldehyderesins, were used to cold-glue beechand spruce lamellas to form a structural timber likeglued laminated timber. Adhesive formulations includedmixed furan resin with furfuryl alcohol (FC2 and twomodified furan resins with urea-formaldehyde resin(UR/FC2 and UR/FC3 at 50% UR. Bond shearstrength by longitudinal tensile and resistance todelamination were performed according to SR EN302:2004. The best performance was obtained withadhesive FC2 which showed shear strength above thevalues indicated for structural adhesives in EN301:2004. FC2 adhesive performed significantly betterin delamination tests too, both in dry and wetconditions, compared to the other two adhesives,showing promise for its use in load-bearing timberstructures.

  3. Reliability-Based Structural Optimization of Wave Energy Converters

    Directory of Open Access Journals (Sweden)

    Simon Ambühl


    Full Text Available More and more wave energy converter (WEC concepts are reaching prototypelevel. Once the prototype level is reached, the next step in order to further decrease thelevelized cost of energy (LCOE is optimizing the overall system with a focus on structuraland maintenance (inspection costs, as well as on the harvested power from the waves.The target of a fully-developed WEC technology is not maximizing its power output,but minimizing the resulting LCOE. This paper presents a methodology to optimize thestructural design of WECs based on a reliability-based optimization problem and the intentto maximize the investor’s benefits by maximizing the difference between income (e.g., fromselling electricity and the expected expenses (e.g., structural building costs or failure costs.Furthermore, different development levels, like prototype or commercial devices, may havedifferent main objectives and will be located at different locations, as well as receive varioussubsidies. These points should be accounted for when performing structural optimizationsof WECs. An illustrative example on the gravity-based foundation of the Wavestar deviceis performed showing how structural design can be optimized taking target reliability levelsand different structural failure modes due to extreme loads into account.

  4. Capacitance-based damage detection sensing for aerospace structural composites (United States)

    Bahrami, P.; Yamamoto, N.; Chen, Y.; Manohara, H.


    Damage detection technology needs improvement for aerospace engineering application because detection within complex composite structures is difficult yet critical to avoid catastrophic failure. Damage detection is challenging in aerospace structures because not all the damage detection technology can cover the various defect types (delamination, fiber fracture, matrix crack etc.), or conditions (visibility, crack length size, etc.). These defect states are expected to become even more complex with future introduction of novel composites including nano-/microparticle reinforcement. Currently, non-destructive evaluation (NDE) methods with X-ray, ultrasound, or eddy current have good resolutions (< 0.1 mm), but their detection capabilities is limited by defect locations and orientations and require massive inspection devices. System health monitoring (SHM) methods are often paired with NDE technologies to signal out sensed damage, but their data collection and analysis currently requires excessive wiring and complex signal analysis. Here, we present a capacitance sensor-based, structural defect detection technology with improved sensing capability. Thin dielectric polymer layer is integrated as part of the structure; the defect in the structure directly alters the sensing layer's capacitance, allowing full-coverage sensing capability independent of defect size, orientation or location. In this work, capacitance-based sensing capability was experimentally demonstrated with a 2D sensing layer consisting of a dielectric layer sandwiched by electrodes. These sensing layers were applied on substrate surfaces. Surface indentation damage (~1mm diameter) and its location were detected through measured capacitance changes: 1 to 250 % depending on the substrates. The damage detection sensors are light weight, and they can be conformably coated and can be part of the composite structure. Therefore it is suitable for aerospace structures such as cryogenic tanks and rocket

  5. High efficiency tantalum-based ceramic composite structures (United States)

    Stewart, David A. (Inventor); Leiser, Daniel B. (Inventor); DiFiore, Robert R. (Inventor); Katvala, Victor W. (Inventor)


    Tantalum-based ceramics are suitable for use in thermal protection systems. These composite structures have high efficiency surfaces (low catalytic efficiency and high emittance), thereby reducing heat flux to a spacecraft during planetary re-entry. These ceramics contain tantalum disilicide, molybdenum disilicide and borosilicate glass. The components are milled, along with a processing aid, then applied to a surface of a porous substrate, such as a fibrous silica or carbon substrate. Following application, the coating is then sintered on the substrate. The composite structure is substantially impervious to hot gas penetration and capable of surviving high heat fluxes at temperatures approaching F. and above.

  6. Structural design methodologies for ceramic-based material systems (United States)

    Duffy, Stephen F.; Chulya, Abhisak; Gyekenyesi, John P.


    One of the primary pacing items for realizing the full potential of ceramic-based structural components is the development of new design methods and protocols. The focus here is on low temperature, fast-fracture analysis of monolithic, whisker-toughened, laminated, and woven ceramic composites. A number of design models and criteria are highlighted. Public domain computer algorithms, which aid engineers in predicting the fast-fracture reliability of structural components, are mentioned. Emphasis is not placed on evaluating the models, but instead is focused on the issues relevant to the current state of the art.

  7. Bending-active reciprocal structures based on equilateral polyhedral geometries

    DEFF Research Database (Denmark)

    Popovic Larsen, Olga; BRANCART, Stijn; DE TEMMERMAN, Niels


    of parts of reciprocal bending-active components based on a selection of polyhedral dome types. To simplify the assembly of the structures and avoid the manual bending of the components on site, we introduce the concept of a double-layered, pre-bent component. Finally, this paper presents the development......, fabrication and assembly of the ReciPlyDome, a full-scale prototype of a bending-active reciprocal dome with double-layered components. Preliminary analyses of the load-bearing behaviour show the potential of these systems for material-efficient, lightweight structures. The research presented in this paper...

  8. Miniature Microwave Bandpass Filter Based on EBG Structures

    DEFF Research Database (Denmark)

    Zhurbenko, Vitaliy; Krozer, Viktor; Meincke, Peter


    as compared to stepped-impedance hairpin (SIH) resonators with similar response. The new bandpass filter has a reduced footprint and can be fabricated in standard thick-film manufacturing technology. Measured and simulated results exhibit good agreement. The measured results show improvement in the filter......A new design of a planar microwave filter, based on rejection band properties of an electrically small electromagnetic bandgap (EBG) structure, is proposed. The proposed EBG structure demonstrates effective impedance manipulation, exhibits a simple analysis, and is about three times smaller...... characteristics in comparison to existing SIH filter design....

  9. Particle filtering based structural assessment with acoustic emission sensing (United States)

    Yan, Wuzhao; Abdelrahman, Marwa; Zhang, Bin; Ziehl, Paul


    Nuclear structures are designed to withstand severe loading events under various stresses. Over time, aging of structural systems constructed with concrete and steel will occur. This deterioration may reduce service life of nuclear facilities and/or lead to unnecessary or untimely repairs. Therefore, online monitoring of structures in nuclear power plants and waste storage has drawn significant attention in recent years. Of many existing non-destructive evaluation and structural monitoring approaches, acoustic emission is promising for assessment of structural damage because it is non-intrusive and is sensitive to corrosion and crack growth in reinforced concrete elements. To provide a rapid, actionable, and graphical means for interpretation Intensity Analysis plots have been developed. This approach provides a means for classification of damage. Since the acoustic emission measurement is only an indirect indicator of structural damage, potentially corrupted by non-genuine data, it is more suitable to estimate the states of corrosion and cracking in a Bayesian estimation framework. In this paper, we will utilize the accelerated corrosion data from a specimen at the University of South Carolina to develop a particle filtering-based diagnosis and prognosis algorithm. Promising features of the proposed algorithm are described in terms of corrosion state estimation and prediction of degradation over time to a predefined threshold.

  10. Value of information-based inspection planning for offshore structures

    DEFF Research Database (Denmark)

    Irman, Arifian Agusta; Thöns, Sebastian; Leira, Bernt J.


    and risk- based inspection (RRBI) constitutes an efficient method to optimize inspection planning. Basing the inspection planning on pre-posterior Bayesian decision analysis and especially a Value of Information analysis allows to explicitly quantify the expected benefits, costs and risks associated...... with each inspection strategy. A simplified and generic risk-based inspection planning utilizing pre- posterior Bayesian decision analysis had been proposed by Faber et al. [1] and Straub [2]. This paper provides considerations on the theoretical background and a Value of Information analysis......-based inspection planning. The paper will start out with a review of the state-of-art RBI planning procedure based on Bayesian decision theory and its application in offshore structure integrity management. An example of the Value of Information approach is illustrated and it is pointed to further research...

  11. Design and Additive Manufacturing of 3D Phononic Band Gap Structures Based on Gradient Based Optimization. (United States)

    Wormser, Maximilian; Wein, Fabian; Stingl, Michael; Körner, Carolin


    We present a novel approach for gradient based maximization of phononic band gaps. The approach is a geometry projection method combining parametric shape optimization with density based topology optimization. By this approach, we obtain, in a two dimension setting, cellular structures exhibiting relative and normalized band gaps of more than 8 and 1.6, respectively. The controlling parameter is the minimal strut size, which also corresponds with the obtained stiffness of the structure. The resulting design principle is manually interpreted into a three dimensional structure from which cellular metal samples are fabricated by selective electron beam melting. Frequency response diagrams experimentally verify the numerically determined phononic band gaps of the structures. The resulting structures have band gaps down to the audible frequency range, qualifying the structures for an application in noise isolation.

  12. Design and Additive Manufacturing of 3D Phononic Band Gap Structures Based on Gradient Based Optimization

    Directory of Open Access Journals (Sweden)

    Maximilian Wormser


    Full Text Available We present a novel approach for gradient based maximization of phononic band gaps. The approach is a geometry projection method combining parametric shape optimization with density based topology optimization. By this approach, we obtain, in a two dimension setting, cellular structures exhibiting relative and normalized band gaps of more than 8 and 1.6, respectively. The controlling parameter is the minimal strut size, which also corresponds with the obtained stiffness of the structure. The resulting design principle is manually interpreted into a three dimensional structure from which cellular metal samples are fabricated by selective electron beam melting. Frequency response diagrams experimentally verify the numerically determined phononic band gaps of the structures. The resulting structures have band gaps down to the audible frequency range, qualifying the structures for an application in noise isolation.

  13. Linear algebra-based matrix structural analysis of two-dimensional reciprocal structures

    DEFF Research Database (Denmark)

    Parigi, Dario


    The following paper proposes a formulation for the extension of linear algebra-based matrix structural analysis to assemblies in which elements join in intermediate points. Such a formulation in particular must include now the possibility to describe an expanded set of joints as prismatic joint...

  14. Gradient based structural optimization with fatigue constraints of jacket structures for offshore wind turbines

    DEFF Research Database (Denmark)

    Oest, Jacob; Overgaard, Lars Christian; Lund, Erik


    without the need for extensive manual post-processing. Ultimately, the optimized design may be lighter and thus reduce both production and installation cost. The aim of this work is to present such a gradient based optimization method with fatigue constraints of jacket structures for the preliminary......Investigating the fatigue life of support structures of offshore wind turbines is imperative to avoid unexpected failure. Therefore, in the context of structural optimization, including fatigue constraints is crucial, as the optimized design will meet the design criteria early in the design process...... design phase. The key challenge is to efficiently deal with the very large number of non-linear fatigue constraints and the very large time-history loads that are used in the design of offshore support structures. In this paper main emphasis will be on the analytical design sensitivity analysis used...

  15. Integrated Teaching of Structure-Based Drug Design and Biopharmaceutics: A Computer-Based Approach (United States)

    Sutch, Brian T.; Romero, Rebecca M.; Neamati, Nouri; Haworth, Ian S.


    Rational drug design requires expertise in structural biology, medicinal chemistry, physiology, and related fields. In teaching structure-based drug design, it is important to develop an understanding of the need for early recognition of molecules with "drug-like" properties as a key component. That is, it is not merely sufficient to teach…

  16. Diode rectifier bridge-based structure for DFIG-based wind turbine

    DEFF Research Database (Denmark)

    Zhu, Rongwu; Chen, Zhe; Wu, Xiaojie


    This paper proposes a new structure for the doubly-fed induction generator (DFIG)-based wind turbine. The proposed structure consists of a DFIG controlled by a partial rated power converter in the rotor side, a three-phase diode rectifier bridge (DRB) connected to the stator, and a DC/AC full rated...

  17. Scalable, ultra-resistant structural colors based on network metamaterials

    CERN Document Server

    Galinski, Henning; Dong, Hao; Gongora, Juan S Totero; Favaro, Grégory; Döbeli, Max; Spolenak, Ralph; Fratalocchi, Andrea; Capasso, Federico


    Structural colours have drawn wide attention for their potential as a future printing technology for various applications, ranging from biomimetic tissues to adaptive camouflage materials. However, an efficient approach to realise robust colours with a scalable fabrication technique is still lacking, hampering the realisation of practical applications with this platform. Here we develop a new approach based on large scale network metamaterials, which combine dealloyed subwavelength structures at the nanoscale with loss-less, ultra-thin dielectrics coatings. By using theory and experiments, we show how sub-wavelength dielectric coatings control a mechanism of resonant light coupling with epsilon-near-zero (ENZ) regions generated in the metallic network, manifesting the formation of highly saturated structural colours that cover a wide portion of the spectrum. Ellipsometry measurements report the efficient observation of these colours even at angles of $70$ degrees. The network-like architecture of these nanoma...

  18. Capacidade Preditiva de Modelos de Insolvência com Base em Números Contábeis e Dados Descritivos

    Directory of Open Access Journals (Sweden)

    Ricardo Luiz Wüst Corrêa de Lyra


    Full Text Available No Brasil a pesquisa sobre modelos de previsão de insolvência iniciou na década de 1970, sendo que a maior parte dos trabalhos fez uso da Análise Discriminante como ferramenta estatística do modelo. Nos últimos anos, buscou-se verificar se é possível prever a insolvência das empresas utilizando dados descritivos contidos nos relatórios das organizações. Assim, este estudo tem como objetivo verificar a capacidade de alguns modelos de previsão de insolvência em prever a descontinuidade de empresas brasileiras que decretaram falência. A pesquisa caracteriza-se como descritiva e possui abordagem quantitativa, realizada por meio de pesquisa documental. A amostra totalizou 13 empresas que decretaram falência entre os anos de 1997 e 2003. Os resultados indicam que a maioria dos modelos de previsão de falência testados apresentou resultados elevados de previsões corretas. Os modelos de previsão de descontinuidade com base em relatórios descritivos obtiveram na média mais previsões assertivas quanto à capacidade de prever a falência das empresas. Esses achados demonstram que, apesar de algumas pesquisas apontarem para a falta de validade de preditores criados em realidades empresariais diferentes, alguns modelos ainda possuem boa capacidade de previsão de insolvência. Conclui-se que tanto os modelos de previsão de insolvência com base em números contábeis quanto os modelos que se utilizam de dados de relatórios descritivos podem prever a descontinuidade das organizações. Por fim, pode-se inferir que a maioria dos modelos de previsão de falência que fazem uso de números contábeis podem ser funcionais e capazes de prever a descontinuidade das organizações.

  19. Accuracy of structure-based sequence alignment of automatic methods

    Directory of Open Access Journals (Sweden)

    Lee Byungkook


    similarity is low, structure-based methods produce better sequence alignments than by using sequence similarities alone. However, current structure-based methods still mis-align 11–19% of the conserved core residues when compared to the human-curated CDD alignments. The alignment quality of each program depends on the protein structural type and similarity, with DaliLite showing the most agreement with CDD on average.

  20. Moire-Fringe-Based Fiber Optic Tiltmeter for Structural Health Monitoring

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Dae Hyun [Seoul National of Technology, Seoul (Korea, Republic of)


    This paper presents a novel fiber optic tiltmeter system for the health monitoring of large-size structures. The system is composed of a sensor head, a light control unit and a signal processing unit. The sensing mechanism of the sensor head is based on a novel integration of the moire fringe phenomenon with fiber optics to achieve a robust performance in addition to its immunity to EM interference, easy ratting, and low cost. In this paper, a prototype of the fiber optic tiltmeter system has been developed successfully. A low-cost light control unit has been developed to drive the system's optic and electronic components. From an experimental test, the fiber optic tiltmeter is proven to be a prospective sensor for the monitoring of the tilting angle of civil structure with a good linearity. Finally, the test also successfully demonstrates the performance and the potential of the novel fiber optic tiltmeter system to monitor the health of civil infrastructures.

  1. Structure-based design of cyclooxygenase-2 selectivity into ketoprofen. (United States)

    Palomer, Albert; Pascual, Jaume; Cabré, Marta; Borràs, Liset; González, Gracia; Aparici, Mònica; Carabaza, Assumpta; Cabré, Francesc; García, M Luisa; Mauleón, David


    We have recently described how to achieve COX-2 selectivity from the non-selective inhibitor indomethacin (1) using a combination of a pharmacophore and computer 3-D models based on the known X-ray crystal structures of cyclooxygenases. In the present study we have focused on the design of COX-2 selective analogues of the NSAID ketoprofen (2). The design is similarly based on the combined use of the previous pharmacophore together with traditional medicinal chemistry techniques motivated by the comparative modeling of the 3-D structures of 2 docked into the COX active sites. The analysis includes use of the program GRID to detect isoenzyme differences near the active site region and is aimed at suggesting modifications of the basic benzophenone frame of the lead compound 2. The resulting series of compounds bearing this central framework is exemplified by the potent and selective COX-2 inhibitor 17 (LM-1669).

  2. Experimental demonstration of dielectric structure based two beam acceleration.

    Energy Technology Data Exchange (ETDEWEB)

    Gai, W.; Conde, M. E.; Konecny, R.; Power, J. G.; Schoessow, P.; Sun, X.; Zou, P.


    We report on the experimental results of the dielectric based two beam accelerator (step-up transformer). By using a single high charge beam, we have generated and extracted a high power RF pulse from a 7.8 GHz primary dielectric structure and then subsequently transferred to a second accelerating structure with higher dielectric constant and smaller transverse dimensions. We have measured the energy change of a second (witness) beam passing through the acceleration stage. The measured gradient is >4 times the deceleration gradient. The detailed experiment of set-up and results of the measurements are dimmed. Future plans for the development of a 100 MeV demonstration accelerator based on this technique is presented.

  3. Structuring User Involvement in Panel-Based Living Labs

    Directory of Open Access Journals (Sweden)

    Lieven De Marez


    Full Text Available A shift towards open innovation approaches with systematic user involvement has occurred within media and ICT. One of the emerging frameworks structuring these initiatives is the "living lab" approach. Despite the growing evidence of the beneficial nature of customer involvement in product development, research into specific user characteristics for innovation is still scarce, particularly in living labs, with the notable exception of literature on lead users. Especially within the context of living labs for ICT and media innovation, an application of the lead-user framework looks promising as a way to structure and facilitate user involvement. This article is based on the experiences of three Flemish living lab initiatives with a panel-based approach and provides a customer characteristics framework that guides user involvement in living labs.

  4. The structure of the complex between a branched pentasaccharide and <em>Thermobacillus xylanilyticus em>GH-51 arabinofuranosidase reveals xylan-binding determinants and induced fit

    DEFF Research Database (Denmark)

    Paës, Gabriel; Skov, Lars K; O'Donohue, Michael J


    substrate xylan. The overall structure shows the two characteristic GH-51 domains: a catalytic domain that is folded into a (beta/alpha) 8-barrel and a C-terminal domain that displays jelly roll architecture. The pentasaccharide is bound in a groove on the surface of the enzyme, with the mono arabinosyl....... In the absence of substrate, the enzyme adopts an open conformation. In the substrate-bound form, the long loop connecting beta-strand 2 to alpha-helix 2 closes the active site and interacts with the substrate through residues His98 and Trp99. The results of kinetic and fluorescence titration studies using......The crystal structure of the family GH-51 alpha- l-arabinofuranosidase from Thermobacillus xylanilyticus has been solved as a seleno-methionyl derivative. In addition, the structure of an inactive mutant Glu176Gln is presented in complex with a branched pentasaccharide, a fragment of its natural...

  5. SAGPAR: structural grammar-based automated pathway reconstruction. (United States)

    Tagore, Somnath; De, Rajat K


    In-silico metabolic engineering is a very useful branch of systems biology for modeling, analysis and prediction of various outcomes of metabolic pathways. It can also be used for detecting interactions and dynamics within a network. Various protocols have been proposed for modeling a pathway. But most of these protocols have various disadvantages and shortcomings with respect to automated pathway modeling and analysis. In the present article, we have proposed a novel algorithm for automated pathway reconstruction. We have also made a comparative study of our algorithm with other standard protocols and discussed its advantages over others. We present StructurAl Grammar-based automated PAthway Reconstruction (SAGPAR), a fast and robust algorithm that generates any metabolic pathway using some given structural representations of metabolites. Users can model any pathway based on some pre-required features that are asked as an input by the algorithm. The algorithm also takes into considerations various thermodynamic thresholds and structural properties while modeling a pathway. The given algorithm has been tested on the standard pathway datasets of 25 pathways of Mycoplasma pneumoniae M129 and 24 pathways of Homo sapiens. The dataset is taken from KEGG and PubChem Compound data repositories. SAGPAR performs much better than some already present metabolic pathway analysis tools like Copasi, PHT, Gepasi, Jarnac and Path-A.

  6. Structural health monitoring methodology for aircraft condition-based maintenance (United States)

    Saniger, Jordi; Reithler, Livier; Guedra-Degeorges, Didier; Takeda, Nobuo; Dupuis, Jean Pierre


    Reducing maintenance costs while keeping a constant level of safety is a major issue for Air Forces and airlines. The long term perspective is to implement condition based maintenance to guarantee a constant safety level while decreasing maintenance costs. On this purpose, the development of a generalized Structural Health Monitoring System (SHMS) is needed. The objective of such a system is to localize the damages and to assess their severity, with enough accuracy to allow low cost corrective actions. The present paper describes a SHMS based on acoustic emission technology. This choice was driven by its reliability and wide use in the aerospace industry. The described SHMS uses a new learning methodology which relies on the generation of artificial acoustic emission events on the structure and an acoustic emission sensor network. The calibrated acoustic emission events picked up by the sensors constitute the knowledge set that the system relies on. With this methodology, the anisotropy of composite structures is taken into account, thus avoiding the major cause of errors of classical localization methods. Moreover, it is adaptive to different structures as it does not rely on any particular model but on measured data. The acquired data is processed and the event's location and corrected amplitude are computed. The methodology has been demonstrated and experimental tests on elementary samples presented a degree of accuracy of 1cm.

  7. Theoretical investigation of pressure-induced structural transitions in americium using GGA+<em>U> and hybrid density functional theory methods

    DEFF Research Database (Denmark)

    Verma, Ashok K.; Modak, P.; Sharma, Surinder M.


    -I to Am-II transition. Good agreement was found between calculated and experimental equations of states for all phases, but the first three phases need larger U (α) parameters (where α represents the fraction of Hartree-Fock exchange energy replacing the DFT exchange energy) than the fourth phase in order...... and pressure-induced structural transitions. Both methods yield equilibrium volume and bulk modulus in good agreement with the experimental results. The GGA+spin orbit coupling+U method reproduced all structural transitions under pressure correctly, but the HYB-DFT method failed to reproduce the observed Am...

  8. Quality-based Multimodal Classification Using Tree-Structured Sparsity (United States)


    ASI Series F, Computer and Systems Sciences, 163:446–456, 1999. 5 [7] D. Hall and J. Llinas. An introduction to multisensor data fusion . Proceedings of...advantages of in- formation fusion based on sparsity models for multi- modal classification. Among several sparsity models, tree- structured sparsity provides...rithm is proposed to solve the optimization problem, which is an efficient tool for feature-level fusion among either ho- mogeneous or heterogeneous

  9. From crystal to compound: structure-based antimalarial drug discovery. (United States)

    Drinkwater, Nyssa; McGowan, Sheena


    Despite a century of control and eradication campaigns, malaria remains one of the world's most devastating diseases. Our once-powerful therapeutic weapons are losing the war against the Plasmodium parasite, whose ability to rapidly develop and spread drug resistance hamper past and present malaria-control efforts. Finding new and effective treatments for malaria is now a top global health priority, fuelling an increase in funding and promoting open-source collaborations between researchers and pharmaceutical consortia around the world. The result of this is rapid advances in drug discovery approaches and technologies, with three major methods for antimalarial drug development emerging: (i) chemistry-based, (ii) target-based, and (iii) cell-based. Common to all three of these approaches is the unique ability of structural biology to inform and accelerate drug development. Where possible, SBDD (structure-based drug discovery) is a foundation for antimalarial drug development programmes, and has been invaluable to the development of a number of current pre-clinical and clinical candidates. However, as we expand our understanding of the malarial life cycle and mechanisms of resistance development, SBDD as a field must continue to evolve in order to develop compounds that adhere to the ideal characteristics for novel antimalarial therapeutics and to avoid high attrition rates pre- and post-clinic. In the present review, we aim to examine the contribution that SBDD has made to current antimalarial drug development efforts, covering hit discovery to lead optimization and prevention of parasite resistance. Finally, the potential for structural biology, particularly high-throughput structural genomics programmes, to identify future targets for drug discovery are discussed.

  10. Structural Differentiation of Graphs Using Hosoya-Based Indices (United States)

    Dehmer, Matthias; Mowshowitz, Abbe; Shi, Yongtang


    In this paper, we introduce the Hosoya-Spectral indices and the Hosoya information content of a graph. The first measure combines structural information captured by partial Hosoya polynomials and graph spectra. The latter is a graph entropy measure which is based on blocks consisting of vertices with the same partial Hosoya polynomial. We evaluate the discrimination power of these quantities by interpreting numerical results. PMID:25019933

  11. Automated glioblastoma segmentation based on a multiparametric structured unsupervised classification. (United States)

    Juan-Albarracín, Javier; Fuster-Garcia, Elies; Manjón, José V; Robles, Montserrat; Aparici, F; Martí-Bonmatí, L; García-Gómez, Juan M


    Automatic brain tumour segmentation has become a key component for the future of brain tumour treatment. Currently, most of brain tumour segmentation approaches arise from the supervised learning standpoint, which requires a labelled training dataset from which to infer the models of the classes. The performance of these models is directly determined by the size and quality of the training corpus, whose retrieval becomes a tedious and time-consuming task. On the other hand, unsupervised approaches avoid these limitations but often do not reach comparable results than the supervised methods. In this sense, we propose an automated unsupervised method for brain tumour segmentation based on anatomical Magnetic Resonance (MR) images. Four unsupervised classification algorithms, grouped by their structured or non-structured condition, were evaluated within our pipeline. Considering the non-structured algorithms, we evaluated K-means, Fuzzy K-means and Gaussian Mixture Model (GMM), whereas as structured classification algorithms we evaluated Gaussian Hidden Markov Random Field (GHMRF). An automated postprocess based on a statistical approach supported by tissue probability maps is proposed to automatically identify the tumour classes after the segmentations. We evaluated our brain tumour segmentation method with the public BRAin Tumor Segmentation (BRATS) 2013 Test and Leaderboard datasets. Our approach based on the GMM model improves the results obtained by most of the supervised methods evaluated with the Leaderboard set and reaches the second position in the ranking. Our variant based on the GHMRF achieves the first position in the Test ranking of the unsupervised approaches and the seventh position in the general Test ranking, which confirms the method as a viable alternative for brain tumour segmentation.

