WorldWideScience

Sample records for unique structural information

  1. Fossil insects may provide unique information on structures and disturbances in past forest ecosystems - examples from Holocene studies in southern Sweden

    Science.gov (United States)

    Lemdahl, Geoffrey; Gustavsson, Gunnar; Olsson, Fredrik; Gaillard, Marie-José

    2010-05-01

    Insects are complex organisms that play an important role in all types of forest ecosystems. Insect remains are often abundant in waterlogged sediments and peat, and the majority of the fossils may be identified to species level, thus contributing with specific information. The occurrence of species feeding or confined to one or a few species of herbaceous plants, shrubs and trees may confirm or improve/refine the interpretations based on pollen and plant macrofossil analyses. Many insects, particularly ground living animals, select open, sun exposed habitats or closed shaded areas. Such indicators are valuable for reconstructions of forest/landscape openness. However, unique information can be provided by fossil insect assemblages. Insect studies carried out at two natural sites in southern Sweden with complete Holocene peat stratigraphies (Olsson and Lemdahl 2009) and a number of sites covering parts of the Holocene (e.g. Gaillard and Lemdahl 1994, Gustavsson et al. 2009) provide strong evidence on changes in forest structure and the occurrence and nature of disturbances. Studies in Britain have yielded similar results (e.g. Whitehouse 2006). Saproxylic beetles indicate the presence of dead wood, which clearly was a more prominent component in ancient woodlands than in present forests, and beetles confined to wood mould suggest the presence of large hollow trees. Finds of pyrophilic species, of which some are very rare in European woodlands today, together with layers of charcoal, suggest that fire was a major disturbance factor during most of the Holocene in southern Sweden. Whereas macroscopic charcoal fragments indicate local fires, the presence of pyrophilic insects is an indication of continuous fire activity at the regional spatial scale. Remains of dung beetles indicate extensive grazing by megaherbivores during early Holocene, and more intensive grazing during late Holocene, whereas such indicators are absent from mid Holocene records, which correlates

  2. Unique strategies for technical information management at Johnson Space Center

    Science.gov (United States)

    Krishen, Vijay

    1994-01-01

    In addition to the current NASA manned programs, the maturation of Space Station and the introduction of the Space Exploration programs are anticipated to add substantially to the number and variety of data and documentation at NASA Johnson Space Center (JSC). This growth in the next decade has been estimated at five to ten fold compared to the current numbers. There will be an increased requirement for the tracking and currency of space program data and documents with National pressures to realize economic benefits from the research and technological developments of space programs. From a global perspective the demand for NASA's technical data and documentation is anticipated to increase at local, national, and international levels. The primary users will be government, industry, and academia. In our present national strategy, NASA's research and technology will assume a great role in the revitalization of the economy and gaining international competitiveness. Thus, greater demand will be placed on NASA's data and documentation resources. In this paper the strategies and procedures developed by DDMS, Inc., to accommodate the present and future information utilization needs are presented. The DDMS, Inc., strategies and procedures rely on understanding user requirements, library management issues, and technological applications for acquiring, searching, storing, and retrieving specific information accurately and quickly. The proposed approach responds to changing customer requirements and product deliveries. The unique features of the proposed strategy include: (1) To establish customer driven data and documentation management through an innovative and unique methods to identify needs and requirements. (2) To implement a structured process which responds to user needs, aimed at minimizing costs and maximizing services, resulting in increased productivity. (3) To provide a process of standardization of services and procedures. This standardization is the central

  3. Deciphering the structure of isomeric oligosaccharides in a complex mixture by tandem mass spectrometry: Photon activation with vacuum ultra-violet brings unique information and enables definitive structure assignment

    Energy Technology Data Exchange (ETDEWEB)

    Ropartz, David, E-mail: David.Ropartz@nantes.inra.fr [INRA, UR1268 Biopolymers Interactions Assemblies, F-44316 Nantes (France); Lemoine, Jérôme [Institut des Sciences Analytiques, UMR 5280, Université Lyon 1-CNRS, Université de Lyon, F-69622 Villeurbanne cedex (France); Giuliani, Alexandre [Synchrotron SOLEIL, L’Orme des Merisiers, F-91190 Gif-sur-Yvette (France); UAR 1008 CEPIA, INRA, F-44316 Nantes (France); Bittebière, Yann [INRA, UR1268 Biopolymers Interactions Assemblies, F-44316 Nantes (France); Enjalbert, Quentin [Institut des Sciences Analytiques, UMR 5280, Université Lyon 1-CNRS, Université de Lyon, F-69622 Villeurbanne cedex (France); Institut Lumière Matière, UMR5306, Université Lyon 1-CNRS, Université de Lyon, F-69622 Villeurbanne cedex (France); Antoine, Rodolphe; Dugourd, Philippe [Institut Lumière Matière, UMR5306, Université Lyon 1-CNRS, Université de Lyon, F-69622 Villeurbanne cedex (France); Ralet, Marie-Christine; Rogniaux, Hélène [INRA, UR1268 Biopolymers Interactions Assemblies, F-44316 Nantes (France)

    2014-01-07

    Graphical abstract: -- Highlights: •A complex mixture of methylated oligogalacturonans was fractionated by IP-RP-UHPLC. •Synchrotron-radiation in VUV range was used as an activation process for tandem MS. •VUV activation brought rich structural information compared to LE-CAD. •Resolution of more than 35 structures, including isomers, was successfully completed. -- Abstract: Carbohydrates have a wide variety of structures whose complexity and heterogeneity challenge the field of analytical chemistry. Tandem mass spectrometry, with its remarkable sensitivity and high information content, provides key advantages to addressing the structural elucidation of polysaccharides. Yet, classical fragmentation by collision-activated dissociation (CAD) in many cases fails to reach a comprehensive structural determination, especially when isomers have to be differentiated. In this work, for the first time, vacuum ultra-violet (VUV) synchrotron radiation is used as the activation process in tandem mass spectrometry of large oligosaccharides. Compared to low energy CAD (LE-CAD), photon activated dissociation brought more straightforward and valuable structural information. The outstanding feature was that complete series of informative ions were produced, with only minor neutral losses. Moreover, systematic fragmentation rules could be drawn thus facilitating the definitive assignments of fragment identities. As a result, most of the structures present in a complex mixture of oligogalacturonans could be comprehensively resolved, including many isomers differing in the position of methyl groups along the galacturonic acid backbone.

  4. Affective and cognitive meta-bases of attitudes: Unique effects on information interest and persuasion.

    Science.gov (United States)

    See, Ya Hui Michelle; Petty, Richard E; Fabrigar, Leandre R

    2008-06-01

    The authors investigated the predictive utility of people's subjective assessments of whether their evaluations are affect- or cognition driven (i.e., meta-cognitive bases) as separate from whether people's attitudes are actually affect- or cognition based (i.e., structural bases). Study 1 demonstrated that meta-bases uniquely predict interest in affective versus cognitive information above and beyond structural bases and other related variables (i.e., need for cognition and need for affect). In Study 2, meta-bases were shown to account for unique variance in attitude change as a function of appeal type. Finally, Study 3 showed that as people became more deliberative in their judgments, meta-bases increased in predictive utility, and structural bases decreased in predictive utility. These findings support the existence of meta-bases of attitudes and demonstrate that meta-bases are distinguishable from structural bases in their predictive utility. (PsycINFO Database Record (c) 2008 APA, all rights reserved).

  5. 77 FR 57055 - Agency Information Collection Activities; Proposed Collection; Unique Device Identification...

    Science.gov (United States)

    2012-09-17

    ... PRA) associated with the proposed rule, Unique Device Identification System, that appeared in the... 830 RIN 0910-AG31 Agency Information Collection Activities; Proposed Collection; Unique Device Identification System; Extension of Comment Period AGENCY: Food and Drug Administration, HHS. ACTION...

  6. Constructing Black Titania with Unique Nanocage Structure for Solar Desalination.

    Science.gov (United States)

    Zhu, Guilian; Xu, Jijian; Zhao, Wenli; Huang, Fuqiang

    2016-11-23

    Solar desalination driven by solar radiation as heat source is freely available, however, hindered by low efficiency. Herein, we first design and synthesize black titania with a unique nanocage structure simultaneously with light trapping effect to enhance light harvesting, well-crystallized interconnected nanograins to accelerate the heat transfer from titania to water and with opening mesopores (4-10 nm) to facilitate the permeation of water vapor. Furthermore, the coated self-floating black titania nanocages film localizes the temperature increase at the water-air interface rather than uniformly heating the bulk of the water, which ultimately results in a solar-thermal conversion efficiency as high as 70.9% under a simulated solar light with an intensity of 1 kW m(-2) (1 sun). This finding should inspire new black materials with rationally designed structure for superior solar desalination performance.

  7. Structuring the Information Gap.

    Science.gov (United States)

    Edge, Julian

    1984-01-01

    Describes an information gap procedure to teach a new structure which requires students to look for and exchange information in order to complete a task in an English as a second language class. Illustrates the method with a set of materials and suggests ways for teachers to produce similar materials. (SED)

  8. Growth Mechanism of a Unique Hierarchical Vaterite Structure

    Science.gov (United States)

    Ma, Guobin; Xu, Yifei; Wang, Mu

    2013-03-01

    Calcium carbonate is one of the most significant minerals in nature as well as in biogenic sources. Calcium carbonate occurs naturally in three crystalline polymorphs, i.e., calcite, aragonite, and vaterite. Although it has been attracted much research attention to understanding of the formation mechanisms of the material, the properties of the vaterite polymorph is not well known. Here we report synthesis and formation mechanism of a unique hierarchical structure of vaterite. The material is grown by a controlled diffusion method. The structure possesses a core and an outer part. The core is convex lens-like and is formed by vaterite nanocrystals that have small misorientations. The outer part is separated into six garlic clove-like segments. Each segment possesses piles of plate-like vaterite crystals, and the orientations of the plates continuously change from pile to pile. Based on real-time experimental results and the structural analysis, a growth mechanism is presented. Work supported by NSFC (Grant No. 51172104) and MOST of China (Grant No. 2101CB630705)

  9. Information Structure: Afterword

    Directory of Open Access Journals (Sweden)

    Craige Roberts

    2012-12-01

    Full Text Available This is the afterword to the 2012 republication of "Information structure in discourse: Towards an integrated formal theory of pragmatics". See also the annotated bibliography on related topics at http://www.ling.ohio-state.edu/~croberts/QUDbib/. http://dx.doi.org/10.3765/sp.5.7 BibTeX info

  10. Unique Structural Features of Influenza Virus H15 Hemagglutinin

    Energy Technology Data Exchange (ETDEWEB)

    Tzarum, Netanel; McBride, Ryan; Nycholat, Corwin M.; Peng, Wenjie; Paulson, James C.; Wilson, Ian A. (Scripps)

    2017-04-12

    Influenza A H15 viruses are members of a subgroup (H7-H10-H15) of group 2 hemagglutinin (HA) subtypes that include H7N9 and H10N8 viruses that were isolated from humans during 2013. The isolation of avian H15 viruses is, however, quite rare and, until recently, geographically restricted to wild shorebirds and waterfowl in Australia. The HAs of H15 viruses contain an insertion in the 150-loop (loop beginning at position 150) of the receptor-binding site common to this subgroup and a unique insertion in the 260-loop compared to any other subtype. Here, we show that the H15 HA has a high preference for avian receptor analogs by glycan array analyses. The H15 HA crystal structure reveals that it is structurally closest to H7N9 HA, but the head domain of the H15 trimer is wider than all other HAs due to a tilt and opening of the HA1 subunits of the head domain. The extended 150-loop of the H15 HA retains the conserved conformation as in H7 and H10 HAs. Furthermore, the elongated 260-loop increases the exposed HA surface and can contribute to antigenic variation in H15 HAs. Since avian-origin H15 HA viruses have been shown to cause enhanced disease in mammalian models, further characterization and immune surveillance of H15 viruses are warranted.

    IMPORTANCEIn the last 2 decades, an apparent increase has been reported for cases of human infection by emerging avian influenza A virus subtypes, including H7N9 and H10N8 viruses isolated during 2013. H15 is the other member of the subgroup of influenza A virus group 2 hemagglutinins (HAs) that also include H7 and H10. H15 viruses have been restricted to Australia, but recent isolation of H15 viruses in western Siberia suggests that they could be spread more globally via the avian flyways that converge and emanate from this region. Here we report on characterization of the three-dimensional structure and receptor specificity of the H15 hemagglutinin, revealing distinct features and specificities that can

  11. Information Transmission in Emerging Markets: The Case of a Unique Financing Instrument

    OpenAIRE

    Siddiqi, Hammad

    2008-01-01

    Information flows are necessary for well-functioning financial markets. However, in many emerging markets, the legal and institutional preconditions for proper information flow are not met. How do such markets respond? We argue that they respond by developing innovative information transmission mechanisms. We identify one such mechanism associated with the evolution of equity markets in South Asia. The mechanism operates through a financing instrument unique to India and Pakistan, called badl...

  12. Information Structures and Undergraduate Students

    Science.gov (United States)

    Lee, Hur-Li

    2008-01-01

    This study explores how undergraduates seek information across various information structures. Taking part in an interview, fifteen students of diverse backgrounds described their information seeking. The findings pointed to several issues relating to the underlying structures of information resources. Suggestions are made for structural…

  13. Homodiselenacalix[4]arenes: Molecules with Unique Channelled Crystal Structures.

    Science.gov (United States)

    Thomas, Joice; Dobrzańska, Liliana; Van Meervelt, Luc; Quevedo, Mario Alfredo; Woźniak, Krzysztof; Stachowicz, Marcin; Smet, Mario; Maes, Wouter; Dehaen, Wim

    2016-01-18

    A synthetic route towards homodiselenacalix[4]arene macrocycles is presented, based on the dynamic covalent chemistry of diselenides. The calixarene inner rim is decorated with either alkoxy or tert-butyl ester groups. Single-crystal X-ray analysis of two THF solvates with methoxy and ethoxy substituents reveals the high similarity of their molecular structures and alterations on the supramolecular level. In both crystal structures, solvent channels are present and differ in both shape and capacity. Furthermore, the methoxy-substituted macrocycle undergoes a single-crystal-to-single-crystal transformation during which the molecular structure changes its conformation from 1,3-alternate (loaded with THF/water) to 1,2-alternate (apohost form). Molecular modelling techniques were applied to explore the conformational and energetic behaviour of the macrocycles.

  14. Gelled Complex Fluids: Combining Unique Structures with Mechanical Stability.

    Science.gov (United States)

    Stubenrauch, Cosima; Gießelmann, Frank

    2016-03-01

    Gelled complex fluids are soft materials in which the microstructure of the complex fluid is combined with the mechanical stability of a gel. To obtain a gelled complex fluid one either adds a gelator to a complex fluid or replaces the solvent in a gel by a complex fluid. The most prominent example of a "natural" gelled complex fluid is the cell. There are various strategies by which one can form a gelled complex fluid; one such strategy is orthogonal self-assembly, that is, the independent but simultaneous formation of two coexisting self-assembled structures within one system. The aim of this Review is to describe the structure and potential applications of various man-made gelled complex fluids and to clarify whether or not the respective system is formed by orthogonal self-assembly.

  15. Understanding `galaxy groups' as a unique structure in the universe

    Science.gov (United States)

    Paul, S.; John, R. S.; Gupta, P.; Kumar, H.

    2017-10-01

    'Galaxy groups' have hardly been realized as a separate class of objects with specific characteristics in the structural hierarchy. The presumption that the self-similarity of dark matter structures is a valid prescription for the baryonic universe at all scales has rendered smaller structures undetectable by current observational facilities, leading to lesser dedicated studies on them. Some recent reports that indicate a deviation from LX-T scaling in groups compared to clusters have motivated us to study their physical properties in depth. In this article, we report the extensive study on physical properties of groups in comparison to the clusters through cosmological hydrodynamic plus N-body simulations using enzo 2.2 code. As additional physics, radiative cooling, heating due to supernova and star motions, star formation and stellar feedback have been implemented. We have produced a mock sample of 362 objects with mass ranging from 5 × 1012 M⊙ to 2.5 × 1015 M⊙. Strikingly, we have found that objects with mass below ∼8 × 1013 M⊙ do not follow any of the cluster self-similar laws in hydrostatics, not even in thermal and non-thermal energies. Two distinct scaling laws are observed to be followed with breaks at ∼8 × 1013 M⊙ for mass, ∼1 keV for temperature and ∼1 Mpc for radius. This places groups as a distinct entity in the hierarchical structures, well demarcated from clusters. This study reveals that groups are mostly far away from virialization, suggesting the need for formulating new models for deciphering their physical parameters. They are also shown to have high turbulence and more non-thermal energy stored, indicating better visibility in the non-thermal regime.

  16. Electrospun superhydrophobic membranes with unique structures for membrane distillation.

    Science.gov (United States)

    Liao, Yuan; Loh, Chun-Heng; Wang, Rong; Fane, Anthony G

    2014-09-24

    With modest temperature demand, low operating pressure, and high solute rejection, membrane distillation (MD) is an attractive option for desalination, waste treatment, and food and pharmaceutical processing. However, large-scale practical applications of MD are still hindered by the absence of effective membranes with high hydrophobicity, high porosity, and adequate mechanical strength, which are important properties for MD permeation fluxes, stable long-term performance, and effective packing in modules without damage. This study describes novel design strategies for highly robust superhydrophobic dual-layer membranes for MD via electrospinning. One of the newly developed membranes comprises a durable and ultrathin 3-dimensional (3D) superhydrophobic skin and porous nanofibrous support whereas another was fabricated by electrospinning 3D superhydrophobic layers on a nonwoven support. These membranes exhibit superhydrophobicity toward distilled water, salty water, oil-in-water emulsion, and beverages, which enables them to be used not only for desalination but also for other processes. The superhydrophobic dual-layer membrane #3S-N with nanofibrous support has a competitive permeation flux of 24.6 ± 1.2 kg m(-2) h(-1) in MD (feed and permeate temperate were set as 333 and 293 K, respectively) due to the higher porosity of the nanofibrous scaffold. Meanwhile, the membranes with the nonwoven support exhibit greater mechanical strength due to this support combined with better long-term performance because of the thicker 3D superhydrophobic layers. The morphology, pore size, porosity, mechanical properties, and liquid enter pressure of water of these superhydrophobic composite membranes with two different structures are reported and compared with commercial polyvinylidene fluoride membranes.

  17. Short Cycle Structure of Graphs on Surfaces (1)-the Uniqueness Theorems

    Institute of Scientific and Technical Information of China (English)

    Han Ren; Mo Deng

    2008-01-01

    In this paper we investigate cycle base structures of a (weighted) graph and show that much information of short cycles is contained in a MCB (minimum cycle base). After setting up a Hall type theorem for base-transformation, we give a sufficient and necessary condition for a cycle base to be a MCB. Further more, we show that the structure of MCB in a (weighted) graph is unique. In the case of nonnegative weight,every pair of MCB have the same number of k-cycles for each integer k>3. The property is also true for those having longest length (although much work has been down in evaluating MCB, little is known for those having longest length).

  18. Invalidating Policies using Structural Information

    DEFF Research Database (Denmark)

    Kammuller, Florian; Probst, Christian W.

    2013-01-01

    by invalidating policies using structural information of the organisational model. Based on this structural information and a description of the organisation's policies, our approach invalidates the policies and identifies exemplary sequences of actions that lead to a violation of the policy in question. Based...... on these examples, the organisation can identify real attack vectors that might result in an insider attack. This information can be used to refine access control system or policies....

  19. Existence and Uniqueness of Endemic States for the Age-structured MSEIR Epidemic Model

    Institute of Scientific and Technical Information of China (English)

    Xue-zhi Li; Geni Gupur; Guang-tian Zhu

    2002-01-01

    The existence and uniqueness of positive steady states for the age-structured MSEIR epidemic model with age-dependent transmission coefficient is considered. Threshold results for the existence of endemic states are established; under certain conditions, uniqueness is also shown.

  20. Identifying Non-Volatile Data Storage Areas: Unique Notebook Identification Information as Digital Evidence

    Directory of Open Access Journals (Sweden)

    Nikica Budimir

    2007-03-01

    Full Text Available The research reported in this paper introduces new techniques to aid in the identification of recovered notebook computers so they may be returned to the rightful owner. We identify non-volatile data storage areas as a means of facilitating the safe storing of computer identification information. A forensic proof of concept tool has been designed to test the feasibility of several storage locations identified within this work to hold the data needed to uniquely identify a computer. The tool was used to perform the creation and extraction of created information in order to allow the analysis of the non-volatile storage locations as valid storage areas capable of holding and preserving the data created within them.  While the format of the information used to identify the machine itself is important, this research only discusses the insertion, storage and ability to retain such information.

  1. Invalidating Policies using Structural Information

    DEFF Research Database (Denmark)

    Kammuller, Florian; Probst, Christian W.

    2014-01-01

    by invalidating policies using structural information of the organisational model. Based on this structural information and a description of the organisation’s policies, our approach invalidates the policies and identifies exemplary sequences of actions that lead to a violation of the policy in question. Based...... on these examples, the organisation can identify real attack vectors that might result in an insider attack. This information can be used to refine access control systems or policies. We provide case studies showing how mechanical verification tools, i.e. modelchecking with MCMAS and interactive theorem proving...

  2. Generic uniqueness of a structured matrix factorization and applications in blind source separation

    OpenAIRE

    Domanov, Ignat; De Lathauwer, Lieven

    2016-01-01

    Algebraic geometry, although little explored in signal processing, provides tools that are very convenient for investigating generic properties in a wide range of applications. Generic properties are properties that hold "almost everywhere". We present a set of conditions that are sufficient for demonstrating the generic uniqueness of a certain structured matrix factorization. This set of conditions may be used as a checklist for generic uniqueness in different settings. We discuss two partic...

  3. Europium-based iron pnictides: a unique laboratory for magnetism, superconductivity and structural effects.

    Science.gov (United States)

    Zapf, Sina; Dressel, Martin

    2017-01-01

    Despite decades of intense research, the origin of high-temperature superconductivity in cuprates and iron-based compounds is still a mystery. Magnetism and superconductivity are traditionally antagonistic phenomena; nevertheless, there is basically no doubt left that unconventional superconductivity is closely linked to magnetism. But this is not the whole story; recently, also structural effects related to the so-called nematic phase gained considerable attention. In order to obtain more information about this peculiar interplay, systematic material research is one of the most important attempts, revealing from time to time unexpected effects. Europium-based iron pnictides are the latest example of such a completely paradigmatic material, as they display not only spin-density-wave and superconducting ground states, but also local Eu(2+) magnetism at a similar temperature scale. Here we review recent experimental progress in determining the complex phase diagrams of europium-based iron pnictides. The conclusions drawn from the observations reach far beyond these model systems. Thus, although europium-based iron pnictides are very peculiar, they provide a unique platform to study the common interplay of structural-nematic, magnetic and electronic effects in high-temperature superconductors.

  4. Europium-based iron pnictides: a unique laboratory for magnetism, superconductivity and structural effects

    Science.gov (United States)

    Zapf, Sina; Dressel, Martin

    2017-01-01

    Despite decades of intense research, the origin of high-temperature superconductivity in cuprates and iron-based compounds is still a mystery. Magnetism and superconductivity are traditionally antagonistic phenomena; nevertheless, there is basically no doubt left that unconventional superconductivity is closely linked to magnetism. But this is not the whole story; recently, also structural effects related to the so-called nematic phase gained considerable attention. In order to obtain more information about this peculiar interplay, systematic material research is one of the most important attempts, revealing from time to time unexpected effects. Europium-based iron pnictides are the latest example of such a completely paradigmatic material, as they display not only spin-density-wave and superconducting ground states, but also local Eu2+ magnetism at a similar temperature scale. Here we review recent experimental progress in determining the complex phase diagrams of europium-based iron pnictides. The conclusions drawn from the observations reach far beyond these model systems. Thus, although europium-based iron pnictides are very peculiar, they provide a unique platform to study the common interplay of structural-nematic, magnetic and electronic effects in high-temperature superconductors.

  5. Structure information from fusion barriers

    Indian Academy of Sciences (India)

    S V S Sastry; S Santra

    2000-06-01

    It is shown that the analysis of fusion barrier distributions is not always an unambiguous test or a ‘fingerprint’ of the structure information of the colliding nuclei. Examples are presented with same fusion barrier distributions for nuclei having different structures. The fusion excitation functions for 16O+208Pb, using the coupled reaction channel (CRC) method and correct structure information, have been analysed. The barrier distributions derived from these excitation functions including many of the significant channels are featureless, although these channels have considerable effects on the fusion excitation function. However, a simultaneous analysis of the fusion, elastic and quasi-elastic channels would fix the structure and the reaction unambiguously

  6. Generic Uniqueness of a Structured Matrix Factorization and Applications in Blind Source Separation

    Science.gov (United States)

    Domanov, Ignat; Lathauwer, Lieven De

    2016-06-01

    Algebraic geometry, although little explored in signal processing, provides tools that are very convenient for investigating generic properties in a wide range of applications. Generic properties are properties that hold "almost everywhere". We present a set of conditions that are sufficient for demonstrating the generic uniqueness of a certain structured matrix factorization. This set of conditions may be used as a checklist for generic uniqueness in different settings. We discuss two particular applications in detail. We provide a relaxed generic uniqueness condition for joint matrix diagonalization that is relevant for independent component analysis in the underdetermined case. We present generic uniqueness conditions for a recently proposed class of deterministic blind source separation methods that rely on mild source models. For the interested reader we provide some intuition on how the results are connected to their algebraic geometric roots.

  7. On the Half Shell: An Introduction to Oysters and Their Unique Structures and Function

    Science.gov (United States)

    Frederick, J. Adam; Haines, Sarah; Romano, Christina; Takacs, Jacqueline

    2017-01-01

    The eastern oyster, "Crassostrea virginica," is an ecologically and economically important species in Chesapeake Bay. Oysters are ecologically unique in the Chesapeake Bay because they build a structure known as a bar or reef by attaching to one another over a 45 long period of time. They have been coined the "Ecological Engineers…

  8. On the Half Shell: An Introduction to Oysters and Their Unique Structures and Function

    Science.gov (United States)

    Frederick, J. Adam; Haines, Sarah; Romano, Christina; Takacs, Jacqueline

    2017-01-01

    The eastern oyster, "Crassostrea virginica," is an ecologically and economically important species in Chesapeake Bay. Oysters are ecologically unique in the Chesapeake Bay because they build a structure known as a bar or reef by attaching to one another over a 45 long period of time. They have been coined the "Ecological Engineers…

  9. EXISTENCE AND UNIQUENESS OF ENDEMIC STATES FOR THE AGE-STRUCTURED SEIR EPIDEMIC MODEL

    Institute of Scientific and Technical Information of China (English)

    Xuezhi LI; Jing CHEN

    2006-01-01

    An age-structured SEIR epidemic model of a vertically as well as horizontally transmitted disease is investigated. Threshold results for the existence of endemic states are established for most cases. Under certain conditions, uniqueness is also shown. Threshold used are explicitly computable in term of demographic and epidemiological parameters of the model.

  10. Exploiting Unique Structural and Functional Properties of Malarial Glycolytic Enzymes for Antimalarial Drug Development

    Directory of Open Access Journals (Sweden)

    Asrar Alam

    2014-01-01

    Full Text Available Metabolic enzymes have been known to carry out a variety of functions besides their normal housekeeping roles known as “moonlighting functions.” These functionalities arise from structural changes induced by posttranslational modifications and/or binding of interacting proteins. Glycolysis is the sole source of energy generation for malaria parasite Plasmodium falciparum, hence a potential pathway for therapeutic intervention. Crystal structures of several P. falciparum glycolytic enzymes have been solved, revealing that they exhibit unique structural differences from the respective host enzymes, which could be exploited for their selective targeting. In addition, these enzymes carry out many parasite-specific functions, which could be of potential interest to control parasite development and transmission. This review focuses on the moonlighting functions of P. falciparum glycolytic enzymes and unique structural differences and functional features of the parasite enzymes, which could be exploited for therapeutic and transmission blocking interventions against malaria.

  11. Exploiting Unique Structural and Functional Properties of Malarial Glycolytic Enzymes for Antimalarial Drug Development

    Science.gov (United States)

    Neyaz, Md. Kausar; Ikramul Hasan, Syed

    2014-01-01

    Metabolic enzymes have been known to carry out a variety of functions besides their normal housekeeping roles known as “moonlighting functions.” These functionalities arise from structural changes induced by posttranslational modifications and/or binding of interacting proteins. Glycolysis is the sole source of energy generation for malaria parasite Plasmodium falciparum, hence a potential pathway for therapeutic intervention. Crystal structures of several P. falciparum glycolytic enzymes have been solved, revealing that they exhibit unique structural differences from the respective host enzymes, which could be exploited for their selective targeting. In addition, these enzymes carry out many parasite-specific functions, which could be of potential interest to control parasite development and transmission. This review focuses on the moonlighting functions of P. falciparum glycolytic enzymes and unique structural differences and functional features of the parasite enzymes, which could be exploited for therapeutic and transmission blocking interventions against malaria. PMID:25580350

  12. Genetic structure of a unique admixed population: implications for medical research.

    Science.gov (United States)

    Patterson, Nick; Petersen, Desiree C; van der Ross, Richard E; Sudoyo, Herawati; Glashoff, Richard H; Marzuki, Sangkot; Reich, David; Hayes, Vanessa M

    2010-02-01

    STATEMENT: In naming population groups, we think a chief aim is to use terms that the group members use themselves, or find familiar and comfortable. The terms used in this manuscript to describe populations are as historically correct as possible and are chosen so as not to offend any population group. Two of the authors (DCP and REvdR) belong to the Coloured population, with one of the authors (REvdR) having contributed extensively to current literature on the history of the Coloured people of South Africa and served as Vice-President of the South African Institute of Race Relations. According to the 2001 South African census (http://www.statssa.gov.za/census01/HTML/CInBrief/CIB2001.pdf), "Statistics South Africa continues to classify people by population group, in order to monitor progress in moving away from the apartheid-based discrimination of the past. However, membership of a population group is now based on self-perception and self-classification, not on a legal definition. Five options were provided on the questionnaire, Black African, Coloured, Indian or Asian, White and Other. Responses in the category 'Other' were very few and were therefore imputed". We have elected to use the term Bushmen rather than San to refer to the hunter-gatherer people of Southern Africa. Although they have no collective name for themselves, this decision was based on the term Bushmen (or Bossiesman) being the more familiar to the communities themselves, while the term San is the more accepted academic classification. Understanding human genetic structure has fundamental implications for understanding the evolution and impact of human diseases. In this study, we describe the complex genetic substructure of a unique and recently admixed population arising approximately 350 years ago as a direct result of European settlement in South Africa. Analysis was performed using over 900 000 genome-wide single nucleotide polymorphisms in 20 unrelated ancestry-informative marker selected

  13. Unique Concept for a Low Cost, Light Weight Space Deployable Antenna Structure

    Science.gov (United States)

    Freeland, Robert E.; Bilyeu, Gayle D.; Veal, Gordon R.

    1993-01-01

    Large space deployable antennas are needed for a variety of applications that include Mobile Communications, Radiometry, Active Microwave Sensing, Very Long Baseline Interferometry and DoD Space Based Radar. These user requirements identify the need for structures up to tens of meters in size for operation from 1 to 90 GHz, based on different aperture configurations. However, the one thing the users have in common is a concept selection criteria for low cost, light weight and highly reliable deployable structures. Fortunately, a unique class of space structures has recently emerged that have tremendous potential for satisfying these criteria. They are referred to as inflatable deployable structures.

  14. Discovery of a Structurally Unique Small Molecule that Inhibits Protein Synthesis

    Science.gov (United States)

    Thakral, Durga; Tae, Hyun Seop

    2017-01-01

    Identifying and characterizing natural products and synthetic small molecules that inhibit biochemical processes such as ribosomal translation can lead to novel sources of molecular probes and therapeutics. The search for new antibiotics has been invigorated by the increasing burden of drug-resistant bacteria and has identified many clinically essential prokaryote-specific ribosome inhibitors. However, the current cohort of antibiotics is limited with regards to bacterial resistance mechanisms because of structural similarity within classes. From a high-throughput screen for translation inhibitors, we discovered a new compound, T6102, which inhibits bacterial protein synthesis in vitro, inhibits bacterial growth of Bacillus subtilis in vivo, and has a chemical structure that appears to be unique among known classes of translation-inhibiting antibiotics. T6102’s unique structure compared to current clinically-utilized antibiotics makes it an exciting new candidate for the development of next-generation antibiotics.

  15. Informational laws of genome structures

    Science.gov (United States)

    Bonnici, Vincenzo; Manca, Vincenzo

    2016-06-01

    In recent years, the analysis of genomes by means of strings of length k occurring in the genomes, called k-mers, has provided important insights into the basic mechanisms and design principles of genome structures. In the present study, we focus on the proper choice of the value of k for applying information theoretic concepts that express intrinsic aspects of genomes. The value k = lg2(n), where n is the genome length, is determined to be the best choice in the definition of some genomic informational indexes that are studied and computed for seventy genomes. These indexes, which are based on information entropies and on suitable comparisons with random genomes, suggest five informational laws, to which all of the considered genomes obey. Moreover, an informational genome complexity measure is proposed, which is a generalized logistic map that balances entropic and anti-entropic components of genomes and is related to their evolutionary dynamics. Finally, applications to computational synthetic biology are briefly outlined.

  16. Structural Perspectives on the Evolutionary Expansion of Unique Protein-Protein Binding Sites.

    Science.gov (United States)

    Goncearenco, Alexander; Shaytan, Alexey K; Shoemaker, Benjamin A; Panchenko, Anna R

    2015-09-15

    Structures of protein complexes provide atomistic insights into protein interactions. Human proteins represent a quarter of all structures in the Protein Data Bank; however, available protein complexes cover less than 10% of the human proteome. Although it is theoretically possible to infer interactions in human proteins based on structures of homologous protein complexes, it is still unclear to what extent protein interactions and binding sites are conserved, and whether protein complexes from remotely related species can be used to infer interactions and binding sites. We considered biological units of protein complexes and clustered protein-protein binding sites into similarity groups based on their structure and sequence, which allowed us to identify unique binding sites. We showed that the growth rate of the number of unique binding sites in the Protein Data Bank was much slower than the growth rate of the number of structural complexes. Next, we investigated the evolutionary roots of unique binding sites and identified the major phyletic branches with the largest expansion in the number of novel binding sites. We found that many binding sites could be traced to the universal common ancestor of all cellular organisms, whereas relatively few binding sites emerged at the major evolutionary branching points. We analyzed the physicochemical properties of unique binding sites and found that the most ancient sites were the largest in size, involved many salt bridges, and were the most compact and least planar. In contrast, binding sites that appeared more recently in the evolution of eukaryotes were characterized by a larger fraction of polar and aromatic residues, and were less compact and more planar, possibly due to their more transient nature and roles in signaling processes.

  17. Non-redundant unique interface structures as templates for modeling protein interactions

    OpenAIRE

    Engin Cukuroglu; Attila Gursoy; Ruth Nussinov; Ozlem Keskin

    2014-01-01

    Non-Redundant Unique Interface Structures as Templates for Modeling Protein Interactions Engin Cukuroglu1, Attila Gursoy1*, Ruth Nussinov2,3, Ozlem Keskin1* 1 Center for Computational Biology and Bioinformatics and College of Engineering, Koc University, Istanbul, Turkey, 2 National Cancer Institute, Cancer and Inflammation Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., National Cancer Institute, Frederick, Maryland, United States of ...

  18. Rhamnogalacturonan lyase reveals a unique three-domain modular structure for polysaccharide lyase family 4

    DEFF Research Database (Denmark)

    McDonough, Michael A.; Kadirvelraj, Renuka; Harris, Pernille

    2004-01-01

    Rhamnogalacturonan lyase (RG-lyase) specifically recognizes and cleaves alpha-1,4 glycosidic bonds between L-rhamnose and D-galacturonic acids in the backbone of rhamno galacturonan-I, a major component of the plant cell wall polysaccharide, pectin. The three-dimensional structure of RG-lyase fro...... structural homology to non-catalytic domains from other carbohydrate active enzymes.......Rhamnogalacturonan lyase (RG-lyase) specifically recognizes and cleaves alpha-1,4 glycosidic bonds between L-rhamnose and D-galacturonic acids in the backbone of rhamno galacturonan-I, a major component of the plant cell wall polysaccharide, pectin. The three-dimensional structure of RG-lyase from...... Aspergillus aculeatus has been determined to 1.5 Angstrom resolution representing the first known structure from polysaccharide lyase family 4 and of an enzyme with this catalytic specificity. The 508-amino acid polypeptide displays a unique arrangement of three distinct modular domains. Each domain shows...

  19. Uranium(VI) coordination polymers with pyromellitate ligand: Unique 1D channel structures and diverse fluorescence

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Yingjie, E-mail: yzx@ansto.gov.au [Australian Nuclear Science and Technology Organization, Locked Bag 2001, Kirrawee DC, NSW 2232 (Australia); Bhadbhade, Mohan [Mark Wainwright Analytical Centre, University of New South Wales, Kensington, NSW 2052 (Australia); Karatchevtseva, Inna [Australian Nuclear Science and Technology Organization, Locked Bag 2001, Kirrawee DC, NSW 2232 (Australia); Price, Jason R. [Australian Synchrotron, 800 Blackburn Road, Clayton, VIC 3168 (Australia); Liu, Hao [Centre for Clean Energy Technology, School of Chemistry and Forensic Science, University of Technology Sydney, PO Box 123, Broadway, Sydney, NSW 2007 (Australia); Zhang, Zhaoming; Kong, Linggen [Australian Nuclear Science and Technology Organization, Locked Bag 2001, Kirrawee DC, NSW 2232 (Australia); Čejka, Jiří [Department of Mineralogy, National Museum, Václavské náměstí, 68, Prague 1, 115 79-CZ (Czech Republic); Lu, Kim; Lumpkin, Gregory R. [Australian Nuclear Science and Technology Organization, Locked Bag 2001, Kirrawee DC, NSW 2232 (Australia)

    2015-03-15

    Three new coordination polymers of uranium(VI) with pyromellitic acid (H{sub 4}btca) have been synthesized and structurally characterized. (ED)[(UO{sub 2})(btca)]·(DMSO)·3H{sub 2}O (1) (ED=ethylenediammonium; DMSO=dimethylsulfoxide) has a lamellar structure with intercalation of ED and DMSO. (NH{sub 4}){sub 2}[(UO{sub 2}){sub 6}O{sub 2}(OH){sub 6}(btca)]·~6H{sub 2}O (2) has a 3D framework built from 7-fold coordinated uranyl trinuclear units and btca ligands with 1D diamond-shaped channels (~8.5 Å×~8.6 Å). [(UO{sub 2}){sub 2}(H{sub 2}O)(btca)]·4H{sub 2}O (3) has a 3D network constructed by two types of 7-fold coordinated uranium polyhedron. The unique μ{sub 5}-coordination mode of btca in 3 enables the formation of 1D olive-shaped large channels (~4.5 Å×~19 Å). Vibrational modes, thermal stabilities and fluorescence properties have been investigated. - Graphical abstract: Table of content: three new uranium(VI) coordination polymers with pyromellitic acid (H{sub 4}btca) have been synthesized via room temperature and hydrothermal synthesis methods, and structurally characterized. Two to three dimensional (3D) frameworks are revealed. All 3D frameworks have unique 1D large channels. Their vibrational modes, thermal stabilities and photoluminescence properties have been investigated. - Highlights: • Three new coordination polymers of U(VI) with pyromellitic acid (H{sub 4}btca). • Structures from a 2D layer to 3D frameworks with unique 1D channels. • Unusual µ{sub 5}-(η{sub 1}:η{sub 2}:η{sub 1}:η{sub 2:}η{sub 1}) coordination mode of btca ligand. • Vibrational modes, thermal stabilities and luminescent properties reported.

  20. Encoding information into precipitation structures

    Science.gov (United States)

    Martens, Kirsten; Bena, Ioana; Droz, Michel; Rácz, Zoltan

    2008-12-01

    Material design at submicron scales would be profoundly affected if the formation of precipitation patterns could be easily controlled. It would allow the direct building of bulk structures, in contrast to traditional techniques which consist of removing material in order to create patterns. Here, we discuss an extension of our recent proposal of using electrical currents to control precipitation bands which emerge in the wake of reaction fronts in A+ + B- → C reaction-diffusion processes. Our main result, based on simulating the reaction-diffusion-precipitation equations, is that the dynamics of the charged agents can be guided by an appropriately designed time-dependent electric current so that, in addition to the control of the band spacing, the width of the precipitation bands can also be tuned. This makes straightforward the encoding of information into precipitation patterns and, as an amusing example, we demonstrate the feasibility by showing how to encode a musical rhythm.

  1. Quantum Information with Structured Light

    Science.gov (United States)

    Mirhosseini, Mohammad

    Quantum information science promises dramatic progress in a variety of fields such as cryptography, computation, and metrology. Although the proof-of-principle attempts for implementing quantum protocols have often relied on only a few qubits, the utilization of more sophisticated quantum systems is required for practical applications. In this thesis, we investigate the emerging role of high-dimensional optical states as a resource for encoding quantum information. We begin the first chapter with a review of orbital angular momentum (OAM) as a prime candidate for realizing multilevel quantum states and follow with a brief introduction to the quantum measurement theory. The second and the third chapters are dedicated to the application of OAM modes in quantum cryptography. In the second chapter, we discuss the challenges of projective measurement of OAM at the single-photon level, a crucial task required for quantum information processing. We then present our development of an efficient and accurate mode-sorting device that is capable of projectively measuring the orbital angular momentum of single photons. In the third chapter, we discuss the role of OAM modes in increasing the information capacity of quantum cryptography. We start this chapter by establishing the merits of encoding information on the quantum index of OAM modes in a free-space link. We then generalizing the BB-84 QKD protocol to the Hilbert space spanned by a finite number of OAM modes and outline our experimental realization. The last two chapters are dedicated to the tomography of structured light fields. We start the fourth chapter by applying the recently found method of direct measurement to the characterization of OAM superpositions. We find the quantum state in the Hilbert space spanned by 27 OAM modes by performing a weak measurement of orbital angular momentum (OAM) followed by a strong measurement of azimuthal angle. We then introduce the concept of compressive direct measurement (CDM

  2. Unique structure and optics of the lesser eyes of the box jellyfish Tripedalia cystophora

    DEFF Research Database (Denmark)

    Garm, A; Andersson, F; Nilsson, Dan-E

    2008-01-01

    The visual system of box jellyfish comprises a total of 24 eyes. These are of four types and each probably has a special function. To investigate this hypothesis the morphology and optics of the lesser eyes, the pit and slit eyes, were examined. The pit eyes hold one cell type only and are probably...... mere light meters. The slit eyes, comprising four cell types, are complex and highly asymmetric. They also hold a lens-like structure, but its optical power is minute. Optical modeling suggests spatial resolution, but only in one plane. These unique and intriguing traits support strong peripheral...

  3. How Unique Are Our Users? Comparing Responses Regarding the Information-Seeking Habits of Engineering Faculty

    Science.gov (United States)

    Robbins, Sarah; Engel, Debra; Kulp, Christina

    2011-01-01

    Studies of information-seeking behaviors are common in the professional literature for library and information studies. This study examines the generalizability of findings of single-institution studies to other institutions by performing an institution-to-institution comparison of the results obtained from an information-seeking behavior survey…

  4. How Unique Are Our Users? Comparing Responses Regarding the Information-Seeking Habits of Engineering Faculty

    Science.gov (United States)

    Robbins, Sarah; Engel, Debra; Kulp, Christina

    2011-01-01

    Studies of information-seeking behaviors are common in the professional literature for library and information studies. This study examines the generalizability of findings of single-institution studies to other institutions by performing an institution-to-institution comparison of the results obtained from an information-seeking behavior survey…

  5. Structural insights into the unique inhibitory mechanism of the silkworm protease inhibitor serpin18

    Science.gov (United States)

    Guo, Peng-Chao; Dong, Zhaoming; Zhao, Ping; Zhang, Yan; He, Huawei; Tan, Xiang; Zhang, Weiwei; Xia, Qingyou

    2015-01-01

    Serpins generally serve as inhibitors that utilize a mobile reactive center loop (RCL) as bait to trap protease targets. Here, we present the crystal structure of serpin18 from Bombyx mori at 1.65 Å resolution, which has a very short and stable RCL. Activity analysis showed that the inhibitory target of serpin18 is a cysteine protease rather than a serine protease. Notably, this inhibitiory reaction results from the formation of an intermediate complex, which then follows for the digestion of protease and inhibitor into small fragments. This activity differs from previously reported modes of inhibition for serpins. Our findings have thus provided novel structural insights into the unique inhibitory mechanism of serpin18. Furthermore, one physiological target of serpin18, fibroinase, was identified, which enables us to better define the potential role for serpin18 in regulating fibroinase activity during B. mori development. PMID:26148664

  6. Measurement of MMP-9 and -12 degraded elastin (ELM) provides unique information on lung tissue degradation

    DEFF Research Database (Denmark)

    Skjøt-Arkil, Helene; Clausen, Rikke E; Nguyen, Quoc Hai Trieu;

    2012-01-01

    Elastin is an essential component of selected connective tissues that provides a unique physiological elasticity. Elastin may be considered a signature protein of lungs where matrix metalloprotease (MMP) -9-and -12, may be considered the signature proteases of the macrophages, which in part...... are responsible for tissue damage during disease progression. Thus, we hypothesized that a MMP-9/-12 generated fragment of elastin may be a relevant biochemical maker for lung diseases....

  7. Unique structural modulation of a non-native substrate by cochaperone DnaJ.

    Science.gov (United States)

    Tiwari, Satyam; Kumar, Vignesh; Jayaraj, Gopal Gunanathan; Maiti, Souvik; Mapa, Koyeli

    2013-02-12

    The role of bacterial DnaJ protein as a cochaperone of DnaK is strongly appreciated. Although DnaJ unaccompanied by DnaK can bind unfolded as well as native substrate proteins, its role as an individual chaperone remains elusive. In this study, we demonstrate that DnaJ binds a model non-native substrate with a low nanomolar dissociation constant and, more importantly, modulates the structure of its non-native state. The structural modulation achieved by DnaJ is different compared to that achieved by the DnaK-DnaJ complex. The nature of structural modulation exerted by DnaJ is suggestive of a unique unfolding activity on the non-native substrate by the chaperone. Furthermore, we demonstrate that the zinc binding motif along with the C-terminal substrate binding domain of DnaJ is necessary and sufficient for binding and the subsequent binding-induced structural alterations of the non-native substrate. We hypothesize that this hitherto unknown structural alteration of non-native states by DnaJ might be important for its chaperoning activity by removing kinetic traps of the folding intermediates.

  8. Computerized management information systems and organizational structures

    Science.gov (United States)

    Zannetos, Z. S.; Sertel, M. R.

    1970-01-01

    The computerized management of information systems and organizational structures is discussed. The subjects presented are: (1) critical factors favoring centralization and decentralization of organizations, (2) classification of organizations by relative structure, (3) attempts to measure change in organization structure, and (4) impact of information technology developments on organizational structure changes.

  9. The not so unique Global Trade Identification Number : Exploring inconsistencies in online product information sources

    OpenAIRE

    Karpischek, Stephan; Michahelles, Florian; Fleisch, Elgar

    2011-01-01

    Mobile shopping apps for consumers often identify retail products by Global Trade Identification Number (GTIN) using barcodes or RFID technology and rely on online data sources to provide basic product information. Several different sources exist, and reports show that the available product information in them is often inconsistent with implications for both retail businesses and consumers. In this paper we compare the product information provided by 10 different online sources for more than ...

  10. Structural Basis of Natural Promoter Recognition by a Unique Nuclear Receptor, HNF4[alpha

    Energy Technology Data Exchange (ETDEWEB)

    Lu, Peng; Rha, Geun Bae; Melikishvili, Manana; Wu, Guangteng; Adkins, Brandon C.; Fried, Michael G.; Chi, Young-In (Kentucky)

    2010-11-09

    HNF4{alpha} (hepatocyte nuclear factor 4{alpha}) plays an essential role in the development and function of vertebrate organs, including hepatocytes and pancreatic {beta}-cells by regulating expression of multiple genes involved in organ development, nutrient transport, and diverse metabolic pathways. As such, HNF4{alpha} is a culprit gene product for a monogenic and dominantly inherited form of diabetes, known as maturity onset diabetes of the young (MODY). As a unique member of the nuclear receptor superfamily, HNF4{alpha} recognizes target genes containing two hexanucleotide direct repeat DNA-response elements separated by one base pair (DR1) by exclusively forming a cooperative homodimer. We describe here the 2.0 {angstrom} crystal structure of human HNF4{alpha} DNA binding domain in complex with a high affinity promoter element of another MODY gene, HNF1{alpha}, which reveals the molecular basis of unique target gene selection/recognition, DNA binding cooperativity, and dysfunction caused by diabetes-causing mutations. The predicted effects of MODY mutations have been tested by a set of biochemical and functional studies, which show that, in contrast to other MODY gene products, the subtle disruption of HNF4{alpha} molecular function can cause significant effects in afflicted MODY patients.

  11. Changing nuclear landscape and unique PML structures during early epigenetic transitions of human embryonic stem cells.

    Science.gov (United States)

    Butler, John T; Hall, Lisa L; Smith, Kelly P; Lawrence, Jeanne B

    2009-07-01

    The complex nuclear structure of somatic cells is important to epigenomic regulation, yet little is known about nuclear organization of human embryonic stem cells (hESC). Here we surveyed several nuclear structures in pluripotent and transitioning hESC. Observations of centromeres, telomeres, SC35 speckles, Cajal Bodies, lamin A/C and emerin, nuclear shape and size demonstrate a very different "nuclear landscape" in hESC. This landscape is remodeled during a brief transitional window, concomitant with or just prior to differentiation onset. Notably, hESC initially contain abundant signal for spliceosome assembly factor, SC35, but lack discrete SC35 domains; these form as cells begin to specialize, likely reflecting cell-type specific genomic organization. Concomitantly, nuclear size increases and shape changes as lamin A/C and emerin incorporate into the lamina. During this brief window, hESC exhibit dramatically different PML-defined structures, which in somatic cells are linked to gene regulation and cancer. Unlike the numerous, spherical somatic PML bodies, hES cells often display approximately 1-3 large PML structures of two morphological types: long linear "rods" or elaborate "rosettes", which lack substantial SUMO-1, Daxx, and Sp100. These occur primarily between Day 0-2 of differentiation and become rare thereafter. PML rods may be "taut" between other structures, such as centromeres, but clearly show some relationship with the lamina, where PML often abuts or fills a "gap" in early lamin A/C staining. Findings demonstrate that pluripotent hES cells have a markedly different overall nuclear architecture, remodeling of which is linked to early epigenomic programming and involves formation of unique PML-defined structures.

  12. Experimental study of wind loads on unique buildings and structures in Russia

    Directory of Open Access Journals (Sweden)

    Poddaeva Olga

    2016-01-01

    Full Text Available Design and construction of unique buildings and structures (sports arenas, airport complexes, business centres, etc. from an engineering point of view is a very difficult task as in most cases these facilities have an original architectural form. Therefore, consideration of wind loads is an important part of the design. The paper presents the definition of wind load for two complex of airport. Researches was applied the combined calculation an experimental method. During the experimental study a wind tunnel architectural and construction type NRU MSUCE was used. Numerical simulations were performed using the software package ANSYS. The result of research on each object are integral aerodynamic loads on the object (coefficients Cx, Cy, Cmz and picture of the distribution of aerodynamic pressure coefficient Cp obtained in the numerical simulation. In conclusion, we discuss the possible formation of deposits of snow and recommendations to eliminate them from the roof of researched objects.

  13. Existence and uniqueness of endemic states for the age-structured S-I-R epidemic model.

    Science.gov (United States)

    Cha, Y; Iannelli, M; Milner, F A

    1998-06-15

    The existence and uniqueness of positive steady states for the age structured S-I-R epidemic model with intercohort transmission is considered. Threshold results for the existence of endemic states are established for most cases. Uniqueness is shown in each case. Threshold used are explicitly computable in terms of demographic and epidemiological parameters of the model.

  14. Dissecting structural basis of the unique substrate selectivity of human enteropeptidase catalytic subunit.

    Science.gov (United States)

    Ostapchenko, Valeriy G; Gasparian, Marine E; Kosinsky, Yurij A; Efremov, Roman G; Dolgikh, Dmitry A; Kirpichnikov, Mikhail P

    2012-01-01

    Enteropeptidase is a key enzyme in the digestion system of higher animals. It initiates enzymatic cascade cleaving trypsinogen activation peptide after a unique sequence DDDDK. Recently, we have found specific activity of human enteropeptidase catalytic subunit (L-HEP) being significantly higher than that of its bovine ortholog (L-BEP). Moreover, we have discovered that L-HEP hydrolyzed several nonspecific peptidic substrates. In this work, we aimed to further characterize species-specific enteropeptidase activities and to reveal their structural basis. First, we compared hydrolysis of peptides and proteins lacking DDDDK sequence by L-HEP and L-BEP. In each case human enzyme was more efficient, with the highest hydrolysis rate observed for substrates with a large hydrophobic residue in P2-position. Computer modeling suggested enzyme exosite residues 96 (Arg in L-HEP, Lys in L-BEP) and 219 (Lys in L-HEP, Gln in L-BEP) to be responsible for these differences in enteropeptidase catalytic activity. Indeed, human-to-bovine mutations Arg96Lys, Lys219Gln shifted catalytic properties of L-HEP toward those of L-BEP. This effect was amplified in case of the double mutation Arg96Lys/Lys219Gln, but still did not cover the full difference in catalytic activities of human and bovine enzymes. To find a missing link, we studied monopeptide benzyl-arginine-β-naphthylamide hydrolysis. L-HEP catalyzed it with an order lower K (m) than L-BEP, suggesting the monopeptide-binding S1 site input into catalytic distinction between two enteropeptidase species. Together, our findings suggest structural basis of the unique catalytic properties of human enteropeptidase and instigate further studies of its tentative physiological and pathological roles.

  15. In situ structure of trypanosomal ATP synthase dimer reveals a unique arrangement of catalytic subunits

    Science.gov (United States)

    Mühleip, Alexander W.; Dewar, Caroline E.; Schnaufer, Achim; Kühlbrandt, Werner; Davies, Karen M.

    2017-01-01

    We used electron cryotomography and subtomogram averaging to determine the in situ structures of mitochondrial ATP synthase dimers from two organisms belonging to the phylum euglenozoa: Trypanosoma brucei, a lethal human parasite, and Euglena gracilis, a photosynthetic protist. At a resolution of 32.5 Å and 27.5 Å, respectively, the two structures clearly exhibit a noncanonical F1 head, in which the catalytic (αβ)3 assembly forms a triangular pyramid rather than the pseudo-sixfold ring arrangement typical of all other ATP synthases investigated so far. Fitting of known X-ray structures reveals that this unusual geometry results from a phylum-specific cleavage of the α subunit, in which the C-terminal αC fragments are displaced by ∼20 Å and rotated by ∼30° from their expected positions. In this location, the αC fragment is unable to form the conserved catalytic interface that was thought to be essential for ATP synthesis, and cannot convert γ-subunit rotation into the conformational changes implicit in rotary catalysis. The new arrangement of catalytic subunits suggests that the mechanism of ATP generation by rotary ATPases is less strictly conserved than has been generally assumed. The ATP synthases of these organisms present a unique model system for discerning the individual contributions of the α and β subunits to the fundamental process of ATP synthesis. PMID:28096380

  16. Unique genomic structure and distinct mitotic behavior of ring chromosome 21 in two unrelated cases.

    Science.gov (United States)

    Zhang, H Z; Xu, F; Seashore, M; Li, P

    2012-01-01

    A ring chromosome replacing a normal chromosome could involve variable structural rearrangements and mitotic instability. However, most previously reported cases lacked further genomic characterization. High-resolution oligonucleotide array comparative genomic hybridization with single-nucleotide polymorphism typing (aCGH+SNP) was used to study 2 unrelated cases with a ring chromosome 21. Case 1 had severe myopia, hypotonia, joint hypermobility, speech delay, and dysmorphic features. aCGH detected a 1.275-Mb duplication of 21q22.12-q22.13 and a 6.731-Mb distal deletion at 21q22.2. Case 2 showed severe growth and developmental retardations, intractable seizures, and dysmorphic features. aCGH revealed a contiguous pattern of a 3.612- Mb deletion of 21q22.12-q22.2, a 4.568-Mb duplication of 21q22.2-q22.3, and a 2.243-Mb distal deletion at 21q22.3. Mitotic instability was noted in 13, 30, and 76% of in vitro cultured metaphase cells, interphase cells, and leukocyte DNA, respectively. The different phenotypes of these 2 cases are likely associated with the unique genomic structure and distinct mitotic behavior of their ring chromosome 21. These 2 cases represent a subtype of ring chromosome 21 probably involving somatic dicentric ring breakage and reunion. A cytogenomic approach is proposed for characterizing the genomic structure and mitotic instability of ring chromosome abnormalities.

  17. The JFFMA assessment of flavoring substances structurally related to menthol and uniquely used in Japan.

    Science.gov (United States)

    Mirokuji, Yoshiharu; Abe, Hajime; Okamura, Hiroyuki; Saito, Kenji; Sekiya, Fumiko; Hayashi, Shim-mo; Maruyama, Shinpei; Ono, Atsushi; Nakajima, Madoka; Degawa, Masakuni; Ozawa, Shogo; Shibutani, Makoto; Maitani, Tamio

    2014-02-01

    Using the procedure devised by the Joint FAO/WHO Expert Committee on Food Additives (JECFA), we performed safety evaluations on four flavoring substances structurally related to menthol (L-menthyl 2-methylbutyrate, DL-menthyl octanoate, DL-menthyl palmitate, and DL-menthyl stearate) uniquely used in Japan. While no genotoxicity study data were available in the literature, all four substances had no chemical structural alerts predictive of genotoxicity. Moreover, they all four are esters consisting of menthol and simple carboxylic acids that were assumed to be immediately hydrolyzed after ingestion and metabolized into innocuous substances for excretion. As menthol and carboxylic acids have no known genotoxicity, it was judged that the JECFA procedure could be applied to these four substances. According to Cramer's classification, these substances were categorized as class I based on their chemical structures. The estimated daily intakes for all four substances were within the range of 1.54-4.71 μg/person/day and 60-1250 μg/person/day, using the methods of Maximized Survey-Derived Intake and Single Portion Exposure Technique, respectively, based on the annual usage data of 2001, 2005, and 2010 in Japan. As the daily intakes of these substances were below the threshold of concern applied to class I substances viz., 1800 μg/person/day, it was concluded that all four substances raise no safety concerns when used for flavoring foods under the currently estimated intake levels.

  18. News from the Library: Online particle physics information: a unique compilation of information resources in particle physics

    CERN Multimedia

    CERN Library

    2012-01-01

    Are you looking for some specific information in particle physics? For example, the main literature databases, data repositories or laboratories...   Just go to the Libary's Online Particle Physics Information page. There you'll find a wide selection of relevant information, as well as resources in particle physics and related areas. The collection covers all aspects of the discipline - in addition to traditional scientific information resources you can find, for example, a selection of relevant blogs and art websites. This webpage is an extended and regularly updated version of the chapter on Online Particle Physics Information in the Review of Particle Properties. It is maintained by the CERN Library team which welcomes suggestions for additions and updates: library.desk@cern.ch.  

  19. Sources semiconductrices de photons uniques ou de photons jumeaux pour l'information quantique

    Science.gov (United States)

    Berger, Vincent; Gérard, Jean-Michel

    2003-07-01

    A large number of scientific proposals in recent years are based on transport and manipulation of information using single quantum objects. Although very impressive theoretical perspectives have been envisaged, experimental demonstrations are still limited due to technological difficulties with present state-of-the-art devices. This paper presents various approaches aiming at efficient single or twin photons semiconductor sources. The emergence of these devices will be an important technological breakthrough in the field of quantum information. To cite this article: V. Berger, J.-M. Gérard, C. R. Physique 4 (2003).

  20. Aphis Glycines Virus 2, a Novel Insect Virus with a Unique Genome Structure

    Directory of Open Access Journals (Sweden)

    Sijun Liu

    2016-11-01

    Full Text Available The invasive soybean aphid, Aphis glycines, is a major pest in soybeans, resulting in substantial economic loss. We analyzed the A. glycines transcriptome to identify sequences derived from viruses of A. glycines. We identified sequences derived from a novel virus named Aphis glycines virus 2 (ApGlV2. The assembled virus genome sequence was confirmed by reverse transcription polymerase chain reaction (RT-PCR and Sanger sequencing, conserved domains were characterized, and distribution, and transmission examined. This virus has a positive sense, single-stranded RNA genome of ~4850 nt that encodes three proteins. The RNA-dependent RNA polymerase (RdRp of ApGlV2 is a permuted RdRp similar to those of some tetraviruses, while the capsid protein is structurally similar to the capsid proteins of plant sobemoviruses. ApGlV2 also encodes a larger minor capsid protein, which is translated by a readthrough mechanism. ApGlV2 appears to be widespread in A. glycines populations and to persistently infect aphids with a 100% vertical transmission rate. ApGlV2 is susceptible to the antiviral RNA interference (RNAi pathway. This virus, with its unique genome structure with both plant- and insect-virus characteristics, is of particular interest from an evolutionary standpoint.

