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Sample records for anti-bixbyite-type structure analysed

  1. Spin Structure Analyses of Antiferromagnets

    International Nuclear Information System (INIS)

    Chung, Jae Ho; Song, Young Sang; Lee, Hak Bong

    2010-05-01

    We have synthesized series of powder sample of incommensurate antiferromagnetic multiferroics, (Mn, Co)WO 4 and Al doped Ba 0.5 Sr 1.5 Zn 2 Fe 12 O 22 , incommensurate antiferromagnetic multiferroics. Their spin structure was studied by using the HRPD. In addition, we have synthesized series of crystalline samples of incommensurate multiferroics, (Mn, Co)WO 4 and olivines. Their spin structure was investigated using neutron diffraction under high magnetic field. As a result, we were able to draw the phase diagram of (Mn, Co)WO 4 as a function of composition and temperature. We learned the how the spin structure changes with increased ionic substitution. Finally we have drawn the phase diagram of the multicritical olivine Mn2SiS4/Mn2GeS4 as a function of filed and temperature through the spin structure studies

  2. Fully Coupled FE Analyses of Buried Structures

    Directory of Open Access Journals (Sweden)

    James T. Baylot

    1994-01-01

    Full Text Available Current procedures for determining the response of buried structures to the effects of the detonation of buried high explosives recommend decoupling the free-field stress analysis from the structure response analysis. A fully coupled (explosive–soil structure finite element analysis procedure was developed so that the accuracies of current decoupling procedures could be evaluated. Comparisons of the results of analyses performed using this procedure with scale-model experiments indicate that this finite element procedure can be used to effectively evaluate the accuracies of the methods currently being used to decouple the free-field stress analysis from the structure response analysis.

  3. Modelling and analysing oriented fibrous structures

    International Nuclear Information System (INIS)

    Rantala, M; Lassas, M; Siltanen, S; Sampo, J; Takalo, J; Timonen, J

    2014-01-01

    A mathematical model for fibrous structures using a direction dependent scaling law is presented. The orientation of fibrous nets (e.g. paper) is analysed with a method based on the curvelet transform. The curvelet-based orientation analysis has been tested successfully on real data from paper samples: the major directions of fibrefibre orientation can apparently be recovered. Similar results are achieved in tests on data simulated by the new model, allowing a comparison with ground truth

  4. Water channel structures analysed by electron crystallography.

    Science.gov (United States)

    Tani, Kazutoshi; Fujiyoshi, Yoshinori

    2014-05-01

    The mechanisms underlying water transport through aquaporin (AQP) have been debated for two decades. The water permeation phenomenon of AQP seems inexplicable because the Grotthuss mechanism does not allow for simultaneous fast water permeability and inhibition of proton transfer through the hydrogen bonds of water molecules. The AQP1 structure determined by electron crystallography provided the first insights into the proton exclusion mechanism despite fast water permeation. Although several studies have provided clues about the mechanism based on the AQP structure, each proposed mechanism remains incomplete. The present review is focused on AQP function and structure solved by electron crystallography in an attempt to fill the gaps between the findings in the absence and presence of lipids. Many AQP structures can be superimposed regardless of the determination method. The AQP fold is preserved even under conditions lacking lipids, but the water arrangement in the channel pore differs. The differences might be explained by dipole moments formed by the two short helices in the lipid bilayer. In addition, structure analyses of double-layered two-dimensional crystals of AQP suggest an array formation and cell adhesive function. Electron crystallography findings not only have contributed to resolve some of the water permeation mechanisms, but have also elucidated the multiple functions of AQPs in the membrane. The roles of AQPs in the brain remain obscure, but their multiple activities might be important in the regulation of brain and other biological functions. This article is part of a Special Issue entitled Aquaporins. © 2013.

  5. DEPUTY: analysing architectural structures and checking style

    International Nuclear Information System (INIS)

    Gorshkov, D.; Kochelev, S.; Kotegov, S.; Pavlov, I.; Pravilnikov, V.; Wellisch, J.P.

    2001-01-01

    The DepUty (dependencies utility) can be classified as a project and process management tool. The main goal of DepUty is to assist by means of source code analysis and graphical representation using UML, in understanding dependencies of sub-systems and packages in CMS Object Oriented software, to understand architectural structure, and to schedule code release in modularised integration. It also allows a new-comer to more easily understand the global structure of CMS software, and to void circular dependencies up-front or re-factor the code, in case it was already too close to the edge of non-maintainability. The authors will discuss the various views DepUty provides to analyse package dependencies, and illustrate both the metrics and style checking facilities it provides

  6. Activation analyses for different fusion structural alloys

    International Nuclear Information System (INIS)

    Attaya, H.; Smith, D.

    1991-01-01

    The leading candidate structural materials, viz., the vanadium alloys, the nickel or the manganese stabilized austenitic steels, and the ferritic steels, are analysed in terms of their induced activation in the TPSS fusion power reactor. The TPSS reactor has 1950 MW fusion power and inboard and outboard average neutron wall loading of 3.75 and 5.35 MW/m 2 respectively. The results shows that, after one year of continuous operation, the vanadium alloys have the least radioactivity at reactor shutdown. The maximum difference between the induced radioactivity in the vanadium alloys and in the other iron-based alloys occurs at about 10 years after reactor shutdown. At this time, the total reactor radioactivity, using the vanadium alloys, is about two orders of magnitude less than the total reactor radioactivity utilizing any other alloy. The difference is even larger in the first wall, the FW-vanadium activation is 3 orders of magnitude less than other alloys' FW activation. 2 refs., 7 figs

  7. Special analyses reveal coke-deposit structure

    International Nuclear Information System (INIS)

    Albright, L.F.

    1988-01-01

    A scanning electron microscope (SEM) and an energy dispersive X-ray analyzer (EDAX) have been used to obtain information that clarifies the three mechanisms of coke formation in ethylene furnaces, and to analyze the metal condition at the exit of furnace. The results can be used to examine furnace operations and develop improved ethylene plant practices. In this first of four articles on the analyses of coke and metal samples, the coking mechanisms and coke deposits in a section of tube from an actual ethylene furnace (Furnace A) from a plant on the Texas Gulf Coast are discussed. The second articles in the series will analyze the condition of the tube metal in the same furnace. To show how coke deposition and metal condition dependent on the operating parameters of an ethylene furnace, the third article in the series will show the coke deposition in a Texas Gulf Coast furnace tube (Furnace B) that operated at shorter residence time. The fourth article discusses the metal condition in that furnace. Some recommendations, based on the analyses and findings, are offered in the fourth article that could help extend the life of ethylene furnace tubes, and also improve overall ethylene plant operations

  8. Analysing the nanoporous structure of aramid fibres

    DEFF Research Database (Denmark)

    Pauw, Brian Richard; Vigild, Martin Etchells; Mortensen, Kell

    2010-01-01

    After consideration of the applicability of classical methods, a novel analysis method for the characterization of fibre void structures is presented, capable of fitting the entire anisotropic two-dimensional scattering pattern to a model of perfectly aligned, polydisperse ellipsoids. It is tested...... for validity against the computed scattering pattern for a simulated nanostructure, after which it is used to fit the scattering from the void structure of commercially available heat-treated poly(p-phenylene terephtalamide) fibre and its as-spun precursor fibre. The application shows a reasonable fit...... and results in size distributions for both the lengths and the widths of the ellipsoidal voids. Improvements to the analysis methods are compared, consisting of the introduction of an orientation distribution for the nano-ellipsoids, and the addition of large scatterers to account for the effect of fibrillar...

  9. Complex Analyses of Plankton Structure and Function

    Directory of Open Access Journals (Sweden)

    Karl E. Havens

    2001-01-01

    Full Text Available This paper critically evaluates some complex methods that have been used to characterize the structure and function of freshwater plankton communities. The focus is on methods related to plankton size structure and carbon transfer. The specific methods reviewed are 1 size spectrum analysis, 2 size-fractionated phytoplankton productivity, 3 size-fractionated zooplankton grazing, 4 plankton ecological transfer efficiency, and 5 grazer effects on phytoplankton community structure. Taken together, these methods can provide information on community ecological properties that are directly related to practical issues including water quality and fisheries productivity. However, caution is warranted since application without a complete understanding of assumptions and context of the manipulations could lead to erroneous conclusions. As an example, experimental studies involving the addition or removal of zooplankton, especially when coupled with nutrient addition treatments, could provide information on the degree of consumer vs. resource control of phytoplankton. Resource managers subsequently could use this information in developing effective measures for controlling nuisance algal biomass. However, the experiments must be done critically and with sufficient safeguards and other measurements to ensure that treatments (e.g., zooplankton exclosure by screening of water actually are successful and do not introduce other changes in the community (e.g., removal of large algae. In all of the methods described here, the investigator must take care when generalizing results and, in particular, carry out a sufficient number of replications to encompass both the major seasonal and spatial variation that occurs in the ecosystem.

  10. Accelerated safety analyses - structural analyses Phase I - structural sensitivity evaluation of single- and double-shell waste storage tanks

    International Nuclear Information System (INIS)

    Becker, D.L.

    1994-11-01

    Accelerated Safety Analyses - Phase I (ASA-Phase I) have been conducted to assess the appropriateness of existing tank farm operational controls and/or limits as now stipulated in the Operational Safety Requirements (OSRs) and Operating Specification Documents, and to establish a technical basis for the waste tank operating safety envelope. Structural sensitivity analyses were performed to assess the response of the different waste tank configurations to variations in loading conditions, uncertainties in loading parameters, and uncertainties in material characteristics. Extensive documentation of the sensitivity analyses conducted and results obtained are provided in the detailed ASA-Phase I report, Structural Sensitivity Evaluation of Single- and Double-Shell Waste Tanks for Accelerated Safety Analysis - Phase I. This document provides a summary of the accelerated safety analyses sensitivity evaluations and the resulting findings

  11. Masonry structures built with fictile tubules: Experimental and numerical analyses

    Science.gov (United States)

    Tiberti, Simone; Scuro, Carmelo; Codispoti, Rosamaria; Olivito, Renato S.; Milani, Gabriele

    2017-11-01

    Masonry structures with fictile tubules were a distinctive building technique of the Mediterranean area. This technique dates back to Roman and early Christian times, used to build vaulted constructions and domes with various geometrical forms by virtue of their modular structure. In the present work, experimental tests were carried out to identify the mechanical properties of hollow clay fictile tubules and a possible reinforcing technique for existing buildings employing such elements. The experimental results were then validated by devising and analyzing numerical models with the FE software Abaqus, also aimed at investigating the structural behavior of an arch via linear and nonlinear static analyses.

  12. Secondary structural analyses of ITS1 in Paramecium.

    Science.gov (United States)

    Hoshina, Ryo

    2010-01-01

    The nuclear ribosomal RNA gene operon is interrupted by internal transcribed spacer (ITS) 1 and ITS2. Although the secondary structure of ITS2 has been widely investigated, less is known about ITS1 and its structure. In this study, the secondary structure of ITS1 sequences for Paramecium and other ciliates was predicted. Each Paramecium ITS1 forms an open loop with three helices, A through C. Helix B was highly conserved among Paramecium, and similar helices were found in other ciliates. A phylogenetic analysis using the ITS1 sequences showed high-resolution, implying that ITS1 is a good tool for species-level analyses.

  13. Seismic Soil-Structure Interaction Analyses of a Deeply Embedded Model Reactor – SASSI Analyses

    Energy Technology Data Exchange (ETDEWEB)

    Nie J.; Braverman J.; Costantino, M.

    2013-10-31

    This report summarizes the SASSI analyses of a deeply embedded reactor model performed by BNL and CJC and Associates, as part of the seismic soil-structure interaction (SSI) simulation capability project for the NEAMS (Nuclear Energy Advanced Modeling and Simulation) Program of the Department of Energy. The SASSI analyses included three cases: 0.2 g, 0.5 g, and 0.9g, all of which refer to nominal peak accelerations at the top of the bedrock. The analyses utilized the modified subtraction method (MSM) for performing the seismic SSI evaluations. Each case consisted of two analyses: input motion in one horizontal direction (X) and input motion in the vertical direction (Z), both of which utilized the same in-column input motion. Besides providing SASSI results for use in comparison with the time domain SSI results obtained using the DIABLO computer code, this study also leads to the recognition that the frequency-domain method should be modernized so that it can better serve its mission-critical role for analysis and design of nuclear power plants.

  14. Static and Dynamic Structure Analyses of Polymer Crystals

    Science.gov (United States)

    Tashiro, Kohji

    Recent development in static and dynamic structure analyses of polymer crystals has been reviewed. Various methods were developed to enhance the reliability of static structure analysis. Usage of synchrotron high-energy X-ray beam allowed us to increase the total number of observed X-ray reflections by one order. Wide-angle neutron diffraction revealed the hydrogen atomic positions accurately, making it possible to evaluate the mechanical property of polymer crystals quantitatively. Time-resolved measurements of wide-angle and small-angle X-ray scatterings as well as infrared and Raman spectra have revealed the structural revolution processes as seen in the studies of isothermal crystallization and mechanical deformation processes.

  15. Static and dynamic structure analyses of polymer crystals

    International Nuclear Information System (INIS)

    Tashiro, Kohji

    2011-01-01

    Recent development in static and dynamic structure analyses of polymer crystals has been reviewed. Various methods were developed to enhance the reliability of static structure analysis. Usage of synchrotron high-energy X-ray beam allowed us to increase the total number of observed X-ray reflections by one order. Wide-angle neutron diffraction revealed the hydrogen atomic positions accurately, making it possible to evaluate the mechanical property of polymer crystals quantitatively. Time-resolved measurements of wide-angle and small-angle X-ray scatterings as well as infrared and Raman spectra have revealed the structural revolution processes as seen in the studies of isothermal crystallization and mechanical deformation processes. (author)

  16. Front lines of structural analyses by pulsed Neutron Diffraction

    International Nuclear Information System (INIS)

    Shamoto, Shin-ichi; Kodama, Katsuaki; Suzuya, Kentaro; Kamiyama, Takashi; Otomo, Toshiya; Fukunaga, Toshiharu

    2008-01-01

    The neutron is a subatomic particle without electronic charge, but has a magnetic moment. This nature leads high permeability compared to x-rays, and therefore neutrons become the powerful nondestructive probe for measurements. Diffraction patterns for wide reciprocal space can be measured by pulsed neutrons, which have been exploited for the structural analyses from amorphous materials to crystalline solids. Further, the pulsed neutrons have been applied to the structural studies of highly disordered materials, and also nanometer size materials. The structural studies using pulsed neutrons are reviewed in this paper from pioneering researches to the latest results in comparison with those by synchrotron radiation x-rays. For the amorphous hydrogen storage material, TbFe 2 D 3.0 , the structure factor and atomic pair distribution function (PDF) by neutron diffraction are compared with those by x-ray diffraction. The local crystal structure of a multiferroic system has been studied by means of PDF analysis on neutron powder diffraction data. PDF analysis is employed in order to determine the precise lattice parameters of nano-structure materials. The three distinctive neutron diffractometers, super high resolution powder diffractometer, high intensity total diffractometer and iMATERIA (IBARAKI materials design diffractometer), under construction at Material and Life Science Facility in J-PARC are introduced. (Y.K.)

  17. A database structure for radiological optimization analyses of decommissioning operations

    International Nuclear Information System (INIS)

    Zeevaert, T.; Van de Walle, B.

    1995-09-01

    The structure of a database for decommissioning experiences is described. Radiological optimization is a major radiation protection principle in practices and interventions, involving radiological protection factors, economic costs, social factors. An important lack of knowledge with respect to these factors exists in the domain of the decommissioning of nuclear power plants, due to the low number of decommissioning operations already performed. Moreover, decommissioning takes place only once for a installation. Tasks, techniques, and procedures are in most cases rather specific, limiting the use of past experiences in the radiological optimization analyses of new decommissioning operations. Therefore, it is important that relevant data or information be acquired from decommissioning experiences. These data have to be stored in a database in a way they can be used efficiently in ALARA analyses of future decommissioning activities

  18. Structure and chemistry of coals: calorimetric analyses. [Wetting heat

    Energy Technology Data Exchange (ETDEWEB)

    ,

    1979-01-01

    Heats of immersion (h/sub i/) of coals have been shown to be a valuable means of investigating structure and chemistry of coals. This report outlines some of the factors involved. Lower ranked coals imbibe more liquids (i.e., H/sub 2/O) onto more polar sites (carbonyl, phenolic, etc.) than higher ranked coals. Mineral matter reacts strongly with polar liquids (i.e., H/sub 2/O) giving rise to enhanced h/sub i/. Grinding of coals not only decreases particle size but modifies the coal structure to an increasing degree dependent upon the extent and severity of grinding. The magnitude of h/sub i/ and the rate of reaction are both modified consistent with the existence of a shrinking core or unperturbed coal structure serving as substrate to which the modified (less ordered) material is bound. Chemical (alkali) attack seems to loosen the coal structure markedly to allow enhanced access to fluid reagents. These exploratory studies have shown that calorimetric analyses similar to those developed and used by A.C. Zettlemoyer and his coworkers are excellent means for elucidating the structure and chemistry of coals and related materials.

  19. DMPD: Structural and functional analyses of bacterial lipopolysaccharides. [Dynamic Macrophage Pathway CSML Database

    Lifescience Database Archive (English)

    Full Text Available 12106784 Structural and functional analyses of bacterial lipopolysaccharides. Carof...html) (.csml) Show Structural and functional analyses of bacterial lipopolysaccharides. PubmedID 12106784 Ti...tle Structural and functional analyses of bacterial lipopolysaccharides. Authors

  20. Structural integrity analyses: can we manage the advances?

    International Nuclear Information System (INIS)

    Sauve, R.

    2006-01-01

    Engineering has been one of a number of disciplines in which significant advances in analysis procedures has taken place in the last two decades. In particular, advances in computer technology and engineering software have revolutionized the assessment of component structural integrity for a wide range of applications. A significant development in computational mechanics directly related to computer technology that has had a profound impact on the field of structural integrity is the finite element method. The finite element method has re-defined and expanded the role of structural integrity assessments by providing comprehensive modelling capabilities to engineers involved in design and failure analyses. As computer processing speeds and capacity have increased, so has the role of computer modelling in assessments of component structural integrity. With new product development cycles shrinking, the role of initial testing is being reduced in favour of computer modelling and simulation to assess component life and durability. For ageing structures, the evaluation of remaining life and the impact of degraded structural integrity becomes tractable with the modern advances in computational methods. The areas of structural integrity that have derived great benefit from the advances in numerical techniques include stress analysis, fracture mechanics, dynamics, heat transfer, structural reliability, probabilistic methods and continuum mechanics in general. One of the salient features of the current methods is the ability to handle large complex steady state or transient dynamic problems that exhibit highly non-linear behaviour. With the ever-increasing usage of these advanced methods, the question is posed: Can we manage the advances? Better still are we managing the advances? As with all technological advances that enter mainstream use, comes the need for education, training and certification in the application of these methods, improved quality assurance procedures and

  1. Analysing the magnetopause internal structure: new possibilities offered by MMS

    Science.gov (United States)

    Belmont, G.; Rezeau, L.; Manuzzo, R.; Aunai, N.; Dargent, J.

    2017-12-01

    We explore the structure of the magnetopause using a crossing observed by the MMS spacecraft on October 16th, 2015. Several methods (MVA, BV, CVA) are first applied to compute the normal to the magnetopause considered as a whole. The different results obtained are not identical and we show that the whole boundary is not stationary and not planar, so that basic assumptions of these methods are not well satisfied. We then analyse more finely the internal structure for investigating the departures from planarity. Using the basic mathematical definition of what is a one-dimensional physical problem, we introduce a new method, called LNA (Local Normal Analysis) for determining the varying normal, and we compare the results so obtained with those coming from the MDD tool developed by [Shi et al., 2005]. This method gives the dimensionality of the magnetic variations from multi-point measurements and allows estimating the direction of the local normal using the magnetic field. On the other hand, LNA is a single-spacecraft method which gives the local normal from the magnetic field and particle data. This study shows that the magnetopause does include approximate one-dimensional sub-structures but also two and three dimensional intervals. It also shows that the dimensionality of the magnetic variations can differ from the variations of the other fields so that, at some places, the magnetic field can have a 1D structure although all the plasma variations do not verify the properties of a global one-dimensional problem. Finally a generalisation and a systematic application of the MDD method to the physical quantities of interest is shown.

  2. Evolution and Structural Analyses of Glossina morsitans (Diptera; Glossinidae Tetraspanins

    Directory of Open Access Journals (Sweden)

    Edwin K. Murungi

    2014-11-01

    Full Text Available Tetraspanins are important conserved integral membrane proteins expressed in many organisms. Although there is limited knowledge about the full repertoire, evolution and structural characteristics of individual members in various organisms, data obtained so far show that tetraspanins play major roles in membrane biology, visual processing, memory, olfactory signal processing, and mechanosensory antennal inputs. Thus, these proteins are potential targets for control of insect pests. Here, we report that the genome of the tsetse fly, Glossina morsitans (Diptera: Glossinidae encodes at least seventeen tetraspanins (GmTsps, all containing the signature features found in the tetraspanin superfamily members. Whereas six of the GmTsps have been previously reported, eleven could be classified as novel because their amino acid sequences do not map to characterized tetraspanins in the available protein data bases. We present a model of the GmTsps by using GmTsp42Ed, whose presence and expression has been recently detected by transcriptomics and proteomics analyses of G. morsitans. Phylogenetically, the identified GmTsps segregate into three major clusters. Structurally, the GmTsps are largely similar to vertebrate tetraspanins. In view of the exploitation of tetraspanins by organisms for survival, these proteins could be targeted using specific antibodies, recombinant large extracellular loop (LEL domains, small-molecule mimetics and siRNAs as potential novel and efficacious putative targets to combat African trypanosomiasis by killing the tsetse fly vector.

  3. Site response - a critical problem in soil-structure interaction analyses for embedded structures

    International Nuclear Information System (INIS)

    Seed, H.B.; Lysmer, J.

    1986-01-01

    Soil-structure interaction analyses for embedded structures must necessarily be based on a knowledge of the manner in which the soil would behave in the absence of any structure - that is on a knowledge and understanding of the spatial distribution of motions in the ground within the depth of embedment of the structure. The nature of these spatial variations is discussed and illustrated by examples of recorded motions. It is shown that both the amplitude of peak acceleration and the form of the acceleration response spectrum for earthquake motions will necessarily vary with depth and failure to take these variations into account may introduce an unwarranted degree of conservatism into the soil-structure interaction analysis procedure

  4. Analyses Of Techniques On Structural Fatigue Failure Detection ...

    African Journals Online (AJOL)

    Machines and structures are subjected to variable loading conditions where the stress cycle does not remain the same during the operation of the machine. Fatigue is undoubtedly one of the most serious of all causes of breakdowns of machines and structures which results in sudden failures. The use of the time domain ...

  5. Evolution and Structural Analyses of Glossina morsitans (Diptera; Glossinidae) Tetraspanins

    NARCIS (Netherlands)

    Murungi, E.K.; Kariithi, H.M.; Adunga, V.; Obonyo, M.; Christoffels, A.

    2014-01-01

    Tetraspanins are important conserved integral membrane proteins expressed in many organisms. Although there is limited knowledge about the full repertoire, evolution and structural characteristics of individual members in various organisms, data obtained so far show that tetraspanins play major

  6. Secretory Structure, Histochemistry and Phytochemistry Analyses of Stimulant Plant

    Science.gov (United States)

    Umah, C.; Dorly; Sulistyaningsih, Y. C.

    2017-03-01

    Plants that are used as stimulant supposed to contains various metabolit compounds that are produced or secreted by secretory structures. This study aimed to identify the secretory structure of plant used as stimulant and chemical compounds accumulated in it. The secretory structure and its histochemistry were observed on plant material that are used as herbal ingredient. Phytochemical content was analyzed by using a qualitative test. The result showed that the idioblast cells and secretory cavities were found in the leaves of Decaspermum fruticosum, and Polyalthia rumphii. Most idioblast cells contained lipophilic substances and terpenoids or alkaloids, while secretory cavity contained alkaloid. Phytochemical analysis for D. fruticosum, and P. rumphii contain terpenoids, phenols, steroids, and flavonoids

  7. Structured Intuition: A Methodology to Analyse Entity Authentication

    DEFF Research Database (Denmark)

    Ahmed, Naveed

    and the level of abstraction used in the analysis. Thus, the goal of developing a high level methodology that can be used with different notions of security, authentication, and abstraction is worth considering. In this thesis, we propose a new methodology, called the structured intuition (SI), which addresses...

  8. Bioinformatics analyses of Shigella CRISPR structure and spacer classification.

    Science.gov (United States)

    Wang, Pengfei; Zhang, Bing; Duan, Guangcai; Wang, Yingfang; Hong, Lijuan; Wang, Linlin; Guo, Xiangjiao; Xi, Yuanlin; Yang, Haiyan

    2016-03-01

    Clustered regularly interspaced short palindromic repeats (CRISPR) are inheritable genetic elements of a variety of archaea and bacteria and indicative of the bacterial ecological adaptation, conferring acquired immunity against invading foreign nucleic acids. Shigella is an important pathogen for anthroponosis. This study aimed to analyze the features of Shigella CRISPR structure and classify the spacers through bioinformatics approach. Among 107 Shigella, 434 CRISPR structure loci were identified with two to seven loci in different strains. CRISPR-Q1, CRISPR-Q4 and CRISPR-Q5 were widely distributed in Shigella strains. Comparison of the first and last repeats of CRISPR1, CRISPR2 and CRISPR3 revealed several base variants and different stem-loop structures. A total of 259 cas genes were found among these 107 Shigella strains. The cas gene deletions were discovered in 88 strains. However, there is one strain that does not contain cas gene. Intact clusters of cas genes were found in 19 strains. From comprehensive analysis of sequence signature and BLAST and CRISPRTarget score, the 708 spacers were classified into three subtypes: Type I, Type II and Type III. Of them, Type I spacer referred to those linked with one gene segment, Type II spacer linked with two or more different gene segments, and Type III spacer undefined. This study examined the diversity of CRISPR/cas system in Shigella strains, demonstrated the main features of CRISPR structure and spacer classification, which provided critical information for elucidation of the mechanisms of spacer formation and exploration of the role the spacers play in the function of the CRISPR/cas system.

  9. Analysing inequalities in Germany a structured additive distributional regression approach

    CERN Document Server

    Silbersdorff, Alexander

    2017-01-01

    This book seeks new perspectives on the growing inequalities that our societies face, putting forward Structured Additive Distributional Regression as a means of statistical analysis that circumvents the common problem of analytical reduction to simple point estimators. This new approach allows the observed discrepancy between the individuals’ realities and the abstract representation of those realities to be explicitly taken into consideration using the arithmetic mean alone. In turn, the method is applied to the question of economic inequality in Germany.

  10. Thermal Shock Structural Analyses of a Positron Target

    International Nuclear Information System (INIS)

    2002-01-01

    In the positron source of the Stanford Linear Collider (SLC), the electron beam collides with a tungsten-rhenium target. As the beam passes into the material, thermal energy is created that heats the material to several hundred degrees centigrade on a time scale of nanoseconds. The heating of the material results in thermal stresses that may be large enough to cause material failure. The analyses calculate the thermal shock pressure and stress pulses as they move throughout the material due to the rapid energy deposition. Failure of the target occurred after three years of operation with an elevated power deposition toward the end of the three years. The calculations were made with the LLNL coupled heat transfer and dynamic solid mechanics analysis codes, TOPAZ3D and DYNA3D, and the thermal energy deposition was calculated with the SLAC Electron Gamma Shower (EGS) code simulating the electron-induced cascade. Material fatigue strength, experimentally measured properties for the non-irradiated and irradiated material, as well as the calculated stress state are evaluated in assessing the cause for the target failure

  11. Structural analyses of sucrose laurate regioisomers by mass spectrometry techniques

    DEFF Research Database (Denmark)

    Lie, Aleksander; Stensballe, Allan; Pedersen, Lars Haastrup

    2015-01-01

    6- And 6′-O-lauroyl sucrose were isolated and analyzed by matrix-assisted laser desorption/ionisation (MALDI) time-of-flight (TOF) mass spectrometry (MS), Orbitrap high-resolution (HR) MS, and electrospray-ionization (ESI) tandem mass spectrometry (MS/MS). The analyses aimed to explore.......8, respectively, and Orbitrap HRMS confirmed the mass of [M+Na]+ (m/z 547.2712). ESI-MS/MS on the precursor ion [M+Na]+ resulted in product ion mass spectra showing two high-intensity signals for each sample. 6-O-Lauroyl sucrose produced signals located at m/z 547.27 and m/z 385.21, corresponding to the 6-O......-lauroyl glucose sodium adduct ions, while the signals for 6′-O-lauroyl sucrose were located at m/z 385.22 and 367.20, respectively corresponding to the sodium adduct ions with 6-O-lauroyl fructose and 6-O-lauroyl fructosyl. The mass spectra of the two regioisomers were clearly different, and the investigation...

  12. Lipids: From Chemical Structures, Biosynthesis, and Analyses to Industrial Applications.

    Science.gov (United States)

    Li-Beisson, Yonghua; Nakamura, Yuki; Harwood, John

    2016-01-01

    Lipids are one of the major subcellular components, and play numerous essential functions. As well as their physiological roles, oils stored in biomass are useful commodities for a variety of biotechnological applications including food, chemical feedstocks, and fuel. Due to their agronomic as well as economic and societal importance, lipids have historically been subjected to intensive studies. Major current efforts are to increase the energy density of cell biomass, and/or create designer oils suitable for specific applications. This chapter covers some basic aspects of what one needs to know about lipids: definition, structure, function, metabolism and focus is also given on the development of modern lipid analytical tools and major current engineering approaches for biotechnological applications. This introductory chapter is intended to serve as a primer for all subsequent chapters in this book outlining current development in specific areas of lipids and their metabolism.

  13. Analysing Vibrations of Dissipative Structures with Connection Disruption

    Science.gov (United States)

    Potapov, A.

    2017-11-01

    The article contains the mathematical models of vibrations and the algorithm to calculate a constructive nonlinear system in case of a sudden failure process in a connection. The calculation model of the structure is viewed as a discreet dissipative system. From the position of time analysis, the author derives the governing equation of the system reaction under static load before the failure. The author has conducted the analysis of the system reaction and has proved certain dependence for its parameters at the moment of connection fracture. For the critical time point we obtained the kinematic (movements, velocities and accelerations) and force parameters of reaction (restoring, dissipative and inertial forces) in two states of the calculation model: before and after the fracture. The article contains the derivation of analytical expressions defining the leap size of the dynamic reaction parameters of the calculation model at the moment of its damage. The author has presented the auxiliary reaction which allows one to evaluate the side effect caused by the constructive element disruption. The side effect reaction equation presents a vector difference of the reaction after and before the damage. The results are illustrated by the example of a two span steel beam the vibrations of which were caused by the sudden destruction of an intermediate support. The evaluation of the solution accuracy is also presented.

  14. Three new hydrochlorothiazide cocrystals: Structural analyses and solubility studies

    Science.gov (United States)

    Ranjan, Subham; Devarapalli, Ramesh; Kundu, Sudeshna; Vangala, Venu R.; Ghosh, Animesh; Reddy, C. Malla

    2017-04-01

    Hydrochlorothiazide (HCT) is a diuretic BCS class IV drug with poor aqueous solubility and low permeability leading to poor oral absorption. The present work explores the cocrystallization technique to enhance the aqueous solubility of HCT. Three new cocrystals of HCT with water soluble coformers phenazine (PHEN), 4-dimethylaminopyridine (DMAP) and picolinamide (PICA) were prepared successfully by solution crystallization method and characterized by single crystal X-ray diffraction (SCXRD), powder X-ray diffraction (PXRD), fourier transform -infraredspectroscopy (FT-IR), differential scanning calorimetry (DSC) and thermogravimetric analysis (TGA). Structural characterization revealed that the cocrystals with PHEN, DMAP and PICA exists in P21/n, P21/c and P21/n space groups, respectively. The improved solubility of HCT-DMAP (4 fold) and HCT-PHEN (1.4 fold) cocrystals whereas decreased solubility of HCT-PICA (0.5 fold) as compared to the free drug were determined after 4 h in phosphate buffer, pH 7.4, at 25 °C by using shaking flask method. HCT-DMAP showed a significant increase in solubility than all previously reported cocrystals of HCT suggest the role of a coformer. The study demonstrates that the selection of coformer could have pronounced impact on the physicochemical properties of HCT and cocrystallization can be a promising approach to improve aqueous solubility of drugs.

  15. Molecular, structural, and phylogenetic analyses of Taxus chinensis JAZs.

    Science.gov (United States)

    Zhang, Meng; Chen, Ying; Nie, Lin; Jin, Xiaofei; Fu, Chunhua; Yu, Longjiang

    2017-07-15

    Taxus spp. are ancient gymnosperms that produce a unique secondary metabolite, namely, taxol, an anticancer drug. JAZ proteins are key regulators of the JA signaling pathway, which control taxol biosynthesis. However, the JAZ proteins of Taxus spp. are poorly studied. In this work, nine JAZ genes from Taxus chinensis were identified using our previous transcriptome data and named as TcJAZ1-TcJAZ9. Of these nine TcJAZ proteins, eight contain Jas and TIFY domains, and the Jas domain of TcJAZ6 is incomplete. Most TcJAZs and PsJAZs are not related to AtJAZs and OsJAZs. Phylogenetic analysis divided all JAZ proteins from Arabidopsis thaliana, Oryza sativa, Picea sitchensis, and T. chinensis into eight subgroups; gymnosperms JAZs were classified into subgroups V-VIII, and angiosperm JAZs were categorized into subgroups I-V. Three motifs of subgroups VI-VIII were identified in gymnosperm JAZs, indicating that gymnosperm JAZ proteins exhibit a different evolutionary process from those of angiosperms. The expression patterns of nine TcJAZs showed that TcJAZ2/3/8 was a key regulator, indicating their important roles in T. chinensis. Results revealed that gymnosperm JAZs differ from angiosperm JAZs in terms of molecular structure. Three novel conserved motifs were found in TcJAZs and PsJAZs. This study provides a basis for research on JA regulatory system in Taxus spp. and for elucidating the significance of JA signaling pathway to land plants. Copyright © 2017. Published by Elsevier B.V.

  16. ASSESSMENT OF CHAROLAIS BULLS POPULATION STRUCTURE BASED ON SNPs ANALYSES

    Directory of Open Access Journals (Sweden)

    Nina Moravčíková

    2014-02-01

    Full Text Available The aim of this study was identification of SNPs in leptin (LEP, leptin receptor (LEPR, growth hormone (GH and specific pituitary transcription factor (Pit-1 genes in order to analyze genetic structure of Charolais bulls’ population. The total numbers of genomic DNA samples were taken from 52 breeding bulls and analyzed by PCR-RFLP method. After digestion with restriction enzymes were detected in bulls’ population alleles with frequency: LEP/Sau3AI A 0.83 and B 0.17 (±0.037; LEPR/BseGI C 0.95 and T 0.05 (±0.021, GH/AluI L 0.62 and V 0.38 (±0.048 and Pit1/HinfI A 0.40 and B 0.60 (±0.048. Based on the observed vs. expected genotypes frequencies population across loci were in Hardy-Weinberg equilibrium (P>0.05, only in case of Pit-1 locus was detected disequilibrium. Predominant were in analyzed breeding bulls LEP/Sau3AIAA (0.69, LEPR/T945MCC (0.90, GH/AluILL (0.43 and Pit-1/HinfIAB (0.65 genotypes. The observed heterozygosity of SNPs was also transferred to the low (LEP/Sau3AI/0.248 and LEPR/T945M/0.088 or median polymorphic information content (GH/AluI/0.366 and Pit-1/HinfI/0.370. Within genetic variability estimating negative (LEPR/T945M and Pit-1/HinfI and positive values (LEP/Sau3AI and GH/AluI of fixation indexes FIS indicating slight heterozygote excess or deficiency based on analyzed genetic marker were observed.

  17. Generalized structural equations improve sexual-selection analyses.

    Directory of Open Access Journals (Sweden)

    Sonia Lombardi

    Full Text Available Sexual selection is an intense evolutionary force, which operates through competition for the access to breeding resources. There are many cases where male copulatory success is highly asymmetric, and few males are able to sire most females. Two main hypotheses were proposed to explain this asymmetry: "female choice" and "male dominance". The literature reports contrasting results. This variability may reflect actual differences among studied populations, but it may also be generated by methodological differences and statistical shortcomings in data analysis. A review of the statistical methods used so far in lek studies, shows a prevalence of Linear Models (LM and Generalized Linear Models (GLM which may be affected by problems in inferring cause-effect relationships; multi-collinearity among explanatory variables and erroneous handling of non-normal and non-continuous distributions of the response variable. In lek breeding, selective pressure is maximal, because large numbers of males and females congregate in small arenas. We used a dataset on lekking fallow deer (Dama dama, to contrast the methods and procedures employed so far, and we propose a novel approach based on Generalized Structural Equations Models (GSEMs. GSEMs combine the power and flexibility of both SEM and GLM in a unified modeling framework. We showed that LMs fail to identify several important predictors of male copulatory success and yields very imprecise parameter estimates. Minor variations in data transformation yield wide changes in results and the method appears unreliable. GLMs improved the analysis, but GSEMs provided better results, because the use of latent variables decreases the impact of measurement errors. Using GSEMs, we were able to test contrasting hypotheses and calculate both direct and indirect effects, and we reached a high precision of the estimates, which implies a high predictive ability. In synthesis, we recommend the use of GSEMs in studies on

  18. Seismic design technology for breeder reactor structures. Volume 2. Special topics in soil/structure interaction analyses

    International Nuclear Information System (INIS)

    Reddy, D.P.

    1983-04-01

    This volume is divided into six chapters: definition of seismic input ground motion, review of state-of-the-art procedures, analysis guidelines, rock/structure interaction analysis example, comparison of two- and three-dimensional analyses, and comparison of analyses using FLUSH and TRI/SAC Codes

  19. Non-linear finite element analyses applicable for the design of large reinforced concrete structures

    NARCIS (Netherlands)

    Engen, M; Hendriks, M.A.N.; Øverli, Jan Arve; Åldstedt, Erik

    2017-01-01

    In order to make non-linear finite element analyses applicable during assessments of the ultimate load capacity or the structural reliability of large reinforced concrete structures, there is need for an efficient solution strategy with a low modelling uncertainty. A solution strategy comprises

  20. 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.

  1. ObStruct: A Method to Objectively Analyse Factors Driving Population Structure Using Bayesian Ancestry Profiles

    Science.gov (United States)

    Gayevskiy, Velimir; Klaere, Steffen; Knight, Sarah; Goddard, Matthew R.

    2014-01-01

    Bayesian inference methods are extensively used to detect the presence of population structure given genetic data. The primary output of software implementing these methods are ancestry profiles of sampled individuals. While these profiles robustly partition the data into subgroups, currently there is no objective method to determine whether the fixed factor of interest (e.g. geographic origin) correlates with inferred subgroups or not, and if so, which populations are driving this correlation. We present ObStruct, a novel tool to objectively analyse the nature of structure revealed in Bayesian ancestry profiles using established statistical methods. ObStruct evaluates the extent of structural similarity between sampled and inferred populations, tests the significance of population differentiation, provides information on the contribution of sampled and inferred populations to the observed structure and crucially determines whether the predetermined factor of interest correlates with inferred population structure. Analyses of simulated and experimental data highlight ObStruct's ability to objectively assess the nature of structure in populations. We show the method is capable of capturing an increase in the level of structure with increasing time since divergence between simulated populations. Further, we applied the method to a highly structured dataset of 1,484 humans from seven continents and a less structured dataset of 179 Saccharomyces cerevisiae from three regions in New Zealand. Our results show that ObStruct provides an objective metric to classify the degree, drivers and significance of inferred structure, as well as providing novel insights into the relationships between sampled populations, and adds a final step to the pipeline for population structure analyses. PMID:24416362

  2. ObStruct: a method to objectively analyse factors driving population structure using Bayesian ancestry profiles.

    Directory of Open Access Journals (Sweden)

    Velimir Gayevskiy

    Full Text Available Bayesian inference methods are extensively used to detect the presence of population structure given genetic data. The primary output of software implementing these methods are ancestry profiles of sampled individuals. While these profiles robustly partition the data into subgroups, currently there is no objective method to determine whether the fixed factor of interest (e.g. geographic origin correlates with inferred subgroups or not, and if so, which populations are driving this correlation. We present ObStruct, a novel tool to objectively analyse the nature of structure revealed in Bayesian ancestry profiles using established statistical methods. ObStruct evaluates the extent of structural similarity between sampled and inferred populations, tests the significance of population differentiation, provides information on the contribution of sampled and inferred populations to the observed structure and crucially determines whether the predetermined factor of interest correlates with inferred population structure. Analyses of simulated and experimental data highlight ObStruct's ability to objectively assess the nature of structure in populations. We show the method is capable of capturing an increase in the level of structure with increasing time since divergence between simulated populations. Further, we applied the method to a highly structured dataset of 1,484 humans from seven continents and a less structured dataset of 179 Saccharomyces cerevisiae from three regions in New Zealand. Our results show that ObStruct provides an objective metric to classify the degree, drivers and significance of inferred structure, as well as providing novel insights into the relationships between sampled populations, and adds a final step to the pipeline for population structure analyses.

  3. Non Linear Analyses for the Evaluation of Seismic Behavior of Mixed R.C.-Masonry Structures

    International Nuclear Information System (INIS)

    Liberatore, Laura; Tocci, Cesare; Masiani, Renato

    2008-01-01

    In this work the seismic behavior of masonry buildings with mixed structural system, consisting of perimeter masonry walls and internal r.c. frames, is studied by means of non linear static (pushover) analyses. Several aspects, like the distribution of seismic action between masonry and r.c. elements, the local and global behavior of the structure, the crisis of the connections and the attainment of the ultimate strength of the whole structure are examined. The influence of some parameters, such as the masonry compressive and tensile strength, on the structural behavior is investigated. The numerical analyses are also repeated on a building in which the r.c. internal frames are replaced with masonry walls

  4. Structural and seismic analyses of waste facility reinforced concrete storage vaults

    International Nuclear Information System (INIS)

    Wang, C.Y.

    1995-01-01

    Facility 317 of Argonne National Laboratory consists of several reinforced concrete waste storage vaults designed and constructed in the late 1940's through the early 1960's. In this paper, structural analyses of these concrete vaults subjected to various natural hazards are described, emphasizing the northwest shallow vault. The natural phenomenon hazards considered include both earthquakes and tornados. Because these vaults are deeply embedded in the soil, the SASSI (System Analysis of Soil-Structure Interaction) code was utilized for the seismic calculations. The ultimate strength method was used to analyze the reinforced concrete structures. In all studies, moment and shear strengths at critical locations of the storage vaults were evaluated. Results of the structural analyses show that almost all the waste storage vaults meet the code requirements according to ACI 349--85. These vaults also satisfy the performance goal such that confinement of hazardous materials is maintained and functioning of the facility is not interrupted

  5. 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. © 2010 The Authors, Animal Genetics © 2010 Stichting International Foundation for Animal Genetics.

  6. Analyses of a steel containment vessel with an outer contact structure under severe internal overpressurization conditions

    International Nuclear Information System (INIS)

    Porter, V.L.

    1994-01-01

    Many Mark-I and Mark-II BWR plants are designed with a steel vessel as the primary containment. Typically, the steel containment vessel (SCV) is enclosed within a reinforced concrete shield building with only a small gap (74-90 mm) separating the two structures. This paper describes finite element analyses performed to evaluate the effects of contact and friction between a steel containment vessel and an outer contact structure when the containment vessel is subjected to large internal pressures. These computations were motivated by a joint program on containment integrity involving the Nuclear Power Engineering Corporation (NUPEC) of Japan, the US Nuclear Regulatory Commission (NRC), and Sandia National Laboratories for testing model containments. Under severe accident loading conditions, the steel containment vessel in a typical Mark-I or Mark-II plant may deform under internal pressurization such that it contacts the inner surface of a shield building wall. (Thermal expansion from increasing accident temperatures would also close the gap between the SCV and the shield building, but temperature effects are not considered in these analyses.) The amount and location of contact and the pressure at which it occurs all affect how the combined structure behaves. A preliminary finite element model has been developed to analyze a model of a typical steel containment vessel con-ling into contact with an outer structure. Both the steel containment vessel and the outer contact structure were modelled with axisymmetric shell finite elements. Of particular interest are the influence that the contact structure has on deformation and potential failure modes of the containment vessel. Furthermore, the coefficient of friction between the two structures was varied to study its effects on the behavior of the containment vessel and on the uplift loads transmitted to the contact structure. These analyses show that the material properties of an outer contact structure and the amount

  7. SYNTHESIS AND STRUCTURAL ANALYSES OF BIS(2-OXO-2,3 ...

    African Journals Online (AJOL)

    SYNTHESIS AND STRUCTURAL ANALYSES OF BIS(2-OXO-2,3-. DIHYDROPYRIMIDIN-1-IUM) TETRACHLORO ZINCATE (II). [H2pymo][ZnCl4] AND BIS(PYRIMIDIN-2-OLATE) ZINC(II). [Zn(PYMO)2]. Mukhtar A. Kurawa. Department of Pure and Industrial Chemistry, Bayero University Kano. P. M. B. 3011 Kano Nigeria.

  8. Comparative sequence and structural analyses of G-protein-coupled receptor crystal structures and implications for molecular models.

    Directory of Open Access Journals (Sweden)

    Catherine L Worth

    Full Text Available BACKGROUND: Up until recently the only available experimental (high resolution structure of a G-protein-coupled receptor (GPCR was that of bovine rhodopsin. In the past few years the determination of GPCR structures has accelerated with three new receptors, as well as squid rhodopsin, being successfully crystallized. All share a common molecular architecture of seven transmembrane helices and can therefore serve as templates for building molecular models of homologous GPCRs. However, despite the common general architecture of these structures key differences do exist between them. The choice of which experimental GPCR structure(s to use for building a comparative model of a particular GPCR is unclear and without detailed structural and sequence analyses, could be arbitrary. The aim of this study is therefore to perform a systematic and detailed analysis of sequence-structure relationships of known GPCR structures. METHODOLOGY: We analyzed in detail conserved and unique sequence motifs and structural features in experimentally-determined GPCR structures. Deeper insight into specific and important structural features of GPCRs as well as valuable information for template selection has been gained. Using key features a workflow has been formulated for identifying the most appropriate template(s for building homology models of GPCRs of unknown structure. This workflow was applied to a set of 14 human family A GPCRs suggesting for each the most appropriate template(s for building a comparative molecular model. CONCLUSIONS: The available crystal structures represent only a subset of all possible structural variation in family A GPCRs. Some GPCRs have structural features that are distributed over different crystal structures or which are not present in the templates suggesting that homology models should be built using multiple templates. This study provides a systematic analysis of GPCR crystal structures and a consistent method for identifying

  9. Comparative sequence and structural analyses of G-protein-coupled receptor crystal structures and implications for molecular models.

    Science.gov (United States)

    Worth, Catherine L; Kleinau, Gunnar; Krause, Gerd

    2009-09-16

    Up until recently the only available experimental (high resolution) structure of a G-protein-coupled receptor (GPCR) was that of bovine rhodopsin. In the past few years the determination of GPCR structures has accelerated with three new receptors, as well as squid rhodopsin, being successfully crystallized. All share a common molecular architecture of seven transmembrane helices and can therefore serve as templates for building molecular models of homologous GPCRs. However, despite the common general architecture of these structures key differences do exist between them. The choice of which experimental GPCR structure(s) to use for building a comparative model of a particular GPCR is unclear and without detailed structural and sequence analyses, could be arbitrary. The aim of this study is therefore to perform a systematic and detailed analysis of sequence-structure relationships of known GPCR structures. We analyzed in detail conserved and unique sequence motifs and structural features in experimentally-determined GPCR structures. Deeper insight into specific and important structural features of GPCRs as well as valuable information for template selection has been gained. Using key features a workflow has been formulated for identifying the most appropriate template(s) for building homology models of GPCRs of unknown structure. This workflow was applied to a set of 14 human family A GPCRs suggesting for each the most appropriate template(s) for building a comparative molecular model. The available crystal structures represent only a subset of all possible structural variation in family A GPCRs. Some GPCRs have structural features that are distributed over different crystal structures or which are not present in the templates suggesting that homology models should be built using multiple templates. This study provides a systematic analysis of GPCR crystal structures and a consistent method for identifying suitable templates for GPCR homology modelling that will

  10. The structure of the General Health Questionnaire (GHQ-12): two meta-analytic factor analyses.

    Science.gov (United States)

    Gnambs, Timo; Staufenbiel, Thomas

    2018-01-30

    The General Health Questionnaire (GHQ-12) is a popular measure of psychological distress. Despite its widespread use, an ongoing controversy pertains to its internal structure. Although the GHQ-12 was originally constructed to capture a unitary construct, empirical studies identified different factor structures. Therefore, this study examined the dimensionality of the GHQ-12 in two independent meta-analyses. The first meta-analysis used summary data published in 38 primary studies (total N = 76,473). Meta-analytic exploratory factor analyses identified two factors formed by negatively and positively worded items. The second meta-analysis included individual responses of 410,640 participants from 84 independent samples. Meta-analytic confirmatory factor analyses corroborated the two-dimensional structure of the GHQ-12. However, bifactor modelling showed that most of the variance was explained by a general factor. Therefore, subscale scores reflected rather limited unique variance. Overall, the two meta-analyses demonstrated that the GHQ-12 is essentially unidimensional. It is not recommended to use and interpret subscale scores because they primarily reflect general mental health rather than distinct constructs.

  11. Fine-scale genetic structure analyses suggest further male than female dispersal in mountain gorillas.

    Science.gov (United States)

    Roy, Justin; Gray, Maryke; Stoinski, Tara; Robbins, Martha M; Vigilant, Linda

    2014-07-07

    Molecular studies in social mammals rarely compare the inferences gained from genetic analyses with field information, especially in the context of dispersal. In this study, we used genetic data to elucidate sex-specific dispersal dynamics in the Virunga Massif mountain gorilla population (Gorilla beringei beringei), a primate species characterized by routine male and female dispersal from stable mixed-sex social groups. Specifically, we conducted spatial genetic structure analyses for each sex and linked our genetically-based observations with some key demographic and behavioural data from this population. To investigate the spatial genetic structure of mountain gorillas, we analysed the genotypes of 193 mature individuals at 11 microsatellite loci by means of isolation-by-distance and spatial autocorrelation analyses. Although not all males and females disperse, female gorillas displayed an isolation-by-distance pattern among groups and a signal of dispersal at short distances from their natal group based on spatial autocorrelation analyses. In contrast, male genotypes were not correlated with spatial distance, thus suggesting a larger mean dispersal distance for males as compared to females. Both within sex and mixed-sex pairs were on average genetically more related within groups than among groups. Our study provides evidence for an intersexual difference in dispersal distance in the mountain gorilla. Overall, it stresses the importance of investigating spatial genetic structure patterns on a sex-specific basis to better understand the dispersal dynamics of the species under investigation. It is currently poorly understood why some male and female gorillas disperse while others remain in the natal group. Our results on average relatedness within and across groups confirm that groups often contain close relatives. While inbreeding avoidance may play a role in driving female dispersal, we note that more detailed dyadic genetic analyses are needed to shed light on

  12. Who will volunteer? Analysing individual and structural factors of volunteering in Swiss sports clubs.

    Science.gov (United States)

    Schlesinger, Torsten; Nagel, Siegfried

    2013-01-01

    This article analyses the conditions influencing volunteering in sports clubs. It focuses not only on individual characteristics of volunteers but also on the corresponding structural conditions of sports clubs. It proposes a model of voluntary work in sports clubs based on economic behaviour theory. The influences of both the individual and context levels on the decision to engage in voluntary work are estimated in different multilevel models. Results of these multilevel analyses indicate that volunteering is not just an outcome of individual characteristics such as lower workloads, higher income, children belonging to the sports club, longer club memberships, or a strong commitment to the club. It is also influenced by club-specific structural conditions; volunteering is more probable in rural sports clubs whereas growth-oriented goals in clubs have a destabilising effect.

  13. Population structure of the wild soybean (Glycine soja) in China: implications from microsatellite analyses.

    Science.gov (United States)

    Guo, Juan; Liu, Yifei; Wang, Yunsheng; Chen, Jianjun; Li, Yinghui; Huang, Hongwen; Qiu, Lijuan; Wang, Ying

    2012-09-01

    Wild soybean (Glycine soja), a native species of East Asia, is the closest wild relative of the cultivated soybean (G. max) and supplies valuable genetic resources for cultivar breeding. Analyses of the genetic variation and population structure of wild soybean are fundamental for effective conservation studies and utilization of this valuable genetic resource. In this study, 40 wild soybean populations from China were genotyped with 20 microsatellites to investigate the natural population structure and genetic diversity. These results were integrated with previous microsatellite analyses for 231 representative individuals from East Asia to investigate the genetic relationships of wild soybeans from China. Analysis of molecular variance (AMOVA) revealed that 43·92 % of the molecular variance occurred within populations, although relatively low genetic diversity was detected for natural wild soybean populations. Most of the populations exhibited significant effects of a genetic bottleneck. Principal co-ordinate analysis, construction of a Neighbor-Joining tree and Bayesian clustering indicated two main genotypic clusters of wild soybean from China. The wild soybean populations, which are distributed in north-east and south China, separated by the Huang-Huai Valley, displayed similar genotypes, whereas those populations from the Huang-Huai Valley were different. The previously unknown population structure of the natural populations of wild soybean distributed throughout China was determined. Two evolutionarily significant units were defined and further analysed by combining genetic diversity and structure analyses from Chinese populations with representative samples from Eastern Asia. The study suggests that during the glacial period there may have been an expansion route between south-east and north-east China, via the temperate forests in the East China Sea Land Bridge, which resulted in similar genotypes of wild soybean populations from these regions. Genetic

  14. Improving small-angle X-ray scattering data for structural analyses of the RNA world.

    Science.gov (United States)

    Rambo, Robert P; Tainer, John A

    2010-03-01

    Defining the shape, conformation, or assembly state of an RNA in solution often requires multiple investigative tools ranging from nucleotide analog interference mapping to X-ray crystallography. A key addition to this toolbox is small-angle X-ray scattering (SAXS). SAXS provides direct structural information regarding the size, shape, and flexibility of the particle in solution and has proven powerful for analyses of RNA structures with minimal requirements for sample concentration and volumes. In principle, SAXS can provide reliable data on small and large RNA molecules. In practice, SAXS investigations of RNA samples can show inconsistencies that suggest limitations in the SAXS experimental analyses or problems with the samples. Here, we show through investigations on the SAM-I riboswitch, the Group I intron P4-P6 domain, 30S ribosomal subunit from Sulfolobus solfataricus (30S), brome mosaic virus tRNA-like structure (BMV TLS), Thermotoga maritima asd lysine riboswitch, the recombinant tRNA(val), and yeast tRNA(phe) that many problems with SAXS experiments on RNA samples derive from heterogeneity of the folded RNA. Furthermore, we propose and test a general approach to reducing these sample limitations for accurate SAXS analyses of RNA. Together our method and results show that SAXS with synchrotron radiation has great potential to provide accurate RNA shapes, conformations, and assembly states in solution that inform RNA biological functions in fundamental ways.

  15. BranchAnalysis2D/3D automates morphometry analyses of branching structures.

    Science.gov (United States)

    Srinivasan, Aditya; Muñoz-Estrada, Jesús; Bourgeois, Justin R; Nalwalk, Julia W; Pumiglia, Kevin M; Sheen, Volney L; Ferland, Russell J

    2018-01-15

    Morphometric analyses of biological features have become increasingly common in recent years with such analyses being subject to a large degree of observer bias, variability, and time consumption. While commercial software packages exist to perform these analyses, they are expensive, require extensive user training, and are usually dependent on the observer tracing the morphology. To address these issues, we have developed a broadly applicable, no-cost ImageJ plugin we call 'BranchAnalysis2D/3D', to perform morphometric analyses of structures with branching morphologies, such as neuronal dendritic spines, vascular morphology, and primary cilia. Our BranchAnalysis2D/3D algorithm allows for rapid quantification of the length and thickness of branching morphologies, independent of user tracing, in both 2D and 3D data sets. We validated the performance of BranchAnalysis2D/3D against pre-existing software packages using trained human observers and images from brain and retina. We found that the BranchAnalysis2D/3D algorithm outputs results similar to available software (i.e., Metamorph, AngioTool, Neurolucida), while allowing faster analysis times and unbiased quantification. BranchAnalysis2D/3D allows inexperienced observers to output results like a trained observer but more efficiently, thereby increasing the consistency, speed, and reliability of morphometric analyses. Copyright © 2017 Elsevier B.V. All rights reserved.

  16. Insulin mimetics in Urtica dioica: structural and computational analyses of Urtica dioica extracts.

    Science.gov (United States)

    Domola, Masoud Shabani; Vu, Vivian; Robson-Doucette, Christine A; Sweeney, Gary; Wheeler, Michael B

    2010-06-01

    Urtica Dioica (UD) is a plant shown to reduce blood glucose levels upon oral ingestion; however, neither its active component nor its mechanism of action has been identified. One active fraction of this extract, termed UD-1, was separated by molecular sieve column chromatography and purified by high performance liquid chromatography (HPLC). While UD-1 did not stimulate insulin secretion in glucose-responsive MIN6 clonal beta-cells, chronic exposure (24 h) significantly enhanced glucose uptake (approximately 1.5-fold) in L6-GLUT4myc myoblast cells. Using HPLC and MALDI-TOF, we further purified the UD-1 fraction into two fractions termed UD-1A and UD-1B. Computational and structural analyses strongly suggested that the antidiabetic component of UD-1 was due to one or more structurally related cyclical peptides that facilitate glucose uptake by forming unique glucose permeable pores. The structure and function of these glucose-conducting pores are discussed herein.

  17. Seismic fragility analyses of nuclear power plant structures based on the recorded earthquake data in Korea

    International Nuclear Information System (INIS)

    Cho, Sung Gook; Joe, Yang Hee

    2005-01-01

    By nature, the seismic fragility analysis results will be considerably affected by the statistical data of design information and site-dependent ground motions. The engineering characteristics of small magnitude earthquake spectra recorded in the Korean peninsula during the last several years are analyzed in this paper. An improved method of seismic fragility analysis is evaluated by comparative analyses to verify its efficiency for practical application to nuclear power plant structures. The effects of the recorded earthquake on the seismic fragilities of Korean nuclear power plant structures are also evaluated from the comparative studies. Observing the obtained results, the proposed method is more efficient for the multi-modes structures. The case study results show that seismic fragility analysis based on the Newmark's spectra in Korea might over-estimate the seismic capacities of Korean facilities

  18. Seismic fragility analyses of nuclear power plant structures based on the recorded earthquake data in Korea

    Energy Technology Data Exchange (ETDEWEB)

    Cho, Sung Gook [Department of Civil and Environmental System Engineering, University of Incheon, 177 Dohwa-dong, Nam-gu, Incheon 402-749 (Korea, Republic of)]. E-mail: sgcho@incheon.ac.kr; Joe, Yang Hee [Department of Civil and Environmental System Engineering, University of Incheon, 177 Dohwa-dong, Nam-gu, Incheon 402-749 (Korea, Republic of)

    2005-08-01

    By nature, the seismic fragility analysis results will be considerably affected by the statistical data of design information and site-dependent ground motions. The engineering characteristics of small magnitude earthquake spectra recorded in the Korean peninsula during the last several years are analyzed in this paper. An improved method of seismic fragility analysis is evaluated by comparative analyses to verify its efficiency for practical application to nuclear power plant structures. The effects of the recorded earthquake on the seismic fragilities of Korean nuclear power plant structures are also evaluated from the comparative studies. Observing the obtained results, the proposed method is more efficient for the multi-modes structures. The case study results show that seismic fragility analysis based on the Newmark's spectra in Korea might over-estimate the seismic capacities of Korean facilities.

  19. Wave response analyses of floating crane structure; Crane sen no jobu kozobutsu no haro oto

    Energy Technology Data Exchange (ETDEWEB)

    Nobukawa, H.; Takaki, M.; Kitamura, M.; Ahou, G. [Hiroshima University, Hiroshima (Japan). Faculty of Engineering; Higashimura, M. [Fukada Salvage and Marine Works Co. Ltd., Osaka (Japan)

    1996-12-31

    Identifying a dynamic load acting on a lifted load in a floating crane moving in waves is important for preparing an operation manual for the floating crane. Analyses were made on motions in waves of a floating crane with a lifting load of 3,600 tons, with considerations given to deformation of the crane structure. Discussions were given on a dynamic load acting on a lifted load. If a case that considers elastic deformation in the crane structure is compared with a case that does not consider same in calculating hull motions of the floating crane, the difference between them is small if wave length {lambda} to the ship length L is about 0.5. However, if {lambda}/L is 1.0 and 1.5, the difference grows very large. Therefore, the effect of deformation in the crane structure on hull motions of the floating crane cannot be ignored in these cases. A dynamic load acting on a lifted load that considers deformation in the crane structure is about 5% of lifted weight in a headsea condition in which the wave height is 2 m and {lambda}/L is 1.5. As opposed, an estimated value of a dynamic load when the crane structure is regarded as a rigid body is 13%, which is 2.6 times as great as the case that considers deformation of the crane structure. 3 refs., 17 figs., 1 tab.

  20. A structured and qualitative systems approach to analysing hydrogen transitions: Key changes and actor mapping

    Energy Technology Data Exchange (ETDEWEB)

    Hugh, Michael J.; Yetano Roche, Maria [Departamento de Engenharia Mecanica (IDMEC), Pav. De Mecanica 1-2, Av. Rovisco Pais, 1049-001 Lisboa (Portugal); Bennett, Simon J. [Imperial College Centre for Energy Policy and Technology (ICCEPT), Imperial College London, Fourth Floor RSM Building, Prince Consort Road, London SW7 2BP (United Kingdom)

    2007-07-15

    A number of 'roadmapping' activities are being carried out internationally with the aim of planning and facilitating transitions to hydrogen energy systems. However, there is an evident discrepancy between the treatment of quantitative and qualitative information in the majority of roadmapping efforts. Whilst quantitative information is frequently analysed in numerical and computational models, conversely qualitative information tends to be incorporated on a significantly more ad hoc basis. Previous attempts at incorporating qualitative considerations have not usually been systematised. In this paper we present a methodology aimed at increasing the rigour with which qualitative information is treated in hydrogen roadmapping activities. The key changes and actor mapping (KCAM) methodology was developed as the primary qualitative component of the European Hydrogen Energy Roadmap project 'HyWays'. KCAM, developed from a well known general systems development model, constitutes a means of qualitatively analysing variable hydrogen supply chains that is structured, systematic and flexible. (author)

  1. EXANA, a program for analysing EXtended energy loss fine structures, EXELFS spectra

    International Nuclear Information System (INIS)

    Tafreshi, M.A.; Bohm, C.; Csillag, S.

    1992-09-01

    This paper is a users guide and reference manual for the EXANA, an IBM or IBM compatible PC-based program used for analysing extended fine structures occurring on the high energy side of the ionisation edges. The RDF (Radial Distance Function) obtained from this analysis contains information about the number, distance, and type of the nearby atoms, as well as the inelastic mean free path and disorder in distances from the centre atom to the atoms in a atomic shell around it. The program can be made available on request. (au)

  2. X-ray structure analyses of biological molecules and particles in Japan. A brief history and future prospect

    International Nuclear Information System (INIS)

    Nakasako, Masayoshi; Yamamoto, Masaki

    2015-01-01

    In Japan, X-ray structure analyses of molecules and particles from biology started in the 1970s. The structure analysis methods have been developed through the innovation of various techniques in advance, and have contributed for understanding the elementary and microscopic processes in life. Here we summarize briefly the history of X-ray structure analyses for structural biology in Japan and think about the prospect. (author)

  3. Analyses of structure and spectroscopic property in amorphous oxides and chalcogenides

    Energy Technology Data Exchange (ETDEWEB)

    Iwadate, Yasuhiko; Hattori, Takeo; Nishiyama, Shin; Fukushima, Kazuko; Yokota, Hideki [Chiba Univ. (Japan). Faculty of Engineering; Noda, Kenji; Nakazawa, Tetsuya

    1998-01-01

    Li{sub 2}O-TeO{sub 2} glasses studied in the present work are known to possess high densities, refractive indexes, dielectric constants, and transmittance against the lights at infrared wavelength region. In spite of their usefulness, there exists little work on the short range structure of Li{sub 2}O-TeO{sub 2} glasses analyzed by not spectroscopy but diffraction experiments. The structure of Li{sub 2}O(15mol%)-TeO{sub 2}(85mol%) and Li{sub 2}O(25mol%)-TeO{sub 2}(75mol%) glasses was analysed by X-ray diffraction in which an interpretation of the radial distribution function was discussed on the basis of the correlation method. (author)

  4. Analysing structural and cultural change in acute settings using a Giddens-Weick paradigmatic approach.

    Science.gov (United States)

    Braithwaite, Jeffrey

    2006-06-01

    An examination of the salient literature on hospital clinical directorates (CDs) is presented. A critique of the largely managerialist, instrumental, hortatory and normative extant literature about CDs is offered. In analysing the literature this way the earlier promotional and critical literature is eschewed in favour of an evaluative approach. CDs are then reconceptualised by locating them within two overarching accounts of social structure--formalised, prescribed frameworks, and enacted, patterned interactions--following the kinds of distinctions made by Giddens, Weick, social action and institutional theorists. Social structure as it relates to culture is also considered, following Martin. Such an approach facilitates an understanding of the general weaknesses of health service perspectives and methods of analysis, and exposes the strengths of Giddens-Weick type paradigms.

  5. Analyses of a steel containment vessel with an outer contact structure under severe internal overpressurization conditions

    International Nuclear Information System (INIS)

    Porter, V.L.

    1993-01-01

    Many Mark-I and Mark-II BWR plants are designed with a steel vessel as the primary containment. Typically, the steel containment vessel (SCV) is enclosed within a reinforced concrete shield building with only a small gap (50--90mm) separating the two structures. This paper describes finite element analyses performed to evaluate the effects of contact and friction between a steel containment vessel and an outer contact structure when the containment vessel is subjected to large internal pressures. These computations were motivated by a joint program on containment integrity involving the Nuclear Power Engineering Corporation (NUPEC) of Japan, the US Nuclear Regulatory Commission (NRC), and Sandia National Laboratories for testing model containments

  6. The Use of Gene Modification and Advanced Molecular Structure Analyses towards Improving Alfalfa Forage

    Energy Technology Data Exchange (ETDEWEB)

    Lei, Yaogeng; Hannoufa, Abdelali; Yu, Peiqiang

    2017-01-29

    Alfalfa is one of the most important legume forage crops in the world. In spite of its agronomic and nutritive advantages, alfalfa has some limitations in the usage of pasture forage and hay supplement. High rapid degradation of protein in alfalfa poses a risk of rumen bloat to ruminants which could cause huge economic losses for farmers. Coupled with the relatively high lignin content, which impedes the degradation of carbohydrate in rumen, alfalfa has unbalanced and asynchronous degradation ratio of nitrogen to carbohydrate (N/CHO) in rumen. Genetic engineering approaches have been used to manipulate the expression of genes involved in important metabolic pathways for the purpose of improving the nutritive value, forage yield, and the ability to resist abiotic stress. Such gene modification could bring molecular structural changes in alfalfa that are detectable by advanced structural analytical techniques. These structural analyses have been employed in assessing alfalfa forage characteristics, allowing for rapid, convenient and cost-effective analysis of alfalfa forage quality. In this article, we review two major obstacles facing alfalfa utilization, namely poor protein utilization and relatively high lignin content, and highlight genetic studies that were performed to overcome these drawbacks, as well as to introduce other improvements to alfalfa quality. We also review the use of advanced molecular structural analysis in the assessment of alfalfa forage for its potential usage in quality selection in alfalfa breeding.

  7. Structural and functional analyses of DNA-sensing and immune activation by human cGAS.

    Directory of Open Access Journals (Sweden)

    Kazuki Kato

    Full Text Available The detection of cytosolic DNA, derived from pathogens or host cells, by cytosolic receptors is essential for appropriate host immune responses. Cyclic GMP-AMP synthase (cGAS is a newly identified cytosolic DNA receptor that produces cyclic GMP-AMP, which activates stimulator of interferon genes (STING, resulting in TBK1-IRF3 pathway activation followed by the production of type I interferons. Here we report the crystal structure of human cGAS. The structure revealed that a cluster of lysine and arginine residues forms the positively charged DNA binding surface of human cGAS, which is important for the STING-dependent immune activation. A structural comparison with other previously determined cGASs and our functional analyses suggested that a conserved zinc finger motif and a leucine residue on the DNA binding surface are crucial for the DNA-specific immune response of human cGAS, consistent with previous work. These structural features properly orient the DNA binding to cGAS, which is critical for DNA-induced cGAS activation and STING-dependent immune activation. Furthermore, we showed that the cGAS-induced activation of STING also involves the activation of the NF-κB and IRF3 pathways. Our results indicated that cGAS is a DNA sensor that efficiently activates the host immune system by inducing two distinct pathways.

  8. Numerical Analyses of Subsoil-structure Interaction in Original Non-commercial Software based on FEM

    Science.gov (United States)

    Cajka, R.; Vaskova, J.; Vasek, J.

    2018-04-01

    For decades attention has been paid to interaction of foundation structures and subsoil and development of interaction models. Given that analytical solutions of subsoil-structure interaction could be deduced only for some simple shapes of load, analytical solutions are increasingly being replaced by numerical solutions (eg. FEM – Finite element method). Numerical analyses provides greater possibilities for taking into account the real factors involved in the subsoil-structure interaction and was also used in this article. This makes it possible to design the foundation structures more efficiently and still reliably and securely. Currently there are several software that, can deal with the interaction of foundations and subsoil. It has been demonstrated that non-commercial software called MKPINTER (created by Cajka) provides appropriately results close to actual measured values. In MKPINTER software stress-strain analysis of elastic half-space by means of Gauss numerical integration and Jacobean of transformation is done. Input data for numerical analysis were observed by experimental loading test of concrete slab. The loading was performed using unique experimental equipment which was constructed in the area Faculty of Civil Engineering, VŠB-TU Ostrava. The purpose of this paper is to compare resulting deformation of the slab with values observed during experimental loading test.

  9. Assessment of abnormal brain structures and networks in major depressive disorder using morphometric and connectome analyses.

    Science.gov (United States)

    Chen, Vincent Chin-Hung; Shen, Chao-Yu; Liang, Sophie Hsin-Yi; Li, Zhen-Hui; Tyan, Yeu-Sheng; Liao, Yin-To; Huang, Yin-Chen; Lee, Yena; McIntyre, Roger S; Weng, Jun-Cheng

    2016-11-15

    It is hypothesized that the phenomenology of major depressive disorder (MDD) is subserved by disturbances in the structure and function of brain circuits; however, findings of structural abnormalities using MRI have been inconsistent. Generalized q-sampling imaging (GQI) methodology provides an opportunity to assess the functional integrity of white matter tracts in implicated circuits. The study population was comprised of 16 outpatients with MDD (mean age 44.81±2.2 years) and 30 age- and gender-matched healthy controls (mean age 45.03±1.88 years). We excluded participants with any other primary mental disorder, substance use disorder, or any neurological illnesses. We used T1-weighted 3D MRI with voxel-based morphometry (VBM) and vertex-wise shape analysis, and GQI with voxel-based statistical analysis (VBA), graph theoretical analysis (GTA) and network-based statistical (NBS) analysis to evaluate brain structure and connectivity abnormalities in MDD compared to healthy controls correlates with clinical measures of depressive symptom severity, Hamilton Depression Rating Scale 17-item (HAMD) and Hospital Anxiety and Depression Scale (HADS). Using VBM and vertex-wise shape analyses, we found significant volumetric decreases in the hippocampus and amygdala among subjects with MDD (pbrain disorder with abnormal circuit structure and connectivity. Copyright © 2016 Elsevier B.V. All rights reserved.

  10. Analysing the relationship between traumatic biographical events and the current structural functioning of personality.

    Science.gov (United States)

    Schiltz, L; Schiltz, J

    2008-01-01

    We present the general structure of a multi-annual research project. Our general expectancy concerns the possibilities of arts psychotherapy as a means of launching the blocked process of subjectivation with people suffering from exclusion, precarity and marginalization. The research project follows a complex research design with a sequential strategy, the first part consisting in an integrated psychosocial and clinical study using a mixed methodology. We constructed special rating scales for the analysis of the data of a semi-structured biographical interview and also for the holistic interpretation of the Rotter Blank Sentences Test, separating the associations to sentences beginning with the third and first person. The correlations between two sets of variables (biographical interview and Rotter test) were computed for the total experimental group (N=206), and for clinical subgroups. We shall analyse the matrices of correlations (Spearman's Rho) with the help of optimal scaling procedures (OVERALS). The links between traumatic biographical events and responses to the 3rd, respectively 1st person items of the Rotter test are interpreted in terms of unconscious versus conscious psychological processes and allow us analysing the expression of defence mechanisms and coping strategies. The results of the study are discussed in the light of the recent traumatogenic hypothesis of borderline functioning.

  11. Structural and functional analyses of the putrescine binding protein PotF from Xanthomonas citri

    International Nuclear Information System (INIS)

    Santana, L.D.F.; Balan, A.