  12. Automated glioblastoma segmentation based on a multiparametric structured unsupervised classification.

    Directory of Open Access Journals (Sweden)

    Javier Juan-Albarracín

    Full Text Available Automatic brain tumour segmentation has become a key component for the future of brain tumour treatment. Currently, most of brain tumour segmentation approaches arise from the supervised learning standpoint, which requires a labelled training dataset from which to infer the models of the classes. The performance of these models is directly determined by the size and quality of the training corpus, whose retrieval becomes a tedious and time-consuming task. On the other hand, unsupervised approaches avoid these limitations but often do not reach comparable results than the supervised methods. In this sense, we propose an automated unsupervised method for brain tumour segmentation based on anatomical Magnetic Resonance (MR images. Four unsupervised classification algorithms, grouped by their structured or non-structured condition, were evaluated within our pipeline. Considering the non-structured algorithms, we evaluated K-means, Fuzzy K-means and Gaussian Mixture Model (GMM, whereas as structured classification algorithms we evaluated Gaussian Hidden Markov Random Field (GHMRF. An automated postprocess based on a statistical approach supported by tissue probability maps is proposed to automatically identify the tumour classes after the segmentations. We evaluated our brain tumour segmentation method with the public BRAin Tumor Segmentation (BRATS 2013 Test and Leaderboard datasets. Our approach based on the GMM model improves the results obtained by most of the supervised methods evaluated with the Leaderboard set and reaches the second position in the ranking. Our variant based on the GHMRF achieves the first position in the Test ranking of the unsupervised approaches and the seventh position in the general Test ranking, which confirms the method as a viable alternative for brain tumour segmentation.

  13. Fire Performance-Based Design of Building Structures

    Directory of Open Access Journals (Sweden)

    C. Muñoz Blanc


    Full Text Available This Paper presents the advantages of Performance-Based Design regarding safety of structures under fire action. A general vision of this method is provided, and the advantages of its application are shown through a real case study. Although Performance Based Design has a long career in countries such as United Kingdom, United States or Japan, with more than 30 years of development and evolution, in Spain the code has allowed to use this method since just a decade ago. Nevertheless, although Spanish Building Technical Code encourages designers to carry out this work strategy, the information that is included for this purpose is yet scarce.

  14. Ab Initio Protein Structure Assembly Using Continuous Structure Fragments and Optimized Knowledge-based Force Field (United States)

    Xu, Dong; Zhang, Yang


    Ab initio protein folding is one of the major unsolved problems in computational biology due to the difficulties in force field design and conformational search. We developed a novel program, QUARK, for template-free protein structure prediction. Query sequences are first broken into fragments of 1–20 residues where multiple fragment structures are retrieved at each position from unrelated experimental structures. Full-length structure models are then assembled from fragments using replica-exchange Monte Carlo simulations, which are guided by a composite knowledge-based force field. A number of novel energy terms and Monte Carlo movements are introduced and the particular contributions to enhancing the efficiency of both force field and search engine are analyzed in detail. QUARK prediction procedure is depicted and tested on the structure modeling of 145 non-homologous proteins. Although no global templates are used and all fragments from experimental structures with template modeling score (TM-score) >0.5 are excluded, QUARK can successfully construct 3D models of correct folds in 1/3 cases of short proteins up to 100 residues. In the ninth community-wide Critical Assessment of protein Structure Prediction (CASP9) experiment, QUARK server outperformed the second and third best servers by 18% and 47% based on the cumulative Z-score of global distance test-total (GDT-TS) scores in the free modeling (FM) category. Although ab initio protein folding remains a significant challenge, these data demonstrate new progress towards the solution of the most important problem in the field. PMID:22411565

  15. Defect classification in sparsity-based structural health monitoring (United States)

    Golato, Andrew; Ahmad, Fauzia; Santhanam, Sridhar; Amin, Moeness G.


    Guided waves have gained popularity in structural health monitoring (SHM) due to their ability to inspect large areas with little attenuation, while providing rich interactions with defects. For thin-walled structures, the propagating waves are Lamb waves, which are a complex but well understood type of guided waves. Recent works have cast the defect localization problem of Lamb wave based SHM within the sparse reconstruction framework. These methods make use of a linear model relating the measurements with the scene reflectivity under the assumption of point-like defects. However, most structural defects are not perfect points but tend to assume specific forms, such as surface cracks or internal cracks. Knowledge of the "type" of defects is useful in the assessment phase of SHM. In this paper, we present a dual purpose sparsity-based imaging scheme which, in addition to accurately localizing defects, properly classifies the defects present simultaneously. The proposed approach takes advantage of the bias exhibited by certain types of defects toward a specific Lamb wave mode. For example, some defects strongly interact with the anti-symmetric modes, while others strongly interact with the symmetric modes. We build model based dictionaries for the fundamental symmetric and anti-symmetric wave modes, which are then utilized in unison to properly localize and classify the defects present. Simulated data of surface and internal defects in a thin Aluminum plate are used to validate the proposed scheme.

  16. Microscopic neural image registration based on the structure of mitochondria (United States)

    Cao, Huiwen; Han, Hua; Rao, Qiang; Xiao, Chi; Chen, Xi


    Microscopic image registration is a key component of the neural structure reconstruction with serial sections of neural tissue. The goal of microscopic neural image registration is to recover the 3D continuity and geometrical properties of specimen. During image registration, various distortions need to be corrected, including image rotation, translation, tissue deformation, which come from the procedure of sample cutting, staining and imaging. Furthermore, there is only certain similarity between adjacent sections, and the degree of similarity depends on local structure of the tissue and the thickness of the sections. These factors make the microscopic neural image registration a challenging problem. To tackle the difficulty of corresponding landmarks extraction, we introduce a novel image registration method for Scanning Electron Microscopy (SEM) images of serial neural tissue sections based on the structure of mitochondria. The ellipsoidal shape of mitochondria ensures that the same mitochondria has similar shape between adjacent sections, and its characteristic of broad distribution in the neural tissue guarantees that landmarks based on the mitochondria distributed widely in the image. The proposed image registration method contains three parts: landmarks extraction between adjacent sections, corresponding landmarks matching and image deformation based on the correspondences. We demonstrate the performance of our method with SEM images of drosophila brain.

  17. Prioridades estratégicas em serviços de pós-venda de uma empresa de manufatura de base tecnológica Strategic prioritization in after-sales services in a manufacturing technology center

    Directory of Open Access Journals (Sweden)

    Miguel Afonso Sellitto


    Full Text Available O objetivo deste artigo foi construir uma estrutura de temas estratégicos em serviços de pós-venda de uma empresa de manufatura de base tecnológica. O artigo faz uma revisão sobre operações e estratégia de pós-venda e apresenta a metodologia de pesquisa, o método de trabalho e os resultados de um caso-piloto em uma empresa de fabricação de equipamentos eletrônicos industriais. O método compreendeu sessões de grupos focados com especialistas que construíram uma estrutura de quatro temas estratégicos e vinte e três fatores de competição em pós-venda. A estrutura foi testada em questionário respondido por gestores da operação. Foram indagadas a importância e o desempenho da empresa nos fatores de competição da estrutura. Verificou-se que o fator reparos em bancada ou oficina tem mais desempenho que importância e está sobrevalorizado pela gestão. Também se verificou que os fatores testes acelerados, uso de confiabilidade em projeto e em garantia e uso de sistemas de informação para prospecção e para tratamento de clientes estão subvalorizados e poderiam receber mais recursos em uma eventual reformulação da estratégia de pós-venda. Os outros fatores mostraram-se equilibrados: os desempenhos avaliados são similares às importâncias atribuídas. Na continuidade, a pesquisa será estendida aos distribuidores da empresa que operam em campo a estratégia de pós-venda.This paper aimed at constructing a structure for strategic themes in after-sales services of a manufacturing technology center. After-sales service operations and strategy are reviewed and the research methodology, and the findings of a case study in an industrial electronic equipment manufacturer were presented. The method included team work that together with experts developed a structure composed of four strategic themes and twenty-three after sale competitive factors. The structure was tested by a questionnaire administered to operations managers

  18. Cyclic Bis-1,3-dialkylpyridiniums from the Sponge <em>Haliclona> sp.

    Directory of Open Access Journals (Sweden)

    Jongheon Shin


    Full Text Available Eight novel cyclic bis-1,3-dialkylpyridiniums, as well as two known compounds from the cyclostellettamine class, were isolated from the sponge <em>Haliclona> sp. from Korea. Structures of these novel compounds were determined using combined NMR and FAB-MS/MS analyses. Several of these compounds exhibited moderate cytotoxic and antibacterial activities against A549 cell-line and Gram-positive strains, respectively. The structure-activity relationships of cyclostellettamines are discussed based on their bioactivities.

  19. Electronic structure of layered ferroelectric high-<em>k> titanate Pr2Ti2O7

    DEFF Research Database (Denmark)

    Atuchin, V.V.; Gavrilova, T.A.; Grivel, Jean-Claude


    The spectroscopic parameters and electronic structure of binary titanate Pr2Ti2O7 have been studied by IR-, Raman and X-ray photoelectron spectroscopy (XPS) for the powder sample prepared by solid state synthesis. The spectral features of valence band and all constituent element core levels have ...... parameters in comparison with those of other titanium- and praseodymium-bearing oxides....

  20. EM structure of a helicase-loader complex depicting a 6:2 binding sub-stoichiometry from Geobacillus kaustophilus HTA426

    Energy Technology Data Exchange (ETDEWEB)

    Lin, Yen-Chen [Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan (China); Naveen, Vankadari [Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan (China); Molecular Cell Biology, Taiwan International Graduate Program, Institute of Molecular Biology, Academia Sinica, and Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan (China); Hsiao, Chwan-Deng, E-mail: [Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan (China); Molecular Cell Biology, Taiwan International Graduate Program, Institute of Molecular Biology, Academia Sinica, and Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan (China)


    During DNA replication, bacterial helicase is recruited as a complex in association with loader proteins to unwind the parental duplex. Previous structural studies have reported saturated 6:6 helicase-loader complexes with different conformations. However, structural information on the sub-stoichiometric conformations of these previously-documented helicase-loader complexes remains elusive. Here, with the aid of single particle electron-microscopy (EM) image reconstruction, we present the Geobacillus kaustophilus HTA426 helicase-loader (DnaC-DnaI) complex with a 6:2 binding stoichiometry in the presence of ATPγS. In the 19 Å resolution EM map, the undistorted and unopened helicase ring holds a robust loader density above the C-terminal RecA-like domain. Meanwhile, the path of the central DNA binding channel appears to be obstructed by the reconstructed loader density, implying its potential role as a checkpoint conformation to prevent the loading of immature complex onto DNA. Our data also reveals that the bound nucleotides and the consequently induced conformational changes in the helicase hexamer are essential for active association with loader proteins. These observations provide fundamental insights into the formation of the helicase-loader complex in bacteria that regulates the DNA replication process. - Highlights: • Helicase-loader complex structure with 6:2 sub-stoichiometry is resolved by EM. • Helicase hexamer in 6:2 sub-stoichiometry is constricted and un-opened. • 6:2 binding ratio of helicase-loader complex could act as a DNA loading checkpoint. • Nucleotides stabilize helicase-loader complex at low protein concentrations.

  1. Structural Analysis of a Heteropolysaccharide from <em>Saccharina japonicaem> by Electrospray Mass Spectrometry in Tandem with Collision-Induced Dissociation Tandem Mass Spectrometry (ESI-CID-MS/MS

    Directory of Open Access Journals (Sweden)

    Weihua Jin


    Full Text Available A fucoidan extracted from <em>Saccharina japonicaem> was fractionated by anion exchange chromatography. The most complex fraction F0.5 was degraded by dilute sulphuric acid and then separated by use of an activated carbon column. Fraction Y1 was fractionated by anion exchange and gel filtration chromatography while Fraction Y2 was fractionated by gel filtration chromatography. The fractions were determined by ESI-MS and analyzed by ESI-CID-MS/MS. It was concluded that F0.5 had a backbone of alternating 4-linked GlcA and 2-linked Man with the first Man residue from the nonreducing end accidentally sulfated at C6. In addition, F0.5 had a 3-linked glucuronan, in accordance with a previous report by NMR. Some other structural characteristics included GlcA 1→3 Man 1→4 GlcA, Man 1→3 GlcA 1→4 GlcA, Fuc 1→4 GlcA and Fuc 1→3 Fuc. Finally, it was shown that fucose was sulfated at C2 or C4 while galactose was sulfated at C2, C4 or C6.

  2. A probabilistic fragment-based protein structure prediction algorithm. (United States)

    Simoncini, David; Berenger, Francois; Shrestha, Rojan; Zhang, Kam Y J


    Conformational sampling is one of the bottlenecks in fragment-based protein structure prediction approaches. They generally start with a coarse-grained optimization where mainchain atoms and centroids of side chains are considered, followed by a fine-grained optimization with an all-atom representation of proteins. It is during this coarse-grained phase that fragment-based methods sample intensely the conformational space. If the native-like region is sampled more, the accuracy of the final all-atom predictions may be improved accordingly. In this work we present EdaFold, a new method for fragment-based protein structure prediction based on an Estimation of Distribution Algorithm. Fragment-based approaches build protein models by assembling short fragments from known protein structures. Whereas the probability mass functions over the fragment libraries are uniform in the usual case, we propose an algorithm that learns from previously generated decoys and steers the search toward native-like regions. A comparison with Rosetta AbInitio protocol shows that EdaFold is able to generate models with lower energies and to enhance the percentage of near-native coarse-grained decoys on a benchmark of [Formula: see text] proteins. The best coarse-grained models produced by both methods were refined into all-atom models and used in molecular replacement. All atom decoys produced out of EdaFold's decoy set reach high enough accuracy to solve the crystallographic phase problem by molecular replacement for some test proteins. EdaFold showed a higher success rate in molecular replacement when compared to Rosetta. Our study suggests that improving low resolution coarse-grained decoys allows computational methods to avoid subsequent sampling issues during all-atom refinement and to produce better all-atom models. EdaFold can be downloaded from [corrected].

  3. Sobre as bases dos procedimentos investigativos em psicanálise On the basis of investigation procedures in psychoanalysis

    Directory of Open Access Journals (Sweden)

    Anna Carolina Lo Bianco


    Full Text Available O presente trabalho examina as bases da pesquisa psicanalítica. Parte das marcas deixadas nas investigações psicanalíticas pelos procedimentos científicos de disciplinas como a neurologia e a neurofisiologia no século XIX. Em seguida, acompanha o surgimento de um novo objeto, o sujeito do inconsciente, o qual, ainda que requeira operações que mantenham o rigor e a precisão característicos do pensamento científico, implica formas de investigação mais apropriadas ao campo recém-constituído. Por fim, conclui que, ao contrário de emular os procedimentos das ciências naturais, a pesquisa em psicanálise tem de reconhecer a especificidade de seu objeto, pois este só se deixa circunscrever em análise, na qual analista e analisante estão implicados nas próprias produções inconscientes sob investigação. Essa é a particularidade da nova forma de saber que marca de modo indelével o pensamento do século XX em diante.The work examines the basis of psychoanalytical research. It begins by examining the influence of scientific procedures, used by neurology and neurophysiology in the nineteenth century, on psychoanalysis. It then observes the discovery of a new subject matter of research the unconscious. The latter following the rules of rigorous and precise scientific thought still implies the need for new, adequate forms of investigation for the recently forged field of research. As a conclusion it states that rather than imitating the natural sciences procedures, psychoanalytical research needs to recognise the specificity of its subject matter. Such subject matter can only be apprehended during the analytic session, where analyst and analysand are involved in the very unconscious productions under investigation. This constitutes the particular, new kind of knowledge that so much has influenced the twentieth century thought and beyond.

  4. Eficiência de fosfitos no controle da podridão da base do estipe em mudas de pupunheira

    Directory of Open Access Journals (Sweden)

    Eduardo Jun Fuzitani


    Full Text Available A exploração de palmito no Brasil está deixando de ser uma atividade extrativista para tornar-se agrícola, devido ao plantio de palmeiras, como a pupunheira (Bactris gasipaes Kunth var. gasipaes Henderson. A podridão da base do estipe (PBE, causada por Phytophthora palmivora, vem destacando-se como uma importante doença, que poderá limitar o cultivo da pupunheira em várias regiões produtoras. Esta doença ocorre em plantas jovens e adultas. O objetivo do presente trabalho foi avaliar a eficiência da aplicação preventiva e curativa de fosfitos sobre a incidência e a severidade da PBE em mudas de pupunheira, em casa de vegetação. Para tal, três experimentos foram conduzidos, conforme segue: I - Efeito preventivo e curativo de fosfitos, seguindo o esquema fatorial 6 x 2 (tipos de fosfitos x épocas de aplicação; II - Efeito da aplicação preventiva de fosfito de potássio, seguindo o esquema fatorial 6 x 4 (número de aplicações x épocas de avaliação; e III - Efeito preventivo do número de aplicações e dosagens de fosfitos de potássio, seguindo o esquema fatorial 3 x 2 (dosagens x número de aplicações. A severidade da doença foi avaliada aos 28 dias no experimento I e no experimento III, enquanto no experimento II foi avaliada aos 7; 14; 21 e 28 dias após a inoculação, baseada em escala descritiva, com nota de 0 a 4. Os tratamentos foram dispostos no delineamento inteiramente casualizado, com 10 repetições de uma muda cada. Os dados foram submetidos à análise de variância e, quando significativos, pelo teste F (p < 0,05, e as médias dos tratamentos foram comparadas pelo teste de Tukey, a 5% de probabilidade. Pelos resultados obtidos, pôde-se concluir que o fosfito de potássio proporcionou melhor controle entre os fosfitos testados, e quando aplicado de forma preventiva na dosagem de 2,5 mL.L-1 com 3 aplicações e na dosagem de 5,0 mL.L-1 com 2 ou 3 aplicações, reduziu significativamente a incidência e

  5. SA-Search: a web tool for protein structure mining based on a Structural Alphabet (United States)

    Guyon, Frédéric; Camproux, Anne-Claude; Hochez, Joëlle; Tufféry, Pierre


    SA-Search is a web tool that can be used to mine for protein structures and extract structural similarities. It is based on a hidden Markov model derived Structural Alphabet (SA) that allows the compression of three-dimensional (3D) protein conformations into a one-dimensional (1D) representation using a limited number of prototype conformations. Using such a representation, classical methods developed for amino acid sequences can be employed. Currently, SA-Search permits the performance of fast 3D similarity searches such as the extraction of exact words using a suffix tree approach, and the search for fuzzy words viewed as a simple 1D sequence alignment problem. SA-Search is available at PMID:15215446

  6. Estratégia de capacitação em cirurgia palpebral baseada em modelo animal Animal model-based strategy of palpebral surgery training

    Directory of Open Access Journals (Sweden)

    João França Lopes


    Full Text Available OBJETIVO: Desenvolvimento de método de treinamento prático em cirurgia palpebral baseado em modelo animal, orientado para o oftalmologista geral e para o iniciante em cirurgia palpebral. MÉTODOS: O modelo porcino foi selecionado devido à semelhança com relação à pálpebra humana. Após breve estudo dirigido com material didático abordando aspectos básicos em cirurgia palpebral e roteiro prático detalhado dos procedimentos a serem realizados, passou-se ao treinamento prático. As técnicas de cirurgia palpebral abordadas foram ressecção pentagonal com reconstrução direta e por planos da pálpebra e técnica original de Bick. O treinamento foi monitorizado cuidadosamente por instrutores com ampla experiência no assunto. Cada aluno tinha à disposição 4 pálpebras. RESULTADOS: Quatorze oftalmologistas foram treinados por meio deste modelo no 1º Curso de Cirurgia Palpebral em Animal em dezembro de 2001. Ao final do treinamento, os alunos se mostraram mais confiantes na realização dos procedimentos realizados, acreditando que a experiência havia contribuído positivamente para o desenvolvimento prático em cirurgia palpebral. CONCLUSÃO: O modelo animal porcino de treinamento pode ser etapa valiosa na transição da esfera teórica para a habilitação prática em Plástica Ocular, e pode ser utilizado como estratégia eficaz na capacitação em ressecção pentagonal com reconstrução direta e por planos da pálpebra e técnica original de Bick.OBJETIVE: Development of an animal model for practical instruction of eyelid surgery, directed to the general ophthalmologist and to the beginner in ophthalmic plastic surgery. METHODS: The porcine model was selected due to its similarity with the human lid anatomy. After a quick guided study with instructive material concerning basic aspects in eyelid surgery, with detailed instructions on the procedures to be performed, the practical training was started. The trained surgery

  7. Dendritic growth and structure of undercooled nickel base alloys (United States)

    Flemings, M. C.; Shiohara, Y.


    The principal objectives of this overall investigation are to: study means for obtaining high undercooling in levitation melted droplets, and study structures produced upon the solidification of these undercooled specimens. Thermal measurements are made of the undercooling, and of the rapid recalescence, to develop an understanding of the solidification mechanism. Comparison of results is made with the modeling studies. Characterization and metallographic work is done to gain an understanding of the relationship between rapid solidification variables and the structures so produced. In ground based work to date, solidification of undercooled Ni-25 wt percent Sn alloy was observed by high-speed cinematography and the results compared with optical temperature measurements. Also in ground based work, high-speed optical temperature measurements were made of the solidification behavior of levitated metal samples within a transparent glass medium. Two undercooled Ni-Sn alloys were examined. Measurements were carried out on samples at undercoolings up to 330 K. Microstructures of samples produced in ground based work were determined by optical metallography and by SEM, and microsegregation by electron microprobe measurements. A series of flight tests were planned to conduct experiments similar to the ground based experiments. The Space Shuttle Columbia carried an alloy undercooled experiment in the STS 61-C mission in January 1986. A sample of Ni-32.5 wt percent Sn eutectic was melted and solidified under microgravity conditions.

  8. <em>In Vivoem> Histamine Optical Nanosensors

    Directory of Open Access Journals (Sweden)

    Heather A. Clark


    Full Text Available In this communication we discuss the development of ionophore based nanosensors for the detection and monitoring of histamine levels <em>in vivoem>. This approach is based on the use of an amine-reactive, broad spectrum ionophore which is capable of recognizing and binding to histamine. We pair this ionophore with our already established nanosensor platform, and demonstrate <em>in vitroem> and <em>in vivoem> monitoring of histamine levels. This approach enables capturing rapid kinetics of histamine after injection, which are more difficult to measure with standard approaches such as blood sampling, especially on small research models. The coupling together of <em>in vivoem> nanosensors with ionophores such as nonactin provide a way to generate nanosensors for novel targets without the difficult process of designing and synthesizing novel ionophores.

  9. A population on the edge: genetic diversity and population structure of the world's northernmost harbour seals (<em>Phoca vitulinaem>)

    DEFF Research Database (Denmark)

    Andersen, Liselotte Wesley; Lydersen, Christian; Frie, Anne Kirstine


      It is crucial to examine the genetic diversity and structure of small, isolated populations, especially those at the edge of their distribution range, because they are vulnerable to stochastic processes if genetic diversity is low and isolation level high, and because such populations provide...... harbour seal populations, but if it the Svalbard population is experiencing inbreeding, this could reduce its resilience to climate change, disease outbreaks or other perturbations. Udgivelsesdato: 2010...

  10. Prevalência de Diabetes Mellitus em Pelotas, RS: um estudo de base populacional Prevalence of Diabetes Mellitus in Southern Brazil: a population-based study

    Directory of Open Access Journals (Sweden)

    Juvenal Soares Dias da Costa


    Full Text Available OBJETIVO: Comparar a prevalência de Diabetes Mellitus em população adulta, residente em área urbana, segundo auto-referência e valores de exame de glicemia de jejum. MÉTODOS: Realizou-se um estudo transversal de base populacional, com 1.968 pessoas de 20 a 69 anos, residentes na zona urbana da cidade de Pelotas, Estado do Rio Grande do Sul, em 2000. Estimou-se uma amostra de 1.800 indivíduos. Realizaram-se visitas domiciliares em 40 setores censitários sorteados aleatoriamente. Foi aplicado um questionário padronizado a todos participantes da pesquisa, incluindo perguntas sobre a presença de "açúcar no sangue", e quando afirmativo, se algum médico havia confirmado a doença. Uma subamostra de 367 participantes foi sorteada para realização de exames, entre os quais glicemia de jejum. Adotou-se como ponto de corte da glicemia de jejum para reconhecimento de diabetes 126 mg/dl e 140 mg/dl. Os resultados foram apresentados na forma de freqüência e respectivos intervalos de confiança de 95%. RESULTADOS: Dos entrevistados, 110 (5,6%; IC 95%: 4,6-6,6 referiram a presença de Diabetes Mellitus com diagnóstico confirmado pelo médico. Para as 367 pessoas submetidas aos exames laboratoriais, a prevalência de diabetes auto-referido e confirmada por médico foi de 7,1% (IC 95%: 4,5-9,7. CONCLUSÕES: As estimativas de prevalência encontradas são compatíveis com as obtidas em outras investigações nacionais. Os estudos epidemiológicos de base populacional são raros no Brasil e podem contribuir para o planejamento em saúde.OBJECTIVE: To compare the prevalence of Diabetes Mellitus among the adult population of an urban area, according to self-reported diabetes and fasting glucose test results. METHODS: We carried out a population-based cross-sectional study of 1,968 subjects aged 20-69 years, living in the urban area of the city of Pelotas, Southern Brazil, in the year 2000. Sample size was calculated at 1,800 subjects. We visited the

  11. Monitoring of pipeline deformations using optical fiber sensors based on Bragg lattices; Monitoracao de deformacoes em dutos utilizando sensores a fibra optica com base em redes de Bragg

    Energy Technology Data Exchange (ETDEWEB)

    Moszkowica, Viktor Nigri [Pontificia Univ. Catolica do Rio de Janeiro, RJ (Brazil)]. E-mail:


    In the petroleum sector there is a growing need for the use of pipelines as well as for their monitoring. A way to avoid leaks that can cause great damage to the environment is by the monitoring of deformations. In case failures can not be avoided through operational procedures, the monitoring of deformations can identify the initial moment and location of the leak, allowing for quick action on the part of the cleaning and depollution teams. Also important is the monitoring of slopes and soil movements. The same thing applies to production and transfer submarine pipelines subject to complex dynamic loadings that combine internal and external pressure, torsion, axial stress and, the most common of all, flexion loading. For this type of application, optical fiber sensors present a number of interesting features. Multiplexing, remote operation and long distance distribution of sensors are characteristics that attract their use in deformation monitoring systems. Presented herein are the research results of works that had the objective of developing deformation monitoring techniques in pipelines using optical fiber sensors based on Bragg grating. The technical feasibility of this technology is demonstrated through laboratorial tests. Also discussed herein are methods for field implementation of sensors, optical signal multiplexing techniques and potential advantages of applying this technology. (author)

  12. Towards improving compound selection in structure-based virtual screening. (United States)

    Waszkowycz, Bohdan


    Structure-based virtual screening is now an established technology for supporting hit finding and lead optimisation in drug discovery. Recent validation studies have highlighted the poor performance of currently used scoring functions in estimating binding affinity and hence in ranking large datasets of docked ligands. Progress in the analysis of large datasets can be made through the use of appropriate data mining techniques and the derivation of a broader range of descriptors relevant to receptor-ligand binding. In addition, simple scoring functions can be supplemented by simulation-based scoring protocols. Developments in workflow design allow the automation of repetitive tasks, and also encourage the routine use of simulation-based methods and the rapid prototyping of novel modelling and analysis procedures.