  1. Understanding the Unique Electronic Properties of Nano Structures Using Photoemission Theory.

    Science.gov (United States)

    Kwon, Soonnam; Choi, Won Kook

    2015-12-04

    Newly emerging experimental techniques such as nano-ARPES are expected to provide an opportunity to measure the electronic properties of nano-materials directly. However, the interpretation of the spectra is not simple because it must consider quantum mechanical effects related to the measurement process itself. Here, we demonstrate a novel approach that can overcome this problem by using an adequate simulation to corroborate the experimental results. Ab initio calculation on arbitrarily-shaped or chemically ornamented nano-structures is elaborately correlated to photoemission theory. This correlation can be directly exploited to interpret the experimental results. To test this method, a direct comparison was made between the calculation results and experimental results on highly-oriented pyrolytic graphite (HOPG). As a general extension, the unique electronic structures of nano-sized graphene oxide and features from the experimental result of black phosphorous (BP) are disclosed for the first time as supportive evidence of the usefulness of this method. This work pioneers an approach to intuitive and practical understanding of the electronic properties of nano-materials.

  2. Mining chemical structural information from the drug literature.

    Science.gov (United States)

    Banville, Debra L

    2006-01-01

    It is easier to find too many documents on a life science topic than to find the right information inside these documents. With the application of text data mining to biological documents, it is no surprise that researchers are starting to look at applications that mine out chemical information. The mining of chemical entities--names and structures--brings with it some unique challenges, which commercial and academic efforts are beginning to address. Ultimately, life science text data mining applications need to focus on the marriage of biological and chemical information.

  3. Unique Structural and Nucleotide Exchange Features of the Rho1 GTPase of Entamoeba histolytica*

    Science.gov (United States)

    Bosch, Dustin E.; Wittchen, Erika S.; Qiu, Connie; Burridge, Keith; Siderovski, David P.

    2011-01-01

    The single-celled human parasite Entamoeba histolytica possesses a dynamic actin cytoskeleton vital for its intestinal and systemic pathogenicity. The E. histolytica genome encodes several Rho family GTPases known to regulate cytoskeletal dynamics. EhRho1, the first family member identified, was reported to be insensitive to the Rho GTPase-specific Clostridium botulinum C3 exoenzyme, raising the possibility that it may be a misclassified Ras family member. Here, we report the crystal structures of EhRho1 in both active and inactive states. EhRho1 is activated by a conserved switch mechanism, but diverges from mammalian Rho GTPases in lacking a signature Rho insert helix. EhRho1 engages a homolog of mDia, EhFormin1, suggesting a role in mediating serum-stimulated actin reorganization and microtubule formation during mitosis. EhRho1, but not a constitutively active mutant, interacts with a newly identified EhRhoGDI in a prenylation-dependent manner. Furthermore, constitutively active EhRho1 induces actin stress fiber formation in mammalian fibroblasts, thereby identifying it as a functional Rho family GTPase. EhRho1 exhibits a fast rate of nucleotide exchange relative to mammalian Rho GTPases due to a distinctive switch one isoleucine residue reminiscent of the constitutively active F28L mutation in human Cdc42, which for the latter protein, is sufficient for cellular transformation. Nonconserved, nucleotide-interacting residues within EhRho1, revealed by the crystal structure models, were observed to contribute a moderating influence on fast spontaneous nucleotide exchange. Collectively, these observations indicate that EhRho1 is a bona fide member of the Rho GTPase family, albeit with unique structural and functional aspects compared with mammalian Rho GTPases. PMID:21930699

  4. Unique structural and nucleotide exchange features of the Rho1 GTPase of Entamoeba histolytica.

    Science.gov (United States)

    Bosch, Dustin E; Wittchen, Erika S; Qiu, Connie; Burridge, Keith; Siderovski, David P

    2011-11-11

    The single-celled human parasite Entamoeba histolytica possesses a dynamic actin cytoskeleton vital for its intestinal and systemic pathogenicity. The E. histolytica genome encodes several Rho family GTPases known to regulate cytoskeletal dynamics. EhRho1, the first family member identified, was reported to be insensitive to the Rho GTPase-specific Clostridium botulinum C3 exoenzyme, raising the possibility that it may be a misclassified Ras family member. Here, we report the crystal structures of EhRho1 in both active and inactive states. EhRho1 is activated by a conserved switch mechanism, but diverges from mammalian Rho GTPases in lacking a signature Rho insert helix. EhRho1 engages a homolog of mDia, EhFormin1, suggesting a role in mediating serum-stimulated actin reorganization and microtubule formation during mitosis. EhRho1, but not a constitutively active mutant, interacts with a newly identified EhRhoGDI in a prenylation-dependent manner. Furthermore, constitutively active EhRho1 induces actin stress fiber formation in mammalian fibroblasts, thereby identifying it as a functional Rho family GTPase. EhRho1 exhibits a fast rate of nucleotide exchange relative to mammalian Rho GTPases due to a distinctive switch one isoleucine residue reminiscent of the constitutively active F28L mutation in human Cdc42, which for the latter protein, is sufficient for cellular transformation. Nonconserved, nucleotide-interacting residues within EhRho1, revealed by the crystal structure models, were observed to contribute a moderating influence on fast spontaneous nucleotide exchange. Collectively, these observations indicate that EhRho1 is a bona fide member of the Rho GTPase family, albeit with unique structural and functional aspects compared with mammalian Rho GTPases.

  5. Unique Structural and Nucleotide Exchange Features of the Rho1 GTPase of Entamoeba histolytica

    Energy Technology Data Exchange (ETDEWEB)

    Bosch, Dustin E.; Wittchen, Erika S.; Qiu, Connie; Burridge, Keith; Siderovski, David P. (UNC)

    2012-08-10

    The single-celled human parasite Entamoeba histolytica possesses a dynamic actin cytoskeleton vital for its intestinal and systemic pathogenicity. The E. histolytica genome encodes several Rho family GTPases known to regulate cytoskeletal dynamics. EhRho1, the first family member identified, was reported to be insensitive to the Rho GTPase-specific Clostridium botulinum C3 exoenzyme, raising the possibility that it may be a misclassified Ras family member. Here, we report the crystal structures of EhRho1 in both active and inactive states. EhRho1 is activated by a conserved switch mechanism, but diverges from mammalian Rho GTPases in lacking a signature Rho insert helix. EhRho1 engages a homolog of mDia, EhFormin1, suggesting a role in mediating serum-stimulated actin reorganization and microtubule formation during mitosis. EhRho1, but not a constitutively active mutant, interacts with a newly identified EhRhoGDI in a prenylation-dependent manner. Furthermore, constitutively active EhRho1 induces actin stress fiber formation in mammalian fibroblasts, thereby identifying it as a functional Rho family GTPase. EhRho1 exhibits a fast rate of nucleotide exchange relative to mammalian Rho GTPases due to a distinctive switch one isoleucine residue reminiscent of the constitutively active F28L mutation in human Cdc42, which for the latter protein, is sufficient for cellular transformation. Nonconserved, nucleotide-interacting residues within EhRho1, revealed by the crystal structure models, were observed to contribute a moderating influence on fast spontaneous nucleotide exchange. Collectively, these observations indicate that EhRho1 is a bona fide member of the Rho GTPase family, albeit with unique structural and functional aspects compared with mammalian Rho GTPases.

  6. Typography, Color, and Information Structure.

    Science.gov (United States)

    Keyes, Elizabeth

    1993-01-01

    Focuses on how typography and color complement and differ from each other in signaling an underlying content structure; the synergism between typography, color, and page layout (use of white space) that aids audience understanding and use; and the characteristics of typography and of color that are most important in these contexts. (SR)

  7. Typography, Color, and Information Structure.

    Science.gov (United States)

    Keyes, Elizabeth

    1993-01-01

    Focuses on how typography and color complement and differ from each other in signaling an underlying content structure; the synergism between typography, color, and page layout (use of white space) that aids audience understanding and use; and the characteristics of typography and of color that are most important in these contexts. (SR)

  8. Human blood basophils display a unique phenotype including activation linked membrane structures.

    Science.gov (United States)

    Stain, C; Stockinger, H; Scharf, M; Jäger, U; Gössinger, H; Lechner, K; Bettelheim, P

    1987-12-01

    To evaluate the membrane marker profile of human basophils a panel of well-established monoclonal antibodies (MoAbs, n = 60) was used for a combined toluidine/immunofluorescence staining procedure. Myeloid-associated MoAbs (particularly MoAbs against the LFA-1 family (CD11, CDw18), MoAbs directed against lactosylceramide (CDw17), anti-glycoprotein (gp) 150 MoAbs MCS 2 and MY 7 (CDw13), anti-gp 67 MoAb MY 9, anti Fc gamma-receptor (mol wt 40 kd) MoAb CIKM5, anti-CR 1 MoAb E 11, and the antiglycolipid MoAb VIM-2) were reactive with basophils, indicating a close relationship to other mature myeloid cells. Under normal conditions, basophils surprisingly express at least three activation-linked structures not detectable on mature neutrophils, ie, the p45 structure defined by MoAbs OKT-10 and VIP-2b, the p24 structure identified by the CD9 MoAb BA-2, and the receptor for interleukin 2 (IL 2) recognized by three different MoAbs (anti-TAC, IL2RI, anti-IL 2). Moreover, under short-term culture conditions basophils both in mononuclear cell (MNC) suspension and as purified fractions display the HLA-DR and T4 antigens. The neutrophilic/eosinophilic structure 3-fucosyl-N-acetyllactosamine is expressed on basophils only after neuraminidase treatment. Basophils were not stained at all by CD 16 MoAbs directed against the Fc gamma-receptor (mol wt 50 to 70 kd) of neutrophils, by the MoAb 63D3 (CDw12) recognizing the monocyte/granulocyte-associated p 200 antigen, and by the CDw 14 antibodies (VIM-13, Mo 2) defining the monocyte-specific structure p 55. Enriched basophils freshly obtained from chronic granulocytic leukemia (CGL) patients yielded identical results in FACS analyses. In summary, these data indicate that basophils generate a unique combination of surface determinants and possibly represent an activated cell population.

  9. Information Handling, Organizational Structure, and Power.

    Science.gov (United States)

    Buckland, Michael K.

    1989-01-01

    Uses examples from military strategic communications to demonstrate that organizational structures and the distribution of power within organizational structures adapt to changes in information handling capability. It is concluded that delegation and decentralization can be viewed as indicative of inadequate information handling and that improved…

  10. Information Structure, Grammar and Strategy in Discourse

    Science.gov (United States)

    Stevens, Jon

    2013-01-01

    This dissertation examines two information-structural phenomena, Givenness and Focus, from the perspective of both syntax and pragmatics. Evidence from English, German and other languages suggests a "split" analysis of information structure--the notions of Focus and Givenness, often thought to be closely related, exist independently at…

  11. A Grammar Library for Information Structure

    Science.gov (United States)

    Song, Sanghoun

    2014-01-01

    This dissertation makes substantial contributions to both the theoretical and computational treatment of information structure, with an eye toward creating natural language processing applications such as multilingual machine translation systems. The aim of the present dissertation is to create a grammar library of information structure for the…

  12. Antinociceptive profile of salvinorin A, a structurally unique kappa opioid receptor agonist.

    Science.gov (United States)

    McCurdy, Christopher R; Sufka, Kenneth J; Smith, Grant H; Warnick, Jason E; Nieto, Marcelo J

    2006-01-01

    Salvinorin A, is a structurally unique, non-nitrogenous, kappa opioid receptor (KOP) agonist. Given the role of KOPs in analgesic processes, we set out to determine whether salvinorin A has antinociceptive activity in thermal and chemo-nociceptive assays. The tail-flick assay was employed to investigate 1) salvinorin A's (0.5, 1.0, 2.0, and 4.0 mg/kg) dose-response and time-course (10, 20, and 30 min) effects in a thermal nociceptive assay, and 2) the ability for the KOP antagonist norBNI (10.0 mg/kg) to prevent salvinorin A antinociception. The hotplate assay was utilized as a second thermal nociceptive measure to test salvinorin A's dose-response effects. The acetic acid abdominal constriction assay was used to study salvinorin A's dose-response and time-course (over 30 min) effects in a chemo-nociceptive assay. Together, these studies revealed that salvinorin A produces a dose-dependent antinociception that peaked at 10 min post-injection but rapidly returned to baseline. Additionally, pretreatment with the KOP antagonist norbinaltorphimine (norBNI) reversed salvinorin A-induced antinociception. These findings demonstrate that salvinorin A produces a KOP mediated antinociceptive effect with a short duration of action.

  13. Structure Of Management Information In SNMP

    Directory of Open Access Journals (Sweden)

    Oancea DANIEL

    2003-12-01

    Full Text Available In this article we present the Structure of Management Information from SNMP, for all three versions of SNMP, as well as the main differences between them. In the first part, two version of SNMP are presented: version 1, version 2; and in the last part the third version, that uses a security model for information protection, is presented.

  14. Structural Information Retention in Visual Art Processing.

    Science.gov (United States)

    Koroscik, Judith Smith

    The accuracy of non-art college students' longterm retention of structural information presented in Leonardo da Vinci's "Mona Lisa" was tested. Seventeen female undergraduates viewed reproductions of the painting and copies that closely resembled structural attributes of the original. Only 3 of the 17 subjects reported having viewed a reproduction…

  15. Structural Information Retention in Visual Art Processing.

    Science.gov (United States)

    Koroscik, Judith Smith

    The accuracy of non-art college students' longterm retention of structural information presented in Leonardo da Vinci's "Mona Lisa" was tested. Seventeen female undergraduates viewed reproductions of the painting and copies that closely resembled structural attributes of the original. Only 3 of the 17 subjects reported having viewed a reproduction…

  16. Structural characterization and antioxidative activity of lancifonins: unique nortriterpenoids from Schisandra lancifolia.

    Science.gov (United States)

    Shi, Yi-Ming; Yang, Jie; Xu, Li; Li, Xiao-Nian; Shang, Shan-Zhai; Cao, Peng; Xiao, Wei-Lie; Sun, Han-Dong

    2014-03-01

    Six unique nortriterpenoids, lancifonins A-F (1-6), were isolated from Schisandra lancifolia. Their absolute configurations were determined by X-ray diffraction and ECD calculation. The conformational analysis of 1 was performed due to the unanticipated changes of Cotton effects in its ECD spectrum. Compounds 5 and 6 possess a unique 7/7 fused carbocyclic core with an internal ester bridge between C-9 and C-14, and 5 exhibited protective activity against H2O2-induced oxidative damage on Caco-2 cells.

  17. Value of Information Analysis in Structural Safety

    DEFF Research Database (Denmark)

    Konakli, Katerina; Faber, Michael Havbro

    2014-01-01

    of structural systems. In this context, experiments may refer to inspections or techniques of structural health monitoring. The Value of Information concept provides a powerful tool for determining whether the experimental cost is justified by the expected benefit and for identifying the optimal among different......Pre-posterior analysis can be used to assess the potential of an experiment to enhance decision making by providing information on parameters characterized by uncertainty. The present paper describes a framework for pre-posterior analysis for support of decisions related to maintenance...... and quality of information and the probabilistic dependencies between components of a system....

  18. Advanced Data Structure and Geographic Information Systems

    Science.gov (United States)

    Peuquet, D. (Principal Investigator)

    1984-01-01

    The current state of the art in specified areas of Geographic Information Systems GIS technology is examined. Study of the question of very large, efficient, heterogeneous spatial databases is required in order to explore the potential application of remotely sensed data for studying the long term habitability of the Earth. Research includes a review of spatial data structures and storage, development of operations required by GIS, and preparation of a testbed system to compare Vaster data structure with NASA's Topological Raster Structure.

  19. A unique structure for the multiplexer in quantum-dot cellular automata to create a revolution in design of nanostructures

    Energy Technology Data Exchange (ETDEWEB)

    Naji Asfestani, Mazaher; Rasouli Heikalabad, Saeed, E-mail: s.rasouli@iaut.ac.ir

    2017-05-01

    Quantum-dot cellular automata (QCA) is the advent of technology and suitable replacement for semiconductor transistor technology. In this paper, a unique structure for the 2:1 multiplexer is presented in QCA. The structure of this component is simple, ultra-efficient and very useful to implement the various logical functions. The proposed structure does not follow any Boolean function. It takes advantage of the inherent characteristics of quantum technology to produce the desired output. Based on these principles, we design the new and efficient structures for the 4:1 multiplexer and 8:1 multiplexer in the QCA technology. These structures are designed with QCADesigner simulator and simulation results are examined. Investigation results indicate the amazing performance of proposed structure compared to existing structures in terms of area, complexity, power consumption and latency.

  20. Structured pedigree information for distributed fusion systems

    Science.gov (United States)

    Arambel, Pablo O.

    2008-04-01

    One of the most critical challenges in distributed data fusion is the avoidance of information double counting (also called "data incest" or "rumor propagation"). This occurs when a node in a network incorporates information into an estimate - e.g. the position of an object - and the estimate is injected into the network. Other nodes fuse this estimate with their own estimates, and continue to propagate estimates through the network. When the first node receives a fused estimate from the network, it does not know if it already contains its own contributions or not. Since the correlation between its own estimate and the estimate received from the network is not known, the node can not fuse the estimates in an optimal way. If it assumes that both estimates are independent from each other, it unknowingly double counts the information that has already being used to obtain the two estimates. This leads to overoptimistic error covariance matrices. If the double-counting is not kept under control, it may lead to serious performance degradation. Double counting can be avoided by propagating uniquely tagged raw measurements; however, that forces each node to process all the measurements and precludes the propagation of derived information. Another approach is to fuse the information using the Covariance Intersection (CI) equations, which maintain consistent estimates irrespective of the cross-correlation among estimates. However, CI does not exploit pedigree information of any kind. In this paper we present an approach that propagates multiple covariance matrices, one for each uncorrelated source in the network. This is a way to compress the pedigree information and avoids the need to propagate raw measurements. The approach uses a generalized version of the Split CI to fuse different estimates with appropriate weights to guarantee the consistency of the estimates.

  1. Information Processing Structure of Quantum Gravity

    Science.gov (United States)

    Gyongyosi, Laszlo; Imre, Sandor

    2014-05-01

    The theory of quantum gravity is aimed to fuse general relativity with quantum theory into a more fundamental framework. Quantum gravity provides both the non-fixed causality of general relativity and the quantum uncertainty of quantum mechanics. In a quantum gravity scenario, the causal structure is indefinite and the processes are causally non-separable. We provide a model for the information processing structure of quantum gravity. We show that the quantum gravity environment is an information resource-pool from which valuable information can be extracted. We analyze the structure of the quantum gravity space and the entanglement of the space-time geometry. We study the information transfer capabilities of quantum gravity space and define the quantum gravity channel. We characterize the information transfer of the gravity space and the correlation measure functions of the gravity channel. We investigate the process of stimulated storage for quantum gravity memories, a phenomenon that exploits the information resource-pool property of quantum gravity. The results confirm that the benefits of the quantum gravity space can be exploited in quantum computations, particularly in the development of quantum computers. The results are supported by the grant COST Action MP1006.

  2. Structuring medication related activities for information management.

    Science.gov (United States)

    Luukkonen, Irmeli; Mykkänen, Juha; Kivekäs, Eija; Saranto, Kaija

    2014-01-01

    Medication treatment and the related information management are central parts of a patient's health care. As a cross-organizational and cooperative process, medication information management is a complex domain for development activities. We studied medication activities and related information management in a regional project in order to produce a shared broad picture of its processes and to understand the main issues and the needs for improvement. In this paper we provide a summary of the findings in a structured form, based on a six-dimensioned framework for design and analysis of activities and processes.

  3. Unique Reversible Crystal-to-Crystal Phase Transition – Structural and Functional Properties of Fused Ladder Thienoarenes

    KAUST Repository

    Abe, Yuichiro

    2017-08-15

    Donor-acceptor type molecules based on fused ladder thienoarenes, indacenodithiophene (IDT) and dithienocyclopenta-thienothiophene (DTCTT), coupled with benzothiadiazole, are prepared and their solid-state structures are investigated. They display a rich variety of solid phases ranging from amorphous glass states to crystalline states, upon changes in the central aromatic core and side group structures. Most notably, the DTCTT-based derivatives showed reversible crystal-to-crystal phase transitions in heating and cooling cycles. Unlike what has been seen in π−conjugated molecules variable temperature XRD revealed that structural change occurs continuously during the transition. A columnar self-assembled structure with slip-stacked π−π interaction is proposed to be involved in the solid-state. This research provides the evidence of unique structural behavior of the DTCTT-based molecules through the detailed structural analysis. This unique structural transition paves the way for these materials to have self-healing of crystal defects, leading to improved optoelectronic properties.

  4. Management Information Systems and Organizational Structure.

    Science.gov (United States)

    Cox, Bruce B.

    1987-01-01

    Discusses the context within which office automation takes place by using the models of the Science of Creative Intelligence and Transcendental Meditation. Organizational structures are compared to the phenomenon of the "collective consciousness" and the development of automated information systems from manual methods of organizational…

  5. INFORMATION ON THE NEW CAREER STRUCTURE

    CERN Multimedia

    Human Resources Division

    2001-01-01

    Since Council approved the new Career Structure last December, work has been progressing to prepare for the implementation of the new scheme on 1 September 2001. The necessary amendments to the Staff Rules and Regulations were approved by the Finance Committee and Council last week, and related explanatory documents are being drawn up and will be available shortly for consultation. As announced earlier, a series of information meetings has started in the Divisions in order to present the new scheme and to give the opportunity for questions from the staff. These information meetings are being held over the period from 20 June to 4 July. Further information concerning the new Career Structure will be announced in the coming weeks.

  6. An information criterion for marginal structural models.

    Science.gov (United States)

    Platt, Robert W; Brookhart, M Alan; Cole, Stephen R; Westreich, Daniel; Schisterman, Enrique F

    2013-04-15

    Marginal structural models were developed as a semiparametric alternative to the G-computation formula to estimate causal effects of exposures. In practice, these models are often specified using parametric regression models. As such, the usual conventions regarding regression model specification apply. This paper outlines strategies for marginal structural model specification and considerations for the functional form of the exposure metric in the final structural model. We propose a quasi-likelihood information criterion adapted from use in generalized estimating equations. We evaluate the properties of our proposed information criterion using a limited simulation study. We illustrate our approach using two empirical examples. In the first example, we use data from a randomized breastfeeding promotion trial to estimate the effect of breastfeeding duration on infant weight at 1 year. In the second example, we use data from two prospective cohorts studies to estimate the effect of highly active antiretroviral therapy on CD4 count in an observational cohort of HIV-infected men and women. The marginal structural model specified should reflect the scientific question being addressed but can also assist in exploration of other plausible and closely related questions. In marginal structural models, as in any regression setting, correct inference depends on correct model specification. Our proposed information criterion provides a formal method for comparing model fit for different specifications.

  7. Optimal Control Strategies in Delayed Sharing Information Structures

    CERN Document Server

    Nayyar, Ashutosh; Teneketzis, Demosthenis

    2010-01-01

    The $n$-step delayed sharing information structure is investigated. This information structure comprises of $K$ controllers that share their information with a delay of $n$ time steps. This information structure is a link between the classical information structure, where information is shared perfectly between the controllers, and a non-classical information structure, where there is no "lateral" sharing of information among the controllers. Structural results for optimal control strategies for systems with such information structures are presented. A sequential methodology for finding the optimal strategies is also derived. The solution approach provides an insight for identifying structural results and sequential decomposition for general decentralized stochastic control problems.

  8. Unique Gene-Silencing and Structural Properties of 2;#8242;-Fluoro-Modified siRNAs

    Energy Technology Data Exchange (ETDEWEB)

    Manoharan, Muthiah; Akinc, Akin; Pandey, Rajendra K.; Qin, June; Hadwiger, Philipp; John, Matthias; Mills, Kathy; Charisse, Klaus; Maier, Martin A.; Nechev, Lubomir; Greene, Emily M.; Pallan, Pradeep S.; Rozners, Eriks; Rajeev, Kallanthottathil G.; Egli, Martin (Binghamton); (Alnylam Pharm.); (Vanderbilt)

    2015-10-15

    With little or no negative impact on the activity of small interfering RNAs (siRNAs), regardless of the number of modifications or the positions within the strand, the 2'-deoxy-2'-fluoro (2'-F) modification is unique. Furthermore, the 2'-F-modified siRNA (see crystal structure) was thermodynamically more stable and more nuclease-resistant than the parent siRNA, and produced no immunostimulatory response.

  9. Nuclear Resonance Scattering of Synchrotron Radiation as a Unique Electronic, Structural, and Thermodynamic Probe

    Science.gov (United States)

    Alp, E. Ercan; Sturhahn, Wolfgang; Toellner, Thomas S.; Zhao, Jiyong; Leu, Bogdan M.

    Discovery of Mössbauer effect [1] in a nuclear transition was a remarkable development. It revealed how long-lived nuclear states with relatively low energies in the kiloelectron volt (keV) region can be excited without recoil. This new effect had a unique feature involving a coupling between nuclear physics and solid-state physics, both in terms of physics and sociology. Physics coupling originates from the fact that recoilless emission and absorption or resonance is only possible if the requirement that nuclei have to be bound in a lattice with quantized vibrational states is fulfilled, and that the finite electron density on the nucleus couples to nuclear degrees of freedom leading to hyperfine interactions. Thus, Mössbauer spectroscopy allows peering into solid-state effects using unique nuclear transitions. Sociological aspects of this coupling had been equally startling and fruitful. The interaction between diverse scientific communities, who learned to use Mössbauer spectroscopy proved to be very valuable. For example, biologists, geologists, chemists, physicists, materials scientists, and archeologists, all sharing a common spectroscopic technique, also learned to appreciate the beauty and intricacies of each other's fields. As a laboratory-based technique, Mössbauer spectroscopy matured by the end of the 1970s. Further exciting developments took place when accelerator-based techniques were employed, like synchrotron radiation or "in-beam" Mössbauer experiments with implanted radioactive ions. More recently, two Mössbauer spectrometers on the surface of the Mars kept the technique vibrant and viable up until present time.

  10. Informational technologies in modern educational structure

    Science.gov (United States)

    Fedyanin, A. B.

    2017-01-01

    The article represents the structure of informational technologies complex that is applied in modern school education, describes the most important educational methods, shows the results of their implementation. It represents the forms and methods of educational process informative support usage, examined in respects of different aspects of their using that take into account also the psychological features of students. A range of anxious facts and dangerous trends connected with the usage and distribution of the informational technologies that are to be taken into account in the educational process of informatization is also indicated in the article. Materials of the article are based on the experience of many years in operation and development of the informational educational sphere on the basis of secondary school of the physics and mathematics specialization.

  11. Validation of a unique concept for a low-cost, lightweight space-deployable antenna structure

    Science.gov (United States)

    Freeland, R. E.; Bilyeu, G. D.; Veal, G. R.

    1993-01-01

    An experiment conducted in the framework of a NASA In-Space Technology Experiments Program based on a concept of inflatable deployable structures is described. The concept utilizes very low inflation pressure to maintain the required geometry on orbit and gravity-induced deflection of the structure precludes any meaningful ground-based demonstrations of functions performance. The experiment is aimed at validating and characterizing the mechanical functional performance of a 14-m-diameter inflatable deployable reflector antenna structure in the orbital operational environment. Results of the experiment are expected to significantly reduce the user risk associated with using large space-deployable antennas by demonstrating the functional performance of a concept that meets the criteria for low-cost, lightweight, and highly reliable space-deployable structures.

  12. Nuclear Magnetic Resonance Structure Shows that the Severe Acute Respiratory Syndrome Coronavirus-Unique Domain Contains a Macrodomain Fold▿

    Science.gov (United States)

    Chatterjee, Amarnath; Johnson, Margaret A.; Serrano, Pedro; Pedrini, Bill; Joseph, Jeremiah S.; Neuman, Benjamin W.; Saikatendu, Kumar; Buchmeier, Michael J.; Kuhn, Peter; Wüthrich, Kurt

    2009-01-01

    The nuclear magnetic resonance (NMR) structure of a central segment of the previously annotated severe acute respiratory syndrome (SARS)-unique domain (SUD-M, for “middle of the SARS-unique domain”) in SARS coronavirus (SARS-CoV) nonstructural protein 3 (nsp3) has been determined. SUD-M(513-651) exhibits a macrodomain fold containing the nsp3 residues 528 to 648, and there is a flexibly extended N-terminal tail with the residues 513 to 527 and a C-terminal flexible tail of residues 649 to 651. As a follow-up to this initial result, we also solved the structure of a construct representing only the globular domain of residues 527 to 651 [SUD-M(527-651)]. NMR chemical shift perturbation experiments showed that SUD-M(527-651) binds single-stranded poly(A) and identified the contact area with this RNA on the protein surface, and electrophoretic mobility shift assays then confirmed that SUD-M has higher affinity for purine bases than for pyrimidine bases. In a further search for clues to the function, we found that SUD-M(527-651) has the closest three-dimensional structure homology with another domain of nsp3, the ADP-ribose-1"-phosphatase nsp3b, although the two proteins share only 5% sequence identity in the homologous sequence regions. SUD-M(527-651) also shows three-dimensional structure homology with several helicases and nucleoside triphosphate-binding proteins, but it does not contain the motifs of catalytic residues found in these structural homologues. The combined results from NMR screening of potential substrates and the structure-based homology studies now form a basis for more focused investigations on the role of the SARS-unique domain in viral infection. PMID:19052085

  13. Information Processing Structure of Quantum Gravity

    CERN Document Server

    Gyongyosi, Laszlo

    2014-01-01

    The theory of quantum gravity is aimed to fuse general relativity with quantum theory into a more fundamental framework. The space of quantum gravity provides both the non-fixed causality of general relativity and the quantum uncertainty of quantum mechanics. In a quantum gravity scenario, the causal structure is indefinite and the processes are causally non-separable. In this work, we provide a model for the information processing structure of quantum gravity. We show that the quantum gravity environment is an information resource-pool from which valuable information can be extracted. We analyze the structure of the quantum gravity space and the entanglement of the space-time geometry. We study the information transfer capabilities of quantum gravity space and define the quantum gravity channel. We reveal that the quantum gravity space acts as a background noise on the local environment states. We characterize the properties of the noise of the quantum gravity space and show that it allows the separate local...

  14. Crystal structure of Mox-1, a unique plasmid-mediated class C β-lactamase with hydrolytic activity towards moxalactam.

    Science.gov (United States)

    Oguri, Takuma; Furuyama, Takamitsu; Okuno, Takashi; Ishii, Yoshikazu; Tateda, Kazuhiro; Bonomo, Robert A; Shimizu-Ibuka, Akiko

    2014-07-01

    Mox-1 is a unique plasmid-mediated class C β-lactamase that hydrolyzes penicillins, cephalothin, and the expanded-spectrum cephalosporins cefepime and moxalactam. In order to understand the unique substrate profile of this enzyme, we determined the X-ray crystallographic structure of Mox-1 β-lactamase at a 1.5-Å resolution. The overall structure of Mox-1 β-lactamase resembles that of other AmpC enzymes, with some notable exceptions. First, comparison with other enzymes whose structures have been solved reveals significant differences in the composition of amino acids that make up the hydrogen-bonding network and the position of structural elements in the substrate-binding cavity. Second, the main-chain electron density is not observed in two regions, one containing amino acid residues 214 to 216 positioned in the Ω loop and the other in the N terminus of the B3 β-strand corresponding to amino acid residues 303 to 306. The last two observations suggest that there is significant structural flexibility of these regions, a property which may impact the recognition and binding of substrates in Mox-1. These important differences allow us to propose that the binding of moxalactam in Mox-1 is facilitated by the avoidance of steric clashes, indicating that a substrate-induced conformational change underlies the basis of the hydrolytic profile of Mox-1 β-lactamase.

  15. O'nyong nyong virus molecular determinants of unique vector specificity reside in non-structural protein 3.

    Directory of Open Access Journals (Sweden)

    Kali D Saxton-Shaw

    Full Text Available O'nyong nyong virus (ONNV and Chikungunya virus (CHIKV are two closely related alphaviruses with very different infection patterns in the mosquito, Anopheles gambiae. ONNV is the only alphavirus transmitted by anopheline mosquitoes, but specific molecular determinants of infection of this unique vector specificity remain unidentified. Fifteen distinct chimeric viruses were constructed to evaluate both structural and non-structural regions of the genome and infection patterns were determined through artificial infectious feeds in An. gambiae with each of these chimeras. Only one region, non-structural protein 3 (nsP3, was sufficient to up-regulate infection to rates similar to those seen with parental ONNV. When ONNV non-structural protein 3 (nsP3 replaced nsP3 from CHIKV virus in one of the chimeric viruses, infection rates in An. gambiae went from 0% to 63.5%. No other single gene or viral region addition was able to restore infection rates. Thus, we have shown that a non-structural genome element involved in viral replication is a major element involved in ONNV's unique vector specificity.

  16. O'nyong nyong virus molecular determinants of unique vector specificity reside in non-structural protein 3.

    Science.gov (United States)

    Saxton-Shaw, Kali D; Ledermann, Jeremy P; Borland, Erin M; Stovall, Janae L; Mossel, Eric C; Singh, Amber J; Wilusz, Jeffrey; Powers, Ann M

    2013-01-01

    O'nyong nyong virus (ONNV) and Chikungunya virus (CHIKV) are two closely related alphaviruses with very different infection patterns in the mosquito, Anopheles gambiae. ONNV is the only alphavirus transmitted by anopheline mosquitoes, but specific molecular determinants of infection of this unique vector specificity remain unidentified. Fifteen distinct chimeric viruses were constructed to evaluate both structural and non-structural regions of the genome and infection patterns were determined through artificial infectious feeds in An. gambiae with each of these chimeras. Only one region, non-structural protein 3 (nsP3), was sufficient to up-regulate infection to rates similar to those seen with parental ONNV. When ONNV non-structural protein 3 (nsP3) replaced nsP3 from CHIKV virus in one of the chimeric viruses, infection rates in An. gambiae went from 0% to 63.5%. No other single gene or viral region addition was able to restore infection rates. Thus, we have shown that a non-structural genome element involved in viral replication is a major element involved in ONNV's unique vector specificity.

  17. Crystal structure of an invertebrate cytolysin pore reveals unique properties and mechanism of assembly

    Science.gov (United States)

    Podobnik, Marjetka; Savory, Peter; Rojko, Nejc; Kisovec, Matic; Wood, Neil; Hambley, Richard; Pugh, Jonathan; Wallace, E. Jayne; McNeill, Luke; Bruce, Mark; Liko, Idlir; Allison, Timothy M.; Mehmood, Shahid; Yilmaz, Neval; Kobayashi, Toshihide; Gilbert, Robert J. C.; Robinson, Carol V.; Jayasinghe, Lakmal; Anderluh, Gregor

    2016-05-01

    The invertebrate cytolysin lysenin is a member of the aerolysin family of pore-forming toxins that includes many representatives from pathogenic bacteria. Here we report the crystal structure of the lysenin pore and provide insights into its assembly mechanism. The lysenin pore is assembled from nine monomers via dramatic reorganization of almost half of the monomeric subunit structure leading to a β-barrel pore ~10 nm long and 1.6-2.5 nm wide. The lysenin pore is devoid of additional luminal compartments as commonly found in other toxin pores. Mutagenic analysis and atomic force microscopy imaging, together with these structural insights, suggest a mechanism for pore assembly for lysenin. These insights are relevant to the understanding of pore formation by other aerolysin-like pore-forming toxins, which often represent crucial virulence factors in bacteria.

  18. KLIKK proteases of Tannerella forsythia: putative virulence factors with a unique domain structure

    Science.gov (United States)

    Ksiazek, Miroslaw; Mizgalska, Danuta; Eick, Sigrum; Thøgersen, Ida B.; Enghild, Jan J.; Potempa, Jan

    2015-01-01

    Comparative genomics of virulent Tannerella forsythia ATCC 43037 and a close health-associated relative, Tannerella BU063, revealed, in the latter, the absence of an entire array of genes encoding putative secretory proteases that possess a nearly identical C-terminal domain (CTD) that ends with a -Lys-Leu-Ile-Lys-Lys motif. This observation suggests that these proteins, referred to as KLIKK proteases, may function as virulence factors. Re-sequencing of the loci of the KLIKK proteases found only six genes grouped in two clusters. All six genes were expressed by T. forsythia in routine culture conditions, although at different levels. More importantly, a transcript of each gene was detected in gingival crevicular fluid (GCF) from periodontitis sites infected with T. forsythia indicating that the proteases are expressed in vivo. In each protein, a protease domain was flanked by a unique N-terminal profragment and a C-terminal extension ending with the CTD. Partially purified recombinant proteases showed variable levels of proteolytic activity in zymography gels and toward protein substrates, including collagen, gelatin, elastin, and casein. Taken together, these results indicate that the pathogenic strain of T. forsythia secretes active proteases capable of degrading an array of host proteins, which likely represents an important pathogenic feature of this bacterium. PMID:25954253

  19. KLIKK proteases of Tannerella forsythia: putative virulence factors with a unique domain structure

    Directory of Open Access Journals (Sweden)

    Miroslaw eKsiazek

    2015-04-01

    Full Text Available Comparative genomics of virulent Tannerella forsythia ATCC 43037 and a close health-associated relative, Tannerella BU063, revealed, in the latter, the absence of an entire array of genes encoding putative secretory proteases that possess a nearly identical C-terminal domain (CTD that ends with a -Lys-Leu-Ile-Lys-Lys motif. This observation suggests that these proteins, referred to as KLIKK proteases, may function as virulence factors. Re-sequencing of the loci of the KLIKK proteases found only six genes grouped in two clusters. All six genes were expressed by T. forsythia in routine culture conditions, although at different levels. More importantly, a transcript of each gene was detected in gingival crevicular fluid (GCF from periodontitis sites infected with T. forsythia indicating that the proteases are expressed in vivo. In each protein, a protease domain was flanked by a unique N-terminal profragment and a C-terminal extension ending with the CTD. Partially purified recombinant proteases showed variable levels of proteolytic activity in zymography gels and toward protein substrates, including collagen, gelatin, elastin, and casein. Taken together, these results indicate that the pathogenic strain of T. forsythia secretes active proteases capable of degrading an array of host proteins, which likely represents an important pathogenic feature of this bacterium.

  20. KLIKK proteases of Tannerella forsythia: putative virulence factors with a unique domain structure.

    Science.gov (United States)

    Ksiazek, Miroslaw; Mizgalska, Danuta; Eick, Sigrum; Thøgersen, Ida B; Enghild, Jan J; Potempa, Jan

    2015-01-01

    Comparative genomics of virulent Tannerella forsythia ATCC 43037 and a close health-associated relative, Tannerella BU063, revealed, in the latter, the absence of an entire array of genes encoding putative secretory proteases that possess a nearly identical C-terminal domain (CTD) that ends with a -Lys-Leu-Ile-Lys-Lys motif. This observation suggests that these proteins, referred to as KLIKK proteases, may function as virulence factors. Re-sequencing of the loci of the KLIKK proteases found only six genes grouped in two clusters. All six genes were expressed by T. forsythia in routine culture conditions, although at different levels. More importantly, a transcript of each gene was detected in gingival crevicular fluid (GCF) from periodontitis sites infected with T. forsythia indicating that the proteases are expressed in vivo. In each protein, a protease domain was flanked by a unique N-terminal profragment and a C-terminal extension ending with the CTD. Partially purified recombinant proteases showed variable levels of proteolytic activity in zymography gels and toward protein substrates, including collagen, gelatin, elastin, and casein. Taken together, these results indicate that the pathogenic strain of T. forsythia secretes active proteases capable of degrading an array of host proteins, which likely represents an important pathogenic feature of this bacterium.

  1. Information transfer in community structured multiplex networks

    Directory of Open Access Journals (Sweden)

    Albert eSolé Ribalta

    2015-08-01

    Full Text Available The study of complex networks that account for different types of interactions has become a subject of interest in the last few years, specially because its representational power in the description of users interactions in diverse online social platforms (Facebook, Twitter, Instagram, etc.. The mathematical description of these interacting networks has been coined under the name of multilayer networks, where each layer accounts for a type of interaction. It has been shown that diffusive processes on top of these networks present a phenomenology that cannot be explained by the naive superposition of single layer diffusive phenomena but require the whole structure of interconnected layers. Nevertheless, the description of diffusive phenomena on multilayer networks has obviated the fact that social networks have strong mesoscopic structure represented by different communities of individuals driven by common interests, or any other social aspect. In this work, we study the transfer of information in multilayer networks with community structure. The final goal is to understand and quantify, if the existence of well-defined community structure at the level of individual layers, together with the multilayer structure of the whole network, enhances or deteriorates the diffusion of packets of information.

  2. Creating Imaginative Worlds: Unique Details and Structure in Norma Fox Mazer's Young Adult Fiction.

    Science.gov (United States)

    Angel, Ann

    2001-01-01

    Discusses how writer Norma Fox Mazer has helped many readers make the leap between reality and imagination simply in the way she handles details in the lives of her characters. Explores the ideas of communicating with detail, experimenting with structure, and playing with time in crucial scenes. (SG)

  3. CDK1 structures reveal conserved and unique features of the essential cell cycle CDK

    Science.gov (United States)

    Brown, Nicholas R.; Korolchuk, Svitlana; Martin, Mathew P.; Stanley, Will A.; Moukhametzianov, Rouslan; Noble, Martin E. M.; Endicott, Jane A.

    2015-04-01

    CDK1 is the only essential cell cycle CDK in human cells and is required for successful completion of M-phase. It is the founding member of the CDK family and is conserved across all eukaryotes. Here we report the crystal structures of complexes of CDK1-Cks1 and CDK1-cyclin B-Cks2. These structures confirm the conserved nature of the inactive monomeric CDK fold and its ability to be remodelled by cyclin binding. Relative to CDK2-cyclin A, CDK1-cyclin B is less thermally stable, has a smaller interfacial surface, is more susceptible to activation segment dephosphorylation and shows differences in the substrate sequence features that determine activity. Both CDK1 and CDK2 are potential cancer targets for which selective compounds are required. We also describe the first structure of CDK1 bound to a potent ATP-competitive inhibitor and identify aspects of CDK1 structure and plasticity that might be exploited to develop CDK1-selective inhibitors.

  4. Creating Imaginative Worlds: Unique Details and Structure in Norma Fox Mazer's Young Adult Fiction.

    Science.gov (United States)

    Angel, Ann

    2001-01-01

    Discusses how writer Norma Fox Mazer has helped many readers make the leap between reality and imagination simply in the way she handles details in the lives of her characters. Explores the ideas of communicating with detail, experimenting with structure, and playing with time in crucial scenes. (SG)

  5. Information and hierarchical structure in financial markets

    Science.gov (United States)

    Mantegna, R. N.

    1999-09-01

    I investigate the information content present in the time series of stock prices of a portfolio of stocks traded in a financial market. By investigating the correlation coefficient between pairs of stocks I provide a working definition of a generalized distance between the stocks of the portfolio. This generalized distance is used to obtain an ultrametric distance matrix between the stocks. The ultrametric structure of the portfolio investigated has associated a taxonomy which is meaningful from an economic point of view.

  6. Syndecans as cell surface receptors: Unique structure equates with functional diversity

    DEFF Research Database (Denmark)

    Choi, Youngsil; Chung, Heesung; Jung, Heyjung

    2011-01-01

    An increasing number of functions for syndecan cell surface heparan sulfate proteoglycans have been proposed over the last decade. Moreover, aberrant syndecan regulation has been found to play a critical role in multiple pathologies, including cancers, as well as wound healing and inflammation. A...... glycosaminoglycan chains, especially heparan sulfate. This heterodisperse polysaccharide has the potential to interact with many ligands from diverse protein families. Here, we relate the structural features of syndecans to some of their known functions....

  7. Enhancing community detection by local structural information

    CERN Document Server

    Xiang, Ju; Zhang, Yan; Bao, Mei-Hua; Tang, Liang; Tang, Yan-Ni; Gao, Yuan-Yuan; Li, Jian-Ming; Chen, Benyan; Hu, Jing-Bo

    2016-01-01

    Many real-world networks such as the gene networks, protein-protein interaction networks and metabolic networks exhibit community structures, meaning the existence of groups of densely connected vertices in the networks. Many local similarity measures in the networks are closely related to the concept of the community structures, and may have positive effect on community detection in the networks. Here, various local similarity measures are used to extract the local structural information and then are applied to community detection in the networks by using the edge-reweighting strategy. The effect of the local similarity measures on community detection is carefully investigated and compared in various networks. The experimental results show that the local similarity measures are crucial to the improvement for the community detection methods, while the positive effect of the local similarity measures is closely related to the networks under study and the applied community detection methods.

  8. Euglena gracilis ascorbate peroxidase forms an intramolecular dimeric structure: its unique molecular characterization.

    Science.gov (United States)

    Ishikawa, Takahiro; Tajima, Naoko; Nishikawa, Hitoshi; Gao, Yongshun; Rapolu, Madhusudhan; Shibata, Hitoshi; Sawa, Yoshihiro; Shigeoka, Shigeru

    2010-02-09

    Euglena gracilis lacks a catalase and contains a single APX (ascorbate peroxidase) and enzymes related to the redox cycle of ascorbate in the cytosol. In the present study, a full-length cDNA clone encoding the Euglena APX was isolated and found to contain an open reading frame encoding a protein of 649 amino acids with a calculated molecular mass of 70.5 kDa. Interestingly, the enzyme consisted of two entirely homologous catalytic domains, designated APX-N and APX-C, and an 102 amino acid extension in the N-terminal region, which had a typical class II signal proposed for plastid targeting in Euglena. A computer-assisted analysis indicated a novel protein structure with an intramolecular dimeric structure. The analysis of cell fractionation showed that the APX protein is distributed in the cytosol, but not the plastids, suggesting that Euglena APX becomes mature in the cytosol after processing of the precursor. The kinetics of the recombinant mature FL (full-length)-APX and the APX-N and APX-C domains with ascorbate and H2O2 were almost the same as that of the native enzyme. However, the substrate specificity of the mature FL-APX and the native enzyme was different from that of APX-N and APX-C. The mature FL-APX, but not the truncated forms, could reduce alkyl hydroperoxides, suggesting that the dimeric structure is correlated with substrate recognition. In Euglena cells transfected with double-stranded RNA, the silencing of APX expression resulted in a significant increase in the cellular level of H2O2, indicating the physiological importance of APX to the metabolism of H2O2.

  9. Strong guest binding by cyclodextrin hosts in competing nonpolar solvents and the unique crystalline structure.

    Science.gov (United States)

    Kida, Toshiyuki; Iwamoto, Takuya; Fujino, Yoshinori; Tohnai, Norimitsu; Miyata, Mikiji; Akashi, Mitsuru

    2011-09-02

    6-O-Modified β-cyclodextrins, such as heptakis(6-O-triisopropylsilyl)-β-cyclodextrin (TIPS-β-CD) and heptakis(6-O-tert-butyldimethylsilyl)-β-cyclodextrin (TBDMS-β-CD), formed 2:1 inclusion complexes with pyrene in benzene and cyclohexane with high association constants. The X-ray crystalline structure of the TIPS-β-CD-pyrene complex obtained from the benzene solution showed that one pyrene molecule was incorporated in the form of a sandwich-type complex with two benzene molecules within the cavity of the dimer formed by two TIPS-β-CD molecules.

  10. Structural, Bioinformatic, and In Vivo Analyses of Two Treponema pallidum Lipoproteins Reveal a Unique TRAP Transporter

    Energy Technology Data Exchange (ETDEWEB)

    Deka, Ranjit K.; Brautigam, Chad A.; Goldberg, Martin; Schuck, Peter; Tomchick, Diana R.; Norgard, Michael V. (NIH); (UTSMC)

    2012-05-25

    Treponema pallidum, the bacterial agent of syphilis, is predicted to encode one tripartite ATP-independent periplasmic transporter (TRAP-T). TRAP-Ts typically employ a periplasmic substrate-binding protein (SBP) to deliver the cognate ligand to the transmembrane symporter. Herein, we demonstrate that the genes encoding the putative TRAP-T components from T. pallidum, tp0957 (the SBP), and tp0958 (the symporter), are in an operon with an uncharacterized third gene, tp0956. We determined the crystal structure of recombinant Tp0956; the protein is trimeric and perforated by a pore. Part of Tp0956 forms an assembly similar to those of 'tetratricopeptide repeat' (TPR) motifs. The crystal structure of recombinant Tp0957 was also determined; like the SBPs of other TRAP-Ts, there are two lobes separated by a cleft. In these other SBPs, the cleft binds a negatively charged ligand. However, the cleft of Tp0957 has a strikingly hydrophobic chemical composition, indicating that its ligand may be substantially different and likely hydrophobic. Analytical ultracentrifugation of the recombinant versions of Tp0956 and Tp0957 established that these proteins associate avidly. This unprecedented interaction was confirmed for the native molecules using in vivo cross-linking experiments. Finally, bioinformatic analyses suggested that this transporter exemplifies a new subfamily of TPATs (TPR-protein-associated TRAP-Ts) that require the action of a TPR-containing accessory protein for the periplasmic transport of a potentially hydrophobic ligand(s).

  11. Structure of the Membrane-tethering GRASP Domain Reveals a Unique PDZ Ligand Interaction That Mediates Golgi Biogenesis

    Energy Technology Data Exchange (ETDEWEB)

    S Truschel; D Sengupta; A Foote; A Heroux; M Macbeth; A Linstedt

    2011-12-31

    Biogenesis of the ribbon-like membrane network of the mammalian Golgi requires membrane tethering by the conserved GRASP domain in GRASP65 and GRASP55, yet the tethering mechanism is not fully understood. Here, we report the crystal structure of the GRASP55 GRASP domain, which revealed an unusual arrangement of two tandem PDZ folds that more closely resemble prokaryotic PDZ domains. Biochemical and functional data indicated that the interaction between the ligand-binding pocket of PDZ1 and an internal ligand on PDZ2 mediates the GRASP self-interaction, and structural analyses suggest that this occurs via a unique mode of internal PDZ ligand recognition. Our data uncover the structural basis for ligand specificity and provide insight into the mechanism of GRASP-dependent membrane tethering of analogous Golgi cisternae.

  12. Structure of the Membrane-tethering GRASP Domain Reveals a Unique PDZ Ligand Interaction That Mediates Golgi Biogenesis

    Energy Technology Data Exchange (ETDEWEB)

    Truschel, S.T.; Heroux, A.; Sengupta, D.; Foote, A.; Macbeth, M. R.; Linstedt, A. D.

    2011-06-10

    Biogenesis of the ribbon-like membrane network of the mammalian Golgi requires membrane tethering by the conserved GRASP domain in GRASP65 and GRASP55, yet the tethering mechanism is not fully understood. Here, we report the crystal structure of the GRASP55 GRASP domain, which revealed an unusual arrangement of two tandem PDZ folds that more closely resemble prokaryotic PDZ domains. Biochemical and functional data indicated that the interaction between the ligand-binding pocket of PDZ1 and an internal ligand on PDZ2 mediates the GRASP self-interaction, and structural analyses suggest that this occurs via a unique mode of internal PDZ ligand recognition. Our data uncover the structural basis for ligand specificity and provide insight into the mechanism of GRASP-dependent membrane tethering of analogous Golgi cisternae.

  13. Novel Fluorinated Indanone, Tetralone and Naphthone Derivatives: Synthesis and Unique Structural Features

    Directory of Open Access Journals (Sweden)

    Joseph C. Sloop

    2012-02-01

    Full Text Available Several fluorinated and trifluoromethylated indanone, tetralone and naphthone derivatives have been prepared via Claisen condensations and selective fluorinations in yields ranging from 22–60%. In addition, we report the synthesis of new, selectively fluorinated bindones in yields ranging from 72–92%. Of particular interest is the fluorination and trifluoroacetylation regiochemistry observed in these fluorinated products. We also note unusual transformations including a novel one pot, dual trifluoroacetylation, trifluoroacetylnaphthone synthesis via a deacetylation as well as an acetyl-trifluoroacetyl group exchange. Solid-state structural features exhibited by these compounds were investigated using crystallographic methods. Crystallographic results, supported by spectroscopic data, show that trifluoroacetylated ketones prefer a chelated cis-enol form whereas fluorinated bindone products exist primarily as the cross-conjugated triketo form.

  14. Poly(ADP-ribose)--a unique natural polymer structural features, biological role and approaches to the chemical synthesis.

    Science.gov (United States)

    Drenichev, Mikhail S; Mikhailov, Sergey N

    2015-01-01

    Poly(ADP-ribose) (PAR) is a natural polymer, taking part in numerous important cellular processes. Several enzymes are involved in biosynthesis and degradation of PAR. One of them, poly(ADP-ribose)polymerase-1 (PARP-1) is considered to be a perspective target for the design of new drugs, affecting PAR metabolism. The structure of PAR was established by enzymatic hydrolysis and further analysis of the products, but total chemical synthesis of PAR hasn't been described yet. Several approaches have been developed on the way to chemical synthesis of this unique biopolymer.

  15. Weak Genetic Structure in Northern African Dromedary Camels Reflects Their Unique Evolutionary History

    Science.gov (United States)

    Cherifi, Youcef Amine; Gaouar, Suheil Bechir Semir; Guastamacchia, Rosangela; El-Bahrawy, Khalid Ahmed; Abushady, Asmaa Mohammed Aly; Sharaf, Abdoallah Aboelnasr; Harek, Derradji; Lacalandra, Giovanni Michele; Saïdi-Mehtar, Nadhira

    2017-01-01

    Knowledge on genetic diversity and structure of camel populations is fundamental for sustainable herd management and breeding program implementation in this species. Here we characterized a total of 331 camels from Northern Africa, representative of six populations and thirteen Algerian and Egyptian geographic regions, using 20 STR markers. The nineteen polymorphic loci displayed an average of 9.79 ± 5.31 alleles, ranging from 2 (CVRL8) to 24 (CVRL1D). Average He was 0.647 ± 0.173. Eleven loci deviated significantly from Hardy-Weinberg proportions (P<0.05), due to excess of homozygous genotypes in all cases except one (CMS18). Distribution of genetic diversity along a weak geographic gradient as suggested by network analysis was not supported by either unsupervised and supervised Bayesian clustering. Traditional extensive/nomadic herding practices, together with the historical use as a long-range beast of burden and its peculiar evolutionary history, with domestication likely occurring from a bottlenecked and geographically confined wild progenitor, may explain the observed genetic patterns. PMID:28103238

  16. Structure of CARDS toxin, a unique ADP-ribosylating and vacuolating cytotoxin from Mycoplasma pneumoniae.

    Science.gov (United States)

    Becker, Argentina; Kannan, T R; Taylor, Alexander B; Pakhomova, Olga N; Zhang, Yanfeng; Somarajan, Sudha R; Galaleldeen, Ahmad; Holloway, Stephen P; Baseman, Joel B; Hart, P John

    2015-04-21

    Mycoplasma pneumoniae (Mp) infections cause tracheobronchitis and "walking" pneumonia, and are linked to asthma and other reactive airway diseases. As part of the infectious process, the bacterium expresses a 591-aa virulence factor with both mono-ADP ribosyltransferase (mART) and vacuolating activities known as Community-Acquired Respiratory Distress Syndrome Toxin (CARDS TX). CARDS TX binds to human surfactant protein A and annexin A2 on airway epithelial cells and is internalized, leading to a range of pathogenetic events. Here we present the structure of CARDS TX, a triangular molecule in which N-terminal mART and C-terminal tandem β-trefoil domains associate to form an overall architecture distinct from other well-recognized ADP-ribosylating bacterial toxins. We demonstrate that CARDS TX binds phosphatidylcholine and sphingomyelin specifically over other membrane lipids, and that cell surface binding and internalization activities are housed within the C-terminal β-trefoil domain. The results enhance our understanding of Mp pathogenicity and suggest a novel avenue for the development of therapies to treat Mp-associated asthma and other acute and chronic airway diseases.

  17. Structuring Broadcast Audio for Information Access

    Directory of Open Access Journals (Sweden)

    Jean-Luc Gauvain

    2003-02-01

    Full Text Available One rapidly expanding application area for state-of-the-art speech recognition technology is the automatic processing of broadcast audiovisual data for information access. Since much of the linguistic information is found in the audio channel, speech recognition is a key enabling technology which, when combined with information retrieval techniques, can be used for searching large audiovisual document collections. Audio indexing must take into account the specificities of audio data such as needing to deal with the continuous data stream and an imperfect word transcription. Other important considerations are dealing with language specificities and facilitating language portability. At Laboratoire d′Informatique pour la Mécanique et les Sciences de l′Ingénieur (LIMSI, broadcast news transcription systems have been developed for seven languages: English, French, German, Mandarin, Portuguese, Spanish, and Arabic. The transcription systems have been integrated into prototype demonstrators for several application areas such as audio data mining, structuring audiovisual archives, selective dissemination of information, and topic tracking for media monitoring. As examples, this paper addresses the spoken document retrieval and topic tracking tasks.

  18. An informationally structured room for robotic assistance.

    Science.gov (United States)

    Tsuji, Tokuo; Mozos, Oscar Martinez; Chae, Hyunuk; Pyo, Yoonseok; Kusaka, Kazuya; Hasegawa, Tsutomu; Morooka, Ken'ichi; Kurazume, Ryo

    2015-04-22

    The application of assistive technologies for elderly people is one of the most promising and interesting scenarios for intelligent technologies in the present and near future. Moreover, the improvement of the quality of life for the elderly is one of the first priorities in modern countries and societies. In this work, we present an informationally structured room that is aimed at supporting the daily life activities of elderly people. This room integrates different sensor modalities in a natural and non-invasive way inside the environment. The information gathered by the sensors is processed and sent to a centralized management system, which makes it available to a service robot assisting the people. One important restriction of our intelligent room is reducing as much as possible any interference with daily activities. Finally, this paper presents several experiments and situations using our intelligent environment in cooperation with our service robot.

  19. Extensive genetic diversity, unique population structure and evidence of genetic exchange in the sexually transmitted parasite Trichomonas vaginalis.

    Directory of Open Access Journals (Sweden)

    Melissa D Conrad

    Full Text Available Trichomonas vaginalis is the causative agent of human trichomoniasis, the most common non-viral sexually transmitted infection world-wide. Despite its prevalence, little is known about the genetic diversity and population structure of this haploid parasite due to the lack of appropriate tools. The development of a panel of microsatellite makers and SNPs from mining the parasite's genome sequence has paved the way to a global analysis of the genetic structure of the pathogen and association with clinical phenotypes.Here we utilize a panel of T. vaginalis-specific genetic markers to genotype 235 isolates from Mexico, Chile, India, Australia, Papua New Guinea, Italy, Africa and the United States, including 19 clinical isolates recently collected from 270 women attending New York City sexually transmitted disease clinics. Using population genetic analysis, we show that T. vaginalis is a genetically diverse parasite with a unique population structure consisting of two types present in equal proportions world-wide. Parasites belonging to the two types (type 1 and type 2 differ significantly in the rate at which they harbor the T. vaginalis virus, a dsRNA virus implicated in parasite pathogenesis, and in their sensitivity to the widely-used drug, metronidazole. We also uncover evidence of genetic exchange, indicating a sexual life-cycle of the parasite despite an absence of morphologically-distinct sexual stages.Our study represents the first robust and comprehensive evaluation of global T. vaginalis genetic diversity and population structure. Our identification of a unique two-type structure, and the clinically relevant phenotypes associated with them, provides a new dimension for understanding T. vaginalis pathogenesis. In addition, our demonstration of the possibility of genetic exchange in the parasite has important implications for genetic research and control of the disease.

  20. English-Chinese Translating from Perspective of Information Structure

    Institute of Scientific and Technical Information of China (English)

    汪世纪

    2014-01-01

    The application of information structure theory in translation is a dynamic communicative approach. The fluency of translation relies on the rearrangement of the given information and the new information and as well as the proper reproduction of information focuses. Therefore, a translator should be aware of information structure and information focus and thus make some adjustments while translating.

  1. Information transfer in community structured multiplex networks

    CERN Document Server

    Solé-Ribalta, Albert; Gómez, Sergio; Arenas, Alex

    2015-01-01

    The study of complex networks that account for different types of interactions has become a subject of interest in the last few years, specially because its representational power in the description of users interactions in diverse online social platforms (Facebook, Twitter, Instagram, etc.). The mathematical description of these interacting networks has been coined under the name of multilayer networks, where each layer accounts for a type of interaction. It has been shown that diffusive processes on top of these networks present a phenomenology that cannot be explained by the naive superposition of single layer diffusive phenomena but require the whole structure of interconnected layers. Nevertheless, the description of diffusive phenomena on multilayer networks has obviated the fact that social networks have strong mesoscopic structure represented by different communities of individuals driven by common interests, or any other social aspect. In this work, we study the transfer of information in multilayer ...

  2. Crystal structure of lactose permease in complex with an affinity inactivator yields unique insight into sugar recognition

    Energy Technology Data Exchange (ETDEWEB)

    Chaptal, Vincent; Kwon, Seunghyug; Sawaya, Michael R.; Guan, Lan; Kaback, H. Ronald; Abramson, Jeff (UCLA); (TTU)

    2011-08-29

    Lactose permease of Escherichia coli (LacY) with a single-Cys residue in place of A122 (helix IV) transports galactopyranosides and is specifically inactivated by methanethiosulfonyl-galactopyranosides (MTS-gal), which behave as unique suicide substrates. In order to study the mechanism of inactivation more precisely, we solved the structure of single-Cys122 LacY in complex with covalently bound MTS-gal. This structure exhibits an inward-facing conformation similar to that observed previously with a slight narrowing of the cytoplasmic cavity. MTS-gal is bound covalently, forming a disulfide bond with C122 and positioned between R144 and W151. E269, a residue essential for binding, coordinates the C-4 hydroxyl of the galactopyranoside moiety. The location of the sugar is in accord with many biochemical studies.