    2012-01-01

    Full text: The focus of our group is to determinate the role of ABC transporters in the physiology and growth of Xanthomonas citri, a phytopathogenic bacteria that infects citrus plants causing significant losses for the economy. One of the ABC transporters identified in the X. citri genome and that was showed to be active during the infection in Citrus sinensis plants was the putrescine transporter. This transporter consists of two internal membrane proteins PotG and PotH that form a pore, a cytoplasmic protein that gives energy for the transport and the periplasmic-binding protein PotF, which is responsible for the affinity and specificity of the system. Its function is associated to the microbial carcinogenesis, biofilm formation, escape from phagolysosomes, bacteriocin production, toxin activity and protection from oxidative and acid stress. In this work, we show for the first time, the expression, purification, functional and structural analyses of the X. citri PotF protein. The PotF was expressed from Escherichia coli cells strain Arctic, as a 40 kDa soluble protein, after induction of IPTG for twenty four hours at thirteen deg C. Using immobilized metal affinity chromatography for purification, the protein was eluted in the fractions with 10-500 mM of imidazole. To test the folding and cability to bind putrescine, spectroscopic analyses were performed using circular dichroism and intrinsic fluorescence. The data showed that PotF suffers conformational changes in presence of ligands and in different pH, suggesting a possible interaction with the tested ligand. Moreover, based on bioinformatics studies and molecular modeling analyses, we showed that X. citri PotF is highly conserved when compared to orthologs present in other bacteria, including the residues that form the ligand-binding site. The production of PotF in a soluble and stable form will allow us to start the crystallization trials in attempt to solve its structure. (author)

  12. Structural and functional analyses of the putrescine binding protein PotF from Xanthomonas citri

    Energy Technology Data Exchange (ETDEWEB)

    Santana, L.D.F.; Balan, A. [Laboratorio Nacional de Biociencias - LNBIO, Campinas, SP (Brazil)

    2012-07-01

    Full text: The focus of our group is to determinate the role of ABC transporters in the physiology and growth of Xanthomonas citri, a phytopathogenic bacteria that infects citrus plants causing significant losses for the economy. One of the ABC transporters identified in the X. citri genome and that was showed to be active during the infection in Citrus sinensis plants was the putrescine transporter. This transporter consists of two internal membrane proteins PotG and PotH that form a pore, a cytoplasmic protein that gives energy for the transport and the periplasmic-binding protein PotF, which is responsible for the affinity and specificity of the system. Its function is associated to the microbial carcinogenesis, biofilm formation, escape from phagolysosomes, bacteriocin production, toxin activity and protection from oxidative and acid stress. In this work, we show for the first time, the expression, purification, functional and structural analyses of the X. citri PotF protein. The PotF was expressed from Escherichia coli cells strain Arctic, as a 40 kDa soluble protein, after induction of IPTG for twenty four hours at thirteen deg C. Using immobilized metal affinity chromatography for purification, the protein was eluted in the fractions with 10-500 mM of imidazole. To test the folding and cability to bind putrescine, spectroscopic analyses were performed using circular dichroism and intrinsic fluorescence. The data showed that PotF suffers conformational changes in presence of ligands and in different pH, suggesting a possible interaction with the tested ligand. Moreover, based on bioinformatics studies and molecular modeling analyses, we showed that X. citri PotF is highly conserved when compared to orthologs present in other bacteria, including the residues that form the ligand-binding site. The production of PotF in a soluble and stable form will allow us to start the crystallization trials in attempt to solve its structure. (author)

  13. Identification of a Herbal Powder by Deoxyribonucleic Acid Barcoding and Structural Analyses.

    Science.gov (United States)

    Sheth, Bhavisha P; Thaker, Vrinda S

    2015-10-01

    Authentic identification of plants is essential for exploiting their medicinal properties as well as to stop the adulteration and malpractices with the trade of the same. To identify a herbal powder obtained from a herbalist in the local vicinity of Rajkot, Gujarat, using deoxyribonucleic acid (DNA) barcoding and molecular tools. The DNA was extracted from a herbal powder and selected Cassia species, followed by the polymerase chain reaction (PCR) and sequencing of the rbcL barcode locus. Thereafter the sequences were subjected to National Center for Biotechnology Information (NCBI) basic local alignment search tool (BLAST) analysis, followed by the protein three-dimension structure determination of the rbcL protein from the herbal powder and Cassia species namely Cassia fistula, Cassia tora and Cassia javanica (sequences obtained in the present study), Cassia Roxburghii, and Cassia abbreviata (sequences retrieved from Genbank). Further, the multiple and pairwise structural alignment were carried out in order to identify the herbal powder. The nucleotide sequences obtained from the selected species of Cassia were submitted to Genbank (Accession No. JX141397, JX141405, JX141420). The NCBI BLAST analysis of the rbcL protein from the herbal powder showed an equal sequence similarity (with reference to different parameters like E value, maximum identity, total score, query coverage) to C. javanica and C. roxburghii. In order to solve the ambiguities of the BLAST result, a protein structural approach was implemented. The protein homology models obtained in the present study were submitted to the protein model database (PM0079748-PM0079753). The pairwise structural alignment of the herbal powder (as template) and C. javanica and C. roxburghii (as targets individually) revealed a close similarity of the herbal powder with C. javanica. A strategy as used here, incorporating the integrated use of DNA barcoding and protein structural analyses could be adopted, as a novel

  14. Quantification of rock heterogeneities by structural geological field studies combined with laboratory analyses

    Science.gov (United States)

    Reyer, Dorothea; Afsar, Filiz; Philipp, Sonja

    2013-04-01

    Heterogeneous rock properties in terms of layering and complex infrastructure of fault zones are typical in sedimentary successions. The knowledge of in-situ mechanical rock properties is crucial for a better understanding of processes such as fracturing and fluid transport in fractured reservoirs. To estimate in situ rock properties at different depths it is important to understand how rocks from outcrops differ from rocks at depth, for example due to alteration and removal of the overburden load. We aim at quantifying these properties by performing structural geological field studies in outcrop analogues combined with laboratory analyses of outcrop samples and drill-cores. The field studies focus on 1) fault zone infrastructure and 2) host rock fracture systems in two different study areas with different lithologies, the North German and the Bristol Channel Basin. We analyse quantitatively the dimension, geometry, persistence and connectivity of fracture systems. The field studies are complemented by systematic sampling to obtain the parameters Young's modulus, compressive and tensile strengths and elastic strain energy (also referred to as destruction work) from which we estimate rock and fracture toughnesses. The results show that in rocks with distinctive layering fractures are often restricted to individual layers, that is, stratabound. The probability of arrest seems to depend on the stiffness contrast between two single layers as well as on the thickness of the softer layer. The results also show that there are clear differences between fault zones in the different lithologies in terms of damage zone thicknesses and fracture system parameters. The results of laboratory analyses show that the mechanical properties vary considerably and for many samples there are clear directional differences. That is, samples taken perpendicular to layering commonly have higher stiffnesses and strengths than those taken parallel to layering. We combine the results of

  15. System response analyses of base-isolated structures to earthquake ground motions

    International Nuclear Information System (INIS)

    Wang, C.Y.; Tang, Y.; Marchertas, A.H.

    1991-01-01

    Seismic isolation is one of the most significant earthquake engineering developments in recent years. This paper describes system response analyses of base-isolated structures to earthquake ground motions. Emphasis is placed on the adaptation of a nonlinear constitutive model for the elastomeric isolation bearing together with the treatment of foundation embedment for the soil-structure- interaction analysis. The constitutive model requires six input parameters derived from bearing experimental data under sinusoidal loading. The characteristic behavior of bearing, such as the variation of shear modulus and material damping with the change of maximum shear deformation, can be captured closely by the formulation. In the treatment of soil embedment a spring method is utilized to evaluate the foundation input motion as well as soil stiffness and damping. The above features have been incorporated into a three-dimensional system response program, SISEC, developed at Argonne National Laboratory (ANL) (Wang et al. 1991). Sample problems are presented to illustrate the relative response of isolated and unisolated structures. 5 refs., 7 figs

  16. Experimental and theoretical analyses of package-on-package structure under three-point bending loading

    International Nuclear Information System (INIS)

    Jia Su; Wang Xi-Shu; Ren Huai-Hui

    2012-01-01

    High density packaging is developing toward miniaturization and integration, which causes many difficulties in designing, manufacturing, and reliability testing. Package-on-Package (PoP) is a promising three-dimensional high-density packaging method that integrates a chip scale package (CSP) in the top package and a fine-pitch ball grid array (FBGA) in the bottom package. In this paper, in-situ scanning electron microscopy (SEM) observation is carried out to detect the deformation and damage of the PoP structure under three-point bending loading. The results indicate that the cracks occur in the die of the top package, then cause the crack deflection and bridging in the die attaching layer. Furthermore, the mechanical principles are used to analyse the cracking process of the PoP structure based on the multi-layer laminating hypothesis and the theoretical analysis results are found to be in good agreement with the experimental results. (condensed matter: structural, mechanical, and thermal properties)

  17. Structural integrity analyses for preemptive weld overlay on the dissimilar metal weld of a pressurizer nozzle

    Energy Technology Data Exchange (ETDEWEB)

    Huang, Chin-Cheng, E-mail: cchuang@iner.gov.tw [Institute of Nuclear Energy Research, Taiwan (China); Liu, Ru-Feng [Institute of Nuclear Energy Research, Taiwan (China)

    2012-02-15

    This paper presents structural integrity analyses for preemptive weld overlay on the dissimilar metal weld (DMW) of a pressurizer nozzle in a pressurized water reactor (PWR). Based on MRP-169 and ASME Code Case N-504-2, weld overlay sizing calculation, residual stress improvement, shrinkage evaluation, fatigue crack growth and fatigue usage analysis are performed. The weld overlay procedure has to be confirmed to improve the residual stresses around the inside surface of DMW. The residual compressive stress distribution is thus addressed to be resistant to subsequent primary water stress corrosion cracking (PWSCC) initiation and further crack growth. To ensure the structural integrity of the original attached piping system, the measured displacement is transformed to temperature gradient to simulate the shrinkage after overlay and is used to determine the post weld distortion and stress situation. Further, the conservative postulated surface cracks are assumed in the DMW for fatigue crack growth analysis with system design cycles. The stress limits and cumulative fatigue usages of the pressurizer nozzle with overlay are also evaluated to meet ASME Code, Section III. Based on the present results, the structural integrity of the pressurizer nozzle with preemptive weld overlay is shown.

  18. Computer-aided analyses of transport protein sequences: gleaning evidence concerning function, structure, biogenesis, and evolution.

    Science.gov (United States)

    Saier, M H

    1994-03-01

    Three-dimensional structures have been elucidated for very few integral membrane proteins. Computer methods can be used as guides for estimation of solute transport protein structure, function, biogenesis, and evolution. In this paper the application of currently available computer programs to over a dozen distinct families of transport proteins is reviewed. The reliability of sequence-based topological and localization analyses and the importance of sequence and residue conservation to structure and function are evaluated. Evidence concerning the nature and frequency of occurrence of domain shuffling, splicing, fusion, deletion, and duplication during evolution of specific transport protein families is also evaluated. Channel proteins are proposed to be functionally related to carriers. It is argued that energy coupling to transport was a late occurrence, superimposed on preexisting mechanisms of solute facilitation. It is shown that several transport protein families have evolved independently of each other, employing different routes, at different times in evolutionary history, to give topologically similar transmembrane protein complexes. The possible significance of this apparent topological convergence is discussed.

  19. Comparing of Normal Stress Distribution in Static and Dynamic Soil-Structure Interaction Analyses

    International Nuclear Information System (INIS)

    Kholdebarin, Alireza; Massumi, Ali; Davoodi, Mohammad; Tabatabaiefar, Hamid Reza

    2008-01-01

    It is important to consider the vertical component of earthquake loading and inertia force in soil-structure interaction analyses. In most circumstances, design engineers are primarily concerned about the analysis of behavior of foundations subjected to earthquake-induced forces transmitted from the bedrock. In this research, a single rigid foundation with designated geometrical parameters located on sandy-clay soil has been modeled in FLAC software with Finite Different Method and subjected to three different vertical components of earthquake records. In these cases, it is important to evaluate effect of footing on underlying soil and to consider normal stress in soil with and without footing. The distribution of normal stress under the footing in static and dynamic states has been studied and compared. This Comparison indicated that, increasing in normal stress under the footing caused by vertical component of ground excitations, has decreased dynamic vertical settlement in comparison with static state

  20. Multistable Microactuators Functioning on the Basis of Electromagnetic Lorentz Force: Nonlinear Structural and Electrothermal Analyses

    International Nuclear Information System (INIS)

    Han, Jeong Sam

    2010-01-01

    In this paper, the design and nonlinear simulation of a multistable electromagnetic microactuator, which provides four stable equilibrium positions within its operating range, have been discussed. Quadstable actuator motion has been made possible by using both X- and Y-directional bistable structures with snapping curved beams. Two pairs of the curved beams are attached to an inner frame in both X- and Y-directions to realize independent bistable behavior in each direction. For the actuation of the actuator at the micrometer scale, an electromagnetic actuation method in which Lorentz force is taken into consideration was used. By using this method, micrometer-stroke quadstability in a plane parallel to a substrate was possible. The feasibility of designing an actuator that can realize quadstable motion by using the electromagnetic actuation method has been thoroughly clarified by performing nonlinear static and dynamic analyses and electrothermal coupled-field analysis of the multistable microactuator

  1. Iran, the bomb and the pursuit of security. Structured conflict analyses

    International Nuclear Information System (INIS)

    Bock, Andreas M.; Henneberg, Ingo

    2014-01-01

    This volume introduces readers to the structured conflict analysis as a tool of social science research and uses this instrument exemplarily to analyze systematically and on a broad basis the various conflicts that are associated with Iran both domestically and in foreign policy - beyond popular stereotypes such as the ''bomb''. The 13 contributions draw a complex picture of the conflicts with and in Iran and reflect the various aspects of these conflicts from different perspectives and at a high methodological and theoretical level. The nuclear program is examined, inter alia through the eyes of four major theories of International Relations. In addition, the analyses are concerned with the regional security dimension, the relationship USA-Iran, the role of national preferences, and the effect of national processes to the Iranian foreign policy.

  2. Impact of reading habit on white matter structure: Cross-sectional and longitudinal analyses.

    Science.gov (United States)

    Takeuchi, Hikaru; Taki, Yasuyuki; Hashizume, Hiroshi; Asano, Kohei; Asano, Michiko; Sassa, Yuko; Yokota, Susumu; Kotozaki, Yuka; Nouchi, Rui; Kawashima, Ryuta

    2016-06-01

    Psychological studies showed the quantity of reading habit affects the development of their reading skills, various language skills, and knowledge. However, despite a vast amount of literature, the effects of reading habit on the development of white matter (WM) structures critical to language and reading processes have never been investigated. In this study, we used the fractional anisotropy (FA) measure of diffusion tensor imaging to measure WM microstructural properties and examined cross-sectional and longitudinal correlations between reading habit and FA of the WM bundles in a large sample of normal children. In both cross-sectional and longitudinal analyses, we found that greater strength of reading habit positively affected FA in the left arcuate fasciculus (AF), in the left inferior fronto-occipital fasciculus (IFOF), and in the left posterior corona radiata (PCR). Consistent with previous studies, we also confirmed the significance or a tendency for positive correlation between the strength of reading habit and the Verbal Comprehension score in cross-sectional and longitudinal analyses. These cross-sectional and longitudinal findings indicate that a healthy reading habit may be directly or indirectly associated with the advanced development of WM critical to reading and language processes. Future intervention studies are needed to determine the causal effects of reading habits on WM in normal children. Copyright © 2016 Elsevier Inc. All rights reserved.

  3. Analyses of Markov decision process structure regarding the possible strategic use of interacting memory systems

    Directory of Open Access Journals (Sweden)

    Eric A Zilli

    2008-12-01

    Full Text Available Behavioral tasks are often used to study the different memory systems present in humans and animals. Such tasks are usually designed to isolate and measure some aspect of a single memory system. However, it is not necessarily clear that any given task actually does isolate a system or that the strategy used by a subject in the experiment is the one desired by the experimenter. We have previously shown that when tasks are written mathematically as a form of partially-observable Markov decision processes, the structure of the tasks provide information regarding the possible utility of certain memory systems. These previous analyses dealt with the disambiguation problem: given a specific ambiguous observation of the environment, is there information provided by a given memory strategy that can disambiguate that observation to allow a correct decisionµ Here we extend this approach to cases where multiple memory systems can be strategically combined in different ways. Specifically, we analyze the disambiguation arising from three ways by which episodic-like memory retrieval might be cued (by another episodic-like memory, by a semantic association, or by working memory for some earlier observation. We also consider the disambiguation arising from holding earlier working memories, episodic-like memories or semantic associations in working memory. From these analyses we can begin to develop a quantitative hierarchy among memory systems in which stimulus-response memories and semantic associations provide no disambiguation while the episodic memory system provides the most flexible

  4. Analysing taxonomic structures and local ecological processes in temperate forests in North Eastern China.

    Science.gov (United States)

    Fan, Chunyu; Tan, Lingzhao; Zhang, Chunyu; Zhao, Xiuhai; von Gadow, Klaus

    2017-10-30

    considered the spatial dispersion of species generated a taxonomic structure which proved to be more consistent with that in the observed community. As sampling sizes increased from 20 m × 20 m to 50 m × 50 m, the magnitudes of SESs of taxonomic ratios increased. Based on the phylogenetic analysis, we found that the Jiaohe plot was phylogenetically clustered at almost all scales. We detected significant phylogenetically overdispersion at the 20 m × 20 m and 30 m × 30 m scales in the Liangshui plot. The results suggest that the effect of abiotic filtering is greater than the effects of interspecific competition in shaping the local community at almost all scales. Local processes influence the taxonomic structures, but their combined effects vary with the spatial scale. The taxonomic approach provides similar insights as the phylogenetic approach, especially when we applied a more conservative null model. Analysing taxonomic structure may be a useful tool for communities where well-resolved phylogenetic data are not available.

  5. Trophic structure in a seabird host-parasite food web: insights from stable isotope analyses.

    Directory of Open Access Journals (Sweden)

    Elena Gómez-Díaz

    2010-05-01

    Full Text Available Ecological studies on food webs rarely include parasites, partly due to the complexity and dimensionality of host-parasite interaction networks. Multiple co-occurring parasites can show different feeding strategies and thus lead to complex and cryptic trophic relationships, which are often difficult to disentangle by traditional methods. We analyzed stable isotope ratios of C ((13C/(12C, delta(13C and N ((15N/(14N, delta(15N of host and ectoparasite tissues to investigate trophic structure in 4 co-occurring ectoparasites: three lice and one flea species, on two closely related and spatially segregated seabird hosts (Calonectris shearwaters. delta(13C isotopic signatures confirmed feathers as the main food resource for the three lice species and blood for the flea species. All ectoparasite species showed a significant enrichment in delta(15N relatively to the host tissue consumed (discrimination factors ranged from 2 to 5 per thousand depending on the species. Isotopic differences were consistent across multiple host-ectoparasite locations, despite of some geographic variability in baseline isotopic levels. Our findings illustrate the influence of both ectoparasite and host trophic ecology in the isotopic structuring of the Calonectris ectoparasite community. This study highlights the potential of stable isotope analyses in disentangling the nature and complexity of trophic relationships in symbiotic systems.

  6. Structural and magnetic properties of multi-core nanoparticles analysed using a generalised numerical inversion method

    Science.gov (United States)

    Bender, P.; Bogart, L. K.; Posth, O.; Szczerba, W.; Rogers, S. E.; Castro, A.; Nilsson, L.; Zeng, L. J.; Sugunan, A.; Sommertune, J.; Fornara, A.; González-Alonso, D.; Barquín, L. Fernández; Johansson, C.

    2017-01-01

    The structural and magnetic properties of magnetic multi-core particles were determined by numerical inversion of small angle scattering and isothermal magnetisation data. The investigated particles consist of iron oxide nanoparticle cores (9 nm) embedded in poly(styrene) spheres (160 nm). A thorough physical characterisation of the particles included transmission electron microscopy, X-ray diffraction and asymmetrical flow field-flow fractionation. Their structure was ultimately disclosed by an indirect Fourier transform of static light scattering, small angle X-ray scattering and small angle neutron scattering data of the colloidal dispersion. The extracted pair distance distribution functions clearly indicated that the cores were mostly accumulated in the outer surface layers of the poly(styrene) spheres. To investigate the magnetic properties, the isothermal magnetisation curves of the multi-core particles (immobilised and dispersed in water) were analysed. The study stands out by applying the same numerical approach to extract the apparent moment distributions of the particles as for the indirect Fourier transform. It could be shown that the main peak of the apparent moment distributions correlated to the expected intrinsic moment distribution of the cores. Additional peaks were observed which signaled deviations of the isothermal magnetisation behavior from the non-interacting case, indicating weak dipolar interactions. PMID:28397851

  7. Analyses of the Sequence and Structural Properties Corresponding to Pentapeptide and Large Palindromes in Proteins.

    Directory of Open Access Journals (Sweden)

    Settu Sridhar

    Full Text Available The analyses of 3967 representative proteins selected from the Protein Data Bank revealed the presence of 2803 pentapeptide and large palindrome sequences with known secondary structure conformation. These represent 2014 unique palindrome sequences. 60% palindromes are not associated with any regular secondary structure and 28% are in helix conformation, 11% in strand conformation and 1% in the coil conformation. The average solvent accessibility values are in the range between 0-155.28 Å2 suggesting that the palindromes in proteins can be either buried, exposed to the solvent or share an intermittent property. The number of residue neighborhood contacts defined by interactions ≤ 3.2 Ǻ is in the range between 0-29 residues. Palindromes of the same length in helix, strand and coil conformation are associated with different amino acid residue preferences at the individual positions. Nearly, 20% palindromes interact with catalytic/active site residues, ligand or metal ions in proteins and may therefore be important for function in the corresponding protein. The average hydrophobicity values for the pentapeptide and large palindromes range between -4.3 to +4.32 and the number of palindromes is almost equally distributed between the negative and positive hydrophobicity values. The palindromes represent 107 different protein families and the hydrolases, transferases, oxidoreductases and lyases contain relatively large number of palindromes.

  8. Structural and magnetic properties of multi-core nanoparticles analysed using a generalised numerical inversion method

    Science.gov (United States)

    Bender, P.; Bogart, L. K.; Posth, O.; Szczerba, W.; Rogers, S. E.; Castro, A.; Nilsson, L.; Zeng, L. J.; Sugunan, A.; Sommertune, J.; Fornara, A.; González-Alonso, D.; Barquín, L. Fernández; Johansson, C.

    2017-04-01

    The structural and magnetic properties of magnetic multi-core particles were determined by numerical inversion of small angle scattering and isothermal magnetisation data. The investigated particles consist of iron oxide nanoparticle cores (9 nm) embedded in poly(styrene) spheres (160 nm). A thorough physical characterisation of the particles included transmission electron microscopy, X-ray diffraction and asymmetrical flow field-flow fractionation. Their structure was ultimately disclosed by an indirect Fourier transform of static light scattering, small angle X-ray scattering and small angle neutron scattering data of the colloidal dispersion. The extracted pair distance distribution functions clearly indicated that the cores were mostly accumulated in the outer surface layers of the poly(styrene) spheres. To investigate the magnetic properties, the isothermal magnetisation curves of the multi-core particles (immobilised and dispersed in water) were analysed. The study stands out by applying the same numerical approach to extract the apparent moment distributions of the particles as for the indirect Fourier transform. It could be shown that the main peak of the apparent moment distributions correlated to the expected intrinsic moment distribution of the cores. Additional peaks were observed which signaled deviations of the isothermal magnetisation behavior from the non-interacting case, indicating weak dipolar interactions.

  9. 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).

  10. Structural analyses of choroid after half-dose verteporfin photodynamic therapy for central serous chorioretinopathy.

    Science.gov (United States)

    Izumi, Takahiko; Koizumi, Hideki; Maruko, Ichiro; Takahashi, Yohei; Sonoda, Shozo; Sakamoto, Taiji; Iida, Tomohiro

    2017-04-01

    To investigate the changes in the intrachoroidal structures after half-dose verteporfin photodynamic therapy (PDT) for central serous chorioretinopathy (CSC). Swept-source optical coherence tomography cross-sectional images of 22 eyes of 22 patients with CSC were retrospectively analysed by a manual delineation technique and binarisation method. In the 22 eyes, the mean subfoveal choroidal thickness decreased from 412.9±112.9 μm at baseline to 340.0±111.0 μm at 3 months (p<0.0001). The mean thickness of the large choroidal vessel layer decreased from 368.7±112.7 μm at baseline to 292.2±118.0 μm at 3 months (p<0.0001), but the mean choriocapillaris-medium choroidal vessel layer thickness did not change from 44.2±29.2 μm at baseline to 47.8±25.7 μm at 3 months (p=0.85). Analyses of the binarised choroidal images showed that a 3 mm subfoveal choroidal area decreased from 1.141±0.290 mm 2 at baseline to 0.962±0.320 mm 2 at 3 months after PDT (p=0.0001). The mean luminal areas decreased from 0.826±0.246 mm 2 at baseline to 0.665±0.234 mm 2 at 3 months (p=0.0001), however, the mean stromal areas did not change from 0.315±0.066 mm 2 at baseline to 0.297±0.095 mm 2 at 3 months (p=0.60). Half-dose PDT reduces subfoveal choroidal thickness and alters the intrachoroidal structures in eyes with CSC. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

  11. Thermo-mechanical finite element analyses of bolted cask lid structures

    International Nuclear Information System (INIS)

    Wieser, G.; Qiao Linan; Eberle, A.; Voelzke, H.

    2004-01-01

    The analysis of complex bolted cask lid structures under mechanical or thermal accident conditions is important for the evaluation of cask integrity and leak-tightness in package design assessment according to the Transport Regulations or in aircraft crash scenarios. In this context BAM is developing methods based on Finite Elements to calculate the effects of mechanical impacts onto the bolted lid structures as well as effects caused by severe fire scenarios. I n case of fire it might be not enough to perform only a thermal heat transfer analysis. The complex cask design in connection with a severe hypothetical time-temperature-curve representing an accident fire scenario will create a strong transient heating up of the cask body and its lid system. This causes relative displacements between the seals and its counterparts that can be analyzed by a so-called thermo-mechanical calculation. Although it is currently not possible to correlate leakage rates with results from deformation analyses directly an appropriate Finite Element model of the considered type of metallic lid seal has been developed. For the present it is possible to estimate the behaviour of the seal based on the calculated relative displacements at its seating and the behaviour of the lid bolts under the impact load or the temperature field respectively. Except of the lid bolts the geometry of the cask and the mechanical loading is axial-symmetric which simplifies the analysis considerably and a two-dimensional Finite Element model with substitute lid bolts may be used. The substitute bolts are modelled as one-dimensional truss or beam elements. An advanced two-dimensional bolt submodel represents the bolts with plane stress continuum elements. This paper discusses the influence of different bolt modelling on the relative displacements at the seating of the seals. Besides this, the influence of bolt modelling, thermal properties and detail in geometry of the two-dimensional Finite Element models on

  12. Methodological effects in Fourier transform infrared (FTIR) spectroscopy: Implications for structural analyses of biomacromolecular samples

    Science.gov (United States)

    Kamnev, Alexander A.; Tugarova, Anna V.; Dyatlova, Yulia A.; Tarantilis, Petros A.; Grigoryeva, Olga P.; Fainleib, Alexander M.; De Luca, Stefania

    2018-03-01

    A set of experimental data obtained by Fourier transform infrared (FTIR) spectroscopy (involving the use of samples ground and pressed with KBr, i.e. in a polar halide matrix) and by matrix-free transmission FTIR or diffuse reflectance infrared Fourier transform (DRIFT) spectroscopic methodologies (involving measurements of thin films or pure powdered samples, respectively) were compared for several different biomacromolecular substances. The samples under study included poly-3-hydroxybutyrate (PHB) isolated from cell biomass of the rhizobacterium Azospirillum brasilense; dry PHB-containing A. brasilense biomass; pectin (natural carboxylated heteropolysaccharide of plant origin; obtained from apple peel) as well as its chemically modified derivatives obtained by partial esterification of its galacturonide-chain hydroxyl moieties with palmitic, oleic and linoleic acids. Significant shifts of some FTIR vibrational bands related to polar functional groups of all the biomacromolecules under study, induced by the halide matrix used for preparing the samples for spectroscopic measurements, were shown and discussed. A polar halide matrix used for preparing samples for FTIR measurements was shown to be likely to affect band positions not only per se, by affecting band energies or via ion exchange (e.g., with carboxylate moieties), but also by inducing crystallisation of metastable amorphous biopolymers (e.g., PHB of microbial origin). The results obtained have important implications for correct structural analyses of polar, H-bonded and/or amphiphilic biomacromolecular systems using different methodologies of FTIR spectroscopy.

  13. Structural analyses and immunomodulatory properties of fructo-oligosaccharides from onion (Allium cepa).

    Science.gov (United States)

    Kumar, V Prasanna; Prashanth, K V Harish; Venkatesh, Y P

    2015-03-06

    Onion (Allium cepa) is an immune-boosting food rich in fructans. The major aim of this study is to characterize and investigate the immunomodulatory properties of onion fructo-oligosaccharides (FOS). FOS was isolated from onion bulbs by hot 80% ethanol extraction (yield: ∼4.5 g/100 g fw) followed by gel permeation chromatography. NMR of onion FOS revealed unusual β-D-Glc terminal residue at the non-reducing end. TLC and ESI-MS analyses showed that onion FOS ranged from trisaccharides to hexasaccharides. Onion FOS (50 μg/mL) significantly increased (∼3-fold) the proliferation of mouse splenocytes/thymocytes vs. control. Further, onion FOS enhanced (∼2.5-fold) the production of nitric oxide by peritoneal exudates cells (PECs) from Wistar rats; intracellular free radicals production and phagocytic activity of isolated murine PECs were also augmented. Our structural and in vitro results indicate that onion FOS comprising of tri- to hexasaccharide units belongs to inulin-type fructans, and possess immunostimulatory activities towards murine lymphocytes and macrophages. Copyright © 2014 Elsevier Ltd. All rights reserved.

  14. Synthesis, characterization, and structural analyses of two cyanide-bridged bimetallic complexes

    Science.gov (United States)

    Kautz, J. A.; Mullica, D. F.; Cunningham, B. P.; Combs, R. A.; Farmer, J. M.

    2000-05-01

    The crystal structures of two bimetallic cyanide-bridged lanthanide (Ln) complexes were obtained by means of three-dimensional single-crystal X-ray diffraction techniques. The isostructural complexes (DMF)4(H2O)3LaFe(CN)6·H2O (I) and (DMF)4(H2O)3CeFe(CN)6·H2O (II) crystallize in the monoclinic system with Z=4 having respective lattice constants of a=17.660(2), 17.633(4); b=8.952(1), 8.920(2); c=20.017(2), 19.950(4) Å; and β=95.68(1), 95.72(3). In each complex, the coordination about the central lanthanide ion is eight in a square antiprism arrangement while the coordination about the iron(III) ion is six, oriented octahedrally. Molecules in the crystal lattice of each complex are held together by normal van der Waals forces and a network of hydrogen bonding. Characterization includes physical property determinations, conoscopic studies, thermal gravimetric analyses (TGA), and IR spectrometric identifications. Select geometric parameters are tabulated and a synthesis of these compounds is presented.

  15. Family structure and posttraumatic stress reactions: a longitudinal study using multilevel analyses

    Directory of Open Access Journals (Sweden)

    Nygaard Egil

    2011-12-01

    Full Text Available Abstract Background There is limited research on the relevance of family structures to the development and maintenance of posttraumatic stress following disasters. We longitudinally studied the effects of marital and parental statuses on posttraumatic stress reactions after the 2004 Southeast Asian tsunami and whether persons in the same households had more shared stress reactions than others. Method The study included a tourist population of 641 Norwegian adult citizens, many of them from families with children. We measured posttraumatic stress symptoms with the Impact of Event Scale-Revised at 6 months and 2 years post-disaster. Analyses included multilevel methods with mixed effects models. Results Results showed that neither marital nor parental status was significantly related to posttraumatic stress. At both assessments, adults living in the same household reported levels of posttraumatic stress that were more similar to one another than adults who were not living together. Between households, disaster experiences were closely related to the variance in posttraumatic stress symptom levels at both assessments. Within households, however, disaster experiences were less related to the variance in symptom level at 2 years than at 6 months. Conclusions These results indicate that adult household members may influence one another's posttraumatic stress reactions as well as their interpretations of the disaster experiences over time. Our findings suggest that multilevel methods may provide important information about family processes after disasters.

  16. Development of NUPREP PC Version and Input Structures for NUCIRC Single Channel Analyses

    Energy Technology Data Exchange (ETDEWEB)

    Yoon, Churl; Jun, Ji Su; Park, Joo Hwan

    2007-12-15

    The input file for a steady-state thermal-hydraulic code NUCIRC consists of common channel input data and specific channel input data in a case of single channel analysis. Even when all the data is ready for the 380 channels' single channel analyses, it takes long time and requires enormous effort to compose an input file by hand-editing. The automatic pre-processor for this tedious job is a NUPREP code. In this study, a NUPREP PC version has been developed from the source list in the program manual of NUCIRC-MOD2.000 that is imported in a form of an execution file. In this procedure, some errors found in PC executions and lost statements are fixed accordingly. It is confirmed that the developed NUPREP code produces input file correctly for the CANDU-6 single channel analysis. Additionally, the NUCIRC input structure and data format are summarized for a single channel analysis and the input CARDs required for the creep information of aged channels are listed.

  17. Development of NUPREP PC Version and Input Structures for NUCIRC Single Channel Analyses

    International Nuclear Information System (INIS)

    Yoon, Churl; Jun, Ji Su; Park, Joo Hwan

    2007-12-01

    The input file for a steady-state thermal-hydraulic code NUCIRC consists of common channel input data and specific channel input data in a case of single channel analysis. Even when all the data is ready for the 380 channels' single channel analyses, it takes long time and requires enormous effort to compose an input file by hand-editing. The automatic pre-processor for this tedious job is a NUPREP code. In this study, a NUPREP PC version has been developed from the source list in the program manual of NUCIRC-MOD2.000 that is imported in a form of an execution file. In this procedure, some errors found in PC executions and lost statements are fixed accordingly. It is confirmed that the developed NUPREP code produces input file correctly for the CANDU-6 single channel analysis. Additionally, the NUCIRC input structure and data format are summarized for a single channel analysis and the input CARDs required for the creep information of aged channels are listed

  18. Energetic, Structural, and Antimicrobial Analyses of [beta]-Lactam Side Chain Recognition by [beta]-Lactamases

    Energy Technology Data Exchange (ETDEWEB)

    Caselli, E.; Powers, R.A.; Blaszczak, L.C.; Wu, C.Y.E.; Prati, F.; Shoichet, B.K. (NWU)

    2010-03-05

    Penicillins and cephalosporins are among the most widely used and successful antibiotics. The emergence of resistance to these {beta}-lactams, most often through bacterial expression of {beta}-lactamases, threatens public health. To understand how {beta}-lactamases recognize their substrates, it would be helpful to know their binding energies. Unfortunately, these have been difficult to measure because {beta}-lactams form covalent adducts with {beta}-lactamases. This has complicated functional analyses and inhibitor design. To investigate the contribution to interaction energy of the key amide (R1) side chain of {beta}-lactam antibiotics, eight acylglycineboronic acids that bear the side chains of characteristic penicillins and cephalosporins, as well as four other analogs, were synthesized. These transition-state analogs form reversible adducts with serine {beta}-lactamases. Therefore, binding energies can be calculated directly from K{sub i} values. The K{sub i} values measured span four orders of magnitude against the Group I {beta}-lactamase AmpC and three orders of magnitude against the Group II {beta}-lactamase TEM-1. The acylglycineboronic acids have K{sub i} values as low as 20 nM against AmpC and as low as 390 nM against TEM-1. The inhibitors showed little activity against serine proteases, such as chymotrypsin. R1 side chains characteristic of {beta}-lactam inhibitors did not have better affinity for AmpC than did side chains characteristic of {beta}-lactam substrates. Two of the inhibitors reversed the resistance of pathogenic bacteria to {beta}-lactams in cell culture. Structures of two inhibitors in their complexes with AmpC were determined by X-ray crystallography to 1.90 {angstrom} and 1.75 {angstrom} resolution; these structures suggest interactions that are important to the affinity of the inhibitors. Acylglycineboronic acids allow us to begin to dissect interaction energies between {beta}-lactam side chains and {beta}-lactamases. Surprisingly

  19. 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…

  20. Characterization of bud emergence 46 (BEM46) protein: Sequence, structural, phylogenetic and subcellular localization analyses

    Energy Technology Data Exchange (ETDEWEB)

    Kumar, Abhishek; Kollath-Leiß, Krisztina; Kempken, Frank, E-mail: fkempken@bot.uni-kiel.de

    2013-08-30

    Highlights: •All eukaryotes have at least a single copy of a bem46 ortholog. •The catalytic triad of BEM46 is illustrated using sequence and structural analysis. •We identified indels in the conserved domain of BEM46 protein. •Localization studies of BEM46 protein were carried out using GFP-fusion tagging. -- Abstract: The bud emergence 46 (BEM46) protein from Neurospora crassa belongs to the α/β-hydrolase superfamily. Recently, we have reported that the BEM46 protein is localized in the perinuclear ER and also forms spots close by the plasma membrane. The protein appears to be required for cell type-specific polarity formation in N. crassa. Furthermore, initial studies suggested that the BEM46 amino acid sequence is conserved in eukaryotes and is considered to be one of the widespread conserved “known unknown” eukaryotic genes. This warrants for a comprehensive phylogenetic analysis of this superfamily to unravel origin and molecular evolution of these genes in different eukaryotes. Herein, we observe that all eukaryotes have at least a single copy of a bem46 ortholog. Upon scanning of these proteins in various genomes, we find that there are expansions leading into several paralogs in vertebrates. Usingcomparative genomic analyses, we identified insertion/deletions (indels) in the conserved domain of BEM46 protein, which allow to differentiate fungal classes such as ascomycetes from basidiomycetes. We also find that exonic indels are able to differentiate BEM46 homologs of different eukaryotic lineage. Furthermore, we unravel that BEM46 protein from N. crassa possess a novel endoplasmic-retention signal (PEKK) using GFP-fusion tagging experiments. We propose that three residues namely a serine 188S, a histidine 292H and an aspartic acid 262D are most critical residues, forming a catalytic triad in BEM46 protein from N. crassa. We carried out a comprehensive study on bem46 genes from a molecular evolution perspective with combination of functional

  1. Characterization of bud emergence 46 (BEM46) protein: Sequence, structural, phylogenetic and subcellular localization analyses

    International Nuclear Information System (INIS)

    Kumar, Abhishek; Kollath-Leiß, Krisztina; Kempken, Frank

    2013-01-01

    Highlights: •All eukaryotes have at least a single copy of a bem46 ortholog. •The catalytic triad of BEM46 is illustrated using sequence and structural analysis. •We identified indels in the conserved domain of BEM46 protein. •Localization studies of BEM46 protein were carried out using GFP-fusion tagging. -- Abstract: The bud emergence 46 (BEM46) protein from Neurospora crassa belongs to the α/β-hydrolase superfamily. Recently, we have reported that the BEM46 protein is localized in the perinuclear ER and also forms spots close by the plasma membrane. The protein appears to be required for cell type-specific polarity formation in N. crassa. Furthermore, initial studies suggested that the BEM46 amino acid sequence is conserved in eukaryotes and is considered to be one of the widespread conserved “known unknown” eukaryotic genes. This warrants for a comprehensive phylogenetic analysis of this superfamily to unravel origin and molecular evolution of these genes in different eukaryotes. Herein, we observe that all eukaryotes have at least a single copy of a bem46 ortholog. Upon scanning of these proteins in various genomes, we find that there are expansions leading into several paralogs in vertebrates. Usingcomparative genomic analyses, we identified insertion/deletions (indels) in the conserved domain of BEM46 protein, which allow to differentiate fungal classes such as ascomycetes from basidiomycetes. We also find that exonic indels are able to differentiate BEM46 homologs of different eukaryotic lineage. Furthermore, we unravel that BEM46 protein from N. crassa possess a novel endoplasmic-retention signal (PEKK) using GFP-fusion tagging experiments. We propose that three residues namely a serine 188S, a histidine 292H and an aspartic acid 262D are most critical residues, forming a catalytic triad in BEM46 protein from N. crassa. We carried out a comprehensive study on bem46 genes from a molecular evolution perspective with combination of functional

  2. Comparative Genome Analyses Reveal Distinct Structure in the Saltwater Crocodile MHC

    Science.gov (United States)

    Jaratlerdsiri, Weerachai; Deakin, Janine; Godinez, Ricardo M.; Shan, Xueyan; Peterson, Daniel G.; Marthey, Sylvain; Lyons, Eric; McCarthy, Fiona M.; Isberg, Sally R.; Higgins, Damien P.; Chong, Amanda Y.; John, John St; Glenn, Travis C.; Ray, David A.; Gongora, Jaime

    2014-01-01

    The major histocompatibility complex (MHC) is a dynamic genome region with an essential role in the adaptive immunity of vertebrates, especially antigen presentation. The MHC is generally divided into subregions (classes I, II and III) containing genes of similar function across species, but with different gene number and organisation. Crocodylia (crocodilians) are widely distributed and represent an evolutionary distinct group among higher vertebrates, but the genomic organisation of MHC within this lineage has been largely unexplored. Here, we studied the MHC region of the saltwater crocodile (Crocodylus porosus) and compared it with that of other taxa. We characterised genomic clusters encompassing MHC class I and class II genes in the saltwater crocodile based on sequencing of bacterial artificial chromosomes. Six gene clusters spanning ∼452 kb were identified to contain nine MHC class I genes, six MHC class II genes, three TAP genes, and a TRIM gene. These MHC class I and class II genes were in separate scaffold regions and were greater in length (2–6 times longer) than their counterparts in well-studied fowl B loci, suggesting that the compaction of avian MHC occurred after the crocodilian-avian split. Comparative analyses between the saltwater crocodile MHC and that from the alligator and gharial showed large syntenic areas (>80% identity) with similar gene order. Comparisons with other vertebrates showed that the saltwater crocodile had MHC class I genes located along with TAP, consistent with birds studied. Linkage between MHC class I and TRIM39 observed in the saltwater crocodile resembled MHC in eutherians compared, but absent in avian MHC, suggesting that the saltwater crocodile MHC appears to have gene organisation intermediate between these two lineages. These observations suggest that the structure of the saltwater crocodile MHC, and other crocodilians, can help determine the MHC that was present in the ancestors of archosaurs. PMID:25503521

  3. Comparative genome analyses reveal distinct structure in the saltwater crocodile MHC.

    Directory of Open Access Journals (Sweden)

    Weerachai Jaratlerdsiri

    Full Text Available The major histocompatibility complex (MHC is a dynamic genome region with an essential role in the adaptive immunity of vertebrates, especially antigen presentation. The MHC is generally divided into subregions (classes I, II and III containing genes of similar function across species, but with different gene number and organisation. Crocodylia (crocodilians are widely distributed and represent an evolutionary distinct group among higher vertebrates, but the genomic organisation of MHC within this lineage has been largely unexplored. Here, we studied the MHC region of the saltwater crocodile (Crocodylus porosus and compared it with that of other taxa. We characterised genomic clusters encompassing MHC class I and class II genes in the saltwater crocodile based on sequencing of bacterial artificial chromosomes. Six gene clusters spanning ∼452 kb were identified to contain nine MHC class I genes, six MHC class II genes, three TAP genes, and a TRIM gene. These MHC class I and class II genes were in separate scaffold regions and were greater in length (2-6 times longer than their counterparts in well-studied fowl B loci, suggesting that the compaction of avian MHC occurred after the crocodilian-avian split. Comparative analyses between the saltwater crocodile MHC and that from the alligator and gharial showed large syntenic areas (>80% identity with similar gene order. Comparisons with other vertebrates showed that the saltwater crocodile had MHC class I genes located along with TAP, consistent with birds studied. Linkage between MHC class I and TRIM39 observed in the saltwater crocodile resembled MHC in eutherians compared, but absent in avian MHC, suggesting that the saltwater crocodile MHC appears to have gene organisation intermediate between these two lineages. These observations suggest that the structure of the saltwater crocodile MHC, and other crocodilians, can help determine the MHC that was present in the ancestors of archosaurs.

  4. Analyses of the sucrose synthase gene family in cotton: structure, phylogeny and expression patterns

    Directory of Open Access Journals (Sweden)

    Chen Aiqun

    2012-06-01

    Full Text Available Abstract Background In plants, sucrose synthase (Sus is widely considered as a key enzyme involved in sucrose metabolism. Several paralogous genes encoding different isozymes of Sus have been identified and characterized in multiple plant genomes, while limited information of Sus genes is available to date for cotton. Results Here, we report the molecular cloning, structural organization, phylogenetic evolution and expression profiles of seven Sus genes (GaSus1 to 7 identified from diploid fiber cotton (Gossypium arboreum. Comparisons between cDNA and genomic sequences revealed that the cotton GaSus genes were interrupted by multiple introns. Comparative screening of introns in homologous genes demonstrated that the number and position of Sus introns are highly conserved among Sus genes in cotton and other more distantly related plant species. Phylogenetic analysis showed that GaSus1, GaSus2, GaSus3, GaSus4 and GaSus5 could be clustered together into a dicot Sus group, while GaSus6 and GaSus7 were separated evenly into other two groups, with members from both dicot and monocot species. Expression profiles analyses of the seven Sus genes indicated that except GaSus2, of which the transcripts was undetectable in all tissues examined, and GaSus7, which was only expressed in stem and petal, the other five paralogues were differentially expressed in a wide ranges of tissues, and showed development-dependent expression profiles in cotton fiber cells. Conclusions This is a comprehensive study of the Sus gene family in cotton plant. The results presented in this work provide new insights into the evolutionary conservation and sub-functional divergence of the cotton Sus gene family in response to cotton fiber growth and development.

  5. PEG/CaFe2O4 nanocomposite: Structural, morphological, magnetic and thermal analyses

    International Nuclear Information System (INIS)

    Khanna, Lavanya; Verma, Narendra K.

    2013-01-01

    The coating of Polyethylene Glycol (PEG) on calcium ferrite (CaFe 2 O 4 ) nanoparticles has been reported in the present study. The X-ray diffraction pattern revealed the formation of orthorhombic structure of bare CaFe 2 O 4 nanoparticles, which was also retained after the PEG coating, along with additional characteristic peaks of PEG at 19° and 23°. The rings of CaFe 2 O 4 nanoparticles were identified by the selected area electron diffraction pattern. The characteristic bands of PEG as observed in its Fourier transform infrared spectrum were also present in PEG coated CaFe 2 O 4 nanoparticles, hence confirming its presence. In the thermal gravimetric studies, the complete thermal decomposition of PEG occurred in a one step process, but in case of PEG coated CaFe 2 O 4 nanoparticles, the decomposition took place at a higher temperature owing to the formation of covalent bonds of PEG with CaFe 2 O 4 nanoparticles. The presence of PEG on CaFe 2 O 4 nanoparticles, spherical formation of PEG coated CaFe 2 O 4 nanoparticles and reduced agglomeration in the CaFe 2 O 4 nanoparticles were revealed by high resolution transmission electron microscope, transmission electron microscope and scanning electron microscope studies, respectively. In vibrating sample magnetometer analysis, both bare as well as coated CaFe 2 O 4 nanoparticles exhibited superparamagnetic behavior. However, a drop in the magnetic saturation value was observed from 36.76 emu/g for CaFe 2 O 4 nanoparticles to 6.74 emu/g for PEG coated CaFe 2 O 4 nanoparticles, due to the formation of magnetically dead layer of PEG. In ZFC and FC analyses, superparamagnetic behavior with blocking temperature for bare and coated nanoparticles has been observed at ∼40 K and ∼60 K, respectively. The increase in the blocking temperature is attributed to the increase in the particle size after PEG coating

  6. Un modèle d’analyse de structures situationnelles de discours

    Directory of Open Access Journals (Sweden)

    Ewa Miczka

    2015-11-01

    Full Text Available A model for the analysis of situational discourse structures In this paper the author presents a model for the analysis of situational discourse structures applied to fait divers. Situational structures of discourse are defined as a sequence of experiential frames. Each frame permits to conceptualize one event forming a part of information introduced in discourse. The proposed model permits to analyze (1 the internal structure of experiencial frames activated in discours and (2 possible relations between frames identified in discourse. The author aims to present the role of situational structures in discourse comprehension – the process which implicates creation of discourse representation.

  7. Using enterprise architecture to analyse how organisational structure impact motivation and learning

    Science.gov (United States)

    Närman, Pia; Johnson, Pontus; Gingnell, Liv

    2016-06-01

    When technology, environment, or strategies change, organisations need to adjust their structures accordingly. These structural changes do not always enhance the organisational performance as intended partly because organisational developers do not understand the consequences of structural changes in performance. This article presents a model-based analysis framework for quantitative analysis of the effect of organisational structure on organisation performance in terms of employee motivation and learning. The model is based on Mintzberg's work on organisational structure. The quantitative analysis is formalised using the Object Constraint Language (OCL) and the Unified Modelling Language (UML) and implemented in an enterprise architecture tool.

  8. Robust, high-throughput solution structural analyses by small angle X-ray scattering (SAXS)

    Energy Technology Data Exchange (ETDEWEB)

    Hura, Greg L.; Menon, Angeli L.; Hammel, Michal; Rambo, Robert P.; Poole II, Farris L.; Tsutakawa, Susan E.; Jenney Jr, Francis E.; Classen, Scott; Frankel, Kenneth A.; Hopkins, Robert C.; Yang, Sungjae; Scott, Joseph W.; Dillard, Bret D.; Adams, Michael W. W.; Tainer, John A.

    2009-07-20

    We present an efficient pipeline enabling high-throughput analysis of protein structure in solution with small angle X-ray scattering (SAXS). Our SAXS pipeline combines automated sample handling of microliter volumes, temperature and anaerobic control, rapid data collection and data analysis, and couples structural analysis with automated archiving. We subjected 50 representative proteins, mostly from Pyrococcus furiosus, to this pipeline and found that 30 were multimeric structures in solution. SAXS analysis allowed us to distinguish aggregated and unfolded proteins, define global structural parameters and oligomeric states for most samples, identify shapes and similar structures for 25 unknown structures, and determine envelopes for 41 proteins. We believe that high-throughput SAXS is an enabling technology that may change the way that structural genomics research is done.

  9. Histochemical analyses of hepatic architecture of the hagfish with special attention to periportal biliary structures.

    Science.gov (United States)

    Umezu, Arisa; Kametani, Harunobu; Akai, Yusuke; Koike, Toru; Shiojiri, Nobuyoshi

    2012-07-01

    The hagfish liver was histochemically examined with special attention to biliary structures around the portal veins. Hepatocytes were organized into tubular structures surrounded by sinusoids. Biliary ductule structures, which resemble the ductal plates transiently appearing in mammalian liver development, were observed around the portal veins, but they did not appear around central veins. Thus, the hagfish liver demonstrates the same basic structure as the mammalian liver; that is, a vascular system from portal to central veins via sinusoids, and portal triad structures consisting of portal veins, hepatic arteries, and intrahepatic bile ducts. The epithelial cells of the ductal platelike structures strongly expressed cytokeratin, had some lectin-binding sites, and were delineated by the basal lamina, which was reactive for periodic acid-Schiff (PAS) staining and Iectin histochemistry. The lumina of the ductal plate-like structures were comparatively small and heterogeneous in diameter around the portal veins, suggesting that the biliary structures may not be efficient for bile secretion. The epithelial cells of the gall bladder had a simple columnar shape and were a PAS-positive cytoplasm. Those of bile ducts near the hilus, including extrahepatic and hepatic ducts, were simple columnar or cuboidal cells, and had large lumina. The cytoplasm in these cells was PAS-positive. These phenotypes with the expression of lectin-binding sites were clearly different from those of the ductal plate-like structures in the liver proper, suggesting that the extrahepatic and intrahepatic biliary structures may have different developmental origins.

  10. Proceedings of the international workshop on structural analyses bridging over between amorphous and crystalline materials (SABAC2008)

    International Nuclear Information System (INIS)

    Shamoto, Shin-ichi; Kodama, Katsuaki

    2008-07-01

    International workshop entitled 'Structural Analyses Bridging over between Amorphous and Crystalline Materials' (SABAC2008) was held on January 10 and 11, 2007 at Techno Community Square 'RICOTTI' in Tokai. Amorphous and crystalline materials are studied historically by various approaches. Recent industrial functional materials such as optical memory material, thermoelectric material, hydrogen storage material, and ionic conductor have intrinsic atomic disorders in their lattices. These local lattice disorders cannot be studied by conventional crystal structure analyses such as Rietveld analysis. Similar difficulty also exists in the structure analysis of nanomaterials. In the workshop, new approaches to the structural analysis on these materials were discussed. This report includes abstracts and materials of the presentations in the workshop. (author)

  11. Atmospheric moisture and cloud structure determined from SSM/I and global gridpoint analyses. [Special Sensor Microwave Imager

    Science.gov (United States)

    Robertson, Franklin R.; Huang, Huo-Jin

    1989-01-01

    Data from the Special Sensor Microwave Imager/I on the DMSP satellite are used to study atmospheric moisture and cloud structure. Column-integrated water vapor and total liquid water retrievals are obtained using an algorithm based on a radiative model for brightness temperature (Wentz, 1983). The results from analyzing microwave and IR measurements are combined with independent global gridpoint analyses to study the distribution and structure of atmospheric moisture over oceanic regions.

  12. Study of parameters important to soil-structure interaction in seismic analyses of nuclear power plants

    International Nuclear Information System (INIS)

    Nelson, T.A.

    1983-12-01

    The development of state-of-the-art techniques for analyzing the effects of soil-structure interaction (SSI) on structures during earthquakes is outlined. Emphasis is placed on methods to account for energy dissipation as a result of both wave propagation away from the structure's foundation and hysteretic soil response. Solution techniques are grouped into two major types: substructure methods, which break the problem into a series of steps; and direct methods, which analyze the soil-structure model in one step. In addition to theoretical and historical development of SSI methodology, case studies are presented illustrating the application of these solution techniques. 94 references

  13. Structure Analyses of Fe-based Metallic Glasses by Electron Diffraction

    Directory of Open Access Journals (Sweden)

    Akihiko Hirata

    2010-12-01

    Full Text Available Nanoscale structural information of amorphous structures has become obtainable by using nanobeam electron diffraction in combination with high resolution imaging. In addition, accurate radial distribution function analysis using energy filter has also become available to know averaged amorphous structures. In this paper, we introduce some applications of these techniques, especially to several Fe-based metallic glasses. On the basis of these results, we discuss a relationship between the glass structure and the glass stability in Fe-based metallic glasses

  14. Bending analyses for 3D engineered structural panels made from laminated paper and carbon fabric

    Science.gov (United States)

    Jinghao Li; John F. Hunt; Zhiyong Cai; Xianyan Zhou

    2013-01-01

    This paper presents analysis of a 3-dimensional engineered structural panel (3DESP) having a tri-axial core structure made from phenolic impregnated laminated-paper composites with and without high strength composite carbon-fiber fabric laminated to the outside of both faces. Both I-beam equations and finite element method were used to analyze four-point bending of the...

  15. Structural and Treatment Analyses of Safe and At-Risk Behaviors and Postures Performed by Pharmacy Employees

    Science.gov (United States)

    Fante, Rhiannon; Gravina, Nicole; Betz, Alison; Austin, John

    2010-01-01

    This study employed structural and treatment analyses to determine factors that contributed to wrist posture safety in a small pharmacy. The pharmacy was located on a university campus and participants were three female pharmacy technicians. These particular employees had experienced various repetitive-motion injuries that resulted in a total of…

  16. Population-based analyses of Giardia duodenalis is consistent with the clonal assemblage structure

    Directory of Open Access Journals (Sweden)

    Takumi Katsuhisa

    2012-08-01

    Full Text Available Abstract Background Giardia duodenalis is a common protozoan parasite of humans and animals. Genetic characterization of single loci indicates the existence of eight groups called assemblages, which differ in their host distribution. Molecular analyses challenged the idea that G. duodenalis is a strictly clonal diplomonad by providing evidence of recombination within and between assemblages. Particularly, inter-assemblage recombination events would complicate the interpretation of multi-locus genotyping data from field isolates: where is a host infected with multiple Giardia genotypes or with a single, recombined Giardia genotype. Methods Population genetic analyses on the single and multiple-locus level on an extensive dataset of G. duodenalis isolates from humans and animals were performed. Results Our analyses indicate that recombination between isolates from different assemblages are apparently very rare or absent in the natural population of Giardia duodenalis. At the multi-locus level, our statistical analyses are more congruent with clonal reproduction and can equally well be explained with the presence of multiple G. duodenalis genotypes within one field isolate. Conclusions We conclude that recombination between G. duodenalis assemblages is either very rare or absent. Recombination between genotypes from the same assemblage and genetic exchange between the nuclei of a single cyst needs further investigation.

  17. Crystallization and preliminary structural analyses of glutamate dehydrogenase from Peptoniphilus asaccharolyticus

    OpenAIRE

    Oliveira, Tania F.; Carrigan, John B.; Hamza, Muaawia A.; Sharkey, Michael A.; Engel, Paul C.; Khan, Amir R.

    2010-01-01

    Selenomethionine-derivatized glutamate dehydrogenase from P. asaccharolyticus has been crystallized. Diffraction data were collected to 3.5 Å resolution from crystals belonging to the rhombohedral space group H32 and structure determination is in progress.

  18. Structural Performance’s Optimally Analysing and Implementing Based on ANSYS Technology

    Science.gov (United States)

    Han, Na; Wang, Xuquan; Yue, Haifang; Sun, Jiandong; Wu, Yongchun

    2017-06-01

    Computer-aided Engineering (CAE) is a hotspot both in academic field and in modern engineering practice. Analysis System(ANSYS) simulation software for its excellent performance become outstanding one in CAE family, it is committed to the innovation of engineering simulation to help users to shorten the design process, improve product innovation and performance. Aimed to explore a structural performance’s optimally analyzing model for engineering enterprises, this paper introduced CAE and its development, analyzed the necessity for structural optimal analysis as well as the framework of structural optimal analysis on ANSYS Technology, used ANSYS to implement a reinforced concrete slab structural performance’s optimal analysis, which was display the chart of displacement vector and the chart of stress intensity. Finally, this paper compared ANSYS software simulation results with the measured results,expounded that ANSYS is indispensable engineering calculation tools.

  19. Research resource: novel structural insights bridge gaps in glycoprotein hormone receptor analyses.

    Science.gov (United States)

    Kreuchwig, Annika; Kleinau, Gunnar; Krause, Gerd

    2013-08-01

    The first version of a glycoprotein hormone receptor (GPHR) information resource was designed to link functional with structural GPHR information, in order to support sequence-structure-function analysis of the LH, FSH, and TSH receptors (http://ssfa-gphr.de). However, structural information on a binding- and signaling-sensitive extracellular fragment (∼100 residues), the hinge region, had been lacking. A new FSHR crystal structure of the hormone-bound extracellular domain has recently been solved. The structure comprises the leucine-rich repeat domain and most parts of the hinge region. We have not only integrated the new FSHR/FSH structure and the derived homology models of TSHR/TSH, LHCGR/CG, and LHCGR/LH into our web-based information resource, but have additionally provided novel tools to analyze the advanced structural features, with the common characteristics and distinctions between GPHRs, in a more precise manner. The hinge region with its second hormone-binding site allows us to assign functional data to the new structural features between hormone and receptor, such as binding details of a sulfated tyrosine (conserved throughout the GPHRs) extending into a pocket of the hormone. We have also implemented a protein interface analysis tool that enables the identification and visualization of extracellular contact points between interaction partners. This provides a starting point for comparing the binding patterns of GPHRs. Together with the mutagenesis data stored in the database, this will help to decipher the essential residues for ligand recognition and the molecular mechanisms of signal transduction, extending from the extracellular hormone-binding site toward the intracellular G protein-binding sites.

  20. Structural Analyses of Avocado sunblotch viroid Reveal Differences in the Folding of Plus and Minus RNA Strands

    Directory of Open Access Journals (Sweden)

    Clémentine Delan-Forino

    2014-01-01

    Full Text Available Viroids are small pathogenic circular single-stranded RNAs, present in two complementary sequences, named plus and minus, in infected plant cells. A high degree of complementarities between different regions of the RNAs allows them to adopt complex structures. Since viroids are naked non-coding RNAs, interactions with host factors appear to be closely related to their structural and catalytic characteristics. Avocado sunblotch viroid (ASBVd, a member of the family Avsunviroidae, replicates via a symmetric RNA-dependant rolling-circle process, involving self-cleavage via hammerhead ribozymes. Consequently, it is assumed that ASBVd plus and minus strands adopt similar structures. Moreover, by computer analyses, a quasi-rod-like secondary structure has been predicted. Nevertheless, secondary and tertiary structures of both polarities of ASBVd remain unsolved. In this study, we analyzed the characteristic of each strand of ASBVd through biophysical analyses. We report that ASBVd transcripts of plus and minus polarities exhibit differences in electrophoretic mobility under native conditions and in thermal denaturation profiles. Subsequently, the secondary structures of plus and minus polarities of ASBVd were probed using the RNA-selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE method. The models obtained show that both polarities fold into different structures. Moreover, our results suggest the existence of a kissing-loop interaction within the minus strand that may play a role in in vivo viroid life cycle.

  1. Detailed Structural Analyses of KOH Activated Carbon from Waste Coffee Beans

    Science.gov (United States)

    Takahata, Tomokazu; Toda, Ikumi; Ono, Hiroki; Ohshio, Shigeo; Akasaka, Hiroki; Himeno, Syuji; Kokubu, Toshinori; Saitoh, Hidetoshi

    2009-11-01

    The relationship of the detailed structural change of KOH activated carbon and hydrogen storage ability was investigated in activated carbon materials fabricated from waste coffee beans. The specific surface area of porous carbon materials calculated from N2 adsorption isotherms stood at 2070 m2/g when the weight ratio of KOH to carbon materials was 5:1, and pore size was in the range of approximately 0.6 to 1.1 nm as micropores. In the structural analysis, X-ray diffraction analysis and Raman spectroscopy indicated structural change in these carbon materials through KOH activation. The order of the graphite structure changed to a smaller scale with this activation. It is theorized that specific surface area increased using micropores provided by carbon materials developed from the descent of the graphite structure. Hydrogen storage ability improved with these structural changes, and reached 0.6 wt % at 2070 m2/g. These results suggest that hydrogen storage ability is conferred by the chemical effect on graphite of carbon materials.

  2. A protein relational database and protein family knowledge bases to facilitate structure-based design analyses.

    Science.gov (United States)

    Mobilio, Dominick; Walker, Gary; Brooijmans, Natasja; Nilakantan, Ramaswamy; Denny, R Aldrin; Dejoannis, Jason; Feyfant, Eric; Kowticwar, Rupesh K; Mankala, Jyoti; Palli, Satish; Punyamantula, Sairam; Tatipally, Maneesh; John, Reji K; Humblet, Christine

    2010-08-01

    The Protein Data Bank is the most comprehensive source of experimental macromolecular structures. It can, however, be difficult at times to locate relevant structures with the Protein Data Bank search interface. This is particularly true when searching for complexes containing specific interactions between protein and ligand atoms. Moreover, searching within a family of proteins can be tedious. For example, one cannot search for some conserved residue as residue numbers vary across structures. We describe herein three databases, Protein Relational Database, Kinase Knowledge Base, and Matrix Metalloproteinase Knowledge Base, containing protein structures from the Protein Data Bank. In Protein Relational Database, atom-atom distances between protein and ligand have been precalculated allowing for millisecond retrieval based on atom identity and distance constraints. Ring centroids, centroid-centroid and centroid-atom distances and angles have also been included permitting queries for pi-stacking interactions and other structural motifs involving rings. Other geometric features can be searched through the inclusion of residue pair and triplet distances. In Kinase Knowledge Base and Matrix Metalloproteinase Knowledge Base, the catalytic domains have been aligned into common residue numbering schemes. Thus, by searching across Protein Relational Database and Kinase Knowledge Base, one can easily retrieve structures wherein, for example, a ligand of interest is making contact with the gatekeeper residue.

  3. Comparative Analyses of Aryl Hydrocarbon Receptor Structure, Function, and Evolution in Marine Mammals

    Science.gov (United States)

    2007-02-01

    to assess biological parameters in large whales. Sloughed skin and fecal samples have been used with success; however, the utility of such samples is...applying our approach to fecal or sloughed skin samples . The minimally invasive nature of remote live biopsy is justified for gaining access to the...stable- isotope analyses of biopsy samples . Canadian Journal of Zoology 79:1442-1454. Hunt, K.E., R.M. Rolland, S.D. Kraus and S.K. Wasser. 2006. Analysis

  4. Using analyses of amino Acid coevolution to understand protein structure and function.

    Science.gov (United States)

    Ashenberg, Orr; Laub, Michael T

    2013-01-01

    Determining which residues of a protein contribute to a specific function is a difficult problem. Analyses of amino acid covariation within a protein family can serve as a useful guide by identifying residues that are functionally coupled. Covariation analyses have been successfully used on several different protein families to identify residues that work together to promote folding, enable protein-protein interactions, or contribute to an enzymatic activity. Covariation is a statistical signal that can be measured in a multiple sequence alignment of homologous proteins. As sequence databases have expanded dramatically, covariation analyses have become easier and more powerful. In this chapter, we describe how functional covariation arises during the evolution of proteins and how this signal can be distinguished from various background signals. We discuss the basic methodology for performing amino acid covariation analysis, using bacterial two-component signal transduction proteins as an example. We provide practical suggestions for each step of the process including assembly of protein sequences, construction of a multiple sequence alignment, measurement of covariation, and analysis of results. Copyright © 2013 Elsevier Inc. All rights reserved.

  5. CASKET: a computer code system for thermal and structural analyses of radioactive material transport and/or storage cask

    Energy Technology Data Exchange (ETDEWEB)

    Ikushima, Takeshi [Japan Atomic Energy Research Inst., Tokai, Ibaraki (Japan). Tokai Research Establishment

    1998-05-01

    A computer code system CASKET (CASK thermal and structural analyses and Evaluation code system) for the thermal and structural analyses which are indispensable for radioactive material transport and/or storage cask designs has been developed. The CASKET is a simplified computer code system to perform parametric analyses on sensitivity evaluations in designing a cask and conducting its safety analysis. Main features of the CASKET are as follow: (1) it is capable to perform impact analysis of casks with shock absorbers, (2) it is capable to perform impact analysis of casks with fins. (3) puncture analysis of casks is capable, (4) rocking analysis of casks during seismic load is capable, (5) material property data library are provided for impact analysis of casks, (6) material property data library are provided for thermal analysis of casks, (7) fin energy absorption data library are provided for impact analysis of casks with fins are and (8) not only main frame computers (OS MSP) but also work stations (OS UNIX) and personal computers (OS Windows 3.1) are available. In the paper, brief illustrations of calculation methods are presented. Some calculation results are compared with experimental ones to confirm the computer programs are useful for thermal and structural analyses. (author)

  6. A new analysing approach for the structure of density fluctuation of supercritical fluid

    International Nuclear Information System (INIS)

    Sato, T; Sugiyama, M; Itoh, K; Mori, K; Fukunaga, T; Misawa, M; Otomo, T; Takata, S

    2008-01-01

    Large scale structural evolution of supercritical carbon dioxide along the isotherm at 32 deg. C was investigated with small-angle neutron scattering. The maximum of the density fluctuation, the so-called 'ridge', was confirmed with Ornstein-Zernike analysis. To investigate the structural change in more detail, the molecular distribution over a large domain was determined with a newly developed reverse Monte Carlo method. From the molecular distribution obtained, the pair distribution function and cluster-size distribution can be calculated. With increasing density of carbon dioxide, the cluster size increases monotonically, whereas the pair distribution function for the range of sizes shorter than 10 A shows a monotonic decrease. From this result, it is suggested that the structural change along the isotherm is caused by the change of balance between growth of clusters and increase of the average density

  7. Seismic response analyses of base isolated structures with high damping elastomeric bearings

    Energy Technology Data Exchange (ETDEWEB)

    Wang, C.Y.; Tang, Y.; Chang, Y.W.; Seidensticker, R.W. (Argonne National Lab., IL (USA)); Marchertas, A.H. (Northern Illinois Univ., De Kalb, IL (USA))

    1991-01-01

    Seismic response analysis of base-isolated structures with high damping elastomeric bearings is described. Emphasis is placed on the adaptation of a nonlinear constitutive model for the isolation bearing together with the treatment of foundation embedment for the soil-structure-interaction analysis. The constitutive model requires six input parameters derived from bearing experimental data under sinusoidal loading. The characteristic behavior of bearing, such as the variation of shear modulus and material damping with the change of maximum shear deformation, can be captured closely by the formulation. In the treatment of soil embedment a spring method is utilized to evaluate the foundation input motion as well as soil stiffness and damping. The above features have been incorporated into a three-dimensional system response program, SISEC, developed at Argonne National Laboratory. Sample problems are presented to illustrate the relative response of isolated and unisolated structures. 11 refs., 12 figs.

  8. Factor analyses of the Hospital Anxiety and Depression Scale: a Bayesian structural equation modeling approach.

    Science.gov (United States)

    Fong, Ted Chun Tat; Ho, Rainbow Tin Hung

    2013-12-01

    The latent structure of the Hospital Anxiety and Depression Scale (HADS) has caused inconsistent results in the literature. The HADS is frequently analyzed via maximum likelihood confirmatory factor analysis (ML-CFA). However, the overly restrictive assumption of exact zero cross-loadings and residual correlations in ML-CFA can lead to poor model fits and distorted factor structures. This study applied Bayesian structural equation modeling (BSEM) to evaluate the latent structure of the HADS. Three a priori models, the two-factor, three-factor, and bifactor models, were investigated in a Chinese community sample (N = 312) and clinical sample (N = 198) using ML-CFA and BSEM. BSEM specified approximate zero cross-loadings and residual correlations through the use of zero-mean, small-variance informative priors. The model comparison was based on the Bayesian information criterion (BIC). Using ML-CFA, none of the three models provided an adequate fit for either sample. The BSEM two-factor model with approximate zero cross-loadings and residual correlations fitted both samples well with the lowest BIC of the three models and displayed a simple and parsimonious factor-loading pattern. The study demonstrated that the two-factor structure fitted the HADS well, suggesting its usefulness in assessing the symptoms of anxiety and depression in clinical practice. BSEM is a sophisticated and flexible statistical technique that better reflects substantive theories and locates the source of model misfit. Future use of BSEM is recommended to evaluate the latent structure of other psychological instruments.

  9. Novel gene-brain structure relationships in psychotic disorder revealed using parallel independent component analyses.

    Science.gov (United States)

    Tandon, Neeraj; Nanda, Pranav; Padmanabhan, Jaya L; Mathew, Ian T; Eack, Shaun M; Narayanan, Balaji; Meda, Shashwath A; Bergen, Sarah E; Ruaño, Gualbert; Windemuth, Andreas; Kocherla, Mohan; Petryshen, Tracey L; Clementz, Brett; Sweeney, John; Tamminga, Carol; Pearlson, Godfrey; Keshavan, Matcheri S

    2017-04-01

    Schizophrenia, schizoaffective disorder, and psychotic bipolar disorder overlap with regard to symptoms, structural and functional brain abnormalities, and genetic risk factors. Neurobiological pathways connecting genes to clinical phenotypes across the spectrum from schizophrenia to psychotic bipolar disorder remain largely unknown. We examined the relationship between structural brain changes and risk alleles across the psychosis spectrum in the multi-site Bipolar-Schizophrenia Network for Intermediate Phenotypes (B-SNIP) cohort. Regional MRI brain volumes were examined in 389 subjects with a psychotic disorder (139 schizophrenia, 90 schizoaffective disorder, and 160 psychotic bipolar disorder) and 123 healthy controls. 451,701 single-nucleotide polymorphisms were screened and processed using parallel independent component analysis (para-ICA) to assess associations between genes and structural brain abnormalities in probands. 482 subjects were included after quality control (364 individuals with psychotic disorder and 118 healthy controls). Para-ICA identified four genetic components including several risk genes already known to contribute to schizophrenia and bipolar disorder and revealed three structural components that showed overlapping relationships with the disease risk genes across the three psychotic disorders. Functional ontologies representing these gene clusters included physiological pathways involved in brain development, synaptic transmission, and ion channel activity. Heritable brain structural findings such as reduced cortical thickness and surface area in probands across the psychosis spectrum were associated with somewhat distinct genes related to putative disease pathways implicated in psychotic disorders. This suggests that brain structural alterations might represent discrete psychosis intermediate phenotypes along common neurobiological pathways underlying disease expression across the psychosis spectrum. Copyright © 2016 Elsevier B.V. All

  10. The evaluation method of soil-spring for the analyses of foundation structures on layered bedsoil

    International Nuclear Information System (INIS)

    Satoh, S.; Sasaki, F.

    1985-01-01

    When performing the finite element method analysis of foundation structures, such as mat slab of reactor buildings and turbine buildings, it is very important to evaluate and model the soil-spring mechanism between foundation and soil correctly. In this model, this paper presents the method in which soil-spring mechanism is evaluated from the theoretical solution. In this theory the semi-infinite elastic solid is assumed to be made of multi-layered soil systems. From the analytical example, it is concluded that the stress analysis of foundation structures on multi-layered soil systems cannot be evaluated by the conventional methods. (orig.)

  11. Analysing the impact of buyers' personality constructs on the market structure of brands

    DEFF Research Database (Denmark)

    Chrysochou, Polymeros; Krystallis, Athanasios; Rungie, Cam

    2008-01-01

    In order to operationalize brand loyalty, various models have been applied that estimate brand measures and further describe patterns and the structure of the markets. A well known model in this area is the Dirichlet-NBD model. Despite major advancements to those models, how buyers' characteristics...... and psychographics influence actual brand measures and the overall market structure in repeat purchase occasions is still under-researched. Moreover, measuring the type and magnitude of buyer-related effects on brand loyalty could provide additional valuable information to brand managers. Aim of this paper...

  12. Phytophthora community structure analyses in Oregon nurseries inform systems approaches to disease management

    Science.gov (United States)

    J.L. Parke; B.J. Knaus; V.J. Fieland; C. Lewis; N.J. Grünwald

    2014-01-01

    Nursery plants are important vectors for plant pathogens. Understanding what pathogens occur in nurseries in different production stages can be useful to the development of integrated systems approaches. Four horticultural nurseries in Oregon were sampled every 2 months for 4 years to determine the identity and community structure of Phytophthora...

  13. Total risk-analysing methods for dam structures and a case study in Turkey

    Energy Technology Data Exchange (ETDEWEB)

    Tosun, H. [Turkish Association of Dam Safety, Ankara (Turkey); Turkoz, M. [Osmangazi Univ., Eskisehir (Turkey). Dept. of Civil Engineering

    2007-07-01

    By considering the various factors of hazard, the total risk of dam structures in a basin can be systematically analyzed. These factors include structural factors such as settlement, seepage, leakage, and internal erosion; and, dam site factors such as seismic activity, landslide, rockfall and flooding. In order to increase safety, these hazards can be analyzed in detail and design and construction measures can be taken into account. This paper outlined the main principles of total risk analysis of dams in a basin. The paper discussed the geological setting and structural geology of the Euphrates-Tigris basin located in Turkey and dam properties of thirty-two large dams, which are located on different seismic zones of the Euphrates basin. Properties that were identified and compared included: structural height, function, type, completed year, volume of dam fill, and reservoir capacity. The paper discussed the methods of analysis using a computer program for the probabilistic and deterministic assessment of seismic hazard. It was concluded that peak ground acceleration changes within a wide range for the dam sites of the basins. In addition, sixteen large dams were in the high-risk class in the basins. 21 refs., 2 tabs., 2 figs.

  14. Testing Mediation Using Multiple Regression and Structural Equation Modeling Analyses in Secondary Data

    Science.gov (United States)

    Li, Spencer D.

