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

PubMed

Stokes-Rees, Ian; Sliz, Piotr

2010-12-14

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

Automated crystallographic system for high-throughput protein structure determination.

PubMed

Brunzelle, Joseph S; Shafaee, Padram; Yang, Xiaojing; Weigand, Steve; Ren, Zhong; Anderson, Wayne F

2003-07-01

High-throughput structural genomic efforts require software that is highly automated, distributive and requires minimal user intervention to determine protein structures. Preliminary experiments were set up to test whether automated scripts could utilize a minimum set of input parameters and produce a set of initial protein coordinates. From this starting point, a highly distributive system was developed that could determine macromolecular structures at a high throughput rate, warehouse and harvest the associated data. The system uses a web interface to obtain input data and display results. It utilizes a relational database to store the initial data needed to start the structure-determination process as well as generated data. A distributive program interface administers the crystallographic programs which determine protein structures. Using a test set of 19 protein targets, 79% were determined automatically.

Real-space processing of helical filaments in SPARX

PubMed Central

Behrmann, Elmar; Tao, Guozhi; Stokes, David L.; Egelman, Edward H.; Raunser, Stefan; Penczek, Pawel A.

2012-01-01

We present a major revision of the iterative helical real-space refinement (IHRSR) procedure and its implementation in the SPARX single particle image processing environment. We built on over a decade of experience with IHRSR helical structure determination and we took advantage of the flexible SPARX infrastructure to arrive at an implementation that offers ease of use, flexibility in designing helical structure determination strategy, and high computational efficiency. We introduced the 3D projection matching code which now is able to work with non-cubic volumes, the geometry better suited for long helical filaments, we enhanced procedures for establishing helical symmetry parameters, and we parallelized the code using distributed memory paradigm. Additional feature includes a graphical user interface that facilitates entering and editing of parameters controlling the structure determination strategy of the program. In addition, we present a novel approach to detect and evaluate structural heterogeneity due to conformer mixtures that takes advantage of helical structure redundancy. PMID:22248449

Linking microbial community structure and microbial processes: An empirical and conceptual overview

USGS Publications Warehouse

Bier, R.L.; Bernhardt, Emily S.; Boot, Claudia M.; Graham, Emily B.; Hall, Edward K.; Lennon, Jay T.; Nemergut, Diana R.; Osborne, Brooke B.; Ruiz-Gonzalez, Clara; Schimel, Joshua P.; Waldrop, Mark P.; Wallenstein, Matthew D.

2015-01-01

A major goal of microbial ecology is to identify links between microbial community structure and microbial processes. Although this objective seems straightforward, there are conceptual and methodological challenges to designing studies that explicitly evaluate this link. Here, we analyzed literature documenting structure and process responses to manipulations to determine the frequency of structure-process links and whether experimental approaches and techniques influence link detection. We examined nine journals (published 2009–13) and retained 148 experimental studies measuring microbial community structure and processes. Many qualifying papers (112 of 148) documented structure and process responses, but few (38 of 112 papers) reported statistically testing for a link. Of these tested links, 75% were significant and typically used Spearman or Pearson's correlation analysis (68%). No particular approach for characterizing structure or processes was more likely to produce significant links. Process responses were detected earlier on average than responses in structure or both structure and process. Together, our findings suggest that few publications report statistically testing structure-process links. However, when links are tested for they often occur but share few commonalities in the processes or structures that were linked and the techniques used for measuring them.

An Integrated Approach Linking Process to Structural Modeling With Microstructural Characterization for Injections-Molded Long-Fiber Thermoplastics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nguyen, Ba Nghiep; Bapanapalli, Satish K.; Smith, Mark T.

2008-09-01

The objective of our work is to enable the optimum design of lightweight automotive structural components using injection-molded long fiber thermoplastics (LFTs). To this end, an integrated approach that links process modeling to structural analysis with experimental microstructural characterization and validation is developed. First, process models for LFTs are developed and implemented into processing codes (e.g. ORIENT, Moldflow) to predict the microstructure of the as-formed composite (i.e. fiber length and orientation distributions). In parallel, characterization and testing methods are developed to obtain necessary microstructural data to validate process modeling predictions. Second, the predicted LFT composite microstructure is imported into amore » structural finite element analysis by ABAQUS to determine the response of the as-formed composite to given boundary conditions. At this stage, constitutive models accounting for the composite microstructure are developed to predict various types of behaviors (i.e. thermoelastic, viscoelastic, elastic-plastic, damage, fatigue, and impact) of LFTs. Experimental methods are also developed to determine material parameters and to validate constitutive models. Such a process-linked-structural modeling approach allows an LFT composite structure to be designed with confidence through numerical simulations. Some recent results of our collaborative research will be illustrated to show the usefulness and applications of this integrated approach.« less

Structure of catalase determined by MicroED

PubMed Central

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

2014-01-01

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

Flow directionality, mountain barriers and functional traits determine diatom metacommunity structuring of high mountain streams.

PubMed

Dong, Xiaoyu; Li, Bin; He, Fengzhi; Gu, Yuan; Sun, Meiqin; Zhang, Haomiao; Tan, Lu; Xiao, Wen; Liu, Shuoran; Cai, Qinghua

2016-04-19

Stream metacommunities are structured by a combination of local (environmental filtering) and regional (dispersal) processes. The unique characters of high mountain streams could potentially determine metacommunity structuring, which is currently poorly understood. Aiming at understanding how these characters influenced metacommunity structuring, we explored the relative importance of local environmental conditions and various dispersal processes, including through geographical (overland), topographical (across mountain barriers) and network (along flow direction) pathways in shaping benthic diatom communities. From a trait perspective, diatoms were categorized into high-profile, low-profile and motile guild to examine the roles of functional traits. Our results indicated that both environmental filtering and dispersal processes influenced metacommunity structuring, with dispersal contributing more than environmental processes. Among the three pathways, stream corridors were primary pathway. Deconstructive analysis suggested different responses to environmental and spatial factors for each of three ecological guilds. However, regardless of traits, dispersal among streams was limited by mountain barriers, while dispersal along stream was promoted by rushing flow in high mountain stream. Our results highlighted that directional processes had prevailing effects on metacommunity structuring in high mountain streams. Flow directionality, mountain barriers and ecological guilds contributed to a better understanding of the roles that mountains played in structuring metacommunity.

Process for fabricating a microelectromechanical structure

DOEpatents

Sniegowski, Jeffry J.; Krygowski, Thomas W.; Mani, Seethambal S.; Habermehl, Scott D.; Hetherington, Dale L.; Stevens, James E.; Resnick, Paul J.; Volk, Steven R.

2004-10-26

A process is disclosed for forming a microelectromechanical (MEM) structure on a substrate having from 5 to 6 or more layers of deposited and patterned polysilicon. The process is based on determining a radius of curvature of the substrate which is bowed due to accumulated stress in the layers of polysilicon and a sacrificial material used to buildup the MEM structure, and then providing one or more stress-compensation layers on a backside of the substrate to flatten the substrate and allow further processing.

Multiscale regression modeling in mouse supraspinatus tendons reveals that dynamic processes act as mediators in structure-function relationships.

PubMed

Connizzo, Brianne K; Adams, Sheila M; Adams, Thomas H; Jawad, Abbas F; Birk, David E; Soslowsky, Louis J

2016-06-14

Recent advances in technology have allowed for the measurement of dynamic processes (re-alignment, crimp, deformation, sliding), but only a limited number of studies have investigated their relationship with mechanical properties. The overall objective of this study was to investigate the role of composition, structure, and the dynamic response to load in predicting tendon mechanical properties in a multi-level fashion mimicking native hierarchical collagen structure. Multiple linear regression models were investigated to determine the relationships between composition/structure, dynamic processes, and mechanical properties. Mediation was then used to determine if dynamic processes mediated structure-function relationships. Dynamic processes were strong predictors of mechanical properties. These predictions were location-dependent, with the insertion site utilizing all four dynamic responses and the midsubstance responding primarily with fibril deformation and sliding. In addition, dynamic processes were moderately predicted by composition and structure in a regionally-dependent manner. Finally, dynamic processes were partial mediators of the relationship between composition/structure and mechanical function, and results suggested that mediation is likely shared between multiple dynamic processes. In conclusion, the mechanical properties at the midsubstance of the tendon are controlled primarily by fibril structure and this region responds to load via fibril deformation and sliding. Conversely, the mechanical function at the insertion site is controlled by many other important parameters and the region responds to load via all four dynamic mechanisms. Overall, this study presents a strong foundation on which to design future experimental and modeling efforts in order to fully understand the complex structure-function relationships present in tendon. Copyright © 2016 Elsevier Ltd. All rights reserved.

Challenges in NMR-based structural genomics

NASA Astrophysics Data System (ADS)

Sue, Shih-Che; Chang, Chi-Fon; Huang, Yao-Te; Chou, Ching-Yu; Huang, Tai-huang

2005-05-01

Understanding the functions of the vast number of proteins encoded in many genomes that have been completely sequenced recently is the main challenge for biologists in the post-genomics era. Since the function of a protein is determined by its exact three-dimensional structure it is paramount to determine the 3D structures of all proteins. This need has driven structural biologists to undertake the structural genomics project aimed at determining the structures of all known proteins. Several centers for structural genomics studies have been established throughout the world. Nuclear magnetic resonance (NMR) spectroscopy has played a major role in determining protein structures in atomic details and in a physiologically relevant solution state. Since the number of new genes being discovered daily far exceeds the number of structures determined by both NMR and X-ray crystallography, a high-throughput method for speeding up the process of protein structure determination is essential for the success of the structural genomics effort. In this article we will describe NMR methods currently being employed for protein structure determination. We will also describe methods under development which may drastically increase the throughput, as well as point out areas where opportunities exist for biophysicists to make significant contribution in this important field.

Education, the Process of Attainment and the Structure of Inequality. Discussion Papers #393-77.

ERIC Educational Resources Information Center

Sorensen, Aage B.

This paper analyzes the properties of the process of social and economic attainments in two contrasting situations: (1) when the process of attainment generates the distribution of attainments, and (2) when the structure of attainments is seen as exogenously determined. It is argued that the neoclassical economic theory of earnings determination…

Rate Kinetics and Molecular Dynamics of the Structural Transitions in Amyloidogenic Proteins

NASA Astrophysics Data System (ADS)

Steckmann, Timothy M.

Amyloid fibril aggregation is associated with several horrific diseases such as Alzheimer's, Creutzfeld-Jacob, diabetes, Parkinson's and others. The process of amyloid aggregation involves forming myriad different metastable intermediate aggregates. Amyloid fibrils are composed of proteins that originate in an innocuous alpha-helix or random-coil structure. The alpha-helices convert their structure to beta-strands that aggregate into beta-sheets, and then into protofibrils, and ultimately into fully formed amyloid fibrils. On the basis of experimental data, I have developed a mathematical model for the kinetics of the reaction pathways and determined rate parameters for peptide secondary structural conversion and aggregation during the entire fibrillogenesis process from random coil to fibrils, including the molecular species that accelerate the conversions. The specific steps of the model and the rate constants that are determined by fitting to experimental data provide insight on the molecular species involved in the fibril formation process. To better understand the molecular basis of the protein structural transitions and aggregation, I report on molecular dynamics (MD) computational studies on the formation of amyloid protofibrillar structures in the small model protein ccbeta, which undergoes many of the structural transitions of the larger, naturally occurring amyloid forming proteins. Two different structural transition processes involving hydrogen bonds are observed for aggregation into fibrils: the breaking of intrachain hydrogen bonds to allow beta-hairpin proteins to straighten, and the subsequent formation of interchain hydrogen bonds during aggregation into amyloid fibrils. For my MD simulations, I found that the temperature dependence of these two different structural transition processes results in the existence of a temperature window that the ccbeta protein experiences during the process of forming protofibrillar structures. Both the mathematical modeling of the kinetics and the MD simulations show that molecular structural heterogeneity is a major factor in the process. The MD simulations also show that intrachain and interchain hydrogen bonds breaking and forming is strongly correlated to the process of amyloid formation.

Structural design/margin assessment

NASA Technical Reports Server (NTRS)

Ryan, R. S.

1993-01-01

Determining structural design inputs and the structural margins following design completion is one of the major activities in space exploration. The end result is a statement of these margins as stability, safety factors on ultimate and yield stresses, fracture limits (fracture control), fatigue lifetime, reuse criteria, operational criteria and procedures, stability factors, deflections, clearance, handling criteria, etc. The process is normally called a load cycle and is time consuming, very complex, and involves much more than structures. The key to successful structural design is the proper implementation of the process. It depends on many factors: leadership and management of the process, adequate analysis and testing tools, data basing, communications, people skills, and training. This process and the various factors involved are discussed.

A World of Information at Their Fingertips: College Students' Motivations and Practices in Their Self-Determined Information Seeking

ERIC Educational Resources Information Center

Nadelson, Louis S.; Sias, Christina M.; Matyi, Joshua; Morris, Sterling R.; Cain, Ryan; Cromwell, Matthew; Lund, Emily M.; Furse, Joseph; Hofmannova, Adela; Johnson, McKenzie; Seegmiller, Janiece; Xie, Tianyi

2016-01-01

People frequently engage in the process of "heutagogy" (i.e., self-determined learning). Unlike pedagogy and andragogy, heutagogy occurs without a structure or leader setting the context and directing the learning toward a specific goal. The lack of structure and the possible self-determination of topic, value, source, and trust in…

Combustion: Structural interaction in a viscoelastic material

NASA Technical Reports Server (NTRS)

Chang, T. Y.; Chang, J. P.; Kumar, M.; Kuo, K. K.

1980-01-01

The effect of interaction between combustion processes and structural deformation of solid propellant was considered. The combustion analysis was performed on the basis of deformed crack geometry, which was determined from the structural analysis. On the other hand, input data for the structural analysis, such as pressure distribution along the crack boundary and ablation velocity of the crack, were determined from the combustion analysis. The interaction analysis was conducted by combining two computer codes, a combustion analysis code and a general purpose finite element structural analysis code.

Determination of bulk domain structure and magnetization processes in bcc ferromagnetic alloys: Analysis of magnetostriction in F e83G a17

NASA Astrophysics Data System (ADS)

He, Yangkun; Coey, J. M. D.; Schaefer, Rudolf; Jiang, Chengbao

2018-01-01

The ground state of macroscopic samples of magnetically ordered materials is a domain state because of magnetostatic energy or entropy, yet we have limited experimental means for imaging the bulk domain structure and the magnetization process directly. The common methods available reveal the domains at the surface or in electron- or x-ray transparent lamellae, not those in the bulk. The magnetization curve just reflects the vector sum of the moments of all the domains in the sample, but magnetostriction curves are more informative. They are strongly influenced by the domain structure in the unmagnetized state and its evolution during the magnetization process in an applied field. Here we report a method of determining the bulk domain structure in a cubic magnetostrictive material by combining magneto-optic Kerr microscopy with magnetostriction and magnetization measurements on single crystals as a function of applied field. We analyze the magnetostriction of F e83G a17 crystals in terms of a domain structure that is greatly influenced by sample shape and heat treatment. Saturation magnetostriction measurements are used to determine the fraction of domains orientated along the three 〈100 〉 axes in the initial state. Domain wall motion and rotation process have characteristic signatures in the magnetostriction curves, including those associated with the Δ E effect and domain rotation through a 〈110 〉 auxetic direction.

Automated protein NMR structure determination using wavelet de-noised NOESY spectra.

PubMed

Dancea, Felician; Günther, Ulrich

2005-11-01

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

On vital aid: the why, what and how of validation

PubMed Central

Kleywegt, Gerard J.

2009-01-01

Limitations to the data and subjectivity in the structure-determination process may cause errors in macromolecular crystal structures. Appropriate validation techniques may be used to reveal problems in structures, ideally before they are analysed, published or deposited. Additionally, such tech­niques may be used a posteriori to assess the (relative) merits of a model by potential users. Weak validation methods and statistics assess how well a model reproduces the information that was used in its construction (i.e. experimental data and prior knowledge). Strong methods and statistics, on the other hand, test how well a model predicts data or information that were not used in the structure-determination process. These may be data that were excluded from the process on purpose, general knowledge about macromolecular structure, information about the biological role and biochemical activity of the molecule under study or its mutants or complexes and predictions that are based on the model and that can be tested experimentally. PMID:19171968

Representing Personal Determinants in Causal Structures.

ERIC Educational Resources Information Center

Bandura, Albert

1984-01-01

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

On a Molecular Basis, Investigate Association of Molecular Structure with Bioactive Compounds, Anti-Nutritional Factors and Chemical and Nutrient Profiles of Canola Seeds and Co-Products from Canola Processing: Comparison Crusher Plants within Canada and within China as well as between Canada and China.

PubMed

Gomaa, Walaa M S; Mosaad, Gamal M; Yu, Peiqiang

2018-04-21

The objectives of this study were to: (1) Use molecular spectroscopy as a novel technique to quantify protein molecular structures in relation to its chemical profiles and bioenergy values in oil-seeds and co-products from bio-oil processing. (2) Determine and compare: (a) protein molecular structure using Fourier transform infrared (FT/IR-ATR) molecular spectroscopy technique; (b) bioactive compounds, anti-nutritional factors, and chemical composition; and (c) bioenergy values in oil seeds (canola seeds), co-products (meal or pellets) from bio-oil processing plants in Canada in comparison with China. (3) Determine the relationship between protein molecular structural features and nutrient profiles in oil-seeds and co-products from bio-oil processing. Our results showed the possibility to characterize protein molecular structure using FT/IR molecular spectroscopy. Processing induced changes between oil seeds and co-products were found in the chemical, bioenergy profiles and protein molecular structure. However, no strong correlation was found between the chemical and nutrient profiles of oil seeds (canola seeds) and their protein molecular structure. On the other hand, co-products were strongly correlated with protein molecular structure in the chemical profile and bioenergy values. Generally, comparisons of oil seeds (canola seeds) and co-products (meal or pellets) in Canada, in China, and between Canada and China indicated the presence of variations among different crusher plants and bio-oil processing products.

Automatic protein structure solution from weak X-ray data

NASA Astrophysics Data System (ADS)

Skubák, Pavol; Pannu, Navraj S.

2013-11-01

Determining new protein structures from X-ray diffraction data at low resolution or with a weak anomalous signal is a difficult and often an impossible task. Here we propose a multivariate algorithm that simultaneously combines the structure determination steps. In tests on over 140 real data sets from the protein data bank, we show that this combined approach can automatically build models where current algorithms fail, including an anisotropically diffracting 3.88 Å RNA polymerase II data set. The method seamlessly automates the process, is ideal for non-specialists and provides a mathematical framework for successfully combining various sources of information in image processing.

Automation of NMR structure determination of proteins.

PubMed

Altieri, Amanda S; Byrd, R Andrew

2004-10-01

The automation of protein structure determination using NMR is coming of age. The tedious processes of resonance assignment, followed by assignment of NOE (nuclear Overhauser enhancement) interactions (now intertwined with structure calculation), assembly of input files for structure calculation, intermediate analyses of incorrect assignments and bad input data, and finally structure validation are all being automated with sophisticated software tools. The robustness of the different approaches continues to deal with problems of completeness and uniqueness; nevertheless, the future is very bright for automation of NMR structure generation to approach the levels found in X-ray crystallography. Currently, near completely automated structure determination is possible for small proteins, and the prospect for medium-sized and large proteins is good. Copyright 2004 Elsevier Ltd.

The Internal Structure of "Chaos": Letter Category Determines Visual Word Perceptual Units

ERIC Educational Resources Information Center

Chetail, Fabienne; Content, Alain

2012-01-01

The processes and the cues determining the orthographic structure of polysyllabic words remain far from clear. In the present study, we investigated the role of letter category (consonant vs. vowels) in the perceptual organization of letter strings. In the syllabic counting task, participants were presented with written words matched for the…

A programmable nanoreplica molding for the fabrication of nanophotonic devices.

PubMed

Liu, Longju; Zhang, Jingxiang; Badshah, Mohsin Ali; Dong, Liang; Li, Jingjing; Kim, Seok-min; Lu, Meng

2016-03-01

The ability to fabricate periodic structures with sub-wavelength features has a great potential for impact on integrated optics, optical sensors, and photovoltaic devices. Here, we report a programmable nanoreplica molding process to fabricate a variety of sub-micrometer periodic patterns using a single mold. The process utilizes a stretchable mold to produce the desired periodic structure in a photopolymer on glass or plastic substrates. During the replica molding process, a uniaxial force is applied to the mold and results in changes of the periodic structure, which resides on the surface of the mold. Direction and magnitude of the force determine the array geometry, including the lattice constant and arrangement. By stretching the mold, 2D arrays with square, rectangular, and triangular lattice structures can be fabricated. As one example, we present a plasmonic crystal device with surface plasmon resonances determined by the force applied during molding. In addition, photonic crystal slabs with different array patterns are fabricated and characterized. This unique process offers the capability of generating various periodic nanostructures rapidly and inexpensively.

A programmable nanoreplica molding for the fabrication of nanophotonic devices

PubMed Central

Liu, Longju; Zhang, Jingxiang; Badshah, Mohsin Ali; Dong, Liang; Li, Jingjing; Kim, Seok-min; Lu, Meng

2016-01-01

The ability to fabricate periodic structures with sub-wavelength features has a great potential for impact on integrated optics, optical sensors, and photovoltaic devices. Here, we report a programmable nanoreplica molding process to fabricate a variety of sub-micrometer periodic patterns using a single mold. The process utilizes a stretchable mold to produce the desired periodic structure in a photopolymer on glass or plastic substrates. During the replica molding process, a uniaxial force is applied to the mold and results in changes of the periodic structure, which resides on the surface of the mold. Direction and magnitude of the force determine the array geometry, including the lattice constant and arrangement. By stretching the mold, 2D arrays with square, rectangular, and triangular lattice structures can be fabricated. As one example, we present a plasmonic crystal device with surface plasmon resonances determined by the force applied during molding. In addition, photonic crystal slabs with different array patterns are fabricated and characterized. This unique process offers the capability of generating various periodic nanostructures rapidly and inexpensively. PMID:26925828

Models of determining deformations

NASA Astrophysics Data System (ADS)

Gladilin, V. N.

2016-12-01

In recent years, a lot of functions designed to determine deformation values that occur mostly as a result of settlement of structures and industrial equipment. Some authors suggest such advanced mathematical functions approximating deformations as general methods for the determination of deformations. The article describes models of deformations as physical processes. When comparing static, cinematic and dynamic models, it was found that the dynamic model reflects the deformation of structures and industrial equipment most reliably.

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

NASA Technical Reports Server (NTRS)

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

1986-01-01

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

Cloud computing method for dynamically scaling a process across physical machine boundaries

DOEpatents

Gillen, Robert E.; Patton, Robert M.; Potok, Thomas E.; Rojas, Carlos C.

2014-09-02

A cloud computing platform includes first device having a graph or tree structure with a node which receives data. The data is processed by the node or communicated to a child node for processing. A first node in the graph or tree structure determines the reconfiguration of a portion of the graph or tree structure on a second device. The reconfiguration may include moving a second node and some or all of its descendant nodes. The second and descendant nodes may be copied to the second device.

Influence of Structural Features and Fracture Processes on Surface Roughness: A Case Study from the Krosno Sandstones of the Górka-Mucharz Quarry (Little Beskids, Southern Poland)

NASA Astrophysics Data System (ADS)

Pieczara, Łukasz

2015-09-01

The paper presents the results of analysis of surface roughness parameters in the Krosno Sandstones of Mucharz, southern Poland. It was aimed at determining whether these parameters are influenced by structural features (mainly the laminar distribution of mineral components and directional distribution of non-isometric grains) and fracture processes. The tests applied in the analysis enabled us to determine and describe the primary statistical parameters used in the quantitative description of surface roughness, as well as specify the usefulness of contact profilometry as a method of visualizing spatial differentiation of fracture processes in rocks. These aims were achieved by selecting a model material (Krosno Sandstones from the Górka-Mucharz Quarry) and an appropriate research methodology. The schedule of laboratory analyses included: identification analyses connected with non-destructive ultrasonic tests, aimed at the preliminary determination of rock anisotropy, strength point load tests (cleaved surfaces were obtained due to destruction of rock samples), microscopic analysis (observation of thin sections in order to determine the mechanism of inducing fracture processes) and a test method of measuring surface roughness (two- and three-dimensional diagrams, topographic and contour maps, and statistical parameters of surface roughness). The highest values of roughness indicators were achieved for surfaces formed under the influence of intragranular fracture processes (cracks propagating directly through grains). This is related to the structural features of the Krosno Sandstones (distribution of lamination and bedding).

Epidemic spreading on complex networks with community structures

PubMed Central

Stegehuis, Clara; van der Hofstad, Remco; van Leeuwaarden, Johan S. H.

2016-01-01

Many real-world networks display a community structure. We study two random graph models that create a network with similar community structure as a given network. One model preserves the exact community structure of the original network, while the other model only preserves the set of communities and the vertex degrees. These models show that community structure is an important determinant of the behavior of percolation processes on networks, such as information diffusion or virus spreading: the community structure can both enforce as well as inhibit diffusion processes. Our models further show that it is the mesoscopic set of communities that matters. The exact internal structures of communities barely influence the behavior of percolation processes across networks. This insensitivity is likely due to the relative denseness of the communities. PMID:27440176

Role of Thermal Process on Self-Assembled Structures of 4′-([2,2′:6′,2″-Terpyridin]-4′-Yl)-[1,1′-Biphenyl]-4-Carboxylic Acid on Au(III)

PubMed Central

Liu, Xiaoqing; Wang, Yongli; Song, Xin; Chen, Feng; Ouyang, Hongping; Zhang, Xueao; Cai, Yingxiang; Liu, Xiaoming; Wang, Li

2013-01-01

The role of dynamic processes on self-assembled structures of 4′-([2,2′:6′, 2″-terpyridin]-4′-yl)-[1,1′-biphenyl]-4-carboxylic acid (l) molecules on Au(III) has been studied by scanning tunneling microscopy. The as-deposited monolayer is closed-packed and periodic in a short-range due to dipole forces. A thermal annealing process at 110 degrees drives such disordered monolayer into ordered chain-like structures, determined by the combination of the dipole forces and hydrogen bonding. Further annealing at 130 degrees turns the whole monolayer into a bowknot-like structure in which hydrogen bonding plays the dominant role in the formation of assembled structures. Such dependence of an assembled structure on the process demonstrates that an assembled structure can be regulated and controlled not only by the molecular structure but also by the thermal process to form the assembled structure. PMID:23478440

The Structural Underpinnings of Policy Learning: A Classroom Policy Simulation

NASA Astrophysics Data System (ADS)

Bird, Stephen

This paper investigates the relationship between the centrality of individual actors in a social network structure and their policy learning performance. In a dynamic comparable to real-world policy networks, results from a classroom simulation demonstrate a strong relationship between centrality in social learning networks and grade performance. Previous research indicates that social network centrality should have a positive effect on learning in other contexts and this link is tested in a policy learning context. Second, the distinction between collaborative learning versus information diffusion processes in policy learning is examined. Third, frequency of interaction is analyzed to determine whether consistent, frequent tics have a greater impact on the learning process. Finally, the data arc analyzed to determine if the benefits of centrality have limitations or thresholds when benefits no longer accrue. These results demonstrate the importance of network structure, and support a collaborative conceptualization of the policy learning process.