  3. Crystal structure of lactose permease in complex with an affinity inactivator yields unique insight into sugar recognition.

    Science.gov (United States)

    Chaptal, Vincent; Kwon, Seunghyug; Sawaya, Michael R; Guan, Lan; Kaback, H Ronald; Abramson, Jeff

    2011-06-07

    Lactose permease of Escherichia coli (LacY) with a single-Cys residue in place of A122 (helix IV) transports galactopyranosides and is specifically inactivated by methanethiosulfonyl-galactopyranosides (MTS-gal), which behave as unique suicide substrates. In order to study the mechanism of inactivation more precisely, we solved the structure of single-Cys122 LacY in complex with covalently bound MTS-gal. This structure exhibits an inward-facing conformation similar to that observed previously with a slight narrowing of the cytoplasmic cavity. MTS-gal is bound covalently, forming a disulfide bond with C122 and positioned between R144 and W151. E269, a residue essential for binding, coordinates the C-4 hydroxyl of the galactopyranoside moiety. The location of the sugar is in accord with many biochemical studies.

  4. Shot detection combining Bayesian and structural information

    Science.gov (United States)

    Han, Seung H.; Kweon, In-So

    2000-12-01

    There are a number of shots in a video, each of which has boundary types, such as cut, fade, dissolve and wipe. Many previous approaches can find the cut boundary without difficulty. However, most of them often produce false alarms for the videos with large motions of camera and objects. We propose a shot boundary detection method combining Bayesian and structural information. In the Bayesian approach, a probability distribution function models each transition type, e.g., normal, abrupt, gradual transition, and also models shot length. But inseparability between those distributions causes unwanted results and degrades the precision. In this paper, we demonstrate that the shape of the filtered frame difference, called the structural information, provides an important cue to distinguish fade and dissolve effects form cut effects and gradual changes caused by motion of camera and objects. The proposed method has been tested for a few golf video segments and shown good performances in detecting fade and dissolve effects as well as cut.

  5. Visualization of database structures for information retrieval

    Directory of Open Access Journals (Sweden)

    Grete Lisbjerg Jensen

    1994-12-01

    Full Text Available This paper describes the Book House system, which is designed to support children's information retrieval in libraries as part of their education. It is a shareware program available on CD-ROM or floppy disks, and comprises functionality for database searching as well as for classifying and storing book information in the database. The system concept is based on an understanding of children's domain structures and their capabilities for categorization of information needs in connection with their activities in schools, in school libraries or in public libraries. These structures are visualized in the interface by using metaphors and multimedia technology. Through the use of text, images and animation, the Book House encourages children - even at a very early age - to learn by doing in an enjoyable way, which plays on their previous experiences with computer games. Both words and pictures can be used for searching; this makes the system suitable for all age groups. Even children who have not yet learned to read properly can, by selecting pictures, search for and find those books they would like to have read aloud. Thus, at the very beginning of their school life, they can learn to search for books on their own. For the library community, such a system will provide an extended service which will increase the number of children's own searches and also improve the relevance, quality and utilization of the book collections in the libraries. A market research report on the need for an annual indexing service for books in the Book House format is in preparation by the Danish Library Centre A/S.

  6. Grammar and information structure. A study with reference to Russian

    NARCIS (Netherlands)

    Slioussar, N.

    2007-01-01

    This thesis is dedicated to the study of information structure (IS) dividing information into given/new, salient/backgrounded etc. There is an information structure represented in the discourse mental model and an information structure encoded in the grammar, which indirectly reflects it (as the ten

  7. A unique semiconductor-carbon-metal hybrid structure design as a counter electrode in dye-sensitized solar cells.

    Science.gov (United States)

    Guo, Sheng-Qi; Wang, Ling-Chang; Zhang, Chen-Guang; Qi, Gao-Can; Gu, Bing-Chuan; Liu, Lu; Yuan, Zhi-Hao

    2017-05-25

    The catalytic activity of counter electrodes (CEs) severely restricts the photovoltaic conversion efficiency of dye-sensitized solar cells. However, electrons trapped by bulk defects greatly reduce the catalytic activity of the CE. In this study, we report a novel In2S3-C-Au hybrid structure designed by simply decorating Au particles on the surface of carbon-coated hierarchical In2S3 flower-like architectures, which could avoid the abovementioned problems. This effect can be attributed to the unique contribution of indium sulfide, carbon, and Au from the hybrid structure, as well as to their synergy. Electrochemical measurements revealed that the hybrid structure possessed high catalytic activity and electrochemical stability for the interconversion of the redox couple I3(-)/I(-). Moreover, this superior performance can be incorporated into the dye-sensitized solar cells system. We used this hybrid structure as a counter electrode by casting it on an FTO substrate to form a film, which displayed better photovoltaic conversion efficiency (8.91%) than the commercial Pt counterpart (7.67%).

  8. Temporal decoding by phase-locked loops: unique features of circuit-level implementations and their significance for vibrissal information processing.

    Science.gov (United States)

    Zacksenhouse, Miriam; Ahissar, Ehud

    2006-07-01

    Rhythmic active touch, such as whisking, evokes a periodic reference spike train along which the timing of a novel stimulus, induced, for example, when the whiskers hit an external object, can be interpreted. Previous work supports the hypothesis that the whisking-induced spike train entrains a neural implementation of a phase-locked loop (NPLL) in the vibrissal system. Here we extend this work and explore how the entrained NPLL decodes the delay of the novel, contact-induced stimulus and facilitates object localization. We consider two implementations of NPLLs, which are based on a single neuron or a neural circuit, respectively, and evaluate the resulting temporal decoding capabilities. Depending on the structure of the NPLL, it can lock in either a phase- or co-phase-sensitive mode, which is sensitive to the timing of the input with respect to the beginning of either the current or the next cycle, respectively. The co-phase-sensitive mode is shown to be unique to circuit-based NPLLs. Concentrating on temporal decoding in the vibrissal system of rats, we conclude that both the nature of the information processing task and the response characteristics suggest that the computation is sensitive to the co-phase. Consequently, we suggest that the underlying thalamocortical loop should implement a circuit-based NPLL.

  9. Crystal structures and inhibitor binding properties of plant class V chitinases: the cycad enzyme exhibits unique structural and functional features.

    Science.gov (United States)

    Umemoto, Naoyuki; Kanda, Yuka; Ohnuma, Takayuki; Osawa, Takuo; Numata, Tomoyuki; Sakuda, Shohei; Taira, Toki; Fukamizo, Tamo

    2015-04-01

    A class V (glycoside hydrolase family 18) chitinase from the cycad Cycas revoluta (CrChiA) is a plant chitinase that has been reported to possess efficient transglycosylation (TG) activity. We solved the crystal structure of CrChiA, and compared it with those of class V chitinases from Nicotiana tabacum (NtChiV) and Arabidopsis thaliana (AtChiC), which do not efficiently catalyze the TG reaction. All three chitinases had a similar (α/β)8 barrel fold with an (α + β) insertion domain. In the acceptor binding site (+1, +2 and +3) of CrChiA, the Trp168 side chain was found to stack face-to-face with the +3 sugar. However, this interaction was not found in the identical regions of NtChiV and AtChiC. In the DxDxE motif, which is essential for catalysis, the carboxyl group of the middle Asp (Asp117) was always oriented toward the catalytic acid Glu119 in CrChiA, whereas the corresponding Asp in NtChiV and AtChiC was oriented toward the first Asp. These structural features of CrChiA appear to be responsible for the efficient TG activity. When binding of the inhibitor allosamidin was evaluated using isothermal titration calorimetry, the changes in binding free energy of the three chitinases were found to be similar to each other, i.e. between -9.5 and -9.8 kcal mol(-1) . However, solvation and conformational entropy changes in CrChiA were markedly different from those in NtChiV and AtChiC, but similar to those of chitinase A from Serratia marcescens (SmChiA), which also exhibits significant TG activity. These results provide insight into the molecular mechanism underlying the TG reaction and the molecular evolution from bacterial chitinases to plant class V chitinases.

  10. Trends in information theory-based chemical structure codification.

    Science.gov (United States)

    Barigye, Stephen J; Marrero-Ponce, Yovani; Pérez-Giménez, Facundo; Bonchev, Danail

    2014-08-01

    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.

  11. MULTILEVEL INDEX STRUCTURE FOR INFORMATION FILTERING BASED ON USER CHARACTERISTIC

    Institute of Scientific and Technical Information of China (English)

    He jun; Zhou Mingtian

    2001-01-01

    Aimed at information overload and personalized characteristic of user information requirement, this letter presents a type of multilevel index structure and algorithm which is applied to large scale information filtering system and has better performance and stronger scalability.

  12. Hepatic crown-like structure: a unique histological feature in non-alcoholic steatohepatitis in mice and humans.

    Directory of Open Access Journals (Sweden)

    Michiko Itoh

    Full Text Available Although macrophages are thought to be crucial for the pathogenesis of chronic inflammatory diseases, how they are involved in disease progression from simple steatosis to non-alcoholic steatohepatitis (NASH is poorly understood. Here we report the unique histological structure termed "hepatic crown-like structures (hCLS" in the mouse model of human NASH; melanocortin-4 receptor deficient mice fed a Western diet. In hCLS, CD11c-positive macrophages aggregate to surround hepatocytes with large lipid droplets, which is similar to those described in obese adipose tissue. Histological analysis revealed that hCLS is closely associated with activated fibroblasts and collagen deposition. When treatment with clodronate liposomes effectively depletes macrophages scattered in the liver, with those in hCLS intact, hepatic expression of inflammatory and fibrogenic genes is unaffected, suggesting that hCLS is an important source of inflammation and fibrosis during the progression of NASH. Notably, the number of hCLS is positively correlated with the extent of liver fibrosis. We also observed increased number of hCLS in the liver of non-alcoholic fatty liver disease/NASH patients. Collectively, our data provide evidence that hCLS is involved in the development of hepatic inflammation and fibrosis, thereby suggesting its pathophysiologic role in disease progression from simple steatosis to NASH.

  13. The structure of a bottlenose dolphin society is coupled to a unique foraging cooperation with artisanal fishermen.

    Science.gov (United States)

    Daura-Jorge, F G; Cantor, M; Ingram, S N; Lusseau, D; Simões-Lopes, P C

    2012-10-23

    Diverse and localized foraging behaviours have been reported in isolated populations of many animal species around the world. In Laguna, southern Brazil, a subset of resident bottlenose dolphins (Tursiops truncatus) uses a foraging tactic involving cooperative interactions with local, beach-casting fishermen. We used individual photo-identification data to assess whether cooperative and non-cooperative dolphins were socially segregated. The social structure of the population was found to be a fission-fusion system with few non-random associations, typical for this species. However, association values were greater among cooperative dolphins than among non-cooperative dolphins or between dolphins from different foraging classes. Furthermore, the dolphin social network was divided into three modules, clustering individuals that shared or lacked the cooperative foraging tactic. Space-use patterns were not sufficient to explain this partitioning, indicating a behavioural factor. The segregation of dolphins using different foraging tactics could result from foraging behaviour driving social structure, while the closer association between dolphins engaged in the cooperation could facilitate the transmission and learning of this behavioural trait from conspecifics. This unique case of a dolphin-human interaction represents a valuable opportunity to explore hypotheses on the role of social learning in wild cetaceans.

  14. Structure-affinity relationships of a unique nicotinic ligand: N(1)-dimethyl-N(4)-phenylpiperazinium iodide (DMPP).

    Science.gov (United States)

    Romanelli, M N; Manetti, D; Scapecchi, S; Borea, P A; Dei, S; Bartolini, A; Ghelardini, C; Gualtieri, F; Guandalini, L; Varani, K

    2001-11-08

    DMPP is a well-known nicotinic agonist that does not fit any proposed pharmacophore for nicotinic binding and represents a unique ligand among the hundreds of nicotinic agonists studied in the past decades. A systematic modulation of the chemical structure of DMPP, aimed to establish its structure-affinity relationships, is reported. The research has allowed to identify molecules such as 11c, 13c, 14c, and 28c, with affinities for alpha(4)beta(2) receptors in the low nanomolar range, some 2 orders of magnitude lower than the lead compound. The agonistic properties of the most interesting compounds have been assessed by measuring their analgesic activity on mice (hot-plate test). Another result of the research was the identification of DMPP analogues, such as 3a (K(i) = 90 nM) and 14b (K(i) = 180 nM), that maintain affinity for the central nicotinic receptor when the ammonium function is changed into an aminic one and are therefore possible leads for drug development in neurodegenerative diseases.

  15. Information diffusion in structured online social networks

    Science.gov (United States)

    Li, Pei; Zhang, Yini; Qiao, Fengcai; Wang, Hui

    2015-05-01

    Nowadays, due to the word-of-mouth effect, online social networks have been considered to be efficient approaches to conduct viral marketing, which makes it of great importance to understand the diffusion dynamics in online social networks. However, most research on diffusion dynamics in epidemiology and existing social networks cannot be applied directly to characterize online social networks. In this paper, we propose models to characterize the information diffusion in structured online social networks with push-based forwarding mechanism. We introduce the term user influence to characterize the average number of times that messages are browsed which is incurred by a given type user generating a message, and study the diffusion threshold, above which the user influence of generating a message will approach infinity. We conduct simulations and provide the simulation results, which are consistent with the theoretical analysis results perfectly. These results are of use in understanding the diffusion dynamics in online social networks and also critical for advertisers in viral marketing who want to estimate the user influence before posting an advertisement.

  16. Structure of the PSD-95/MAP1A complex reveals a unique target recognition mode of the MAGUK GK domain.

    Science.gov (United States)

    Xia, Yitian; Shang, Yuan; Zhang, Rongguang; Zhu, Jinwei

    2017-08-10

    The PSD-95 family of membrane-associated guanylate kinases (MAGUKs) are major synaptic scaffold proteins and play crucial roles in the dynamic regulation of dendritic remodelling, which is understood to be the foundation of synaptogenesis and synaptic plasticity. The guanylate kinase (GK) domain of MAGUK family proteins functions as a phosphor-peptide binding module. However, the GK domain of PSD-95 has been found to directly bind to a peptide sequence within the C-terminal region of neuronal-specific microtubule-associated protein 1A (MAP1A), although the detailed molecular mechanism governing this phosphorylation-independent interaction at the atomic level is missing. In the present study, we determine the crystal structure of PSD-95 GK in complex with the MAP1A peptide at 2.6-Å resolution. The complex structure reveals that, unlike a linear and elongated conformation in the phosphor-peptide/GK complexes, the MAP1A peptide adopts a unique conformation with a stretch of hydrophobic residues far from each other in the primary sequence clustering and interacting with the 'hydrophobic site' of PSD-95 GK and a highly conserved aspartic acid of MAP1A (D2117) mimicking the phosphor-serine/threonine in binding to the 'phosphor-site' of PSD-95 GK. We demonstrate that the MAP1A peptide may undergo a conformational transition upon binding to PSD-95 GK. Further structural comparison of known DLG GK-mediated complexes reveals the target recognition specificity and versatility of DLG GKs. © 2017 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society.

  17. Two unique ligand-binding clamps of Rhizopus oryzae starch binding domain for helical structure disruption of amylose.

    Directory of Open Access Journals (Sweden)

    Ting-Ying Jiang

    Full Text Available The N-terminal starch binding domain of Rhizopus oryzae glucoamylase (RoSBD has a high binding affinity for raw starch. RoSBD has two ligand-binding sites, each containing a ligand-binding clamp: a polyN clamp residing near binding site I is unique in that it is expressed in only three members of carbohydrate binding module family 21 (CBM21 members, and a Y32/F58 clamp located at binding site II is conserved in several CBMs. Here we characterized different roles of these sites in the binding of insoluble and soluble starches using an amylose-iodine complex assay, atomic force microscopy, isothermal titration calorimetry, site-directed mutagenesis, and structural bioinformatics. RoSBD induced the release of iodine from the amylose helical cavity and disrupted the helical structure of amylose type III, thereby significantly diminishing the thickness and length of the amylose type III fibrils. A point mutation in the critical ligand-binding residues of sites I and II, however, reduced both the binding affinity and amylose helix disruption. This is the first molecular model for structure disruption of the amylose helix by a non-hydrolytic CBM21 member. RoSBD apparently twists the helical amylose strands apart to expose more ligand surface for further SBD binding. Repeating the process triggers the relaxation and unwinding of amylose helices to generate thinner and shorter amylose fibrils, which are more susceptible to hydrolysis by glucoamylase. This model aids in understanding the natural roles of CBMs in protein-glycan interactions and contributes to potential molecular engineering of CBMs.

  18. How Unique Are Our Users? Part 2: Comparing Responses Regarding the Information-Seeking Habits of Education Faculty

    Science.gov (United States)

    Robbins, Sarah; Rupp-Serrano, Karen

    2013-01-01

    This follow-up study examines whether or not findings of single institution studies are applicable to other institutions by performing an institution-to-institution comparison of the results obtained from an information-seeking behavior survey sent to education faculty at twenty research institutions. The results from this study corroborated what…

  19. How Unique Are Our Users? Part 2: Comparing Responses Regarding the Information-Seeking Habits of Education Faculty

    Science.gov (United States)

    Robbins, Sarah; Rupp-Serrano, Karen

    2013-01-01

    This follow-up study examines whether or not findings of single institution studies are applicable to other institutions by performing an institution-to-institution comparison of the results obtained from an information-seeking behavior survey sent to education faculty at twenty research institutions. The results from this study corroborated what…

  20. Dragon pulse information management system (DPIMS): A unique model-based approach to implementing domain agnostic system of systems and behaviors

    Science.gov (United States)

    Anderson, Thomas S.

    2016-05-01

    The Global Information Network Architecture is an information technology based on Vector Relational Data Modeling, a unique computational paradigm, DoD network certified by USARMY as the Dragon Pulse Informa- tion Management System. This network available modeling environment for modeling models, where models are configured using domain relevant semantics and use network available systems, sensors, databases and services as loosely coupled component objects and are executable applications. Solutions are based on mission tactics, techniques, and procedures and subject matter input. Three recent ARMY use cases are discussed a) ISR SoS. b) Modeling and simulation behavior validation. c) Networked digital library with behaviors.

  1. Structural and biochemical analysis of a unique phosphatase from Bdellovibrio bacteriovorus reveals its structural and functional relationship with the protein tyrosine phosphatase class of phytase.

    Directory of Open Access Journals (Sweden)

    Robert J Gruninger

    Full Text Available Bdellovibrio bacteriovorus is an unusual δ-proteobacterium that invades and preys on other Gram-negative bacteria and is of potential interest as a whole cell therapeutic against pathogens of man, animals and crops. PTPs (protein tyrosine phosphatases are an important class of enzyme involved in desphosphorylating a variety of substrates, often with implications in cell signaling. The B. bacteriovorus open reading frame Bd1204 is predicted to encode a PTP of unknown function. Bd1204 is both structurally and mechanistically related to the PTP-like phytase (PTPLP class of enzymes and possesses a number of unique properties not observed in any other PTPLPs characterized to date. Bd1204 does not display catalytic activity against some common protein tyrosine phosphatase substrates but is highly specific for hydrolysis of phosphomonoester bonds of inositol hexakisphosphate. The structure reveals that Bd1204 has the smallest and least electropositive active site of all characterized PTPLPs to date yet possesses a unique substrate specificity characterized by a strict preference for inositol hexakisphosphate. These two active site features are believed to be the most significant contributors to the specificity of phytate degrading enzymes. We speculate that Bd1204 may be involved in phosphate acquisition outside of prey.

  2. Temporal and Statistical Information in Causal Structure Learning

    Science.gov (United States)

    McCormack, Teresa; Frosch, Caren; Patrick, Fiona; Lagnado, David

    2015-01-01

    Three experiments examined children's and adults' abilities to use statistical and temporal information to distinguish between common cause and causal chain structures. In Experiment 1, participants were provided with conditional probability information and/or temporal information and asked to infer the causal structure of a 3-variable mechanical…

  3. Ideologically Structured Information Exchange among Environmental Groups

    Science.gov (United States)

    Lhotka, Laura; Bailey, Conner; Dubois, Mark

    2008-01-01

    We use social network analysis to test the hypothesis that group ideology affects information exchange among environmental groups. The analysis is based on interviews with leaders of 136 environmental groups in Alabama. This paper adds to the literature on resource mobilization among social movement organizations by exploring information exchange…

  4. Qanat -a unique system of water supply in iran. Specifics of structures and principles of engineering devices

    Directory of Open Access Journals (Sweden)

    Rodionovskaya Inna Serafimovna

    2016-11-01

    Full Text Available A considerable part of the world population is living in a geographical belt of hot and dry climate. The rainfalls there are rare and there is lack of fresh water basins and water sources. That’s why a powerful water supply system was developed here, which has been operating for centuries, and a technology of its construction has been improved to the level of art. The specific nature of hydro-technical water supply system of Iranian settlements is considered in this article. Such specificity is typical for the regions with mountain relief in the conditions of hot-dry climate. Also, the construction characteristics of the system, its structure and building components are given as well as short information about the features of buildings constructions and their technical operation. Functional, urban-architectural and environmental aspects are considered; the influence of the hydraulic system on the population resettlement is specified. The role of these structures is noted in respect of environment greening. Informational and cognitive nature of the given material allows using it in educational process of architects and civil engineers, expanding their professional horizons, as well as in scientific researches aimed at finding the ways of ecologization of modern architectural environment in the condition of urbanization development.

  5. Pattern information extraction from crystal structures

    OpenAIRE

    Okuyan, Erhan

    2005-01-01

    Cataloged from PDF version of article. Determining crystal structure parameters of a material is a quite important issue in crystallography. Knowing the crystal structure parameters helps to understand physical behavior of material. For complex structures, particularly for materials which also contain local symmetry as well as global symmetry, obtaining crystal parameters can be quite hard. This work provides a tool that will extract crystal parameters such as primitive vect...

  6. Musical information processing reflecting its structure

    OpenAIRE

    Hiraga, Rumi

    1999-01-01

    In pursuit of generating expressive musical rendition with rules, the computer music project Psyche has greatly concerned musical structure. Although described implicitly, musical structure exists innately and absolutely in musical scores. This thesis demonstrates the successful introduction of musical structure to computer music systems that are related to performance synthesis. Two systems, a performance visualization system and a computer-assisted musical analysis system Daphne, are descri...

  7. Predicting RNA Structure Using Mutual Information

    DEFF Research Database (Denmark)

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

    2005-01-01

    Background: With the ever-increasing number of sequenced RNAs and the establishment of new RNA databases, such as the Comparative RNA Web Site and Rfam, there is a growing need for accurately and automatically predicting RNA structures from multiple alignments. Since RNA secondary structure is of...

  8. Predicting RNA Structure Using Mutual Information

    DEFF Research Database (Denmark)

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

    2005-01-01

    Background: With the ever-increasing number of sequenced RNAs and the establishment of new RNA databases, such as the Comparative RNA Web Site and Rfam, there is a growing need for accurately and automatically predicting RNA structures from multiple alignments. Since RNA secondary structure......, to display and predict conserved RNA secondary structure (including pseudoknots) from an alignment. Results: We show that MIfold can be used to predict simple pseudoknots, and that the performance can be adjusted to make it either more sensitive or more selective. We also demonstrate that the overall...... performance of MIfold improves with the number of aligned sequences for certain types of RNA sequences. In addition, we show that, for these sequences, MIfold is more sensitive but less selective than the related RNAalifold structure prediction program and is comparable with the COVE structure prediction...

  9. Geographic Names Information System (GNIS) Structures

    Data.gov (United States)

    Department of Homeland Security — The Geographic Names Information System (GNIS) is the Federal standard for geographic nomenclature. The U.S. Geological Survey developed the GNIS for the U.S. Board...

  10. Unique transcriptome patterns of the white and grey matter corroborate structural and functional heterogeneity in the human frontal lobe.

    Directory of Open Access Journals (Sweden)

    James D Mills

    Full Text Available The human frontal lobe has undergone accelerated evolution, leading to the development of unique human features such as language and self-reflection. Cortical grey matter and underlying white matter reflect distinct cellular compositions in the frontal lobe. Surprisingly little is known about the transcriptomal landscape of these distinct regions. Here, for the first time, we report a detailed transcriptomal profile of the frontal grey (GM and white matter (WM with resolution to alternatively spliced isoforms obtained using the RNA-Seq approach. We observed more vigorous transcriptome activity in GM compared to WM, presumably because of the presence of cellular bodies of neurons in the GM and RNA associated with the nucleus and perinuclear space. Among the top differentially expressed genes, we also identified a number of long intergenic non-coding RNAs (lincRNAs, specifically expressed in white matter, such as LINC00162. Furthermore, along with confirmation of expression of known markers for neurons and oligodendrocytes, we identified a number of genes and splicing isoforms that are exclusively expressed in GM or WM with examples of GABRB2 and PAK2 transcripts, respectively. Pathway analysis identified distinct physiological and biochemical processes specific to grey and white matter samples with a prevalence of synaptic processes in GM and myelination regulation and axonogenesis in the WM. Our study also revealed that expression of many genes, for example, the GPR123, is characterized by isoform switching, depending in which structure the gene is expressed. Our report clearly shows that GM and WM have perhaps surprisingly divergent transcriptome profiles, reflecting distinct roles in brain physiology. Further, this study provides the first reference data set for a normal human frontal lobe, which will be useful in comparative transcriptome studies of cerebral disorders, in particular, neurodegenerative diseases.

  11. A real-time in-memory discovery service leveraging hierarchical packaging information in a unique identifier network to retrieve track and trace information

    CERN Document Server

    Müller, Jürgen

    2014-01-01

    This book examines how to efficiently retrieve track and trace information for an item that took a certain path through a complex network of manufacturers, wholesalers, retailers and consumers. It includes valuable tips on in-memory data management.

  12. Structure and reactivity of a unique Y-shaped tricoordinate bis(silyl)platinum(II)-NHC complex

    NARCIS (Netherlands)

    Berthon-Gelloz, G.; de Bruin, B.; Tinant, B.; Markó, I.E.

    2009-01-01

    A unique, three-coordinate Y-shaped bis(silyl)platinum(II) complex was isolated and characterized. DFT studies on a model system shed light on the nature of this unusual coordination mode for platinum(II).

  13. Do You Want to Know What I Learned? Using Informational Trade Books as Models to Teach Text Structure

    Science.gov (United States)

    Read, Sylvia; Reutzel, D. Ray; Fawson, Parker C.

    2008-01-01

    Informational text is an important resource for classroom teachers that places unique comprehension demands on young students. Research on teaching expository text structure to young children shows that explicit instruction improves student comprehension. This practical article addresses how to use "well-structured" expository trade book titles to…

  14. Observability and Information Structure of Nonlinear Systems,

    Science.gov (United States)

    1985-10-01

    defined by Shannon and used as a measure of mut.:al infor-mation between event x. and y4. If p(x.l IY.) I I(x., y.) xil -in (1/p(x.)) =- JInp (x.) (2...entropy H(x,y) in a similar way as H(x,y) = - fx,yp(xiy)lnp(x,y)cdlY, = -E[ JInp (x,y)]. (3-13) With the above definitions, mutual information between x...Observabiity of Nonlinear Systems, Eng. Cybernetics, Volume 1, pp 338-345, 1972. 18. Sen , P., Chidambara, M.R., Observability of a Class of Nonli-.ear

  15. Pattern information extraction from crystal structures

    Science.gov (United States)

    Okuyan, Erhan; Güdükbay, Uğur; Gülseren, Oğuz

    2007-04-01

    Determining the crystal structure parameters of a material is an important issue in crystallography and material science. Knowing the crystal structure parameters helps in understanding the physical behavior of material. It can be difficult to obtain crystal parameters for complex structures, particularly those materials that show local symmetry as well as global symmetry. This work provides a tool that extracts crystal parameters such as primitive vectors, basis vectors and space groups from the atomic coordinates of crystal structures. A visualization tool for examining crystals is also provided. Accordingly, this work could help crystallographers, chemists and material scientists to analyze crystal structures efficiently. Program summaryTitle of program: BilKristal Catalogue identifier: ADYU_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADYU_v1_0 Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Licensing provisions: None Programming language used: C, C++, Microsoft .NET Framework 1.1 and OpenGL Libraries Computer: Personal Computers with Windows operating system Operating system: Windows XP Professional RAM: 20-60 MB No. of lines in distributed program, including test data, etc.:899 779 No. of bytes in distributed program, including test date, etc.:9 271 521 Distribution format:tar.gz External routines/libraries: Microsoft .NET Framework 1.1. For visualization tool, graphics card driver should also support OpenGL Nature of problem: Determining crystal structure parameters of a material is a quite important issue in crystallography. Knowing the crystal structure parameters helps to understand physical behavior of material. For complex structures, particularly, for materials which also contain local symmetry as well as global symmetry, obtaining crystal parameters can be quite hard. Solution method: The tool extracts crystal parameters such as primitive vectors, basis vectors and identify the space group from

  16. A reactive data structure for geographic information systems

    NARCIS (Netherlands)

    Oosterom, P.J.M. van

    1989-01-01

    We introduce a Reactive Data Structure, that is a spatial data structure with detail levels. The two properties, spatial organization and detail levels, are the basis for a Geographic Information System with a multi-scale database. A reactive data structure is a novel type of data structure catering

  17. Phase structure rewrite systems in information retrieval

    Science.gov (United States)

    Klingbiel, P. H.

    1985-01-01

    Operational level automatic indexing requires an efficient means of normalizing natural language phrases. Subject switching requires an efficient means of translating one set of authorized terms to another. A phrase structure rewrite system called a Lexical Dictionary is explained that performs these functions. Background, operational use, other applications and ongoing research are explained.

  18. Reduction of Ambiguity in Phosphorylation-site Localization in Large-scale Phosphopeptide Profiling by Data Filter using Unique Mass Class Information

    Energy Technology Data Exchange (ETDEWEB)

    Madar, Inamul Hasan; Back, Seunghoon; Mun, Donggi; Kim, Hokeun; Lee, Sangwon [Korea Univ., Seoul (Korea, Republic of); Jung, Jae Hun; Kim, Kwang Pyo [Kyung Hee Univ., Yongin (Korea, Republic of)

    2014-03-15

    The rapid development of shotgun proteomics is paving the way for extensive proteome profiling, while providing extensive information on various post translational modifications (PTMs) that occur to a proteome of interest. For example, the current phosphoproteomic methods can yield more than 10,000 phosphopeptides identified from a proteome sample. Despite these developments, it remains a challenging issue to pinpoint the true phosphorylation sites, especially when multiple sites are possible for phosphorylation in the peptides. We developed the Phospho-UMC filter, which is a simple method of localizing the site of phosphorylation using unique mass classes (UMCs) information to differentiate phosphopeptides with different phosphorylation sites and increase the confidence in phosphorylation site localization. The method was applied to large scale phosphopeptide profiling data and was demonstrated to be effective in the reducing ambiguity associated with the tandem mass spectrometric data analysis of phosphopeptides.

  19. The unique architecture and function of cellulose-interacting proteins in oomycetes revealed by genomic and structural analyses

    Directory of Open Access Journals (Sweden)

    Larroque Mathieu

    2012-11-01

    Full Text Available Abstract Background Oomycetes are fungal-like microorganisms evolutionary distinct from true fungi, belonging to the Stramenopile lineage and comprising major plant pathogens. Both oomycetes and fungi express proteins able to interact with cellulose, a major component of plant and oomycete cell walls, through the presence of carbohydrate-binding module belonging to the family 1 (CBM1. Fungal CBM1-containing proteins were implicated in cellulose degradation whereas in oomycetes, the Cellulose Binding Elicitor Lectin (CBEL, a well-characterized CBM1-protein from Phytophthora parasitica, was implicated in cell wall integrity, adhesion to cellulosic substrates and induction of plant immunity. Results To extend our knowledge on CBM1-containing proteins in oomycetes, we have conducted a comprehensive analysis on 60 fungi and 7 oomycetes genomes leading to the identification of 518 CBM1-containing proteins. In plant-interacting microorganisms, the larger number of CBM1-protein coding genes is expressed by necrotroph and hemibiotrophic pathogens, whereas a strong reduction of these genes is observed in symbionts and biotrophs. In fungi, more than 70% of CBM1-containing proteins correspond to enzymatic proteins in which CBM1 is associated with a catalytic unit involved in cellulose degradation. In oomycetes more than 90% of proteins are similar to CBEL in which CBM1 is associated with a non-catalytic PAN/Apple domain, known to interact with specific carbohydrates or proteins. Distinct Stramenopile genomes like diatoms and brown algae are devoid of CBM1 coding genes. A CBM1-PAN/Apple association 3D structural modeling was built allowing the identification of amino acid residues interacting with cellulose and suggesting the putative interaction of the PAN/Apple domain with another type of glucan. By Surface Plasmon Resonance experiments, we showed that CBEL binds to glycoproteins through galactose or N-acetyl-galactosamine motifs. Conclusions This study

  20. Digital Learning Characteristics and Principles of Information Resources Knowledge Structuring

    Science.gov (United States)

    Belichenko, Margarita; Davidovitch, Nitza; Kravchenko, Yuri

    2017-01-01

    Analysis of principles knowledge representation in information systems led to the necessity of improving the structuring knowledge. It is caused by the development of software component and new possibilities of information technologies. The article combines methodological aspects of structuring knowledge and effective usage of information…

  1. The Interaction of Information Structure and Syntactic Representation in Chinese

    Science.gov (United States)

    Hsu, Yu-Yin

    2013-01-01

    This dissertation concerns the interaction of syntax and information structure in Mandarin Chinese and puts the theoretical assumption of parallelism between clauses and noun phrases to the test. It examines and validates the information structural status of the object phrases preposed to clause-internal positions. I argue that Rizzi's (1997)…

  2. Teaching Text Structure: Examining the Affordances of Children's Informational Texts

    Science.gov (United States)

    Jones, Cindy D.; Clark, Sarah K.; Reutzel, D. Ray

    2016-01-01

    This study investigated the affordances of informational texts to serve as model texts for teaching text structure to elementary school children. Content analysis of a random sampling of children's informational texts from top publishers was conducted on text structure organization and on the inclusion of text features as signals of text…

  3. Information Architecture and the Comic Arts: Knowledge Structure and Access

    Science.gov (United States)

    Farmer, Lesley S. J.

    2015-01-01

    This article explains information architecture, focusing on comic arts' features for representing and structuring knowledge. Then it details information design theory and information behaviors relative to this format, also noting visual literacy. Next , applications of comic arts in education are listed. With this background, several research…

  4. Semantic illusion depends on information structure: ERP evidence

    NARCIS (Netherlands)

    Wang, L.; Hagoort, P.; Yang, Y.

    2009-01-01

    Next to propositional content, speakers distribute information in their utterances in such a way that listeners can make a distinction between new (focused) and given (non-focused) information. This is referred to as information structure. We measured event-related potentials (ERPs) to explore the r

  5. Structural and functional studies on a unique linear neutralizing antigenic site (G5) of the rabies virus glycoprotein.

    NARCIS (Netherlands)

    R.W.J. van der Heijden (Roger); J.P.M. Langedijk; J. Groen (Jan); F.G.C.M. Uytdehaag (Fons); R.H. Meloen; A.D.M.E. Osterhaus (Albert)

    1993-01-01

    textabstractThe core of a unique linear neutralization epitope (G5) on the glycoprotein of rabies virus, recognized by a virus-neutralizing mouse monoclonal antibody (MAb 6-15C4), was determined by Pepscan analysis. The G5 epitope was defined as an octapeptide (LHDFRSDE). The contribution of the

  6. Unique Structural Properties of the Mg-Al Hydrotalcite Solid Base Catalyst : An In Situ Study using Mg and Al K-edge XAFS during Calcination and Rehydration

    NARCIS (Netherlands)

    Koningsberger, D.C.; Bokhoven, J.A. van; Roelofs, J.C.A.A.; Jong, K.P. de

    2001-01-01

    The changes in the layered structure of Mg-Al hydrotalcite (Mg/Al=2) during heat treatment have been investigated by using in situ XAFS simultaneously at the Mg and Al K-edges. The development of unique in situ instrumentation allowed the coordination environments at both the Mg and Al centers to be

  7. Structural aesthetics in molecular nanoscience: a unique Ni26 cluster with a 'rabbit-face' topology and a discrete Ni18 'molecular chain'.

    Science.gov (United States)

    Athanasopoulou, Angeliki A; Pilkington, Melanie; Raptopoulou, Catherine P; Escuer, Albert; Stamatatos, Theocharis C

    2014-12-11

    The use of a previously unexplored Schiff-base ligand in Ni(II) carboxylate chemistry has afforded a Ni26 cluster with a record nuclearity that crystallizes with a unique 'rabbit-face'-like topology, and a Ni18 compound that adopts an unusual 'molecular chain' structure.

  8. Constructing the informatics and information technology foundations of a medical device evaluation system: a report from the FDA unique device identifier demonstration.

    Science.gov (United States)

    Drozda, Joseph P; Roach, James; Forsyth, Thomas; Helmering, Paul; Dummitt, Benjamin; Tcheng, James E

    2017-05-03

    The US Food and Drug Administration (FDA) has recognized the need to improve the tracking of medical device safety and performance, with implementation of Unique Device Identifiers (UDIs) in electronic health information as a key strategy. The FDA funded a demonstration by Mercy Health wherein prototype UDIs were incorporated into its electronic information systems. This report describes the demonstration's informatics architecture. Prototype UDIs for coronary stents were created and implemented across a series of information systems, resulting in UDI-associated data flow from manufacture through point of use to long-term follow-up, with barcode scanning linking clinical data with UDI-associated device attributes. A reference database containing device attributes and the UDI Research and Surveillance Database (UDIR) containing the linked clinical and device information were created, enabling longitudinal assessment of device performance. The demonstration included many stakeholders: multiple Mercy departments, manufacturers, health system partners, the FDA, professional societies, the National Cardiovascular Data Registry, and information system vendors. The resulting system of systems is described in detail, including entities, functions, linkage between the UDIR and proprietary systems using UDIs as the index key, data flow, roles and responsibilities of actors, and the UDIR data model. The demonstration provided proof of concept that UDIs can be incorporated into provider and enterprise electronic information systems and used as the index key to combine device and clinical data in a database useful for device evaluation. Keys to success and challenges to achieving this goal were identified. Fundamental informatics principles were central to accomplishing the system of systems model.

  9. Analysis of crack propagation in concrete structures with structural information entropy

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    The propagation of cracks in concrete structures causes energy dissipation and release, and also causes energy redistribution in the structures. Entropy can characterize the energy redistribution. To investigate the relation between the propagation of cracks and the entropy in concrete structures, cracked concrete structures are treated as dissipative structures. Structural information entropy is defined for concrete structures. A compact tension test is conducted. Meanwhile, numerical simulations are also carried out. Both the test and numerical simulation results show that the structural information entropy in the structures can characterize the propagation of cracks in concrete structures.

  10. Protein structure and evolution: are they constrained globally by a principle derived from information theory?

    Science.gov (United States)

    Hatton, Leslie; Warr, Gregory

    2015-01-01

    That the physicochemical properties of amino acids constrain the structure, function and evolution of proteins is not in doubt. However, principles derived from information theory may also set bounds on the structure (and thus also the evolution) of proteins. Here we analyze the global properties of the full set of proteins in release 13-11 of the SwissProt database, showing by experimental test of predictions from information theory that their collective structure exhibits properties that are consistent with their being guided by a conservation principle. This principle (Conservation of Information) defines the global properties of systems composed of discrete components each of which is in turn assembled from discrete smaller pieces. In the system of proteins, each protein is a component, and each protein is assembled from amino acids. Central to this principle is the inter-relationship of the unique amino acid count and total length of a protein and its implications for both average protein length and occurrence of proteins with specific unique amino acid counts. The unique amino acid count is simply the number of distinct amino acids (including those that are post-translationally modified) that occur in a protein, and is independent of the number of times that the particular amino acid occurs in the sequence. Conservation of Information does not operate at the local level (it is independent of the physicochemical properties of the amino acids) where the influences of natural selection are manifest in the variety of protein structure and function that is well understood. Rather, this analysis implies that Conservation of Information would define the global bounds within which the whole system of proteins is constrained; thus it appears to be acting to constrain evolution at a level different from natural selection, a conclusion that appears counter-intuitive but is supported by the studies described herein.

  11. Protein structure and evolution: are they constrained globally by a principle derived from information theory?

    Directory of Open Access Journals (Sweden)

    Leslie Hatton

    Full Text Available That the physicochemical properties of amino acids constrain the structure, function and evolution of proteins is not in doubt. However, principles derived from information theory may also set bounds on the structure (and thus also the evolution of proteins. Here we analyze the global properties of the full set of proteins in release 13-11 of the SwissProt database, showing by experimental test of predictions from information theory that their collective structure exhibits properties that are consistent with their being guided by a conservation principle. This principle (Conservation of Information defines the global properties of systems composed of discrete components each of which is in turn assembled from discrete smaller pieces. In the system of proteins, each protein is a component, and each protein is assembled from amino acids. Central to this principle is the inter-relationship of the unique amino acid count and total length of a protein and its implications for both average protein length and occurrence of proteins with specific unique amino acid counts. The unique amino acid count is simply the number of distinct amino acids (including those that are post-translationally modified that occur in a protein, and is independent of the number of times that the particular amino acid occurs in the sequence. Conservation of Information does not operate at the local level (it is independent of the physicochemical properties of the amino acids where the influences of natural selection are manifest in the variety of protein structure and function that is well understood. Rather, this analysis implies that Conservation of Information would define the global bounds within which the whole system of proteins is constrained; thus it appears to be acting to constrain evolution at a level different from natural selection, a conclusion that appears counter-intuitive but is supported by the studies described herein.

  12. On the Possibility of Quantum Informational Structural Realism

    CERN Document Server

    Bynum, Terrell Ward

    2013-01-01

    In The Philosophy of Information (2011 book), Luciano Floridi presents an ontological theory of Being qua Being, which he calls "Informational Structural Realism", a theory which applies, he says, to every possible world. He identifies primordial information ("dedomena") as the foundation of any structure in any possible world. The present essay examines Floridi's defense of that theory, as well as his refutation of "Digital Ontology" (which some people might confuse with his own). Then, using Floridi's ontology as a starting point, the present essay adds quantum features to dedomena, yielding an ontological theory for our own universe, Quantum Informational Structural Realism, which provides a metaphysical interpretation of key quantum phenomena, and diminishes the "weirdness" or "spookiness" of quantum mechanics. Key Words: digital ontology, dedomena, structural realism, quantum information, primordial qubit

  13. Laboratory information management system for membrane protein structure initiative--from gene to crystal.

    Science.gov (United States)

    Troshin, Petr V; Morris, Chris; Prince, Stephen M; Papiz, Miroslav Z

    2008-12-01

    Membrane Protein Structure Initiative (MPSI) exploits laboratory competencies to work collaboratively and distribute work among the different sites. This is possible as protein structure determination requires a series of steps, starting with target selection, through cloning, expression, purification, crystallization and finally structure determination. Distributed sites create a unique set of challenges for integrating and passing on information on the progress of targets. This role is played by the Protein Information Management System (PIMS), which is a laboratory information management system (LIMS), serving as a hub for MPSI, allowing collaborative structural proteomics to be carried out in a distributed fashion. It holds key information on the progress of cloning, expression, purification and crystallization of proteins. PIMS is employed to track the status of protein targets and to manage constructs, primers, experiments, protocols, sample locations and their detailed histories: thus playing a key role in MPSI data exchange. It also serves as the centre of a federation of interoperable information resources such as local laboratory information systems and international archival resources, like PDB or NCBI. During the challenging task of PIMS integration, within the MPSI, we discovered a number of prerequisites for successful PIMS integration. In this article we share our experiences and provide invaluable insights into the process of LIMS adaptation. This information should be of interest to partners who are thinking about using LIMS as a data centre for their collaborative efforts.

  14. Theory on Structure and Coloring of Maximal Planar Graphs (3)Purely Tree-colorable and Uniquely 4-colorable Maximal Planar Graph Conjectures

    Institute of Scientific and Technical Information of China (English)

    XU Jin

    2016-01-01

    A maximal planar graph is called the recursive maximal planar graph if it can be obtained from 4 K by embedding a 3-degree vertex in some triangular face continuously. The uniquely 4-colorable maximal planar graph conjecture states that a planar graph is uniquely 4-colorable if and only if it is a recursive maximal planar graph. This conjecture, which has 43 years of history, is a very influential conjecture in graph coloring theory after the Four-Color Conjecture. In this paper, the structures and properties of dumbbell maximal planar graphs and recursive maximal planar graphs are studied, and an idea of proving the uniquely 4-colorable maximal planar graph conjecture is proposed based on the extending-contracting operation proposed in this series of article (2).

  15. Information Entropy Measures for Stand Structural Diversity:Joint Entropy

    Institute of Scientific and Technical Information of China (English)

    Lei Xiangdong; Lu Yuanchang

    2004-01-01

    Structural diversity is the key attribute of a stand. A set of biodiversity measures in ecology was introduced in forest management for describing stand structure, of which Shannon information entropy (Shannon index) has been the most widely used measure of species diversity. It is generally thought that tree size diversity could serve as a good proxy for height diversity. However, tree size diversity and height diversity for stand structure is not completely consistent. Stand diameter cannot reflect height information completely. Either tree size diversity or height diversity is one-dimensional information entropy measure. This paper discussed the method of multiple-dimensional information entropy measure with the concept of joint entropy. It is suggested that joint entropy is a good measure for describing overall stand structural diversity.

  16. Structural prediction of dynamic Bayesian network with partial prior information.

    Science.gov (United States)

    Maiti, Aniruddha; Reddy, Ramakanth; Mukherjee, Anirban

    2015-01-01

    The prediction of the structure of a hidden dynamic Bayesian network (DBN) from a noisy dataset is an important and challenging task. This work presents a generalized framework to infer the DBN network structure with partial prior information. In the proposed framework, the partial information about the network structure is provided in the form of prior. The proposed method makes use of the prior information regarding the presence and as well as absence of some of the edges. Using the noisy dataset and partial prior information, this method is able to infer nearly accurate structure of the network. The proposed method is validated using simulated datasets. In addition, two real biological datasets are used to infer hidden biological interaction networks.

  17. Structured Information Management Using New Techniques for Processing Text.

    Science.gov (United States)

    Gibb, Forbes; Smart, Godfrey

    1990-01-01

    Describes the development of a software system, SIMPR (Structured Information Management: Processing and Retrieval), that will process documents by indexing them and classifying their subjects. Topics discussed include information storage and retrieval, file inversion techniques, modelling the user, natural language searching, automatic indexing,…

  18. Information Structure and the Licensing of English Subjects

    Science.gov (United States)

    Mack, Jennifer Elaine

    2010-01-01

    Most approaches to argument realization in English are grounded in lexical semantic structure. While it is widely acknowledged that there is an intimate relationship between information structure and grammatical relations such as "subject," there have been few attempts to formalize this observation. This dissertation proposes an "interface model…

  19. Nuclear Structure References (NSR) file. [Mostly information for input

    Energy Technology Data Exchange (ETDEWEB)

    Ewbank, W.B.

    1978-08-01

    The use of the Nuclear Structure References file by the Nuclear Data Project at ORNL is described. Much of the report concerns format information of interest only to those preparing input to the system or otherwise needing detailed knowledge of its internal structure. 17 figures. (RWR)

  20. Fine Structure in the Circumstellar Environment of a Young, Solar-like Star the Unique Eclipses of KH 15D

    CERN Document Server

    Herbst, W; Vrba, F J; Ibrahimov, M A; Bailer-Jones, C A L; Mundt, R; Lamm, M J; Mazeh, T; Webster, Z T; Haisch, K E; Williams, E C; Rhodes, A H; Balonek, T J; Riffeser, A; Herbst, William; Hamilton, Catrina M.; Vrba, Frederick J.; Ibrahimov, Mansur A.; Bailer-Jones, Coryn A.L.; Mundt, Reinhard; Lamm, Markus; Mazeh, Tsevi; Webster, Zodiac T.; Haisch, Karl E.; Williams, Eric C.; Rhodes, Andrew H.; Balonek, Thomas J.; Riffeser, Alexander Scholz and Arno

    2002-01-01

    Results of an international campaign to photometrically monitor the unique pre-main sequence eclipsing object KH 15D are reported. An updated ephemeris for the eclipse is derived that incorporates a slightly revised period of 48.36 d. There is some evidence that the orbital period is actually twice that value, with two eclipses occurring per cycle. The extraordinary depth (~3.5 mag) and duration (~18 days) of the eclipse indicate that it is caused by circumstellar matter, presumably the inner portion of a disk. The eclipse has continued to lengthen with time and the central brightness reversals are not as extreme as they once were. V-R and V-I colors indicate that the system is slightly bluer near minimum light. Ingress and egress are remarkably well modeled by the passage of a knife-edge across a limb-darkened star. Possible models for the system are briefly discussed.

  1. A large scale analysis of information-theoretic network complexity measures using chemical structures.

    Directory of Open Access Journals (Sweden)

    Matthias Dehmer

    Full Text Available This paper aims to investigate information-theoretic network complexity measures which have already been intensely used in mathematical- and medicinal chemistry including drug design. Numerous such measures have been developed so far but many of them lack a meaningful interpretation, e.g., we want to examine which kind of structural information they detect. Therefore, our main contribution is to shed light on the relatedness between some selected information measures for graphs by performing a large scale analysis using chemical networks. Starting from several sets containing real and synthetic chemical structures represented by graphs, we study the relatedness between a classical (partition-based complexity measure called the topological information content of a graph and some others inferred by a different paradigm leading to partition-independent measures. Moreover, we evaluate the uniqueness of network complexity measures numerically. Generally, a high uniqueness is an important and desirable property when designing novel topological descriptors having the potential to be applied to large chemical databases.

  2. Complementary molecular information changes our perception of food web structure.

    Science.gov (United States)

    Wirta, Helena K; Hebert, Paul D N; Kaartinen, Riikka; Prosser, Sean W; Várkonyi, Gergely; Roslin, Tomas

    2014-02-04

    How networks of ecological interactions are structured has a major impact on their functioning. However, accurately resolving both the nodes of the webs and the links between them is fraught with difficulties. We ask whether the new resolution conferred by molecular information changes perceptions of network structure. To probe a network of antagonistic interactions in the High Arctic, we use two complementary sources of molecular data: parasitoid DNA sequenced from the tissues of their hosts and host DNA sequenced from the gut of adult parasitoids. The information added by molecular analysis radically changes the properties of interaction structure. Overall, three times as many interaction types were revealed by combining molecular information from parasitoids and hosts with rearing data, versus rearing data alone. At the species level, our results alter the perceived host specificity of parasitoids, the parasitoid load of host species, and the web-wide role of predators with a cryptic lifestyle. As the northernmost network of host-parasitoid interactions quantified, our data point exerts high leverage on global comparisons of food web structure. However, how we view its structure will depend on what information we use: compared with variation among networks quantified at other sites, the properties of our web vary as much or much more depending on the techniques used to reconstruct it. We thus urge ecologists to combine multiple pieces of evidence in assessing the structure of interaction webs, and suggest that current perceptions of interaction structure may be strongly affected by the methods used to construct them.

  3. Interconvertions between delta-lactam and delta-lactone derivatives initiated by unique transannular interactions of the rigid cyclohexane boat structure in pentacycloundecane.

    Science.gov (United States)

    Kruger, Hendrik G; Martins, Frans J C; Viljoen, Agatha M

    2004-07-09

    The pentacycloundecane (PCU) cage structure resembles a perfect boat conformation, and for the first time unique lactam/lactone interconversions on the flagpole carbons of a cyclohexane boat structure are reported. The syntheses of a novel dihydroxy-PCU-delta-lactone and two novel N-substituted PCU-delta-lactams are reported. Hydrolysis of some of the PCU-delta-lactam compounds produced delta-lactones, and reaction of the lactones with ammonia or primary amines again produced delta-lactams. Reaction mechanisms to account for the unusual interconversion reactions induced by transannular interactions are proposed.

  4. Cosmological parameters from large scale structure - geometric versus shape information

    CERN Document Server

    Hamann, Jan; Lesgourgues, Julien; Rampf, Cornelius; Wong, Yvonne Y Y

    2010-01-01

    The matter power spectrum as derived from large scale structure (LSS) surveys contains two important and distinct pieces of information: an overall smooth shape and the imprint of baryon acoustic oscillations (BAO). We investigate the separate impact of these two types of information on cosmological parameter estimation, and show that for the simplest cosmological models, the broad-band shape information currently contained in the SDSS DR7 halo power spectrum (HPS) is by far superseded by geometric information derived from the baryonic features. An immediate corollary is that contrary to popular beliefs, the upper limit on the neutrino mass m_\

  5. The Structure of the Poxvirus A33 Protein Reveals a Dimer of Unique C-Type Lectin-Like Domains

    Energy Technology Data Exchange (ETDEWEB)

    Su, Hua-Poo; Singh, Kavita; Gittis, Apostolos G.; Garboczi, David N. (NIH)

    2010-11-03

    The current vaccine against smallpox is an infectious form of vaccinia virus that has significant side effects. Alternative vaccine approaches using recombinant viral proteins are being developed. A target of subunit vaccine strategies is the poxvirus protein A33, a conserved protein in the Chordopoxvirinae subfamily of Poxviridae that is expressed on the outer viral envelope. Here we have determined the structure of the A33 ectodomain of vaccinia virus. The structure revealed C-type lectin-like domains (CTLDs) that occur as dimers in A33 crystals with five different crystal lattices. Comparison of the A33 dimer models shows that the A33 monomers have a degree of flexibility in position within the dimer. Structural comparisons show that the A33 monomer is a close match to the Link module class of CTLDs but that the A33 dimer is most similar to the natural killer (NK)-cell receptor class of CTLDs. Structural data on Link modules and NK-cell receptor-ligand complexes suggest a surface of A33 that could interact with viral or host ligands. The dimer interface is well conserved in all known A33 sequences, indicating an important role for the A33 dimer. The structure indicates how previously described A33 mutations disrupt protein folding and locates the positions of N-linked glycosylations and the epitope of a protective antibody.

  6. The structural chemistry of metallocorroles: combined X-ray crystallography and quantum chemistry studies afford unique insights.

    Science.gov (United States)

    Thomas, Kolle E; Alemayehu, Abraham B; Conradie, Jeanet; Beavers, Christine M; Ghosh, Abhik

    2012-08-21

    Although they share some superficial structural similarities with porphyrins, corroles, trianionic ligands with contracted cores, give rise to fundamentally different transition metal complexes in comparison with the dianionic porphyrins. Many metallocorroles are formally high-valent, although a good fraction of them are also noninnocent, with significant corrole radical character. These electronic-structural characteristics result in a variety of fascinating spectroscopic behavior, including highly characteristic, paramagnetically shifted NMR spectra and textbook cases of charge-transfer spectra. Although our early research on corroles focused on spectroscopy, we soon learned that the geometric structures of metallocorroles provide a fascinating window into their electronic-structural characteristics. Thus, we used X-ray structure determinations and quantum chemical studies, chiefly using DFT, to obtain a comprehensive understanding of metallocorrole geometric and electronic structures. This Account describes our studies of the structural chemistry of metallocorroles. At first blush, the planar or mildly domed structure of metallocorroles might appear somewhat uninteresting particularly when compared to metalloporphyrins. Metalloporphyrins, especially sterically hindered ones, are routinely ruffled or saddled, but the missing meso carbon apparently makes the corrole skeleton much more resistant to nonplanar distortions. Ruffling, where the pyrrole rings are alternately twisted about the M-N bonds, is energetically impossible for metallocorroles. Saddling is also uncommon; thus, a number of sterically hindered, fully substituted metallocorroles exhibit almost perfectly planar macrocycle cores. Against this backdrop, copper corroles stand out as an important exception. As a result of an energetically favorable Cu(d(x2-y2))-corrole(π) orbital interaction, copper corroles, even sterically unhindered ones, are inherently saddled. Sterically hindered substituents

  7. Community detection using global and local structural information

    Indian Academy of Sciences (India)

    Hai-Long Yan; Ju Xiang; Xiao-Yu Zhang; Jun-Feng Fan; Fang Chane; Gen-Yi Fu; Er-Min Guo; Xin-Guang Hu; Ke Hu; Ru-Min Wang

    2013-01-01

    Community detection is of considerable importance for understanding both the structure and function of complex networks. In this paper, we introduced the general procedure of the community detection algorithms using global and local structural information, where the edge betweenness and the local similarity measures respectively based on local random walk dynamics and local cyclic structures were used. The algorithms were tested on artificial and real-world networks. The results clearly show that all the algorithms have excellent performance in the tests and the local similarity measure based on local random walk dynamics is superior to that based on local cyclic structures.

  8. Correlating structural order with structural rearrangement in dusty plasma liquids: can structural rearrangement be predicted by static structural information?

    Science.gov (United States)

    Su, Yen-Shuo; Liu, Yu-Hsuan; I, Lin

    2012-11-09

    Whether the static microstructural order information is strongly correlated with the subsequent structural rearrangement (SR) and their predicting power for SR are investigated experimentally in the quenched dusty plasma liquid with microheterogeneities. The poor local structural order is found to be a good alarm to identify the soft spot and predict the short term SR. For the site with good structural order, the persistent time for sustaining the structural memory until SR has a large mean value but a broad distribution. The deviation of the local structural order from that averaged over nearest neighbors serves as a good second alarm to further sort out the short time SR sites. It has the similar sorting power to that using the temporal fluctuation of the local structural order over a small time interval.

  9. Reinforcing Visual Grouping Cues to Communicate Complex Informational Structure.

    Science.gov (United States)

    Bae, Juhee; Watson, Benjamin

    2014-12-01

    In his book Multimedia Learning [7], Richard Mayer asserts that viewers learn best from imagery that provides them with cues to help them organize new information into the correct knowledge structures. Designers have long been exploiting the Gestalt laws of visual grouping to deliver viewers those cues using visual hierarchy, often communicating structures much more complex than the simple organizations studied in psychological research. Unfortunately, designers are largely practical in their work, and have not paused to build a complex theory of structural communication. If we are to build a tool to help novices create effective and well structured visuals, we need a better understanding of how to create them. Our work takes a first step toward addressing this lack, studying how five of the many grouping cues (proximity, color similarity, common region, connectivity, and alignment) can be effectively combined to communicate structured text and imagery from real world examples. To measure the effectiveness of this structural communication, we applied a digital version of card sorting, a method widely used in anthropology and cognitive science to extract cognitive structures. We then used tree edit distance to measure the difference between perceived and communicated structures. Our most significant findings are: 1) with careful design, complex structure can be communicated clearly; 2) communicating complex structure is best done with multiple reinforcing grouping cues; 3) common region (use of containers such as boxes) is particularly effective at communicating structure; and 4) alignment is a weak structural communicator.

  10. Structural Identification and Monitoring based on Uncertain/Limited Information

    Directory of Open Access Journals (Sweden)

    Chatzi Eleni N.

    2015-01-01

    Full Text Available The goal of the present study is to propose a structural identification framework able to exploit both vibrational response and operational condition information in extracting structural models, able to represent the systemspecific structural behavior in its complete operational spectrum. In doing so, a scheme need be derived for the extraction of salient features, which are indicative of structural condition. Such a scheme should account for variations attributed to operational effects, such as environmental and operational load variations, and which likely lie within regular structural condition bounds, versus variations which indicate short- or long-term damage effects. The latter may be achieved via coupling of sparse, yet diverse, monitoring information with appropriate stochastic tools, able to infer the underlying dependences between the monitored input and output data. This in turn allows for extraction of quantities, or features, relating to structural condition, which may further be utilized as performance indicators. The computational tool developed herein for realizing such a framework, termed the PCE-ICA scheme, is based on the use of Polynomial Chaos Expansion (PCE tool, along with an Independent Component Analysis (ICA algorithm. The benefits of additionally fusing a data-driven system model will further be discussed for the case of complex structural response. The method is assessed via implementation on field data acquired from diverse structural systems, namely a benchmark bridge case study and a wind turbine tower structure, revealing a robust condition assessment tool.

  11. Interaction between Syntactic Structure and Information Structure in the Processing of a Head-Final Language

    Science.gov (United States)

    Koizumi, Masatoshi; Imamura, Satoshi

    2017-01-01

    The effects of syntactic and information structures on sentence processing load were investigated using two reading comprehension experiments in Japanese, a head-final SOV language. In the first experiment, we discovered the main effects of syntactic and information structures, as well as their interaction, showing that interaction of these two…

  12. Kinetic and structural studies reveal a unique binding mode of sulfite to the nickel center in urease

    OpenAIRE

    Mazzei, Luca; Cianci, Michele; Benini, Stefano; Bertini, Leonardo; Musiani, Francesco; Ciurli, Stefano

    2016-01-01

    Urease is the most efficient enzyme known to date, and catalyzes the hydrolysis of urea using two Ni(II) ions in the active site. Urease is a virulence factor in several human pathogens, while causing severe environmental and agronomic problems. Sporosarcina pasteurii urease has been used extensively in the structural characterization of the enzyme. Sodium sulfite has been widely used as a preservative in urease solutions to prevent oxygen-induced oxidation, but its role as an inhibitor has a...