    2011-01-01

    Mediation analysis in child and adolescent development research is possible using large secondary data sets. This article provides an overview of two statistical methods commonly used to test mediated effects in secondary analysis: multiple regression and structural equation modeling (SEM). Two empirical studies are presented to illustrate the…

  15. Community structure of arbuscular mycorrhizal fungi in undisturbed vegetation revealed by analyses of LSU rdna sequences

    DEFF Research Database (Denmark)

    Rosendahl, Søren; Holtgrewe-Stukenbrock, Eva

    2004-01-01

    Arbuscular mycorrhizal fungi (AMF) form a mutualistic symbiosis with plant roots and are found in most ecosystems. In this study the community structure of AMF in a clade of the genus Glomus was examined in undisturbed costal grassland using LSU rDNA sequences amplified from roots of Hieracium...

  16. Second Order Nonlinear Hydroelastic Analyses of Floating Bodies - the Primary Consideration of Nonlinear Structure

    DEFF Research Database (Denmark)

    Chen, X.; Cui, W.; Jensen, Jørgen Juncher

    2003-01-01

    The theory and typical numerical results of a second order nonlinear hydroelastic analysis of floating bodies are presented in a series of papers in which only nonlinearity in fluids is considered. Under the assumption of linear fluid, the hydroelastic analysis methods of nonlinear structure are ...

  17. Sequence analyses and 3D structure prediction of two Type III ...

    African Journals Online (AJOL)

    Internet

    2012-04-17

    Apr 17, 2012 ... the usefulness of protein structure models for molecular replacement. Bioinformatics, 21(2): 72-76. Gomez JM, Loir M, Le Gac F (1998). Growth hormone receptors in testis and liver during the spermatogenetic cycle in rainbow trout. (Oncorhynchus mykiss). Biol. Reprod. 58: 483-491. Harvey S, Scanes CG.

  18. Ultra-Structure database design methodology for managing systems biology data and analyses

    Directory of Open Access Journals (Sweden)

    Hemminger Bradley M

    2009-08-01

    Full Text Available Abstract Background Modern, high-throughput biological experiments generate copious, heterogeneous, interconnected data sets. Research is dynamic, with frequently changing protocols, techniques, instruments, and file formats. Because of these factors, systems designed to manage and integrate modern biological data sets often end up as large, unwieldy databases that become difficult to maintain or evolve. The novel rule-based approach of the Ultra-Structure design methodology presents a potential solution to this problem. By representing both data and processes as formal rules within a database, an Ultra-Structure system constitutes a flexible framework that enables users to explicitly store domain knowledge in both a machine- and human-readable form. End users themselves can change the system's capabilities without programmer intervention, simply by altering database contents; no computer code or schemas need be modified. This provides flexibility in adapting to change, and allows integration of disparate, heterogenous data sets within a small core set of database tables, facilitating joint analysis and visualization without becoming unwieldy. Here, we examine the application of Ultra-Structure to our ongoing research program for the integration of large proteomic and genomic data sets (proteogenomic mapping. Results We transitioned our proteogenomic mapping information system from a traditional entity-relationship design to one based on Ultra-Structure. Our system integrates tandem mass spectrum data, genomic annotation sets, and spectrum/peptide mappings, all within a small, general framework implemented within a standard relational database system. General software procedures driven by user-modifiable rules can perform tasks such as logical deduction and location-based computations. The system is not tied specifically to proteogenomic research, but is rather designed to accommodate virtually any kind of biological research. Conclusion We find

  19. Organic chemistry as a language and the implications of chemical linguistics for structural and retrosynthetic analyses.

    Science.gov (United States)

    Cadeddu, Andrea; Wylie, Elizabeth K; Jurczak, Janusz; Wampler-Doty, Matthew; Grzybowski, Bartosz A

    2014-07-28

    Methods of computational linguistics are used to demonstrate that a natural language such as English and organic chemistry have the same structure in terms of the frequency of, respectively, text fragments and molecular fragments. This quantitative correspondence suggests that it is possible to extend the methods of computational corpus linguistics to the analysis of organic molecules. It is shown that within organic molecules bonds that have highest information content are the ones that 1) define repeat/symmetry subunits and 2) in asymmetric molecules, define the loci of potential retrosynthetic disconnections. Linguistics-based analysis appears well-suited to the analysis of complex structural and reactivity patterns within organic molecules. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  20. Electrochemical alloying of immiscible Ag and Co for their structural and magnetic analyses

    Science.gov (United States)

    Santhi, Kalavathy; Kumarsan, Dhanapal; Vengidusamy, Naryanan; Arumainathan, Stephen

    2017-07-01

    Electrochemical alloying of immiscible Ag and Co was carried out at different current densities from electrolytes of two different concentrations, after optimizing the electrolytic bath and operating conditions. The samples obtained were characterized using X-ray diffraction to confirm the simultaneous deposition of Ag and Co and to determine their crystallographic structure. The atomic percentage of Ag and Co contents in the granular alloy was determined by ICP-OES analysis. The XPS spectra were observed to confirm the presence of Ag and Co in the metallic form in the granular alloy samples. The micrographs observed using scanning and transmission electron microscopes threw light on the surface morphology and the size of the particles. The magnetic nature of the samples was analyzed at room temperature by a vibration sample magnetometer. Their magnetic phase transition while heating was also studied to provide further evidence for the magnetic behaviour and the structure of the deposits.

  1. ANALYSING THE SOIL STRUCTURE UNDER DIFFERENT TILLAGE SYSTEMS USING X-RAY MICROTOMOGRAPHY AND PF CURVES

    OpenAIRE

    Beekkerk van Ruth, Jöran; Degre, Aurore; Aubinet, Marc; Roisin, Christian; Léonard, Angélique; Beckers, Eléonore

    2011-01-01

    Assessing soil structure is primordial when comparing tillage systems. Whilst most conventional techniques characterize global parameters, X-ray microtomography allows a characterization of the poral space at a µm-scale. These results, combined with data from pF curves, can form a solid basis in order to quantify soil physical fertility. Soil samples were taken from the organic topsoil on two Belgian experimental sites implementing both conventional tillage (CT, ploughing) and simplified ...

  2. A systematic method for analysing the protein hydration structure of T4 lysozyme

    Czech Academy of Sciences Publication Activity Database

    Kysilka, Jiří; Vondrášek, Jiří

    2013-01-01

    Roč. 26, č. 10 (2013), s. 479-487 ISSN 0952-3499 R&D Projects: GA ČR GAP208/10/0725; GA MŠk(CZ) LH11020 Grant - others:GA ČR(CZ) GAP302/10/0427 Institutional support: RVO:61388963 Keywords : protein hydration structure * water * X-ray crystallography * cluster algorithm * interaction enthalpy Subject RIV: CE - Biochemistry Impact factor: 2.337, year: 2013

  3. Membrane-interaction quantitative structure--activity relationship (MI-QSAR) analyses of skin penetration enhancers.

    Science.gov (United States)

    Zheng, Tao; Hopfinger, A J; Esposito, Emilio X; Liu, Jianzhong; Tseng, Yufeng J

    2008-06-01

    Membrane-interaction quantitative structure-activity relationship (MI-QSAR) models for two skin penetration enhancer data sets of 61 and 42 compounds were constructed and compared to QSAR models constructed for the same two data sets using only classic intramolecular QSAR descriptors. These two data sets involve skin penetration enhancement of hydrocortisone and hydrocortisone acetate, and the enhancers are generally similar in structure to lipids and surfactants. A new MI-QSAR descriptor, the difference in the integrated cylindrical distribution functions over the phospholipid monolayer model, in and out of the presence of the skin penetration enhancer, DeltaSigma h(r), was developed. This descriptor is dominant in the optimized MI-QSAR models of both training sets studied and greatly reduces the size and complexity of the MI-QSAR models as compared to those QSAR models developed using the classic intramolecular descriptors. The MI-QSAR models indicate that good penetration enhancers make bigger "holes" in the monolayer and are less aqueous-soluble, so as to preferentially enter the monolayer, than are poor penetration enhancers. The skin penetration enhancer thus alters the structure and organization of the monolayer. This space and time alteration in the structure and dynamics of the membrane monolayer is captured by DeltaSigma h(r) and is simplistically referred to as "holes" in the monolayer. The MI-QSAR models explain 70-80% of the variance in skin penetration enhancement across each of the two training sets and are stable predictive models using accepted diagnostic measures of robustness and predictivity.

  4. Nanometer-resolved chemical analyses of femtosecond laser-induced periodic surface structures on titanium

    Science.gov (United States)

    Kirner, Sabrina V.; Wirth, Thomas; Sturm, Heinz; Krüger, Jörg; Bonse, Jörn

    2017-09-01

    The chemical characteristics of two different types of laser-induced periodic surface structures (LIPSS), so-called high and low spatial frequency LIPSS (HSFL and LSFL), formed upon irradiation of titanium surfaces by multiple femtosecond laser pulses in air (30 fs, 790 nm, 1 kHz), are analyzed by various optical and electron beam based surface analytical techniques, including micro-Raman spectroscopy, energy dispersive X-ray analysis, X-ray photoelectron spectroscopy, and Auger electron spectroscopy. The latter method was employed in a high-resolution mode being capable of spatially resolving even the smallest HSFL structures featuring spatial periods below 100 nm. In combination with an ion sputtering technique, depths-resolved chemical information of superficial oxidation processes was obtained, revealing characteristic differences between the two different types of LIPSS. Our results indicate that a few tens of nanometer shallow HSFL are formed on top of a ˜150 nm thick graded superficial oxide layer without sharp interfaces, consisting of amorphous TiO2 and partially crystallized Ti2O3. The larger LSFL structures with periods close to the irradiation wavelength originate from the laser-interaction with metallic titanium. They are covered by a ˜200 nm thick amorphous oxide layer, which consists mainly of TiO2 (at the surface) and other titanium oxide species of lower oxidation states underneath.

  5. Structural and Kinetic Analyses of Macrophage Migration Inhibitory Factor Active Site Interactions

    Energy Technology Data Exchange (ETDEWEB)

    Crichlow, G.; Lubetsky, J; Leng, L; Bucala, R; Lolis, E

    2009-01-01

    Macrophage migration inhibitory factor (MIF) is a secreted protein expressed in numerous cell types that counters the antiinflammatory effects of glucocorticoids and has been implicated in sepsis, cancer, and certain autoimmune diseases. Interestingly, the structure of MIF contains a catalytic site resembling the tautomerase/isomerase sites of microbial enzymes. While bona fide physiological substrates remain unknown, model substrates have been identified. Selected compounds that bind in the tautomerase active site also inhibit biological functions of MIF. It had previously been shown that the acetaminophen metabolite, N-acetyl-p-benzoquinone imine (NAPQI), covalently binds to the active site of MIF. In this study, kinetic data indicate that NAPQI inhibits MIF both covalently and noncovalently. The structure of MIF cocrystallized with NAPQI reveals that the NAPQI has undergone a chemical alteration forming an acetaminophen dimer (bi-APAP) and binds noncovalently to MIF at the mouth of the active site. We also find that the commonly used protease inhibitor, phenylmethylsulfonyl fluoride (PMSF), forms a covalent complex with MIF and inhibits the tautomerase activity. Crystallographic analysis reveals the formation of a stable, novel covalent bond for PMSF between the catalytic nitrogen of the N-terminal proline and the sulfur of PMSF with complete, well-defined electron density in all three active sites of the MIF homotrimer. Conclusions are drawn from the structures of these two MIF-inhibitor complexes regarding the design of novel compounds that may provide more potent reversible and irreversible inhibition of MIF.

  6. Multivariate Analyses of Quality Metrics for Crystal Structures in the PDB Archive.

    Science.gov (United States)

    Shao, Chenghua; Yang, Huanwang; Westbrook, John D; Young, Jasmine Y; Zardecki, Christine; Burley, Stephen K

    2017-03-07

    Following deployment of an augmented validation system by the Worldwide Protein Data Bank (wwPDB) partnership, the quality of crystal structures entering the PDB has improved. Of significance are improvements in quality measures now prominently displayed in the wwPDB validation report. Comparisons of PDB depositions made before and after introduction of the new reporting system show improvements in quality measures relating to pairwise atom-atom clashes, side-chain torsion angle rotamers, and local agreement between the atomic coordinate structure model and experimental electron density data. These improvements are largely independent of resolution limit and sample molecular weight. No significant improvement in the quality of associated ligands was observed. Principal component analysis revealed that structure quality could be summarized with three measures (Rfree, real-space R factor Z score, and a combined molecular geometry quality metric), which can in turn be reduced to a single overall quality metric readily interpretable by all PDB archive users. Copyright © 2017 Elsevier Ltd. All rights reserved.

  7. Factors governing the metal coordination number in metal complexes from Cambridge Structural Database analyses.

    Science.gov (United States)

    Dudev, Minko; Wang, Jonathan; Dudev, Todor; Lim, Carmay

    2006-02-02

    The metal coordination number (CN) is a key determinant of the structure and properties of metal complexes. It also plays an important role in metal selectivity in certain metalloproteins. Despite its central role, the preferred CN for several metal cations remains ambiguous, and the factors determining the metal CN are not fully understood. Here, we evaluate how the CN depends on (1) the metal's size, charge, and charge-accepting ability for a given set of ligands, and (2) the ligand's size, charge, charge-donating ability, and denticity for a given metal by analyzing the Cambridge Structural Database (CSD) structures of metal ions in the periodic table. The results show that for a given ligand type, the metal's size seems to affect its CN more than its charge, especially if the ligand is neutral, whereas, for a given metal type, the ligand's charge and charge-donating ability appear to affect the metal CN more than the ligand's size. Interestingly, all 98 metal cations surveyed could adopt more than than one CN, and most of them show an apparent preference toward even rather than odd CNs. Furthermore, as compared to the preferred metal CNs observed in the CSD, those in protein binding sites generally remain the same. This implies that the protein matrix (excluding amino acid residues in the metal's first and second coordination shell) does not impose severe geometrical restrictions on the bound metal cation.

  8. Sensitivity Study of Poisson's Ratio Used in Soil Structure Interaction (SSI) Analyses

    Energy Technology Data Exchange (ETDEWEB)

    Han, Seung-ju [KHNP CRI, Daejeon (Korea, Republic of); You, Dong-Hyun [KEPCO Engineering and Construction, Gimcheon (Korea, Republic of); Jang, Jung-bum; Yun, Kwan-hee [KEPCO Research Institute, Daejeon (Korea, Republic of)

    2016-10-15

    The preliminary review for Design Certification (DC) of APR1400 was accepted by NRC on March 4, 2015. After the acceptance of the application for standard DC of APR1400, KHNP has responded the Request for Additional Information (RAI) raised by NRC to undertake a full design certification review. Design certification is achieved through the NRC's rulemaking process, and is founded on the staff's review of the application, which addresses the various safety issues associated with the proposed nuclear power plant design, independent of a specific site. The USNRC issued RAIs pertain to Design Control Document (DCD) Ch.3.7 'Seismic Design' is DCD Tables 3.7A-1 and 3.7A-2 show Poisson’s ratios in the S1 and S2 soil profiles used for SSI analysis as great as 0.47 and 0.48 respectively. Based on staff experience, use of Poisson's ratio approaching these values may result in numerical instability of the SSI analysis results. Sensitivity study is performed using the ACS SASSI NI model of APR1400 with S1 and S2 soil profiles to demonstrate that the Poisson’s ratio values used in the SSI analyses of S1 and S2 soil profile cases do not produce numerical instabilities in the SSI analysis results. No abrupt changes or spurious peaks, which tend to indicate existence of numerical sensitivities in the SASSI solutions, appear in the computed transfer functions of the original SSI analyses that have the maximum dynamic Poisson’s ratio values of 0.47 and 0.48 as well as in the re-computed transfer functions that have the maximum dynamic Poisson’s ratio values limited to 0.42 and 0.45.

  9. NUMERICAL MODELLING AS NON-DESTRUCTIVE METHOD FOR THE ANALYSES AND DIAGNOSIS OF STONE STRUCTURES: MODELS AND POSSIBILITIES

    Directory of Open Access Journals (Sweden)

    Nataša Štambuk-Cvitanović

    1999-12-01

    Full Text Available Assuming the necessity of analysis, diagnosis and preservation of existing valuable stone masonry structures and ancient monuments in today European urban cores, numerical modelling become an efficient tool for the structural behaviour investigation. It should be supported by experimentally found input data and taken as a part of general combined approach, particularly non-destructive techniques on the structure/model within it. For the structures or their detail which may require more complex analyses three numerical models based upon finite elements technique are suggested: (1 standard linear model; (2 linear model with contact (interface elements; and (3 non-linear elasto-plastic and orthotropic model. The applicability of these models depend upon the accuracy of the approach or type of the problem, and will be presented on some characteristic samples.

  10. Numerical analyses of the effect of SG-interlayer shear stiffness on the structural performance of reinforced glass beams

    DEFF Research Database (Denmark)

    Louter, C.; Nielsen, Jens Henrik

    2013-01-01

    of SentryGlas (SG) interlayer sheets. The current contribution numerically investigates the effect of the SG-interlayer shear stiffness on the overall structural response of the beams. This is done by means of a 3D finite element model in which the individual glass layers, the SG......-interlayers and the reinforcement are incorporated. In the model, the glass parts are allowed to crack, but all other parts are assumed linear elastic throughout the analyses. By changing the shear modulus of the SG-interlayer in multiple analyses, its contribution to the overall structural performance of the beams - especially......This paper focuses on the numerical modelling of SentryGlas-laminated reinforced glass beams. In these beams, which have been experimentally investigated in preceding research, a stainless steel reinforcement section is laminated at the inner recessed edge of a triple-layer glass beam by means...

  11. Numerical analyses of the effect of SG-interlayer shear stiffness on the structural performance of reinforced glass beams

    DEFF Research Database (Denmark)

    Louter, C.; Nielsen, Jens Henrik

    2013-01-01

    -interlayers and the reinforcement are incorporated. In the model, the glass parts are allowed to crack, but all other parts are assumed linear elastic throughout the analyses. By changing the shear modulus of the SG-interlayer in multiple analyses, its contribution to the overall structural performance of the beams - especially......This paper focuses on the numerical modelling of SentryGlas-laminated reinforced glass beams. In these beams, which have been experimentally investigated in preceding research, a stainless steel reinforcement section is laminated at the inner recessed edge of a triple-layer glass beam by means...... of SentryGlas (SG) interlayer sheets. The current contribution numerically investigates the effect of the SG-interlayer shear stiffness on the overall structural response of the beams. This is done by means of a 3D finite element model in which the individual glass layers, the SG...

  12. Structure analyses of swollen rubber-filler systems by using contrast variation Small angle neutron scattering (SANS)

    International Nuclear Information System (INIS)

    Takenaka, Mikihito; Nishitsuji, Shotaro; Yamaguchi, Daisuke; Koizumi, Satoshi

    2009-01-01

    Full text: The polymer layers absorbed on silica particles in rubber-silica systems have investigated with contrast variation small-angle neutron scattering (SANS) method. The scattering intensities of specimens swollen by the solvents having various scattering length densities were measured. The contrast variation SANS for the specimens yielded partial scattering functions: the scattering function for polymer-polymer correlation SPP(q), the scattering function for silica- silica correlation SSS(q), and the scattering function for polymer- silica correlation SPS(q). The analyses of SSS(q) explored the hierarchical structures formed by silica particles. The analyses of SPS(q) and SSS(q) clarified the existence of dense polymer layers around silica aggregates. Several characteristic parameters are estimated from the analyses, such as the size of aggregates, the thickness of layers, the volume fractions of polymer of layers and matrix, and the correlation length of the matrix network. The contrast variation SANS is found to be a powerful tool of the analyses of the structures of the rubber-filler systems. (author)

  13. Tenant mix structure in shopping centres: some empirical analyses from Poland

    Directory of Open Access Journals (Sweden)

    Bartłomiej Marona

    2016-06-01

    Full Text Available Objective: The objective of this paper is to find an ideal tenant mix structure for the current shopping centres in Upper Silesian Urban Area Region in Poland, taking under consideration consumer preferences and behaviour. Research Design & Methods: Apart from literature review, empirical research is based on a survey questionnaire. The Analytic Hierarchy Process was applied in the analysis of the data collected. Findings: The research confirmed that to a great extent the valid tenant mix structure in the surveyed shopping centres meets with friendly attitude of customers. However, there are areas where improvement can increase the visitors’ satisfaction. Moreover, it was proven that shopping remains the main reason for customers’ visits in shopping centres, in spite of extending the offer of this type of places with new functions. Implications & Recommendations: Real estate managers are recommended to take actions aiming at increasing competitiveness on the market via the extension of the proposed shopping offer and their adjustment to customers’ expectations. For the managers, the results of the conducted research suggest lack of the necessity for radical transformations, and transforming Polish shopping centres into facilities of the fourth and fifth generation, which is slow in Poland, is, as it turns out, not necessarily expected, since customers identify shopping centres mainly with their traditional function. Contribution & Value Added: The proposed research model and findings can serve as a useful lens within the research of tenant mix structure in shopping centres in other parts of the Poland.

  14. Hydrogen and hydration structures of macromolecule revealed by neutron crystallographic analyses

    International Nuclear Information System (INIS)

    Chatake, Toshiyuki; Morimoto, Yukio

    2007-01-01

    In order to reveal the hydration structure of B-DNA and Z-DNA, a neutron diffraction study has been performed at 3.5 and 1.8 A resolution, respectively. The results of Z-DNA are mainly described in this report. It has been generally accepted that almost all water molecules in the minor groove are well ordered in the crystal, while 40% of the water molecules in the major groove are rotationally disordered. However, partial fluctuation of the water molecules is observed even in the minor groove. Hemoglobin (Hb) consists of two α and β subunits and transports oxygen. The α and β subunits are structurally and evolutionarily related each other and each subunit has an oxygen binding site which is called heme. Depending on oxygen attachment, Hb has two structural states, T(tense) which has low O 2 affinity and R(relax) which has high O 2 affinity. Neutron diffraction crystallography has been performed in deoxygenated Hb in the T state without oxygen bonds, and the hydrogen-binding process of histidine residue is discussed in detail. Allosteric effects in Nb arise from the equilibrium between T and R states. The importance of the hydrogen bond between α and β subunits was pointed out in the allosteric effects. The solvent exchange rates of side chain protons of His α 103 and His α 122 have been measured in both deoxygenated and ligated Hb by NMR. This mechanism of the difference of the exchange rate between R and T states in His α 103 and His α 122 is discussed. (author)

  15. Structural analyses of a constitutively active mutant of exchange protein directly activated by cAMP.

    Science.gov (United States)

    White, Mark A; Li, Sheng; Tsalkova, Tamara; Mei, Fang C; Liu, Tong; Woods, Virgil L; Cheng, Xiaodong

    2012-01-01

    Exchange proteins directly activated by cAMP (EPACs) are important allosteric regulators of cAMP-mediated signal transduction pathways. To understand the molecular mechanism of EPAC activation, we have combined site-directed mutagenesis, X-ray crystallography, and peptide amide hydrogen/deuterium exchange mass spectrometry (DXMS) to probe the structural and conformational dynamics of EPAC2-F435G, a constitutively active EPAC2 mutant. Our study demonstrates that conformational dynamics plays a critical role in cAMP-induced EPAC activation. A glycine mutation at 435 position shifts the equilibrium of conformational dynamics towards the extended active conformation.

  16. Structural analyses of a constitutively active mutant of exchange protein directly activated by cAMP.

    Directory of Open Access Journals (Sweden)

    Mark A White

    Full Text Available Exchange proteins directly activated by cAMP (EPACs are important allosteric regulators of cAMP-mediated signal transduction pathways. To understand the molecular mechanism of EPAC activation, we have combined site-directed mutagenesis, X-ray crystallography, and peptide amide hydrogen/deuterium exchange mass spectrometry (DXMS to probe the structural and conformational dynamics of EPAC2-F435G, a constitutively active EPAC2 mutant. Our study demonstrates that conformational dynamics plays a critical role in cAMP-induced EPAC activation. A glycine mutation at 435 position shifts the equilibrium of conformational dynamics towards the extended active conformation.

  17. GSEVM v.2: MCMC software to analyse genetically structured environmental variance models

    DEFF Research Database (Denmark)

    Ibáñez-Escriche, N; Garcia, M; Sorensen, D

    2010-01-01

    This note provides a description of software that allows to fit Bayesian genetically structured variance models using Markov chain Monte Carlo (MCMC). The gsevm v.2 program was written in Fortran 90. The DOS and Unix executable programs, the user's guide, and some example files are freely available...... for research purposes at http://www.bdporc.irta.es/estudis.jsp. The main feature of the program is to compute Monte Carlo estimates of marginal posterior distributions of parameters of interest. The program is quite flexible, allowing the user to fit a variety of linear models at the level of the mean...

  18. Second Order Nonlinear Hydroelastic Analyses of Floating Bodies - the Primary Consideration of Nonlinear Structure

    DEFF Research Database (Denmark)

    Chen, X.; Cui, W.; Jensen, Jørgen Juncher

    2003-01-01

    The theory and typical numerical results of a second order nonlinear hydroelastic analysis of floating bodies are presented in a series of papers in which only nonlinearity in fluids is considered. Under the assumption of linear fluid, the hydroelastic analysis methods of nonlinear structure...... are introduced in this paper. With the examples of the motion and displacement reponses of a floating plate undergoing large vertical deflections in multidirectional waves, the analysis method of the couple action between the vertical deflections in multidirectional waves, the analysis method of the couple...

  19. Seismic fragility analyses of nuclear power plant structures based on the recorded earthquake data in Korea

    International Nuclear Information System (INIS)

    Joe, Yang Hee; Cho, Sung Gook

    2003-01-01

    This paper briefly introduces an improved method for evaluating seismic fragilities of components of nuclear power plants in Korea. Engineering characteristics of small magnitude earthquake spectra recorded in the Korean peninsula during the last several years are also discussed in this paper. For the purpose of evaluating the effects of the recorded earthquake on the seismic fragilities of Korean nuclear power plant structures, several cases of comparative studies have been performed. The study results show that seismic fragility analysis based on the Newmark's spectra in Korea might over-estimate the seismic capacities of Korean facilities. (author)

  20. Quantitative structure-activity relationship models of chemical transformations from matched pairs analyses.

    Science.gov (United States)

    Beck, Jeremy M; Springer, Clayton

    2014-04-28

    The concepts of activity cliffs and matched molecular pairs (MMP) are recent paradigms for analysis of data sets to identify structural changes that may be used to modify the potency of lead molecules in drug discovery projects. Analysis of MMPs was recently demonstrated as a feasible technique for quantitative structure-activity relationship (QSAR) modeling of prospective compounds. Although within a small data set, the lack of matched pairs, and the lack of knowledge about specific chemical transformations limit prospective applications. Here we present an alternative technique that determines pairwise descriptors for each matched pair and then uses a QSAR model to estimate the activity change associated with a chemical transformation. The descriptors effectively group similar transformations and incorporate information about the transformation and its local environment. Use of a transformation QSAR model allows one to estimate the activity change for novel transformations and therefore returns predictions for a larger fraction of test set compounds. Application of the proposed methodology to four public data sets results in increased model performance over a benchmark random forest and direct application of chemical transformations using QSAR-by-matched molecular pairs analysis (QSAR-by-MMPA).

  1. Functional and structural analyses of a 1,4-β-endoglucanase from Ganoderma lucidum.

    Science.gov (United States)

    Liu, Guizhi; Li, Qian; Shang, Na; Huang, Jian-Wen; Ko, Tzu-Ping; Liu, Weidong; Zheng, Yingying; Han, Xu; Chen, Yun; Chen, Chun-Chi; Jin, Jian; Guo, Rey-Ting

    2016-05-01

    Ganoderma lucidum is a saprotrophic white-rot fungus which contains a rich set of cellulolytic enzymes. Here, we screened an array of potential 1,4-β-endoglucanases from G. lucidum based on the gene annotation library and found that one candidate gene, GlCel5A, exhibits CMC-hydrolyzing activity. The recombinant GlCel5A protein expressed in Pichia pastoris is able to hydrolyze CMC and β-glucan but not xylan and mannan. The enzyme exhibits optimal activity at 60°C and pH 3-4, and retained 50% activity at 80 and 90°C for at least 15 and 10min. The crystal structure of GlCel5A and its complex with cellobiose, solved at 2.7 and 2.86Å resolution, shows a classical (β/α)8 TIM-barrel fold as seen in other members of glycoside hydrolase family 5. The complex structure contains a cellobiose molecule in the +1 and +2 subsites, and reveals the interactions with the positive sites of the enzyme. Collectively, the present work provides the first comprehensive characterization of an endoglucanase from G. lucidum that possesses properties for industrial applications, and strongly encourages further studying in the cellulolytic enzyme system of G. lucidum. Copyright © 2016. Published by Elsevier Inc.

  2. Structural and Functional Analyses of the Severe Acute Respiratory Syndrome Coronavirus Endoribonuclease Nsp15

    Energy Technology Data Exchange (ETDEWEB)

    Bhardwaj, Kanchan; Palaninathan, Satheesh; Alcantara, Joanna Maria Ortiz; Yi, Lillian Li; Guarino, Linda; Sacchettini, James C.; Kao, C. Cheng (TAM)

    2008-03-31

    The severe acute respiratory syndrome (SARS) coronavirus encodes several RNA-processing enzymes that are unusual for RNA viruses, including Nsp15 (nonstructural protein 15), a hexameric endoribonuclease that preferentially cleaves 3' of uridines. We solved the structure of a catalytically inactive mutant version of Nsp15, which was crystallized as a hexamer. The structure contains unreported flexibility in the active site of each subunit. Substitutions in the active site residues serine 293 and proline 343 allowed Nsp15 to cleave at cytidylate, whereas mutation of leucine 345 rendered Nsp15 able to cleave at purines as well as pyrimidines. Mutations that targeted the residues involved in subunit interactions generally resulted in the formation of catalytically inactive monomers. The RNA-binding residues were mapped by a method linking reversible cross-linking, RNA affinity purification, and peptide fingerprinting. Alanine substitution of several residues in the RNA-contacting portion of Nsp15 did not affect hexamer formation but decreased the affinity of RNA binding and reduced endonuclease activity. This suggests a model for Nsp15 hexamer interaction with RNA.

  3. Electrochemical alloying of immiscible Ag and Co for their structural and magnetic analyses

    Energy Technology Data Exchange (ETDEWEB)

    Santhi, Kalavathy [Material Science Centre, Department of Nuclear Physics, University of Madras, Guindy Campus, Chennai 600025 (India); Department of Physics, Women’s Christian College, Chennai 600006 (India); Kumarsan, Dhanapal [Material Science Centre, Department of Nuclear Physics, University of Madras, Guindy Campus, Chennai 600025 (India); Vengidusamy, Naryanan [Department of Inorganic Chemistry, University of Madras, Guindy Campus, Chennai 600025 (India); Arumainathan, Stephen, E-mail: stephen_arum@hotmail.com [Material Science Centre, Department of Nuclear Physics, University of Madras, Guindy Campus, Chennai 600025 (India)

    2017-07-01

    Highlights: • Ag-Co alloy has been prepared using pulsed electrodeposition method. • Wide range of Ag composition in the alloy was obtained. • XPS measurement evident the Ag and Co in metallic nature. • The electrodeposition method develop dendrite like morphology. • Detailed analysis of magnetic behaviour is carried out. - Abstract: Electrochemical alloying of immiscible Ag and Co was carried out at different current densities from electrolytes of two different concentrations, after optimizing the electrolytic bath and operating conditions. The samples obtained were characterized using X-ray diffraction to confirm the simultaneous deposition of Ag and Co and to determine their crystallographic structure. The atomic percentage of Ag and Co contents in the granular alloy was determined by ICP-OES analysis. The XPS spectra were observed to confirm the presence of Ag and Co in the metallic form in the granular alloy samples. The micrographs observed using scanning and transmission electron microscopes threw light on the surface morphology and the size of the particles. The magnetic nature of the samples was analyzed at room temperature by a vibration sample magnetometer. Their magnetic phase transition while heating was also studied to provide further evidence for the magnetic behaviour and the structure of the deposits.

  4. Adolf Hitler's Parkinson's disease and an attempt to analyse his personality structure.

    Science.gov (United States)

    Gerstenbrand, F; Karamat, E

    1999-03-01

    It has been proved that Adolf Hitler suffered from idiopathic Parkinson's disease. No indication for postencephalitic parkinsonism was found in the clinical symptoms or the case history. Professor Max de Crinis established his diagnosis of Parkinson's disease in Hitler early in 1945 and informed the SS leadership, who decided to initiate treatment with a specially prepared 'antiparkinsonian mixture' to be administered by a physician. However, Hitler never received the mixture, this implies that the SS intended to remove the severely diseased 'Leader'. Two different character traits can be analysed in Hitler's personality: on the one hand the typical premorbid personality of parkinsonian patients with uncorrectable mental rigidity, extreme inflexibility and insupportable pedantry. On the other an antisocial personality disorder with lack of ethical and social values, a deeply rooted tendency to betray others and to deceive himself and uncontrollable emotional reactions. This special combination in Hitler's personality resulted in the uncritical conviction of his mission and an enormous driving for recognition. The neuropsychiatric analysis of Hitler's personality could lead to a better explanation of the pathological traits of one of the most conspicuous historical personalities. Copyright 1999 Lippincott Williams & Wilkins.

  5. Anatomical variations of trabecular bone structure in intraoral radiographs using fractal and particles count analyses

    International Nuclear Information System (INIS)

    Amer, Maha Eshak; Heo, Min Suk; Brooks, Sharon L; Benavides, Erika

    2012-01-01

    This study was performed to evaluate possible variations in maxillary and mandibular bone texture of normal population using the fractal analysis, particles count, and area fraction in intraoral radiographs. Periapical radiographs of patients who had full mouth intraoral radiographs were collected. Regions of interest (100X100 pixels) were located between the teeth of the maxillary anterior, premolar, and molar area, as well as the mandibular anterior, premolar, and molar areas. The fractal dimension (FD) was calculated by using the box counting method. The particle count (PC) and area fraction (AF) analyses were also performed. There was no significant difference in the FD values among the different groups of age, gender, upper, and lower jaws. The mean FD value was 1.49±0.01. The mean PC ranged from 44 to 54, and the mean AF ranged from 10.92 to 11.85. The values of FD, PC, and AF were significantly correlated with each other except for the upper molar area. According to the results, patients with normal trabecular pattern showed a FD of approximately 1.5. Based on these results, further investigation would be recommended if the FD value of patient significantly different from this number, since the alteration of this value indicates microstructural modification of trabecular pattern of the jaws. Additionally, with periapical radiographs, simple and cost-effective, PC and AF could be used to assess the deviation from the normal.

  6. Comparative analyses of glycerotoxin expression unveil a novel structural organization of the bloodworm venom system.

    Science.gov (United States)

    Richter, Sandy; Helm, Conrad; Meunier, Frederic A; Hering, Lars; Campbell, Lahcen I; Drukewitz, Stephan H; Undheim, Eivind A B; Jenner, Ronald A; Schiavo, Giampietro; Bleidorn, Christoph

    2017-03-04

    We present the first molecular characterization of glycerotoxin (GLTx), a potent neurotoxin found in the venom of the bloodworm Glycera tridactyla (Glyceridae, Annelida). Within the animal kingdom, GLTx shows a unique mode of action as it can specifically up-regulate the activity of Ca v 2.2 channels (N-type) in a reversible manner. The lack of sequence information has so far hampered a detailed understanding of its mode of action. Our analyses reveal three ~3.8 kb GLTx full-length transcripts, show that GLTx represents a multigene family, and suggest it functions as a dimer. An integrative approach using transcriptomics, quantitative real-time PCR, in situ hybridization, and immunocytochemistry shows that GLTx is highly expressed exclusively in four pharyngeal lobes, a previously unrecognized part of the venom apparatus. Our results overturn a century old textbook view on the glycerid venom system, suggesting that it is anatomically and functionally much more complex than previously thought. The herein presented GLTx sequence information constitutes an important step towards the establishment of GLTx as a versatile tool to understand the mechanism of synaptic function, as well as the mode of action of this novel neurotoxin.

  7. Diversity and evolution of plant diacylglycerol acyltransferase (DGATs unveiled by phylogenetic, gene structure and expression analyses

    Directory of Open Access Journals (Sweden)

    Andreia Carina Turchetto-Zolet

    Full Text Available Abstract Since the first diacylglycerol acyltransferase (DGAT gene was characterized in plants, a number of studies have focused on understanding the role of DGAT activity in plant triacylglycerol (TAG biosynthesis. DGAT enzyme is essential in controlling TAGs synthesis and is encoded by different genes. DGAT1 and DGAT2 are the two major types of DGATs and have been well characterized in many plants. On the other hand, the DGAT3 and WS/DGAT have received less attention. In this study, we present the first general view of the presence of putative DGAT3 and WS/DGAT in several plant species and report on the diversity and evolution of these genes and its relationships with the two main DGAT genes (DGAT1 and DGAT2. According to our analyses DGAT1, DGAT2, DGAT3 and WS/DGAT are very divergent genes and may have distinct origin in plants. They also present divergent expression patterns in different organs and tissues. The maintenance of several types of genes encoding DGAT enzymes in plants demonstrates the importance of DGAT activity for TAG biosynthesis. Evolutionary history studies of DGATs coupled with their expression patterns help us to decipher their functional role in plants, helping to drive future biotechnological studies.

  8. Microbial community structure in autotrophic nitrifying granules characterized by experimental and simulation analyses

    DEFF Research Database (Denmark)

    Matsumoto, S.; Katoku, M.; Saeki, G.

    2010-01-01

    the bacterial distribution obtained by fluorescence in situ hybridization analysis, as well as the measured oxygen, nitrite, nitrate and ammonium concentration profiles. Results of this study are important because they show that a combination of simulation and experimental techniques can better explain......This study evaluates the community structure in nitrifying granules (average diameter of 1600 mu m) produced in an aerobic reactor fed with ammonia as the sole energy source by a multivalent approach combining molecular techniques, microelectrode measurements and mathematical modelling...... the observed granule development as a result of the multiple bacteria-substrate interactions. The interaction between nitrifying and heterotrophic bacteria was evaluated by assuming three types of heterotrophic bacterial growth on soluble microbial products from nitrifying bacteria. The models described well...

  9. Analysis of metal-matrix composite structures. I - Micromechanics constitutive theory. II - Laminate analyses

    Science.gov (United States)

    Arenburg, R. T.; Reddy, J. N.

    1991-01-01

    The micromechanical constitutive theory is used to examine the nonlinear behavior of continuous-fiber-reinforced metal-matrix composite structures. Effective lamina constitutive relations based on the Abouli micromechanics theory are presented. The inelastic matrix behavior is modeled by the unified viscoplasticity theory of Bodner and Partom. The laminate constitutive relations are incorporated into a first-order deformation plate theory. The resulting boundary value problem is solved by utilizing the finite element method. Attention is also given to computational aspects of the numerical solution, including the temporal integration of the inelastic strains and the spatial integration of bending moments. Numerical results the nonlinear response of metal matrix composites subjected to extensional and bending loads are presented.

  10. Extra-regulatory impact tests and analyses of the structural evaluation test unit

    International Nuclear Information System (INIS)

    Ludwigsen, J.S.; Ammerman, D.J.

    1995-01-01

    The structural evaluation test unit is roughly equivalent to a 1/3 scale model of a high level waste rail cask. The test unit was designed to just meet the requirements of NRC Regulatory Guide 7.6 when subjected to a 9 m (30 ft) free drop resulting in an impact velocity of 13.4 m/s (30 mph) onto an unyielding target in the end-on orientation. The test unit was then subjected to impacts with higher velocities to determine the amount of built-in conservatism in this design approach. Test impacts of 13.4, 20.1 and 26.8 m/s (30, 45, and 60 mph) were performed. This paper will describe the design, testing, and comparison of measured strains and deformations to the equivalent analytical predictions

  11. Structural Response of Submerged Air-Backed Plates by Experimental and Numerical Analyses

    Directory of Open Access Journals (Sweden)

    Lloyd Hammond

    2000-01-01

    Full Text Available This paper presents the results of a series of small-scale underwater shock experiments that measured the structural responses of submerged, fully clamped, air-backed, steel plates to a range of high explosive charge sizes. The experimental results were subsequently used to validate a series of simulations using the coupled LS-DYNA/USA finite element/boundary element codes. The modelling exercise was complicated by a significant amount of local cavitation occurring in the fluid adjacent to the plate and difficulties in modelling the boundary conditions of the test plates. The finite element model results satisfactorily predicted the displacement-time history of the plate over a range of shock loadings although a less satisfactory correlation was achieved for the peak velocities. It is expected that the predictive capability of the finite element model will be significantly improved once hydrostatic initialisation can be fully utilised with the LS-DYNA/USA software.

  12. Mathematical and computational analyses of cracking formation fracture morphology and its evolution in engineering materials and structures

    CERN Document Server

    Sumi, Yoichi

    2014-01-01

    This book is about the pattern formation and the evolution of crack propagation in engineering materials and structures, bridging mathematical analyses of cracks based on singular integral equations, to computational simulation of engineering design. The first two parts of this book focus on elasticity and fracture and provide the basis for discussions on fracture morphology and its numerical simulation, which may lead to a simulation-based fracture control in engineering structures. Several design concepts are discussed for the prevention of fatigue and fracture in engineering structures, including safe-life design, fail-safe design, damage tolerant design. After starting with basic elasticity and fracture theories in parts one and two, this book focuses on the fracture morphology that develops due to the propagation of brittle cracks or fatigue cracks.   In part three, the mathematical analysis of a curved crack is precisely described, based on the perturbation method. The stability theory of interactive ...

  13. An improved lake model for climate simulations: Model structure, evaluation, and sensitivity analyses in CESM1

    Directory of Open Access Journals (Sweden)

    Zachary Subin

    2012-02-01

    Full Text Available Lakes can influence regional climate, yet most general circulation models have, at best, simple and largely untested representations of lakes. We developed the Lake, Ice, Snow, and Sediment Simulator(LISSS for inclusion in the land-surface component (CLM4 of an earth system model (CESM1. The existing CLM4 lake modelperformed poorly at all sites tested; for temperate lakes, summer surface water temperature predictions were 10–25uC lower than observations. CLM4-LISSS modifies the existing model by including (1 a treatment of snow; (2 freezing, melting, and ice physics; (3 a sediment thermal submodel; (4 spatially variable prescribed lakedepth; (5 improved parameterizations of lake surface properties; (6 increased mixing under ice and in deep lakes; and (7 correction of previous errors. We evaluated the lake model predictions of water temperature and surface fluxes at three small temperate and boreal lakes where extensive observational data was available. We alsoevaluated the predicted water temperature and/or ice and snow thicknesses for ten other lakes where less comprehensive forcing observations were available. CLM4-LISSS performed very well compared to observations for shallow to medium-depth small lakes. For large, deep lakes, the under-prediction of mixing was improved by increasing the lake eddy diffusivity by a factor of 10, consistent with previouspublished analyses. Surface temperature and surface flux predictions were improved when the aerodynamic roughness lengths were calculated as a function of friction velocity, rather than using a constant value of 1 mm or greater. We evaluated the sensitivity of surface energy fluxes to modeled lake processes and parameters. Largechanges in monthly-averaged surface fluxes (up to 30 W m22 were found when excluding snow insulation or phase change physics and when varying the opacity, depth, albedo of melting lake ice, and mixing strength across ranges commonly found in real lakes. Typical

  14. A large format in operando wound cell for analysing the structural dynamics of lithium insertion materials

    Science.gov (United States)

    Brant, William R.; Roberts, Matthew; Gustafsson, Torbjörn; Biendicho, Jordi Jacas; Hull, Stephen; Ehrenberg, Helmut; Edström, Kristina; Schmid, Siegbert

    2016-12-01

    This paper presents a large wound cell for in operando neutron diffraction (ND) from which high quality diffraction patterns are collected every 15 min while maintaining conventional electrochemical performance. Under in operando data collection conditions the oxygen atomic displacement parameters (ADPs) and cell parameters were extracted for Li0.18Sr0.66Ti0.5Nb0.5O3. Analysis of diffraction data collected under in situ conditions revealed that the lithium is located on the (0.5 0.5 0) site, corresponding to the 3c Wyckoff position in the cubic perovskite unit cell, after the cell is discharged to 1 V. When the cell is discharged under potentiostatic conditions the quantity of lithium on this site increases, indicating a potential position where lithium becomes pinned in the thermodynamically stable phase. During this potentiostatic step the oxygen ADPs reduce significantly. On discharge, however, the oxygen ADPs were observed to increase gradually as more lithium is inserted into the structure. Finally, the rate of unit cell expansion changed by ∼44% once the lithium content approached ∼0.17 Li per formula unit. A link between lithium content and degree of mobility, disorder of the oxygen positions and changing rate of unit cell expansion at various stages during lithium insertion and extraction is thus presented.

  15. Phytophthora community structure analyses in Oregon nurseries inform systems approaches to disease management.

    Science.gov (United States)

    Parke, Jennifer L; Knaus, Brian J; Fieland, Valerie J; Lewis, Carrie; Grünwald, Niklaus J

    2014-10-01

    Nursery plants are important vectors for plant pathogens. Understanding what pathogens occur in nurseries in different production stages can be useful to the development of integrated systems approaches. Four horticultural nurseries in Oregon were sampled every 2 months for 4 years to determine the identity and community structure of Phytophthora spp. associated with different sources and stages in the nursery production cycle. Plants, potting media, used containers, water, greenhouse soil, and container yard substrates were systematically sampled from propagation to the field. From 674 Phytophthora isolates recovered, 28 different species or taxa were identified. The most commonly isolated species from plants were Phytophthora plurivora (33%), P. cinnamomi (26%), P. syringae (19%), and P. citrophthora (11%). From soil and gravel substrates, P. plurivora accounted for 25% of the isolates, with P. taxon Pgchlamydo, P. cryptogea, and P. cinnamomi accounting for 18, 17, and 15%, respectively. Five species (P. plurivora, P. syringae, P. taxon Pgchlamydo, P. gonapodyides, and P. cryptogea) were found in all nurseries. The greatest diversity of taxa occurred in irrigation water reservoirs (20 taxa), with the majority of isolates belonging to internal transcribed spacer clade 6, typically including aquatic opportunists. Nurseries differed in composition of Phytophthora communities across years, seasons, and source within the nursery. These findings suggest likely contamination hazards and target critical control points for management of Phytophthora disease using a systems approach.

  16. Nanoscale “Quantum” Islands on Metal Substrates: Microscopy Studies and Electronic Structure Analyses

    Directory of Open Access Journals (Sweden)

    Da-Jiang Liu

    2010-07-01

    Full Text Available Confinement of electrons can occur in metal islands or in continuous films grown heteroepitaxially upon a substrate of a different metal or on a metallic alloy. Associated quantum size effects (QSE can produce a significant height-dependence of the surface free energy for nanoscale thicknesses of up to 10–20 layers. This may suffice to induce height selection during film growth. Scanning STM analysis has revealed remarkable flat-topped or mesa-like island and film morphologies in various systems. We discuss in detail observations of QSE and associated film growth behavior for Pb/Cu(111, Ag/Fe(100, and Cu/fcc-Fe/Cu(100 [A/B or A/B/A], and for Ag/NiAl(110 with brief comments offered for Fe/Cu3Au(001 [A/BC binary alloys]. We also describe these issues for Ag/5-fold i-Al-Pd-Mn and Bi/5-fold i-Al-Cu-Fe [A/BCD ternary icosohedral quasicrystals]. Electronic structure theory analysis, either at the level of simple free electron gas models or more sophisticated Density Functional Theory calculations, can provide insight into the QSE-mediated thermodynamic driving force underlying height selection.

  17. Comparative analyses of microbial structures and gene copy numbers in the anaerobic digestion of various types of sewage sludge.

    Science.gov (United States)

    Hidaka, Taira; Tsushima, Ikuo; Tsumori, Jun

    2018-04-01

    Anaerobic co-digestion of various sewage sludges is a promising approach for greater recovery of energy, but the process is more complicated than mono-digestion of sewage sludge. The applicability of microbial structure analyses and gene quantification to understand microbial conditions was evaluated. The results show that information from gene analyses is useful in managing anaerobic co-digestion and damaged microbes in addition to conventional parameters like total solids, pH and biogas production. Total bacterial 16S rRNA gene copy numbers are the most useful tools for evaluating unstable anaerobic digestion of sewage sludge, rather than mcrA and total archaeal 16S rRNA gene copy numbers, and high-throughput sequencing. First order decay rates of gene copy numbers during pH failure were higher than typical decay rates of microbes in stable operation. The sequencing analyses, including multidimensional scaling, showed very different microbial structure shifts, but the results were not consistent. Copyright © 2017 Elsevier Ltd. All rights reserved.

  18. Social Capital and Well-Being: Structural Analyses of Latina Mothers by Nativity.

    Science.gov (United States)

    Held, Mary L; Cuellar, Matthew

    2016-09-01

    Objective This study examined the direct and mediating effects of maternal social capital on health and well-being for native- and foreign-born Latina mothers and their children. Methods Data were drawn from the baseline and nine-year follow up waves of the Fragile Families and Child Well-being Study. The study included a sample of 874 Latina mothers. Mplus7 was used to perform structural equation modeling to determine whether exogenous indicators (age, education, and economic well-being) predicted social capital, whether social capital predicted mother and child well-being, and whether mediating effects helped explain each relationship. Results For native-born Latinas (n = 540), social capital did not predict maternal or child well-being. However, social capital significantly mediated the effects of age, education, and economic well-being on maternal well-being. For foreign-born Latinas (n = 334), social capital was a significant predictor of maternal well-being. Social capital also mediated the effects of age, education, and economic well-being on maternal, but not child well-being. Younger and foreign-born Latinas who report higher educational attainment and economic well-being have greater social capital, and thus better self-reported health. Conclusion Findings suggest that social capital is particularly relevant to the health of foreign-born Latinas. For all Latina mothers, social capital may serve as a protective mitigating factor to better health. Health service providers should evaluate the potential to integrate programs that promote social capital accumulation for Latinas. Further research should examine factors to improve the health of Latinas' children.

  19. Experiments and analyses on melt-structure-water interactions during severe accidents

    Energy Technology Data Exchange (ETDEWEB)

    Seghal, B.R.; Dinh, T.N.; Bui, V.A.; Green, J.A.; Nourgaliev, R.R.; Okkonen, T.O.; Dinh, A.T. [Royal Inst. of Tech., Stockholm (Sweden). Div. of Nuclear Power Safety

    1998-04-01

    This report is the final report for the research project Melt Structure Water Interactions (MSWI). It describes results of analytical and experimental studies concerning MSWI during the course of a hypothetical core meltdown accident in a LWR. Emphasis has been placed on phenomena which govern vessel failure mode and timing and the mechanisms and properties which govern the fragmentation and breakup of melt jets and droplets. It was found that: 2-D effects significantly diminished the focusing effect of an overlying metallic layer on top of an oxide melt pool. This result improves the feasibility of in-vessel retention of a melt pool through external cooling of the lower head; phenomena related to hole ablation and melt discharge, in the event of vessel failure, are affected significantly by crust formation; the jet fragmentation process is a function of many related phenomena. The fragmentation rate depends not only on the traditional parameters but also on the melt physical properties, which change as the melt cools down from liquid to solid temperature; film boiling was investigated by developing a two-phase flow model and inserting it in a multi-D fluid dynamics code. It was concluded that the thickness of the film on the surface of a melt jet would be small and that the effects of the film on the process should not be large. This conclusion is contrary to the modeling employed in some other codes. The computer codes were developed and validated against the data obtained in the MSWI Project. The melt vessel interaction thermal analysis code describes the process of melt pool formation and convection and the resulting vessel thermal loadings. In addition, several innovative models were developed to describe the melt-water interaction process. The code MELT-3D treats the melt jet as a collection of particles whose movement is described with a three-dimensional Eulerian formulation. The model (SIPHRA) tracks the melt jet with an additional equation, using the

  20. Structure-from-Motion Using Historical Aerial Images to Analyse Changes in Glacier Surface Elevation

    Directory of Open Access Journals (Sweden)

    Nico Mölg

    2017-10-01

    Full Text Available The application of structure-from-motion (SfM to generate digital terrain models (DTMs derived from different image sources has strongly increased, the major reason for this being that processing is substantially easier with SfM than with conventional photogrammetry. To test the functionality in a demanding environment, we applied SfM and conventional photogrammetry to archival aerial images from Zmuttgletscher, a mountain glacier in Switzerland, for nine dates between 1946 and 2005 using the most popular software packages, and compared the results regarding bundle adjustment and final DTM quality. The results suggest that by using SfM it is possible to produce DTMs of similar quality as with conventional photogrammetry. Higher point cloud density and less noise allow a higher ground resolution of the final DTM, and the time effort from the user is 3–6 times smaller, while the controls of the commercial software packages Agisoft PhotoScan (Version 1.2; Agisoft, St. Petersburg, Russia and Pix4Dmapper (Version 3.0; Pix4D, Lausanne, Switzerland are limited in comparison to ERDAS photogrammetry. SfM performs less reliably when few images with little overlap are processed. Even though SfM facilitates the largely automated production of high quality DTMs, the user is not exempt from a thorough quality check, at best with reference data where available. The resulting DTM time series revealed an average change in surface elevation at the glacier tongue of −67.0 ± 5.3 m. The spatial pattern of changes over time reflects the influence of flow dynamics and the melt of clean ice and that under debris cover. With continued technological advances, we expect to see an increasing use of SfM in glaciology for a variety of purposes, also in processing archival aerial imagery.

  1. Impact of branched structures on cycloalkane ignition in a motored engine: Detailed product and conformational analyses

    KAUST Repository

    Kang, Dongil

    2015-04-01

    The ignition process of ethylcyclohexane (ECH) and its two isomers, 1,3-dimethylcyclohexane (13DMCH) and 1,2-dimethylcyclohexane (12DMCH) was investigated in a modified CFR engine. The experiment was conducted with intake air temperature of 155. °C, equivalence ratio of 0.5 and engine speed of 600. rpm. The engine compression ratio (CR) was gradually increased in a stepwise manner until autoignition occurred. It was found that ECH exhibited a significantly higher oxidation reactivity compared to its two isomers. The autoignition criterion was based on CO emissions and the apparent heat release rates. Ethylcyclohexane (ECH) indicated noticeable two stage ignition behavior, while less significant heat release occurred for the two isomers at comparable conditions. The mole fractions of unreacted fuel and stable intermediate species over a wide range of compression ratios were analyzed by GC-MS and GC-FID. Most of the species indicated constant rates of formation and the trends of relative yield to unreacted fuel are well in agreement with the oxidation reactivity in the low temperature regime. The major intermediate species are revealed as a group of conjugate olefins, which possess the same molecular structure as the original fuel compound except for the presence of a double carbon bond. Conjugate olefins were mostly formed through (1,4) H-shift isomerization during the low temperature oxidation of alkylcyclohexanes. Conformation analysis explains the reactivity differences in the three isomers as well as the fractions of intermediate species. The hydrogen availability located in alkyl substituents plays an important role in determining oxidation reactivity, requiring less activation energy for abstraction through the (1,5) H-shift isomerization. This reactivity difference contributes to building up the major intermediate species observed during oxidation of each test fuel. 12DMCH, whose ignition reactivity is the lowest, less favors β-scission of C-C backbone of

  2. Clustering structures of large proteins using multifractal analyses based on a 6-letter model and hydrophobicity scale of amino acids

    International Nuclear Information System (INIS)

    Yang Jianyi; Yu Zuguo; Anh, Vo

    2009-01-01

    The Schneider and Wrede hydrophobicity scale of amino acids and the 6-letter model of protein are proposed to study the relationship between the primary structure and the secondary structural classification of proteins. Two kinds of multifractal analyses are performed on the two measures obtained from these two kinds of data on large proteins. Nine parameters from the multifractal analyses are considered to construct the parameter spaces. Each protein is represented by one point in these spaces. A procedure is proposed to separate large proteins in the α, β, α + β and α/β structural classes in these parameter spaces. Fisher's linear discriminant algorithm is used to assess our clustering accuracy on the 49 selected large proteins. Numerical results indicate that the discriminant accuracies are satisfactory. In particular, they reach 100.00% and 84.21% in separating the α proteins from the {β, α + β, α/β} proteins in a parameter space; 92.86% and 86.96% in separating the β proteins from the {α + β, α/β} proteins in another parameter space; 91.67% and 83.33% in separating the α/β proteins from the α + β proteins in the last parameter space.

  3. Phylogeographic analyses of submesophotic snappers Etelis coruscans and Etelis "marshi" (family Lutjanidae reveal concordant genetic structure across the Hawaiian Archipelago.

    Directory of Open Access Journals (Sweden)

    Kimberly R Andrews

    Full Text Available The Hawaiian Archipelago has become a natural laboratory for understanding genetic connectivity in marine organisms as a result of the large number of population genetics studies that have been conducted across this island chain for a wide taxonomic range of organisms. However, population genetic studies have been conducted for only two species occurring in the mesophotic or submesophotic zones (30+m in this archipelago. To gain a greater understanding of genetic connectivity in these deepwater habitats, we investigated the genetic structure of two submesophotic fish species (occurring ∼200-360 m in this archipelago. We surveyed 16 locations across the archipelago for submesophotic snappers Etelis coruscans (N = 787 and E. "marshi" (formerly E. carbunculus; N = 770 with 436-490 bp of mtDNA cytochrome b and 10-11 microsatellite loci. Phylogeographic analyses reveal no geographic structuring of mtDNA lineages and recent coalescence times that are typical of shallow reef fauna. Population genetic analyses reveal no overall structure across most of the archipelago, a pattern also typical of dispersive shallow fishes. However some sites in the mid-archipelago (Raita Bank to French Frigate Shoals had significant population differentiation. This pattern of no structure between ends of the Hawaiian range, and significant structure in the middle, was previously observed in a submesophotic snapper (Pristipomoides filamentosus and a submesophotic grouper (Hyporthodus quernus. Three of these four species also have elevated genetic diversity in the mid-archipelago. Biophysical larval dispersal models from previous studies indicate that this elevated diversity may result from larval supplement from Johnston Atoll, ∼800 km southwest of Hawaii. In this case the boundaries of stocks for fishery management cannot be defined simply in terms of geography, and fishery management in Hawaii may need to incorporate external larval supply into management

  4. Numerical analyses of the effect of SG‐interlayer shear stiffness on the structural performance of reinforced glass beams

    DEFF Research Database (Denmark)

    Louter, C.; Nielsen, Jens Henrik

    2013-01-01

    at the post-breakage stage –is investigated. From the results of the analyses it is observed that the residual load-bearing capacity, i.e. the load-bearing capacity after glass fracture, increases with an increasing shear modulus of the SG-interlayer. Furthermore, the load-displacement response from...... the numerical model is predicting experimental observations very well. However, the crack pattern resulting from the numerical model is not matching the experimental observations. Further studies are thus needed to fully understand the mechanisms involved in the structural behaviour of SGlaminated reinforced...

  5. Structure-function analyses of a PL24 family ulvan lyase reveal key features and suggest its catalytic mechanism.

    Science.gov (United States)

    Ulaganathan, ThirumalaiSelvi; Helbert, William; Kopel, Moran; Banin, Ehud; Cygler, Miroslaw

    2018-01-30

    Ulvan is a major cell wall component of green algae of the genus Ulva and some marine bacteria encode enzymes that can degrade this polysaccharide. The first ulvan degrading lyases have been recently characterized and several putative ulvan lyases have been recombinantly expressed, confirmed as ulvan lyases and partially characterized. Two families of ulvan degrading lyases, PL24 and PL25, have recently been established. The PL24 lyase LOR_107 from the bacterial Alteromonadales sp. strain LOR degrades ulvan endolytically, cleaving the bond at the C4 of a glucuronic acid. However, the mechanism and LOR_107 structural features involved are unknown. We present here the crystal structure of LOR_107, representing the first PL24 family structure. We found that LOR_107 adopts a seven-bladed β-propeller fold with a deep canyon on one side of the protein. Comparative sequence analysis revealed a cluster of conserved residues within this canyon, and site-directed mutagenesis disclosed several residues essential for catalysis. We also found that LOR_107 uses the His/Tyr catalytic mechanism, common to several PL families. We captured a tetrasaccharide substrate in the structures of two inactive mutants, which indicated a two-step binding event, with the first substrate interaction near the top of the canyon coordinated by Arg-320, followed by sliding of the substrate into the canyon toward the active-site residues. Surprisingly, the LOR_107 structure was very similar to that of PL25 family PLSV_3936, despite only ~14% sequence identity between the two enzymes. On the basis of our structural and mutational analyses, we propose a catalytic mechanism for LOR_107 that differs from the typical His/Tyr mechanism. Published under license by The American Society for Biochemistry and Molecular Biology, Inc.

  6. Novel evolutionary lineages revealed in the Chaetothyriales (fungi based on multigene phylogenetic analyses and comparison of its secondary structure.

    Directory of Open Access Journals (Sweden)

    Martina Réblová

    Full Text Available Cyphellophora and Phialophora (Chaetothyriales, Pezizomycota comprise species known from skin infections of humans and animals and from a variety of environmental sources. These fungi were studied based on the comparison of cultural and morphological features and phylogenetic analyses of five nuclear loci, i.e., internal transcribed spacer rDNA operon (ITS, large and small subunit nuclear ribosomal DNA (nuc28S rDNA, nuc18S rDNA, β-tubulin, DNA replication licensing factor (mcm7 and second largest subunit of RNA polymerase II (rpb2. Phylogenetic results were supported by comparative analysis of ITS1 and ITS2 secondary structure of representatives of the Chaetothyriales and the identification of substitutions among the taxa analyzed. Base pairs with non-conserved, co-evolving nucleotides that maintain base pairing in the RNA transcript and unique evolutionary motifs in the ITS2 that characterize whole clades or individual taxa were mapped on predicted secondary structure models. Morphological characteristics, structural data and phylogenetic analyses of three datasets, i.e., ITS, ITS-β-tubulin and 28S-18S-rpb2-mcm7, define a robust clade containing eight species of Cyphellophora (including the type and six species of Phialophora. These taxa are now accommodated in the Cyphellophoraceae, a novel evolutionary lineage within the Chaetothyriales. Cyphellophora is emended and expanded to encompass species with both septate and nonseptate conidia formed on discrete, intercalary, terminal or lateral phialides. Six new combinations in Cyphellophora are proposed and a dichotomous key to species accepted in the genus is provided. Cyphellophora eugeniae and C. hylomeconis, which grouped in the Chaetothyriaceae, represent another novel lineage and are introduced as the type species of separate genera.

  7. Extensive structural change of the envelope protein of dengue virus induced by a tuned ionic strength: conformational and energetic analyses

    Science.gov (United States)

    Degrève, Léo; Fuzo, Carlos A.; Caliri, Antonio

    2012-12-01

    The Dengue has become a global public health threat, with over 100 million infections annually; to date there is no specific vaccine or any antiviral drug. The structures of the envelope (E) proteins of the four known serotype of the dengue virus (DENV) are already known, but there are insufficient molecular details of their structural behavior in solution in the distinct environmental conditions in which the DENVs are submitted, from the digestive tract of the mosquito up to its replication inside the host cell. Such detailed knowledge becomes important because of the multifunctional character of the E protein: it mediates the early events in cell entry, via receptor endocytosis and, as a class II protein, participates determinately in the process of membrane fusion. The proposed infection mechanism asserts that once in the endosome, at low pH, the E homodimers dissociate and insert into the endosomal lipid membrane, after an extensive conformational change, mainly on the relative arrangement of its three domains. In this work we employ all-atom explicit solvent Molecular Dynamics simulations to specify the thermodynamic conditions in that the E proteins are induced to experience extensive structural changes, such as during the process of reducing pH. We study the structural behavior of the E protein monomer at acid pH solution of distinct ionic strength. Extensive simulations are carried out with all the histidine residues in its full protonated form at four distinct ionic strengths. The results are analyzed in detail from structural and energetic perspectives, and the virtual protein movements are described by means of the principal component analyses. As the main result, we found that at acid pH and physiological ionic strength, the E protein suffers a major structural change; for lower or higher ionic strengths, the crystal structure is essentially maintained along of all extensive simulations. On the other hand, at basic pH, when all histidine residues are in

  8. Structure elucidation and toxicity analyses of the radiolytic products of aflatoxin B{sub 1} in methanol-water solution

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Feng [Institute of Agro-food Science and Technology of Chinese Academy of Agricultural Sciences, 2nd Yuanmingyuan West Road, Hai Dian District, Beijing 100193 (China); Key Opening Laboratory of Agricultural Products Processing and Quality Control, Ministry of Agriculture, 2nd Yuanmingyuan West Road, Hai Dian District, Beijing 100193 (China); Graduate School of Chinese Academy of Agricultural Sciences, 12th Zhongguancun South Road, Hai Dian District, Beijing 100081 (China); Xie, Fang [Institute of Agro-food Science and Technology of Chinese Academy of Agricultural Sciences, 2nd Yuanmingyuan West Road, Hai Dian District, Beijing 100193 (China); Key Opening Laboratory of Agricultural Products Processing and Quality Control, Ministry of Agriculture, 2nd Yuanmingyuan West Road, Hai Dian District, Beijing 100193 (China); Xue, Xiaofeng [Bee Research Institute of Chinese Academy of Agricultural Sciences, 1st Xiangshan North Ditch, Hai Dian District, Beijing 100093 (China); Wang, Zhidong; Fan, Bei [Institute of Agro-food Science and Technology of Chinese Academy of Agricultural Sciences, 2nd Yuanmingyuan West Road, Hai Dian District, Beijing 100193 (China); Key Opening Laboratory of Agricultural Products Processing and Quality Control, Ministry of Agriculture, 2nd Yuanmingyuan West Road, Hai Dian District, Beijing 100193 (China); Ha, Yiming, E-mail: wxfay2011@hotmail.com [Institute of Agro-food Science and Technology of Chinese Academy of Agricultural Sciences, 2nd Yuanmingyuan West Road, Hai Dian District, Beijing 100193 (China); Key Opening Laboratory of Agricultural Products Processing and Quality Control, Ministry of Agriculture, 2nd Yuanmingyuan West Road, Hai Dian District, Beijing 100193 (China)

    2011-09-15

    Highlights: {yields} Radiolytic products of aflatoxin B{sub 1} were produced under gamma irradiation. {yields} Seven key radiolytic products were structure-elucidated. {yields} Free-radical species in radiolytic solution resulted in the formation of products. {yields} Based on the structure-activity relationship analysis, the toxicity of radiolytic products was significantly reduced compared with that of AFB{sub 1}. {yields} The addition reaction on furan ring double bond was the reason for the reduced toxicity. - Abstract: The identification of the radiolytic products of mycotoxins is a key issue in the feasibility study of gamma ray radiation detoxification. Methanol-water solution (60:40, v/v) spiked with aflatoxin B{sub 1} (AFB{sub 1}; 20 mg L{sup -1}) was irradiated with Co{sup 60} gamma ray to generate radiolytic products. Liquid chromatography-quadruple time-of-flight mass spectrometry was applied to identify the radiolytic products of AFB{sub 1}. Accurate mass and proposed molecular formulas with a high-matching property of more than 20 radiolytic products were obtained. Seven key radiolytic products were proposed based on the molecular formulas and tandem mass spectrometry spectra. The analyses of toxicity and formation pathways were proposed based on the structure of the radiolytic products. The addition reaction caused by the free-radical species in the methanol-water solution resulted in the formation of most radiolytic products. Based on the structure-activity relationship analysis, the toxicity of radiolytic products was significantly reduced compared with that of AFB{sub 1} because of the addition reaction that occurred on the double bond in the terminal furan ring. For this reason, gamma irradiation is deemed an effective tool for the detoxification of AFB{sub 1}.

  9. Genome-wide Single Nucleotide Polymorphism Analyses Reveal Genetic Diversity and Structure of Wild and Domestic Cattle in Bangladesh

    Directory of Open Access Journals (Sweden)

    Md. Rasel Uzzaman

    2014-10-01

    Full Text Available In spite of variation in coat color, size, and production traits among indigenous Bangladeshi cattle populations, genetic differences among most of the populations have not been investigated or exploited. In this study, we used a high-density bovine single nucleotide polymorphism (SNP 80K Bead Chip derived from Bos indicus breeds to assess genetic diversity and population structure of 2 Bangladeshi zebu cattle populations (red Chittagong, n = 28 and non-descript deshi, n = 28 and a semi-domesticated population (gayal, n = 17. Overall, 95% and 58% of the total SNPs (69,804 showed polymorphisms in the zebu and gayal populations, respectively. Similarly, the average minor allele frequency value was as high 0.29 in zebu and as low as 0.09 in gayal. The mean expected heterozygosity varied from 0.42±0.14 in zebu to 0.148±0.14 in gayal with significant heterozygosity deficiency of 0.06 (FIS in the latter. Coancestry estimations revealed that the two zebu populations are weakly differentiated, with over 99% of the total genetic variation retained within populations and less than 1% accounted for between populations. Conversely, strong genetic differentiation (FST = 0.33 was observed between zebu and gayal populations. Results of population structure and principal component analyses suggest that gayal is distinct from Bos indicus and that the two zebu populations were weakly structured. This study provides basic information about the genetic diversity and structure of Bangladeshi cattle and the semi-domesticated gayal population that can be used for future appraisal of breed utilization and management strategies.

  10. Structural Stability and Vibrational Analyses of Haloselenonyl Azides, XSeO2-NNN, where X is F, Cl, Br

    Directory of Open Access Journals (Sweden)

    Wolfgang Förِner

    2005-10-01

    Full Text Available The structural stability of haloselenonyl azides was investigated by quantum mechanical Møller-Plesset perturbation theory of second order and density functional theory calculations. The 6-311+G** basis set was used to include polarization and diffuse functions in the calculations at the DFT-B3LYP level. The potential scans for the rotation of the -NNN rotor were calculated and found to be consistent with a single minimum that corresponds to a gauche conformation (-NNN moiety nearly eclipses one of the two selenonyl Se=O bonds for the three halogens at ambient temperature. The structural parameters for the minima calculated by MP2 and DFT turned out to be very similar. The vibrational modes, infrared and Raman intensities as well as depolarization ratios were calculated at DFT-B3LYP/6-311+G** level for the three molecules in their gauche conformations. The potential energy distributions among symmetry coordinates of the normal modes of the molecules in their gauche conformation were then computed from normal coordinate analyses.

  11. Analyse économique de la structure des coûts de production apicole au Cameroun

    Directory of Open Access Journals (Sweden)

    Muluh, GA.

    2008-01-01

    Full Text Available Economic Analysis of the Bee Farming Costs Structure in Cameroon. Beekeeping is spreading in Cameroon, and contributes to the sustainable management of the non timber forest products. This study presents the structure of the bee farms production factors in the North-West of the aforesaid country. The assumption is that there would be a significant difference in the production costs components between the types of bee-farms in the North-West of Cameroon. The data collected in 2005 related to the operation of the exploitations, the cost factors and income. The analyses were made using Excel and SPSS software, and the principal results are the following. Bee farming returns to scale are decreasing in the North-West of Cameroon. The bee farms of this zone invest more in the capital factor. Their follow-up is very insufficient, whereas all can maximize profit. Although there is a significant difference of the total fixed costs of production between the traditional bee exploitations and the semi modern ones, there is no difference in variable costs, nor in total cost of production between them. The setting-up of an apiculture policy which insists on extension services close to the bee-farmers is essential for the rise of this sub sector.

  12. Response patterns on interview and questionnaire versions of the Eating Disorder Examination and their impact on latent structure analyses.

    Science.gov (United States)

    Berg, Kelly C; Swanson, Sonja A; Stiles-Shields, E Colleen; Eddy, Kamryn T; Peterson, Carol B; Le Grange, Daniel

    2013-07-01

    The purpose of this investigation was to compare the latent structures of the interview (EDE) and questionnaire (EDE-Q) versions of the Eating Disorder Examination. Participants were 280 children, adolescents, and young adults seeking eating disorder treatment. Two separate latent structure analyses (LSAs) were conducted; one used variables from the EDE as indicators and the other used the corresponding variables from the EDE-Q as indicators. The EDE and EDE-Q models both yielded four-class solutions. Three of the four classes from the EDE-Q model demonstrated moderate to high concordance with their paired class from the EDE model. Using the EDE-Q to detect the EDE, the sensitivity and specificity of measuring certain classes varied from poor (18.6%) to excellent (93.7%). The overall concordance was moderate (κ=.49). These data suggest that LSAs using the EDE and EDE-Q may be directly compared; however, differences between results may represent inconsistencies in response patterns rather than true differences in psychopathology. Copyright © 2013 Elsevier Inc. All rights reserved.

  13. Paleostress Reconstruction from 3D seismic, Natural Fracture and Calcite Twin Analyses: Structural Insights into the Otway Basin, Australia

    Science.gov (United States)

    Burgin, Hugo; Amrouch, Khalid; Holford, Simon

    2017-04-01

    The Otway Basin, Australia, is of particular interest due to its significance as an Australian hydrocarbon producing province and a major global CO2 burial project. Structural data was collected in the form of natural fractures from wellbore image logs and outcrop in addition to calcite twin analyses, within formations from the mid cretaceous from both on and offshore. Evidence for four structural events within the study area have been identified including NE-SW and NW-SE orientated extension, in addition to a NW-SE compressive event. Natural fracture data also reveals a previously "un-detected" NE-SW compression within the Otway Basin. This study presents the first investigation of paleostress environments within the region from micro, meso and macro scale tectonic data in both onshore and offshore in addition to the first quantification of differential paleostresses. This work highlights the importance of a comprehensive understanding of four dimensional stress evolution within the sedimentary basins of Australia's southern margin.

  14. Controlled cobalt doping in the spinel structure of magnetosome magnetite: New evidences from element- and site-specific XMCD analyses

    Science.gov (United States)

    Pan, Y.; LI, J.; Menguy, N.; Arrio, M. A.; Sainctavit, P.; Juhin, A.; Wang, Y.; Chen, H.; Bunau, O.; Otero, E.; Ohresser, P.