Molecular Dynamics Studies of Structure and Functions of Water-Membrane Interfaces

NASA Technical Reports Server (NTRS)

Pohorille, Andrew; Wilson, Michael A.; DeVincenzi, Donald L. (Technical Monitor)

2001-01-01

A large number of essential cellular processes occur at the interfaces between water and membranes. The selectivity and dynamics of these processes are largely determined by the structural and electrical properties of the water-membrane interface. We investigate these properties by the molecular dynamics method. Over the time scales of the simulations, the membrane undergoes fluctuations described by the capillary wave model. These fluctuations produce occasional thinning defects in the membrane which provide effective pathways for passive transport of ions and small molecules across the membrane. Ions moving through the membrane markedly disrupt its structure and allow for significant water penetration into the membrane interior. Selectivity of transport, with respect to ionic charge, is determined by the interfacial electrostatic potential. Many small molecules. of potential significance in catalysis, bioenergetics and pharmacology, are shown to bind to the interface. The energetics and dynamics of this process will be discussed.

Do's and don'ts of cryo-electron microscopy: a primer on sample preparation and high quality data collection for macromolecular 3D reconstruction.

PubMed

Cabra, Vanessa; Samsó, Montserrat

2015-01-09

Cryo-electron microscopy (cryoEM) entails flash-freezing a thin layer of sample on a support, and then visualizing the sample in its frozen hydrated state by transmission electron microscopy (TEM). This can be achieved with very low quantity of protein and in the buffer of choice, without the use of any stain, which is very useful to determine structure-function correlations of macromolecules. When combined with single-particle image processing, the technique has found widespread usefulness for 3D structural determination of purified macromolecules. The protocol presented here explains how to perform cryoEM and examines the causes of most commonly encountered problems for rational troubleshooting; following all these steps should lead to acquisition of high quality cryoEM images. The technique requires access to the electron microscope instrument and to a vitrification device. Knowledge of the 3D reconstruction concepts and software is also needed for computerized image processing. Importantly, high quality results depend on finding the right purification conditions leading to a uniform population of structurally intact macromolecules. The ability of cryoEM to visualize macromolecules combined with the versatility of single particle image processing has proven very successful for structural determination of large proteins and macromolecular machines in their near-native state, identification of their multiple components by 3D difference mapping, and creation of pseudo-atomic structures by docking of x-ray structures. The relentless development of cryoEM instrumentation and image processing techniques for the last 30 years has resulted in the possibility to generate de novo 3D reconstructions at atomic resolution level.

Friction Stir Welding

NASA Technical Reports Server (NTRS)

Nunes, Arthur C., Jr.

2008-01-01

Friction stir welding (FSW) is a solid state welding process invented in 1991 at The Welding Institute in the United Kingdom. A weld is made in the FSW process by translating a rotating pin along a weld seam so as to stir the sides of the seam together. FSW avoids deleterious effects inherent in melting and promises to be an important welding process for any industries where welds of optimal quality are demanded. This article provides an introduction to the FSW process. The chief concern is the physical effect of the tool on the weld metal: how weld seam bonding takes place, what kind of weld structure is generated, potential problems, possible defects for example, and implications for process parameters and tool design. Weld properties are determined by structure, and the structure of friction stir welds is determined by the weld metal flow field in the vicinity of the weld tool. Metal flow in the vicinity of the weld tool is explained through a simple kinematic flow model that decomposes the flow field into three basic component flows: a uniform translation, a rotating solid cylinder, and a ring vortex encircling the tool. The flow components, superposed to construct the flow model, can be related to particular aspects of weld process parameters and tool design; they provide a bridge to an understanding of a complex-at-first-glance weld structure. Torques and forces are also discussed. Some simple mathematical models of structural aspects, torques, and forces are included.

Evaluation of uncertainty in determination of neutral axis and deformed shape of beam structures : final report.

DOT National Transportation Integrated Search

2016-01-01

With aging infrastructure, it becomes crucial to make informed decisions about maintenance and : preservation actions, as well as renewal of civil structures. Structural Health Monitoring (SHM) can be : an important aid in this decision process, but ...

Choosing to Be a Defender or an Outsider in a School Bullying Incident: Determining Factors and the Defending Process

ERIC Educational Resources Information Center

Chen, Li-Ming; Chang, Lennon Y. C.; Cheng, Ying-Yao

2016-01-01

This study examined the determinants of students' willingness to intervene in bullying incidents, as well as the process underlying students' defending behaviors. The participants were 24 students (12 defenders and 12 outsiders) recruited from six secondary schools in southern Taiwan. The study used semi-structured interviews to collect…

Study of mould design and forming process on advanced polymer-matrix composite complex structure

NASA Astrophysics Data System (ADS)

Li, S. J.; Zhan, L. H.; Bai, H. M.; Chen, X. P.; Zhou, Y. Q.

2015-07-01

Advanced carbon fibre-reinforced polymer-matrix composites are widely applied to aviation manufacturing field due to their outstanding performance. In this paper, the mould design and forming process of the complex composite structure were discussed in detail using the hat stiffened structure as an example. The key issues of the moulddesign were analyzed, and the corresponding solutions were also presented. The crucial control points of the forming process such as the determination of materials and stacking sequence, the temperature and pressure route of the co-curing process were introduced. In order to guarantee the forming quality of the composite hat stiffened structure, a mathematical model about the aperture of rubber mandrel was introduced. The study presented in this paper may provide some actual references for the design and manufacture of the important complex composite structures.

Design and Optimization of Composite Automotive Hatchback Using Integrated Material-Structure-Process-Performance Method

NASA Astrophysics Data System (ADS)

Yang, Xudong; Sun, Lingyu; Zhang, Cheng; Li, Lijun; Dai, Zongmiao; Xiong, Zhenkai

2018-03-01

The application of polymer composites as a substitution of metal is an effective approach to reduce vehicle weight. However, the final performance of composite structures is determined not only by the material types, structural designs and manufacturing process, but also by their mutual restrict. Hence, an integrated "material-structure-process-performance" method is proposed for the conceptual and detail design of composite components. The material selection is based on the principle of composite mechanics such as rule of mixture for laminate. The design of component geometry, dimension and stacking sequence is determined by parametric modeling and size optimization. The selection of process parameters are based on multi-physical field simulation. The stiffness and modal constraint conditions were obtained from the numerical analysis of metal benchmark under typical load conditions. The optimal design was found by multi-discipline optimization. Finally, the proposed method was validated by an application case of automotive hatchback using carbon fiber reinforced polymer. Compared with the metal benchmark, the weight of composite one reduces 38.8%, simultaneously, its torsion and bending stiffness increases 3.75% and 33.23%, respectively, and the first frequency also increases 44.78%.

Investigation of selected structural parameters in Fe 95Si 5 amorphous alloy during crystallization process

NASA Astrophysics Data System (ADS)

Fronczyk, Adam

2007-04-01

In this study, we report on a crystallization behavior of the Fe 95Si 5 metallic glasses using a differential scanning cabrimetry (DSC), and X-ray diffraction. The paper presents the results of experimental investigation of Fe 95Si 5 amorphous alloy, subjected to the crystallizing process by the isothermal annealing. The objective of the experiment was to determine changes in the structural parameters during crystallization process of the examined alloy. Crystalline diameter and the lattice constant of the crystallizing phase were used as parameters to evaluate structural changes in material.

A Brief Introduction to the Theory of Friction Stir Welding

NASA Technical Reports Server (NTRS)

Nunes, Arthur C., Jr.

2008-01-01

Friction stir welding (FSW) is a solid state welding process invented in 1991 at The Welding Institute in the United Kingdom. A weld is made in the FSW process by translating a rotating pin along a weld seam so as to stir the sides of the seam together. FSW avoids deleterious effects inherent in melting and is already an important welding process for the aerospace industry, where welds of optimal quality are demanded. The structure of welds determines weld properties. The structure of friction stir welds is determined by the flow field in the weld metal in the vicinity of the weld tool. A simple kinematic model of the FSW flow field developed at Marshall Space Flight Center, which enables the basic features of FSW microstructure to be understood and related to weld process parameters and tool design, is explained.

Atoms in Action: Observing Atomic Motion with Dynamic in situ X-ray Diffraction

NASA Astrophysics Data System (ADS)

Cox, Jordan Michael

Metal-organic framework (MOF) materials are rich in both structural diversity and application. These materials are comprised of metal atoms or clusters which are connected in a three-dimensional polymer-like network by bridging organic linker molecules. One of the major attractive features in MOFs is their permanent pore space which can potentially be used to adsorb or exchange foreign molecules from/with the surrounding environment. While MOFs are an active area of scientific interest, MOF materials are still relatively new, only 20 years old. As such, there is still much that needs to be understood about these materials before they can be effectively applied to widespread chemical problems like CO2 sequestration or low-pressure hydrogen fuel storage. One of the most important facets of MOF chemistry to understand in order to rationally design MOF materials with tailor-made properties is the relationship between the structural features in a MOF and the chemical and physical properties of that material. By examining in detail the atomic structure of a MOF with known properties under a variety of conditions, scientists can begin to unravel the guiding principles which govern these relationships. X-ray diffraction remains one of the most effective tools for determining the structure of a crystalline material with atomic resolution, and has been applied to the determination of MOF structures for years. Typically these experiments have been carried out using powder X-ray diffraction, but this technique lacks the high-resolution structural information found in single-crystal methods. Some studies have been reported which use specialized devices, sometimes called Environmental Control Cells, to study single crystalline MOFs under non-ambient chemical conditions in situ . However, these in situ studies are performed under static conditions. Even in cases where the ECC provides continued access to the local chemical environment during diffraction data collections, the environment is left static or data is not collected until after the material has equilibrated to its new environment. First, a unique ECC has been designed and constructed which allows continuous access to the local chemical environment of a single-crystal sample while maintaining ease of use, minimizing size, and which is easily adaptable to a wide variety of gaseous and liquid chemical stimuli. Novel methods have been developed and are herein described for utilizing this ECC and in situ X-ray diffraction methods in a dynamic manner for monitoring the structural responses of single crystals to changes in their local chemical environment. These methods provide the opportunity for the determination of changes in unit cell parameters and even complete crystal structures during adsorption, desorption, and exchange processes in MOF materials. The application of these methods to the determination of the dehydration process of a previously reported cobalt-based MOF have revealed surprising structural and dynamics data. Several new intermediate structures have been determined in this process, including one metastable species and several actively transitioning species during the dehydration process. Applying these methods to the ethanol solvation process in the same material again yielded results which were richer in structural information than the previously reported ex situ structures. A computational study of rotational potential energy surfaces in a family of photochromic MOF linkers revealed the important role rotational stereoisomers can play in maintaining light-activated functionality when these linkers are incorporated into next-generation functional MOF materials. Finally, the application of novel photocrystallography techniques were used in conjunction with spectroscopic methods to determine the nature of the anomalous behavior of a photochromic diarylethene single-crystal.

Pulse - Accelerator Science in Medicine

Science.gov Websites

the structure of biological molecules. They use the energy that charged particles emit when powerful than the sun and focused on a pinpoint. Deciphering the structure of proteins is key to understanding biological processes and healing disease. To determine a protein’s structure, researchers direct

Johann Deisenhofer, Crystallography, and Proteins

Science.gov Websites

research using X-ray crystallography to elucidate for the first time the three-dimensional structure of a large membrane-bound protein molecule. This structure helped explain the process of photosynthesis, by a protein structure determination that relied on complementary features of two different beam lines

A Bayesian Approach for Determining Protein Side-Chain Rotamer Conformations Using Unassigned NOE Data

PubMed Central

Zeng, Jianyang; Roberts, Kyle E.; Zhou, Pei

2011-01-01

Abstract A major bottleneck in protein structure determination via nuclear magnetic resonance (NMR) is the lengthy and laborious process of assigning resonances and nuclear Overhauser effect (NOE) cross peaks. Recent studies have shown that accurate backbone folds can be determined using sparse NMR data, such as residual dipolar couplings (RDCs) or backbone chemical shifts. This opens a question of whether we can also determine the accurate protein side-chain conformations using sparse or unassigned NMR data. We attack this question by using unassigned nuclear Overhauser effect spectroscopy (NOESY) data, which records the through-space dipolar interactions between protons nearby in three-dimensional (3D) space. We propose a Bayesian approach with a Markov random field (MRF) model to integrate the likelihood function derived from observed experimental data, with prior information (i.e., empirical molecular mechanics energies) about the protein structures. We unify the side-chain structure prediction problem with the side-chain structure determination problem using unassigned NMR data, and apply the deterministic dead-end elimination (DEE) and A* search algorithms to provably find the global optimum solution that maximizes the posterior probability. We employ a Hausdorff-based measure to derive the likelihood of a rotamer or a pairwise rotamer interaction from unassigned NOESY data. In addition, we apply a systematic and rigorous approach to estimate the experimental noise in NMR data, which also determines the weighting factor of the data term in the scoring function derived from the Bayesian framework. We tested our approach on real NMR data of three proteins: the FF Domain 2 of human transcription elongation factor CA150 (FF2), the B1 domain of Protein G (GB1), and human ubiquitin. The promising results indicate that our algorithm can be applied in high-resolution protein structure determination. Since our approach does not require any NOE assignment, it can accelerate the NMR structure determination process. PMID:21970619

The JCSG high-throughput structural biology pipeline.

PubMed

Elsliger, Marc André; Deacon, Ashley M; Godzik, Adam; Lesley, Scott A; Wooley, John; Wüthrich, Kurt; Wilson, Ian A

2010-10-01

The Joint Center for Structural Genomics high-throughput structural biology pipeline has delivered more than 1000 structures to the community over the past ten years. The JCSG has made a significant contribution to the overall goal of the NIH Protein Structure Initiative (PSI) of expanding structural coverage of the protein universe, as well as making substantial inroads into structural coverage of an entire organism. Targets are processed through an extensive combination of bioinformatics and biophysical analyses to efficiently characterize and optimize each target prior to selection for structure determination. The pipeline uses parallel processing methods at almost every step in the process and can adapt to a wide range of protein targets from bacterial to human. The construction, expansion and optimization of the JCSG gene-to-structure pipeline over the years have resulted in many technological and methodological advances and developments. The vast number of targets and the enormous amounts of associated data processed through the multiple stages of the experimental pipeline required the development of variety of valuable resources that, wherever feasible, have been converted to free-access web-based tools and applications.

Structure of a low-population intermediate state in the release of an enzyme product.

PubMed

De Simone, Alfonso; Aprile, Francesco A; Dhulesia, Anne; Dobson, Christopher M; Vendruscolo, Michele

2015-01-09

Enzymes can increase the rate of biomolecular reactions by several orders of magnitude. Although the steps of substrate capture and product release are essential in the enzymatic process, complete atomic-level descriptions of these steps are difficult to obtain because of the transient nature of the intermediate conformations, which makes them largely inaccessible to standard structure determination methods. We describe here the determination of the structure of a low-population intermediate in the product release process by human lysozyme through a combination of NMR spectroscopy and molecular dynamics simulations. We validate this structure by rationally designing two mutations, the first engineered to destabilise the intermediate and the second to stabilise it, thus slowing down or speeding up, respectively, product release. These results illustrate how product release by an enzyme can be facilitated by the presence of a metastable intermediate with transient weak interactions between the enzyme and product.

NMR studies of protein-nucleic acid interactions.

PubMed

Varani, Gabriele; Chen, Yu; Leeper, Thomas C

2004-01-01

Protein-DNA and protein-RNA complexes play key functional roles in every living organism. Therefore, the elucidation of their structure and dynamics is an important goal of structural and molecular biology. Nuclear magnetic resonance (NMR) studies of protein and nucleic acid complexes have common features with studies of protein-protein complexes: the interaction surfaces between the molecules must be carefully delineated, the relative orientation of the two species needs to be accurately and precisely determined, and close intermolecular contacts defined by nuclear Overhauser effects (NOEs) must be obtained. However, differences in NMR properties (e.g., chemical shifts) and biosynthetic pathways for sample productions generate important differences. Chemical shift differences between the protein and nucleic acid resonances can aid the NMR structure determination process; however, the relatively limited dispersion of the RNA ribose resonances makes the process of assigning intermolecular NOEs more difficult. The analysis of the resulting structures requires computational tools unique to nucleic acid interactions. This chapter summarizes the most important elements of the structure determination by NMR of protein-nucleic acid complexes and their analysis. The main emphasis is on recent developments (e.g., residual dipolar couplings and new Web-based analysis tools) that have facilitated NMR studies of these complexes and expanded the type of biological problems to which NMR techniques of structural elucidation can now be applied.

Experimental analysis for fabrication of high-aspect-ratio piezoelectric ceramic structure by micro-powder injection molding process

NASA Astrophysics Data System (ADS)

Han, Jun Sae; Gal, Chang Woo; Park, Jae Man; Kim, Jong Hyun; Park, Seong Jin

2018-04-01

Aspect ratio effects in the micro-powder injection molding process were experimentally analyzed for fabrication of high-aspect-ratio piezoelectric ceramic structure. The mechanisms of critical defects have been studied according to individual manufacturing steps. In the molding process, incomplete filling phenomenon determines the critical aspect ratios of a micro pattern. According to mold temperature, an incomplete filling phenomenon has been analyzed with respect to different pattern sizes and aspect ratio. In demolding and drying process, the capillary behavior of sacrificial polymeric mold insert determines the critical aspect ratio of a micro pattern. With respect to pattern dimensions, slumping behavior has been analyzed. Based on our current systems, micro PZT feature has stability when it has lower aspect ratio than 5. Under optimized processing conditions, 20 μm and 40 μm ceramic rod array feature which has 5 of aspect ratio were successfully fabricated by the developed process. Further modification points to fabricate the smaller and higher feature were specifically addressed.

PDBStat: a universal restraint converter and restraint analysis software package for protein NMR.

PubMed

Tejero, Roberto; Snyder, David; Mao, Binchen; Aramini, James M; Montelione, Gaetano T

2013-08-01

The heterogeneous array of software tools used in the process of protein NMR structure determination presents organizational challenges in the structure determination and validation processes, and creates a learning curve that limits the broader use of protein NMR in biology. These challenges, including accurate use of data in different data formats required by software carrying out similar tasks, continue to confound the efforts of novices and experts alike. These important issues need to be addressed robustly in order to standardize protein NMR structure determination and validation. PDBStat is a C/C++ computer program originally developed as a universal coordinate and protein NMR restraint converter. Its primary function is to provide a user-friendly tool for interconverting between protein coordinate and protein NMR restraint data formats. It also provides an integrated set of computational methods for protein NMR restraint analysis and structure quality assessment, relabeling of prochiral atoms with correct IUPAC names, as well as multiple methods for analysis of the consistency of atomic positions indicated by their convergence across a protein NMR ensemble. In this paper we provide a detailed description of the PDBStat software, and highlight some of its valuable computational capabilities. As an example, we demonstrate the use of the PDBStat restraint converter for restrained CS-Rosetta structure generation calculations, and compare the resulting protein NMR structure models with those generated from the same NMR restraint data using more traditional structure determination methods. These results demonstrate the value of a universal restraint converter in allowing the use of multiple structure generation methods with the same restraint data for consensus analysis of protein NMR structures and the underlying restraint data.

PDBStat: A Universal Restraint Converter and Restraint Analysis Software Package for Protein NMR

PubMed Central

Tejero, Roberto; Snyder, David; Mao, Binchen; Aramini, James M.; Montelione, Gaetano T

2013-01-01

The heterogeneous array of software tools used in the process of protein NMR structure determination presents organizational challenges in the structure determination and validation processes, and creates a learning curve that limits the broader use of protein NMR in biology. These challenges, including accurate use of data in different data formats required by software carrying out similar tasks, continue to confound the efforts of novices and experts alike. These important issues need to be addressed robustly in order to standardize protein NMR structure determination and validation. PDBStat is a C/C++ computer program originally developed as a universal coordinate and protein NMR restraint converter. Its primary function is to provide a user-friendly tool for interconverting between protein coordinate and protein NMR restraint data formats. It also provides an integrated set of computational methods for protein NMR restraint analysis and structure quality assessment, relabeling of prochiral atoms with correct IUPAC names, as well as multiple methods for analysis of the consistency of atomic positions indicated by their convergence across a protein NMR ensemble. In this paper we provide a detailed description of the PDBStat software, and highlight some of its valuable computational capabilities. As an example, we demonstrate the use of the PDBStat restraint converter for restrained CS-Rosetta structure generation calculations, and compare the resulting protein NMR structure models with those generated from the same NMR restraint data using more traditional structure determination methods. These results demonstrate the value of a universal restraint converter in allowing the use of multiple structure generation methods with the same restraint data for consensus analysis of protein NMR structures and the underlying restraint data. PMID:23897031

Investigating the high school students' cognitive structures about the work concept

NASA Astrophysics Data System (ADS)

Tavukçuoǧlu, Erdem; Özcan, Özgür

2018-02-01

The purpose of this study is to determine the high school students' cognitive structures related to the concepts of work. The participants of the study were composed of the students enrolled in 11. and 12. class of an Anatolian high school in Turkey. The data were collected via word association test related to the key concept to determine the students' cognitive structures. The collected data were analyzed according to the content analysis method. In the data analysis process, we determined firstly the number of words, the number of answers and the semantic relations between the words written by students. The words having semantic connections were grouped under the same category. Thus, at the end of the study, high school students' cognitive structures and some alternative conceptions were determined related to concepts of work.

AFRL Solid Propellant Laboratory Explosive Siting and Renovation Lessons Learned

DTIC Science & Technology

2010-07-01

Area 1-30A explosive facility and provide consultation/support during the review process for each of the site plans. • Applied Engineering Services...provided consultation/support during the siting review process. • Applied Engineering Services (AES) Inc. performed a detailed structural, blast, thermal... Applied Engineering Services (AES) Inc. structural, blast, thermal and fragment hazard analysis to determine the appropriate siting values based on

Coalescence and Collisions of Gold Nanoparticles

PubMed Central

Antúnez-García, Joel; Mejía-Rosales, Sergio; Pérez-Tijerina, Eduardo; Montejano-Carrizales, Juan Martín; José-Yacamán, Miguel

2011-01-01

We study the assembling of small gold clusters subject to collisions and close contact coalescence by using molecular dynamics simulations to simulate events that occur typically in the sputtering process of synthesis. Our results support the notion that the kinetics of coalescence processes strongly determine the geometry and structure of the final particle. While impact velocities, relative orientations, and the initial shape of the interacting particles are unlikely to strictly determine the structural details of the newly formed particle, we found that high initial temperatures and/or impact velocities increase the probability of appearance of icosahedral-like structures, Wulff polyhedra are likely to be formed as a product of the interactions between nanospheres, while the appearance of fcc particles of approximately cuboctahedral shape is mainly due to the interaction between icosahedra. PMID:28879995

Coalescence and Collisions of Gold Nanoparticles.

PubMed

Antúnez-García, Joel; Mejía-Rosales, Sergio; Pérez-Tijerina, Eduardo; Montejano-Carrizales, Juan Martín; José-Yacamán, Miguel

2011-01-28

We study the assembling of small gold clusters subject to collisions and close contact coalescence by using molecular dynamics simulations to simulate events that occur typically in the sputtering process of synthesis. Our results support the notion that the kinetics of coalescence processes strongly determine the geometry and structure of the final particle. While impact velocities, relative orientations, and the initial shape of the interacting particles are unlikely to strictly determine the structural details of the newly formed particle, we found that high initial temperatures and/or impact velocities increase the probability of appearance of icosahedral-like structures, Wulff polyhedra are likely to be formed as a product of the interactions between nanospheres, while the appearance of fcc particles of approximately cuboctahedral shape is mainly due to the interaction between icosahedra.

Multi-target parallel processing approach for gene-to-structure determination of the influenza polymerase PB2 subunit.

PubMed

Armour, Brianna L; Barnes, Steve R; Moen, Spencer O; Smith, Eric; Raymond, Amy C; Fairman, James W; Stewart, Lance J; Staker, Bart L; Begley, Darren W; Edwards, Thomas E; Lorimer, Donald D

2013-06-28

Pandemic outbreaks of highly virulent influenza strains can cause widespread morbidity and mortality in human populations worldwide. In the United States alone, an average of 41,400 deaths and 1.86 million hospitalizations are caused by influenza virus infection each year (1). Point mutations in the polymerase basic protein 2 subunit (PB2) have been linked to the adaptation of the viral infection in humans (2). Findings from such studies have revealed the biological significance of PB2 as a virulence factor, thus highlighting its potential as an antiviral drug target. The structural genomics program put forth by the National Institute of Allergy and Infectious Disease (NIAID) provides funding to Emerald Bio and three other Pacific Northwest institutions that together make up the Seattle Structural Genomics Center for Infectious Disease (SSGCID). The SSGCID is dedicated to providing the scientific community with three-dimensional protein structures of NIAID category A-C pathogens. Making such structural information available to the scientific community serves to accelerate structure-based drug design. Structure-based drug design plays an important role in drug development. Pursuing multiple targets in parallel greatly increases the chance of success for new lead discovery by targeting a pathway or an entire protein family. Emerald Bio has developed a high-throughput, multi-target parallel processing pipeline (MTPP) for gene-to-structure determination to support the consortium. Here we describe the protocols used to determine the structure of the PB2 subunit from four different influenza A strains.