  13. DNA nanotechnology based on i-motif structures. (United States)

    Dong, Yuanchen; Yang, Zhongqiang; Liu, Dongsheng


    CONSPECTUS: Most biological processes happen at the nanometer scale, and understanding the energy transformations and material transportation mechanisms within living organisms has proved challenging. To better understand the secrets of life, researchers have investigated artificial molecular motors and devices over the past decade because such systems can mimic certain biological processes. DNA nanotechnology based on i-motif structures is one system that has played an important role in these investigations. In this Account, we summarize recent advances in functional DNA nanotechnology based on i-motif structures. The i-motif is a DNA quadruplex that occurs as four stretches of cytosine repeat sequences form C·CH(+) base pairs, and their stabilization requires slightly acidic conditions. This unique property has produced the first DNA molecular motor driven by pH changes. The motor is reliable, and studies show that it is capable of millisecond running speeds, comparable to the speed of natural protein motors. With careful design, the output of these types of motors was combined to drive micrometer-sized cantilevers bend. Using established DNA nanostructure assembly and functionalization methods, researchers can easily integrate the motor within other DNA assembled structures and functional units, producing DNA molecular devices with new functions such as suprahydrophobic/suprahydrophilic smart surfaces that switch, intelligent nanopores triggered by pH changes, molecular logic gates, and DNA nanosprings. Recently, researchers have produced motors driven by light and electricity, which have allowed DNA motors to be integrated within silicon-based nanodevices. Moreover, some devices based on i-motif structures have proven useful for investigating processes within living cells. The pH-responsiveness of the i-motif structure also provides a way to control the stepwise assembly of DNA nanostructures. In addition, because of the stability of the i-motif, this

  14. Ultrasonic wave-based structural health monitoring embedded instrument

    Energy Technology Data Exchange (ETDEWEB)

    Aranguren, G.; Monje, P. M., E-mail: [Electronic Design Group, Faculty of Engineering of Bilbao, University of the Basque Country, Bilbao (Spain); Cokonaj, Valerijan [AERnnova Engineering Solutions Ibérica S.A., Madrid (Spain); Barrera, Eduardo; Ruiz, Mariano [Instrumentation and Applied Acoustic Research Group of the Technical University of Madrid, Madrid (Spain)


    Piezoelectric sensors and actuators are the bridge between electronic and mechanical systems in structures. This type of sensor is a key element in the integrity monitoring of aeronautic structures, bridges, pressure vessels, wind turbine blades, and gas pipelines. In this paper, an all-in-one system for Structural Health Monitoring (SHM) based on ultrasonic waves is presented, called Phased Array Monitoring for Enhanced Life Assessment. This integrated instrument is able to generate excitation signals that are sent through piezoelectric actuators, acquire the received signals in the piezoelectric sensors, and carry out signal processing to check the health of structures. To accomplish this task, the instrument uses a piezoelectric phased-array transducer that performs the actuation and sensing of the signals. The flexibility and strength of the instrument allow the user to develop and implement a substantial part of the SHM technique using Lamb waves. The entire system is controlled using configuration software and has been validated through functional, electrical loading, mechanical loading, and thermal loading resistance tests.

  15. Ultrasonic wave-based structural health monitoring embedded instrument. (United States)

    Aranguren, G; Monje, P M; Cokonaj, Valerijan; Barrera, Eduardo; Ruiz, Mariano


    Piezoelectric sensors and actuators are the bridge between electronic and mechanical systems in structures. This type of sensor is a key element in the integrity monitoring of aeronautic structures, bridges, pressure vessels, wind turbine blades, and gas pipelines. In this paper, an all-in-one system for Structural Health Monitoring (SHM) based on ultrasonic waves is presented, called Phased Array Monitoring for Enhanced Life Assessment. This integrated instrument is able to generate excitation signals that are sent through piezoelectric actuators, acquire the received signals in the piezoelectric sensors, and carry out signal processing to check the health of structures. To accomplish this task, the instrument uses a piezoelectric phased-array transducer that performs the actuation and sensing of the signals. The flexibility and strength of the instrument allow the user to develop and implement a substantial part of the SHM technique using Lamb waves. The entire system is controlled using configuration software and has been validated through functional, electrical loading, mechanical loading, and thermal loading resistance tests.

  16. Impedance based sensor technology to monitor stiffness of biological structures (United States)

    Annamdas, Venu Gopal Madhav; Annamdas, Kiran Kishore Kumar


    In countries like USA or Japan it is not so uncommon to have wooden structures in their homes. However, metals and its alloys are the most widely used engineering materials in construction of any military or civil structure. Revisiting natural disasters like the recent Haiti earthquake (12 Jan 2010) or Katrina (cyclones) reminds the necessity to have better housing infrastructure with robust monitoring systems. Traditionally wood is accepted as excellent rehabilitation material, after any disaster. The recycling materials extracted from in-organic, biodegradable wastes, also can be used for rehabilitation. The key issue which dampens the life of these rehabilitated structure including green materials (like wood) is unnecessary deposits (nails, screws, bolts etc)/damages due to insect attack. Thus, a few health monitoring techniques have emerged in the recent past. Electromechanical Impedance technique is one such technique, which is simple but robust to detect variations in the integrity of structures. In this paper, impedance based piezoceramic sensor was bonded on wooden sample, which was used to study changes due to metallic (steel nails) deposits at various locations. A study of weight deposits on aluminum plate was used for comparisons.

  17. Table of periodic properties of fullerenes based on structural parameters. (United States)

    Torrens, Francisco


    The periodic table (PT) of the elements suggests that hydrogen could be the origin of everything else. The construction principle is an evolutionary process that is formally similar to those of Darwin and Oparin. The Kekulé structure count and permanence of the adjacency matrix of fullerenes are related to structural parameters involving the presence of contiguous pentagons p, q and r. Let p be the number of edges common to two pentagons, q the number of vertices common to three pentagons, and r the number of pairs of nonadjacent pentagon edges shared between two other pentagons. Principal component analysis (PCA) of the structural parameters and cluster analysis (CA) of the fullerenes permit classifying them and agree. A PT of the fullerenes is built based on the structural parameters, PCA and CA. The periodic law does not have the rank of the laws of physics. (1) The properties of the fullerenes are not repeated; only, and perhaps, their chemical character. (2) The order relationships are repeated, although with exceptions. The proposed statement is the following: The relationships that any fullerene p has with its neighbor p + 1 are approximately repeated for each period.

  18. Ultrasonic wave-based structural health monitoring embedded instrument (United States)

    Aranguren, G.; Monje, P. M.; Cokonaj, Valerijan; Barrera, Eduardo; Ruiz, Mariano


    Piezoelectric sensors and actuators are the bridge between electronic and mechanical systems in structures. This type of sensor is a key element in the integrity monitoring of aeronautic structures, bridges, pressure vessels, wind turbine blades, and gas pipelines. In this paper, an all-in-one system for Structural Health Monitoring (SHM) based on ultrasonic waves is presented, called Phased Array Monitoring for Enhanced Life Assessment. This integrated instrument is able to generate excitation signals that are sent through piezoelectric actuators, acquire the received signals in the piezoelectric sensors, and carry out signal processing to check the health of structures. To accomplish this task, the instrument uses a piezoelectric phased-array transducer that performs the actuation and sensing of the signals. The flexibility and strength of the instrument allow the user to develop and implement a substantial part of the SHM technique using Lamb waves. The entire system is controlled using configuration software and has been validated through functional, electrical loading, mechanical loading, and thermal loading resistance tests.

  19. Structural Optimization of Slender Robot Arm Based on Sensitivity Analysis

    Directory of Open Access Journals (Sweden)

    Zhong Luo


    Full Text Available An effective structural optimization method based on a sensitivity analysis is proposed to optimize the variable section of a slender robot arm. The structure mechanism and the operating principle of a polishing robot are introduced firstly, and its stiffness model is established. Then, a design of sensitivity analysis method and a sequential linear programming (SLP strategy are developed. At the beginning of the optimization, the design sensitivity analysis method is applied to select the sensitive design variables which can make the optimized results more efficient and accurate. In addition, it can also be used to determine the scale of moving step which will improve the convergency during the optimization process. The design sensitivities are calculated using the finite difference method. The search for the final optimal structure is performed using the SLP method. Simulation results show that the proposed structure optimization method is effective in enhancing the stiffness of the robot arm regardless of the robot arm suffering either a constant force or variable forces.

  20. Carbon Nanotube-Based Structural Health Monitoring Sensors (United States)

    Wincheski, Russell; Jordan, Jeffrey; Oglesby, Donald; Watkins, Anthony; Patry, JoAnne; Smits, Jan; Williams, Phillip


    Carbon nanotube (CNT)-based sensors for structural health monitoring (SHM) can be embedded in structures of all geometries to monitor conditions both inside and at the surface of the structure to continuously sense changes. These CNTs can be manipulated into specific orientations to create small, powerful, and flexible sensors. One of the sensors is a highly flexible sensor for crack growth detection and strain field mapping that features a very dense and highly ordered array of single-walled CNTs. CNT structural health sensors can be mass-produced, are inexpensive, can be packaged in small sizes (0.5 micron(sup 2)), require less power than electronic or piezoelectric transducers, and produce less waste heat per square centimeter than electronic or piezoelectric transducers. Chemically functionalized lithographic patterns are used to deposit and align the CNTs onto metallic electrodes. This method consistently produces aligned CNTs in the defined locations. Using photo- and electron-beam lithography, simple Cr/Au thin-film circuits are patterned onto oxidized silicon substrates. The samples are then re-patterned with a CNT-attracting, self-assembled monolayer of 3-aminopropyltriethoxysilane (APTES) to delineate the desired CNT locations between electrodes. During the deposition of the solution-suspended single- wall CNTs, the application of an electric field to the metallic contacts causes alignment of the CNTs along the field direction. This innovation is a prime candidate for smart skin technologies with applications ranging from military, to aerospace, to private industry.

  1. Coordinate-based versus structural approaches to brain image analysis. (United States)

    Mangin, J-F; Rivière, D; Coulon, O; Poupon, C; Cachia, A; Cointepas, Y; Poline, J-B; Le Bihan, D; Régis, J; Papadopoulos-Orfanos, D


    A basic issue in neurosciences is to look for possible relationships between brain architecture and cognitive models. The lack of architectural information in magnetic resonance images, however, has led the neuroimaging community to develop brain mapping strategies based on various coordinate systems without accurate architectural content. Therefore, the relationships between architectural and functional brain organizations are difficult to study when analyzing neuroimaging experiments. This paper advocates that the design of new brain image analysis methods inspired by the structural strategies often used in computer vision may provide better ways to address these relationships. The key point underlying this new framework is the conversion of the raw images into structural representations before analysis. These representations are made up of data-driven elementary features like activated clusters, cortical folds or fiber bundles. Two classes of methods are introduced. Inference of structural models via matching across a set of individuals is described first. This inference problem is illustrated by the group analysis of functional statistical parametric maps (SPMs). Then, the matching of new individual data with a priori known structural models is described, using the recognition of the cortical sulci as a prototypical example.

  2. Monaural Sound Localization Based on Reflective Structure and Homomorphic Deconvolution (United States)

    Park, Yeonseok; Choi, Anthony


    The asymmetric structure around the receiver provides a particular time delay for the specific incoming propagation. This paper designs a monaural sound localization system based on the reflective structure around the microphone. The reflective plates are placed to present the direction-wise time delay, which is naturally processed by convolutional operation with a sound source. The received signal is separated for estimating the dominant time delay by using homomorphic deconvolution, which utilizes the real cepstrum and inverse cepstrum sequentially to derive the propagation response’s autocorrelation. Once the localization system accurately estimates the information, the time delay model computes the corresponding reflection for localization. Because of the structure limitation, two stages of the localization process perform the estimation procedure as range and angle. The software toolchain from propagation physics and algorithm simulation realizes the optimal 3D-printed structure. The acoustic experiments in the anechoic chamber denote that 79.0% of the study range data from the isotropic signal is properly detected by the response value, and 87.5% of the specific direction data from the study range signal is properly estimated by the response time. The product of both rates shows the overall hit rate to be 69.1%. PMID:28946625

  3. Análise de necessidades com base em gênero para orientar a produção de material didático em espanhol: gêneros profissionais do ramo imobiliário

    Directory of Open Access Journals (Sweden)

    Natalia Labella-Sánchez


    Full Text Available Considerando que a análise de necessidades é fundamental para estruturar o ensino de línguas para fins específicos e para identificar os conteúdos a serem ensinados (DUDLEY-EVANS; ST. JOHN, 1998; RAMOS et al., 2004, este artigo objetiva trazer algumas reflexões teórico-metodológicas a respeito de uma análise de necessidades com base em gêneros de texto. Para isso, utilizamos a proposta de análise do sistema de atividades de Bazerman (2005. O resultado de tal análise permitiu identificar os conjuntos de gênero que caracterizam o contexto laboral dos profissionais do ramo imobiliário e propiciou subsídios para direcionar uma futura elaboração de material didático em torno a gêneros, já que os dados revelaram quais gêneros de texto precisam ser utilizados em espanhol pelos corretores e em quais situações comunicativas isso ocorre dentro do sistema de atividade.

  4. Structural level characterization of base oils using advanced analytical techniques

    KAUST Repository

    Hourani, Nadim


    Base oils, blended for finished lubricant formulations, are classified by the American Petroleum Institute into five groups, viz., groups I-V. Groups I-III consist of petroleum based hydrocarbons whereas groups IV and V are made of synthetic polymers. In the present study, five base oil samples belonging to groups I and III were extensively characterized using high performance liquid chromatography (HPLC), comprehensive two-dimensional gas chromatography (GC×GC), and Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) equipped with atmospheric pressure chemical ionization (APCI) and atmospheric pressure photoionization (APPI) sources. First, the capabilities and limitations of each analytical technique were evaluated, and then the availed information was combined to reveal compositional details on the base oil samples studied. HPLC showed the overwhelming presence of saturated over aromatic compounds in all five base oils. A similar trend was further corroborated using GC×GC, which yielded semiquantitative information on the compound classes present in the samples and provided further details on the carbon number distributions within these classes. In addition to chromatography methods, FT-ICR MS supplemented the compositional information on the base oil samples by resolving the aromatics compounds into alkyl- and naphtheno-subtituted families. APCI proved more effective for the ionization of the highly saturated base oil components compared to APPI. Furthermore, for the detailed information on hydrocarbon molecules FT-ICR MS revealed the presence of saturated and aromatic sulfur species in all base oil samples. The results presented herein offer a unique perspective into the detailed molecular structure of base oils typically used to formulate lubricants. © 2015 American Chemical Society.

  5. Níveis crescentes de feno em dietas à base de palma forrageira para caprinos em confinamento:comportamento ingestivo - DOI: 10.4025/actascianimsci.v27i4.1152 Increasing hay levels in forage cactus based diets for goats in feedlot: ingestive behavior - DOI: 10.4025/actascianimsci.v27i4.1152

    Directory of Open Access Journals (Sweden)

    Marcelo de Andrade Ferreira


    Full Text Available O experimento foi realizado de janeiro a abril de 2004, com o objetivo de avaliar o comportamento ingestivo de caprinos alimentados com rações contendo 5; 15; 25; 35; e 45% de feno de capim-tifton (Cynodon dactylon, (L Pers em dietas à base de palma forrageira (Opuntia ficus-indica, Mill. Foram utilizados 5 animais, fistulados no rúmen, distribuídos em quadrado latino 5x5. Os consumos de matéria seca, em kg/dia e em % do peso vivo (PV, e de fibra em detergente neutro, em % PV, apresentaram comportamento quadrático ( P 0,05 dos níveis de feno sobre as atividades de defecação, micção, procura pela água e posição preferencial em deitarThe experiment was carried out from January to April 2004. Five animals fed with ruminal cannula were randomly allocated in 5x5 square, to evaluate ingestive behavior and physiologic parameters. Animals were fed with forage cactus (Opuntia ficus-indica, Mill - based diets with 5; 15; 25; 35; and 45% tifton hay (Cynodon dactylon,(L. Pers. There was a quadratic relationship between dry matter (kg/day and % live weight (LW and neutral detergent fiber (% LW intake and tifton hay inclusion. Idleness time reduced whereas rumination, eating and chewing time increased linearly ( P 0.05 defecation, urination, water search and lying down position

  6. A community detection algorithm based on structural similarity (United States)

    Guo, Xuchao; Hao, Xia; Liu, Yaqiong; Zhang, Li; Wang, Lu


    In order to further improve the efficiency and accuracy of community detection algorithm, a new algorithm named SSTCA (the community detection algorithm based on structural similarity with threshold) is proposed. In this algorithm, the structural similarities are taken as the weights of edges, and the threshold k is considered to remove multiple edges whose weights are less than the threshold, and improve the computational efficiency. Tests were done on the Zachary’s network, Dolphins’ social network and Football dataset by the proposed algorithm, and compared with GN and SSNCA algorithm. The results show that the new algorithm is superior to other algorithms in accuracy for the dense networks and the operating efficiency is improved obviously.

  7. Ultrafast Dynamic Pressure Sensors Based on Graphene Hybrid Structure. (United States)

    Liu, Shanbiao; Wu, Xing; Zhang, Dongdong; Guo, Congwei; Wang, Peng; Hu, Weida; Li, Xinming; Zhou, Xiaofeng; Xu, Hejun; Luo, Chen; Zhang, Jian; Chu, Junhao


    Mechanical flexible electronic skin has been focused on sensing various physical parameters, such as pressure and temperature. The studies of material design and array-accessible devices are the building blocks of strain sensors for subtle pressure sensing. Here, we report a new and facile preparation of a graphene hybrid structure with an ultrafast dynamic pressure response. Graphene oxide nanosheets are used as a surfactant to prevent graphene restacking in aqueous solution. This graphene hybrid structure exhibits a frequency-independent pressure resistive sensing property. Exceeding natural skin, such pressure sensors, can provide transient responses from static up to 10 000 Hz dynamic frequencies. Integrated by the controlling system, the array-accessible sensors can manipulate a robot arm and self-rectify the temperature of a heating blanket. This may pave a path toward the future application of graphene-based wearable electronics.

  8. Structure-based control of complex networks with nonlinear dynamics

    CERN Document Server

    Zañudo, Jorge G T; Albert, Réka


    Given the network of interactions underlying a complex system, what can we learn about controlling such a system solely from its structure? Over a century of research in control theory has given us tools to answer this question, which were widely applied in science and engineering. Yet the current tools do not always consider the inherently nonlinear dynamics of real systems and the naturally occurring system states in their definition of "control", a term whose interpretation varies across disciplines. Here we use a new mathematical framework for structure-based control of networks governed by a broad class of nonlinear dynamics that includes the major dynamic models of biological, technological, and social processes. This framework provides realizable node overrides that steer a system towards any of its natural long term dynamic behaviors and which are guaranteed to be effective regardless of the dynamic details and parameters of the underlying system. We use this framework on several real networks, compar...

  9. Realization of Broadband Matched Filter Structures Based on Dual Networks

    Directory of Open Access Journals (Sweden)

    M. Gerding


    Full Text Available This paper deals with the basic electrical properties of dual networks and with their application in broadband matched filter structures. Starting with the main characteristics and different realization methods of dual networks, a filter structure is presented, which is based on a combination of dual networks and which provides a broadband matched input and two decoupled output ports. This filter synthesis focuses on the design of high pass filters, which are suitable to be used as differentiating stages in electrical pulse generators as a part of the so-called pulse shaping network. In order to achieve a proper pulse shape and for the prevention of multiple reflections between the switching circuit and the differentiating network, a broadband matched filter is a basic requirement.

  10. Evidence-based ergonomics: a model and conceptual structure proposal. (United States)

    Silveira, Dierci Marcio


    In Human Factors and Ergonomics Science (HFES), it is difficult to identify what is the best approach to tackle the workplace and systems design problems which needs to be solved, and it has been also advocated as transdisciplinary and multidisciplinary the issue of "How to solve the human factors and ergonomics problems that are identified?". The proposition on this study is to combine the theoretical approach for Sustainability Science, the Taxonomy of the Human Factors and Ergonomics (HFE) discipline and the framework for Evidence-Based Medicine in an attempt to be applied in Human Factors and Ergonomics. Applications of ontologies are known in the field of medical research and computer science. By scrutinizing the key requirements for the HFES structuring of knowledge, it was designed a reference model, First, it was identified the important requirements for HFES Concept structuring, as regarded by Meister. Second, it was developed an evidence-based ergonomics framework as a reference model composed of six levels based on these requirements. Third, it was devised a mapping tool using linguistic resources to translate human work, systems environment and the complexities inherent to their hierarchical relationships to support future development at Level 2 of the reference model and for meeting the two major challenges for HFES, namely, identifying what problems should be addressed in HFE as an Autonomous Science itself and proposing solutions by integrating concepts and methods applied in HFES for those problems.

  11. Structure-specific ribonucleases for MS-based elucidation of higher-order RNA structure. (United States)

    Scalabrin, Matteo; Siu, Yik; Asare-Okai, Papa Nii; Fabris, Daniele


    Supported by high-throughput sequencing technologies, structure-specific nucleases are experiencing a renaissance as biochemical probes for genome-wide mapping of nucleic acid structure. This report explores the benefits and pitfalls of the application of Mung bean (Mb) and V1 nuclease, which attack specifically single- and double-stranded regions of nucleic acids, as possible structural probes to be employed in combination with MS detection. Both enzymes were found capable of operating in ammonium-based solutions that are preferred for high-resolution analysis by direct infusion electrospray ionization (ESI). Sequence analysis by tandem mass spectrometry (MS/MS) was performed to confirm mapping assignments and to resolve possible ambiguities arising from the concomitant formation of isobaric products with identical base composition and different sequences. The observed products grouped together into ladder-type series that facilitated their assignment to unique regions of the substrate, but revealed also a certain level of uncertainty in identifying the boundaries between paired and unpaired regions. Various experimental factors that are known to stabilize nucleic acid structure, such as higher ionic strength, presence of Mg(II), etc., increased the accuracy of cleavage information, but did not completely eliminate deviations from expected results. These observations suggest extreme caution in interpreting the results afforded by these types of reagents. Regardless of the analytical platform of choice, the results highlighted the need to repeat probing experiments under the most diverse possible conditions to recognize potential artifacts and to increase the level of confidence in the observed structural information.

  12. Modeling ultrasonic NDE and guided wave based structural health monitoring (United States)

    Ravi, Nitin B.; Rathod, Vivek T.; Chakraborty, Nibir.; Mahapatra, D. R.; Sridaran, Ramanan; Boller, Christian


    Structural Health Monitoring (SHM) systems require integration of non-destructive technologies into structural design and operational processes. Modeling and simulation of complex NDE inspection processes are important aspects in the development and deployment of SHM technologies. Ray tracing techniques are vital simulation tools to visualize the wave path inside a material. These techniques also help in optimizing the location of transducers and their orientation with respect to the zone of interrogation. It helps in increasing the chances of detection and identification of a flaw in that zone. While current state-of-the-art techniques such as ray tracing based on geometric principle help in such visualization, other information such as signal losses due to spherical or cylindrical shape of wave front are rarely taken into consideration. The problem becomes a little more complicated in the case of dispersive guided wave propagation and near-field defect scattering. We review the existing models and tools to perform ultrasonic NDE simulation in structural components. As an initial step, we develop a ray-tracing approach, where phase and spectral information are preserved. This enables one to study wave scattering beyond simple time of flight calculation of rays. Challenges in terms of theory and modelling of defects of various kinds are discussed. Various additional considerations such as signal decay and physics of scattering are reviewed and challenges involved in realistic computational implementation are discussed. Potential application of this approach to SHM system design is highlighted and by applying this to complex structural components such as airframe structures, SHM is demonstrated to provide additional value in terms of lighter weight and/or longevity enhancement resulting from an extension of the damage tolerance design principle not compromising safety and reliability.

  13. Hidratação e equilíbrio ácido-base em pacientes cirúrgicos Hydration and acid-base balance in surgical patients

    Directory of Open Access Journals (Sweden)

    Takachi Moriya


    Full Text Available Estudou-se a influência da hidratação em 30 pacientes submetidos a cirurgia de pequeno e grande porte. Os pacientes foram divididos em grupos de 5 conforme o porte cirúrgico e o tipo de hidratação: restrição hídrica, segundo o balanço diário e sobrecarga hidrossalina. As alterações mais relevantes do equilíbrio ácido base foram: pré-operatório - alcalose respiratória; pós-operatório imediato - acidose respiratória; 1º, 2º e 3º dias de pós-operatório - alcalose respiratória, metabólica ou mista. Os métodos de hidratação com restrição hídrica ou segundo o balanço não afetaram o equilíbrio ácido-base, enquanto que a sobrecarga hidrossalina reduziu de modo significativo a incidência de alcalose metabólica no pós-operatório.