    2016-12-01

    Controlled cobalt doping in the spinel structure of magnetosome magnetite: New evidences from element- and site-specific XMCD analyses Jinhua Li1,2*, Nicolas Menguy2,3, Marie-Anne Arrio3, Philippe Sainctavit3,4, Amélie Juhin3, Yinzhao Wang1,2, Haitao Chen5, Oana Bunau3, Edwige Otero4, Philippe Ohresser4, Yongxin Pan1,21Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing 100029, China. 2France-China Biomineralization and Nano-structures Laboratory, Chinese Academy of Sciences, Beijing 100029, China. 3IMPMC, CNRS UMR 7590, Sorbonne Universités, MNHN, UPMC, IRD UMR 206, 75005 Paris, France. 4Synchrotron SOLEIL, L'Orme des Merisiers Saint-Aubin, 91192 Gif-sur-Yvette Cedex, France. 5Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China *To whom correspondence may be addressed. Email: lijinhua@mail.iggcas.ac.cnThe biomineralization of magnetite nanocrystals (called magnetosomes) by magnetotactic bacteria (MTB) has attracted intense interest in biology, geology and materials science. Great efforts have been recently made in producing transition metal-doped magnetosomes with modified magnetic properties for a range of applications. However, the coordination chemistry and magnetism of such metal-doped magnetosomes still remains largely unknown. Here, we present new evidences from X-ray magnetic circular dichroism (XMCD) for element- and site-specific magnetic analyses that cobalt is incorporated in the spinel structure of the magnetosomes within Magnetospirillum magneticum AMB-1 through the replacement of Fe2+ ions by Co2+ ions in octahedral (Oh) sites of magnetite. Compared with non-doped one, cobalt-doped magnetosome sample has lower Verwey transition temperature and larger magnetic coercivity, related to the amount of doped cobalt. This study this study indicates a biologically controlled process on cobalt doping and magnetic alteration by MTB system

  15. Virulence Structure of Blumeria graminis f. sp. tritici and Its Genetic Diversity by ISSR and SRAP Profiling Analyses.

    Directory of Open Access Journals (Sweden)

    Na Liu

    Full Text Available Blumeria graminis f. sp. tritici, which causes wheat powdery mildew, is an obligate biotrophic pathogen that can easily genetically adapt to its host plant. Understanding the virulence structure of and genetic variations in this pathogen is essential for disease control and for breeding resistance to wheat powdery mildew. This study investigated 17 pathogenic populations in Sichuan, China and classified 109 isolates into two distinct groups based on pathogenicity analysis: high virulence (HV, 92 isolates and low virulence (LV, 17 isolates. Populations from Yibin (Southern region, Xichang (Western region, and Meishan (Middle region showed lower virulence frequencies than populations from other regions. Many of the previously known resistance genes did not confer resistance in this study. The resistance gene Pm21 displayed an immune response to pathogenic challenge with all populations in Sichuan, and Pm13, Pm5b, Pm2+6, and PmXBD maintained resistance. AMOVA revealed significantly higher levels of variation within populations and lower levels of variation among populations within regions. High levels of gene flow were detected among populations in the four regions. Closely related populations within each region were distinguished by cluster analyses using ISSR and SRAP alleles. Both ISSR and SRAP allele profiling analyses revealed high levels of genetic diversity among pathogenic populations in Sichuan. Although ISSR and SRAP profiling analysis showed similar resolutions, the SRAP alleles appeared to be more informative. We did not detect any significant association between these alleles and the virulence or pathogenicity of the pathogen. Our results suggest that ISSR and SRAP alleles are more efficient for the characterization of small or closely related populations versus distantly related populations.

  16. Virulence Structure of Blumeria graminis f. sp. tritici and Its Genetic Diversity by ISSR and SRAP Profiling Analyses.

    Science.gov (United States)

    Liu, Na; Liu, Z Lewis; Gong, Guoshu; Zhang, Min; Wang, Xu; Zhou, You; Qi, Xiaobo; Chen, Huabao; Yang, Jizhi; Luo, Peigao; Yang, Chunping

    2015-01-01

    Blumeria graminis f. sp. tritici, which causes wheat powdery mildew, is an obligate biotrophic pathogen that can easily genetically adapt to its host plant. Understanding the virulence structure of and genetic variations in this pathogen is essential for disease control and for breeding resistance to wheat powdery mildew. This study investigated 17 pathogenic populations in Sichuan, China and classified 109 isolates into two distinct groups based on pathogenicity analysis: high virulence (HV, 92 isolates) and low virulence (LV, 17 isolates). Populations from Yibin (Southern region), Xichang (Western region), and Meishan (Middle region) showed lower virulence frequencies than populations from other regions. Many of the previously known resistance genes did not confer resistance in this study. The resistance gene Pm21 displayed an immune response to pathogenic challenge with all populations in Sichuan, and Pm13, Pm5b, Pm2+6, and PmXBD maintained resistance. AMOVA revealed significantly higher levels of variation within populations and lower levels of variation among populations within regions. High levels of gene flow were detected among populations in the four regions. Closely related populations within each region were distinguished by cluster analyses using ISSR and SRAP alleles. Both ISSR and SRAP allele profiling analyses revealed high levels of genetic diversity among pathogenic populations in Sichuan. Although ISSR and SRAP profiling analysis showed similar resolutions, the SRAP alleles appeared to be more informative. We did not detect any significant association between these alleles and the virulence or pathogenicity of the pathogen. Our results suggest that ISSR and SRAP alleles are more efficient for the characterization of small or closely related populations versus distantly related populations.

  17. Trophic structure of mesopelagic fishes in the Gulf of Mexico revealed by gut content and stable isotope analyses

    Science.gov (United States)

    McClain-Counts, Jennifer P.; Demopoulos, Amanda W.J.; Ross, Steve W.

    2017-01-01

    Mesopelagic fishes represent an important component of the marine food web due to their global distributions, high abundances and ability to transport organic material throughout a large part of the water column. This study combined stable isotope (SIAs) and gut content analyses (GCAs) to characterize the trophic structure of mesopelagic fishes in the North-Central Gulf of Mexico. Additionally, this study examined whether mesopelagic fishes utilized chemosynthetic energy from cold seeps. Specimens were collected (9–25 August 2007) over three deep (>1,000 m) cold seeps at discrete depths (surface to 1,503 m) over the diurnal cycle. GCA classified 31 species (five families) of mesopelagic fishes into five feeding guilds: piscivores, large crustacean consumers, copepod consumers, generalists and mixed zooplanktivores. However, these guilds were less clearly defined based on stable isotope mixing model (MixSIAR) results, suggesting diets may be more mixed over longer time periods (weeks–months) and across co-occurring species. Copepods were likely important for the majority of mesopelagic fishes, consistent with GCA (this study) and previous literature. MixSIAR results also identified non-crustacean prey items, including salps and pteropods, as potentially important prey items for mesopelagic fishes, including those fishes not analysed in GCA (Sternoptyx spp. and Melamphaidae). Salps and other soft-bodied species are often missed in GCAs. Mesopelagic fishes had δ13C results consistent with particulate organic matter serving as the baseline organic carbon source, fueling up to three trophic levels. Fishes that undergo diel vertical migration were depleted in 15N relative to weak migrators, consistent with depth-specific isotope trends in sources and consumers, and assimilation of 15N-depleted organic matter in surface waters. Linear correlations between fish size and δ15N values suggested ontogenetic changes in fish diets for several species. While there was

  18. Molecular and functional analyses of a maize autoactive NB-LRR protein identify precise structural requirements for activity.

    Science.gov (United States)

    Wang, Guan-Feng; Ji, Jiabing; El-Kasmi, Farid; Dangl, Jeffery L; Johal, Guri; Balint-Kurti, Peter J

    2015-02-01

    Plant disease resistance is often mediated by nucleotide binding-leucine rich repeat (NLR) proteins which remain auto-inhibited until recognition of specific pathogen-derived molecules causes their activation, triggering a rapid, localized cell death called a hypersensitive response (HR). Three domains are recognized in one of the major classes of NLR proteins: a coiled-coil (CC), a nucleotide binding (NB-ARC) and a leucine rich repeat (LRR) domains. The maize NLR gene Rp1-D21 derives from an intergenic recombination event between two NLR genes, Rp1-D and Rp1-dp2 and confers an autoactive HR. We report systematic structural and functional analyses of Rp1 proteins in maize and N. benthamiana to characterize the molecular mechanism of NLR activation/auto-inhibition. We derive a model comprising the following three main features: Rp1 proteins appear to self-associate to become competent for activity. The CC domain is signaling-competent and is sufficient to induce HR. This can be suppressed by the NB-ARC domain through direct interaction. In autoactive proteins, the interaction of the LRR domain with the NB-ARC domain causes de-repression and thus disrupts the inhibition of HR. Further, we identify specific amino acids and combinations thereof that are important for the auto-inhibition/activity of Rp1 proteins. We also provide evidence for the function of MHD2, a previously uncharacterized, though widely conserved NLR motif. This work reports several novel insights into the precise structural requirement for NLR function and informs efforts towards utilizing these proteins for engineering disease resistance.

  19. Molecular and functional analyses of a maize autoactive NB-LRR protein identify precise structural requirements for activity.

    Directory of Open Access Journals (Sweden)

    Guan-Feng Wang

    2015-02-01

    Full Text Available Plant disease resistance is often mediated by nucleotide binding-leucine rich repeat (NLR proteins which remain auto-inhibited until recognition of specific pathogen-derived molecules causes their activation, triggering a rapid, localized cell death called a hypersensitive response (HR. Three domains are recognized in one of the major classes of NLR proteins: a coiled-coil (CC, a nucleotide binding (NB-ARC and a leucine rich repeat (LRR domains. The maize NLR gene Rp1-D21 derives from an intergenic recombination event between two NLR genes, Rp1-D and Rp1-dp2 and confers an autoactive HR. We report systematic structural and functional analyses of Rp1 proteins in maize and N. benthamiana to characterize the molecular mechanism of NLR activation/auto-inhibition. We derive a model comprising the following three main features: Rp1 proteins appear to self-associate to become competent for activity. The CC domain is signaling-competent and is sufficient to induce HR. This can be suppressed by the NB-ARC domain through direct interaction. In autoactive proteins, the interaction of the LRR domain with the NB-ARC domain causes de-repression and thus disrupts the inhibition of HR. Further, we identify specific amino acids and combinations thereof that are important for the auto-inhibition/activity of Rp1 proteins. We also provide evidence for the function of MHD2, a previously uncharacterized, though widely conserved NLR motif. This work reports several novel insights into the precise structural requirement for NLR function and informs efforts towards utilizing these proteins for engineering disease resistance.

  20. Structural characterizations, Hirshfeld surface analyses, and third-order nonlinear optical properties of two novel chalcone derivatives

    Science.gov (United States)

    Maidur, Shivaraj R.; Jahagirdar, Jitendra R.; Patil, Parutagouda Shankaragouda; Chia, Tze Shyang; Quah, Ching Kheng

    2018-01-01

    We report synthesis, characterizations, structure-property relationships, and third-order nonlinear optical studies for two new chalcone derivatives, (2E)-1-(anthracen-9-yl)-3-(4-bromophenyl)prop-2-en-1-one (Br-ANC) and (2E)-1-(anthracen-9-yl)-3-(4-chlorophenyl)prop-2-en-1-one (Cl-ANC). These derivatives were crystallized in the centrosymmetric monoclinic P21/c crystal structure. The intermolecular interactions of both the crystals were visualized by Hirshfeld surface analyses (HSA). The crystals are thermally stable up to their melting points (180.82 and 191.16 °C for Cl-ANC and Br-ANC, respectively). The geometry optimizations, FT-IR spectra, 1H and 13C NMR spectra, electronic absorption spectra, electronic transitions, and HOMO-LUMO energy gaps were studied by Density Functional Theory (DFT) at B3LYP/6-311+G(d, p) level. The theoretical results provide excellent agreement with experimental findings. The electric dipole moments, static polarizabilities, molecular electrostatic potentials (MEP) and global chemical reactivity descriptors (GCRD) were also theoretically computed. The materials exhibited good nonlinear absorption (NLA), nonlinear refraction (NLR) and optical limiting (OL) behavior under diode-pumped solid-state (DPSS) continuous wave (CW) laser excitation (532 nm and 200 mW). The NLO parameters such as NLA coefficient (β∼10-5 cmW-1), NLR index (n2∼10-10 cm2 W-1) and third-order NLO susceptibilities (χ(3) ∼10-7 esu) were measured. Further, we estimated one-photon and two-photon figures of merit, which satisfy the demands (W > 1 and T < 1) for all-optical switching. Thus, the present chalcone derivatives with anthracene moiety are potential materials for OL and optical switching applications.

  1. New five coordinated supramolecular structured cadmium complex as precursor for CdO nanoparticles: Synthesis, crystal structure, theoretical and 3D Hirshfeld surface analyses

    Science.gov (United States)

    Ghanbari Niyaky, S.; Montazerozohori, M.; Masoudiasl, A.; White, J. M.

    2017-03-01

    In this paper, a combined experimental and theoretical study on a new CdLBr2 complex (L = N1-(2-bromobenzylidene)-N2-(2-((E)-(2-bromobenzylidene) amino)ethyl) ethane-1,2-diamine) synthesized via template method, is described. The crystal structure analysis of the complex indicates that, the Cd(II) ion is centered in a distorted square pyramidal space constructed by three iminic nitrogens of the ligand as well as two bromide anions. More analysis of crystal packing proposed a supramolecular structure stabilized by some non-covalent interactions such as Br⋯Br and Xsbnd H⋯Br (X = N and C) in solid state. Furthermore, 3D Hirshfeld surface analyses and DFT studies were applied for theoretical investigation of the complexes. Theoretical achievements were found in a good agreement with respect to the experimental data. To evaluate the nature of bonding and the strength of the intra and inter-molecular interactions a natural bond orbital (NBO) analysis on the complex structure was performed. Time dependent density functional theory (TD-DFT) was also applied to predict the electronic spectral data of the complex as compared with the experimental ones. CdLBr2 complex as nano-structure compound was also prepared under ultrasonic conditions and characterized by scanning electron microscopy (SEM) and X-ray powder diffraction (XRPD). Finally, it was found that the cadmium complex can be used as a suitable precursor for preparation of CdO nanoparticles via calcination process at 600 °C under air atmosphere.

  2. Microsatellite and mitochondrial DNA analyses of Atlantic bluefin tuna (Thunnus thynnus thynnus) population structure in the Mediterranean Sea.

    Science.gov (United States)

    Carlsson, Jens; McDowell, Jan R; Díaz-Jaimes, Píndaro; Carlsson, Jeanette E L; Boles, Sandra B; Gold, John R; Graves, John E

    2004-11-01

    Genetic variation was surveyed at nine microsatellite loci and the mitochondrial control region (868 bp) to test for the presence of genetic stock structure in young-of-the-year Atlantic bluefin tuna (Thunnus thynnus thynnus) from the Mediterranean Sea. Bluefin tuna were sampled over a period of 5 years from the Balearic and Tyrrhenian seas in the western basin of the Mediterranean Sea, and from the southern Ionian Sea in the eastern basin of the Mediterranean Sea. Analyses of multilocus microsatellite genotypes and mitochondrial control region sequences revealed no significant heterogeneity among collections taken from the same location in different years; however, significant spatial genetic heterogeneity was observed across all samples for both microsatellite markers and mitochondrial control region sequences (FST=0.0023, P=0.038 and PhiST=0.0233, P=0.000, respectively). Significant genetic differentiation between the Tyrrhenian and Ionian collections was found for both microsatellite and mitochondrial markers (FST=0.0087, P=0.015 and PhiST=0.0367, P=0.030, respectively). These results suggest the possibility of a genetically discrete population in the eastern basin of the Mediterranean Sea.

  3. Control volume analyses of glottal flow using a fully-coupled numerical fluid-structure interaction model

    Science.gov (United States)

    Yang, Jubiao; Krane, Michael; Zhang, Lucy

    2013-11-01

    Vocal fold vibrations and the glottal jet are successfully simulated using the modified Immersed Finite Element method (mIFEM), a fully coupled dynamics approach to model fluid-structure interactions. A self-sustained and steady vocal fold vibration is captured given a constant pressure input at the glottal entrance. The flow rates at different axial locations in the glottis are calculated, showing small variations among them due to the vocal fold motion and deformation. To further facilitate the understanding of the phonation process, two control volume analyses, specifically with Bernoulli's equation and Newton's 2nd law, are carried out for the glottal flow based on the simulation results. A generalized Bernoulli's equation is derived to interpret the correlations between the velocity and pressure temporally and spatially along the center line which is a streamline using a half-space model with symmetry boundary condition. A specialized Newton's 2nd law equation is developed and divided into terms to help understand the driving mechanism of the glottal flow.

  4. Combining satellite and seismic images to analyse the shallow structure of the Dead Sea Transform near the DESERT transect

    Science.gov (United States)

    Kesten, D.; Weber, M.; Haberland, Ch.; Janssen, Ch.; Agnon, A.; Bartov, Y.; Rabba, I.

    2008-02-01

    The left-lateral Dead Sea Transform (DST) in the Middle East is one of the largest continental strike-slip faults of the world. The southern segment of the DST in the Arava/Araba Valley between the Dead Sea and the Red Sea, called Arava/Araba Fault (AF), has been studied in detail in the multidisciplinary DESERT (DEad SEa Rift Transect) project. Based on these results, here, the interpretations of multi-spectral (ASTER) satellite images and seismic reflection studies have been combined to analyse geologic structures. Whereas satellite images reveal neotectonic activity in shallow young sediments, reflection seismic image deep faults that are possibly inactive at present. The combination of the two methods allows putting some age constraint on the activity of individual fault strands. Although the AF is clearly the main active fault segment of the southern DST, we propose that it has accommodated only a limited (up to 60 km) part of the overall 105 km of sinistral plate motion since Miocene times. There is evidence for sinistral displacement along other faults, based on geological studies, including satellite image interpretation. Furthermore, a subsurface fault is revealed ≈4 km west of the AF on two ≈E-W running seismic reflection profiles. Whereas these seismic data show a flower structure typical for strike-slip faults, on the satellite image this fault is not expressed in the post-Miocene sediments, implying that it has been inactive for the last few million years. About 1 km to the east of the AF another, now buried fault, was detected in seismic, magnetotelluric and gravity studies of DESERT. Taking together various evidences, we suggest that at the beginning of transform motion deformation occurred in a rather wide belt, possibly with the reactivation of older ≈N-S striking structures. Later, deformation became concentrated in the region of today’s Arava Valley. Till ≈5 Ma ago there might have been other, now inactive fault traces in the vicinity

  5. Structures des fractions lourdes. Méthodes d'analyse et préparation des charges Structures of Heavy Fractions. Feedstock Analysis and Preparation Methods

    Directory of Open Access Journals (Sweden)

    Vercier P.

    2006-11-01

    Full Text Available Après avoir défini les termes fractions lourdes et pétroles bruts lourds, et avoir souligné l'intérêt économique qu'il y a à utiliser ces matériaux, on passera en revue les techniques analytiques disponibles pour aborder les difficiles problèmes technologiques que soulève l'emploi des équipements et des méthodes conventionnels. On montrera que les analystes auront besoin de techniques améliorées ou même entièrement nouvelles pour séparer ces produits en des fractions plus simples, susceptibles d'être alors analysées par les méthodes plus traditionnelles : distillation à haute température (jusqu'à 650 °C ; séparation en asphaltènes, résines et huile ; séparation en acides, bases, neutres, saturés, mono-, di-, poly-aromatiques ; analyses structurales (analyses élémentaires, détermination des masses moléculaires, spectrométrie de masse, RMN, pyrolyse et détection à l'aide de détecteurs spécifiques pour le soufre et l'azote. Comme le facteur temps est important dans les études pilote, il sera montré que la mise au point des méthodes rapides et modernes de chromatographie liquide sera l'objectif prioritaire de la recherche analytique dans le futur proche. After defining the terms heavy fractionsand heavy crudesand then stressing the economic interest there is in using such materials, a survey is made of the analytical techniques available for tackling the difficult technological problems arising from the use of conventional equipment and methods. It is shown that analysts will need improved or even completely new techniques for separating such products into simpler fractions so that they can be analyzed by more traditional methods, i. e. high-temperature distillation (up to 650°C; separation into asphaltenes, resins and oils; structural analyses (elemental analyses, determining molecular weights, mass spectrometry, NMR, pyrolysis and detection with specific sulfur and nitrogen detectors. Since the time

  6. Structural, micro-structural and kinematic analyses of channel flow in the Karmostaj salt diapir in the Zagros foreland folded belt, Fars province, Iran

    Science.gov (United States)

    Sarkarinejad, Khalil; Sarshar, Maryam Asadi; Adineh, Sadegh

    2018-02-01

    One of the main characteristic of the Zagros foreland fold-and-thrust belt and the Zagros foreland folded belt are wide distributions of surface extrusion from the Hormuz salt diapirs. This study examines the structure and kinematic of channel flow in the Karmostaj salt diapir in the southwestern part of the Zagros foreland folded belt. This diapir has reached the surface as a result of the channel flow mechanism and has extruded in the southern limb of the Kuh-Gach anticline which is an asymmetric décollement fold with convergence to the south. Structural and microstructural studies and quantitative finite strain (Rs) and kinematic vorticity number (Wk) analyses were carried out within this salt diapir and its namakier. This was in order to investigate the structural evolution in the salt diapiric system, the characteristics and mechanism of the salt flow and the distribution of flow regimes within the salt diapir and interaction of regional tectonics and salt diaprism. The extruded salt has developed a flow foliation sub-parallel to the remnant bedding recorded by different colors, a variety of internal folds including symmetrical and asymmetrical folds and interference fold patterns, shear zones, and boudins. These structures were used to analyze mechanisms and history of diapiric flow and extrusion. The microstructures, reveal various deformation mechanisms in various parts of salt diapir. The measurements of finite strain show that Rs values in the margin of salt diapir are higher than within its namakier which is consistent with the results of structural studies. Mean kinematic vorticity number (Wm) measured in steady state deformation of diapir and namakier is Wm = 0.45-0.48 ± 0.13. The estimated mean finite deformation (Wm) values indicate that 67.8% pure shear and 32.2% simple shear deformation were involved; the implications of which are discussed. The vorticity of flow indicates that in the early stage of growth, Poiseuille flow was the dominate

  7. European Phaseolus coccineus L. landraces: population structure and adaptation, as revealed by cpSSRs and phenotypic analyses.

    Directory of Open Access Journals (Sweden)

    Monica Rodriguez

    Full Text Available Relatively few studies have extensively analysed the genetic diversity of the runner bean through molecular markers. Here, we used six chloroplast microsatellites (cpSSRs to investigate the cytoplasmic diversity of 331 European domesticated accessions of the scarlet runner bean (Phaseolus coccineus L., including the botanical varieties albiflorus, bicolor and coccineus, and a sample of 49 domesticated and wild accessions from Mesoamerica. We further explored the pattern of diversity of the European landraces using 12 phenotypic traits on 262 individuals. For 158 European accessions, we studied the relationships between cpSSR polymorphisms and phenotypic traits. Additionally, to gain insights into the role of gene flow and migration, for a subset of 115 accessions, we compared and contrasted the results obtained by cpSSRs and phenotypic traits with those obtained in a previous study with 12 nuclear microsatellites (nuSSRs. Our results suggest that both demographic and selective factors have roles in the shaping of the population genetic structure of the European runner bean. In particular, we infer the existence of a moderate-to-strong cytoplasmic bottleneck that followed the expansion of the crop into Europe, and we deduce multiple domestication events for this species. We also observe an adaptive population differentiation in the phenology across a latitudinal gradient, which suggests that selection led to the diversification of the runner bean in Europe. The botanical varieties albiflorus, bicolor and coccineus, which are based solely on flower colour, cannot be distinguished based on these cpSSRs and nuSSRs, nor according to the 12 quantitative traits.

  8. Coupled optical-thermal-fluid and structural analyses of novel light-trapping tubular panels for concentrating solar power receivers

    Science.gov (United States)

    Ortega, Jesus D.; Christian, Joshua M.; Yellowhair, Julius E.; Ho, Clifford K.

    2015-09-01

    Traditional tubular receivers used in concentrating solar power are formed using tubes connected to manifolds to form panels; which in turn are arranged in cylindrical or rectangular shapes. Previous and current tubular receivers, such as the ones used in Solar One, Solar Two, and most recently the Ivanpah solar plants, have used a black paint coating to increase the solar absorptance of the receiver. However, these coatings degrade over time and must be reapplied, increasing the receiver maintenance cost. This paper presents the thermal efficiency evaluation of novel receiver tubular panels that have a higher effective solar absorptance due to a light-trapping effect created by arranging the tubes in each panel into unique geometric configurations. Similarly, the impact of the incidence angle on the effective solar absorptance and thermal efficiency is evaluated. The overarching goal of this work is to achieve effective solar absorptances of ~90% and thermal efficiencies above 85% without using an absorptance coating. Several panel geometries were initially proposed and were down-selected based on structural analyses considering the thermal and pressure loading requirements of molten salt and supercritical carbon-dioxide receivers. The effective solar absorptance of the chosen tube geometries and panel configurations were evaluated using the ray-tracing modeling capabilities of SolTrace. The thermal efficiency was then evaluated by coupling computational fluid dynamics with the ray-tracing results using ANSYS Fluent. Compared to the base case analysis (flat tubular panel), the novel tubular panels have shown an increase in effective solar absorptance and thermal efficiency by several percentage points.

  9. Population genetic structure of Santa Ynez rainbow trout – 2001 based on microsatellite and mtDNA analyses

    Science.gov (United States)

    Nielsen, Jennifer L.; Zimmerman, Christian E.; Olsen, Jeffrey B.; Wiacek, Talia; Kretschmer, E.J.; Greenwald, Glenn M.; Wenburg, John K.

    2003-01-01

    Microsatellite allelic and mitochondrial DNA (mtDNA) haplotype diversity are analyzed in eight rainbow trout (Oncorhynchus mykiss) collections: two from tributaries flowing into the upper Santa Ynez River watershed at Gibraltar Reservoir (Camuesa and Gidney creeks); three from tributaries between Gibraltar and Jameson reservoirs (Fox, Blue Canyon, and Alder creeks); one from a tributary above Jameson Reservoir (Juncal Creek); Jameson Reservoir; and one from the mainstem Santa Ynez River above the Jameson Reservoir. Both analyses reveal a high degree of population structure. Thirteen microsatellite loci are amplified from 376 fish. Population pairwise comparisons show significant differences in allelic frequency among all populations with the exception of Juncal Creek and Jameson Reservoir (p = 0.4). Pairwise Fst values range from 0.001 (Juncal Creek and Jameson Reservoir) to 0.17 (Camuesa and Juncal creeks) with an overall value of 0.021. Regression analyses (Slatkin 1993) supports an isolation-bydistance model in the five populations below Jameson Reservoir (intercept = 1.187, slope = -0.41, r2 = 0.67). A neighbor-joining bootstrap value of 100% (based on 2000 replicate trees) separates the populations sampled above and below Juncal Dam. Composite haplotypes from 321 fish generated using mtDNA sequence data (Dloop) reveal four previously described haplotypes (MYS1, MYS3, MYS5 and MYS8; Nielsen et al. 1994a), and one (MYS5) was found in all populations. Mean haplotype diversity is 0.48. Pairwise Fst values from mtDNA range from -0.019 to 0.530 (0.177 over all populations) and are larger than those for microsatellites in 26 of 28 pairwise comparisons. In addition, the mtDNA and microsatellites provide contrasting evidence of the relationship of Fox and Alder creeks to the other six populations. Discrepancies between the two markers are likely due to the unique properties of the two marker types and their value in revealing historic (mtDNA) versus contemporary

  10. 3D/4D analyses of damage and fracture behaviours in structural materials via synchrotron X-ray tomography.

    Science.gov (United States)

    Toda, Hiroyuki

    2014-11-01

    X-ray microtomography has been utilized for the in-situ observation of various structural metals under external loading. Recent advances in X-ray microtomography provide remarkable tools to image the interior of materials. In-situ X-ray microtomography provides a unique possibility to access the 3D character of internal microstructure and its time evolution behaviours non-destructively, thereby enabling advanced techniques for measuring local strain distribution. Local strain mapping is readily enabled by processing such high-resolution tomographic images either by the particle tracking technique or the digital image correlation technique [1]. Procedures for tracking microstructural features which have been developed by the authors [2], have been applied to analyse localised deformation and damage evolution in a material [3]. Typically several tens of thousands of microstructural features, such as particles and pores, are tracked in a tomographic specimen (0.2 - 0.3 mm(3) in volume). When a sufficient number of microstructural features is dispersed in 3D space, the Delaunay tessellation algorithm is used to obtain local strain distribution. With these techniques, 3D strain fields can be measured with reasonable accuracy. Even local crack driving forces, such as local variations in the stress intensity factor, crack tip opening displacement and J integral along a crack front line, can be measured from discrete crack tip displacement fields [4]. In the present presentation, complicated crack initiation and growth behaviour and the extensive formation of micro cracks ahead of a crack tip are introduced as examples.A novel experimental method has recently been developed by amalgamating a pencil beam X-Ray diffraction (XRD) technique with the microstructural tracking technique [5]. The technique provides information about individual grain orientations and 1-micron-level grain morphologies in 3D together with high-density local strain mapping. The application of this

  11. Proposal of the Methodology for Analysing the Structural Relationship in the System of Random Process Using the Data Mining Methods

    Directory of Open Access Journals (Sweden)

    Michaľčonok German

    2014-12-01

    Full Text Available The aim of this paper is to present the possibilities of applying data mining techniques to the problem of analysis of structural relationships in the system of stationary random processes. In this paper, we will approach the area of the random processes, present the process of structural analysis and select suitable circuit data mining methods applicable to the area of structural analysis. We will propose the methodology for the structural analysis in the system of stationary stochastic processes using data mining methods for active experimental approach, based on the theoretical basis.

  12. structure-chemical analyses of half-antiperovskites and superconductivity of parkerites; Strukturchemische Untersuchungen an Halbantiperowskiten und Supraleitung der Parkerite

    Energy Technology Data Exchange (ETDEWEB)

    Peter, Philipp

    2015-04-22

    The aim of this work was the structural investigation on Halfantiperowskites. In the process four new compounds were synthesized and a new ordering variant was found. Furthermore superconductivity was measured on selected compounds of the Parkerite-type of structure and an attempt was made to change the transition temperature by selective doping.

  13. The changing structure of fears during childhood and adolescence: Confirmatory factor analyses of the Fear Survey Schedule for Children - Revised

    NARCIS (Netherlands)

    Bokhorst, C.L.; Westenberg, P.M.; Oosterlaan, J.; Heyne, D.A.

    2008-01-01

    The (in)variance of the structure of fear across child and adolescent development was investigated using the response of 3,803 young people (aged 6-18 years) to the Fear Survey Schedule for Children-Revised (FSSC-R). It was hypothesized that the structure of fear, particularly social fear, would

  14. Effects of Cooperative, Competitive, and Individualistic Learning Structures on College Student Achievement and Peer Relationships: A Series of Meta-Analyses

    Science.gov (United States)

    Hilk, Caroline Lual

    2013-01-01

    This series of meta-analyses investigates the effects of social interdependence (cooperative, competitive, and individualistic learning structures) on achievement and peer relationships among college students. This study quantitatively synthesized the literature on the effects of social interdependence on achievement and peer relationship outcomes…

  15. Response Analyses of Tuned Mass Dampers to Structures Exposed to Vortex Loading of Simiu-Scanlan Type

    DEFF Research Database (Denmark)

    Andersen, Lars; Birch, N. W.; Hansen, A. H.

    2001-01-01

    Vortex-induced loads on slender one-dimensional structures vibrating at lock-in conditions consist of a self-induced part in phase with the velocity of the structure in addition to an additive, almost harmonially varying component representing the same type of load as the vortex-induced force...... on a fixed cylinder. Simiu and Scanlan (1996 Wind Effects on Structures. New York: John Wiley & Sons Inc.) have proposed a widely used model for the self-induced part of the load based on a van der Pol oscillator. The aim of this paper is to investigate the optimal design of tuned mass dampers...

  16. Structural Conditions for Collaboration and Learning in Innovation Networks: Using an Innovation System Performance Lens to Analyse Agricultural Knowledge Systems

    NARCIS (Netherlands)

    Hermans, F.; Klerkx, L.W.A.; Roep, D.

    2015-01-01

    Purpose: We investigate how the structural conditions of eight different European agricultural innovation systems can facilitate or hinder collaboration and social learning in multidisciplinary innovation networks. Methodology: We have adapted the Innovation System Failure Matrix to investigate the

  17. Structural brain alterations of Down's syndrome in early childhood evaluation by DTI and volumetric analyses

    International Nuclear Information System (INIS)

    Gunbey, Hediye Pinar; Bilgici, Meltem Ceyhan; Aslan, Kerim; Incesu, Lutfi; Has, Arzu Ceylan; Ogur, Methiye Gonul; Alhan, Aslihan

    2017-01-01

    To provide an initial assessment of white matter (WM) integrity with diffusion tensor imaging (DTI) and the accompanying volumetric changes in WM and grey matter (GM) through volumetric analyses of young children with Down's syndrome (DS). Ten children with DS and eight healthy control subjects were included in the study. Tract-based spatial statistics (TBSS) were used in the DTI study for whole-brain voxelwise analysis of fractional anisotropy (FA) and mean diffusivity (MD) of WM. Volumetric analyses were performed with an automated segmentation method to obtain regional measurements of cortical volumes. Children with DS showed significantly reduced FA in association tracts of the fronto-temporo-occipital regions as well as the corpus callosum (CC) and anterior limb of the internal capsule (p < 0.05). Volumetric reductions included total cortical GM, cerebellar GM and WM volume, basal ganglia, thalamus, brainstem and CC in DS compared with controls (p < 0.05). These preliminary results suggest that DTI and volumetric analyses may reflect the earliest complementary changes of the neurodevelopmental delay in children with DS and can serve as surrogate biomarkers of the specific elements of WM and GM integrity for cognitive development. (orig.)

  18. Structural brain alterations of Down's syndrome in early childhood evaluation by DTI and volumetric analyses

    Energy Technology Data Exchange (ETDEWEB)

    Gunbey, Hediye Pinar; Bilgici, Meltem Ceyhan; Aslan, Kerim; Incesu, Lutfi [Ondokuz Mayis University, Faculty of Medicine, Department of Radiology, Kurupelit, Samsun (Turkey); Has, Arzu Ceylan [Bilkent University, National Magnetic Resonance Research Center, Ankara (Turkey); Ogur, Methiye Gonul [Ondokuz Mayis University, Department of Genetics, Samsun (Turkey); Alhan, Aslihan [Ufuk University, Department of Statistics, Ankara (Turkey)

    2017-07-15

    To provide an initial assessment of white matter (WM) integrity with diffusion tensor imaging (DTI) and the accompanying volumetric changes in WM and grey matter (GM) through volumetric analyses of young children with Down's syndrome (DS). Ten children with DS and eight healthy control subjects were included in the study. Tract-based spatial statistics (TBSS) were used in the DTI study for whole-brain voxelwise analysis of fractional anisotropy (FA) and mean diffusivity (MD) of WM. Volumetric analyses were performed with an automated segmentation method to obtain regional measurements of cortical volumes. Children with DS showed significantly reduced FA in association tracts of the fronto-temporo-occipital regions as well as the corpus callosum (CC) and anterior limb of the internal capsule (p < 0.05). Volumetric reductions included total cortical GM, cerebellar GM and WM volume, basal ganglia, thalamus, brainstem and CC in DS compared with controls (p < 0.05). These preliminary results suggest that DTI and volumetric analyses may reflect the earliest complementary changes of the neurodevelopmental delay in children with DS and can serve as surrogate biomarkers of the specific elements of WM and GM integrity for cognitive development. (orig.)

  19. Structural and spectral analyses of N,N'-(2,2'-dithiodi-o-phenylene)bis-(furan-2-carboxamide)

    Science.gov (United States)

    Yıldırım, Sema Öztürk; Büyükmumcu, Zeki; Pekdur, Özlem Savaş; Butcher, Ray J.; Doǧan, Şengül Dilem

    2018-02-01

    In this study we report structure determination of N,N'-(2,2'-dithiodi-o-phenylene)bis-(furan-2-carboxamide). 2,2'-Dithiobis(benzamide) derivatives have been reported to possess important biological properties such as antibacterial, antifungal activities and inhibition of blood platelet aggregation and redeterrmined at 100(2)K from the data published by Raftery, Lallbeeharry, Bhowon, Laulloo & Joulea [Acta Cryst. 2009, E65, o16]. 2,2'-Dithiobis(N-butyl-benzamide) has been reported to be useful as an antiseptic for cosmetics. The structural properties of the compound have been characterized by using 1H NMR and the structure were determined by single-crystal X-ray diffraction. Molecular structure crystallizes in triclinic form, space group with a = 9.6396(7) Å, b = 9.9115(7) Å, c = 12.0026(8) Å, α = 109.743(6)°, β = 103.653(6)°, γ = 104.633(6)° and V = 977.15(13) Å3. In the solid state of the molecular structure N-H…S, N-H…O and C-H…O, type interactions provide for stabilization. The geometries of the title compound have been optimized using density functional theory (DFT) method. The calculated values were found to be in agreement with the experimental data.

  20. Accurate structure analyses of polymer crystals on the basis of wide-angle X-ray and neutron diffractions

    International Nuclear Information System (INIS)

    Tashiro, Kohji; Hanesaka, Makoto; Yamamoto, Hiroko; Wasanasuk, Kaewkan; Jayaratri, Paramita; Yoshizawa, Yoshinori; Tanaka, Ichiro; Niimura, Nobuo; Kusaka, Katsuhiro; Hosoya, Takaaki; Ohhara, Takashi; Kurihara, Kazuo; Kuroki, Ryota; Tamada, Taro; Fujiwara, Satoru; Katsube, Katsuyoshi; Morikawa, Keisuke; Komiya, Yukiatsu; Kitano, Toshiaki; Nishu, Takashi; Ozeki, Tomoji

    2014-01-01

    The crystal structure analysis of various polymer substances has been reviewed on the basis of wide-angle high-energy X-ray and neutron diffraction data. The progress in structural analytical techniques of polymer crystals have been reviewed at first. The structural models proposed so far were reinvestigated and new models have been proposed for various kinds of polymer crystals including polyethylene, poly(vinyl alcohol), poly(lactic acid) and its stereocomplex etc. The hydrogen atomic positions were also clarified by the quantitative analysis of wide-angle neutron diffraction data, from which the physical properties of polymer crystals have been evaluated theoretically. The bonded electron density distribution has been estimated for a polydiacetylene single crystal on the basis of the so-called X-N method or by the combination of structural information derived from X-ray and neutron diffraction data analysis. Some comments have been added about future developments in the field of structure-property relationship determination. (author)

  1. Constitutive Relations Analyses of Plastic Flow in Dual-Phase Steels to Elucidate Structure-Strength-Ductility Correlations

    Science.gov (United States)

    Saimoto, S.; Timokhina, I. B.; Pereloma, E. V.

    2017-07-01

    The structure-strength characterization is typically performed by correlating the structure with x-ray, electron, or atomic imaging devices to the bulk mechanical tensile parameters of yield stress and the plastic yielding response. The problem is that structure parameters embedded in the stress-strain data cannot be revealed without an analyzable constitutive relation. New functional slip-based constitutive formulation with precise digital fitting parameters can replicate the measured data with at least two loci. Thus, this study examines the possibility of identifying the mechanical response as a result of the various microstructure components. The key parameter, the mean slip distance, can be calibrated from the initial work-hardening slope at 0.2% strain from which all the fit parameters can be determined. In this process, a newly derived friction stress is defined to separate the yield phenomenon from the plastic strains beyond yield-point elongation. This methodology has been applied to dual-phase steel specimens that resulted in excellent predictive correlations with prior structure-strength characterization. Hence, the structure-strength-ductility changes resulting from processing conditions can be more precisely surmised from mechanical testing. Thus, a method to delineate the nanostructure evolution with deformation using mesoscopic mechanical parameters has been introduced.

  2. Nanoscale Stress Field Evaluation with Shallow Trench Isolation Structure Assessed by Cathodoluminescence Spectroscopy, Raman Spectroscopy, and Finite Element Method Analyses

    Science.gov (United States)

    Kodera, Masako; Iguchi, Tadashi; Tsuchiya, Norihiko; Tamura, Mizuki; Kakinuma, Shigeru; Naka, Nobuyuki; Kashiwagi, Shinsuke

    2008-04-01

    Stress engineering related to the LSI process is required. With shallow trench isolation (STI) structures, a high stress field causes a variation in electrical characteristics. Although stress fields in a Si substrate can be detected by Raman spectroscopy, no effective technique has been reported for the measurement of nanoscale stress fields in a dielectric material used for STI filling. Recently, we have reported that “cathodoluminescence (CL) spectroscopy” enables us to detect nanometer-scale stress fields in LSI structures. In this study, we performed the first estimation of the stress fields with a STI structure by CL and Raman spectroscopy, as well as finite element method (FEM) calculation. We were able to repeatedly acquire clear stress distributions by CL and Raman spectroscopy. Moreover, CL, Raman, and FEM results showed excellent agreement with one another, revealing that a large variation in stresses along the AA/STI boundary was induced by the intrinsic tensile stress of the SiO2 film.

  3. A comparative proteomic approach to analyse structure, function and evolution of rice chitinases: a step towards increasing plant fungal resistance.

    Science.gov (United States)

    Sarma, Kishore; Dehury, Budheswar; Sahu, Jagajjit; Sarmah, Ranjan; Sahoo, Smita; Sahu, Mousumi; Sen, Priyabrata; Modi, Mahendra Kumar; Barooah, Madhumita

    2012-11-01

    Glycoside hydrolase family 19 chitinases (EC 3.2.1.14) widely distributed in plants, bacteria and viruses catalyse the hydrolysis of chitin and play a major role in plant defense mechanisms and development. Rice possesses several classes of chitinase, out of which a single structure of class I has been reported in PDB to date. In the present study an attempt was made to gain more insight into the structure, function and evolution of class I, II and IV chitinases of GH family 19 from rice. The three-dimensional structures of chitinases were modelled and validated based on available X-ray crystal structures. The structural study revealed that they are highly α-helical and bilobed in nature. These enzymes are single or multi domain and multi-functional in which chitin-binding domain (CBD) and catalytic domain (CatD) are present in class I and IV whereas class II lacks CBD. The CatD possesses a catalytic triad which is thought to be involved in catalytic process. Loop III, which is common in all three classes of chitinases, reflects that it may play a significant role in their function. Our study also confirms that the absence and presence of different loops in GH family 19 of rice may be responsible for various sized products. Molecular phylogeny revealed chitinases in monocotyledons and dicotyledons differed from each other forming two different clusters and may have evolved differentially. More structural study of this enzyme from different plants is required to enhance the knowledge of catalytic mechanism and substrate binding.

  4. Information content of X-ray analyses characterizing the structural state of cocoa butter and their manufacturing conditions

    International Nuclear Information System (INIS)

    Foersterling, G.; Kleinstueck, K.; Loeser, U.; Tscheuschner, H.D.

    1980-01-01

    Direct X-ray analyses performed on the model substance cocoa butter revealed a direct relation between the easily measurable quantities of the diffraction pattern (site, intensity and sharpness of the reflexes) and the characteristic parameters of the sample (lattice constants, 'perfection' and crystalline fraction), which can be derived from these measured quantities, on the one side, and the technological parameters of the manufacturing process (tempering regimen and storage conditions) on the other side. An automated X-ray diffractometer was used and an optimal measuring strategy was developed the measuring effects being sufficiently great as compared to the measuring errors and the characterization of one sample requiring only 30 - 60 minutes. (author)

  5. Complete Soil-Structure Interaction (SSI) Analyses of I-walls Embedded in Level Ground During Flood Loading

    Science.gov (United States)

    2012-09-01

    75  4  Analyses of I-wall Site Founded on a Clay with Undrained Shear Strenght (Su) of 300 psf...Zero tensile strength capability is assumed along this soil-to-I-wall interface. ERDC/ITL TR-12-4 5 are discussed. A design flood depth of 9 ft1...the steel sheet-pile and the concrete I-wall section. Plate elements were used to model the concrete I-wall to process bending moment and shear

  6. On the Structure of Personality Disorder Traits: Conjoint Analyses of the CAT-PD, PID-5, and NEO-PI-3 Trait Models

    Science.gov (United States)

    Wright, Aidan G.C.; Simms, Leonard J.

    2014-01-01

    The current study examines the relations among contemporary models of pathological and normal range personality traits. Specifically, we report on (a) conjoint exploratory factor analyses of the Computerized Adaptive Test of Personality Disorder static form (CAT-PD-SF) with the Personality Inventory for the DSM-5 (PID-5; Krueger et al., 2012) and NEO Personality Inventory-3 First Half (NEI-PI-3FH; McCrae & Costa, 2007), and (b) unfolding hierarchical analyses of the three measures in a large general psychiatric outpatient sample (N = 628; 64% Female). A five-factor solution provided conceptually coherent alignment among the CAT-PD-SF, PID-5, and NEO-PI-3FH scales. Hierarchical solutions suggested that higher-order factors bear strong resemblance to dimensions that emerge from structural models of psychopathology (e.g., Internalizing and Externalizing spectra). These results demonstrate that the CAT-PD-SF adheres to the consensual structure of broad trait domains at the five-factor level. Additionally, patterns of scale loadings further inform questions of structure and bipolarity of facet and domain level constructs. Finally, hierarchical analyses strengthen the argument for using broad dimensions that span normative and pathological functioning to scaffold a quantitatively derived phenotypic structure of psychopathology to orient future research on explanatory, etiological, and maintenance mechanisms. PMID:24588061

  7. On the structure of personality disorder traits: conjoint analyses of the CAT-PD, PID-5, and NEO-PI-3 trait models.

    Science.gov (United States)

    Wright, Aidan G C; Simms, Leonard J

    2014-01-01

    The current study examines the relations among contemporary models of pathological and normal range personality traits. Specifically, we report on (a) conjoint exploratory factor analyses of the Computerized Adaptive Test of Personality Disorder static form (CAT-PD-SF) with the Personality Inventory for the Diagnostic and Statistical Manual of Mental Disorders, fifth edition and NEO Personality Inventory-3 First Half, and (b) unfolding hierarchical analyses of the three measures in a large general psychiatric outpatient sample (n = 628; 64% Female). A five-factor solution provided conceptually coherent alignment among the CAT-PD-SF, PID-5, and NEO-PI-3FH scales. Hierarchical solutions suggested that higher-order factors bear strong resemblance to dimensions that emerge from structural models of psychopathology (e.g., Internalizing and Externalizing spectra). These results demonstrate that the CAT-PD-SF adheres to the consensual structure of broad trait domains at the five-factor level. Additionally, patterns of scale loadings further inform questions of structure and bipolarity of facet and domain level constructs. Finally, hierarchical analyses strengthen the argument for using broad dimensions that span normative and pathological functioning to scaffold a quantitatively derived phenotypic structure of psychopathology to orient future research on explanatory, etiological, and maintenance mechanisms.

  8. A Penicillium chrysogenum-based expression system for the production of small, cysteine-rich antifungal proteins for structural and functional analyses.

    Science.gov (United States)

    Sonderegger, Christoph; Galgóczy, László; Garrigues, Sandra; Fizil, Ádám; Borics, Attila; Manzanares, Paloma; Hegedüs, Nikoletta; Huber, Anna; Marcos, Jose F; Batta, Gyula; Marx, Florentine

    2016-11-11

    Small, cysteine-rich and cationic antifungal proteins (APs) from filamentous ascomycetes, such as NFAP from Neosartorya fischeri and PAF from Penicillium chrysogenum, are promising candidates for novel drug development. A prerequisite for their application is a detailed knowledge about their structure-function relation and mode of action, which would allow protein modelling to enhance their toxicity and specificity. Technologies for structure analyses, such as electronic circular dichroism (ECD) or NMR spectroscopy, require highly purified samples and in case of NMR milligrams of uniformly 15 N-/ 13 C-isotope labelled protein. To meet these requirements, we developed a P. chrysogenum-based expression system that ensures sufficient amount and optimal purity of APs for structural and functional analyses. The APs PAF, PAF mutants and NFAP were expressed in a P. chrysogenum ∆paf mutant strain that served as perfect microbial expression factory. This strain lacks the paf-gene coding for the endogenous antifungal PAF and is resistant towards several APs from other ascomycetes. The expression of the recombinant proteins was under the regulation of the strong paf promoter, and the presence of a paf-specific pre-pro sequence warranted the secretion of processed proteins into the supernatant. The use of defined minimal medium allowed a single-step purification of the recombinant proteins. The expression system could be extended to express PAF in the related fungus Penicillium digitatum, which does not produce detectable amounts of APs, demonstrating the versatility of the approach. The molecular masses, folded structures and antifungal activity of the recombinant proteins were analysed by ESI-MS, ECD and NMR spectroscopy and growth inhibition assays. This study demonstrates the implementation of a paf promoter driven expression cassettes for the production of cysteine-rich, cationic, APs in different Penicillium species. The system is a perfect tool for the generation of

  9. Novel evolutionary lineages revealed in the Chaetothyriales (Fungi) based on multigene phylogenetic analyses and comparison of ITS secondary structure

    Czech Academy of Sciences Publication Activity Database

    Réblová, Martina; Untereiner, W. A.; Réblová, K.

    2013-01-01

    Roč. 8, č. 5 (2013), e63547 E-ISSN 1932-6203 R&D Projects: GA ČR GAP506/12/0038 Institutional support: RVO:67985939 Keywords : Cyphelophora * Phialophora * secondary structure Subject RIV: EF - Botanics Impact factor: 3.534, year: 2013

  10. Isolation, Structural Analyses and Biological Activity Assays against Chronic Lymphocytic Leukemia of Two Novel Cytochalasins - Sclerotionigrin A and B

    DEFF Research Database (Denmark)

    Petersen, Lene Maj; Bladt, Tanja Thorskov; Duerr, Claudia

    2014-01-01

    Two new cytochalasins, sclerotionigrin A (1) and B (2) were isolated together with the known proxiphomin (3) from the filamentous fungus Aspergillus sclerotioniger. The structures and relative stereochemistry of 1 and 2 were determined based on comparison with 3, and from extensive 1D and 2D NMR ...

  11. Guided waves based SHM systems for composites structural elements: statistical analyses finalized at probability of detection definition and assessment

    Science.gov (United States)

    Monaco, E.; Memmolo, V.; Ricci, F.; Boffa, N. D.; Maio, L.

    2015-03-01

    Maintenance approaches based on sensorised structures and Structural Health Monitoring systems could represent one of the most promising innovations in the fields of aerostructures since many years, mostly when composites materials (fibers reinforced resins) are considered. Layered materials still suffer today of drastic reductions of maximum allowable stress values during the design phase as well as of costly and recurrent inspections during the life cycle phase that don't permit of completely exploit their structural and economic potentialities in today aircrafts. Those penalizing measures are necessary mainly to consider the presence of undetected hidden flaws within the layered sequence (delaminations) or in bonded areas (partial disbonding); in order to relax design and maintenance constraints a system based on sensors permanently installed on the structure to detect and locate eventual flaws can be considered (SHM system) once its effectiveness and reliability will be statistically demonstrated via a rigorous Probability Of Detection function definition and evaluation. This paper presents an experimental approach with a statistical procedure for the evaluation of detection threshold of a guided waves based SHM system oriented to delaminations detection on a typical wing composite layered panel. The experimental tests are mostly oriented to characterize the statistical distribution of measurements and damage metrics as well as to characterize the system detection capability using this approach. Numerically it is not possible to substitute part of the experimental tests aimed at POD where the noise in the system response is crucial. Results of experiments are presented in the paper and analyzed.

  12. Structural Conditions for Collaboration and Learning in Innovation Networks: Using an Innovation System Performance Lens to Analyse Agricultural Knowledge Systems

    Science.gov (United States)

    Hermans, Frans; Klerkx, Laurens; Roep, Dirk

    2015-01-01

    Purpose: We investigate how the structural conditions of eight different European agricultural innovation systems can facilitate or hinder collaboration and social learning in multidisciplinary innovation networks. Methodology: We have adapted the Innovation System Failure Matrix to investigate the main barriers and enablers eight countries…

  13. Mutational and structural analyses of Caldanaerobius polysaccharolyticus Man5B reveal novel active site residues for family 5 glycoside hydrolases.

    Directory of Open Access Journals (Sweden)

    Takuji Oyama

    Full Text Available CpMan5B is a glycoside hydrolase (GH family 5 enzyme exhibiting both β-1,4-mannosidic and β-1,4-glucosidic cleavage activities. To provide insight into the amino acid residues that contribute to catalysis and substrate specificity, we solved the structure of CpMan5B at 1.6 Å resolution. The structure revealed several active site residues (Y12, N92 and R196 in CpMan5B that are not present in the active sites of other structurally resolved GH5 enzymes. Residue R196 in GH5 enzymes is thought to be strictly conserved as a histidine that participates in an electron relay network with the catalytic glutamates, but we show that an arginine fulfills a functionally equivalent role and is found at this position in every enzyme in subfamily GH5_36, which includes CpMan5B. Residue N92 is required for full enzymatic activity and forms a novel bridge over the active site that is absent in other family 5 structures. Our data also reveal a role of Y12 in establishing the substrate preference for CpMan5B. Using these molecular determinants as a probe allowed us to identify Man5D from Caldicellulosiruptor bescii as a mannanase with minor endo-glucanase activity.

  14. Mutational and structural analyses of Caldanaerobius polysaccharolyticus Man5B reveal novel active site residues for family 5 glycoside hydrolases.

    Science.gov (United States)

    Oyama, Takuji; Schmitz, George E; Dodd, Dylan; Han, Yejun; Burnett, Alanna; Nagasawa, Naoko; Mackie, Roderick I; Nakamura, Haruki; Morikawa, Kosuke; Cann, Isaac

    2013-01-01

    CpMan5B is a glycoside hydrolase (GH) family 5 enzyme exhibiting both β-1,4-mannosidic and β-1,4-glucosidic cleavage activities. To provide insight into the amino acid residues that contribute to catalysis and substrate specificity, we solved the structure of CpMan5B at 1.6 Å resolution. The structure revealed several active site residues (Y12, N92 and R196) in CpMan5B that are not present in the active sites of other structurally resolved GH5 enzymes. Residue R196 in GH5 enzymes is thought to be strictly conserved as a histidine that participates in an electron relay network with the catalytic glutamates, but we show that an arginine fulfills a functionally equivalent role and is found at this position in every enzyme in subfamily GH5_36, which includes CpMan5B. Residue N92 is required for full enzymatic activity and forms a novel bridge over the active site that is absent in other family 5 structures. Our data also reveal a role of Y12 in establishing the substrate preference for CpMan5B. Using these molecular determinants as a probe allowed us to identify Man5D from Caldicellulosiruptor bescii as a mannanase with minor endo-glucanase activity.

  15. Analyses of the temporal and spatial structures of heavy rainfall from a catalog of high-resolution radar rainfall fields

    DEFF Research Database (Denmark)

    Thorndahl, Søren; Smith, James A.; Baeck, Mary Lynn

    2014-01-01

    that relate to size, structure and evolution of heavy rainfall. Extreme rainfall is also linked with severe weather (tornados, large hail and damaging wind). The diurnal cycle of rainfall for heavy rain days is characterized by an early peak in the largest rainfall rates, an afternoon-evening peak in rain...

  16. The Decline of Industrial Unionism in the Meatpacking Industry: Event-Structure Analyses of Labor Unrest, 1946-1987.

    Science.gov (United States)

    Brueggemann, John; Brown, Cliff

    2003-01-01

    A study of the United Packinghouse Workers of America compared the postwar years and the Reagan era. Using event-structure analysis, the development of new corporate strategies (new technologies, production reorganization, cheap nonunion labor) fundamentally transformed the capital-labor relationship and led to the collapse of industrial unionism…

  17. Pseudomonas community structure and antagonistic potential in the rhizosphere : insights gained by combining phylogenetic and functional gene-based analyses

    NARCIS (Netherlands)

    Costa, Rodrigo; Gomes, Newton C. M.; Kroegerrecklenfort, Ellen; Opelt, Katja; Berg, Gabriele; Smalla, Kornelia

    The Pseudomonas community structure and antagonistic potential in the rhizospheres of strawberry and oilseed rape (host plants of the fungal phytopathogen Verticillium dahliae) were assessed. The use of a new PCR-DGGE system, designed to target Pseudomonas-specific gacA gene fragments in

  18. Thermal/structural analyses of several hydrogen-cooled leading-edge concepts for hypersonic flight vehicles

    Science.gov (United States)

    Gladden, Herbert J.; Melis, Matthew E.; Mockler, Theodore T.; Tong, Mike

    1990-01-01

    The aerodynamic heating at high flight Mach numbers, when shock interference heating is included, can be extremely high and can exceed the capability of most conventional metallic and potential ceramic materials available. Numerical analyses of the heat transfer and thermal stresses are performed on three actively cooled leading-edge geometries (models) made of three different materials to address the issue of survivability in a hostile environment. These analyses show a mixture of results from one configuration to the next. Results for each configuration are presented and discussed. Combinations of enhanced internal film coefficients and high material thermal conductivity of copper and tungsten are predicted to maintain the maximum wall temperature for each concept within acceptable operating limits. The exception is the TD nickel material which is predicted to melt for most cases. The wide range of internal impingement film coefficients (based on correlations) for these conditions can lead to a significant uncertainty in expected leading-edge wall temperatures. The equivalent plastic strain, inherent in each configuration which results from the high thermal gradients, indicates a need for further cyclic analysis to determine component life.

  19. Electronic structure analyses of BN network materials using high energy-resolution spectroscopy methods based on transmission electron microscopy.

    Science.gov (United States)

    Terauchi, M

    2006-07-01

    Electronic structures of boron-nitride (BN) nanotubes and a BN cone-structure material were studied by using a high energy-resolution electron energy-loss spectroscopy (EELS) microscope. A trial of the whole electronic structure study of hexagonal BN (h-BN), which consists of flat BN honeycomb layers, was conducted by a combination of EELS and X-ray emission spectroscopy (XES) based on transmission electron microscopy (TEM) (TEM-EELS/XES). The pi and pi+sigma plasmon energies of BN nanotubes (BNT) were smaller than those of h-BN. The pi+sigma energy was explained by the surface plasmon excitation. The spectrum of a two-wall BNT of 2.7 nm in diameter showed a new spectral onset at 4 eV. The valence electron excitation spectra obtained from the tip region of the BN cone with an apex angle of 20 degrees showed similar intensity distribution with those of BNTs. The B K-shell electron excitation spectra obtained from the bottom edge region of the BN cone showed additional peak intensity when compared with those of h-BN and BNT. The B K-shell electron excitation spectra and B K-emission spectra of h-BN were compared with a result of a LDA band calculation. It showed that high symmetry points in the band diagram appear as peak and/or shoulder structures in the EELS and XES spectra. Interband transitions appeared in the imaginary part of the dielectric function of h-BN experimentally obtained were assigned in the band diagram. The analysis also presented that the LDA calculation estimated the bandgap energy smaller than the real material by an amount of 2 eV. Those results of TEM-EELS/XES analysis presented that high energy-resolution spectroscopy methods combined with TEM is a promising method to analyze whole electronic structures of nanometer scale materials. Copyright (c) 2006 Wiley-Liss, Inc.

  20. Structural and mutational analyses of the Leptospira interrogans virulence-related heme oxygenase provide insights into its catalytic mechanism.

    Directory of Open Access Journals (Sweden)

    Anabel Soldano

    Full Text Available Heme oxygenase from Leptospira interrogans is an important virulence factor. During catalysis, redox equivalents are provided to this enzyme by the plastidic-type ferredoxin-NADP+ reductase also found in L. interrogans. This process may have evolved to aid this bacterial pathogen to obtain heme-iron from their host and enable successful colonization. Herein we report the crystal structure of the heme oxygenase-heme complex at 1.73 Å resolution. The structure reveals several distinctive features related to its function. A hydrogen bonded network of structural water molecules that extends from the catalytic site to the protein surface was cleared observed. A depression on the surface appears to be the H+ network entrance from the aqueous environment to the catalytic site for O2 activation, a key step in the heme oxygenase reaction. We have performed a mutational analysis of the F157, located at the above-mentioned depression. The mutant enzymes were unable to carry out the complete degradation of heme to biliverdin since the reaction was arrested at the verdoheme stage. We also observed that the stability of the oxyferrous complex, the efficiency of heme hydroxylation and the subsequent conversion to verdoheme was adversely affected. These findings underscore a long-range communication between the outer fringes of the hydrogen-bonded network of structural waters and the heme active site during catalysis. Finally, by analyzing the crystal structures of ferredoxin-NADP+ reductase and heme oxygenase, we propose a model for the productive association of these proteins.

  1. Comprehensive separation and structural analyses of polyphenols and related compounds from bracts of hops (Humulus lupulus L.).

    Science.gov (United States)

    Tanaka, Yoshihisa; Yanagida, Akio; Komeya, Satoshi; Kawana, Miho; Honma, Daiki; Tagashira, Motoyuki; Kanda, Tomomasa; Shibusawa, Yoichi

    2014-03-12

    A novel sequential chromatographic technique was applied to the comprehensive separation of polyphenols and related compounds from a hop bract extract. Over 100 types of constituents were effectively isolated from only 25 g of extract in high yields by high-speed countercurrent chromatography followed by hydrophilic interaction chromatography and reversed-phase high performance liquid chromatography. Among the materials isolated, the structures of 39 compounds were elucidated on the basis of their spectroscopic data including electrospray ionization time-of-flight mass spectrometry and one-dimensional/two-dimensional nuclear magnetic resonance. Three new compounds, 1 known compound identified for the first time in plants, and 20 known compounds that have not been reported in hops, were found. The hop bract extract also contained an abundance of highly oligomeric proanthocyanidins, which consisted of B-type procyanidin structures.

  2. Structured modelling and nonlinear analysis of PEM fuel cells; Strukturierte Modellierung und nichtlineare Analyse von PEM-Brennstoffzellen

    Energy Technology Data Exchange (ETDEWEB)

    Hanke-Rauschenbach, R.

    2007-10-26

    In the first part of this work a model structuring concept for electrochemical systems is presented. The application of such a concept for the structuring of a process model allows it to combine different fuel cell models to form a whole model family, regardless of their level of detail. Beyond this the concept offers the opportunity to flexibly exchange model entities on different model levels. The second part of the work deals with the nonlinear behaviour of PEM fuel cells. With the help of a simple, spatially lumped and isothermal model, bistable current-voltage characteristics of PEM fuel cells operated with low humidified feed gases are predicted and discussed in detail. The cell is found to exhibit current-voltage curves with pronounced local extrema in a parameter range that is of practical interest when operated at constant feed gas flow rates. (orig.)

  3. Experimental and Numerical Analyses of Dynamic Deformation and Failure in Marine Structures Subjected to Underwater Impulsive Loads

    Science.gov (United States)

    2012-08-01

    M.Y. He, and A.G. Evans, Application of a dynamic constitutive law to multilayer metallic sandwich panels subject to impulsive loads. Journal of...Impulsive Loads. 9th International Conference on Sandwich Structures, ICSS9, 2010. 146 93. Wadley, H., et al., Compressive response of multilayered ... extrusions . International Journal of Crashworthiness, 2004. 9(5): p. 449-463. 103. D’Alembert, J.R., Recherches sur la courbe que forme une corde tenduë

  4. Structural features of the southern Tulum Fault System, western central Argentina, through gravimetric data and geomorphologic analyses

    Science.gov (United States)

    Rodríguez, Aixa I.; Christiansen, Rodolfo O.; Suvires, Graciela M.; Lince Klinger, Federico; Martinez, M. Patricia

    2016-12-01

    A gravimetric analysis over the Tulum Valley was made. This data was used to reveal the structural setting of the Tulum Fault System situated in the southeastern part of San Juan province in the arid western part of Argentina. This system is the boundary between two geological provinces, the eastern Precordillera Oriental and the Sierras Pampeanas Occidentales. Gravity data was processed using upward continuation and vertical derivative filters and all the results were compared with the geomorphological and the drainage systems maps of the area. Our assessment confirms the presence of two structures in the Pampeano basement with positive anomalies similar to those found in Valdivia and Barboza hills, two important depocenters with low gravimetric gradients separated by a zone with higher gravity anomalies than the depocenters to the east and west. In view of this, a structural map is proposed for the area. This system is important not only because it is the boundary between two geological provinces and has significance regarding regional tectonic issues but also because it controls the surface drainage, soils distribution and groundwater flow of the Tulum basin conditioning the land use distribution.

  5. Differential CLE peptide perception by plant receptors implicated from structural and functional analyses of TDIF-TDR interactions

    Energy Technology Data Exchange (ETDEWEB)

    Li, Zhijie; Chakraborty, Sayan; Xu, Guozhou; Kobe, Bostjan

    2017-04-06

    Tracheary Element Differentiation Inhibitory Factor (TDIF) belongs to the family of post-translationally modified CLE (CLAVATA3/embryo surrounding region (ESR)-related) peptide hormones that control root growth and define the delicate balance between stem cell proliferation and differentiation in SAM (shoot apical meristem) or RAM (root apical meristem). In Arabidopsis, Tracheary Element Differentiation Inhibitory Factor Receptor (TDR) and its ligand TDIF signaling pathway is involved in the regulation of procambial cell proliferation and inhibiting its differentiation into xylem cells. Here we present the crystal structures of the extracellular domains (ECD) of TDR alone and in complex with its ligand TDIF resolved at 2.65 Åand 2.75 Å respectively. These structures provide insights about the ligand perception and specific interactions between the CLE peptides and their cognate receptors. Our in vitro biochemical studies indicate that the interactions between the ligands and the receptors at the C-terminal anchoring site provide conserved binding. While the binding interactions occurring at the N-terminal anchoring site dictate differential binding specificities between different ligands and receptors. Our studies will open different unknown avenues of TDR-TDIF signaling pathways that will enhance our knowledge in this field highlighting the receptor ligand interaction, receptor activation, signaling network, modes of action and will serve as a structure function relationship model between the ligand and the receptor for various similar leucine-rich repeat receptor-like kinases (LRR-RLKs).

  6. Hirshfeld surface analyses and crystal structures of supramolecular self-assembly thiourea derivatives directed by non-covalent interactions

    Science.gov (United States)

    Gumus, Ilkay; Solmaz, Ummuhan; Binzet, Gun; Keskin, Ebru; Arslan, Birdal; Arslan, Hakan

    2018-04-01

    The novel N-(bis(3,5-dimethoxybenzyl)carbamothioyl)-4-R-benzamide (R: H, Cl, CH3 and OCH3) compounds have been synthesized and characterized by FT-IR, 1H NMR and 13C NMR spectroscopy. Their crystal structures were also determined by single-crystal X-ray diffraction studies. Hirshfeld surfaces analysis and their associated two dimensional fingerprint plots of compounds were used as theoretical approach to assess driving force for crystal structure formation via the intermolecular interactions in the crystal lattices of synthesized compounds. The study of X-ray single crystal diffraction and Hirshfeld surfaces analysis of the prepared compounds shows that hydrogen bonding and other weaker interactions such as Nsbnd H⋯S, weak Csbnd H⋯S, Csbnd H⋯O, Csbnd H⋯N and Csbnd H···π intermolecular interactions and π-π stacking, among molecules of synthesized compounds participate in a cooperative way to stabilize the supramolecular structures.

  7. Combining microsatellite, otolith shape and parasites community analyses as a holistic approach to assess population structure of Dentex dentex

    Science.gov (United States)

    Marengo, M.; Baudouin, M.; Viret, A.; Laporte, M.; Berrebi, P.; Vignon, M.; Marchand, B.; Durieux, E. D. H.

    2017-10-01

    The common dentex, Dentex dentex, is an iconic marine coastal fish of the Mediterranean Sea. Despite its economic and ecological importance, data on the population structure of this species are still very limited. The aim of this study was to identify the stock structure of the common dentex at relatively fine spatial scale around Corsica Island, using a combination of markers that have different spatial and temporal scales of integration: microsatellite DNA markers, otolith shape analysis and parasites communities. Microsatellite analysis indicated that there was no significant genetic differentiation in D. dentex between the four sampling sites around Corsica. Otolith shape analysis suggests one potential distinct population unit of D. dentex centered in one site (Cap Corse) varying in their degree of differentiation from those in the other zones. Multivariate analysis on parasite abundance data highlights to a lower extent two sites (Bonifacio and Galeria) with some connectivity between adjacent zones. The combination of these three markers together highlights the resulting three sites while giving complementary insights and an opportunity to compare their utility and potential to understand population interactions. A complex population structure around Corsican coasts is then proposed, providing a new perspective on common dentex fishery stock conservation and management strategies.

  8. Zinc(II) halide complexes with 2-methoxyaniline ligand: Synthesis, characterization, thermal analyses, crystal structure determination and luminescent properties

    Science.gov (United States)

    Amani, Vahid

    2018-03-01

    Three new mononuclear zinc(II) complexes, [Zn(2-MeO-C6H4NH2)2X2] (X is Cl in 1, Br in 2 and I in 3), were prepared from the reactions of ZnX2 with 2-methoxyaniline (2-MeO-C6H4NH2) ligand in methanol. Suitable crystals of these complexes were obtained for X-ray diffraction measurements by slow evaporation of methanol solution at room temperature. The three complexes were thoroughly characterized by thermogravimetric analysis, elemental analysis (CHNO), spectral methods (IR, UV-Vis, 13C{1H}NMR, 1H NMR and luminescence), and single crystal X-ray diffraction. The X-ray structural analysis indicated that in the structures of these complexes, the zinc(II) cation is four-coordinated in a distorted tetrahedral configuration by two N atoms from two 2-methoxyanyline ligands and two halide anions. Also, in these complexes intermolecular interactions, for example Nsbnd H⋯X hydrogen bonds (in 1-3), Csbnd H⋯X hydrogen bonds (in 3), Csbnd H⋯π interactions (in 1 and 2) and π⋯π interactions (in 3), are effective in the stabilization of the crystal structures. In addition, the luminescence spectra of all complexes in methanolic solution show that the intensity of their emission bands is stronger than that for free 2-methoxyaniline ligand.

  9. Synchrotron radiation structure analyses of the light-induced radical pair of a hexaarylbiimidazolyl derivative. Origin of the spin-multiplicity change

    CERN Document Server

    Kawano, M; Matsubara, K; Imabayashi, H; Mitsumi, M; Toriumi, K; Ohashi, Y

    2002-01-01

    In situ synchrotron radiation structure analyses of a light-induced radical pair from o-Cl-HABI were performed by using an X-ray vacuum camera at 23-70K at the BL02B1 station of SPring-8. The combined results of X-ray analysis with theoretical calculation, IR, and UV-vis spectroscopy reveal that a slight conformational change of the radical pair causes the drastic spin-multiplicity change during 2-140K. (author)

  10. Biochemical and Structural Analyses of Two Cryptic Esterases in Bacteroides intestinalis and their Synergistic Activities with Cognate Xylanases.

    Science.gov (United States)

    Wefers, Daniel; Cavalcante, Janaina J V; Schendel, Rachel R; Deveryshetty, Jaigeeth; Wang, Kui; Wawrzak, Zdzislaw; Mackie, Roderick I; Koropatkin, Nicole M; Cann, Isaac

    2017-08-04

    Arabinoxylans are constituents of the human diet. Although not utilizable by the human host, they can be fermented by colonic bacteria. The arabinoxylan backbone is decorated with arabinose side chains that may be substituted with ferulic acid, thus limiting depolymerization to fermentable sugars. We investigated the polypeptides encoded by two genes upregulated during growth of the colonic bacterium Bacteroides intestinalis on wheat arabinoxylan. The recombinant proteins, designated BiFae1A and BiFae1B, were functionally assigned esterase activities. Both enzymes were active on acetylated substrates, although each showed a higher ferulic acid esterase activity on methyl-ferulate. BiFae1A showed a catalytic efficiency of 12mM s -1 on para-nitrophenyl-acetate, and on methyl-ferulate, the value was 27 times higher. BiFae1B showed low catalytic efficiencies for both substrates. Furthermore, the two enzymes released ferulic acid from various structural elements, and NMR spectroscopy indicated complete de-esterification of arabinoxylan oligosaccharides from wheat bran. BiFae1A is a tetramer based on the crystal structure, whereas BiFae1B is a dimer in solution based on size exclusion chromatography. The structure of BiFae1A was solved to 1.98Å resolution, and two tetramers were observed in the asymmetric unit. A flexible loop that may act as a hinge over the active site and likely coordinates critical interactions with the substrate was prominent in BiFae1A. Sequence alignments of the esterase domains in BiFae1B with the feruloyl esterase from Clostridium thermocellum suggest that both domains lack the flexible hinge in BiFae1A, an observation that may partly provide a molecular basis for the differences in activities in the two esterases. Copyright © 2017 Elsevier Ltd. All rights reserved.

  11. Combining Internet monitoring processes, packaging and isotopic analyses to determine the market structure: example of Gamma Butyrolactone.

    Science.gov (United States)

    Pazos, Diego; Giannasi, Pauline; Rossy, Quentin; Esseiva, Pierre

    2013-07-10

    The Internet is becoming more and more popular among drug users. The use of websites and forums to obtain illicit drugs and relevant information about the means of consumption is a growing phenomenon mainly for new synthetic drugs. Gamma Butyrolactone (GBL), a chemical precursor of Gamma Hydroxy Butyric acid (GHB), is used as a "club drug" and also in drug facilitated sexual assaults. Its market takes place mainly on the Internet through online websites but the structure of the market remains unknown. This research aims to combine digital, physical and chemical information to help understand the distribution routes and the structure of the GBL market. Based on an Internet monitoring process, thirty-nine websites selling GBL, mainly in the Netherlands, were detected between January 2010 and December 2011. Seventeen websites were categorized into six groups based on digital traces (e.g. IP addresses and contact information). In parallel, twenty-five bulk GBL specimens were purchased from sixteen websites for packaging comparisons and carbon isotopic measurements. Packaging information showed a high correlation with digital data confirming the links previously established whereas chemical information revealed undetected links and provided complementary information. Indeed, while digital and packaging data give relevant information about the retailers, the supply routes and the distribution close to the consumer, the carbon isotopic data provides upstream information about the production level and in particular the synthesis pathways and the chemical precursors. A three-level structured market has been thereby identified with a production level mainly located in China and in Germany, an online distribution level mainly hosted in the Netherlands and the customers who order on the Internet. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

  12. In silico Analyses of Subtype Specific HIV-1 Tat-TAR RNA Interaction Reveals the Structural Determinants for Viral Activity

    Directory of Open Access Journals (Sweden)

    Larance Ronsard

    2017-08-01

    Full Text Available HIV-1 Tat transactivates viral genes through strong interaction with TAR RNA. The stem-loop bulged region of TAR consisting of three nucleotides at the position 23–25 and the loop region consisting of six nucleotides at the position 30–35 are essential for viral transactivation. The arginine motif of Tat (five arginine residues on subtype TatC is critically important for TAR interaction. Any mutations in this motif could lead to reduce transactivation ability and pathogenesis. Here, we identified structurally important residues (arginine and lysine residues of Tat in this motif could bind to TAR via hydrogen bond interactions which is critical for transactivation. Natural mutant Ser46Phe in the core motif could likely led to conformational change resulting in more hydrogen bond interactions than the wild type Tat making it highly potent transactivator. Importantly, we report the possible probabilities of number of hydrogen bond interactions in the wild type Tat and the mutants with TAR complexes. This study revealed the differential transactivation of subtype B and C Tat could likely be due to the varying number of hydrogen bonds with TAR. Our data support that the N-terminal and the C-terminal domains of Tat is involved in the TAR interactions through hydrogen bonds which is important for transactivation. This study highlights the evolving pattern of structurally important determinants of Tat in the arginine motif for viral transactivation.