  13. Risk Management of Large RC Structures within Spatial Information System

    DEFF Research Database (Denmark)

    Qin, Jianjun; Faber, Michael Havbro

    2012-01-01

    subject to corrosion and geographical information system based risk modeling concerning large‐scale risk management. The term “risk management” here refers in particular to the process of condition assessment and optimization of the inspection and repair activities. The SIS facilitates the storage......Abstract: The present article addresses the development of a spatial information system (SIS), which aims to facilitate risk management of large‐scale concrete structures. The formulation of the SIS is based on ideas developed in the context of indicator‐based risk modeling for concrete structures...... and handling of all relevant information to the risk management. The probabilistic modeling utilized in the condition assessment takes basis in a Bayesian hierarchical modeling philosophy. It facilitates the updating of risks as well as optimizing inspection plans whenever new information about the condition...

  14. The structure of Aquifex aeolicus ribosomal protein S8 reveals a unique subdomain that contributes to an extremely tight association with 16S rRNA.

    Science.gov (United States)

    Menichelli, Elena; Edgcomb, Stephen P; Recht, Michael I; Williamson, James R

    2012-01-20

    The assembly of ribonucleoprotein complexes occurs under a broad range of conditions, but the principles that promote assembly and allow function at high temperature are poorly understood. The ribosomal protein S8 from Aquifex aeolicus (AS8) is unique in that there is a 41-residue insertion in the consensus S8 sequence. In addition, AS8 exhibits an unusually high affinity for the 16S ribosomal RNA, characterized by a picomolar dissociation constant that is approximately 26,000-fold tighter than the equivalent interaction from Escherichia coli. Deletion analysis demonstrated that binding to the minimal site on helix 21 occurred at the same nanomolar affinity found for other bacterial species. The additional affinity required the presence of a three-helix junction between helices 20, 21, and 22. The crystal structure of AS8 was solved, revealing the helix-loop-helix geometry of the unique AS8 insertion region, while the core of the molecule is conserved with known S8 structures. The AS8 structure was modeled onto the structure of the 30S ribosomal subunit from E. coli, suggesting the possibility that the unique subdomain provides additional backbone and side-chain contacts between the protein and an unpaired base within the three-way junction of helices 20, 21, and 22. Point mutations in the protein insertion subdomain resulted in a significantly reduced RNA binding affinity with respect to wild-type AS8. These results indicate that the AS8-specific subdomain provides additional interactions with the three-way junction that contribute to the extremely tight binding to ribosomal RNA.

  15. Designing quantum information processing via structural physical approximation

    Science.gov (United States)

    Bae, Joonwoo

    2017-10-01

    In quantum information processing it may be possible to have efficient computation and secure communication beyond the limitations of classical systems. In a fundamental point of view, however, evolution of quantum systems by the laws of quantum mechanics is more restrictive than classical systems, identified to a specific form of dynamics, that is, unitary transformations and, consequently, positive and completely positive maps to subsystems. This also characterizes classes of disallowed transformations on quantum systems, among which positive but not completely maps are of particular interest as they characterize entangled states, a general resource in quantum information processing. Structural physical approximation offers a systematic way of approximating those non-physical maps, positive but not completely positive maps, with quantum channels. Since it has been proposed as a method of detecting entangled states, it has stimulated fundamental problems on classifications of positive maps and the structure of Hermitian operators and quantum states, as well as on quantum measurement such as quantum design in quantum information theory. It has developed efficient and feasible methods of directly detecting entangled states in practice, for which proof-of-principle experimental demonstrations have also been performed with photonic qubit states. Here, we present a comprehensive review on quantum information processing with structural physical approximations and the related progress. The review mainly focuses on properties of structural physical approximations and their applications toward practical information applications.

  16. Unique structure and stability of HmuY, a novel heme-binding protein of Porphyromonas gingivalis.

    Directory of Open Access Journals (Sweden)

    Halina Wójtowicz

    2009-05-01

    Full Text Available Infection, survival, and proliferation of pathogenic bacteria in humans depend on their capacity to impair host responses and acquire nutrients in a hostile environment. Among such nutrients is heme, a co-factor for oxygen storage, electron transport, photosynthesis, and redox biochemistry, which is indispensable for life. Porphyromonas gingivalis is the major human bacterial pathogen responsible for severe periodontitis. It recruits heme through HmuY, which sequesters heme from host carriers and delivers it to its cognate outer-membrane transporter, the TonB-dependent receptor HmuR. Here we report that heme binding does not significantly affect the secondary structure of HmuY. The crystal structure of heme-bound HmuY reveals a new all-beta fold mimicking a right hand. The thumb and fingers pinch heme iron through two apical histidine residues, giving rise to highly symmetric octahedral iron co-ordination. The tetrameric quaternary arrangement of the protein found in the crystal structure is consistent with experiments in solution. It shows that thumbs and fingertips, and, by extension, the bound heme groups, are shielded from competing heme-binding proteins from the host. This may also facilitate heme transport to HmuR for internalization. HmuY, both in its apo- and in its heme-bound forms, is resistant to proteolytic digestion by trypsin and the major secreted proteases of P. gingivalis, gingipains K and R. It is also stable against thermal and chemical denaturation. In conclusion, these studies reveal novel molecular properties of HmuY that are consistent with its role as a putative virulence factor during bacterial infection.

  17. A New Star-shaped Carbazole Derivative with Polyhedral Oligomeric Silsesquioxane Core: Crystal Structure and Unique Photoluminescence Property.

    Science.gov (United States)

    Xu, Zixuan; Yu, Tianzhi; Zhao, Yuling; Zhang, Hui; Zhao, Guoyun; Li, Jianfeng; Chai, Lanqin

    2016-01-01

    A new inorganic–organic hybrid material based on polyhedral oligomeric silsesquioxane (POSS) capped with carbazolyl substituents, octakis[3-(carbazol-9-yl)propyldimethylsiloxy]-silsesquioxane (POSS-8Cz), was successfully synthesized and characterized. The X-ray crystal structure of POSS-8Cz were described. The photophysical properties of POSS-8Cz were investigated by using UV–vis,photoluminescence spectroscopic analysis. The hybrid material exhibits blue emission in the solution and the solid film.The morphology and thermal stablity properties were measured by X-ray diffraction (XRD) and TG-DTA analysis.

  18. Information and computer-aided system for structural materials

    Energy Technology Data Exchange (ETDEWEB)

    Nekrashevitch, Yu.G.; Nizametdinov, Sh.U.; Polkovnikov, A.V.; Rumjantzev, V.P.; Surina, O.N. (Engineering Physics Inst., Moscow (Russia)); Kalinin, G.M.; Sidorenkov, A.V.; Strebkov, Yu.S. (Research and Development Inst. of Power Engineering, Moscow (Russia))

    1992-09-01

    An information and computer-aided system for structural materials data has been developed to provide data for the fusion and fission reactor system design. It is designed for designers, industrial engineers, and material science specialists and provides a friendly interface in an interactive mode. The database for structural materials contains the master files: Chemical composition, physical, mechanical, corrosion, technological properties, regulatory and technical documentation. The system is implemented on a PC/AT running the PS /2 operating system. (orig.).

  19. Integrating "Free" Word Order Syntax and Information Structure

    CERN Document Server

    Hoffman, B

    1995-01-01

    This paper describes a combinatory categorial formalism called Multiset-CCG that can capture the syntax and interpretation of ``free'' word order in languages such as Turkish. The formalism compositionally derives the predicate-argument structure and the information structure (e.g. topic, focus) of a sentence in parallel, and uniformly handles word order variation among the arguments and adjuncts within a clause, as well as in complex clauses and across clause boundaries.

  20. Kinetic and structural studies reveal a unique binding mode of sulfite to the nickel center in urease.

    Science.gov (United States)

    Mazzei, Luca; Cianci, Michele; Benini, Stefano; Bertini, Leonardo; Musiani, Francesco; Ciurli, Stefano

    2016-01-01

    Urease is the most efficient enzyme known to date, and catalyzes the hydrolysis of urea using two Ni(II) ions in the active site. Urease is a virulence factor in several human pathogens, while causing severe environmental and agronomic problems. Sporosarcina pasteurii urease has been used extensively in the structural characterization of the enzyme. Sodium sulfite has been widely used as a preservative in urease solutions to prevent oxygen-induced oxidation, but its role as an inhibitor has also been suggested. In the present study, isothermal titration microcalorimetry was used to establish sulfite as a competitive inhibitor for S. pasteurii urease, with an inhibition constant of 0.19mM at pH7. The structure of the urease-sulfite complex, determined at 1.65Å resolution, shows the inhibitor bound to the dinuclear Ni(II) center of urease in a tridentate mode involving bonds between the two Ni(II) ions in the active site and all three oxygen atoms of the inhibitor, supporting the observed competitive inhibition kinetics. This coordination mode of sulfite has never been observed, either in proteins or in small molecule complexes, and could inspire synthetic coordination chemists as well as biochemists to develop urease inhibitors based on this chemical moiety.

  1. Adaptive evolvement of information age C4ISR structure

    Institute of Scientific and Technical Information of China (English)

    Yushi Lan; Kebo Deng; Shaojie Mao; Heng Wang; Kan Yi; Ming Lei

    2015-01-01

    Command, control, communication, computing, intel-ligence, surveil ance and reconnaissance (C4ISR) in information age is a complex system whose structure always changes ac-tively or passively during the warfare. Therefore, it is important to optimize the structure, especial y in ambiguous and quick-tempo modern warfare. This paper proposes an adaptive evolvement mechanism for the C4ISR structure to survive the changeable warfare. Firstly, the information age C4ISR structure is defined and modeled based on the complex network theory. Secondly, taking the observe, orient, decide and act (OODA) model into consideration, four kinds of loops in the C4ISR structure are pro-posed and their coefficient of networked effects (CNE) is further defined. Then, the adaptive evolvement mechanisms of the four kinds of loops are presented respectively. Final y, taking the joint air-defense C4ISR as an example, simulation experiments are im-plemented, which validate the evolvement mechanism and show that the information age C4ISR structure has some characteristics of smal-world network and scale-free network.

  2. Information-theoretical noninvasive damage detection in bridge structures

    Science.gov (United States)

    Sudu Ambegedara, Amila; Sun, Jie; Janoyan, Kerop; Bollt, Erik

    2016-11-01

    Damage detection of mechanical structures such as bridges is an important research problem in civil engineering. Using spatially distributed sensor time series data collected from a recent experiment on a local bridge in Upper State New York, we study noninvasive damage detection using information-theoretical methods. Several findings are in order. First, the time series data, which represent accelerations measured at the sensors, more closely follow Laplace distribution than normal distribution, allowing us to develop parameter estimators for various information-theoretic measures such as entropy and mutual information. Second, as damage is introduced by the removal of bolts of the first diaphragm connection, the interaction between spatially nearby sensors as measured by mutual information becomes weaker, suggesting that the bridge is "loosened." Finally, using a proposed optimal mutual information interaction procedure to prune away indirect interactions, we found that the primary direction of interaction or influence aligns with the traffic direction on the bridge even after damaging the bridge.

  3. Crystal structure of TNF-α-inducing protein from Helicobacter pylori in active form reveals the intrinsic molecular flexibility for unique DNA-binding.

    Directory of Open Access Journals (Sweden)

    Mingming Gao

    Full Text Available Tipα (TNF-α-inducing protein from Helicobacter pylori is a carcinogenic effector. Studies on this protein revealed that a homodimer linked by a pair of intermolecular disulfide bridges (Cys25-Cys25 and Cys27-Cys27 was absolutely necessary for its biological functions. The activities of Tipα would be abolished when both disulfide bridges were disrupted. The crystal structures of Tipα reported to date, however, were based on inactive, monomeric mutants with their N-terminal, including residues Cys25 and Cys27, truncated. Here we report the crystal structure of H. pylori Tipα protein, TipαN(25, at 2.2Å resolution, in which Cys25 and Cys27 form a pair of inter-chain disulfide bridges linking an active dimer. The disulfide bridges exhibit structural flexibility in the present structure. A series of structure-based mutagenesis, biochemical assays and molecular dynamic simulations on DNA-Tipα interactions reveal that Tipα utilizes the dimeric interface as the DNA-binding site and that residues His60, Arg77 and Arg81 located at the interface are crucial for DNA binding. Tipα could bind to one ssDNA, two ssDNA or one dsDNA in experiments, respectively, in the native or mutant states. The unique DNA-binding activities of Tipα indicate that the intrinsic flexible nature of disulfide bridges could endow certain elasticity to the Tipα dimer for its unique bioactivities. The results shed light on the possible structural mechanism for the functional performances of Tipα.

  4. The crystal structure of Haloferax volcanii proliferating cell nuclear antigen reveals unique surface charge characteristics due to halophilic adaptation

    Directory of Open Access Journals (Sweden)

    Morroll Shaun

    2009-08-01

    Full Text Available Abstract Background The high intracellular salt concentration required to maintain a halophilic lifestyle poses challenges to haloarchaeal proteins that must stay soluble, stable and functional in this extreme environment. Proliferating cell nuclear antigen (PCNA is a fundamental protein involved in maintaining genome integrity, with roles in both DNA replication and repair. To investigate the halophilic adaptation of such a key protein we have crystallised and solved the structure of Haloferax volcanii PCNA (HvPCNA to a resolution of 2.0 Å. Results The overall architecture of HvPCNA is very similar to other known PCNAs, which are highly structurally conserved. Three commonly observed adaptations in halophilic proteins are higher surface acidity, bound ions and increased numbers of intermolecular ion pairs (in oligomeric proteins. HvPCNA possesses the former two adaptations but not the latter, despite functioning as a homotrimer. Strikingly, the positive surface charge considered key to PCNA's role as a sliding clamp is dramatically reduced in the halophilic protein. Instead, bound cations within the solvation shell of HvPCNA may permit sliding along negatively charged DNA by reducing electrostatic repulsion effects. Conclusion The extent to which individual proteins adapt to halophilic conditions varies, presumably due to their diverse characteristics and roles within the cell. The number of ion pairs observed in the HvPCNA monomer-monomer interface was unexpectedly low. This may reflect the fact that the trimer is intrinsically stable over a wide range of salt concentrations and therefore additional modifications for trimer maintenance in high salt conditions are not required. Halophilic proteins frequently bind anions and cations and in HvPCNA cation binding may compensate for the remarkable reduction in positive charge in the pore region, to facilitate functional interactions with DNA. In this way, HvPCNA may harness its environment as

  5. Evidence for predilection of macrophage infiltration patterns in the deeper midline and mesial temporal structures of the brain uniquely in patients with HIV-associated dementia

    Directory of Open Access Journals (Sweden)

    Hsu Kenneth

    2009-12-01

    Full Text Available Abstract Background HIV-1 penetrates the central nervous system, which is vital for HIV-associated dementia (HAD. But the role of cellular infiltration and activation together with HIV in the development of HAD is poorly understood. Methods To study activation and infiltration patterns of macrophages, CD8+ T cells in relation to HIV in diverse CNS areas of patients with and without dementia. 46 brain regions from two rapidly progressing severely demented patients and 53 regions from 4 HIV+ non-dementia patients were analyzed. Macrophage and CD8+ T cell infiltration of the CNS in relation to HIV was assessed using immuno-histochemical analysis with anti-HIV (P24, anti-CD8 and anti-CD68, anti-S-100A8 and granzyme B antibodies (cellular activation. Statistical analysis was performed with SPSS 12.0 with Student's t test and ANOVA. Results Overall, the patterns of infiltration of macrophages and CD8+ T cells were indiscernible between patients with and without dementia, but the co-localization of macrophages and CD8+ T cells along with HIV P24 antigen in the deeper midline and mesial temporal structures of the brain segregated the two groups. This predilection of infected macrophages and CD8+ T cells to the middle part of the brain was unique to both HAD patients, along with unique nature of provirus gag gene sequences derived from macrophages in the midline and mesial temporal structures. Conclusion Strong predilection of infected macrophages and CD8+ T cells was typical of the deeper midline and mesial temporal structures uniquely in HAD patients, which has some influence on neurocognitive impairment during HIV infection.

  6. Structural Characterization of Proline-rich Tyrosine Kinase 2 (PYK2) Reveals a Unique (DFG-out) Conformation and Enables Inhibitor Design

    Energy Technology Data Exchange (ETDEWEB)

    Han, Seungil; Mistry, Anil; Chang, Jeanne S.; Cunningham, David; Griffor, Matt; Bonnette, Peter C.; Wang, Hong; Chrunyk, Boris A.; Aspnes, Gary E.; Walker, Daniel P.; Brosius, Arthur D.; Buckbinder, Leonard; Pfizer

    2009-05-21

    Proline-rich tyrosine kinase 2 (PYK2) is a cytoplasmic, non-receptor tyrosine kinase implicated in multiple signaling pathways. It is a negative regulator of osteogenesis and considered a viable drug target for osteoporosis treatment. The high-resolution structures of the human PYK2 kinase domain with different inhibitor complexes establish the conventional bilobal kinase architecture and show the conformational variability of the DFG loop. The basis for the lack of selectivity for the classical kinase inhibitor, PF-431396, within the FAK family is explained by our structural analyses. Importantly, the novel DFG-out conformation with two diarylurea inhibitors (BIRB796, PF-4618433) reveals a distinct subclass of non-receptor tyrosine kinases identifiable by the gatekeeper Met-502 and the unique hinge loop conformation of Leu-504. This is the first example of a leucine residue in the hinge loop that blocks the ATP binding site in the DFG-out conformation. Our structural, biophysical, and pharmacological studies suggest that the unique features of the DFG motif, including Leu-504 hinge-loop variability, can be exploited for the development of selective protein kinase inhibitors.

  7. Thesaurus of terms for information on mechanics of structural failure

    Science.gov (United States)

    Carpenter, J. L., Jr.; Moya, N.

    1973-01-01

    A Thesaurus of approximately 700 subject terms used to describe the six problem areas in the mechanics of structural failure is presented. The initial criteria for the selection of terms are their significance and frequency of use in the literature describing the mechanics of structural failure. The purpose of the Thesaurus is to provide the Aerospace Safety Research and Data Institute a list of key works and identifiers that afford effective retrieval of information regarding failure modes and mechanisms for aerospace structures. The Thesaurus includes both a conventional listing of subject terms and a Key Words In Context (KWIC) listing.

  8. Quantitative Analysis of Major Factors Affecting Black Carbon Transport and Concentrations in the Unique Atmospheric Structures of Urban Environment

    Science.gov (United States)

    Liang, Marissa Shuang

    Black carbon (BC) from vehicular emission in transportation is a principal component of particulate matters ≤ 2.5 mum (PM2.5). PM2.5 and other diesel emission pollutants (e.g., NOx) are regulated by the Clean Air Act (CAA) according to the National Ambient Air Quality standards (NAAQS). This doctoral dissertation details a study on transport behaviors of black carbon and PM2.5 from transportation routes, their relations with the atmospheric structure of an urban formation, and their relations with the use of biodiesel fuels. The results have implications to near-road risk assessment and to the development of sustainable transportation solutions in urban centers. The first part of study quantified near-roadside black carbon transport as a function of particulate matter (PM) size and composition, as well as microclimatic variables (temperature and wind fields) at the interstate highway I-75 in northern Cincinnati, Ohio. Among variables examined, wind speed and direction significantly affect the roadside transport of black carbon and hence its effective emission factor. Observed non-Gaussian dispersion occurred during low wind and for wind directions at acute angles or upwind to the receptors, mostly occurring in the morning hours. Meandering of air pollutant mass under thermal inversion is likely the driving force. In contrary, Gaussian distribution predominated in daytime of strong downwinds. The roles of urban atmospheric structure, wind fields, and the urban heat island (UHI) effects were further examined on pollutant dispersion and transport. Spatiotemporal variations of traffic flow, atmospheric structure, ambient temperature and PM2.5 concentration data from 14 EPA-certified NAAQS monitoring stations, were analyzed in relation to land-use in the Cincinnati metropolitan area. The results show a decade-long UHI effects with higher interior temperature than that in exurban, and a prominent nocturnal thermal inversion frequent in urban boundary layer. The

  9. Prenuclear Accentuation in English: Phonetics, Phonology, Information Structure

    Science.gov (United States)

    Bishop, Jason Brandon

    2013-01-01

    A primary function of prosody in many languages is to convey information structure--the "packaging" of a sentence's content into categories such as "focus", "given" and "topic". In English and other West Germanic languages it is widely assumed that focus is signaled prosodically by the location of a…

  10. Prosodic Marking of Information Structure by Malaysian Speakers of English

    Science.gov (United States)

    Gut, Ulrike; Pillai, Stefanie

    2014-01-01

    Various researchers have shown that second language (L2) speakers have difficulties with marking information structure in English prosodically: They deviate from native speakers not only in terms of pitch accent placement (Grosser, 1997; Gut, 2009; Ramírez Verdugo, 2002) and the type of pitch accent they produce (Wennerstrom, 1994, 1998) but also…

  11. Impact of Information Technology Governance Structures on Strategic Alignment

    Science.gov (United States)

    Gordon, Fitzroy R.

    2013-01-01

    This dissertation is a study of the relationship between Information Technology (IT) strategic alignment and IT governance structure within the organization. This dissertation replicates Asante (2010) among a different population where the prior results continue to hold, the non-experimental approach explored two research questions but include two…

  12. Impact of Information Technology Governance Structures on Strategic Alignment

    Science.gov (United States)

    Gordon, Fitzroy R.

    2013-01-01

    This dissertation is a study of the relationship between Information Technology (IT) strategic alignment and IT governance structure within the organization. This dissertation replicates Asante (2010) among a different population where the prior results continue to hold, the non-experimental approach explored two research questions but include two…

  13. Exploiting structural information in patent specifications for key compound prediction.

    Science.gov (United States)

    Tyrchan, Christian; Boström, Jonas; Giordanetto, Fabrizio; Winter, Jon; Muresan, Sorel

    2012-06-25

    Patent specifications are one of many information sources needed to progress drug discovery projects. Understanding compound prior art and novelty checking, validation of biological assays, and identification of new starting points for chemical explorations are a few areas where patent analysis is an important component. Cheminformatics methods can be used to facilitate the identification of so-called key compounds in patent specifications. Such methods, relying on structural information extracted from documents by expert curation or text mining, can complement or in some cases replace the traditional manual approach of searching for clues in the text. This paper describes and compares three different methods for the automatic prediction of key compounds in patent specifications using structural information alone. For this data set, the cluster seed analysis described by Hattori et al. (Hattori, K.; Wakabayashi, H.; Tamaki, K. Predicting key example compounds in competitors' patent applications using structural information alone. J. Chem. Inf. Model.2008, 48, 135-142) is superior in terms of prediction accuracy with 26 out of 48 drugs (54%) correctly predicted from their corresponding patents. Nevertheless, the two new methods, based on frequency of R-groups (FOG) and maximum common substructure (MCS) similarity measures, show significant advantages due to their inherent ability to visualize relevant structural features. The results of the FOG method can be enhanced by manual selection of the scaffolds used in the analysis. Finally, a successful example of applying FOG analysis for designing potent ATP-competitive AXL kinase inhibitors with improved properties is described.

  14. Prenuclear Accentuation in English: Phonetics, Phonology, Information Structure

    Science.gov (United States)

    Bishop, Jason Brandon

    2013-01-01

    A primary function of prosody in many languages is to convey information structure--the "packaging" of a sentence's content into categories such as "focus", "given" and "topic". In English and other West Germanic languages it is widely assumed that focus is signaled prosodically by the location of a…

  15. The value of structural information in the VAR model

    NARCIS (Netherlands)

    R.W. Strachan (Rodney); H.K. van Dijk (Herman)

    2003-01-01

    textabstractEconomic policy decisions are often informed by empirical economic analysis. While the decision-maker is usually only interested in good estimates of outcomes, the analyst is interested in estimating the model. Accurate inference on the structural features of a model, such as cointegrati

  16. Systematic study of aggregation structure and thermal behavior of a series of unique H-shape alkane molecules.

    Science.gov (United States)

    Yamamoto, Hiroko; Tashiro, Kohji; Nemoto, Norio; Motoyama, Yukihiro; Takahashi, Yoshiaki

    2011-08-11

    The H-shape alkanes of various arm lengths have been synthesized successfully through the Grignard reaction. The detailed investigation of these novel compounds may allow us to widen the topological chemistry field furthermore. The molecular form and molecular packing structure in the crystal lattice have been revealed successfully on the basis of X-ray structure analysis as well as the analysis of Raman longitudinal acoustic modes (LAM) sensitive to the alkyl zigzag chain segments. The molecular conformation in the crystal lattice is deformed markedly from the originally imagined H-shape. In the cases of C3HOH to C6HOH, for example, the molecules are packed in a complicated manner and the OH···O hydrogen bonds govern the whole intermolecular interactions mainly. Since the alkyl segmental length is not very long, the conformational change is not very drastic, i.e., the small configurational entropy. Synergic effect of the hydrogen bonds and the small configurational entropy gives the higher melting point as known from the thermal data. On the other hand, in the cases of C10HOH and C12HOH, one of the long alkyl chain arms is found to be bent by 90° so that all of the alky chain segments of planar-zigzag conformation can be packed as closely as possible, and the intermolecular OH···O hydrogen bonds are also formed effectively without any mistake. As a result, the contribution of nonbonded intra- and intermolecular van der Waals interactions between the trans-zigzag alkyl chain segments become major, and the coupling of this enthalpy effect with the larger configurational entropy effect of the molecular shape results in the decrement of the melting point which approaches gradually that of longer n-alkane compound. In this way a sensitive balance between the nonbonded van der Waals interactions, the OH···O hydrogen bonds, as well as the configurational entropy effect gives the characteristic thermal behavior of the H-shape compounds. The thus

  17. Reduced graphene oxide composites with water soluble copolymers having tailored lower critical solution temperatures and unique tube-like structure

    Science.gov (United States)

    Namvari, Mina; Biswas, Chandra S.; Galluzzi, Massimiliano; Wang, Qiao; Du, Bing; Stadler, Florian J.

    2017-01-01

    Nanohybrids of graphene with water soluble polymer were synthesized using ‘grafting from’ method. GO, prepared by modified Hummers’ method, was first reacted with sodium azide. Alkyne-terminated RAFT-CTA was synthesized by reaction of propargyl alcohol and S-1-dodecyl-S’-(α,α‘-dimethyl-α”-acetic acid) trithiocarbonate. RAFT-CTA was grafted onto the GO sheets by facile click-reaction and subsequently, N-isopropylacrylamide (NIPAM) and N-ethyleacrylamide (NEAM) were polymerized on graphene sheets via RAFT polymerization method. The respective copolymers with different ratios were also prepared. The nanohybrids were characterized by FTIR, XRD, TGA, Raman, SEM, and AFM. Both SEM and AFM clearly showed rod-like structures for rGO-PNEAM. XRD showed a small peak at 2θ = 19.21°, corresponding to d-spacing ≈ 4.6 Å. In addition, the nanohybrids showed a very broad temperature range for the LCST in water between ca. 30 and 70 °C. PMID:28291225

  18. 3-cm Fine Structure Masers: A Unique Signature of Supermassive Black Hole Formation via Direct Collapse in the Early Universe

    CERN Document Server

    Dijkstra, Mark; Loeb, Abraham

    2016-01-01

    The direct collapse black hole (DCBH) scenario describes the isothermal collapse of a pristine gas cloud directly into a massive, M_BH=10^4-10^6 M_sun black hole. In this paper we show that large HI column densities of primordial gas at T~10^4 K with low molecular abundance - which represent key aspects of the DCBH scenario - provide optimal conditions for pumping of the 2p-level of atomic hydrogen by trapped Lyman alpha (Lya) photons. This Lya pumping mechanism gives rise to inverted level population of the 2s_1/2-2p_3/2 transition, and therefore to stimulated fine structure emission at 3.04 cm (rest-frame). We show that simplified models of the DCBH scenario amplify the CMB by up to a factor of 10^5, above which the maser saturates. Hyperfine splitting of the 3-cm transition gives rise to a characteristic broad (FWHM ~ tens of MHz in the observers frame) asymmetric line profile. This signal subtends an angular scale of ~ 1-10 mas, which translates to a flux of ~ 0.3-3 microJy, which is detectable with ultra...

  19. Reduced graphene oxide composites with water soluble copolymers having tailored lower critical solution temperatures and unique tube-like structure

    Science.gov (United States)

    Namvari, Mina; Biswas, Chandra S.; Galluzzi, Massimiliano; Wang, Qiao; Du, Bing; Stadler, Florian J.

    2017-03-01

    Nanohybrids of graphene with water soluble polymer were synthesized using ‘grafting from’ method. GO, prepared by modified Hummers’ method, was first reacted with sodium azide. Alkyne-terminated RAFT-CTA was synthesized by reaction of propargyl alcohol and S-1-dodecyl-S’-(α,α‘-dimethyl-α”-acetic acid) trithiocarbonate. RAFT-CTA was grafted onto the GO sheets by facile click-reaction and subsequently, N-isopropylacrylamide (NIPAM) and N-ethyleacrylamide (NEAM) were polymerized on graphene sheets via RAFT polymerization method. The respective copolymers with different ratios were also prepared. The nanohybrids were characterized by FTIR, XRD, TGA, Raman, SEM, and AFM. Both SEM and AFM clearly showed rod-like structures for rGO-PNEAM. XRD showed a small peak at 2θ = 19.21°, corresponding to d-spacing ≈ 4.6 Å. In addition, the nanohybrids showed a very broad temperature range for the LCST in water between ca. 30 and 70 °C.

  20. Information diversity in structure and dynamics of simulated neuronal networks.

    Science.gov (United States)

    Mäki-Marttunen, Tuomo; Aćimović, Jugoslava; Nykter, Matti; Kesseli, Juha; Ruohonen, Keijo; Yli-Harja, Olli; Linne, Marja-Leena

    2011-01-01

    Neuronal networks exhibit a wide diversity of structures, which contributes to the diversity of the dynamics therein. The presented work applies an information theoretic framework to simultaneously analyze structure and dynamics in neuronal networks. Information diversity within the structure and dynamics of a neuronal network is studied using the normalized compression distance. To describe the structure, a scheme for generating distance-dependent networks with identical in-degree distribution but variable strength of dependence on distance is presented. The resulting network structure classes possess differing path length and clustering coefficient distributions. In parallel, comparable realistic neuronal networks are generated with NETMORPH simulator and similar analysis is done on them. To describe the dynamics, network spike trains are simulated using different network structures and their bursting behaviors are analyzed. For the simulation of the network activity the Izhikevich model of spiking neurons is used together with the Tsodyks model of dynamical synapses. We show that the structure of the simulated neuronal networks affects the spontaneous bursting activity when measured with bursting frequency and a set of intraburst measures: the more locally connected networks produce more and longer bursts than the more random networks. The information diversity of the structure of a network is greatest in the most locally connected networks, smallest in random networks, and somewhere in between in the networks between order and disorder. As for the dynamics, the most locally connected networks and some of the in-between networks produce the most complex intraburst spike trains. The same result also holds for sparser of the two considered network densities in the case of full spike trains.

  1. Structural Simulations and Conservation Analysis -Historic Building Information Model (HBIM

    Directory of Open Access Journals (Sweden)

    C. Dore

    2015-02-01

    Full Text Available In this paper the current findings to date of the Historic Building Information Model (HBIM of the Four Courts in Dublin are presented. The Historic Building Information Model (HBIM forms the basis for both structural and conservation analysis to measure the impact of war damage which still impacts on the building. The laser scan survey was carried out in the summer of 2014 of the internal and external structure. After registration and processing of the laser scan survey, the HBIM was created of the damaged section of the building and is presented as two separate workflows in this paper. The first is the model created from historic data, the second a procedural and segmented model developed from laser scan survey of the war damaged drum and dome. From both models structural damage and decay simulations will be developed for documentation and conservation analysis.

  2. 3-cm Fine Structure Masers: A Unique Signature of Supermassive Black Hole Formation via Direct Collapse in the Early Universe

    Science.gov (United States)

    Dijkstra, Mark; Sethi, Shiv; Loeb, Abraham

    2016-03-01

    The direct collapse black hole (DCBH) scenario describes the isothermal collapse of a pristine gas cloud directly into a massive, {M}{BH} = 104-106{M}⊙ black hole. In this paper we show that large H i column densities of primordial gas at T˜ {10}4 K with low molecular abundance—which represent key aspects of the DCBH scenario—provide optimal conditions for the pumping of the 2p-level of atomic hydrogen by trapped Lyα photons. This Lyα pumping mechanism gives rise to an inverted level population of the 2{s}1/2-2{p}3/2 transition, and therefore also gives rise to stimulated fine structure emission at λ =3.04 {cm} (rest-frame). We show that simplified models of the DCBH scenario amplify the CMB by up to a factor of ˜ {10}5, above which the maser saturates. Hyperfine splitting of the 3 cm transition gives rise to a characteristic broad (FWHM ˜ tens of MHz in the observers frame) asymmetric line profile. This signal subtends an angular scale of ˜1-10 mas, which translates to a flux of ˜0.3-3 μJy, which is detectable with ultra-deep surveys being planned with SKA1-MID. While challenging, as the signal is visible for a fraction of the collapse time of the cloud, the matching required physical conditions imply that a detection of the redshifted 3-cm emission line could provide direct evidence for the DCBH scenario.

  3. Structural and functional characterization of the Geobacillus copper nitrite reductase: involvement of the unique N-terminal region in the interprotein electron transfer with its redox partner.

    Science.gov (United States)

    Fukuda, Yohta; Koteishi, Hiroyasu; Yoneda, Ryohei; Tamada, Taro; Takami, Hideto; Inoue, Tsuyoshi; Nojiri, Masaki

    2014-03-01

    The crystal structures of copper-containing nitrite reductase (CuNiR) from the thermophilic Gram-positive bacterium Geobacillus kaustophilus HTA426 and the amino (N)-terminal 68 residue-deleted mutant were determined at resolutions of 1.3Å and 1.8Å, respectively. Both structures show a striking resemblance with the overall structure of the well-known CuNiRs composed of two Greek key β-barrel domains; however, a remarkable structural difference was found in the N-terminal region. The unique region has one β-strand and one α-helix extended to the northern surface of the type-1 copper site. The superposition of the Geobacillus CuNiR model on the electron-transfer complex structure of CuNiR with the redox partner cytochrome c551 in other denitrifier system led us to infer that this region contributes to the transient binding with the partner protein during the interprotein electron transfer reaction in the Geobacillus system. Furthermore, electron-transfer kinetics experiments using N-terminal residue-deleted mutant and the redox partner, Geobacillus cytochrome c551, were carried out. These structural and kinetics studies demonstrate that the region is directly involved in the specific partner recognition.

  4. Quantification of the Value of Structural Health Monitoring Information for Fatigue Deteriorating Structural Systems

    DEFF Research Database (Denmark)

    Thöns, Sebastian; Schneider, Ronald; Faber, Michael Havbro

    2015-01-01

    This paper addresses the quantification of the value of structural health monitoring (SHM) before its implementation for structural systems on the basis of its Value of Information (VoI). The value of SHM is calculated utilizing the Bayesian pre-posterior decision analysis modelling the structural...... life cycle performance, the integrity management and the structural risks. The relevance and precision of SHM information for the reduction of the structural system risks and the expected cost of the structural integrity management throughout the life cycle constitutes the value of SHM....... The influence of and the value of SHM in regard to the structural system risks and the integrity management is explicated and explained. The results are pointing to the importance of the consideration of the structural system risks for the quantification of the value of SHM....

  5. Diabetes: Unique to Older Adults

    Science.gov (United States)

    ... Stroke Urinary Incontinence Related Documents PDF Choosing Wisely: Diabetes Tests and Treatments Download Related Video Join our e-newsletter! Aging & Health A to Z Diabetes Unique to Older Adults This section provides information ...

  6. Osteoporosis: Unique to Older Adults

    Science.gov (United States)

    ... our e-newsletter! Aging & Health A to Z Osteoporosis Unique to Older Adults This section provides information ... and widely-prescribed medications for the treatment of osteoporosis. Some serious side effects of these medication have ...

  7. Nutrition: Unique to Older Adults

    Science.gov (United States)

    ... our e-newsletter! Aging & Health A to Z Nutrition Unique to Older Adults This section provides information ... teeth that are needed for grinding up food, nutrition suffers. If you are unable to chew and ...

  8. On the complexity and the information content of cosmic structures

    Science.gov (United States)

    Vazza, F.

    2017-03-01

    The emergence of cosmic structure is commonly considered one of the most complex phenomena in nature. However, this complexity has never been defined nor measured in a quantitative and objective way. In this work, we propose a method to measure the information content of cosmic structure and to quantify the complexity that emerges from it, based on Information Theory. The emergence of complex evolutionary patterns is studied with a statistical symbolic analysis of the datastream produced by state-of-the-art cosmological simulations of forming galaxy clusters. This powerful approach allows us to measure how many bits of information is necessary to predict the evolution of energy fields in a statistical way, and it offers a simple way to quantify when, where and how the cosmic gas behaves in complex ways. The most complex behaviours are found in the peripheral regions of galaxy clusters, where supersonic flows drive shocks and large energy fluctuations over a few tens of million years. Describing the evolution of magnetic energy requires at least twice as large amount of bits as required for the other energy fields. When radiative cooling and feedback from galaxy formation are considered, the cosmic gas is overall found to double its degree of complexity. In the future, Cosmic Information Theory can significantly increase our understanding of the emergence of cosmic structure as it represents an innovative framework to design and analyse complex simulations of the Universe in a simple, yet powerful way.

  9. MPOD: A Material Property Open Database linked to structural information

    Science.gov (United States)

    Pepponi, Giancarlo; Gražulis, Saulius; Chateigner, Daniel

    2012-08-01

    Inspired by the Crystallography Open Database (COD), the Material Properties Open Database (MPOD) was given birth. MPOD aims at collecting and making publicly available at no charge tensorial properties (including scalar properties) of phases and linking such properties to structural information of the COD when available. MPOD files are written with the STAR file syntax, used and developed for the Crystallographic Information Files. A dictionary containing new definitions has been written according to the Dictionary Definition Language 1, although some tricks were adopted to allow for multiple entries still avoiding ambiguousness. The initial set includes mechanical properties, elastic stiffness and compliance, internal friction; electrical properties, resistivity, dielectric permittivity and stiffness, thermodynamic properties, heat capacity, thermal conductivity, diffusivity and expansion; electromechanical properties, piezoelectricity, electrostriction, electromechanical coupling; optical properties; piezooptic and photoelastic properties; superconducting properties, critical fields, penetration and coherence lengths. Properties are reported in MPOD files where the original published paper containing the data is cited and structural and experimental information is also given. One MPOD file contains information relative to only one publication and one phase. The files and the information contained therein can also be consulted on-line at http://www.materialproperties.org.

  10. Physicists' Information Tasks: Structure, Length and Retrieval Performance

    DEFF Research Database (Denmark)

    Lykke, Marianne; Ingwersen, Peter; Bogers, Toine;

    2010-01-01

    to describe the tasks, 3) what semantic categories were used to express the search facets, and 4) retrieval performance. Results show variety in structure and length across task descriptions and task purposes. The results indicate effect of length and, in particular, of task purpose on retrieval performance......In this poster, we describe central aspects of 65 natural information tasks from 23 senior researchers, PhDs, and experienced MSc students from three different university departments of physics. We analyze 1) the main purpose of the information task, 2) which and how many search facets were used...

  11. Physicists' Information Tasks: Structure, Length and Retrieval Performance

    DEFF Research Database (Denmark)

    Lykke, Marianne; Ingwersen, Peter; Bogers, Toine

    2010-01-01

    to describe the tasks, 3) what semantic categories were used to express the search facets, and 4) retrieval performance. Results show variety in structure and length across task descriptions and task purposes. The results indicate effect of length and, in particular, of task purpose on retrieval performance......In this poster, we describe central aspects of 65 natural information tasks from 23 senior researchers, PhDs, and experienced MSc students from three different university departments of physics. We analyze 1) the main purpose of the information task, 2) which and how many search facets were used...

  12. Extracting structural information from the polarization dependence of one- and two-dimensional sum frequency generation spectra.

    Science.gov (United States)

    Laaser, Jennifer E; Zanni, Martin T

    2013-07-25

    We present ways in which pulse sequences and polarizations can be used to extract structural information from one- and two-dimensional vibrational sum frequency generation (2D SFG) spectra. We derive analytic expressions for the polarization dependence of systems containing coupled vibrational modes, and we present simulated spectra to identify the features of different molecular geometries. We discuss several useful polarization combinations for suppressing strong diagonal peaks and emphasizing weaker cross-peaks. We investigate unique capabilities of 2D SFG spectra for obtaining structural information about SFG-inactive modes and for identifying coupled achiral chromophores. This work builds on techniques that have been developed for extracting structural information from 2D IR spectra. This paper discusses how to utilize these concepts in 2D SFG experiments to probe multioscillator systems at interfaces. The sample code for calculating polarization dependence of 1D and 2D SFG spectra is provided in the Supporting Information .

  13. Utilizing the Structure and Content Information for XML Document Clustering

    Science.gov (United States)

    Tran, Tien; Kutty, Sangeetha; Nayak, Richi

    This paper reports on the experiments and results of a clustering approach used in the INEX 2008 document mining challenge. The clustering approach utilizes both the structure and content information of the Wikipedia XML document collection. A latent semantic kernel (LSK) is used to measure the semantic similarity between XML documents based on their content features. The construction of a latent semantic kernel involves the computing of singular vector decomposition (SVD). On a large feature space matrix, the computation of SVD is very expensive in terms of time and memory requirements. Thus in this clustering approach, the dimension of the document space of a term-document matrix is reduced before performing SVD. The document space reduction is based on the common structural information of the Wikipedia XML document collection. The proposed clustering approach has shown to be effective on the Wikipedia collection in the INEX 2008 document mining challenge.

  14. Deep and Structured Robust Information Theoretic Learning for Image Analysis.

    Science.gov (United States)

    Deng, Yue; Bao, Feng; Deng, Xuesong; Wang, Ruiping; Kong, Youyong; Dai, Qionghai

    2016-07-07

    This paper presents a robust information theoretic (RIT) model to reduce the uncertainties, i.e. missing and noisy labels, in general discriminative data representation tasks. The fundamental pursuit of our model is to simultaneously learn a transformation function and a discriminative classifier that maximize the mutual information of data and their labels in the latent space. In this general paradigm, we respectively discuss three types of the RIT implementations with linear subspace embedding, deep transformation and structured sparse learning. In practice, the RIT and deep RIT are exploited to solve the image categorization task whose performances will be verified on various benchmark datasets. The structured sparse RIT is further applied to a medical image analysis task for brain MRI segmentation that allows group-level feature selections on the brain tissues.

  15. Information structure and reference tracking in complex sentences

    CERN Document Server

    Gijn, Rik van; Matic, Dejan

    2014-01-01

    This paper discusses argument marking and reference tracking in Mekens complex clauses and their correlation to information structure. The distribution of pronominal arguments in Mekens simple clauses follows an absolutive pattern with main verbs. Complex clauses maintain the morphological absolutive argument marking, but show a nominative pattern with respect to argument reference tracking, since transitive and intransitive subjects function as syntactic pivots. The language extends the use of argument-marking verb morphology to control the reference of discourse participants across clauses.

  16. 11Li structural information from inclusive break-up measurements

    Directory of Open Access Journals (Sweden)

    Fernández-García J. P.

    2015-01-01

    Full Text Available Structure information of 11Li halo nucleus has been obtained from the inclusive break-up measurements of the 11Li+208Pb reactions at energies around the Coulomb barrier (Elab = 24.3 and 29.8 MeV. The effective break-up energy and the slope of B(E1 distribution close to the threshold have been extracted from the experimental data.

  17. ANNIS: a linguistic database for exploring information structure

    OpenAIRE

    Dipper, Stefanie; Götze, Michael; Stede, Manfred; Wegst, Tillmann

    2008-01-01

    In this paper, we discuss the design and implementation of our first version of the database "ANNIS" (ANNotation of Information Structure). For research based on empirical data, ANNIS provides a uniform environment for storing this data together with its linguistic annotations. A central database promotes standardized annotation, which facilitates interpretation and comparison of the data. ANNIS is used through a standard web browser and offers tier-based visualization of data and annotations...

  18. The Effect of Information and Communication Technologies on Urban Structure

    OpenAIRE

    Ioannides, Yannis M.; Overman, Henry G.; Rossi-Hansberg, Esteban; Schmidheiny, Kurt

    2007-01-01

    The geographic concentration of economic activity occurs because transport costs for goods, people and ideas give individuals and organisations incentives to locate close to each other. Historically, all of these costs have been falling. Such changes could lead us to predict the death of distance. This paper is concerned with one aspect of this prediction: the impact that less costly communication and transmission of information might have on cities and the urban structure. We develop a model...

  19. The effect of information and communication technologies on urban structure

    OpenAIRE

    Ioannides, Yannis M.; Overman, Henry G.; Rossi-Hansberg, Esteban; Schmidheiny, Kurt

    2007-01-01

    The geographic concentration of economic activity occurs because transport costs for goods, people and ideas give individuals and organisations incentives to locate close to each other. Historically, all of these costs have been falling. Such changes could lead us to predict the death of distance. This paper is concerned with one aspect of this prediction: the impact that less costly communication and transmission of information might have on cities and the urban structure. We develop a model...

  20. Automated extraction of chemical structure information from digital raster images

    Directory of Open Access Journals (Sweden)

    Shedden Kerby A

    2009-02-01

    Full Text Available Abstract Background To search for chemical structures in research articles, diagrams or text representing molecules need to be translated to a standard chemical file format compatible with cheminformatic search engines. Nevertheless, chemical information contained in research articles is often referenced as analog diagrams of chemical structures embedded in digital raster images. To automate analog-to-digital conversion of chemical structure diagrams in scientific research articles, several software systems have been developed. But their algorithmic performance and utility in cheminformatic research have not been investigated. Results This paper aims to provide critical reviews for these systems and also report our recent development of ChemReader – a fully automated tool for extracting chemical structure diagrams in research articles and converting them into standard, searchable chemical file formats. Basic algorithms for recognizing lines and letters representing bonds and atoms in chemical structure diagrams can be independently run in sequence from a graphical user interface-and the algorithm parameters can be readily changed-to facilitate additional development specifically tailored to a chemical database annotation scheme. Compared with existing software programs such as OSRA, Kekule, and CLiDE, our results indicate that ChemReader outperforms other software systems on several sets of sample images from diverse sources in terms of the rate of correct outputs and the accuracy on extracting molecular substructure patterns. Conclusion The availability of ChemReader as a cheminformatic tool for extracting chemical structure information from digital raster images allows research and development groups to enrich their chemical structure databases by annotating the entries with published research articles. Based on its stable performance and high accuracy, ChemReader may be sufficiently accurate for annotating the chemical database with links

  1. Structural Studies of Geosmin Synthase, a Bifunctional Sesquiterpene Synthase with αα Domain Architecture That Catalyzes a Unique Cyclization-Fragmentation Reaction Sequence.

    Science.gov (United States)

    Harris, Golda G; Lombardi, Patrick M; Pemberton, Travis A; Matsui, Tsutomu; Weiss, Thomas M; Cole, Kathryn E; Köksal, Mustafa; Murphy, Frank V; Vedula, L Sangeetha; Chou, Wayne K W; Cane, David E; Christianson, David W

    2015-12-01

    Geosmin synthase from Streptomyces coelicolor (ScGS) catalyzes an unusual, metal-dependent terpenoid cyclization and fragmentation reaction sequence. Two distinct active sites are required for catalysis: the N-terminal domain catalyzes the ionization and cyclization of farnesyl diphosphate to form germacradienol and inorganic pyrophosphate (PPi), and the C-terminal domain catalyzes the protonation, cyclization, and fragmentation of germacradienol to form geosmin and acetone through a retro-Prins reaction. A unique αα domain architecture is predicted for ScGS based on amino acid sequence: each domain contains the metal-binding motifs typical of a class I terpenoid cyclase, and each domain requires Mg(2+) for catalysis. Here, we report the X-ray crystal structure of the unliganded N-terminal domain of ScGS and the structure of its complex with three Mg(2+) ions and alendronate. These structures highlight conformational changes required for active site closure and catalysis. Although neither full-length ScGS nor constructs of the C-terminal domain could be crystallized, homology models of the C-terminal domain were constructed on the basis of ∼36% sequence identity with the N-terminal domain. Small-angle X-ray scattering experiments yield low-resolution molecular envelopes into which the N-terminal domain crystal structure and the C-terminal domain homology model were fit, suggesting possible αα domain architectures as frameworks for bifunctional catalysis.

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

    DEFF Research Database (Denmark)

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

    2017-01-01

    -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...... 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...

  3. Information-driven structural modelling of protein-protein interactions.

    Science.gov (United States)

    Rodrigues, João P G L M; Karaca, Ezgi; Bonvin, Alexandre M J J

    2015-01-01

    Protein-protein docking aims at predicting the three-dimensional structure of a protein complex starting from the free forms of the individual partners. As assessed in the CAPRI community-wide experiment, the most successful docking algorithms combine pure laws of physics with information derived from various experimental or bioinformatics sources. Of these so-called "information-driven" approaches, HADDOCK stands out as one of the most successful representatives. In this chapter, we briefly summarize which experimental information can be used to drive the docking prediction in HADDOCK, and then focus on the docking protocol itself. We discuss and illustrate with a tutorial example a "classical" protein-protein docking prediction, as well as more recent developments for modelling multi-body systems and large conformational changes.

  4. Encoding techniques for complex information structures in connectionist systems

    Science.gov (United States)

    Barnden, John; Srinivas, Kankanahalli

    1990-01-01

    Two general information encoding techniques called relative position encoding and pattern similarity association are presented. They are claimed to be a convenient basis for the connectionist implementation of complex, short term information processing of the sort needed in common sense reasoning, semantic/pragmatic interpretation of natural language utterances, and other types of high level cognitive processing. The relationships of the techniques to other connectionist information-structuring methods, and also to methods used in computers, are discussed in detail. The rich inter-relationships of these other connectionist and computer methods are also clarified. The particular, simple forms are discussed that the relative position encoding and pattern similarity association techniques take in the author's own connectionist system, called Conposit, in order to clarify some issues and to provide evidence that the techniques are indeed useful in practice.

  5. Instruction in Information Structuring Improves Bayesian Judgment in Intelligence Analysts

    Directory of Open Access Journals (Sweden)

    David R. Mandel

    2015-04-01

    Full Text Available An experiment was conducted to test the effectiveness of brief instruction in information structuring (i.e., representing and integrating information for improving the coherence of probability judgments and binary choices among intelligence analysts. Forty-three analysts were presented with comparable sets of Bayesian judgment problems before and immediately after instruction. After instruction, analysts’ probability judgments were more coherent (i.e., more additive and compliant with Bayes theorem. Instruction also improved the coherence of binary choices regarding category membership: after instruction, subjects were more likely to invariably choose the category to which they assigned the higher probability of a target’s membership. The research provides a rare example of evidence-based validation of effectiveness in instruction to improve the statistical assessment skills of intelligence analysts. Such instruction could also be used to improve the assessment quality of other types of experts who are required to integrate statistical information or make probabilistic assessments.

  6. Internal Structure of Information Packages in Digital Preservation

    Directory of Open Access Journals (Sweden)

    Lee, Seungmin

    2014-12-01

    Full Text Available The description of preserved resources is one of the requirements in digital preservation. The description is generally created in the format of metadata records, and those records are combined to generate information packages to support the process of digital preservation. However, current strategies or models of digital preservation may not generate information packages in efficient ways. To overcome these problems, this research proposed an internal structure of information packages in digital preservation. In order to construct the internal structure, this research analyzed existing metadata standards and cataloging rules such as Dublin Core, MARC, and FRBR to extract the core elements of resource description. The extracted elements were categorized according to their semantics and functions, which resulted in three categories of core elements. These categories and core elements were manifested by using RDF syntax in order to be substantially applied to combine metadata records in digital preservation. Although the internal structure is not intended to create metadata records, it is expected to provide an alternative approach to enable combining existing metadata records in the context of digital preservation in a more flexible way.

  7. Enhancing community detection by using local structural information

    Science.gov (United States)

    Xiang, Ju; Hu, Ke; Zhang, Yan; Bao, Mei-Hua; Tang, Liang; Tang, Yan-Ni; Gao, Yuan-Yuan; Li, Jian-Ming; Chen, Benyan; Hu, Jing-Bo

    2016-03-01

    Many real-world networks, such as gene networks, protein-protein interaction networks and metabolic networks, exhibit community structures, meaning the existence of groups of densely connected vertices in the networks. Many local similarity measures in the networks are closely related to the concept of the community structures, and may have a positive effect on community detection in the networks. Here, various local similarity measures are used to extract local structural information, which is then applied to community detection in the networks by using the edge-reweighting strategy. The effect of the local similarity measures on community detection is carefully investigated and compared in various networks. The experimental results show that the local similarity measures are crucial for the improvement of community detection methods, while the positive effect of the local similarity measures is closely related to the networks under study and applied community detection methods.

  8. PROGRAM SYSTEM AND INFORMATION METADATA BANK OF TERTIARY PROTEIN STRUCTURES

    Directory of Open Access Journals (Sweden)

    T. A. Nikitin

    2013-01-01

    Full Text Available The article deals with the architecture of metadata storage model for check results of three-dimensional protein structures. Concept database model was built. The service and procedure of database update as well as data transformation algorithms for protein structures and their quality were presented. Most important information about entries and their submission forms to store, access, and delivery to users were highlighted. Software suite was developed for the implementation of functional tasks using Java programming language in the NetBeans v.7.0 environment and JQL to query and interact with the database JavaDB. The service was tested and results have shown system effectiveness while protein structures filtration.

  9. Register of experts for information on mechanics of structural failure

    Science.gov (United States)

    Carpenter, J. L., Jr.; Stuhrke, W. F.

    1975-01-01

    This register is comprised of a list of approximately 300 experts from approximately 90 organizations who have published results of theoretical and/or experimental research related to six problem areas in the mechanics of structural failure: (1) life prediction for structural materials, (2) fracture toughness testing, (3) fracture mechanics analysis; (4) hydrogen embrittlement; (5) protective coatings; and (6) composite materials. The criteria for the selection of names for the register are recent contributions to the literature, participation in or support of relevant research programs, and referral by peers. Each author included is listed by organizational affiliation, address, and principal field of expertise. The purpose of the register is to present, in easy reference form, sources for dependable information regarding failure modes and mechanisms of aerospace structures. The register includes two indexes; an alphabetical listing of the experts and an alphabetical listing of the organizations with whom they are affiliated.

  10. Point and line geologic structure information in "Structure, outcrop, and subcrop of the geologic structure information for the Arapahoe and Laramie-Fox Hills aquifers.

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — This digital geospatial data set consists of points and lines representing symbolization of geologic structure information for the Arapahoe and Laramie-Fox Hills...

  11. Enabling cell-cell communication via nanopore formation: structure, function and localization of the unique cell wall amidase AmiC2 of Nostoc punctiforme.

    Science.gov (United States)

    Büttner, Felix M; Faulhaber, Katharina; Forchhammer, Karl; Maldener, Iris; Stehle, Thilo

    2016-04-01

    To orchestrate a complex life style in changing environments, the filamentous cyanobacterium Nostoc punctiforme facilitates communication between neighboring cells through septal junction complexes. This is achieved by nanopores that perforate the peptidoglycan (PGN) layer and traverse the cell septa. The N-acetylmuramoyl-l-alanine amidase AmiC2 (Npun_F1846; EC 3.5.1.28) in N. punctiforme generates arrays of such nanopores in the septal PGN, in contrast to homologous amidases that mediate daughter cell separation after cell division in unicellular bacteria. Nanopore formation is therefore a novel property of AmiC homologs. Immunofluorescence shows that native AmiC2 localizes to the maturing septum. The high-resolution crystal structure (1.12 Å) of its catalytic domain (AmiC2-cat) differs significantly from known structures of cell splitting and PGN recycling amidases. A wide and shallow binding cavity allows easy access of the substrate to the active site, which harbors an essential zinc ion. AmiC2-cat exhibits strong hydrolytic activity in vitro. A single point mutation of a conserved glutamate near the zinc ion results in total loss of activity, whereas zinc removal leads to instability of AmiC2-cat. An inhibitory α-helix, as found in the Escherichia coli AmiC(E. coli) structure, is absent. Taken together, our data provide insight into the cell-biological, biochemical and structural properties of an unusual cell wall lytic enzyme that generates nanopores for cell-cell communication in multicellular cyanobacteria. The novel structural features of the catalytic domain and the unique biological function of AmiC2 hint at mechanisms of action and regulation that are distinct from other amidases. The AmiC2-cat structure has been deposited in the Protein Data Bank under accession number 5EMI. © 2016 Federation of European Biochemical Societies.

  12. Unique Physically Anchored Cryptographic Theoretical Calculation of the Fine-Structure Constant {\\alpha} Matching both the g/2 and Interferometric High-Precision Measurements

    CERN Document Server

    Rhodes, Charles Kirkham

    2010-01-01

    The fine-structure constant {\\alpha}, the dimensionless number that represents the strength of electromagnetic coupling in the limit of sufficiently low energy interactions, is the crucial fundamental physical parameter that governs a nearly limitless range of phenomena involving the interaction of radiation with materials. Ideally, the apparatus of physical theory should be competent to provide a calculational procedure that yields a quantitatively correct value for {\\alpha} and the physical basis for its computation. This study presents the first demonstration of an observationally anchored theoretical procedure that predicts a unique value for {\\alpha} that stands in full agreement with the best (~370 ppt) high-precision experimental determinations. In a directly connected cryptographic computation, the method that gives these results also yields the magnitude of the cosmological constant {\\Omega}{\\Lambda} in conformance with the observational data and the condition of perfect flatness ({\\Omega}{\\Lambda} +...

  13. The Structure of the RAGE:S100A6 Complex Reveals a Unique Mode of Homodimerization for S100 Proteins.

    Science.gov (United States)

    Yatime, Laure; Betzer, Cristine; Jensen, Rasmus Kjeldsen; Mortensen, Sofia; Jensen, Poul Henning; Andersen, Gregers Rom

    2016-12-06

    S100 proteins are calcium-dependent regulators of homeostatic processes. Upon cellular response to stress, and notably during tumorigenesis, they relocalize to the extracellular environment where they induce pro-inflammatory signals by activating the receptor for advanced glycation end products (RAGE), thereby facilitating tumor growth and metastasis. Despite its importance in sustaining inflammation, the structural basis for RAGE-S100 crosstalk is still unknown. Here we report two crystal structures of the RAGE:S100A6 complex encompassing a full-length RAGE ectodomain. The structures, in combination with a comprehensive interaction analysis, suggest that the primary S100A6 binding site is formed by the RAGE C1 domain. Complex formation with S100A6 induces a unique dimeric conformation of RAGE that appears suited for signal transduction and intracellular effector recruitment. Intriguingly, S100A6 adopts a dimeric conformation radically different from all known S100 dimers. We discuss the physiological relevance of this non-canonical homodimeric form in vivo. Copyright © 2016 Elsevier Ltd. All rights reserved.

  14. Structural and mechanistic studies on carboxymethylproline synthase (CarB), a unique member of the crotonase superfamily catalyzing the first step in carbapenem biosynthesis.

    Science.gov (United States)

    Sleeman, Mark C; Sorensen, John L; Batchelar, Edward T; McDonough, Michael A; Schofield, Christopher J

    2005-10-14

    The first step in the biosynthesis of the medicinally important carbapenem family of beta-lactam antibiotics is catalyzed by carboxymethylproline synthase (CarB), a unique member of the crotonase superfamily. CarB catalyzes formation of (2S,5S)-carboxymethylproline [(2S,5S)-t-CMP] from malonyl-CoA and l-glutamate semialdehyde. In addition to using a cosubstrate, CarB catalyzes C-C and C-N bond formation processes as well as an acyl-coenzyme A hydrolysis reaction. We describe the crystal structure of CarB in the presence and absence of acetyl-CoA at 2.24 A and 3.15 A resolution, respectively. The structures reveal that CarB contains a conserved oxy-anion hole probably required for decarboxylation of malonyl-CoA and stabilization of the resultant enolate. Comparison of the structures reveals that conformational changes (involving His(229)) in the cavity predicted to bind l-glutamate semialdehyde occur on (co)substrate binding. Mechanisms for the formation of the carboxymethylproline ring are discussed in the light of the structures and the accompanying studies using isotopically labeled substrates; cyclization via 1,4-addition is consistent with the observed labeling results (providing that hydrogen exchange at the C-6 position of carboxymethylproline does not occur). The side chain of Glu(131) appears to be positioned to be involved in hydrolysis of the carboxymethylproline-CoA ester intermediate. Labeling experiments ruled out the possibility that hydrolysis proceeds via an anhydride in which water attacks a carbonyl derived from Glu(131), as proposed for 3-hydroxyisobutyryl-CoA hydrolase. The structural work will aid in mutagenesis studies directed at altering the selectivity of CarB to provide intermediates for the production of clinically useful carbapenems.

  15. FLEXIBILITY ANALYSIS IN AN INFORMATION ECONOMY: STRUCTURAL EQUATION MODELING

    Directory of Open Access Journals (Sweden)

    Ricardo da Silva

    2006-11-01

    Full Text Available This paper analyzes the new concept of flexibility in organizations – of relevance both at micro and macro level. Information Economy (IE modern function is specifically analyzed. The purpose of this paper is not limited to the study of information economy flexibility, but extends its focus to other areas of organization and economic studies, having as reference the proposed model. Although not covering all aspects regarding objectives and hypotheses, results obtained demonstrate that subsequent studies can lead to success experiences, since the models presented are: stability in relation to the deviations presented in the resulting equations; values that are very close to what is desirable for adjustment indexes, factorial loads, t-values, extracted variances and reliability; as well as other necessary aspects for the application of the technique. The approach focuses the analysis of information economy flexibility based on structural equations modeling to serve as reference for the development of adaptation phenomenon studies in relation to structures, strategies and organizational processes, against the environmental dynamics contemporary society is faced with.