  14. Gigascale Silicon Photonic Transmitters Integrating HBT-based Carrier-injection Electroabsorption Modulator Structures (United States)

    Fu, Enjin

    injection modulators and light-emitting diodes (LED) with drive voltage requirements below 1.5V. Measurement results show an optical link based on a 70MHz red LED work well at 300Mbps by using the pre-emphasis driver module. A traveling wave electrode (TWE) modulator structure is presented, including a novel design methodology to address process limitations imposed by a commercial silicon fabrication technology. Results from 3D full wave EM simulation demonstrate the application of the design methodology to achieve specifications, including phase velocity matching, insertion loss, and impedance matching. Results show the HBT-based TWE-EAM system has the bandwidth higher than 60GHz.

  15. Resonance phenomena in one-dimensional grating-based structures

    Directory of Open Access Journals (Sweden)

    I.Ya. Yaremchuk


    Full Text Available Enhanced optical transmission through metallic 1-D grating-based structures has been studied using the rigorous coupled wave analysis. The results have shown that optical transmission is determined by waveguide properties of the grating slit, and there is a minimum width of slit for TE polarization, when high transmission occurs due to waveguide effect. In contrast, this limitation doesn’t exist for TM polarization, and extraordinary transmission is obtained at the sub-wavelength slit. As a result, high transmission is reached due to resonance of electromagnetic field inside the grating slit.

  16. Sistema local de pesquisa e desenvolvimento de empresas de base tecnológica em Juiz de Fora

    Directory of Open Access Journals (Sweden)

    Eduardo Gonçalves


    Full Text Available Este artigo aborda o desenvolvimento de empresas de base tecnológica em Juiz de Fora baseado nas vantagens locacionais, infra-estrutura de pesquisa e iniciativas de apoio à criação deste tipo de empresa. Há uma recuperação da história econômica da cidade, diferenciando-a do novo tipo de desenvolvimento que pode ocorrer a partir do sucesso de algumas experiências, do suporte institucional montado e das vantagens locacionais identificadas. A superação de certas limitações, a consolidação das iniciativas e o aumento dos spin-offs determinarão a viabilidade deste tipo de industrialização.

  17. Recuperação de informações em bases de dados: usos de tesauro

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    Leonardo Fernandes Souto

    Full Text Available Uma das maiores dificuldades enfrentadas na obtenção de informações relevantes é quanto à filtragem de informações. Nesse sentido é bom destacar que o profissional da informação pode ser considerado como o primeiro filtro do sistema. O uso de instrumentos de linguagem documentária se faz necessário e contribui de forma substancial para o sucesso do serviço oferecido. Esse trabalho defende a necessidade de um profissional da informação, na contribuição ao gerenciamento de sistemas de recuperação da informação, e tem como foco, o uso de tesauros em bases de dados, analisando-os sobre dois aspectos: como uma ferramenta de trabalho do indexador e como um poderoso recurso facilitador para a busca de informações.

  18. Gestão baseada em valor aplicada ao terceiro setor Value based management applied to the tertiary sector

    Directory of Open Access Journals (Sweden)

    Alexandre Assaf Neto


    Full Text Available Nos últimos anos, o mundo assistiu ao crescimento do assistencialismo e das preocupações sociais. Pessoas se reúnem e formam instituições cujo único objetivo é tentar amenizar problemas sociais. Surge o chamado Terceiro Setor, que vem crescendo e conseguindo ajudar no suprimento das carências resultantes da incapacidade do governo em exercer o seu papel. No entanto, muitas organizações desse setor apresentam problemas de gestão. A metodologia centra-se em revisão bibliográfica sobre os temas principais do trabalho, além de uma pesquisa empírica. A pesquisa empírica mostrou que, na prática, é possível aplicar a GBV, sendo necessárias adaptações para a avaliação econômica da entidade. Este trabalho apresenta uma adequação da gestão baseada em valor, ferramenta sedimentada nas empresas lucrativas, para as empresas desse setor e apresenta o cálculo do EVA® para uma organização sem fins lucrativos.In recent years, the world has witnessed growing concern about social issues and assistance. People join to create organizations with the only goal of trying to mitigate social problems. This gives rise to the so-called Tertiary Sector, which is expanding and manages to help to fulfill the needs generated by the government's incapacity to play its role. Nevertheless, many organizations in this sector present management problems. The methodology focuses on a bibliographic review of the subject, as well as an empirical research. The empirical research has shown that it is actually possible to apply value based management, provided that modifications are made for the organization's economic assessment. This study presents an adaptation of value based management, a tool used by for-profit companies, to tertiary-sector organizations, as well as the calculation of EVA TM for not-for-profit organizations.

  19. Effects of <em>Citrus aurantiumem> (Bitter Orange Fruit Extracts and <em>p>-Synephrine on Metabolic Fluxes in the Rat Liver

    Directory of Open Access Journals (Sweden)

    Rosane Marina Peralta


    Full Text Available The fruit extracts of <em>Citrus aurantiumem> (bitter orange are traditionally used as weight-loss products and as appetite supressants. An important fruit component is <em>p>-synephrine, which is structurally similar to the adrenergic agents. Weight-loss and adrenergic actions are always related to metabolic changes and this work was designed to investigate a possible action of the <em>C. aurantiumem> extract on liver metabolism. The isolated perfused rat liver was used to measure catabolic and anabolic pathways, including oxygen uptake and perfusion pressure. The <em>C. aurantiumem> extract and <em>p>-synephrine increased glycogenolysis, glycolysis, oxygen uptake and perfusion pressure. These changes were partly sensitive to a- and b-adrenergic antagonists. <em>p>-Synephrine (200 mM produced an increase in glucose output that was only 15% smaller than the increment caused by the extract containing 196 mM <em>p>-synephrine. At low concentrations the <em>C. aurantiumem> extract tended to increase gluconeogenesis, but at high concentrations it was inhibitory, opposite to what happened with <em>p>-synephrine. The action of the <em>C. aurantiumem> extract on liver metabolism is similar to the well known actions of adrenergic agents and can be partly attributed to its content in <em>p>-synephrine. Many of these actions are catabolic and compatible with the weight-loss effects usually attributed to <em>C. aurantiumem>.

  20. Synthesis/literature review for determining structural layer coefficients (SLC) of bases. (United States)


    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...

  1. Somente um deve vencer: as bases de recrutamento dos candidatos à Prefeitura das capitais brasileiras em 2008

    Directory of Open Access Journals (Sweden)

    Riberti de Almeida Felisbino


    Full Text Available Não é segredo para os estudiosos e é reconhecido pelos atores envolvidos no jogo político que o Prefeito desempenha importantes atividades, podendo influenciar o dia-a-dia da população, a relação com outras esferas de governo e as eleições gerais. Tomando como universo empírico os candidatos ao cargo de Prefeito das capitais brasileiras em 2008, procuramos identificar e analisar as bases de recrutamento desses concorrentes ao principal posto político do município. As interpretações correntes na literatura concentram-se sobre os vencedores da disputa eleitoral, deixando de lado os derrotados. O que os vencedores têm que os derrotados não têm? Seria o perfil dos vencedores diferente daquele encontrado no grupo dos derrotados? Com o propósito de oferecer uma contribuição aos estudos das bases de recrutamento dos membros pertencentes às elites locais, o texto está organizado em uma única seção, onde vamos discutir três dimensões: (i gênero, faixa etária e naturalidade; (ii nível de instrução, grupo profissional e mandato executivo e (iii gastos com campanha e tamanho do patrimônio. Essas características podem ajudar a construir um perfil sociopolítico dos membros pertencentes aos grupos dos vencedores e dos derrotados nas eleições municipais de 2008 para o cargo de Prefeito das capitais brasileiras. Além disso, o estudo desses atributos pode indicar quais predominaram na disputa eleitoral, isto é, quais deles podem mostrar as características que circundam o processo seletivo dos integrantes do distinto grupo político.

  2. Prevalência e fatores associados ao excesso de peso em adultos do Brasil: um estudo de base populacional em todo território nacional

    Directory of Open Access Journals (Sweden)

    Vladimir Schuindt da Silva


    Full Text Available Avaliou-se a prevalência e fatores associados ao excesso de peso (IMC > 25kg/m ² em adultos (81.745 do Brasil. Realizou-se regressão de Poisson, bruta e ajustada. Os resultados mostraram maiores prevalências de excesso de peso em adultos de 50 a 59 anos (RP=1,21, IC95%: 1,20;1,22, do sexo masculino (RP=1,01, IC95%: 1,01;1,02, da cor-raça negra (RP=1,01, IC95%: 1,00;1,02, nível de escolaridade médio (RP=1,02, IC95%: 1,01;1,02, renda alta (RP=1,09, IC95%: 1,08;1,10 e da Região Sul (RP=1,02, IC95%: 1,01;1,02. Os resultados apontam para a necessidade de ações estratégicas que levem em conta as prevalências de excesso de peso verificadas nos diferentes estratos da população brasileira.

  3. Automatic Structure-Based Code Generation from Coloured Petri Nets

    DEFF Research Database (Denmark)

    Kristensen, Lars Michael; Westergaard, Michael


    Automatic code generation based on Coloured Petri Net (CPN) models is challenging because CPNs allow for the construction of abstract models that intermix control flow and data processing, making translation into conventional programming constructs difficult. We introduce Process-Partitioned CPNs...... (PP-CPNs) which is a subclass of CPNs equipped with an explicit separation of process control flow, message passing, and access to shared and local data. We show how PP-CPNs caters for a four phase structure-based automatic code generation process directed by the control flow of processes....... The viability of our approach is demonstrated by applying it to automatically generate an Erlang implementation of the Dynamic MANET On-demand (DYMO) routing protocol specified by the Internet Engineering Task Force (IETF)....

  4. Structural eigenfrequency optimization based on local sub-domain "frequencies"

    DEFF Research Database (Denmark)

    Pedersen, Pauli; Pedersen, Niels Leergaard


    eigenfrequencies may also be controlled in this manner.The presented examples are based on 2D finite element models with the use of subspace iteration for analysis and a recursive design procedure based on the derived optimality condition. The design that maximize a frequency depend on the total amount......The engineering approach of fully stressed design is a practical tool with a theoretical foundation. The analog approach to structural eigenfrequency optimization is presented here with its theoretical foundation. A numerical redesign procedure is proposed and illustrated with examples.......For the ideal case, an optimality criterion is fulfilled if the design have the same sub-domain ”frequency” (local Rayleigh quotient). Sensitivity analysis shows an important relation between squared system eigenfrequency and squared local sub-domain frequency for a given eigenmode. Higher order...

  5. Method of pectus excavatum measurement based on structured light technique (United States)

    Glinkowski, Wojciech; Sitnik, Robert; Witkowski, Marcin; Kocoń, Hanna; Bolewicki, Pawel; Górecki, Andrzej


    We present an automatic method for assessment of pectus excavatum severity based on an optical 3-D markerless shape measurement. A four-directional measurement system based on a structured light projection method is built to capture the shape of the body surface of the patients. The system setup is described and typical measurement parameters are given. The automated data analysis path is explained. Their main steps are: normalization of trunk model orientation, cutting the model into slices, analysis of each slice shape, selecting the proper slice for the assessment of pectus excavatum of the patient, and calculating its shape parameter. We develop a new shape parameter (I3ds) that shows high correlation with the computed tomography (CT) Haller index widely used for assessment of pectus excavatum. Clinical results and the evaluation of developed indexes are presented.

  6. Structure- and oil type-based efficacy of emulsion adjuvants. (United States)

    Jansen, Theo; Hofmans, Marij P M; Theelen, Marc J G; Manders, Frans; Schijns, Virgil E J C


    Oil-based emulsions are well-known immunopotentiators for inactivated, "killed" vaccines. We addressed the relationship between emulsion structure and levels of in vivo antibody formation to inactivated New Castle Disease virus (NDV) and Infectious Bronchitis virus (IBV) as antigens in 3-week-old chickens. The use of a polymeric emulsifier allowed for direct comparison of three types of emulsions, water-in-oil (W/O), oil-in-water (O/W) and W/O-in-water (W/O/W), while maintaining an identical content of components for each vehicle. They were prepared with either non-metabolizable, mineral oil or metabolizable, Miglyol 840. In addition, we assessed the inherent release capacity of each emulsion variant in vitro. Remarkably, we noted that W/O-type emulsions induced the best immune responses, while they released no antigen during 3 weeks. In general, mineral oil vaccines showed superior efficacy compared to Miglyol 840-based vaccines.

  7. Structured Light-Based Hazard Detection For Planetary Surface Navigation (United States)

    Nefian, Ara; Wong, Uland Y.; Dille, Michael; Bouyssounouse, Xavier; Edwards, Laurence; To, Vinh; Deans, Matthew; Fong, Terry


    This paper describes a structured light-based sensor for hazard avoidance in planetary environments. The system presented here can also be used in terrestrial applications constrained by reduced onboard power and computational complexity and low illumination conditions. The sensor is on a calibrated camera and laser dot projector system. The onboard hazard avoidance system determines the position of the projected dots in the image and through a triangulation process detects potential hazards. The paper presents the design parameters for this sensor and describes the image based solution for hazard avoidance. The system presented here was tested extensively in day and night conditions in Lunar analogue environments. The current system achieves over 97 detection rate with 1.7 false alarms over 2000 images.

  8. Band structure engineering in topological insulator based heterostructures. (United States)

    Menshchikova, T V; Otrokov, M M; Tsirkin, S S; Samorokov, D A; Bebneva, V V; Ernst, A; Kuznetsov, V M; Chulkov, E V


    The ability to engineer an electronic band structure of topological insulators would allow the production of topological materials with tailor-made properties. Using ab initio calculations, we show a promising way to control the conducting surface state in topological insulator based heterostructures representing an insulator ultrathin films on the topological insulator substrates. Because of a specific relation between work functions and band gaps of the topological insulator substrate and the insulator ultrathin film overlayer, a sizable shift of the Dirac point occurs resulting in a significant increase in the number of the topological surface state charge carriers as compared to that of the substrate itself. Such an effect can also be realized by applying the external electric field that allows a gradual tuning of the topological surface state. A simultaneous use of both approaches makes it possible to obtain a topological insulator based heterostructure with a highly tunable topological surface state.

  9. Sinterização de cerâmicas à base de PZT em forno de microondas Microwave synthesis of PZT based ceramics

    Directory of Open Access Journals (Sweden)

    M. V. Gelfuso


    Full Text Available Cerâmicas de titanato e zirconato de chumbo dopadas com neodímio foram sinterizadas em um forno de microondas de uso doméstico modificado. Neste tipo de aquecimento, a energia eletromagnética é transferida diretamente para o material, sendo convertida em calor pelo material cerâmico, reduzindo o tempo e energia durante o processamento. Desta forma, foram produzidos corpos cerâmicos com tempo de sinterização que variou até 30 min, a 1100 e 1200 ºC. As fases foram investigadas por meio de difratometria de raios X. Corpos cerâmicos com densidade de 95% da teórica foram obtidos com tempo de sinterização de 10 min em 1100 ºC, com uma taxa de aquecimento de 400 ºC/min. Para as cerâmicas com densidade superior a 90% da teórica foram medidos os valores de constante dielétrica e fator de perda.Ferroelectric ceramics based on lead zirconate titanate doped with neodymium were sintered using a modified microwave oven. In this process the energy is transferred directly to the material through the interaction between molecules of the material with the electromagnetic field. The microwave sintering process has an advantage to reduce the time and save energy. This type of process involves energy conversion, opposing to heat transfer. Ceramic parts were produced by thermal treatments at 1100 ºC and 1200 ºC up to 30 min. The formed crystalline phases were investigated by X-ray diffraction. Ceramic parts with densities above 95% of the theoretical density were produced in 10 min by heating at 1100 ºC, with heating rate of 400 ºC/min. Values of dielectric constant and loss factor of ceramics with density above 90%T.D. were determined.

  10. Near-Atomic Resolution Structure Determination in Over-Focus with Volta Phase Plate by Cs-Corrected Cryo-EM. (United States)

    Fan, Xiao; Zhao, Lingyun; Liu, Chuan; Zhang, Jin-Can; Fan, Kelong; Yan, Xiyun; Peng, Hai-Lin; Lei, Jianlin; Wang, Hong-Wei


    Volta phase plate (VPP) is a recently developed transmission electron microscope (TEM) apparatus that can significantly enhance the image contrast of biological samples in cryoelectron microscopy, and therefore provide the possibility to solve structures of relatively small macromolecules at high-resolution. In this work, we performed theoretical analysis and found that using phase plate on objective lens spherical aberration (Cs)-corrected TEM may gain some interesting optical properties, including the over-focus imaging of macromolecules. We subsequently evaluated the imaging strategy of frozen-hydrated apo-ferritin with VPP on a Cs-corrected TEM and obtained the structure of apo-ferritin at near-atomic resolution from both under- and over-focused dataset, illustrating the feasibility and new potential of combining VPP with Cs-corrected TEM for high-resolution cryo-EM. Copyright © 2017 Elsevier Ltd. All rights reserved.

  11. Neuronal bases of structural coherence in contemporary dance observation. (United States)

    Bachrach, Asaf; Jola, Corinne; Pallier, Christophe


    The neuronal processes underlying dance observation have been the focus of an increasing number of brain imaging studies over the past decade. However, the existing literature mainly dealt with effects of motor and visual expertise, whereas the neural and cognitive mechanisms that underlie the interpretation of dance choreographies remained unexplored. Hence, much attention has been given to the action observation network (AON) whereas the role of other potentially relevant neuro-cognitive mechanisms such as mentalizing (theory of mind) or language (narrative comprehension) in dance understanding is yet to be elucidated. We report the results of an fMRI study where the structural coherence of short contemporary dance choreographies was manipulated parametrically using the same taped movement material. Our participants were all trained dancers. The whole-brain analysis argues that the interpretation of structurally coherent dance phrases involves a subpart (superior parietal) of the AON as well as mentalizing regions in the dorsomedial prefrontal cortex. An ROI analysis based on a similar study using linguistic materials (Pallier et al., 2011) suggests that structural processing in language and dance might share certain neural mechanisms. Copyright © 2015 Elsevier Inc. All rights reserved.

  12. Structure and Dynamics of Water at Carbon-Based Interfaces

    Directory of Open Access Journals (Sweden)

    Jordi Martí


    Full Text Available Water structure and dynamics are affected by the presence of a nearby interface. Here, first we review recent results by molecular dynamics simulations about the effect of different carbon-based materials, including armchair carbon nanotubes and a variety of graphene sheets—flat and with corrugation—on water structure and dynamics. We discuss the calculations of binding energies, hydrogen bond distributions, water’s diffusion coefficients and their relation with surface’s geometries at different thermodynamical conditions. Next, we present new results of the crystallization and dynamics of water in a rigid graphene sieve. In particular, we show that the diffusion of water confined between parallel walls depends on the plate distance in a non-monotonic way and is related to the water structuring, crystallization, re-melting and evaporation for decreasing inter-plate distance. Our results could be relevant in those applications where water is in contact with nanostructured carbon materials at ambient or cryogenic temperatures, as in man-made superhydrophobic materials or filtration membranes, or in techniques that take advantage of hydrated graphene interfaces, as in aqueous electron cryomicroscopy for the analysis of proteins adsorbed on graphene.

  13. Scalable, ultra-resistant structural colors based on network metamaterials

    KAUST Repository

    Galinski, Henning


    Structural colors have drawn wide attention for their potential as a future printing technology for various applications, ranging from biomimetic tissues to adaptive camouflage materials. However, an efficient approach to realize robust colors with a scalable fabrication technique is still lacking, hampering the realization of practical applications with this platform. Here, we develop a new approach based on large-scale network metamaterials that combine dealloyed subwavelength structures at the nanoscale with lossless, ultra-thin dielectric coatings. By using theory and experiments, we show how subwavelength dielectric coatings control a mechanism of resonant light coupling with epsilon-near-zero regions generated in the metallic network, generating the formation of saturated structural colors that cover a wide portion of the spectrum. Ellipsometry measurements support the efficient observation of these colors, even at angles of 70°. The network-like architecture of these nanomaterials allows for high mechanical resistance, which is quantified in a series of nano-scratch tests. With such remarkable properties, these metastructures represent a robust design technology for real-world, large-scale commercial applications.

  14. Identification of Novel Smoothened Ligands Using Structure-Based Docking.

    Directory of Open Access Journals (Sweden)

    Celine Lacroix

    Full Text Available The seven transmembrane protein Smoothened is required for Hedgehog signaling during embryonic development and adult tissue homeostasis. Inappropriate activation of the Hedgehog signalling pathway leads to cancers such as basal cell carcinoma and medulloblastoma, and Smoothened inhibitors are now available clinically to treat these diseases. However, resistance to these inhibitors rapidly develops thereby limiting their efficacy. The determination of Smoothened crystal structures enables structure-based discovery of new ligands with new chemotypes that will be critical to combat resistance. In this study, we docked 3.2 million available, lead-like molecules against Smoothened, looking for those with high physical complementarity to its structure; this represents the first such campaign against the class Frizzled G-protein coupled receptor family. Twenty-one high-ranking compounds were selected for experimental testing, and four, representing three different chemotypes, were identified to antagonize Smoothened with IC50 values better than 50 μM. A screen for analogs revealed another six molecules, with IC50 values in the low micromolar range. Importantly, one of the most active of the new antagonists continued to be efficacious at the D473H mutant of Smoothened, which confers clinical resistance to the antagonist vismodegib in cancer treatment.

  15. Structural damage diagnostics via wave propagation-based filtering techniques (United States)

    Ayers, James T., III

    Structural health monitoring (SHM) of aerospace components is a rapidly emerging field due in part to commercial and military transport vehicles remaining in operation beyond their designed life cycles. Damage detection strategies are sought that provide real-time information of the structure's integrity. One approach that has shown promise to accurately identify and quantify structural defects is based on guided ultrasonic wave (GUW) inspections, where low amplitude attenuation properties allow for long range and large specimen evaluation. One drawback to GUWs is that they exhibit a complex multi-modal response, such that each frequency corresponds to at least two excited modes, and thus intelligent signal processing is required for even the simplest of structures. In addition, GUWs are dispersive, whereby the wave velocity is a function of frequency, and the shape of the wave packet changes over the spatial domain, requiring sophisticated detection algorithms. Moreover, existing damage quantification measures are typically formulated as a comparison of the damaged to undamaged response, which has proven to be highly sensitive to changes in environment, and therefore often unreliable. As a response to these challenges inherent to GUW inspections, this research develops techniques to locate and estimate the severity of the damage. Specifically, a phase gradient based localization algorithm is introduced to identify the defect position independent of excitation frequency and damage size. Mode separation through the filtering technique is central in isolating and extracting single mode components, such as reflected, converted, and transmitted modes that may arise from the incident wave impacting a damage. Spatially-integrated single and multiple component mode coefficients are also formulated with the intent to better characterize wave reflections and conversions and to increase the signal to noise ratios. The techniques are applied to damaged isotropic finite

  16. Protein Function Prediction Based on Sequence and Structure Information

    KAUST Repository

    Smaili, Fatima Z.


    The number of available protein sequences in public databases is increasing exponentially. However, a significant fraction of these sequences lack functional annotation which is essential to our understanding of how biological systems and processes operate. In this master thesis project, we worked on inferring protein functions based on the primary protein sequence. In the approach we follow, 3D models are first constructed using I-TASSER. Functions are then deduced by structurally matching these predicted models, using global and local similarities, through three independent enzyme commission (EC) and gene ontology (GO) function libraries. The method was tested on 250 “hard” proteins, which lack homologous templates in both structure and function libraries. The results show that this method outperforms the conventional prediction methods based on sequence similarity or threading. Additionally, our method could be improved even further by incorporating protein-protein interaction information. Overall, the method we use provides an efficient approach for automated functional annotation of non-homologous proteins, starting from their sequence.

  17. (Biodegradable Ionomeric Polyurethanes Based on Xanthan: Synthesis, Properties, and Structure

    Directory of Open Access Journals (Sweden)

    T. V. Travinskaya


    Full Text Available New (biodegradable environmentally friendly film-forming ionomeric polyurethanes (IPU based on renewable biotechnological polysaccharide xanthan (Xa have been obtained. The influence of the component composition on the colloidal-chemical and physic-mechanical properties of IPU/Xa and based films, as well as the change of their properties under the influence of environmental factors, have been studied. The results of IR-, PMS-, DMA-, and X-ray scattering study indicate that incorporation of Xa into the polyurethane chain initiates the formation of a new polymer structure different from the structure of the pure IPU (matrix: an amorphous polymer-polymer microdomain has occurred as a result of the chemical interaction of Xa and IPU. It predetermines the degradation of the IPU/Xa films as a whole, unlike the mixed polymer systems, and plays a key role in the improvement of material performance. The results of acid, alkaline hydrolysis, and incubation into the soil indicate the increase of the intensity of degradation processes occurring in the IPU/Xa in comparison with the pure IPU. It has been shown that the introduction of Xa not only imparts the biodegradability property to polyurethane, but also improves the mechanical properties.

  18. Seismic assessment of reinforced concrete frame structures with a new flexibility based element (United States)

    Arede, Antonio Jose Coelho Dias

    diopsidio contendo Al na estrutura, sinterizacao e no comportamento durante a cristalizacao de vidros e nas propriedades dos materiais vitro-cerâmicos, com relevância para a sua aplicacao como selantes em SOFC. Verificou-se que Foi observado que os vidros/vitro-cerâmicos a base de enstatite nao apresentavam as caracteristicas necessarias para serem usados como materiais selantes em SOFC, enquanto as melhores propriedades apresentadas pelos vitro-cerâmicos a base de diopsidio qualificaram-nos para futuros estudos neste tipo de aplicacoes. Para alem de investigar a adequacao dos vitro-cerâmicos a base de clinopyroxene como selantes, esta tese tem tambem como objetivo estudar a influencia dos agentes de nucleacao na nucleacao em volume dos vitro-cerâmicos resultantes a base de diopsidio, de modo a qualifica-los como potenciais materiais hopedeiros de residuos nucleares radioactivos.