  13. Phylogenetic Spread of Sequence Data Affects Fitness of SOD1 Consensus Enzymes: Insights from Sequence Statistics and Structural Analyses.

    Science.gov (United States)

    Goyal, Venuka Durani; Magliery, Thomas J

    2018-02-28

    Non-natural protein sequences with native-like structures and functions can be constructed successfully using consensus design. This design strategy is relatively well understood in repeat proteins with simple binding function, however detailed studies are lacking in globular enzymes. The SOD1 family is a good model for such studies due to the availability of large amount of sequence and structure data motivated by involvement of human SOD1 in the fatal motor neuron disease amyotrophic lateral sclerosis (ALS). We constructed two consensus SOD1 enzymes from multiple sequence alignments from all organisms and eukaryotic organisms. A significant difference in their catalytic activities shows that the phylogenetic spread of the sequences used affects the fitness of the construct obtained. A mutation in an electrostatic loop and overall design incompatibilities between bacterial and eukaryotic sequences were implicated in this disparity. Based on this analysis, a bioinformatics approach was used to classify mutations thought to cause familial ALS providing a unique high level view of the physical basis of disease-causing aggregation of human SOD1. This article is protected by copyright. All rights reserved. © 2018 Wiley Periodicals, Inc.

  14. Structural and biochemical analyses indicate that a bacterial persulfide dioxygenase–rhodanese fusion protein functions in sulfur assimilation

    Energy Technology Data Exchange (ETDEWEB)

    Motl, Nicole; Skiba, Meredith A.; Kabil, Omer; Smith, Janet L.; Banerjee, Ruma

    2017-07-06

    Hydrogen sulfide (H2S) is a signaling molecule that is toxic at elevated concentrations. In eukaryotes, it is cleared via a mitochondrial sulfide oxidation pathway, which comprises sulfide quinone oxidoreductase, persulfide dioxygenase (PDO), rhodanese, and sulfite oxidase and converts H2S to thiosulfate and sulfate. Natural fusions between the non-heme iron containing PDO and rhodanese, a thiol sulfurtransferase, exist in some bacteria. However, little is known about the role of the PDO–rhodanese fusion (PRF) proteins in sulfur metabolism. Herein, we report the kinetic properties and the crystal structure of a PRF from the Gram-negative endophytic bacterium Burkholderia phytofirmans. The crystal structures of wild-type PRF and a sulfurtransferase-inactivated C314S mutant with and without glutathione were determined at 1.8, 2.4, and 2.7 Å resolution, respectively. We found that the two active sites are distant and do not show evidence of direct communication. The B. phytofirmans PRF exhibited robust PDO activity and preferentially catalyzed sulfur transfer in the direction of thiosulfate to sulfite and glutathione persulfide; sulfur transfer in the reverse direction was detectable only under limited turnover conditions. Together with the kinetic data, our bioinformatics analysis reveals that B. phytofirmans PRF is poised to metabolize thiosulfate to sulfite in a sulfur assimilation pathway rather than in sulfide stress response as seen, for example, with the Staphylococcus aureus PRF or sulfide oxidation and disposal as observed with the homologous mammalian proteins.

  15. Biochemical, structural and molecular dynamics analyses of the potential virulence factor RipA from Yersinia pestis.

    Directory of Open Access Journals (Sweden)

    Rodrigo Torres

    Full Text Available Human diseases are attributed in part to the ability of pathogens to evade the eukaryotic immune systems. A subset of these pathogens has developed mechanisms to survive in human macrophages. Yersinia pestis, the causative agent of the bubonic plague, is a predominately extracellular pathogen with the ability to survive and replicate intracellularly. A previous study has shown that a novel rip (required for intracellular proliferation operon (ripA, ripB and ripC is essential for replication and survival of Y. pestis in postactivated macrophages, by playing a role in lowering macrophage-produced nitric oxide (NO levels. A bioinformatics analysis indicates that the rip operon is conserved among a distally related subset of macrophage-residing pathogens, including Burkholderia and Salmonella species, and suggests that this previously uncharacterized pathway is also required for intracellular survival of these pathogens. The focus of this study is ripA, which encodes for a protein highly homologous to 4-hydroxybutyrate-CoA transferase; however, biochemical analysis suggests that RipA functions as a butyryl-CoA transferase. The 1.9 Å X-ray crystal structure reveals that RipA belongs to the class of Family I CoA transferases and exhibits a unique tetrameric state. Molecular dynamics simulations are consistent with RipA tetramer formation and suggest a possible gating mechanism for CoA binding mediated by Val227. Together, our structural characterization and molecular dynamic simulations offer insights into acyl-CoA specificity within the active site binding pocket, and support biochemical results that RipA is a butyryl-CoA transferase. We hypothesize that the end product of the rip operon is butyrate, a known anti-inflammatory, which has been shown to lower NO levels in macrophages. Thus, the results of this molecular study of Y. pestis RipA provide a structural platform for rational inhibitor design, which may lead to a greater understanding of the

  16. Structural and Functional Analyses of the Six1 Transcriptional Complex for Anti-Breast Cancer Drug Design

    Science.gov (United States)

    2011-04-01

    expertise of a cancer/molecular biologist with a structural biologist/ biochemist . Within the proposal, we will identify multiple avenues for targeting the...32129‐34.   Ford HL (1998). Homeobox genes: a link between development, cell  cycle , and cancer? Cell Biol  Int 22: 397‐400.   Ford HL, Kabingu EN...Bump EA, Mutter GL, Pardee AB (1998). Abrogation of the G2 cell  cycle   checkpoint associated with overexpression of HSIX1: a possible mechanism of

  17. Combined genomic and structural analyses of a cultured magnetotactic bacterium reveals its niche adaptation to a dynamic environment

    Directory of Open Access Journals (Sweden)

    Ana Carolina Vieira Araujo

    2016-10-01

    Full Text Available Abstract Background Magnetotactic bacteria (MTB are a unique group of prokaryotes that have a potentially high impact on global geochemical cycling of significant primary elements because of their metabolic plasticity and the ability to biomineralize iron-rich magnetic particles called magnetosomes. Understanding the genetic composition of the few cultivated MTB along with the unique morphological features of this group of bacteria may provide an important framework for discerning their potential biogeochemical roles in natural environments. Results Genomic and ultrastructural analyses were combined to characterize the cultivated magnetotactic coccus Magnetofaba australis strain IT-1. Cells of this species synthesize a single chain of elongated, cuboctahedral magnetite (Fe3O4 magnetosomes that cause them to align along magnetic field lines while they swim being propelled by two bundles of flagella at velocities up to 300 μm s−1. High-speed microscopy imaging showed the cells move in a straight line rather than in the helical trajectory described for other magnetotactic cocci. Specific genes within the genome of Mf. australis strain IT-1 suggest the strain is capable of nitrogen fixation, sulfur reduction and oxidation, synthesis of intracellular polyphosphate granules and transporting iron with low and high affinity. Mf. australis strain IT-1 and Magnetococcus marinus strain MC-1 are closely related phylogenetically although similarity values between their homologous proteins are not very high. Conclusion Mf. australis strain IT-1 inhabits a constantly changing environment and its complete genome sequence reveals a great metabolic plasticity to deal with these changes. Aside from its chemoautotrophic and chemoheterotrophic metabolism, genomic data indicate the cells are capable of nitrogen fixation, possess high and low affinity iron transporters, and might be capable of reducing and oxidizing a number of sulfur compounds. The relatively

  18. The Pectin Methylesterase Gene Complement of Phytophthora sojae: Structural and Functional Analyses, and the Evolutionary Relationships with Its Oomycete Homologs.

    Science.gov (United States)

    Horowitz, Brent B; Ospina-Giraldo, Manuel D

    2015-01-01

    Phytophthora sojae is an oomycete pathogen that causes the disease known as root and stem rot in soybean plants, frequently leading to massive economic damage. Additionally, P. sojae is increasingly being utilized as a model for phytopathogenic oomycete research. Despite the economic and scientific importance of P. sojae, the mechanism by which it penetrates the host roots is not yet fully understood. It has been found that oomycetes are not capable of penetrating the cell wall solely through mechanical force, suggesting that alternative factors facilitate breakdown of the host cell wall. Pectin methylesterases have been suggested to be important for Phytophthora pathogenicity, but no data exist on their role in the P. sojae infection process. We have scanned the newly revised version of the annotated P. sojae genome for the presence of putative pectin methylesterases genes and conducted a sequence analysis of all gene models found. We also searched for potential regulatory motifs in the promoter region of the proposed P. sojae models, and investigated the gene expression levels throughout the early course of infection on soybean plants. We found that P. sojae contains a large repertoire of pectin methylesterase-coding genes and that most of these genes display similar motifs in the promoter region, indicating the possibility of a shared regulatory mechanism. Phylogenetic analyses confirmed the evolutionary relatedness of the pectin methylesterase-coding genes within and across Phytophthora spp. In addition, the gene duplication events that led to the emergence of this gene family appear to have occurred prior to many speciation events in the genus Phytophthora. Our results also indicate that the highest levels of expression occurred in the first 24 hours post inoculation, with expression falling after this time. Our study provides evidence that pectin methylesterases may be important for the early action of the P. sojae infection process.

  19. Analysing urban planning implications from an electric vehicles scenario for urban structure-, transport- and energy-systems

    Energy Technology Data Exchange (ETDEWEB)

    Rid, Wolfgang [Stuttgart Univ. (Germany). Lehrstuhl Stadtplanung und Entwerfen; Fachhochschule Erfurt (Germany). Fachgebiet Stadt- und Regionaloekonomie; Pesch, Franz; Wewer, Max; Sperle, Tilman [Stuttgart Univ. (Germany). Lehrstuhl Stadtplanung und Entwerfen

    2013-06-01

    Depending on scenarios of actual electric vehicles on the road, ''electric mobility'' will heavily affect urban planning and infrastructure. We analyze these effects by developing an ''urban typology for electro-mobility''. By doing so, we seek to demonstrate that both requirements from electric vehicle scenarios (infrastructure, on-site provision of renewable energy etc.) and potential benefits (noise-reduction, NOx-reduction, modal-split etc.) are dependent on the urban context. The typology was developed according to preliminary studies' results recommending to use the GFZ (Gross Floor Area) and residential density to describe different types of urban structure, but additionally makes use of the proportion of public space and number of resident families (per ha net residential area) to extract five different ''urban types for electro-mobility''. Electro-mobility will have a significant climate effect only if 'green' electric power production is able to provide the additional amount of renewable energy needed. On-site power plants must be further developed to reduce externalities from large scale power plants providing C02-free energy (e.g. externalities from offshore wind energy plants). The potential to produce renewable energy from on-site power plants is dependent on the type of the urban context: Advanced ''plus-energy-concepts'' for example, today, are restricted to building scales of low-density residential zones, whereas in inner city zones, buildings have to provide energy for far more people per floorspace or for cooling purposes, as well. On-site renewable energy plants should be placed in urban settings, where they can work most efficiently and where they can be best integrated into the urban context given, hence, electro-mobility needs to be viewed from an urban perspective. Many other projects, so far, have investigated technical solutions to improve

  20. Discovery of potent NEK2 inhibitors as potential anticancer agents using structure-based exploration of NEK2 pharmacophoric space coupled with QSAR analyses.

    Science.gov (United States)

    Khanfar, Mohammad A; Banat, Fahmy; Alabed, Shada; Alqtaishat, Saja

    2017-02-01

    High expression of Nek2 has been detected in several types of cancer and it represents a novel target for human cancer. In the current study, structure-based pharmacophore modeling combined with multiple linear regression (MLR)-based QSAR analyses was applied to disclose the structural requirements for NEK2 inhibition. Generated pharmacophoric models were initially validated with receiver operating characteristic (ROC) curve, and optimum models were subsequently implemented in QSAR modeling with other physiochemical descriptors. QSAR-selected models were implied as 3D search filters to mine the National Cancer Institute (NCI) database for novel NEK2 inhibitors, whereas the associated QSAR model prioritized the bioactivities of captured hits for in vitro evaluation. Experimental validation identified several potent NEK2 inhibitors of novel structural scaffolds. The most potent captured hit exhibited an [Formula: see text] value of 237 nM.

  1. Proteomic and 3D structure analyses highlight the C/D box snoRNP assembly mechanism and its control

    Science.gov (United States)

    Bizarro, Jonathan; Charron, Christophe; Boulon, Séverine; Westman, Belinda; Pradet-Balade, Bérengère; Vandermoere, Franck; Chagot, Marie-Eve; Hallais, Marie; Ahmad, Yasmeen; Leonhardt, Heinrich; Lamond, Angus; Manival, Xavier; Branlant, Christiane; Charpentier, Bruno

    2014-01-01

    In vitro, assembly of box C/D small nucleolar ribonucleoproteins (snoRNPs) involves the sequential recruitment of core proteins to snoRNAs. In vivo, however, assembly factors are required (NUFIP, BCD1, and the HSP90–R2TP complex), and it is unknown whether a similar sequential scheme applies. In this paper, we describe systematic quantitative stable isotope labeling by amino acids in cell culture proteomic experiments and the crystal structure of the core protein Snu13p/15.5K bound to a fragment of the assembly factor Rsa1p/NUFIP. This revealed several unexpected features: (a) the existence of a protein-only pre-snoRNP complex containing five assembly factors and two core proteins, 15.5K and Nop58; (b) the characterization of ZNHIT3, which is present in the protein-only complex but gets released upon binding to C/D snoRNAs; (c) the dynamics of the R2TP complex, which appears to load/unload RuvBL AAA+ adenosine triphosphatase from pre-snoRNPs; and (d) a potential mechanism for preventing premature activation of snoRNP catalytic activity. These data provide a framework for understanding the assembly of box C/D snoRNPs. PMID:25404746

  2. Structural and biochemical analyses of the DEAD-box ATPase Sub2 in association with THO or Yra1

    Energy Technology Data Exchange (ETDEWEB)

    Ren, Yi [Laboratory of Cell Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, United States; Schmiege, Philip [Laboratory of Cell Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, United States; Blobel, Günter [Laboratory of Cell Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, United States

    2017-01-06

    mRNA is cotranscrptionally processed and packaged into messenger ribonucleoprotein particles (mRNPs) in the nucleus. Prior to export through the nuclear pore, mRNPs undergo several obligatory remodeling reactions. In yeast, one of these reactions involves loading of the mRNA-binding protein Yra1 by the DEAD-box ATPase Sub2 as assisted by the hetero-pentameric THO complex. To obtain molecular insights into reaction mechanisms, we determined crystal structures of two relevant complexes: a THO hetero-pentamer bound to Sub2 at 6.0 Å resolution; and Sub2 associated with an ATP analogue, RNA, and a C-terminal fragment of Yra1 (Yra1-C) at 2.6 Å resolution. We found that the 25 nm long THO clamps Sub2 in a half-open configuration; in contrast, when bound to the ATP analogue, RNA and Yra1-C, Sub2 assumes a closed conformation. Both THO and Yra1-C stimulated Sub2’s intrinsic ATPase activity. We propose that THO surveys common landmarks in each nuclear mRNP to localize Sub2 for targeted loading of Yra1.

  3. Structural and biochemical analyses of the DEAD-box ATPase Sub2 in association with THO or Yra1.

    Science.gov (United States)

    Ren, Yi; Schmiege, Philip; Blobel, Günter

    2017-01-06

    mRNA is cotranscrptionally processed and packaged into messenger ribonucleoprotein particles (mRNPs) in the nucleus. Prior to export through the nuclear pore, mRNPs undergo several obligatory remodeling reactions. In yeast, one of these reactions involves loading of the mRNA-binding protein Yra1 by the DEAD-box ATPase Sub2 as assisted by the hetero-pentameric THO complex. To obtain molecular insights into reaction mechanisms, we determined crystal structures of two relevant complexes: a THO hetero-pentamer bound to Sub2 at 6.0 Å resolution; and Sub2 associated with an ATP analogue, RNA, and a C-terminal fragment of Yra1 (Yra1-C) at 2.6 Å resolution. We found that the 25 nm long THO clamps Sub2 in a half-open configuration; in contrast, when bound to the ATP analogue, RNA and Yra1-C, Sub2 assumes a closed conformation. Both THO and Yra1-C stimulated Sub2's intrinsic ATPase activity. We propose that THO surveys common landmarks in each nuclear mRNP to localize Sub2 for targeted loading of Yra1.

  4. Histochemical analyses of anti-microbial substances in canine perianal skin with special reference to glandular structures.

    Science.gov (United States)

    Nara, T; Yasui, T; Fujimori, O; Meyer, W; Tsukise, A

    2013-04-01

    Circumanal glands are prominent features of the canine perianal skin, which are often located near to the sebaceous glands and apocrine glands. As the functional relevance of circumanal glands is yet unknown, we studied the localisation of sialic acids and anti-microbial substances (lysozyme, immunoglobulin A, lactoferrin, β-defensin) in these glandular structures by lectin histochemistry and immunohistochemistry. The glands exhibited a number of sialic acids that were linked to α2-6Gal/GalNAc and α2-3Galβ1-4GlcNAc. Additionally, lysozyme, lactoferrin and β-defensin could be demonstrated in the three types of skin glands, whereas IgA was only detectable in the apocrine glands. The results of the study suggest the specific significance of the circumanal glands. Independent of a certain endocrine role, their products may mainly function as protective agents to preserve the integrity of the anal region, considering that sialic acids and anti-microbial substances are important in defence mechanisms. © 2012 Blackwell Verlag GmbH.

  5. Impact of forest harvesting on trophic structure of eastern Canadian Boreal Shield lakes: insights from stable isotope analyses.

    Directory of Open Access Journals (Sweden)

    Patricia Glaz

    Full Text Available Perturbations on ecosystems can have profound immediate effects and can, accordingly, greatly alter the natural community. Land-use such as forestry activities in the Canadian Boreal region have increased in the last decades, raising concerns about their potential impact on aquatic ecosystems. The objective of this study was to evaluate the impact of forest harvesting on trophic structure in eastern Canadian Boreal Shield lakes. We measured carbon and nitrogen stable isotopes values for aquatic primary producers, terrestrial detritus, benthic macroinvertebrates, zooplankton and brook trout (Salvelinus fontinalis over a three-year period in eight eastern Boreal Shield lakes. Four lakes were studied before, one and two years after forest harvesting (perturbed lakes and compared with four undisturbed reference lakes (unperturbed lakes sampled at the same time. Stable isotope mixing models showed leaf-litter to be the main food source for benthic primary consumers in both perturbed and unperturbed lakes, suggesting no logging impact on allochthonous subsidies to the littoral food web. Brook trout derived their food mainly from benthic predatory macroinvertebrates in unperturbed lakes. However, in perturbed lakes one year after harvesting, zooplankton appeared to be the main contributor to brook trout diet. This change in brook trout diet was mitigated two years after harvesting. Size-related diet shift were also observed for brook trout, indicating a diet shift related to size. Our study suggests that carbon from terrestrial habitat may be a significant contribution to the food web of oligotrophic Canadian Boreal Shield lakes. Forest harvesting did not have an impact on the diet of benthic primary consumers. On the other hand, brook trout diet composition was affected by logging with greater zooplankton contribution in perturbed lakes, possibly induced by darker-colored environment in these lakes one year after logging.

  6. Impact of forest harvesting on trophic structure of eastern Canadian Boreal Shield lakes: insights from stable isotope analyses.

    Science.gov (United States)

    Glaz, Patricia; Sirois, Pascal; Archambault, Philippe; Nozais, Christian

    2014-01-01

    Perturbations on ecosystems can have profound immediate effects and can, accordingly, greatly alter the natural community. Land-use such as forestry activities in the Canadian Boreal region have increased in the last decades, raising concerns about their potential impact on aquatic ecosystems. The objective of this study was to evaluate the impact of forest harvesting on trophic structure in eastern Canadian Boreal Shield lakes. We measured carbon and nitrogen stable isotopes values for aquatic primary producers, terrestrial detritus, benthic macroinvertebrates, zooplankton and brook trout (Salvelinus fontinalis) over a three-year period in eight eastern Boreal Shield lakes. Four lakes were studied before, one and two years after forest harvesting (perturbed lakes) and compared with four undisturbed reference lakes (unperturbed lakes) sampled at the same time. Stable isotope mixing models showed leaf-litter to be the main food source for benthic primary consumers in both perturbed and unperturbed lakes, suggesting no logging impact on allochthonous subsidies to the littoral food web. Brook trout derived their food mainly from benthic predatory macroinvertebrates in unperturbed lakes. However, in perturbed lakes one year after harvesting, zooplankton appeared to be the main contributor to brook trout diet. This change in brook trout diet was mitigated two years after harvesting. Size-related diet shift were also observed for brook trout, indicating a diet shift related to size. Our study suggests that carbon from terrestrial habitat may be a significant contribution to the food web of oligotrophic Canadian Boreal Shield lakes. Forest harvesting did not have an impact on the diet of benthic primary consumers. On the other hand, brook trout diet composition was affected by logging with greater zooplankton contribution in perturbed lakes, possibly induced by darker-colored environment in these lakes one year after logging.

  7. Wolfram syndrome: structural and functional analyses of mutant and wild-type wolframin, the WFS1 gene product.

    Science.gov (United States)

    Hofmann, Sabine; Philbrook, Christine; Gerbitz, Klaus-Dieter; Bauer, Matthias F

    2003-08-15

    Mutations of the WFS1 gene are responsible for Wolfram syndrome, a rare, recessive disorder characterized by early-onset, non-autoimmune diabetes mellitus, optic atrophy and further neurological and endocrinological abnormalities. The WFS1 gene encodes wolframin, a putative multispanning membrane glycoprotein of the endoplasmic reticulum. The function of wolframin is completely unknown. In order to characterize wolframin, we have generated polyclonal antibodies against both hydrophilic termini of the protein. Wolframin was found to be ubiquitously expressed with highest levels in brain, pancreas, heart and insulinoma beta-cell lines. Analysis of the structural features provides experimental evidence that wolframin contains nine transmembrane segments and is embedded in the membrane in an N(cyt)/C(lum) topology. Wolframin assembles into higher molecular weight complexes of approximately 400 kDa in the membrane. Pulse-chase experiments demonstrate that during maturation wolframin is N-glycosylated but lacks proteolytical processing. Moreover, N-glycosylation appears to be essential for the biogenesis and stability of wolframin. Here we investigate, for the first time, the molecular mechanisms that cause loss-of-function of wolframin in affected individuals. In patients harboring nonsense mutations complete absence of the mutated wolframin is caused by instability and rapid decay of WFS1 nonsense transcripts. In a patient carrying a compound heterozygous missense mutation, R629W, we found markedly reduced steady-state levels of wolframin. Pulse-chase experiments of mutant wolframin expressed in COS-7 cells indicated that the R629W mutation leads to instability and strongly reduced half-life of wolframin. Thus, the Wolfram syndrome in patients investigated here is caused by reduced protein dosage rather than dysfunction of the mutant wolframin.

  8. Structural Changes of Desertified and Managed Shrubland Landscapes in Response to Drought: Spectral, Spatial and Temporal Analyses

    Directory of Open Access Journals (Sweden)

    Tarin Paz-Kagan

    2014-08-01

    Full Text Available Drought events cause changes in ecosystem function and structure by reducing the shrub abundance and expanding the biological soil crusts (biocrusts. This change increases the leakage of nutrient resources and water into the river streams in semi-arid areas. A common management solution for decreasing this loss of resources is to create a runoff-harvesting system (RHS. The objective of the current research is to apply geo-information techniques, including remote sensing and geographic information systems (GIS, on the watershed scale, to monitor and analyze the spatial and temporal changes in response to drought of two source-sink systems, the natural shrubland and the human-made RHSs in the semi-arid area of the northern Negev Desert, Israel. This was done by evaluating the changes in soil, vegetation and landscape cover. The spatial changes were evaluated by three spectral indices: Normalized Difference Vegetation Index (NDVI, Crust Index (CI and landscape classification change between 2003 and 2010. In addition, we examined the effects of environmental factors on NDVI, CI and their clustering after successive drought years. The results show that vegetation cover indicates a negative ∆NDVI change due to a reduction in the abundance of woody vegetation. On the other hand, the soil cover change data indicate a positive ∆CI change due to the expansion of the biocrusts. These two trends are evidence for degradation processes in terms of resource conservation and bio-production. A considerable part of the changed area (39% represents transitions between redistribution processes of resources, such as water, sediments, nutrients and seeds, on the watershed scale. In the pre-drought period, resource redistribution mainly occurred on the slope scale, while in the post-drought period, resource redistribution occurred on the whole watershed scale. However, the RHS management is effective in reducing leakage, since these systems are located on the

  9. 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

  10. Analyses of magnetic structures and nuclear-density distribution by the structure-refinement and three-dimensional visualization systems RIETAN-FP-VENUS

    International Nuclear Information System (INIS)

    Izumi, Fujio; Momma, Koichi

    2010-01-01

    We have been developing a multi-purpose pattern-fitting system RIETAN-FP and a three-dimensional visualization system VENUS, which have been extensively used for structure refinements of various metal and inorganic materials from neutron powder diffraction data. At first, their outlines and the history of their developments are shortly looked back. The second part describes procedures for analyzing collinear magnetic structures with the combination of VESTA in the VENUS system and RIETAN-FP by taking BiCoO 3 for instance. Finally, a new C++ program, Dysnomia, for the maximum entropy method is introduced with emphasis on its new features. Dysnomia excels its predecessor, PRIMA, in computation speed, memory efficiency, scalability, and reliability. In particular, addition of a normal-distribution constraint is effective in obtaining nuclear-density distribution that is physically and chemically reasonable. (author)

  11. Rationale for the closure of the soil density unreviewed safety question and recommended structural analyses improvements for the Tank Waste Remidiation System underground storage facilities

    International Nuclear Information System (INIS)

    Morris, K.H.

    1998-01-01

    The purpose of this report is twofold. First, this report documents the technical evaluation supporting the Project Hanford Management Contract (PHMC) contractor recommendation to close the Unreviewed Safety Question (USQ) as originally evaluated in TF-94-0260, Soil Compaction Test Data Indicates Soil Density in Excess of Density Used in Tank Qualification Analysis for AP Tank Farm. Second, this report describes the status of existing structural analyses for the Tank Waste Remediation System (TWRS) waste storage structures and outlines the associated technical upgrades being considered by the contractor. This second feature of the report serves to communicate the distinction between the soil density issue which is the topic of the open USQ and other technical issues which are important to the contractor from a programmatic standpoint. Contractor actions to address the latter technical issues would support improvements in day-to-day operations (e.g., provide possible relaxations in soil load restrictions) but are not necessary to close the soil density USQ. Section 2.0 of this report documents the rationale for the PHMC contractor recommendation to the Department of Energy (DOE) to close the soil density USQ. Section 3.0 documents the recommended structural analyses improvements for the double-shell tanks (DSTs) which are the structures associated with the soil density USQ. Sections 4.0 and 5.0 provide, for completeness, the same information for single-shell tanks (SSTs), double-contained receiver tanks (DCRTs), catch tanks and inactive miscellaneous underground storage tanks (IMUSTs). Section 6.0 provides the conclusions of this report

  12. High resolution crustal structure for the region between the Chilenia and Cuyania terrane above the Pampean flat slab of Argentina from local receiver function and petrological analyses

    Science.gov (United States)

    Ammirati, J. B.; Alvarado, P. M.; Pérez, S. B.; Beck, S. L.; Porter, R. C.; Zandt, G.

    2015-12-01

    Jean-Baptiste Ammirati 1,Sofía Perez 1, Patricia Alvarado 1, Susan L. Beck 2, Ryan Porter 3 and George Zandt 2(1) CIGEOBIO-CONICET, Universidad Nacional de San Juan, Argentina (2) The University of Arizona, USA (3) Northern Arizona University, USA At ~31ºS, The subduction of the Nazca plate under the South American plate presents along-strike variations of its dip angle referred to the Chilean-Pampean flat slab. Geological observations suggest that the regional crustal structure is inherited from the accretion of different terranes at Ordovician times and later reactivated during Andean compression since Miocene. Geophysical observations confirmed that the structure is extending in depth with décollement levels that accommodate crustal shortening in the region. In order to get a better insight on the shallow tectonics we computed high frequency local receiver functions from slab seismicity (~100 km depth). Local earthquakes present a higher frequency content that permits a better vertical resolution. Using a common conversion point (CCP) stacking method we obtained cross sections showing high-resolution crustal structure in the western part of the Pampean flat slab region, at the transition between the Precordillera and the Frontal Cordillera. Our results show a well-defined structure and their lateral extent for both units down to 80 km depth. In good agreement with previous studies, our higher resolution images better identify very shallow discontinuities putting more constraints on the relationships with the regional structural geology. Recent petrological analyses combined with RF high-resolution structure also allow us to better understand the regional crustal composition. Interestingly, we are able to observe a shifting structure beneath the Uspallata-Calingasta Valley, highlighting the differences in terms of crustal structure between the Precordillera and the Frontal Cordillera. Previously determined focal mechanisms in the region match well this

  13. Determining the Architecture of a Protein-DNA Complex by Combining FeBABE Cleavage Analyses, 3-D Printed Structures, and the ICM Molsoft Program.

    Science.gov (United States)

    James, Tamara; Hsieh, Meng-Lun; Knipling, Leslie; Hinton, Deborah

    2015-01-01

    Determining the structure of a protein-DNA complex can be difficult, particularly if the protein does not bind tightly to the DNA, if there are no homologous proteins from which the DNA binding can be inferred, and/or if only portions of the protein can be crystallized. If the protein comprises just a part of a large multi-subunit complex, other complications can arise such as the complex being too large for NMR studies, or it is not possible to obtain the amounts of protein and nucleic acids needed for crystallographic analyses. Here, we describe a technique we used to map the position of an activator protein relative to the DNA within a large transcription complex. We determined the position of the activator on the DNA from data generated using activator proteins that had been conjugated at specific residues with the chemical cleaving reagent, iron bromoacetamidobenzyl-EDTA (FeBABE). These analyses were combined with 3-D models of the available structures of portions of the activator protein and B-form DNA to obtain a 3-D picture of the protein relative to the DNA. Finally, the Molsoft program was used to refine the position, revealing the architecture of the protein-DNA within the transcription complex.

  14. Sequence, secondary structure, and phylogenetic analyses of the ribosomal internal transcribed spacer 2 (ITS2) in members of the North American Signifera Group of Orthopodomyia (Diptera: Culicidae).

    Science.gov (United States)

    Byrd, Brian D; Harrison, Bruce A; Zavortink, Thomas J; Wesson, Dawn M

    2012-11-01

    Mosquitoes of the genus Orthopodomyia (Diptera: Culicidae) are little known and of uncertain epidemiological importance. In the United States, there are three Orthopodomyia species (i.e., Or. signifera (Coquillett), Or. alba Baker, and Or. kummi Edwards); they are all members of the Signifera Group based on the current morphological taxonomy. In the course of identifying recently collected specimens, a problem was found with the current key morphological characters for separating the fourth instar larvae of Or. signifera and Or. kummi. Internal transcribed spacer two sequences of the rDNA were obtained to resolve the identities. The Orthopodomyia internal transcribed spacer two ranged in size from 193 (Or. kummi) to 244 bp (Or. signifera) (mean = 218 bp) and were slightly Adenine/Thymine enriched (44.7% Guanine/Cytosine on average). Putative secondary structures reveal structural homologies (four domains) consistent between species that also feature conserved sequences specific to mosquitoes (e.g., a conserved motif on the 3' aspect of the longest helix: GARTACATCC). Sequence analyses suggest that in certain areas of southwestern North America, hybridization may occur between Or. kummi and Or. signifera. Furthermore, our analyses confirm that Or. californica (a junior synonym of Or. signifera) is indeed Or. signifera. To our knowledge, this is the first sequence-based phylogenetic and molecular analysis of the Orthopodomyia.

  15. Multigene-based analyses of the phylogenetic evolution of oligotrich ciliates, with consideration of the internal transcribed spacer 2 secondary structure of three systematically ambiguous genera.

    Science.gov (United States)

    Li, Jiamei; Liu, Weiwei; Gao, Shan; Warren, Alan; Song, Weibo

    2013-03-01

    Oligotrichs are ciliates of great abundance, but their molecular systematics are rarely studied. In this study, nine species representing three genera (Strombidium, Novistrombidium, and Omegastrombidium) of marine oligotrich ciliates were collected from coastal waters of China. The small subunit (SSU) rRNA gene of two species and the internal transcribed spacers and 5.8S region (ITS1-5.8S-ITS2) for all nine species were sequenced for the first time. Phylogenetic trees using both the SSU rRNA gene and ITS1-5.8S-ITS2 region sequences were generated. In addition, the secondary structures of ITS2 RNA transcripts of 11 taxa representing four genera (Novistrombidium, Strombidium, Omegastrombidium, and Laboea) were investigated. The phylogenetic analyses show that (i) the family Strombidiidae is polyphyletic, (ii) the genus Novistrombidium is probably paraphyletic, containing at least two subclades, which is consistent with recent cladistic analyses based on morphological data, and (iii) the tail-less genus Laboea is separate from other genera of Strombidiidae, clustering instead with the tontoniids. Comparisons of the secondary structure of ITS2 regions also show that Laboea is clearly different from other strombidiids. These findings cast doubt on the monophyly of the family Strombidiidae.

  16. Chemical Characterization and Determination of the Anti-Oxidant Capacity of Two Brown Algae with Respect to Sampling Season and Morphological Structures Using Infrared Spectroscopy and Multivariate Analyses.

    Science.gov (United States)

    Beratto, Angelo; Agurto, Cristian; Freer, Juanita; Peña-Farfal, Carlos; Troncoso, Nicolás; Agurto, Andrés; Castillo, Rosario Del P

    2017-10-01

    Brown algae biomass has been shown to be a highly important industrial source for the production of alginates and different nutraceutical products. The characterization of this biomass is necessary in order to allocate its use to specific applications according to the chemical and biological characteristics of this highly variable resource. The methods commonly used for algae characterization require a long time for the analysis and rigorous pretreatments of samples. In this work, nondestructive and fast analyses of different morphological structures from Lessonia spicata and Macrocystis pyrifera, which were collected during different seasons, were performed using Fourier transform infrared (FT-IR) techniques in combination with chemometric methods. Mid-infrared (IR) and near-infrared (NIR) spectral ranges were tested to evaluate the spectral differences between the species, seasons, and morphological structures of algae using a principal component analysis (PCA). Quantitative analyses of the polyphenol and alginate contents and the anti-oxidant capacity of the samples were performed using partial least squares (PLS) with both spectral ranges in order to build a predictive model for the rapid quantification of these parameters with industrial purposes. The PCA mainly showed differences in the samples based on seasonal sampling, where changes were observed in the bands corresponding to polysaccharides, proteins, and lipids. The obtained PLS models had high correlation coefficients (r) for the polyphenol content and anti-oxidant capacity (r > 0.9) and lower values for the alginate determination (0.7 algae biomass, in which high variability in the samples was incorporated for the qualitative and quantitative analyses, and have the potential to be used on an industrial scale.

  17. Accounting for age Structure in Ponderosa Pine Ecosystem Analyses: Integrating Management, Disturbance Histories and Observations with the BIOME-BGC Model

    Science.gov (United States)

    Hibbard, K. A.; Law, B.; Thornton, P.

    2003-12-01

    Disturbance and management regimes in forested ecosystems have been recently highlighted as important factors contributing to quantification of carbon stocks and fluxes. Disturbance events, such as stand-replacing fires and current management regimes that emphasize understory and tree thinning are primary suspects influencing ecosystem processes, including net ecosystem productivity (NEP) in forests of the Pacific Northwest. Several recent analyses have compared simulated to measured component stocks and fluxes of carbon in Ponderosa Pine (Pinus ponderosa var. Laws) at 12 sites ranging from 9 to 300 years in central Oregon (Law et al. 2001, Law et al. 2003) using the BIOME-BGC model. Major emphases on ecosystem model developments include improving allocation logic, integrating ecosystem processes with disturbance such as fire and including nitrogen in biogeochemical cycling. In Law et al. (2001, 2003), field observations prompted BIOME-BGC improvements including dynamic allocation of carbon to fine root mass through the life of a stand. A sequence of simulations was also designed to represent both management and disturbance histories for each site, however, current age structure of each sites wasn't addressed. Age structure, or cohort management has largely been ignored by ecosystem models, however, some studies have sought to incorporate stand age with disturbance and management (e.g. Hibbard et al. 2003). In this analyses, we regressed tree ages against height (R2 = 0.67) to develop a proportional distribution of age structure for each site. To preserve the integrity of the comparison between Law et al. (2003) and this study, we maintained the same timing of harvest, however, based on the distribution of age structures, we manipulated the amount of removal. Harvest by Law et al. (2003) was set at stand-replacement (99%) levels to simulate clear-cutting and reflecting the average top 10% of the age in each plot. For the young sites, we set removal at 73%, 51% and

  18. Systematic approaches for targeting an atom-probe tomography sample fabricated in a thin TEM specimen: Correlative structural, chemical and 3-D reconstruction analyses.

    Science.gov (United States)

    Baik, Sung-Il; Isheim, Dieter; Seidman, David N

    2018-01-01

    Atom-probe tomography (APT) is a unique analysis tool that enables true three-dimensional (3-D) analyses with sub-nano scale spatial resolution. Recent implementations of the local-electrode atom-probe (LEAP) tomograph with ultraviolet laser pulsing have significantly expanded the research applications of APT. The small field-of-view of a needle-shaped specimen with a less than 100 nm diam. is, however, a major limitation for analyzing materials. The systematic approaches for site-specific targeting of an APT nanotip in a transmission electron microscope (TEM) of a thin sample are introduced to solve the geometrical limitations of a sharpened APT nanotip. In addition to "coupling APT to TEM", the technique presented here allows for targeting the preparation of an APT tip based on TEM observation of a much larger area than what is captured in the APT tip. The correlative methods have synergies for not only high-resolution structural analyses but also for obtaining chemical information. Chemical analyses in a TEM, both energy-dispersive X-ray spectroscopy (EDS) and electron energy-loss spectroscopy (EELS), are performed and compared with the APT chemical analyses of a carbide phase (M 7 C 3 ) precipitate at a grain boundary in a Ni-based alloy. Additionally, a TEM image of a sharpened APT nanotip is utilized for calculation of the detection area ratio of an APT nanotip by comparison with a TEM image for precise tomographic reconstructions. A grain-boundary/carbide precipitate triple junction is used to attain precise positioning of an APT nanotip in an analyzed TEM specimen. Copyright © 2017 Elsevier B.V. All rights reserved.

  19. What is the Relationship Between “Personality” and “Social” Psychologies? Network, Community, and Whole Text Analyses of The Structure of Contemporary Scholarship

    Directory of Open Access Journals (Sweden)

    Kevin Lanning

    2017-03-01

    Full Text Available The structure of social/personality psychology, including the relationship between the areas of “social” and “personality,” is empirically examined in a series of network, community, and text analyses. In a study of keywords, both attitudes and social cognition and group processes appear as communities; the role of personality is more diffuse. In a larger analysis of citations in the four primary journals in the combined social/personality area, personality appears as a large community which surrounds a well-defined core (the Five-Factor Model but which lies on the periphery of social/personality psychology. Interpersonal relations and attachment are central in social/personality, and appear largely distinct from the study of groups. Attitudes and social cognition are broadly studied, but, in contrast with personality and interpersonal relations, are not structured around a simple core. These methods and results collectively inform the relationship between personality and social psychologies and provide an early step towards an empirical understanding of the structure of the discipline.

  20. Spatial genetic analyses reveal cryptic population structure and migration patterns in a continuously harvested grey wolf (Canis lupus population in north-eastern Europe.

    Directory of Open Access Journals (Sweden)

    Maris Hindrikson

    Full Text Available Spatial genetics is a relatively new field in wildlife and conservation biology that is becoming an essential tool for unravelling the complexities of animal population processes, and for designing effective strategies for conservation and management. Conceptual and methodological developments in this field are therefore critical. Here we present two novel methodological approaches that further the analytical possibilities of STRUCTURE and DResD. Using these approaches we analyse structure and migrations in a grey wolf (Canislupus population in north-eastern Europe. We genotyped 16 microsatellite loci in 166 individuals sampled from the wolf population in Estonia and Latvia that has been under strong and continuous hunting pressure for decades. Our analysis demonstrated that this relatively small wolf population is represented by four genetic groups. We also used a novel methodological approach that uses linear interpolation to statistically test the spatial separation of genetic groups. The new method, which is capable of using program STRUCTURE output, can be applied widely in population genetics to reveal both core areas and areas of low significance for genetic groups. We also used a recently developed spatially explicit individual-based method DResD, and applied it for the first time to microsatellite data, revealing a migration corridor and barriers, and several contact zones.

  1. Vascugraft polyurethane arterial prosthesis as femoro-popliteal and femoro-peroneal bypasses in humans: pathological, structural and chemical analyses of four excised grafts.

    Science.gov (United States)

    Zhang, Z; Marois, Y; Guidoin, R G; Bull, P; Marois, M; How, T; Laroche, G; King, M W

    1997-01-01

    Following positive results obtained in in vitro studies and in vivo implantations in animals, a clinical trial using the Vascugraft polyurethane arterial prosthesis as a below-knee substitute was undertaken in 15 patients. Eight grafts became occluded during the first year, and segments from four of them were explanted and made available for pathological, structural and chemical investigations. The implantation periods ranged from 21 to 358 days. Failures were associated with kinking (one case), possible anastomotic mismatch between the graft and the artery (one case), and poor run-off (two cases). No organized collagenous internal encapsulation was noted; however, endothelial-like cells were observed at the anastomotic site of one graft. No significant structural degradation of the prostheses was observed in those grafts implanted for 21, 38 and 46 days. Some deteriorations in the fibrous structure were observed on the external surface of the prosthesis implanted for 358 days. High-resolution carbon C1s analysis by ESCA demonstrated a 60 to 80% decrease in carbonate content on the surface of all explanted prostheses. Chemical analyses of each polyurethane graft by IR, SEC and DSC revealed no significant chemical changes. The clinical performance of the Vascugraft prosthesis for below-knee implantation proved to be no more impressive than that of expanded polytetrafluorethylene, the currently accepted reference. The decision by B. Braun Melsungen AG to end this program is therefore to be regarded as highly professional.

  2. Iran, the bomb and the pursuit of security. Structured conflict analyses; Iran, die Bombe und das Streben nach Sicherheit. Strukturierte Konfliktanalysen

    Energy Technology Data Exchange (ETDEWEB)

    Bock, Andreas M. [Akkon-Hochschule fuer Humanwissenschaften, Berlin (Germany); Henneberg, Ingo (ed.) [Freiburg Univ. (Germany). Professur fuer Governance in Mehrebenensystemen

    2014-07-01

    This volume introduces readers to the structured conflict analysis as a tool of social science research and uses this instrument exemplarily to analyze systematically and on a broad basis the various conflicts that are associated with Iran both domestically and in foreign policy - beyond popular stereotypes such as the ''bomb''. The 13 contributions draw a complex picture of the conflicts with and in Iran and reflect the various aspects of these conflicts from different perspectives and at a high methodological and theoretical level. The nuclear program is examined, inter alia through the eyes of four major theories of International Relations. In addition, the analyses are concerned with the regional security dimension, the relationship USA-Iran, the role of national preferences, and the effect of national processes to the Iranian foreign policy.

  3. Matrix metalloproteinase-10/TIMP-2 structure and analyses define conserved core interactions and diverse exosite interactions in MMP/TIMP complexes.

    Directory of Open Access Journals (Sweden)

    Jyotica Batra

    Full Text Available Matrix metalloproteinases (MMPs play central roles in vertebrate tissue development, remodeling, and repair. The endogenous tissue inhibitors of metalloproteinases (TIMPs regulate proteolytic activity by binding tightly to the MMP active site. While each of the four TIMPs can inhibit most MMPs, binding data reveal tremendous heterogeneity in affinities of different TIMP/MMP pairs, and the structural features that differentiate stronger from weaker complexes are poorly understood. Here we report the crystal structure of the comparatively weakly bound human MMP-10/TIMP-2 complex at 2.1 Å resolution. Comparison with previously reported structures of MMP-3/TIMP-1, MT1-MMP/TIMP-2, MMP-13/TIMP-2, and MMP-10/TIMP-1 complexes offers insights into the structural basis of binding selectivity. Our analyses identify a group of highly conserved contacts at the heart of MMP/TIMP complexes that define the conserved mechanism of inhibition, as well as a second category of diverse adventitious contacts at the periphery of the interfaces. The AB loop of the TIMP N-terminal domain and the contact loops of the TIMP C-terminal domain form highly variable peripheral contacts that can be considered as separate exosite interactions. In some complexes these exosite contacts are extensive, while in other complexes the AB loop or C-terminal domain contacts are greatly reduced and appear to contribute little to complex stability. Our data suggest that exosite interactions can enhance MMP/TIMP binding, although in the relatively weakly bound MMP-10/TIMP-2 complex they are not well optimized to do so. Formation of highly variable exosite interactions may provide a general mechanism by which TIMPs are fine-tuned for distinct regulatory roles in biology.

  4. Matrix metalloproteinase-10/TIMP-2 structure and analyses define conserved core interactions and diverse exosite interactions in MMP/TIMP complexes.

    Science.gov (United States)

    Batra, Jyotica; Soares, Alexei S; Mehner, Christine; Radisky, Evette S

    2013-01-01

    Matrix metalloproteinases (MMPs) play central roles in vertebrate tissue development, remodeling, and repair. The endogenous tissue inhibitors of metalloproteinases (TIMPs) regulate proteolytic activity by binding tightly to the MMP active site. While each of the four TIMPs can inhibit most MMPs, binding data reveal tremendous heterogeneity in affinities of different TIMP/MMP pairs, and the structural features that differentiate stronger from weaker complexes are poorly understood. Here we report the crystal structure of the comparatively weakly bound human MMP-10/TIMP-2 complex at 2.1 Å resolution. Comparison with previously reported structures of MMP-3/TIMP-1, MT1-MMP/TIMP-2, MMP-13/TIMP-2, and MMP-10/TIMP-1 complexes offers insights into the structural basis of binding selectivity. Our analyses identify a group of highly conserved contacts at the heart of MMP/TIMP complexes that define the conserved mechanism of inhibition, as well as a second category of diverse adventitious contacts at the periphery of the interfaces. The AB loop of the TIMP N-terminal domain and the contact loops of the TIMP C-terminal domain form highly variable peripheral contacts that can be considered as separate exosite interactions. In some complexes these exosite contacts are extensive, while in other complexes the AB loop or C-terminal domain contacts are greatly reduced and appear to contribute little to complex stability. Our data suggest that exosite interactions can enhance MMP/TIMP binding, although in the relatively weakly bound MMP-10/TIMP-2 complex they are not well optimized to do so. Formation of highly variable exosite interactions may provide a general mechanism by which TIMPs are fine-tuned for distinct regulatory roles in biology.

  5. Controlled cobalt doping in the spinel structure of magnetosome magnetite: new evidences from element- and site-specific X-ray magnetic circular dichroism analyses.

    Science.gov (United States)

    Li, Jinhua; Menguy, Nicolas; Arrio, Marie-Anne; Sainctavit, Philippe; Juhin, Amélie; Wang, Yinzhao; Chen, Haitao; Bunau, Oana; Otero, Edwige; Ohresser, Philippe; Pan, Yongxin

    2016-08-01

    The biomineralization of magnetite nanocrystals (called magnetosomes) by magnetotactic bacteria (MTB) has attracted intense interest in biology, geology and materials science due to the precise morphology of the particles, the chain-like assembly and their unique magnetic properties. Great efforts have been recently made in producing transition metal-doped magnetosomes with modified magnetic properties for a range of applications. Despite some successful outcomes, the coordination chemistry and magnetism of such metal-doped magnetosomes still remain largely unknown. Here, we present new evidences from X-ray magnetic circular dichroism (XMCD) for element- and site-specific magnetic analyses that cobalt is incorporated in the spinel structure of the magnetosomes within Magnetospirillum magneticum AMB-1 through the replacement of Fe(2+) ions by Co(2+) ions in octahedral (Oh) sites of magnetite. Both XMCD at Fe and Co L2,3 edges, and energy-dispersive X-ray spectroscopy on transmission electron microscopy analyses reveal a heterogeneous distribution of cobalt occurring either in different particles or inside individual particles. Compared with non-doped one, cobalt-doped magnetosome sample has lower Verwey transition temperature and larger magnetic coercivity, related to the amount of doped cobalt. This study also demonstrates that the addition of trace cobalt in the growth medium can significantly improve both the cell growth and the magnetosome formation within M. magneticum AMB-1. Together with the cobalt occupancy within the spinel structure of magnetosomes, this study indicates that MTB may provide a promising biomimetic system for producing chains of metal-doped single-domain magnetite with an appropriate tuning of the magnetic properties for technological and biomedical applications. © 2016 The Author(s).

  6. Detecting molecular features of spectra mainly associated with structural and non-structural carbohydrates in co-products from bioEthanol production using DRIFT with uni- and multivariate molecular spectral analyses.

    Science.gov (United States)

    Yu, Peiqiang; Damiran, Daalkhaijav; Azarfar, Arash; Niu, Zhiyuan

    2011-01-01

    The objective of this study was to use DRIFT spectroscopy with uni- and multivariate molecular spectral analyses as a novel approach to detect molecular features of spectra mainly associated with carbohydrate in the co-products (wheat DDGS, corn DDGS, blend DDGS) from bioethanol processing in comparison with original feedstock (wheat (Triticum), corn (Zea mays)). The carbohydrates related molecular spectral bands included: A_Cell (structural carbohydrates, peaks area region and baseline: ca. 1485-1188 cm(-1)), A_1240 (structural carbohydrates, peak area centered at ca. 1240 cm(-1) with region and baseline: ca. 1292-1198 cm(-1)), A_CHO (total carbohydrates, peaks region and baseline: ca. 1187-950 cm(-1)), A_928 (non-structural carbohydrates, peak area centered at ca. 928 cm(-1) with region and baseline: ca. 952-910 cm(-1)), A_860 (non-structural carbohydrates, peak area centered at ca. 860 cm(-1) with region and baseline: ca. 880-827 cm(-1)), H_1415 (structural carbohydrate, peak height centered at ca. 1415 cm(-1) with baseline: ca. 1485-1188 cm(-1)), H_1370 (structural carbohydrate, peak height at ca. 1370 cm(-1) with a baseline: ca. 1485-1188 cm(-1)). The study shows that the grains had lower spectral intensity (KM Unit) of the cellulosic compounds of A_1240 (8.5 vs. 36.6, P bioethanol processing. There were no differences (P > 0.05) in the peak area intensities of A_Cell (structural CHO) at 1292-1198 cm(-1) and A_CHO (total CHO) at 1187-950 cm(-1) with average molecular infrared intensity KM unit of 226.8 and 508.1, respectively. There were no differences (P > 0.05) in the peak height intensities of H_1415 and H_1370 (structural CHOs) with average intensities 1.35 and 1.15, respectively. The multivariate molecular spectral analyses were able to discriminate and classify between the corn and corn DDGS molecular spectra, but not wheat and wheat DDGS. This study indicated that the bioethanol processing changes carbohydrate molecular structural profiles, compared

  7. Structural and Biochemical Analyses of Swine Major Histocompatibility Complex Class I Complexes and Prediction of the Epitope Map of Important Influenza A Virus Strains.

    Science.gov (United States)

    Fan, Shuhua; Wu, Yanan; Wang, Song; Wang, Zhenbao; Jiang, Bo; Liu, Yanjie; Liang, Ruiying; Zhou, Wenzhong; Zhang, Nianzhi; Xia, Chun

    2016-08-01

    , the skewing of the α1 and α2 helixes is important in the different peptide conformations in SLA-3*hs0202. We also determined the fundamental motif for SLA-3*hs0202 to be X-(M/A/R)-(N/Q/R/F)-X-X-X-X-X-(V/I) based on a series of structural and biochemical analyses, and 28 SLA-3*hs0202-restricted epitope candidates were identified from important IAV strains. We believe our structure and analyses of pSLA-3*hs0202 can benefit vaccine development to control IAV in swine. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

  8. A Combination of Structural and Empirical Analyses Delineates the Key Contacts Mediating Stability and Affinity Increases in an Optimized Biotherapeutic Single-chain Fv (scFv)*

    Science.gov (United States)

    Tu, Chao; Terraube, Virginie; Tam, Amy Sze Pui; Stochaj, Wayne; Fennell, Brian J.; Lin, Laura; Stahl, Mark; LaVallie, Edward R.; Somers, Will; Finlay, William J. J.; Mosyak, Lydia; Bard, Joel; Cunningham, Orla

    2016-01-01

    Fully-human single-chain Fv (scFv) proteins are key potential building blocks of bispecific therapeutic antibodies, but they often suffer from manufacturability and clinical development limitations such as instability and aggregation. The causes of these scFv instability problems, in proteins that should be theoretically stable, remains poorly understood. To inform the future development of such molecules, we carried out a comprehensive structural analysis of the highly stabilized anti-CXCL13 scFv E10. E10 was derived from the parental 3B4 using complementarity-determining region (CDR)-restricted mutagenesis and tailored selection and screening strategies, and carries four mutations in VL-CDR3. High-resolution crystal structures of parental 3B4 and optimized E10 scFvs were solved in the presence and absence of human CXCL13. In parallel, a series of scFv mutants was generated to interrogate the individual contribution of each of the four mutations to stability and affinity improvements. In combination, these analyses demonstrated that the optimization of E10 was primarily mediated by removing clashes between both the VL and the VH, and between the VL and CXCL13. Importantly, a single, germline-encoded VL-CDR3 residue mediated the key difference between the stable and unstable forms of the scFv. This work demonstrates that, aside from being the critical mediators of specificity and affinity, CDRs may also be the primary drivers of biotherapeutic developability. PMID:26515064

  9. Evolution of a passive crustal-scale detachment (Syros, Aegean region): Insights from structural and petrofabric analyses in the hanging-wall

    Science.gov (United States)

    Aravadinou, E.; Xypolias, P.

    2017-10-01

    New detailed (micro-)structural investigations, quartz petrofabric analyses and geological/structural mapping in southeast Syros (Cycladic massif, Aegean region) allow us to place new constraints on the tectonic evolution of the Uppermost unit, which occupies the immediate hanging-wall of the crustal-scale Vari Detachment. We show that the Eocene ‒ Oligocene deformation history in the hanging-wall of this detachment is associated with SW-directed ductile shearing. This history includes an early distributed constrictional deformation expressed by transport-parallel upright folds, L-tectonites and cleft-girdles quartz c-axis fabrics that were formed at temperatures ∼500 °C. Ductile deformation progressively localized at the bottom of the Uppermost unit leading to the formation of a greenschist-facies mylonitic zone under plane strain conditions inferred from Type-I cross-girdles quartz c-axis fabrics. The ongoing mylonitization was also associated with temporally increasing pure shear component of deformation coupled with cooling from ∼500 °C to ∼400 °C. We suggest that the Vari Detachment represents a passive normal-sense roof fault resulted from the NE-directed ductile extrusion of the Blueschist unit (footwall) at middle Eocene ‒ Oligocene times. In the middle Miocene, the activation of the brittle SSW-directed Late Vari Detachment enhanced the brittle exhumation of both the Blueschist unit and the Vari Detachment.

  10. Structural and mutational analyses of cis-acting sequences in the 5'-untranslated region of satellite RNA of bamboo mosaic potexvirus

    International Nuclear Information System (INIS)

    Annamalai, Padmanaban; Hsu, Y.-H.; Liu, Y.-P.; Tsai, C.-H.; Lin, N.-S.

    2003-01-01

    The satellite RNA of Bamboo mosaic virus (satBaMV) contains on open reading frame for a 20-kDa protein that is flanked by a 5'-untranslated region (UTR) of 159 nucleotides (nt) and a 3'-UTR of 129 nt. A secondary structure was predicted for the 5'-UTR of satBaMV RNA, which folds into a large stem-loop (LSL) and a small stem-loop. Enzymatic probing confirmed the existence of LSL (nt 8-138) in the 5'-UTR. The essential cis-acting sequences in the 5'-UTR required for satBaMV RNA replication were determined by deletion and substitution mutagenesis. Their replication efficiencies were analyzed in Nicotiana benthamiana protoplasts and Chenopodium quinoa plants coinoculated with helper BaMV RNA. All deletion mutants abolished the replication of satBaMV RNA, whereas mutations introduced in most of the loop regions and stems showed either no replication or a decreased replication efficiency. Mutations that affected the positive-strand satBaMV RNA accumulation also affected the accumulation of negative-strand RNA; however, the accumulation of genomic and subgenomic RNAs of BaMV were not affected. Moreover, covariation analyses of natural satBaMV variants provide substantial evidence that the secondary structure in the 5'-UTR of satBaMV is necessary for efficient replication

  11. Grid integration of electric-powered vehicles in existing and future energy supply structures. Advances in systems analyses 1. Final report; Netzintegration von Fahrzeugen mit elektrifizierten Antriebssystemen in bestehende und zukuenftige Energieversorgungsstrukturen. Advances in System Analyses 1. Endbericht

    Energy Technology Data Exchange (ETDEWEB)

    Linssen, Jochen; Bickert, Stefan; Hennings, Wilfried [Forschungszentrum Juelich GmbH (Germany). Inst. fuer Energie- und Klimaforschung, Systemforschung und Technologische Entwicklung (IEK-STE)] [and others

    2012-07-01

    The research project examines whether a fleet of vehicles with electric propulsion system (xEV) can be integrated into existing and future energy supply systems for effective integration of fluctuating power production as well as for energy storage. A multi-sectoral, system-wide scenario analysis is performed to evaluate the grid integration of electric vehicles. The effect of an xEV fleet and the impacts of various battery charging scenarios, including the option of feeding power back into the grid, are addressed by detailed technical and economic models and summarized by an energy system model. The suitability of different powertrain concepts is analysed, giving consideration to their individual applications by users. Based on the results of a German nationwide survey of mobility patterns and analyses of 47 test subjects, individual driving profiles for private cars are drawn up and stored in a database. They are used as input for the vehicle energy model. This model calculates the energy requirements of different xEV concepts and facilitates optimized powertrain design and battery sizing for the respective applications. The results show that if the batteries are charged overnight it is possible to cover a major fraction of daily driving distances by electric power. Additional charging during the day does not significantly improve this fraction. The auxiliaries have a greater influence on the vehicle's energy demand than individual driving patterns. Battery lifetime is extended by recharging the battery as required and preferably as late as possible before the next trip. In most cases, using the batteries for grid services reduces battery lifetime and leads to higher specific costs. Models of the transmission grid and typical distribution grids are developed. It is shown that charging one million xEV in 2020 and six million in 2030 (as envisaged by the German Federal Government) is technically feasible without major structural modifications of the

  12. The use of IR, magnetism, reflectance, and mass spectra together with thermal analyses in structure investigation of codeine phosphate complexes of d-block elements

    Science.gov (United States)

    Zayed, M. A.; El-shahat, M. F.; Abdullah, S. M.

    2005-06-01

    Codeine is an analgesic with uses similar to morphines, but it is of much less effect, i.e., it had a mild sedative effect; codeine is usually used as the phosphate form (Cod.P) and is often administrated by mouth with aspirin of paracetamol. Due to its serious use, if it is in large dose, attention is paid in this research to the synthesis and stereochemistry of new iron, cobalt, nickel, copper, and zinc complexes of this drug in both solution and the solid states. The spectra of these complexes in solution and the study of their stoichiometry refer to the formation of 1:1 ratio of metal (M) to ligand (L). The steriochemical structures of the solid complexes were studied on the basis of their analytical, spectroscopic, magnetic, and thermal data. Infrared spectra proved the presence of M sbnd O bonds. Magnetic susceptibility and solid reflectance spectral measurements were used to infer the structures. The prepared complexes were found to have the general formulae [ML(OH) x(H 2O) y](H 2O) zH 3PO 4, M: Co(II), Ni(II), and Cu(II), x = 1, y = 0, z = 0; M: Fe(II), x = 1, y = 2, z = 1; Fe(III), x = 2, y = 1, z = 0; Co(III), x = 0, y = 2, z = 1; Zn(II), x = 1, y = 0, z = 3; and L: (Cod.P) of the general formula C 18H 24NO 7P (anhydrate). Octahedral, tetrahedral, and square planer structures were proposed for these complexes depending upon the magnetic and reflectance data and were confirmed by detailed mass and thermal analyses comparative studies.

  13. Preliminary examination of food web structure of Nicola Lake (Taim Hydrological System, south Brazil using dual C and N stable isotope analyses

    Directory of Open Access Journals (Sweden)

    Alexandre M. Garcia

    Full Text Available Taim Ecological Reserve is located within the Taim Hydrological System and was created to protect a heterogeneous and productive landscape harboring exceptional biological diversity in southern Brazil. Using stable isotope ratio analyses of carbon (delta13C and nitrogen (delta15N, we provide a preliminary description of the food web structure, including estimates of production sources supporting fish populations and vertical trophic structure, within a representative lake of this system. A total of 21 organisms (5 macrophytes, 3 mollusks and 13 adult fishes representing 16 species were collected for isotope analysis. Fishes had delta13C values ranging from -24.30º/oo to -28.31º/oo , showing concordance with the range of values observed for macrophytes (-25.49 to -27.10º/oo, and suggesting that these plants could be a major carbon source supporting these fishes. delta13C signatures of Corbicula (-30.81º/oo and Pomacea (-24.26º/oo indirectly suggest that phytoplankton and benthic algae could be alternative carbon sources for some consumers. Nitrogen isotope ratios indicated approximately three consumer trophic levels. The pearl cichlid Geophagus brasiliensis was a primary consumer. Two catfishes (Trachelyopterus lucenai and Loricariichthys anus were secondary consumers. Two congeneric pike cichclids (Crenicichla lepidota and C. punctata, a catfish (Pimelodus maculatus and the characids Astyanax fasciatus and Oligosarcus robustus were tertiary consumers. Further studies including additional primary producers and consumers and greater sample numbers should be conducted to provide a more complete and detailed description of food web structure and dynamics within the reserve.

  14. Single crystal structure analyses of scheelite-powellite CaW1-xMoxO4 solidsolutions and unique occurrence in Jisyakuyama skarn deposits

    Science.gov (United States)

    Yamashita, K.; Yoshiasa, A.; Miyazaki, H.; Tokuda, M.; Tobase, T.; Isobe, H.; Nishiyama, T.; Sugiyama, K.; Miyawaki, R.

    2017-12-01

    Jisyakuyama skarn deposit, Fukuchi, Fukuoka, Japan, shows a simple occurrenceformed by penetration of hot water into limestone cracks. A unique occurrence of scheelite-powellite CaW1-xMoxO4 minerals is observed in the skarn deposit. Many syntheticexperiments for scheelite-powellite solid solutions have been reported as research onfluorescent materials. In this system it is known that a complete continuous solid solution isformed even at room temperature. In this study, we have carried out the chemical analyses,crystal structural refinements and detail description of occurrence on scheelite-powelliteminerals. We have also attempted synthesis of single crystal of solid solution in a widecomposition range. The chemical compositions were determined by JEOL scanningelectron microscope and EDS, INCA system. We have performed the crystal structurerefinements of the scheelite-powellite CaW1-xMoxO4 solid solutions (x=0.0-1.0) byRIGAKU single-crystal structure analysis system RAPID. The R and S values are around0.0s and 1.03. As the result of structural refinements of natural products and many solidsolutions, we confirm that most large natural single crystals have compositions at bothendmembers, and large solid solution crystals are rare. The lattice constants, interatomicdistances and other crystallographic parameters for the solid solution change uniquely withcomposition and it was confirmed as a continuous solid solution. Single crystals of scheeliteendmember + powellite endmember + solid solution with various compositions form anaggregate in the deposit (Figure 1). Crystal shapes of powellite and scheelite arehypidiomorphic and allotriomorphic, respectively. Many solid solution crystals areaccompanied by scheelite endmember and a compositional gap is observed betweenpowellite and solid-solution crystals. The presence of several penetration solutions withsignificantly different W and Mo contents may be assumed. This research can be expectedto lead to giving restrictive

  15. Genetic Structuration, Demography and Evolutionary History of Mycobacterium tuberculosis LAM9 Sublineage in the Americas as Two Distinct Subpopulations Revealed by Bayesian Analyses

    Science.gov (United States)

    Reynaud, Yann; Millet, Julie; Rastogi, Nalin

    2015-01-01

    Tuberculosis (TB) remains broadly present in the Americas despite intense global efforts for its control and elimination. Starting from a large dataset comprising spoligotyping (n = 21183 isolates) and 12-loci MIRU-VNTRs data (n = 4022 isolates) from a total of 31 countries of the Americas (data extracted from the SITVIT2 database), this study aimed to get an overview of lineages circulating in the Americas. A total of 17119 (80.8%) strains belonged to the Euro-American lineage 4, among which the most predominant genotypic family belonged to the Latin American and Mediterranean (LAM) lineage (n = 6386, 30.1% of strains). By combining classical phylogenetic analyses and Bayesian approaches, this study revealed for the first time a clear genetic structuration of LAM9 sublineage into two subpopulations named LAM9C1 and LAM9C2, with distinct genetic characteristics. LAM9C1 was predominant in Chile, Colombia and USA, while LAM9C2 was predominant in Brazil, Dominican Republic, Guadeloupe and French Guiana. Globally, LAM9C2 was characterized by higher allelic richness as compared to LAM9C1 isolates. Moreover, LAM9C2 sublineage appeared to expand close to twenty times more than LAM9C1 and showed older traces of expansion. Interestingly, a significant proportion of LAM9C2 isolates presented typical signature of ancestral LAM-RDRio MIRU-VNTR type (224226153321). Further studies based on Whole Genome Sequencing of LAM strains will provide the needed resolution to decipher the biogeographical structure and evolutionary history of this successful family. PMID:26517715

  16. A Combination of Structural and Empirical Analyses Delineates the Key Contacts Mediating Stability and Affinity Increases in an Optimized Biotherapeutic Single-chain Fv (scFv).

    Science.gov (United States)

    Tu, Chao; Terraube, Virginie; Tam, Amy Sze Pui; Stochaj, Wayne; Fennell, Brian J; Lin, Laura; Stahl, Mark; LaVallie, Edward R; Somers, Will; Finlay, William J J; Mosyak, Lydia; Bard, Joel; Cunningham, Orla

    2016-01-15

    Fully-human single-chain Fv (scFv) proteins are key potential building blocks of bispecific therapeutic antibodies, but they often suffer from manufacturability and clinical development limitations such as instability and aggregation. The causes of these scFv instability problems, in proteins that should be theoretically stable, remains poorly understood. To inform the future development of such molecules, we carried out a comprehensive structural analysis of the highly stabilized anti-CXCL13 scFv E10. E10 was derived from the parental 3B4 using complementarity-determining region (CDR)-restricted mutagenesis and tailored selection and screening strategies, and carries four mutations in VL-CDR3. High-resolution crystal structures of parental 3B4 and optimized E10 scFvs were solved in the presence and absence of human CXCL13. In parallel, a series of scFv mutants was generated to interrogate the individual contribution of each of the four mutations to stability and affinity improvements. In combination, these analyses demonstrated that the optimization of E10 was primarily mediated by removing clashes between both the VL and the VH, and between the VL and CXCL13. Importantly, a single, germline-encoded VL-CDR3 residue mediated the key difference between the stable and unstable forms of the scFv. This work demonstrates that, aside from being the critical mediators of specificity and affinity, CDRs may also be the primary drivers of biotherapeutic developability. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

  17. Polycystic liver in the adult (PLA in Spain: analysis of a structured survey analysing the experience and attitude of gastroenterologists in Spain

    Directory of Open Access Journals (Sweden)

    Javier Ampuero

    2014-04-01

    Full Text Available Background: Polycystic liver in the adult (PLA is a rare disease characterized by chronic liver enlargement. Objective: To analyse gastroenterologists' involvement in, experience with, and attitude toward diagnosing, monitoring, and treating patients with PLA in Spain. Methods: Each of seven study coordinators contacted 15 specialists in their geographic area about participating in the study via an online structured survey. Results: Of the 105 clinics contacted, 88 completed the questionnaire, with a mean of 3 patients being followed per practice, although 6 clinics were following more than 20 patients with PLA. Patients were being followed mainly by the Department of Hepatology (81 % and/or the Department of Gastroenterology (33 %. The majority of patients were diagnosed (98 % and monitored (97 % using liver ultrasound. When diagnosed, 76 % of patients were under 50 years of age, females predominating. The primary treatment objective for the patients was symptomatic management. Pharmacotherapy was prescribed by 28 % of physicians: Somatostatin analogues, primarily, followed by mTOR inhibitors. One-third of the clinics indicated that they had patients who had undergone liver transplant and/or surgery. Conclusions: Ultrasound is the diagnosing and monitoring method of choice. Among the clinics using pharmacotherapy for symptomatic management, somatostatin analogues were the drugs of choice. These clinics' infrequent use of invasive procedures suggests that they perceive the various invasive techniques as not very effective.

  18. Structural changes in Parkinson's disease. Voxel-based morphometry and diffusion tensor imaging analyses based on 123I-MIBG uptake

    International Nuclear Information System (INIS)

    Kikuchi, Kazufumi; Hiwatashi, Akio; Togao, Osamu; Yamashita, Koji; Somehara, Ryo; Kamei, Ryotaro; Baba, Shingo; Honda, Hiroshi; Yamaguchi, Hiroo; Kira, Jun-ichi

    2017-01-01

    Patients with Parkinson's disease (PD) may exhibit symptoms of sympathetic dysfunction that can be measured using 123 I-metaiodobenzylguanidine (MIBG) myocardial scintigraphy. We investigated the relationship between microstructural brain changes and 123 I-MIBG uptake in patients with PD using voxel-based morphometry (VBM) and diffusion tensor imaging (DTI) analyses. This retrospective study included 24 patients with PD who underwent 3 T magnetic resonance imaging and 123 I-MIBG scintigraphy. They were divided into two groups: 12 MIBG-positive and 12 MIBG-negative cases (10 men and 14 women; age range: 60-81 years, corrected for gender and age). The heart/mediastinum count (H/M) ratio was calculated on anterior planar 123 I-MIBG images obtained 4 h post-injection. VBM and DTI were performed to detect structural differences between these two groups. Patients with low H/M ratio had significantly reduced brain volume at the right inferior frontal gyrus (uncorrected p < 0.0001, K > 90). Patients with low H/M ratios also exhibited significantly lower fractional anisotropy than those with high H/M ratios (p < 0.05) at the left anterior thalamic radiation, the left inferior fronto-occipital fasciculus, the left superior longitudinal fasciculus, and the left uncinate fasciculus. VBM and DTI may reveal microstructural changes related to the degree of 123 I-MIBG uptake in patients with PD. (orig.)

  19. Structural changes in Parkinson's disease: voxel-based morphometry and diffusion tensor imaging analyses based on 123I-MIBG uptake.

    Science.gov (United States)

    Kikuchi, Kazufumi; Hiwatashi, Akio; Togao, Osamu; Yamashita, Koji; Somehara, Ryo; Kamei, Ryotaro; Baba, Shingo; Yamaguchi, Hiroo; Kira, Jun-Ichi; Honda, Hiroshi

    2017-12-01

    Patients with Parkinson's disease (PD) may exhibit symptoms of sympathetic dysfunction that can be measured using 123 I-metaiodobenzylguanidine (MIBG) myocardial scintigraphy. We investigated the relationship between microstructural brain changes and 123 I-MIBG uptake in patients with PD using voxel-based morphometry (VBM) and diffusion tensor imaging (DTI) analyses. This retrospective study included 24 patients with PD who underwent 3 T magnetic resonance imaging and 123 I-MIBG scintigraphy. They were divided into two groups: 12 MIBG-positive and 12 MIBG-negative cases (10 men and 14 women; age range: 60-81 years, corrected for gender and age). The heart/mediastinum count (H/M) ratio was calculated on anterior planar 123 I-MIBG images obtained 4 h post-injection. VBM and DTI were performed to detect structural differences between these two groups. Patients with low H/M ratio had significantly reduced brain volume at the right inferior frontal gyrus (uncorrected p  90). Patients with low H/M ratios also exhibited significantly lower fractional anisotropy than those with high H/M ratios (p based morphometry can detect grey matter changes in Parkinson's disease. • Diffusion tensor imaging can detect white matter changes in Parkinson's disease.

  20. Structural changes in Parkinson's disease. Voxel-based morphometry and diffusion tensor imaging analyses based on {sup 123}I-MIBG uptake

    Energy Technology Data Exchange (ETDEWEB)

    Kikuchi, Kazufumi; Hiwatashi, Akio; Togao, Osamu; Yamashita, Koji; Somehara, Ryo; Kamei, Ryotaro; Baba, Shingo; Honda, Hiroshi [Kyushu University, Department of Clinical Radiology, Graduate School of Medical Sciences, Fukuoka (Japan); Yamaguchi, Hiroo; Kira, Jun-ichi [Kyushu University, Department of Neurology, Graduate School of Medical Sciences, Fukuoka (Japan)

    2017-12-15

    Patients with Parkinson's disease (PD) may exhibit symptoms of sympathetic dysfunction that can be measured using {sup 123}I-metaiodobenzylguanidine (MIBG) myocardial scintigraphy. We investigated the relationship between microstructural brain changes and {sup 123}I-MIBG uptake in patients with PD using voxel-based morphometry (VBM) and diffusion tensor imaging (DTI) analyses. This retrospective study included 24 patients with PD who underwent 3 T magnetic resonance imaging and {sup 123}I-MIBG scintigraphy. They were divided into two groups: 12 MIBG-positive and 12 MIBG-negative cases (10 men and 14 women; age range: 60-81 years, corrected for gender and age). The heart/mediastinum count (H/M) ratio was calculated on anterior planar {sup 123}I-MIBG images obtained 4 h post-injection. VBM and DTI were performed to detect structural differences between these two groups. Patients with low H/M ratio had significantly reduced brain volume at the right inferior frontal gyrus (uncorrected p < 0.0001, K > 90). Patients with low H/M ratios also exhibited significantly lower fractional anisotropy than those with high H/M ratios (p < 0.05) at the left anterior thalamic radiation, the left inferior fronto-occipital fasciculus, the left superior longitudinal fasciculus, and the left uncinate fasciculus. VBM and DTI may reveal microstructural changes related to the degree of {sup 123}I-MIBG uptake in patients with PD. (orig.)