Transcript Lifetime Is Balanced between Stabilizing Stem-Loop Structures and Degradation-Promoting Polyadenylation in Plant Mitochondria

PubMed Central

Kuhn, Josef; Tengler, Ulrike; Binder, Stefan

2001-01-01

To determine the influence of posttranscriptional modifications on 3′ end processing and RNA stability in plant mitochondria, pea atp9 and Oenothera atp1 transcripts were investigated for the presence and function of 3′ nonencoded nucleotides. A 3′ rapid amplification of cDNA ends approach initiated at oligo(dT)-adapter primers finds the expected poly(A) tails predominantly attached within the second stem or downstream of the double stem-loop structures at sites of previously mapped 3′ ends. Functional studies in a pea mitochondrial in vitro processing system reveal a rapid removal of the poly(A) tails up to termini at the stem-loop structure but little if any influence on further degradation of the RNA. In contrast 3′ poly(A) tracts at RNAs without such stem-loop structures significantly promote total degradation in vitro. To determine the in vivo identity of 3′ nonencoded nucleotides more accurately, pea atp9 transcripts were analyzed by a direct anchor primer ligation-reverse transcriptase PCR approach. This analysis identified maximally 3-nucleotide-long nonencoded extensions most frequently of adenosines combined with cytidines. Processing assays with substrates containing homopolymer stretches of different lengths showed that 10 or more adenosines accelerate RNA processivity, while 3 adenosines have no impact on RNA life span. Thus polyadenylation can generally stimulate the decay of RNAs, but processivity of degradation is almost annihilated by the stabilizing effect of the stem-loop structures. These antagonistic actions thus result in the efficient formation of 3′ processed and stable transcripts. PMID:11154261

Organizational Perspectives on Rapid Response Team Structure, Function, and Cost: A Qualitative Study.

PubMed

Smith, Patricia L; McSweeney, Jean

Understanding how an organization determines structure and function of a rapid response team (RRT), as well as cost evaluation and implications, can provide foundational knowledge to guide decisions about RRTs. The objectives were to (1) identify influencing factors in organizational development of RRT structure and function and (2) describe evaluation of RRT costs. Using a qualitative, ethnographic design, nurse executives and experts in 15 moderate-size hospitals were interviewed to explore their decision-making processes in determining RRT structure and function. Face-to-face interviews were audio recorded and transcribed verbatim and verified for accurateness. Using content analysis and constant comparison, interview data were analyzed. Demographic data were analyzed using descriptive statistics. The sample included 27 participants from 15 hospitals in 5 south-central states. They described a variety of RRT responders and functions, with the majority of hospitals having a critical care charge nurse attending all RRT calls for assistance. Others described a designated RRT nurse with primary RRT duties as responder to all RRT calls. Themes of RRT development from the data included influencers, decision processes, and thoughts about cost. It is important to understand how hospitals determine optimal structure and function to enhance support of quality nursing care. Determining the impact of an RRT on costs and benefits is vital in balancing patient safety and limited resources. Future research should focus on clarifying differences between team structure and function in outcomes as well as the most effective means to estimate costs and benefits.

Molecular disassembly of rice and lotus starches during thermal processing and its effect on starch digestibility.

PubMed

Wang, Shujun; Sun, Yue; Wang, Jinrong; Wang, Shuo; Copeland, Les

2016-02-01

The molecular disassembly of starch during thermal processing is a major determinant for the susceptibility of starch to enzymatic digestion. In the present study, the effects of thermal processing on the disassembly of the granular structure and the in vitro enzymatic digestibility of rice and lotus starches were investigated. After heating at 50 °C, rice and lotus starches did not show significant changes in granular morphology, long-range crystallinity and short-range molecular order. As the temperature increased to 60 °C, rice starch underwent a partial gelatinization followed by an incomplete disruption of granular morphology, crystallites and molecular order. In contrast, lotus starch was almost completely gelatinized at 60 °C. At 70 °C or higher, both starches were fully gelatinized with complete disruption of the micro and macro structures. Our results show that gelatinization greatly increased the in vitro enzymatic digestibility of both starches, but that the degree of disassembly of the starch structure during thermal processing was not a major determinant of the digestibility of gelatinized starch.

Kinetic products in coordination networks: ab initio X-ray powder diffraction analysis.

PubMed

Martí-Rujas, Javier; Kawano, Masaki

2013-02-19

Porous coordination networks are materials that maintain their crystal structure as molecular "guests" enter and exit their pores. They are of great research interest with applications in areas such as catalysis, gas adsorption, proton conductivity, and drug release. As with zeolite preparation, the kinetic states in coordination network preparation play a crucial role in determining the final products. Controlling the kinetic state during self-assembly of coordination networks is a fundamental aspect of developing further functionalization of this class of materials. However, unlike for zeolites, there are few structural studies reporting the kinetic products made during self-assembly of coordination networks. Synthetic routes that produce the necessary selectivity are complex. The structural knowledge obtained from X-ray crystallography has been crucial for developing rational strategies for design of organic-inorganic hybrid networks. However, despite the explosive progress in the solid-state study of coordination networks during the last 15 years, researchers still do not understand many chemical reaction processes because of the difficulties in growing single crystals suitable for X-ray diffraction: Fast precipitation can lead to kinetic (metastable) products, but in microcrystalline form, unsuitable for single crystal X-ray analysis. X-ray powder diffraction (XRPD) routinely is used to check phase purity, crystallinity, and to monitor the stability of frameworks upon guest removal/inclusion under various conditions, but rarely is used for structure elucidation. Recent advances in structure determination of microcrystalline solids from ab initio XRPD have allowed three-dimensional structure determination when single crystals are not available. Thus, ab initio XRPD structure determination is becoming a powerful method for structure determination of microcrystalline solids, including porous coordination networks. Because of the great interest across scientific disciplines in coordination networks, especially porous coordination networks, the ability to determine crystal structures when the crystals are not suitable for single crystal X-ray analysis is of paramount importance. In this Account, we report the potential of kinetic control to synthesize new coordination networks and we describe ab initio XRPD structure determination to characterize these networks' crystal structures. We describe our recent work on selective instant synthesis to yield kinetically controlled porous coordination networks. We demonstrate that instant synthesis can selectively produce metastable networks that are not possible to synthesize by conventional solution chemistry. Using kinetic products, we provide mechanistic insights into thermally induced (573-723 K) (i.e., annealing method) structural transformations in porous coordination networks as well as examples of guest exchange/inclusion reactions. Finally, we describe a memory effect that allows the transfer of structural information from kinetic precursor structures to thermally stable structures through amorphous intermediate phases. We believe that ab initio XRPD structure determination will soon be used to investigate chemical processes that lead intrinsically to microcrystalline solids, which up to now have not been fully understood due to the unavailability of single crystals. For example, only recently have researchers used single-crystal X-ray diffraction to elucidate crystal-to-crystal chemical reactions taking place in the crystalline scaffold of coordination networks. The potential of ab initio X-ray powder diffraction analysis goes beyond single-crystal-to-single-crystal processes, potentially allowing members of this field to study intriguing in situ reactions, such as reactions within pores.

Structural study of (N{sub 2}H{sub 5},H){sub 2.9}U{sub 1.1}Ce{sub 0.9}(C{sub 2}O{sub 4}){sub 5}·10H{sub 2}O from a conventional X-ray diffraction diagram obtained on a powder synthesized by a fast vortex process

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brackx, E., E-mail: Emmanuelle.brackx@cea.fr; Laval, J.P.; Dugne, O.

2015-01-15

In the context of research on U/minor actinides for nuclear fuel reprocessing in the transmutation process, developments are first studied with surrogates containing uranium and lanthanides to facilitate testing. The tests consist of precipitating and calcining a hydrazinium uranium/cerium oxalate. The structure of this oxalate had not been previously determined, but was necessary to validate the physicochemical mechanisms involved. The present study, firstly demonstrates the structural similarity of the U/Ce oxalate phase (N{sub 2}H{sub 5},H){sub 2.9}U{sub 1.1}Ce{sub 0.9}(C{sub 2}O{sub 4}){sub 5}·10H{sub 2}O, synthesized using a vortex precipitator for continuous synthesis of actinide oxalates, with previously known oxalates, crystallizing in P6{submore » 3}/mmc symmetry, obtained by more classical methods. This fast precipitation process induces massive nucleation of fine powders. Their structural and microstructural determination confirms that the raw and dried phases belong to the same structural family as (NH{sub 4}){sub 2}U{sub 2}(C{sub 2}O{sub 4}){sub 5}·0.7H{sub 2}O whose structure was described by Chapelet-Arab in P6{sub 3}/mmc symmetry, using single crystal data. However, they present an extended disorder inside the tunnels of the structure, even after drying at 100 °C, between water and hydrazinium ions. This disorder is directly related to the fast vortex method. This structure determination can be used as a basis for further semi-quantitative analysis on the U/minor actinides products formed under various experimental conditions. - Highlights: • Uranium cerium oxalate precipitate characterization by X-ray powder diffraction. • Morphology characterization by SEM analysis. • Structure determination by unit cell Rietveld refinement.« less

Porous calcium polyphosphate bone substitutes: additive manufacturing versus conventional gravity sinter processing-effect on structure and mechanical properties.

PubMed

Hu, Youxin; Shanjani, Yaser; Toyserkani, Ehsan; Grynpas, Marc; Wang, Rizhi; Pilliar, Robert

2014-02-01

Porous calcium polyphosphate (CPP) structures proposed as bone-substitute implants and made by sintering CPP powders to form bending test samples of approximately 35 vol % porosity were machined from preformed blocks made either by additive manufacturing (AM) or conventional gravity sintering (CS) methods and the structure and mechanical characteristics of samples so made were compared. AM-made samples displayed higher bending strengths (≈1.2-1.4 times greater than CS-made samples), whereas elastic constant (i.e., effective elastic modulus of the porous structures) that is determined by material elastic modulus and structural geometry of the samples was ≈1.9-2.3 times greater for AM-made samples. X-ray diffraction analysis showed that samples made by either method displayed the same crystal structure forming β-CPP after sinter annealing. The material elastic modulus, E, determined using nanoindentation tests also showed the same value for both sample types (i.e., E ≈ 64 GPa). Examination of the porous structures indicated that significantly larger sinter necks resulted in the AM-made samples which presumably resulted in the higher mechanical properties. The development of mechanical properties was attributed to the different sinter anneal procedures required to make 35 vol % porous samples by the two methods. A primary objective of the present study, in addition to reporting on bending strength and sample stiffness (elastic constant) characteristics, was to determine why the two processes resulted in the observed mechanical property differences for samples of equivalent volume percentage of porosity. An understanding of the fundamental reason(s) for the observed effect is considered important for developing improved processes for preparation of porous CPP implants as bone substitutes for use in high load-bearing skeletal sites. Copyright © 2013 Wiley Periodicals, Inc.

Do changes in coronal emission structure imply magnetic reconnection

NASA Technical Reports Server (NTRS)

Nolte, J. T.; Gerassimenko, M.; Krieger, A. S.; Petrasso, R. D.; Svestka, Z.; Wentzel, D. G.

1977-01-01

Several physical processes that can affect the emission from structures in the corona are investigated on the basis of images of coronal X-ray and XUV emission structures. Changes in emission accompanied by little or no change in large-scale magnetic structure are examined, and three theoretically distinct processes by which magnetic structure can change are discussed: reconfiguration of potential (current-free) fields, reconfiguration of frozen-in fields, and reconfiguration by magnetic-field-line reconnection. The possibility is considered of determining by observation whether a change in emission results from a magnetic change and, if so, what kind of magnetic change has occurred. It is concluded that changes in coronal emission structure do not necessarily imply magnetic reconnection.

Generalized Processing Tree Models: Jointly Modeling Discrete and Continuous Variables.

PubMed

Heck, Daniel W; Erdfelder, Edgar; Kieslich, Pascal J

2018-05-24

Multinomial processing tree models assume that discrete cognitive states determine observed response frequencies. Generalized processing tree (GPT) models extend this conceptual framework to continuous variables such as response times, process-tracing measures, or neurophysiological variables. GPT models assume finite-mixture distributions, with weights determined by a processing tree structure, and continuous components modeled by parameterized distributions such as Gaussians with separate or shared parameters across states. We discuss identifiability, parameter estimation, model testing, a modeling syntax, and the improved precision of GPT estimates. Finally, a GPT version of the feature comparison model of semantic categorization is applied to computer-mouse trajectories.

Signal processing techniques for damage detection with piezoelectric wafer active sensors and embedded ultrasonic structural radar

NASA Astrophysics Data System (ADS)

Yu, Lingyu; Bao, Jingjing; Giurgiutiu, Victor

2004-07-01

Embedded ultrasonic structural radar (EUSR) algorithm is developed for using piezoelectric wafer active sensor (PWAS) array to detect defects within a large area of a thin-plate specimen. Signal processing techniques are used to extract the time of flight of the wave packages, and thereby to determine the location of the defects with the EUSR algorithm. In our research, the transient tone-burst wave propagation signals are generated and collected by the embedded PWAS. Then, with signal processing, the frequency contents of the signals and the time of flight of individual frequencies are determined. This paper starts with an introduction of embedded ultrasonic structural radar algorithm. Then we will describe the signal processing methods used to extract the time of flight of the wave packages. The signal processing methods being used include the wavelet denoising, the cross correlation, and Hilbert transform. Though hardware device can provide averaging function to eliminate the noise coming from the signal collection process, wavelet denoising is included to ensure better signal quality for the application in real severe environment. For better recognition of time of flight, cross correlation method is used. Hilbert transform is applied to the signals after cross correlation in order to extract the envelope of the signals. Signal processing and EUSR are both implemented by developing a graphical user-friendly interface program in LabView. We conclude with a description of our vision for applying EUSR signal analysis to structural health monitoring and embedded nondestructive evaluation. To this end, we envisage an automatic damage detection application utilizing embedded PWAS, EUSR, and advanced signal processing.

Topology synthesis and size optimization of morphing wing structures

NASA Astrophysics Data System (ADS)

Inoyama, Daisaku

This research demonstrates a novel topology and size optimization methodology for synthesis of distributed actuation systems with specific applications to morphing air vehicle structures. The main emphasis is placed on the topology and size optimization problem formulations and the development of computational modeling concepts. The analysis model is developed to meet several important criteria: It must allow a rigid-body displacement, as well as a variation in planform area, with minimum strain on structural members while retaining acceptable numerical stability for finite element analysis. Topology optimization is performed on a semi-ground structure with design variables that control the system configuration. In effect, the optimization process assigns morphing members as "soft" elements, non-morphing load-bearing members as "stiff' elements, and non-existent members as "voids." The optimization process also determines the optimum actuator placement, where each actuator is represented computationally by equal and opposite nodal forces with soft axial stiffness. In addition, the configuration of attachments that connect the morphing structure to a non-morphing structure is determined simultaneously. Several different optimization problem formulations are investigated to understand their potential benefits in solution quality, as well as meaningfulness of the formulations. Extensions and enhancements to the initial concept and problem formulations are made to accommodate multiple-configuration definitions. In addition, the principal issues on the external-load dependency and the reversibility of a design, as well as the appropriate selection of a reference configuration, are addressed in the research. The methodology to control actuator distributions and concentrations is also discussed. Finally, the strategy to transfer the topology solution to the sizing optimization is developed and cross-sectional areas of existent structural members are optimized under applied aerodynamic loads. That is, the optimization process is implemented in sequential order: The actuation system layout is first determined through multi-disciplinary topology optimization process, and then the thickness or cross-sectional area of each existent member is optimized under given constraints and boundary conditions. Sample problems are solved to demonstrate the potential capabilities of the presented methodology. The research demonstrates an innovative structural design procedure from a computational perspective and opens new insights into the potential design requirements and characteristics of morphing structures.

Influence of Building Material Solution of Structures to Effectiveness of Real Estate Development

NASA Astrophysics Data System (ADS)

Somorová, Viera

2015-11-01

Real estate development is in its essence the development process characterized by a considerable dynamics. The purpose of the development process is the creation of buildings which can be either rented by future unknown users or sold in the real estate market. A first part of the paper is dedicated to the analysis of the parameters of buildings solutions considering the future operating costs in a phase of designing. Material solution of external structures is a main factor not only in determining the future operating costs but also in achieving the subsequent economic effectiveness of the real estate development. To determine the relationship between economic efficiency criteria and determine the optimal material variant of building constructions for the specific example is the aim of the second part of paper.

Fragmentation of structural energetic materials: implications for performance

NASA Astrophysics Data System (ADS)

Aydelotte, B.; Braithwaite, C. H.; Thadhani, N. N.

2014-05-01

Fragmentation results for structural energetic materials based on intermetallic forming mixtures are reviewed and the implications of the fragment populations are discussed. Cold sprayed Ni+Al and explosively compacted mixtures of Ni+Al+W and Ni+Al+W+Zr powders were fabricated into ring shaped samples and explosively fragmented. Ring velocity was monitored and fragments were soft captured in order to study the fragmentation process. It was determined that the fragments produced by these structural energetic materials are much smaller than those typically produced by ductile metals such as steel or aluminum. This has implications for combustion processes that may occur subsequent to the fragmentation process.

Quantum imaging with incoherently scattered light from a free-electron laser

NASA Astrophysics Data System (ADS)

Schneider, Raimund; Mehringer, Thomas; Mercurio, Giuseppe; Wenthaus, Lukas; Classen, Anton; Brenner, Günter; Gorobtsov, Oleg; Benz, Adrian; Bhatti, Daniel; Bocklage, Lars; Fischer, Birgit; Lazarev, Sergey; Obukhov, Yuri; Schlage, Kai; Skopintsev, Petr; Wagner, Jochen; Waldmann, Felix; Willing, Svenja; Zaluzhnyy, Ivan; Wurth, Wilfried; Vartanyants, Ivan A.; Röhlsberger, Ralf; von Zanthier, Joachim

2018-02-01

The advent of accelerator-driven free-electron lasers (FEL) has opened new avenues for high-resolution structure determination via diffraction methods that go far beyond conventional X-ray crystallography methods. These techniques rely on coherent scattering processes that require the maintenance of first-order coherence of the radiation field throughout the imaging procedure. Here we show that higher-order degrees of coherence, displayed in the intensity correlations of incoherently scattered X-rays from an FEL, can be used to image two-dimensional objects with a spatial resolution close to or even below the Abbe limit. This constitutes a new approach towards structure determination based on incoherent processes, including fluorescence emission or wavefront distortions, generally considered detrimental for imaging applications. Our method is an extension of the landmark intensity correlation measurements of Hanbury Brown and Twiss to higher than second order, paving the way towards determination of structure and dynamics of matter in regimes where coherent imaging methods have intrinsic limitations.

Product development using process monitoring and NDE data fusion

NASA Astrophysics Data System (ADS)

Peterson, Todd; Bossi, Richard H.

1998-03-01

Composite process/product development relies on both process monitoring information and nondestructive evaluation measurements for determining application suitability. In the past these activities have been performed and analyzed independently. Our present approach is to present the process monitoring and NDE data together in a data fusion workstation. This methodology leads to final product acceptance based on a combined process monitoring and NDE criteria. The data fusion work station combines process parameter and NDE data in a single workspace enabling all the data to be used in the acceptance/rejection decision process. An example application is the induction welding process, a unique joining method for assembling primary composite structure, that offers significant cost and weight advantages over traditional fasted structure. The determination of the required time, temperature and pressure conditions used in the process to achieve a complete weld is being aided by the use of ultrasonic inspection techniques. Full waveform ultrasonic inspection data is employed to evaluate the quality of spar cap to skin fit, an essential element of the welding process, and is processed to find a parameter that can be used for weld acceptance. Certification of the completed weld incorporates the data fusion methodology.

Invasive Processes, Mosaics and the Structure of Helminth Parasite Faunas

USDA-ARS?s Scientific Manuscript database

The biosphere in evolutionary and ecological time has been structured by episodes of geographic and host colonization that have determined distributions for complex assemblages of microparasites and macroparasites including helminths circulating among vertebrates. Biological invasion is an intricat...

The study of membrane formation via phase inversion method by cloud point and light scattering experiment

NASA Astrophysics Data System (ADS)

Arahman, Nasrul; Maimun, Teuku; Mukramah, Syawaliah

2017-01-01

The composition of polymer solution and the methods of membrane preparation determine the solidification process of membrane. The formation of membrane structure prepared via non-solvent induced phase separation (NIPS) method is mostly determined by phase separation process between polymer, solvent, and non-solvent. This paper discusses the phase separation process of polymer solution containing Polyethersulfone (PES), N-methylpirrolidone (NMP), and surfactant Tetronic 1307 (Tet). Cloud point experiment is conducted to determine the amount of non-solvent needed on induced phase separation. Amount of water required as a non-solvent decreases by the addition of surfactant Tet. Kinetics of phase separation for such system is studied by the light scattering measurement. With the addition of Tet., the delayed phase separation is observed and the structure growth rate decreases. Moreover, the morphology of fabricated membrane from those polymer systems is analyzed by scanning electron microscopy (SEM). The images of both systems show the formation of finger-like macrovoids through the cross-section.

Detection of LiveLock in BPMN Using Process Expression

NASA Astrophysics Data System (ADS)

Tantitharanukul, Nasi; Jumpamule, Watcharee

Although the Business Process Modeling Notation (BPMN) is a popular tool for modeling business process in conceptual level, the result diagram may contain structural problem. One of the structural problems is livelock. In this problem, one token proceeds to end event, while other token is still in process with no progression. In this paper, we introduce an expression liked method to detect livelock in the BPMN diagram. Our approach utilizes the power of the declarative ability of expression to determine all of the possible process chains, and indicate whether there are livelock or not. As a result, we have shown that our method can detect livelock, if any.

Critical considerations for the qualitative and quantitative determination of process-induced disorder in crystalline solids.

PubMed

Newman, Ann; Zografi, George

2014-09-01

Solid-state instabilities in crystalline solids arise during processing primarily because a certain level of structural disorder has been introduced into the crystal. Many physical instabilities appear to be associated with the recrystallization of molecules from these disordered regions, while chemical instabilities arise from sufficient molecular mobility to allow solid-state chemical reactivity. In this Commentary we discuss the various forms of structural disorder, processing which can produce disorder, the quantitative analysis of process-induced order, and strategies to limit disorder and its effects. © 2014 Wiley Periodicals, Inc. and the American Pharmacists Association.

Bridging the gap between individual-level risk for HIV and structural determinants: using root cause analysis in strategic planning.

PubMed

Willard, Nancy; Chutuape, Kate; Stines, Stephanie; Ellen, Jonathan M

2012-01-01

HIV prevention efforts have expanded beyond individual-level interventions to address structural determinants of risk. Coalitions have been an important vehicle for addressing similar intractable and deeply rooted health-related issues. A root cause analysis process may aid coalitions in identifying fundamental, structural-level contributors to risk and in identifying appropriate solutions. For this article, strategic plans for 13 coalitions were analyzed both before and after a root cause analysis approach was applied to determine the coalitions' strategic plans potential impact and comprehensiveness. After root cause analysis, strategic plans trended toward targeting policies and practices rather than on single agency programmatic changes. Plans expanded to target multiple sectors and several changes within sectors to penetrate deeply into a sector or system. Findings suggest that root cause analysis may be a viable tool to assist coalitions in identifying structural determinants and possible solutions for HIV risk.

Structural analysis of vibroacoustical processes

NASA Technical Reports Server (NTRS)

Gromov, A. P.; Myasnikov, L. L.; Myasnikova, Y. N.; Finagin, B. A.

1973-01-01

The method of automatic identification of acoustical signals, by means of the segmentation was used to investigate noises and vibrations in machines and mechanisms, for cybernetic diagnostics. The structural analysis consists of presentation of a noise or vibroacoustical signal as a sequence of segments, determined by the time quantization, in which each segment is characterized by specific spectral characteristics. The structural spectrum is plotted as a histogram of the segments, also as a relation of the probability density of appearance of a segment to the segment type. It is assumed that the conditions of ergodic processes are maintained.

Determinants of women's satisfaction with maternal health care: a review of literature from developing countries.

PubMed

Srivastava, Aradhana; Avan, Bilal I; Rajbangshi, Preety; Bhattacharyya, Sanghita

2015-04-18

Developing countries account for 99 percent of maternal deaths annually. While increasing service availability and maintaining acceptable quality standards, it is important to assess maternal satisfaction with care in order to make it more responsive and culturally acceptable, ultimately leading to enhanced utilization and improved outcomes. At a time when global efforts to reduce maternal mortality have been stepped up, maternal satisfaction and its determinants also need to be addressed by developing country governments. This review seeks to identify determinants of women's satisfaction with maternity care in developing countries. The review followed the methodology of systematic reviews. Public health and social science databases were searched. English articles covering antenatal, intrapartum or postpartum care, for either home or institutional deliveries, reporting maternal satisfaction from developing countries (World Bank list) were included, with no year limit. Out of 154 shortlisted abstracts, 54 were included and 100 excluded. Studies were extracted onto structured formats and analyzed using the narrative synthesis approach. Determinants of maternal satisfaction covered all dimensions of care across structure, process and outcome. Structural elements included good physical environment, cleanliness, and availability of adequate human resources, medicines and supplies. Process determinants included interpersonal behavior, privacy, promptness, cognitive care, perceived provider competency and emotional support. Outcome related determinants were health status of the mother and newborn. Access, cost, socio-economic status and reproductive history also influenced perceived maternal satisfaction. Process of care dominated the determinants of maternal satisfaction in developing countries. Interpersonal behavior was the most widely reported determinant, with the largest body of evidence generated around provider behavior in terms of courtesy and non-abuse. Other aspects of interpersonal behavior included therapeutic communication, staff confidence and competence and encouragement to laboring women. Quality improvement efforts in developing countries could focus on strengthening the process of care. Special attention is needed to improve interpersonal behavior, as evidence from the review points to the importance women attach to being treated respectfully, irrespective of socio-cultural or economic context. Further research on maternal satisfaction is required on home deliveries and relative strength of various determinants in influencing maternal satisfaction.