  16. On the complexity and the information content of cosmic structures

    CERN Document Server

    Vazza, Franco

    2016-01-01

    The emergence of cosmic structure is commonly considered one of the most complex phenomena in Nature. However, this complexity has never been defined nor measured in a quantitative and objective way. In this work we propose a method to measure the information content of cosmic structure and to quantify the complexity that emerges from it, based on Information Theory. The emergence of complex evolutionary patterns is studied with a statistical symbolic analysis of the datastream produced by state-of-the-art cosmological simulations of forming galaxy clusters. This powerful approach allows us to measure how many bits of information are necessary to predict the evolution of energy fields in a statistical way, and it offers a simple way to quantify when, where and how the cosmic gas behaves in complex ways. The most complex behaviors are found in the peripheral regions of galaxy clusters, where supersonic flows drive shocks and large energy fluctuations over a few tens of million years. Describing the evolution o...

  17. Web Structure Mining: Exploring Hyperlinks and Algorithms for Information Retrieval

    Directory of Open Access Journals (Sweden)

    P. R. Kumar

    2010-01-01

    Full Text Available Problem statement: A study on hyperlink analysis and the algorithms used for link analysis in the Web Information retrieval was done. Approach: This research was initiated because of the dependability of search engines for information retrieval in the web. Understand the web structure mining and determine the importance of hyperlink in web information retrieval particularly using the Google Search engine. Hyperlink analysis was important methodology used by famous search engine Google to rank the pages. Results: The different algorithms used for link analysis like PageRank (PR, Weighted PageRank (WPR and Hyperlink-Induced Topic Search (HITS algorithms are discussed and compared. PageRank algorithm was implemented using a Java program and the convergence of the PageRank values are shown in a chart form. Conclusion: This study was done basically to explore the link structure algorithms for ranking and compare those algorithms. The further research on this area will be problems facing PageRank algorithm and how to handle those problems.

  18. Development of XAFS for multi-dimensional structural information

    CERN Document Server

    Cheung, K

    1998-01-01

    time-resolved XAFS data on dilute metal systems. The development .also involved off-line commissioning of a UV/visible stopped-flow unit and adapting it to carry out time-resolved fluorescence XAFS data. The rest of the upgrade in implementing sagittal focusing optics are in progress. Similarly a novel fast count rate and compact solid state fluorescence detector has also been designed and is to be commissioned shortly. Our aim is to reduce sample size and data integration lime for obtaining high quality time-resolved XAFS data. There were two distinct projects which this thesis reports. The overall aim was to extend the XAFS technique to a multi-dimensional structural technique. First of the projects, concerned with the development of the EXAFS analysis method. This new approach in EXAFS analysis aims to extend it to give 3-D structural information with atomic precision and accuracy. The method involves making use of the structural information available from the vast library of the PDB database on protein mo...

  19. Information Technology from Theory to Practice in Higher Education Structure

    Directory of Open Access Journals (Sweden)

    Tooraj Sadeghi

    2016-12-01

    Full Text Available In the past two decades, developments process of higher education dependence on the increased demand for admission to higher education, development of communication technologies, need for human resource development, rapid technological changes, accumulated knowledge and information and leads to serious challenges and changes in the role of universities and higher education in the new millennium. So dramatic changes of higher education and move it towards the universalization and interpretations of the common need for higher education has created new perspectives in the development of higher education that under the influence of the information revolution and paradigm of information technology added new funds to higher education charter. The article discussed after several years of theorizing, turns and focuses on research into fundamental processes and IT operations in higher education are essential. In this study, using theoretical method and library studies gap between theory and deployment procedures were evaluated and the results showed that " there is still the gap between the theory of information technology in higher education structure and deployment procedures in practice between theory and practice]".

  20. Structural information revealed by the dispersion of ADC with frequency.

    Science.gov (United States)

    Li, Hua; Jiang, Xiaoyu; Wang, Feng; Xu, Junzhong; Gore, John C

    2015-11-01

    Diffusion MRI provides a non-invasive means to characterize tissue microstructure at varying length scales. Temporal diffusion spectra reveal how the apparent diffusion coefficient (ADC) varies with frequency. When measured using oscillating gradient spin echo sequences, the manner in which ADC disperses with gradient frequency (which is related to the reciprocal of diffusion time) provides information on the characteristic dimensions of restricting structures within the medium. For example, the dispersion of ADC with oscillating gradient frequency (ΔfADC) has been shown to correlate with axon sizes in white matter and provide novel tissue contrast in images of mouse hippocampus and cerebellum. However, despite increasing interest in applying frequency-dependent ADC to derive novel information on tissue, the interpretations of ADC spectra are not always clear. In this study, the relation between ADC spectra and restricting dimensions are further elucidated and used to derive novel image contrast related to the sizes of intrinsic microstructures.

  1. Optical flow with structure information for epithelial image mosaicing.

    Science.gov (United States)

    Ali, Sharib; Faraz, Khuram; Daul, Christian; Blondel, Walter

    2015-01-01

    Mosaicing of biological tissue surfaces is challenging due to the weak image textures. This contribution presents a mosaicing algorithm based on a robust and accurate variational optical flow scheme. A Riesz pyramid based multiscale approach aims at overcoming the "flattening-out" problem at coarser levels. Moreover, the structure information present in images of epithelial surfaces is incorporated into the data-term to improve the algorithm robustness. The algorithm accuracy is first assessed with simulated sequences and then used for mosaicing standard clinical endoscopic data.

  2. The Atypical Response Regulator Protein ChxR Has Structural Characteristics and Dimer Interface Interactions That Are Unique within the OmpR/PhoB Subfamily

    Energy Technology Data Exchange (ETDEWEB)

    Hickey, John M.; Lovell, Scott; Battaile, Kevin P.; Hu, Lei; Middaugh, C. Russell; Hefty, P. Scott (Kansas); (HWMRI)

    2013-05-29

    Typically as a result of phosphorylation, OmpR/PhoB response regulators form homodimers through a receiver domain as an integral step in transcriptional activation. Phosphorylation stabilizes the ionic and hydrophobic interactions between monomers. Recent studies have shown that some response regulators retain functional activity in the absence of phosphorylation and are termed atypical response regulators. The two currently available receiver domain structures of atypical response regulators are very similar to their phospho-accepting homologs, and their propensity to form homodimers is generally retained. An atypical response regulator, ChxR, from Chlamydia trachomatis, was previously reported to form homodimers; however, the residues critical to this interaction have not been elucidated. We hypothesize that the intra- and intermolecular interactions involved in forming a transcriptionally competent ChxR are distinct from the canonical phosphorylation (activation) paradigm in the OmpR/PhoB response regulator subfamily. To test this hypothesis, structural and functional studies were performed on the receiver domain of ChxR. Two crystal structures of the receiver domain were solved with the recently developed method using triiodo compound I3C. These structures revealed many characteristics unique to OmpR/PhoB subfamily members: typical or atypical. Included was the absence of two {alpha}-helices present in all other OmpR/PhoB response regulators. Functional studies on various dimer interface residues demonstrated that ChxR forms relatively stable homodimers through hydrophobic interactions, and disruption of these can be accomplished with the introduction of a charged residue within the dimer interface. A gel shift study with monomeric ChxR supports that dimerization through the receiver domain is critical for interaction with DNA.

  3. Informational structure of genetic sequences and nature of gene splicing

    Science.gov (United States)

    Trifonov, E. N.

    1991-10-01

    Only about 1/20 of DNA of higher organisms codes for proteins, by means of classical triplet code. The rest of DNA sequences is largely silent, with unclear functions, if any. The triplet code is not the only code (message) carried by the sequences. There are three levels of molecular communication, where the same sequence ``talks'' to various bimolecules, while having, respectively, three different appearances: DNA, RNA and protein. Since the molecular structures and, hence, sequence specific preferences of these are substantially different, the original DNA sequence has to carry simultaneously three types of sequence patterns (codes, messages), thus, being a composite structure in which one had the same letter (nucleotide) is frequently involved in several overlapping codes of different nature. This multiplicity and overlapping of the codes is a unique feature of the Gnomic, language of genetic sequences. The coexisting codes have to be degenerate in various degrees to allow an optimal and concerted performance of all the encoded functions. There is an obvious conflict between the best possible performance of a given function and necessity to compromise the quality of a given sequence pattern in favor of other patterns. It appears that the major role of various changes in the sequences on their ``ontogenetic'' way from DNA to RNA to protein, like RNA editing and splicing, or protein post-translational modifications is to resolve such conflicts. New data are presented strongly indicating that the gene splicing is such a device to resolve the conflict between the code of DNA folding in chromatin and the triplet code for protein synthesis.

  4. A High-Resolution Crystal Structure of a Psychrohalophilic α–Carbonic Anhydrase from Photobacterium profundum Reveals a Unique Dimer Interface

    Energy Technology Data Exchange (ETDEWEB)

    Somalinga, Vijayakumar; Buhrman, Greg; Arun, Ashikha; Rose, Robert B.; Grunden, Amy M. (NCSU)

    2016-12-09

    Bacterial α–carbonic anhydrases (α-CA) are zinc containing metalloenzymes that catalyze the rapid interconversion of CO2 to bicarbonate and a proton. We report the first crystal structure of a pyschrohalophilic α–CA from a deep-sea bacterium, Photobacterium profundum. Size exclusion chromatography of the purified P. profundum α–CA (PprCA) reveals that the protein is a heterogeneous mix of monomers and dimers. Furthermore, an “in-gel” carbonic anhydrase activity assay, also known as protonography, revealed two distinct bands corresponding to monomeric and dimeric forms of PprCA that are catalytically active. The crystal structure of PprCA was determined in its native form and reveals a highly conserved “knot-topology” that is characteristic of α–CA’s. Similar to other bacterial α–CA’s, PprCA also crystallized as a dimer. Furthermore, dimer interface analysis revealed the presence of a chloride ion (Cl-) in the interface which is unique to PprCA and has not been observed in any other α–CA’s characterized so far. Molecular dynamics simulation and chloride ion occupancy analysis shows 100% occupancy for the Cl- ion in the dimer interface. Zinc coordinating triple histidine residues, substrate binding hydrophobic patch residues, and the hydrophilic proton wire residues are highly conserved in PprCA and are identical to other well-studied α–CA’s.

  5. Structures of the Bacillus subtilis glutamine synthetase dodecamer reveal large intersubunit catalytic conformational changes linked to a unique feedback inhibition mechanism.

    Science.gov (United States)

    Murray, David S; Chinnam, Nagababu; Tonthat, Nam Ky; Whitfill, Travis; Wray, Lewis V; Fisher, Susan H; Schumacher, Maria A

    2013-12-13

    Glutamine synthetase (GS), which catalyzes the production of glutamine, plays essential roles in nitrogen metabolism. There are two main bacterial GS isoenzymes, GSI-α and GSI-β. GSI-α enzymes, which have not been structurally characterized, are uniquely feedback-inhibited by Gln. To gain insight into GSI-α function, we performed biochemical and cellular studies and obtained structures for all GSI-α catalytic and regulatory states. GSI-α forms a massive 600-kDa dodecameric machine. Unlike other characterized GS, the Bacillus subtilis enzyme undergoes dramatic intersubunit conformational alterations during formation of the transition state. Remarkably, these changes are required for active site construction. Feedback inhibition arises from a hydrogen bond network between Gln, the catalytic glutamate, and the GSI-α-specific residue, Arg(62), from an adjacent subunit. Notably, Arg(62) must be ejected for proper active site reorganization. Consistent with these findings, an R62A mutation abrogates Gln feedback inhibition but does not affect catalysis. Thus, these data reveal a heretofore unseen restructuring of an enzyme active site that is coupled with an isoenzyme-specific regulatory mechanism. This GSI-α-specific regulatory network could be exploited for inhibitor design against Gram-positive pathogens.

  6. BiOI/TiO2 nanotube arrays, a unique flake-tube structured p-n junction with remarkable visible-light photoelectrocatalytic performance and stability.

    Science.gov (United States)

    Liu, Jiaqin; Ruan, Lili; Adeloju, Samuel B; Wu, Yucheng

    2014-01-28

    A series of unique flake-tube structured p-n heterojunctions of BiOI/TiO2 nanotube arrays (TNTAs) were successfully prepared by loading large amounts of BiOI nanoflakes onto both the outer and inner walls of well-separated TiO2 nanotubes using anodization followed by the sequential chemical bath deposition (S-CBD) method. The as-prepared BiOI/TNTAs samples were characterized by X-ray diffraction, electron microscopy, X-ray photoelectron spectroscopy, UV-vis diffuse reflectance spectroscopy and nitrogen sorption. The photoelectrocatalytic (PEC) activity and stability of the BiOI/TNTAs samples toward degradation of methyl orange (MO) solutions under visible-light irradiation (λ > 420 nm) were evaluated. The visible-light PEC performance of BiOI/TNTAs samples was further confirmed by the transient photocurrent response test. The results from the current study revealed that the 5-BiOI/TNTAs sample exhibited the best PEC activity, favourable stability, and the highest photocurrent density among all the BiOI/TNTAs heterostructured samples. The combined effects of several factors may contribute to the remarkable visible-light PEC performance for the 5-BiOI/TNTAs sample including a 3D connected intertube spacing system and an open tube-mouth structure, strong visible-light absorption by BiOI, the formation of a p-n junction, larger specific surface area, and the impact of the applied external electrostatic field.

  7. The crystal structure of an HSL-homolog EstE5 complex with PMSF reveals a unique configuration that inhibits the nucleophile Ser144 in catalytic triads.

    Science.gov (United States)

    Nam, Ki Hyun; Kim, Soo-Jin; Priyadarshi, Amit; Kim, Hyun Sook; Hwang, Kwang Yeon

    2009-11-13

    The esterase/lipase family (EC 3.1.1.3/EC 3.1.1.1) represents a diverse group of hydrolases that catalyze the cleavage of ester bonds and are widely distributed in animals, plants and microorganisms. Among these enzymes, hormone-sensitive lipases, play a critical role in the regulation of rodent fat cell lipolysis and are regarded as adipose tissue-specific enzymes. Recently, we reported the structural and biological characterization of EstE5 from the metagenome library [K.H. Nam, M.Y. Kim, S.J. Kim, A. Priyadarshi, W.H. Lee, K.Y. Hwang, Structural and functional analysis of a novel EstE5 belonging to the subfamily of hormone-sensitive lipase, Biochem. Biophys. Res. Commun. 379 (2009) 553-556]. The structure of this protein revealed that it belongs to the HSL-family. Here, we report the inhibition of the activity of the HSL-homolog EstE5 protein as determined by the use of esterase/lipase inhibitors. Our results revealed that the EstE5 protein is significantly inhibited by PMSF. In addition, this is the first study to identify the crystal structures of EstE5-PMSF at 2.4 and 2.5A among the HSL-homolog structures. This structural configuration is similar to that adopted when serine proteases are inhibited by PMSF. The results presented here provide valuable information regarding the properties of the HSL-family.

  8. Cardiac contractility structure-activity relationship and ligand-receptor interactions; the discovery of unique and novel molecular switches in myosuppressin signaling.

    Directory of Open Access Journals (Sweden)

    Megan Leander

    Full Text Available Peptidergic signaling regulates cardiac contractility; thus, identifying molecular switches, ligand-receptor contacts, and antagonists aids in exploring the underlying mechanisms to influence health. Myosuppressin (MS, a decapeptide, diminishes cardiac contractility and gut motility. Myosuppressin binds to G protein-coupled receptor (GPCR proteins. Two Drosophila melanogaster myosuppressin receptors (DrmMS-Rs exist; however, no mechanism underlying MS-R activation is reported. We predicted DrmMS-Rs contained molecular switches that resembled those of Rhodopsin. Additionally, we believed DrmMS-DrmMS-R1 and DrmMS-DrmMS-R2 interactions would reflect our structure-activity relationship (SAR data. We hypothesized agonist- and antagonist-receptor contacts would differ from one another depending on activity. Lastly, we expected our study to apply to other species; we tested this hypothesis in Rhodnius prolixus, the Chagas disease vector. Searching DrmMS-Rs for molecular switches led to the discovery of a unique ionic lock and a novel 3-6 lock, as well as transmission and tyrosine toggle switches. The DrmMS-DrmMS-R1 and DrmMS-DrmMS-R2 contacts suggested tissue-specific signaling existed, which was in line with our SAR data. We identified R. prolixus (RhpMS-R and discovered it, too, contained the unique myosuppressin ionic lock and novel 3-6 lock found in DrmMS-Rs as well as transmission and tyrosine toggle switches. Further, these motifs were present in red flour beetle, common water flea, honey bee, domestic silkworm, and termite MS-Rs. RhpMS and DrmMS decreased R. prolixus cardiac contractility dose dependently with EC50 values of 140 nM and 50 nM. Based on ligand-receptor contacts, we designed RhpMS analogs believed to be an active core and antagonist; testing on heart confirmed these predictions. The active core docking mimicked RhpMS, however, the antagonist did not. Together, these data were consistent with the unique ionic lock, novel 3-6 lock

  9. Cosmological parameters from large scale structure - geometric versus shape information

    Science.gov (United States)

    Hamann, Jan; Hannestad, Steen; Lesgourgues, Julien; Rampf, Cornelius; Wong, Yvonne Y. Y.

    2010-07-01

    The matter power spectrum as derived from large scale structure (LSS) surveys contains two important and distinct pieces of information: an overall smooth shape and the imprint of baryon acoustic oscillations (BAO). We investigate the separate impact of these two types of information on cosmological parameter estimation for current data, and show that for the simplest cosmological models, the broad-band shape information currently contained in the SDSS DR7 halo power spectrum (HPS) is by far superseded by geometric information derived from the baryonic features. An immediate corollary is that contrary to popular beliefs, the upper limit on the neutrino mass mν presently derived from LSS combined with cosmic microwave background (CMB) data does not in fact arise from the possible small-scale power suppression due to neutrino free-streaming, if we limit the model framework to minimal ΛCDM+mν. However, in more complicated models, such as those extended with extra light degrees of freedom and a dark energy equation of state parameter w differing from -1, shape information becomes crucial for the resolution of parameter degeneracies. This conclusion will remain true even when data from the Planck spacecraft are combined with SDSS DR7 data. In the course of our analysis, we update both the BAO likelihood function by including an exact numerical calculation of the time of decoupling, as well as the HPS likelihood, by introducing a new dewiggling procedure that generalises the previous approach to models with an arbitrary sound horizon at decoupling. These changes allow a consistent application of the BAO and HPS data sets to a much wider class of models, including the ones considered in this work. All the cases considered here are compatible with the conservative 95%-bounds ∑mν < 1.16eV, Neff = 4.8±2.0.

  10. Incorporating secondary structural features into sequence information for predicting protein structural class.

    Science.gov (United States)

    Liao, Bo; Peng, Ting; Chen, Haowen; Lin, Yaping

    2013-10-01

    Knowledge of structural classes is applied in numerous important predictive tasks that address structural and functional features of proteins, although the prediction accuracy of the protein structural classes is not high. In this study, 45 different features were rationally designed to model the differences between protein structural classes, among which, 30 of them reflect the combined protein sequence information. In terms of correlation function, the protein sequence can be converted to a digital signal sequence, from which we can generate 20 discrete Fourier spectrum numbers. According to the segments of amino with different characteristics occurring in protein sequences, the frequencies of the 10 kinds of segments of amino acid (motifs) in protein are calculated. Other features include the secondary structural information :10 features were proposed to model the strong adjacent correlations in the secondary structural elements and capture the long-range spatial interactions between secondary structures, other 5 features were designed to differentiate α/β from α+β classes , which is a major problem of the existing algorithm. The methods were proposed based on a large set of low-identity sequences for which secondary structure is predicted from their sequence (based on PSI-PRED). By means of this method, the overall prediction accuracy of four benchmark datasets were all improved. Especially for the dataset FC699, 25PDB and D1189 which are 1.26%, 1% and 0.85% higher than the best previous method respectively.

  11. A cautionary note on the use of information fit indexes in covariance structure modeling with means

    NARCIS (Netherlands)

    Wicherts, J.M.; Dolan, C.V.

    2004-01-01

    Information fit indexes such as Akaike Information Criterion, Consistent Akaike Information Criterion, Bayesian Information Criterion, and the expected cross validation index can be valuable in assessing the relative fit of structural equation models that differ regarding restrictiveness. In cases i

  12. The Generalization of Mutual Information as the Information between a Set of Variables: The Information Correlation Function Hierarchy and the Information Structure of Multi-Agent Systems

    Science.gov (United States)

    Wolf, David R.

    2004-01-01

    The topic of this paper is a hierarchy of information-like functions, here named the information correlation functions, where each function of the hierarchy may be thought of as the information between the variables it depends upon. The information correlation functions are particularly suited to the description of the emergence of complex behaviors due to many- body or many-agent processes. They are particularly well suited to the quantification of the decomposition of the information carried among a set of variables or agents, and its subsets. In more graphical language, they provide the information theoretic basis for understanding the synergistic and non-synergistic components of a system, and as such should serve as a forceful toolkit for the analysis of the complexity structure of complex many agent systems. The information correlation functions are the natural generalization to an arbitrary number of sets of variables of the sequence starting with the entropy function (one set of variables) and the mutual information function (two sets). We start by describing the traditional measures of information (entropy) and mutual information.

  13. Structure of the human angiotensin II type 1 (AT1) receptor bound to angiotensin II from multiple chemoselective photoprobe contacts reveals a unique peptide binding mode.

    Science.gov (United States)

    Fillion, Dany; Cabana, Jérôme; Guillemette, Gaétan; Leduc, Richard; Lavigne, Pierre; Escher, Emanuel

    2013-03-22

    Breakthroughs in G protein-coupled receptor structure determination based on crystallography have been mainly obtained from receptors occupied in their transmembrane domain core by low molecular weight ligands, and we have only recently begun to elucidate how the extracellular surface of G protein-coupled receptors (GPCRs) allows for the binding of larger peptide molecules. In the present study, we used a unique chemoselective photoaffinity labeling strategy, the methionine proximity assay, to directly identify at physiological conditions a total of 38 discrete ligand/receptor contact residues that form the extracellular peptide-binding site of an activated GPCR, the angiotensin II type 1 receptor. This experimental data set was used in homology modeling to guide the positioning of the angiotensin II (AngII) peptide within several GPCR crystal structure templates. We found that the CXC chemokine receptor type 4 accommodated the results better than the other templates evaluated; ligand/receptor contact residues were spatially grouped into defined interaction clusters with AngII. In the resulting receptor structure, a β-hairpin fold in extracellular loop 2 in conjunction with two extracellular disulfide bridges appeared to open and shape the entrance of the ligand-binding site. The bound AngII adopted a somewhat vertical binding mode, allowing concomitant contacts across the extracellular surface and deep within the transmembrane domain core of the receptor. We propose that such a dualistic nature of GPCR interaction could be well suited for diffusible linear peptide ligands and a common feature of other peptidergic class A GPCRs.

  14. Structure of the Human Angiotensin II Type 1 (AT1) Receptor Bound to Angiotensin II from Multiple Chemoselective Photoprobe Contacts Reveals a Unique Peptide Binding Mode*

    Science.gov (United States)

    Fillion, Dany; Cabana, Jérôme; Guillemette, Gaétan; Leduc, Richard; Lavigne, Pierre; Escher, Emanuel

    2013-01-01

    Breakthroughs in G protein-coupled receptor structure determination based on crystallography have been mainly obtained from receptors occupied in their transmembrane domain core by low molecular weight ligands, and we have only recently begun to elucidate how the extracellular surface of G protein-coupled receptors (GPCRs) allows for the binding of larger peptide molecules. In the present study, we used a unique chemoselective photoaffinity labeling strategy, the methionine proximity assay, to directly identify at physiological conditions a total of 38 discrete ligand/receptor contact residues that form the extracellular peptide-binding site of an activated GPCR, the angiotensin II type 1 receptor. This experimental data set was used in homology modeling to guide the positioning of the angiotensin II (AngII) peptide within several GPCR crystal structure templates. We found that the CXC chemokine receptor type 4 accommodated the results better than the other templates evaluated; ligand/receptor contact residues were spatially grouped into defined interaction clusters with AngII. In the resulting receptor structure, a β-hairpin fold in extracellular loop 2 in conjunction with two extracellular disulfide bridges appeared to open and shape the entrance of the ligand-binding site. The bound AngII adopted a somewhat vertical binding mode, allowing concomitant contacts across the extracellular surface and deep within the transmembrane domain core of the receptor. We propose that such a dualistic nature of GPCR interaction could be well suited for diffusible linear peptide ligands and a common feature of other peptidergic class A GPCRs. PMID:23386604

  15. Unique structure of iC3b resolved at a resolution of 24 Å by 3D-electron microscopy.

    Science.gov (United States)

    Alcorlo, Martin; Martínez-Barricarte, Ruben; Fernández, Francisco J; Rodríguez-Gallego, César; Round, Adam; Vega, M Cristina; Harris, Claire L; de Cordoba, Santiago Rodríguez; Llorca, Oscar

    2011-08-01

    Activation of C3, deposition of C3b on the target surface, and subsequent amplification by formation of a C3-cleaving enzyme (C3-convertase; C3bBb) triggers the effector functions of complement that result in inflammation and cell lysis. Concurrently, surface-bound C3b is proteolyzed to iC3b by factor I and appropriate cofactors. iC3b then interacts with the complement receptors (CR) of the Ig superfamily, CR2 (CD21), CR3 (CD11b/CD18), and CR4 (CD11c/CD18) on leukocytes, down-modulating inflammation, enhancing B cell-mediated immunity, and targeting pathogens for clearance by phagocytosis. Using EM and small-angle X-ray scattering, we now present a medium-resolution structure of iC3b (24 Å). iC3b displays a unique conformation with structural features distinct from any other C3 fragment. The macroglobulin ring in iC3b is similar to that in C3b, whereas the TED (thioester-containing domain) domain and the remnants of the CUB (complement protein subcomponents C1r/C1s, urchin embryonic growth factor and bone morphogenetic protein 1) domain have moved to locations more similar to where they were in native C3. A consequence of this large conformational change is the disruption of the factor B binding site, which renders iC3b unable to assemble a C3-convertase. This structural model also justifies the decreased interaction between iC3b and complement regulators and the recognition of iC3b by the CR of the Ig superfamily, CR2, CR3, and CR4. These data further illustrate the extraordinary conformational versatility of C3 to accommodate a great diversity of functional activities.

  16. Unique structure of iC3b resolved at a resolution of 24 Å by 3D-electron microscopy

    Science.gov (United States)

    Alcorlo, Martin; Martínez-Barricarte, Ruben; Fernández, Francisco J.; Rodríguez-Gallego, César; Round, Adam; Vega, M. Cristina; Harris, Claire L.; de Cordoba, Santiago Rodríguez; Llorca, Oscar

    2011-01-01

    Activation of C3, deposition of C3b on the target surface, and subsequent amplification by formation of a C3-cleaving enzyme (C3-convertase; C3bBb) triggers the effector functions of complement that result in inflammation and cell lysis. Concurrently, surface-bound C3b is proteolyzed to iC3b by factor I and appropriate cofactors. iC3b then interacts with the complement receptors (CR) of the Ig superfamily, CR2 (CD21), CR3 (CD11b/CD18), and CR4 (CD11c/CD18) on leukocytes, down-modulating inflammation, enhancing B cell-mediated immunity, and targeting pathogens for clearance by phagocytosis. Using EM and small-angle X-ray scattering, we now present a medium-resolution structure of iC3b (24 Å). iC3b displays a unique conformation with structural features distinct from any other C3 fragment. The macroglobulin ring in iC3b is similar to that in C3b, whereas the TED (thioester-containing domain) domain and the remnants of the CUB (complement protein subcomponents C1r/C1s, urchin embryonic growth factor and bone morphogenetic protein 1) domain have moved to locations more similar to where they were in native C3. A consequence of this large conformational change is the disruption of the factor B binding site, which renders iC3b unable to assemble a C3-convertase. This structural model also justifies the decreased interaction between iC3b and complement regulators and the recognition of iC3b by the CR of the Ig superfamily, CR2, CR3, and CR4. These data further illustrate the extraordinary conformational versatility of C3 to accommodate a great diversity of functional activities. PMID:21788512

  17. tRNA[superscript His] guanylyltransferase (THG1), a unique 3;#8242;-5;#8242; nucleotidyl transferase, shares unexpected structural homology with canonical 5;#8242;-3;#8242; DNA polymerases

    Energy Technology Data Exchange (ETDEWEB)

    Hyde, Samantha J.; Eckenroth, Brian E.; Smith, Brian A.; Eberley, William A.; Heintz, Nicholas H.; Jackman, Jane E.; Doublié, Sylvie (OSU); (Vermont)

    2011-11-07

    All known DNA and RNA polymerases catalyze the formation of phosphodiester bonds in a 5' to 3' direction, suggesting this property is a fundamental feature of maintaining and dispersing genetic information. The tRNA{sup His} guanylyltransferase (Thg1) is a member of a unique enzyme family whose members catalyze an unprecedented reaction in biology: 3'-5' addition of nucleotides to nucleic acid substrates. The 2.3-{angstrom} crystal structure of human THG1 (hTHG1) reported here shows that, despite the lack of sequence similarity, hTHG1 shares unexpected structural homology with canonical 5'-3' DNA polymerases and adenylyl/guanylyl cyclases, two enzyme families known to use a two-metal-ion mechanism for catalysis. The ability of the same structural architecture to catalyze both 5'-3' and 3'-5' reactions raises important questions concerning selection of the 5'-3' mechanism during the evolution of nucleotide polymerases.

  18. Unsupervised discovery of information structure in biomedical documents.

    Science.gov (United States)

    Kiela, Douwe; Guo, Yufan; Stenius, Ulla; Korhonen, Anna

    2015-04-01

    Information structure (IS) analysis is a text mining technique, which classifies text in biomedical articles into categories that capture different types of information, such as objectives, methods, results and conclusions of research. It is a highly useful technique that can support a range of Biomedical Text Mining tasks and can help readers of biomedical literature find information of interest faster, accelerating the highly time-consuming process of literature review. Several approaches to IS analysis have been presented in the past, with promising results in real-world biomedical tasks. However, all existing approaches, even weakly supervised ones, require several hundreds of hand-annotated training sentences specific to the domain in question. Because biomedicine is subject to considerable domain variation, such annotations are expensive to obtain. This makes the application of IS analysis across biomedical domains difficult. In this article, we investigate an unsupervised approach to IS analysis and evaluate the performance of several unsupervised methods on a large corpus of biomedical abstracts collected from PubMed. Our best unsupervised algorithm (multilevel-weighted graph clustering algorithm) performs very well on the task, obtaining over 0.70 F scores for most IS categories when applied to well-known IS schemes. This level of performance is close to that of lightly supervised IS methods and has proven sufficient to aid a range of practical tasks. Thus, using an unsupervised approach, IS could be applied to support a wide range of tasks across sub-domains of biomedicine. We also demonstrate that unsupervised learning brings novel insights into IS of biomedical literature and discovers information categories that are not present in any of the existing IS schemes. The annotated corpus and software are available at http://www.cl.cam.ac.uk/∼dk427/bio14info.html. © The Author 2014. Published by Oxford University Press. All rights reserved. For

  19. Competing Structure, Competing Views: The Role of Formal and Informal Social Structures in Shaping Stakeholder Perceptions

    Directory of Open Access Journals (Sweden)

    Christina Prell

    2010-12-01

    Full Text Available What is social structure, and how does it influence the views and behaviors of land managers? In this paper, we unpack the term "social structure" in the context of current research on institutions, social networks, and their role(s in resource management. We identify two different kinds of structure, formal and informal, and explore how these link to views of land management and management practice. Formal structures refer to intentionally designed organizations that arise out of larger institutional arrangements; informal ones refer to social networks, based on the communication contacts individuals possess. Our findings show significant correlations between respondents' views regarding land management and their social networks; it is these informal structures that have greater influence on what stakeholders perceive. These findings suggest that stakeholders are less influenced by their particular organizational affiliation or category (e.g., "conservationist" versus "farmer", and more by whom they speak with on a regular basis regarding land management. We conclude with a discussion on the practical implications for resource managers wishing to "design" participatory management, arguing that, if "diversity" is the goal in designing such participatory processes, then diversity needs to translate beyond stakeholder categories to include consideration for the personal, social networks surrounding stakeholders.

  20. Improving protein structural class prediction using novel combined sequence information and predicted secondary structural features.

    Science.gov (United States)

    Dai, Qi; Wu, Li; Li, Lihua

    2011-12-01

    Protein structural class prediction solely from protein sequences is a challenging problem in bioinformatics. Numerous efficient methods have been proposed for protein structural class prediction, but challenges remain. Using novel combined sequence information coupled with predicted secondary structural features (PSSF), we proposed a novel scheme to improve prediction of protein structural classes. Given an amino acid sequence, we first transformed it into a reduced amino acid sequence and calculated its word frequencies and word position features to combine novel sequence information. Then we added the PSSF to the combine sequence information to predict protein structural classes. The proposed method was tested on four benchmark datasets in low homology and achieved the overall prediction accuracies of 83.1%, 87.0%, 94.5%, and 85.2%, respectively. The comparison with existing methods demonstrates that the overall improvements range from 2.3% to 27.5%, which indicates that the proposed method is more efficient, especially for low-homology amino acid sequences.

  1. Primary structure and phosphorylation of dentin matrix protein 1 (DMP1) and dentin phosphophoryn (DPP) uniquely determine their role in biomineralization.

    Science.gov (United States)

    Deshpande, Atul Suresh; Fang, Ping-An; Zhang, Xiaoyuan; Jayaraman, Thottala; Sfeir, Charles; Beniash, Elia

    2011-08-08

    The SIBLING (small integrin-binding ligand N-linked glycoproteins) family is the major group of noncollagenous proteins in bone and dentin. These extremely acidic and highly phosphorylated extracellular proteins play critical roles in the formation of collagenous mineralized tissues. Whereas the lack of individual SIBLINGs causes significant mineralization defects in vivo, none of them led to a complete cessation of mineralization suggesting that these proteins have overlapping functions. To assess whether different SIBLINGs regulate biomineralization in a similar manner and how phosphorylation impacts their activity, we studied the effects of two SIBLINGs, dentin matrix protein 1 (DMP1) and dentin phosphophoryn (DPP), on mineral morphology and organization in vitro. Our results demonstrate distinct differences in the effects of these proteins on mineralization. We show that phosphorylation has a profound effect on the regulation of mineralization by both proteins. Specifically, both phosphorylated proteins facilitated organized mineralization of collagen fibrils and phosphorylated DMP1-induced formation of organized mineral bundles in the absence of collagen. In summary, these results indicate that the primary structure and phosphorylation uniquely determine functions of individual SIBLINGs in regulation of mineral morphology and organization.

  2. Unique structural properties of 2,4,6-tri-tert-butylanilide: isomerization and switching between separable amide rotamers through the reaction of anilide enolates.

    Science.gov (United States)

    Tsukagoshi, Shiori; Ototake, Nobutaka; Ohnishi, Yusuke; Shimizu, Mayu; Kitagawa, Osamu

    2013-05-17

    Herein, we report a unique structural property of 2,4,6-tri-tert-butylanilide, which can be separated into its amide rotamers at room temperature. Interconversion between the rotamers of anilide enolates occurs readily at room temperature and their reaction with electrophiles gives mixtures of the rotamers in a ratio that depends on the reactivity of the corresponding electrophile. That is, the reaction of the 2,4,6-tri-tert-butylacetanilide enolate with reactive electrophiles, such as allyl bromide or protic acids, gives mixtures of the anilide rotamers in which the E rotamer is the major component, whereas less-reactive electrophiles, such as 1-bromopropane and 2-iodopropane, yield mixtures of the rotamers in which the Z rotamer is the major component. The rotameric ratio of the product is also strongly dependent on the reactivity of the anilide enolate. Switching between the anilide rotamers can be achieved through protonation of a less-reactive enolate by a less-reactive protic acid and thermal isomerization of the anilide.

  3. Nanoporous PdZr surface alloy as highly active non-platinum electrocatalyst toward oxygen reduction reaction with unique structure stability and methanol-tolerance

    Science.gov (United States)

    Duan, Huimei; Xu, Caixia

    2016-06-01

    Nanoporous (NP) PdZr alloy with controllable bimetallic ratio is successfully fabricated by a simple dealloying method. By leaching out the more reactive Al from PdZrAl precursor alloy, NP-PdZr alloy with smaller ligament size was generated, characterized by the nanoscaled interconnected network skeleton and hollow channels extending in all three dimensions. Upon voltammetric scan in acid solution, the dissolution of surface Zr atoms generates the highly active Pd-Zr surface alloy with a nearly pure Pd surface and Pd-Zr alloy core. The NP-Pd80Zr20 surface alloy exhibits markedly enhanced specific and mass activities as well as higher catalytic stability toward oxygen reduction reaction (ORR) compared with NP-Pd and the state-of-the-art Pt/C catalysts. In addition, the NP-Pd80Zr20 surface alloy shows a better selectivity for ORR than methanol in the 0.1 M HClO4 and 0.1 M methanol mixed solution. X-ray photoelectron spectroscopy and density functional theory calculations both demonstrate that the weakened Pd-O bond and improved ORR performances in turn depend on the downshifted d-band center of Pd due to the alloying Pd with Zr (20 at.%). The as-made NP-PdZr alloy holds prospective applications as a cathode electrocatalyst in fuel-cell-related technologies with the advantages of superior overall ORR performances, unique structure stability, and easy preparation.

  4. Formation of a unique cluster of G-quadruplex structures in the HIV-1 Nef coding region: implications for antiviral activity.

    Directory of Open Access Journals (Sweden)

    Rosalba Perrone

    Full Text Available G-quadruplexes are tetraplex structures of nucleic acids that can form in G-rich sequences. Their presence and functional role have been established in telomeres, oncogene promoters and coding regions of the human chromosome. In particular, they have been proposed to be directly involved in gene regulation at the level of transcription. Because the HIV-1 Nef protein is a fundamental factor for efficient viral replication, infectivity and pathogenesis in vitro and in vivo, we investigated G-quadruplex formation in the HIV-1 nef gene to assess the potential for viral inhibition through G-quadruplex stabilization. A comprehensive computational analysis of the nef coding region of available strains showed the presence of three conserved sequences that were uniquely clustered. Biophysical testing proved that G-quadruplex conformations were efficiently stabilized or induced by G-quadruplex ligands in all three sequences. Upon incubation with a G-quadruplex ligand, Nef expression was reduced in a reporter gene assay and Nef-dependent enhancement of HIV-1 infectivity was significantly repressed in an antiviral assay. These data constitute the first evidence of the possibility to regulate HIV-1 gene expression and infectivity through G-quadruplex targeting and therefore open a new avenue for viral treatment.

  5. Quantum information analysis of electronic states at different molecular structures

    CERN Document Server

    Barcza, G; Marti, K H; Reiher, M

    2010-01-01

    We have studied transition metal clusters from a quantum information theory perspective using the density-matrix renormalization group (DMRG) method. We demonstrate the competition between entanglement and interaction localization. We also discuss the application of the configuration interaction based dynamically extended active space procedure which significantly reduces the effective system size and accelerates the speed of convergence for complicated molecular electronic structures to a great extent. Our results indicate the importance of taking entanglement among molecular orbitals into account in order to devise an optimal orbital ordering and carry out efficient calculations on transition metal clusters. We propose a recipe to perform DMRG calculations in a black-box fashion and we point out the connections of our work to other tensor network state approaches.

  6. Electronic structure of atoms: atomic spectroscopy information system

    Science.gov (United States)

    Kazakov, V. V.; Kazakov, V. G.; Kovalev, V. S.; Meshkov, O. I.; Yatsenko, A. S.

    2017-10-01

    The article presents a Russian atomic spectroscopy, information system electronic structure of atoms (IS ESA) (http://grotrian.nsu.ru), and describes its main features and options to support research and training. The database contains over 234 000 records, great attention paid to experimental data and uniform filling of the database for all atomic numbers Z, including classified levels and transitions of rare earth and transuranic elements and their ions. Original means of visualization of scientific data in the form of spectrograms and Grotrian diagrams have been proposed. Presentation of spectral data in the form of interactive color charts facilitates understanding and analysis of properties of atomic systems. The use of the spectral data of the IS ESA together with its functionality is effective for solving various scientific problems and training of specialists.

  7. Displaying the information contents of structural RNA alignments: the structure logos

    DEFF Research Database (Denmark)

    Gorodkin, Jan; Heyer, L.J.; Brunak, Søren

    1997-01-01

    We extend the standard `Sequence Logo' method of Schneider and Stevens to incorporate prior frequencies on the bases, allow for gaps in the alignments, and indicate the mutual information of base-paired regions in RNA. Given an alignment of RNA sequences with the base pairings indicated, the prog......We extend the standard `Sequence Logo' method of Schneider and Stevens to incorporate prior frequencies on the bases, allow for gaps in the alignments, and indicate the mutual information of base-paired regions in RNA. Given an alignment of RNA sequences with the base pairings indicated......, the program will calculate the information at each position, including the mutual information of the base pairs, and display the results in a `Structure Logo'. Alignments without base pairing can also be displayed in a `Sequence Logo', but still allowing gaps and incorporating prior frequencies if desired...

  8. Unique Physician Identification Number (UPIN) Directory

    Data.gov (United States)

    U.S. Department of Health & Human Services — The Unique Physician Identification Number (UPIN) Directory contains selected information on physicians, doctors of Osteopathy, limited licensed practitioners and...

  9. Information structures in economics studies in the theory of markets with imperfect information

    CERN Document Server

    Nermuth, Manfred

    1982-01-01

    This book is intended as a contribution to the theory of markets with imperfect information. The subject being nearly limitless, only certain selected topics are discussed. These are outlined in the Introduction (Ch. 0). The remainder of the book is divided into three parts. All results of economic significance are contained in Parts II & III. Part I introduces the main tools for the analysis, in particular the concept of an information structure. Although most of the material presented in Part I is not original, it is hoped that the detailed and self-contained exposition will help the reader to understand not only the following pages, but also the existing technical and variegated literature on markets with imperfect information. The mathematical prerequisites needed, but not explained in the text rarely go beyond elementary calculus and probability theory. Whenever more advanced concepts are used, I have made an effort to give an intuitive explanation as well, so that the argument can also be followed o...

  10. Geometric structure and information change in phase transitions

    Science.gov (United States)

    Kim, Eun-jin; Hollerbach, Rainer

    2017-06-01

    We propose a toy model for a cyclic order-disorder transition and introduce a geometric methodology to understand stochastic processes involved in transitions. Specifically, our model consists of a pair of forward and backward processes (FPs and BPs) for the emergence and disappearance of a structure in a stochastic environment. We calculate time-dependent probability density functions (PDFs) and the information length L , which is the total number of different states that a system undergoes during the transition. Time-dependent PDFs during transient relaxation exhibit strikingly different behavior in FPs and BPs. In particular, FPs driven by instability undergo the broadening of the PDF with a large increase in fluctuations before the transition to the ordered state accompanied by narrowing the PDF width. During this stage, we identify an interesting geodesic solution accompanied by the self-regulation between the growth and nonlinear damping where the time scale τ of information change is constant in time, independent of the strength of the stochastic noise. In comparison, BPs are mainly driven by the macroscopic motion due to the movement of the PDF peak. The total information length L between initial and final states is much larger in BPs than in FPs, increasing linearly with the deviation γ of a control parameter from the critical state in BPs while increasing logarithmically with γ in FPs. L scales as |lnD | and D-1 /2 in FPs and BPs, respectively, where D measures the strength of the stochastic forcing. These differing scalings with γ and D suggest a great utility of L in capturing different underlying processes, specifically, diffusion vs advection in phase transition by geometry. We discuss physical origins of these scalings and comment on implications of our results for bistable systems undergoing repeated order-disorder transitions (e.g., fitness).

  11. Protein Function Prediction Based on Sequence and Structure Information

    KAUST Repository

    Smaili, Fatima Z.

    2016-05-25

    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.

  12. Structure of the hypothetical protein Ton1535 from Thermococcus onnurineus NA1 reveals unique structural properties by a left-handed helical turn in normal α-solenoid protein.

    Science.gov (United States)

    Jeong, Jae-Hee; Kim, Yi-Seul; Rojvirija, Catleya; Cha, Hyung Jin; Kim, Yeon-Gil; Ha, Sung Chul

    2014-06-01

    The crystal structure of Ton1535, a hypothetical protein from Thermococcus onnurineus NA1, was determined at 2.3 Å resolution. With two antiparallel α-helices in a helix-turn-helix motif as a repeating unit, Ton1535 consists of right-handed coiled N- and C-terminal regions that are stacked together using helix bundles containing a left-handed helical turn. One left-handed helical turn in the right-handed coiled structure produces two unique structural properties. One is the presence of separated concave grooves rather than one continuous concave groove, and the other is the contribution of α-helices on the convex surfaces of the N-terminal region to the extended surface of the concave groove of the C-terminal region and vice versa.

  13. A novel predictor for protein structural class based on integrated information of the secondary structure sequence.

    Science.gov (United States)

    Zhang, Lichao; Zhao, Xiqiang; Kong, Liang; Liu, Shuxia

    2014-08-01

    The structural class has become one of the most important features for characterizing the overall folding type of a protein and played important roles in many aspects of protein research. At present, it is still a challenging problem to accurately predict protein structural class for low-similarity sequences. In this study, an 18-dimensional integrated feature vector is proposed by fusing the information about content and position of the predicted secondary structure elements. The consistently high accuracies of jackknife and 10-fold cross-validation tests on different low-similarity benchmark datasets show that the proposed method is reliable and stable. Comparison of our results with other methods demonstrates that our method is an effective computational tool for protein structural class prediction, especially for low-similarity sequences.

  14. Personalized Information Access in a Wiki Using Structured Tagging

    NARCIS (Netherlands)

    Singh, A. V.; Wombacher, A.; Aberer, K.

    2007-01-01

    Environmental engineers from different organizations work in interdisciplinary projects having the need of information exchange. In particular, a collaborative environment with personalized access to information is needed, which supports strongly varying information needs of the users. This scenario

  15. Threat and efficacy uncertainty in news coverage about bed bugs as unique predictors of information seeking and avoidance: an extension of the EPPM.

    Science.gov (United States)

    Goodall, Catherine E; Reed, Phillip

    2013-01-01

    An experiment was conducted from the perspective of the Extended Parallel Process Model (EPPM) investigating readers' responses to print news stories about the issue of bed bugs. Stories containing reference to (a) the threat of bed bugs and (b) efficacy of the solution were manipulated to vary the level of certainty with which the variables were discussed. Results suggest that stories referencing uncertainty regarding presence of the bed-bug threat may be more likely to motivate intention to seek information than stories referencing certainty of the threat. Results also suggest that stories referencing uncertainty regarding feasibility/effectiveness of proposed solutions may be more likely to motivate intention to avoid information than stories referencing certainty of proposed solutions. Given that information avoidance is one of various types of maladaptive responses to fear appeal messages (according to EPPM), results suggest that the presence of uncertainty when discussing solutions to threats in news stories might result in problematic avoidance responses that discourage people from taking protective action.

  16. SVM-based method for protein structural class prediction using secondary structural content and structural information of amino acids.

    Science.gov (United States)

    Mohammad, Tabrez Anwar Shamim; Nagarajaram, Hampapathalu Adimurthy

    2011-08-01

    The knowledge collated from the known protein structures has revealed that the proteins are usually folded into the four structural classes: all-α, all-β, α/β and α + β. A number of methods have been proposed to predict the protein's structural class from its primary structure; however, it has been observed that these methods fail or perform poorly in the cases of distantly related sequences. In this paper, we propose a new method for protein structural class prediction using low homology (twilight-zone) protein sequences dataset. Since protein structural class prediction is a typical classification problem, we have developed a Support Vector Machine (SVM)-based method for protein structural class prediction that uses features derived from the predicted secondary structure and predicted burial information of amino acid residues. The examination of different individual as well as feature combinations revealed that the combination of secondary structural content, secondary structural and solvent accessibility state frequencies of amino acids gave rise to the best leave-one-out cross-validation accuracy of ~81% which is comparable to the best accuracy reported in the literature so far.

  17. An Improved Protein Structural Prediction Method by Incorporating Both Sequence and Structure Information.

    Science.gov (United States)

    Wei, Leyi; Liao, Minghong; Gao, Xing; Zou, Quan

    2014-09-15

    Protein structural classes information is beneficial for secondary and tertiary structure prediction, protein folds prediction, and protein function analysis. Thus, predicting protein structural classes is of vital importance. In recent years, several computational methods have been developed for low-sequence-similarity (25% - 40%) protein structural classes prediction. However, the reported prediction accuracies are actually not satisfactory. Aiming to further improve the prediction accuracies, we propose three different feature extraction methods and construct a comprehensive feature set that captures both sequence and structure information. By applying a random forest (RF) classifier to the feature set, we further develop a novel method for structural classes prediction. We test the proposed method on three benchmark datasets (25PDB, 640, and 1189) with low sequence similarity, and obtain the overall prediction accuracies of 93.5%, 92.6%, and 93.4%, respectively. Compared with six competing methods, the accuracies we achieved are 3.4%, 6.2%, and 8.7% higher than that achieved by the best-performing methods, showing the superiority of our method. Moreover, due to the limitation of the size of the three benchmark datasets, we further test the proposed method on three updated large-scale datasets with different sequence similarity (40%, 30%, and 25%). The proposed method achieves above 90% accuracies for all the three datasets, consistency with the accuracies on the above three benchmark datasets. Experimental results suggest our method as an effective and promising tool for structural classes prediction. Currently, a webserver that implements the proposed method is available on http://121.192.180.204:8080/RF_PSCP/Index.html.

  18. Nucleosomes, Linker DNA, and Linker Histone form a Unique Structural Motif that Directs the Higher-Order Folding and Compaction of Chromatin

    Science.gov (United States)

    Bednar, Jan; Horowitz, Rachel A.; Grigoryev, Sergei A.; Carruthers, Lenny M.; Hansen, Jeffrey C.; Koster, Abraham J.; Woodcock, Christopher L.

    1998-11-01

    The compaction level of arrays of nucleosomes may be understood in terms of the balance between the self-repulsion of DNA (principally linker DNA) and countering factors including the ionic strength and composition of the medium, the highly basic N termini of the core histones, and linker histones. However, the structural principles that come into play during the transition from a loose chain of nucleosomes to a compact 30-nm chromatin fiber have been difficult to establish, and the arrangement of nucleosomes and linker DNA in condensed chromatin fibers has never been fully resolved. Based on images of the solution conformation of native chromatin and fully defined chromatin arrays obtained by electron cryomicroscopy, we report a linker histone-dependent architectural motif beyond the level of the nucleosome core particle that takes the form of a stem-like organization of the entering and exiting linker DNA segments. DNA completes ≈ 1.7 turns on the histone octamer in the presence and absence of linker histone. When linker histone is present, the two linker DNA segments become juxtaposed ≈ 8 nm from the nucleosome center and remain apposed for 3-5 nm before diverging. We propose that this stem motif directs the arrangement of nucleosomes and linker DNA within the chromatin fiber, establishing a unique three-dimensional zigzag folding pattern that is conserved during compaction. Such an arrangement with peripherally arranged nucleosomes and internal linker DNA segments is fully consistent with observations in intact nuclei and also allows dramatic changes in compaction level to occur without a concomitant change in topology.

  19. The role of governance structures in supply chain information sharing

    NARCIS (Netherlands)

    Denolf, J.M.; Trienekens, J.H.; Vorst, Van Der J.G.A.J.; Omta, S.W.F.

    2015-01-01

    Information sharing in supply chains may result in concerns related to information security, information access privileges, and allocation of claimed benefits. To mitigate such concerns in order to efficiently and effectively share information, relationships among the supply chain actors need to

  20. Discourse-level structuring of information in narrative:Signalling structural, interactional and cognitive shifts

    Directory of Open Access Journals (Sweden)

    Tuija Virtanen

    2011-07-01

    Full Text Available Discourse-level structuring of information is explored in narrative in the light of three parameters subsumed under this umbrella notion: (i the structural concepts of “theme-rheme”, connected to “position”; (ii the interaction-oriented pair of concepts “topic-comment”, grounded in the notion of “aboutness”; and (iii the cognitively motivated gradient from “given” to “new” information, related to interlocutors’ assumptions of their memory constraints as well as those of others. In each pair/gradient of concepts one member/pole – “theme”, “comment”, and “new” – is argued to constitute the Figure, against the (necessary Ground of the other. The linguistic signalling of the structural, interactional and cognitive shifts in information structuring is examined in two different kinds of narratives in written French. The analysis of a short legend, in its entirety, and a narrative paragraph from a news story both point to high context-sensitivity in the signalling of the three parameters of discourse-level structuring of information, with that of the discourse level “newness” differing most markedly from the others.Cet article étudie la structure informationnelle dans des textes narratifs en observant trois distinctions linguistiques que recouvre cette structure : (i au niveau textuel, le couple « thème-rhème » défini par une distinction positionnelle ; (ii au niveau interactionnel, l’opposition « topique-commentaire » reposant sur la notion d’« à propos » ; et (iii la distinction cognitive entre information donnée et information nouvelle, mettant en jeu les présomptions des interlocuteurs sur les contraintes mémorielles de l’autre. Dans chacune de ces oppositions binaires ou graduelles, l’un des concepts joue le rôle de Figure (le « thème », le « commentaire » et l’information nouvelle par rapport à un Fond, joué par l’autre concept (le « rhème », le

  1. Crystal Structure of the Human Cytomegalovirus pUL50-pUL53 Core Nuclear Egress Complex Provides Insight into a Unique Assembly Scaffold for Virus-Host Protein Interactions.

    Science.gov (United States)

    Walzer, Sascha A; Egerer-Sieber, Claudia; Sticht, Heinrich; Sevvana, Madhumati; Hohl, Katharina; Milbradt, Jens; Muller, Yves A; Marschall, Manfred

    2015-11-13

    Nuclear replication of cytomegalovirus relies on elaborate mechanisms of nucleocytoplasmic egress of viral particles. Thus, the role of two essential and conserved viral nuclear egress proteins, pUL50 and pUL53, is pivotal. pUL50 and pUL53 heterodimerize and form a core nuclear egress complex (NEC), which is anchored to the inner nuclear membrane and provides a scaffold for the assembly of a multimeric viral-cellular NEC. Here, we report the crystal structure of the pUL50-pUL53 heterodimer (amino acids 1-175 and 50-292, respectively) at 2.44 Å resolution. Both proteins adopt a globular fold with mixed α and β secondary structure elements. pUL53-specific features include a zinc-binding site and a hook-like N-terminal extension, the latter representing a hallmark element of the pUL50-pUL53 interaction. The hook-like extension (amino acids 59-87) embraces pUL50 and contributes 1510 Å(2) to the total interface area (1880 Å(2)). The pUL50 structure overall resembles the recently published NMR structure of the murine cytomegalovirus homolog pM50 but reveals a considerable repositioning of the very C-terminal α-helix of pUL50 upon pUL53 binding. pUL53 shows structural resemblance with the GHKL domain of bacterial sensory histidine kinases. A close examination of the crystal structure indicates partial assembly of pUL50-pUL53 heterodimers to hexameric ring-like structures possibly providing additional scaffolding opportunities for NEC. In combination, the structural information on pUL50-pUL53 considerably improves our understanding of the mechanism of HCMV nuclear egress. It may also accelerate the validation of the NEC as a unique target for developing a novel type of antiviral drug and improved options of broad-spectrum antiherpesviral therapy.

  2. Syntax Encodes Information Structure: Evidence from On-Line Reading Comprehension

    Science.gov (United States)

    Brown, Meredith; Savova, Virginia; Gibson, Edward

    2012-01-01

    Although sentences are thought to be generally easier to process when given information precedes new information, closer examination reveals that these preferences only manifest within some syntactic structures. Here, we examine the consequences of the relative ordering of given and new information ("information structure") for the on-line…

  3. The Informational Text Structure Survey (ITS[superscript 2]): An Exploration of Primary Grade Teachers' Sensitivity to Text Structure in Young Children's Informational Texts

    Science.gov (United States)

    Reutzel, D. Ray; Jones, Cindy D.; Clark, Sarah K.; Kumar, Tamara

    2016-01-01

    There has been no research reported about if or how well primary grade teachers can identify information text structures in children's authentic informational texts. The ability to do so accurately and reliably is a prerequisite for teachers to be able to teach students how to recognize and use text structures to assist them in comprehending…

  4. Integration of spectral domain optical coherence tomography with microperimetry generates unique datasets for the simultaneous identification of visual function and retinal structure in ophthalmological applications

    Science.gov (United States)

    Koulen, Peter; Gallimore, Gary; Vincent, Ryan D.; Sabates, Nelson R.; Sabates, Felix N.

    2011-06-01

    Conventional perimeters are used routinely in various eye disease states to evaluate the central visual field and to quantitatively map sensitivity. However, standard automated perimetry proves difficult for retina and specifically macular disease due to the need for central and steady fixation. Advances in instrumentation have led to microperimetry, which incorporates eye tracking for placement of macular sensitivity values onto an image of the macular fundus thus enabling a precise functional and anatomical mapping of the central visual field. Functional sensitivity of the retina can be compared with the observed structural parameters that are acquired with high-resolution spectral domain optical coherence tomography and by integration of scanning laser ophthalmoscope-driven imaging. Findings of the present study generate a basis for age-matched comparison of sensitivity values in patients with macular pathology. Microperimetry registered with detailed structural data performed before and after intervention treatments provides valuable information about macular function, disease progression and treatment success. This approach also allows for the detection of disease or treatment related changes in retinal sensitivity when visual acuity is not affected and can drive the decision making process in choosing different treatment regimens and guiding visual rehabilitation. This has immediate relevance for applications in central retinal vein occlusion, central serous choroidopathy, age-related macular degeneration, familial macular dystrophy and several other forms of retina related visual disability.

  5. Unique Path Partitions

    DEFF Research Database (Denmark)

    Bessenrodt, Christine; Olsson, Jørn Børling; Sellers, James A.

    2013-01-01

    We give a complete classification of the unique path partitions and study congruence properties of the function which enumerates such partitions.......We give a complete classification of the unique path partitions and study congruence properties of the function which enumerates such partitions....

  6. Recognition and stabilization of a unique CPRI--structural motif in cucurbitaceae family trypsin inhibitor peptides: molecular dynamics based homology modeling using the X-ray structure of MCTI-II.

    Science.gov (United States)

    Chakraborty, S; Haldar, U; Bera, A K; Pal, A K; Bhattacharya, S; Ghosh, S; Mukhopadhyay, B P; Banerjee, A

    2001-02-01

    The high resolution crystallographic structure of MCTI-II complexed with beta trypsin (PDB entry 1MCT) was used to model the corresponding structures of the six inhibitor peptides belonging to Cucurbitaceae family (MCTI-I, LA-1, LA-2, CMTI-I, CMTI-III, CMTI-IV). Two model inhibitors, LA-1 and LA-2 were refined by molecular dynamics to estimate the average solution structure. The difference accessible surface area (DASA) study of the inhibitors with and without trypsin revealed the Arginine and other residues of the inhibitors which bind to trypsin. The hydration dynamics study of LA1 and LA2 also confirm the suitability of water molecules at the active Arg site. Moreover, the presence of a unique 3D-structural motif comprises with the four CPRI residues from the amino terminal is thought to be conserved in all the six studied inhibitors, which seems essential for the directional fixation for proper complexation of the Arg (5) residue towards the trypsin S1-binding pocket. The role of the disulphide linkage in the geometrical stabilization of CPRI (Cysteine, Proline, Arginine, Isoleucine) motif has also been envisaged from the comparative higher intra molecular Cys (3) -Cys (20) disulphide dihedral energies.

  7. Information structure design for databases a practical guide to data modelling

    CERN Document Server

    Mortimer, Andrew J

    2014-01-01

    Computer Weekly Professional Series: Information Structure Design for Databases: A Practical Guide to Data modeling focuses on practical data modeling covering business and information systems. The publication first offers information on data and information, business analysis, and entity relationship model basics. Discussions cover degree of relationship symbols, relationship rules, membership markers, types of information systems, data driven systems, cost and value of information, importance of data modeling, and quality of information. The book then takes a look at entity relationship mode

  8. A Structural Optimization Method for Information Resource Management.

    Science.gov (United States)

    1985-12-01

    1982; Hirschheim, 1983). According to Matlin (1980), management of a resource suggests opportunities to conserve that resource, be effective and...1982; Matlin , 1980). It is this continuing and expanding reuse of the information resource that determines the well being of organizations in an...Rita. "Records, Words, Data...The Stage of Information Management - Part 2." Information and R rCLds _ng1Huin=Me 16 (July 1982): 18-20. Matlin , Gerald

  9. Information structure influences depth of syntactic processing: event-related potential evidence for the Chomsky illusion.