  1. Detecting Molecular Features of Spectra Mainly Associated with Structural and Non-Structural Carbohydrates in Co-Products from BioEthanol Production Using DRIFT with Uni- and Multivariate Molecular Spectral Analyses

    Directory of Open Access Journals (Sweden)

    Zhiyuan Niu

    2011-03-01

    Full Text Available The objective of this study was to use DRIFT spectroscopy with uni- and multivariate molecular spectral analyses as a novel approach to detect molecular features of spectra mainly associated with carbohydrate in the co-products (wheat DDGS, corn DDGS, blend DDGS from bioethanol processing in comparison with original feedstock (wheat (Triticum, corn (Zea mays. The carbohydrates related molecular spectral bands included: A_Cell (structural carbohydrates, peaks area region and baseline: ca. 1485–1188 cm−1, A_1240 (structural carbohydrates, peak area centered at ca. 1240 cm−1 with region and baseline: ca. 1292–1198 cm−1, A_CHO (total carbohydrates, peaks region and baseline: ca. 1187–950 cm-1, A_928 (non-structural carbohydrates, peak area centered at ca. 928 cm−1 with region and baseline: ca. 952–910 cm−1, A_860 (non-structural carbohydrates, peak area centered at ca. 860 cm−1 with region and baseline: ca. 880–827 cm-1, H_1415 (structural carbohydrate, peak height centered at ca. 1415 cm−1 with baseline: ca. 1485–1188 cm−1, H_1370 (structural carbohydrate, peak height at ca. 1370 cm−1 with a baseline: ca. 1485–1188 cm−1. The study shows that the grains had lower spectral intensity (KM Unit of the cellulosic compounds of A_1240 (8.5 vs. 36.6, P < 0.05, higher (P < 0.05 intensities of the non-structural carbohydrate of A_928 (17.3 vs. 2.0 and A_860 (20.7 vs. 7.6 than their co-products from bioethanol processing. There were no differences (P > 0.05 in the peak area intensities of A_Cell (structural CHO at 1292–1198 cm−1 and A_CHO (total CHO at 1187–950 cm−1 with average molecular infrared intensity KM unit of 226.8 and 508.1, respectively. There were no differences (P > 0.05 in the peak height intensities of H_1415 and H_1370 (structural CHOs with average intensities 1.35 and 1.15, respectively. The multivariate molecular spectral analyses were able to discriminate and classify between the corn and corn DDGS

  2. Detecting Molecular Features of Spectra Mainly Associated with Structural and Non-Structural Carbohydrates in Co-Products from BioEthanol Production Using DRIFT with Uni- and Multivariate Molecular Spectral Analyses

    Science.gov (United States)

    Yu, Peiqiang; Damiran, Daalkhaijav; Azarfar, Arash; Niu, Zhiyuan

    2011-01-01

    The objective of this study was to use DRIFT spectroscopy with uni- and multivariate molecular spectral analyses as a novel approach to detect molecular features of spectra mainly associated with carbohydrate in the co-products (wheat DDGS, corn DDGS, blend DDGS) from bioethanol processing in comparison with original feedstock (wheat (Triticum), corn (Zea mays)). The carbohydrates related molecular spectral bands included: A_Cell (structural carbohydrates, peaks area region and baseline: ca. 1485–1188 cm−1), A_1240 (structural carbohydrates, peak area centered at ca. 1240 cm−1 with region and baseline: ca. 1292–1198 cm−1), A_CHO (total carbohydrates, peaks region and baseline: ca. 1187–950 cm−1), A_928 (non-structural carbohydrates, peak area centered at ca. 928 cm−1 with region and baseline: ca. 952–910 cm−1), A_860 (non-structural carbohydrates, peak area centered at ca. 860 cm−1 with region and baseline: ca. 880–827 cm−1), H_1415 (structural carbohydrate, peak height centered at ca. 1415 cm−1 with baseline: ca. 1485–1188 cm−1), H_1370 (structural carbohydrate, peak height at ca. 1370 cm−1 with a baseline: ca. 1485–1188 cm−1). The study shows that the grains had lower spectral intensity (KM Unit) of the cellulosic compounds of A_1240 (8.5 vs. 36.6, P carbohydrate of A_928 (17.3 vs. 2.0) and A_860 (20.7 vs. 7.6) than their co-products from bioethanol processing. There were no differences (P > 0.05) in the peak area intensities of A_Cell (structural CHO) at 1292–1198 cm−1 and A_CHO (total CHO) at 1187–950 cm−1 with average molecular infrared intensity KM unit of 226.8 and 508.1, respectively. There were no differences (P > 0.05) in the peak height intensities of H_1415 and H_1370 (structural CHOs) with average intensities 1.35 and 1.15, respectively. The multivariate molecular spectral analyses were able to discriminate and classify between the corn and corn DDGS molecular spectra, but not wheat and wheat DDGS. This

  3. Cocrystals of kaempferol, quercetin and myricetin with 4,4‧-bipyridine: Crystal structures, analyses of intermolecular interactions and antibacterial properties

    Science.gov (United States)

    Zhang, Yu-Nan; Yin, He-Mei; Zhang, Yu; Zhang, Da-Jun; Su, Xin; Kuang, Hai-Xue

    2017-02-01

    With an aim to explore the interactions of Osbnd H⋯N between hydroxyl moiety of the flavonoids and the pyridyl ring of N-containing aromatic amines, three flavonols with varying B-ring-hydroxyl groups (kaempferol, quercetin, and myricetin) were selected to combine with 4,4‧-bipyridine. As a result, three new cocrystals of flavonols were obtained with a solution evaporation approach. These three cocrystals were characterized by single crystal X-ray diffraction, XPRD, IR and NMR methods. The resulting cocrystals were kaempferol: 4,4‧-bipyridine (2:1) (KAE·BPY·2H2O), quercetin: 4,4‧-bipyridine (1:1.5) (QUE·BPY), and myricetin: 4,4‧-bipyridine (1:2) (MYR·BPY·H2O). Structural analyses show that an array of hydrogen bonds and π-π stacking interactions interconnect the molecules to form a two-dimensional (2D) supramolecular layer in KAE·BPY·2H2O, QUE·BPY, and MYR·BPY·H2O. In the three cocrystals, they present as three different synthons-ⅠR88(58), Ⅳ R44(42) and, Ⅶ R66(29) with 4,4‧-bipyridine, respectively-which may yield a strategy for constructing the supramolecule. Cocrystals of flavonols combined with N-containing aromatic amines, 7-OH, B-ring-hydroxyl number and/or the location of the flavonols to play a significant part in extending the dimensionality of the cocrystals. The resulting motif formation and crystal packing in these flavonols cocrystals has combined with N-containing aromatic amines. Additionally, the antibacterial properties of the three cocrystals against Staphylococcus aureus (S. aureus) and Escherichia coli (E. coli) have been investigated.

  4. Synthesis, structural analyses and antimicrobial activity of the water soluble 1D coordination polymer [Ag(3-aminopyridine)]ClO4

    Science.gov (United States)

    Soliman, Saied M.; Elsilk, Sobhy E.

    2017-12-01

    The synthesis, characterization and molecular structure aspects of the [Ag(3-aminopyridine)]ClO4 coordination polymer have been presented. Single crystal X-ray diffraction (SC-XRD) analysis showed that the asymmetric unit consists of two Ag, one 3-aminopyridine (3APy) and one ionic perchlorate anion. The 3-aminpyridine (3APy) acts as a bridged ligand connecting the Ag-atoms via the amine and pyridine ring N-atoms leading to the formation of 1D coordination polymer. The perchlorate anion connects the 1D chains via a complicated set of Nsbnd H⋯O and Csbnd H⋯O hydrogen bonding interactions. Strong FTIR spectral bands at 1143.1, 1116.7 and 1085.6 cm-1 and a weak band at 932.9 cm-1 revealed the ionic character of the complex. Single point DFT calculations combined with atoms in molecules (AIM) and natural bond orbital (NBO) analyses indicated stronger Agsbnd N(py) than Agsbnd N(NH2) interaction. The former has more covalent character according to the AIM topological parameters. The Ag⋯O interactions are weak and are mainly affected by dispersion interactions. Of the six DFT methods used for geometry optimizations, the TPSSTPSS then PBEPBE are the most powerful DFT methods to predict the Agsbnd N distances. Effect of methods on the frontier molecular orbitals energies and shapes are also presented. Preliminary antimicrobial studies showed that the [Ag(3APy)]ClO4 complex has more activity against all the studied microorganisms than the free 3APy.

  5. Decomposition of Intermolecular Interactions in the Crystal Structure of Some Diacetyl Platinum(II Complexes: Combined Hirshfeld, AIM, and NBO Analyses

    Directory of Open Access Journals (Sweden)

    Saied M. Soliman

    2016-12-01

    Full Text Available Intermolecular interactions play a vital role in crystal structures. Therefore, we conducted a topological study, using Hirshfeld surfaces and atom in molecules (AIM analysis, to decompose and analyze, respectively, the different intermolecular interactions in six hydrazone-diacetyl platinum(II complexes. Using AIM and natural bond orbital (NBO analyses, we determined the type, nature, and strength of the interactions. All the studied complexes contain C-H⋯O interactions, and the presence of bond critical points along the intermolecular paths underlines their significance. The electron densities (ρ(r at the bond critical points (0.0031–0.0156 e/a03 fall within the typical range for H-bonding interactions. Also, the positive values of the Laplacian of the electron density (∇2ρ(r revealed the depletion of electronic charge on the interatomic path, another characteristic feature of closed-shell interactions. The ratios of the absolute potential energy density to the kinetic energy density (|V(r|/G(r and ρ(r are highest for the O2⋯H15-N3 interaction in [Pt(COMe2(2-pyCMe=NNH2] (1; hence, this interaction has the highest covalent character of all the O⋯H intermolecular interactions. Interestingly, in [Pt(COMe2(H2NN=CMe-CMe=NNH2] (3, there are significant N-H⋯Pt interactions. Using the NBO method, the second-order interaction energies, E(2, of these interactions range from 3.894 to 4.061 kJ/mol. Furthermore, the hybrid Pt orbitals involved in these interactions are comprised of dxy, dxz, and s atomic orbitals.

  6. Periodic safety analyses

    International Nuclear Information System (INIS)

    Gouffon, A.; Zermizoglou, R.

    1990-12-01

    The IAEA Safety Guide 50-SG-S8 devoted to 'Safety Aspects of Foundations of Nuclear Power Plants' indicates that operator of a NPP should establish a program for inspection of safe operation during construction, start-up and service life of the plant for obtaining data needed for estimating the life time of structures and components. At the same time the program should ensure that the safety margins are appropriate. Periodic safety analysis are an important part of the safety inspection program. Periodic safety reports is a method for testing the whole system or a part of the safety system following the precise criteria. Periodic safety analyses are not meant for qualification of the plant components. Separate analyses are devoted to: start-up, qualification of components and materials, and aging. All these analyses are described in this presentation. The last chapter describes the experience obtained for PWR-900 and PWR-1300 units from 1986-1989

  7. Metagenomic and Metatranscriptomic Analyses Reveal the Structure and Dynamics of a Dechlorinating Community Containing Dehalococcoides mccartyi and Corrinoid-Providing Microorganisms under Cobalamin-Limited Conditions

    Energy Technology Data Exchange (ETDEWEB)

    Men, Yujie; Yu, Ke; Bælum, Jacob; Gao, Ying; Tremblay, Julien; Prestat, Emmanuel; Stenuit, Ben; Tringe, Susannah G.; Jansson, Janet; Zhang, Tong; Alvarez-Cohen, Lisa; Liu, Shuang-Jiang

    2017-02-10

    ABSTRACT

    The aim of this study is to obtain a systems-level understanding of the interactions betweenDehalococcoidesand corrinoid-supplying microorganisms by analyzing community structures and functional compositions, activities, and dynamics in trichloroethene (TCE)-dechlorinating enrichments. Metagenomes and metatranscriptomes of the dechlorinating enrichments with and without exogenous cobalamin were compared. Seven putative draft genomes were binned from the metagenomes. At an early stage (2 days), more transcripts of genes in theVeillonellaceaebin-genome were detected in the metatranscriptome of the enrichment without exogenous cobalamin than in the one with the addition of cobalamin. Among these genes, sporulation-related genes exhibited the highest differential expression when cobalamin was not added, suggesting a possible release route of corrinoids from corrinoid producers. Other differentially expressed genes include those involved in energy conservation and nutrient transport (including cobalt transport). The most highly expressed corrinoidde novobiosynthesis pathway was also assigned to theVeillonellaceaebin-genome. Targeted quantitative PCR (qPCR) analyses confirmed higher transcript abundances of those corrinoid biosynthesis genes in the enrichment without exogenous cobalamin than in the enrichment with cobalamin. Furthermore, the corrinoid salvaging and modification pathway ofDehalococcoideswas upregulated in response to the cobalamin stress. This study provides important insights into the microbial interactions and roles played by members of dechlorinating communities under cobalamin-limited conditions.

    IMPORTANCEThe key

  8. Herbivory of Omnivorous Fish Shapes the Food Web Structure of a Chinese Tropical Eutrophic Lake: Evidence from Stable Isotope and Fish Gut Content Analyses

    Directory of Open Access Journals (Sweden)

    Jian Gao

    2017-01-01

    Full Text Available Studies suggest that, unlike the situation in temperate lakes, high biomasses of omnivorous fish are maintained in subtropical and tropical lakes when they shift from a turbid phytoplankton-dominated state to a clear water macrophyte-dominated state, and the predation pressure on large-bodied zooplankton therefore remains high. Whether this reflects a higher degree of herbivory in warm lakes than in temperate lakes is debatable. We combined food web studies using stable isotopes with gut content analyses of the most dominant fish species to elucidate similarities and differences in food web structure between a clear water macrophyte-dominated basin (MDB and a turbid phytoplankton-dominated basin (PDB of Huizhou West Lake, a shallow tropical Chinese lake. The δ13C–δ15N biplot of fish and invertebrates revealed community-wide differences in isotope-based metrics of the food webs between MDB and PDB. The range of consumer δ15N (NR was lower in MDB than in PDB, indicating shorter food web length in MDB. The mean nearest neighbor distance (MNND and standard deviation around MNND (SDNND were higher in MDB than in PDB, showing a markedly low fish trophic overlap and a more uneven packing of species in niches in MDB than in PDB. The range of fish δ13C (CR of consumers was more extensive in MDB than in PDB, indicating a wider feeding range for fish in MDB. Mixing model results showed that macrophytes and associated periphyton constituted a large fraction of basal production sources for the fish in MDB, while particulate organic matter (POM contributed a large fraction in PDB. In MDB, the diet of the dominant fish species, crucian carp (Carassius carassius, consisted mainly of vegetal matter (macrophytes and periphyton and zooplankton, while detritus was the most important food item in PDB. Our results suggest that carbon from macrophytes with associated periphyton may constitute an important food resource for omnivorous fish, and this may strongly

  9. Theoretical study of the electronic structure of f-element complexes by quantum chemical methods; Analyse de la structure electronique des complexes contenant des elements F par des methodes de la chimie quantique

    Energy Technology Data Exchange (ETDEWEB)

    Vetere, V

    2002-09-15

    This thesis is related to comparative studies of the chemical properties of molecular complexes containing lanthanide or actinide trivalent cations, in the context of the nuclear waste disposal. More precisely, our aim was a quantum chemical analysis of the metal-ligand bonding in such species. Various theoretical approaches were compared, for the inclusion of correlation (density functional theory, multiconfigurational methods) and of relativistic effects (relativistic scalar and 2-component Hamiltonians, relativistic pseudopotentials). The performance of these methods were checked by comparing computed structural properties to published experimental data, on small model systems: lanthanide and actinide tri-halides and on X{sub 3}M-L species (X=F, Cl; M=La, Nd, U; L = NH{sub 3}, acetonitrile, CO). We have thus shown the good performance of density functionals combined with a quasi-relativistic method, as well as of gradient-corrected functionals associated with relativistic pseudopotentials. In contrast, functionals including some part of exact exchange are less reliable to reproduce experimental trends, and we have given a possible explanation for this result . Then, a detailed analysis of the bonding has allowed us to interpret the discrepancies observed in the structural properties of uranium and lanthanides complexes, based on a covalent contribution to the bonding, in the case of uranium(III), which does not exist in the lanthanide(III) homologues. Finally, we have examined more sizeable systems, closer to experimental species, to analyse the influence of the coordination number, of the counter-ions and of the oxidation state of uranium, on the metal-ligand bonding. (author)

  10. A systematic study of coordinate precision in X-ray structure analyses. Pt. 2. Predictive estimates of E.S.D.'s for the general-atom case

    International Nuclear Information System (INIS)

    Allen, F.H.; Cole, J.C.; Durham Univ.; Howard, J.A.K.; Durham Univ.

    1995-01-01

    The relationship between the mean isotropic e.s.d. anti σ(A) o of any element type A in a crystal structure and the R factor and atomic constitution of that structure is explored for 124 905 element-type occurrences calculated from 33 955 entries in the Cambridge Structural Database. On the basis of the work of Cruickshank [Acta Cryst. (1960), 13, 774-777], it is shown that anti σ(A) p values can be estimated by equations of the form anti σ(A) p = KRN 1/2 c /Z A where N c is taken as ΣZ 2 i /Z 2 C , the Z i are atomic numbers and the summation is over all atoms in the asymmetric unit. Values of K were obtained by regression techniques using the anti σ(A) o as basis. The constant K nc for noncentrosymmetric structures is found to be larger than K c for centrosymmetric structures by a factor of ∼2 1/2 , as predicted by Cruickshank (1960). Two predictive equations are generated, one for first-row elements and the second for elements with Z A > 10. The relationship between the different constants K that arise in these two situations is linked to shape differentials in scattering-factor (f i ) curves for light and heavy atoms. It is found that predictive equations in which the Z i are selectively replaced by f i at a constant sinθ/λ of 0.30 A -1 generate closely similar values of K for the light-atom and heavy-atom subsets. The overall analysis indicates that atomic e.s.d.'s may be seriously underestimated in the more precise structure determinations, that e.s.d.'s for the heaviest atoms may be less reliable than those for lighter atoms and that e.s.d.'s in noncentrosymmetric structures may be less accurate than those in centrosymmetric structures. (orig.)

  11. Structure of the Bro1 domain protein BROX and functional analyses of the ALIX Bro1 domain in HIV-1 budding.

    Directory of Open Access Journals (Sweden)

    Qianting Zhai

    Full Text Available Bro1 domains are elongated, banana-shaped domains that were first identified in the yeast ESCRT pathway protein, Bro1p. Humans express three Bro1 domain-containing proteins: ALIX, BROX, and HD-PTP, which function in association with the ESCRT pathway to help mediate intraluminal vesicle formation at multivesicular bodies, the abscission stage of cytokinesis, and/or enveloped virus budding. Human Bro1 domains share the ability to bind the CHMP4 subset of ESCRT-III proteins, associate with the HIV-1 NC(Gag protein, and stimulate the budding of viral Gag proteins. The curved Bro1 domain structure has also been proposed to mediate membrane bending. To date, crystal structures have only been available for the related Bro1 domains from the Bro1p and ALIX proteins, and structures of additional family members should therefore aid in the identification of key structural and functional elements.We report the crystal structure of the human BROX protein, which comprises a single Bro1 domain. The Bro1 domains from BROX, Bro1p and ALIX adopt similar overall structures and share two common exposed hydrophobic surfaces. Surface 1 is located on the concave face and forms the CHMP4 binding site, whereas Surface 2 is located at the narrow end of the domain. The structures differ in that only ALIX has an extended loop that projects away from the convex face to expose the hydrophobic Phe105 side chain at its tip. Functional studies demonstrated that mutations in Surface 1, Surface 2, or Phe105 all impair the ability of ALIX to stimulate HIV-1 budding.Our studies reveal similarities in the overall folds and hydrophobic protein interaction sites of different Bro1 domains, and show that a unique extended loop contributes to the ability of ALIX to function in HIV-1 budding.

  12. Seismic fragility analyses

    International Nuclear Information System (INIS)

    Kostov, Marin

    2000-01-01

    In the last two decades there is increasing number of probabilistic seismic risk assessments performed. The basic ideas of the procedure for performing a Probabilistic Safety Analysis (PSA) of critical structures (NUREG/CR-2300, 1983) could be used also for normal industrial and residential buildings, dams or other structures. The general formulation of the risk assessment procedure applied in this investigation is presented in Franzini, et al., 1984. The probability of failure of a structure for an expected lifetime (for example 50 years) can be obtained from the annual frequency of failure, β E determined by the relation: β E ∫[d[β(x)]/dx]P(flx)dx. β(x) is the annual frequency of exceedance of load level x (for example, the variable x may be peak ground acceleration), P(fI x) is the conditional probability of structure failure at a given seismic load level x. The problem leads to the assessment of the seismic hazard β(x) and the fragility P(fl x). The seismic hazard curves are obtained by the probabilistic seismic hazard analysis. The fragility curves are obtained after the response of the structure is defined as probabilistic and its capacity and the associated uncertainties are assessed. Finally the fragility curves are combined with the seismic loading to estimate the frequency of failure for each critical scenario. The frequency of failure due to seismic event is presented by the scenario with the highest frequency. The tools usually applied for probabilistic safety analyses of critical structures could relatively easily be adopted to ordinary structures. The key problems are the seismic hazard definitions and the fragility analyses. The fragility could be derived either based on scaling procedures or on the base of generation. Both approaches have been presented in the paper. After the seismic risk (in terms of failure probability) is assessed there are several approaches for risk reduction. Generally the methods could be classified in two groups. The

  13. Kinematics, dynamics and structural analyses of a semi-passive mechanical arm; Analise cinematica, dinamica e estrutural de um manipulador semi-passivo

    Energy Technology Data Exchange (ETDEWEB)

    Ferreira, Claudio Violante [PETROBRAS S.A., Rio de Janeiro, RJ (Brazil); Romano, Vitor Ferreira [Universidade Federal do Rio de Janeiro (UFRJ), RJ (Brazil). Escola Politecnica

    2008-07-01

    This work presents the dynamics and kinematics modeling, and the structural analysis (including modal analysis) of a gantry type Semi-Passive mechanical Arm (SPA). The kinematics analysis of the SPA is referred in the Joints Space Coordinates. The Denavit-Hartenberg (D-H) parameterization method is used in the manipulator kinematics model. The dynamics analysis is also referred in the Joints Space, and done by means of Lagrange Equations. To develop the dynamic equations it were considered the joints friction and the external loads related to marine currents and the AUV/SPA interaction. The dynamics analysis it was done in two SPA configurations: all joints with activated brakes (locked) and all joints with not activated brakes. A commercial FEM program, ANSYS{sup R} 5.5.1, was used to calculate the structural deformations and tensions, and these results were used to define the final structure configuration. This program has a Static Analysis Package which permits to determine the displacements, stresses, strains and forces in structures caused by external loads. In order to evaluate the SPA structural stiffness it was done the modal analysis and the determination of five SPA vibration modes and natural frequencies. (author)

  14. Possible future HERA analyses

    International Nuclear Information System (INIS)

    Geiser, Achim

    2015-12-01

    A variety of possible future analyses of HERA data in the context of the HERA data preservation programme is collected, motivated, and commented. The focus is placed on possible future analyses of the existing ep collider data and their physics scope. Comparisons to the original scope of the HERA pro- gramme are made, and cross references to topics also covered by other participants of the workshop are given. This includes topics on QCD, proton structure, diffraction, jets, hadronic final states, heavy flavours, electroweak physics, and the application of related theory and phenomenology topics like NNLO QCD calculations, low-x related models, nonperturbative QCD aspects, and electroweak radiative corrections. Synergies with other collider programmes are also addressed. In summary, the range of physics topics which can still be uniquely covered using the existing data is very broad and of considerable physics interest, often matching the interest of results from colliders currently in operation. Due to well-established data and MC sets, calibrations, and analysis procedures the manpower and expertise needed for a particular analysis is often very much smaller than that needed for an ongoing experiment. Since centrally funded manpower to carry out such analyses is not available any longer, this contribution not only targets experienced self-funded experimentalists, but also theorists and master-level students who might wish to carry out such an analysis.

  15. Structural and Enzymatic Analyses Reveal the Binding Mode of a Novel Series of Francisella tularensis Enoyl Reductase (FabI) Inhibitors

    Energy Technology Data Exchange (ETDEWEB)

    Mehboob, Shahila; Hevener, Kirk E.; Truong, Kent; Boci, Teuta; Santarsiero, Bernard D.; Johnson, Michael E. (UIC)

    2012-10-10

    Because of structural and mechanistic differences between eukaryotic and prokaryotic fatty acid synthesis enzymes, the bacterial pathway, FAS-II, is an attractive target for the design of antimicrobial agents. We have previously reported the identification of a novel series of benzimidazole compounds with particularly good antibacterial effect against Francisella tularensis, a Category A biowarfare pathogen. Herein we report the crystal structure of the F. tularensis FabI enzyme in complex with our most active benzimidazole compound bound with NADH. The structure reveals that the benzimidazole compounds bind to the substrate site in a unique conformation that is distinct from the binding motif of other known FabI inhibitors. Detailed inhibition kinetics have confirmed that the compounds possess a novel inhibitory mechanism that is unique among known FabI inhibitors. These studies could have a strong impact on future antimicrobial design efforts and may reveal new avenues for the design of FAS-II active antibacterial compounds.

  16. SEM and Raman spectroscopy analyses of laser-induced periodic surface structures grown by ethanol-assisted femtosecond laser ablation of chromium

    Science.gov (United States)

    Bashir, Shazia; Shahid Rafique, M.; Nathala, Chandra S. R.; Ajami, Ali; Husinsky, Wolfgang

    2015-05-01

    The effect of fluence and pulse duration on the growth of nanostructures on chromium (Cr) surfaces has been investigated upon irradiation of femtosecond (fs) laser pulses in a liquid confined environment of ethanol. In order to explore the effect of fluence, targets were exposed to 1000 pulses at various peak fluences ranging from 4.7 to 11.8 J cm-2 for pulse duration of ∼25 fs. In order to explore the effect of pulse duration, targets were exposed to fs laser pulses of various pulse durations ranging from 25 to 100 fs, for a constant fluence of 11.8 J cm-2. Surface morphology and structural transformations have been analyzed by scanning electron microscopy and Raman spectroscopy, respectively. After laser irradiation, disordered sputtered surface with intense melting and cracking is obtained at the central ablated areas, which are augmented with increasing laser fluence due to enhanced thermal effects. At the peripheral ablated areas, where local fluence is approximately in the range of 1.4-4 mJ cm-2, very well-defined laser-induced periodic surface structures (LIPSS) with periodicity ranging from 270 to 370 nm along with dot-like structures are formed. As far as the pulse duration is concerned, a significant effect on the surface modification of Cr has been revealed. In the central ablated areas, for the shortest pulse duration (25 fs), only melting has been observed. However, LIPSS with dot-like structures and droplets have been grown for longer pulse durations. The periodicity of LIPSS increases and density of dot-like structures decreases with increasing pulse duration. The chemical and structural modifications of irradiated Cr have been revealed by Raman spectroscopy. It confirms the formation of new bands of chromium oxides and enol complexes or Cr-carbonyl compounds. The peak intensities of identified bands are dependent upon laser fluence and pulse duration.

  17. Better Transitions for Troops: An Application of Schlossberg's Transition Framework to Analyses of Barriers and Institutional Support Structures for Student Veterans

    Science.gov (United States)

    Griffin, Kimberly A.; Gilbert, Claire K.

    2015-01-01

    Scholssberg's transition theory is used to frame qualitative analysis of narratives from veterans, administrators, and student affairs professionals, examining whether and how institutions can influence veterans' transitions to higher education. Findings suggest how institutional structures assist students in developing navigational…

  18. Social Network Analyses (SNA) as a method to study the structure of contacts within teams of a school for secondary education

    NARCIS (Netherlands)

    Meijs, Celeste; De Laat, Maarten

    2017-01-01

    This paper reports findings from a study using social network analysis techniques to understand social learning relationships within and between teacher teams in a large secondary school in the Netherlands (n=117 teachers). The findings suggest a relationship between the social structure of a team

  19. Analysis of structural heterogeneities on drilled cores: a reservoir modeling oriented methodology; Analyse des heterogeneites structurales sur carottes: une methodologie axee vers la modelisation des reservoirs

    Energy Technology Data Exchange (ETDEWEB)

    Cortes, P.; Petit, J.P. [Montpellier-2 Univ., Lab. de Geophysique, Tectonique et Sedimentologie, UMR CNRS 5573, 34 (France); Guy, L. [ELF Aquitaine Production, 64 - Pau (France); Thiry-Bastien, Ph. [Lyon-1 Univ., 69 (France)

    1999-07-01

    The characterization of structural heterogeneities of reservoirs is of prime importance for hydrocarbons recovery. A methodology is presented which allows to compare the dynamic behaviour of fractured reservoirs and the observation of microstructures on drilled cores or surface reservoir analogues. (J.S.)

  20. Detection of Differential Item Functioning on the Kirton Adaption-Innovation Inventory Using Multiple-Group Mean and Covariance Structure Analyses.

    Science.gov (United States)

    Chan, David

    2000-01-01

    Demonstrates how the mean and covariance structure analysis model of D. Sorbom (1974) can be used to detect uniform and nonuniform differential item functioning (DIF) on polytomous ordered response items assumed to approximate a continuous scale. Uses results from 773 civil service employees administered the Kirton Adaption-Innovation Inventory…

  1. The structure of post-traumatic stress symptoms in survivors of war: confirmatory factor analyses of the Impact of Event Scale—Revised

    NARCIS (Netherlands)

    Morina, N.; Böhme, H.F.; Ajdukovic, D.; Bogic, M.; Franciskovic, T.; Galeazzi, G.M.; Kucukalic, A.; Lecic-Tosevski, D.; Popovski, M.; Schützwohl, M.; Stangier, U.; Priebe, S.

    2010-01-01

    The study aimed at establishing the factor structure of the Impact of Event Scale—Revised (IES-R) in survivors of war. A total sample of 4167 participants with potentially traumatic experiences during the war in Ex-Yugoslavia was split into three samples: two independent samples of people who stayed

  2. Signal frequency distribution and natural-time analyses from acoustic emission monitoring of an arched structure in the Castle of Racconigi

    Directory of Open Access Journals (Sweden)

    G. Niccolini

    2017-07-01

    Full Text Available The stability of an arch as a structural element in the thermal bath of King Charles Albert (Carlo Alberto in the Royal Castle of Racconigi (on the UNESCO World Heritage List since 1997 was assessed by the acoustic emission (AE monitoring technique with application of classical inversion methods to recorded AE data. First, damage source location by means of triangulation techniques and signal frequency analysis were carried out. Then, the recently introduced method of natural-time analysis was preliminarily applied to the AE time series in order to reveal a possible entrance point to a critical state of the monitored structural element. Finally, possible influence of the local seismic and microseismic activity on the stability of the monitored structure was investigated. The criterion for selecting relevant earthquakes was based on the estimation of the size of earthquake preparation zones. The presented results suggest the use of the AE technique as a tool for detecting both ongoing structural damage processes and microseismic activity during preparation stages of seismic events.

  3. Signal frequency distribution and natural-time analyses from acoustic emission monitoring of an arched structure in the Castle of Racconigi

    Science.gov (United States)

    Niccolini, Gianni; Manuello, Amedeo; Marchis, Elena; Carpinteri, Alberto

    2017-07-01

    The stability of an arch as a structural element in the thermal bath of King Charles Albert (Carlo Alberto) in the Royal Castle of Racconigi (on the UNESCO World Heritage List since 1997) was assessed by the acoustic emission (AE) monitoring technique with application of classical inversion methods to recorded AE data. First, damage source location by means of triangulation techniques and signal frequency analysis were carried out. Then, the recently introduced method of natural-time analysis was preliminarily applied to the AE time series in order to reveal a possible entrance point to a critical state of the monitored structural element. Finally, possible influence of the local seismic and microseismic activity on the stability of the monitored structure was investigated. The criterion for selecting relevant earthquakes was based on the estimation of the size of earthquake preparation zones. The presented results suggest the use of the AE technique as a tool for detecting both ongoing structural damage processes and microseismic activity during preparation stages of seismic events.

  4. Extending Structural Analyses of the Rosenberg Self-Esteem Scale to Consider Criterion-Related Validity: Can Composite Self-Esteem Scores Be Good Enough?

    Science.gov (United States)

    Donnellan, M Brent; Ackerman, Robert A; Brecheen, Courtney

    2016-01-01

    Although the Rosenberg Self-Esteem Scale (RSES) is the most widely used measure of global self-esteem in the literature, there are ongoing disagreements about its factor structure. This methodological debate informs how the measure should be used in substantive research. Using a sample of 1,127 college students, we test the overall fit of previously specified models for the RSES, including a newly proposed bifactor solution (McKay, Boduszek, & Harvey, 2014 ). We extend previous work by evaluating how various latent factors from these structural models are related to a set of criterion variables frequently studied in the self-esteem literature. A strict unidimensional model poorly fit the data, whereas models that accounted for correlations between negatively and positively keyed items tended to fit better. However, global factors from viable structural models had similar levels of association with criterion variables and with the pattern of results obtained with a composite global self-esteem variable calculated from observed scores. Thus, we did not find compelling evidence that different structural models had substantive implications, thereby reducing (but not eliminating) concerns about the integrity of the self-esteem literature based on overall composite scores for the RSES.

  5. Crustal and upper mantle S-wave velocity structures across the Taiwan Strait from ambient seismic noise and teleseismic Rayleigh wave analyses

    Science.gov (United States)

    Huang, Y.; Yao, H.; Wu, F. T.; Liang, W.; Huang, B.; Lin, C.; Wen, K.

    2013-12-01

    Although orogeny seems to have stopped in western Taiwan large and small earthquakes do occur in the Taiwan Strait. Limited studies have focused on this region before and were barely within reach for comprehensive projects like TAICRUST and TAIGER for logistical reasons; thus, the overall crustal structures of the Taiwan Strait remain unknown. Time domain empirical Green's function (TDEGF) from ambient seismic noise to determine crustal velocity structure allows us to study an area using station pairs on its periphery. This research aims to resolve 1-D average crustal and upper mantle S-wave velocity (Vs) structures alone paths of several broadband station-pairs across the Taiwan Strait; 5-120 s Rayleigh wave phase velocity dispersion data derived by combining TDEGF and traditional surface wave two-station method (TS). The average Vs structures show significant differences in the upper 15 km as expected. In general, the highest Vs are observed in the coastal area of Mainland China and the lowest Vs appear along the southwest offshore of the Taiwan Island; they differ by about 0.6-1.1 km/s. For different parts of the Strait, the Vs are lower in the middle by about 0.1-0.2 km/s relative to those in the northern and southern parts. The overall crustal thickness is approximately 30 km, much thinner and less variable than under the Taiwan Island.

  6. Structural, biochemical, and phylogenetic analyses suggest that indole-3-acetic acid methyltransferase is an evolutionarily ancient member of the SABATH family.

    Science.gov (United States)

    Zhao, Nan; Ferrer, Jean-Luc; Ross, Jeannine; Guan, Ju; Yang, Yue; Pichersky, Eran; Noel, Joseph P; Chen, Feng

    2008-02-01

    The plant SABATH protein family encompasses a group of related small-molecule methyltransferases (MTs) that catalyze the S-adenosyl-L-methionine-dependent methylation of natural chemicals encompassing widely divergent structures. Indole-3-acetic acid (IAA) methyltransferase (IAMT) is a member of the SABATH family that modulates IAA homeostasis in plant tissues through methylation of IAA's free carboxyl group. The crystal structure of Arabidopsis (Arabidopsis thaliana) IAMT (AtIAMT1) was determined and refined to 2.75 A resolution. The overall tertiary and quaternary structures closely resemble the two-domain bilobed monomer and the dimeric arrangement, respectively, previously observed for the related salicylic acid carboxyl methyltransferase from Clarkia breweri (CbSAMT). To further our understanding of the biological function and evolution of SABATHs, especially of IAMT, we analyzed the SABATH gene family in the rice (Oryza sativa) genome. Forty-one OsSABATH genes were identified. Expression analysis showed that more than one-half of the OsSABATH genes were transcribed in one or multiple organs. The OsSABATH gene most similar to AtIAMT1 is OsSABATH4. Escherichia coli-expressed OsSABATH4 protein displayed the highest level of catalytic activity toward IAA and was therefore named OsIAMT1. OsIAMT1 exhibited kinetic properties similar to AtIAMT1 and poplar IAMT (PtIAMT1). Structural modeling of OsIAMT1 and PtIAMT1 using the experimentally determined structure of AtIAMT1 reported here as a template revealed conserved structural features of IAMTs within the active-site cavity that are divergent from functionally distinct members of the SABATH family, such as CbSAMT. Phylogenetic analysis revealed that IAMTs from Arabidopsis, rice, and poplar (Populus spp.) form a monophyletic group. Thus, structural, biochemical, and phylogenetic evidence supports the hypothesis that IAMT is an evolutionarily ancient member of the SABATH family likely to play a critical role in IAA

  7. Structural mapping of the coiled-coil domain of a bacterial condensin and comparative analyses across all domains of life suggest conserved features of SMC proteins.

    Science.gov (United States)

    Waldman, Vincent M; Stanage, Tyler H; Mims, Alexandra; Norden, Ian S; Oakley, Martha G

    2015-06-01

    The structural maintenance of chromosomes (SMC) proteins form the cores of multisubunit complexes that are required for the segregation and global organization of chromosomes in all domains of life. These proteins share a common domain structure in which N- and C- terminal regions pack against one another to form a globular ATPase domain. This "head" domain is connected to a central, globular, "hinge" or dimerization domain by a long, antiparallel coiled coil. To date, most efforts for structural characterization of SMC proteins have focused on the globular domains. Recently, however, we developed a method to map interstrand interactions in the 50-nm coiled-coil domain of MukB, the divergent SMC protein found in γ-proteobacteria. Here, we apply that technique to map the structure of the Bacillus subtilis SMC (BsSMC) coiled-coil domain. We find that, in contrast to the relatively complicated coiled-coil domain of MukB, the BsSMC domain is nearly continuous, with only two detectable coiled-coil interruptions. Near the middle of the domain is a break in coiled-coil structure in which there are three more residues on the C-terminal strand than on the N-terminal strand. Close to the head domain, there is a second break with a significantly longer insertion on the same strand. These results provide an experience base that allows an informed interpretation of the output of coiled-coil prediction algorithms for this family of proteins. A comparison of such predictions suggests that these coiled-coil deviations are highly conserved across SMC types in a wide variety of organisms, including humans. © 2015 Wiley Periodicals, Inc.

  8. Using Instrumental Neutron Activation Analysis for geochemical analyses of terrestrial impact structures: Current analytical procedures at the University of Vienna Geochemistry Activation Analysis Laboratory

    International Nuclear Information System (INIS)

    Mader, Dieter; Koeberl, Christian

    2009-01-01

    The Instrumental Neutron Activation Analysis Gamma Spectroscopy Laboratory at the Department of Lithospheric Research, University of Vienna, has been upgraded in the year 2006. This paper describes the sample preparation, new instrumentation and data evaluation for hundreds of rock samples of two terrestrial impact structures. The measurement and data evaluation are done by using Genie TM 2000 and a custom-made batch software for the used analysis sequences.

  9. Structure and microstructure of Ni-Mn-Ga single crystal exhibiting magnetic shape memory effect analysed by high resolution X-ray diffraction

    Czech Academy of Sciences Publication Activity Database

    Heczko, Oleg; Cejpek, P.; Drahokoupil, Jan; Holý, V.

    2016-01-01

    Roč. 115, Aug (2016), s. 250-258 ISSN 1359-6454 R&D Projects: GA ČR GA13-30397S; GA ČR GA15-00262S Institutional support: RVO:68378271 Keywords : magnetic field-induced strain * magnetic shape memory effect * X-ray diffraction * structure of Ni-Mn-Ga Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 5.301, year: 2016

  10. Comparative sequence, structure and redox analyses of Klebsiella pneumoniae DsbA show that anti-virulence target DsbA enzymes fall into distinct classes.

    Directory of Open Access Journals (Sweden)

    Fabian Kurth

    Full Text Available Bacterial DsbA enzymes catalyze oxidative folding of virulence factors, and have been identified as targets for antivirulence drugs. However, DsbA enzymes characterized to date exhibit a wide spectrum of redox properties and divergent structural features compared to the prototypical DsbA enzyme of Escherichia coli DsbA (EcDsbA. Nonetheless, sequence analysis shows that DsbAs are more highly conserved than their known substrate virulence factors, highlighting the potential to inhibit virulence across a range of organisms by targeting DsbA. For example, Salmonella enterica typhimurium (SeDsbA, 86 % sequence identity to EcDsbA shares almost identical structural, surface and redox properties. Using comparative sequence and structure analysis we predicted that five other bacterial DsbAs would share these properties. To confirm this, we characterized Klebsiella pneumoniae DsbA (KpDsbA, 81 % identity to EcDsbA. As expected, the redox properties, structure and surface features (from crystal and NMR data of KpDsbA were almost identical to those of EcDsbA and SeDsbA. Moreover, KpDsbA and EcDsbA bind peptides derived from their respective DsbBs with almost equal affinity, supporting the notion that compounds designed to inhibit EcDsbA will also inhibit KpDsbA. Taken together, our data show that DsbAs fall into different classes; that DsbAs within a class may be predicted by sequence analysis of binding loops; that DsbAs within a class are able to complement one another in vivo and that compounds designed to inhibit EcDsbA are likely to inhibit DsbAs within the same class.

  11. Realistic Features in Analysing the Effect of the Seismic Motion upon Localized Structures Considering Base Isolation Influence on Their Dynamic Behaviour

    Science.gov (United States)

    Apostol, Bogdan Felix; Florin Balan, Stefan; Ionescu, Constantin

    2017-12-01

    The effects of the earthquakes on buildings and the concept of seismic base isolation are investigated by using the model of the vibrating bar embedded at one end. The normal modes and the eigenfrequencies of the bar are highlighted and the amplification of the response due to the excitation of the normal modes (eigenmodes) is computed. The effect is much enhanced at resonance, for oscillating shocks which contain eigenfrequencies of the bar. Also, the response of two linearly joined bars with one end embedded is calculated. It is shown that for very different elastic properties the eigenfrequencies are due mainly to the “softer” bar. The effect of the base isolation in seismic structural engineering is assessed by formulating the model of coupled harmonic oscillators, as a simplified model for the structure building-foundation viewed as two coupled vibrating bars. The coupling decreases the lower eigenfrequencies of the structure and increases the higher ones. Similar amplification factors are derived for coupled oscillators at resonance with an oscillating shock.

  12. Insights into the potential function and membrane organization of the TP0435 (Tp17) lipoprotein from Treponema pallidum derived from structural and biophysical analyses.

    Science.gov (United States)

    Brautigam, Chad A; Deka, Ranjit K; Liu, Wei Z; Norgard, Michael V

    2015-01-01

    The sexually transmitted disease syphilis is caused by the bacterial spirochete Treponema pallidum. This microorganism is genetically intractable, accounting for the large number of putative and undercharacterized members of the pathogen's proteome. In an effort to ascribe a function(s) to the TP0435 (Tp17) lipoprotein, we engineered a soluble variant of the protein (rTP0435) and determined its crystal structure at a resolution of 2.42 Å. The structure is characterized by an eight-stranded β-barrel protein with a shallow "basin" at one end of the barrel and an α-helix stacked on the opposite end. Furthermore, there is a disulfide-linked dimer of the protein in the asymmetric unit of the crystals. Solution hydrodynamic experiments established that purified rTP0435 is monomeric, but specifically forms the disulfide-stabilized dimer observed in the crystal structure. The data herein, when considered with previous work on TP0435, imply plausible roles for the protein in either ligand binding, treponemal membrane architecture, and/or pathogenesis. © 2014 The Protein Society.

  13. Population genetic structure and approximate Bayesian computation analyses reveal the southern origin and northward dispersal of the oriental fruit moth Grapholita molesta (Lepidoptera: Tortricidae) in its native range.

    Science.gov (United States)

    Wei, Shu-Jun; Cao, Li-Jun; Gong, Ya-Jun; Shi, Bao-Cai; Wang, Su; Zhang, Fan; Guo, Xiao-Jun; Wang, Yuan-Min; Chen, Xue-Xin

    2015-08-01

    The oriental fruit moth (OFM) Grapholita molesta is one of the most destructive orchard pests. Assumed to be native to China, the moth is now distributed throughout the world. However, the evolutionary history of this moth in its native range remains unknown. In this study, we explored the population genetic structure, dispersal routes and demographic history of the OFM in China and South Korea based on mitochondrial genes and microsatellite loci. The Mantel test indicated a significant correlation between genetic distance and geographical distance in the populations. Bayesian analysis of population genetic structure (baps) identified four nested clusters, while the geneland analysis inferred five genetic groups with spatial discontinuities. Based on the approximate Bayesian computation approach, we found that the OFM was originated from southern China near the Shilin area of Yunnan Province. The early divergence and dispersal of this moth was dated to the Penultimate glaciation of Pleistocene. Further dispersal from southern to northern region of China occurred before the last glacial maximum, while the expansion of population size in the derived populations in northern region of China occurred after the last glacial maximum. Our results indicated that the current distribution and structure of the OFM were complicatedly influenced by climatic and geological events and human activities of cultivation and wide dissemination of peach in ancient China. We provide an example on revealing the origin and dispersal history of an agricultural pest insect in its native range as well as the underlying factors. © 2015 The Authors. Molecular Ecology Published by John Wiley & Sons Ltd.

  14. Electrochemical cycling effect on structural parameters and electron density of Li1-xNi0.5Mn1.5O4 using synchrotron X-ray analyses

    Science.gov (United States)

    Itoh, Takanori; Imai, Hideto

    2018-03-01

    We investigated the electrochemical cycling effects on the average, local, and electronic structures of 1st and 28th cycled Li1-xNi0.5Mn1.5O4 (LNMO) by Rietveld refinements, the maximum entropy method (MEM) for synchrotron X-ray, and X-ray absorption spectroscopy (XAS) using unexposed cathode materials. The results obtained with Rietveld refinements and XAS showed that the electrochemical cycling increases the transition metal valences, distorts the (Ni, Mn)-O6 octahedral, and decreases the Ni content in LNMO. Through MEM analyses we found that Li ions were stabilized by the electrochemical cycling. We also used synchrotron X-ray analyses to ascertain the correlation among specific capacity degradation, average and local structures, and the electron density before and after cycled LNMO.

  15. Canopy structure of tropical and sub-tropical rain forests in relation to conifer dominance analysed with a portable LIDAR system.

    Science.gov (United States)

    Aiba, Shin-ichiro; Akutsu, Kosuke; Onoda, Yusuke

    2013-12-01

    Globally, conifer dominance is restricted to nutient-poor habitats in colder, drier or waterlogged environments, probably due to competition with angiosperms. Analysis of canopy structure is important for understanding the mechanism of plant coexistence in relation to competition for light. Most conifers are shade intolerant, and often have narrow, deep, conical crowns. In this study it is predicted that conifer-admixed forests have less distinct upper canopies and more undulating canopy surfaces than angiosperm-dominated forests. By using a ground-based, portable light detection and ranging (LIDAR) system, canopy structure was quantified for old-growth evergreen rainforests with varying dominance of conifers along altitudinal gradients (200-3100 m a.s.l.) on tropical and sub-tropical mountains (Mount Kinabalu, Malaysian Borneo and Yakushima Island, Japan) that have different conifer floras. Conifers dominated at higher elevations on both mountains (Podocarpaceae and Araucariaceae on Kinabalu and Cupressaceae and Pinaceae on Yakushima), but conifer dominance also varied with soil/substrate conditions on Kinabalu. Conifer dominance was associated with the existence of large-diameter conifers. Forests with higher conifer dominance showed a canopy height profile (CHP) more skewed towards the understorey on both Kinabalu and Yakushima. In contrast, angiosperm-dominated forests had a CHP skewed towards upper canopy, except for lowland dipterocarp forests and a sub-alpine scrub dominated by small-leaved Leptospermum recurvum (Myrtaceae) on Kinabalu. Forests with a less dense upper canopy had more undulating outer canopy surfaces. Mixed conifer-angiosperm forests on Yakushima and dipterocarp forests on Kinabalu showed similar canopy structures. The results generally supported the prediction, suggesting that lower growth of angiosperm trees (except L. recurvum on Kinabalu) in cold and nutrient-poor environments results in a sparser upper canopy, which allows shade

  16. Structural and Biochemical Analyses Reveal the Mechanism of Glutathione S-Transferase Pi 1 Inhibition by the Anti-cancer Compound Piperlongumine.

    Science.gov (United States)

    Harshbarger, Wayne; Gondi, Sudershan; Ficarro, Scott B; Hunter, John; Udayakumar, Durga; Gurbani, Deepak; Singer, William D; Liu, Yan; Li, Lianbo; Marto, Jarrod A; Westover, Kenneth D

    2017-01-06

    Glutathione S-transferase pi 1 (GSTP1) is frequently overexpressed in cancerous tumors and is a putative target of the plant compound piperlongumine (PL), which contains two reactive olefins and inhibits proliferation in cancer cells but not normal cells. PL exposure of cancer cells results in increased reactive oxygen species and decreased GSH. These data in tandem with other information led to the conclusion that PL inhibits GSTP1, which forms covalent bonds between GSH and various electrophilic compounds, through covalent adduct formation at the C7-C8 olefin of PL, whereas the C2-C3 olefin of PL was postulated to react with GSH. However, direct evidence for this mechanism has been lacking. To investigate, we solved the X-ray crystal structure of GSTP1 bound to PL and GSH at 1.1 Å resolution to rationalize previously reported structure activity relationship studies. Surprisingly, the structure showed that a hydrolysis product of PL (hPL) was conjugated to glutathione at the C7-C8 olefin, and this complex was bound to the active site of GSTP1; no covalent bond formation between hPL and GSTP1 was observed. Mass spectrometry (MS) analysis of the reactions between PL and GSTP1 confirmed that PL does not label GSTP1. Moreover, MS data also indicated that nucleophilic attack on PL at the C2-C3 olefin led to PL hydrolysis. Although hPL inhibits GSTP1 enzymatic activity in vitro, treatment of cells susceptible to PL with hPL did not have significant anti-proliferative effects, suggesting that hPL is not membrane-permeable. Altogether, our data suggest a model wherein PL is a prodrug whose intracellular hydrolysis initiates the formation of the hPL-GSH conjugate, which blocks the active site of and inhibits GSTP1 and thereby cancer cell proliferation. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  17. Structural analyses of the CRISPR protein Csc2 reveal the RNA-binding interface of the type I-D Cas7 family.

    Science.gov (United States)

    Hrle, Ajla; Maier, Lisa-Katharina; Sharma, Kundan; Ebert, Judith; Basquin, Claire; Urlaub, Henning; Marchfelder, Anita; Conti, Elena

    2014-01-01

    Upon pathogen invasion, bacteria and archaea activate an RNA-interference-like mechanism termed CRISPR (clustered regularly interspaced short palindromic repeats). A large family of Cas (CRISPR-associated) proteins mediates the different stages of this sophisticated immune response. Bioinformatic studies have classified the Cas proteins into families, according to their sequences and respective functions. These range from the insertion of the foreign genetic elements into the host genome to the activation of the interference machinery as well as target degradation upon attack. Cas7 family proteins are central to the type I and type III interference machineries as they constitute the backbone of the large interference complexes. Here we report the crystal structure of Thermofilum pendens Csc2, a Cas7 family protein of type I-D. We found that Csc2 forms a core RRM-like domain, flanked by three peripheral insertion domains: a lid domain, a Zinc-binding domain and a helical domain. Comparison with other Cas7 family proteins reveals a set of similar structural features both in the core and in the peripheral domains, despite the absence of significant sequence similarity. T. pendens Csc2 binds single-stranded RNA in vitro in a sequence-independent manner. Using a crosslinking - mass-spectrometry approach, we mapped the RNA-binding surface to a positively charged surface patch on T. pendens Csc2. Thus our analysis of the key structural and functional features of T. pendens Csc2 highlights recurring themes and evolutionary relationships in type I and type III Cas proteins.

  18. Structural and mutational analyses of the receptor binding domain of botulinum D/C mosaic neurotoxin: Insight into the ganglioside binding mechanism

    Energy Technology Data Exchange (ETDEWEB)

    Nuemket, Nipawan [Graduate School of Life Sciences, Hokkaido University, Sapporo 060-0810 (Japan); Tanaka, Yoshikazu [Creative Research Institution ' Sousei,' Hokkaido University, Sapporo 001-0021 (Japan); Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0810 (Japan); Tsukamoto, Kentaro; Tsuji, Takao [Department of Microbiology, Fujita Health University School of Medicine, Toyoake, Aichi 470-1192 (Japan); Nakamura, Keiji; Kozaki, Shunji [Department of Veterinary Science, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Osaka 598-8531 (Japan); Yao, Min [Graduate School of Life Sciences, Hokkaido University, Sapporo 060-0810 (Japan); Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0810 (Japan); Tanaka, Isao, E-mail: tanaka@castor.sci.hokudai.ac.jp [Graduate School of Life Sciences, Hokkaido University, Sapporo 060-0810 (Japan); Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0810 (Japan)

    2011-07-29

    Highlights: {yields} We determined the crystal structure of the receptor binding domain of BoNT in complex with 3'-sialyllactose. {yields} An electron density derived from the 3'-sialyllactose was confirmed at the cleft in the C-terminal subdomain. {yields} Alanine site-directed mutagenesis showed that GBS and GBL are important for ganglioside binding. {yields} A cell binding mechanism, which involves cooperative contribution of two sites, was proposed. -- Abstract: Clostridium botulinum type D strain OFD05, which produces the D/C mosaic neurotoxin, was isolated from cattle killed by the recent botulism outbreak in Japan. The D/C mosaic neurotoxin is the most toxic of the botulinum neurotoxins (BoNT) characterized to date. Here, we determined the crystal structure of the receptor binding domain of BoNT from strain OFD05 in complex with 3'-sialyllactose at a resolution of 3.0 A. In the structure, an electron density derived from the 3'-sialyllactose was confirmed at the cleft in the C-terminal subdomain. Alanine site-directed mutagenesis showed the significant contribution of the residues surrounding the cleft to ganglioside recognition. In addition, a loop adjoining the cleft also plays an important role in ganglioside recognition. In contrast, little effect was observed when the residues located around the surface previously identified as the protein receptor binding site in other BoNTs were substituted. The results of cell binding analysis of the mutants were significantly correlated with the ganglioside binding properties. Based on these observations, a cell binding mechanism of BoNT from strain OFD05 is proposed, which involves cooperative contribution of two ganglioside binding sites.

  19. Structural and mutational analyses of the receptor binding domain of botulinum D/C mosaic neurotoxin: Insight into the ganglioside binding mechanism

    International Nuclear Information System (INIS)

    Nuemket, Nipawan; Tanaka, Yoshikazu; Tsukamoto, Kentaro; Tsuji, Takao; Nakamura, Keiji; Kozaki, Shunji; Yao, Min; Tanaka, Isao

    2011-01-01

    Highlights: → We determined the crystal structure of the receptor binding domain of BoNT in complex with 3'-sialyllactose. → An electron density derived from the 3'-sialyllactose was confirmed at the cleft in the C-terminal subdomain. → Alanine site-directed mutagenesis showed that GBS and GBL are important for ganglioside binding. → A cell binding mechanism, which involves cooperative contribution of two sites, was proposed. -- Abstract: Clostridium botulinum type D strain OFD05, which produces the D/C mosaic neurotoxin, was isolated from cattle killed by the recent botulism outbreak in Japan. The D/C mosaic neurotoxin is the most toxic of the botulinum neurotoxins (BoNT) characterized to date. Here, we determined the crystal structure of the receptor binding domain of BoNT from strain OFD05 in complex with 3'-sialyllactose at a resolution of 3.0 A. In the structure, an electron density derived from the 3'-sialyllactose was confirmed at the cleft in the C-terminal subdomain. Alanine site-directed mutagenesis showed the significant contribution of the residues surrounding the cleft to ganglioside recognition. In addition, a loop adjoining the cleft also plays an important role in ganglioside recognition. In contrast, little effect was observed when the residues located around the surface previously identified as the protein receptor binding site in other BoNTs were substituted. The results of cell binding analysis of the mutants were significantly correlated with the ganglioside binding properties. Based on these observations, a cell binding mechanism of BoNT from strain OFD05 is proposed, which involves cooperative contribution of two ganglioside binding sites.

  20. Preparation and structure investigation of novel Schiff bases using spectroscopic, thermal analyses and molecular orbital calculations and studying their biological activities

    Science.gov (United States)

    Zayed, Ehab M.; Zayed, M. A.; El-Desawy, M.

    2015-01-01

    Two novel Schiff's bases (EB1 and L1) as new macrocyclic compounds were prepared via condensation reactions between bisaldehyde (2,2‧-(ethane-1,2-diylbis(oxy))dibenzaldehyde): firstly with hydrazine carbothioamide to give (EB1), secondly with 4,6-diaminopyrimidine-2-thiol to give (L1). EB1 has a general formula C18H20N6O2S2 of mole mass = 416.520, and IUPAC name ((N,N‧Z,N,N‧E)-N,N‧-(((ethane1,2diylbis(oxy))bis(2,1phenylene))bis(methanylylidene))bis(1hydrazinylmethanethioamide). L1 has a general formula C20H16N4O2S of mole mass = 376.10; and IUPAC name 1,2-bis(2-vinylphenoxy)ethane4,6-diaminopyrimidine-2-thiol). The structures of the compounds obtained were characterized based on elemental analysis, FT-IR and 1H NMR spectra, mass, and thermogravimetric analysis (TG, DTG). The activation thermodynamic parameters, such as, ΔE*, ΔH*, ΔS* and ΔG* were calculated from the TG curves using Coats-Redfern method. It is important to investigate their structures to know the active groups and weak bond responsible for their biological activities. The obtained thermal (TA) and mass (MS) practical results are confirmed by semi-empirical MO-calculation using PM3 procedure, on the neutral and positively charged forms of these novel Schiff bases. Therefore, comparison between MS and TA helps in selection of the proper pathway representing the decomposition of these compounds to give indication about their structures and consequently their biological activities. Their biological activities have been tested in vitro against Escherichia coli, Proteus vulgaris, Bacillissubtilies and Staphylococcus aurous bacteria in order to assess their antimicrobial potential.

  1. Characterization of [4Fe-4S] Cluster Vibrations and Structure in Nitrogenase Fe Protein at Three Oxidation Levels via Combined NRVS, EXAFS and DFT Analyses

    Science.gov (United States)

    Mitra, Devrani; George, Simon J.; Guo, Yisong; Kamali, Saeed; Keable, Stephen; Peters, John W.; Pelmenschikov, Vladimir; Case, David A.; Cramer, Stephen P.

    2013-01-01

    Azotobacter vinelandii nitrogenase Fe protein (Av2) provides a rare opportunity to investigate a [4Fe-4S] cluster at three oxidation levels in the same protein environment. Here, we report the structural and vibrational changes of this cluster upon reduction using a combination of NRVS and EXAFS spectroscopies and DFT calculations. Key to this work is the synergy between these three techniques as each generates highly complementary information and their analytical methodologies are interdependent. Importantly, the spectroscopic samples contained no glassing agents. NRVS and DFT reveal a systematic 10-30 cm−1 decrease in Fe-S stretching frequencies with each added electron. The “oxidized” [4Fe-4S]2+ state spectrum is consistent with and extends previous resonance Raman spectra. For the “reduced” [4Fe-4S]1+ state in Fe protein, and for any “all-ferrous” [4Fe-4S]0 cluster, these NRVS spectra are the first available vibrational data. NRVS simulations also allow estimation of the vibrational disorder for Fe-S and Fe-Fe distances, constraining the EXAFS analysis and allowing structural disorder to be estimated. For oxidized Av2, EXAFS and DFT indicate nearly equal Fe-Fe distances, while addition of one electron decreases the cluster symmetry. However, addition of the second electron to form the all-ferrous state induces significant structural change. EXAFS data recorded to k = 21 Å−1 indicates a 1:1 ratio of Fe-Fe interactions at 2.56 Å and 2.75 Å, a result consistent with DFT. Broken symmetry (BS) DFT rationalizes the interplay between redox state and the Fe-S and Fe-Fe distances as predominantly spin-dependent behavior inherent to the [4Fe-4S] cluster and perturbed by the Av2 protein environment. PMID:23282058

  2. Quartz: structural and thermodynamic analyses across the α ↔ β transition with origin of negative thermal expansion (NTE) in β quartz and calcite

    Energy Technology Data Exchange (ETDEWEB)

    Antao, Sytle M.

    2016-04-01

    The temperature variation,T, of the crystal structure of quartz, SiO2, from 298 to 1235 K was obtained with synchrotron powder X-ray diffraction data and Rietveld structure refinements. The polymorphic transformation fromP3221 (low-T, α quartz) toP6222 (high-T, β quartz) occurs at a transition temperature,Ttr= 847 K. TheTvariations of spontaneous strains and several structural parameters are fitted to an order parameter,Q, using Landau theory. The change in Si atom coordinate, Six, givesTtr-Tc= 0.49 K, which indicates an α ↔ β transition that is weakly first order and nearly tricritical in character (Q4T). Strains give higherTtr-Tcvalues (≃ 7 K). Other fitted parameters are the oxygen Ozcoordinate, Si—Si distance, Si—O—Si and φ angles, and intensity of the (111) reflection,I111. In α quartz, the Si—Si distance increases withTbecause of cation repulsion, so the Si—O—Si angle increases (and φ decreases) and causes the thermal expansion of the framework structure that consists of corner-sharing distorted rigid SiO4tetrahedra. The Si—Si distances contract withTand cause negative thermal expansion (NTE) in β quartz because of increasing thermal librations of the O atom in the Si—O—Si linkage that occur nearly perpendicular to the Si—Si contraction. In calcite, CaCO3, the short Ca—Ca distance expands withT, but the next-nearest Ca—Ca distance, which is of equal length to theaaxis, contracts withTand causes NTE along

  3. Size Matters: Assessing Optimum Soil Sample Size for Fungal and Bacterial Community Structure Analyses Using High Throughput Sequencing of rRNA Gene Amplicons

    Directory of Open Access Journals (Sweden)

    Christopher Ryan Penton

    2016-06-01

    Full Text Available We examined the effect of different soil sample sizes obtained from an agricultural field, under a single cropping system uniform in soil properties and aboveground crop responses, on bacterial and fungal community structure and microbial diversity indices. DNA extracted from soil sample sizes of 0.25, 1, 5 and 10 g using MoBIO kits and from 10 and 100 g sizes using a bead-beating method (SARDI were used as templates for high-throughput sequencing of 16S and 28S rRNA gene amplicons for bacteria and fungi, respectively, on the Illumina MiSeq and Roche 454 platforms. Sample size significantly affected overall bacterial and fungal community structure, replicate dispersion and the number of operational taxonomic units (OTUs retrieved. Richness, evenness and diversity were also significantly affected. The largest diversity estimates were always associated with the 10 g MoBIO extractions with a corresponding reduction in replicate dispersion. For the fungal data, smaller MoBIO extractions identified more unclassified Eukaryota incertae sedis and unclassified glomeromycota while the SARDI method retrieved more abundant OTUs containing unclassified Pleosporales and the fungal genera Alternaria and Cercophora. Overall, these findings indicate that a 10 g soil DNA extraction is most suitable for both soil bacterial and fungal communities for retrieving optimal diversity while still capturing rarer taxa in concert with decreasing replicate variation.

  4. Network class superposition analyses.

    Directory of Open Access Journals (Sweden)

    Carl A B Pearson

    Full Text Available Networks are often used to understand a whole system by modeling the interactions among its pieces. Examples include biomolecules in a cell interacting to provide some primary function, or species in an environment forming a stable community. However, these interactions are often unknown; instead, the pieces' dynamic states are known, and network structure must be inferred. Because observed function may be explained by many different networks (e.g., ≈ 10(30 for the yeast cell cycle process, considering dynamics beyond this primary function means picking a single network or suitable sample: measuring over all networks exhibiting the primary function is computationally infeasible. We circumvent that obstacle by calculating the network class ensemble. We represent the ensemble by a stochastic matrix T, which is a transition-by-transition superposition of the system dynamics for each member of the class. We present concrete results for T derived from boolean time series dynamics on networks obeying the Strong Inhibition rule, by applying T to several traditional questions about network dynamics. We show that the distribution of the number of point attractors can be accurately estimated with T. We show how to generate Derrida plots based on T. We show that T-based Shannon entropy outperforms other methods at selecting experiments to further narrow the network structure. We also outline an experimental test of predictions based on T. We motivate all of these results in terms of a popular molecular biology boolean network model for the yeast cell cycle, but the methods and analyses we introduce are general. We conclude with open questions for T, for example, application to other models, computational considerations when scaling up to larger systems, and other potential analyses.

  5. Effect of Synthesis Temperature on the Growth Iron-Filled Carbon Nanotubes as Evidenced by Structural, Micro-Raman, and Thermogravimetric Analyses

    Directory of Open Access Journals (Sweden)

    M. S. Shamsudin

    2012-01-01

    Full Text Available Tubular structure and well dense of aligned carbon nanotubes (CNTs were formulated using two-stage catalytic chemical vapor deposition apparatus. In this experiment, aligned CNT was synthesized in the range of 700–900°C temperatures with increment rate of 50°C per sample. The aligned CNT properties were investigated via field emission scanning electron microscope, micro-Raman spectrometer and thermogravimetric analyzer. The experimental results showed that aligned CNT properties were highly dependent on synthesis temperature changes. The optimum temperature of higher crystallinity was observed at 800°C synthesis temperature. However, the highest yield of nanotubes (~99.99% was obtained at 900°C synthesis temperature. Aligned CNT orientation was in a parallel form and packed together in orderly manner. The behaviors of aligned CNT will be discussed in detail in this paper.

  6. Structural and biochemical analyses reveal insights into covalent flavinylation of the Escherichia coli Complex II homolog quinol:fumarate reductase

    Energy Technology Data Exchange (ETDEWEB)

    Starbird, C.A.; Maklashina, Elena; Sharma, Pankaj; Qualls-Histed, Susan; Cecchini, Gary; Iverson, T.M. (VA); (UCSF); (Vanderbilt)

    2017-06-14

    The Escherichia coli Complex II homolog quinol:fumarate reductase (QFR, FrdABCD) catalyzes the interconversion of fumarate and succinate at a covalently attached FAD within the FrdA subunit. The SdhE assembly factor enhances covalent flavinylation of Complex II homologs, but the mechanisms underlying the covalent attachment of FAD remain to be fully elucidated. Here, we explored the mechanisms of covalent flavinylation of the E. coli QFR FrdA subunit. Using a ΔsdhE E. coli strain, we show that the requirement for the assembly factor depends on the cellular redox environment. We next identified residues important for the covalent attachment and selected the FrdAE245 residue, which contributes to proton shuttling during fumarate reduction, for detailed biophysical and structural characterization. We found that QFR complexes containing FrdAE245Q have a structure similar to that of the WT flavoprotein, but lack detectable substrate binding and turnover. In the context of the isolated FrdA subunit, the anticipated assembly intermediate during covalent flavinylation, FrdAE245 variants had stability similar to that of WT FrdA, contained noncovalent FAD, and displayed a reduced capacity to interact with SdhE. However, small-angle X-ray scattering (SAXS) analysis of WT FrdA cross-linked to SdhE suggested that the FrdAE245 residue is unlikely to contribute directly to the FrdA-SdhE protein-protein interface. We also found that no auxiliary factor is absolutely required for flavinylation, indicating that the covalent flavinylation is autocatalytic. We propose that multiple factors, including the SdhE assembly factor and bound dicarboxylates, stimulate covalent flavinylation by preorganizing the active site to stabilize the quinone-methide intermediate.

  7. Analysing the Structural Effect of Point Mutations of Cytotoxic Necrotizing Factor 1 (CNF1 on Lu/BCAM Adhesion Glycoprotein Association

    Directory of Open Access Journals (Sweden)

    Alexandre G. de Brevern

    2018-03-01

    Full Text Available Cytotoxic Necrotizing Factor 1 (CNF1 was identified in 1983 as a protein toxin produced by certain pathogenic strains of Escherichia coli. Since then, numerous studies have investigated its particularities. For instance, it is associated with the single chain AB-toxin family, and can be divided into different functional and structural domains, e.g., catalytic and transmembrane domain and interaction sites. A few years ago, the identification of the Lutheran (Lu adhesion glycoprotein/basal cell adhesion molecule (BCAM as a cellular receptor for CNF1 provided new insights into the adhesion process of CNF1. Very recently, the Ig-like domain 2 of Lu/BCAM was confirmed as the main interaction site using protein-protein interaction and competition studies with various different mutants. Here, I present in silico approaches that precisely explain the impact of these mutations, leading to a better explanation of these experimental studies. These results can be used in the development of future antitoxin strategies.

  8. Structural and spectroscopic analyses of copper doped P2O5 -ZnO-K2O-Bi2O3 glasses

    Directory of Open Access Journals (Sweden)

    Yahia H. Elbashar

    2015-09-01

    Full Text Available Homogeneous glass samples with different compositions 42 (P2O5·40 (ZnO·(16 −x(K2O·2 (Bi2O3·x(Cu2O (where x = 1, 2 and 3 mol% were prepared by conventional melt-quenched technique under controlled conditions. The structure of the prepared glass samples was investigated by X-ray diffraction. Optical properties (transmittance and reflectance of the glasses were measured in the wavelength range 200–900 nm. The optical band gap energy of the investigated glasses with 1, 2 and 3 mol% Cu2O was estimated from absorption data using the Mott and Davis relation and found to be 2.33, 2.45 and 2.53 eV, respectively. The mechanism of optical absorption was found to be direct. The band tail width was also estimated and found to lay in the acceptable range. Refractive index, absorption coefficient, extinction coefficient and real/imaginary parts of dielectric constants were calculated. Further to this, some theoretical investigation of the spectral problems was carried out. The investigation was based on finite difference method.

  9. Late-Miocene thrust fault-related folding in the northern Tibetan Plateau: Insight from paleomagnetic and structural analyses of the Kumkol basin

    Science.gov (United States)

    Lu, Haijian; Fu, Bihong; Shi, Pilong; Xue, Guoliang; Li, Haibing

    2018-05-01

    Constraints on the timing and style of the Tibetan Plateau growth help spur new understanding of the tectonic evolution of the northern Tibetan Plateau and its relation to the India-Asia continental collision. In this regard, records of tectonic deformation with accurate ages are urgently needed, especially in regions without relevant studies. The Kumkol basin, located between two major intermontane basins (the Hoh Xil and Qaidam basins), may hold clues to how these major basins evolve during the Cenozoic. However, little has been known about the exact ages of the strata and tectonic deformation of the basin. Herein, detailed paleomagnetic and structural studies are conducted on the southern Baiquanhe section in the central Kumkol basin, northern Tibetan Plateau. The magnetostratigraphic study indicates that the southern Baiquanhe section spans a time interval of 8.2-4.2 Ma. Well-preserved growth strata date to 7.5 Ma, providing evidence for a significant thrust fault-related folding. This thrust-related folding has also been identified in the Tian Shan foreland and in the northern Tibetan Plateau, most likely implying a pulsed basinward deformation during the late Miocene.

  10. Tem analyses of the local crystal and domain structures in (Na(1-x)K(x))0.5Bi(0.5)TiO3 perovskite ceramics.

    Science.gov (United States)

    Otonicar, Mojca; Skapin, Sreco D; Jancar, Bostjan

    2011-09-01

    The local crystal and domain structures of the ((Na(1-x)K(x))(0.5)Bi(0.5)TiO(3) (NBT-KBT) solid solutions were studied because of their influence on the enhanced electromechanical properties of ceramics. Based on X-ray diffraction, the morphotropic phase boundary (MPB) was determined for the composition x = 0.20, in which the rhombohedral and the tetragonal structures were observed to coexist. However, detailed domain-structure analyses using transmission electron microscopy (TEM), performed on the NBT, KBT, and five NBT-KBT solid-solution compositions, revealed some structural changes at/near the MPB. In the samples on the tetragonal side of the MPB, the grains showed a lamellar domain structure with 90° orientations of the individual domains, separated by straight domain boundaries, i.e., (011)/(101) twin planes. The rhombohedral samples on the other side of the MPB showed a typical square-net pattern with needle-like or lamellar ~71°/109° rhombohedral domains with (001) and/or (110) twin planes separating the individual domains. The domain structure at the MPB showed well-defined lamellar domains. Based on the occurrence of the superstructure reflections in the SAED patterns of various crystallographic zones, on the characteristic splitting of the reflections, and on the domain morphology observations, the crystal structure in/near the boundary region was determined to be a tetragonal structure with an in-phase oxygen octahedral tilt system (probably a(0)a(0)c(+)). It is suggested that the tetragonal polar order is partly induced from the rhombohedral structure at the MPB as a result of mechanical loading during TEM sample preparation.

  11. Mechanical and deformation analyses of pile foundation for supporting structure of off-shore wind turbine at Changhua coast in Taiwan

    Science.gov (United States)

    Wang, W. C.; Lin, D. G.

    2015-12-01

    This study investigates the bearing capacities and mechanical behaviors of pile foundation installed on the seabed of wind farm near Chang-Hua coast of western Taiwan for the supporting structure of offshore wind turbine. A series of three-dimensional (3-D) numerical modeling of pile foundation subjected to various types of combined loading were carried out using Plaix-3D finite element program to investigate the interactive behaviors between soil and pile. In the numerical modeling, pile diameter, pile length and pile spacing were selected as design parameters to inspect their effects on the bearing capacities and deformation behaviors of the pile foundation. For a specific design parameter combination, one can obtain the corresponding loading-displacement curve, various ultimate bearing capacities, V-H (Vertical-Horizontal combined loading) ultimate bearing capacity envelope, and p-ycurve of pile foundation. Numerical results indicate that: (1) Large displacement and plastic points at ultimate state mostly distribute and concentrate in the topsoil of seabed and around pile head. (2) The soil resistance on the soil-pile interface is ascending with the increases of depth, pile diameter and pile length. (3) The vertical and horizontal bearing capacities of pile group increase significantly with the increase of pile diameter. (4) The vertical and bending moment capacities of pile group increase greatly with the increase of pile length whereas the horizontal capacity is almost insensitive to pile length. (5) The bending moment of pile is highly influenced by the pile spacing. (6) For different design parameters, the shape of ultimate bearing capacity envelopes of pile group on V-H plane is similar while the envelopes will expand as the design parameters increase. For different loading levels of bending moment, the envelopes on V-H plane will contract gradually as the bending moment loading increasing.

  12. Investigating population structure of Sea Lamprey (Petromyzon marinus, L.) in Western Iberian Peninsula using morphological characters and heart fatty acid signature analyses.