The Scottish Structural Proteomics Facility: targets, methods and outputs.

PubMed

Oke, Muse; Carter, Lester G; Johnson, Kenneth A; Liu, Huanting; McMahon, Stephen A; Yan, Xuan; Kerou, Melina; Weikart, Nadine D; Kadi, Nadia; Sheikh, Md Arif; Schmelz, Stefan; Dorward, Mark; Zawadzki, Michal; Cozens, Christopher; Falconer, Helen; Powers, Helen; Overton, Ian M; van Niekerk, C A Johannes; Peng, Xu; Patel, Prakash; Garrett, Roger A; Prangishvili, David; Botting, Catherine H; Coote, Peter J; Dryden, David T F; Barton, Geoffrey J; Schwarz-Linek, Ulrich; Challis, Gregory L; Taylor, Garry L; White, Malcolm F; Naismith, James H

2010-06-01

The Scottish Structural Proteomics Facility was funded to develop a laboratory scale approach to high throughput structure determination. The effort was successful in that over 40 structures were determined. These structures and the methods harnessed to obtain them are reported here. This report reflects on the value of automation but also on the continued requirement for a high degree of scientific and technical expertise. The efficiency of the process poses challenges to the current paradigm of structural analysis and publication. In the 5 year period we published ten peer-reviewed papers reporting structural data arising from the pipeline. Nevertheless, the number of structures solved exceeded our ability to analyse and publish each new finding. By reporting the experimental details and depositing the structures we hope to maximize the impact of the project by allowing others to follow up the relevant biology.

Identifying influential factors of business process performance using dependency analysis

NASA Astrophysics Data System (ADS)

Wetzstein, Branimir; Leitner, Philipp; Rosenberg, Florian; Dustdar, Schahram; Leymann, Frank

2011-02-01

We present a comprehensive framework for identifying influential factors of business process performance. In particular, our approach combines monitoring of process events and Quality of Service (QoS) measurements with dependency analysis to effectively identify influential factors. The framework uses data mining techniques to construct tree structures to represent dependencies of a key performance indicator (KPI) on process and QoS metrics. These dependency trees allow business analysts to determine how process KPIs depend on lower-level process metrics and QoS characteristics of the IT infrastructure. The structure of the dependencies enables a drill-down analysis of single factors of influence to gain a deeper knowledge why certain KPI targets are not met.

Biotechnology Science Experiments on Mir

NASA Technical Reports Server (NTRS)

Kroes, Roger L.

1999-01-01

This paper describes the microgravity biotechnology experiments carried out on the Shuttle/Mir program. Four experiments investigated the growth of protein crystals, and three investigated cellular growth. Many hundreds of protein samples were processed using four different techniques. The objective of these experiments was to determine optimum conditions for the growth of very high quality single crystals to be used for structure determination. The Biotechnology System (BTS) was used to process the three cell growth investigations. The samples processed by these experiments were: bovine chondrocytes, human renal epithelial cells, and human breast cancer cells and endothelial cells. The objective was to determine the unique properties of cell aggregates produced in the microgravity environment.

Use of Structure as a Basis for Abstraction in Air Traffic Control

NASA Technical Reports Server (NTRS)

Davison, Hayley J.; Hansman, R. John

2004-01-01

The safety and efficiency of the air traffic control domain is highly dependent on the capabilities and limitations of its human controllers. Past research has indicated that structure provided by the airspace and procedures could aid in simplifying the controllers cognitive tasks. In this paper, observations, interviews, voice command data analyses, and radar analyses were conducted at the Boston Terminal Route Control (TRACON) facility to determine if there was evidence of controllers using structure to simplify their cognitive processes. The data suggest that controllers do use structure-based abstractions to simplify their cognitive processes, particularly the projection task. How structure simplifies the projection task and the implications of understanding the benefits structure provides to the projection task was discussed.

Multi-target Parallel Processing Approach for Gene-to-structure Determination of the Influenza Polymerase PB2 Subunit

PubMed Central

Moen, Spencer O.; Smith, Eric; Raymond, Amy C.; Fairman, James W.; Stewart, Lance J.; Staker, Bart L.; Begley, Darren W.; Edwards, Thomas E.; Lorimer, Donald D.

2013-01-01

Pandemic outbreaks of highly virulent influenza strains can cause widespread morbidity and mortality in human populations worldwide. In the United States alone, an average of 41,400 deaths and 1.86 million hospitalizations are caused by influenza virus infection each year 1. Point mutations in the polymerase basic protein 2 subunit (PB2) have been linked to the adaptation of the viral infection in humans 2. Findings from such studies have revealed the biological significance of PB2 as a virulence factor, thus highlighting its potential as an antiviral drug target. The structural genomics program put forth by the National Institute of Allergy and Infectious Disease (NIAID) provides funding to Emerald Bio and three other Pacific Northwest institutions that together make up the Seattle Structural Genomics Center for Infectious Disease (SSGCID). The SSGCID is dedicated to providing the scientific community with three-dimensional protein structures of NIAID category A-C pathogens. Making such structural information available to the scientific community serves to accelerate structure-based drug design. Structure-based drug design plays an important role in drug development. Pursuing multiple targets in parallel greatly increases the chance of success for new lead discovery by targeting a pathway or an entire protein family. Emerald Bio has developed a high-throughput, multi-target parallel processing pipeline (MTPP) for gene-to-structure determination to support the consortium. Here we describe the protocols used to determine the structure of the PB2 subunit from four different influenza A strains. PMID:23851357

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

PubMed

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

2018-06-01

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

Crack propagation analysis using acoustic emission sensors for structural health monitoring systems.

PubMed

Kral, Zachary; Horn, Walter; Steck, James

2013-01-01

Aerospace systems are expected to remain in service well beyond their designed life. Consequently, maintenance is an important issue. A novel method of implementing artificial neural networks and acoustic emission sensors to form a structural health monitoring (SHM) system for aerospace inspection routines was the focus of this research. Simple structural elements, consisting of flat aluminum plates of AL 2024-T3, were subjected to increasing static tensile loading. As the loading increased, designed cracks extended in length, releasing strain waves in the process. Strain wave signals, measured by acoustic emission sensors, were further analyzed in post-processing by artificial neural networks (ANN). Several experiments were performed to determine the severity and location of the crack extensions in the structure. ANNs were trained on a portion of the data acquired by the sensors and the ANNs were then validated with the remaining data. The combination of a system of acoustic emission sensors, and an ANN could determine crack extension accurately. The difference between predicted and actual crack extensions was determined to be between 0.004 in. and 0.015 in. with 95% confidence. These ANNs, coupled with acoustic emission sensors, showed promise for the creation of an SHM system for aerospace systems.

Information Security Management (ISM)

NASA Astrophysics Data System (ADS)

Šalgovičová, Jarmila; Prajová, Vanessa

2012-12-01

Currently, all organizations have to tackle the issue of information security. The paper deals with various aspects of Information Security Management (ISM), including procedures, processes, organizational structures, policies and control processes. Introduction of Information Security Management should be a strategic decision. The concept and implementation of Information Security Management in an organization are determined by the corporate needs and objectives, security requirements, the processes deployed as well as the size and structure of the organization. The implementation of ISM should be carried out to the extent consistent with the needs of the organization.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nelson, Stacy; English, Shawn; Briggs, Timothy

Fiber-reinforced composite materials offer light-weight solutions to many structural challenges. In the development of high-performance composite structures, a thorough understanding is required of the composite materials themselves as well as methods for the analysis and failure prediction of the relevant composite structures. However, the mechanical properties required for the complete constitutive definition of a composite material can be difficult to determine through experimentation. Therefore, efficient methods are necessary that can be used to determine which properties are relevant to the analysis of a specific structure and to establish a structure's response to a material parameter that can only be definedmore » through estimation. The objectives of this paper deal with demonstrating the potential value of sensitivity and uncertainty quantification techniques during the failure analysis of loaded composite structures; and the proposed methods are applied to the simulation of the four-point flexural characterization of a carbon fiber composite material. Utilizing a recently implemented, phenomenological orthotropic material model that is capable of predicting progressive composite damage and failure, a sensitivity analysis is completed to establish which material parameters are truly relevant to a simulation's outcome. Then, a parameter study is completed to determine the effect of the relevant material properties' expected variations on the simulated four-point flexural behavior as well as to determine the value of an unknown material property. This process demonstrates the ability to formulate accurate predictions in the absence of a rigorous material characterization effort. Finally, the presented results indicate that a sensitivity analysis and parameter study can be used to streamline the material definition process as the described flexural characterization was used for model validation.« less

Structural Insights into the HIV-1 Minus-strand Strong-stop DNA*

PubMed Central

Chen, Yingying; Maskri, Ouerdia; Chaminade, Françoise; René, Brigitte; Benkaroun, Jessica; Godet, Julien; Mély, Yves; Mauffret, Olivier; Fossé, Philippe

2016-01-01

An essential step of human immunodeficiency virus type 1 (HIV-1) reverse transcription is the first strand transfer that requires base pairing of the R region at the 3′-end of the genomic RNA with the complementary r region at the 3′-end of minus-strand strong-stop DNA (ssDNA). HIV-1 nucleocapsid protein (NC) facilitates this annealing process. Determination of the ssDNA structure is needed to understand the molecular basis of NC-mediated genomic RNA-ssDNA annealing. For this purpose, we investigated ssDNA using structural probes (nucleases and potassium permanganate). This study is the first to determine the secondary structure of the full-length HIV-1 ssDNA in the absence or presence of NC. The probing data and phylogenetic analysis support the folding of ssDNA into three stem-loop structures and the presence of four high-affinity binding sites for NC. Our results support a model for the NC-mediated annealing process in which the preferential binding of NC to four sites triggers unfolding of the three-dimensional structure of ssDNA, thus facilitating interaction of the r sequence of ssDNA with the R sequence of the genomic RNA. In addition, using gel retardation assays and ssDNA mutants, we show that the NC-mediated annealing process does not rely on a single pathway (zipper intermediate or kissing complex). PMID:26668324

Parton distributions in the LHC era

NASA Astrophysics Data System (ADS)

Del Debbio, Luigi

2018-03-01

Analyses of LHC (and other!) experiments require robust and statistically accurate determinations of the structure of the proton, encoded in the parton distribution functions (PDFs). The standard description of hadronic processes relies on factorization theorems, which allow a separation of process-dependent short-distance physics from the universal long-distance structure of the proton. Traditionally the PDFs are obtained from fits to experimental data. However, understanding the long-distance properties of hadrons is a nonperturbative problem, and lattice QCD can play a role in providing useful results from first principles. In this talk we compare the different approaches used to determine PDFs, and try to assess the impact of existing, and future, lattice calculations.

Study of XAFS of some Fe compounds and determination of first shell radial distance

NASA Astrophysics Data System (ADS)

Parsai, Neetu; Mishra, Ashutosh

2017-05-01

X-ray absorption fine structure (XAFS) of some Fe compounds have been studied using the latest XAFS analysis software Demeter with Strawberry Perl. The processed XAFS data of the Fe compounds have been taken from available model compound library. The XAFS data have been processed to plot the µ(E) verses E spectra. These spectra have been converted into K-space, R-space and q-space. R-space spectra have been used to obtain first shell radial distance in Fe compounds. Structural parameters like first shell radial distance is useful in determination of bond length in Fe compounds. Hence the study play important role in biological applications.

Health Care Merged With Senior Housing: Description and Evaluation of a Successful Program.

PubMed

Barry, Theresa Teta

2017-01-01

Objective: This article describes and evaluates a successful partnership between a large health care organization and housing for seniors. The program provides on-site, primary care visits by a physician and a nurse in addition to intensive social services to residents in an affordable senior housing apartment building located in Pennsylvania. Per Donabedian's "Structure-Process-Outcome" model, the program demonstrated positive health care outcomes for its participants via a prescribed structure. To provide guidance for replication in similar settings, we qualitatively evaluated the processes by which successful outcomes were obtained. Methods: With program structures in place and outcomes measured, this case study collected and analyzed qualitative information taken from key informant interviews on care processes involved in the program. Themes were extracted from semistructured interviews and used to describe the processes that helped and hindered the program. Results and Discussion: Common processes were identified across respondents; however, the nuanced processes that lead to successful outcomes suggest that defined structures and processes may not be sufficient to produce similar outcomes in other settings. Further research is needed to determine the program's replicability and policy implications.

Mixing and Matching Detergents for Membrane Protein NMR Structure Determination

DOE Office of Scientific and Technical Information (OSTI.GOV)

Columbus, Linda; Lipfert, Jan; Jambunathan, Kalyani

2009-10-21

One major obstacle to membrane protein structure determination is the selection of a detergent micelle that mimics the native lipid bilayer. Currently, detergents are selected by exhaustive screening because the effects of protein-detergent interactions on protein structure are poorly understood. In this study, the structure and dynamics of an integral membrane protein in different detergents is investigated by nuclear magnetic resonance (NMR) and electron paramagnetic resonance (EPR) spectroscopy and small-angle X-ray scattering (SAXS). The results suggest that matching of the micelle dimensions to the protein's hydrophobic surface avoids exchange processes that reduce the completeness of the NMR observations. Based onmore » these dimensions, several mixed micelles were designed that improved the completeness of NMR observations. These findings provide a basis for the rational design of mixed micelles that may advance membrane protein structure determination by NMR.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Singh, Surendra; Jauriqui, Leanne; Sloan, Trista

We have used Process Compensated Resonant Testing (PCRT) for studying structural integrity and functional performance of ceramic balls used in various auxiliary power units (APUs), propulsion engines, and defense and space missiles. The results show that PCRT is successful in sorting acceptable parts from parts with defects such as micro-structural changes, C-cracks, and scuffs. However, PCRT suffers from limitations, generally not determining the type, size or location of the anomaly. The pursuit of improvements to PCRT is an on-going process.

Solution NMR Refinement of a Metal Ion Bound Protein Using Metal Ion Inclusive Restrained Molecular Dynamics Methods

PubMed Central

Chakravorty, Dhruva K.; Wang, Bing; Lee, Chul Won; Guerra, Alfredo J.; Giedroc, David P.; Merz, Kenneth M.

2013-01-01

Correctly calculating the structure of metal coordination sites in a protein during the process of nuclear magnetic resonance (NMR) structure determination and refinement continues to be a challenging task. In this study, we present an accurate and convenient means by which to include metal ions in the NMR structure determination process using molecular dynamics (MD) constrained by NMR-derived data to obtain a realistic and physically viable description of the metal binding site(s). This method provides the framework to accurately portray the metal ions and its binding residues in a pseudo-bond or dummy-cation like approach, and is validated by quantum mechanical/molecular mechanical (QM/MM) MD calculations constrained by NMR-derived data. To illustrate this approach, we refine the zinc coordination complex structure of the zinc sensing transcriptional repressor protein Staphylococcus aureus CzrA, generating over 130 ns of MD and QM/MM MD NMR-data compliant sampling. In addition to refining the first coordination shell structure of the Zn(II) ion, this protocol benefits from being performed in a periodically replicated solvation environment including long-range electrostatics. We determine that unrestrained (not based on NMR data) MD simulations correlated to the NMR data in a time-averaged ensemble. The accurate solution structure ensemble of the metal-bound protein accurately describes the role of conformational dynamics in allosteric regulation of DNA binding by zinc and serves to validate our previous unrestrained MD simulations of CzrA. This methodology has potentially broad applicability in the structure determination of metal ion bound proteins, protein folding and metal template protein-design studies. PMID:23609042

In vitro organogenesis of gut-like structures from mouse embryonic stem cells.

PubMed

Kuwahara, M; Ogaeri, T; Matsuura, R; Kogo, H; Fujimoto, T; Torihashi, S

2004-04-01

Embryonic stem (ES) cells have pluripotency and give rise to many cell types and tissues, including representatives of all three germ layers in the embryo. We have reported previously that mouse ES cells formed contracting gut-like organs from embryoid bodies (EBs). These gut-like structures contracted spontaneously, and had large lumens surrounded by three layers, i.e. epithelium, lamina propria and muscularis. Ganglia were scattered along the periphery, and interstitial cells of Cajal (ICC) were distributed among the smooth muscle cells. In the present study, to determine whether they can be a model of gut organogenesis, we investigated the formation process of the gut-like structures in comparison with embryonic gut development. As a result, we found that the fundamental process of formation in vitro was similar to embryonic gut development in vivo. The result indicates that the gut-like structure is a useful tool not only for developmental study to determine the factors that induce gut organogenesis, but also for studies of enteric neurone and ICC development.

X-ray free electron laser: opportunities for drug discovery.

PubMed

Cheng, Robert K Y; Abela, Rafael; Hennig, Michael

2017-11-08

Past decades have shown the impact of structural information derived from complexes of drug candidates with their protein targets to facilitate the discovery of safe and effective medicines. Despite recent developments in single particle cryo-electron microscopy, X-ray crystallography has been the main method to derive structural information. The unique properties of X-ray free electron laser (XFEL) with unmet peak brilliance and beam focus allow X-ray diffraction data recording and successful structure determination from smaller and weaker diffracting crystals shortening timelines in crystal optimization. To further capitalize on the XFEL advantage, innovations in crystal sample delivery for the X-ray experiment, data collection and processing methods are required. This development was a key contributor to serial crystallography allowing structure determination at room temperature yielding physiologically more relevant structures. Adding the time resolution provided by the femtosecond X-ray pulse will enable monitoring and capturing of dynamic processes of ligand binding and associated conformational changes with great impact to the design of candidate drug compounds. © 2017 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society.

The role of predictability and structure in word stress processing: an ERP study on Cairene Arabic and a cross-linguistic comparison

PubMed Central

Domahs, Ulrike; Knaus, Johannes A.; El Shanawany, Heba; Wiese, Richard

2014-01-01

This article presents neurolinguistic data on word stress perception in Cairene Arabic, in comparison to previous results on German and Turkish. The main goal is to investigate how central properties of stress systems such as predictability of stress and metrical structure are reflected in the prosodic processing of words. Cairene Arabic is a language with a regular foot-based word stress system, leading to highly predictable placement of word stress. An ERP study on Cairene Arabic is reported, in which a stress violation paradigm is used to investigate the factors predictability of stress and foot structure. The results of the experiment show that for Cairene Arabic the internal structure of prosodic words in terms of feet determines prosodic processing. This structure effect is complemented by a frequency effect for stress patterns. PMID:25374546

Silicon-based Porous Ceramics via Freeze Casting of Preceramic Polymers

NASA Astrophysics Data System (ADS)

Naviroj, Maninpat

Freeze casting is a technique for processing porous materials that has drawn significant attention for its effectiveness in producing a variety of tailorable pore structures for ceramics, metals, and polymers. With freeze casting, pores are generated based on a solidification process where ice crystals act as a sacrificial template which can eventually be sublimated to create pores. While the majority of freeze-casting studies have been performed using conventional ceramic suspensions, this work explores an alternative processing route by freeze casting with preceramic polymer solutions. Significant differences exist between freeze casting of a particulate suspension and a polymeric solution. These changes affect the processing method, solidification behavior, and pore structure, thereby introducing new challenges and possibilities for the freeze-casting technique. The first part of this study explored the processing requirements involved with freeze casting of preceramic polymers, along with methods to control the resulting pore structure. Solvent choice, freezing front velocity, and polymer concentration were used as processing variables to manipulate the pore structures. A total of seven organic solvents were freeze cast with a polymethylsiloxane preceramic polymer to produce ceramics with isotropic, dendritic, prismatic, and lamellar pore morphologies. Changes in freezing front velocity and polymer concentration were shown to influence pore size, shape, and connectivity. Differences between suspension- and solution-based samples freeze cast under equivalent conditions were also investigated. Certain solidification microstructures were strongly affected by the presence of suspended particles, creating differences between pore structures generated from the same solvents. Additionally, processing of solution-based samples were found to be the more facile technique. Compressive strength and water permeability of dendritic and lamellar structures were analyzed to determine functional differences between the pore structures. Results show that dendritic structures were up to 30 times stronger, while lamellar structures provided higher permeability constants. A change in freezing front velocity was shown to significantly affect permeability but not compressive strength. Finally, improved pore alignment along the freezing direction was achieved by controlling the nucleation and growth of solvent crystals through the use of a grain-selection template. Dendritic samples freeze cast with a template showed substantial increase in pore alignment, as determined by image analysis and permeability tests, with the permeability constant increasing by up to 6-fold when compared to a control sample.

Competition between crystallization and vitrification of the rigid amorphous fraction in poly(3-hydroxybutyrate)

NASA Astrophysics Data System (ADS)

Di Lorenzo, Maria Laura; Righetti, Maria Cristina; Gazzano, Massimo

2012-07-01

Semicrystalline polymers have a metastable nanophase structure, where the various nanophases can be crystal, liquid, glass, or mesophase. This multi-level structure is determined by a competition among self-organization, crystallization, and vitrification of the amorphous segments and is established during material processing. The kinetics of such competition is here determined for poly(3-hydroxybutyrate) (PHB), as vitrification/devitrification of the rigid amorphous fraction strongly affects crystallization kinetics of PHB.

Deoxyribonucleoprotein structure and radiation injury - Cellular radiosensitivity is determined by LET-infinity-dependent DNA damage in hydrated deoxyribonucleoproteins and the extent of its repair

NASA Technical Reports Server (NTRS)

Lett, J. T.; Peters, E. L.

1992-01-01

Until recently, OH radicals formed in bulk nuclear water were believed to be the major causes of DNA damage that results in cell death, especially for sparsely ionizing radiations. That hypothesis has now been challenged, if not refuted. Lethal genomic DNA damage is determined mainly by energy deposition in deoxyribonucleoproteins, and their hydration shells, and charge (energy) transfer processes within those structures.

Periodic surface structure creation by UV femtosecond pulses on silicon

NASA Astrophysics Data System (ADS)

Gilicze, Barnabás; Moczok, Márió; Madarász, Dániel; Juhász, Nóra; Racskó, Bence; Nánai, László

2017-01-01

Laser-induced periodic surface structures are created on Si (100) and Si (111) wafers by 500 fs laser pulses at 248 nm. The periodic structure is concentric and highly regular. The spatial period is consistently varying between 1.1 µm and 3.3 µm in the radial direction. It is shown that the fluence of the irradiation at the same pulse number determines the size of the area where the periodic structure is created and for the same fluence the pulse number determines the regularity of the created grooves by melting processes. The origin of this structure is identified as the inhomogeneity of the laser beam profile caused by Fresnel diffraction close to the focal plane. Further improvement of the formation of periodic structure with femtosecond laser pulses is suggested.

Detecting Structural Failures Via Acoustic Impulse Responses

NASA Technical Reports Server (NTRS)

Bayard, David S.; Joshi, Sanjay S.

1995-01-01

Advanced method of acoustic pulse reflectivity testing developed for use in determining sizes and locations of failures within structures. Used to detect breaks in electrical transmission lines, detect faults in optical fibers, and determine mechanical properties of materials. In method, structure vibrationally excited with acoustic pulse (a "ping") at one location and acoustic response measured at same or different location. Measured acoustic response digitized, then processed by finite-impulse-response (FIR) filtering algorithm unique to method and based on acoustic-wave-propagation and -reflection properties of structure. Offers several advantages: does not require training, does not require prior knowledge of mathematical model of acoustic response of structure, enables detection and localization of multiple failures, and yields data on extent of damage at each location.

Measurement methods of building structures deflections

NASA Astrophysics Data System (ADS)

Wróblewska, Magdalena

2018-04-01

Underground mining exploitation is leading to the occurrence of deformations manifested by, in particular, sloping terrain. The structures situated on the deforming subsoil are subject to uneven subsidence which is leading in consequence to their deflection. Before a building rectification process takes place by, e.g. uneven raising, the structure's deflection direction and value is determined so that the structure is restored to its vertical position as a result of the undertaken remedial measures. Deflection can be determined by applying classical as well as modern measurement techniques. The article presents examples of measurement methods used considering the measured elements of building structures' constructions and field measurements. Moreover, for a given example of a mining area, the existing deflections of buildings were compared with mining terrain sloping.

Heat and mass transfer models to understand the drying mechanisms of a porous substrate.

PubMed

Songok, Joel; Bousfield, Douglas W; Gane, Patrick A C; Toivakka, Martti

2016-02-01

While drying of paper and paper coatings is expensive, with significant energy requirements, the rate controlling mechanisms are not currently fully understood. Two two-dimensional models are used as a first approximation to predict the heat transfer during hot air drying and to evaluate the role of various parameters on the drying rates of porous coatings. The models help determine the structural limiting factors during the drying process, while applying for the first time the recently known values of coating thermal diffusivity. The results indicate that the thermal conductivity of the coating structure is not the controlling factor, but the drying rate is rather determined by the thermal transfer process at the structure surface. This underlines the need for ensuring an efficient thermal transfer from hot air to coating surface during drying, before considering further measures to increase the thermal conductivity of porous coatings.

Direct detection of x-rays for protein crystallography employing a thick, large area CCD

DOEpatents

Atac, Muzaffer; McKay, Timothy

1999-01-01

An apparatus and method for directly determining the crystalline structure of a protein crystal. The crystal is irradiated by a finely collimated x-ray beam. The interaction of the x-ray beam with the crystal produces scattered x-rays. These scattered x-rays are detected by means of a large area, thick CCD which is capable of measuring a significant number of scattered x-rays which impact its surface. The CCD is capable of detecting the position of impact of the scattered x-ray on the surface of the CCD and the quantity of scattered x-rays which impact the same cell or pixel. This data is then processed in real-time and the processed data is outputted to produce a image of the structure of the crystal. If this crystal is a protein the molecular structure of the protein can be determined from the data received.

Contemporary Methodology for Protein Structure Determination.

ERIC Educational Resources Information Center

Hunkapiller, Michael W.; And Others

1984-01-01

Describes the nature and capabilities of methods used to characterize protein and peptide structure, indicating that they have undergone changes which have improved the speed, reliability, and applicability of the process. Also indicates that high-performance liquid chromatography and gel electrophoresis have made purifying proteins and peptides a…

Use of MAGSAT anomaly data for crustal structure and mineral resources in the US Midcontinent

NASA Technical Reports Server (NTRS)

Carmichael, R. S. (Principal Investigator)

1982-01-01

Personnel matters related to the processing and interpretation of MAGSAT data are reported. Efforts are being initiated to determine the crustal geology, structure, and potential economic consequences to be deduced from the satellite magnetic anomalies in conjuction with correlative data.