  19. Decomposition Criterion-based Redundancy Removal in Mechanical Structures

    Directory of Open Access Journals (Sweden)

    A. N. Bozhko


    Full Text Available The most important design solutions of production engineering for the assembly operation are an assembly sequence and assembly chart. Both are closely linked with each other and therefore are recorded in the single process flow sheet that is an assembly chart.Capability for successive order assembling and splitting into assembly units depends on a set of the product design properties from which the main ones are position mechanical connections used to locate details within a product. An adequate mathematical model of the mechanical connections of technical system is a hyper graph. It allows us to give the correct description of the location relation of variable-locality.The analysis of the array of drawings shows that many designs contain redundant mechanical connections. The inequality is a criterion of redundancy, where |X| is the number of tops of the hyper graph (details, and |R| is the number of hyper edges (full assembly bases. Excess of mutual coordination is a harmful phenomenon which at designing stage exhibits as unsolvable dimension chains, while at the assembly stage it shows as relocation. Redundant connections should be removed from a design at the earliest design-for-manufacturing stages. Removal of connections generates mechanical structures with different assembly properties. The work offers some important criteria of generation of irredundant mechanical structures. The paper considers in detail a maximum decomposition criterion, which allows us to receive structures with the greatest capability to split into assembly units. It shows that such structures exhibit high flexibility in assembling and are adaptable to various specifications and production processes.

  20. The mechanosensitive Piezo1 channel: structural features and molecular bases underlying its ion permeation and mechanotransduction. (United States)

    Wang, Yubo; Xiao, Bailong


    The evolutionarily conserved Piezo family of proteins, including Piezo1 and Piezo2, encodes the long-sought-after mammalian mechanosensitive cation channels that play critical roles in various mechanotransduction processes such as touch, pain, proprioception, vascular development and blood pressure regulation. Mammalian Piezo proteins contain over 2500 amino acids with numerous predicted transmembrane segments, and do not bear sequence homology with any known class of ion channels. Thus, it is imperative, but challenging, to understand how they serve as effective mechanotransducers for converting mechanical force into electrochemical signals. Here, we review the recent major breakthroughs in determining the three-bladed, propeller-shaped structure of mouse Piezo1 using the state-of-the-art cryo-electron microscopy (cryo-EM) and functionally dissecting out the molecular bases that define its ion permeation and mechanotransduction properties, which provide key insights into clarifying its oligomeric status and pore-forming region. We also discuss the hypothesis that the complex Piezo proteins can be deduced into discrete mechanotransduction and ion-conducting pore modules, which coordinate to fulfill their specialized function in mechanical sensing and transduction, ion permeation and selection. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

  1. A structure-based model of semantic integrity constraints for relational data bases (United States)

    Rasdorf, William J.; Ulberg, Karen J.; Baugh, John W., Jr.


    Data base management systems (DBMSs) are in widespread use because of the ease and flexibility with which users access large volumes of data. Ensuring data accuracy through integrity constraints is a central aspect of DBMS use. However, many DBMSs still lack adequate integrity support. In additon, a comprehensive theoretical basis for such support the role of a constraint classification system - has yet to be developed. This paper presents a formalism that classifies semantic integrity constraints based on the structure of the relational model. Integrity constraints are characterized by the portion of the data base structure they access, whether one or more relations, attributes, or tuples. Thus, the model is completely general, allowing the arbitrary specification of any constraint. Examples of each type of constraint are illustrated using a small engineering data base, and various implementation issues are discussed.

  2. Emergy-based life cycle assessment (Em-LCA of multi-unit and single-family residential buildings in Canada

    Directory of Open Access Journals (Sweden)

    Bahareh Reza


    Full Text Available The construction and building process depends on substantial consumption of natural resources with far-reaching impacts beyond their development area. In general, a significant portion of annual resource consumption by the building and construction industry is a result of applying traditional building strategies and practices such as designing and selecting types of development (e.g. multi-unit condo and single-family house, etc., building materials and structure, heating/cooling systems, and planning renovation and maintenance practices. On the other hand, apart from structural suitability, building developers mostly consider the basic requirements of public owners or private occupants of the buildings, where the main criteria for selecting building strategies are costs, and long-term environmental and socio-economic impacts are generally ignored. The main purpose of this paper is to develop an improved building sustainability assessment framework to measure and integrate different sustainability factors, i.e. long-term environmental upstream and downstream impacts and associated socio-economic costs, in a unified and quantitative basis. The application of the proposed framework has been explained through a case study of single-family houses and multi-unit residential buildings in Canada. A comprehensive framework based on the integration of emergy synthesis and life cycle assessment (LCA has been developed and applied. The results of this research prove that the proposed emergy-based life cycle assessment (Em-LCA framework offers a practical sustainability assessment tool by providing quantitative and transparent results for informed decision-making.

  3. Analysis of Hybrid-Integrated High-Speed Electro-Absorption Modulated Lasers Based on EM/Circuit Co-simulation

    DEFF Research Database (Denmark)

    Johansen, Tom Keinicke; Krozer, Viktor; Kazmierski, C.


    An improved electromagnetic simulation (EM) based approach has been developed for optimization of the electrical to optical (E/O) transmission properties of integrated electro-absorption modulated lasers (EMLs) aiming at 100 Gbit/s Ethernet applications. Our approach allows for an accurate analysis...

  4. Structure Based Predictive Model for Coal Char Combustion

    Energy Technology Data Exchange (ETDEWEB)

    Robert Hurt; Joseph Calo; Robert Essenhigh; Christopher Hadad


    This unique collaborative project has taken a very fundamental look at the origin of structure, and combustion reactivity of coal chars. It was a combined experimental and theoretical effort involving three universities and collaborators from universities outside the U.S. and from U.S. National Laboratories and contract research companies. The project goal was to improve our understanding of char structure and behavior by examining the fundamental chemistry of its polyaromatic building blocks. The project team investigated the elementary oxidative attack on polyaromatic systems, and coupled with a study of the assembly processes that convert these polyaromatic clusters to mature carbon materials (or chars). We believe that the work done in this project has defined a powerful new science-based approach to the understanding of char behavior. The work on aromatic oxidation pathways made extensive use of computational chemistry, and was led by Professor Christopher Hadad in the Department of Chemistry at Ohio State University. Laboratory experiments on char structure, properties, and combustion reactivity were carried out at both OSU and Brown, led by Principle Investigators Joseph Calo, Robert Essenhigh, and Robert Hurt. Modeling activities were divided into two parts: first unique models of crystal structure development were formulated by the team at Brown (PI'S Hurt and Calo) with input from Boston University and significant collaboration with Dr. Alan Kerstein at Sandia and with Dr. Zhong-Ying chen at SAIC. Secondly, new combustion models were developed and tested, led by Professor Essenhigh at OSU, Dieter Foertsch (a collaborator at the University of Stuttgart), and Professor Hurt at Brown. One product of this work is the CBK8 model of carbon burnout, which has already found practical use in CFD codes and in other numerical models of pulverized fuel combustion processes, such as EPRI's NOxLOI Predictor. The remainder of the report consists of detailed

  5. Supercapacitors based on carbon nanotube fuzzy fabric structural composites (United States)

    Alresheedi, Bakheet Awad

    Supercapacitors used in conjunction with batteries offer a solution to energy storage and delivery problems in systems where high power output is required, such as in fully electric cars. This project aimed to enhance current supercapacitor technology by fabricating activated carbon on a substrate consisting of carbon nanotubes (CNTs) grown on a carbon fiber fabric (fuzzy fabric). The fuzzy surface of CNTs lowers electrical resistance and increases porosity, resulting in a flexible fabric with high specific capacitance. Experimental results confirm that the capacitance of activated carbon fabricated on the fuzzy fiber composite is significantly higher than when activated carbon is formed simply on a bare carbon fiber substrate, indicating the usefulness of CNTs in supercapacitor technology. The fabrication of the fuzzy fiber based carbon electrode was fairly complex. The processing steps included composite curing, stabilization, carbonization and activation. Ratios of the three basic ingredients for the supercapacitor (fiber, CNT and polymer matrix) were investigated through experimentation and Grey relational analysis. The aim of Grey relational analysis was to examine factors that affect the overall performance of the supercapacitor. It is based on finding relationships in both independent and interrelated data series (parameters). Using this approach, it was determined that the amount of CNTs on the fiber surface plays a major role in the capacitor properties. An increased amount of CNTs increases the surface area and electrical conductivity of the substrate, while also reducing the required time of activation. Technical advances in the field of Materials and Structures are usually focused on attaining superior performance while reducing weight and cost. To achieve such combinations, multi-functionality has become essential; namely, to reduce weight by imparting additional functions simultaneously to a single material. In this study, a structural composite with

  6. Desindustrialização e o investimento em infraestrutura como instrumento conciliador de uma política industrial base no Brasil

    Directory of Open Access Journals (Sweden)



    Full Text Available RESUMOO fraco desempenho da indústria brasileira no período pós-crise de 2008 retomou o debate em torno da necessidade de um esboço de política industrial. Por conseguinte, e dadas as suas características, o investimento em infraestrutura se apresenta como uma alternativa conciliadora e eficiente na tarefa de devolver a competitividade a este setor. Este trabalho tem como objetivo aprofundar o debate sobre a questão da desindustrialização da economia brasileira e contribuir para a discussão sobre a funcionalidade do investimento em infraestrutura como instrumento de política industrial, enfatizando seu caráter conciliador no que chamamos aqui de uma política industrial base.

  7. Gradient-based optimization in nonlinear structural dynamics

    DEFF Research Database (Denmark)

    Dou, Suguang

    , frequency stabilization, and disk resonator gyroscope. For advanced design of these structures, it is of considerable value to extend current optimization in linear structural dynamics into nonlinear structural dynamics. In this thesis, we present a framework for modelling, analysis, characterization...

  8. Pre-Stressing Timber-Based Plate Tensegrity Structures

    DEFF Research Database (Denmark)

    Falk, Andreas; Kirkegaard, Poul Henning


    Tensile structures occur in numerous varieties utilising combinations of tension and compression. Introducing structural plates in the basic tensegrity unit and tensegric assemblies varies the range of feasible topologies and provides the structural system with an integrated surface. The present...

  9. Hierarchical structure analysis describing abnormal base composition of genomes (United States)

    Ouyang, Zhengqing; Liu, Jian-Kun; She, Zhen-Su


    Abnormal base compositional patterns of genomic DNA sequences are studied in the framework of a hierarchical structure (HS) model originally proposed for the study of fully developed turbulence [She and Lévêque, Phys. Rev. Lett. 72, 336 (1994)]. The HS similarity law is verified over scales between 103bp and 105bp , and the HS parameter β is proposed to describe the degree of heterogeneity in the base composition patterns. More than one hundred bacteria, archaea, virus, yeast, and human genome sequences have been analyzed and the results show that the HS analysis efficiently captures abnormal base composition patterns, and the parameter β is a characteristic measure of the genome. Detailed examination of the values of β reveals an intriguing link to the evolutionary events of genetic material transfer. Finally, a sequence complexity (S) measure is proposed to characterize gradual increase of organizational complexity of the genome during the evolution. The present study raises several interesting issues in the evolutionary history of genomes.

  10. Electron Cryo-microscopy as a Tool for Structure-Based Drug Development. (United States)

    Merino, Felipe; Raunser, Stefan


    For decades, X-ray crystallography and NMR have been the most important techniques for studying the atomic structure of macromolecules. However, as a result of size, instability, low yield, and other factors, many macromolecules are difficult to crystallize or unsuitable for NMR studies. Electron cryo-microscopy (cryo-EM) does not depend on crystals and has therefore been the method of choice for many macromolecular complexes that cannot be crystallized, but atomic resolution has mostly been beyond its reach. A new generation of detectors that are capable of sensing directly the incident electrons has recently revolutionized the field, with structures of macromolecules now routinely being solved to near-atomic resolution. In this review, we summarize some of the most recent examples of high-resolution cryo-EM structures. We put particular emphasis on proteins with pharmacological relevance that have traditionally been inaccessible to crystallography. Furthermore, we discuss examples where interactions with small molecules have been fully characterized at atomic resolution. Finally, we stress the current limits of cryo-EM, and methodological issues related to its usage as a tool for drug development. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. Origem, sucessão e estrutura de uma floresta de galeria periodicamente alagada em Viçosa-MG Origin, sucession and structure of a periodically flooded gallery forest in Viçosa, Minas Gerais, Brazil

    Directory of Open Access Journals (Sweden)

    João Augusto Alves Meira Neto


    possuir condições biológicas e ecológicas para iniciar a sucessão secundária. A alta diversidade genética da população de Erythrina falcata pode ter sido um dos fatores determinantes do sucesso de colonização da área. A associação de Erythrina falcata com figueiras pode ter sido determinante no sucesso desse processo em seu início, e a associação inicial deve ter funcionado como sistema de baixa diversidade de espécies, comparável a outras florestas alagadas do Sudeste brasileiro.The study of the phytosociological structures and sizes in secondary forest fragments allows to make inferences on the original composition and structures at the beginning of the secondary succession. The importance of gallery or riparian forest studies increases with the increasing concerns on the impacts caused by water courses and their borders, specially the building of power plant dams. The objectives of this work were to describe the structure of a secondary gallery forest to identify an arboreous species population which participated at the beginning of the successional process in this forest and based on these data, to study the genetic structure and to assess the biology of the species which probably started the successional process. A survey of all the trees with a 1,3 m stem circumference from the ground greater than or equal to 10 cm was carried out. Out of the 48 tree species already included, 87.5% are endozoochoric and 12.5% are anemochoric. Out of the latter those with the smallest propagules presented greater density in this forest, which is isolated from others by pastures. The most important species (VI presented by this gallery forest were: Talauma ovata, Erythrina falcata and Euterpe edulis. Ficus species from the subgenus Urostigma presented a great biomass in spite of its low density. Erythrina falcata was considered one of the species of greater importance, probably associated to the Ficus species at the beginning of the secondary succession, due to the

  12. Equilíbrio eletrolítico e ácido-base em bovinos Eletroctrolyte and acid-base balance in bovines

    Directory of Open Access Journals (Sweden)

    Moisés Dias Freitas


    Full Text Available O conhecimento sobre a fisiologia e regulação dos eletrólitos e do equilíbrio ácido-base é necessário, pois a saúde do animal depende diretamente da composição normal dos fluídos nos diversos compartimentos corporais. Esta regulação está intimamente entrelaçada em um rigoroso e preciso controle, de modo que uma anormalidade em um destes compartimentos reflete na alteração dos demais. A avaliação do equilíbrio eletrolítico e ácido-base pode fornecer informações fundamentais para o diagnóstico, prognóstico e decisão terapêutica de diversas enfermidades nos bovinos, tais como diarreias neonatais, hemoparasitoses (anaplasmose e a babesiose, deslocamento de abomaso e processos de sépticos. As correções destas alterações com medidas terapêuticas adequadas são pontos chave para minimizar as perdas por mortalidade causadas por estas enfermidades.The knowledge of the physiology and regulation of electrolytes and blood gas parameters is necessary because the health of the animal depends directly on the normal composition of fluid in body compartments. The regulation of these is closely intertwined with a rigorous and precise control so that an abnormality in one of these compartments reflects the change in the other. The evaluation of electrolyte and acid-base balance can provide key information for diagnosis, prognosis and therapeutic decision for several diseases in animals such as neonatal diarrhea, anaplasmosis and babesiosis, displacement of abomasum and septic processes. The corrections of these changes with appropriate treatment are key to minimizing losses due to mortality in these diseases.

  13. Shape Memory Alloy-Based Periodic Cellular Structures Project (United States)

    National Aeronautics and Space Administration — This SBIR Phase I effort will develop and demonstrate an innovative shape memory alloy (SMA) periodic cellular structural technology. Periodic cellular structures...

  14. Antibody humanization by structure-based computational protein design. (United States)

    Choi, Yoonjoo; Hua, Casey; Sentman, Charles L; Ackerman, Margaret E; Bailey-Kellogg, Chris


    Antibodies derived from non-human sources must be modified for therapeutic use so as to mitigate undesirable immune responses. While complementarity-determining region (CDR) grafting-based humanization techniques have been successfully applied in many cases, it remains challenging to maintain the desired stability and antigen binding affinity upon grafting. We developed an alternative humanization approach called CoDAH ("Computationally-Driven Antibody Humanization") in which computational protein design methods directly select sets of amino acids to incorporate from human germline sequences to increase humanness while maintaining structural stability. Retrospective studies show that CoDAH is able to identify variants deemed beneficial according to both humanness and structural stability criteria, even for targets lacking crystal structures. Prospective application to TZ47, a murine anti-human B7H6 antibody, demonstrates the approach. Four diverse humanized variants were designed, and all possible unique VH/VL combinations were produced as full-length IgG1 antibodies. Soluble and cell surface expressed antigen binding assays showed that 75% (6 of 8) of the computationally designed VH/VL variants were successfully expressed and competed with the murine TZ47 for binding to B7H6 antigen. Furthermore, 4 of the 6 bound with an estimated KD within an order of magnitude of the original TZ47 antibody. In contrast, a traditional CDR-grafted variant could not be expressed. These results suggest that the computational protein design approach described here can be used to efficiently generate functional humanized antibodies and provide humanized templates for further affinity maturation.

  15. Welding studs detection based on line structured light (United States)

    Geng, Lei; Wang, Jia; Wang, Wen; Xiao, Zhitao


    The quality of welding studs is significant for installation and localization of components of car in the process of automobile general assembly. A welding stud detection method based on line structured light is proposed. Firstly, the adaptive threshold is designed to calculate the binary images. Then, the light stripes of the image are extracted after skeleton line extraction and morphological filtering. The direction vector of the main light stripe is calculated using the length of the light stripe. Finally, the gray projections along the orientation of the main light stripe and the vertical orientation of the main light stripe are computed to obtain curves of gray projection, which are used to detect the studs. Experimental results demonstrate that the error rate of proposed method is lower than 0.1%, which is applied for automobile manufacturing.

  16. Study of structural-mechanical properties of the ointment base

    Directory of Open Access Journals (Sweden)

    V. V. Rudenko


    Full Text Available The ENTRY. For the local treatment of surgical wounds basis of a medicine plays an important role in ensuring its therapeutic effect. Ointment framework depends on adequate frequency of applications, pharmacokinetics, therapeutic effect and absence/presence of side effects. Unjustifiable selected the basis of a medicinal product may cause not only the increase or reduction of the actions of the active substance, but also a total absence of it. The AIM of the WORK was to develop composition and technology of production of combined emulsion of a medicine for the treatment of surgical wounds that meet the modern medical-biological requirements. MATERIALS AND METHODS OF RESEARCH. Rheological studies carried out with the help of rotary viscometer with coaxial cylinders «Rheotest-2» (Germany. For the study took the hinge of a pilot sample. RESULTS AND THEIR DISCUSSION. Based on the biomedical requirements to create a combination of soft drugs for the treatment of wound healing we conducted research to establish ointments emulsion based on first order. As emulsifier of the first kind were used twin-80 and stearic acid, and emulsifier of the second kind - monostearat glycerin. For the comparative analysis was taken a comprehensive emulsifier No.1. It is established, that the use of a complex of emulsifiers stearic acid, emulsifier No.1 the highest structural-mechanical parameters have emulsion with the ratio of surface-active substances of 2.5 % and 5.5%, respectively. With the increase in the stearic acid emulsion was increase in the rheological parameters of the model for all shear rates. Also the composition of model samples at different ratios of emulsifier No.1 and the twin-80. Determined that the maximum value rheological parameters observed in the ratio of: emulsifier No.1-twin-80 (1:7. With the increase in the emulsions quantity of emulsifier No.1 rheological parameters increases sharply for all speeds of the shift. This non-linear dependence

  17. Au-Based Catalysts: Electrochemical Characterization for Structural Insights

    Directory of Open Access Journals (Sweden)

    Valentina Pifferi


    Full Text Available Au-based catalysts are widely used in important processes because of their peculiar characteristics. The catalyst performance depends strongly on the nature and structure of the metal nanoparticles, especially in the case of bimetallic catalysts where synergistic effects between the two metals can be occasionally seen. In this paper, it is shown that electrochemical characterisation (cyclovoltammetry CV and electrochemical impedance spectroscopy EIS of AuPd systems can be used to determine the presence of an electronic interaction between the two metals, thus providing a strong support in the determination of the nature of the synergy between Au and Pd in the liquid phase oxidation of alcohols. However, it seems likely that the strong difference in the catalytic behavior between the single metals and the bimetallic system is connected not only to the redox behaviour, but also to the energetic balance between the different elementary steps of the reaction.

  18. MEMS magnetic field sensor based on silicon bridge structure

    Energy Technology Data Exchange (ETDEWEB)

    Du Guangtao; Chen Xiangdong; Lin Qibin; Li Hui; Guo Huihui, E-mail: [School of Information Science and Technology, Southwest Jiaotong University, Chengdu 610031 (China)


    A MEMS piezoresistive magnetic field sensor based on a silicon bridge structure has been simulated and tested. The sensor consists of a silicon sensitivity diaphragm embedded with a piezoresistive Wheatstone bridge, and a ferromagnetic magnet adhered to the sensitivity diaphragm. When the sensor is subjected to an external magnetic field, the magnetic force bends the silicon sensitivity diaphragm, producing stress and resistors change of the Wheatstone bridge and the output voltage of the sensor. Good agreement is observed between the theory and measurement behavior of the magnetic field sensor. Experimental results demonstrate that the maximum sensitivity and minimum resolution are 48 m V/T and 160 {mu}T, respectively, making this device suitable for strong magnetic field measurement. Research results indicate that the sensor repeatability and dynamic response time are about 0.66% and 150 ms, respectively. (semiconductor devices)

  19. Controlling pesticide release via structuring agropolymer and nanoclays based materials. (United States)

    Chevillard, Anne; Angellier-Coussy, Hélène; Guillard, Valérie; Gontard, Nathalie; Gastaldi, Emmanuelle


    The potential use of nanoclays for modulating transfer properties of active agents in bio-sourced polymers was explored. For this purpose, new pesticide formulations were designed by combining wheat gluten, ethofumesate (model pesticide) and three montmorillonites (MMT) using a bi-vis extrusion process. Controlled release properties, evaluated through release experiments in water, were discussed in relation to the material formulations and their resulting structure. Partition coefficients were calculated from experimental data and diffusivity values were identified with a Fick's second law mechanistic model. The effect of temperature on release pattern was also evaluated and the activation energy of diffusion was determined. Ethofumesate release was slowed down for all wheat gluten based-formulations as compared to the commercial product. This slow release effect was increased in the presence of hydrophobic MMTs, due to a higher affinity for ethofumesate than for wheat gluten. Contrarily, hydrophilic MMT, displaying a greater affinity for wheat gluten than for ethofumesate seemed ineffective to slow down its release despite the tortuous pathway achieved through a well-exfoliated structure. To conclude, the release mechanisms would be rather governed by pesticide/MMT interactions than MMT/polymer matrix in the case of a hydrophobic pesticide such as ethofumesate and a hydrophilic matrix such as wheat gluten. Copyright © 2011 Elsevier B.V. All rights reserved.

  20. Glass-based confined structures enabling light control

    Energy Technology Data Exchange (ETDEWEB)

    Chiappini, Andrea; Normani, Simone; Chiasera, Alessandro [IFN–CNR CSMFO Lab., and FBK Photonics Unit via alla Cascata 56/C Povo, 38123 Trento (Italy); Lukowiak, Anna [Institute of Low Temperature and Structure Research PAS, Okolna St. 2, 50-422 Wroclaw (Poland); Vasilchenko, Iustyna [IFN–CNR CSMFO Lab., and FBK Photonics Unit via alla Cascata 56/C Povo, 38123 Trento (Italy); Dipartimento di Fisica, Università di Trento, via Sommarive 14 Povo, 38123Trento (Italy); Ristic, Davor [Institut Ruđer Bošković, Bijenička cesta 54, 10000 Zagreb (Croatia); Boulard, Brigitte [IMMM, CNRS Equipe Fluorures, Université du Maine, Av. Messiaen, 72085 Le Mans cedex 9 (France); Dorosz, Dominik [Department of Power Engineering, Photonics and Lighting Technology, Bialystok University of Technology, Wiejska Street 45D, 15-351 Bialystok (Poland); Scotognella, Francesco [Center for Nano Science and Technology@PoliMi, Istituto Italiano di Tecnologia, Via Giovanni Pascoli, 70/3, 20133, Milan (Italy); Politecnico di Milano, Dipartimento di Fisica and Istituto di Fotonica e Nanotecnologie CNR, Piazza Leonardo da Vinci 32, 20133 Milano (Italy); Vaccari, Alessandro [FBK -CMM, ARES Unit, 38123 Trento (Italy); Taccheo, Stefano [College of Engineering, Swansea University, Singleton Park, SA2 8PP, Swansea (United Kingdom); Pelli, Stefano; Righini, Giancarlo C. [IFAC - CNR, MiPLab., 50019 Sesto Fiorentino (Italy); Museo Storico della Fisica e Centro di Studi e Ricerche “Enrico Fermi”, Piazza del Viminale 1, 00184 Roma (Italy); Conti, Gualtiero Nunzi [IFAC - CNR, MiPLab., 50019 Sesto Fiorentino (Italy); Ramponi, Roberta [Politecnico di Milano, Dipartimento di Fisica and Istituto di Fotonica e Nanotecnologie CNR, Piazza Leonardo da Vinci 32, 20133 Milano (Italy); and others


    When a luminescent ion is confined in a system characterized by one or more specific properties such as spatial size, geometrical dimension and shape, refractive index, local crystal field, cut-off vibrational energy and so on, it's possible to control its emission. The control of branching ratios as a function of the composition, the luminescence enhancement induced by a photonic crystal, or the laser action in a microresonator, are well known examples of light control. Photonic glass-based structures are extremely viable systems to exploit the above mentioned properties and in our research team we have successfully fabricated luminescent photonic structures by different techniques, including sol-gel, rf sputtering, drawing, melting, and physical vapour deposition. Here we will discuss some of them with the aim to make the reader aware of the chemical-physical properties related to each specific system. We will demonstrate that glass ceramic waveguides in some cases present superior spectroscopic properties in respect to the parent glass, that compositional properties can play a positive role in reducing luminescence quenching and in developing novel planar waveguides and fibers, that colloids allow to obtain high internal quantum efficiency and that photonic crystals, microcavities and microresonators can enable the handling of the rare earth luminescence. Finally, the pros and cons of the systems and of the different techniques employed for their fabrication will be discussed and some perspectives concerning the glass photonics will be proposed looking at both possible applications and investigation of physical properties.