    Science.gov (United States)

    Lança, Maria João; Machado, Maria; Mateus, Catarina S; Lourenço, Marta; Ferreira, Ana F; Quintella, Bernardo R; Almeida, Pedro R

    2014-01-01

    This study hypothesizes the existence of three groups of sea lamprey Petromyzon marinus L. in Portugal (North/Central group, Tagus group, and Guadiana group), possibly promoted by seabed topography isolation during the oceanic phase of the life cycle. Within this context, our purpose was to analyze the existence of a stock structure on sea lamprey populations sampled in the major Portuguese river basins using both morphological characters and heart tissue fatty acid signature. In both cases, the multiple discriminant analysis revealed statistically significant differences among groups, and the overall corrected classification rate estimated from cross-validation procedure was particularly high for the cardiac muscle fatty acid profiles (i.e. 83.8%). Morphometric characters were much more useful than meristic ones to discriminate stocks, and the most important variables for group differentiation were eye length, second dorsal fin length and branchial length. Fatty acid analysis showed that all lampreys from the southern Guadiana group were correctly classified and not mixing with individuals from any other group, reflecting a typical heart fatty acid signature. Our results revealed that 89.5% and 72.2% of the individuals from the Tagus and North/Central groups, respectively, were also correctly classified, despite some degree of overlap between individuals from these groups. The fatty acids that contributed to the observed segregation were C16:0; C17:0; C18:1ω9; C20:3ω6 and C22:2ω6. Detected differences are probably related with environmental variables to which lampreys may have been exposed, which leaded to different patterns of gene expression. These results suggest the existence of three different sea lamprey stocks in Portugal, with implication in terms of management and conservation.

  13. Investigating population structure of Sea Lamprey (Petromyzon marinus, L. in Western Iberian Peninsula using morphological characters and heart fatty acid signature analyses.

    Directory of Open Access Journals (Sweden)

    Maria João Lança

    Full Text Available This study hypothesizes the existence of three groups of sea lamprey Petromyzon marinus L. in Portugal (North/Central group, Tagus group, and Guadiana group, possibly promoted by seabed topography isolation during the oceanic phase of the life cycle. Within this context, our purpose was to analyze the existence of a stock structure on sea lamprey populations sampled in the major Portuguese river basins using both morphological characters and heart tissue fatty acid signature. In both cases, the multiple discriminant analysis revealed statistically significant differences among groups, and the overall corrected classification rate estimated from cross-validation procedure was particularly high for the cardiac muscle fatty acid profiles (i.e. 83.8%. Morphometric characters were much more useful than meristic ones to discriminate stocks, and the most important variables for group differentiation were eye length, second dorsal fin length and branchial length. Fatty acid analysis showed that all lampreys from the southern Guadiana group were correctly classified and not mixing with individuals from any other group, reflecting a typical heart fatty acid signature. Our results revealed that 89.5% and 72.2% of the individuals from the Tagus and North/Central groups, respectively, were also correctly classified, despite some degree of overlap between individuals from these groups. The fatty acids that contributed to the observed segregation were C16:0; C17:0; C18:1ω9; C20:3ω6 and C22:2ω6. Detected differences are probably related with environmental variables to which lampreys may have been exposed, which leaded to different patterns of gene expression. These results suggest the existence of three different sea lamprey stocks in Portugal, with implication in terms of management and conservation.

  14. Toward the bioremediation of dioxin-polluted soil: structural and functional analyses of in situ microbial populations by quinone profiling and culture-dependent methods.

    Science.gov (United States)

    Hiraishi, A; Miyakoda, H; Lim, B R; Hu, H Y; Fujie, K; Suzuki, J

    2001-10-01

    In order to obtain basic information toward the bioremediation of dioxin-polluted soil, microbial communities in farmland soils polluted with high concentrations of polychlorinated dibenzo-p-dioxins (PCDDs) and polychlorinated dibenzofurans (PCDFs) were studied by quinone profiling as well as conventional microbiological methods. The concentration of PCDD/Fs in the polluted soils ranged from 36 to 4,980 pg toxicity equivalent quality (TEQ) g(-1) dry weight of soil. There was an inverse relationship between the levels of PCDD/Fs and microbial biomass as measured by direct cell counting and quinone profiling. The most abundant quinone type detected was either MK-6 or Q-10. In addition, MK-8, MK-8(H2), and MK-9(H8) were detected in significant amounts. Numerical analysis of quinone profiles showed that the heavily polluted soils (> or = 1,430 pg TEQ g(-1)) contained different community structures from lightly polluted soils (polluted soils with dibenzofuran or 2-chlorodibenzofuran resulted in enrichment of Q-10-containing bacteria. When the heavily polluted soil was incubated in static bottles with autoclaved compost as an organic nutrient additive, the concentrations of PCDD/Fs in the soil were decreased by 22% after 3 months of incubation. These results indicate that dioxin pollution exerted a significant effect on microbial populations in soil in terms of quantity, quality, and activity. The in situ microbial populations in the dioxin-polluted soil were suggested to have a potential for the transformation of PCDD/Fs and oxidative degradation of the lower chlorinated ones thus produced.

  15. Structure-function analyses of a pertussis-like toxin from pathogenicEscherichia colireveal a distinct mechanism of inhibition of trimeric G-proteins.

    Science.gov (United States)

    Littler, Dene R; Ang, Sheng Y; Moriel, Danilo G; Kocan, Martina; Kleifeld, Oded; Johnson, Matthew D; Tran, Mai T; Paton, Adrienne W; Paton, James C; Summers, Roger J; Schembri, Mark A; Rossjohn, Jamie; Beddoe, Travis

    2017-09-08

    Pertussis-like toxins are secreted by several bacterial pathogens during infection. They belong to the AB 5 virulence factors, which bind to glycans on host cell membranes for internalization. Host cell recognition and internalization are mediated by toxin B subunits sharing a unique pentameric ring-like assembly. Although the role of pertussis toxin in whooping cough is well-established, pertussis-like toxins produced by other bacteria are less studied, and their mechanisms of action are unclear. Here, we report that some extra-intestinal Escherichia coli pathogens ( i.e. those that reside in the gut but can spread to other bodily locations) encode a pertussis-like toxin that inhibits mammalian cell growth in vitro We found that this protein, Ec Plt, is related to toxins produced by both nontyphoidal and typhoidal Salmonella serovars. Pertussis-like toxins are secreted as disulfide-bonded heterohexamers in which the catalytic ADP-ribosyltransferase subunit is activated when exposed to the reducing environment in mammalian cells. We found here that the reduced Ec Plt exhibits large structural rearrangements associated with its activation. We noted that inhibitory residues tethered within the NAD + -binding site by an intramolecular disulfide in the oxidized state dissociate upon the reduction and enable loop restructuring to form the nucleotide-binding site. Surprisingly, although pertussis toxin targets a cysteine residue within the α subunit of inhibitory trimeric G-proteins, we observed that activated Ec Plt toxin modifies a proximal lysine/asparagine residue instead. In conclusion, our results reveal the molecular mechanism underpinning activation of pertussis-like toxins, and we also identified differences in host target specificity. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  16. Infrared and X-ray Absorption Near Edge Structure Spectroscopy Analyses of the Titan Haze Simulation (THS) Aerosols Produced at Low Temperature (200 K)

    Science.gov (United States)

    Sciamma-O'Brien, Ella; Salama, Farid

    2016-10-01

    We present our latest results on the Titan Haze Simulation (THS) experiment developed on the COSmIC simulation chamber at NASA Ames. In Titan's atmosphere, a complex organic chemistry induced by UV radiation and electron bombardment occurs between N2 and CH4 and leads to the production of larger molecules and solid aerosols. In the THS, Titan's chemistry is simulated by pulsed plasma in the stream of a supersonic expansion, at Titan-like temperature (200 K). The residence time of the gas in the pulsed plasma discharge is ~3 µs, hence the chemistry is truncated allowing us to probe the first and intermediate steps of the chemistry, by adding heavier precursors into the initial N2-CH4 gas mixture. Experiments have been performed in different gas mixtures from the simpler N2-CH4 (98:2 and 95:5), to more complex mixtures: N2-CH4-C2H2 (91:5:4 and 94.5:5:0.5), N2-CH4-C6H6 (90:5:5) and N2-CH4-C2H2-C6H6 (86:5:4:5). Both the gas and solid phases have been analyzed using a combination of in situ and ex situ diagnostics.A recent mass spectrometry analysis of the gas phase demonstrated that the THS is a unique tool to monitor the different steps of the N2-CH4 chemistry [1]. The results of the solid phase study are consistent with the chemical growth evolution observed in the gas phase. The solid phase products are in the form of grains produced in volume and not from interaction on the substrate's surface. Scanning Electron Microscopy images have shown that more complex mixtures produce larger aggregates (100-500 nm in N2-CH4, up to 5 µm in N2-CH4-C2H2-C6H6). Moreover, the morphology of the grains seems to depend on the precursors, a finding that could have an impact on Titan haze microphysical models. We will present the latest results of the infrared and x-ray absorption near edge structure spectroscopic measurements that have been performed on all four mixtures. These results provide information on the nature of the different functional groups present in our samples as

  17. Structural and Spectroscopic Characterization of 17- and 18-Electron Piano-Stool Complexes of Chromium. Thermochemical Analyses of Weak Cr–H Bonds

    Energy Technology Data Exchange (ETDEWEB)

    van der Eide, Edwin F.; Helm, Monte L.; Walter, Eric D.; Bullock, R. Morris

    2013-02-04

    The 17-electron radical CpCr(CO)2(IMe)• (IMe = 1,3-dimethylimidazol-2-ylidene) was synthesized by the reaction of IMe with [CpCr(CO)3]2, and characterized by single crystal X-ray diffraction and by EPR, IR and variable temperature 1H NMR spectroscopy. The metal-centered radical is monomeric under all conditions and exhibits Curie paramagnetic behavior in solution. An electrochemically reversible reduction to 18-electron CpCr(CO)2(IMe)- takes place at E½ = -1.89(1) V vs Cp2Fe+•/0 in MeCN, and was accomplished chemically with KC8 in THF. The salts K+(18-crown-6)[CpCr(CO)2(IMe)]- • ½THF and K+[CpCr(CO)2(IMe)]- • ¾THF were crystallographically characterized. Monomeric ion pairs are found in the former, whereas the latter has a polymeric structure due to a network of K∙∙∙O(CO) interactions. Protonation of K+(18-crown-6)[CpCr(CO)2(IMe)]- • ½THF gives the hydride CpCr(CO)2(IMe)H, which could not be isolated, but was characterized in solution; a pKa of 27.2(4) was determined in MeCN. A thermochemical analysis provides the Cr-H bond dissociation free energy (BDFE) for CpCr(CO)2(IMe)H in MeCN solution as 47.3(6) kcal mol-1. This value is exceptionally low for a transition metal hydride, and implies that the reaction 2 [Cr-H] → 2 [Cr•] + H2 is exergonic (ΔG = -9.0(8) kcal mol-1). This analysis explains the experimental observation that generated solutions of the hydride produce CpCr(CO)2(IMe)• (typically on the timescale of days). By contrast, CpCr(CO)2(PCy3)H has a higher Cr-H BDFE (52.9(4) kcal mol-1), is more stable with respect to H2 loss, and is isolable. We thank the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences and Biosciences for support. M.L.H. carried out the crystallographic studies and was supported as part of the Center for Molecular Electrocatalysis, an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science, Office of Basic

  18. A structural basis for LCMV immune evasion: subversion of H-2D(b) and H-2K(b) presentation of gp33 revealed by comparative crystal structure.Analyses.

    Science.gov (United States)

    Achour, Adnane; Michaëlsson, Jakob; Harris, Robert A; Odeberg, Jacob; Grufman, Per; Sandberg, Johan K; Levitsky, Victor; Kärre, Klas; Sandalova, Tatyana; Schneider, Gunter

    2002-12-01

    LCMV infection of H-2(b) mice generates a CD8(+) CTL response mainly directed toward three immunodominant epitopes. One of these, gp33, is presented by both H-2D(b) and H-2K(b) MHC class I molecules. The virus can escape immune recognition in the context of both these MHC class I molecules through single mutations of the peptide. In order to understand the underlying structural mechanism, we determined the crystal structures of both complexes. The structures reveal that the peptide is presented in two diametrically opposed manners by H-2D(b) and H-2K(b), with residues used as anchor positions in one MHC class I molecule interacting with the TCR in the other. Importantly, the peptide's N-terminal residue p1K protrudes from the binding cleft in H-2K(b). We present structural evidence that explains the functional consequences of single mutations found in escape variants.

  19. Analysis of self-organized In(Ga)As quantum structures with the scanning transmission electron microscope; Analyse selbstorganisierter In(Ga)As-Quantenstrukturen mit dem Raster-Transmissionselektronenmikroskop

    Energy Technology Data Exchange (ETDEWEB)

    Sauerwald, Andres

    2008-05-27

    Aim of this thesis was to apply the analytical methods of the scanning transmission electron microscopy to the study of self-organized In(Ga)As quantum structures. With the imaging methods Z contrast and bright field (position resolutions in the subnanometer range) and especially with the possibilities of the quantitative chemical EELS analysis of the scanning transmission electron microscope (STEM) fundamental questions concerning morphology and chemical properties of self-organized quantum structures should be answered. By the high position resolution of the STEM among others essentail morphological and structural parameters in the growth behaviour of 'dot in a well' (DWell) structures and of vertically correlated quantum dots (QDs) could be analyzed. For the optimization of DWell structures samples were studied, the nominal InAs-QD growth position was directedly varied within the embedding InGaAs quantum wells. The STEM offers in connection with the EELS method a large potential for the chemical analysis of quantum structures. Studied was a sample series of self-organized InGaAs/GaAs structures on GaAs substrate, the stress of which was changed by varying the Ga content of the INGaAs material between 2.4 % and 4.3 %. [German] Ziel dieser Arbeit war es, die analytischen Methoden der Raster-Transmissionselektronenmikroskopie zur Untersuchung selbstorganisierter In(Ga)As-Quantenstrukturen anzuwenden. Mit den abbildenden Methoden Z-Kontrast und Hellfeld (Ortsaufloesungen im Subnanometerbereich) und insbesondere mit den Moeglichkeiten der quantitativen chemischen EELS-Analyse des Raster-Transmissionselektronenmikroskops (RTEMs) sollten grundsaetzliche Fragestellungen hinsichtlich der Morphologie und der chemischen Eigenschaften selbstorganisierter Quantenstrukturen beantwortet werden. Durch die hohe Ortsaufloesung des RTEMs konnten u.a. essentielle morphologische und strukturelle Parameter im Wachstumsverhalten von 'Dot in a Well

  20. Click one pot synthesis, spectral analyses, crystal structures, DFT studies and brine shrimp cytotoxicity assay of two newly synthesized 1,4,5-trisubstituted 1,2,3-triazoles

    Science.gov (United States)

    Ahmed, Muhammad Naeem; Yasin, Khawaja Ansar; Ayub, Khurshid; Mahmood, Tariq; Tahir, M. Nawaz; Khan, Bilal Ahmad; Hafeez, Muhammad; Ahmed, Madiha; ul-Haq, Ihsan

    2016-02-01

    Methyl-2-(1-benzyl-4-phenyl-1H-1,2,3-triazol-5-yl)-2-oxoacetate (1) and ethyl-2-(1-benzyl-4-phenyl-1H-1,2,3-triazol-5-yl)-2-oxoacetate (2) were synthesized by one pot three component strategy, and characterized by FT-IR, NMR (1H and 13C) spectroscopy and TOF-MS spectrometry. Finally, the structures were unequivocally confirmed by single crystal X-ray diffraction analyses. Both compounds, 1 and 2 exist in monoclinic crystal packing having space group P21/n and P21/c, respectively. Crystal structures investigations revealed that the molecular structures of the title compounds are stabilized by weak intermolecular hydrogen bonding interactions to form dimers. Density functional theory (DFT) calculations were performed not only to compare with the experimental spectroscopic results but also to probe structural properties. The molecular electrostatic potential (MEP) mapped over the entire stabilized geometries of the molecules delivered information about the electrophilic and nucleophilic sites. Furthermore, frontier molecular orbital analysis gave the idea about stability and reactivity of compounds. Both compounds were also screened for brine shrimp cytotoxicity assay.

  1. Analyses of Concrete Structures Exposed to Fire

    DEFF Research Database (Denmark)

    Hertz, Kristian

    The text book contains the data and methods necessary for fire safety design of concrete constructions. The methods relate to standard fire as well as to any time of any other fire course.Material data are presented for concretes exposed to fire, and calculation methods are given for the ultimate...... bending capacity of beams and slabs, the ultimate shear capacity of beams, for the instability of columns and walls and for the deflection of prestressed and non-prestressed beams, slabs, walls and columns.All methods have been derived and compared to tests by Kristian Hertz....

  2. Understanding complex structures in fold-and-thrust belts. Integration of geometric and growth strata analyses, paleomagnetism, AMS and analogue models in the Western termination of the Southern Pyrenees

    Science.gov (United States)

    Pueyo, Emilio L.; Sánchez, Elisa; Oliva-Urcia, Belén; José Ramón, Ma

    2014-05-01

    Classic 2D approaches have helped the understanding of the geometry and kinematics of fold-and-thrust belts belts (FAT belts) but are insufficient to unravel many natural cases. This is because deformation is 3D from the geometric point of view and, thus, cylindrical features may be considered as a simplification. On the other hand, deformation kinematics is usually complex, diachronic and poliphasic in real cases. Therefore, FAT belts have to be always considered in 4D. In this sense, the Southern Pyrenees is a perfect location to study the evolution of FAT belts because of the exceptional outcropping conditions of growth strata, the proven diachronic kinematics and the non-coaxial interference of deformation events. Within the vast catalogue of complex structures that includes superposed folding, conical and plunging folds, oblique thrust ramps, etc here, we have selected the westernmost termination of the South Pyrenean sole thrust to illustrate how the integration of geometric and kinematic analysis can help unraveling complex structures in FAT belts. The San Marzal pericline (4 km2 surface extension) is the lateral termination of the Sto. Domingo deca-kilometric fold. San Marzal looks like a large 70° plunging cylindrical structure. However the large magnitude (≡ 60-70°) of vertical axis rotations accommodated between its flanks cannot be explained without a conical geometry. In this work we will show how the structural analysis performed on this structure has disentangled its complex geometry. This analyses comprises several hundreds of bedding data, joints and veins and more than 150 standard paleomagnetic and AMS sites. Besides, we will show how the kinematic information derived from magnetostratigraphic sections (more than 8 km of sampled profiles) has helped to constraint the folding and rotation ages and velocities. Finally, all these complex geometric and kinematic features have inspired us to build an analogue model where we can explore the 3D

  3. Evaluation of fluid-coupled seismic buckling strength for FBRs' reactor vessel wall protective structures. Validation of the applicability of the finite element procedures for dynamic buckling analyses of a fluid-filled thin cylindrical shell by dynamic buckling tests

    International Nuclear Information System (INIS)

    Toyoda, Yukihiro; Matsuura, Shinichi

    1997-01-01

    The demonstration FBRs' reactor vessel wall protective structures, which are composed of thin shell structures, may fail by dynamic buckling due to seismically induced hydrodynamic effects. In order to clarify the dynamic buckling characteristics of the shells, numerical analysis can be a useful tool. However, it generally takes an enormous amount of computational time to execute dynamic buckling analysis by the finite element method. Therefore, one of the authors has developed an elastic-plastic large displacement analysis computer program for shells of revolution with high efficiency. The objectives of this study are to investigate the buckling behaviour of a partially liquid-filled cantilevered thin cylindrical shell subjected to harmonic excitation, and to validate the applicability of the improved computer program which has the capability of elastic-plastic dynamic buckling analysis including fluid-structure interaction. Numerical simulations were performed using the computer program under the conditions corresponding to shaking table tests of the tank. It is confirmed that the dynamic buckling analyses of the liquid-filled thin shell are possible by using the computer program within reasonable computational time. (author)

  4. Crystal structures and Hirshfeld surface analyses of bis[N,N-bis(2-methoxyethyldithiocarbamato-κ2S,S′]di-n-butyltin(IV and [N-(2-methoxyethyl-N-methyldithiocarbamato-κ2S,S′]triphenyltin(IV

    Directory of Open Access Journals (Sweden)

    Rapidah Mohamad

    2018-03-01

    Full Text Available The crystal and molecular structures of the two title organotin dithiocarbamate compounds, [Sn(C4H92(C7H14NO2S22], (I, and [Sn(C6H53(C5H10NOS2], (II, are described. Both structures feature asymmetrically bound dithiocarbamate ligands leading to a skew-trapezoidal bipyramidal geometry for the metal atom in (I and a distorted tetrahedral geometry in (II. The complete molecule of (I is generated by a crystallographic twofold axis (Sn site symmetry 2. In the crystal of (I, molecules self-assemble into a supramolecular array parallel to (10-1 via methylene-C—H...O(methoxy interactions. In the crystal of (II, supramolecular dimers are formed via pairs of weak phenyl-C—H...π(phenyl contacts. In each of (I and (II, the specified assemblies connect into a three-dimensional architecture without directional interactions between them. Hirshfeld surface analyses confirm the importance of H...H contacts in the molecular packing of each of (I and (II, and in the case of (I, highlight the importance of short methoxy-H...H(butyl contacts between layers.

  5. Laser Beam Focus Analyser

    DEFF Research Database (Denmark)

    Nielsen, Peter Carøe; Hansen, Hans Nørgaard; Olsen, Flemming Ove

    2007-01-01

    the obtainable features in direct laser machining as well as heat affected zones in welding processes. This paper describes the development of a measuring unit capable of analysing beam shape and diameter of lasers to be used in manufacturing processes. The analyser is based on the principle of a rotating...... mechanical wire being swept through the laser beam at varying Z-heights. The reflected signal is analysed and the resulting beam profile determined. The development comprised the design of a flexible fixture capable of providing both rotation and Z-axis movement, control software including data capture...... and finally data analysis based on the ISO approach. The device was calibrated and tested on commercially available laser systems. It showed good reproducibility. It was the target to be able to measure CW lasers with a power up to 200 W, focused down to spot diameters in the range of 10µm. In order...

  6. Analyses of the radiation of birnaviruses from diverse host phyla and of their evolutionary affinities with other double-stranded RNA and positive strand RNA viruses using robust structure-based multiple sequence alignments and advanced phylogenetic methods.

    Science.gov (United States)

    Gibrat, Jean-François; Mariadassou, Mahendra; Boudinot, Pierre; Delmas, Bernard

    2013-07-17

    Birnaviruses form a distinct family of double-stranded RNA viruses infecting animals as different as vertebrates, mollusks, insects and rotifers. With such a wide host range, they constitute a good model for studying the adaptation to the host. Additionally, several lines of evidence link birnaviruses to positive strand RNA viruses and suggest that phylogenetic analyses may provide clues about transition. We characterized the genome of a birnavirus from the rotifer Branchionus plicalitis. We used X-ray structures of RNA-dependent RNA polymerases and capsid proteins to obtain multiple structure alignments that allowed us to obtain reliable multiple sequence alignments and we employed "advanced" phylogenetic methods to study the evolutionary relationships between some positive strand and double-stranded RNA viruses. We showed that the rotifer birnavirus genome exhibited an organization remarkably similar to other birnaviruses. As this host was phylogenetically very distant from the other known species targeted by birnaviruses, we revisited the evolutionary pathways within the Birnaviridae family using phylogenetic reconstruction methods. We also applied a number of phylogenetic approaches based on structurally conserved domains/regions of the capsid and RNA-dependent RNA polymerase proteins to study the evolutionary relationships between birnaviruses, other double-stranded RNA viruses and positive strand RNA viruses. We show that there is a good correlation between the phylogeny of the birnaviruses and that of their hosts at the phylum level using the RNA-dependent RNA polymerase (genomic segment B) on the one hand and a concatenation of the capsid protein, protease and ribonucleoprotein (genomic segment A) on the other hand. This correlation tends to vanish within phyla. The use of advanced phylogenetic methods and robust structure-based multiple sequence alignments allowed us to obtain a more accurate picture (in terms of probability of the tree topologies) of the

  7. Contesting Citizenship: Comparative Analyses

    DEFF Research Database (Denmark)

    Siim, Birte; Squires, Judith

    2007-01-01

    importance of particularized experiences and multiple ineequality agendas). These developments shape the way citizenship is both practiced and analysed. Mapping neat citizenship modles onto distinct nation-states and evaluating these in relation to formal equality is no longer an adequate approach....... Comparative citizenship analyses need to be considered in relation to multipleinequalities and their intersections and to multiple governance and trans-national organisinf. This, in turn, suggests that comparative citizenship analysis needs to consider new spaces in which struggles for equal citizenship occur...

  8. Diversity of primary care systems analysed.

    NARCIS (Netherlands)

    Kringos, D.; Boerma, W.; Bourgueil, Y.; Cartier, T.; Dedeu, T.; Hasvold, T.; Hutchinson, A.; Lember, M.; Oleszczyk, M.; Pavlick, D.R.

    2015-01-01

    This chapter analyses differences between countries and explains why countries differ regarding the structure and process of primary care. The components of primary care strength that are used in the analyses are health policy-making, workforce development and in the care process itself (see Fig.

  9. A Multi-Faceted Approach to Analyse the Effects of Environmental Variables on Geographic Range and Genetic Structure of a Perennial Psammophilous Geophyte: The Case of the Sea Daffodil Pancratium maritimum L. in the Mediterranean Basin.

    Directory of Open Access Journals (Sweden)

    Olga De Castro

    Full Text Available The Mediterranean coastline is a dynamic and complex system which owes its complexity to its past and present vicissitudes, e.g. complex tectonic history, climatic fluctuations, and prolonged coexistence with human activities. A plant species that is widespread in this habitat is the sea daffodil, Pancratium maritimum (Amaryllidaceae, which is a perennial clonal geophyte of the coastal sands of the Mediterranean and neighbouring areas, well adapted to the stressful conditions of sand dune environments. In this study, an integrated approach was used, combining genetic and environmental data with a niche modelling approach, aimed to investigate: (1 the effect of climate change on the geographic range of this species at different times {past (last inter-glacial, LIG; and last glacial maximum, LGM, present (CURR, near-future (FUT} and (2 the possible influence of environmental variables on the genetic structure of this species in the current period. The genetic results show that 48 sea daffodil populations (867 specimens display a good genetic diversity in which the marginal populations (i.e. Atlantic Sea populations present lower values. Recent genetic signature of bottleneck was detected in few populations (8%. The molecular variation was higher within the populations (77% and two genetic pools were well represented. Comparing the different climatic simulations in time, the global range of this plant increased, and a further extension is foreseen in the near future thanks to projections on the climate of areas currently-more temperate, where our model suggested a forecast for a climate more similar to the Mediterranean coast. A significant positive correlation was observed between the genetic distance and Precipitation of Coldest Quarter variable in current periods. Our analyses support the hypothesis that geomorphology of the Mediterranean coasts, sea currents, and climate have played significant roles in shaping the current genetic structure of

  10. A Multi-Faceted Approach to Analyse the Effects of Environmental Variables on Geographic Range and Genetic Structure of a Perennial Psammophilous Geophyte: The Case of the Sea Daffodil Pancratium maritimum L. in the Mediterranean Basin.

    Science.gov (United States)

    De Castro, Olga; Di Maio, Antonietta; Di Febbraro, Mirko; Imparato, Gennaro; Innangi, Michele; Véla, Errol; Menale, Bruno

    2016-01-01

    The Mediterranean coastline is a dynamic and complex system which owes its complexity to its past and present vicissitudes, e.g. complex tectonic history, climatic fluctuations, and prolonged coexistence with human activities. A plant species that is widespread in this habitat is the sea daffodil, Pancratium maritimum (Amaryllidaceae), which is a perennial clonal geophyte of the coastal sands of the Mediterranean and neighbouring areas, well adapted to the stressful conditions of sand dune environments. In this study, an integrated approach was used, combining genetic and environmental data with a niche modelling approach, aimed to investigate: (1) the effect of climate change on the geographic range of this species at different times {past (last inter-glacial, LIG; and last glacial maximum, LGM), present (CURR), near-future (FUT)} and (2) the possible influence of environmental variables on the genetic structure of this species in the current period. The genetic results show that 48 sea daffodil populations (867 specimens) display a good genetic diversity in which the marginal populations (i.e. Atlantic Sea populations) present lower values. Recent genetic signature of bottleneck was detected in few populations (8%). The molecular variation was higher within the populations (77%) and two genetic pools were well represented. Comparing the different climatic simulations in time, the global range of this plant increased, and a further extension is foreseen in the near future thanks to projections on the climate of areas currently-more temperate, where our model suggested a forecast for a climate more similar to the Mediterranean coast. A significant positive correlation was observed between the genetic distance and Precipitation of Coldest Quarter variable in current periods. Our analyses support the hypothesis that geomorphology of the Mediterranean coasts, sea currents, and climate have played significant roles in shaping the current genetic structure of the sea

  11. Dialogisk kommunikationsteoretisk analyse

    DEFF Research Database (Denmark)

    Phillips, Louise Jane

    2018-01-01

    analysemetode, der er blevet udviklet inden for dialogisk kommunikationsforskning - The Integrated Framework for Analysing Dialogic Knowledge Production and Communication (IFADIA). IFADIA-metoden bygger på en kombination af Bakhtins dialogteori og Foucaults teori om magt/viden og diskurs. Metoden er beregnet...

  12. Probabilistic safety analyses (PSA)

    International Nuclear Information System (INIS)

    1997-01-01

    The guide shows how the probabilistic safety analyses (PSA) are used in the design, construction and operation of light water reactor plants in order for their part to ensure that the safety of the plant is good enough in all plant operational states

  13. Meta-analyses

    NARCIS (Netherlands)

    Hendriks, Maria A.; Luyten, Johannes W.; Scheerens, Jaap; Sleegers, P.J.C.; Scheerens, J

    2014-01-01

    In this chapter results of a research synthesis and quantitative meta-analyses of three facets of time effects in education are presented, namely time at school during regular lesson hours, homework, and extended learning time. The number of studies for these three facets of time that could be used

  14. Analysing Access Control Specifications

    DEFF Research Database (Denmark)

    Probst, Christian W.; Hansen, René Rydhof

    2009-01-01

    . Recent events have revealed intimate knowledge of surveillance and control systems on the side of the attacker, making it often impossible to deduce the identity of an inside attacker from logged data. In this work we present an approach that analyses the access control configuration to identify the set...

  15. Wavelet Analyses and Applications

    Science.gov (United States)

    Bordeianu, Cristian C.; Landau, Rubin H.; Paez, Manuel J.

    2009-01-01

    It is shown how a modern extension of Fourier analysis known as wavelet analysis is applied to signals containing multiscale information. First, a continuous wavelet transform is used to analyse the spectrum of a nonstationary signal (one whose form changes in time). The spectral analysis of such a signal gives the strength of the signal in each…

  16. Filmstil - teori og analyse

    DEFF Research Database (Denmark)

    Hansen, Lennard Højbjerg

    Filmstil påvirker på afgørende vis vores oplevelse af film. Men filmstil, måden, de levende billeder organiserer fortællingen på fylder noget mindre end filmens handling, når vi taler om film. Filmstil - teori og analyse er en rigt eksemplificeret præsentation, kritik og videreudvikling af...

  17. Risico-analyse brandstofpontons

    NARCIS (Netherlands)

    Uijt de Haag P; Post J; LSO

    2001-01-01

    Voor het bepalen van de risico's van brandstofpontons in een jachthaven is een generieke risico-analyse uitgevoerd. Er is een referentiesysteem gedefinieerd, bestaande uit een betonnen brandstofponton met een relatief grote inhoud en doorzet. Aangenomen is dat de ponton gelegen is in een

  18. Revealing the functional structure of a new PLA2 K49 from Bothriopsis taeniata snake venom employing automatic "de novo" sequencing using CID/HCD/ETD MS/MS analyses.

    Science.gov (United States)

    Carregari, Victor Corasolla; Dai, Jie; Verano-Braga, Thiago; Rocha, Thalita; Ponce-Soto, Luis Alberto; Marangoni, Sergio; Roepstorff, Peter

    2016-01-10

    Snake venoms are composed of approximately 90% of proteins with several pharmacological activities having high potential in research as biological tools. One of the most abundant compounds is phospholipases A2 (PLA2), which are the most studied venom protein due to their wide pharmacological activity. Using a combination of chromatographic steps, a new PLA2 K49 was isolated and purified from the whole venom of the Bothriopsis taeniata and submitted to analyses mass spectrometry. An automatic “de novo” sequencing of this new PLA2 K49 denominated Btt-TX was performed using Peaks Studio 6 for analysis of the spectra. Additionally, a triplex approach CID/HCD/ETD has been performed, to generate higher coverage of the sequence of the protein. Structural studies correlating biological activities were made associating specific Btt-TX regions and myotoxic activity. Lysine acetylation was performed to better understand the mechanism of membrane interaction, identifying the extreme importance of the highly hydrophobic amino acids L, P and F for disruption of the membrane. Our myotoxical studies show a possible membrane disruption mechanism by Creatine Kinase release without a noticeable muscle damage, that probably occurred without phospholipid hydrolyses, but with a probable penetration of the hydrophobic amino acids present in the C-terminal region of the protein.

  19. Interaction of vanadium (IV) solvates (L) with second-generation fluoroquinolone antibacterial drug ciprofloxacin: Spectroscopic, structure, thermal analyses, kinetics and biological evaluation (L = An, DMF, Py and Et3N)

    Science.gov (United States)

    Zordok, Wael A.

    2014-08-01

    The preparation and characterization of the new solid complexes [VO(CIP)2L]SO4ṡnH2O, where L = aniline (An), dimethylformamide (DMF), pyridine (Py) and triethylamine (Et3N) in the reaction of ciprofloxacin (CIP) with VO(SO4)2·2H2O in ethanol. The isolated complexes have been characterized with their melting points, elemental analysis, IR spectroscopy, magnetic properties, conductance measurements, UV-Vis. and 1H NMR spectroscopic methods and thermal analyses. The results supported the formation of the complexes and indicated that ciprofloxacin reacts as a bidentate ligand bound to the vanadium ion through the pyridone oxygen and one carboxylato oxygen. The activation energies, E*; entropies, ΔS*; enthalpies, ΔH*; Gibbs free energies, ΔG*, of the thermal decomposition reactions have been derived from thermo gravimetric (TGA) and differential thermo gravimetric (DTG) curves, using Coats-Redfern and Horowitz-Metzeger methods. The lowest energy model structure of each complex has been proposed by using the density functional theory (DFT) at the B3LYP/CEP-31G level of theory. The ligand and their metal complexes were also evaluated for their antibacterial activity against several bacterial species, such as Bacillus Subtilis (B. Subtilis), Staphylococcus aureus (S. aureus), Nesseria Gonorrhoeae (N. Gonorrhoeae), Pseudomonas aeruginosa (P. aeruginosa) and Escherichia coli (E. coli).

  20. Biomass feedstock analyses

    Energy Technology Data Exchange (ETDEWEB)

    Wilen, C.; Moilanen, A.; Kurkela, E. [VTT Energy, Espoo (Finland). Energy Production Technologies

    1996-12-31

    The overall objectives of the project `Feasibility of electricity production from biomass by pressurized gasification systems` within the EC Research Programme JOULE II were to evaluate the potential of advanced power production systems based on biomass gasification and to study the technical and economic feasibility of these new processes with different type of biomass feed stocks. This report was prepared as part of this R and D project. The objectives of this task were to perform fuel analyses of potential woody and herbaceous biomasses with specific regard to the gasification properties of the selected feed stocks. The analyses of 15 Scandinavian and European biomass feed stock included density, proximate and ultimate analyses, trace compounds, ash composition and fusion behaviour in oxidizing and reducing atmospheres. The wood-derived fuels, such as whole-tree chips, forest residues, bark and to some extent willow, can be expected to have good gasification properties. Difficulties caused by ash fusion and sintering in straw combustion and gasification are generally known. The ash and alkali metal contents of the European biomasses harvested in Italy resembled those of the Nordic straws, and it is expected that they behave to a great extent as straw in gasification. Any direct relation between the ash fusion behavior (determined according to the standard method) and, for instance, the alkali metal content was not found in the laboratory determinations. A more profound characterisation of the fuels would require gasification experiments in a thermobalance and a PDU (Process development Unit) rig. (orig.) (10 refs.)

  1. AMS analyses at ANSTO

    International Nuclear Information System (INIS)

    Lawson, E.M.

    1998-01-01

    The major use of ANTARES is Accelerator Mass Spectrometry (AMS) with 14 C being the most commonly analysed radioisotope - presently about 35 % of the available beam time on ANTARES is used for 14 C measurements. The accelerator measurements are supported by, and dependent on, a strong sample preparation section. The ANTARES AMS facility supports a wide range of investigations into fields such as global climate change, ice cores, oceanography, dendrochronology, anthropology, and classical and Australian archaeology. Described here are some examples of the ways in which AMS has been applied to support research into the archaeology, prehistory and culture of this continent's indigenous Aboriginal peoples. (author)

  2. Multi-Omics and Integrated Network Analyses Reveal New Insights into the Systems Relationships between Metabolites, Structural Genes, and Transcriptional Regulators in Developing Grape Berries (Vitis vinifera L. Exposed to Water Deficit

    Directory of Open Access Journals (Sweden)

    Stefania Savoi

    2017-07-01

    Full Text Available Grapes are one of the major fruit crops and they are cultivated in many dry environments. This study comprehensively characterizes the metabolic response of grape berries exposed to water deficit at different developmental stages. Increases of proline, branched-chain amino acids, phenylpropanoids, anthocyanins, and free volatile organic compounds have been previously observed in grape berries exposed to water deficit. Integrating RNA-sequencing analysis of the transcriptome with large-scale analysis of central and specialized metabolites, we reveal that these increases occur via a coordinated regulation of key structural pathway genes. Water deficit-induced up-regulation of flavonoid genes is also coordinated with the down-regulation of many stilbene synthases and a consistent decrease in stilbenoid concentration. Water deficit activated both ABA-dependent and ABA-independent signal transduction pathways by modulating the expression of several transcription factors. Gene-gene and gene-metabolite network analyses showed that water deficit-responsive transcription factors such as bZIPs, AP2/ERFs, MYBs, and NACs are implicated in the regulation of stress-responsive metabolites. Enrichment of known and novel cis-regulatory elements in the promoters of several ripening-specific/water deficit-induced modules further affirms the involvement of a transcription factor cross-talk in the berry response to water deficit. Together, our integrated approaches show that water deficit-regulated gene modules are strongly linked to key fruit-quality metabolites and multiple signal transduction pathways may be critical to achieve a balance between the regulation of the stress-response and the berry ripening program. This study constitutes an invaluable resource for future discoveries and comparative studies, in grapes and other fruits, centered on reproductive tissue metabolism under abiotic stress.

  3. Analysis of existing structure and emissions of wood combustion plants for the production of heat and electricity in Bavaria; Analyse der Bestandesstruktur und der Emissionen von Holzfeuerungsanlagen zur Erzeugung von Waerme und Strom in Bayern.

    Energy Technology Data Exchange (ETDEWEB)

    Joa, Bettina

    2014-07-01

    This work deals with the detailed analysis of the existing structure of all Bavarian wood burning plants for the generation of heat and electricity as well as the determination of the resulting emission emissions in 2013. The number of wood burning plants in the single-chamber fireplaces, wood central heating and wood-fired heating plants which are in operation in the year 2013 were determined, and how many plants are existing in the various areas like pellet stoves, traditional ovens, wood-burning fireplace, pellet central heating systems, wood chips central heating systems, fire-wood central heating systems, wood combined heat and power plant (electricity and heat) and wood power plants (heat). In addition, the regional distribution of the wood burning plants in the Bavarian governmental districts is investigated as well as the type and amount of energy produced by them (heat, electricity). [German] Diese Arbeit behandelt die detaillierte Analyse der Bestandesstruktur saemtlicher bayerischer Holzfeuerungsanlagen zur Erzeugung von Waerme und Strom sowie die Ermittlung des dabei entstehenden Emissionsausstosses im Jahr 2013. Dabei wurde ermittelt wie viele Holzfeuerungsanlagen in den Segmenten Einzelraumfeuerstaetten, Holz-Zentralheizungen und Holzheiz(kraft)werke im Jahr 2013 in Bayern in Betrieb sind und wie viele Anlagen es in den einzelnen Bereichen Pelletoefen, traditionelle Oefen, Kaminoefen, Heizkamine, offene Kamine, Kacheloefen, Pellet-Zentralheizungen, Hackschnitzel-Zentralheizungen, Scheitholz-Zentralheizungen, Holzheizkraftwerke (Waerme und Strom), Holzheizwerke (Waerme) sowie Holzkraftwerke (Strom) gibt. Des Weiteren wird die regionale Verteilung der Holzfeuerungsanlagen in den bayerischen Regierungsbezirken erforscht sowie die durch sie produzierte Art und Menge an Energie (Waerme, Strom).

  4. Multi-Omics and Integrated Network Analyses Reveal New Insights into the Systems Relationships between Metabolites, Structural Genes, and Transcriptional Regulators in Developing Grape Berries (Vitis viniferaL.) Exposed to Water Deficit.

    Science.gov (United States)

    Savoi, Stefania; Wong, Darren C J; Degu, Asfaw; Herrera, Jose C; Bucchetti, Barbara; Peterlunger, Enrico; Fait, Aaron; Mattivi, Fulvio; Castellarin, Simone D

    2017-01-01

    Grapes are one of the major fruit crops and they are cultivated in many dry environments. This study comprehensively characterizes the metabolic response of grape berries exposed to water deficit at different developmental stages. Increases of proline, branched-chain amino acids, phenylpropanoids, anthocyanins, and free volatile organic compounds have been previously observed in grape berries exposed to water deficit. Integrating RNA-sequencing analysis of the transcriptome with large-scale analysis of central and specialized metabolites, we reveal that these increases occur via a coordinated regulation of key structural pathway genes. Water deficit-induced up-regulation of flavonoid genes is also coordinated with the down-regulation of many stilbene synthases and a consistent decrease in stilbenoid concentration. Water deficit activated both ABA-dependent and ABA-independent signal transduction pathways by modulating the expression of several transcription factors. Gene-gene and gene-metabolite network analyses showed that water deficit-responsive transcription factors such as bZIPs, AP2/ERFs, MYBs, and NACs are implicated in the regulation of stress-responsive metabolites. Enrichment of known and novel cis -regulatory elements in the promoters of several ripening-specific/water deficit-induced modules further affirms the involvement of a transcription factor cross-talk in the berry response to water deficit. Together, our integrated approaches show that water deficit-regulated gene modules are strongly linked to key fruit-quality metabolites and multiple signal transduction pathways may be critical to achieve a balance between the regulation of the stress-response and the berry ripening program. This study constitutes an invaluable resource for future discoveries and comparative studies, in grapes and other fruits, centered on reproductive tissue metabolism under abiotic stress.

  5. Analyses of Sickness Absence

    NARCIS (Netherlands)

    Heijnen, S.M.M.

    2014-01-01

    Sickness absence is an empirical phenomenon of all time. Generally, it has a medical cause. However, other factors also appear to have an impact on the actual rate of sickness absence, such as the institutional setting, the business cycle and the economic structure. Many questions on the different

  6. Uncertainty Analyses and Strategy

    International Nuclear Information System (INIS)

    Kevin Coppersmith

    2001-01-01

    The DOE identified a variety of uncertainties, arising from different sources, during its assessment of the performance of a potential geologic repository at the Yucca Mountain site. In general, the number and detail of process models developed for the Yucca Mountain site, and the complex coupling among those models, make the direct incorporation of all uncertainties difficult. The DOE has addressed these issues in a number of ways using an approach to uncertainties that is focused on producing a defensible evaluation of the performance of a potential repository. The treatment of uncertainties oriented toward defensible assessments has led to analyses and models with so-called ''conservative'' assumptions and parameter bounds, where conservative implies lower performance than might be demonstrated with a more realistic representation. The varying maturity of the analyses and models, and uneven level of data availability, result in total system level analyses with a mix of realistic and conservative estimates (for both probabilistic representations and single values). That is, some inputs have realistically represented uncertainties, and others are conservatively estimated or bounded. However, this approach is consistent with the ''reasonable assurance'' approach to compliance demonstration, which was called for in the U.S. Nuclear Regulatory Commission's (NRC) proposed 10 CFR Part 63 regulation (64 FR 8640 [DIRS 101680]). A risk analysis that includes conservatism in the inputs will result in conservative risk estimates. Therefore, the approach taken for the Total System Performance Assessment for the Site Recommendation (TSPA-SR) provides a reasonable representation of processes and conservatism for purposes of site recommendation. However, mixing unknown degrees of conservatism in models and parameter representations reduces the transparency of the analysis and makes the development of coherent and consistent probability statements about projected repository

  7. EEG analyses with SOBI.

    Energy Technology Data Exchange (ETDEWEB)

    Glickman, Matthew R.; Tang, Akaysha (University of New Mexico, Albuquerque, NM)

    2009-02-01

    The motivating vision behind Sandia's MENTOR/PAL LDRD project has been that of systems which use real-time psychophysiological data to support and enhance human performance, both individually and of groups. Relevant and significant psychophysiological data being a necessary prerequisite to such systems, this LDRD has focused on identifying and refining such signals. The project has focused in particular on EEG (electroencephalogram) data as a promising candidate signal because it (potentially) provides a broad window on brain activity with relatively low cost and logistical constraints. We report here on two analyses performed on EEG data collected in this project using the SOBI (Second Order Blind Identification) algorithm to identify two independent sources of brain activity: one in the frontal lobe and one in the occipital. The first study looks at directional influences between the two components, while the second study looks at inferring gender based upon the frontal component.

  8. A simple beam analyser

    International Nuclear Information System (INIS)

    Lemarchand, G.

    1977-01-01

    (ee'p) experiments allow to measure the missing energy distribution as well as the momentum distribution of the extracted proton in the nucleus versus the missing energy. Such experiments are presently conducted on SACLAY's A.L.S. 300 Linac. Electrons and protons are respectively analysed by two spectrometers and detected in their focal planes. Counting rates are usually low and include time coincidences and accidentals. Signal-to-noise ratio is dependent on the physics of the experiment and the resolution of the coincidence, therefore it is mandatory to get a beam current distribution as flat as possible. Using new technologies has allowed to monitor in real time the behavior of the beam pulse and determine when the duty cycle can be considered as being good with respect to a numerical basis

  9. Analyse af elbilers forbrug

    DEFF Research Database (Denmark)

    Andersen, Ove; Krogh, Benjamin Bjerre; Torp, Kristian

    2014-01-01

    Denne rapport undersøger GPS og CAN bus datagrundlaget opsamlet ved kørsel med elbiler og analysere på elbilers forbrug. Analyserne er baseret på godt 133 millioner GPS og CAN bus målinger opsamlet fra 164 elbiler (Citroen C-Zero, Mitsubishi iMiev og Peugeot Ion) i kalenderåret 2012....... For datagrundlaget kan det konstateres, at der er behov for væsentlige, men simple opstramninger for fremadrettet at gøre det nemmere at anvende GPS/CAN bus data fra elbiler i andre analyser. Brugen af elbiler er sammenlignet med brændstofbiler og konklusionen er, at elbiler generelt kører 10-15 km/t langsommere på...

  10. Analyse de "La banlieue"

    Directory of Open Access Journals (Sweden)

    Nelly Morais

    2006-11-01

    Full Text Available 1. Préambule - Conditions de réalisation de la présente analyse Un groupe d'étudiants de master 1 de FLE de l'université Paris 3 (donc des étudiants en didactique des langues se destinant à l'enseignement du FLE a observé le produit au cours d'un module sur les TIC (Technologies de l'Information et de la Communication et la didactique des langues. Une discussion s'est ensuite engagée sur le forum d'une plate-forme de formation à distance à partir de quelques questions posées par l'enseigna...

  11. A History of Rotorcraft Comprehensive Analyses

    Science.gov (United States)

    Johnson, Wayne

    2013-01-01

    A history of the development of rotorcraft comprehensive analyses is presented. Comprehensive analyses are digital computer programs that calculate the aeromechanical behavior of the rotor and aircraft, bringing together the most advanced models of the geometry, structure, dynamics, and aerodynamics available in rotary wing technology. The development of the major codes of the last five decades from industry, government, and universities is described. A number of common themes observed in this history are discussed.

  12. Thermal Analyse sof Cross-Linked Polyethylene

    Directory of Open Access Journals (Sweden)

    Radek Polansky

    2007-01-01

    Full Text Available The paper summarizes results obtained during the structural analyses measurements (Differential Scanning Calorimetry DSC, Thermogravimetry TG, Thermomechanical analysis TMA and Fourier transform infrared spectroscopy FT-IR. The samples of cross-linked polyethylene cable insulation were tested via these analyses. The DSC and TG were carried out using simultaneous thermal analyzer TA Instruments SDT Q600 with connection of Fourier transform infrared spectrometer Nicolet 380. Thermomechanical analysis was carried out by TMA Q400EM TA Instruments apparatus.

  13. Website-analyse

    DEFF Research Database (Denmark)

    Thorlacius, Lisbeth

    2009-01-01

    eller blindgyder, når han/hun besøger sitet. Studier i design og analyse af de visuelle og æstetiske aspekter i planlægning og brug af websites har imidlertid kun i et begrænset omfang været under reflektorisk behandling. Det er baggrunden for dette kapitel, som indleder med en gennemgang af æstetikkens......Websitet er i stigende grad det foretrukne medie inden for informationssøgning,virksomhedspræsentation, e-handel, underholdning, undervisning og social kontakt. I takt med denne voksende mangfoldighed af kommunikationsaktiviteter på nettet, er der kommet mere fokus på at optimere design og...... planlægning af de funktionelle og indholdsmæssige aspekter ved websites. Der findes en stor mængde teori- og metodebøger, som har specialiseret sig i de tekniske problemstillinger i forbindelse med interaktion og navigation, samt det sproglige indhold på websites. Den danske HCI (Human Computer Interaction...

  14. A channel profile analyser

    International Nuclear Information System (INIS)

    Gobbur, S.G.

    1983-01-01

    It is well understood that due to the wide band noise present in a nuclear analog-to-digital converter, events at the boundaries of adjacent channels are shared. It is a difficult and laborious process to exactly find out the shape of the channels at the boundaries. A simple scheme has been developed for the direct display of channel shape of any type of ADC on a cathode ray oscilliscope display. This has been accomplished by sequentially incrementing the reference voltage of a precision pulse generator by a fraction of a channel and storing ADC data in alternative memory locations of a multichannel pulse height analyser. Alternative channels are needed due to the sharing at the boundaries of channels. In the flat region of the profile alternate memory locations are channels with zero counts and channels with the full scale counts. At the boundaries all memory locations will have counts. The shape of this is a direct display of the channel boundaries. (orig.)

  15. Analyse de la vulnérabilité sismique des structures à ossature en bois avec remplissage : essais expérimentaux - modélisation numérique - calculs parasismiques

    OpenAIRE

    Vieux-Champagne, Florent

    2013-01-01

    The seismic vulnerabilty is an important issue in the design of a building. The seismicresistant behavior of timber-framed structures is particularly relevant. Two types of timberframedstructures can be distinguished : the timber-framed structures using industrial products,such as wood-products panels used to brace the structure or metal fasteners, and traditionaltimber-framed structures included infill made of natuarl materials (earth or stones masonry).The seismic resistant behavior efficie...

  16. Molecular ecological network analyses

    Directory of Open Access Journals (Sweden)

    Deng Ye

    2012-05-01

    Full Text Available Abstract Background Understanding the interaction among different species within a community and their responses to environmental changes is a central goal in ecology. However, defining the network structure in a microbial community is very challenging due to their extremely high diversity and as-yet uncultivated status. Although recent advance of metagenomic technologies, such as high throughout sequencing and functional gene arrays, provide revolutionary tools for analyzing microbial community structure, it is still difficult to examine network interactions in a microbial community based on high-throughput metagenomics data. Results Here, we describe a novel mathematical and bioinformatics framework to construct ecological association networks named molecular ecological networks (MENs through Random Matrix Theory (RMT-based methods. Compared to other network construction methods, this approach is remarkable in that the network is automatically defined and robust to noise, thus providing excellent solutions to several common issues associated with high-throughput metagenomics data. We applied it to determine the network structure of microbial communities subjected to long-term experimental warming based on pyrosequencing data of 16 S rRNA genes. We showed that the constructed MENs under both warming and unwarming conditions exhibited topological features of scale free, small world and modularity, which were consistent with previously described molecular ecological networks. Eigengene analysis indicated that the eigengenes represented the module profiles relatively well. In consistency with many other studies, several major environmental traits including temperature and soil pH were found to be important in determining network interactions in the microbial communities examined. To facilitate its application by the scientific community, all these methods and statistical tools have been integrated into a comprehensive Molecular Ecological

  17. 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

    NARCIS (Netherlands)

    Oosthuysen, W. F.; Orth, H.; Lombard, C. J.; Sinha, B.; Wasserman, E.

    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

  18. Development of a stage-structured process-based predator–prey model to analyse biological control of cotton aphid, Aphis gossypii, by the sevenspot ladybeetle, Coccinella septempunctata, in cotton

    NARCIS (Netherlands)

    Xia, J.Y.; Wang, J.; Cui, J.J.; Leffelaar, P.A.; Rabbinge, R.; Werf, van der W.

    2018-01-01

    Agricultural system diversification is well known to affect the population dynamics of crop pests, but predator–prey dynamics in crop systems are difficult to analyse due to interactions between multiple life stages of predator and prey, the modulating effect of temperature, the actions of

  19. Hybrid Logical Analyses of the Ambient Calculus

    DEFF Research Database (Denmark)

    Bolander, Thomas; Hansen, Rene Rydhof

    2010-01-01

    In this paper, hybrid logic is used to formulate three control flow analyses for Mobile Ambients, a process calculus designed for modelling mobility. We show that hybrid logic is very well-suited to express the semantic structure of the ambient calculus and how features of hybrid logic can...

  20. Comparison of elastic and inelastic analyses

    International Nuclear Information System (INIS)

    Ammerman, D.J.; Heinstein, M.W.; Wellman, G.W.

    1993-01-01

    In this paper, comparisons between elastic and inelastic analyses are made for a simple ring structure and for a package to transport a large quantity of RAM by rail (rail cask) with lead gamma shielding to illustrate the differences in the two analysis techniques. (J.P.N.)

  1. New developments in the simultaneous measurement system of wide-angle and small-angle x-ray scatterings and vibrational spectra for the static and dynamic analyses of the hierarchical structures of polymer solids

    International Nuclear Information System (INIS)

    Tashiro, Kohji; Yamamoto, Hiroko; Yoshioka, Taiyo; Ninh, Tran Hai; Shimada, Shigeru; Nakatani, Takeshi; Iwamoto, Hiroyuki; Ohta, Noboru; Masunaga, Hiroyasu

    2012-01-01

    A simultaneous measurement system of wide-angle X-ray diffraction (WAXD), small-angle X-ray scattering (SAXS) and Raman or transmission-type infrared spectroscopy was developed by us. Its purposes is to clarify the static and dynamic structural changes of polymer materials subjected to the various external condition changes. Some examples described here include the study of the stretch-induced reorientation phenomenon of a-axially-oriented polyethylene, the study of structural change in photo-induced solid-state polymerization reaction of muconic acid ester monomer crystal, the study of the two-stage high-temperature phase transitions of aliphatic nylons, the study of stress-induced crystalline phase transition of an oriented poly(tetramethylene terephthalate) sample and its relation to the higher-order structural change, and the study of structural regularization process of poly(L-lactic acid) in the isothermal crystallization of the meso phase. These case studies in the clarification of hierarchical structural changes of polymer materials have proven that the simultaneous measurement systems can be useful to examine the structural changes in polymer systems. (author)

  2. The nature of the Ailao Shan-Red River (ASRR) shear zone: Constraints from structural, microstructural and fabric analyses of metamorphic rocks from the Diancang Shan, Ailao Shan and Day Nui Con Voi massifs

    Science.gov (United States)

    Liu, Junlai; Tang, Yuan; Tran, My-Dung; Cao, Shuyun; Zhao, Li; Zhang, Zhaochong; Zhao, Zhidan; Chen, Wen

    2012-03-01

    The structural geology, timing of shearing, and tectonic implications of the ASRR shear zone, one of the most striking lineaments in Southeast Asia, have been the topics of extensive studies over the past few decades. The Xuelong Shan (XLS), Diancang Shan (DCS), Ailao Shan (ALS) and Day Nui Con Voi (DNCV) metamorphic massifs along the shear zone have preserved important information on its structural and tectonic evolution. Our field structural analysis, detailed microstructural and fabric analysis, as well as the quartz, sillimanite and garnet fabric studies of the sheared rocks from the massifs demonstrate the dominant roles of three deformation episodes during Cenozoic tectonic evolution in the shear zone. Among the contrasting structural and microstructural associations in the shear zone, D2 structures, which were formed at the brittle to ductile transition during large-scale left-lateral shearing in the second deformation episode, predominate over the structural styles of the other two deformation episodes. Discrete micro-shear zones with intensive grain size reduction compose the characteristic structural style of D2 deformation. In addition, several types of folds (early shearing folds, F21, and late-shearing folds, F22) were formed in the sheared rocks, including discrete to distributed mylonitic foliation, stretching lineation and shear fabrics (e.g., mica fish, domino structures, as well as sigma and delta fabrics). A sequence of microstructures from syn-kinematic magmatic flow, high-temperature solid-state deformation, to brittle-ductile shearing is well-preserved in the syn-kinematic leucocratic intrusions. Deformation structures from the first episode (D1) are characterized by F1 folds and distributed foliations (S1) in rocks due to pure shearing at high temperatures. They are preserved in weakly sheared (D2) rocks along the eastern margin of the ALS belt or in certain low-strain tectonic enclaves within the shear zone. Furthermore, semi

  3. XPS-and-DFT analyses of the Pb 4f — Zn 3s and Pb 5d — O 2s overlapped ambiguity contributions to the final electronic structure of bulk and thin-film Pb-modulated zincite

    Energy Technology Data Exchange (ETDEWEB)

    Zatsepin, D.A. [M.N. Miheev Institute of Metal Physics of Ural Branch of Russian Academy of Sciences, 620990 Yekaterinburg (Russian Federation); Institute of Physics and Technology, Ural Federal University, 620002 Yekaterinburg (Russian Federation); Boukhvalov, D.W., E-mail: danil@hanyang.ac.kr [Department of Chemistry, Hanyang University, 17 Haengdang-dong, Seongdong-gu, Seoul 133-791 (Korea, Republic of); Theoretical Physics and Applied Mathematics Department, Ural Federal University,Mira Street 19, 620002 Yekaterinburg (Russian Federation); Gavrilov, N.V. [Institute of Electrophysics, Russian Academy of Sciences, Ural Branch, 620990 Yekaterinburg (Russian Federation); Kurmaev, E.Z. [M.N. Miheev Institute of Metal Physics of Ural Branch of Russian Academy of Sciences, 620990 Yekaterinburg (Russian Federation); Institute of Physics and Technology, Ural Federal University, 620002 Yekaterinburg (Russian Federation); Zatsepin, A.F. [Institute of Physics and Technology, Ural Federal University, 620002 Yekaterinburg (Russian Federation); Cui, L. [Shenzhen Graduate School, Harbin Institute of Technology, Shenzhen 518055 (China); Shur, V. Ya.; Esin, A.A. [Institute of Natural Sciences, Ural Federal University, 51 Lenin Ave, 620000 Yekaterinburg (Russian Federation)

    2017-05-31

    Highlights: • Two modes of ZnO:Pb in the bulk and surface morphologies were established: the high- and low-interaction. • It was shown the ambiguity contribution of Pb 4f − Zn 3s and Pb 5d − O 2s states into final electronic structure. • The main type of defects is PbO-like with some PbO{sub 2}-like contributions. • An applied wurzite-like structural model well agrees with experimental data obtained for zincite. - Abstract: The electronic structures of zincite Pb-modulated bulk and thin-films were studied via X-ray photoelectron spectroscopy (XPS) and density functional theory (DFT) techniques. Both XPS data and DFT-calculations allowed the derivation of two different Pb-embedding scenarios into the ZnO-hosts. These included the high-interaction mode of Pb-impurity with initial zinc-oxygen host-lattice for the bulk morphology, accompanied with low Pb-metal losses; and the low-interaction mode for thin-films, where there was intake of Pb-impurities into the hollows of the surface. Despite dissimilar mechanisms of Pb-impurity accumulation and distribution in the bulk and thin-films zincite host-matrices, the strong Pb 4f — Zn 3s and Pb 5d — O 2s overlapped ambiguity contribution to the appropriate core-level structure and valence bands was established by XPS analysis and reproduced with the help of DFT-calculations. It was shown that the microscopic structure of the embedded lead-impurity played a crucial role in the Pb ion-beam stimulated synthesis of secondary lead-oxygen phases via large-area defect fabrication, and the difference among zincite and wurzite polymorphs played almost no role in this case.

  4. Advanced toroidal facility vaccuum vessel stress analyses

    International Nuclear Information System (INIS)

    Hammonds, C.J.; Mayhall, J.A.

    1987-01-01

    The complex geometry of the Advance Toroidal Facility (ATF) vacuum vessel required special analysis techniques in investigating the structural behavior of the design. The response of a large-scale finite element model was found for transportation and operational loading. Several computer codes and systems, including the National Magnetic Fusion Energy Computer Center Cray machines, were implemented in accomplishing these analyses. The work combined complex methods that taxed the limits of both the codes and the computer systems involved. Using MSC/NASTRAN cyclic-symmetry solutions permitted using only 1/12 of the vessel geometry to mathematically analyze the entire vessel. This allowed the greater detail and accuracy demanded by the complex geometry of the vessel. Critical buckling-pressure analyses were performed with the same model. The development, results, and problems encountered in performing these analyses are described. 5 refs., 3 figs

  5. Advanced Toroidal Facility vacuum vessel stress analyses

    International Nuclear Information System (INIS)

    Hammonds, C.J.; Mayhall, J.A.

    1987-01-01

    The complex geometry of the Advanced Toroidal Facility (ATF) vacuum vessel required special analysis techniques in investigating the structural behavior of the design. The response of a large-scale finite element model was found for transportation and operational loading. Several computer codes and systems, including the National Magnetic Fusion Energy Computer Center Cray machines, were implemented in accomplishing these analyses. The work combined complex methods that taxed the limits of both the codes and the computer systems involved. Using MSC/NASTRAN cyclic-symmetry solutions permitted using only 1/12 of the vessel geometry to mathematically analyze the entire vessel. This allowed the greater detail and accuracy demanded by the complex geometry of the vessel. Critical buckling-pressure analyses were performed with the same model. The development, results, and problems encountered in performing these analyses are described

  6. Sorption analyses in materials science: selected oxides

    International Nuclear Information System (INIS)

    Fuller, E.L. Jr.; Condon, J.B.; Eager, M.H.; Jones, L.L.

    1981-01-01

    Physical adsorption studies have been shown to be extremely valuable in studying the chemistry and structure of dispersed materials. Many processes rely on the access to the large amount of surface made available by the high degree of dispersion. Conversely, there are many applications where consolidation of the dispersed solids is required. Several systems (silica gel, alumina catalysts, mineralogic alumino-silicates, and yttrium oxide plasters) have been studied to show the type and amount of chemical and structural information that can be obtained. Some review of current theories is given and additional concepts are developed based on statistical and thermodynamic arguments. The results are applied to sorption data to show that detailed sorption analyses are extremely useful and can provide valuable information that is difficult to obtain by any other means. Considerable emphasis has been placed on data analyses and interpretation of a nonclassical nature to show the potential of such studies that is often not recognized nor utilized

  7. Multiple Imputation for Network Analyses

    NARCIS (Netherlands)

    Krause, Robert; Huisman, Mark; Steglich, Christian; Snijders, Thomas

    2016-01-01

    Missing data on network ties is a fundamental problem for network analyses. The biases induced by missing edge data, even when missing completely at random (MCAR), are widely acknowledged and problematic for network analyses (Kossinets, 2006; Huisman & Steglich, 2008; Huisman, 2009). Although

  8. Low temperature X-ray structure analyses combined with NBO studies of a new heteroleptic octa-coordinated Holmium(III) complex with N,N,N-tridentate hydrazono-phthalazine-type ligand

    Science.gov (United States)

    Soliman, Saied M.; El-Faham, Ayman

    2018-04-01

    The new heteroleptic [HoL(H2O)5]Br3 complex, L is hydrazono-phthalazine ligand, is synthesized and its molecular structure aspects were analyzed using single crystal X-ray structure (SCXRD), Hirshfeld (HF) analysis, quantum theory of atoms in molecules (QTAIM) and natural bond orbital (NBO) method. The SCXRD showed that the Ho is octa-coordinated with one N,N,N-tridentate ligand L and five water molecules. The HF analysis is used to analyze the molecular packing in the [HoL(H2O)5]Br3crystal structure. The complex cations are connected via strong Osbnd H⋯Br and Nsbnd H⋯Br H-bonding interactions which have greater importance than the Csbnd H⋯Br contacts. Also, all the Hosbnd N and Hosbnd O bonds have the characteristics of closed shell interactions using QTAIM. The natural orbitals included in these interactions were analyzed using NBO method. The alpha LP*(8)Ho and beta LP*(4)Ho which have mainly s-orbital characters are the most important anti-bonding natural orbitals included in all Ho-N and Hosbnd O bonds. The rest of the Ho anti-bonding orbitals which have either p or d-orbital characters shared partially in the Ho-ligands interactions. Natural charges analysis revealed the presence of significant amount of electron density (0.9225-0.9300 e) transferred from the ligands to Ho (2.0700-2.0775 e). Spherical spin density with ∼4.0 e is predicted over the Ho atom.

  9. Report of the experts' mission to review thermal hydraulic and structural analyses for PTS assessment of Kozloduy NPP units 1-4 reactor pressure vessels, Sofia, Bulgaria 3-7 April 1995

    International Nuclear Information System (INIS)

    1995-01-01

    Based upon a request of the Government of Bulgaria and in order to assist its Regulatory Body, an experts' mission was carried out to Sofia and Kozloduy, 21-25 November 1994 within the framework of the IAEA TC Project BUL/9/013-05 and of the IAEA Extrabudgetary Programme on the Safety of the WWER NPPs. The mission also specified the technical content of further assistance by the IAEA. With respect to the findings and recommendations made in November 1994, WWER-SC-109, a follow-up expert's mission was carried out to Sofia, Bulgaria, April 3-7, 1995. The objective of the mission was to review the selection of transients, thermal hydraulic, stress and fracture mechanics analyses for reactor pressure vessel integrity assessment of Kozloduy unit 1-4. In addition, an update on the activities completed, underway and planned related to unit 1 reactor pressure vessel embrittlement was presented and discussed. The review was carried out by 4 international experts from Finland, France, Russia and IAEA in co-operation with the Bulgarian regulatory body, plant, Energoproject Sofia and Institute of Metals staff. The mission was conducted out within the frame of the IAEA TC Project BUL/9/013-05 and of the IAEA Extrabudgetary Programme on the Safety of the WWER NPPs. 18 refs

  10. Comparative structure analyses of cystine knot-containing molecules with eight aminoacyl ring including glycoprotein hormones (GPH alpha and beta subunits and GPH-related A2 (GPA2 and B5 (GPB5 molecules

    Directory of Open Access Journals (Sweden)

    Combarnous Yves

    2009-08-01

    Full Text Available Abstract Background Cystine-knot (cys-knot structure is found in a rather large number of secreted proteins and glycoproteins belonging to the TGFbeta and glycoprotein hormone (GPH superfamilies, many of which are involved in endocrine control of reproduction. In these molecules, the cys-knot is formed by a disulfide (SS bridge penetrating a ring formed by 8, 9 or 10 amino-acid residues among which four are cysteine residues forming two SS bridges. The glycoprotein hormones Follicle-Stimulating Hormone (FSH, Luteinizing Hormone (LH, Thyroid-Stimulating Hormone (TSH and Chorionic Gonadotropin (CG are heterodimers consisting of non-covalently associated alpha and beta subunits that possess cys-knots with 8-amino-acyl (8aa rings. In order to get better insight in the structural evolution of glycoprotein hormones, we examined the number and organization of SS bridges in the sequences of human 8-aa-ring cys-knot proteins having 7 (gremlins, 9 (cerberus, DAN, 10 (GPA2, GPB5, GPHα and 12 (GPHβ cysteine residues in their sequence. Discussion The comparison indicated that the common GPH-alpha subunit exhibits a SS bridge organization ressembling that of DAN and GPA2 but possesses a unique bridge linking an additional cysteine inside the ring to the most N-terminal cysteine residue. The specific GPHbeta subunits also exhibit a SS bridge organization close to that of DAN but it has two additional C-terminal cysteine residues which are involved in the formation of the "seat belt" fastened by a SS "buckle" that ensures the stability of the heterodimeric structure of GPHs. GPA2 and GPB5 exhibit no cys residue potentially involved in interchain SS bridge and GPB5 does not possess a sequence homologous to that of the seatbelt in GPH β-subunits. GPA2 and GPB5 are thus not expected to form a stable heterodimer at low concentration in circulation. Summary The 8-aa cys-knot proteins GPA2 and GPB5 are expected to form a heterodimer only at concentrations above 0

  11. A new 1D manganese(II) coordination polymer with end-to-end azide bridge and isonicotinoylhydrazone Schiff base ligand: Crystal structure, Hirshfeld surface, NBO and thermal analyses

    Science.gov (United States)

    Khani, S.; Montazerozohori, M.; Masoudiasl, A.; White, J. M.

    2018-02-01

    A new manganese (II) coordination polymer, [MnL2 (μ-1,3-N3)2]n, with co-ligands including azide anion and Schiff base based on isonicotinoylhydrazone has been synthesized and characterized. The crystal structure determination shows that the azide ligand acts as end-to-end (EE) bridging ligand and generates a one-dimensional coordination polymer. In this compound, each manganes (II) metal center is hexa-coordinated by four azide nitrogens and two pyridinic nitrogens for the formation of octahedral geometry. The analysis of crystal packing indicates that the 1D chain of [MnL2 (μ-1,3-N3)2]n, is stabilized as a 3D supramolecular network by intra- and inter-chain intermolecular interactions of X-H···Y (X = N and C, Y = O and N). Hirshfeld surface analysis and 2D fingerprint plots have been used for a more detailed investigation of intermolecular interactions. Also, natural bond orbital (NBO) analysis was performed to get information about atomic charge distributions, hybridizations and the strength of interactions. Finally, thermal analysis of compound showed its complete decomposition during three thermal steps.

  12. Melatonin charge transfer complex with 2,3-dichloro-5,6-dicyano-1,4-benzoquinone: Molecular structure, DFT studies, thermal analyses, evaluation of biological activity and utility for determination of melatonin in pure and dosage forms

    Science.gov (United States)

    Mohamed, Gehad G.; Hamed, Maher M.; Zaki, Nadia G.; Abdou, Mohamed M.; Mohamed, Marwa El-Badry; Abdallah, Abanoub Mosaad

    2017-07-01

    A simple, accurate and fast spectrophotometric method for the quantitative determination of melatonin (ML) drug in its pure and pharmaceutical forms was developed based on the formation of its charge transfer complex with 2,3-dichloro-5,6-dicyano-1,4-benzoquinone (DDQ) as an electron acceptor. The different conditions for this method were optimized accurately. The Lambert-Beer's law was found to be valid over the concentration range of 4-100 μg mL- 1 ML. The solid form of the CT complex was structurally characterized by means of different spectral methods. Density functional theory (DFT) and time-dependent density functional theory (TD-DFT) calculations were carried out. The different quantum chemical parameters of the CT complex were calculated. Thermal properties of the CT complex and its kinetic thermodynamic parameters were studied, as well as its antimicrobial and antifungal activities were investigated. Molecular docking studies were performed to predict the binding modes of the CT complex components towards E. coli bacterial RNA and the receptor of breast cancer mutant oxidoreductase.

  13. Hyperfine structure analysis in magnetic resonance spectroscopy: from astrophysical measurements towards endogenous biosensors in human tissue; Hyperfeinstruktur-Analyse in der Magnetresonanzspektroskopie: von astrophysikalischen Messungen zu endogenen Biosensoren in menschlichem Gewebe

    Energy Technology Data Exchange (ETDEWEB)

    Schroeder, L. [Deutsches Krebsforschungszentrum, Heidelberg (Germany). Medizinische Physik in der Radiologie; California Univ., Berkeley, CA (United States). Dept. of Chemistry; Lawrence Berkeley National Lab., Berkeley, CA (United States). Dept. of Chemistry

    2007-07-01

    The hyperfine interaction of two spins is a well studied effect in atomic systems. Magnetic resonance experiments demonstrate that the detectable dipole transitions are determined by the magnetic moments of the constituents and the external magnetic field. Transferring the corresponding quantum mechanics to molecular bound nuclear spins allows for precise prediction of NMR spectra obtained from metabolites in human tissue. This molecular hyperfine structure has been neglected so far in in vivo NMR spectroscopy but contains useful information, especially when studying molecular dynamics. This contribution represents a review of the concept of applying the Breit-Rabi formalism to coupled nuclear spins and discusses the immobilization of different metabolites in anisotropic tissue revealed by 1H NMR spectra of carnosine, phosphocreatine and taurine. Comparison of atomic and molecular spin systems allows for statements on the biological constraints for direct spin-spin interactions. Moreover, the relevance of hyperfine effects on the line shapes of multiplets of indirectly-coupled spin systems with more than two constituents can be predicted by analyzing quantum mechanical parameters. As an example, the superposition of eigenstates of the AMX system of adenosine 5'-triphosphate and its application for better quantification of 31P-NMR spectra will be discussed. (orig.)

  14. Structure, spectroscopic analyses (FT-IR and NMR), vibrational study, chemical reactivity and molecular docking study on 3,3'-((4-(trifluoromethyl)phenyl)methylene)bis(2-hydroxynaphthalene-1,4-dione), a promising anticancerous bis-lawsone derivative

    Science.gov (United States)

    Yadav, Krishna Kant; Kumar, Abhishek; Kumar, Amarendra; Misra, Neeraj; Brahmachari, Goutam

    2018-02-01

    Lawsone (2-hydroxy-1,4-naphthoquinone)has been evaluated to possess a wide range of biological and pharmacological activities. The interesting structural pattern of lawsone coupled with its so-called multifaceted pharmacological potential have made this scaffolds useful in certain chemical processes, particularly in synthesizing ligands for metal complexations, and also few of its derivatives have shown a number of biological activities. The equilibrium geometry of 3,3‧-((4-(trifluoromethyl)phenyl)methylene)bis(2-hydroxynaphthalene-1,4-dione) (1; TPMHD), a promising anticancerous lawsone derivative, has been determined and analyzed at DFT method employingB3LYP/6-311++G(d,p) level of theory. The reactivity descriptors such as Fukui functions and HOMO-LUMO gap are calculated and discussed. The infrared spectra of TPMHD(1) are calculated and compared with the experimentally observed ones. Moreover, 1H and 13C NMR spectra have been calculated by using the gauge independent atomic orbital method. The docking studies reveal that the TPMHD has strong binding affinity toward target protein 2SHP. Thus the compound has a possible use as a drug in cancer therapy. The study suggests further investigation on TPMHD for their in-depth biological and pharmaceutical importance.