Measurements of Shock Effects Recorded by Hayabusa Samples

NASA Technical Reports Server (NTRS)

Zolensky, Michael; Mikouchi, Takashi; Hagiya, Kenji; Ohsumi, Kazumasa; Martinez, James; Komatsu, Mutsumi; Chan, Queenie H-.S.

2015-01-01

We requested and have been approved for 5 Hayabusa samples in order definitively establish the degree of shock experienced by the regolith of asteroid Itokawa, and to devise a bridge between shock determinations by standard light optical petrography, crystal structures as determined by synchrotron X-ray diffraction (SXRD), and degree of crystallinity as determined by electron back-scattered diffraction (EBSD) [1,2]. As of the writing of this abstract we are awaiting the approved samples. We propose measurements of astromaterial crystal structures and regolith processes. The proposed research work will improve our understanding of how small, primitive solar system bodies formed and evolved, and improve understanding of the processes that determine the history and future of habitability of environments on other solar system bodies. The results of the proposed research will directly enrich the ongoing asteroid and comet exploration missions by NASA, JAXA and ESA, and broaden our understanding of the origin and evolution of small bodies in the early solar system, and elucidate the nature of asteroid and comet regolith.

Measurements of Shock Effects Recorded by Itokawa Samples

NASA Technical Reports Server (NTRS)

Zolensky, Michael; Mikouchi, Takashi; Hagiya, Kenji; Ohsumi, Kazumasa; Martinez, James; Komatsu, Mutsumi; Chan, Queenie H-.S.

2016-01-01

We requested and have been approved for 5 Hayabusa samples in order definitively establish the degree of shock experienced by the regolith of asteroid Itokawa, and to devise a bridge between shock determinations by standard light optical petrography, crystal structures as determined by synchrotron X-ray diffraction (SXRD), and degree of crystallinity as determined by electron back-scattered diffraction (EBSD). As of the writing of this abstract we are awaiting the approved samples. We propose measurements of astromaterial crystal structures and regolith processes. The proposed research work will improve our understanding of how small, primitive solar system bodies formed and evolved, and improve understanding of the processes that determine the history and future of habitability of environments on other solar system bodies. The results of the proposed research will directly enrich the ongoing asteroid and comet exploration missions by NASA, JAXA and ESA, and broaden our understanding of the origin and evolution of small bodies in the early solar system, and elucidate the nature of asteroid and comet regolith.

Determinants of parental satisfaction with ultrasound hip screening in child health care.

PubMed

Witting, Marjon; Boere-Boonekamp, Magda M; Fleuren, Margot A H; Sakkers, Ralph J B; Ijzerman, Maarten J

2012-06-01

Prior research has shown ultrasound (US) screening for developmental dysplasia of the hip (DDH) in preventive child health care to be more effective than the current screening method. In the present study, 3-month-old infants were screened for DDH with US. The objective of this study was to examine parental satisfaction with the screening and determinants that affect satisfaction. Parental satisfaction was measured using a questionnaire. Independent variables included socio-demographic determinants, structure, process and outcome-related determinants and the meeting of expectations. Satisfaction with the screening was high. Parents who perceived the screener as competent, had enough time to ask questions, perceived the proceeding as fluent, perceived a low burden on their infant and whose expectations were met, were more likely to be satisfied. Satisfaction was influenced by process-related factors and not by factors related to the structure and the outcome of the screening. Good information provision before the screening and communication during the screening are means by which parental satisfaction can be influenced positively.

Solidification Based Grain Refinement in Steels

DTIC Science & Technology

2009-07-24

pearlite (See Figure 1). No evidence of the as-cast austenite dendrite structure was observed. The gating system for this sample resides at the thermal...possible nucleating compounds. 3) Extend grain refinement theory and solidification knowledge through experimental data. 4) Determine structure ...refine the structure of a casting through heat treatment. The energy required for grain refining via thermomechanical processes or heat treatment

Low frequency vibration approach for assessing performance of wood floor systems

Treesearch

Xiping Wang; Robert J. Ross; Michael O. Hunt; John R. Erickson; John W. Forsman

2005-01-01

The primary means of inspecting buildings and other structures is to evaluate each structure member individually. This is a time-consuming and expensive process, particularly if sheathing or other covering materials must be removed to access the structural members. The objective of this study was to determine if a low frequency vibration method could be used to...

Sum rules across the unpolarized Compton processes involving generalized polarizabilities and moments of nucleon structure functions

NASA Astrophysics Data System (ADS)

Lensky, Vadim; Hagelstein, Franziska; Pascalutsa, Vladimir; Vanderhaeghen, Marc

2018-04-01

We derive two new sum rules for the unpolarized doubly virtual Compton scattering process on a nucleon, which establish novel low-Q2 relations involving the nucleon's generalized polarizabilities and moments of the nucleon's unpolarized structure functions F1(x ,Q2) and F2(x ,Q2). These relations facilitate the determination of some structure constants which can only be accessed in off-forward doubly virtual Compton scattering, not experimentally accessible at present. We perform an empirical determination for the proton and compare our results with a next-to-leading-order chiral perturbation theory prediction. We also show how these relations may be useful for a model-independent determination of the low-Q2 subtraction function in the Compton amplitude, which enters the two-photon-exchange contribution to the Lamb shift of (muonic) hydrogen. An explicit calculation of the Δ (1232 )-resonance contribution to the muonic-hydrogen 2 P -2 S Lamb shift yields -1 ±1 μ eV , confirming the previously conjectured smallness of this effect.

On the importance of cotranscriptional RNA structure formation

PubMed Central

Lai, Daniel; Proctor, Jeff R.; Meyer, Irmtraud M.

2013-01-01

The expression of genes, both coding and noncoding, can be significantly influenced by RNA structural features of their corresponding transcripts. There is by now mounting experimental and some theoretical evidence that structure formation in vivo starts during transcription and that this cotranscriptional folding determines the functional RNA structural features that are being formed. Several decades of research in bioinformatics have resulted in a wide range of computational methods for predicting RNA secondary structures. Almost all state-of-the-art methods in terms of prediction accuracy, however, completely ignore the process of structure formation and focus exclusively on the final RNA structure. This review hopes to bridge this gap. We summarize the existing evidence for cotranscriptional folding and then review the different, currently used strategies for RNA secondary-structure prediction. Finally, we propose a range of ideas on how state-of-the-art methods could be potentially improved by explicitly capturing the process of cotranscriptional structure formation. PMID:24131802

A Mössbauer spectroscopic study of an industrial catalyst for dehydrogenation of etylbenzene to styrene

NASA Astrophysics Data System (ADS)

Jiang, K. Y.; Fan, Q.; Zhao, Z. J.; Mao, L. S.; Yang, X. L.

2006-01-01

Iron oxide catalyst with spinel structure used for dehydrogenation of ethylbenzene is one kind of important catalyst in petrochemical industry. In this work several series of industrial catalyst were prepared with different components and different manufacturing processes. Mössbauer Spectroscopy has been used to determine the optimal components and the better manufacturing process for spinel structure formation. The results may prove useful for producing the industrial dehydrogenation catalyst with better catalytic property.

A Mössbauer spectroscopic study of an industrial catalyst for dehydrogenation of etylbenzene to styrene

NASA Astrophysics Data System (ADS)

Jiang, K. Y.; Fan, Q.; Zhao, Z. J.; Mao, L. S.; Yang, X. L.

Iron oxide catalyst with spinel structure used for dehydrogenation of ethylbenzene is one kind of importantcatalyst in petrochemical industry. In this work several series of industrial catalyst were prepared with differentcomponents and differentmanufacturing processes. Mössbauer Spectroscopy has been used to determine the optimal components and the better manufacturing process for spinel structure formation. The results may prove useful for producing the industrial dehydrogenation catalyst with better catalytic property.

Skin age testing criteria: characterization of human skin structures by 500 MHz MRI multiple contrast and image processing.

PubMed

Sharma, Rakesh

2010-07-21

Ex vivo magnetic resonance microimaging (MRM) image characteristics are reported in human skin samples in different age groups. Human excised skin samples were imaged using a custom coil placed inside a 500 MHz NMR imager for high-resolution microimaging. Skin MRI images were processed for characterization of different skin structures. Contiguous cross-sectional T1-weighted 3D spin echo MRI, T2-weighted 3D spin echo MRI and proton density images were compared with skin histopathology and NMR peaks. In all skin specimens, epidermis and dermis thickening and hair follicle size were measured using MRM. Optimized parameters TE and TR and multicontrast enhancement generated better MRI visibility of different skin components. Within high MR signal regions near to the custom coil, MRI images with short echo time were comparable with digitized histological sections for skin structures of the epidermis, dermis and hair follicles in 6 (67%) of the nine specimens. Skin % tissue composition, measurement of the epidermis, dermis, sebaceous gland and hair follicle size, and skin NMR peaks were signatures of skin type. The image processing determined the dimensionality of skin tissue components and skin typing. The ex vivo MRI images and histopathology of the skin may be used to measure the skin structure and skin NMR peaks with image processing may be a tool for determining skin typing and skin composition.

Skin age testing criteria: characterization of human skin structures by 500 MHz MRI multiple contrast and image processing

NASA Astrophysics Data System (ADS)

Sharma, Rakesh

2010-07-01

Ex vivo magnetic resonance microimaging (MRM) image characteristics are reported in human skin samples in different age groups. Human excised skin samples were imaged using a custom coil placed inside a 500 MHz NMR imager for high-resolution microimaging. Skin MRI images were processed for characterization of different skin structures. Contiguous cross-sectional T1-weighted 3D spin echo MRI, T2-weighted 3D spin echo MRI and proton density images were compared with skin histopathology and NMR peaks. In all skin specimens, epidermis and dermis thickening and hair follicle size were measured using MRM. Optimized parameters TE and TR and multicontrast enhancement generated better MRI visibility of different skin components. Within high MR signal regions near to the custom coil, MRI images with short echo time were comparable with digitized histological sections for skin structures of the epidermis, dermis and hair follicles in 6 (67%) of the nine specimens. Skin % tissue composition, measurement of the epidermis, dermis, sebaceous gland and hair follicle size, and skin NMR peaks were signatures of skin type. The image processing determined the dimensionality of skin tissue components and skin typing. The ex vivo MRI images and histopathology of the skin may be used to measure the skin structure and skin NMR peaks with image processing may be a tool for determining skin typing and skin composition.

The Structured Interview and Interviewer Training in the Admissions Process

PubMed Central

Cox, Wendy C.; White-Harris, Carla; Blalock, Susan J.

2007-01-01

Objectives To determine the extent to which the structured interview is used in the PharmD admissions process in US colleges and schools of pharmacy, and the prevalence and content of interviewer training. Methods A survey instrument consisting of 7 questions regarding interviews and interviewer training was sent to 92 colleges and schools of pharmacy in the United States that were accredited or seeking accreditation. Results Sixty survey instruments (65% response rate) were returned. The majority of the schools that responded (80%) used interviews as part of the PharmD admissions process. Of the schools that used an interview as part of the admissions process, 86% provided some type of interviewer training and 13% used a set of predefined questions in admissions interviews. Conclusions Most colleges and schools of pharmacy use some components of the structured interview in the PharmD admissions process; however, training for interviewers varies widely among colleges and schools of pharmacy. PMID:17998980

Quantum structures: An attempt to explain the origin of their appearance in nature

NASA Astrophysics Data System (ADS)

Aerts, Diederik

1995-08-01

We explain quantum structure as due to two effects: (a) a real change of state of the entity under the influence of the measurement and (b) a lack of knowledge about a deeper deterministic reality of the measurement process. We present a quantum machine, with which we can illustrate in a simple way how the quantum structure arises as a consequence of the two mentioned effects. We introduce a parameter ɛ that measures the size of the lack of knowledge of the measurement process, and by varying this parameter, we describe a continuous evolution from a quantum structure (maximal lack of knowledge) to a classical structure (zero lack of knowledge). We show that for intermediate values of ɛ we find a new type of structure that is neither quantum nor classical. We apply the model to situations of lack of knowledge about the measurement process appearing in other aspects of reality. Specifically, we investigate the quantumlike structures that appear in the situation of psychological decision processes, where the subject is influenced during the testing and forms some opinions during the testing process. Our conclusion is that in the light of this explanation, the quantum probabilities are epistemic and not ontological, which means that quantum mechanics is compatible with a determinism of the whole.

A review of visual memory capacity: Beyond individual items and towards structured representations

PubMed Central

Brady, Timothy F.; Konkle, Talia; Alvarez, George A.

2012-01-01

Traditional memory research has focused on identifying separate memory systems and exploring different stages of memory processing. This approach has been valuable for establishing a taxonomy of memory systems and characterizing their function, but has been less informative about the nature of stored memory representations. Recent research on visual memory has shifted towards a representation-based emphasis, focusing on the contents of memory, and attempting to determine the format and structure of remembered information. The main thesis of this review will be that one cannot fully understand memory systems or memory processes without also determining the nature of memory representations. Nowhere is this connection more obvious than in research that attempts to measure the capacity of visual memory. We will review research on the capacity of visual working memory and visual long-term memory, highlighting recent work that emphasizes the contents of memory. This focus impacts not only how we estimate the capacity of the system - going beyond quantifying how many items can be remembered, and moving towards structured representations - but how we model memory systems and memory processes. PMID:21617025

Studies of the General Parton Distributions.

NASA Astrophysics Data System (ADS)

Goloskokov, Sergey

2017-12-01

We discuss possibility to study Generalized Parton Distributions (GPSs) induced processes using polarized beams at NICA. We show that important information on GPDs structure can be obtained at NICA in exclusive meson production and in Drell-Yan (D-Y) process that determined by the double GPDs contribution.

Uncertainty Reduction for Stochastic Processes on Complex Networks

NASA Astrophysics Data System (ADS)

Radicchi, Filippo; Castellano, Claudio

2018-05-01

Many real-world systems are characterized by stochastic dynamical rules where a complex network of interactions among individual elements probabilistically determines their state. Even with full knowledge of the network structure and of the stochastic rules, the ability to predict system configurations is generally characterized by a large uncertainty. Selecting a fraction of the nodes and observing their state may help to reduce the uncertainty about the unobserved nodes. However, choosing these points of observation in an optimal way is a highly nontrivial task, depending on the nature of the stochastic process and on the structure of the underlying interaction pattern. In this paper, we introduce a computationally efficient algorithm to determine quasioptimal solutions to the problem. The method leverages network sparsity to reduce computational complexity from exponential to almost quadratic, thus allowing the straightforward application of the method to mid-to-large-size systems. Although the method is exact only for equilibrium stochastic processes defined on trees, it turns out to be effective also for out-of-equilibrium processes on sparse loopy networks.

Structure Property Studies for Additively Manufactured Parts

DOE Office of Scientific and Technical Information (OSTI.GOV)

Milenski, Helen M; Schmalzer, Andrew Michael; Kelly, Daniel

2015-08-17

Since the invention of modern Additive Manufacturing (AM) processes engineers and designers have worked hard to capitalize on the unique building capabilities that AM allows. By being able to customize the interior fill of parts it is now possible to design components with a controlled density and customized internal structure. The creation of new polymers and polymer composites allow for even greater control over the mechanical properties of AM parts. One of the key reasons to explore AM, is to bring about a new paradigm in part design, where materials can be strategically optimized in a way that conventional subtractivemore » methods cannot achieve. The two processes investigated in my research were the Fused Deposition Modeling (FDM) process and the Direct Ink Write (DIW) process. The objectives of the research were to determine the impact of in-fill density and morphology on the mechanical properties of FDM parts, and to determine if DIW printed samples could be produced where the filament diameter was varied while the overall density remained constant.« less

Analysis of cold worked holes for structural life extension

NASA Technical Reports Server (NTRS)

Wieland, David H.; Cutshall, Jon T.; Burnside, O. Hal; Cardinal, Joseph W.

1994-01-01

Cold working holes for improved fatigue life of fastener holes are widely used on aircraft. This paper presents methods used by the authors to determine the percent of cold working to be applied and to analyze fatigue crack growth of cold worked fastener holes. An elastic, perfectly-plastic analysis of a thick-walled tube is used to determine the stress field during the cold working process and the residual stress field after the process is completed. The results of the elastic/plastic analysis are used to determine the amount of cold working to apply to a hole. The residual stress field is then used to perform damage tolerance analysis of a crack growing out of a cold worked fastener hole. This analysis method is easily implemented in existing crack growth computer codes so that the cold worked holes can be used to extend the structural life of aircraft. Analytical results are compared to test data where appropriate.

Striatal and Hippocampal Entropy and Recognition Signals in Category Learning: Simultaneous Processes Revealed by Model-Based fMRI

ERIC Educational Resources Information Center

Davis, Tyler; Love, Bradley C.; Preston, Alison R.

2012-01-01

Category learning is a complex phenomenon that engages multiple cognitive processes, many of which occur simultaneously and unfold dynamically over time. For example, as people encounter objects in the world, they simultaneously engage processes to determine their fit with current knowledge structures, gather new information about the objects, and…

[Structural elements of critical thinking of nurses in emergency care].

PubMed

Crossetti, Maria da Graça Oliveira; Bittencourt, Greicy Kelly Gouveia Dias; Lima, Ana Amélia Antunes; de Góes, Marta Georgina Oliveira; Saurin, Gislaine

2014-09-01

The objective of this study was to analyze the structural elements of critical thinking (CT) of nurses in the clinical decision-making process. This exploratory, qualitative study was conducted with 20 emergency care nurses in three hospitals in southern Brazil. Data were collected from April to June 2009, and a validated clinical case was applied from which nurses listed health problems, prescribed care and listed the structural elements of CT. Content analysis resulted in categories used to determine priority structural elements of CT, namely theoretical foundations and practical relationship to clinical decision making; technical and scientific knowledge and clinical experience, thought processes and clinical decision making: clinical reasoning and basis for clinical judgments of nurses: patient assessment and ethics. It was concluded that thinking critically is a skill that enables implementation of a secure and effective nursing care process.

Structural Genomics of Protein Phosphatases

DOE Office of Scientific and Technical Information (OSTI.GOV)

Almo,S.; Bonanno, J.; Sauder, J.

The New York SGX Research Center for Structural Genomics (NYSGXRC) of the NIGMS Protein Structure Initiative (PSI) has applied its high-throughput X-ray crystallographic structure determination platform to systematic studies of all human protein phosphatases and protein phosphatases from biomedically-relevant pathogens. To date, the NYSGXRC has determined structures of 21 distinct protein phosphatases: 14 from human, 2 from mouse, 2 from the pathogen Toxoplasma gondii, 1 from Trypanosoma brucei, the parasite responsible for African sleeping sickness, and 2 from the principal mosquito vector of malaria in Africa, Anopheles gambiae. These structures provide insights into both normal and pathophysiologic processes, including transcriptionalmore » regulation, regulation of major signaling pathways, neural development, and type 1 diabetes. In conjunction with the contributions of other international structural genomics consortia, these efforts promise to provide an unprecedented database and materials repository for structure-guided experimental and computational discovery of inhibitors for all classes of protein phosphatases.« less

Glycobiology of Reproductive Processes in Marine Animals: The State of the Art

PubMed Central

Gallo, Alessandra; Costantini, Maria

2012-01-01

Glycobiology is the study of complex carbohydrates in biological systems and represents a developing field of science that has made huge advances in the last half century. In fact, it combines all branches of biomedical research, revealing the vast and diverse forms of carbohydrate structures that exist in nature. Advances in structure determination have enabled scientists to study the function of complex carbohydrates in more depth and to determine the role that they play in a wide range of biological processes. Glycobiology research in marine systems has primarily focused on reproduction, in particular for what concern the chemical communication between the gametes. The current status of marine glycobiology is primarily descriptive, devoted to characterizing marine glycoconjugates with potential biomedical and biotechnological applications. In this review, we describe the current status of the glycobiology in the reproductive processes from gametogenesis to fertilization and embryo development of marine animals. PMID:23247316

What Shapes the Phylogenetic Structure of Anuran Communities in a Seasonal Environment? The Influence of Determinism at Regional Scale to Stochasticity or Antagonistic Forces at Local Scale

PubMed Central

Ferreira, Vanda Lúcia; Strüssmann, Christine; Tomas, Walfrido Moraes

2015-01-01

Ecological communities are structured by both deterministic and stochastic processes. We investigated phylogenetic patterns at regional and local scales to understand the influences of seasonal processes in shaping the structure of anuran communities in the southern Pantanal wetland, Brazil. We assessed the phylogenetic structure at different scales, using the Net Relatedness Index (NRI), the Nearest Taxon Index (NTI), and phylobetadiversity indexes, as well as a permutation test, to evaluate the effect of seasonality. The anuran community was represented by a non-random set of species with a high degree of phylogenetic relatedness at the regional scale. However, at the local scale the phylogenetic structure of the community was weakly related with the seasonality of the system, indicating that oriented stochastic processes (e.g. colonization, extinction and ecological drift) and/or antagonist forces drive the structure of such communities in the southern Pantanal. PMID:26102202

What Shapes the Phylogenetic Structure of Anuran Communities in a Seasonal Environment? The Influence of Determinism at Regional Scale to Stochasticity or Antagonistic Forces at Local Scale.

PubMed

Martins, Clarissa de Araújo; Roque, Fabio de Oliveira; Santos, Bráulio A; Ferreira, Vanda Lúcia; Strüssmann, Christine; Tomas, Walfrido Moraes

2015-01-01

Ecological communities are structured by both deterministic and stochastic processes. We investigated phylogenetic patterns at regional and local scales to understand the influences of seasonal processes in shaping the structure of anuran communities in the southern Pantanal wetland, Brazil. We assessed the phylogenetic structure at different scales, using the Net Relatedness Index (NRI), the Nearest Taxon Index (NTI), and phylobetadiversity indexes, as well as a permutation test, to evaluate the effect of seasonality. The anuran community was represented by a non-random set of species with a high degree of phylogenetic relatedness at the regional scale. However, at the local scale the phylogenetic structure of the community was weakly related with the seasonality of the system, indicating that oriented stochastic processes (e.g. colonization, extinction and ecological drift) and/or antagonist forces drive the structure of such communities in the southern Pantanal.

The Economics of Structured Continuing Education in Selected Professional Journals.

ERIC Educational Resources Information Center

Sasmor, James C.

A study determined what business administration considerations were elements in the managerial decision making process to include structured continuing education in a professional journal and what the positive or negative results have been in terms of operating benefits and profits. An initial literature review showed the need for exploratory…

12 CFR Appendix C to Part 360 - Deposit File Structure

Code of Federal Regulations, 2011 CFR

2011-01-01

... structure for the data file to provide deposit data to the FDIC. If data or information are not maintained... covered institution's understanding of its customers and the data maintained around deposit accounts... complete its insurance determination process, it may add this information to the end of this data file...

Pedagogical Interaction in High School, the Structural and Functional Model of Pedagogical Interaction

ERIC Educational Resources Information Center

Semenova, Larissa A.; Kazantseva, Anastassiya I.; Sergeyeva, Valeriya V.; Raklova, Yekaterina M.; Baiseitova, Zhanar B.

2016-01-01

The study covers the problems of pedagogical technologies and their experimental implementation in the learning process. The theoretical aspects of the "student-teacher" interaction are investigated. A structural and functional model of pedagogical interaction is offered, which determines the conditions for improving pedagogical…

The Employer Perspective: A Survey of Employer Participation in Structured Workplace Learning, 2000.

ERIC Educational Resources Information Center

AMR Interactive (Australia).

In 2000, a quantitative telephone survey of 2,098 businesses in Australia determined employer awareness of and participation in structured workplace learning (SWL) programs. It explored "drivers" of participation and employers' decision-making process. Comparisons with a 1998 survey identified changes in employer awareness, attitudes,…

[Immunochemistry of eukaryotic ribosomes].

PubMed

Lopaczyński, W; Gałasiński, W

1990-01-01

Immunochemical investigations of ribosomes should correlate with basic knowledge of the function, structure and activity of organelles in the cell processes. Our paper presents data of immunochemical methods used to determine the structure, function and differences of ribosomes. We present the usefulness of immunochemical methods to test human ribosomes, diagnosis and therapy of many diseases.

Modeling the assembly order of multimeric heteroprotein complexes

PubMed Central

Esquivel-Rodriguez, Juan; Terashi, Genki; Christoffer, Charles; Shin, Woong-Hee

2018-01-01

Protein-protein interactions are the cornerstone of numerous biological processes. Although an increasing number of protein complex structures have been determined using experimental methods, relatively fewer studies have been performed to determine the assembly order of complexes. In addition to the insights into the molecular mechanisms of biological function provided by the structure of a complex, knowing the assembly order is important for understanding the process of complex formation. Assembly order is also practically useful for constructing subcomplexes as a step toward solving the entire complex experimentally, designing artificial protein complexes, and developing drugs that interrupt a critical step in the complex assembly. There are several experimental methods for determining the assembly order of complexes; however, these techniques are resource-intensive. Here, we present a computational method that predicts the assembly order of protein complexes by building the complex structure. The method, named Path-LzerD, uses a multimeric protein docking algorithm that assembles a protein complex structure from individual subunit structures and predicts assembly order by observing the simulated assembly process of the complex. Benchmarked on a dataset of complexes with experimental evidence of assembly order, Path-LZerD was successful in predicting the assembly pathway for the majority of the cases. Moreover, when compared with a simple approach that infers the assembly path from the buried surface area of subunits in the native complex, Path-LZerD has the strong advantage that it can be used for cases where the complex structure is not known. The path prediction accuracy decreased when starting from unbound monomers, particularly for larger complexes of five or more subunits, for which only a part of the assembly path was correctly identified. As the first method of its kind, Path-LZerD opens a new area of computational protein structure modeling and will be an indispensable approach for studying protein complexes. PMID:29329283

Modeling the assembly order of multimeric heteroprotein complexes.