  1. A Lightweight Structure Redesign Method Based on Selective Laser Melting

    Directory of Open Access Journals (Sweden)

    Li Tang


    Full Text Available The purpose of this paper is to present a new design method of lightweight parts fabricated by selective laser melting (SLM based on the “Skin-Frame” and to explore the influence of fabrication defects on SLM parts with different sizes. Some standard lattice parts were designed according to the Chinese GB/T 1452-2005 standard and manufactured by SLM. Then these samples were tested in an MTS Insight 30 compression testing machine to study the trends of the yield process with different structure sizes. A set of standard cylinder samples were also designed according to the Chinese GB/T 228-2010 standard. These samples, which were made of iron-nickel alloy (IN718, were also processed by SLM, and then tested in the universal material testing machine INSTRON 1346 to obtain their tensile strength. Furthermore, a lightweight redesigned method was researched. Then some common parts such as a stopper and connecting plate were redesigned using this method. These redesigned parts were fabricated and some application tests have already been performed. The compression testing results show that when the minimum structure size is larger than 1.5 mm, the mechanical characteristics will hardly be affected by process defects. The cylinder parts were fractured by the universal material testing machine at about 1069.6 MPa. These redesigned parts worked well in application tests, with both the weight and fabrication time of these parts reduced more than 20%.

  2. Frequency-based similarity detection of structures in human brain (United States)

    Sims, Dave I.; Siadat, Mohammad-Reza


    Advancements in 3D scanning and volumetric imaging methods have motivated researchers to tackle new challenges related to storing, retrieving and comparing 3D models, especially in medical domain. Comparing natural rigid shapes and detecting subtle changes in 3D models of brain structures is of great importance. Precision in capturing surface details and insensitivity to shape orientation are highly desirable properties of good shape descriptors. In this paper, we propose a new method, Spherical Harmonics Distance (SHD), which leverages the power of spherical harmonics to provide more accurate representation of surface details. At the same time, the proposed method incorporates the features of a shape distribution method (D2) and inherits its insensitivity to shape orientation. Comparing SHD to a spherical harmonics based method (SPHARM) shows that the performance of the proposed method is less sensitive to rotation. Also, comparing SHD to D2 shows that the proposed method is more accurate in detecting subtle changes. The performance of the proposed method is verified by calculating the Fisher measure (FM) of extracted feature vectors. The FM of the vectors generated by SHD on average shows 27 times higher values than that of D2. Our preliminary results show that SHD successfully combines desired features from two different methods and paves the way towards better detection of subtle dissimilarities among natural rigid shapes (e.g. structures of interest in human brain). Detecting these subtle changes can be instrumental in more accurate diagnosis, prognosis and treatment planning.

  3. Structural and mechanistic insights into human splicing factor SF3b complex derived using an integrated approach guided by the cryo-EM density maps. (United States)

    Rakesh, Ramachandran; Joseph, Agnel Praveen; Bhaskara, Ramachandra M; Srinivasan, Narayanaswamy


    Pre-mRNA splicing in eukaryotes is performed by the spliceosome, a highly complex macromolecular machine. SF3b is a multi-protein complex which recognizes the branch point adenosine of pre-mRNA as part of a larger U2 snRNP or U11/U12 di-snRNP in the dynamic spliceosome machinery. Although a cryo-EM map is available for human SF3b complex, the structure and relative spatial arrangement of all components in the complex are not yet known. We have recognized folds of domains in various proteins in the assembly and generated comparative models. Using an integrative approach involving structural and other experimental data, guided by the available cryo-EM density map, we deciphered a pseudo-atomic model of the closed form of SF3b which is found to be a "fuzzy complex" with highly flexible components and multiplicity of folds. Further, the model provides structural information for 5 proteins (SF3b10, SF3b155, SF3b145, SF3b130 and SF3b14b) and localization information for 4 proteins (SF3b10, SF3b145, SF3b130 and SF3b14b) in the assembly for the first time. Integration of this model with the available U11/U12 di-snRNP cryo-EM map enabled elucidation of an open form. This now provides new insights on the mechanistic features involved in the transition between closed and open forms pivoted by a hinge region in the SF3b155 protein that also harbors cancer causing mutations. Moreover, the open form guided model of the 5' end of U12 snRNA, which includes the branch point duplex, shows that the architecture of SF3b acts as a scaffold for U12 snRNA: pre-mRNA branch point duplex formation with potential implications for branch point adenosine recognition fidelity.

  4. A school-based oral health educational program: the experience of Maringa- PR, Brazil Programa educacional em saúde bucal baseado em escolas: a experiência de Maringá- PR, Brasil

    Directory of Open Access Journals (Sweden)

    Carlos Alberto Conrado


    Full Text Available The main purpose of this study was to evaluate the preliminary results of a school-based oral health educational strategy adopted in public primary schools from the city of Maringa, State of Parana, Brazil. The study sample was composed by 556 children and adolescents aged 6 to 17 years old, 124 schoolteachers and a group of 55 mothers. The educational approach was implemented for 18 months and consisted of reinforcements of interventions addressed to students and schoolteachers at school level and few activities targeted at the mothers, performed by means of home visits. Baseline and follow-up interviews focused on oral health care were undertaken for the entire study population. As a stimulus for the students to achieve proper oral hygiene habits, the simplified oral hygiene index was assessed at three different moments. A statistically significant improvement in their oral hygiene index (pO principal propósito deste estudo foi avaliar os resultados preliminares de uma estratégia educacional baseada em escolas sobre saúde bucal adotada em escolas públicas de ensino fundamental da cidade de Maringá, estado do Paraná, Brasil. A amostra de estudo foi composta por 556 crianças e adolescentes entre 6 e 17 anos de idade, 124 professoras e um grupo de 55 mães. A abordagem educacional foi implementada por um período de 18 meses e consistiu de reforços das intervenções educativas dirigidas aos estudantes e professores a nível escolar e de poucas atividades tendo como alvo as mães, desenvolvidas através de visitas domiciliares. Entrevistas iniciais e de acompanhamento focando cuidados em saúde bucal foram realizadas com toda a população de estudo. Como um estímulo aos estudantes para assumirem hábitos apropriados de higiene bucal, o índice de higiene oral simplificado foi avaliado em três diferentes momentos. Uma melhora estatisticamente significante em seus índices de higiene oral (p< 0,001 foi registrada. Os resultados alcan

  5. Conformational specificity of non-canonical base pairs and higher order structures in nucleic acids: crystal structure database analysis (United States)

    Mukherjee, Shayantani; Bansal, Manju; Bhattacharyya, Dhananjay


    Non-canonical base pairs contribute immensely to the structural and functional variability of RNA, which calls for a detailed characterization of their spatial conformation. Intra-base pair parameters, namely propeller, buckle, open-angle, stagger, shear and stretch describe structure of base pairs indicating planarity and proximity of association between the two bases. In order to study the conformational specificities of non-canonical base pairs occurring in RNA crystal structures, we have upgraded NUPARM software to calculate these intra-base pair parameters using a new base pairing edge specific axis system. Analysis of base pairs and base triples with the new edge specific axis system indicate the presence of specific structural signatures for different classes of non-canonical pairs and triples. Differentiating features could be identified for pairs in cis or trans orientation, as well as those involving sugar edges or C-H-mediated hydrogen bonds. It was seen that propeller for all types of base pairs in cis orientation are generally negative, while those for trans base pairs do not have any preference. Formation of a base triple is seen to reduce propeller of the associated base pair along with reduction of overall flexibility of the pairs. We noticed that base pairs involving sugar edge are generally more non-planar, with large propeller or buckle values, presumably to avoid steric clash between the bulky sugar moieties. These specific conformational signatures often provide an insight into their role in the structural and functional context of RNA.

  6. Non-Watson Crick base pairs might stabilize RNA structural motifs in ...

    Indian Academy of Sciences (India)

    Watson Crick base pairs, internal loops and pseudoknots have been the highlighting feature of recent structural determination of RNAs. The recent crystal structure of group-I introns has demonstrated that these might constitute RNA structural ...

  7. Aflatoxins, ochratoxin A and zearalenone in maize-based food products Aflatoxinas, ocratoxina A e zearalenona em produtos alimentícios à base de milho

    Directory of Open Access Journals (Sweden)

    Beatriz Leiko Sekiyama


    Full Text Available The occurrence of aflatoxins B1 (AFB1, B2 (AFB2 , G1 (AFG1 and G2 (AFG2 , ochratoxin A (OA and zearalenone (ZEA was evaluated in 121 maize-based food samples collected in the commerce of Maringá City, Paraná State, Brazil. The study was carried out between January 2002 and February 2003. Thin-layer chromatographic method was used to determine the mycotoxins. The recovery averages were 106.6%, 109.4%, 106.6%, 109.4%, 101.8% and 101.7% to AFB1, AFB2, AFG1, AFG2, OA and ZEA, respectively. Three samples (2.5% were positive to AFB1 (8 to 59 µg/kg, two (1.7% to AFB2 (2.4 µg/kg, one (0.8% to OA (64 µg/kg and one (0.8% to ZEA (448 µg/kg. The greater frequency of positive samples and also the highest concentration of AFB1 were found in popcorn samples (8.3%, 59 µg/kg. The data showed a low frequency of mycotoxins in products based on maize traded in Maringá, but the Probable Average Daily Intake (PDI of AFB1 in them was high. Therefore, it is necessary to accomplish an active vigilance of these mycotoxins in such food products in order to provide safety to Brazilian people health.A ocorrência de aflatoxinas B1 (AFB1, B2 (AFB2, G1 (AFG1 e G2 (AFG2, ocratoxina A (OA e zearalenona (ZEA foi avaliada em 121 amostras de alimentos à base de milho, que foram coletadas no comércio da cidade de Maringá, PR, Brasil, entre os meses de Janeiro/2002 a Fevereiro/2003. A cromatografia em camada delgada foi empregada para a determinação das micotoxinas. As médias das recuperações foram 106,6%, 109,4%, 106,6%, 109,4%, 101,8% e 101,7% para AFB1, AFB2, AFG1, AFG2, OA e ZEA, respectivamente. Três amostras (2,5% foram positivas para AFB1 (8 a 59 µg/kg, duas (1,7% para AFB2 (2,4 µg/kg, uma (0,8% para OA (64 µg/kg e uma (0,8% para ZEA (448 µg/kg. A maior freqüência de amostras positivas e também a mais alta concentração de AFB1 foi encontrada nas amostras de pipoca (8,3%, 59 µg/kg. Os dados demonstraram uma baixa freqüência de micotoxinas em

  8. Strain-based energy harvesting for structural health monitoring

    Energy Technology Data Exchange (ETDEWEB)

    Debeaux, S.; Masson, P.; Frechette, L. [Sherbrooke Univ., PQ (Canada). Dept. of Mechanical Engineering


    Structural health monitoring (SHM) has been proposed for the maintenance of aircraft fuselage and wings. Wireless sensors and self-powered actuators are recommended in order to avoid extensive wiring of the nodes. One idea is to convert the mechanical energy (vibrations) in an aircraft into electricity using piezoelectric materials. This study investigated the potential of strain-based energy harvesters as opposed to inertial harvesters to supply wireless nodes on typical aircraft structures. In particular, it experimentally compared different piezoelectric energy harvesting devices for use in structural health monitoring. The experimental setup reproduced the simple vibration behaviour of an aircraft wing with respect to frequency and strain level. The study examined 2 distinct groups of piezoelectric harvesting devices, notably piezoelectric harvesting devices polarized in 3-3, and piezoelectric harvesting devices polarized in 3-1. Power dissipation in a resistive load was tested along with energy storage in a capacitance. The optimal voltage was linearly dependent on the strain, but independent of the frequency. The optimal current was linearly dependent on both the frequency and the strain level. The power dissipated in a resistive load was linearly dependent on the frequency but quadratically related to the strain level. The dissipated power in the piezoelectric material was a linear function of the capacitance and inversely proportional to the relative permittivity. The study results were in agreement with literature which indicates that power density in the order of 100 {mu}W/cm{sup 3} is sufficient for many applications, including structural health monitoring. Larger devices will be needed to increase the harvested energy. A simple model was used to describe typical dynamic behaviour of aircraft components, notably a beam representing the whole wing subjected to atmospheric effects, and a plate representing a fuselage panel. Different configurations of

  9. Men's health: a population-based study on social inequalities A saúde dos homens: desigualdades sociais em estudo de base populacional

    Directory of Open Access Journals (Sweden)

    Tássia Fraga Bastos


    Full Text Available This study evaluates social inequalities in health according to level of schooling in the male population. This was a cross-sectional, population-based study with a sample of 449 men ranging from 20 to 59 years of age and living in Campinas, São Paulo State, Brazil. The chi-square test was used to verify associations, and a Poisson regression model was used to estimate crude and adjusted prevalence ratios. Men with less schooling showed higher rates of alcohol consumption and dependence, smoking, sedentary lifestyle during leisure time, and less healthy eating habits, in addition to higher prevalence of bad or very bad self-rated health, at least one chronic disease, hypertension, and other health problems. No differences were detected between the two schooling strata in terms of use of health services, except for dental services. The findings point to social inequality in health-related behaviors and in some health status indicators. However, possible equity was observed in the use of nearly all types of health services.Este trabalho avalia as desigualdades sociais em saúde, segundo escolaridade, na população masculina. Trata-se de um estudo transversal de base populacional, envolvendo 449 homens, de 20 a 59 anos, residentes em Campinas, São Paulo, Brasil. Realizou-se o teste qui-quadrado para verificar as associações e o modelo de regressão de Poisson para estimar as razões de prevalência brutas e ajustadas. O segmento de menor escolaridade apresentou maiores proporções de consumo e dependência de bebida alcoólica, tabagismo, sedentarismo e de consumo alimentar menos saudável, além de maiores prevalências de autoavaliação da saúde como ruim/muito ruim, pelo menos uma doença crônica, hipertensão, dentre outros problemas de saúde. Não foram detectadas diferenças entre os segmentos com relação ao uso de serviços de saúde, à exceção da utilização de serviços odontológicos. Os achados revelam que h

  10. A dinuclear dysprosium complex based on schiff base ligand: synthesis, structure and magnetic property (United States)

    Hu, Peng; Xiao, Fengping; Wu, Lihuan; Chen, Zhisheng


    A novel dinuclear dysprosium complex, namely [Dy2 (L) 4 (COO) 2 (CH3OH)2] (1) (L = 2-hydroxy-3-methodxybenzaldehyde-5-bromo oxime), was synthesized, structurally and magnetically characterized. Single-crystal X-ray structural analysis reveals that complex 1 is neutral dinuclear complex, in which two Dy(III) ions with nine-coordinated environment are bridged by two phenoxide groups from two schiff base ligands and four O ions from two molecules of methanoic acid. The magnetic study of complex 1 indicates the slow relaxation of magnetization.

  11. Synthesis of 1,2,3-Triazole Derivatives and <em>in Vitroem> Antifungal Evaluation on <em>Candida> Strains

    Directory of Open Access Journals (Sweden)

    Almir G. Wanderley


    Full Text Available 1,2,3-Triazoles have been extensively studied as compounds possessing important biological activities. In this work, we describe the synthesis of ten 2-(1-aryl-1<em>H>-1,2,3-triazol-4-ylpropan-2-ols via copper catalyzed azide alkyne cycloaddition (CuAAc or <em>click chemistryem>. Next the<em> in vitroem> antifungal activity of these ten compounds was evaluated using the microdilution broth method against 42 isolates of four different <em>Candida> species. Among all tested compounds, the halogen substituted triazole 2-[1-(4-chlorophenyl-1<em>H>-(1,2,3triazol-4-yl]propan-2-ol, revealed the best antifungal profile, showing that further modifications could be done in the structure to obtain a better drug candidate in the future.

  12. Brain structure correlates of emotion-based rash impulsivity. (United States)

    Muhlert, N; Lawrence, A D


    Negative urgency (the tendency to engage in rash, ill-considered action in response to intense negative emotions), is a personality trait that has been linked to problematic involvement in several risky and impulsive behaviours, and to various forms of disinhibitory psychopathology, but its neurobiological correlates are poorly understood. Here, we explored whether inter-individual variation in levels of trait negative urgency was associated with inter-individual variation in regional grey matter volumes. Using voxel-based morphometry (VBM) in a sample (n=152) of healthy participants, we found that smaller volumes of the dorsomedial prefrontal cortex and right temporal pole, regions previously linked to emotion appraisal, emotion regulation and emotion-based decision-making, were associated with higher levels of trait negative urgency. When controlling for other impulsivity linked personality traits (sensation seeking, lack of planning/perseverance) and negative emotionality per se (neuroticism), these associations remained, and an additional relationship was found between higher levels of trait negative urgency and smaller volumes of the left ventral striatum. This latter finding mirrors recent VBM findings in an animal model of impulsivity. Our findings offer novel insight into the brain structure correlates of one key source of inter-individual differences in impulsivity. Copyright © 2015. Published by Elsevier Inc.

  13. Coevolutionary Structure-Redesigned-Based Bacterial Foraging Optimization. (United States)

    Niu, B; Liu, J; Wu, T; Chu, X H; Wang, Z X; Liu, Y M


    This paper presents a Coevolutionary Structure-Redesigned-Based Bacteria Foraging Optimization (CSRBFO) based on the natural phenomenon that most living creatures tend to cooperate with each other so as to fulfill tasks more effectively. Aiming at lowering computational complexity while maintaining the critical search capability of standard bacterial foraging optimization (BFO), we employ a general loop to replace the nested loop and eliminate the reproduction step of BFO. Hence, the proposed CSRBFO only consists of two main steps: (1) chemotaxis and (2) elimination & dispersal. A coevolutionary strategy by which all bacteria can learn from each other and search for optima cooperatively is incorporated into the chemotactic step to accelerate convergence and facilitate accurate search. In the elimination & dispersal step, the three-stage evolutionary strategy with different learning methods for maintaining diversity is studied. An evaluation of the convergence status is then added to determine whether bacteria should move on to the next stage or not. The combination of coevolutionary strategy and convergence status evaluation is expected to balance exploration and exploitation. Experimental results comparing 7 well-known heuristic algorithms on 24 benchmark functions demonstrate that the proposed CSRBFO outperforms the comparison algorithms significantly in most of the cases.

  14. Reconstructing Carotenoid-Based and Structural Coloration in Fossil Skin. (United States)

    McNamara, Maria E; Orr, Patrick J; Kearns, Stuart L; Alcalá, Luis; Anadón, Pere; Peñalver, Enrique


    Evidence of original coloration in fossils provides insights into the visual communication strategies used by ancient animals and the functional evolution of coloration over time [1-7]. Hitherto, all reconstructions of the colors of reptile integument and the plumage of fossil birds and feathered dinosaurs have been of melanin-based coloration [1-6]. Extant animals also use other mechanisms for producing color [8], but these have not been identified in fossils. Here we report the first examples of carotenoid-based coloration in the fossil record, and of structural coloration in fossil integument. The fossil skin, from a 10 million-year-old colubrid snake from the Late Miocene Libros Lagerstätte (Teruel, Spain) [9, 10], preserves dermal pigment cells (chromatophores)-xanthophores, iridophores, and melanophores-in calcium phosphate. Comparison with chromatophore abundance and position in extant reptiles [11-15] indicates that the fossil snake was pale-colored in ventral regions; dorsal and lateral regions were green with brown-black and yellow-green transverse blotches. Such coloration most likely functioned in substrate matching and intraspecific signaling. Skin replicated in authigenic minerals is not uncommon in exceptionally preserved fossils [16, 17], and dermal pigment cells generate coloration in numerous reptile, amphibian, and fish taxa today [18]. Our discovery thus represents a new means by which to reconstruct the original coloration of exceptionally preserved fossil vertebrates. Copyright © 2016 Elsevier Ltd. All rights reserved.

  15. Corrosion of structural materials by lead-based reactor coolants.

    Energy Technology Data Exchange (ETDEWEB)

    Abraham, D. P.; Leibowitz, L.; Maroni, V. A.; McDeavitt, S. M.; Raraz, A. G.


    Advanced nuclear reactor design has, in recent years, focused increasingly on the use of heavy-liquid-metal coolants, such as lead and lead-bismuth eutectic. Similarly, programs on accelerator-based transmutation systems have also considered the use of such coolants. Russian experience with heavy-metal coolants for nuclear reactors has lent credence to the validity of this approach. Of significant concern is the compatibility of structural materials with these coolants. We have used a thermal convection-based test method to allow exposure of candidate materials to molten lead and lead-bismuth flowing under a temperature gradient. The gradient was deemed essential in evaluating the behavior of the test materials in that should preferential dissolution of components of the test material occur we would expect dissolution in the hotter regions and deposition in the colder regions, thus promoting material transport. Results from the interactions of a Si-rich mild steel alloy, AISI S5, and a ferritic-martensitic stainless steel, HT-9, with the molten lead-bismuth are presented.

  16. Steel catenary riser design based on coupled analysis methodology; Projeto de um riser rigido em catenaria baseado em metodologia de analise acoplada

    Energy Technology Data Exchange (ETDEWEB)

    Bahiense, Rodrigo A.; Rodrigues, Marcos V. [Det Norske Veritas (DNV), Rio de Janeiro, RJ (Brazil)


    Due to adoption of oil and gas production systems to deep and ultra-deep water, achieving frontiers that were not conceivable before, research in computational methods has contributed to implementation of sophisticated and efficient numerical tools in order to perform simulations considering those operational conditions. Thus, this work presents a steel catenary riser (SCR) design which is connected to a semi-submersible platform where the applied motions to SCR are obtained from analyses based on de-coupled and coupled methodologies. With increase of the line number of the system and water depth, the effects due to coupling of the lines on the platform motions are significant. It can be observed from performed evaluations for a floating production system, comparing the obtained results for SCR under extreme and fatigue conditions when it was submitted to the platform motions considering both methodologies mentioned. So, from the results obtained it can be concluded that for production system evaluated the adoption of decoupled methodology presents more conservative results. Thus the adoption of the coupled model associated to design practice of production lines presents as an alternative more realist and accurate to provide the optimization in the design of these structures. (author)

  17. Pressão arterial elevada em adolescentes e fatores associados: um estudo de base escolar em Uruguaiana, Rio Grande do Sul, 2011

    Directory of Open Access Journals (Sweden)

    Mauren Lúcia de Araújo Bergmann


    Full Text Available Resumo Objetivos: identificar a prevalência de pressão arterial (PA elevada e seus fatores associados em adolescentes de Uruguaiana (RS, 2011. Métodos: amostra probabilística composta por adolescentes de 10 a 17 anos de escolas públicas. A PA foi aferida pelo método auscultatório e classificada em normal ou elevada (PA acima do percentil 90. Fatores sociodemográficos, psicossociais, comportamentais, estado nutricional e aptidão física foram analisados. Foi realizada uma análise de regressão logística considerando um modelo teórico hierárquico. Resultados: participaram do estudo 1455 adolescentes (741 do sexo feminino. A prevalência de PA sistólica e PA diastólica elevadas foram de 16,4% (IC95%: 14,4-18,4 e de 18,5% (IC95%: 16,4-20,6, respectivamente. Permaneceram associados à PA sistólica e diastólica elevadas no modelo final: se perceber menos em forma que seus pares (sistólica OR: 2,27; IC95%: 1,22-4,23; diastólica OR: 2,99; IC95%: 1,34-6,70 e o sobrepeso e obesidade (sistólica OR: 9,29; IC95%: 4,89-17,69; diastólica OR: 4,70; IC95%: 2,61-8,45. Ainda, adolescentes do sexo feminino (OR: 1,39; IC95%: 1,02-1,90 e de maior nível socioeconômico (OR: 2,39; IC95%: 1,31- 4,36 têm mais chance de apresentarem PA sistólica elevada. Conclusões: a prevalência de PA elevada encontrada entre os adolescentes é alta. Para sua prevenção, programas de combate ao excesso de peso considerando características sociodemográficas como o sexo e nível socioeconômico devem ser elaboradas

  18. Origem, prática educativa e evolução do movimento de educação de base (MEB em Itacoatiara - AM

    Directory of Open Access Journals (Sweden)

    Alderlene Lima de Souza


    Full Text Available Este estudo visou analisar a relevância do Movimento de Educação de Base (MEB, no município de Itacoatiara-AM, no período de 1998 a 2003. Tendo em vista o caráter político-pedagógico das práticas educativas forjadas por este movimento durante a sua 3ª fase a nível nacional. O Movimento de Educação de Base foi criado em 1961 pela Conferência Nacional dos Bispos do Brasil (CNBB. O objetivo principal do MEB era desenvolver um programa de educação de base, por meio de escolas radiofônicas, principalmente nas zonas rurais das áreas subdesenvolvidas do Norte, Nordeste e Centro-Oeste do país, expandindo-se posteriormente para outras regiões do Brasil de acordo com o decreto 5.2267/61. Assim, pautou-se a análise em fontes primárias (documentos que estão localizadas na Cúria Prelatícia da cidade. E também no levantamento bibliográfico, pois, é praticamente impossível desenvolver um estudo científico, sem a fundamentação em um ou mais pressupostos que direcionem a “reconstrução” do objeto. Apesar da diversidade de informações contida nos documentos, ainda são escassos os estudos que visam historiar o MEB da região Norte do país. Os dados da pesquisa apontam que, durante a atuação do MEB em Itacoatiara o rádio não era o principal meio de transmissão das aulas, os professores utilizavam cartilhas elaboradas pelo MEB de acordo com a realidade local.


    Energy Technology Data Exchange (ETDEWEB)

    Robert H. Hurt; Eric M. Suuberg


    This report is part on the ongoing effort at Brown University and Ohio State University to develop structure based models of coal combustion. A very fundamental approach is taken to the description of coal chars and their reaction processes, and the results are therefore expected to have broad applicability to the spectrum of carbon materials of interest in energy technologies. This quarter, our work on structure development in carbons continued. A combination of hot stage in situ and ex situ polarized light microscopy was used to identify the preferred orientational of graphene layers at gas interfaces in pitches used as carbon material precursors. The experiments show that edge-on orientation is the equilibrium state of the gas/pitch interface, implying that basal-rich surfaces have higher free energies than edge-rich surfaces in pitch. This result is in agreement with previous molecular modeling studies and TEM observations in the early stages of carbonization. The results may have important implications for the design of tailored carbons with edge-rich or basal-rich surfaces. In the computational chemistry task, we have continued our investigations into the reactivity of large aromatic rings. The role of H-atom abstraction as well as radical addition to monocyclic aromatic rings has been examined, and a manuscript is currently being revised after peer review. We have also shown that OH radical is more effective than H atom in the radical addition process with monocyclic rings. We have extended this analysis to H-atom and OH-radical addition to phenanthrene. Work on combustion kinetics focused on the theoretical analysis of the data previously gathered using thermogravametric analysis.