  15. Competitive effects and instruments of power sector reforms. International reform concepts blockade structures, risk distribution. A political economy analysis; Wettbewerbseffekte und Instrumente von Stromsektorreformen. Internationale Reformkonzepte, Blockadestrukturen, Risikoverteilung. Eine politoekonomische Analyse

    Energy Technology Data Exchange (ETDEWEB)

    Liebchen, Armin [Liebchen Consulting, Berlin (Germany)

    2014-07-01

    Power sectors with weak or inadequate competition structures are the rule, despite numerous attempts at reform. But can afford modern economies this defect for a long time? Why can the implementation of competition are blocked so effectively? The author studied international reform experiences and opens up interesting insights that can also reflect on problems of the German energy turnaround: The difficulty of timing and coordination of the reform components, the development of resistance levels of individual interest groups, breach of contract as a rational alternative, causes unwanted price effects, shifting interest situations of major stakeholders, change dynamics impending regulatory risks, pending financing risks, stranded cost-conflict situations for power stations disconnected from the grid and facilities and instruments of a political and regulatory risk management for reforms. With numerous examples, background analyzes and instruments to reform analysis, this book is aimed at investors, policy planners and analysts. [German] Stromsektoren mit schwachen oder unzulaenglichen Wettbewerbsstrukturen sind trotz zahlreicher Reformversuche die Regel. Aber koennen sich moderne Volkswirtschaften diesen Mangel dauerhaft leisten? Warum kann die Einfuehrung von Wettbewerb so wirksam blockiert werden? Der Autor untersucht internationale Reformerfahrungen und eroeffnet interessante Einsichten, die sich auch auf Problemlagen der deutschen Energiewende spiegeln lassen: Die Schwierigkeit des richtigen Timings und der Abstimmung der Reformteile, dem Aufbau von Widerstandslinien einzelner Interessensgruppen, Vertragsbruch als rationaler Alternative, Ursachen unerwuenschter Preiseffekte, sich verschiebenden Interessenslagen wichtiger Akteure, Veraenderungsdynamik drohender Regulierungsrisiken, schwebenden Finanzierungsrisiken, stranded-cost-Konfliktlagen fuer vom Netz genommene Kraftwerke und Moeglichkeiten und Instrumenten eines politisch-regulatorischen Risikomanagements

  16. Métodos estatísticos e estrutura espacial de populações: uma análise comparativa = Statistic methods and population spatial structure: a comparative analyses

    Directory of Open Access Journals (Sweden)

    Matheus de Souza Lima-Ribeiro

    2006-07-01

    Full Text Available O presente estudo teve por objetivo comparar os resultados de distribuição espacial obtidos entre os métodos clássicos e os métodos que estimam a variância entre parcelas. Foram analisadas duas espécies, Vernonia aurea e Duguetia furfuracea. Foram utilizados a Distribuição de Poisson (padrão aleatório, a Distribuição Binomial Negativa (padrão agregado e os métodos BQV, TTLQV e PQV (variância entre parcelas, bem como a razão variância:média (I, coeficiente de Green (Ig e o índice de dispersão de Morisita (Im. Ambas metodologias detectaram padrão de distribuição espacial agregado para as populações analisadas, com resultados similares quanto ao nível de agregação, além de complementação das informações, em diferentes escalas, entre os métodos clássicos e de variância entre parcelas. Desse modo, recomenda-se a utilização desses métodos estatísticos em estudos de estrutura espacial, uma vez que os testes são robustos e complementares e os dados são de fácil coleta em campo.This study aims to compare the results of spatial structure obtained between the classic and quadrat variance methods. Two species were analised, Vernonia aurea and Duguetia furfuracea. The Poisson distribution (random pattern, the Negative Binomial distribution (aggregate pattern, the BQV, TTLQV and PQV methods, the ratiovariance: mean (I, the Green coefficient (Ig and the Morisita’s index of dispersion (Im were used to detect the populations spatial pattern. An aggregated spatial pattern distribution was detected through both methodologies, with similar results as for the aggregation level and the complementation of the information in different scales between classic and quadrat variance methods. Thus, the utilization of these statistic methods in studies of the spatialstructure is recommended, given that tests are robust and complementary and field data samples are easy to collect.

  17. An extensible analysable system model

    DEFF Research Database (Denmark)

    Probst, Christian W.; Hansen, Rene Rydhof

    2008-01-01

    Analysing real-world systems for vulnerabilities with respect to security and safety threats is a difficult undertaking, not least due to a lack of availability of formalisations for those systems. While both formalisations and analyses can be found for artificial systems such as software......, this does not hold for real physical systems. Approaches such as threat modelling try to target the formalisation of the real-world domain, but still are far from the rigid techniques available in security research. Many currently available approaches to assurance of critical infrastructure security...... are based on (quite successful) ad-hoc techniques. We believe they can be significantly improved beyond the state-of-the-art by pairing them with static analyses techniques. In this paper we present an approach to both formalising those real-world systems, as well as providing an underlying semantics, which...

  18. Sample preparation in foodomic analyses.

    Science.gov (United States)

    Martinović, Tamara; Šrajer Gajdošik, Martina; Josić, Djuro

    2018-04-16

    Representative sampling and adequate sample preparation are key factors for successful performance of further steps in foodomic analyses, as well as for correct data interpretation. Incorrect sampling and improper sample preparation can be sources of severe bias in foodomic analyses. It is well known that both wrong sampling and sample treatment cannot be corrected anymore. These, in the past frequently neglected facts, are now taken into consideration, and the progress in sampling and sample preparation in foodomics is reviewed here. We report the use of highly sophisticated instruments for both high-performance and high-throughput analyses, as well as miniaturization and the use of laboratory robotics in metabolomics, proteomics, peptidomics and genomics. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

  19. Mitogenomic analyses from ancient DNA

    DEFF Research Database (Denmark)

    Paijmans, Johanna L. A.; Gilbert, Tom; Hofreiter, Michael

    2013-01-01

    The analysis of ancient DNA is playing an increasingly important role in conservation genetic, phylogenetic and population genetic analyses, as it allows incorporating extinct species into DNA sequence trees and adds time depth to population genetics studies. For many years, these types of DNA...... analyses (whether using modern or ancient DNA) were largely restricted to the analysis of short fragments of the mitochondrial genome. However, due to many technological advances during the past decade, a growing number of studies have explored the power of complete mitochondrial genome sequences...... (mitogenomes). Such studies were initially limited to analyses of extant organisms, but developments in both DNA sequencing technologies and general methodological aspects related to working with degraded DNA have resulted in complete mitogenomes becoming increasingly popular for ancient DNA studies as well...

  20. Pawnee Nation Energy Option Analyses

    Energy Technology Data Exchange (ETDEWEB)

    Matlock, M.; Kersey, K.; Riding In, C.

    2009-07-21

    Pawnee Nation of Oklahoma Energy Option Analyses In 2003, the Pawnee Nation leadership identified the need for the tribe to comprehensively address its energy issues. During a strategic energy planning workshop a general framework was laid out and the Pawnee Nation Energy Task Force was created to work toward further development of the tribe’s energy vision. The overarching goals of the “first steps” project were to identify the most appropriate focus for its strategic energy initiatives going forward, and to provide information necessary to take the next steps in pursuit of the “best fit” energy options. Description of Activities Performed The research team reviewed existing data pertaining to the availability of biomass (focusing on woody biomass, agricultural biomass/bio-energy crops, and methane capture), solar, wind and hydropower resources on the Pawnee-owned lands. Using these data, combined with assumptions about costs and revenue streams, the research team performed preliminary feasibility assessments for each resource category. The research team also reviewed available funding resources and made recommendations to Pawnee Nation highlighting those resources with the greatest potential for financially-viable development, both in the near-term and over a longer time horizon. Findings and Recommendations Due to a lack of financial incentives for renewable energy, particularly at the state level, combined mediocre renewable energy resources, renewable energy development opportunities are limited for Pawnee Nation. However, near-term potential exists for development of solar hot water at the gym, and an exterior wood-fired boiler system at the tribe’s main administrative building. Pawnee Nation should also explore options for developing LFGTE resources in collaboration with the City of Pawnee. Significant potential may also exist for development of bio-energy resources within the next decade. Pawnee Nation representatives should closely monitor

  1. Finite element analyses for RF photoinjector gun cavities

    International Nuclear Information System (INIS)

    Marhauser, F.

    2006-01-01

    This paper details electromagnetical, thermal and structural 3D Finite Element Analyses (FEA) for normal conducting RF photoinjector gun cavities. The simulation methods are described extensively. Achieved results are presented. (orig.)

  2. Structural Behaviour of Reciprocal Structures

    DEFF Research Database (Denmark)

    Parigi, Dario; Kirkegaard, Poul Henning

    2013-01-01

    The present paper focuses on the comparison of several two-dimensional and three-dimensional reciprocal configurations. The goal of such comparison is to analyse the structural behaviour when changing the geometric parameters used to describe the geometry of reciprocal structures.......The present paper focuses on the comparison of several two-dimensional and three-dimensional reciprocal configurations. The goal of such comparison is to analyse the structural behaviour when changing the geometric parameters used to describe the geometry of reciprocal structures....

  3. Analyses Of High Voltage Transmission Cables In South Western ...

    African Journals Online (AJOL)

    ... unit diameter) of the analysed underground cable is good compared with the standard conductor, the overhead cable has a poor load bearing capability. SEM and EDX analyses show that both the underground and the overhead cables contain impurities that are deleterious to the structure and their functional properties.

  4. Finite strain analyses of deformations in polymer specimens

    DEFF Research Database (Denmark)

    Tvergaard, Viggo

    2016-01-01

    Analyses of the stress and strain state in test specimens or structural components made of polymer are discussed. This includes the Izod impact test, based on full 3D transient analyses. Also a long thin polymer tube under internal pressure has been studied, where instabilities develop, such as b...

  5. BWR core melt progression phenomena: Experimental analyses

    International Nuclear Information System (INIS)

    Ott, L.J.

    1992-01-01

    In the BWR Core Melt in Progression Phenomena Program, experimental results concerning severe fuel damage and core melt progression in BWR core geometry are used to evaluate existing models of the governing phenomena. These include control blade eutectic liquefaction and the subsequent relocation and attack on the channel box structure; oxidation heating and hydrogen generation; Zircaloy melting and relocation; and the continuing oxidation of zirconium with metallic blockage formation. Integral data have been obtained from the BWR DF-4 experiment in the ACRR and from BWR tests in the German CORA exreactor fuel-damage test facility. Additional integral data will be obtained from new CORA BWR test, the full-length FLHT-6 BWR test in the NRU test reactor, and the new program of exreactor experiments at Sandia National Laboratories (SNL) on metallic melt relocation and blockage formation. an essential part of this activity is interpretation and use of the results of the BWR tests. The Oak Ridge National Laboratory (ORNL) has developed experiment-specific models for analysis of the BWR experiments; to date, these models have permitted far more precise analyses of the conditions in these experiments than has previously been available. These analyses have provided a basis for more accurate interpretation of the phenomena that the experiments are intended to investigate. The results of posttest analyses of BWR experiments are discussed and significant findings from these analyses are explained. The ORNL control blade/canister models with materials interaction, relocation and blockage models are currently being implemented in SCDAP/RELAP5 as an optional structural component

  6. Analysing and Comparing Encodability Criteria

    Directory of Open Access Journals (Sweden)

    Kirstin Peters

    2015-08-01

    Full Text Available Encodings or the proof of their absence are the main way to compare process calculi. To analyse the quality of encodings and to rule out trivial or meaningless encodings, they are augmented with quality criteria. There exists a bunch of different criteria and different variants of criteria in order to reason in different settings. This leads to incomparable results. Moreover it is not always clear whether the criteria used to obtain a result in a particular setting do indeed fit to this setting. We show how to formally reason about and compare encodability criteria by mapping them on requirements on a relation between source and target terms that is induced by the encoding function. In particular we analyse the common criteria full abstraction, operational correspondence, divergence reflection, success sensitiveness, and respect of barbs; e.g. we analyse the exact nature of the simulation relation (coupled simulation versus bisimulation that is induced by different variants of operational correspondence. This way we reduce the problem of analysing or comparing encodability criteria to the better understood problem of comparing relations on processes.

  7. Descriptive Analyses of Mechanical Systems

    DEFF Research Database (Denmark)

    Andreasen, Mogens Myrup; Hansen, Claus Thorp

    2003-01-01

    Forord Produktanalyse og teknologianalyse kan gennmføres med et bredt socio-teknisk sigte med henblik på at forstå kulturelle, sociologiske, designmæssige, forretningsmæssige og mange andre forhold. Et delområde heri er systemisk analyse og beskrivelse af produkter og systemer. Nærværende kompend...

  8. Millifluidic droplet analyser for microbiology

    NARCIS (Netherlands)

    Baraban, L.; Bertholle, F.; Salverda, M.L.M.; Bremond, N.; Panizza, P.; Baudry, J.; Visser, de J.A.G.M.; Bibette, J.

    2011-01-01

    We present a novel millifluidic droplet analyser (MDA) for precisely monitoring the dynamics of microbial populations over multiple generations in numerous (=103) aqueous emulsion droplets (100 nL). As a first application, we measure the growth rate of a bacterial strain and determine the minimal

  9. Workload analyse of assembling process

    Science.gov (United States)

    Ghenghea, L. D.

    2015-11-01

    The workload is the most important indicator for managers responsible of industrial technological processes no matter if these are automated, mechanized or simply manual in each case, machines or workers will be in the focus of workload measurements. The paper deals with workload analyses made to a most part manual assembling technology for roller bearings assembling process, executed in a big company, with integrated bearings manufacturing processes. In this analyses the delay sample technique have been used to identify and divide all bearing assemblers activities, to get information about time parts from 480 minutes day work time that workers allow to each activity. The developed study shows some ways to increase the process productivity without supplementary investments and also indicated the process automation could be the solution to gain maximum productivity.

  10. Safety analyses of surface facilities

    International Nuclear Information System (INIS)

    Anspach, W.; Baran, A.; Dorst, H.J.; Eifert, B.; Gruen, M.; Behrendt, V.; Berkhan, W.; Dincklage, R.D. v.; Doehler, J.; Bruecher, H.

    1981-01-01

    The investigations were carried out using the example of the Gorleben waste disposal center and the planning documents established for this center. The safety analyses refer to the transport of spent fuel elements, the water-cooled interin storage and the reprocessing stage. Regarding the risk analysis of the technical systems the dynamics of the courses of incidents can be better taken into account by doing a methodical development. (DG) [de

  11. Technical center for transportation analyses

    International Nuclear Information System (INIS)

    Foley, J.T.

    1978-01-01

    A description is presented of an information search/retrieval/research activity of Sandia Laboratories which provides technical environmental information which may be used in transportation risk analyses, environmental impact statements, development of design and test criteria for packaging of energy materials, and transportation mode research studies. General activities described are: (1) history of center development; (2) environmental information storage/retrieval system; (3) information searches; (4) data needs identification; and (5) field data acquisition system and applications

  12. Methodology of cost benefit analyses

    International Nuclear Information System (INIS)

    Patrik, M.; Babic, P.

    2000-10-01

    The report addresses financial aspects of proposed investments and other steps which are intended to contribute to nuclear safety. The aim is to provide introductory insight into the procedures and potential of cost-benefit analyses as a routine guide when making decisions on costly provisions as one of the tools to assess whether a particular provision is reasonable. The topic is applied to the nuclear power sector. (P.A.)

  13. Uncertainty in Operational Atmospheric Analyses and Re-Analyses

    Science.gov (United States)

    Langland, R.; Maue, R. N.

    2016-12-01

    This talk will describe uncertainty in atmospheric analyses of wind and temperature produced by operational forecast models and in re-analysis products. Because the "true" atmospheric state cannot be precisely quantified, there is necessarily error in every atmospheric analysis, and this error can be estimated by computing differences ( variance and bias) between analysis products produced at various centers (e.g., ECMWF, NCEP, U.S Navy, etc.) that use independent data assimilation procedures, somewhat different sets of atmospheric observations and forecast models with different resolutions, dynamical equations, and physical parameterizations. These estimates of analysis uncertainty provide a useful proxy to actual analysis error. For this study, we use a unique multi-year and multi-model data archive developed at NRL-Monterey. It will be shown that current uncertainty in atmospheric analyses is closely correlated with the geographic distribution of assimilated in-situ atmospheric observations, especially those provided by high-accuracy radiosonde and commercial aircraft observations. The lowest atmospheric analysis uncertainty is found over North America, Europe and Eastern Asia, which have the largest numbers of radiosonde and commercial aircraft observations. Analysis uncertainty is substantially larger (by factors of two to three times) in most of the Southern hemisphere, the North Pacific ocean, and under-developed nations of Africa and South America where there are few radiosonde or commercial aircraft data. It appears that in regions where atmospheric analyses depend primarily on satellite radiance observations, analysis uncertainty of both temperature and wind remains relatively high compared to values found over North America and Europe.

  14. Exploratory structural assessment in craniocervical dystonia: Global and differential analyses.

    Directory of Open Access Journals (Sweden)

    Larissa Vilany

    Full Text Available Our goal was to investigate the cortical thickness and subcortical volume in subjects with craniocervical dystonia and its subgroups.We studied 49 subjects, 17 with cervical dystonia, 18 with blepharospasm or oromandibular dystonia, and 79 healthy controls. We performed a whole group analysis, followed by a subgroup analysis. We used Freesurfer software to measure cortical thickness, subcortical volume and to perform a primary exploratory analysis in the craniocervical dystonia group, complemented by a region of interest analysis. We also performed a secondary analysis, with data generated from Freesurfer for subgroups, corrected by false discovery rate. We then performed an exploratory generalized linear model with significant areas for the previous steps using clinical features as independent variables.The primary exploratory analysis demonstrated atrophy in visual processing regions in craniocervical dystonia. The secondary analysis demonstrated atrophy in motor, sensory, and visual regions in blepharospasm or oromandibular dystonia, as well as in limbic regions in cervical dystonia. Cervical dystonia patients also had greater cortical thickness than blepharospasm or oromandibular dystonia patients in frontal pole and medial orbitofrontal regions. Finally, we observed an association between precuneus, age of onset of dystonia and age at the MRI exam, in craniocervical dystonia; between motor and limbic regions and age at the exam, clinical score and time on botulinum toxin in cervical dystonia and sensory regions and age of onset and time on botulinum toxin in blepharospasm or oromandibular dystonia.We detected involvement of visual processing regions in craniocervical dystonia, and a pattern of involvement in cervical dystonia and blepharospasm or oromandibular dystonia, including motor, sensory and limbic areas. We also showed an association of cortical thickness atrophy and younger onset age, older age at the MRI exam, higher clinical score and an uncertain association with longer time on botulinum toxin.

  15. Analyse des structures planaires multicouches à ferrite par la ...

    African Journals Online (AJOL)

    Electromagnetic Analysis of microwave integrated circuits is an attractive subject do to the recent development and use of new materials such as magnetic anisotropic materials (hexaferrite, ...). These materials are used in many microwave components (isolator, circulator, phase shifter) employed in telecommunication ...

  16. UNDERSTANDING RELIGIOUS VIOLENCE IN INDONESIA: Theological, Structural and Cultural Analyses

    Directory of Open Access Journals (Sweden)

    Ahmad Salehudin

    2012-12-01

    Full Text Available Lately Indonesia is facing a lot of tremendous experience about religious violence. Indonesian Islam which is previously assumed as peaceful religion is suddenly changing to be frightening religion. The destruction in some places such as Bali Bombing, JW Marriot Bombing, and Sampang riot in some places Islam is the trigger of religious violence. This paper discusses the repetition of religious violence in Indonesia especially after New Order era. The writer argues that religious violence in Indonesia is as natural disaster, historical process in human evolution and as close experience that presenting and relating to human history. It may be caused by political condition and the response to economic injustice. In doing so, it is kind of social acceleration toward the process of change and also being a factor of the emergence of new agenda. This is because every disaster, including religious violence, requires an adjustment and a new formulation of the functions that have been damaged.

  17. Structural and gene expression analyses of uptake hydrogenases ...

    Indian Academy of Sciences (India)

    2013-10-01

    Oct 1, 2013 ... Bioinformatics Conference, Proceedings 728–729. Fleming AI, Wittenberg JB, Wittenberg BA, Dudman WF and. Appleby CA 1987 The purification, characterization and ligand-binding kinetics of hemoglobins from root-nodules of the non-leguminous Casuarina-Glauca-Frankia symbiosis. Biochim. Biophys.

  18. A variable thickness window: Thermal and structural analyses

    International Nuclear Information System (INIS)

    Wang, Zhibi; Kuzay, T.M.

    1994-01-01

    In this paper, the finite difference formulations for variable thickness thermal analysis and variable thickness plane stress analysis are presented. In heat transfer analysis, radiation effects and temperature-dependent thermal conductivity are taken into account. While in thermal stress analysis, the thermal expansion coefficient is considered as temperature dependent. An application of the variable thickness window to an Advanced Photon Source beamline is presented

  19. Providing traceability for neuroimaging analyses.

    Science.gov (United States)

    McClatchey, Richard; Branson, Andrew; Anjum, Ashiq; Bloodsworth, Peter; Habib, Irfan; Munir, Kamran; Shamdasani, Jetendr; Soomro, Kamran

    2013-09-01

    With the increasingly digital nature of biomedical data and as the complexity of analyses in medical research increases, the need for accurate information capture, traceability and accessibility has become crucial to medical researchers in the pursuance of their research goals. Grid- or Cloud-based technologies, often based on so-called Service Oriented Architectures (SOA), are increasingly being seen as viable solutions for managing distributed data and algorithms in the bio-medical domain. For neuroscientific analyses, especially those centred on complex image analysis, traceability of processes and datasets is essential but up to now this has not been captured in a manner that facilitates collaborative study. Few examples exist, of deployed medical systems based on Grids that provide the traceability of research data needed to facilitate complex analyses and none have been evaluated in practice. Over the past decade, we have been working with mammographers, paediatricians and neuroscientists in three generations of projects to provide the data management and provenance services now required for 21st century medical research. This paper outlines the finding of a requirements study and a resulting system architecture for the production of services to support neuroscientific studies of biomarkers for Alzheimer's disease. The paper proposes a software infrastructure and services that provide the foundation for such support. It introduces the use of the CRISTAL software to provide provenance management as one of a number of services delivered on a SOA, deployed to manage neuroimaging projects that have been studying biomarkers for Alzheimer's disease. In the neuGRID and N4U projects a Provenance Service has been delivered that captures and reconstructs the workflow information needed to facilitate researchers in conducting neuroimaging analyses. The software enables neuroscientists to track the evolution of workflows and datasets. It also tracks the outcomes of

  20. Fractal and multifractal analyses of bipartite networks

    Science.gov (United States)

    Liu, Jin-Long; Wang, Jian; Yu, Zu-Guo; Xie, Xian-Hua

    2017-03-01

    Bipartite networks have attracted considerable interest in various fields. Fractality and multifractality of unipartite (classical) networks have been studied in recent years, but there is no work to study these properties of bipartite networks. In this paper, we try to unfold the self-similarity structure of bipartite networks by performing the fractal and multifractal analyses for a variety of real-world bipartite network data sets and models. First, we find the fractality in some bipartite networks, including the CiteULike, Netflix, MovieLens (ml-20m), Delicious data sets and (u, v)-flower model. Meanwhile, we observe the shifted power-law or exponential behavior in other several networks. We then focus on the multifractal properties of bipartite networks. Our results indicate that the multifractality exists in those bipartite networks possessing fractality. To capture the inherent attribute of bipartite network with two types different nodes, we give the different weights for the nodes of different classes, and show the existence of multifractality in these node-weighted bipartite networks. In addition, for the data sets with ratings, we modify the two existing algorithms for fractal and multifractal analyses of edge-weighted unipartite networks to study the self-similarity of the corresponding edge-weighted bipartite networks. The results show that our modified algorithms are feasible and can effectively uncover the self-similarity structure of these edge-weighted bipartite networks and their corresponding node-weighted versions.

  1. Engineering analyses of large precision cathode strip chambers for GEM

    Energy Technology Data Exchange (ETDEWEB)

    Horvath, J.A.; Belser, F.C.; Pratuch, S.M.; Wuest, C.R. [Lawrence Livermore National Lab., CA (United States); Mitselmakher, G. [Superconducting Super Collider Lab., Dallas, TX (United States); Gordeev, A. [Institute of Theoretical and Experimental Physics, Moscow (Russian Federation); Johnson, C.V. [Lawrence Livermore National Lab., CA (United States)]|[Superconducting Super Collider Lab., Dallas, TX (United States); Polychronakos, V.A. [Brookhaven National Lab., Upton, NY (United States); Golutvin, I.A. [Joint Institute for Nuclear Research, Dubna (Russian Federation)

    1993-10-21

    Structural analyses of large precision cathode strip chambers performed up to the date of this publication are documented. Mechanical property data for typical chamber materials are included. This information, originally intended to be an appendix to the {open_quotes}CSC Structural Design Bible,{close_quotes} is presented as a guide for future designers of large chambers.

  2. Comparison of elastic and inelastic analyses

    International Nuclear Information System (INIS)

    Ammerman, D.J.; Heinstein, M.W.; Wellman, G.W.

    1992-01-01

    The use of inelastic analysis methods instead of the traditional elastic analysis methods in the design of radioactive material (RAM) transport packagings leads to a better understanding of the response of the package to mechanical loadings. Thus, better assessment of the containment, thermal protection, and shielding integrity of the package after a structure accident event can be made. A more accurate prediction of the package response can lead to enhanced safety and also allow for a more efficient use of materials, possibly leading to a package with higher capacity or lower weight. This paper discusses the advantages and disadvantages of using inelastic analysis in the design of RAM shipping packages. The use of inelastic analysis presents several problems to the package designer. When using inelastic analysis the entire nonlinear response of the material must be known, including the effects of temperature changes and strain rate. Another problem is that there currently is not an acceptance criteria for this type of analysis that is approved by regulatory agencies. Inelastic analysis acceptance criteria based on failure stress, failure strain , or plastic energy density could be developed. For both elastic and inelastic analyses it is also important to include other sources of stress in the analyses, such as fabrication stresses, thermal stresses, stresses from bolt preloading, and contact stresses at material interfaces. Offsetting these added difficulties is the improved knowledge of the package behavior. This allows for incorporation of a more uniform margin of safety, which can result in weight savings and a higher level of confidence in the post-accident configuration of the package. In this paper, comparisons between elastic and inelastic analyses are made for a simple ring structure and for a package to transport a large quantity of RAM by rail (rail cask) with lead gamma shielding to illustrate the differences in the two analysis techniques

  3. Methodological challenges in carbohydrate analyses

    Directory of Open Access Journals (Sweden)

    Mary Beth Hall

    2007-07-01

    Full Text Available Carbohydrates can provide up to 80% of the dry matter in animal diets, yet their specific evaluation for research and diet formulation is only now becoming a focus in the animal sciences. Partitioning of dietary carbohydrates for nutritional purposes should reflect differences in digestion and fermentation characteristics and effects on animal performance. Key challenges to designating nutritionally important carbohydrate fractions include classifying the carbohydrates in terms of nutritional characteristics, and selecting analytical methods that describe the desired fraction. The relative lack of information on digestion characteristics of various carbohydrates and their interactions with other fractions in diets means that fractions will not soon be perfectly established. Developing a system of carbohydrate analysis that could be used across animal species could enhance the utility of analyses and amount of data we can obtain on dietary effects of carbohydrates. Based on quantities present in diets and apparent effects on animal performance, some nutritionally important classes of carbohydrates that may be valuable to measure include sugars, starch, fructans, insoluble fiber, and soluble fiber. Essential to selection of methods for these fractions is agreement on precisely what carbohydrates should be included in each. Each of these fractions has analyses that could potentially be used to measure them, but most of the available methods have weaknesses that must be evaluated to see if they are fatal and the assay is unusable, or if the assay still may be made workable. Factors we must consider as we seek to analyze carbohydrates to describe diets: Does the assay accurately measure the desired fraction? Is the assay for research, regulatory, or field use (affects considerations of acceptable costs and throughput? What are acceptable accuracy and variability of measures? Is the assay robust (enhances accuracy of values? For some carbohydrates, we

  4. Defect assessment in nuclear components: R and D related to industrial problems - synthesis of the research, training and teaching activities; Analyse de nocivite de defauts dans les structures nucleaires: R et D associee aux problemes industriels - synthese des activites de recherche, d'encadrement et d'enseignement

    Energy Technology Data Exchange (ETDEWEB)

    Marie, St

    2007-06-15

    Nuclear industry pays a particular attention to structures integrity problems: well-aware of the possible catastrophic consequence of a major accident, everything is carried out to minimise the risk of such a situation. From the design, and during all the operating life of the plant, a high level of safety is required and checks by the safety authorities, on the basis of reports made by the operator. These two entities ask for R and D activities to support the improvement of the knowledge of the phenomena already identified (as in the case of the vessel of the PWR) or to bring some element of understanding to situation not considered yet, up to the first incident (as in 1998 with the fatigue problems in the thermal mixing zone, at the origin of the Civaux arrest). Among the CEA teams concerned with these problems, the Laboratory of the Structures Integrity and of Normalisation aims to study the integrity problems in metallic nuclear structures leaning on exceptional experimental means: the RESEDA platform allows the realisation of large-scaled tests on analytical tests (representative of analysed phenomena) to reproduce the industrial situation, linked to various and accurate equipment for the measures and the analyses. Three industrial thematics represent to main part of my research activities at CEA in the fracture mechanics field: - the industrial case of the PWR vessel is related to brittle fracture of the ferritic steels, - the piping components, related to ductile tearing and fracture in the brittle-to-ductile domain, - the high temperature fracture mechanics for the components submitted to very complex loadings. (author)

  5. Theorising and Analysing Academic Labour

    Directory of Open Access Journals (Sweden)

    Thomas Allmer

    2018-01-01

    Full Text Available The aim of this article is to contextualise universities historically within capitalism and to analyse academic labour and the deployment of digital media theoretically and critically. It argues that the post-war expansion of the university can be considered as medium and outcome of informational capitalism and as a dialectical development of social achievement and advanced commodification. The article strives to identify the class position of academic workers, introduces the distinction between academic work and labour, discusses the connection between academic, information and cultural work, and suggests a broad definition of university labour. It presents a theoretical model of working conditions that helps to systematically analyse the academic labour process and to provide an overview of working conditions at universities. The paper furthermore argues for the need to consider the development of education technologies as a dialectics of continuity and discontinuity, discusses the changing nature of the forces and relations of production, and the impact on the working conditions of academics in the digital university. Based on Erik Olin Wright’s inclusive approach of social transformation, the article concludes with the need to bring together anarchist, social democratic and revolutionary strategies for establishing a socialist university in a commons-based information society.

  6. Incorporating nonlinearity into mediation analyses.

    Science.gov (United States)

    Knafl, George J; Knafl, Kathleen A; Grey, Margaret; Dixon, Jane; Deatrick, Janet A; Gallo, Agatha M

    2017-03-21

    Mediation is an important issue considered in the behavioral, medical, and social sciences. It addresses situations where the effect of a predictor variable X on an outcome variable Y is explained to some extent by an intervening, mediator variable M. Methods for addressing mediation have been available for some time. While these methods continue to undergo refinement, the relationships underlying mediation are commonly treated as linear in the outcome Y, the predictor X, and the mediator M. These relationships, however, can be nonlinear. Methods are needed for assessing when mediation relationships can be treated as linear and for estimating them when they are nonlinear. Existing adaptive regression methods based on fractional polynomials are extended here to address nonlinearity in mediation relationships, but assuming those relationships are monotonic as would be consistent with theories about directionality of such relationships. Example monotonic mediation analyses are provided assessing linear and monotonic mediation of the effect of family functioning (X) on a child's adaptation (Y) to a chronic condition by the difficulty (M) for the family in managing the child's condition. Example moderated monotonic mediation and simulation analyses are also presented. Adaptive methods provide an effective way to incorporate possibly nonlinear monotonicity into mediation relationships.

  7. Incorporating nonlinearity into mediation analyses

    Directory of Open Access Journals (Sweden)

    George J. Knafl

    2017-03-01

    Full Text Available Abstract Background Mediation is an important issue considered in the behavioral, medical, and social sciences. It addresses situations where the effect of a predictor variable X on an outcome variable Y is explained to some extent by an intervening, mediator variable M. Methods for addressing mediation have been available for some time. While these methods continue to undergo refinement, the relationships underlying mediation are commonly treated as linear in the outcome Y, the predictor X, and the mediator M. These relationships, however, can be nonlinear. Methods are needed for assessing when mediation relationships can be treated as linear and for estimating them when they are nonlinear. Methods Existing adaptive regression methods based on fractional polynomials are extended here to address nonlinearity in mediation relationships, but assuming those relationships are monotonic as would be consistent with theories about directionality of such relationships. Results Example monotonic mediation analyses are provided assessing linear and monotonic mediation of the effect of family functioning (X on a child’s adaptation (Y to a chronic condition by the difficulty (M for the family in managing the child's condition. Example moderated monotonic mediation and simulation analyses are also presented. Conclusions Adaptive methods provide an effective way to incorporate possibly nonlinear monotonicity into mediation relationships.

  8. Molecular Analyses of Transgenic Plants.

    Science.gov (United States)

    Trijatmiko, Kurniawan Rudi; Arines, Felichi Mae; Oliva, Norman; Slamet-Loedin, Inez Hortense; Kohli, Ajay

    2016-01-01

    One of the major challenges in plant molecular biology is to generate transgenic plants that express transgenes stably over generations. Here, we describe some routine methods to study transgene locus structure and to analyze transgene expression in plants: Southern hybridization using DIG chemiluminescent technology for characterization of transgenic locus, SYBR Green-based real-time RT-PCR to measure transgene transcript level, and protein immunoblot analysis to evaluate accumulation and stability of transgenic protein product in the target tissue.

  9. Uncertainty and Sensitivity Analyses Plan

    International Nuclear Information System (INIS)

    Simpson, J.C.; Ramsdell, J.V. Jr.

    1993-04-01

    Hanford Environmental Dose Reconstruction (HEDR) Project staff are developing mathematical models to be used to estimate the radiation dose that individuals may have received as a result of emissions since 1944 from the US Department of Energy's (DOE) Hanford Site near Richland, Washington. An uncertainty and sensitivity analyses plan is essential to understand and interpret the predictions from these mathematical models. This is especially true in the case of the HEDR models where the values of many parameters are unknown. This plan gives a thorough documentation of the uncertainty and hierarchical sensitivity analysis methods recommended for use on all HEDR mathematical models. The documentation includes both technical definitions and examples. In addition, an extensive demonstration of the uncertainty and sensitivity analysis process is provided using actual results from the Hanford Environmental Dose Reconstruction Integrated Codes (HEDRIC). This demonstration shows how the approaches used in the recommended plan can be adapted for all dose predictions in the HEDR Project

  10. Hydrogen Analyses in the EPR

    International Nuclear Information System (INIS)

    Worapittayaporn, S.; Eyink, J.; Movahed, M.

    2008-01-01

    In severe accidents with core melting large amounts of hydrogen may be released into the containment. The EPR provides a combustible gas control system to prevent hydrogen combustion modes with the potential to challenge the containment integrity due to excessive pressure and temperature loads. This paper outlines the approach for the verification of the effectiveness and efficiency of this system. Specifically, the justification is a multi-step approach. It involves the deployment of integral codes, lumped parameter containment codes and CFD codes and the use of the sigma criterion, which provides the link to the broad experimental data base for flame acceleration (FA) and deflagration to detonation transition (DDT). The procedure is illustrated with an example. The performed analyses show that hydrogen combustion at any time does not lead to pressure or temperature loads that threaten the containment integrity of the EPR. (authors)

  11. Analysing performance through value creation

    Directory of Open Access Journals (Sweden)

    Adrian TRIFAN

    2015-12-01

    Full Text Available This paper draws a parallel between measuring financial performance in 2 variants: the first one using data offered by accounting, which lays emphasis on maximizing profit, and the second one which aims to create value. The traditional approach to performance is based on some indicators from accounting data: ROI, ROE, EPS. The traditional management, based on analysing the data from accounting, has shown its limits, and a new approach is needed, based on creating value. The evaluation of value based performance tries to avoid the errors due to accounting data, by using other specific indicators: EVA, MVA, TSR, CVA. The main objective is shifted from maximizing the income to maximizing the value created for shareholders. The theoretical part is accompanied by a practical analysis regarding the creation of value and an analysis of the main indicators which evaluate this concept.

  12. HGCal Simulation Analyses for CMS

    CERN Document Server

    Bruno, Sarah Marie

    2015-01-01

    This summer, I approached the topic of fast-timing detection of photons from Higgs decays via simulation analyses, working under the supervision of Dr. Adolf Bornheim of the California Institute of Technology. My specific project focused on simulating the high granularity calorimeter for the Compact Muon Solenoid (CMS) experiment. CMS detects particles using calorimeters. The Electromagnetic Calorimeter (ECal) is arranged cylindrically to form a barrel section and two “endcaps.” Previously, both the barrel and endcap have employed lead tungstate crystal detectors, known as the “shashlik” design. The crystal detectors, however, rapidly degrade from exposure to radiation. This effect is most pronounced in the endcaps. To avoid the high expense of frequently replacing degraded detectors, it was recently decided to eliminate the endcap crystals in favor of an arrangement of silicon detectors known as the “High Granularity Calorimeter” (HGCal), while leaving the barrel detector technology unchanged. T...

  13. Isotopic signatures by bulk analyses

    International Nuclear Information System (INIS)

    Efurd, D.W.; Rokop, D.J.

    1997-01-01

    Los Alamos National Laboratory has developed a series of measurement techniques for identification of nuclear signatures by analyzing bulk samples. Two specific applications for isotopic fingerprinting to identify the origin of anthropogenic radioactivity in bulk samples are presented. The first example is the analyses of environmental samples collected in the US Arctic to determine the impact of dumping of radionuclides in this polar region. Analyses of sediment and biota samples indicate that for the areas sampled the anthropogenic radionuclide content of sediments was predominantly the result of the deposition of global fallout. The anthropogenic radionuclide concentrations in fish, birds and mammals were very low. It can be surmised that marine food chains are presently not significantly affected. The second example is isotopic fingerprinting of water and sediment samples from the Rocky Flats Facility (RFP). The largest source of anthropogenic radioactivity presently affecting surface-waters at RFP is the sediments that are currently residing in the holding ponds. One gram of sediment from a holding pond contains approximately 50 times more plutonium than 1 liter of water from the pond. Essentially 100% of the uranium in Ponds A-1 and A-2 originated as depleted uranium. The largest source of radioactivity in the terminal Ponds A-4, B-5 and C-2 was naturally occurring uranium and its decay product radium. The uranium concentrations in the waters collected from the terminal ponds contained 0.05% or less of the interim standard calculated derived concentration guide for uranium in waters available to the public. All of the radioactivity observed in soil, sediment and water samples collected at RFP was naturally occurring, the result of processes at RFP or the result of global fallout. No extraneous anthropogenic alpha, beta or gamma activities were detected. The plutonium concentrations in Pond C-2 appear to vary seasonally

  14. Modelling and Analysing Socio-Technical Systems

    DEFF Research Database (Denmark)

    Aslanyan, Zaruhi; Ivanova, Marieta Georgieva; Nielson, Flemming

    2015-01-01

    Modern organisations are complex, socio-technical systems consisting of a mixture of physical infrastructure, human actors, policies and processes. An in-creasing number of attacks on these organisations exploits vulnerabilities on all different levels, for example combining a malware attack...... with social engineering. Due to this combination of attack steps on technical and social levels, risk assessment in socio-technical systems is complex. Therefore, established risk assessment methods often abstract away the internal structure of an organisation and ignore human factors when modelling...... and assessing attacks. In our work we model all relevant levels of socio-technical systems, and propose evaluation techniques for analysing the security properties of the model. Our approach simplifies the identification of possible attacks and provides qualified assessment and ranking of attacks based...

  15. On study design in neuroimaging heritability analyses

    Science.gov (United States)

    Koran, Mary Ellen; Li, Bo; Jahanshad, Neda; Thornton-Wells, Tricia A.; Glahn, David C.; Thompson, Paul M.; Blangero, John; Nichols, Thomas E.; Kochunov, Peter; Landman, Bennett A.

    2014-03-01

    Imaging genetics is an emerging methodology that combines genetic information with imaging-derived metrics to understand how genetic factors impact observable structural, functional, and quantitative phenotypes. Many of the most well-known genetic studies are based on Genome-Wide Association Studies (GWAS), which use large populations of related or unrelated individuals to associate traits and disorders with individual genetic factors. Merging imaging and genetics may potentially lead to improved power of association in GWAS because imaging traits may be more sensitive phenotypes, being closer to underlying genetic mechanisms, and their quantitative nature inherently increases power. We are developing SOLAR-ECLIPSE (SE) imaging genetics software which is capable of performing genetic analyses with both large-scale quantitative trait data and family structures of variable complexity. This program can estimate the contribution of genetic commonality among related subjects to a given phenotype, and essentially answer the question of whether or not the phenotype is heritable. This central factor of interest, heritability, offers bounds on the direct genetic influence over observed phenotypes. In order for a trait to be a good phenotype for GWAS, it must be heritable: at least some proportion of its variance must be due to genetic influences. A variety of family structures are commonly used for estimating heritability, yet the variability and biases for each as a function of the sample size are unknown. Herein, we investigate the ability of SOLAR to accurately estimate heritability models based on imaging data simulated using Monte Carlo methods implemented in R. We characterize the bias and the variability of heritability estimates from SOLAR as a function of sample size and pedigree structure (including twins, nuclear families, and nuclear families with grandparents).

  16. Proteins analysed as virtual knots

    Science.gov (United States)

    Alexander, Keith; Taylor, Alexander J.; Dennis, Mark R.

    2017-02-01

    Long, flexible physical filaments are naturally tangled and knotted, from macroscopic string down to long-chain molecules. The existence of knotting in a filament naturally affects its configuration and properties, and may be very stable or disappear rapidly under manipulation and interaction. Knotting has been previously identified in protein backbone chains, for which these mechanical constraints are of fundamental importance to their molecular functionality, despite their being open curves in which the knots are not mathematically well defined; knotting can only be identified by closing the termini of the chain somehow. We introduce a new method for resolving knotting in open curves using virtual knots, which are a wider class of topological objects that do not require a classical closure and so naturally capture the topological ambiguity inherent in open curves. We describe the results of analysing proteins in the Protein Data Bank by this new scheme, recovering and extending previous knotting results, and identifying topological interest in some new cases. The statistics of virtual knots in protein chains are compared with those of open random walks and Hamiltonian subchains on cubic lattices, identifying a regime of open curves in which the virtual knotting description is likely to be important.

  17. Digital image analyser for autoradiography

    International Nuclear Information System (INIS)

    Muth, R.A.; Plotnick, J.

    1985-01-01

    The most critical parameter in quantitative autoradiography for assay of tissue concentrations of tracers is the ability to obtain precise and accurate measurements of optical density of the images. Existing high precision systems for image analysis, rotating drum densitometers, are expensive, suffer from mechanical problems and are slow. More moderately priced and reliable video camera based systems are available, but their outputs generally do not have the uniformity and stability necessary for high resolution quantitative autoradiography. The authors have designed and constructed an image analyser optimized for quantitative single and multiple tracer autoradiography which the authors refer to as a memory-mapped charged-coupled device scanner (MM-CCD). The input is from a linear array of CCD's which is used to optically scan the autoradiograph. Images are digitized into 512 x 512 picture elements with 256 gray levels and the data is stored in buffer video memory in less than two seconds. Images can then be transferred to RAM memory by direct memory-mapping for further processing. Arterial blood curve data and optical density-calibrated standards data can be entered and the optical density images can be converted automatically to tracer concentration or functional images. In double tracer studies, images produced from both exposures can be stored and processed in RAM to yield ''pure'' individual tracer concentration or functional images. Any processed image can be transmitted back to the buffer memory to be viewed on a monitor and processed for region of interest analysis

  18. PROFESSIONALISM: GENESIS AND CATEGORICAL ANALYSES

    Directory of Open Access Journals (Sweden)

    Ирина Олеговна Авдеева

    2013-12-01

    Full Text Available In the article the theoretical-methodological analysis of the concept of «professional», describes the genesis and key aspects of its content and structure. In addition, this publication discusses some of the approaches to the definition of the studied concepts, including: system (professional it seems as multipart strictly organized education of consciousness and psyche of the individual; professional graphic (from a position of objective (professional description and subjective (mental graph the parties; integrative (as property, process, and status of the person; acmeological (as the dialectical the unity of the personality and activity components; in terms of motivation and operating parties and other Stresses the importance of personal (theoretical knowledge, professional qualities, value orientations, motivational orientation of others and specific features of labour employee (practical skills, professional experience and other, determining the effectiveness of its activities.DOI: http://dx.doi.org/10.12731/2218-7405-2013-10-12

  19. Severe Accident Recriticality Analyses (SARA)

    Energy Technology Data Exchange (ETDEWEB)

    Frid, W. [Swedish Nuclear Power Inspectorate, Stockholm (Sweden); Hoejerup, F. [Risoe National Lab. (Denmark); Lindholm, I.; Miettinen, J.; Puska, E.K. [VTT Energy, Helsinki (Finland); Nilsson, Lars [Studsvik Eco and Safety AB, Nykoeping (Sweden); Sjoevall, H. [Teoliisuuden Voima Oy (Finland)

    1999-11-01

    Recriticality in a BWR has been studied for a total loss of electric power accident scenario. In a BWR, the B{sub 4}C control rods would melt and relocate from the core before the fuel during core uncovery and heat-up. If electric power returns during this time-window unborated water from ECCS systems will start to reflood the partly control rod free core. Recriticality might take place for which the only mitigating mechanisms are the Doppler effect and void formation. In order to assess the impact of recriticality on reactor safety, including accident management measures, the following issues have been investigated in the SARA project: 1. the energy deposition in the fuel during super-prompt power burst, 2. the quasi steady-state reactor power following the initial power burst and 3. containment response to elevated quasi steady-state reactor power. The approach was to use three computer codes and to further develop and adapt them for the task. The codes were SIMULATE-3K, APROS and RECRIT. Recriticality analyses were carried out for a number of selected reflooding transients for the Oskarshamn 3 plant in Sweden with SIMULATE-3K and for the Olkiluoto 1 plant in Finland with all three codes. The core state initial and boundary conditions prior to recriticality have been studied with the severe accident codes SCDAP/RELAP5, MELCOR and MAAP4. The results of the analyses show that all three codes predict recriticality - both superprompt power bursts and quasi steady-state power generation - for the studied range of parameters, i. e. with core uncovery and heat-up to maximum core temperatures around 1800 K and water flow rates of 45 kg/s to 2000 kg/s injected into the downcomer. Since the recriticality takes place in a small fraction of the core the power densities are high which results in large energy deposition in the fuel during power burst in some accident scenarios. The highest value, 418 cal/g, was obtained with SIMULATE-3K for an Oskarshamn 3 case with reflooding

  20. Ergonomic analyses of downhill skiing.

    Science.gov (United States)

    Clarys, J P; Publie, J; Zinzen, E

    1994-06-01

    The purpose of this study was to provide electromyographic feedback for (1) pedagogical advice in motor learning, (2) the ergonomics of materials choice and (3) competition. For these purposes: (1) EMG data were collected for the Stem Christie, the Stem Turn and the Parallel Christie (three basic ski initiation drills) and verified for the complexity of patterns; (2) integrated EMG (iEMG) and linear envelopes (LEs) were analysed from standardized positions, motions and slopes using compact, soft and competition skis; (3) in a simulated 'parallel special slalom', the muscular activity pattern and intensity of excavated and flat snow conditions were compared. The EMG data from the three studies were collected on location in the French Alps (Tignes). The analog raw EMG was recorded on the slopes with a portable seven-channel FM recorder (TEAC MR30) and with pre-amplified bipolar surface electrodes supplied with a precision instrumentation amplifier (AD 524, Analog Devices, Norwood, USA). The raw signal was full-wave rectified and enveloped using a moving average principle. This linear envelope was normalized according to the highest peak amplitude procedure per subject and was integrated in order to obtain a reference of muscular intensity. In the three studies and for all subjects (elite skiers: n = 25 in studies 1 and 2, n = 6 in study 3), we found a high level of co-contractions in the lower limb extensors and flexors, especially during the extension phase of the ski movement. The Stem Christie and the Parallel Christie showed higher levels of rhythmic movement (92 and 84%, respectively).(ABSTRACT TRUNCATED AT 250 WORDS)

  1. Genomic analyses of modern dog breeds.

    Science.gov (United States)

    Parker, Heidi G

    2012-02-01

    A rose may be a rose by any other name, but when you call a dog a poodle it becomes a very different animal than if you call it a bulldog. Both the poodle and the bulldog are examples of dog breeds of which there are >400 recognized worldwide. Breed creation has played a significant role in shaping the modern dog from the length of his leg to the cadence of his bark. The selection and line-breeding required to maintain a breed has also reshaped the genome of the dog, resulting in a unique genetic pattern for each breed. The breed-based population structure combined with extensive morphologic variation and shared human environments have made the dog a popular model for mapping both simple and complex traits and diseases. In order to obtain the most benefit from the dog as a genetic system, it is necessary to understand the effect structured breeding has had on the genome of the species. That is best achieved by looking at genomic analyses of the breeds, their histories, and their relationships to each other.

  2. Monitoring of test roads with MSWI bottom ash in the sub-base. Measurements with falling weight deflectometer on test structures in Malmoe and Umeaa. Analyses of ground water and leachate along test structures in Umeaa; Uppfoeljning av slaggrusprovvaegar. Fallviktsmaetning paa provstraeckor paa Toerringevaegen i Malmoe och Daavamyran i Umeaa. Grundvatten- och lakvattenanalyser paa provstraeckor vid Daavamyran i Umeaa

    Energy Technology Data Exchange (ETDEWEB)

    Arm, Maria; Larsson, Lennart; Tiberg, Charlotta; Lind, Bo; Arvidslund, Ola

    2008-12-15

    A number of test roads and test areas with processed municipal solid waste incinerator bottom ash, here called MSWI gravel, have been built in Sweden during the last 10-15 years. The main purpose of the projects reported here was to take advantage of the existing test roads to increase the knowledge of the long-term strength and environmental impact of MSWI gravel, when it is used as a road material. Two test roads with MSWI gravel in the sub-base were monitored through falling weight deflectometer (FWD) measurements and, for one of the roads, by means of sampling and analyses of groundwater and leachate within and along the road. The first road, constructed in 1998, is named Toerringevaegen and is situated outside Malmoe in the south of Sweden. The second road, Daava test road, was constructed in 2001 and is situated outside Umeaa in the north of Sweden. The roads were monitored regarding strength from 2004 to 2008 and Daava test road was also monitored regarding environmental impact from 2006 to 2008. For both roads, comparison was made over time and between the test sections with MSWI gravel and reference sections with crushed rock. Comparison was also made with results from previous studies on these test roads, resulting in a uniquely long monitoring period. The results from Toerringevaegen show that the road section with MSWI gravel in the sub-base retains its strength after several years. The three measurements performed at the Daava road revealed an initially decreasing strength and then a stabilisation. As in previous studies, the strength of the MSWI gravel was found to be about 70% of that of the crushed rock, which has to be taken into account in the design phase. It was concluded that regarding the strength properties MSWI gravel is suitable as sub-base material if the road is properly designed. It can also be used as a filling material, in embankments and as a capping layer. This confirms the conclusions from previous studies. The results from the

  3. Unemployment - Structural

    OpenAIRE

    Lindbeck, Assar

    1999-01-01

    Structural unemployment differs from cyclical unemployment by not disappearing in cyclical booms. In economic theory, structural unemployment is usually analysed in terms of the concept of equilibrium unemployment (the "natural unemployment rate" in Friedman’s terminology). Two elaborate concepts of equilibrium unemployment – the non-accelerating inflation rate of unemployment (the NAIRU) and the unemployment rate that induces firms and workers to accept the same real wage (the PS-WS-model) a...

  4. Automatic incrementalization of Prolog based static analyses

    DEFF Research Database (Denmark)

    Eichberg, Michael; Kahl, Matthias; Saha, Diptikalyan

    2007-01-01

    Modem development environments integrate various static analyses into the build process. Analyses that analyze the whole project whenever the project changes are impractical in this context. We present an approach to automatic incrementalization of analyses that are specified as tabled logic...... incrementalizing a broad range of static analyses....

  5. Uncertainty Analyses for Back Projection Methods

    Science.gov (United States)

    Zeng, H.; Wei, S.; Wu, W.

    2017-12-01

    So far few comprehensive error analyses for back projection methods have been conducted, although it is evident that high frequency seismic waves can be easily affected by earthquake depth, focal mechanisms and the Earth's 3D structures. Here we perform 1D and 3D synthetic tests for two back projection methods, MUltiple SIgnal Classification (MUSIC) (Meng et al., 2011) and Compressive Sensing (CS) (Yao et al., 2011). We generate synthetics for both point sources and finite rupture sources with different depths, focal mechanisms, as well as 1D and 3D structures in the source region. The 3D synthetics are generated through a hybrid scheme of Direct Solution Method and Spectral Element Method. Then we back project the synthetic data using MUSIC and CS. The synthetic tests show that the depth phases can be back projected as artificial sources both in space and time. For instance, for a source depth of 10km, back projection gives a strong signal 8km away from the true source. Such bias increases with depth, e.g., the error of horizontal location could be larger than 20km for a depth of 40km. If the array is located around the nodal direction of direct P-waves the teleseismic P-waves are dominated by the depth phases. Therefore, back projections are actually imaging the reflection points of depth phases more than the rupture front. Besides depth phases, the strong and long lasted coda waves due to 3D effects near trench can lead to additional complexities tested here. The strength contrast of different frequency contents in the rupture models also produces some variations to the back projection results. In the synthetic tests, MUSIC and CS derive consistent results. While MUSIC is more computationally efficient, CS works better for sparse arrays. In summary, our analyses indicate that the impact of various factors mentioned above should be taken into consideration when interpreting back projection images, before we can use them to infer the earthquake rupture physics.

  6. Analyse et conception d'un coupleur coaxial rectangulaire à ...

    African Journals Online (AJOL)

    The modelling of this structure consists in analysing the even and the odd mode characteristic impedances (Zoe, Zoo), the coupling coefficient (k) and the inductance and capacitance matrices ([L] and [C] matrices, respectively). Also we present the results of a directional coupler design. The numerical model developed ...

  7. Analysing social identity in casual Zambian/English conversation: a ...

    African Journals Online (AJOL)

    The study uses systemic functional linguistics' conversational analysis (cf Eggins & Slade, 1997) to investigate role structure as well as to analyse encoded statuses and dimensions of social identity in Zambian/English casual conversation. The focus is on how multilingual Zambians use the repertoire of languages at their ...

  8. Techniques for Analysing Problems in Engineering Projects

    DEFF Research Database (Denmark)

    Thorsteinsson, Uffe

    1998-01-01

    Description of how CPM network can be used for analysing complex problems in engineering projects.......Description of how CPM network can be used for analysing complex problems in engineering projects....

  9. Introduction to nanostructural analyses by small-angle neutron scattering

    International Nuclear Information System (INIS)

    Shibayama, Mitsuhiro

    2010-01-01

    It has already passed more than 30 years since small-angle neutron scattering (SANS) technique was applied in structural analyses. SANS is now one of common tools in structure investigations and SANS instruments can be found in any neutron scattering facilities. In particular, SANS plays an important role in the field of soft matter, such as polymer, micelles, gels, vesicles, as well as biological systems and metallurgy. Here, I give a brief survey on (1) the utility of SANS in structural studies, (2) experimental aspects of SANS, and (3) some results obtained so far. (author)

  10. Improving word coverage using unsupervised morphological analyser

    Indian Academy of Sciences (India)

    Institute of Information Technology (IIIT), Hyderabad. The study was made in various direc- tions to compare the results our system developed with the out put of Hindi Analyser developed by IIIT, Hyderabad. 3.1 Comparison of rule-based morphological analyser with unsupervised morphological analyser. 3.1a Calculation of ...

  11. Nuclear analyses in biology and medical science. Measuring on nucleii in stead of atoms

    International Nuclear Information System (INIS)

    De Goeij, J.J.M.

    1996-01-01

    A brief overview is given of the use of nuclear analyses in life sciences. Features of nuclear analytical methods (NAMs) are grouped into four categories: physical basis, isotopic analyses rather than elemental analyses, no interference of electronic and molecular structure, and penetrating character of nuclear radiation. Obstacles in applying NAMs in the life sciences are outlined. 1 tab

  12. [Anne Arold. Kontrastive Analyse...] / Paul Alvre

    Index Scriptorium Estoniae

    Alvre, Paul, 1921-2008

    2001-01-01

    Arvustus: Arold, Anne. Kontrastive analyse der Wortbildungsmuster im Deutschen und im Estnischen (am Beispiel der Aussehensadjektive). Tartu, 2000. (Dissertationes philologiae germanicae Universitatis Tartuensis)

  13. Towards Reproducible Research Data Analyses in LHC Particle Physics

    CERN Document Server

    Simko, Tibor

    2017-01-01

    The reproducibility of the research data analysis requires having access not only to the original datasets, but also to the computing environment, the analysis software and the workflow used to produce the original results. We present the nascent CERN Analysis Preservation platform with a set of tools developed to support particle physics researchers in preserving the knowledge around analyses so that capturing, sharing, reusing and reinterpreting data becomes easier. The presentation will focus on three pillars: (i) capturing structured knowledge information about data analysis processes; (ii) capturing the computing environment, the software code, the datasets, the configuration and other information assets used in data analyses; (iii) re-instantiating of preserved analyses on a containerised computing cloud for the purposes of re-validation and re-interpretation.

  14. Approximate analyses of inelastic effects in pipework

    International Nuclear Information System (INIS)

    Jobson, D.A.

    1983-01-01

    This presentation shows figures concerned with analyses of inelastic effects in pipework as follows: comparison of experimental and calculated simplified analyses results for free end rotation and for circumferential strain; interrupted stress relaxation; regenerated relaxation caused by reversed yield; buckling of straight pipe under combined bending and torsion; results of fatigues test of pipe bend

  15. Roux 105 PHONETIC DATA AND PHONOLOGICAL ANALYSES ...

    African Journals Online (AJOL)

    This paper is basically concerned with the relationship between phonetic data and phonological analyses. I) It will be shown that phonological analyses based on unverified phonetic data tend to accommodate ad hoc, unmotivated, and even phonetically implausible phonological rules. On the other hand, it will be ...

  16. Random error in cardiovascular meta-analyses

    DEFF Research Database (Denmark)

    Albalawi, Zaina; McAlister, Finlay A; Thorlund, Kristian

    2013-01-01

    BACKGROUND: Cochrane reviews are viewed as the gold standard in meta-analyses given their efforts to identify and limit systematic error which could cause spurious conclusions. The potential for random error to cause spurious conclusions in meta-analyses is less well appreciated. METHODS: We exam...

  17. Novel Algorithms for Astronomical Plate Analyses

    Indian Academy of Sciences (India)

    2016-01-27

    Jan 27, 2016 ... Powerful computers and dedicated software allow effective data mining and scientific analyses in astronomical plate archives. We give and discuss examples of newly developed algorithms for astronomical plate analyses, e.g., searches for optical transients, as well as for major spectral and brightness ...

  18. Cost-Benefit Analyses of Transportation Investments

    DEFF Research Database (Denmark)

    Næss, Petter

    2006-01-01

    -to-pay investigations. Accepting the ontological and epistemological assumptions of cost-benefit analysis involves an implicit acceptance of the ethical and political values favoured by these assumptions. Cost-benefit analyses of transportation investment projects tend to neglect long-term environmental consequences...... and needs among population groups with a low ability to pay. Instead of cost-benefit analyses, impact analyses evaluating the likely effects of project alternatives against a wide range of societal goals is recommended, with quantification and economic valorisation only for impact categories where this can......This paper discusses the practice of cost-benefit analyses of transportation infrastructure investment projects from the meta-theoretical perspective of critical realism. Such analyses are based on a number of untenable ontological assumptions about social value, human nature and the natural...

  19. Numerical analyses for efficient photoionization by nonmonochromatic fields

    International Nuclear Information System (INIS)

    Hasegawa, Shuichi; Suzuki, Atsuyuki

    2000-01-01

    Numerical analyses on excitation and ionization probabilities of atoms with hyperfine structures were performed in order to compare two different excitation methods, adiabatic excitation and broadband excitation. The lifetime of the intermediate states was considered in order to investigate the effect of the absorption line broadening. The dependences of the two excitation methods on the lifetime were found to be quite different. The ionization probability by the adiabatic excitation is higher than that by the broadband excitation for identical excitation laser intensity. (author)

  20. High perfomance liquid chromatography in pharmaceutical analyses.

    Science.gov (United States)

    Nikolin, Branko; Imamović, Belma; Medanhodzić-Vuk, Saira; Sober, Miroslav

    2004-05-01

    compounds often present in concentrations much greater than those of analyte. Analiyte concentrations are often low, and in the case of drugs, the endogenous compounds are sometimes structurally very similar to the drug to be measured. The binding of drugs to the plasma protein also may occur which decreases the amount of free compound that is measured. To undertake the analyses of drugs and metabolites in body fluids the analyst is facet with several problems. The first problem is due to the complex nature of the body fluid, the drugs must be isolated by an extraction technique, which ideally should provide a relatively clean extract, and the separation system must be capable of resolving the drugs of interest from co extractives. All mentioned when we are using high performance liquid chromatography require good selections of detectors, good stationary phase, eluents and adequate program during separation. UV/VIS detector is the most versatile detector used in high performance liquid chromatography it is not always ideal since it is lack of specificity means high resolution of the analyte that may be required. UV detection is preferred since it offers excellent linearity and rapid quantitative analyses can be performed against a single standard of the drug being determined. Diode array and rapid scanning detector are useful for peak identification and monitoring peak purity but they are somewhat less sensitive then single wavelength detectors. In liquid chromatography some components may have a poor UV chromophores if UV detection is being used or be completely retained on the liquid chromatography column. Fluorescence and electrochemical detector are not only considerably more sensitive towed appropriate analytes but also more selective than UV detectors for many compounds. If at all possible fluorescence detectors are sensitive, stable, selective and easy to operate. It is selectivity shows itself in the lack of frontal components observed in plasma extract whereas

  1. Factor analyses of a social support scale using two methods.

    Science.gov (United States)

    Yu, Yu; Shiu, Cheng-Shi; Yang, Joyce P; Wang, Mingjiong; Simoni, Jane M; Chen, Wei-ti; Cheng, Joy; Zhao, Hongxin

    2015-04-01

    Evaluation and comparison of the factor structure of the Medical Outcomes Study Social Support Survey (MOS-SSS) using both confirmatory factor analysis (CFA) and exploratory factor analysis (EFA) with two samples of people living with HIV/AIDS in China. Secondary analyses were conducted with data from two comparable samples of 320 people living with HIV/AIDS from the same hospital using the same inclusion criteria. The first sample of 120 was collected in 2006, and the second sample of 200 was collected in 2012. For each sample, CFA was first performed on the original four-factor structure to check model fit, followed by EFA to explore other factor structures and a subsequent CFA for model fit statistics to be compared to the original four-factor CFA. In both samples, CFA on the originally hypothesized four-factor structure yielded an acceptable model fit. The EFA yielded a two-factor solution in both samples, with different items included in each factor for the two samples. Comparison of CFA on the a priori four-factor structure and the new two-factor structure in both samples indicated that both factor structures were of acceptable model fit, with the four-factor model performing slightly better than the two-factor model. Factor structure of the MOS-SSS is method-dependent, with CFA supporting a four-factor structure, while EFA yielded a two-factor structure in two separate samples. We need to be careful in selecting the analytic method when applying the MOS-SSS to various samples and choose the factor structure that best fits the theoretical model.

  2. Modeling Citable Textual Analyses for the Homer Multitext

    Directory of Open Access Journals (Sweden)

    Christopher William Blackwell

    2016-12-01

    Full Text Available The 'Homer Multitext' project (hmt is documenting the language and structure of Greek epic poetry, and the ancient tradition of commentary on it. The project’s primary data consist of editions of Greek texts; automated and manually created readings analyze the texts across historical and thematic axes. This paper describes an abstract model we follow in documenting an open-ended body of diverse analyses. The analyses apply to passages of texts at different levels of granularity; they may refer to overlapping or mutually exclusive passages of text; and they may apply to non-contiguous passages of text. All are recorded in with explicit, concise, machine-actionable canonical citation of both text passage and analysis in a scheme aligning all analyses to a common notional text. We cite our texts with urns that capture a passage’s position in an 'Ordered Hierarchy of Citation Objects' (ohco2. Analyses are modeled as data-objects with five properties. We create collections of ‘analytical objects’, each uniquely identified by its own urn and each aligned to a particular edition of a text by a urn citation. We can view these analytical objects as an extension of the edition’s citation hierarchy; since they are explicitly ordered by their alignment with the edition they analyze, each collection of analyses meets satisfies the (ohco2 model of a citable text. We call these texts that are derived from and aligned to an edition ‘analytical exemplars’.

  3. Comparison of design and probabilistic analyses of nuclear power plants

    International Nuclear Information System (INIS)

    Maslenikov, O.R.; Johnson, J.J.; Campbell, R.D.

    1995-01-01

    A study was made to evaluate the margin of conservatism introduced into design in-structures response spectra by following standard design analysis procedures according to the U.S.Nuclear Regulatory Commission (NRC) Standard Review Plan and Regulatory Guides for comparing spectra produced by such a design analysis to response from median-centered probabilistic analyses. Three typical nuclear plant structures were studied: PWR reactor building, PWR auxiliary building and BWR reactor building. Each building was assumed to be situated on three idealized sites: a rock site, a medium and a soft soil site. All buildings were assumed to have embedded foundations. The PWR reactor building was also assumed to have a surface foundation. Each design analysis was performed inn accordance with the current SRP criteria. Each probabilistic analysis consisted of 30 earthquake simulations for which the free-field motions and soil and structural properties were varied; the simulated earthquakes were generated such that their mean-plus-one-standard-deviation free-field spectra approximated the Regulatory Guide (RG) 1.60 design spectra. In-structure response spectra from the design analyses were compared with the 84% non-exceedance probability (NEP) spectra from the probabilistic analyses. The comparisons showed that the design method produced conservative results for all cases. The smallest margin was about 10% for buildings on rock sites. Softer sides had larger margins of conservatism; the reactor buildings on the soft soil site had margins of as much as 100% (factor of 2),. The shorter structures and lower locations in all buildings had smaller margins. The margin of conservatism for the surface founded reactor building was about 20% more than for the embedded reactor building. (author). 3 refs., 5 figs., 1 tab

  4. Diagnostic Comparison of Meteorological Analyses during the 2002 Antarctic Winter

    Science.gov (United States)

    Manney, Gloria L.; Allen, Douglas R.; Kruger, Kirstin; Naujokat, Barbara; Santee, Michelle L.; Sabutis, Joseph L.; Pawson, Steven; Swinbank, Richard; Randall, Cora E.; Simmons, Adrian J.; hide

    2005-01-01

    Several meteorological datasets, including U.K. Met Office (MetO), European Centre for Medium-Range Weather Forecasts (ECMWF), National Centers for Environmental Prediction (NCEP), and NASA's Goddard Earth Observation System (GEOS-4) analyses, are being used in studies of the 2002 Southern Hemisphere (SH) stratospheric winter and Antarctic major warming. Diagnostics are compared to assess how these studies may be affected by the meteorological data used. While the overall structure and evolution of temperatures, winds, and wave diagnostics in the different analyses provide a consistent picture of the large-scale dynamics of the SH 2002 winter, several significant differences may affect detailed studies. The NCEP-NCAR reanalysis (REAN) and NCEP-Department of Energy (DOE) reanalysis-2 (REAN-2) datasets are not recommended for detailed studies, especially those related to polar processing, because of lower-stratospheric temperature biases that result in underestimates of polar processing potential, and because their winds and wave diagnostics show increasing differences from other analyses between similar to 30 and 10 hPa (their top level). Southern Hemisphere polar stratospheric temperatures in the ECMWF 40-Yr Re-analysis (ERA-40) show unrealistic vertical structure, so this long-term reanalysis is also unsuited for quantitative studies. The NCEP/Climate Prediction Center (CPC) objective analyses give an inferior representation of the upper-stratospheric vortex. Polar vortex transport barriers are similar in all analyses, but there is large variation in the amount, patterns, and timing of mixing, even among the operational assimilated datasets (ECMWF, MetO, and GEOS-4). The higher-resolution GEOS-4 and ECMWF assimilations provide significantly better representation of filamentation and small-scale structure than the other analyses, even when fields gridded at reduced resolution are studied. The choice of which analysis to use is most critical for detailed transport

  5. Automatic incrementalization of Prolog based static analyses

    DEFF Research Database (Denmark)

    Eichberg, Michael; Kahl, Matthias; Saha, Diptikalyan

    2007-01-01

    Modem development environments integrate various static analyses into the build process. Analyses that analyze the whole project whenever the project changes are impractical in this context. We present an approach to automatic incrementalization of analyses that are specified as tabled logic...... programs and evaluated using incremental tabled evaluation, a technique for efficiently updating memo tables in response to changes in facts and rules. The approach has been implemented and integrated into the Eclipse IDE. Our measurements show that this technique is effective for automatically...

  6. Anthocyanin analyses of Vaccinium fruit dietary supplements

    Science.gov (United States)

    Vaccinium fruit ingredients within dietary supplements were identified by comparisons with anthocyanin analyses of known Vaccinium profiles (demonstration of anthocyanin fingerprinting). Available Vaccinium supplements were purchased and analyzed; their anthocyanin profiles (based on HPLC separation...

  7. Understanding Human Error Based on Automated Analyses

    Data.gov (United States)

    National Aeronautics and Space Administration — This is a report on a continuing study of automated analyses of experiential textual reports to gain insight into the causal factors of human errors in aviation...

  8. Analyse of Maintenance Cost in ST

    CERN Document Server

    Jenssen, B W

    2001-01-01

    An analyse has been carried out in ST concerning the total costs for the division. Even though the target was the maintenance costs in ST, the global budget over has been analysed. This has been done since there is close relation between investments & consolidation and the required level for maintenance. The purpose of the analyse was to focus on maintenance cost in ST as a ratio of total maintenance costs over the replacement value of the equipment, and to make some comparisons with other industries and laboratories. Families of equipment have been defined and their corresponding ratios calculated. This first approach gives us some "quantitative" measurements. This analyse should be combined with performance indicators (more "qualitative" measurements) that are telling us how well we are performing. This will help us in defending our budget, make better priorities, and we will satisfy the requirements from our external auditors.

  9. 7 CFR 94.102 - Analyses available.

    Science.gov (United States)

    2010-01-01

    ... analyses for total ash, fat by acid hydrolysis, moisture, salt, protein, beta-carotene, catalase... glycol, SLS, and zeolex. There are also be tests for starch, total sugars, sugar profile, whey, standard...

  10. Risk analyses of nuclear power plants

    International Nuclear Information System (INIS)

    Jehee, J.N.T.; Seebregts, A.J.

    1991-02-01

    Probabilistic risk analyses of nuclear power plants are carried out by systematically analyzing the possible consequences of a broad spectrum of causes of accidents. The risk can be expressed in the probabilities for melt down, radioactive releases, or harmful effects for the environment. Following risk policies for chemical installations as expressed in the mandatory nature of External Safety Reports (EVRs) or, e.g., the publication ''How to deal with risks'', probabilistic risk analyses are required for nuclear power plants

  11. Global use structures of the magnetic materials neodymium and dysprosium. A scenario-based analysis of the effect of the diffusion of electromobility on the demand for rare earths; Globale Verwendungsstrukturen der Magnetwerkstoffe Neodym und Dysprosium. Eine szenariobasierte Analyse der Auswirkung der Diffusion der Elektromobilitaet auf den Bedarf an Seltenen Erden

    Energy Technology Data Exchange (ETDEWEB)

    Gloeser-Chahoud, Simon; Kuehn, Andre; Tercero Espinoza, Luis

    2016-06-15

    Neodymium-iron-boron magnets (NdFeB) have experienced a significant demand as the most powerful permanent magnet in recent years, especially for the manufacture of compact electric servomotors with high efficiency and high power density, especially for mobile applications in hybrid traction motors and electric vehicles or for electric bikes. However, NdFeB magnets are also increasingly being used in general mechanical engineering (conveying and pumping systems, tools, air conditioning systems, lift motors, etc.), in the small electric motors of conventional passenger cars or in the generators of large wind power plants with permanent magnetic direct drive. Nevertheless, there is still high uncertainty in the use structures of NdFeB magnets and the contained rare earth elements neodymium and dysprosium. An effective instrument for increasing the market transparency and the understanding of complex anthropogenic material cycles is the dynamic material flow modeling. In the present work paper, this instrument is used for an in-depth analysis of the use structures of NdFeB magnets and the contained rare earths on a global scale. The dynamic modeling of product usage cycles reveals today's usage structures and quantifies future magnetic quantities in obsolete product flows. It could be shown that the magnets in today's scrap volume are mainly contained in obsolete electronics applications such as hard disks (HDD), CD and DVD drives, which makes the recycling hardly seem to be economical due to the small magnets and the high material spread, but in the foreseeable future with larger magnetic quantities from synchronous servomotors and generators can be expected, which significantly increases the recycling potential. In a further step, the effect of the diffusion of alternative drives in the automotive market on the dysprosium requirement is analyzed using a system dynamics model and possible adaptation mechanisms in the form of different substitution effects in

  12. Social Network Analyses and Nutritional Behavior: An Integrated Modeling Approach

    Directory of Open Access Journals (Sweden)

    Alistair McNair Senior

    2016-01-01

    Full Text Available Animals have evolved complex foraging strategies to obtain a nutritionally balanced diet and associated fitness benefits. Recent advances in nutrition research, combining state-space models of nutritional geometry with agent-based models of systems biology, show how nutrient targeted foraging behavior can also influence animal social interactions, ultimately affecting collective dynamics and group structures. Here we demonstrate how social network analyses can be integrated into such a modeling framework and provide a tangible and practical analytical tool to compare experimental results with theory. We illustrate our approach by examining the case of nutritionally mediated dominance hierarchies. First we show how nutritionally explicit agent-based models that simulate the emergence of dominance hierarchies can be used to generate social networks. Importantly the structural properties of our simulated networks bear similarities to dominance networks of real animals (where conflicts are not always directly related to nutrition. Finally, we demonstrate how metrics from social network analyses can be used to predict the fitness of agents in these simulated competitive environments. Our results highlight the potential importance of nutritional mechanisms in shaping dominance interactions in a wide range of social and ecological contexts. Nutrition likely influences social interaction in many species, and yet a theoretical framework for exploring these effects is currently lacking. Combining socia