    Science.gov (United States)

    Wang, Lin; Bastiaansen, Marcel; Yang, Yufang; Hagoort, Peter

    2012-01-01

    Information structure facilitates communication between interlocutors by highlighting relevant information. It has previously been shown that information structure modulates the depth of semantic processing. Here we used event-related potentials to investigate whether information structure can modulate the depth of syntactic processing. In question-answer pairs, subtle (number agreement) or salient (phrase structure) syntactic violations were placed either in focus or out of focus through information structure marking. P600 effects to these violations reflect the depth of syntactic processing. For subtle violations, a P600 effect was observed in the focus condition, but not in the non-focus condition. For salient violations, comparable P600 effects were found in both conditions. These results indicate that information structure can modulate the depth of syntactic processing, but that this effect depends on the salience of the information. When subtle violations are not in focus, they are processed less elaborately. We label this phenomenon the Chomsky illusion.

  10. The Structure and Future of the Information Economy.

    Science.gov (United States)

    Cooper, Michael D.

    1983-01-01

    Discusses the United States economy and reviews National Income Accounting concepts and evidence about future of an information economy. It is concluded that information economy growth will be in products, not services, and that it will not continue at same rate it has in past. Thirty-six references are cited. (EJS)

  11. STRUCTURAL AND SEMANTIC FEATURES OF ONLINE INFORMATION RESOURCES

    Directory of Open Access Journals (Sweden)

    Ivan Georgievich Zubkov

    2014-07-01

    Full Text Available Information society is a global economic, political, technological and antroposocial project involving controlled civilizational transition to the world social system in which the dominant role in all spheres of life will play a mass communication system, implemented with the help of computer technology, particularly Internet technology. The question of formation and presentation of information is highly relevant today. The world community has entered a transitional stage from its post-industrial state to the informational. At this stage of the development, society is increasingly dependent on the quality, availability, reliability, timeliness of information, which is created by its own representatives. Especially clearly it is evident in the Internet space, where all information flows merge into a single closed and continuously update system that has its own characteristics, features and qualities.DOI: http://dx.doi.org/10.12731/2218-7405-2014-4-7

  12. The influence of the chain and network information and communication structure on sustainable business development

    NARCIS (Netherlands)

    Bremmers, H.J.; Haverkamp, D.J.; Omta, S.W.F.

    2005-01-01

    This article links the public-private information and communication structure (IC-structure) and Ajzen¿s model of planned behaviour to explain the development of environmental management systems (EMSs). The structure of the IC-system, especially the public-private information exchange, can influence

  13. 75 FR 68809 - Agency Information Collection Activities: Importation Bond Structure

    Science.gov (United States)

    2010-11-09

    ... proposed collection of information, including the validity of the methodology and assumptions used; (3... functionality at http://www.cbp.gov . CBP Forms 301 and 5297 are accessible at http://www.cbp.gov/xp/cgov...

  14. Information theory provides a comprehensive framework for the evaluation of protein structure predictions

    Science.gov (United States)

    Swanson, Rosemarie; Vannucci, Marina; Tsai, Jerry W.

    2008-01-01

    Protein structure prediction has a number of important ad hoc similarity measures for evaluating predictions, but would benefit from a measure that is able to provide a common framework for a broad range of comparisons. Here we show that a mutual information-like measure can provide a comprehensive framework for evaluating protein structure prediction of all types. We discuss the concept of information, its application to secondary structure, and the obstacle to applying it to 3D structure. Based on insights from the secondary structure case, we present an approach to work around the 3D difficulties, and develop a method to measure the mutual information provided by a 3D structure prediction. We integrate the evaluation of all types of protein structure prediction into a single frame work, and compare the amount of information provided by various prediction methods, including secondary structure prediction. Within this broadened framework, the idea that structure is better preserved than sequence during evolution is evaluated quantitatively for the globin family. A nearly perfect sequence match in the globin family corresponds to about 300 bits of information, whereas a nearly perfect structural match for the same two proteins corresponds to about 2500 bits of information, where bits of information describes the probability of obtaining a match of similar closeness by chance. Mutual information provides both a theoretical basis for evaluating structure similarity and an explanatory surround for existing similarity measures. PMID:18704942

  15. Information

    Institute of Scientific and Technical Information of China (English)

    2011-01-01

    There are unstructured abstracts (no more than 256 words) and structured abstracts (no more than 480). The specific requirements for structured abstracts are as follows:An informative, structured abstracts of no more than 4-80 words should accompany each manuscript. Abstracts for original contributions should be structured into the following sections. AIM (no more than 20 words): Only the purpose should be included. Please write the aim as the form of "To investigate/ study/..."; MATERIALS AND METHODS (no more than 140 words); RESULTS (no more than 294 words): You should present P values where appropnate and must provide relevant data to illustrate how they were obtained, e.g. 6.92 ± 3.86 vs 3.61 ± 1.67, P< 0.001; CONCLUSION (no more than 26 words).

  16. A Cautionary Note on the Use of Information Fit Indexes in Covariance Structure Modeling with Means

    Science.gov (United States)

    Wicherts, Jelte M.; Dolan, Conor V.

    2004-01-01

    Information fit indexes such as Akaike Information Criterion, Consistent Akaike Information Criterion, Bayesian Information Criterion, and the expected cross validation index can be valuable in assessing the relative fit of structural equation models that differ regarding restrictiveness. In cases in which models without mean restrictions (i.e.,…

  17. ProCKSI: a decision support system for Protein (Structure Comparison, Knowledge, Similarity and Information

    Directory of Open Access Journals (Sweden)

    Błażewicz Jacek

    2007-10-01

    Full Text Available Abstract Background We introduce the decision support system for Protein (Structure Comparison, Knowledge, Similarity and Information (ProCKSI. ProCKSI integrates various protein similarity measures through an easy to use interface that allows the comparison of multiple proteins simultaneously. It employs the Universal Similarity Metric (USM, the Maximum Contact Map Overlap (MaxCMO of protein structures and other external methods such as the DaliLite and the TM-align methods, the Combinatorial Extension (CE of the optimal path, and the FAST Align and Search Tool (FAST. Additionally, ProCKSI allows the user to upload a user-defined similarity matrix supplementing the methods mentioned, and computes a similarity consensus in order to provide a rich, integrated, multicriteria view of large datasets of protein structures. Results We present ProCKSI's architecture and workflow describing its intuitive user interface, and show its potential on three distinct test-cases. In the first case, ProCKSI is used to evaluate the results of a previous CASP competition, assessing the similarity of proposed models for given targets where the structures could have a large deviation from one another. To perform this type of comparison reliably, we introduce a new consensus method. The second study deals with the verification of a classification scheme for protein kinases, originally derived by sequence comparison by Hanks and Hunter, but here we use a consensus similarity measure based on structures. In the third experiment using the Rost and Sander dataset (RS126, we investigate how a combination of different sets of similarity measures influences the quality and performance of ProCKSI's new consensus measure. ProCKSI performs well with all three datasets, showing its potential for complex, simultaneous multi-method assessment of structural similarity in large protein datasets. Furthermore, combining different similarity measures is usually more robust than

  18. Register of specialized sources for information on mechanics of structural failure

    Science.gov (United States)

    Carpenter, J. L., Jr.; Denny, F. J.

    1973-01-01

    Specialized information sources that generate information relative to six problem areas in aerospace mechanics of structural failure are identified. Selection for inclusion was based upon information obtained from the individual knowledge and professional contacts of Martin Marietta Aerospace staff members and the information uncovered by the staff of technical reviewers. Activities listed perform basic or applied research related to the mechanics of structural failure and publish the results of such research. The purpose of the register is to present, in easy reference form, original sources for dependable information regarding failure modes and mechanisms of aerospace structures.

  19. An approach to knowledge structuring for advanced phases of the Technical and Management Information System (TMIS)

    Science.gov (United States)

    Goranson, H. T.

    1986-01-01

    The Technical and Management Information System (TMIS) must employ on enlightened approach to its object structure, but basic issues in conceptual structuring remain to be resolved. Sirius outlines the necessary agenda and reports on progress toward solutions.

  20. Unique selectivity reversal in Am(3+)-Eu(3+) extraction in a tripodal TREN-based diglycolamide in ionic liquid: extraction, luminescence, complexation and structural studies.

    Science.gov (United States)

    Leoncini, Andrea; Mohapatra, Prasanta K; Bhattacharyya, Arunasis; Raut, Dhaval R; Sengupta, Arijit; Verma, Parveen K; Tiwari, Nidhi; Bhattacharyya, Dibyendu; Jha, Sambhunath; Wouda, Anna M; Huskens, Jurriaan; Verboom, Willem

    2016-02-14

    An N-pivot diglycolamide extractant (DGA-TREN) was synthesized for the first time and its complexation behaviour was studied towards trivalent lanthanide/actinide ions. The solvent extraction studies suggested a unique selectivity reversal in the extraction of trivalent actinides versus trivalent lanthanides which was observed performing extraction studies in an ionic liquid vis-à-vis a molecular diluent for a tripodal TREN-based diglycolamide ligand (DGA-TREN) vs. a tripodal diglycolamide ligand (T-DGA) which may have great significance in radioactive waste remediation. The nature of the bonding to Eu(3+) ion was investigated by EXAFS as well as by DFT calculations.

  1. The Structure of Adjustment Costs in Information Technology Investment

    OpenAIRE

    Hyunbae Chun; Sung-Bae Mun

    2005-01-01

    We examine the pattern of information technology (IT) capital adjustment using data from U.S. industries. Using the gap between actual and desired IT capital stocks, we estimate the shape of the adjustment cost function in IT investment. Both ordinary least squares and nonparametric regression estimates support irreversibility in IT investment.

  2. Structural optimization for materially informed design to robotic production processes

    NARCIS (Netherlands)

    Bier, H.H.; Mostafavi, S.

    2015-01-01

    Hyperbody’s materially informed Design-to-Robotic-Production (D2RP) processes for additive and subtractive manufacturing aim to achieve performative porosity in architecture at various scales. An extended series of D2RP experiments aiming to produce prototypes at 1:1 scale wherein design materiality

  3. Unique Access to Learning

    Science.gov (United States)

    Goble, Don

    2009-01-01

    This article describes the many learning opportunities that broadcast technology students at Ladue Horton Watkins High School in St. Louis, Missouri, experience because of their unique access to technology and methods of learning. Through scaffolding, stepladder techniques, and trial by fire, students learn to produce multiple television programs,…

  4. [Integrating information about imaging biomarkers into structured radiology reports].

    Science.gov (United States)

    Pomar-Nadal, A; Pérez-Castillo, C; Alberich-Bayarri, A; García-Martí, G; Sanz Requena, R; Martí-Bonmatí, L

    2013-01-01

    Imaging biomarkers describe objective characteristics that are related to normal biological processes, diseases, or the response to treatment. They enable radiologists to incorporate into their reports data about structure, function, and tissue components. With the aim of taking maximum advantage of the quantification of medical images, we present a procedure to integrate imaging biomarkers into radiological reports, bringing the new paradigm of personal medicine closer to radiological workflow. In this manner, the results of quantification can complement traditional radiological diagnosis, improving accuracy and the evaluation of the efficacy of treatments. A more personalized, standardized, structured radiological report should include quantitative analyses to complement conventional qualitative reporting in selected cases.

  5. Bibliography of information on mechanics of structural failure

    Science.gov (United States)

    Carpenter, J. L., Jr.; Moya, N.; Shaffer, R. A.; Smith, D. M.

    1973-01-01

    A bibliography of approximately 1500 reference citations related to six problem areas in the mechanics of failure in aerospace structures is presented. The bibliography represents a search of the literature published in the ten year period 1962-1972 and is largely limited to documents published in the United States. Listings are subdivided into the six problem areas: (1) life prediction of structural materials; (2) fracture toughness data; (3) fracture mechanics analysis; (4) hydrogen embrittlement; (5) protective coatings; and (6) composite materials. An author index is included.

  6. Communication by euro area central bankers : structure, information and effectiveness

    NARCIS (Netherlands)

    Jansen, D.J.

    2006-01-01

    This thesis is an empirical study of communication by euro area central bankers. Its remainder is structured as follows: chapter 2, ECB communication during the first years of the EMU, describes communication by euro area central bankers during the period January 1999 to May 2002. Amongst other thin

  7. Score region algebra : a flexible framework for structured information retrieval

    NARCIS (Netherlands)

    Mihajlovic, Vojkan

    2006-01-01

    Approximately three decades ago researchers realized that they would have to structure data to be able to store and access large amounts of data streams that were produced each day. As a result, database management systems were designed and developed, used to keep the data in one place and for findi

  8. Structural information from OH stretching frequencies monohydric saturated alcohols

    NARCIS (Netherlands)

    Maas, J.H. van der; Lutz, E.T.G.

    1974-01-01

    Infrared data have been recorded of the hydroxyl stretching band for about 70 monohydric saturated alcohols in dilute carbon tetrachloride solution. The wavenumber maximum, the half-bandwidth and the band pattern could be related to the structure of the molecules. Not only primary, secondary and ter

  9. Network structure and patterns of information diversity on Twitter

    CERN Document Server

    Shore, Jesse; Dellarocas, Chrysanthos

    2016-01-01

    Social media have great potential to support diverse information sharing, but there is widespread concern that platforms like Twitter do not result in communication between those who hold contradictory viewpoints. Because users can choose whom to follow, prior research suggests that social media users exist in 'echo chambers' or become polarized. We seek evidence of this in a complete cross section of hyperlinks posted on Twitter, using previously validated measures of the political slant of news sources to study information diversity. Contrary to prediction, we find that the average account posts links to more politically moderate news sources than the ones they receive in their own feed. However, members of a tiny network core do exhibit cross-sectional evidence of polarization and are responsible for the majority of tweets received overall due to their popularity and activity, which could explain the widespread perception of polarization on social media.

  10. InterEvDock: a docking server to predict the structure of protein-protein interactions using evolutionary information.

    Science.gov (United States)

    Yu, Jinchao; Vavrusa, Marek; Andreani, Jessica; Rey, Julien; Tufféry, Pierre; Guerois, Raphaël

    2016-07-01

    The structural modeling of protein-protein interactions is key in understanding how cell machineries cross-talk with each other. Molecular docking simulations provide efficient means to explore how two unbound protein structures interact. InterEvDock is a server for protein docking based on a free rigid-body docking strategy. A systematic rigid-body docking search is performed using the FRODOCK program and the resulting models are re-scored with InterEvScore and SOAP-PP statistical potentials. The InterEvScore potential was specifically designed to integrate co-evolutionary information in the docking process. InterEvDock server is thus particularly well suited in case homologous sequences are available for both binding partners. The server returns 10 structures of the most likely consensus models together with 10 predicted residues most likely involved in the interface. In 91% of all complexes tested in the benchmark, at least one residue out of the 10 predicted is involved in the interface, providing useful guidelines for mutagenesis. InterEvDock is able to identify a correct model among the top10 models for 49% of the rigid-body cases with evolutionary information, making it a unique and efficient tool to explore structural interactomes under an evolutionary perspective. The InterEvDock web interface is available at http://bioserv.rpbs.univ-paris-diderot.fr/services/InterEvDock/.

  11. Structural Analysis: Shape Information via Points-To Computation

    CERN Document Server

    Marron, Mark

    2012-01-01

    This paper introduces a new hybrid memory analysis, Structural Analysis, which combines an expressive shape analysis style abstract domain with efficient and simple points-to style transfer functions. Using data from empirical studies on the runtime heap structures and the programmatic idioms used in modern object-oriented languages we construct a heap analysis with the following characteristics: (1) it can express a rich set of structural, shape, and sharing properties which are not provided by a classic points-to analysis and that are useful for optimization and error detection applications (2) it uses efficient, weakly-updating, set-based transfer functions which enable the analysis to be more robust and scalable than a shape analysis and (3) it can be used as the basis for a scalable interprocedural analysis that produces precise results in practice. The analysis has been implemented for .Net bytecode and using this implementation we evaluate both the runtime cost and the precision of the results on a num...

  12. HCM-Linked Δ 160E Cardiac Troponin T Mutation Causes Unique Progressive Structural and Molecular Ventricular Remodeling in Transgenic Mice

    Science.gov (United States)

    Moore, Rachel K.; Grinspan, Lauren Tal; Jimenez, Jesus; Guinto, Pia J.; Ertz-Berger, Briar; Tardiff, Jil C.

    2013-01-01

    Hypertrophic cardiomyopathy (HCM) is a primary disease of cardiac muscle, and one of the most common causes of sudden cardiac death (SCD) in young people. Many mutations in cardiac troponin T (cTnT) lead to a complex form of HCM with varying degrees of ventricular hypertrophy and ~65% of all cTnT mutations occur within or flanking the elongated N-terminal TNT1 domain. Biophysical studies have predicted that distal TNT1 mutations, including Δ160E, cause disease by a novel, yet unknown mechanism as compared to N-terminal mutations. To begin to address the specific effects of this commonly observed cTnT mutation we generated two independent transgenic mouse lines carrying variant doses of the mutant transgene. Hearts from the 30% and 70% cTnT Δ160E lines demonstrated a highly unique, dose-dependent disruption in cellular and sarcomeric architecture and a highly progressive pattern of ventricular remodeling. While adult ventricular myocytes isolated from Δ160E transgenic mice exhibited dosage-independent mechanical impairments, decreased sarcoplasmic reticulum calcium load and SERCA2a calcium uptake activity, the observed decreases in calcium transients were dosage-dependent. The latter findings were concordant with measures of calcium regulatory proteins abundance and phosphorylation state. Finally, studies of whole heart physiology in the isovolumic mode demonstrated dose-dependent differences in the degree of cardiac dysfuction. We conclude that the observed clinical severity of the cTnT Δ160E mutation is caused by a combination of direct sarcomeric disruption coupled to a profound disregulation of Ca2+ homeostasis at the cellular level that results in a unique and highly progressive pattern of ventricular remodeling. PMID:23434821

  13. Incorporating Spatial Structures in Ecological Inference: An Information Theory Approach

    Directory of Open Access Journals (Sweden)

    Rosa Bernardini Papalia

    2010-10-01

    Full Text Available This paper introduces an Information Theory-based method for modeling economic aggregates and estimating their sub-group (sub-area decomposition when no individual or sub-group data are available. This method offers a flexible framework for modeling the underlying variation in sub-group indicators, by addressing the spatial dependency problem. A basic ecological inference problem, which allows for spatial heterogeneity and dependence, is presented with the aim of first estimating the model at the aggregate level, and then of employing the estimated coefficients to obtain the sub-group level indicators.

  14. Encyclopedic Information: Focus on the Structuring of Encyclopedic Information in the Articles of Modern LSP Dictionaries

    DEFF Research Database (Denmark)

    Duvå, Grete; Laursen, Anne Lise

    2001-01-01

    Modern LSP dictionaries differ from LGP dictionaries in many ways, one of which being that they include categories of information not found in traditional LGP dictionaryes. The development in the field lf LSP lexicography, which has taken place over the last ten years, has been based on the need ...

  15. Information Security: A Scientometric Study of the Profile, Structure, and Dynamics of an Emerging Scholarly Specialty

    Science.gov (United States)

    Olijnyk, Nicholas Victor

    2014-01-01

    The central aim of the current research is to explore and describe the profile, dynamics, and structure of the information security specialty. This study's objectives are guided by four research questions: 1. What are the salient features of information security as a specialty? 2. How has the information security specialty emerged and evolved from…

  16. Structure and pragmatics in informal argument: circularity and question-begging.

    Science.gov (United States)

    Brem, Sarah K.

    2003-04-01

    Most everyday arguments are informal, as contrasted with the formal arguments of logic and mathematics. Whereas formal argument is well understood, the nature of informal argument is more elusive. A recent study by Rips (2002) provides further evidence regarding the roles of structure and pragmatics in informal argument.

  17. Pathways of information transmission among wild songbirds follow experimentally imposed changes in social foraging structure.

    Science.gov (United States)

    Firth, Josh A; Sheldon, Ben C; Farine, Damien R

    2016-06-01

    Animals regularly use information from others to shape their decisions. Yet, determining how changes in social structure affect information flow and social learning strategies has remained challenging. We manipulated the social structure of a large community of wild songbirds by controlling which individuals could feed together at automated feeding stations (selective feeders). We then provided novel ephemeral food patches freely accessible to all birds and recorded the spread of this new information. We demonstrate that the discovery of new food patches followed the experimentally imposed social structure and that birds disproportionately learnt from those whom they could forage with at the selective feeders. The selective feeders reduced the number of conspecific information sources available and birds subsequently increased their use of information provided by heterospecifics. Our study demonstrates that changes to social systems carry over into pathways of information transfer and that individuals learn from tutors that provide relevant information in other contexts.

  18. Tensegrity II. How structural networks influence cellular information processing networks

    Science.gov (United States)

    Ingber, Donald E.

    2003-01-01

    The major challenge in biology today is biocomplexity: the need to explain how cell and tissue behaviors emerge from collective interactions within complex molecular networks. Part I of this two-part article, described a mechanical model of cell structure based on tensegrity architecture that explains how the mechanical behavior of the cell emerges from physical interactions among the different molecular filament systems that form the cytoskeleton. Recent work shows that the cytoskeleton also orients much of the cell's metabolic and signal transduction machinery and that mechanical distortion of cells and the cytoskeleton through cell surface integrin receptors can profoundly affect cell behavior. In particular, gradual variations in this single physical control parameter (cell shape distortion) can switch cells between distinct gene programs (e.g. growth, differentiation and apoptosis), and this process can be viewed as a biological phase transition. Part II of this article covers how combined use of tensegrity and solid-state mechanochemistry by cells may mediate mechanotransduction and facilitate integration of chemical and physical signals that are responsible for control of cell behavior. In addition, it examines how cell structural networks affect gene and protein signaling networks to produce characteristic phenotypes and cell fate transitions during tissue development.

  19. Information Structure: Towards an integrated formal theory of pragmatics

    Directory of Open Access Journals (Sweden)

    Craige Roberts

    2012-12-01

    Full Text Available A framework for pragmatic analysis is proposed which treats discourse as a game, with context as a scoreboard organized around the questions under discussion by the interlocutors. The framework is intended to be coordinated with a dynamic compositional semantics. Accordingly, the context of utterance is modeled as a tuple of different types of information, and the questions therein — modeled, as is usual in formal semantics, as alternative sets of propositions — constrain the felicitous flow of discourse. A requirement of Relevance is satisfied by an utterance (whether an assertion, a question or a suggestion iff it addresses the question under discussion. Finally, it is argued that the prosodic focus of an utterance canonically serves to reflect the question under discussion (at least in English, placing additional constraints on felicity in context. http://dx.doi.org/10.3765/sp.5.6 BibTeX info

  20. ERP evidence on the interaction between information structure and emotional salience of words.

    Science.gov (United States)

    Wang, Lin; Bastiaansen, Marcel; Yang, Yufang; Hagoort, Peter

    2013-06-01

    Both emotional words and words focused by information structure can capture attention. This study examined the interplay between emotional salience and information structure in modulating attentional resources in the service of integrating emotional words into sentence context. Event-related potentials (ERPs) to affectively negative, neutral, and positive words, which were either focused or nonfocused in question-answer pairs, were evaluated during sentence comprehension. The results revealed an early negative effect (90-200 ms), a P2 effect, as well as an effect in the N400 time window, for both emotional salience and information structure. Moreover, an interaction between emotional salience and information structure occurred within the N400 time window over right posterior electrodes, showing that information structure influences the semantic integration only for neutral words, but not for emotional words. This might reflect the fact that the linguistic salience of emotional words can override the effect of information structure on the integration of words into context. The interaction provides evidence for attention-emotion interactions at a later stage of processing. In addition, the absence of interaction in the early time window suggests that the processing of emotional information is highly automatic and independent of context. The results suggest independent attention capture systems of emotional salience and information structure at the early stage but an interaction between them at a later stage, during the semantic integration of words.

  1. Evaluating the impact of investments in information technology on structural inertia in health organizations.

    Science.gov (United States)

    Bewley, Lee W

    2010-01-01

    Structural inertia is the overall capacity of an organization to adapt within a market environment. This paper reviews the impact of healthcare investments in information management/information technology (IM/IT) on the strategic management concept of structural inertia. Research indicates that healthcare executives should consider the relative state of structural inertia for their firms and match them with potential IM/IT solutions. Additionally, organizations should favorably consider IM/IT solutions that are comparatively less complex.

  2. Music Information Seeking Behaviour Poses Unique Challenges for the Design of Information Retrieval Systems. A Review of: Lee, J. H. (2010. Analysis of user needs and information features in natural language queries seeking music information. Journal of the American Society for information Science and Technology, 61, 1025-1045.

    Directory of Open Access Journals (Sweden)

    Cari Merkley

    2010-12-01

    Full Text Available Objective – To better understand music information seeking behaviour in a real life situation and to create a taxonomy relating to this behaviour to facilitate better comparison of music information retrieval studies in the future.Design – Content analysis of natural language queries.Setting – Google Answers, a fee based online service.Subjects – 1,705 queries and their related answers and comments posted in the music category of the Google Answers website before April 27, 2005.Methods – A total of 2,208 queries were retrieved from the music category on the Google Answers service. Google Answers was a fee based service in which users posted questions and indicated what they were willing to pay to have them answered. The queries selected for this study were posted prior to April 27, 2005, over a year before the service was discontinued completely. Of the 2208 queries taken from the site, only 1,705 were classified as relevant to the question of music information seeking by the researcher. The off-topic queries were not included in the study. Each of the 1,705 queries was coded according to the needs expressed by the user and the information provided to assist researchers in answering the question. The initial coding framework used by the researcher was informed by previous studies of music information retrieval to facilitate comparison, but was expanded and revised to reflect the evidence itself. Only the questions themselves were subjected to this iterative coding process. The answers provided by the Google Answer researchers and online comments posted by other users were examined by the author, but not coded for inclusion in the study.User needs in the questions were coded for their form and topic. Each question was assigned at least one form and one topic. Form refers to the type of question being asked and consisted of the following 10 categories: identification, location, verification, recommendation, evaluation, ready reference

  3. Minimum information modelling of structural systems with uncertain parameters

    Science.gov (United States)

    Hyland, D. C.

    1983-01-01

    Work is reviewed wherein the design of active structural control is formulated as the mean-square optimal control of a linear mechanical system with stochastic parameters. In practice, a complete probabilistic description of model parameters can never be provided by empirical determinations, and a suitable design approach must accept very limited a priori data on parameter statistics. In consequence, the mean-square optimization problem is formulated using a complete probability assignment which is made to be consistent with available data but maximally unconstrained otherwise through use of a maximum entropy principle. The ramifications of this approach for both robustness and large dimensionality are illustrated by consideration of the full-state feedback regulation problem.

  4. Informing saccharide structural NMR studies with density functional theory calculations.

    Science.gov (United States)

    Klepach, Thomas; Zhao, Hongqiu; Hu, Xiaosong; Zhang, Wenhui; Stenutz, Roland; Hadad, Matthew J; Carmichael, Ian; Serianni, Anthony S

    2015-01-01

    Density functional theory (DFT) is a powerful computational tool to enable structural interpretations of NMR spin-spin coupling constants ( J-couplings) in saccharides, including the abundant (1)H-(1)H ( JHH), (13)C-(1)H ( JCH), and (13)C-(13)C ( JCC) values that exist for coupling pathways comprised of 1-4 bonds. The multiple hydroxyl groups in saccharides, with their attendant lone-pair orbitals, exert significant effects on J-couplings that can be difficult to decipher and quantify without input from theory. Oxygen substituent effects are configurational and conformational in origin (e.g., axial/equatorial orientation of an OH group in an aldopyranosyl ring; C-O bond conformation involving an exocyclic OH group). DFT studies shed light on these effects, and if conducted properly, yield quantitative relationships between a specific J-coupling and one or more conformational elements in the target molecule. These relationships assist studies of saccharide structure and conformation in solution, which are often challenged by the presence of conformational averaging. Redundant J-couplings, defined as an ensemble of J-couplings sensitive to the same conformational element, are particularly helpful when the element is flexible in solution (i.e., samples multiple conformational states on the NMR time scale), provided that algorithms are available to convert redundant J-values into meaningful conformational models. If the latter conversion is achievable, the data can serve as a means of testing, validating, and refining theoretical methods like molecular dynamics (MD) simulations, which are currently relied upon heavily to assign conformational models of saccharides in solution despite a paucity of experimental data needed to independently validate the method.

  5. Selective gas adsorption and unique structural topology of a highly stable guest-free zeolite-type MOF material with N-rich chiral open channels.

    Science.gov (United States)

    Li, Jian-Rong; Tao, Ying; Yu, Qun; Bu, Xian-He; Sakamoto, Hirotoshi; Kitagawa, Susumu

    2008-01-01

    A new multifunctional di-topic tetrazolate-based ligand, 2,3-di-1H-tetrazol-5-ylpyrazine (H(2)dtp) has been designed and synthesized. The solvothermal reaction of this ligand with ZnCl(2) gave a robust guest-free three-dimensional zeolite-like chiral metal-organic framework (MOF) complex, [Zn(dtp)], which crystallized in chiral space group P6(1) and possessed chiral open channels with nitrogen-rich walls and the diameter of approximately 4.1 A. This framework presents a unique uniform etd (8,3) topology, is the first example of its type in MOFs, and exhibits high thermal stability with the decomposition temperature above 380 degrees C and permanent porosity. It is interesting that this material is able to selectively adsorb O(2) and CO(2) over N(2) gas, being a rare example in MOFs. In addition, C(2)H(2) and MeOH adsorption results show that although the framework channel holds nitrogen-rich walls that may provide H-bonding sites, no NH H-bond effect between the guest molecules and microporous surface was observed.

  6. Bayesian Network Structure Learning Based On Rough Set and Mutual Information

    Directory of Open Access Journals (Sweden)

    Zuhong Feng

    2013-09-01

    Full Text Available Abstract In Bayesian network structure learning for incomplete data set, a common problem is too many attributes causing low efficiency and high computation complexity. In this paper, an algorithm of attribute reduction based on rough set is introduced. The algorithm can effectively reduce the dimension of attributes and quickly determine the network structure using mutual information for Bayesian network structure learning.

  7. The structure of somatosensory information for human postural control

    Science.gov (United States)

    Jeka, J. J.; Ribeiro, P.; Oie, K.; Lackner, J. R.

    1998-01-01

    The goal of the present study was to determine the properties of the somatosensory stimulus that alter its temporal coupling to body sway. Six standing subjects were tested while touching a metal plate positioned either directly in front of or lateral to the subject. In each condition, the plate moved 4 mm at 0.2 Hz in either the medial-lateral (ML) or anterior-posterior direction (AP). The results showed that coupling between body sway and touch plate movement was strongest when the touch plate moved in a direction along the longitudinal axis of the arm. Coupling strength was weaker when the touch plate moved perpendicular to the longitudinal axis of the arm. The results consistently show that a radial expansion stimulus was more effective than a lamellar-type stimulus at the fingertip. Moreover, somatosensory information from a surface is interpreted in terms of the orientation of the contact limb and the potential degrees of freedom available through its movement.

  8. Application of a Structured Decision Process for Informing ...

    Science.gov (United States)

    The Guánica Bay watershed has been a priority for research, assessment and management since the 1970s, and since 2008, has been the focus of a U.S. Coral Reef Task Force (USCRTF) research initiative involving multiple agencies assembled to address the effect of land management decisions on coastal resources. Municipal and agricultural growth in the Guánica Bay watershed has provided social and economic value but has led to changes in forest cover (highly valued for biodiversity, endangered species and ecotourism), declining quality and availability of drinking water, and increased sediment and nutrient runoff that adversely affects coastal seagrasses, mangroves and coral reefs. Communities in the coastal region, such as the city of Guánica, rely partially on fishing and tourism economies, both of which are adversely affected by diminishing coastal water quality. In 2008, with funding from NOAA’s Coral Reef Conservation Program, the Center for Watershed Protection developed a Watershed Management Plan (WMP) that included a suite of proposed management actions to reduce sediment runoff and its harmful effects in the coastal zone. The WMP served as the initial SDM decision context for EPA’s research to generate tools and procedures to better inform the decisions made across the watershed and to facilitate complementary actions.Application of SDM in Guánica Bay included archival research on social and economic history of the region and three workshops with s

  9. NASA's unique networking environment

    Science.gov (United States)

    Johnson, Marjory J.

    1988-01-01

    Networking is an infrastructure technology; it is a tool for NASA to support its space and aeronautics missions. Some of NASA's networking problems are shared by the commercial and/or military communities, and can be solved by working with these communities. However, some of NASA's networking problems are unique and will not be addressed by these other communities. Individual characteristics of NASA's space-mission networking enviroment are examined, the combination of all these characteristics that distinguish NASA's networking systems from either commercial or military systems is explained, and some research areas that are important for NASA to pursue are outlined.

  10. The matrix representation for the mathematic structure of Shannon's information measures

    Institute of Scientific and Technical Information of China (English)

    YUAN Yan-hua

    2007-01-01

    Shannon's information measure is a crucial concept in Information Theory. And the research, for the mathematics structure of Shannon's information measure, is to recognize the essence of information measure.The linear relation between Shannon's information measures and some signed measure space by using the formal symbols substitution rule is discussed. Furthermore, the coefficient matrix recurrent formula of the linear relation is obtained. Then the coefficient matrix is proved to be invertible via mathematical induction. This shows that the linear relation is one-to-one, and according to this, it can be concluded that a compact space can be generated from Shannon's information measures.

  11. Exploring the structure and organization of information within nursing clinical handovers.

    Science.gov (United States)

    Johnson, Maree; Jefferies, Diana; Nicholls, Daniel

    2012-10-01

    Clinical handover is the primary source of patient information for nurses; however, inadequate information transfer compromises patient safety. We investigated the content and organization of information conveyed at 81 handovers. A structure that captures and presents the information transferred at handover emerged: identification of the patient and clinical risks, clinical history/presentation, clinical status, care plan and outcomes/goals of care (ICCCO). This approach covers essential information while allowing for prioritization of information when required. Further research into the impact of ICCCO on patient safety is in progress. © 2012 Wiley Publishing Asia Pty Ltd.

  12. Sparse regularization for EIT reconstruction incorporating structural information derived from medical imaging.

    Science.gov (United States)

    Gong, Bo; Schullcke, Benjamin; Krueger-Ziolek, Sabine; Mueller-Lisse, Ullrich; Moeller, Knut

    2016-06-01

    Electrical impedance tomography (EIT) reconstructs the conductivity distribution of a domain using electrical data on its boundary. This is an ill-posed inverse problem usually solved on a finite element mesh. For this article, a special regularization method incorporating structural information of the targeted domain is proposed and evaluated. Structural information was obtained either from computed tomography images or from preliminary EIT reconstructions by a modified k-means clustering. The proposed regularization method integrates this structural information into the reconstruction as a soft constraint preferring sparsity in group level. A first evaluation with Monte Carlo simulations indicated that the proposed solver is more robust to noise and the resulting images show fewer artifacts. This finding is supported by real data analysis. The structure based regularization has the potential to balance structural a priori information with data driven reconstruction. It is robust to noise, reduces artifacts and produces images that reflect anatomy and are thus easier to interpret for physicians.

  13. SMpred: a support vector machine approach to identify structural motifs in protein structure without using evolutionary information.

    Science.gov (United States)

    Pugalenthi, Ganesan; Kandaswamy, Krishna Kumar; Suganthan, P N; Sowdhamini, R; Martinetz, Thomas; Kolatkar, Prasanna R

    2010-12-01

    Knowledge of three dimensional structure is essential to understand the function of a protein. Although the overall fold is made from the whole details of its sequence, a small group of residues, often called as structural motifs, play a crucial role in determining the protein fold and its stability. Identification of such structural motifs requires sufficient number of sequence and structural homologs to define conservation and evolutionary information. Unfortunately, there are many structures in the protein structure databases have no homologous structures or sequences. In this work, we report an SVM method, SMpred, to identify structural motifs from single protein structure without using sequence and structural homologs. SMpred method was trained and tested using 132 proteins domains containing 581 motifs. SMpred method achieved 78.79% accuracy with 79.06% sensitivity and 78.53% specificity. The performance of SMpred was evaluated with MegaMotifBase using 188 proteins containing 1161 motifs. Out of 1161 motifs, SMpred correctly identified 1503 structural motifs reported in MegaMotifBase. Further, we showed that SMpred is useful approach for the length deviant superfamilies and single member superfamilies. This result suggests the usefulness of our approach for facilitating the identification of structural motifs in protein structure in the absence of sequence and structural homologs. The dataset and executable for the SMpred algorithm is available at http://www3.ntu.edu.sg/home/EPNSugan/index_files/SMpred.htm.

  14. Unique fluorophores in the dimeric archaeal histones hMfB and hPyA1 reveal the impact of nonnative structure in a monomeric kinetic intermediate.

    Science.gov (United States)

    Stump, Matthew R; Gloss, Lisa M

    2008-02-01

    Homodimeric archaeal histones and heterodimeric eukaryotic histones share a conserved structure but fold through different kinetic mechanisms, with a correlation between faster folding/association rates and the population of kinetic intermediates. Wild-type hMfB (from Methanothermus fervidus) has no intrinsic fluorophores; Met35, which is Tyr in hyperthermophilic archaeal histones such as hPyA1 (from Pyrococcus strain GB-3A), was mutated to Tyr and Trp. Two Tyr-to-Trp mutants of hPyA1 were also characterized. All fluorophores were introduced into the long, central alpha-helix of the histone fold. Far-UV circular dichroism (CD) indicated that the fluorophores did not significantly alter the helical content of the histones. The equilibrium unfolding transitions of the histone variants were two-state, reversible processes, with DeltaG degrees (H2O) values within 1 kcal/mol of the wild-type dimers. The hPyA1 Trp variants fold by two-state kinetic mechanisms like wild-type hPyA1, but with increased folding and unfolding rates, suggesting that the mutated residues (Tyr-32 and Tyr-36) contribute to transition state structure. Like wild-type hMfB, M35Y and M35W hMfB fold by a three-state mechanism, with a stopped-flow CD burst-phase monomeric intermediate. The M35 mutants populate monomeric intermediates with increased secondary structure and stability but exhibit decreased folding rates; this suggests that nonnative interactions occur from burial of the hydrophobic Tyr and Trp residues in this kinetic intermediate. These results implicate the long central helix as a key component of the structure in the kinetic monomeric intermediates of hMfB as well as the dimerization transition state in the folding of hPyA1.

  15. An integrated health and social care organisation in Sweden: creation and structure of a unique local public health and social care system.

    Science.gov (United States)

    Øvretveit, John; Hansson, Johan; Brommels, Mats

    2010-10-01

    Research and citizens have noted failures in coordinating health and social services and professionals, and the need to address this issue to realize benefits from increasing specialisation. Different methods have been proposed and one has been structural integration of separate services within one organisation. This paper reports an empirical longitudinal study of the development of an integrated health and social care organisation in Sweden combining service provision, purchasing and political governance for a defined population. The study found a combination of influences contributed to the development of this new organisation. The initial structural macro-integration facilitated, but did not of itself result in better clinical care coordination. Other actions were needed to modify the specialised systems and cultures which the organisation inherited. The study design was not able to establish with any degree of certainty whether better patient and cost outcomes resulted, but it did find structural and process changes which make improved outcomes likely. The study concludes that coordinated actions at different levels and of different types were needed to achieve care coordination for patients and that a phased approach was necessary where management capacity and outside expertise are limited.

  16. Crystal structure of Lymnaea stagnalis AChBP complexed with the potent nAChR antagonist DHβE suggests a unique mode of antagonism.

    Directory of Open Access Journals (Sweden)

    Azadeh Shahsavar

    Full Text Available Nicotinic acetylcholine receptors (nAChRs are pentameric ligand-gated ion channels that belong to the Cys-loop receptor superfamily. These receptors are allosteric proteins that exist in different conformational states, including resting (closed, activated (open, and desensitized (closed states. The acetylcholine binding protein (AChBP is a structural homologue of the extracellular ligand-binding domain of nAChRs. In previous studies, the degree of the C-loop radial extension of AChBP has been assigned to different conformational states of nAChRs. It has been suggested that a closed C-loop is preferred for the active conformation of nAChRs in complex with agonists whereas an open C-loop reflects an antagonist-bound (closed state. In this work, we have determined the crystal structure of AChBP from the water snail Lymnaea stagnalis (Ls in complex with dihydro-β-erythroidine (DHβE, which is a potent competitive antagonist of nAChRs. The structure reveals that binding of DHβE to AChBP imposes closure of the C-loop as agonists, but also a shift perpendicular to previously observed C-loop movements. These observations suggest that DHβE may antagonize the receptor via a different mechanism compared to prototypical antagonists and toxins.

  17. FASTR: A novel data format for concomitant representation of RNA sequence and secondary structure information.

    Science.gov (United States)

    Bose, Tungadri; Dutta, Anirban; Mh, Mohammed; Gandhi, Hemang; Mande, Sharmila S

    2015-09-01

    Given the importance of RNA secondary structures in defining their biological role, it would be convenient for researchers seeking RNA data if both sequence and structural information pertaining to RNA molecules are made available together. Current nucleotide data repositories archive only RNA sequence data. Furthermore, storage formats which can frugally represent RNA sequence as well as structure data in a single file, are currently unavailable. This article proposes a novel storage format, 'FASTR', for concomitant representation of RNA sequence and structure. The storage efficiency of the proposed FASTR format has been evaluated using RNA data from various microorganisms. Results indicate that the size of FASTR formatted files (containing both RNA sequence as well as structure information) are equivalent to that of FASTA-format files, which contain only RNA sequence information. RNA secondary structure is typically represented using a combination of a string of nucleotide characters along with the corresponding dot-bracket notation indicating structural attributes. 'FASTR' - the novel storage format proposed in the present study enables a frugal representation of both RNA sequence and structural information in the form of a single string. In spite of having a relatively smaller storage footprint, the resultant 'fastr' string(s) retain all sequence as well as secondary structural information that could be stored using a dot-bracket notation. An implementation of the 'FASTR' methodology is available for download at http://metagenomics.atc.tcs.com/compression/fastr.

  18. FASTR: A novel data format for concomitant representation of RNA sequence and secondary structure information

    Indian Academy of Sciences (India)

    Tungadri Bose; Anirban Dutta; Mohammed Mh; Hemang Gandhi; Sharmila S Mande

    2015-09-01

    Given the importance of RNA secondary structures in defining their biological role, it would be convenient for researchers seeking RNA data if both sequence and structural information pertaining to RNA molecules are made available together. Current nucleotide data repositories archive only RNA sequence data. Furthermore, storage formats which can frugally represent RNA sequence as well as structure data in a single file, are currently unavailable. This article proposes a novel storage format, `FASTR’, for concomitant representation of RNA sequence and structure. The storage efficiency of the proposed FASTR format has been evaluated using RNA data from various microorganisms. Results indicate that the size of FASTR formatted files (containing both RNA sequence as well as structure information) are equivalent to that of FASTA-format files, which contain only RNA sequence information. RNA secondary structure is typically represented using a combination of a string of nucleotide characters along with the corresponding dot-bracket notation indicating structural attributes. `FASTR’ – the novel storage format proposed in the present study enables a frugal representation of both RNA sequence and structural information in the form of a single string. In spite of having a relatively smaller storage footprint, the resultant `fastr’ string(s) retain all sequence as well as secondary structural information that could be stored using a dot-bracket notation. An implementation of the `FASTR’ methodology is available for download at http://metagenomics.atc.tcs.com/compression/fastr.

  19. Graduating to Postdoc: Information-Sharing in Support of Organizational Structures and Needs

    Science.gov (United States)

    Keller, Richard M.; Lucas, Paul J.; Compton, Michael M.; Stewart, Helen J.; Baya, Vinod; DelAlto, Martha

    1999-01-01

    The deployment of information-sharing systems in large organizations can significantly impact existing policies and procedures with regard to authority and control over information. Unless information-sharing systems explicitly support organizational structures and needs, these systems will be rejected summarily. The Postdoc system is a deployed Web-based information-sharing system created specifically to address organizational needs. Postdoc contains various organizational support features including a shared, globally navigable document space, as well as specialized access control, distributed administration, and mailing list features built around the key notion of hierarchical group structures. We review successes and difficulties in supporting organizational needs with Postdoc

  20. Structure of the unique SEFIR domain from human interleukin 17 receptor A reveals a composite ligand-binding site containing a conserved α-helix for Act1 binding and IL-17 signaling

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Bing [Oklahoma State University, Stillwater, OK 74078 (United States); Liu, Caini; Qian, Wen [Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH 44195 (United States); Han, Yue [Oklahoma State University, Stillwater, OK 74078 (United States); Li, Xiaoxia, E-mail: lix@ccf.org [Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH 44195 (United States); Deng, Junpeng, E-mail: lix@ccf.org [Oklahoma State University, Stillwater, OK 74078 (United States)

    2014-05-01

    Crystal structure of the SEFIR domain from human IL-17 receptor A provides new insights into IL-17 signaling. Interleukin 17 (IL-17) cytokines play a crucial role in mediating inflammatory and autoimmune diseases. A unique intracellular signaling domain termed SEFIR is found within all IL-17 receptors (IL-17Rs) as well as the key adaptor protein Act1. SEFIR-mediated protein–protein interaction is a crucial step in IL-17 cytokine signaling. Here, the 2.3 Å resolution crystal structure of the SEFIR domain of IL-17RA, the most commonly shared receptor for IL-17 cytokine signaling, is reported. The structure includes the complete SEFIR domain and an additional α-helical C-terminal extension, which pack tightly together to form a compact unit. Structural comparison between the SEFIR domains of IL-17RA and IL-17RB reveals substantial differences in protein topology and folding. The uniquely long insertion between strand βC and helix αC in IL-17RA SEFIR is mostly well ordered, displaying a helix (αCC′{sub ins}) and a flexible loop (CC′). The DD′ loop in the IL-17RA SEFIR structure is much shorter; it rotates nearly 90° with respect to the counterpart in the IL-17RB SEFIR structure and shifts about 12 Å to accommodate the αCC′{sub ins} helix without forming any knots. Helix αC was identified as critical for its interaction with Act1 and IL-17-stimulated gene expression. The data suggest that the heterotypic SEFIR–SEFIR association via helix αC is a conserved and signature mechanism specific for IL-17 signaling. The structure also suggests that the downstream motif of IL-17RA SEFIR together with helix αC could provide a composite ligand-binding surface for recruiting Act1 during IL-17 signaling.

  1. Building emergency public information structures for response: Lessons learned from New York City.

    Science.gov (United States)

    Silvestri, Nancy

    2017-12-01

    For an effective response, emergency public information operations should be structured to facilitate the provision of timely, accurate, accessible information to the public. A frequent challenge in building a public information structure is identifying the potential staff to allow the operation to get big enough, fast enough. A plan for managing public information operations should define roles to fulfil basic functions (responding to media enquiries, writing materials, disseminating information, media and social media monitoring, community engagement and identifying and addressing rumours). This paper will offer tips for developing a plan and concept of operations for quickly assembling and maintaining public information operations. It will also describe the public information principles implemented during recent incidents in New York City, including the 2015 visit of Pope Francis to New York City. Having a coordinated, flexible model; a trained network of public information officers who are ready to staff public information roles as needed; and a structure that embeds social media into overall public information operations, will leave public information officers and their organisations more prepared to deal with the challenges and opportunities of communicating with the public during emergencies of varying types and sizes.

  2. Use of secondary structural information and C-C distance restraints to model protein structures with MODELLER

    Indian Academy of Sciences (India)

    Boojala V B Reddy; Yiannis N Kaznessis

    2007-08-01

    Protein secondary structure predictions and amino acid long range contact map predictions from primary sequence of proteins have been explored to aid in modelling protein tertiary structures. In order to evaluate the usefulness of secondary structure and 3D-residue contact prediction methods to model protein structures we have used the known Q3 (alpha-helix, beta-strands and irregular turns/loops) secondary structure information, along with residue-residue contact information as restraints for MODELLER. We present here results of our modelling studies on 30 best resolved single domain protein structures of varied lengths. The results shows that it is very difficult to obtain useful models even with 100% accurate secondary structure predictions and accurate residue contact predictions for up to 30% of residues in a sequence. The best models that we obtained for proteins of lengths 37, 70, 118, 136 and 193 amino acid residues are of RMSDs 4.17, 5.27, 9.12, 7.89 and 9.69, respectively. The results show that one can obtain better models for the proteins which have high percent of alpha-helix content. This analysis further shows that MODELLER restrain optimization program can be useful only if we have truly homologous structure(s) as a template where it derives numerous restraints, almost identical to the templates used. This analysis also clearly indicates that even if we satisfy several true residue-residue contact distances, up to 30% of their sequence length with fully known secondary structural information, we end up predicting model structures much distant from their corresponding native structures.

  3. Membrane-Active Epithelial Keratin 6A Fragments (KAMPs Are Unique Human Antimicrobial Peptides with a Non-αβ Structure

    Directory of Open Access Journals (Sweden)

    Judy Tsz Ying Lee

    2016-11-01

    Full Text Available Antibiotic resistance is a pressing global health problem that threatens millions of lives each year. Natural antimicrobial peptides and their synthetic derivatives, including peptoids and peptidomimetics, are promising candidates as novel antibiotics. Recently, the C-terminal glycine-rich fragments of human epithelial keratin 6A were found to have bactericidal and cytoprotective activities. Here, we used an improved 2-dimensional NMR method coupled with a new protocol for structural refinement by low temperature simulated annealing to characterize the solution structure of these kerain-derived antimicrobial peptides (KAMPs. Two specific KAMPs in complex with membrane mimicking sodium dodecyl sulfate (SDS micelles displayed amphipathic conformations with only local bends and turns, and a central 10-residue glycine-rich hydrophobic strip that is central to bactericidal activity. To our knowledge, this is the first report of non-αβ structure for human antimicrobial peptides. Direct observation of Staphylococcus aureus and Pseudomonas aeruginosa by scanning and transmission electron microscopy showed that KAMPs deformed bacterial cell envelopes and induced pore formation. Notably, in competitive binding experiments, KAMPs demonstrated binding affinities to LPS and LTA that did not correlate with their bactericidal activities, suggesting peptide-LPS and peptide-LTA interactions are less important in their mechanisms of action. Moreover, immunoprecipitation of KAMPs-bacterial factor complexes indicated that membrane surface lipoprotein SlyB and intracellular machineries NQR sodium pump and ribosomes are potential molecular targets for the peptides. Results of this study improve our understanding of the bactericidal function of epithelial cytokeratin fragments, and highlight an unexplored class of human antimicrobial peptides, which may serve as non-αβ peptide scaffolds for the design of novel peptide-based antibiotics.

  4. Structural characterization of a unique interface between carbohydrate response element-binding protein (ChREBP) and 14-3-3β protein.

    Science.gov (United States)

    Ge, Qiang; Huang, Nian; Wynn, R Max; Li, Yang; Du, Xinlin; Miller, Bonnie; Zhang, Hong; Uyeda, Kosaku

    2012-12-07

    Carbohydrate response element-binding protein (ChREBP) is an insulin-independent, glucose-responsive transcription factor that is expressed at high levels in liver hepatocytes where it plays a critical role in converting excess carbohydrates to fat for storage. In response to fluctuating glucose levels, hepatic ChREBP activity is regulated in large part by nucleocytoplasmic shuttling of ChREBP protein via interactions with 14-3-3 proteins. The N-terminal ChREBP regulatory region is necessary and sufficient for glucose-responsive ChREBP nuclear import and export. Here, we report the crystal structure of a complex of 14-3-3β bound to the N-terminal regulatory region of ChREBP at 2.4 Å resolution. The crystal structure revealed that the α2 helix of ChREBP (residues 117-137) adopts a well defined α-helical conformation and binds 14-3-3 in a phosphorylation-independent manner that is different from all previously characterized 14-3-3 and target protein-binding modes. ChREBP α2 interacts with 14-3-3 through both electrostatic and van der Waals interactions, and the binding is partially mediated by a free sulfate or phosphate. Structure-based mutagenesis and binding assays indicated that disrupting the observed 14-3-3 and ChREBP α2 interface resulted in a loss of complex formation, thus validating the novel protein interaction mode in the 14-3-3β·ChREBP α2 complex.

  5. Unique properties of C,C'-linked nido-biscarborane tetraanions. Synthesis, structure and bonding of ruthenium monocarbollide via unprecedented cage carbon extrusion.

    Science.gov (United States)

    Zhao, Da; Zhang, Jiji; Lin, Zhenyang; Xie, Zuowei

    2016-08-21

    Four reaction pathways have been found in the reaction of a C,C'-linked nido-biscarborane tetraanionic salt with [Ru(p-cymene)Cl2]2, leading to the isolation and structural characterization of redox, triple cage B-H oxidative addition, cage expansion and cage carbon extrusion products. Among these, the unprecedented cage carbon extrusion results in the formation of a new 6π-electron carboranyl ligand [C2B10H10](2-). The bonding interactions between this ligand and the Ru(ii) center have also been discussed on the basis of DFT calculations.

  6. Structural information in two-dimensional patterns: entropy convergence and excess entropy.

    Science.gov (United States)

    Feldman, David P; Crutchfield, James P

    2003-05-01

    We develop information-theoretic measures of spatial structure and pattern in more than one dimension. As is well known, the entropy density of a two-dimensional configuration can be efficiently and accurately estimated via a converging sequence of conditional entropies. We show that the manner in which these conditional entropies converge to their asymptotic value serves as a measure of global correlation and structure for spatial systems in any dimension. We compare and contrast entropy convergence with mutual-information and structure-factor techniques for quantifying and detecting spatial structure.

  7. Integrating network structure and dynamic information for better routing strategy on scale-free networks

    Science.gov (United States)

    Tang, Xiao-Gai; Wong, Eric W. M.; Wu, Zhi-Xi

    2009-06-01

    We study information packet routing processes on scale-free networks by mimicking the Internet traffic delivery strategies. We incorporate both the global network structure information and local queuing information in the dynamic processes. We propose several new routing strategies to guide the packet routing. The performance of the routing strategies is measured by the average transit time of the packets as well as their dependence on the traffic amount. We find that the routing strategies which integrate both global network structure information and local dynamic information perform much better than the traditional shortest-path routing protocol which takes into account only the global topological information. Moreover, from comparative studies of these routing strategies, we observe that some of our proposed methods can decrease the average transit time of packets but the performance is closely dependent on the total amount of traffic while some other proposed methods can have good performance independent of the total amount of traffic with hyper-excellent average transit time of packets. Also, numerical results show that our proposed methods integrating network structure information and local dynamic information can work much better than the methods recently proposed in [S. Sreenivasan, R. Cohen, E. López, Z. Toroczkai, H.E. Stanley, Phys. Rev. E 75 (2007) 036105, Zhi-Xi Wu, Gang Peng, Eric W.M. Wong, Kai-Hau Yeung, J. Stat. Mech. (2008) P11002.], which only considered network structure information.

  8. Population structure and comparative genome hybridization of European flor yeast reveal a unique group of Saccharomyces cerevisiae strains with few gene duplications in their genome.

    Science.gov (United States)

    Legras, Jean-Luc; Erny, Claude; Charpentier, Claudine

    2014-01-01

    Wine biological aging is a wine making process used to produce specific beverages in several countries in Europe, including Spain, Italy, France, and Hungary. This process involves the formation of a velum at the surface of the wine. Here, we present the first large scale comparison of all European flor strains involved in this process. We inferred the population structure of these European flor strains from their microsatellite genotype diversity and analyzed their ploidy. We show that almost all of these flor strains belong to the same cluster and are diploid, except for a few Spanish strains. Comparison of the array hybridization profile of six flor strains originating from these four countries, with that of three wine strains did not reveal any large segmental amplification. Nonetheless, some genes, including YKL221W/MCH2 and YKL222C, were amplified in the genome of four out of six flor strains. Finally, we correlated ICR1 ncRNA and FLO11 polymorphisms with flor yeast population structure, and associate the presence of wild type ICR1 and a long Flo11p with thin velum formation in a cluster of Jura strains. These results provide new insight into the diversity of flor yeast and show that combinations of different adaptive changes can lead to an increase of hydrophobicity and affect velum formation.

  9. Population structure and comparative genome hybridization of European flor yeast reveal a unique group of Saccharomyces cerevisiae strains with few gene duplications in their genome.

    Directory of Open Access Journals (Sweden)

    Jean-Luc Legras

    Full Text Available Wine biological aging is a wine making process used to produce specific beverages in several countries in Europe, including Spain, Italy, France, and Hungary. This process involves the formation of a velum at the surface of the wine. Here, we present the first large scale comparison of all European flor strains involved in this process. We inferred the population structure of these European flor strains from their microsatellite genotype diversity and analyzed their ploidy. We show that almost all of these flor strains belong to the same cluster and are diploid, except for a few Spanish strains. Comparison of the array hybridization profile of six flor strains originating from these four countries, with that of three wine strains did not reveal any large segmental amplification. Nonetheless, some genes, including YKL221W/MCH2 and YKL222C, were amplified in the genome of four out of six flor strains. Finally, we correlated ICR1 ncRNA and FLO11 polymorphisms with flor yeast population structure, and associate the presence of wild type ICR1 and a long Flo11p with thin velum formation in a cluster of Jura strains. These results provide new insight into the diversity of flor yeast and show that combinations of different adaptive changes can lead to an increase of hydrophobicity and affect velum formation.

  10. Impact melt-bearing breccias of the Mistastin Lake impact structure: A unique planetary analogue for ground-truthing proximal ejecta emplacement

    Science.gov (United States)

    Mader, M. M.; Osinski, G. R.

    2013-12-01

    Impact craters are the dominant geological landform on rocky planetary surfaces; however, relationships between specific craters and their ejecta are typically poorly constrained. With limited planetary samples, scientists look to terrestrial craters as analogues. Impact ejecta is defined here as any target material, regardless of its physical state, that is transported beyond the rim of the transient cavity [1]. The original transient cavity reaches its maximum size during the excavation stage of crater formation, before rim collapse begins in the modification stage [2]. In complex craters, during the modification stage, rocks around the periphery of the bowl-shaped transient crater collapse downward and inward to form a series of terraces along the outer margin of the crater structure [3]. Proximal impact ejecta, can therefore be found on the terraces of the modified rim of a complex crater, interior to the final crater rim [1]. Although typically poorly preserved on Earth due to post-impact erosional processes, impact ejecta have been identified in the terraced rim region of the Mistastin Lake impact structure, located in northern Labrador, Canada (55°53'N; 63°18'W) [4]. The Mistastin Lake impact structure is an intermediate-size, complex crater (28 km apparent crater diameter) formed by a meteorite impact ~36 Ma in crystalline target rocks. The original crater has been differentially eroded; however, a terraced rim and distinct central uplift are still observed [5]. The inner portion of the structure is covered by the Mistastin Lake and the surrounding area is locally covered by soil/glacial deposits and vegetation. Locally, allochthonous impactites overlying fractured target rocks are exposed along the lakeshore and along banks of radially cutting streams. They define a consistent stratigraphy, including, from bottom to top: monomict, lithic breccias, allochthonous polymict lithic breccias, and allochthonous impact melt rocks. Mistastin impact breccias range

  11. Quantifying information transfer by protein domains: Analysis of the Fyn SH2 domain structure

    DEFF Research Database (Denmark)

    Lenaerts, Tom; Ferkinghoff-Borg, Jesper; Stricher, Francois

    2008-01-01

    that directly relates protein structural dynamics to information exchange between functional sites is still lacking. Results: Here we introduce a method to analyze protein dynamics within the framework of information theory and show that signal transduction within proteins can be considered as a particular...... distal communication is achieved. We illustrate the approach by analyzing information transfer by the SH2 domain of Fyn tyrosine kinase, obtained from Monte Carlo dynamics simulations. Our analysis reveals that the Fyn SH2 domain forms a noisy communication channel that couples residues located...... by crossing the core of the SH2 domain. Conclusion: As a result, our method provides a means to directly map the exchange of biological information on the structure of protein domains, making it clear how binding triggers conformational changes in the protein structure. As such it provides a structural road...

  12. Efficient Structural System Reliability Updating with Subspace-Based Damage Detection Information

    DEFF Research Database (Denmark)

    Döhler, Michael; Thöns, Sebastian

    modelling is introduced building upon the non-destructive testing reliability which applies to structural systems and DDS containing a strategy to overcome the high computational efforts for the pre-determination of the DDS reliability. This approach takes basis in the subspace-based damage detection method......Damage detection systems and algorithms (DDS and DDA) provide information of the structural system integrity in contrast to e.g. local information by inspections or non-destructive testing techniques. However, the potential of utilizing DDS information for the structural integrity assessment...... and prognosis is hardly exploited nor treated in scientific literature up to now. In order to utilize the information provided by DDS for the structural performance, usually high computational efforts for the pre-determination of DDS reliability are required. In this paper, an approach for the DDS performance...

  13. The structure and size of sensory bursts encode stimulus information but only size affects behavior.

    Science.gov (United States)

    Marsat, Gary; Pollack, Gerald S

    2010-04-01

    Cricket ultrasound avoidance is a classic model system for neuroethology. Avoidance steering is triggered by high-firing-rate bursts of spikes in the auditory command neuron AN2. Although bursting is common among sensory neurons, and although the detailed structure of bursts may encode information about the stimulus, it is as yet unclear whether this information is decoded. We address this question in two ways: from an information coding point of view, by showing the relationship between stimulus and burst structure; and also from a functional point of view by showing the relationship between burst structure and behavior. We conclude that the burst structure carries detailed temporal information about the stimulus but that this has little impact on the behavioral response, which is affected mainly by burst size.