  20. O uso do custeio baseado em atividades: ABC (Activity Based Costing nas maiores empresas de Santa Catarina

    Directory of Open Access Journals (Sweden)

    Ilse Maria Beuren


    Full Text Available Devido à globalização da economia, as empresas evoluíram para a produção de enormes variedades de produtos personalizados. Com o intuito de atender às exigências dos clientes, surgiu a necessidade de grandes alterações nos processos tecnológicos. Como conseqüência, os custos indiretos passaram a ser mais significativos, o que implicou um novo método de distribuição desses custos, capaz de distribuir melhor os custos indiretos aos produtos e serviços. A esse método foi dado o nome de custeio baseado em atividades - ABC (Activity Based Costing. Esse método foi investigado por Carlos Yorghi Khoury em 1996, numa pesquisa aplicada às 500 maiores empresas do Brasil. O objetivo deste trabalho foi replicar essa pesquisa nas maiores empresas catarinenses, a fim de observar se esses resultados obtidos assemelham-se aos obtidos na pesquisa com as empresas catarinenses.Nesta pesquisa, dos 200 questionários enviados para as maiores empresas de Santa Catarina, 81 retornaram com as questões respondidas. O trabalho levou a conclusões importantes, como: as empresas de Santa Catarina têm amplo conhecimento do sistema ABC; algumas empresas que implantaram esse sistema já estão desistindo de seu uso, em função da complexidade para apropriar os custos indiretos e as despesas às atividades e estas aos produtos.Due to the economic globalization, enterprises have started to produce enormous varieties of personalized products. In order to attend to the requirements of their clients, huge changes in the technological process were needed. Consequently, indirect costs became more significant, which led to a new method for distributing the indirect costs, capable of better distributing the indirect costs of products and services.This method was called Activity Based Costing and was investigated by Carlos Yorghi Khoury in 1996 through a research applied in the 500 biggest companies in Brazil. This paper aims to replicate the 1996 research in the

  1. Synthesis, Structure, Stability and Redispersion of Gold-based Nanoparticles (United States)

    Tiruvalam, Ram Chandra

    Nanoscale gold has been shown to possess an intriguing combination of unexpected optical, photochemical and catalytic properties. The ability to control the size, shape, morphology, composition and dispersion of gold-based nanostructures is key to optimizing their performance for nanotechnology applications. The advanced electron microscopy studies described in this thesis analyze three important aspects of gold and gold-palladium alloy nanoparticles: namely, (i) the ability to synthesize gold nanoparticles of controlled size and shape in an aqueous medium; (ii) the colloidal preparation of designer gold-palladium alloys for selective oxidation catalysis; and (iii) the ability to disperse gold as finely and homogeneously as possible on a metal oxide or carbon support. The ability to exploit the nanoscale properties of gold for various engineering applications often depends on our ability to control size and shape of the nanoscale entity by careful manipulation of the synthesis parameters. We have explored an aqueous based synthesis route, using oleylamine as both a reductant and surfactant, for preparing gold nanostructures. By systematically varying synthesis parameters such as oleylamine concentration, reaction temperature, and aging time it is possible to identify processing regimens that generate Au nanostructures having either pseudo-spherical, faceted polyhedral, nanostar or wire shaped morphologies. Furthermore, by quenching the reaction partway through it is possible to create a class of metastable Au-containing structures such as nanocubes, nanoboxes and nanowires. Possible formation mechanisms for these gold based nano-objects are discussed. There is a growing interest in using supported bimetallic AuPd alloy nanoparticles for selective oxidation reactions. In this study, a systematic series of size controlled AuPd bimetallic particles have been prepared by colloidal synthesis methods. Particles having random alloy structures, as well as `designer

  2. Agendas urbanas intersetoriais em quatro cidades de São Paulo Intersetorial urban agendas based on four cities in São Paulo

    Directory of Open Access Journals (Sweden)

    Rosilda Mendes


    Full Text Available Este artigo visa analisar o processo de implementação e avaliação de projetos de melhoria da qualidade de vida, do ponto de vista dos gestores municipais brasileiros, que têm buscado alternativas para a prática da gestão local. Optou-se por identificar a percepção de gestores, representantes do poder executivo local, prefeitos, secretários de governo e coordenadores, identificados como atores-chave importantes na implementação de projetos de melhoria da qualidade de vida em quatro municípios do Estado de São Paulo/Brasil. Foram feitas entrevistas individuais e em profundidade, com roteiro semi-estruturado. A análise dos quatro projetos por melhoria de qualidade de vida na cidade mostra que o processo de municipalização e descentralização da gestão, que vem sendo impulsionado no Brasil, vem contribuindo para definir uma política local mais autônoma, para criar novas instâncias de decisão, incorporando práticas de controle social e de democratização da gestão. Porém, ainda existem muitas limitações no que se refere à incorporação da avaliação, como elemento retro-alimentador, no planejamento das ações e da prática participativa.This article is designed to analyze the process of implementing and evaluating projects to improve quality of life, based on the view of Brazilian municipal managers who have sought local management alternatives. It was chosen to identify the perception of managers, representatives of local executive authorities, municipal secretaries and coordinators, all identified as key players in implementing quality of life improvement projects in four cities in the State of São Paulo/Brazil. Individual in-depth interviews were carried out using a semi-structured guide and comparative analysis. The analysis of the four projects aiming at improving quality of life in the city shows that the management decentralization processes, which are currently encouraged in Brazil, have contributed to define

  3. EM structure of the ectodomain of integrin CD11b/CD18 and localization of its ligand-binding site relative to the plasma membrane.

    Directory of Open Access Journals (Sweden)

    Brian D Adair

    Full Text Available One-half of the integrin α-subunit Propeller domains contain and extra vWFA domain (αA domain, which mediates integrin binding to extracellular physiologic ligands via its metal-ion-dependent adhesion site (MIDAS. We used electron microscopy to determine the 3D structure of the αA-containing ectodomain of the leukocyte integrin CD11b/CD18 (αMβ2 in its inactive state. A well defined density for αA was observed within a bent ectodomain conformation, while the structure of the ectodomain in complex with the Fab fragment of mAb107, which binds at the MIDAS face of CD11b and stabilizes the inactive state, further revealed that αA is restricted to a relatively small range of orientations relative to the Propeller domain. Using Fab 107 as probe in fluorescent lifetime imaging microscopy (FLIM revealed that αA is positioned relatively far from the membrane surface in the inactive state, and a systematic orientation search revealed that the MIDAS face would be accessible to extracellular ligand in the inactive state of the full-length cellular integrin. These studies are the first to define the 3D EM structure of an αA-containing integrin ectodomain and to position the ligand-binding face of αA domain in relation to the plasma membrane, providing new insights into current models of integrin activation.

  4. Cryo-EM structure of the archaeal 50S ribosomal subunit in complex with initiation factor 6 and implications for ribosome evolution. (United States)

    Greber, Basil J; Boehringer, Daniel; Godinic-Mikulcic, Vlatka; Crnkovic, Ana; Ibba, Michael; Weygand-Durasevic, Ivana; Ban, Nenad


    Translation of mRNA into proteins by the ribosome is universally conserved in all cellular life. The composition and complexity of the translation machinery differ markedly between the three domains of life. Organisms from the domain Archaea show an intermediate level of complexity, sharing several additional components of the translation machinery with eukaryotes that are absent in bacteria. One of these translation factors is initiation factor 6 (IF6), which associates with the large ribosomal subunit. We have reconstructed the 50S ribosomal subunit from the archaeon Methanothermobacter thermautotrophicus in complex with archaeal IF6 at 6.6 Å resolution using cryo-electron microscopy (EM). The structure provides detailed architectural insights into the 50S ribosomal subunit from a methanogenic archaeon through identification of the rRNA expansion segments and ribosomal proteins that are shared between this archaeal ribosome and eukaryotic ribosomes but are mostly absent in bacteria and in some archaeal lineages. Furthermore, the structure reveals that, in spite of highly divergent evolutionary trajectories of the ribosomal particle and the acquisition of novel functions of IF6 in eukaryotes, the molecular binding of IF6 on the ribosome is conserved between eukaryotes and archaea. The structure also provides a snapshot of the reductive evolution of the archaeal ribosome and offers new insights into the evolution of the translation system in archaea. Copyright © 2012 Elsevier Ltd. All rights reserved.

  5. Efficient and versatile graphene-based multilayers for EM field absorption (United States)

    Mencarelli, D.; Pierantoni, L.; Stocchi, M.; Bellucci, S.


    We thoroughly investigate the possibility to absorb most (i.e., up to more than 90%) of the incident electro-magnetic radiations in thin multilayered PMMA/graphene structures, thus proposing the technical realization of a device with an operational frequency range in the millimeter-wave domain, i.e., 30 GHz-300 GHz. Our simulations demonstrate the concrete possibility to enhance the field absorption by means of a selective removal and proper micro-pattering within the graphene material, enabling a complete and efficient control of the graphene sheet conductance. This method is applied to design and engineer a class of devices, endowed with a wideband operation capability, showing almost no fluctuations throughout the whole range of mm-wave frequencies.

  6. Efficient and versatile graphene-based multilayers for EM field absorption

    Energy Technology Data Exchange (ETDEWEB)

    Mencarelli, D.; Pierantoni, L. [Università Politecnica delle Marche, Ancona 60131 (Italy); Istituto Nazionale di Fisica Nucleare (INFN) - Laboratori Nazionali di Frascati (LNF), Frascati, Roma 00044 (Italy); Stocchi, M. [Università Politecnica delle Marche, Ancona 60131 (Italy); Bellucci, S. [Istituto Nazionale di Fisica Nucleare (INFN) - Laboratori Nazionali di Frascati (LNF), Frascati, Roma 00044 (Italy)


    We thoroughly investigate the possibility to absorb most (i.e., up to more than 90%) of the incident electro-magnetic radiations in thin multilayered PMMA/graphene structures, thus proposing the technical realization of a device with an operational frequency range in the millimeter-wave domain, i.e., 30 GHz–300 GHz. Our simulations demonstrate the concrete possibility to enhance the field absorption by means of a selective removal and proper micro-pattering within the graphene material, enabling a complete and efficient control of the graphene sheet conductance. This method is applied to design and engineer a class of devices, endowed with a wideband operation capability, showing almost no fluctuations throughout the whole range of mm-wave frequencies.


    Directory of Open Access Journals (Sweden)

    Nina Moravčíková


    Full Text Available The aim of this study was identification of SNPs in leptin (LEP, leptin receptor (LEPR, growth hormone (GH and specific pituitary transcription factor (Pit-1 genes in order to analyze genetic structure of Charolais bulls’ population. The total numbers of genomic DNA samples were taken from 52 breeding bulls and analyzed by PCR-RFLP method. After digestion with restriction enzymes were detected in bulls’ population alleles with frequency: LEP/Sau3AI A 0.83 and B 0.17 (±0.037; LEPR/BseGI C 0.95 and T 0.05 (±0.021, GH/AluI L 0.62 and V 0.38 (±0.048 and Pit1/HinfI A 0.40 and B 0.60 (±0.048. Based on the observed vs. expected genotypes frequencies population across loci were in Hardy-Weinberg equilibrium (P>0.05, only in case of Pit-1 locus was detected disequilibrium. Predominant were in analyzed breeding bulls LEP/Sau3AIAA (0.69, LEPR/T945MCC (0.90, GH/AluILL (0.43 and Pit-1/HinfIAB (0.65 genotypes. The observed heterozygosity of SNPs was also transferred to the low (LEP/Sau3AI/0.248 and LEPR/T945M/0.088 or median polymorphic information content (GH/AluI/0.366 and Pit-1/HinfI/0.370. Within genetic variability estimating negative (LEPR/T945M and Pit-1/HinfI and positive values (LEP/Sau3AI and GH/AluI of fixation indexes FIS indicating slight heterozygote excess or deficiency based on analyzed genetic marker were observed.

  8. Combining ground-based and airborne EM through Artificial Neural Networks for modelling glacial till under saline groundwater conditions

    Directory of Open Access Journals (Sweden)

    J. L. Gunnink


    Full Text Available Airborne electromagnetic (AEM methods supply data over large areas in a cost-effective way. We used Artificial Neural Networks (ANN to classify the geophysical signal into a meaningful geological parameter. By using examples of known relations between ground-based geophysical data (in this case electrical conductivity, EC, from electrical cone penetration tests and geological parameters (presence of glacial till, we extracted learning rules that could be applied to map the presence of a glacial till using the EC profiles from the airborne EM data. The saline groundwater in the area was obscuring the EC signal from the till but by using ANN we were able to extract subtle and often non-linear, relations in EC that were representative of the presence of the till. The ANN results were interpreted as the probability of having till and showed a good agreement with drilling data. The glacial till is acting as a layer that inhibits groundwater flow, due to its high clay-content, and is therefore an important layer in hydrogeological modelling and for predicting the effects of climate change on groundwater quantity and quality.

  9. Estrutura de espécies arbóreas sob efeito de borda em um fragmento de floresta estacional semidecidual em Pernambuco Edge effect on the structure of tree species in a seasonal forest fragment in Pernambuco

    Directory of Open Access Journals (Sweden)

    Alan Caue de Holanda


    Full Text Available Os fragmentos florestais são considerados os únicos redutos detentores de biodiversidade do planeta. Conhecer os processos que decorrem após a fragmentação, a exemplo da estrutura arbórea ocorrente na borda, é de fundamental importância para se proporem medidas conservacionistas. Os objetivos deste trabalho, desenvolvido em uma área de 83,8 ha, localizada no Município de Nazaré da Mata, PE, foram efetuar o levantamento fitossociológico de espécies arbóreas adultas sob efeito de borda e verificar a similaridade florística entre as parcelas. A área amostral foi de 10.000 m², equivalentes à implantação de 10 transectos de 10 x 100 m perpendiculares à borda, distribuídos de forma sistemática. Foram amostrados, etiquetados e identificados todos os indivíduos arbóreos com CAP e" 15 cm. Posteriormente, realizaram-se os cálculos dos parâmetros fitossociológicos e da similaridade florística. Neste estudo, amostraram-se 1.238 indivíduos, pertencentes a 72 táxons, distribuídos em 26 famílias botânicas. As espécies Campomanesia xanthocarpa, Zanthoxylum rhoifolium e Anadenanthera colubrina apresentaram o maior valor de importância, pois, teoricamente, conseguiram explorar melhor o recurso proporcionado pelo hábitat.Forest fragments are considered the last refuges for biodiversity in the planet. Knowing the processes that occur after fragmentation, such as the tree structure that occurs in the edge, is fundamental to propose conservationist measures. The objective of this work was to carry out a phytosociological survey of adult tree species under edge effect and verify the floristic similarity among the plots. The work was developed in an area of 83,8 ha located in the municipality of Nazaré da Mata - PE. The sample area comprised 10.000 m², equivalent to the implantation of 10 contiguous transects of 10 x 100 m perpendicular to the edge. All tree individuals with CAP e" 15 cm were sampled, labeled and identified

  10. Electronic structure of nitride-based quantum dots

    Energy Technology Data Exchange (ETDEWEB)

    Winkelnkemper, Momme


    In the present work the electronic and optical properties of In{sub x}Ga{sub 1-x}N/GaN and GaN/AlN QDs are studied by means of eight-band k.p theory. Experimental results are interpreted in detail using the theoretical results. The k.p model for the QD electronicstructure calculations accounts for strain, piezo- and pyroelectric effects, spin-orbit and crystal-field splitting, and is implemented for arbitrarily shaped QDs on a finite differences grid. Few-particle corrections are included using the self-consistent Hartree method. Band parameters for the wurtzite and zinc-blende phases of GaN, AlN, and InN are derived from first-principle G{sub 0}W{sub 0} band-structure calculations. Reliable values are also provided for parameters that have not been determined experimentally yet. The electronic properties of nitride QDs are dominated by the large built-in piezo- and pyroelectric fields, which lead to a pronounced red-shift of excitonic transition energies and extremely long radiative lifetimes in large GaN/AlN QDs. In In{sub x}Ga{sub 1-x}N/GaN QDs these fields induce a pronounced dependence of the radiative excitonic lifetimes on the exact QD shape and composition. It is demonstrated that the resulting variations of the radiative lifetimes in an inhomogeneous QD ensemble are the origin of the multi-exponential luminescence decay frequently observed in time-resolved ensemble measurements on In{sub x}Ga{sub 1-x}N/GaN QDs. A polarization mechanism in nitride QDs based on strain-induced valence-band mixing effects is discovered. Due to the valence-band structure of wurtzite group-III nitrides and the specific strain situation in c-plane QDs, the confined hole states are formed predominantly by the two highest valence bands. In particular, the hole ground state (h{sub 0} {identical_to} h{sub A}) is formed by the A band, and the first excited hole state (h{sub 1} {identical_to} h{sub B}) by the B band. It is shown that the interband transitions involving h{sub A} or h

  11. Neutrino-nucleus reactions based on recent structure studies

    Energy Technology Data Exchange (ETDEWEB)

    Suzuki, Toshio [Department of Physics and Graduate School of Integrated Basic Sciences, College of Humanities and Sciences, Nihon University, Sakurajosui 3-25-40, Setagaya-ku, Tokyo 156-8550 (Japan); National Astronomical Observatory of Japan, Mitaka, Tokyo 181-8588 (Japan)


    Neutrino-nucleus reactions are studied with the use of new shell model Hamiltonians, which have proper tensor components in the interactions and prove to be successful in the description of Gamow-Teller (GT) strengths in nuclei. The new Hamiltonians are applied to obtain new neutrino-nucleus reaction cross sections in {sup 12}C, {sup 13}C, {sup 56}Fe and {sup 56}Ni induced by solar and supernova neutrinos. The element synthesis by neutrino processes in supernova explosions is discussed with the new cross sections. The enhancement of the production yields of {sup 7}Li, {sup 11}B and {sup 55}Mn is obtained while fragmented GT strength in {sup 56}Ni with two-peak structure is found to result in smaller e-capture rates at stellar environments. The monopole-based universal interaction with tensor force of π+ρ meson exchanges is used to evaluate GT strength in {sup 40}Ar and ν-induced reactions on {sup 40}Ar. It is found to reproduce well the experimental GT strength in {sup 40}Ar.

  12. Image Registration Based on Autocorrelation of Local Structure. (United States)

    Li, Zhang; Mahapatra, Dwarikanath; Tielbeek, Jeroen A W; Stoker, Jaap; van Vliet, Lucas J; Vos, Frans M


    Registration of images in the presence of intra-image signal fluctuations is a challenging task. The definition of an appropriate objective function measuring the similarity between the images is crucial for accurate registration. This paper introduces an objective function that embeds local phase features derived from the monogenic signal in the modality independent neighborhood descriptor (MIND). The image similarity relies on the autocorrelation of local structure (ALOST) which has two important properties: 1) low sensitivity to space-variant intensity distortions (e.g., differences in contrast enhancement in MRI); 2) high distinctiveness for 'salient' image features such as edges. The ALOST method is quantitatively compared to the MIND approach based on three different datasets: thoracic CT images, synthetic and real abdominal MR images. The proposed method outperformed the NMI and MIND similarity measures on these three datasets. The registration of dynamic contrast enhanced and post-contrast MR images of patients with Crohn's disease led to relative contrast enhancement measures with the highest correlation (r=0.56) to the Crohn's disease endoscopic index of severity.

  13. An ISVD-based Euclidian structure from motion for smartphones (United States)

    Masiero, A.; Guarnieri, A.; Vettore, A.; Pirotti, F.


    The development of Mobile Mapping systems over the last decades allowed to quickly collect georeferenced spatial measurements by means of sensors mounted on mobile vehicles. Despite the large number of applications that can potentially take advantage of such systems, because of their cost their use is currently typically limited to certain specialized organizations, companies, and Universities. However, the recent worldwide diffusion of powerful mobile devices typically embedded with GPS, Inertial Navigation System (INS), and imaging sensors is enabling the development of small and compact mobile mapping systems. More specifically, this paper considers the development of a 3D reconstruction system based on photogrammetry methods for smartphones (or other similar mobile devices). The limited computational resources available in such systems and the users' request for real time reconstructions impose very stringent requirements on the computational burden of the 3D reconstruction procedure. This work takes advantage of certain recently developed mathematical tools (incremental singular value decomposition) and of photogrammetry techniques (structure from motion, Tomasi-Kanade factorization) to access very computationally efficient Euclidian 3D reconstruction of the scene. Furthermore, thanks to the presence of instrumentation for localization embedded in the device, the obtained 3D reconstruction can be properly georeferenced.

  14. Molecular Docking and Structure-Based Drug Design Strategies

    Directory of Open Access Journals (Sweden)

    Leonardo G. Ferreira


    Full Text Available Pharmaceutical research has successfully incorporated a wealth of molecular modeling methods, within a variety of drug discovery programs, to study complex biological and chemical systems. The integration of computational and experimental strategies has been of great value in the identification and development of novel promising compounds. Broadly used in modern drug design, molecular docking methods explore the ligand conformations adopted within the binding sites of macromolecular targets. This approach also estimates the ligand-receptor binding free energy by evaluating critical phenomena involved in the intermolecular recognition process. Today, as a variety of docking algorithms are available, an understanding of the advantages and limitations of each method is of fundamental importance in the development of effective strategies and the generation of relevant results. The purpose of this review is to examine current molecular docking strategies used in drug discovery and medicinal chemistry, exploring the advances in the field and the role played by the integration of structure- and ligand-based methods.

  15. Broadband polarization-insensitive absorber based on gradient structure metamaterial (United States)

    Yang, Guo-Hui; Liu, Xiao-Xin; Lv, Yue-Long; Fu, Jia-Hui; Wu, Qun; Gu, Xuemai


    Metamaterial absorber (MA) is a hot spot in the research on electromagnetic absorbers. In this paper, a metamaterial based broadband polarization-insensitive absorber is proposed. The absorber is fabricated with FR-4 dielectric substrate foiled with copper. The top layer of the unit cell of the MA is composed of resistors mounted crosswire and gradient split ring resonator (SRR) with a square metal patch (SMP) in it. The overall structure is symmetrical, which makes the MA polarization-insensitive. The gradient SRRs and SMPs resonate at adjacent frequencies resulting in broadband property. The absorption rates of the MA for TE and TM wave are calculated through the simulated S-parameters. The bandwidth is 9.9 GHz, where the absorption rate maintains 60% up to 98.28% in both cases and the relative bandwidth is 57.13%. Both broadband and polarization-insensitivity properties are achieved, which demonstrate promising application prospect of the proposed MA in shielding and stealth technology.

  16. Integrated photonic filters based on SiC multilayer structures

    Energy Technology Data Exchange (ETDEWEB)

    Vieira, M.A., E-mail: [Electronics Telecommunication and Computer Dept. ISEL, R. Conselheiro Emídio Navarro, 1949-014, Lisboa (Portugal); CTS-UNINOVA, Quinta da Torre, Monte da Caparica, 2829-516, Caparica (Portugal); Vieira, M. [Electronics Telecommunication and Computer Dept. ISEL, R. Conselheiro Emídio Navarro, 1949-014, Lisboa (Portugal); CTS-UNINOVA, Quinta da Torre, Monte da Caparica, 2829-516, Caparica (Portugal); DEE-FCT-UNL, Quinta da Torre, Monte da Caparica, 2829-516, Caparica (Portugal); Louro, P.; Silva, V.; Fantoni, A. [Electronics Telecommunication and Computer Dept. ISEL, R. Conselheiro Emídio Navarro, 1949-014, Lisboa (Portugal); CTS-UNINOVA, Quinta da Torre, Monte da Caparica, 2829-516, Caparica (Portugal)


    Combined tunable WDM converters based on SiC multilayer photonic active filters are analyzed. The operation combines the properties of active long-pass and short-pass wavelength filter sections into a capacitive active band-pass filter. The sensor element is a multilayered heterostructure produced by PE-CVD. The configuration includes two stacked SiC p–i–n structures sandwiched between two transparent contacts. Transfer function characteristics are studied both theoretically and experimentally. Results show that optical bias activated photonic device combines the demultiplexing operation with the simultaneous photodetection and self amplification of an optical signal acting the device as an integrated photonic filter in the visible range. Depending on the wavelength of the external background and irradiation side, the device acts either as a short- or a long-pass band filter or as a band-stop filter. The output waveform presents a nonlinear amplitude-dependent response to the wavelengths of the input channels. A numerical simulation and a two building-blocks active circuit are presented and give insight into the physics of the device.

  17. Lab-scale periphyton-based system for fish culture Sistema laboratorial baseado em perifíton para piscicultura

    Directory of Open Access Journals (Sweden)

    Davi de Holanda Cavalcante


    Full Text Available The present research aimed to assess a lab-scale model to study periphyton-based systems for fish culture. Twenty-five liters plastic aquaria were stocked with three Nile tilapia, Oreochromis niloticus, juveniles (0.77±0.09g; 12 fish m-2 for 6 weeks in a 2x2 factorial design. Small plastic bottles were placed in some aquaria for periphyton development. Two feeding regimes were employed: "full-fed" (standard feeding rates were fully adopted and "half-fed" (50% of standard feeding rates. Growth performance and limnological variables were observed in each aquarium. There werefive replicates per treatment. Fish have fed actively on periphyton, especially in the half-fed aquaria. The placement of periphyton bottles had no significant effects on the water quality variables, except by the gross primary productivity which became lower. Half-fed aquaria presented lower concentrations of ammonia (0.28-0.29mg L-1, nitrite (0.33-0.37mg L-1 and phosphorus (0.42-0.43mg L-1 than full-fed aquaria (0.57-0.60mg L-1; 0.75-0.77mg L-1; 0.67-0.70mg L-1, respectively. The final body weight of fish in half-fed aquaria with periphyton bottles (6.22±0.64g was significantly higher than in aquaria without bottles (4.65±0.36g. Although the growth rate of fish was lower in the half-fed aquaria (4.27-4.72 vs. 5.29-5.61% BW day-1, survival was significantly higher when compared to the full-fed aquaria (93.3-100.0 vs. 80.0-83.4%. Only in the aquaria with periphyton the feed conversation ratio was improved by the feeding restriction regime.O presente trabalho teve como objetivo avaliar um modelo laboratorial para estudo de sistemas de cultivo de peixes baseados em perifíton. Aquários de 25L foram estocados com três juvenis de tilápia do Nilo, Oreochromis niloticus (0,77±0,09g; 12 peixes m-2 por seis semanas, em arranjo fatorial 2x2. Pequenas garrafas plásticas foram colocadas em determinados aquários para o desenvolvimento de perifíton. Dois regimes alimentares foram

  18. Identification and Determination of <em>Aconitum> Alkaloids in <em>Aconitum> Herbs and <em>Xiaohuoluo Pillem> Using UPLC-ESI-MS

    Directory of Open Access Journals (Sweden)

    Li Yang


    Full Text Available A rapid, specific, and sensitive ultra-performance liquid chromatography-electrospray ionization-mass spectrometry (UPLC-ESI-MS method to examine the chemical differences between <em>Aconitum> herbs and processed products has been developed and validated. Combined with chemometrics analysis of principal component analysis (PCA and orthogonal projection to latent structural discriminate analysis, diester-diterpenoid and monoester-type alkaloids, especially the five alkaloids which contributed to the chemical distinction between <em>Aconitum> herbs and processed products, namely mesaconitine (MA, aconitine (AC, hypaconitine (HA, benzoylmesaconitine (BMA, and benzoylhypaconitine (BHA, were picked out. Further, the five alkaloids and benzoylaconitine (BAC have been simultaneously determined in the <em>Xiaohuoluo pillem>. Chromatographic separations were achieved on a C18 column and peaks were detected by mass spectrometry in positive ion mode and selected ion recording (SIR mode. In quantitative analysis, the six alkaloids showed good regression, (<em>r> > 0.9984, within the test ranges. The lower limit quantifications (LLOQs for MA, AC, HA, BMA, BAC, and BHA were 1.41, 1.20, 1.92, 4.28, 1.99 and 2.02 ng·mL−1, respectively. Recoveries ranged from 99.7% to 101.7%. The validated method was applied successfully in the analysis of the six alkaloids from different samples, in which significant variations were revealed. Results indicated that the developed assay can be used as an appropriate quality control assay for <em>Xiaohuoluo pillem> and other herbal preparations containing <em>Aconitum> roots.