PubMed

Peterson, Lenna X; Togawa, Yoichiro; Esquivel-Rodriguez, Juan; Terashi, Genki; Christoffer, Charles; Roy, Amitava; Shin, Woong-Hee; Kihara, Daisuke

2018-01-01

Protein-protein interactions are the cornerstone of numerous biological processes. Although an increasing number of protein complex structures have been determined using experimental methods, relatively fewer studies have been performed to determine the assembly order of complexes. In addition to the insights into the molecular mechanisms of biological function provided by the structure of a complex, knowing the assembly order is important for understanding the process of complex formation. Assembly order is also practically useful for constructing subcomplexes as a step toward solving the entire complex experimentally, designing artificial protein complexes, and developing drugs that interrupt a critical step in the complex assembly. There are several experimental methods for determining the assembly order of complexes; however, these techniques are resource-intensive. Here, we present a computational method that predicts the assembly order of protein complexes by building the complex structure. The method, named Path-LzerD, uses a multimeric protein docking algorithm that assembles a protein complex structure from individual subunit structures and predicts assembly order by observing the simulated assembly process of the complex. Benchmarked on a dataset of complexes with experimental evidence of assembly order, Path-LZerD was successful in predicting the assembly pathway for the majority of the cases. Moreover, when compared with a simple approach that infers the assembly path from the buried surface area of subunits in the native complex, Path-LZerD has the strong advantage that it can be used for cases where the complex structure is not known. The path prediction accuracy decreased when starting from unbound monomers, particularly for larger complexes of five or more subunits, for which only a part of the assembly path was correctly identified. As the first method of its kind, Path-LZerD opens a new area of computational protein structure modeling and will be an indispensable approach for studying protein complexes.

Arctic systems in the Quaternary: Ecological collision, faunal mosaics and the consequences of wobbling climate

USDA-ARS?s Scientific Manuscript database

Climate oscillations and episodic or recurrent processes interact with evolution, ecology and biogeography determining the structure and complex mosaic that is the biosphere. Parasites and parasite-host assemblages, within an expansive environmental matrix determined by climate, are key components...

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lentine, Anthony L.; Cox, Jonathan Albert

Methods and systems for stabilizing a resonant modulator include receiving pre-modulation and post-modulation portions of a carrier signal, determining the average power from these portions, comparing an average input power to the average output power, and operating a heater coupled to the modulator based on the comparison. One system includes a pair of input structures, one or more processing elements, a comparator, and a control element. The input structures are configured to extract pre-modulation and post-modulation portions of a carrier signal. The processing elements are configured to determine average powers from the extracted portions. The comparator is configured to comparemore » the average input power and the average output power. The control element operates a heater coupled to the modulator based on the comparison.« less

Research and Process-Optimization on Mixed Crystal Caused Uneven-Performance of High-strength Structural Car Steel QStE500TM

NASA Astrophysics Data System (ADS)

Jian-wen, Li; Hong-yan, Liu

Handan Iron and Steel production of high-strength structural car steel QStE500TM thin gauge products using Nb + Ti composite strengthening, with a small amount of Cr element to improve its hardenability, the process parameter control is inappropriate with Nb + Ti complex steel, it is easy to produce in the mixed crystal phenomenon, resulting in decreasing the toughness and uneven performance. In this paper, Gleeble 3500 thermal simulation testing machine for high-strength structural steel car QStE500TM product deformation austenite recrystallization behavior research, determined completely recrystallized, partial recrystallization and non-recrystallization region, provide theoretical basis and necessary data for reasonable controlled rolling process for production.

Poissonian renormalizations, exponentials, and power laws.

PubMed

Eliazar, Iddo

2013-05-01

This paper presents a comprehensive "renormalization study" of Poisson processes governed by exponential and power-law intensities. These Poisson processes are of fundamental importance, as they constitute the very bedrock of the universal extreme-value laws of Gumbel, Fréchet, and Weibull. Applying the method of Poissonian renormalization we analyze the emergence of these Poisson processes, unveil their intrinsic dynamical structures, determine their domains of attraction, and characterize their structural phase transitions. These structural phase transitions are shown to be governed by uniform and harmonic intensities, to have universal domains of attraction, to uniquely display intrinsic invariance, and to be intimately connected to "white noise" and to "1/f noise." Thus, we establish a Poissonian explanation to the omnipresence of white and 1/f noises.

The mind as a process.

PubMed

Bruhn, John G; Wolf, Stewart

2003-01-01

Essentially all behavior is regulated by the brain in response to information received from within the body or from the environment. The tangible structures of the brain serve as devices for processing thoughts and emotions as well as information. Stored among the interacting neural structures are memories of past experiences and responses to them. These intangibles participate in determining the decisions made and the actions performed by the brain's structures. There are valuable studies of the clinical and neurological effects of environmental stimuli, but we need to learn more about the processes that lead to these effects. More definitive correlations could be made between environmental stimuli and the neurological pathways they create by studying individual's real life experiences rather than laboratory simulations alone.

Fragmentation of Structural Energetic Materials: Implications for Performance

NASA Astrophysics Data System (ADS)

Aydelotte, Brady; Braithwaite, Christopher; Thadhani, Naresh

2013-06-01

Fragmentation results for structural energetic materials based on intermetallic forming mixtures are reviewed and the implications of the fragment populations are discussed. Cold Sprayed Ni+Al and explosively compacted mixtures of Ni+Al+W and Ni+Al+W+Zr powders were fabricated into ring shaped samples and subjected to fragmentation tests. Ring velocity was monitored and fragments were soft captured in order to study the fragmentation process. It was determined that the fragments produced by these structural energetic materials are much smaller than those typically produced by ductile metals such as steel or aluminum. This has implications for combustion processes that may occur subsequent to the fragmentation process. ONR/MURI grant No. N00014-07-1-0740 Dr. Cliff Bedford PM.

Efficient packet forwarding using cyber-security aware policies

DOEpatents

Ros-Giralt, Jordi

2017-04-04

For balancing load, a forwarder can selectively direct data from the forwarder to a processor according to a loading parameter. The selective direction includes forwarding the data to the processor for processing, transforming and/or forwarding the data to another node, and dropping the data. The forwarder can also adjust the loading parameter based on, at least in part, feedback received from the processor. One or more processing elements can store values associated with one or more flows into a structure without locking the structure. The stored values can be used to determine how to direct the flows, e.g., whether to process a flow or to drop it. The structure can be used within an information channel providing feedback to a processor.

Efficient packet forwarding using cyber-security aware policies

DOEpatents

Ros-Giralt, Jordi

2017-10-25

For balancing load, a forwarder can selectively direct data from the forwarder to a processor according to a loading parameter. The selective direction includes forwarding the data to the processor for processing, transforming and/or forwarding the data to another node, and dropping the data. The forwarder can also adjust the loading parameter based on, at least in part, feedback received from the processor. One or more processing elements can store values associated with one or more flows into a structure without locking the structure. The stored values can be used to determine how to direct the flows, e.g., whether to process a flow or to drop it. The structure can be used within an information channel providing feedback to a processor.

Improved in-cell structure determination of proteins at near-physiological concentration

PubMed Central

Ikeya, Teppei; Hanashima, Tomomi; Hosoya, Saori; Shimazaki, Manato; Ikeda, Shiro; Mishima, Masaki; Güntert, Peter; Ito, Yutaka

2016-01-01

Investigating three-dimensional (3D) structures of proteins in living cells by in-cell nuclear magnetic resonance (NMR) spectroscopy opens an avenue towards understanding the structural basis of their functions and physical properties under physiological conditions inside cells. In-cell NMR provides data at atomic resolution non-invasively, and has been used to detect protein-protein interactions, thermodynamics of protein stability, the behavior of intrinsically disordered proteins, etc. in cells. However, so far only a single de novo 3D protein structure could be determined based on data derived only from in-cell NMR. Here we introduce methods that enable in-cell NMR protein structure determination for a larger number of proteins at concentrations that approach physiological ones. The new methods comprise (1) advances in the processing of non-uniformly sampled NMR data, which reduces the measurement time for the intrinsically short-lived in-cell NMR samples, (2) automatic chemical shift assignment for obtaining an optimal resonance assignment, and (3) structure refinement with Bayesian inference, which makes it possible to calculate accurate 3D protein structures from sparse data sets of conformational restraints. As an example application we determined the structure of the B1 domain of protein G at about 250 μM concentration in living E. coli cells. PMID:27910948

[Commitment and community participation towards health: knowledge creation from the systematization of social experiences].

PubMed

López-Bolaños, Lizbeth; Campos-Rivera, Marisol; Villanueva-Borbolla, María Ángeles

2018-01-01

Objective. To reflect on the process of committing to participation in the implementation of a health strategic plan, using Participative Systematization of Social Experiences as a tool. Our study was a qualitative research-intervention study, based on the Dialectical Methodological Conception approach. We designed and implemented a two-day workshop, six hours daily, using Systematization methodology with a Community Work Group (CWG). During the workshop, women systematized their experience, with compromise as axis of the process. Using Grounded Theory techniques, we applied micro-analysis to data in order to identify and strengthen categories that emerged during the systematization process. We completed open and axial coding. The CWG identified that commitment and participation itself is influenced by group dynamics and structural determinants. They also reconsidered the way they understood and exercised commitment and participation, and generated knowledge, empowering them to improve their future practice. Commitment and participation were determined by group dynamics and structural factors such as socioeconomic conditions and gender roles. These determinants must be visible and understood in order to generate proposals that are aimed at strengthening the participation and organization of groups.

An approach to functionally relevant clustering of the protein universe: Active site profile-based clustering of protein structures and sequences.

PubMed

Knutson, Stacy T; Westwood, Brian M; Leuthaeuser, Janelle B; Turner, Brandon E; Nguyendac, Don; Shea, Gabrielle; Kumar, Kiran; Hayden, Julia D; Harper, Angela F; Brown, Shoshana D; Morris, John H; Ferrin, Thomas E; Babbitt, Patricia C; Fetrow, Jacquelyn S

2017-04-01

Protein function identification remains a significant problem. Solving this problem at the molecular functional level would allow mechanistic determinant identification-amino acids that distinguish details between functional families within a superfamily. Active site profiling was developed to identify mechanistic determinants. DASP and DASP2 were developed as tools to search sequence databases using active site profiling. Here, TuLIP (Two-Level Iterative clustering Process) is introduced as an iterative, divisive clustering process that utilizes active site profiling to separate structurally characterized superfamily members into functionally relevant clusters. Underlying TuLIP is the observation that functionally relevant families (curated by Structure-Function Linkage Database, SFLD) self-identify in DASP2 searches; clusters containing multiple functional families do not. Each TuLIP iteration produces candidate clusters, each evaluated to determine if it self-identifies using DASP2. If so, it is deemed a functionally relevant group. Divisive clustering continues until each structure is either a functionally relevant group member or a singlet. TuLIP is validated on enolase and glutathione transferase structures, superfamilies well-curated by SFLD. Correlation is strong; small numbers of structures prevent statistically significant analysis. TuLIP-identified enolase clusters are used in DASP2 GenBank searches to identify sequences sharing functional site features. Analysis shows a true positive rate of 96%, false negative rate of 4%, and maximum false positive rate of 4%. F-measure and performance analysis on the enolase search results and comparison to GEMMA and SCI-PHY demonstrate that TuLIP avoids the over-division problem of these methods. Mechanistic determinants for enolase families are evaluated and shown to correlate well with literature results. © 2017 The Authors Protein Science published by Wiley Periodicals, Inc. on behalf of The Protein Society.

Composite laminate failure parameter optimization through four-point flexure experimentation and analysis

DOE PAGES

Nelson, Stacy; English, Shawn; Briggs, Timothy

2016-05-06

Fiber-reinforced composite materials offer light-weight solutions to many structural challenges. In the development of high-performance composite structures, a thorough understanding is required of the composite materials themselves as well as methods for the analysis and failure prediction of the relevant composite structures. However, the mechanical properties required for the complete constitutive definition of a composite material can be difficult to determine through experimentation. Therefore, efficient methods are necessary that can be used to determine which properties are relevant to the analysis of a specific structure and to establish a structure's response to a material parameter that can only be definedmore » through estimation. The objectives of this paper deal with demonstrating the potential value of sensitivity and uncertainty quantification techniques during the failure analysis of loaded composite structures; and the proposed methods are applied to the simulation of the four-point flexural characterization of a carbon fiber composite material. Utilizing a recently implemented, phenomenological orthotropic material model that is capable of predicting progressive composite damage and failure, a sensitivity analysis is completed to establish which material parameters are truly relevant to a simulation's outcome. Then, a parameter study is completed to determine the effect of the relevant material properties' expected variations on the simulated four-point flexural behavior as well as to determine the value of an unknown material property. This process demonstrates the ability to formulate accurate predictions in the absence of a rigorous material characterization effort. Finally, the presented results indicate that a sensitivity analysis and parameter study can be used to streamline the material definition process as the described flexural characterization was used for model validation.« less

Mathematical geophysics: A survey of recent developments in seismology and geodynamics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vlaar, N.J.

1988-01-01

This survey deals with modern methods for the determination of the structure of the Earth and for the analysis and modeling of the dynamic processes in the Earth's interior. Seismology and the three-dimensional structure of the Earth are covered in chapters devoted to waves in the three-dimensional Earth and large-scale inversion, while the discussion of convection and lithospheric processes focuses on geomagnetism, mantle convection, post-glacial rebound, and thermomechanical processes in the lithosphere. The emphasis of the work is theoretical, but the reader will find a discussion of the pertinent observational evidence.

Molecular, mesoscopic and microscopic structure evolution during amylase digestion of extruded maize and high amylose maize starches.

PubMed

Shrestha, Ashok K; Blazek, Jaroslav; Flanagan, Bernadine M; Dhital, Sushil; Larroque, Oscar; Morell, Matthew K; Gilbert, Elliot P; Gidley, Michael J

2015-03-15

Extrusion processing of cereal starch granules with high (>50%) amylose content is a promising approach to create nutritionally desirable resistant starch, i.e. starch that escapes digestion in the small intestine. Whilst high amylose content seems to be required, the structural features responsible for the slow digestion of extrudates are not fully understood. We report the effects of partial enzyme digestion of extruded maize starches on amylopectin branch length profiles, double and single helix contents, crystallinity and lamellar periodicity. Comparing results for three extruded maize starches (27, 57, and 84% apparent amylose) that differ in amylase-sensitivity allows conclusions to be drawn concerning the rate-determining features operating under the digestion conditions used. Enzyme resistance is shown to originate from a combination of molecular and mesoscopic factors, including both recrystallization and an increase in very short branches during the digestion process. This is in contrast to the behaviour of the same starches in the granular form (Shrestha et al., 2012) where molecular and mesoscopic factors are secondary to microscopic structures in determining enzyme susceptibility. Based on the structure of residual material after long-time digestion (>8h), a model for resistant starch from processed high amylose maize starches is proposed based on a fringed micelle structure with lateral aggregation and enzyme susceptibility both limited by attached clusters of branch points. Copyright © 2014 Elsevier Ltd. All rights reserved.

NMR solution structure of the mitochondrial F1beta presequence from Nicotiana plumbaginifolia.

PubMed

Moberg, Per; Nilsson, Stefan; Ståhl, Annelie; Eriksson, Anna-Carin; Glaser, Elzbieta; Mäler, Lena

2004-03-05

We have isolated, characterized and determined the three-dimensional NMR solution structure of the presequence of ATPsynthase F1beta subunit from Nicotiana plumbaginifolia. A general method for purification of presequences is presented. The method is based on overexpression of a mutant precursor containing a methionine residue introduced at the processing site, followed by CNBr-cleavage and purification of the presequence on a cation-exchange column. The F1beta presequence, 53 amino acid residues long, retained its native properties as evidenced by inhibition of in vitro mitochondrial import and processing at micromolar concentrations. CD spectroscopy revealed that the F1beta presequence formed an alpha-helical structure in membrane mimetic environments such as SDS and DPC micelles (approximately 50% alpha-helix), and in acidic phospholipid bicelles (approximately 60% alpha-helix). The NMR solution structure of the F1beta presequence in SDS micelles was determined on the basis of 518 distance and 21 torsion angle constraints. The structure was found to contain two helices, an N-terminal amphipathic alpha-helix (residues 4-15) and a C-terminal alpha-helix (residues 43-53), separated by a largely unstructured 27 residue long internal domain. The N-terminal amphipathic alpha-helix forms the putative Tom20 receptor binding site, whereas the C-terminal alpha-helix is located upstream of the mitochondrial processing peptidase cleavage site.

Developments in signal processing and interpretation in laser tapping

NASA Astrophysics Data System (ADS)

Perton, M.; Neron, C.; Blouin, A.; Monchalin, J.-P.

2013-01-01

A novel technique, called laser-tapping, based on the thermoelastic excitation by laser like laser-ultrasonics has been previously introduced for inspecting honeycomb and foam core structures. If the top skin is delaminated or detached from the substrate, the detached layer is driven into vibration. The interpretation of the vibrations in terms of Lamb wave resonances is first discussed for a flat bottom hole configuration and then used to determine appropriate signal processing for samples such as honeycomb structures.

Crack Propagation Analysis Using Acoustic Emission Sensors for Structural Health Monitoring Systems

DOE PAGES

Kral, Zachary; Horn, Walter; Steck, James

2013-01-01

Aerospace systems are expected to remain in service well beyond their designed life. Consequently, maintenance is an important issue. A novel method of implementing artificial neural networks and acoustic emission sensors to form a structural health monitoring (SHM) system for aerospace inspection routines was the focus of this research. Simple structural elements, consisting of flat aluminum plates of AL 2024-T3, were subjected to increasing static tensile loading. As the loading increased, designed cracks extended in length, releasing strain waves in the process. Strain wave signals, measured by acoustic emission sensors, were further analyzed in post-processing by artificial neural networks (ANN).more » Several experiments were performed to determine the severity and location of the crack extensions in the structure. ANNs were trained on a portion of the data acquired by the sensors and the ANNs were then validated with the remaining data. The combination of a system of acoustic emission sensors, and an ANN could determine crack extension accurately. The difference between predicted and actual crack extensions was determined to be between 0.004 in. and 0.015 in. with 95% confidence. These ANNs, coupled with acoustic emission sensors, showed promise for the creation of an SHM system for aerospace systems.« less

Crack Propagation Analysis Using Acoustic Emission Sensors for Structural Health Monitoring Systems

PubMed Central

Horn, Walter; Steck, James

2013-01-01

Aerospace systems are expected to remain in service well beyond their designed life. Consequently, maintenance is an important issue. A novel method of implementing artificial neural networks and acoustic emission sensors to form a structural health monitoring (SHM) system for aerospace inspection routines was the focus of this research. Simple structural elements, consisting of flat aluminum plates of AL 2024-T3, were subjected to increasing static tensile loading. As the loading increased, designed cracks extended in length, releasing strain waves in the process. Strain wave signals, measured by acoustic emission sensors, were further analyzed in post-processing by artificial neural networks (ANN). Several experiments were performed to determine the severity and location of the crack extensions in the structure. ANNs were trained on a portion of the data acquired by the sensors and the ANNs were then validated with the remaining data. The combination of a system of acoustic emission sensors, and an ANN could determine crack extension accurately. The difference between predicted and actual crack extensions was determined to be between 0.004 in. and 0.015 in. with 95% confidence. These ANNs, coupled with acoustic emission sensors, showed promise for the creation of an SHM system for aerospace systems. PMID:24023536

Crystallization and preliminary X-ray analysis of cryptolepain, a novel glycosylated serine protease from Cryptolepis buchanani

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pande, Monu; Dubey, Vikash K.; Jagannadham, Medicherla V., E-mail: vdubey@iitg.ernet.in

2007-02-01

Cryptolepain is a stable glycosylated novel serine protease was crystallized by hanging-drop method. Crystal data was processed up to 2.25 Å with acceptable statistics and structure determination of the enzyme is under way. Cryptolepain is a stable glycosylated novel serine protease purified from the latex of the medicinally important plant Cryptolepis buchanani. The molecular weight of the enzyme is 50.5 kDa, as determined by mass spectrometry. The sequence of the first 15 N-terminal resides of the protease showed little homology with those of other plant serine proteases, suggesting it to be structurally unique. Thus, it is of interest to solvemore » the structure of the enzyme in order to better understand its structure–function relationship. X-ray diffraction data were collected from a crystal of cryptolepain and processed to 2.25 Å with acceptable statistics. The crystals belong to the orthorhombic space group C222{sub 1}, with unit-cell parameters a = 81.78, b = 108.15, c = 119.86 Å. The Matthews coefficient was 2.62 Å{sup 3} Da{sup −1} with one molecule in the asymmetric unit. The solvent content was found to be 53%. Structure determination of the enzyme is under way.« less

Identification and classification of cathinone unknowns by statistical analysis processing of direct analysis in real time-high resolution mass spectrometry-derived "neutral loss" spectra.

PubMed

Fowble, Kristen L; Shepard, Jason R E; Musah, Rabi A

2018-03-01

An approach to the rapid determination of the structures of novel synthetic cathinone designer drugs, also known as bath salts, is reported. While cathinones fragment so extensively by electron impact mass spectrometry that their mass spectra often cannot be used to identify the structure, collision-induced dissociation (CID) direct analysis in real time-high resolution mass spectrometry (DART-HRMS) experiments furnished spectra that provided diagnostic fragmentation patterns for the analyzed cathinones. From this data, neutral loss spectra, which reflect the presence of specific chemical moieties, could be acquired. These spectra showed striking similarities between cathinones sharing structural features such as pyrrolidine rings and methylenedioxy moieties. Principle component analysis (PCA) of the neutral loss spectra of nine synthetic cathinones of various types including ethcathinones, those containing a methylenedioxy moiety appended to the benzene ring, and pyrrolidine-containing structures, illustrated that cathinones falling within the same class clustered together and could be distinguished from those of other classes. Furthermore, hierarchical clustering analysis of the neutral loss data of a model set derived from 44 synthetic cathinones, furnished a dendrogram in which structurally similar cathinones clustered together. The ability of this model system to facilitate structure determination was tested using 4-fluoroethcathinone, 3,4-methylenedioxy-α-pyrrolidinohexanophenone (MDPHP), and ethylone, which fall into the ethcathinone, pyrrolidine-containing, and methylenedioxy-containing subclasses respectively. The results showed that their neutral loss spectra correctly fell within the ethcathinone, pyrrolidine-containing and methylenedioxy-containing cathinone clades of the dendrogram, and that the neutral loss information could be used to infer the structures of these compounds. The analysis and data processing steps are rapid and samples can be analyzed in their native form without any sample processing steps. The robustness of the dendrogram dataset can be readily increased by continued addition of newly discovered structures. The approach can be broadly applied to structure determination of unknowns, and would be particularly useful for analyses where sample amounts are limited. Copyright © 2017 Elsevier B.V. All rights reserved.

Vascular structure determines pulmonary blood flow distribution

NASA Technical Reports Server (NTRS)

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

1999-01-01

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

The Development and Structure of Professional Examinations Planned for National Use.

ERIC Educational Resources Information Center

Hecht, James T.

The process typically employed by testing services in developing professional tests for national use is described: (1) determination of professional standards; (2) development of test specifications; (3) test construction; (4) test registration and administration; and (5) scoring, analysis, and reporting. To determine professional standards, input…

Inelastic behavior of structural components

NASA Technical Reports Server (NTRS)

Hussain, N.; Khozeimeh, K.; Toridis, T. G.

1980-01-01

A more accurate procedure was developed for the determination of the inelastic behavior of structural components. The actual stress-strain curve for the mathematical of the structure was utilized to generate the force-deformation relationships for the structural elements, rather than using simplified models such as elastic-plastic, bilinear and trilinear approximations. relationships were generated for beam elements with various types of cross sections. In the generational of these curves, stress or load reversals, kinematic hardening and hysteretic behavior were taken into account. Intersections between loading and unloading branches were determined through an iterative process. Using the inelastic properties obtained, the plastic static response of some simple structural systems composed of beam elements was computed. Results were compared with known solutions, indicating a considerable improvement over response predictions obtained by means of simplified approximations used in previous investigations.

Does Initial Leaf Chemistry Affect the Contribution of Insects, Fungi, and Bacteria to Leaf Breakdown in a Lowland Tropical Stream?

NASA Astrophysics Data System (ADS)

Ardon, M.; Pringle, C. M.

2005-05-01

We examined effects of initial leaf chemistry of six common riparian species on the relative contribution of fungi, bacteria, and invertebrates to leaf breakdown in a lowland stream in Costa Rica. We hypothesized that fungi and bacteria would contribute more to the breakdown of species with low concentrations of secondary (tannins and phenolics) and structural (cellulose and lignin) compounds, while invertebrates would be more important in the processing of species with high concentrations of secondary and structural compounds. We incubated single species leaf bags of six common riparian species, representing a range in secondary and structural compounds, in a third-order stream at La Selva Biological Station, Costa Rica. We measured leaf chemistry during the breakdown process. We determined fungal biomass using ergosterol methods, bacteria using DAPI counts, and invertebrate biomass using length-weight regressions. We then used biomass estimates for each group to determine their contribution to the overall breakdown process. Breakdown rates ranged from very fast (Trema integerima, k = 0.23 day-1) to slow (Zygia longifolia , k = 0.011 day-1). While analyses are still under way, preliminary results support our initial hypothesis that fungi contribute more to the break down of leaves from tree species with low concentrations of secondary and structural compounds.

Structural Genomics and Drug Discovery for Infectious Diseases

DOE Office of Scientific and Technical Information (OSTI.GOV)

Anderson, W.F.

The application of structural genomics methods and approaches to proteins from organisms causing infectious diseases is making available the three dimensional structures of many proteins that are potential drug targets and laying the groundwork for structure aided drug discovery efforts. There are a number of structural genomics projects with a focus on pathogens that have been initiated worldwide. The Center for Structural Genomics of Infectious Diseases (CSGID) was recently established to apply state-of-the-art high throughput structural biology technologies to the characterization of proteins from the National Institute for Allergy and Infectious Diseases (NIAID) category A-C pathogens and organisms causing emerging,more » or re-emerging infectious diseases. The target selection process emphasizes potential biomedical benefits. Selected proteins include known drug targets and their homologs, essential enzymes, virulence factors and vaccine candidates. The Center also provides a structure determination service for the infectious disease scientific community. The ultimate goal is to generate a library of structures that are available to the scientific community and can serve as a starting point for further research and structure aided drug discovery for infectious diseases. To achieve this goal, the CSGID will determine protein crystal structures of 400 proteins and protein-ligand complexes using proven, rapid, highly integrated, and cost-effective methods for such determination, primarily by X-ray crystallography. High throughput crystallographic structure determination is greatly aided by frequent, convenient access to high-performance beamlines at third-generation synchrotron X-ray sources.« less

RNA Characterization by Solid-State NMR Spectroscopy.