  14. Hierarchical mutual information for the comparison of hierarchical community structures in complex networks

    CERN Document Server

    Perotti, Juan Ignacio; Caldarelli, Guido

    2015-01-01

    The quest for a quantitative characterization of community and modular structure of complex networks produced a variety of methods and algorithms to classify different networks. However, it is not clear if such methods provide consistent, robust and meaningful results when considering hierarchies as a whole. Part of the problem is the lack of a similarity measure for the comparison of hierarchical community structures. In this work we give a contribution by introducing the {\\it hierarchical mutual information}, which is a generalization of the traditional mutual information, and allows to compare hierarchical partitions and hierarchical community structures. The {\\it normalized} version of the hierarchical mutual information should behave analogously to the traditional normalized mutual information. Here, the correct behavior of the hierarchical mutual information is corroborated on an extensive battery of numerical experiments. The experiments are performed on artificial hierarchies, and on the hierarchical ...

  15. Structural Analysis of β-Fructofuranosidase from Xanthophyllomyces dendrorhous Reveals Unique Features and the Crucial Role of N-Glycosylation in Oligomerization and Activity.

    Science.gov (United States)

    Ramírez-Escudero, Mercedes; Gimeno-Pérez, María; González, Beatriz; Linde, Dolores; Merdzo, Zoran; Fernández-Lobato, María; Sanz-Aparicio, Julia

    2016-03-25

    Xanthophyllomyces dendrorhousβ-fructofuranosidase (XdINV)is a highly glycosylated dimeric enzyme that hydrolyzes sucrose and releases fructose from various fructooligosaccharides (FOS) and fructans. It also catalyzes the synthesis of FOS, prebiotics that stimulate the growth of beneficial bacteria in human gut. In contrast to most fructosylating enzymes, XdINV produces neo-FOS, which makes it an interesting biotechnology target. We present here its three-dimensional structure, which shows the expected bimodular arrangement and also a long extension of its C terminus that together with anN-linked glycan mediate the formation of an unusual dimer. The two active sites of the dimer are connected by a long crevice, which might indicate its potential ability to accommodate branched fructans. This arrangement could be representative of a group of GH32 yeast enzymes having the traits observed in XdINV. The inactive D80A mutant was used to obtain complexes with relevant substrates and products, with their crystals structures showing at least four binding subsites at each active site. Moreover, two different positions are observed from subsite +2 depending on the substrate, and thus, a flexible loop (Glu-334-His-343) is essential in binding sucrose and β(2-1)-linked oligosaccharides. Conversely, β(2-6) and neo-type substrates are accommodated mainly by stacking to Trp-105, explaining the production of neokestose and the efficient fructosylating activity of XdINV on α-glucosides. The role of relevant residues has been investigated by mutagenesis and kinetics measurements, and a model for the transfructosylating reaction has been proposed. The plasticity of its active site makes XdINV a valuable and flexible biocatalyst to produce novel bioconjugates.

  16. Guidance manual for the input of biological information to water-intake-structure design

    Energy Technology Data Exchange (ETDEWEB)

    Neitzel, D.A.; Simmons, M.A.; McKenzie, D.H.

    1981-12-01

    This manual is intended to provide guidance to the biologist who is asked to provide biological input during the construction or subsequent alteration of a water intake structure. Examples of the types of biological information that might be included in intake design are presented. Procedures for quantifying biological information and defining specific tasks that will generate quantifiable data are discussed. Procedures described apply both to new and modified water intake structures.

  17. Preparing to return to the Moon: Lessons from science-driven analogue missions to the Mistastin Lake impact structure, Canada, a unique lunar analogue site

    Science.gov (United States)

    Osinski, G. R.; Barfoot, T.; Chanou, A.; Daly, M. G.; Francis, R.; Hodges, K. V.; Jolliff, B. L.; Mader, M. M.; McCullough, E. M.; Moores, J. E.; Pickersgill, A.; Pontefract, A.; Preston, L.; Shankar, B.; Singleton, A.; Sylvester, P.; Tornabene, L. L.; Young, K. E.

    2013-12-01

    Impact cratering is the dominant geological process on the Moon, Near Earth Asteroids (NEAs) and the moons of Mars - the objectives for the new Solar System Exploration Research Virtual Institute (SSERVI). Led by members of the Canadian Lunar Research Network (CLRN), funded by the Canadian Space Agency, and with participants from the U.S., we carried out a series of analogue missions on Earth in order to prepare and train for future potential robotic and human sample return missions. Critically, these analogue missions were driven by the paradigm that operational and technical objectives are conducted while conducting new science and addressing real overarching scientific objectives. An overarching operational goal was to assess the utility of a robotic field reconnaissance mission as a precursor to a human sortie sample return mission. Here, we focus on the results and lessons learned from a robotic precursor mission and follow on human-robotic mission to the Mistastin Lake impact structure in Labrador, northern Canada (55°53'N; 63°18'W). The Mistastin structure was chosen because it represents an exceptional analogue for lunar craters. This site includes both an anorthositic target, a central uplift, well-preserved impact melt rocks - mostly derived from melting anorthosite - and is (or was) relatively unexplored. This crater formed ~36 million years ago and has a diameter of ~28 km. The scientific goals for these analogue missions were to further our understanding of impact chronology, shock processes, impact ejecta and potential resources within impact craters. By combining these goals in an analogue mission campaign key scientific requirements for a robotic precursor were determined. From the outset, these analogue missions were formulated and executed like an actual space mission. Sites of interest were chosen using remote sensing imagery without a priori knowledge of the site through a rigorous site selection process. The first deployment occurred in

  18. Structure of the Legionella Virulence Factor, SidC Reveals a Unique PI(4P-Specific Binding Domain Essential for Its Targeting to the Bacterial Phagosome.

    Directory of Open Access Journals (Sweden)

    Xi Luo

    2015-06-01

    Full Text Available The opportunistic intracellular pathogen Legionella pneumophila is the causative agent of Legionnaires' disease. L. pneumophila delivers nearly 300 effector proteins into host cells for the establishment of a replication-permissive compartment known as the Legionella-containing vacuole (LCV. SidC and its paralog SdcA are two effectors that have been shown to anchor on the LCV via binding to phosphatidylinositol-4-phosphate [PI(4P] to facilitate the recruitment of ER proteins to the LCV. We recently reported that the N-terminal SNL (SidC N-terminal E3 Ligase domain of SidC is a ubiquitin E3 ligase, and its activity is required for the recruitment of ER proteins to the LCV. Here we report the crystal structure of SidC (1-871. The structure reveals that SidC contains four domains that are packed into an arch-like shape. The P4C domain (PI(4P binding of SidC comprises a four α-helix bundle and covers the ubiquitin ligase catalytic site of the SNL domain. Strikingly, a pocket with characteristic positive electrostatic potentials is formed at one end of this bundle. Liposome binding assays of the P4C domain further identified the determinants of phosphoinositide recognition and membrane interaction. Interestingly, we also found that binding with PI(4P stimulates the E3 ligase activity, presumably due to a conformational switch induced by PI(4P from a closed form to an open active form. Mutations of key residues involved in PI(4P binding significantly reduced the association of SidC with the LCV and abolished its activity in the recruitment of ER proteins and ubiquitin signals, highlighting that PI(4P-mediated targeting of SidC is critical to its function in the remodeling of the bacterial phagosome membrane. Finally, a GFP-fusion with the P4C domain was demonstrated to be specifically localized to PI(4P-enriched compartments in mammalian cells. This domain shows the potential to be developed into a sensitive and accurate PI(4P probe in living cells.

  19. 77 FR 50576 - Fatigue Tolerance Evaluation of Metallic Structures; OMB Approval of Information Collection

    Science.gov (United States)

    2012-08-22

    ... Federal Aviation Administration 14 CFR Part 29 RIN 2120-AJ51 Fatigue Tolerance Evaluation of Metallic Structures; OMB Approval of Information Collection AGENCY: Federal Aviation Administration, DOT. ACTION: Final rule; OMB approval of information collection. SUMMARY: This document notifies the public of...

  20. SAPIENS: Spreading Activation Processor for Information Encoded in Network Structures. Technical Report No. 296.

    Science.gov (United States)

    Ortony, Andrew; Radin, Dean I.

    The product of researchers' efforts to develop a computer processor which distinguishes between relevant and irrelevant information in the database, Spreading Activation Processor for Information Encoded in Network Structures (SAPIENS) exhibits (1) context sensitivity, (2) efficiency, (3) decreasing activation over time, (4) summation of…

  1. Theoretical and practical implacations from the use of structuration theory in public sector information systems research

    NARCIS (Netherlands)

    Veenstra, A.F.E. van; Melin, U.; Axelson, K.

    2014-01-01

    To gain better understanding of the development, implementation and use of information technology (IT), many scholars in the field of information systems (IS) use structuration theory (ST). However, ST is, so far, more seldom applied to, and reflected upon, in studies of public sector IS to account

  2. PHA’s (Polyhydroxyalkanoates): General information on structure and raw materials for their production

    NARCIS (Netherlands)

    Kootstra, A.M.J.; Elissen, H.J.H.; Huurman, Sander

    2017-01-01

    This report provides background information on structure and diversity of different polyhydroxyalkanoates (PHA) and on feedstocks for their microbial production. The information that is contained in this report was compiled as a running document for the project “TKI-AgriFood Kleinschalige Bioraffina

  3. Informal Mealtime Pedagogies: Exploring the Influence of Family Structure on Young People's Healthy Eating Dispositions

    Science.gov (United States)

    Quarmby, Thomas; Dagkas, Symeon

    2015-01-01

    Families are increasingly recognised as informal sites of learning, especially with regard to healthy eating. Through the use of Bourdieu's conceptual tools, this paper explores the role of family meals within different family structures and the informal pedagogic encounters that take place. How they help to construct young people's healthy eating…

  4. Informal Mealtime Pedagogies: Exploring the Influence of Family Structure on Young People's Healthy Eating Dispositions

    Science.gov (United States)

    Quarmby, Thomas; Dagkas, Symeon

    2015-01-01

    Families are increasingly recognised as informal sites of learning, especially with regard to healthy eating. Through the use of Bourdieu's conceptual tools, this paper explores the role of family meals within different family structures and the informal pedagogic encounters that take place. How they help to construct young people's healthy eating…

  5. "Information in Context": Co-Designing Workplace Structures and Systems for Organizational Learning

    Science.gov (United States)

    Somerville, Mary M.; Howard, Zaana

    2010-01-01

    Introduction: This paper discusses an "information in context" design project at Auraria Library in Denver, Colorado which aims to collaboratively create organizational structures and communication systems with and for library employees. Method: This action research project is founded within shared leadership, informed learning and…

  6. A unique manganese (II) complex of 4-methoxy-pyridine-2-carboxylate: Synthesis, crystal structure, FT-IR and UV-Vis spectra and DFT calculations

    Science.gov (United States)

    Tamer, Ömer

    2017-09-01

    The first metal complex of 4-Methoxy-pyridine-2-carboxylic acid, [Mn(4-mpic)2(H2O)2], has been synthesized, and its crystal structure has been determined by X-Ray diffraction method. The FT-IR spectrum for [Mn(4-mpic)2(H2O)2] complex has been presented in this paper, as compared with that of single 4-mpic ligand. The electronic absorption spectrum recorded in DMSO solvent revealed that the ligand metal charge transfer (LMCT) interactions occur in Mn(II) complex. In order to support experimental results, density functional theory (DFT) calculations have been also carried out with the hybrid B3LYP functional. The coordination sphere of central Mn(II) ion has been evaluated by using the hyperconjugative interactions between the lone pair electrons of metal and donor atoms (N and O). The natural charge of Mn(II) ion demonstrated that the electronic transitions from metal ion to 4-mpic are higher than those in reverse direction. The carboxylate group has been determined as the most reactive side of Mn(II) complex in chemical reactions. A comparison among Mulliken, NBO and APT charges has been carried out for Mn(II) complex system. The first static hyperpolarizability parameter for Mn(II) complex has been also investigated by using B3LYP level.

  7. Studies toward the Unique Pederin Family Member Psymberin: Structure Activity Relationships, Biochemical Studies and Genetics Identify the Mode of Action of Psymberin

    Science.gov (United States)

    Wu, Cheng-Yang; Feng, Yu; Cardenas, Eduardo R.; Williams, Noelle; Floreancig, Paul E.; De Brabander, Jef K.; Roth, Michael G.

    2012-01-01

    Psymberin is the only member of the pederin natural product family that contains a dihydroisocoumarin side chain. Structural modifications of psymberin uncoupled inhibition of protein translation from cytotoxicity, suggesting that psymberin has more than one bioactivity. A forward genetic screen in Caenorhabditis elegans was conducted to identify the molecular target(s) of psymberin. Multiple independent psymberin-resistant mutants were isolated, each containing the same point mutation in a gene encoding a ribosomal protein. However, a psymberin-resistant mutant strain bearing this mutation was not cross-resistant to the pederin family member mycalamide A, which binds to the archaeal form of the same protein. Thus, two pederin family members likely differ in how they bind the same molecular target. The accumulation of psymberin in cells was sensitive to the stereochemistry of the amide side chain at C4 or C8 and the presence of the dihydroisocoumarin side chain. The observation that psymberin diastereomers or dihydroisocoumarin-truncated analogs lose all cytotoxic activity while retaining the ability to inhibit protein translation in a cell-free in vitro assay can be explained in the context of these differential cell uptake issues. Finally, we also demonstrate that the blistering activity associated with pederin and other members of the family is not due to their protein synthesis inhibiting activity. Unlike pederin and mycalamide, psymberin does not display irritant or blistering activity. PMID:23088155

  8. Studies toward the unique pederin family member psymberin: structure-activity relationships, biochemical studies, and genetics identify the mode-of-action of psymberin.

    Science.gov (United States)

    Wu, Cheng-Yang; Feng, Yu; Cardenas, Eduardo R; Williams, Noelle; Floreancig, Paul E; De Brabander, Jef K; Roth, Michael G

    2012-11-21

    Psymberin is the only member of the pederin natural product family that contains a dihydroisocoumarin side chain. Structural modifications of psymberin uncoupled inhibition of protein translation from cytotoxicity, suggesting that psymberin has more than one bioactivity. A forward genetic screen in Caenorhabditis elegans was conducted to identify the molecular target(s) of psymberin. Multiple independent psymberin-resistant mutants were isolated, each containing the same point mutation in a gene encoding a ribosomal protein. However, a psymberin-resistant mutant strain bearing this mutation was not cross-resistant to the pederin family member mycalamide A, which binds to the archaeal form of the same protein. Thus, two pederin family members likely differ in how they bind the same molecular target. The accumulation of psymberin in cells was sensitive to the stereochemistry of the amide side chain at C4 or C8 and the presence of the dihydroisocoumarin side chain. The observation that psymberin diastereomers or dihydroisocoumarin-truncated analogs lose all cytotoxic activity while retaining the ability to inhibit protein translation in a cell-free in vitro assay can be explained in the context of these differential cell uptake issues. Finally, we also demonstrate that the blistering activity associated with pederin and other members of the family is not due to their protein synthesis inhibiting activity. Unlike pederin and mycalamide, psymberin does not display irritant or blistering activity.

  9. Information Theory of Networks

    Directory of Open Access Journals (Sweden)

    Matthias Dehmer

    2011-11-01

    Full Text Available The paper puts the emphasis on surveying information-theoretic network measures for analyzing the structure of networks. In order to apply the quantities interdisciplinarily, we also discuss some of their properties such as their structural interpretation and uniqueness.

  10. University Students' Knowledge Structures and Informal Reasoning on the Use of Genetically Modified Foods: Multidimensional Analyses

    Science.gov (United States)

    Wu, Ying-Tien

    2012-12-01

    This study aims to provide insights into the role of learners' knowledge structures about a socio-scientific issue (SSI) in their informal reasoning on the issue. A total of 42 non-science major university students' knowledge structures and informal reasoning were assessed with multidimensional analyses. With both qualitative and quantitative analyses, this study revealed that those students with more extended and better-organized knowledge structures, as well as those who more frequently used higher-order information processing modes, were more oriented towards achieving a higher-level informal reasoning quality. The regression analyses further showed that the "richness" of the students' knowledge structures explained 25 % of the variation in their rebuttal construction, an important indicator of reasoning quality, indicating the significance of the role of students' sophisticated knowledge structure in SSI reasoning. Besides, this study also provides some initial evidence for the significant role of the "core" concept within one's knowledge structure in one's SSI reasoning. The findings in this study suggest that, in SSI-based instruction, science instructors should try to identify students' core concepts within their prior knowledge regarding the SSI, and then they should try to guide students to construct and structure relevant concepts or ideas regarding the SSI based on their core concepts. Thus, students could obtain extended and well-organized knowledge structures, which would then help them achieve better learning transfer in dealing with SSIs.

  11. Value of information: A roadmap to quantifying the benefit of structural health monitoring

    DEFF Research Database (Denmark)

    Straub, D.; Chatzi, E.; Bismut, E.

    2017-01-01

    The concept of value of information (VoI) enables quantification of the benefits provided by structural health monitoring (SHM) systems – in principle. Its implementation is challenging, as it requires an explicit modelling of the structural system’s life cycle, in particular of the decisions...

  12. Hierarchical assembly may be a way to make large information-rich structures

    CERN Document Server

    Whitelam, Stephen

    2015-01-01

    Self-assembly in the laboratory can now yield `information-rich' nanostructures in which each component is of a distinct type and has a defined spatial position. Ensuring the thermodynamic stability of such structures requires inter-component interaction energies to increase logarithmically with structure size, in order to counter the entropy gained upon mixing component types in solution. However, self-assembly in the presence of strong interactions results in general in kinetic trapping, so suggesting a limit to the size of an (equilibrium) structure that can be self-assembled from distinguishable components. Here we study numerically a two-dimensional hierarchical assembly scheme already considered in experiment. We show that this scheme is immune to the kinetic traps associated with strong `native' interactions (interactions designed to stabilize the intended structure), and so, in principle, offers a way to make large information-rich structures. In this scheme the size of an assembled structure scales e...

  13. PROMALS3D: multiple protein sequence alignment enhanced with evolutionary and three-dimensional structural information.

    Science.gov (United States)

    Pei, Jimin; Grishin, Nick V

    2014-01-01

    Multiple sequence alignment (MSA) is an essential tool with many applications in bioinformatics and computational biology. Accurate MSA construction for divergent proteins remains a difficult computational task. The constantly increasing protein sequences and structures in public databases could be used to improve alignment quality. PROMALS3D is a tool for protein MSA construction enhanced with additional evolutionary and structural information from database searches. PROMALS3D automatically identifies homologs from sequence and structure databases for input proteins, derives structure-based constraints from alignments of three-dimensional structures, and combines them with sequence-based constraints of profile-profile alignments in a consistency-based framework to construct high-quality multiple sequence alignments. PROMALS3D output is a consensus alignment enriched with sequence and structural information about input proteins and their homologs. PROMALS3D Web server and package are available at http://prodata.swmed.edu/PROMALS3D.

  14. Representation of information about family relatives as structured data in electronic health records.

    Science.gov (United States)

    Zhou, L; Lu, Y; Vitale, C J; Mar, P L; Chang, F; Dhopeshwarkar, N; Rocha, R A

    2014-01-01

    The ability to manage and leverage family history information in the electronic health record (EHR) is crucial to delivering high-quality clinical care. We aimed to evaluate existing standards in representing relative information, examine this information documented in EHRs, and develop a natural language processing (NLP) application to extract relative information from free-text clinical documents. We reviewed a random sample of 100 admission notes and 100 discharge summaries of 198 patients, and also reviewed the structured entries for these patients in an EHR system's family history module. We investigated the two standards used by Stage 2 of Meaningful Use (SNOMED CT and HL7 Family History Standard) and identified coverage gaps of each standard in coding relative information. Finally, we evaluated the performance of the MTERMS NLP system in identifying relative information from free-text documents. The structure and content of SNOMED CT and HL7 for representing relative information are different in several ways. Both terminologies have high coverage to represent local relative concepts built in an ambulatory EHR system, but gaps in key concept coverage were detected; coverage rates for relative information in free-text clinical documents were 95.2% and 98.6%, respectively. Compared to structured entries, richer family history information was only available in free-text documents. Using a comprehensive lexicon that included concepts and terms of relative information from different sources, we expanded the MTERMS NLP system to extract and encode relative information in clinical documents and achieved a corresponding precision of 100% and recall of 97.4%. Comprehensive assessment and user guidance are critical to adopting standards into EHR systems in a meaningful way. A significant portion of patients' family history information is only documented in free-text clinical documents and NLP can be used to extract this information.

  15. Market structure and the role of consumer information in the physician services industry: an empirical test.

    Science.gov (United States)

    Wong, H S

    1996-04-01

    This paper applies Panzar and Rosse's (1987) econometric test of market structure to examine two long-debated issues: What is the market structure for physician services? Do more physicians in a market area raise the search cost of obtaining consumer information and increase prices (Satterthwaite, 1979, 1985)? For primary care and general and family practice physicians, the monopolistically competitive model prevailed over the competing hypotheses--monopoly, perfect competition, and monopolistic competition characterized by consumer informational confusion. Although less conclisive, there is some evidence to support the monopolistically competitive model for surgeons and the consumer informational confusion model for internal medicine physicians.

  16. AlignHUSH: Alignment of HMMs using structure and hydrophobicity information

    OpenAIRE

    Krishnadev Oruganty; Srinivasan Narayanaswamy

    2011-01-01

    Abstract Background Sensitive remote homology detection and accurate alignments especially in the midnight zone of sequence similarity are needed for better function annotation and structural modeling of proteins. An algorithm, AlignHUSH for HMM-HMM alignment has been developed which is capable of recognizing distantly related domain families The method uses structural information, in the form of predicted secondary structure probabilities, and hydrophobicity of amino acids to align HMMs of t...

  17. Application of Information Processing Theory on the inter-relationship of organizational culture and organizational structure

    OpenAIRE

    Li, YIH; Fellows, RF; Liu, AMM

    2008-01-01

    A conceptual model of the inter-relationship between organizational culture and organizational structure has been formulated. However, it is still unable to explain the direction of interaction of organizational culture and organizational structure in real day-to-day operation. This paper explains this relationship through the application of Information-Processing Theory. It has been established that, on one hand, organizational structure modifies organizational culture and, on the other hand...

  18. The geometrical structure of quantum theory as a natural generalization of information geometry

    Energy Technology Data Exchange (ETDEWEB)

    Reginatto, Marcel [Physikalisch-Technische Bundesanstalt, Braunschweig (Germany)

    2015-01-13

    Quantum mechanics has a rich geometrical structure which allows for a geometrical formulation of the theory. This formalism was introduced by Kibble and later developed by a number of other authors. The usual approach has been to start from the standard description of quantum mechanics and identify the relevant geometrical features that can be used for the reformulation of the theory. Here this procedure is inverted: the geometrical structure of quantum theory is derived from information geometry, a geometrical structure that may be considered more fundamental, and the Hilbert space of the standard formulation of quantum mechanics is constructed using geometrical quantities. This suggests that quantum theory has its roots in information geometry.

  19. Numerical Investigations into the Value of Information in Lifecycle Analysis of Structural Systems

    DEFF Research Database (Denmark)

    Konakli, Katerina; Sudret, Bruno; Faber, Michael Havbro

    2015-01-01

    Preposterior analysis can be used to assess the potential of an experiment to enhance decision-making by providing information on parameters of the decision problem that are surrounded by epistemic uncertainties. The present paper describes a framework for preposterior analysis for support of dec...... dependencies between the components of a system. Furthermore, challenges and potentials in value-of-information analysis for structural systems are discussed.......Preposterior analysis can be used to assess the potential of an experiment to enhance decision-making by providing information on parameters of the decision problem that are surrounded by epistemic uncertainties. The present paper describes a framework for preposterior analysis for support...... of decisions related to maintenance of structural systems. In this context, experiments may refer to inspections or structural health monitoring. The value-of-information concept comprises a powerful tool for determining whether the experimental cost is justified by the expected gained benefit during...

  20. On the Value of Structural Health Monitoring Information for the Operation of Wind Parks

    DEFF Research Database (Denmark)

    Thöns, Sebastian; Faber, Michael H.; Val, Dimitri V.

    2017-01-01

    In the present paper, an approach for the quantification of the Value of Structural Health Monitoring (SHM) Information building upon a framework for infrastructure system utility and decision analysis is developed and applied to the operation of wind parks. The quantification of the value of SHM...... facilitates a benefit and risk informed assessment and optimization of SHM strategies and encompasses models for the infrastructure functionality, the structural constituent and system risks and its management as well as the performance of SHM strategies. A wind park system model incorporating the structural...... for the propagation of SHM information and uncertainties from components to the different system levels and vice versa. The decision to extend the service life and the operation of a wind park is investigated without SHM information and by quantifying the value of several SHM strategies....

  1. Ancestral informative marker selection and population structure visualization using sparse Laplacian eigenfunctions.

    Directory of Open Access Journals (Sweden)

    Jun Zhang

    Full Text Available Identification of a small panel of population structure informative markers can reduce genotyping cost and is useful in various applications, such as ancestry inference in association mapping, forensics and evolutionary theory in population genetics. Traditional methods to ascertain ancestral informative markers usually require the prior knowledge of individual ancestry and have difficulty for admixed populations. Recently Principal Components Analysis (PCA has been employed with success to select SNPs which are highly correlated with top significant principal components (PCs without use of individual ancestral information. The approach is also applicable to admixed populations. Here we propose a novel approach based on our recent result on summarizing population structure by graph laplacian eigenfunctions, which differs from PCA in that it is geometric and robust to outliers. Our approach also takes advantage of the priori sparseness of informative markers in the genome. Through simulation of a ring population and the real global population sample HGDP of 650K SNPs genotyped in 940 unrelated individuals, we validate the proposed algorithm at selecting most informative markers, a small fraction of which can recover the similar underlying population structure efficiently. Employing a standard Support Vector Machine (SVM to predict individuals' continental memberships on HGDP dataset of seven continents, we demonstrate that the selected SNPs by our method are more informative but less redundant than those selected by PCA. Our algorithm is a promising tool in genome-wide association studies and population genetics, facilitating the selection of structure informative markers, efficient detection of population substructure and ancestral inference.

  2. RNACompress: Grammar-based compression and informational complexity measurement of RNA secondary structure

    Directory of Open Access Journals (Sweden)

    Chen Chun

    2008-03-01

    Full Text Available Abstract Background With the rapid emergence of RNA databases and newly identified non-coding RNAs, an efficient compression algorithm for RNA sequence and structural information is needed for the storage and analysis of such data. Although several algorithms for compressing DNA sequences have been proposed, none of them are suitable for the compression of RNA sequences with their secondary structures simultaneously. This kind of compression not only facilitates the maintenance of RNA data, but also supplies a novel way to measure the informational complexity of RNA structural data, raising the possibility of studying the relationship between the functional activities of RNA structures and their complexities, as well as various structural properties of RNA based on compression. Results RNACompress employs an efficient grammar-based model to compress RNA sequences and their secondary structures. The main goals of this algorithm are two fold: (1 present a robust and effective way for RNA structural data compression; (2 design a suitable model to represent RNA secondary structure as well as derive the informational complexity of the structural data based on compression. Our extensive tests have shown that RNACompress achieves a universally better compression ratio compared with other sequence-specific or common text-specific compression algorithms, such as Gencompress, winrar and gzip. Moreover, a test of the activities of distinct GTP-binding RNAs (aptamers compared with their structural complexity shows that our defined informational complexity can be used to describe how complexity varies with activity. These results lead to an objective means of comparing the functional properties of heteropolymers from the information perspective. Conclusion A universal algorithm for the compression of RNA secondary structure as well as the evaluation of its informational complexity is discussed in this paper. We have developed RNACompress, as a useful tool

  3. Structures of two cell wall-associated polysaccharides of a Streptococcus mitis biovar 1 strain. A unique teichoic acid-like polysaccharide and the group O antigen which is a C-polysaccharide in common with pneumococci

    DEFF Research Database (Denmark)

    Bergström, N; Jansson, P.-E.; Kilian, Mogens

    2000-01-01

    The cell wall of Streptococcus mitis biovar 1 strain SK137 contains the C-polysaccharide known as the common antigen of a closely related species Streptococcus pneumoniae, and a teichoic acid-like polysaccharide with a unique structure. The two polysaccharides are different entities and could...... to that of one of the two structures of C-polysaccharide previously identified in S. pneumoniae. C-polysaccharide of S. mitis is characterized by the presence, in each repeating unit, of two residues of phosphocholine and both galactosamine residues in the N-acetylated form. Immunochemical analysis showed that C......-polysaccharide constitutes the Lancefield group O antigen. Studies using mAbs directed against the backbone and against the phosphocholine moiety of the C-polysaccharide revealed several different patterns of these epitopes among 95 S. mitis and Streptococcus oralis strains tested and the exclusive presence of the group O...

  4. Knowledge structure representation and automated updates in intelligent information management systems

    Science.gov (United States)

    Corey, Stephen; Carnahan, Richard S., Jr.

    1990-01-01

    A continuing effort to apply rapid prototyping and Artificial Intelligence techniques to problems associated with projected Space Station-era information management systems is examined. In particular, timely updating of the various databases and knowledge structures within the proposed intelligent information management system (IIMS) is critical to support decision making processes. Because of the significantly large amounts of data entering the IIMS on a daily basis, information updates will need to be automatically performed with some systems requiring that data be incorporated and made available to users within a few hours. Meeting these demands depends first, on the design and implementation of information structures that are easily modified and expanded, and second, on the incorporation of intelligent automated update techniques that will allow meaningful information relationships to be established. Potential techniques are studied for developing such an automated update capability and IIMS update requirements are examined in light of results obtained from the IIMS prototyping effort.

  5. Teaching Three-Dimensional Structural Chemistry Using Crystal Structure Databases. 3. The Cambridge Structural Database System: Information Content and Access Software in Educational Applications

    Science.gov (United States)

    Battle, Gary M.; Allen, Frank H.; Ferrence, Gregory M.

    2011-01-01

    Parts 1 and 2 of this series described the educational value of experimental three-dimensional (3D) chemical structures determined by X-ray crystallography and retrieved from the crystallographic databases. In part 1, we described the information content of the Cambridge Structural Database (CSD) and discussed a representative teaching subset of…

  6. A Survey of Web Link Structure Information Research%Web链接结构信息研究综述

    Institute of Scientific and Technical Information of China (English)

    李剑; 金蓓弘

    2003-01-01

    As the size of WWW is growing at an incredible rate, there is some limitation in the methods that only analyzes the Web pages' information. This paper presents a basic model of Web link structure. Then it classifies the algorithms that analyze the Web link structure information and their applications. At last, it presents the practical approach of analyzing Web link structure information.

  7. Uniqueness is Important in Competition

    Institute of Scientific and Technical Information of China (English)

    FENG Ai-Xia; XV Xiu-Lian; HE Da-Ren

    2009-01-01

    We propose a quantitative network description on the function of uniqueness in a competition system. Two statistical parameters, competition ability and uniqueness are defined, and their relationship in ordinary cases is analytically discussed. The competition between Chinese regional universities is taken as an example. The empirical investigation results show that the uniqueness of a university is really important in competition. Also,uniqueness is very helpful in the promotion of the university overall quality.

  8. A PCA-based method for ancestral informative markers selection in structured populations

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    Identification of population structure can help trace population histories and identify disease genes. Structured association (SA) is a commonly used approach for population structure identification and association mapping. A major issue with SA is that its performance greatly depends on the informa-tiveness and the numbers of ancestral informative markers (AIMs). Present major AIM selection meth-ods mostly require prior individual ancestry information, which is usually not available or uncertain in practice. To address this potential weakness, we herein develop a novel approach for AIM selection based on principle component analysis (PCA), which does not require prior ancestry information of study subjects. Our simulation and real genetic data analysis results suggest that, with equivalent AIMs, PCA-based selected AIMs can significantly increase the accuracy of inferred individual ancestries compared with traditionally randomly selected AIMs. Our method can easily be applied to whole genome data to select a set of highly informative AIMs in population structure, which can then be used to identify potential population structure and correct possible statistical biases caused by population stratification.

  9. A PCA-based method for ancestral informative markers selection in structured populations

    Institute of Scientific and Technical Information of China (English)

    ZHANG Feng; ZHANG Lei; DENG Hong-Wen

    2009-01-01

    Identification of population structure can help trace population histories and identify disease genes.Structured association (SA) is a commonly used approach for population structure identification and association mapping. A major issue with SA is that its performance greatly depends on the informativeness and the numbers of ancestral informative markers (AIMs). Present major AIM selection methods mostly require prior individual ancestry information, which is usually not available or uncertain in practice. To address this potential weakness, we herein develop a novel approach for AIM selection based on principle component analysis (PCA), which does not require prior ancestry information of study subjects. Our simulation and real genetic data analysis results suggest that, with equivalent AIMs,PCA-based selected AIMs can significantly increase the accuracy of inferred individual ancestries compared with traditionally randomly selected AIMs. Our method can easily be applied to whole genome data to select a set of highly informative AIMs in population structure, which can then be used to identify potential population structure and correct possible statistical biases caused by population stratification.

  10. On Uniqueness of coalitional equilibria

    NARCIS (Netherlands)

    Finus, M.; Mouche, van P.H.M.; Rundshagen, B.

    2014-01-01

    For the so-called "new approach" of coalitio formation it is important that coalitional equilibria are unique. Uniqueness comes down to existene and to semi-uniqueness, i.e.\\\\that there exists at most one equilibrium. Although conditions for existence are not problematic, conditions for semi-uniquen

  11. Investigating information-processing performance of different command team structures in the NATO Problem Space.

    Science.gov (United States)

    Stanton, Neville A; Rothrock, Ling; Harvey, Catherine; Sorensen, Linda

    2015-01-01

    The structure of command teams is a significant factor on their communications and ability to process, and act upon, information. The NATO Problem Space was used in this study to represent three of the main dimensions in the battle-space environment: familiarity, rate of change, and strength of information position. Results show that the five common team structures (chain, Y, circle, wheel and all-connected) did not generally perform as predicted in team literature. Findings suggest that under dynamic and highly variable conditions, high levels of synchronisation and trust should be present. On the other hand, synchronisation and trust are less important in hierarchical, highly centralised structures, because team members are more willing to accept the authority of a single leader and this tight control ensures that these teams can perform well as long as the Problem Space is familiar, information is explicit and the environment does not change. Practitioner Summary: Some types of team structures are better suited to particular constraints of the battle-space than others. This research has shown that the much touted all-connected structure is often the worst performing structure and that the traditional hierarchy of command and control has much merit in the digital information age.

  12. Hierarchical structure of the Sicilian goats revealed by Bayesian analyses of microsatellite information.

    Science.gov (United States)

    Siwek, M; Finocchiaro, R; Curik, I; Portolano, B

    2011-02-01

    Genetic structure and relationship amongst the main goat populations in Sicily (Girgentana, Derivata di Siria, Maltese and Messinese) were analysed using information from 19 microsatellite markers genotyped on 173 individuals. A posterior Bayesian approach implemented in the program STRUCTURE revealed a hierarchical structure with two clusters at the first level (Girgentana vs. Messinese, Derivata di Siria and Maltese), explaining 4.8% of variation (amovaФ(ST) estimate). Seven clusters nested within these first two clusters (further differentiations of Girgentana, Derivata di Siria and Maltese), explaining 8.5% of variation (amovaФ(SC) estimate). The analyses and methods applied in this study indicate their power to detect subtle population structure.

  13. The impact of information technology on productivity using structural equations technique in Iran Behnoush Company

    Directory of Open Access Journals (Sweden)

    Mina Beig

    2012-08-01

    Full Text Available Information technology plays an important role on increasing productivity in many organizations. The primary objective of the present survey is to study the impact of information technology on productivity and find a positive and significant relationship between these two factors. Structural equations technique and LISREL software are used for analysis of the questionnaires distributed among managers and some employees of Iran Behnoush Company. Organizations try to improve their performance by investment in information technology. However, many of the previous studies indicate insignificance of the impact of information technology on productivity of the organizations. The present survey studies the impact of information technology on organizations' productivity through the collected data from the above company. Results confirm existence of a positive relationship between information technology and productivity.

  14. Unique Structural Features Facilitate Lizard Tail Autotomy

    DEFF Research Database (Denmark)

    Sanggaard, Kristian Wejse; Danielsen, C. C.; Wogensen, L.

    2012-01-01

    Autotomy refers to the voluntary shedding of a body part; a renowned example is tail loss among lizards as a response to attempted predation. Although many aspects of lizard tail autotomy have been studied, the detailed morphology and mechanism remains unclear. In the present study, we showed...... that tail shedding by the Tokay gecko (Gekko gecko) and the associated extracellular matrix (ECM) rupture were independent of proteolysis. Instead, lizard caudal autotomy relied on biological adhesion facilitated by surface microstructures. Results based on bio-imaging techniques demonstrated that the tail...

  15. Role of a salt bridge in the model protein crambin explored by chemical protein synthesis: X-ray structure of a unique protein analogue, [V15A]crambin-alpha-carboxamide.

    Science.gov (United States)

    Bang, Duhee; Tereshko, Valentina; Kossiakoff, Anthony A; Kent, Stephen B H

    2009-07-01

    We have used total chemical synthesis to prepare [V15A]crambin-alpha-carboxamide, a unique protein analogue that eliminates a salt bridge between the delta-guanidinium of the Arg(10) side chain and the alpha-carboxylate of Asn(46) at the C-terminus of the polypeptide chain. This salt bridge is thought to be important for the folding and stability of the crambin protein molecule. Folding, with concomitant disulfide bond formation, of the fully reduced [V15A]crambin-alpha-carboxamide polypeptide was less efficient than folding/disulfide formation for the [V15A]crambin polypeptide under a standard set of conditions. To probe the origin of this less efficient folding/disulfide bond formation, we separately crystallized purified synthetic [V15A]crambin-alpha-carboxamide and chemically synthesized [V15A]crambin and solved their X-ray structures. The crystal structure of [V15A]crambin-alpha-carboxamide showed that elimination of the Arg(10)-Asn(46) salt bridge caused disorder of the C-terminal region of the polypeptide chain and affected the overall 'tightness' of the structure of the protein molecule. These studies, enabled by chemical protein synthesis, strongly suggest that in native crambin the Arg(10)-Asn(46) salt bridge contributes to efficient formation of correct disulfide bonds and also to the well-ordered structure of the protein molecule.

  16. Behavioral Modernity and the Cultural Transmission of Structured Information: The Semantic Axelrod Model

    CERN Document Server

    Madsen, Mark E

    2014-01-01

    Cultural transmission models are coming to the fore in explaining increases in the Paleolithic toolkit richness and diversity. Analyses suggest that diversity increased due to relaxation of conformism, due to the effects of demographic expansion on cultural diversity, and the effects of extinction and recolonization in metapopulations. During the Paleolithic, however, technologies increase not only in terms of diversity but also in their complexity and interdependence. As Mesoudi and O'Brien (2008) have shown selection broadly favors social learning that is hierarchical and structured, rather than information which is piecemeal and independent. The addition of structured information acquisition potentially explains how the complexity of technology changes along with diversity. Here, we introduce a structured extension of the Axelrod model of cultural differentiation. We examine the conditions under which structured suites of traits develop and differentiate in the model, which can represent the chains of prer...

  17. Structured information analysis for human reliability analysis of emergency tasks in nuclear power plants

    Energy Technology Data Exchange (ETDEWEB)

    Jung, Won Dea; Kim, Jae Whan; Park, Jin Kyun; Ha, Jae Joo [Korea Atomic Energy Research Institute, Taejeon (Korea)

    2000-02-01

    More than twenty HRA (Human Reliability Analysis) methodologies have been developed and used for the safety analysis in nuclear field during the past two decades. However, no methodology appears to have universally been accepted, as various limitations have been raised for more widely used ones. One of the most important limitations of conventional HRA is insufficient analysis of the task structure and problem space. To resolve this problem, we suggest SIA (Structured Information Analysis) for HRA. The proposed SIA consists of three parts. The first part is the scenario analysis that investigates the contextual information related to the given task on the basis of selected scenarios. The second is the goals-means analysis to define the relations between the cognitive goal and task steps. The third is the cognitive function analysis module that identifies the cognitive patterns and information flows involved in the task. Through the three-part analysis, systematic investigation is made possible from the macroscopic information on the tasks to the microscopic information on the specific cognitive processes. It is expected that analysts can attain a structured set of information that helps to predict the types and possibility of human error in the given task. 48 refs., 12 figs., 11 tabs. (Author)

  18. Structured information analysis for human reliability analysis of emergency tasks in nuclear power plants

    Energy Technology Data Exchange (ETDEWEB)

    Jung, Won Dea; Kim, Jae Whan; Park, Jin Kyun; Ha, Jae Joo [Korea Atomic Energy Research Institute, Taejeon (Korea)

    2000-02-01

    More than twenty HRA (Human Reliability Analysis) methodologies have been developed and used for the safety analysis in nuclear field during the past two decades. However, no methodology appears to have universally been accepted, as various limitations have been raised for more widely used ones. One of the most important limitations of conventional HRA is insufficient analysis of the task structure and problem space. To resolve this problem, we suggest SIA (Structured Information Analysis) for HRA. The proposed SIA consists of three parts. The first part is the scenario analysis that investigates the contextual information related to the given task on the basis of selected scenarios. The second is the goals-means analysis to define the relations between the cognitive goal and task steps. The third is the cognitive function analysis module that identifies the cognitive patterns and information flows involved in the task. Through the three-part analysis, systematic investigation is made possible from the macroscopic information on the tasks to the microscopic information on the specific cognitive processes. It is expected that analysts can attain a structured set of information that helps to predict the types and possibility of human error in the given task. 48 refs., 12 figs., 11 tabs. (Author)

  19. Art Libraries: Creating Access to Unique Collections

    Science.gov (United States)

    Falls, Sarah E.

    2009-01-01

    Art libraries face similar issues to other types of libraries during the digital transition but have unique twists driven by the needs of their collections. Art library information seekers may possess a sense of what an art library is: a library, set apart, to support the study of art and art history. For art libraries, it is the collection,…

  20. Modeling proteins using a super-secondary structure library and NMR chemical shift information.

    Science.gov (United States)

    Menon, Vilas; Vallat, Brinda K; Dybas, Joseph M; Fiser, Andras

    2013-06-04

    A remaining challenge in protein modeling is to predict structures for sequences with no sequence similarity to any experimentally solved structure. Based on earlier observations, the library of protein backbone supersecondary structure motifs (Smotifs) saturated about a decade ago. Therefore, it should be possible to build any structure from a combination of existing Smotifs with the help of limited experimental data that are sufficient to relate the backbone conformations of Smotifs between target proteins and known structures. Here, we present a hybrid modeling algorithm that relies on an exhaustive Smotif library and on nuclear magnetic resonance chemical shift patterns without any input of primary sequence information. In a test of 102 proteins, the algorithm delivered 90 homology-model-quality models, among them 24 high-quality ones, and a topologically correct solution for almost all cases. The current approach opens a venue to address the modeling of larger protein structures for which chemical shifts are available.

  1. An analysis of narrative nursing documentation in an otherwise structured intensive care clinical information system.

    Science.gov (United States)

    Moss, Jacqueline; Andison, Margot; Sobko, Heather

    2007-10-11

    Most structured nursing documentation systems allow the entry of data in a free text narrative format. Narrative data, while sometimes necessary, cannot easily be analyzed or linked to the structured portion of the record. This study examined the characteristics of free text narrative documentation entered in an otherwise structured record utilized in a cardiovascular intensive care unit. The analysis revealed that nurses documented 31 categories of narrative entries. Approximately 25% of these entries could have been entered into the structured portion of the record through the use of existing documentation codes. Nurses most frequently used the narrative documentation as a means to communicate summarized information for the coordination of healthcare team members. Development of tools to summarize structured data into an 'at a glance' format could enhance the coordination of healthcare team functioning. The authors discuss these results in the context of developing strategies to increase structured documentation and decrease free text in the patient record.

  2. Computer Simulation of Atoms Nuclei Structure Using Information Coefficients of Proportionality

    OpenAIRE

    Labushev, Mikhail M.

    2012-01-01

    The latest research of the proportionality of atomic weights of chemical elements made it possible to obtain 3 x 3 matrices for the calculation of information coefficients of proportionality Ip that can be used for 3D modeling of the structure of atom nucleus. The results of computer simulation show high potential of nucleus structure research for the characterization of their chemical and physical properties.

  3. Computer Simulation of Atoms Nuclei Structure Using Information Coefficients of Proportionality

    CERN Document Server

    Labushev, Mikhail M

    2012-01-01

    The latest research of the proportionality of atomic weights of chemical elements made it possible to obtain 3 x 3 matrices for the calculation of information coefficients of proportionality Ip that can be used for 3D modeling of the structure of atom nucleus. The results of computer simulation show high potential of nucleus structure research for the characterization of their chemical and physical properties.

  4. Analysis of information gain and Kolmogorov complexity for structural evaluation of cellular automata configurations

    Science.gov (United States)

    Javaheri Javid, Mohammad Ali; Blackwell, Tim; Zimmer, Robert; Majid al-Rifaie, Mohammad

    2016-04-01

    Shannon entropy fails to discriminate structurally different patterns in two-dimensional images. We have adapted information gain measure and Kolmogorov complexity to overcome the shortcomings of entropy as a measure of image structure. The measures are customised to robustly quantify the complexity of images resulting from multi-state cellular automata (CA). Experiments with a two-dimensional multi-state cellular automaton demonstrate that these measures are able to predict some of the structural characteristics, symmetry and orientation of CA generated patterns.

  5. On the Information in the Interest Rate Term Structure and Option Prices

    NARCIS (Netherlands)

    de Jong, F.; Driessen, J.; Pelsser, A.

    2004-01-01

    We examine whether the information in cap and swaption prices is consistent with realized movements of the interest rate term structure. To extract an option-implied interest rate covariance matrix from cap and swaption prices, we use Libor market models as a modelling framework. We propose a

  6. Discovering More Chemical Concepts from 3D Chemical Information Searches of Crystal Structure Databases

    Science.gov (United States)

    Rzepa, Henry S.

    2016-01-01

    Three new examples are presented illustrating three-dimensional chemical information searches of the Cambridge structure database (CSD) from which basic core concepts in organic and inorganic chemistry emerge. These include connecting the regiochemistry of aromatic electrophilic substitution with the geometrical properties of hydrogen bonding…

  7. Speeding up the solution process for the Vehicle Routing Problem with Time Windows using structural information

    DEFF Research Database (Denmark)

    Larsen, Jesper

    2002-01-01

    Two ideas for using structural information for solving the Vehicle Routing Problem with Time Windows (VRPTW) is presented. The VRPTW is a generalization of the well known capacity constrained Vehicle Routing Problem (VRP). Both techniques are based on solving the VRPTW using a Branch...

  8. Discovering More Chemical Concepts from 3D Chemical Information Searches of Crystal Structure Databases

    Science.gov (United States)

    Rzepa, Henry S.

    2016-01-01

    Three new examples are presented illustrating three-dimensional chemical information searches of the Cambridge structure database (CSD) from which basic core concepts in organic and inorganic chemistry emerge. These include connecting the regiochemistry of aromatic electrophilic substitution with the geometrical properties of hydrogen bonding…

  9. Methodology for Simulation and Analysis of Complex Adaptive Supply Network Structure and Dynamics Using Information Theory

    Directory of Open Access Journals (Sweden)

    Joshua Rodewald

    2016-10-01

    Full Text Available Supply networks existing today in many industries can behave as complex adaptive systems making them more difficult to analyze and assess. Being able to fully understand both the complex static and dynamic structures of a complex adaptive supply network (CASN are key to being able to make more informed management decisions and prioritize resources and production throughout the network. Previous efforts to model and analyze CASN have been impeded by the complex, dynamic nature of the systems. However, drawing from other complex adaptive systems sciences, information theory provides a model-free methodology removing many of those barriers, especially concerning complex network structure and dynamics. With minimal information about the network nodes, transfer entropy can be used to reverse engineer the network structure while local transfer entropy can be used to analyze the network structure’s dynamics. Both simulated and real-world networks were analyzed using this methodology. Applying the methodology to CASNs allows the practitioner to capitalize on observations from the highly multidisciplinary field of information theory which provides insights into CASN’s self-organization, emergence, stability/instability, and distributed computation. This not only provides managers with a more thorough understanding of a system’s structure and dynamics for management purposes, but also opens up research opportunities into eventual strategies to monitor and manage emergence and adaption within the environment.

  10. The Low Pitch of High-Frequency Complex Tones Relies on Temporal Fine Structure Information

    DEFF Research Database (Denmark)

    Santurette, Sébastien; Dau, Torsten

    2010-01-01

    structure (TFS) cues has been a matter of debate. It is also controversial up to which frequency TFS information remains available, and to what extent envelope cues become dominant as frequency increases. Using a pitch-matching paradigm, this study investigated whether the pitch of transposed tones...

  11. The Influence of Morphological Structure Information on the Memorization of Chinese Compound Words

    Science.gov (United States)

    Liu, Duo

    2017-01-01

    The present study investigated the influence of morphological structure information on the memorization of Chinese subordinate and coordinative compound words using the memory conjunction error paradigm. During the Study Phase, Hong Kong Chinese college students were asked to either judge the word class (Exp. 1, N = 25) or the orthographic…

  12. Use of Statistical Information for Damage Assessment of Civil Engineering Structures

    DEFF Research Database (Denmark)

    Kirkegaard, Poul Henning; Andersen, P.

    This paper considers the problem of damage assessment of civil engineering structures using statistical information. The aim of the paper is to review how researchers recently have tried to solve the problem. It is pointed out that the problem consists of not only how to use the statistical...

  13. Judgments of Information Structure in L2 French: Nativelike Performance and the Critical Period Hypothesis

    Science.gov (United States)

    Reichle, Robert V.

    2010-01-01

    Previous studies using judgments of morphosyntactic errors have shown mixed evidence for a critical period for L2 acquisition (e.g., Birdsong & Molis, Journal of Memory and Language 44: 235-249, 2001, Johnson & Newport, Cognitive Psychology 21: 60-99, 1989). This study uses anomalies in the domain of information structure, the interface…

  14. Coupled vibrations in peptides and proteins: Structural information using 2D-IR spectroscopy

    NARCIS (Netherlands)

    Huerta Viga, A.

    2014-01-01

    We describe experimental evidence of how detecting the coupling between vibrations can give access to structural information of proteins and peptides at the molecular level. We focus on the investigation of the folded and unfolded states of proteins and peptides in equilibrium. We investigate two

  15. Multimodal Image Reconstruction Using Supplementary Structural Information in Total Variation Regularization.

    Science.gov (United States)

    Kazantsev, Daniil; Lionheart, William R B; Withers, Philip J; Lee, Peter D

    2014-01-01

    In this paper, we propose an iterative reconstruction algorithm which uses available information from one dataset collected using one modality to increase the resolution and signal-to-noise ratio of one collected by another modality. The method operates on the structural information only which increases its suitability across various applications. Consequently, the main aim of this method is to exploit available supplementary data within the regularization framework. The source of primary and supplementary datasets can be acquired using complementary imaging modes where different types of information are obtained (e.g. in medical imaging: anatomical and functional). It is shown by extracting structural information from the supplementary image (direction of level sets) one can enhance the resolution of the other image. Notably, the method enhances edges that are common to both images while not suppressing features that show high contrast in the primary image alone. In our iterative algorithm we use available structural information within a modified total variation penalty term. We provide numerical experiments to show the advantages and feasibility of the proposed technique in comparison to other methods.

  16. Automated refinement of macromolecular structures at low resolution using prior information

    Science.gov (United States)

    Kovalevskiy, Oleg; Nicholls, Robert A.; Murshudov, Garib N.

    2016-01-01

    Since the ratio of the number of observations to adjustable parameters is small at low resolution, it is necessary to use complementary information for the analysis of such data. ProSMART is a program that can generate restraints for macromolecules using homologous structures, as well as generic restraints for the stabilization of secondary structures. These restraints are used by REFMAC5 to stabilize the refinement of an atomic model. However, the optimal refinement protocol varies from case to case, and it is not always obvious how to select appropriate homologous structure(s), or other sources of prior information, for restraint generation. After running extensive tests on a large data set of low-resolution models, the best-performing refinement protocols and strategies for the selection of homologous structures have been identified. These strategies and protocols have been implemented in the Low-Resolution Structure Refinement (LORESTR) pipeline. The pipeline performs auto-detection of twinning and selects the optimal scaling method and solvent parameters. LORESTR can either use user-supplied homologous structures, or run an automated BLAST search and download homologues from the PDB. The pipeline executes multiple model-refinement instances using different parameters in order to find the best protocol. Tests show that the automated pipeline improves R factors, geometry and Ramachandran statistics for 94% of the low-resolution cases from the PDB included in the test set. PMID:27710936

  17. Towards a Structurational Theory of Information Systems: a substantive case analysis

    DEFF Research Database (Denmark)

    Rose, Jeremy; Hackney, R. H

    2003-01-01

    This paper employs the analysis of an interpretive case study within a Regional Train Operating Company (RTOC) to arrive at theoretical understandings of Information Systems (IS). Giddens’ ‘structuration theory’ is developed which offers an account of structure and agency; social practices...... developing and changing over time and space. The most common application of structuration theory to the IS domain is the analysis of empirical situations using the ‘dimensions of the duality of structure’ model. The best-known attempts to theorize IS concerns using this approach have come from Orlikowski...... from whom this paper draws particular attention. Structurational concepts (system integration, time-space distanciation and routinization) as well as Giddens’ conceptualization of social change are further developed to help explain IS phenomena. Some fifty interviews were conducted at every level...

  18. Investigating Information Structure of Phishing Emails Based on Persuasive Communication Perspective

    Directory of Open Access Journals (Sweden)

    Ki Jung Lee

    2007-09-01

    Full Text Available Current approaches of  phishing filters depend on classifying messages based on textually discernable features such as IP-based URLs or domain names as those features that can be easily extracted from a given phishing message. However, in the same sense, those easily perceptible features can be easily manipulated by sophisticated phishers. Therefore, it is important that universal patterns of phishing messages should be identified for feature extraction to serve as a basis for text classification. In this paper, we demonstrate that user perception regarding phishing message can be identified in central and peripheral routes of information processing. We also present a method of formulating quantitative model that can represent persuasive information structure in phishing messages. This paper makes contribution to phishing classification research by presenting the idea of universal information structure in terms of persuasive communication theories.

  19. Prediction of bioactive compound pathways using chemical interaction and structural information.

    Science.gov (United States)

    Cheng, Shiwen; Zhu, Changming; Chu, Chen; Huang, Tao; Kong, Xiangyin; Zhu, Liu Cun

    2016-01-01

    The functional screening of compounds is an important topic in chemistry and biomedicine that can uncover the essential properties of compounds and provide information concerning their correct use. In this study, we investigated the bioactive compounds reported in Selleckchem, which were assigned to 22 pathways. A computational method was proposed to identify the pathways of the bioactive compounds. Unlike most existing methods that only consider compound structural information, the proposed method adopted both the structural and interaction information from the compounds. The total accuracy achieved by our method was 61.79% based on jackknife analysis of a dataset of 1,832 bioactive compounds. Its performance was quite good compared with that of other machine learning algorithms (with total accuracies less than 46%). Finally, some of the false positives obtained by the method were analyzed to investigate the likelihood of compounds being annotated to new pathways.

  20. Not so fast: Fast speech correlates with lower lexical and structural information.

    Science.gov (United States)

    Cohen Priva, Uriel

    2017-03-01

    Speakers dynamically adjust their speech rate throughout conversations. These adjustments have been linked to cognitive and communicative limitations: for example, speakers speak words that are contextually unexpected (and thus add more information) with slower speech rates. This raises the question whether limitations of this type vary wildly across speakers or are relatively constant. The latter predicts that across speakers (or conversations), speech rate and the amount of information content are inversely correlated: on average, speakers can either provide high information content or speak quickly, but not both. Using two corpus studies replicated across two corpora, I demonstrate that indeed, fast speech correlates with the use of less informative words and syntactic structures. Thus, while there are individual differences in overall information throughput, speakers are more similar in this aspect than differences in speech rate would suggest. The results suggest that information theoretic constraints on production operate at a higher level than was observed before and affect language throughout production, not only after words and structures are chosen. Copyright © 2016 Elsevier B.V. All rights reserved.

  1. Investigating dynamical information transfer in the brain following a TMS pulse: Insights from structural architecture.

    Science.gov (United States)

    Amico, Enrico; Van Mierlo, Pieter; Marinazzo, Daniele; Laureys, Steven

    2015-01-01

    Transcranial magnetic stimulation (TMS) has been used for more than 20 years to investigate connectivity and plasticity in the human cortex. By combining TMS with high-density electroencephalography (hd-EEG), one can stimulate any cortical area and measure the effects produced by this perturbation in the rest of the cerebral cortex. The purpose of this paper is to investigate changes of information flow in the brain after TMS from a functional and structural perspective, using multimodal modeling of source reconstructed TMS/hd-EEG recordings and DTI tractography. We prove how brain dynamics induced by TMS is constrained and driven by its structure, at different spatial and temporal scales, especially when considering cross-frequency interactions. These results shed light on the function-structure organization of the brain network at the global level, and on the huge variety of information contained in it.

  2. Structural synaptic plasticity in the hippocampus induced by spatial experience and its implications in information processing.

    Science.gov (United States)

    Carasatorre, M; Ramírez-Amaya, V; Díaz Cintra, S

    2016-10-01

    Long-lasting memory formation requires that groups of neurons processing new information develop the ability to reproduce the patterns of neural activity acquired by experience. Changes in synaptic efficiency let neurons organise to form ensembles that repeat certain activity patterns again and again. Among other changes in synaptic plasticity, structural modifications tend to be long-lasting which suggests that they underlie long-term memory. There is a large body of evidence supporting that experience promotes changes in the synaptic structure, particularly in the hippocampus. Structural changes to the hippocampus may be functionally implicated in stabilising acquired memories and encoding new information. Copyright © 2012 Sociedad Española de Neurología. Publicado por Elsevier España, S.L.U. All rights reserved.

  3. MATHEMATICAL AND INFORMATION SUPPORT FOR CALCULATION AND DESIGN OF TUBE GAS HEATERS LOCATED IN STRUCTURES

    Directory of Open Access Journals (Sweden)

    CHORNOMORETS H. Y.

    2016-02-01

    Full Text Available Raising of problem. For the design and construction of tube gas heaters in building structures to need solve the problems of analysis and synthesis of such heating system. The mathematical model of this system is consists of: mathematical model of the tube gas heater, mathematical model of heat distribution in the building structure and corresponding boundary conditions. To solve the tasks of analysis and synthesis must be appropriate mathematical and information support. Purpose. The purpose of this paper is to describe the developed mathematical and information support that solve the problems of analysis and synthesis of heating systems with gas tube heaters, located in building constructions.Conclusion. Mathematical support includes the development of algorithms and software for the numerical solution of problems analysis and synthesis heating system. Information support includes all the necessary parameters characterizing the thermal properties of materials which used in the heating system, and the parameters characterizing the heat exchange between the coolant and components of the heating system. It was developed algorithms for solving problems of analysis and synthesis heating system with tube gas heater located in structures to use evolutionary search algorithm and software. It was made experimental study and was obtained results allow to calculate the heat transfer from the gas-air mixture to the boundary surface of the building structure. This results and computation will provide full information support for solving problems of analysis and synthesis of the heating system. Was developed mathematical and software support, which allows to solve the problems of analysis and synthesis heating systems with gas tube heaters, located in building structures. Tube gas heaters located in the building structures allows with small capital expenditures to provide space heating. Is necessary to solve the problems of analysis (calculation and

  4. Two applications of information extraction to biological science journal articles: enzyme interactions and protein structures.

    Science.gov (United States)

    Humphreys, K; Demetriou, G; Gaizauskas, R

    2000-01-01

    Information extraction technology, as defined and developed through the U.S. DARPA Message Understanding Conferences (MUCs), has proved successful at extracting information primarily from newswire texts and primarily in domains concerned with human activity. In this paper we consider the application of this technology to the extraction of information from scientific journal papers in the area of molecular biology. In particular, we describe how an information extraction system designed to participate in the MUC exercises has been modified for two bioinformatics applications: EMPathIE, concerned with enzyme and metabolic pathways; and PASTA, concerned with protein structure. Progress to date provides convincing grounds for believing that IE techniques will deliver novel and effective ways for scientists to make use of the core literature which defines their disciplines.

  5. Ab initio protein folding simulations using atomic burials as informational intermediates between sequence and structure.

    Science.gov (United States)

    van der Linden, Marx Gomes; Ferreira, Diogo César; de Oliveira, Leandro Cristante; Onuchic, José N; de Araújo, Antônio F Pereira

    2014-07-01

    The three-dimensional structure of proteins is determined by their linear amino acid sequences but decipherment of the underlying protein folding code has remained elusive. Recent studies have suggested that burials, as expressed by atomic distances to the molecular center, are sufficiently informative for structural determination while potentially obtainable from sequences. Here we provide direct evidence for this distinctive role of burials in the folding code, demonstrating that burial propensities estimated from local sequence can indeed be used to fold globular proteins in ab initio simulations. We have used a statistical scheme based on a Hidden Markov Model (HMM) to classify all heavy atoms of a protein into a small number of burial atomic types depending on sequence context. Molecular dynamics simulations were then performed with a potential that forces all atoms of each type towards their predicted burial level, while simple geometric constraints were imposed on covalent structure and hydrogen bond formation. The correct folded conformation was obtained and distinguished in simulations that started from extended chains for a selection of structures comprising all three folding classes and high burial prediction quality. These results demonstrate that atomic burials can act as informational intermediates between sequence and structure, providing a new conceptual framework for improving structural prediction and understanding the fundamentals of protein folding.