  19. Intervenção educacional com base em modelo para aumentar a atividade física entre adolescentes iranianos

    Directory of Open Access Journals (Sweden)

    Hormoz Sanaeinasab


    Full Text Available OBJETIVO: Avaliar um programa educacional com base no modelo de promoção da saúde (MPS e nos estágios de mudança para melhorar a atividade física (AF entre adolescentes iranianos. MÉTODOS: Este foi um ensaio randomizado controlado com 165 participantes divididos em dois grupos (intervenção/controle. Os dados foram coletados através de questionários de autopreenchimento com base em componentes do MPS (benefícios e barreiras para a ação, autoeficácia, sentimentos em relação ao comportamento, influências interpessoais e situacionais. A escala de estágios de mudança foi utilizada para selecionar participantes aptos (classificados nos estágios de pré-contemplação, contemplação ou preparação e para avaliar a tendência. Após a coleta dos dados de base, a intervenção foi realizada nos participantes e os dados de acompanhamento foram coletados 3 meses depois. RESULTADOS: Ao todo, 88 meninos e 77 meninas com idade média de 13,99±0,4 participaram do estudo. As diferenças em todos os componentes do MPS, exceto os sentimentos em relação ao comportamento e as influências sociais, foram significantes (p < 0,01 entre os valores de base e de acompanhamento. Comparados aos do grupo de controle, os adolescentes do grupo de intervenção foram categorizados nos estágios de ação (70% ou preparação (30% no acompanhamento. A análise de regressão múltipla revelou que preferências concorrentes, normas sociais, modelos sociais (variáveis com p < 0,001 e o compromisso com o plano de ação podem prever consideravelmente o comportamento quanto à AF. O modelo representou 22,5% da variação da AF. CONCLUSÕES: Intervenções educacionais com base nos estágios de mudança podem ter implicações importantes na melhora da AF entre adolescentes em mais componentes do MPS.

  20. Estrutura fatorial da Stages of Change Readiness and Treatment Eagerness Scale (SOCRATES em dependentes de álcool tratados ambulatorialmente Factor structure of the Stages of Change Readiness and Treatment Eagerness Scale (SOCRATES in alcohol dependent outpatients

    Directory of Open Access Journals (Sweden)

    Neliana Buzi Figlie


    Full Text Available OBJETIVO: O objetivo deste estudo foi o de investigar a confiabilidade e a estrutura fatorial da Stages of Change Readiness and Treatment Eagerness Scale (SOCRATES, versão 8,¹ instrumento com 19 itens que mensura a prontidão para a mudança em dependentes de álcool. MÉTODOS: Uma análise fatorial confirmatória da SOCRATES foi realizada em uma amostra de 326 dependentes de álcool, tratados ambulatorialmente, tendo como base a estrutura fatorial demonstrada por Miller & Tonigan² e Maisto et al.³ O questionário foi traduzido e adaptado culturalmente para o idioma português, sendo posteriormente submetido ao procedimento da retradução para o idioma inglês. Durante esse procedimento, foram realizadas algumas modificações, visando a simplificar alguns itens que apresentaram formato complexo. RESULTADOS: As análises estatísticas mostraram a existência de dois fatores correlacionados que melhor exploraram o modelo, sendo este achado similar ao estudo de Maisto et al.³ CONCLUSÕES: Foi constatada menor evidência para o modelo de três fatores. Esses resultados são comparados com estudos prévios e as discrepâncias são discutidas neste artigo.OBJECTIVE: The aim of this study was to investigate the reliability and factor structure of the Stages of Change Readiness and Treatment Eagerness Scale (SOCRATES, version 8,¹ a 19-item self-reported instrument developed to measure readiness to change in alcohol-dependent alcoholics. METHODS: A Confirmatory Factor analysis of the SOCRATES was performed based on the factor structures previously demonstrated by Miller & Tonigan² and Maisto et al.³ in a sample with 326 alcohol-dependent outpatients. The questionnaire was translated into Portuguese, cross-culturally adapted and back-translated into English. During this process SOCRATES underwent some modifications to simplify some complex question formats. RESULTS: The analysis showed that two correlated factors provided the best fit for the

  1. Pulsed EM Field Response of a Thin, High-Contrast, Finely Layered Structure With Dielectric and Conductive Properties

    NARCIS (Netherlands)

    De Hoop, A.T.; Jiang, L.


    The response of a thin, high-contrast, finely layered structure with dielectric and conductive properties to an incident, pulsed, electromagnetic field is investigated theoretically. The fine layering causes the standard spatial discretization techniques to solve Maxwell's equations numerically to

  2. O que é emoção? em busca da organização estrutural do conceito de emoção em crianças What is emotion? searching the organizational structure of children's concept of emotion

    Directory of Open Access Journals (Sweden)

    Antonio Roazzi


    tipo modular.The main aim of this study was to investigate the structural organization of the semantic concept of emotion in children based on an emic perspective. A free word association (emotion and two questions (frequency of emotions and what they knew about emotions was applied to a sample of 247 children aged 7-12 from public and private schools in Brazil. The question concerning what they knew about emotions indicated that most children link emotions to feelings, things their heart feels. Participants also gave examples of positive and negative experiences, specifying certain emotions, mainly emotions classified as primary by researchers in this field. Regarding the question about the frequency of those emotions in their lives, they pointed out joy, happiness and sadness as being the emotions frequently experienced on their daily lives. On the free word association primary emotions predominated being joy the most frequent one, followed by sadness, happiness, anger, fear and love. We also encountered more elaborate emotions (secondary emotions such as missing someone, hatred, peace, and anxiety, among others. In order to verify the structural organization of their semantic conceptual field, we analyzed the categories that participants emitted on the free association task by means of Structural Similarity Analysis (SSA. A method of "external variables as points" was applied with the intention of verifying the relation between the structure created from the semantic field and the variables of age, sex and type of school. Multiple regressions were also computed. It was found that the type of school and, especially, age played a relevant role in predicting the structural organization of emotions, i.e. an ordered modular structure.

  3. Efeito hipoglicêmico de rações à base de berinjela (Solanum melongena,L. em ratos

    Directory of Open Access Journals (Sweden)

    Derivi Sandra Casa Nova


    Full Text Available Os objetivos do presente trabalho foram verificar se dietas ricas em berinjela apresentam efeito hipoglicêmico, se contribuem para o retardamento de absorção da glicose pós-prandial e se a fração fibra solúvel está correlacionada com estes efeitos. Os experimentos foram realizados com ratos Wistar machos adultos, normais e diabéticos, que receberam rações à base de caseína, berinjela com casca e sem casca, e de casca de berinjela por um período de 42 dias. A glicose sangüínea foi determinada no início do experimento e aos 13, 21, 34 e 42 dias. Os testes orais de tolerância à glicose (TOTG foram realizados no final do experimento. Os resultados mostraram que as rações à base de farinha de berinjela com casca e de casca de berinjela apresentaram redução nos níveis de glicose. Este efeito não foi significativo para a ração à base de farinha de berinjela sem casca. Os animais do grupo diabético que receberam ração à base de berinjela com casca apresentaram menor área sob a curva de glicose, do que os dos grupos controle (ração à base de caseína e de berinjela com casca e do que o do grupo diabético que recebeu a ração de caseína. Este efeito não foi observado nos animais que receberam ração à base de berinjela sem casca e casca de berinjela. Estes resultados indicam a presença de um composto responsável pelo efeito hipoglicêmico na casca de berinjela e que a pectina solúvel da ração não foi suficiente para promover tal efeito, mas que a administração contínua de pectina solúvel contribuiu para a melhora da TOTG.



    Lima, Cristiano de; Faculdades Integradas Machado de Assis; Fagundes, Jair Antonio; Silva, Júnior Rogério da; Universidade Federal de Santa Maria - UFSM; Santana, Alex Fabiano Bertollo; ULBRA - Ji-Paraná; Soler, Cristina Crespo; Profesora do PPG em contabilidad de la Universidad de Valencia - España


    It has as main objective of this study is to analyze the contingency variables structure, environment and management indicators of a company's logistics operations, based on contingency theory and the Balanced Scorecard (BSC). To study this unique case, the data were collected through semi-structured interviews, which were based on previous studies on the theory and also contingent on the BSC with the director of costs (supervisor southern) and unit administrator. With a few quirks, like the ...

  5. Development and application of the ultrasonic techniques based in EM AT technology for NDT pipe inspection

    Energy Technology Data Exchange (ETDEWEB)

    Armador Sillero, J.; Calas del Castillo, H. M.; Fernandez, F.J.


    The objective of pipe inspectionsis to detect and evaluate the evolution of the damage caused by degradation phenomena like Erosion/Corrosion and Microbiogically Induced Corrosion (MIC). The technology of Ultrasonic generated by EMAT (ElectroMagnetic Acoustic Transducers) allows the inspection without direct contact with the component. It is possible perform the inspection without couplant, reduces the influence of the component surface and allows to increase the inspection velocity. It is wanted apply a new inspection technique based in EMAT to follow this phenomena to verify the integrity of the components and check if it satisfy the work conditions. (Author)

  6. An EM simulation based design flow for custom-built MR coils incorporating signal and noise. (United States)

    Horneff, Andreas; Eder, Michael; Hell, Erich; Ulrici, Johannes; Felder, Jorg; Rasche, Volker; Anders, Jens


    Developing custom-built MR coils is a cumbersome task, in which an a priori prediction of the coils' SNR performance, their sensitivity pattern and their depth of penetration helps to greatly speed up the design process by reducing the required hardware manufacturing iterations. The simulationbased design flow presented in this paper takes the entire MR imaging process into account. That is, it includes all geometric and material properties of the coil and the phantom, the thermal noise as well as the target MR sequences. The proposed simulation-driven design flow is validated using a manufactured prototype coil, whose performance was optimized regarding its SNR performance, based on the presented design flow, by comparing the coil's measured performance against the simulated results. In these experiments, the mean and the standard deviation of the relative error between the simulated and measured coil sensitivity pattern were found to be μ = 1.79% and σ = 3.15%. Moreover, the peak deviation between the simulated and measured voxel SNR was found to be less than 4%, indicating that simulations are in good accordance with the measured results, validating the proposed software-based design approach.Developing custom-built MR coils is a cumbersome task, in which an a priori prediction of the coils' SNR performance, their sensitivity pattern and their depth of penetration helps to greatly speed up the design process by reducing the required hardware manufacturing iterations. The simulationbased design flow presented in this paper takes the entire MR imaging process into account. That is, it includes all geometric and material properties of the coil and the phantom, the thermal noise as well as the target MR sequences. The proposed simulation-driven design flow is validated using a manufactured prototype coil, whose performance was optimized regarding its SNR performance, based on the presented design flow, by comparing the coil's measured performance against the

  7. Introgression Between Cultivars and Wild Populations of<em> Momordica charantiaem> L. (Cucurbitaceae in Taiwan

    Directory of Open Access Journals (Sweden)

    Yu-Chung Chiang


    Full Text Available The landrace strains of <em>Momordica charantia em>are widely cultivated vegetables throughout the tropics and subtropics, but not in Taiwan, a continental island in Southeast Asia, until a few hundred years ago. In contrast, the related wild populations with smaller fruit sizes are native to Taiwan. Because of the introduction of cultivars for agricultural purposes, these two accessions currently exhibit a sympatric or parapatric distribution in Taiwan. In this study, the cultivars<em> em>and wild samples from Taiwan, India, and Korea<em> em>were collected for testing of their hybridization and evolutionary patterns. The cpDNA marker showed a clear distinction between accessions of cultivars and wild populations of Taiwan and a long divergence time. In contrast, an analysis of eight selectively neutral nuclear microsatellite loci did not reveal a difference between the genetic structures of these two accessions. A relatively short divergence time and frequent but asymmetric gene flows were estimated based on the isolation-with-migration model. Historical and current introgression from cultivars to wild populations of Taiwan was also inferred using MIGRATE-n and BayesAss analyses. Our results showed that these two accessions shared abundant common ancestral polymorphisms, and the timing of the divergence and colonization of the Taiwanese wild populations is consistent with the geohistory of the Taiwan Strait land bridge of the Last Glacial Maximum (LGM. Long-term and recurrent introgression between accessions indicated the asymmetric capacity to receive foreign genes from other accessions. The modern introduction of cultivars of <em>M>. <em>charantia> during the colonization of Taiwan by the Han Chinese ethnic group enhanced the rate of gene replacement in the native populations and resulted in the loss of native genes.

  8. Structure-based inference of molecular functions of proteins of unknown function from Berkeley Structural Genomics Center. (United States)

    Shin, Dong Hae; Hou, Jingtong; Chandonia, John-Marc; Das, Debanu; Choi, In-Geol; Kim, Rosalind; Kim, Sung-Hou


    Advances in sequence genomics have resulted in an accumulation of a huge number of protein sequences derived from genome sequences. However, the functions of a large portion of them cannot be inferred based on the current methods of sequence homology detection to proteins of known functions. Three-dimensional structure can have an important impact in providing inference of molecular function (physical and chemical function) of a protein of unknown function. Structural genomics centers worldwide have been determining many 3-D structures of the proteins of unknown functions, and possible molecular functions of them have been inferred based on their structures. Combined with bioinformatics and enzymatic assay tools, the successful acceleration of the process of protein structure determination through high throughput pipelines enables the rapid functional annotation of a large fraction of hypothetical proteins. We present a brief summary of the process we used at the Berkeley Structural Genomics Center to infer molecular functions of proteins of unknown function.

  9. Structure-based inference of molecular functions of proteins of unknown function from Berkeley Structural Genomics Center

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Sung-Hou; Shin, Dong Hae; Hou, Jingtong; Chandonia, John-Marc; Das, Debanu; Choi, In-Geol; Kim, Rosalind; Kim, Sung-Hou


    Advances in sequence genomics have resulted in an accumulation of a huge number of protein sequences derived from genome sequences. However, the functions of a large portion of them cannot be inferred based on the current methods of sequence homology detection to proteins of known functions. Three-dimensional structure can have an important impact in providing inference of molecular function (physical and chemical function) of a protein of unknown function. Structural genomics centers worldwide have been determining many 3-D structures of the proteins of unknown functions, and possible molecular functions of them have been inferred based on their structures. Combined with bioinformatics and enzymatic assay tools, the successful acceleration of the process of protein structure determination through high throughput pipelines enables the rapid functional annotation of a large fraction of hypothetical proteins. We present a brief summary of the process we used at the Berkeley Structural Genomics Center to infer molecular functions of proteins of unknown function.

  10. Single-step antibody-based affinity cryo-electron microscopy for imaging and structural analysis of macromolecular assemblies. (United States)

    Yu, Guimei; Vago, Frank; Zhang, Dongsheng; Snyder, Jonathan E; Yan, Rui; Zhang, Ci; Benjamin, Christopher; Jiang, Xi; Kuhn, Richard J; Serwer, Philip; Thompson, David H; Jiang, Wen


    Single particle cryo-electron microscopy (cryo-EM) is an emerging powerful tool for structural studies of macromolecular assemblies (i.e., protein complexes and viruses). Although single particle cryo-EM requires less concentrated and smaller amounts of samples than X-ray crystallography, it remains challenging to study specimens that are low-abundance, low-yield, or short-lived. The recent development of affinity grid techniques can potentially further extend single particle cryo-EM to these challenging samples by combining sample purification and cryo-EM grid preparation into a single step. Here we report a new design of affinity cryo-EM approach, cryo-SPIEM, that applies a traditional pathogen diagnosis tool Solid Phase Immune Electron Microscopy (SPIEM) to the single particle cryo-EM method. This approach provides an alternative, largely simplified and easier to use affinity grid that directly works with most native macromolecular complexes with established antibodies, and enables cryo-EM studies of native samples directly from cell cultures. In the present work, we extensively tested the feasibility of cryo-SPIEM with multiple samples including those of high or low molecular weight, macromolecules with low or high symmetry, His-tagged or native particles, and high- or low-yield macromolecules. Results for all these samples (non-purified His-tagged bacteriophage T7, His-tagged Escherichiacoli ribosomes, native Sindbis virus, and purified but low-concentration native Tulane virus) demonstrated the capability of cryo-SPIEM approach in specifically trapping and concentrating target particles on TEM grids with minimal view constraints for cryo-EM imaging and determination of 3D structures. Copyright © 2014 Elsevier Inc. All rights reserved.

  11. New insights into Hoogsteen base pairs in DNA duplexes from a structure-based survey. (United States)

    Zhou, Huiqing; Hintze, Bradley J; Kimsey, Isaac J; Sathyamoorthy, Bharathwaj; Yang, Shan; Richardson, Jane S; Al-Hashimi, Hashim M


    Hoogsteen (HG) base pairs (bps) provide an alternative pairing geometry to Watson-Crick (WC) bps and can play unique functional roles in duplex DNA. Here, we use structural features unique to HG bps (syn purine base, HG hydrogen bonds and constricted C1'-C1' distance across the bp) to search for HG bps in X-ray structures of DNA duplexes in the Protein Data Bank. The survey identifies 106 A•T and 34 G•C HG bps in DNA duplexes, many of which are undocumented in the literature. It also uncovers HG-like bps with syn purines lacking HG hydrogen bonds or constricted C1'-C1' distances that are analogous to conformations that have been proposed to populate the WC-to-HG transition pathway. The survey reveals HG preferences similar to those observed for transient HG bps in solution by nuclear magnetic resonance, including stronger preferences for A•T versus G•C bps, TA versus GG steps, and also suggests enrichment at terminal ends with a preference for 5'-purine. HG bps induce small local perturbations in neighboring bps and, surprisingly, a small but significant degree of DNA bending (∼14°) directed toward the major groove. The survey provides insights into the preferences and structural consequences of HG bps in duplex DNA. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  12. Crystallation, X-Ray Structure Determination and Structure-Based Drug Design for Targeted Malarial Enzymes

    National Research Council Canada - National Science Library

    DeLucas, Lawrence


    .... This structure is currently being used for designing lead inhibitors. We have also purified PFPK-DHPS bifunctional enzyme for structure analysis and are presently screening for crystallization conditions...

  13. Agricultura orgânica em áreas urbanas e periurbanas com base na agroecologia Challenges of organic agriculture in urban and suburban areas

    Directory of Open Access Journals (Sweden)

    Adriana Maria de Aquino


    Full Text Available A agricultura orgânica com base na agroecologia é o mote tecnológico adequado à realidade dos agroecossistemas urbanos. Este artigo ressalta a necessidade de se desenvolver tecnologias e insumos específicos. A partir de experiências com agricultura urbana em diferentes países em desenvolvimento, evidencia-se a necessidade de se buscar capacidades locais e apoio do poder público, especialmente nas iniciativas da sociedade organizada e mobilizada para a produção agrícola urbana.This article presents organic agriculture, based on agroecology, as the appropriate technology for the urban agro-ecosystem. It also points out the need for appropriate technologies and amendments development. Looking at experiences with urban agriculture in development countries, it shows the need for local capacity development and a search for the public sector support, specially of organized groups mobilized for urban agriculture production.

  14. Estrutura do capim-braquiária em relação à planta daninha = Structure of signalgrass in relation to weeds

    Directory of Open Access Journals (Sweden)

    Manoel Eduardo Rozalino Santos


    Full Text Available O objetivo foi avaliar as características estruturais da Brachiaria decumbens cv. Basilisk em relação à planta daninha Solanum sisymbrifolium no pasto. Os tratamentos foram dois locais no mesmo pasto, quais sejam, próximo e distante da planta daninha. O delineamento foi em blocos ao acaso com três repetições. O pasto foi manejado sob lotação contínua, com bovinos e com altura média de aproximadamente 25 cm. Foram quantificadas as densidades populacionais das categorias de tamanho dos perfilhos, a altura, a interceptação de luz, as massas e as densidades volumétricas dos componentes morfológicos do pasto. No local distante da planta daninha houve maior ocorrência de perfilhos com tamanho inferior a 20 cm. Já no local próximo da planta daninha, predominaram perfilhos com tamanho superior a 40 cm. A presença da planta daninha ocasionou aumento na altura do pasto e incremento na interceptação de luz pelo dossel. As massas e as densidades volumétricas de lâmina foliar viva, colmo vivo e material morto foram inferiores no local próximo da planta daninha em relação ao local distante. A ocorrência da planta S. sisymbrifolium provoca variabilidade espacial da vegetação no pasto de B. decumbens manejado sob lotação contínua com bovinos.The objective of this study was to evaluate the structural characteristics of Brachiaria decumbens cv. Basilisk in relation toSolanum sisymbrifolium in pasture. The treatments were two sites in the same pasture, near and far from the weeds. A randomized block design with three replications was used. The pasture was managed under continuous stocking and grass height was kept at about 25cm.Densities were quantified for categories tiller size, height, light interception, masses and volumetric densities of morphological components of the pasture. In the site far from the weeds there is a higher occurrence of tillers with size smaller than 20 cm. In site near the weeds, tillers larger than 40 cm

  15. Obtaining solid electrolytes based on zirconium oxide; Obtencao de eletrolitos solidos baseados em oxido de zirconio

    Energy Technology Data Exchange (ETDEWEB)

    Cajas, P.C.; Munoz, R.; Silva, C.R.M da, E-mail: [Universidade de Brasilia (UnB), Brasilia, DF (Brazil)


    Ceramic materials based on zirconia were synthesized by the controlled precipitation method, ZrO{sub 2}: 3% molY{sub 2}O{sub 3}: η mol% Y{sub 2}O{sub 3} (η = 3,4,5), using commercial zirconia, TZ-3YB-E, and a concentrate of mixed rare earth oxides. The powder samples were thermally treated at 600 ° C (2h) to remove unwanted carbonates formed in the synthesis process, and then subjected to milling using attrition mill and finally compacted by uniaxial pressing and sintered at 1500 ° C (2h). The densities were analyzed by the Archimedes method, obtaining results higher than 96% of theoretical. Using XRD and Rietveld refinements, the phases present in the samples were known qualitatively and quantitatively, observing a mixture of the cubic and tetragonal phases. An improvement in the conductivity in the samples co-doped with complex impedance spectroscopy was determined.

  16. X-ray structure based evaluation of analogs of citalopram

    DEFF Research Database (Denmark)

    Topiol, Sid; Bang-Andersen, Benny; Sanchez, Connie


    The recent publication of X-ray structures of SERT includes structures with the potent antidepressant S-Citalopram (S-Cit). Earlier predictions of ligand binding at both a primary (S1) and an allosteric modulator site (S2), were confirmed. We provide herein examples of a series of Citalopram...... to explain this SAR and demonstrate the potential utility of the newly emerging X-ray structures within the neurotransmitter:sodium Symporter family for drug design....

  17. Trends in information theory-based chemical structure codification. (United States)

    Barigye, Stephen J; Marrero-Ponce, Yovani; Pérez-Giménez, Facundo; Bonchev, Danail


    This report offers a chronological review of the most relevant applications of information theory in the codification of chemical structure information, through the so-called information indices. Basically, these are derived from the analysis of the statistical patterns of molecular structure representations, which include primitive global chemical formulae, chemical graphs, or matrix representations. Finally, new approaches that attempt to go "back to the roots" of information theory, in order to integrate other information-theoretic measures in chemical structure coding are discussed.

  18. Metamaterial based embedded acoustic filters for structural applications

    Directory of Open Access Journals (Sweden)

    Hongfei Zhu


    Full Text Available We investigate the use of acoustic metamaterials to design structural materials with frequency selective characteristics. By exploiting the properties of acoustic metamaterials, we tailor the propagation characteristics of the host structure to effectively filter the constitutive harmonics of an incoming broadband excitation. The design approach exploits the characteristics of acoustic waveguides coupled by cavity modes. By properly designing the cavity we can tune the corresponding resonant mode and, therefore, coupling the waveguide at a prescribed frequency. This structural design can open new directions to develop broadband passive vibrations and noise control systems fully integrated in structural components.

  19. Knowledge-Based Conformer Generation Using the Cambridge Structural Database. (United States)

    Cole, Jason C; Korb, Oliver; McCabe, Patrick; Read, Murray; Taylor, Robin


    Fast generation of plausible molecular conformations is central to molecular modelling. This paper presents an approach to conformer generation that makes extensive use of the information available in the Cambridge Structural Database. By using geometric distributions derived from the Cambridge Structural Database, it is possible to create biologically relevant conformations in the majority of cases analysed. The paper compares the performance of the approach with previously published evaluations, and presents some cases where the method fails. The method appears to show significantly improved performance in reproduction of the conformations of structures observed in the Cambridge Structural Database and the Protein Data Bank as compared to other published methods of a similar speed.

  20. High-Throughput Sequencing Based Methods of RNA Structure Investigation

    DEFF Research Database (Denmark)

    Kielpinski, Lukasz Jan

    In this thesis we describe the development of four related methods for RNA structure probing that utilize massive parallel sequencing. Using them, we were able to gather structural data for multiple, long molecules simultaneously. First, we have established an easy to follow experimental and comp......In this thesis we describe the development of four related methods for RNA structure probing that utilize massive parallel sequencing. Using them, we were able to gather structural data for multiple, long molecules simultaneously. First, we have established an easy to follow experimental...... with known priming sites....