PubMed

Yang, Yufei; Wang, Shenlin

2018-06-21

The structures of RNAs, which play critical roles in various biological processes, provide important clues and insights into the biological functions of these molecules. However, RNA structure determination remains a challenging topic. In recent years, magic-angle-spinning solid-state NMR (MAS SSNMR) has emerged as an alternative technique for structural and dynamic characterization of RNA. MAS SSNMR has been successfully applied to provide atomic-level structural information about several RNA molecules and RNA-protein complexes. In this Minireview, we give an overview of recent progress in the field of MAS SSNMR based RNA structural characterization, and introduce sample preparation strategies and SSNMR spectroscopic techniques that have been incorporated to identify RNA structural elements. We also highlight a few impressive examples of RNAs that have been investigated extensively by SSNMR. Finally, we briefly discuss future technical trends in the use of MAS SSNMR to facilitate RNA structure determination. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Reverse engineering of wörner type drilling machine structure.

NASA Astrophysics Data System (ADS)

Wibowo, A.; Belly, I.; llhamsyah, R.; Indrawanto; Yuwana, Y.

2018-03-01

A product design needs to be modified based on the conditions of production facilities and existing resource capabilities without reducing the functional aspects of the product itself. This paper describes the reverse engineering process of the main structure of the wörner type drilling machine to obtain a machine structure design that can be made by resources with limited ability by using simple processes. Some structural, functional and the work mechanism analyzes have been performed to understand the function and role of each basic components. The process of dismantling of the drilling machine and measuring each of the basic components was performed to obtain sets of the geometry and size data of each component. The geometric model of each structure components and the machine assembly were built to facilitate the simulation process and machine performance analysis that refers to ISO standard of drilling machine. The tolerance stackup analysis also performed to determine the type and value of geometrical and dimensional tolerances, which could affect the ease of the components to be manufactured and assembled

Influence of processing factors over concrete strength.

NASA Astrophysics Data System (ADS)

Kara, K. A.; Dolzhenko, A. V.; Zharikov, I. S.

2018-03-01

Construction of facilities of cast in-situ reinforced concrete poses additional requirements to quality of material, peculiarities of the construction process may sometimes lead to appearance of lamination planes and inhomogeneity of concrete, which reduce strength of the material and structure as a whole. Technology compliance while working with cast in-situ concrete has a significant impact onto the concrete strength. Such process factors as concrete curing, vibration and compaction of the concrete mixture, temperature treatment, etc., when they are countered or inadequately followed lead to a significant reduction in concrete strength. Here, the authors experimentally quantitatively determine the loss of strength in in-situ cast concrete structures due to inadequate following of process requirements, in comparison with full compliance.

Ranking the effects of urban development projects on social determinants of health: health impact assessment.

PubMed

Shojaei, Parisa; Karimlou, Masoud; Nouri, Jafar; Mohammadi, Farahnaz; Malek Afzali, Hosein; Forouzan, Ameneh Setareh

2014-05-30

Health impact assessment (HIA) offer a very logical and interesting approach for those aiming to integrate health issues into planning processes. With a lot of works and plans waiting to be done (e.g., developing and updating plans, counseling planning commissions, cooperation with other organizations), planners find it difficult to prioritize health among a variety of possible issues and solutions they confront. In the present article, first, the list of social determinants of health associated with Chitgar man-made lake was extracted out using a qualitative method and with content analysis approach, and then they were prioritized using analytic hierarchy process. 28 social determinants of health including "intermediary" and "structural" determinants were extracted out. Regarding positive effects of lake on these determinants, "recreational services" and "traffic" received the highest and the lowest weights with 0.895 and 0.638 respectively among structural determinants and with consideration to "construction" option. Furthermore, among intermediary determinants for "construction" option, sub-criteria of both "physical activity" and "air quality" received the final highest weight (0.889) and "pathogenesis" indicated the lowest weight with 0.617. Moreover, lake demonstrated the highest negative effects on "housing" among "structural" determinants which it takes the highest weight (0.476) in "non-construction" option. Additionally, lake had the highest negative effects on "noise pollution" among "intermediary determinants" and it takes the highest weight (0.467) in "non-construction" option. It has been shown that urban development projects such as green spaces, man-made lakes … have a huge range of effects on community's health, and having not considered these effects by urban planners and mangers is going to confront urban health with many challenges.

Evaluation of the effect of roasting process on the energy transition and the crystalline structures of Arabica, Robusta, and Liberica coffee from Jambi Indonesia

NASA Astrophysics Data System (ADS)

Perdana, B. M.; Manihuruk, R.; Ashyar, R.; Heriyanti; Sutrisno

2018-04-01

The effect of the roasting process has been evaluated to determine of the energy transition and the crystalline structure of three types of coffee, Arabica, Robusta, and Liberica coffee both green and roasted coffee with the roasted temperature at 200°C and 230°C. The crystalline structure of the coffee was evaluated with X-ray powder diffraction (XRD). The result exposes that the three types of green coffee showed that an amorphous structure whereas the roasted coffee denotes a crystal structure of sucrose. The varied temperature in the roasting process leads to changes in the crystal structure shown by the peak shift of 2θ for all types of coffee. The added cations, such as Fe2+, Ca2+, and Mg2+ ions on Liberica coffee induced of changes in the crystal structures, which are assigned by the peak shift, that imply of metal ions of the sucrose complexes happened in the solution, except for the addition of Mg2+ ion.

In situ determination of crystal structure and chemistry of minerals at Earth's deep lower mantle conditions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yuan, Hongsheng; Zhang, Li

Recent advances in experimental techniques and data processing allow in situ determination of mineral crystal structure and chemistry up to Mbar pressures in a laser-heated diamond anvil cell (DAC), providing the fundamental information of the mineralogical constitution of our Earth's interior. This work highlights several recent breakthroughs in the field of high-pressure mineral crystallography, including the stability of bridgmanite, the single-crystal structure studies of post-perovskite and H-phase as well as the identification of hydrous minerals and iron oxides in the deep lower mantle. The future development of high-pressure crystallography is also discussed.

Determinants of job stress in chemical process industry: A factor analysis approach.

PubMed

Menon, Balagopal G; Praveensal, C J; Madhu, G

2015-01-01

Job stress is one of the active research domains in industrial safety research. The job stress can result in accidents and health related issues in workers in chemical process industries. Hence it is important to measure the level of job stress in workers so as to mitigate the same to avoid the worker's safety related problems in the industries. The objective of this study is to determine the job stress factors in the chemical process industry in Kerala state, India. This study also aims to propose a comprehensive model and an instrument framework for measuring job stress levels in the chemical process industries in Kerala, India. The data is collected through a questionnaire survey conducted in chemical process industries in Kerala. The collected data out of 1197 surveys is subjected to principal component and confirmatory factor analysis to develop the job stress factor structure. The factor analysis revealed 8 factors that influence the job stress in process industries. It is also found that the job stress in employees is most influenced by role ambiguity and the least by work environment. The study has developed an instrument framework towards measuring job stress utilizing exploratory factor analysis and structural equation modeling.

Suppression of Story Character Goals during Reading

ERIC Educational Resources Information Center

Linderholm, Tracy; Gernsbacher, Morton Ann; van den Broek, Paul; Neninde, Lana; Robertson, Rachel R. W.; Sundermier, Brian

2004-01-01

The objective of this study was to determine how readers process narrative texts when the main character has multiple, and changing, goals. Readers must keep track of such goals to understand the causal relations between text events, an important process for comprehension. The structure building framework theory of reading proposes that readers…

An Organizational Diffusion Study on Distance Education

ERIC Educational Resources Information Center

Smith, Lillian Upton; Richter, Donna L.; Miner, Kathleen R.; Watkins, Ken; Usdan, Stuart

2005-01-01

This research explored the diffusion process of distance education in schools of public health to determine best practices in the planning and implementation of future programs. The researcher traced the diffusion process by utilizing a multiple-case study methodology using a semi-structured interview to collect the perceptions of Distance…

Cruelty in Student Teaching Evaluations

ERIC Educational Resources Information Center

Lindahl, Mary W.; Unger, Michael L.

2010-01-01

Student teaching evaluations (STEs) are increasingly used in the process of determining promotion and tenure. While most research has focused on career consequences, there has been little inquiry into the remarks students write at the end of the evaluation form. The structure of the collection process, involving emotional arousal and anonymity in…

Development of Quantitative Structure-Activity Relationship (QSAR) Models to Predict the Carcinogenic Potency of Chemicals

EPA Science Inventory

Determining the carcinogenicity and carcinogenic potency of new chemicals is both a labor-intensive and time-consuming process. In order to expedite the screening process, there is a need to either: (1) identify alternative toxicity measures (shorter duration) that may be used as...

The Formal Structure of School Summaries.

ERIC Educational Resources Information Center

Flottum, Kjersti

A study compared text summaries produced by French high school students and those written by experts. The study's objective was to determine how language users distinguish the essential from the peripheral information, to describe the summarizing process, and to apply the macrostructure theory to the process of summarizing. The summarized texts…

Event-related brain potentials index cue-based retrieval interference during sentence comprehension.

PubMed

Martin, Andrea E; Nieuwland, Mante S; Carreiras, Manuel

2012-01-16

Successful language use requires access to products of past processing within an evolving discourse. A central issue for any neurocognitive theory of language then concerns the role of memory variables during language processing. Under a cue-based retrieval account of language comprehension, linguistic dependency resolution (e.g., retrieving antecedents) is subject to interference from other information in the sentence, especially information that occurs between the words that form the dependency (e.g., between the antecedent and the retrieval site). Retrieval interference may then shape processing complexity as a function of the match of the information at retrieval with the antecedent versus other recent or similar items in memory. To address these issues, we studied the online processing of ellipsis in Castilian Spanish, a language with morphological gender agreement. We recorded event-related brain potentials while participants read sentences containing noun-phrase ellipsis indicated by the determiner otro/a ('another'). These determiners had a grammatically correct or incorrect gender with respect to their antecedent nouns that occurred earlier in the sentence. Moreover, between each antecedent and determiner, another noun phrase occurred that was structurally unavailable as an antecedent and that matched or mismatched the gender of the antecedent (i.e., a local agreement attractor). In contrast to extant P600 results on agreement violation processing, and inconsistent with predictions from neurocognitive models of sentence processing, grammatically incorrect determiners evoked a sustained, broadly distributed negativity compared to correct ones between 400 and 1000ms after word onset, possibly related to sustained negativities as observed for referential processing difficulties. Crucially, this effect was modulated by the attractor: an increased negativity was observed for grammatically correct determiners that did not match the gender of the attractor, suggesting that structurally unavailable noun phrases were at least temporarily considered for grammatically correct ellipsis. These results constitute the first ERP evidence for cue-based retrieval interference during comprehension of grammatical sentences. Copyright © 2011 Elsevier Inc. All rights reserved.

Special discontinuities in nonlinearly elastic media

NASA Astrophysics Data System (ADS)

Chugainova, A. P.

2017-06-01

Solutions of a nonlinear hyperbolic system of equations describing weakly nonlinear quasitransverse waves in a weakly anisotropic elastic medium are studied. The influence of small-scale processes of dissipation and dispersion is investigated. The small-scale processes determine the structure of discontinuities (shocks) and a set of discontinuities with a stationary structure. Among the discontinuities with a stationary structure, there are special ones that, in addition to relations following from conservation laws, satisfy additional relations required for the existence of their structure. In the phase plane, the structure of such discontinuities is represented by an integral curve joining two saddles. Special discontinuities lead to nonunique self-similar solutions of the Riemann problem. Asymptotics of non-self-similar problems for equations with dissipation and dispersion are found numerically. These asymptotics correspond to self-similar solutions of the problems.

Automatic Control of the Concrete Mixture Homogeneity in Cycling Mixers

NASA Astrophysics Data System (ADS)

Anatoly Fedorovich, Tikhonov; Drozdov, Anatoly

2018-03-01

The article describes the factors affecting the concrete mixture quality related to the moisture content of aggregates, since the effectiveness of the concrete mixture production is largely determined by the availability of quality management tools at all stages of the technological process. It is established that the unaccounted moisture of aggregates adversely affects the concrete mixture homogeneity and, accordingly, the strength of building structures. A new control method and the automatic control system of the concrete mixture homogeneity in the technological process of mixing components have been proposed, since the tasks of providing a concrete mixture are performed by the automatic control system of processing kneading-and-mixing machinery with operational automatic control of homogeneity. Theoretical underpinnings of the control of the mixture homogeneity are presented, which are related to a change in the frequency of vibrodynamic vibrations of the mixer body. The structure of the technical means of the automatic control system for regulating the supply of water is determined depending on the change in the concrete mixture homogeneity during the continuous mixing of components. The following technical means for establishing automatic control have been chosen: vibro-acoustic sensors, remote terminal units, electropneumatic control actuators, etc. To identify the quality indicator of automatic control, the system offers a structure flowchart with transfer functions that determine the ACS operation in transient dynamic mode.

Reference conditions for giant sequoia forest restoration: structure, process, and precision

USGS Publications Warehouse

Stephenson, Nathan L.

1999-01-01

National Park Service policy directs that more natural conditions be restored to giant sequoia groves, which have been altered by a century of fire exclusion. Efforts to find a reasonable and practical definition of “natural” have helped drive scientists and land managers to use past grove conditions as reference conditions for restoration. Extensive research aimed at determining reference conditions has demonstrated that past fire regimes can be characterized with greater precision than past grove structures. Difficulty and imprecision in determining past grove structure has helped fuel a debate between “structural restorationists,” who believe that forest structure should be restored mechanically before fire is reintroduced, and “process restorationists,” who believe that simple reintroduction of fire is appropriate. I evaluate old and new studies from sequoia groves to show that some of the arguments of both groups have been flawed. Importantly, it appears that restoration of fire without a preceding mechanical restoration may restore the pre-Euro-American structure of sequoia groves, at least within the bounds of our imprecise knowledge of past grove structure. However, the same may not be true for all forest types that have experienced lengthy fire exclusion. Our ability to draw robust generalizations about fire's role in forest restoration will depend heavily on a thorough understanding of past and present interactions among climate, fire, and forest structure. Use of reference conditions will be central to developing this understanding.

Ion/Neutral, Ion/Electron, Ion/Photon, and Ion/Ion Interactions in Tandem Mass Spectrometry: Do we need them all? Are they enough?

PubMed Central

McLuckey, Scott A.; Mentinova, Marija

2011-01-01

A range of strategies and tools has been developed to facilitate the determination of primary structures of analyte molecules of interest via tandem mass spectrometry (MS/MS). The two main factors that determine the primary structural information present in an MS/MS spectrum are the type of ion generated from the analyte molecule and the dissociation method. The ion-type subjected to dissociation is determined by the ionization method/conditions and ion transformation processes that might take place after initial gas-phase ion formation. Furthermore, the range of analyte-related ion types can be expanded via derivatization reactions prior to mass spectrometry. Dissociation methods include those that simply alter the population of internal states of the mass-selected ion (i.e., activation methods like collision-induced dissociation) as well as processes that rely on transformation of the ion-type prior to dissociation (e.g., electron capture dissociation). A variety of ionic interactions has been studied for the purpose of ion dissociation and ion transformation that include ion/neutral, ion/photon, ion/electron, and ion/ion interactions. A wide range of phenomena has been observed, many of which have been explored/developed as means for structural analysis. The techniques arising from these phenomena are discussed within the context of the elements of structure determination in tandem mass spectrometry, viz., ion-type definition and dissociation. Unique aspects of the various ion interactions are emphasized along with any barriers to widespread implementation. PMID:21472539

Radiographic analysis of sedimentary structures and depositional histories in Apollo 15 cores

NASA Technical Reports Server (NTRS)

Coch, N. K.

1977-01-01

Radiographs of the Apollo 15 deepdrill drive tubes were analyzed on an SDS electronic enhancer to determine sedimentary structures in the core samples. The data obtained were compared with all other Apollo mission radiographs and used to make inferences on the character of sedimentary depositional processes on the lunar surface.

Responses of redwood soil microbial community structure and N transformations to climate change

Treesearch

Damon C. Bradbury; Mary K. Firestone

2012-01-01

Soil microorganisms perform critical ecosystem functions, including decomposition, nitrogen (N) mineralization and nitrification. Soil temperature and water availability can be critical determinants of the rates of these processes as well as microbial community composition and structure. This research examined how changes in climate affect bacterial and fungal...

Modulation of Endothelial Glycocalyx Structure under Inflammatory Conditions

PubMed Central

Kolářová, Hana; Ambrůzová, Barbora; Švihálková Šindlerová, Lenka; Klinke, Anna; Kubala, Lukáš

2014-01-01

The glycocalyx of the endothelium is an intravascular compartment that creates a barrier between circulating blood and the vessel wall. The glycocalyx is suggested to play an important role in numerous physiological processes including the regulation of vascular permeability, the prevention of the margination of blood cells to the vessel wall, and the transmission of shear stress. Various theoretical models and experimental approaches provide data about changes to the structure and functions of the glycocalyx under various types of inflammatory conditions. These alterations are suggested to promote inflammatory processes in vessels and contribute to the pathogenesis of number of diseases. In this review we summarize current knowledge about the modulation of the glycocalyx under inflammatory conditions and the consequences for the course of inflammation in vessels. The structure and functions of endothelial glycocalyx are briefly discussed in the context of methodological approaches regarding the determination of endothelial glycocalyx and the uncertainty and challenges involved in glycocalyx structure determination. In addition, the modulation of glycocalyx structure under inflammatory conditions and the possible consequences for pathogenesis of selected diseases and medical conditions (in particular, diabetes, atherosclerosis, ischemia/reperfusion, and sepsis) are summarized. Finally, therapeutic strategies to ameliorate glycocalyx dysfunction suggested by various authors are discussed. PMID:24803742

A Method for Assessing the Accuracy of a Photogrammetry System for Precision Deployable Structures

NASA Technical Reports Server (NTRS)

Moore, Ashley

2005-01-01

The measurement techniques used to validate analytical models of large deployable structures are an integral Part of the technology development process and must be precise and accurate. Photogrammetry and videogrammetry are viable, accurate, and unobtrusive methods for measuring such large Structures. Photogrammetry uses Software to determine the three-dimensional position of a target using camera images. Videogrammetry is based on the same principle, except a series of timed images are analyzed. This work addresses the accuracy of a digital photogrammetry system used for measurement of large, deployable space structures at JPL. First, photogrammetry tests are performed on a precision space truss test article, and the images are processed using Photomodeler software. The accuracy of the Photomodeler results is determined through, comparison with measurements of the test article taken by an external testing group using the VSTARS photogrammetry system. These two measurements are then compared with Australis photogrammetry software that simulates a measurement test to predict its accuracy. The software is then used to study how particular factors, such as camera resolution and placement, affect the system accuracy to help design the setup for the videogrammetry system that will offer the highest level of accuracy for measurement of deploying structures.

CCP4i2: the new graphical user interface to the CCP4 program suite.

PubMed

Potterton, Liz; Agirre, Jon; Ballard, Charles; Cowtan, Kevin; Dodson, Eleanor; Evans, Phil R; Jenkins, Huw T; Keegan, Ronan; Krissinel, Eugene; Stevenson, Kyle; Lebedev, Andrey; McNicholas, Stuart J; Nicholls, Robert A; Noble, Martin; Pannu, Navraj S; Roth, Christian; Sheldrick, George; Skubak, Pavol; Turkenburg, Johan; Uski, Ville; von Delft, Frank; Waterman, David; Wilson, Keith; Winn, Martyn; Wojdyr, Marcin

2018-02-01

The CCP4 (Collaborative Computational Project, Number 4) software suite for macromolecular structure determination by X-ray crystallography groups brings together many programs and libraries that, by means of well established conventions, interoperate effectively without adhering to strict design guidelines. Because of this inherent flexibility, users are often presented with diverse, even divergent, choices for solving every type of problem. Recently, CCP4 introduced CCP4i2, a modern graphical interface designed to help structural biologists to navigate the process of structure determination, with an emphasis on pipelining and the streamlined presentation of results. In addition, CCP4i2 provides a framework for writing structure-solution scripts that can be built up incrementally to create increasingly automatic procedures.

Accessibility of selenomethionine proteins by total chemical synthesis: structural studies of human herpesvirus-8 MIP-II.

PubMed

Shao, W; Fernandez, E; Wilken, J; Thompson, D A; Siani, M A; West, J; Lolis, E; Schweitzer, B I

1998-12-11

The determination of high resolution three-dimensional structures by X-ray crystallography or nuclear magnetic resonance (NMR) is a time-consuming process. Here we describe an approach to circumvent the cloning and expression of a recombinant protein as well as screening for heavy atom derivatives. The selenomethionine-modified chemokine macrophage inflammatory protein-II (MIP-II) from human herpesvirus-8 has been produced by total chemical synthesis, crystallized, and characterized by NMR. The protein has a secondary structure typical of other chemokines and forms a monomer in solution. These results indicate that total chemical synthesis can be used to accelerate the determination of three-dimensional structures of new proteins identified in genome programs.

Composite structural materials. [fiber reinforced composites for aircraft structures

NASA Technical Reports Server (NTRS)

Ansell, G. S.; Loewy, R. G.; Wiberly, S. E.

1981-01-01

Physical properties of fiber reinforced composites; structural concepts and analysis; manufacturing; reliability; and life prediction are subjects of research conducted to determine the long term integrity of composite aircraft structures under conditions pertinent to service use. Progress is reported in (1) characterizing homogeneity in composite materials; (2) developing methods for analyzing composite materials; (3) studying fatigue in composite materials; (4) determining the temperature and moisture effects on the mechanical properties of laminates; (5) numerically analyzing moisture effects; (6) numerically analyzing the micromechanics of composite fracture; (7) constructing the 727 elevator attachment rib; (8) developing the L-1011 engine drag strut (CAPCOMP 2 program); (9) analyzing mechanical joints in composites; (10) developing computer software; and (11) processing science and technology, with emphasis on the sailplane project.

Determination of local order in the amorphous precursor to Ba-hexaferrite thin-film recording media

NASA Astrophysics Data System (ADS)

Snyder, J. E.; Harris, V. G.; Das, B. N.; Koon, N. C.; Sui, X.; Kryder, M. H.

1996-04-01

Ba-hexaferrite thin films for recording media applications are often fabricated by a two-step process: sputter deposition of an amorphous precursor, followed by annealing to crystallize the BaFe12O19 phase. The magnetic anisotropy of the crystalline films can be either in-plane or perpendicular, depending on the sputtering process used in the first step. However, conventional structural characterization techniques have not been able to distinguish between different as-sputtered films. Using polarization-dependent extended x-ray absorption fine structure (PD-EXAFS), we have observed anisotropic local structure around both Ba and Fe atoms in the amorphous precursor films. Comparison of the results suggests that the amorphous films consist of networks of Fe atoms surrounded by their O nearest neighbors, with Ba atoms fitting into in-between spaces as network modifiers (there might also be some minor Fe network modifying contribution). The local structural anisotropy of the amorphous films appears to determine the orientation of the fast-growing basal plane directions during annealing, and thus the directions of the c axes and the magnetic anisotropy.

Structural Analysis of the Synaptic Protein Neuroligin and Its β-Neurexin Complex: Determinants for Folding and Cell Adhesion

PubMed Central

Fabrichny, Igor P.; Leone, Philippe; Sulzenbacher, Gerlind; Comoletti, Davide; Miller, Meghan T.; Taylor, Palmer; Bourne, Yves; Marchot, Pascale

2009-01-01

SUMMARY The neuroligins are postsynaptic cell adhesion proteins whose associations with presynaptic neurexins participate in synaptogenesis. Mutations in the neuroligin and neurexin genes appear to be associated with autism and mental retardation. The crystal structure of a neuroligin reveals features not found in its catalytically active relatives, such as the fully hydrophobic interface forming the functional neuroligin dimer; the conformations of surface loops surrounding the vestigial active center; the location of determinants that are critical for folding and processing; and the absence of a macromolecular dipole and presence of an electronegative, hydrophilic surface for neurexin binding. The structure of a β-neurexin-neuroligin complex reveals the precise orientation of the bound neurexin and, despite a limited resolution, provides substantial information on the Ca2+-dependent interactions network involved in trans-synaptic neurexin-neuroligin association. These structures exemplify how an α/β-hydrolase fold varies in surface topography to confer adhesion properties and provide templates for analyzing abnormal processing or recognition events associated with autism. PMID:18093521

Flow processes on the catchment scale - modeling of initial structural states and hydrological behavior in an artificial exemplary catchment

NASA Astrophysics Data System (ADS)

Maurer, Thomas; Caviedes-Voullième, Daniel; Hinz, Christoph; Gerke, Horst H.

2017-04-01

Landscapes that are heavily disturbed or newly formed by either natural processes or human activity are in a state of disequilibrium. Their initial development is thus characterized by highly dynamic processes under all climatic conditions. The primary distribution and structure of the solid phase (i.e. mineral particles forming the pore space) is one of the decisive factors for the development of hydrological behavior of the eco-hydrological system and therefore (co-) determining for its - more or less - stable final state. The artificially constructed ‚Hühnerwasser' catchment (a 6 ha area located in the open-cast lignite mine Welzow-Süd, southern Brandenburg, Germany) is a landscape laboratory where the initial eco-hydrological development is observed since 2005. The specific formation (or construction) processes generated characteristic sediment structures and distributions, resulting in a spatially heterogeneous initial state of the catchment. We developed a structure generator that simulates the characteristic distribution of the solid phase for such constructed landscapes. The program is able to generate quasi-realistic structures and sediment compositions on multiple spatial levels (1 cm up to 100 m scale). The generated structures can be i) conditioned to actual measurement values (e.g., soil texture and bulk distribution); ii) stochastically generated, and iii) calculated deterministically according to the geology and technical processes at the excavation site. Results are visualized using the GOCAD software package and the free software Paraview. Based on the 3D-spatial sediment distributions, effective hydraulic van-Genuchten parameters are calculated using pedotransfer functions. The hydraulic behavior of different sediment distribution (i.e. versions or variations of the catchment's porous body) is calculated using a numerical model developed by one of us (Caviedes-Voullième). Observation data are available from catchment monitoring are available for i) determining the boundary conditions (e.g., precipitation), and ii) the calibration / validation of the model (catchment discharge, ground water). The analysis of multiple sediment distribution scenarios should allow to approximately determine the influx of starting conditions on initial development of hydrological behavior. We present first flow modeling results for a reference (conditioned) catchment model and variations thereof. We will also give an outlook on further methodical development of our approach.