  6. Information

    CERN Document Server

    Ritchie, L David

    1991-01-01

    This volume thoroughly covers the sub-field of information, and is one of the first in a series which synthesizes the research literature on major concepts in the field of communication. Each concise volume includes a research definition (concept explication) and presents a state-of-the-art analysis of theory and empirical findings related to the concept. After defining the word `information', the author contrasts non-linear and reflexive ideas about human communication with linear perspectives. Information is equated with uncertainty. The result presents a pattern for the process of conceptua

  7. SOCIAL NETWORK ANALYSIS FOR THE MEASUREMENT OF FORMAL AND INFORMAL STRUCTURES

    Directory of Open Access Journals (Sweden)

    Siomara Maria Pierangeli Pascotto,

    2013-03-01

    Full Text Available A discussion around the application of the social network analysis methodology has being helped to understand the social dynamic operation of organizations, including governments, which are subject to different management structures that have a high degree of functional hierarchy. This study was developed in a Federal School Institution in Sao Paulo State – Brazil searching to identify the link developed between Institution administrative support staff members and their social networks. The research objective is to establish a comparison between the link data facts with Social Networks Theories which says that the more ties (contacts exist in an informal group, the more the network promotes an open environment for exchanging knowledge and information. The research looked forward to identify how do the social networks are developed, how common objectives and subjects turns people closely connected, how do the focal points and main contacts emerge from this community and what are their influences in the rest of the group. It was applied social network measurement methodologies, combined with qualitative instrument analysis. As a conclusion, was found that the informal structure has influence over the formal structure providing an environment for exchanging knowledge and information, pointing out that some characters are actually responsible for the dynamic of networks, occupying driver and strategic position that gives them recognition as such by the other agents in the net.

  8. Recursively partitioned mixture model clustering of DNA methylation data using biologically informed correlation structures.

    Science.gov (United States)

    Koestler, Devin C; Christensen, Brock C; Marsit, Carmen J; Kelsey, Karl T; Houseman, E Andres

    2013-03-05

    DNA methylation is a well-recognized epigenetic mechanism that has been the subject of a growing body of literature typically focused on the identification and study of profiles of DNA methylation and their association with human diseases and exposures. In recent years, a number of unsupervised clustering algorithms, both parametric and non-parametric, have been proposed for clustering large-scale DNA methylation data. However, most of these approaches do not incorporate known biological relationships of measured features, and in some cases, rely on unrealistic assumptions regarding the nature of DNA methylation. Here, we propose a modified version of a recursively partitioned mixture model (RPMM) that integrates information related to the proximity of CpG loci within the genome to inform correlation structures from which subsequent clustering analysis is based. Using simulations and four methylation data sets, we demonstrate that integrating biologically informative correlation structures within RPMM resulted in improved goodness-of-fit, clustering consistency, and the ability to detect biologically meaningful clusters compared to methods which ignore such correlation. Integrating biologically-informed correlation structures to enhance modeling techniques is motivated by the rapid increase in resolution of DNA methylation microarrays and the increasing understanding of the biology of this epigenetic mechanism.

  9. CYP1B1: a unique gene with unique characteristics.

    Science.gov (United States)

    Faiq, Muneeb A; Dada, Rima; Sharma, Reetika; Saluja, Daman; Dada, Tanuj

    2014-01-01

    CYP1B1, a recently described dioxin inducible oxidoreductase, is a member of the cytochrome P450 superfamily involved in the metabolism of estradiol, retinol, benzo[a]pyrene, tamoxifen, melatonin, sterols etc. It plays important roles in numerous physiological processes and is expressed at mRNA level in many tissues and anatomical compartments. CYP1B1 has been implicated in scores of disorders. Analyses of the recent studies suggest that CYP1B1 can serve as a universal/ideal cancer marker and a candidate gene for predictive diagnosis. There is plethora of literature available about certain aspects of CYP1B1 that have not been interpreted, discussed and philosophized upon. The present analysis examines CYP1B1 as a peculiar gene with certain distinctive characteristics like the uniqueness in its chromosomal location, gene structure and organization, involvement in developmentally important disorders, tissue specific, not only expression, but splicing, potential as a universal cancer marker due to its involvement in key aspects of cellular metabolism, use in diagnosis and predictive diagnosis of various diseases and the importance and function of CYP1B1 mRNA in addition to the regular translation. Also CYP1B1 is very difficult to express in heterologous expression systems, thereby, halting its functional studies. Here we review and analyze these exceptional and startling characteristics of CYP1B1 with inputs from our own experiences in order to get a better insight into its molecular biology in health and disease. This may help to further understand the etiopathomechanistic aspects of CYP1B1 mediated diseases paving way for better research strategies and improved clinical management.

  10. Cognitive Structure of Climate Information System Actors:Using Causal Mapping Approach

    Directory of Open Access Journals (Sweden)

    Maryam Sharifzadeh

    2012-01-01

    Full Text Available Promoting sustainability, productivity, efficiency, and development of agricultural sector are the functions of utilization of appropriate information in terms of agricultural climate information system (ACIS. In this regard, the main question is that, to what extent does the ACIS lead to or provide the necessary context for agricultural development? This research aimed to employ causal mapping approach to investigate cognitive structure of human actors in a climate information system. This explorative qualitative research used case study methodology. This paper is an examination and reflection upon analysis of qualitative data reports, with particular attention to the process of interactively elicited causal maps based on focus group interviews. An exploratory coding approach was used to identify concepts that emerged from the interview transcripts. The relevant knowledge is gathered through the tacit understandings of climate information producers (2 groups, extensionists (6 groups, and users (7 groups in Fars province to reach to the point of redundancy. Investigating causal maps revealed that, actors perceived climate information system challenges as economic, information processing, socio-political, organizational, and technical challenges. The study provided some suggestions to reach to a responsive short term and sustainable long term climate information system in Fars province.

  11. Geometrical analysis of Cys-Cys bridges in proteins and their prediction from incomplete structural information

    Science.gov (United States)

    Goldblum, A.; Rein, R.

    1987-01-01

    Analysis of C-alpha atom positions from cysteines involved in disulphide bridges in protein crystals shows that their geometric characteristics are unique with respect to other Cys-Cys, non-bridging pairs. They may be used for predicting disulphide connections in incompletely determined protein structures, such as low resolution crystallography or theoretical folding experiments. The basic unit for analysis and prediction is the 3 x 3 distance matrix for Cx positions of residues (i - 1), Cys(i), (i +1) with (j - 1), Cys(j), (j + 1). In each of its columns, row and diagonal vector--outer distances are larger than the central distance. This analysis is compared with some analytical models.

  12. Beyond the Twilight Zone: automated prediction of structural properties of proteins by recursive neural networks and remote homology information.

    Science.gov (United States)

    Mooney, Catherine; Pollastri, Gianluca

    2009-10-01

    The prediction of 1D structural properties of proteins is an important step toward the prediction of protein structure and function, not only in the ab initio case but also when homology information to known structures is available. Despite this the vast majority of 1D predictors do not incorporate homology information into the prediction process. We develop a novel structural alignment method, SAMD, which we use to build alignments of putative remote homologues that we compress into templates of structural frequency profiles. We use these templates as additional input to ensembles of recursive neural networks, which we specialise for the prediction of query sequences that show only remote homology to any Protein Data Bank structure. We predict four 1D structural properties - secondary structure, relative solvent accessibility, backbone structural motifs, and contact density. Secondary structure prediction accuracy, tested by five-fold cross-validation on a large set of proteins allowing less than 25% sequence identity between training and test set and query sequences and templates, exceeds 82%, outperforming its ab initio counterpart, other state-of-the-art secondary structure predictors (Jpred 3 and PSIPRED) and two other systems based on PSI-BLAST and COMPASS templates. We show that structural information from homologues improves prediction accuracy well beyond the Twilight Zone of sequence similarity, even below 5% sequence identity, for all four structural properties. Significant improvement over the extraction of structural information directly from PDB templates suggests that the combination of sequence and template information is more informative than templates alone.

  13. A Structural Approach to Performance Monitoring of Waste Sites: Obtaining Actionable Information

    Science.gov (United States)

    Mattson, E. D.; Versteeg, R.; Ankeny, M.; Richardson, A.

    2005-05-01

    Both government and non-government agencies are faced with the challenge of long-term monitoring of waste sites and landfills. Such monitoring should provide actionable information on how these sites are evolving, including (but not limited to) information on the success of remedial treatment methods (either active or passive), compliance with regulatory standards, and evolution of system behavior associated with these sites. Current monitoring efforts suffer from the lack of integration between data collection, data management, information extraction and information use. An alternative to such efforts is the use of a structural approach to performance monitoring developed at Idaho National Laboratory (INL). This approach has the following characteristics (1) tight integration between monitoring objectives and data collection efforts (2) well structured storage of all relevant monitoring data (3) establishment of transparent, reproducible procedures for translation of data to information (including coupling of data to models) (4) development of a web based interface to the monitoring system, providing easy access to data and results by multiple stakeholders. We will discuss several examples of the implementation of the INL monitoring system, including an EPA superfund site and several landfill sites.

  14. Brain white matter structure and information processing speed in healthy older age.

    Science.gov (United States)

    Kuznetsova, Ksenia A; Maniega, Susana Muñoz; Ritchie, Stuart J; Cox, Simon R; Storkey, Amos J; Starr, John M; Wardlaw, Joanna M; Deary, Ian J; Bastin, Mark E

    2016-07-01

    Cognitive decline, especially the slowing of information processing speed, is associated with normal ageing. This decline may be due to brain cortico-cortical disconnection caused by age-related white matter deterioration. We present results from a large, narrow age range cohort of generally healthy, community-dwelling subjects in their seventies who also had their cognitive ability tested in youth (age 11 years). We investigate associations between older age brain white matter structure, several measures of information processing speed and childhood cognitive ability in 581 subjects. Analysis of diffusion tensor MRI data using Tract-based Spatial Statistics (TBSS) showed that all measures of information processing speed, as well as a general speed factor composed from these tests (g speed), were significantly associated with fractional anisotropy (FA) across the white matter skeleton rather than in specific tracts. Cognitive ability measured at age 11 years was not associated with older age white matter FA, except for the g speed-independent components of several individual processing speed tests. These results indicate that quicker and more efficient information processing requires global connectivity in older age, and that associations between white matter FA and information processing speed (both individual test scores and g speed), unlike some other aspects of later life brain structure, are generally not accounted for by cognitive ability measured in youth.

  15. Systematizing Web Search through a Meta-Cognitive, Systems-Based, Information Structuring Model (McSIS)

    Science.gov (United States)

    Abuhamdieh, Ayman H.; Harder, Joseph T.

    2015-01-01

    This paper proposes a meta-cognitive, systems-based, information structuring model (McSIS) to systematize online information search behavior based on literature review of information-seeking models. The General Systems Theory's (GST) prepositions serve as its framework. Factors influencing information-seekers, such as the individual learning…

  16. Mutual information reveals multiple structural relaxation mechanisms in a model glass former.

    Science.gov (United States)

    Dunleavy, Andrew J; Wiesner, Karoline; Yamamoto, Ryoichi; Royall, C Patrick

    2015-01-22

    Among the key challenges to our understanding of solidification in the glass transition is that it is accompanied by little apparent change in structure. Recently, geometric motifs have been identified in glassy liquids, but a causal link between these motifs and solidification remains elusive. One 'smoking gun' for such a link would be identical scaling of structural and dynamic lengthscales on approaching the glass transition, but this is highly controversial. Here we introduce an information theoretic approach to determine correlations in displacement for particle relaxation encoded in the initial configuration of a glass-forming liquid. We uncover two populations of particles, one inclined to relax quickly, the other slowly. Each population is correlated with local density and geometric motifs. Our analysis further reveals a dynamic lengthscale similar to that associated with structural properties, which may resolve the discrepancy between structural and dynamic lengthscales.

  17. Structural elucidation of the nonclassical secondary cell wall polysaccharide from Bacillus cereus ATCC 10987. Comparison with the polysaccharides from Bacillus anthracis and B. cereus type strain ATCC 14579 reveals both unique and common structural features.

    Science.gov (United States)

    Leoff, Christine; Choudhury, Biswa; Saile, Elke; Quinn, Conrad P; Carlson, Russell W; Kannenberg, Elmar L

    2008-10-31

    Nonclassical secondary cell wall polysaccharides constitute a major cell wall structure in the Bacillus cereus group of bacteria. The structure of the secondary cell wall polysaccharide from Bacillus cereus ATCC 10987, a strain that is closely related to Bacillus anthracis, was determined. This polysaccharide was released from the cell wall with aqueous hydrogen fluoride (HF) and purified by gel filtration chromatography. The purified polysaccharide, HF-PS, was characterized by glycosyl composition and linkage analyses, mass spectrometry, and one- and two-dimensional NMR analysis. The results showed that the B. cereus ATCC 10987 HF-PS has a repeating oligosaccharide consisting of a -->6)-alpha-GalNAc-(1-->4)-beta-ManNAc-(1-->4)-beta-GlcNAc-(1--> trisaccharide that is substituted with beta-Gal at O3 of the alpha-GalNAc residue and nonstoichiometrically acetylated at O3 of the N-acetylmannosamine (ManNAc) residue. Comparison of this structure with that of the B. anthracis HF-PS and with structural data obtained for the HF-PS from B. cereus type strain ATCC 14579 revealed that each HF-PS had the same general structural theme consisting of three HexNAc and one Hex residues. A common structural feature in the HF-PSs from B. cereus ATCC 10987 and B. anthracis was the presence of a repeating unit consisting of a HexNAc(3) trisaccharide backbone in which two of the three HexNAc residues are GlcNAc and ManNAc and the third can be either GlcNAc or GalNAc. The implications of these results with regard to the possible functions of the HF-PSs are discussed.

  18. Tracing sub-structure in the European American population with PCA-informative markers.

    Directory of Open Access Journals (Sweden)

    Peristera Paschou

    2008-07-01

    Full Text Available Genetic structure in the European American population reflects waves of migration and recent gene flow among different populations. This complex structure can introduce bias in genetic association studies. Using Principal Components Analysis (PCA, we analyze the structure of two independent European American datasets (1,521 individuals-307,315 autosomal SNPs. Individual variation lies across a continuum with some individuals showing high degrees of admixture with non-European populations, as demonstrated through joint analysis with HapMap data. The CEPH Europeans only represent a small fraction of the variation encountered in the larger European American datasets we studied. We interpret the first eigenvector of this data as correlated with ancestry, and we apply an algorithm that we have previously described to select PCA-informative markers (PCAIMs that can reproduce this structure. Importantly, we develop a novel method that can remove redundancy from the selected SNP panels and show that we can effectively remove correlated markers, thus increasing genotyping savings. Only 150-200 PCAIMs suffice to accurately predict fine structure in European American datasets, as identified by PCA. Simulating association studies, we couple our method with a PCA-based stratification correction tool and demonstrate that a small number of PCAIMs can efficiently remove false correlations with almost no loss in power. The structure informative SNPs that we propose are an important resource for genetic association studies of European Americans. Furthermore, our redundancy removal algorithm can be applied on sets of ancestry informative markers selected with any method in order to select the most uncorrelated SNPs, and significantly decreases genotyping costs.

  19. Resistance and Security Index of Networks: Structural Information Perspective of Network Security

    Science.gov (United States)

    Li, Angsheng; Hu, Qifu; Liu, Jun; Pan, Yicheng

    2016-06-01

    Recently, Li and Pan defined the metric of the K-dimensional structure entropy of a structured noisy dataset G to be the information that controls the formation of the K-dimensional structure of G that is evolved by the rules, order and laws of G, excluding the random variations that occur in G. Here, we propose the notion of resistance of networks based on the one- and two-dimensional structural information of graphs. Given a graph G, we define the resistance of G, written , as the greatest overall number of bits required to determine the code of the module that is accessible via random walks with stationary distribution in G, from which the random walks cannot escape. We show that the resistance of networks follows the resistance law of networks, that is, for a network G, the resistance of G is , where and are the one- and two-dimensional structure entropies of G, respectively. Based on the resistance law, we define the security index of a network G to be the normalised resistance of G, that is, . We show that the resistance and security index are both well-defined measures for the security of the networks.

  20. Doing the Organizational Tango: Symbiotic Relationship between Formal and Informal Organizational Structures for an Agile Organization

    Directory of Open Access Journals (Sweden)

    Irena Malgorzata Ali

    2016-04-01

    Full Text Available This paper reports on research with a broad objective to examine the relationship between two organizational entities, the formally structured organization and informal organizational structures, in a changing operational environment, more specifically during military deployments. The paper draws on organizational and complexity paradigms; based on empirical evidence obtained through qualitative techniques, it describes mechanisms that enable a symbiotic relationship between these two organizational structures in a complex operational landscape. Substantive findings provide insights into the dynamics of the interactions between these structures and illuminate the relationship between three enabling factors – accountability, responsible autonomy, and command and control arrangements – that need to be considered to fully exploit the strengths inherent in both formal and informal structures. Based on these findings, a model for enhancement of organizational agility in response to changes in a complex operational environment is described. The model is predicated on feedback and mutual adjustment of the organization, institution and individual through sensemaking; it illustrates the dynamic nature of interactions that are required for such a response.

  1. Resistance and Security Index of Networks: Structural Information Perspective of Network Security.

    Science.gov (United States)

    Li, Angsheng; Hu, Qifu; Liu, Jun; Pan, Yicheng

    2016-06-03

    Recently, Li and Pan defined the metric of the K-dimensional structure entropy of a structured noisy dataset G to be the information that controls the formation of the K-dimensional structure of G that is evolved by the rules, order and laws of G, excluding the random variations that occur in G. Here, we propose the notion of resistance of networks based on the one- and two-dimensional structural information of graphs. Given a graph G, we define the resistance of G, written , as the greatest overall number of bits required to determine the code of the module that is accessible via random walks with stationary distribution in G, from which the random walks cannot escape. We show that the resistance of networks follows the resistance law of networks, that is, for a network G, the resistance of G is , where and are the one- and two-dimensional structure entropies of G, respectively. Based on the resistance law, we define the security index of a network G to be the normalised resistance of G, that is, . We show that the resistance and security index are both well-defined measures for the security of the networks.

  2. An approach to development of an information geomechanical structural model of the Kuznetsk Coal Basin

    Energy Technology Data Exchange (ETDEWEB)

    Oparin, V.N.; Potapov, V.P.; Yushkin, V.F.; Kiril' tseva, N.A.; Izotov, A.S. [Russian Academy of Science, Novosibirsk (Russian Federation). Inst. of Mining

    2006-05-15

    The geographic information system designed at the Institute of Coal and Coal Chemistry for the Kuznetsk Coal Basin and the non-linear geomechanics researches undertaken at the Institute of Mining has served the basis for analyzing the hierarchical structure of geological faults in the Anzherskiy economic district (Kemerovo Region). The analysis is performed by a new canonical scale for structural-hierarchical representations with base root 2, where A and x are the normalized functionally related values. The recommendations are given on how to utilize the geoinformation system of the Kuznetsk Coal Basin in order to obtain a graphical-analytical representation and a system analysis of experimental geomechanical data.

  3. Algorithm-structured computer arrays and networks architectures and processes for images, percepts, models, information

    CERN Document Server

    Uhr, Leonard

    1984-01-01

    Computer Science and Applied Mathematics: Algorithm-Structured Computer Arrays and Networks: Architectures and Processes for Images, Percepts, Models, Information examines the parallel-array, pipeline, and other network multi-computers.This book describes and explores arrays and networks, those built, being designed, or proposed. The problems of developing higher-level languages for systems and designing algorithm, program, data flow, and computer structure are also discussed. This text likewise describes several sequences of successively more general attempts to combine the power of arrays wi

  4. Structures data collection for The National Map using volunteered geographic information

    Science.gov (United States)

    Poore, Barbara S.; Wolf, Eric B.; Korris, Erin M.; Walter, Jennifer L.; Matthews, Greg D.

    2012-01-01

    The U.S. Geological Survey (USGS) has historically sponsored volunteered data collection projects to enhance its topographic paper and digital map products. This report describes one phase of an ongoing project to encourage volunteers to contribute data to The National Map using online editing tools. The USGS recruited students studying geographic information systems (GIS) at the University of Colorado Denver and the University of Denver in the spring of 2011 to add data on structures - manmade features such as schools, hospitals, and libraries - to four quadrangles covering metropolitan Denver. The USGS customized a version of the online Potlatch editor created by the OpenStreetMap project and populated it with 30 structure types drawn from the Geographic Names Information System (GNIS), a USGS database of geographic features. The students corrected the location and attributes of these points and added information on structures that were missing. There were two rounds of quality control. Student volunteers reviewed each point, and an in-house review of each point by the USGS followed. Nine-hundred and thirty-eight structure points were initially downloaded from the USGS database. Editing and quality control resulted in 1,214 structure points that were subsequently added to The National Map. A post-project analysis of the data shows that after student edit and peer review, 92 percent of the points contributed by volunteers met National Map Accuracy Standards for horizontal accuracy. Lessons from this project will be applied to later phases. These include: simplifying editing tasks and the user interfaces, stressing to volunteers the importance of adding structures that are missing, and emphasizing the importance of conforming to editorial guidelines for formatting names and addresses of structures. The next phase of the project will encompass the entire State of Colorado and will allow any citizen to contribute structures data. Volunteers will benefit from this

  5. Feature selection and the information content of Thematic Mapper simulator data for forest structural assessment

    Science.gov (United States)

    Spanner, M. A.; Brass, J. A.; Peterson, D. L.

    1984-01-01

    An assessment is made of the information content of Thematic Mapper Simulator (TMS) data for the case of a forested region, in order to determine the sensitivity of such data to forest crown closure and tree size class. Principal components analysis and Monte Carlo simulation indicated that channels 4, 7, 5 and 3 were optimal for four-channel forest structure analysis. As the number of channels supplied to the Monte Carlo feature selection routine increased, classification accuracy increased. The greatest sensitivity to the forest structural parameters, which included succession within clearcuts as well as crown closure and size class, was obtained from the 7-channel TMS data.

  6. Amygdalar enlargement associated with unique perception.

    Science.gov (United States)

    Asari, Tomoki; Konishi, Seiki; Jimura, Koji; Chikazoe, Junichi; Nakamura, Noriko; Miyashita, Yasushi

    2010-01-01

    Interference by amygdalar activity in perceptual processes has been reported in many previous studies. Consistent with these reports, previous clinical studies have shown amygdalar volume change in multiple types of psychotic disease presenting with unusual perception. However, the relationship between variation in amygdalar volume in the normal population and the tendency toward unusual or unique perception has never been investigated. To address this issue, we defined an index to represent the tendency toward unique perception using ambiguous stimuli: subjects were instructed to state what the figures looked like to them, and "unique responses" were defined depending on the appearance frequency of the same responses in an age- and gender-matched control group. The index was defined as the ratio of unique responses to total responses per subject. We obtained structural brain images and values of the index from sixty-eight normal subjects. Voxel-based morphometry analyses revealed a positive correlation between amygdalar volume and the index. Since previous reports have indicated that unique responses were observed at higher frequency in the artistic population than in the nonartistic normal population, this positive correlation suggests that amygdalar enlargement in the normal population might be related to creative mental activity.

  7. Information Theory and Voting Based Consensus Clustering for Combining Multiple Clusterings of Chemical Structures.

    Science.gov (United States)

    Saeed, Faisal; Salim, Naomie; Abdo, Ammar

    2013-07-01

    Many consensus clustering methods have been applied in different areas such as pattern recognition, machine learning, information theory and bioinformatics. However, few methods have been used for chemical compounds clustering. In this paper, an information theory and voting based algorithm (Adaptive Cumulative Voting-based Aggregation Algorithm A-CVAA) was examined for combining multiple clusterings of chemical structures. The effectiveness of clusterings was evaluated based on the ability of the clustering method to separate active from inactive molecules in each cluster, and the results were compared with Ward's method. The chemical dataset MDL Drug Data Report (MDDR) and the Maximum Unbiased Validation (MUV) dataset were used. Experiments suggest that the adaptive cumulative voting-based consensus method can improve the effectiveness of combining multiple clusterings of chemical structures.

  8. Structural modelling and control design under incomplete parameter information: The maximum-entropy approach

    Science.gov (United States)

    Hyland, D. C.

    1983-01-01

    A stochastic structural control model is described. In contrast to the customary deterministic model, the stochastic minimum data/maximum entropy model directly incorporates the least possible a priori parameter information. The approach is to adopt this model as the basic design model, thus incorporating the effects of parameter uncertainty at a fundamental level, and design mean-square optimal controls (that is, choose the control law to minimize the average of a quadratic performance index over the parameter ensemble).

  9. Use of Coatings on Hydraulic Steel Structures: Part 2-Supplemental Information

    Science.gov (United States)

    2016-09-01

    are typically applied to structures, are typically regulated at the state level and may have different VOC limits. In some situations, high- solvent ... Industrial maintenance coatings have a federal limit of 450 g/l, but state and local air-quality dis- tricts may have more stringent regulations than the...and coating materials. The handbook contains information on the composition of coat- ings, their mechanisms of curing, environmental and safety

  10. Interaction of negation with tense, modality and information structure in Standard Arabic

    Directory of Open Access Journals (Sweden)

    Nasser Al-Horais

    2013-06-01

    Full Text Available The aim of this paper is to consider the interaction of tense, mood and focus with negation in Standard Arabic. This interaction can be observed via marking the tense and mood of the sentence, or via selecting a particular type of tense, or being associated with Information Structure. Building on this fact, the current paper provides a unified analysis, in which negation in Arabic can be accounted for without a NegP projection.

  11. Statistical Inference on Memory Structure of Processes and Its Applications to Information Theory

    Science.gov (United States)

    2016-05-12

    SECURITY CLASSIFICATION OF: Three areas were investigated. First, new memory models of discrete-time and finitely-valued information sources are...computational and storage complexities are proved. Second, a statistical method is developed to estimate the memory depth of discrete-time and continuously...Distribution Unlimited UU UU UU UU 12-05-2016 15-May-2014 14-Feb-2015 Final Report: Statistical Inference on Memory Structure of Processes and Its Applications

  12. RaptorX: exploiting structure information for protein alignment by statistical inference

    OpenAIRE

    Peng, Jian; Xu, Jinbo

    2011-01-01

    This paper presents RaptorX, a statistical method for template-based protein modeling that improves alignment accuracy by exploiting structural information in a single or multiple templates. RaptorX consists of three major components: single-template threading, alignment quality prediction and multiple-template threading. This paper summarizes the methods employed by RaptorX and presents its CASP9 result analysis, aiming to identify major bottlenecks with RaptorX and template-based modeling a...

  13. Triangle network motifs predict complexes by complementing high-error interactomes with structural information

    Directory of Open Access Journals (Sweden)

    Labudde Dirk

    2009-06-01

    Full Text Available Abstract Background A lot of high-throughput studies produce protein-protein interaction networks (PPINs with many errors and missing information. Even for genome-wide approaches, there is often a low overlap between PPINs produced by different studies. Second-level neighbors separated by two protein-protein interactions (PPIs were previously used for predicting protein function and finding complexes in high-error PPINs. We retrieve second level neighbors in PPINs, and complement these with structural domain-domain interactions (SDDIs representing binding evidence on proteins, forming PPI-SDDI-PPI triangles. Results We find low overlap between PPINs, SDDIs and known complexes, all well below 10%. We evaluate the overlap of PPI-SDDI-PPI triangles with known complexes from Munich Information center for Protein Sequences (MIPS. PPI-SDDI-PPI triangles have ~20 times higher overlap with MIPS complexes than using second-level neighbors in PPINs without SDDIs. The biological interpretation for triangles is that a SDDI causes two proteins to be observed with common interaction partners in high-throughput experiments. The relatively few SDDIs overlapping with PPINs are part of highly connected SDDI components, and are more likely to be detected in experimental studies. We demonstrate the utility of PPI-SDDI-PPI triangles by reconstructing myosin-actin processes in the nucleus, cytoplasm, and cytoskeleton, which were not obvious in the original PPIN. Using other complementary datatypes in place of SDDIs to form triangles, such as PubMed co-occurrences or threading information, results in a similar ability to find protein complexes. Conclusion Given high-error PPINs with missing information, triangles of mixed datatypes are a promising direction for finding protein complexes. Integrating PPINs with SDDIs improves finding complexes. Structural SDDIs partially explain the high functional similarity of second-level neighbors in PPINs. We estimate that

  14. Uniqueness property for quasiharmonic functions

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    Sevdiyor A. Imomkulov

    2014-10-01

    Full Text Available In this paper we consider a class of continuous functions, called quasiaharmonic functions, admitting best approximations by harmonic polynomials. In this class we prove a uniqueness theorem by analogy with the analytic functions.

  15. Knowledge structure of form specification of the next generation GPS information system

    Science.gov (United States)

    Lu, Wenlong; Liu, Xiaojun; Jiang, Xiangqian; Xu, Zhengao

    2006-11-01

    The next generation GPS (Dimensional and Geometrical Product Specification and Verification) is a very important basic technique standard system for manufacturing that aims to enrich the GPS specification language to express the functional requirements of the products, thus to reduce the correlation uncertainty and specification uncertainty, etc. On one facet, it seems that the indication may be richer, precise, and therefore more verbose, and thus probably to take longer time for design. And on another facet, the designer can't use the standards effectively even if he has a well comprehension of them. To resolve the problem, this paper proposes a GPS information system, which will further help to reduce the development cycle and the cost of the products greatly. Acquisition and representation of knowledge are one of the most difficult steps on successfully developing of the knowledge base of this GPS information system, because it affects the development efficiency, speed, and maintenance of the system as data structure in ordinary programming. For knowledge modeling of this GPS information system, a new modeling mechanism based on category theory is put forward in this paper. The knowledge model based on category theory is called Geometrical Knowledge Model (GKM). This information system is built up on the category theory due to its formality and high level of abstraction. Finally, the basic knowledge structure of the next generation GPS roundness specification is given in the paper.

  16. Beyond Categories: A Structural Analysis of the Social Representations of Information Users' Collective Perceptions on 'Relevance'

    Directory of Open Access Journals (Sweden)

    Ju, Boryung

    2013-06-01

    Full Text Available Relevance has a long history of scholarly investigation and discussion in information science. One of its notable concepts is that of 'user-based' relevance. The purpose of this study is to examine how users construct their perspective on the concept of relevance; to analyze what the constituent elements (facets of relevance are, in terms of core-periphery status; and to compare the difference of constructions of two groups of users (information users vs. information professionals as applied with a social representations theory perspective. Data were collected from 244 information users and 123 information professionals through use of a free word association method. Three methods were employed to analyze data: (1 content analysis was used to elicit 26 categories (facets of the concept of relevance; (2 structural analysis of social representations was used to determine the core-periphery status of those facets in terms of coreness, sum of similarity, and weighted frequency; and, (3 maximum tree analysis was used to present and compare the differences between the two groups. Elicited categories in this study overlap with the ones from previous relevance studies, while the findings of a core-periphery analysis show that Topicality, User-needs, Reliability/Credibility, and Importance are configured as core concepts for the information user group, while Topicality, User-needs, Reliability/Credibility, and Currency are core concepts for the information professional group. Differences between the social representations of relevance revealed that Topicality was similar to User-needs and to Importance. Author is closely related to Title while Reliability/Credibility is linked with Currency. Easiness/Clarity is similar to Accuracy. Overall, information users and professionals function with a similar social collective of shared meanings for the concept of relevance. The overall findings identify the core and periphery concepts of relevance and their

  17. Research and design of the structure of information support of road transport

    Directory of Open Access Journals (Sweden)

    V. G. Kozlov

    2016-01-01

    Full Text Available The main issue is to study the interaction between the system of road transport and security of its information systems. The mechanism of this interaction is studied only on the basis of studies of the learning process. These two interacting systems through training react to each other. Due to the strong correlation between these two systems offer the development of the basics of management information support to carry out complex, without violating the integrity of the systems. As the methods of research used methods of system analysis and probability theory. The criteria for the study of the interaction of systems: full-scale technological and economic indicators. By the technological parameters include: completeness of use of the system (load, and performance of information security; to full-scale - the cost of labor, energy, materials; to the economic - the cost, payback, profit, profit. The stages of the development of the structure of information support: the definition of objectives; study of the problems and the choice of solution to the problem; agreed solutions (thematic plan; approval of decisions; Management and Implementation; verification of the effectiveness of decisions. Established shortcomings in the existing system of information support of decentralization processes interrelated technical planning; territorial, institutional and administrative divisions of organizations taking interdependent solutions; the lack of control most of the organizations operating information support for road transport; incomplete information of the absolute majority of publishing houses in the needs of motorists; duplication of the work of many publishers. There are two mechanisms of control information management system. Control enhances performance management system, improves the output characteristics of the system.

  18. Involvement of cortical midline structures in the processing of autobiographical information

    Science.gov (United States)

    Kaplan, Jonas; Damasio, Hanna; Damasio, Antonio

    2014-01-01

    The term autobiographical self has been used to refer to a mental state that permits reflection on self-identity and personality and the answer to related questions (Damasio, 1998). It requires the retrieval and integrated assembly of memories of facts and events that define an individual’s biography. The neural mechanisms behind this state have not been fully elucidated, but it has been suggested that cortical midline structures (CMSs) are critically involved in processing self-related information. To date, the investigation of the involvement of CMSs in autobiographical-self processes has largely focused on the comparison between self and other in relation to one domain of information, personality traits, and has yielded conflicting results. Here, we investigated how activity in CMSs varies with (1) the target of the information (self versus an acquaintance), (2) the domain of information (personality traits versus facts), and (3) differences across individuals regarding how descriptive and how important/relevant the information targeted by the questions was, and regarding the amount of memory retrieved in order to answer the questions. We used an fMRI block-design in which 19 participants answered questions about traits and biographic facts, in relation to themselves and a distant acquaintance. In addition, the participants rated the descriptiveness and importance of the information targeted by the questions, and estimated the amount of memory retrieved to answer the questions. Our results showed that CMSs were active for both facts and traits and for both self and other, and that the level of activity in the posteromedial cortices was generally higher for other than for self. Moreover, the activity in CMSs also varied with the amount of memory retrieved to answer the questions and with descriptiveness and importance of the information. These findings suggest that involvement of CMSs during the evaluation of information is not specific for self, and depends on

  19. Structural Confirmation of a Unique Carotenoid Lactoside, P457, in Symbiodinium sp. Strain nbrc 104787 Isolated from a Sea Anemone and its Distribution in Dinoflagellates and Various Marine Organisms.

    Science.gov (United States)

    Wakahama, Takahiro; Laza-Martínez, Aitor; Bin Haji Mohd Taha, Ahmad Iskandar; Okuyama, Hidetoshi; Yoshida, Kiyohito; Kogame, Kazuhiro; Awai, Koichiro; Kawachi, Masanobu; Maoka, Takashi; Takaichi, Shinichi

    2012-12-01

    The molecular structure of the carotenoid lactoside P457, (3S,5R,6R,3'S,5'R,6'S)-13'-cis-5,6-epoxy-3',5'-dihydroxy-3-(β-d-galactosyl-(1→4)-β-d-glucosyl)oxy-6',7'-didehydro-5,6,7,8,5',6'-hexahydro-β,β-caroten-20-al, was confirmed by spectroscopic methods using Symbiodinium sp. strain NBRC 104787 cells isolated from a sea anemone. Among various algae, cyanobacteria, land plants, and marine invertebrates, the distribution of this unique diglycosyl carotenoid was restricted to free-living peridinin-containing dinoflagellates and marine invertebrates that harbor peridinin-containing zooxanthellae. Neoxanthin appeared to be a common precursor for biosynthesis of peridinin and P457, although neoxanthin was not found in peridinin-containing dinoflagellates. Fucoxanthin-containing dinoflagellates did not possess peridinin or P457; green dinoflagellates, which contain chlorophyll a and b, did not contain peridinin, fucoxanthin, or P457; and no unicellular algae containing both peridinin and P457, other than peridinin-containing dinoflagellates, have been observed. Therefore, the biosynthetic pathways for peridinin and P457 may have been coestablished during the evolution of dinoflagellates after the host heterotrophic eukaryotic microorganism formed a symbiotic association with red alga that does not contain peridinin or P457.

  20. Combining Evolutionary Information and an Iterative Sampling Strategy for Accurate Protein Structure Prediction.

    Directory of Open Access Journals (Sweden)

    Tatjana Braun

    2015-12-01

    Full Text Available Recent work has shown that the accuracy of ab initio structure prediction can be significantly improved by integrating evolutionary information in form of intra-protein residue-residue contacts. Following this seminal result, much effort is put into the improvement of contact predictions. However, there is also a substantial need to develop structure prediction protocols tailored to the type of restraints gained by contact predictions. Here, we present a structure prediction protocol that combines evolutionary information with the resolution-adapted structural recombination approach of Rosetta, called RASREC. Compared to the classic Rosetta ab initio protocol, RASREC achieves improved sampling, better convergence and higher robustness against incorrect distance restraints, making it the ideal sampling strategy for the stated problem. To demonstrate the accuracy of our protocol, we tested the approach on a diverse set of 28 globular proteins. Our method is able to converge for 26 out of the 28 targets and improves the average TM-score of the entire benchmark set from 0.55 to 0.72 when compared to the top ranked models obtained by the EVFold web server using identical contact predictions. Using a smaller benchmark, we furthermore show that the prediction accuracy of our method is only slightly reduced when the contact prediction accuracy is comparatively low. This observation is of special interest for protein sequences that only have a limited number of homologs.

  1. Probing Site-Specific Structural Information of Peptides at Model Membrane Interface In Situ.

    Science.gov (United States)

    Ding, Bei; Panahi, Afra; Ho, Jia-Jung; Laaser, Jennifer E; Brooks, Charles L; Zanni, Martin T; Chen, Zhan

    2015-08-19

    Isotope labeling is a powerful technique to probe detailed structures of biological molecules with a variety of analytical methods such as NMR and vibrational spectroscopies. It is important to obtain molecular structural information on biological molecules at interfaces such as cell membranes, but it is challenging to use the isotope labeling method to study interfacial biomolecules. Here, by individually (13)C═(16)O labeling ten residues of a peptide, Ovispirin-1, we have demonstrated for the first time that a site-specific environment of membrane associated peptide can be probed by the submonolayer surface sensitive sum frequency generation (SFG) vibrational spectroscopy in situ. With the peptide associated with a single lipid bilayer, the sinusoidal trend of the SFG line width and peak-center frequency suggests that the peptide is located at the interface beneath the lipid headgroup region. The constructive interferences between the isotope labeled peaks and the main peptide amide I peak contributed by the unlabeled components were used to determine the membrane orientation of the peptide. From the SFG spectral peak-center frequency, line width, and polarization dependence of the isotope labeled units, we deduced structural information on individual units of the peptide associated with a model cell membrane. We also performed molecular dynamics (MD) simulations to understand peptide-membrane interactions. The physical pictures described by simulation agree well with the SFG experimental result. This research demonstrates the feasibility and power of using isotope labeling SFG to probe molecular structures of interfacial biological molecules in situ in real time.

  2. Crystal structure of the complex between Pseudomonas effector AvrPtoB and the tomato Pto kinase reveals both a shared and a unique interface compared with AvrPto-Pto.

    Science.gov (United States)

    Dong, Jing; Xiao, Fangming; Fan, Fenxia; Gu, Lichuan; Cang, Huaixing; Martin, Gregory B; Chai, Jijie

    2009-06-01

    Resistance to bacterial speck disease in tomato (Solanum lycopersicum) is activated upon recognition by the host Pto kinase of either one of two sequence-unrelated effector proteins, AvrPto or AvrPtoB, from Pseudomonas syringae pv tomato (Pst). Pto induces Pst immunity by acting in concert with the Prf protein. The recently reported structure of the AvrPto-Pto complex revealed that interaction of AvrPto with Pto appears to relieve an inhibitory effect of Pto, allowing Pto to activate Prf. Here, we present the crystal structure of the Pto binding domain of AvrPtoB (residues 121 to 205) at a resolution of 1.9A and of the AvrPtoB(121-205)-Pto complex at a resolution of 3.3 A. AvrPtoB(121-205) exhibits a tertiary fold that is completely different from that of AvrPto, and its conformation remains largely unchanged upon binding to Pto. In common with AvrPto-Pto, the AvrPtoB-Pto complex relies on two interfaces. One of these interfaces is similar in both complexes, although the primary amino acid sequences from the two effector proteins are very different. Amino acid substitutions in Pto at the other interface disrupt the interaction of AvrPtoB-Pto but not that of AvrPto-Pto. Interestingly, substitutions in Pto affecting this unique interface also cause Pto to induce Prf-dependent host cell death independently of either effector protein.

  3. Population structure analyses of Staphylococcus aureus at Tygerberg Hospital, South Africa, reveals a diverse population, a high prevalence of Panton-Valentine leukocidin genes, and unique local methicillin-resistant S. aureus clones.

    Science.gov (United States)

    Oosthuysen, W F; Orth, H; Lombard, C J; Sinha, B; Wasserman, E

    2014-07-01

    Studies reporting on the population structure of Staphylococcus aureus in South Africa have focused only on methicillin-resistant S. aureus (MRSA). This study describes the population structure of S. aureus, including methicillin-susceptible S. aureus (MSSA) isolated from patients at Tygerberg Academic Hospital, Western Cape province. Pulsed-field gel electrophoresis (PFGE), detection of Panton-Valentine leukocidin (PVL), spa typing, multilocus sequence typing (MLST), agr typing and SCCmec typing were used to characterize strains. Of 367 non-repetitive S. aureus isolates collected over a period of 1 year, 56 (15.3%) were MRSA. Skin and soft tissue infections were the most frequent source (54.8%), followed by bone and joint (15.3%) and respiratory tract infections (7.7%). For strain typing, PFGE was the most discriminative method, and resulted in 31 pulsotypes (n = 345, 94.0%), as compared with 16 spa clonal complexes (CCs) (n = 344, 93.4%). Four MLST CCs were identified after eBURST of sequence types (STs) of selected isolates. One hundred and sixty isolates (MSSA, n = 155, 42.2%) were PVL-positive, and agr types I-IV and SCCmec types I-V were identified. Our S. aureus population consisted of genotypically diverse strains, with PVL being a common characteristic of MSSA. MSSA and MRSA isolates clustered in different clones. However, the dominant MRSA clone (ST612) also contained an MSSA isolate, and had a unique genotype. Common global epidemic MRSA clones, such as ST239-MRSA-III and ST36-MRSA-II, were identified. A local clone, ST612-MRSA-IV, was found to be the dominant MRSA clone. © 2013 The Authors Clinical Microbiology and Infection © 2013 European Society of Clinical Microbiology and Infectious Diseases.

  4. Linear versus non-linear structural information limit in high-resolution transmission electron microscopy.

    Science.gov (United States)

    Van Aert, S; Chen, J H; Van Dyck, D

    2010-10-01

    A widely used performance criterion in high-resolution transmission electron microscopy (HRTEM) is the information limit. It corresponds to the inverse of the maximum spatial object frequency that is linearly transmitted with sufficient intensity from the exit plane of the object to the image plane and is limited due to partial temporal coherence. In practice, the information limit is often measured from a diffractogram or from Young's fringes assuming a weak phase object scattering beyond the inverse of the information limit. However, for an aberration corrected electron microscope, with an information limit in the sub-angstrom range, weak phase objects are no longer applicable since they do not scatter sufficiently in this range. Therefore, one relies on more strongly scattering objects such as crystals of heavy atoms observed along a low index zone axis. In that case, dynamical scattering becomes important such that the non-linear and linear interaction may be equally important. The non-linear interaction may then set the experimental cut-off frequency observed in a diffractogram. The goal of this paper is to quantify both the linear and the non-linear information transfer in terms of closed form analytical expressions. Whereas the cut-off frequency set by the linear transfer can be directly related with the attainable resolution, information from the non-linear transfer can only be extracted using quantitative, model-based methods. In contrast to the historic definition of the information limit depending on microscope parameters only, the expressions derived in this paper explicitly incorporate their dependence on the structure parameters as well. In order to emphasize this dependence and to distinguish from the usual information limit, the expressions derived for the inverse cut-off frequencies will be referred to as the linear and non-linear structural information limit. The present findings confirm the well-known result that partial temporal coherence has

  5. Managing Information Uncertainty in Wave Height Modeling for the Offshore Structural Analysis through Random Set

    Directory of Open Access Journals (Sweden)

    Keqin Yan

    2017-01-01

    Full Text Available This chapter presents a reliability study for an offshore jacket structure with emphasis on the features of nonconventional modeling. Firstly, a random set model is formulated for modeling the random waves in an ocean site. Then, a jacket structure is investigated in a pushover analysis to identify the critical wave direction and key structural elements. This is based on the ultimate base shear strength. The selected probabilistic models are adopted for the important structural members and the wave direction is specified in the weakest direction of the structure for a conservative safety analysis. The wave height model is processed in a P-box format when it is used in the numerical analysis. The models are applied to find the bounds of the failure probabilities for the jacket structure. The propagation of this wave model to the uncertainty in results is investigated in both an interval analysis and Monte Carlo simulation. The results are compared in context of information content and numerical accuracy. Further, the failure probability bounds are compared with the conventional probabilistic approach.

  6. Mapping Out Narrative Structures and Dynamics Using Networks and Textual Information

    CERN Document Server

    Min, Semi

    2016-01-01

    Human communication is often executed in the form of a narrative, an account of connected events composed of characters, actions, and settings. A coherent narrative structure is therefore a requisite for a well-formulated narrative -- be it fictional or nonfictional -- for informative and effective communication, opening up the possibility of a deeper understanding of a narrative by studying its structural properties. In this paper we present a network-based framework for modeling and analyzing the structure of a narrative, which is further expanded by incorporating methods from computational linguistics to utilize the narrative text. Modeling a narrative as a dynamically unfolding system, we characterize its progression via the growth patterns of the character network, and use sentiment analysis and topic modeling to represent the actual content of the narrative in the form of interaction maps between characters with associated sentiment values and keywords. This is a network framework advanced beyond the si...

  7. SARANEA: a freely available program to mine structure-activity and structure-selectivity relationship information in compound data sets.

    Science.gov (United States)

    Lounkine, Eugen; Wawer, Mathias; Wassermann, Anne Mai; Bajorath, Jürgen

    2010-01-01

    We introduce SARANEA, an open-source Java application for interactive exploration of structure-activity relationship (SAR) and structure-selectivity relationship (SSR) information in compound sets of any source. SARANEA integrates various SAR and SSR analysis functions and utilizes a network-like similarity graph data structure for visualization. The program enables the systematic detection of activity and selectivity cliffs and corresponding key compounds across multiple targets. Advanced SAR analysis functions implemented in SARANEA include, among others, layered chemical neighborhood graphs, cliff indices, selectivity trees, editing functions for molecular networks and pathways, bioactivity summaries of key compounds, and markers for bioactive compounds having potential side effects. We report the application of SARANEA to identify SAR and SSR determinants in different sets of serine protease inhibitors. It is found that key compounds can influence SARs and SSRs in rather different ways. Such compounds and their SAR/SSR characteristics can be systematically identified and explored using SARANEA. The program and source code are made freely available under the GNU General Public License.

  8. Exploiting structural and topological information to improve prediction of RNA-protein binding sites

    Directory of Open Access Journals (Sweden)

    Yuan Zheng

    2009-10-01

    Full Text Available Abstract Background RNA-protein interactions are important for a wide range of biological processes. Current computational methods to predict interacting residues in RNA-protein interfaces predominately rely on sequence data. It is, however, known that interface residue propensity is closely correlated with structural properties. In this paper we systematically study information obtained from sequences and structures and compare their contributions in this prediction problem. Particularly, different geometrical and network topological properties of protein structures are evaluated to improve interface residue prediction accuracy. Results We have quantified the impact of structural information on the prediction accuracy in comparison to the purely sequence based approach using two machine learning techniques: Naïve Bayes classifiers and Support Vector Machines. The highest AUC of 0.83 was achieved by a Support Vector Machine, exploiting PSI-BLAST profile, accessible surface area, betweenness-centrality and retention coefficient as input features. Taking into account that our results are based on a larger non-redundant data set, the prediction accuracy is considerably higher than reported in previous, comparable studies. A protein-RNA interface predictor (PRIP and the data set have been made available at http://www.qfab.org/PRIP. Conclusion Graph-theoretic properties of residue contact maps derived from protein structures such as betweenness-centrality can supplement sequence or structure features to improve the prediction accuracy for binding residues in RNA-protein interactions. While Support Vector Machines perform better on this task, Naïve Bayes classifiers also have been found to achieve good prediction accuracies but require much less training time and are an attractive choice for large scale predictions.

  9. Theory of uniqueness of Indian Caste System

    Directory of Open Access Journals (Sweden)

    Ashwin Kumar

    2006-08-01

    Full Text Available Classical studies on pre-modern Indian social structure have suggested apparent differences between the Indian caste system and social stratification as one can discern in other parts of the world. However, one needs to question such dogmatic assertions that such vast differences really existed. An endeavor is made in this research paper to reflect on the nature of caste hierarchy in pre-modern India. The caste system forms the significant basis of pre-modern Indian social structure. Early writers conceived the caste system of pre-modern India as something unique to India. An attempt is made to question this application of theory of uniqueness in the case of India.

  10. Theory of uniqueness of Indian Caste System

    Directory of Open Access Journals (Sweden)

    Ashwin Kumar

    2005-11-01

    Full Text Available Classical studies on pre-modern Indian social structure have suggested apparent differences between the Indian caste system and social stratification as one can discern in other parts of the world. However, one needs to question such dogmatic assertions that such vast differences really existed. An endeavor is made in this research paper to reflect on the nature of caste hierarchy in pre-modern India. The caste system forms the significant basis of pre-modern Indian social structure. Early writers conceived the caste system of pre-modern India as something unique to India. An attempt is made to question this application of theory of uniqueness in the case of India.

  11. Processing information about support exchanges in close relationships: The role of a knowledge structure

    Directory of Open Access Journals (Sweden)

    Bulent eTuran

    2016-02-01

    Full Text Available People develop knowledge of interpersonal interaction patterns (e.g., prototypes and schemas, which shape how they process incoming information. One such knowledge structure based on attachment theory was examined: the secure base script (the prototypic sequence of events when an attachment figure comforts a close relationship partner in distress. In two studies (N = 53 and N = 119, participants were shown animated film clips in which geometric figures depicted the secure base script and asked to describe the animations. Both studies found that many people readily recognize the secure-base script from these minimal cues quite well, suggesting that this script is not only available in the context of specific relationships (i.e., a relationship-specific knowledge: The generalized (abstract structure of the script is also readily accessible, which would make it possible to apply it to any relationship (including new relationships. Regression analyses suggested that participants who recognized the script were more likely to (a include more animation elements when describing the animations, (b see a common theme in different animations, (c create better organized stories, and (d later recall more details of the animations. These findings suggest that access to this knowledge structure helps a person organize and remember relevant incoming information. Furthermore, in both Study 1 and Study 2, individual differences in the ready recognition of the script were associated with individual differences in having access to another related knowledge: indicators suggesting that a potential relationship partner can be trusted to be supportive and responsive at times of stress. Results of Study 2 also suggest that recognizing the script is associated with those items of an attachment measure that concern giving and receiving support. Thus, these knowledge structures may shape how people process support-relevant information in their everyday lives, potentially

  12. Processing Information about Support Exchanges in Close Relationships: The Role of a Knowledge Structure.

    Science.gov (United States)

    Turan, Bulent

    2016-01-01

    People develop knowledge of interpersonal interaction patterns (e.g., prototypes and schemas), which shape how they process incoming information. One such knowledge structure based on attachment theory was examined: the secure base script (the prototypic sequence of events when an attachment figure comforts a close relationship partner in distress). In two studies (N = 53 and N = 119), participants were shown animated film clips in which geometric figures depicted the secure base script and asked to describe the animations. Both studies found that many people readily recognize the secure-base script from these minimal cues quite well, suggesting that this script is not only available in the context of specific relationships (i.e., a relationship-specific knowledge): The generalized (abstract) structure of the script is also readily accessible, which would make it possible to apply it to any relationship (including new relationships). Regression analyses suggested that participants who recognized the script were more likely to (a) include more animation elements when describing the animations, (b) see a common theme in different animations, (c) create better organized stories, and (d) later recall more details of the animations. These findings suggest that access to this knowledge structure helps a person organize and remember relevant incoming information. Furthermore, in both Study 1 and Study 2, individual differences in the ready recognition of the script were associated with individual differences in having access to another related knowledge: indicators suggesting that a potential relationship partner can be trusted to be supportive and responsive at times of stress. Results of Study 2 also suggest that recognizing the script is associated with those items of an attachment measure that concern giving and receiving support. Thus, these knowledge structures may shape how people process support-relevant information in their everyday lives, potentially affecting

  13. A Framework for Preliminary Design of Aircraft Structures Based on Process Information. Part 1

    Science.gov (United States)

    Rais-Rohani, Masoud

    1998-01-01

    This report discusses the general framework and development of a computational tool for preliminary design of aircraft structures based on process information. The described methodology is suitable for multidisciplinary design optimization (MDO) activities associated with integrated product and process development (IPPD). The framework consists of three parts: (1) product and process definitions; (2) engineering synthesis, and (3) optimization. The product and process definitions are part of input information provided by the design team. The backbone of the system is its ability to analyze a given structural design for performance as well as manufacturability and cost assessment. The system uses a database on material systems and manufacturing processes. Based on the identified set of design variables and an objective function, the system is capable of performing optimization subject to manufacturability, cost, and performance constraints. The accuracy of the manufacturability measures and cost models discussed here depend largely on the available data on specific methods of manufacture and assembly and associated labor requirements. As such, our focus in this research has been on the methodology itself and not so much on its accurate implementation in an industrial setting. A three-tier approach is presented for an IPPD-MDO based design of aircraft structures. The variable-complexity cost estimation methodology and an approach for integrating manufacturing cost assessment into design process are also discussed. This report is presented in two parts. In the first part, the design methodology is presented, and the computational design tool is described. In the second part, a prototype model of the preliminary design Tool for Aircraft Structures based on Process Information (TASPI) is described. Part two also contains an example problem that applies the methodology described here for evaluation of six different design concepts for a wing spar.

  14. University Students' Knowledge Structures and Informal Reasoning on the Use of Genetically Modified Foods: Multidimensional Analyses

    Science.gov (United States)

    Wu, Ying-Tien

    2013-01-01

    This study aims to provide insights into the role of learners' knowledge structures about a socio-scientific issue (SSI) in their informal reasoning on the issue. A total of 42 non-science major university students' knowledge structures and informal reasoning were assessed with multidimensional analyses. With both qualitative and…

  15. University Students' Knowledge Structures and Informal Reasoning on the Use of Genetically Modified Foods: Multidimensional Analyses

    Science.gov (United States)

    Wu, Ying-Tien

    2013-01-01

    This study aims to provide insights into the role of learners' knowledge structures about a socio-scientific issue (SSI) in their informal reasoning on the issue. A total of 42 non-science major university students' knowledge structures and informal reasoning were assessed with multidimensional analyses. With both qualitative and…

  16. Comparative Analysis of the 15.5kD Box C/D snoRNP Core Protein in the Primitive Eukaryote Giardia lamblia Reveals Unique Structural and Functional Features

    Energy Technology Data Exchange (ETDEWEB)

    Biswas, Shyamasri; Buhrman, Greg; Gagnon, Keith; Mattos, Carla; Brown, II, Bernard A.; Maxwell, E. Stuart (NCSU); (UTSMC)

    2012-07-11

    Box C/D ribonucleoproteins (RNP) guide the 2'-O-methylation of targeted nucleotides in archaeal and eukaryotic rRNAs. The archaeal L7Ae and eukaryotic 15.5kD box C/D RNP core protein homologues initiate RNP assembly by recognizing kink-turn (K-turn) motifs. The crystal structure of the 15.5kD core protein from the primitive eukaryote Giardia lamblia is described here to a resolution of 1.8 {angstrom}. The Giardia 15.5kD protein exhibits the typical {alpha}-{beta}-{alpha} sandwich fold exhibited by both archaeal L7Ae and eukaryotic 15.5kD proteins. Characteristic of eukaryotic homologues, the Giardia 15.5kD protein binds the K-turn motif but not the variant K-loop motif. The highly conserved residues of loop 9, critical for RNA binding, also exhibit conformations similar to those of the human 15.5kD protein when bound to the K-turn motif. However, comparative sequence analysis indicated a distinct evolutionary position between Archaea and Eukarya. Indeed, assessment of the Giardia 15.5kD protein in denaturing experiments demonstrated an intermediate stability in protein structure when compared with that of the eukaryotic mouse 15.5kD and archaeal Methanocaldococcus jannaschii L7Ae proteins. Most notable was the ability of the Giardia 15.5kD protein to assemble in vitro a catalytically active chimeric box C/D RNP utilizing the archaeal M. jannaschii Nop56/58 and fibrillarin core proteins. In contrast, a catalytically competent chimeric RNP could not be assembled using the mouse 15.5kD protein. Collectively, these analyses suggest that the G. lamblia 15.5kD protein occupies a unique position in the evolution of this box C/D RNP core protein retaining structural and functional features characteristic of both archaeal L7Ae and higher eukaryotic 15.5kD homologues.

  17. [Relationship between organisational structure and worksite health management in the information technology and communications sector].

    Science.gov (United States)

    Ansmann, L; Jung, J; Nitzsche, A; Pfaff, H

    2012-05-01

    Worksite health management (WHM) can positively influence employee health and performance. However, it has not yet been comprehensively implemented in companies. This study aims to identify the role of organisational structures in the implementation of WHM. In this cross-sectional study, data were collected on the companies' WHM and the organisational structure. Out of 522 randomly selected companies within the German information technology and communication (ITC) sector, one managing director for each company was being questioned through telephone interviews. Bivariate and multivariate logistic regression analyses were conducted. The results of the study reveal that the implementation of WHM is positively correlated with a large company size (OR 2.75; 95%-CI 1.10-6.88) and with the existence of an employee representation (OR 2.48; 95%-CI 1.54-3.98). Other structural characteristics, such as the employment of a company physician, the percentage of temporary workers as well as the staff's age and sex distribution do not seem to have a significant impact on the implementation of WHM. The results indicate that the implementation of WHM can only be explained to a certain degree by organisational structures. However, the findings highlight the fact that companies with few structural resources are in particular need of tailored support when implementing WHM. © Georg Thieme Verlag KG Stuttgart · New York.

  18. Protein structural information derived from NMR chemical shift with the neural network program TALOS-N.

    Science.gov (United States)

    Shen, Yang; Bax, Ad

    2015-01-01

    Chemical shifts are obtained at the first stage of any protein structural study by NMR spectroscopy. Chemical shifts are known to be impacted by a wide range of structural factors, and the artificial neural network based TALOS-N program has been trained to extract backbone and side-chain torsion angles from (1)H, (15)N, and (13)C shifts. The program is quite robust and typically yields backbone torsion angles for more than 90 % of the residues and side-chain χ 1 rotamer information for about half of these, in addition to reliably predicting secondary structure. The use of TALOS-N is illustrated for the protein DinI, and torsion angles obtained by TALOS-N analysis from the measured chemical shifts of its backbone and (13)C(β) nuclei are compared to those seen in a prior, experimentally determined structure. The program is also particularly useful for generating torsion angle restraints, which then can be used during standard NMR protein structure calculations.

  19. Protein folds recognized by an intelligent predictor based-on evolutionary and structural information.

    Science.gov (United States)

    Cheung, Ngaam J; Ding, Xue-Ming; Shen, Hong-Bin

    2016-02-05

    Protein fold recognition is an important and essential step in determining tertiary structure of a protein in biological science. In this study, a model termed NiRecor is developed for recognizing protein folds based on artificial neural networks incorporated in an adaptive heterogeneous particle swarm optimizer. The main contribution of NiRecor is that it is a data-driven and highly-performing predictor without manually tuning control parameters for different data sets. In biological science, since evolutionary- and structure-based information of amino acid sequences is greatly important in determination of tertiary structure of a protein, accordingly, in NiRecor we employ two different feature sets, which involve position specific scoring matrix and secondary structure prediction matrix, to predict the structural classes of protein folds. The experimental results demonstrate the proposed method is powerful in predicting protein folds with higher precisions by improvements of 1.1 ∼7.8 percentages on three benchmark datasets by comparing with several existing predictors.

  20. Communications tools in research projects to support Semi and Non Structured Information

    Directory of Open Access Journals (Sweden)

    Astrid Jaime

    2005-06-01

    Full Text Available Innovation and thus the production of knowledge becomes a factor of competitiveness. In this context quality management could be complemented by knowledge management to aim the improvement of knowledge production by research activities process. To this end, after describing knowledge and informa-tion typologies in engineering activities, a knowledge man-agement system is proposed. The goal is to support: (1 Semi-Structured Information (e.g. reports, etc. thanks to the BASIC-Lab tool functions, which are based on attributing points of view and annotations to documents and document zones, and (2 Non-Structured Information (such as mail, dialogues, etc., thanks to MICA-Graph approach which intends to support ex-change of technical messages that concerns common resolution of research problems within project teams and to capitalise relevant knowledge. For the both approaches, prototype tools have been developed and evaluated, primarily to feed back with manufacturing knowledge in the EADS industrial envi-ronment.