Microhardness, Friction and Wear of SiC and Si3N4 Materials as a Function of Load, Temperature and Environment.

DTIC Science & Technology

1981-10-01

microstructures which may be developed and finally to relate properties to structure and composition (28-31). Sialon materials are alloys of Si3N4 with oxides...techniques. The effects of specimen microstructure on indentation processes were determined by using materials formed by a wide range of fabrication...microhardness techniques. The effects of specimen microstructure on indentation processes were determined by using materials formed by a wide range of

Using Ultrasonic Lamb Waves To Measure Moduli Of Composites

NASA Technical Reports Server (NTRS)

Kautz, Harold E.

1995-01-01

Measurements of broad-band ultrasonic Lamb waves in plate specimens of ceramic-matrix/fiber and metal-matrix/fiber composite materials used to determine moduli of elasticity of materials. In one class of potential applications of concept, Lamb-wave responses of specimens measured and analyzed at various stages of thermal and/or mechanical processing to determine effects of processing, without having to dissect specimens. In another class, structural components having shapes supporting propagation of Lamb waves monitored ultrasonically to identify signs of deterioration and impending failure.

De Novo Protein Structure Prediction

NASA Astrophysics Data System (ADS)

Hung, Ling-Hong; Ngan, Shing-Chung; Samudrala, Ram

An unparalleled amount of sequence data is being made available from large-scale genome sequencing efforts. The data provide a shortcut to the determination of the function of a gene of interest, as long as there is an existing sequenced gene with similar sequence and of known function. This has spurred structural genomic initiatives with the goal of determining as many protein folds as possible (Brenner and Levitt, 2000; Burley, 2000; Brenner, 2001; Heinemann et al., 2001). The purpose of this is twofold: First, the structure of a gene product can often lead to direct inference of its function. Second, since the function of a protein is dependent on its structure, direct comparison of the structures of gene products can be more sensitive than the comparison of sequences of genes for detecting homology. Presently, structural determination by crystallography and NMR techniques is still slow and expensive in terms of manpower and resources, despite attempts to automate the processes. Computer structure prediction algorithms, while not providing the accuracy of the traditional techniques, are extremely quick and inexpensive and can provide useful low-resolution data for structure comparisons (Bonneau and Baker, 2001). Given the immense number of structures which the structural genomic projects are attempting to solve, there would be a considerable gain even if the computer structure prediction approach were applicable to a subset of proteins.

A NASTRAN model of a large flexible swing-wing bomber. Volume 5: NASTRAN model development-fairing structure

NASA Technical Reports Server (NTRS)

Mock, W. D.; Latham, R. A.

1982-01-01

The NASTRAN model plan for the fairing structure was expanded in detail to generate the NASTRAN model of this substructure. The grid point coordinates, element definitions, material properties, and sizing data for each element were specified. The fairing model was thoroughly checked out for continuity, connectivity, and constraints. The substructure was processed for structural influence coefficients (SIC) point loadings to determine the deflection characteristics of the fairing model. Finally, a demonstration and validation processing of this substructure was accomplished using the NASTRAN finite element program. The bulk data deck, stiffness matrices, and SIC output data were delivered.

Syntactic Approach To Geometric Surface Shell Determination

NASA Astrophysics Data System (ADS)

DeGryse, Donald G.; Panton, Dale J.

1980-12-01

Autonomous terminal homing of a smart missile requires a stored reference scene of the target for which the missle is destined. The reference scene is produced from stereo source imagery by deriving a three-dimensional model containing cultural structures such as buildings, towers, bridges, and tanks. This model is obtained by the precise matching of cultural features from one image of the stereo pair to the other. In the past, this stereo matching process has relied heavily on local edge operators and a gray scale matching metric. The processing is performed line by line over the imagery and the amount of geometric control is minimal. As a result, the gross structure of the scene is determined but the derived three-dimensional data is noisy, oscillatory, and at times significantly inaccurate. This paper discusses new concepts that are currently being developed to stabilize this geometric reference preparation process. The new concepts involve the use of a structural syntax which will be used as a geometric constraint on automatic stereo matching. The syntax arises from the stereo configuration of the imaging platforms at the time of exposure and the knowledge of how various cultural structures are constructed. The syntax is used to parse a scene in terms of its cultural surfaces and to dictate to the matching process the allowable relative positions and orientations of surface edges in the image planes. Using the syntax, extensive searches using a gray scale matching metric are reduced.

High-throughput Crystallography for Structural Genomics

PubMed Central

Joachimiak, Andrzej

2009-01-01

Protein X-ray crystallography recently celebrated its 50th anniversary. The structures of myoglobin and hemoglobin determined by Kendrew and Perutz provided the first glimpses into the complex protein architecture and chemistry. Since then, the field of structural molecular biology has experienced extraordinary progress and now over 53,000 proteins structures have been deposited into the Protein Data Bank. In the past decade many advances in macromolecular crystallography have been driven by world-wide structural genomics efforts. This was made possible because of third-generation synchrotron sources, structure phasing approaches using anomalous signal and cryo-crystallography. Complementary progress in molecular biology, proteomics, hardware and software for crystallographic data collection, structure determination and refinement, computer science, databases, robotics and automation improved and accelerated many processes. These advancements provide the robust foundation for structural molecular biology and assure strong contribution to science in the future. In this report we focus mainly on reviewing structural genomics high-throughput X-ray crystallography technologies and their impact. PMID:19765976

The Scottish Structural Proteomics Facility: targets, methods and outputs

PubMed Central

Oke, Muse; Carter, Lester G.; Johnson, Kenneth A.; Liu, Huanting; McMahon, Stephen A.; Yan, Xuan; Kerou, Melina; Weikart, Nadine D.; Kadi, Nadia; Sheikh, Md. Arif; Schmelz, Stefan; Dorward, Mark; Zawadzki, Michal; Cozens, Christopher; Falconer, Helen; Powers, Helen; Overton, Ian M.; van Niekerk, C. A. Johannes; Peng, Xu; Patel, Prakash; Garrett, Roger A.; Prangishvili, David; Botting, Catherine H.; Coote, Peter J.; Dryden, David T. F.; Barton, Geoffrey J.; Schwarz-Linek, Ulrich; Challis, Gregory L.; Taylor, Garry L.; White, Malcolm F.

2010-01-01

The Scottish Structural Proteomics Facility was funded to develop a laboratory scale approach to high throughput structure determination. The effort was successful in that over 40 structures were determined. These structures and the methods harnessed to obtain them are reported here. This report reflects on the value of automation but also on the continued requirement for a high degree of scientific and technical expertise. The efficiency of the process poses challenges to the current paradigm of structural analysis and publication. In the 5 year period we published ten peer-reviewed papers reporting structural data arising from the pipeline. Nevertheless, the number of structures solved exceeded our ability to analyse and publish each new finding. By reporting the experimental details and depositing the structures we hope to maximize the impact of the project by allowing others to follow up the relevant biology. Electronic supplementary material The online version of this article (doi:10.1007/s10969-010-9090-y) contains supplementary material, which is available to authorized users. PMID:20419351

Potential for on-orbit manufacture of large space structures using the pultrusion process

NASA Technical Reports Server (NTRS)

Wilson, Maywood L.; Macconochie, Ian O.; Johnson, Gary S.

1987-01-01

On-orbit manufacture of lightweight, high-strength, advanced-composite structures using the pultrusion process is proposed. This process is adaptable to a zero-gravity environment by using preimpregnated graphite-fiber reinforcement systems. The reinforcement material is preimpregnated with a high-performance thermoplastic resin at a ground station, is coiled on spools for compact storage, and is transported into Earth orbit. A pultrusion machine is installed in the Shuttle cargo bay from which very long lengths of the desired structure is fabricated on-orbit. Potential structural profiles include rods, angles, channels, hat sections, tubes, honeycomb-cored panels, and T, H, and I beams. A potential pultrudable thermoplastic/graphite composite material is presented as a model for determining the effect on Earth-to-orbit package density of an on-orbit manufacture, the package density is increased by 132 percent, and payload volume requirement is decreased by 56.3 percent. The fabrication method has the potential for on-orbit manufacture of structural members for space platforms, large space antennas, and long tethers.

Promoting quality: the health-care organization from a management perspective.

PubMed

Glickman, Seth W; Baggett, Kelvin A; Krubert, Christopher G; Peterson, Eric D; Schulman, Kevin A

2007-12-01

Although agreement about the need for quality improvement in health care is almost universal, the means of achieving effective improvement in overall care is not well understood. Avedis Donabedian developed the structure-process-outcome framework in which to think about quality-improvement efforts. There is now a robust evidence-base in the quality-improvement literature on process and outcomes, but structure has received considerably less attention. The health-care field would benefit from expanding the current interpretation of structure to include broader perspectives on organizational attributes as primary determinants of process change and quality improvement. We highlight and discuss the following key elements of organizational attributes from a management perspective: (i) executive management, including senior leadership and board responsibilities (ii) culture, (iii) organizational design, (iv) incentive structures and (v) information management and technology. We discuss the relevant contributions from the business and medical literature for each element, and provide this framework as a roadmap for future research in an effort to develop the optimal definition of 'structure' for transforming quality-improvement initiatives.

Poissonian renormalizations, exponentials, and power laws

NASA Astrophysics Data System (ADS)

Eliazar, Iddo

2013-05-01

This paper presents a comprehensive “renormalization study” of Poisson processes governed by exponential and power-law intensities. These Poisson processes are of fundamental importance, as they constitute the very bedrock of the universal extreme-value laws of Gumbel, Fréchet, and Weibull. Applying the method of Poissonian renormalization we analyze the emergence of these Poisson processes, unveil their intrinsic dynamical structures, determine their domains of attraction, and characterize their structural phase transitions. These structural phase transitions are shown to be governed by uniform and harmonic intensities, to have universal domains of attraction, to uniquely display intrinsic invariance, and to be intimately connected to “white noise” and to “1/f noise.” Thus, we establish a Poissonian explanation to the omnipresence of white and 1/f noises.

Heparin Characterization: Challenges and Solutions

NASA Astrophysics Data System (ADS)

Jones, Christopher J.; Beni, Szabolcs; Limtiaco, John F. K.; Langeslay, Derek J.; Larive, Cynthia K.

2011-07-01

Although heparin is an important and widely prescribed pharmaceutical anticoagulant, its high degree of sequence microheterogeneity and size polydispersity make molecular-level characterization challenging. Unlike nucleic acids and proteins that are biosynthesized through template-driven assembly processes, heparin and the related glycosaminoglycan heparan sulfate are actively remodeled during biosynthesis through a series of enzymatic reactions that lead to variable levels of O- and N-sulfonation and uronic acid epimers. As summarized in this review, heparin sequence information is determined through a bottom-up approach that relies on depolymerization reactions, size- and charge-based separations, and sensitive mass spectrometric and nuclear magnetic resonance experiments to determine the structural identity of component oligosaccharides. The structure-elucidation process, along with its challenges and opportunities for future analytical improvements, is reviewed and illustrated for a heparin-derived hexasaccharide.

FRET measurements of kinesin neck orientation reveal a structural basis for processivity and asymmetry.

PubMed

Martin, Douglas S; Fathi, Reza; Mitchison, Timothy J; Gelles, Jeff

2010-03-23

As the smallest and simplest motor enzymes, kinesins have served as the prototype for understanding the relationship between protein structure and mechanochemical function of enzymes in this class. Conventional kinesin (kinesin-1) is a motor enzyme that transports cargo toward the plus end of microtubules by a processive, asymmetric hand-over-hand mechanism. The coiled-coil neck domain, which connects the two kinesin motor domains, contributes to kinesin processivity (the ability to take many steps in a row) and is proposed to be a key determinant of the asymmetry in the kinesin mechanism. While previous studies have defined the orientation and position of microtubule-bound kinesin motor domains, the disposition of the neck coiled-coil remains uncertain. We determined the neck coiled-coil orientation using a multidonor fluorescence resonance energy transfer (FRET) technique to measure distances between microtubules and bound kinesin molecules. Microtubules were labeled with a new fluorescent taxol donor, TAMRA-X-taxol, and kinesin derivatives with an acceptor fluorophore attached at positions on the motor and neck coiled-coil domains were used to reconstruct the positions and orientations of the domains. FRET measurements to positions on the motor domain were largely consistent with the domain orientation determined in previous studies, validating the technique. Measurements to positions on the neck coiled-coil were inconsistent with a radial orientation and instead demonstrated that the neck coiled-coil is parallel to the microtubule surface. The measured orientation provides a structural explanation for how neck surface residues enhance processivity and suggests a simple hypothesis for the origin of kinesin step asymmetry and "limping."

Changes in assembly processes in soil bacterial communities following a wildfire disturbance.

PubMed

Ferrenberg, Scott; O'Neill, Sean P; Knelman, Joseph E; Todd, Bryan; Duggan, Sam; Bradley, Daniel; Robinson, Taylor; Schmidt, Steven K; Townsend, Alan R; Williams, Mark W; Cleveland, Cory C; Melbourne, Brett A; Jiang, Lin; Nemergut, Diana R

2013-06-01

Although recent work has shown that both deterministic and stochastic processes are important in structuring microbial communities, the factors that affect the relative contributions of niche and neutral processes are poorly understood. The macrobiological literature indicates that ecological disturbances can influence assembly processes. Thus, we sampled bacterial communities at 4 and 16 weeks following a wildfire and used null deviation analysis to examine the role that time since disturbance has in community assembly. Fire dramatically altered bacterial community structure and diversity as well as soil chemistry for both time-points. Community structure shifted between 4 and 16 weeks for both burned and unburned communities. Community assembly in burned sites 4 weeks after fire was significantly more stochastic than in unburned sites. After 16 weeks, however, burned communities were significantly less stochastic than unburned communities. Thus, we propose a three-phase model featuring shifts in the relative importance of niche and neutral processes as a function of time since disturbance. Because neutral processes are characterized by a decoupling between environmental parameters and community structure, we hypothesize that a better understanding of community assembly may be important in determining where and when detailed studies of community composition are valuable for predicting ecosystem function.

Changes in assembly processes in soil bacterial communities following a wildfire disturbance

PubMed Central

Ferrenberg, Scott; O'Neill, Sean P; Knelman, Joseph E; Todd, Bryan; Duggan, Sam; Bradley, Daniel; Robinson, Taylor; Schmidt, Steven K; Townsend, Alan R; Williams, Mark W; Cleveland, Cory C; Melbourne, Brett A; Jiang, Lin; Nemergut, Diana R

2013-01-01

Although recent work has shown that both deterministic and stochastic processes are important in structuring microbial communities, the factors that affect the relative contributions of niche and neutral processes are poorly understood. The macrobiological literature indicates that ecological disturbances can influence assembly processes. Thus, we sampled bacterial communities at 4 and 16 weeks following a wildfire and used null deviation analysis to examine the role that time since disturbance has in community assembly. Fire dramatically altered bacterial community structure and diversity as well as soil chemistry for both time-points. Community structure shifted between 4 and 16 weeks for both burned and unburned communities. Community assembly in burned sites 4 weeks after fire was significantly more stochastic than in unburned sites. After 16 weeks, however, burned communities were significantly less stochastic than unburned communities. Thus, we propose a three-phase model featuring shifts in the relative importance of niche and neutral processes as a function of time since disturbance. Because neutral processes are characterized by a decoupling between environmental parameters and community structure, we hypothesize that a better understanding of community assembly may be important in determining where and when detailed studies of community composition are valuable for predicting ecosystem function. PMID:23407312

Resource for structure related information on transmembrane proteins

NASA Astrophysics Data System (ADS)

Tusnády, Gábor E.; Simon, István

Transmembrane proteins are involved in a wide variety of vital biological processes including transport of water-soluble molecules, flow of information and energy production. Despite significant efforts to determine the structures of these proteins, only a few thousand solved structures are known so far. Here, we review the various resources for structure-related information on these types of proteins ranging from the 3D structure to the topology and from the up-to-date databases to the various Internet sites and servers dealing with structure prediction and structure analysis. Abbreviations: 3D, three dimensional; PDB, Protein Data Bank; TMP, transmembrane protein.

Determination of end point of primary drying in freeze-drying process control.

PubMed

Patel, Sajal M; Doen, Takayuki; Pikal, Michael J

2010-03-01

Freeze-drying is a relatively expensive process requiring long processing time, and hence one of the key objectives during freeze-drying process development is to minimize the primary drying time, which is the longest of the three steps in freeze-drying. However, increasing the shelf temperature into secondary drying before all of the ice is removed from the product will likely cause collapse or eutectic melt. Thus, from product quality as well as process economics standpoint, it is very critical to detect the end of primary drying. Experiments were conducted with 5% mannitol and 5% sucrose as model systems. The apparent end point of primary drying was determined by comparative pressure measurement (i.e., Pirani vs. MKS Baratron), dew point, Lyotrack (gas plasma spectroscopy), water concentration from tunable diode laser absorption spectroscopy, condenser pressure, pressure rise test (manometric temperature measurement or variations of this method), and product thermocouples. Vials were pulled out from the drying chamber using a sample thief during late primary and early secondary drying to determine percent residual moisture either gravimetrically or by Karl Fischer, and the cake structure was determined visually for melt-back, collapse, and retention of cake structure at the apparent end point of primary drying (i.e., onset, midpoint, and offset). By far, the Pirani is the best choice of the methods tested for evaluation of the end point of primary drying. Also, it is a batch technique, which is cheap, steam sterilizable, and easy to install without requiring any modification to the existing dryer.

Work function characterization of solution-processed cobalt silicide

DOE PAGES

Ullah, Syed Shihab; Robinson, Matt; Hoey, Justin; ...

2012-05-08

Cobalt silicide thin films were prepared by spin-coating Si6H12-based inks onto various substrates followed by a thermal treatment. The work function of the solution processed Co-Si was determined by both capacitance-voltage (C-V) measurements of metal-oxide-semiconductor (MOS) structures as well as by ultraviolet photoelectron spectroscopy (UPS). The UPS-derived work function was 4.80 eV for a Co-Si film on Si (100) while C-V of MOS structures yielded a work function of 4.36 eV where the metal was solution-processed Co-Si, the oxide was SiO2 and the semiconductor was a B-doped Si wafer.

Simulation of Structural Transformations in Heating of Alloy Steel

NASA Astrophysics Data System (ADS)

Kurkin, A. S.; Makarov, E. L.; Kurkin, A. B.; Rubtsov, D. E.; Rubtsov, M. E.

2017-07-01

Amathematical model for computer simulation of structural transformations in an alloy steel under the conditions of the thermal cycle of multipass welding is presented. The austenitic transformation under the heating and the processes of decomposition of bainite and martensite under repeated heating are considered. Amethod for determining the necessary temperature-time parameters of the model from the chemical composition of the steel is described. Published data are processed and the results used to derive regression models of the temperature ranges and parameters of transformation kinetics of alloy steels. The method developed is used in computer simulation of the process of multipass welding of pipes by the finite-element method.

Ant-mediated ecosystem processes are driven by trophic community structure but mainly by the environment.

PubMed

Salas-Lopez, Alex; Mickal, Houadria; Menzel, Florian; Orivel, Jérôme

2017-01-01

The diversity and functional identity of organisms are known to be relevant to the maintenance of ecosystem processes but can be variable in different environments. Particularly, it is uncertain whether ecosystem processes are driven by complementary effects or by dominant groups of species. We investigated how community structure (i.e., the diversity and relative abundance of biological entities) explains the community-level contribution of Neotropical ant communities to different ecosystem processes in different environments. Ants were attracted with food resources representing six ant-mediated ecosystem processes in four environments: ground and vegetation strata in cropland and forest habitats. The exploitation frequencies of the baits were used to calculate the taxonomic and trophic structures of ant communities and their contribution to ecosystem processes considered individually or in combination (i.e., multifunctionality). We then investigated whether community structure variables could predict ecosystem processes and whether such relationships were affected by the environment. We found that forests presented a greater biodiversity and trophic complementarity and lower dominance than croplands, but this did not affect ecosystem processes. In contrast, trophic complementarity was greater on the ground than on vegetation and was followed by greater resource exploitation levels. Although ant participation in ecosystem processes can be predicted by means of trophic-based indices, we found that variations in community structure and performance in ecosystem processes were best explained by environment. We conclude that determining the extent to which the dominance and complementarity of communities affect ecosystem processes in different environments requires a better understanding of resource availability to different species.

Supercritical transitiometry of polymers.

PubMed

Randzio, S L; Grolier, J P

1998-06-01

Employing supercritical fluids (SCFs) during polymers processing allows the unusual properties of SCFs to be exploited for making polymer products that cannot be obtained by other means. A new supercritical transitiometer has been constructed to permit study of the interactions of SCFs with polymers during processing under well-defined conditions of temperature and pressure. The supercritical transitiometer allows pressure to be exerted by either a supercritical fluid or a neutral medium and enables simultaneous determination of four basic parameters of a transition, i.e., p, T, Δ(tr)H and Δ(tr)V. This permits determination of the SCF effect on modification of the polymer structure at a given pressure and temperature and defines conditions to allow reproducible preparation of new polymer structures. Study of a semicrystalline polyethylene by this method has defined conditions for preparation of new microfoamed phases with good mechanical properties. The low densities and microporous structures of the new materials may make them useful for applications in medicine, pharmacy, or the food industry, for example.

Structural and Nutritional Properties of Pasta from Triticum monococcum and Triticum durum Species. A Combined ¹H NMR, MRI, and Digestibility Study.

PubMed

Pasini, Gabriella; Greco, Fulvia; Cremonini, Mauro A; Brandolini, Andrea; Consonni, Roberto; Gussoni, Maristella

2015-05-27

The aim of the present study was to characterize the structure of two different types of pasta, namely Triticum turgidum ssp. durum (cv. Saragolla) and Triticum monococcum ssp. monococcum (cv. Monlis), under different processing conditions. MRI analysis and NMR spectroscopy (i.e., T1 and T2 NMR relaxation times and diffusion parameters) were conducted on pasta, and (1)H NMR spectroscopic analysis of the chemical compounds released by pasta samples during the cooking process was performed. In addition, starch digestibility (enzimatically determined) was also investigated. The NMR results indicated that Saragolla pasta has a more compact structure, ascribed to pasta network and in particular to different technological gluten properties, that mainly determine the lower ability of Monlis pasta in binding water. These results correlate well with the lower rate of starch hydrolysis measured for Monlis pasta compared to Saragolla when both are dried at high temperature.

Optimization of a Lunar Pallet Lander Reinforcement Structure Using a Genetic Algorithm

NASA Technical Reports Server (NTRS)

Burt, Adam O.; Hull, Patrick V.

2014-01-01

This paper presents a design automation process using optimization via a genetic algorithm to design the conceptual structure of a Lunar Pallet Lander. The goal is to determine a design that will have the primary natural frequencies at or above a target value as well as minimize the total mass. Several iterations of the process are presented. First, a concept optimization is performed to determine what class of structure would produce suitable candidate designs. From this a stiffened sheet metal approach was selected leading to optimization of beam placement through generating a two-dimensional mesh and varying the physical location of reinforcing beams. Finally, the design space is reformulated as a binary problem using 1-dimensional beam elements to truncate the design space to allow faster convergence and additional mechanical failure criteria to be included in the optimization responses. Results are presented for each design space configuration. The final flight design was derived from these results.

Structure Biology of Membrane Bound Enzymes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fu, Dax

The overall goal of the proposed research is to understand the membrane-associated active processes catalyzed by an alkanemore » $$\\square$$-hydroxylase (AlkB) from eubacterium Pseudomonase oleovorans. AlkB performs oxygenation of unactivated hydrocarbons found in crude oils. The enzymatic reaction involves energy-demanding steps in the membrane with the uses of structurally unknown metal active sites featuring a diiron [FeFe] center. At present, a critical barrier to understanding the membrane-associated reaction mechanism is the lack of structural information. The structural biology efforts have been challenged by technical difficulties commonly encountered in crystallization and structural determination of membrane proteins. The specific aims of the current budget cycle are to crystalize AlkB and initiate X-ray analysis to set the stage for structural determination. The long-term goals of our structural biology efforts are to provide an atomic description of AlkB structure, and to uncover the mechanisms of selective modification of hydrocarbons. The structural information will help elucidating how the unactivated C-H bonds of saturated hydrocarbons are oxidized to initiate biodegradation and biotransformation processes. The knowledge gained will be fundamental to biotechnological applications to biofuel transformation of non-edible oil feedstock. Renewable biodiesel is a promising energy carry that can be used to reduce fossil fuel dependency. The proposed research capitalizes on prior BES-supported efforts on over-expression and purification of AlkB to explore the inner workings of a bioenergy-relevant membrane-bound enzyme.« less

Thermoplastic coating of carbon fibers

NASA Technical Reports Server (NTRS)

Edie, D. D.; Lickfield, G. C.; Drews, M. J.; Ellison, M. S.; Allen, L. E.; Mccollum, J. R.; Thomas, H. L.

1988-01-01

Now that quantities of prepreg were made on the thermoplastic coating line, they are being formed into both textile preform structures and directly into composite samples. The textile preforms include both woven and knitted structures which will be thermoformed into a finished part. In order to determine if the matrix resin is properly adhering to the fibers or if voids are being formed in the coating process, the tensile strength and modulus of these samples will be tested. The matrix uniformity of matrix distribution in these samples is also being determined using an image analyzer.

An approach to functionally relevant clustering of the protein universe: Active site profile‐based clustering of protein structures and sequences

PubMed Central

Knutson, Stacy T.; Westwood, Brian M.; Leuthaeuser, Janelle B.; Turner, Brandon E.; Nguyendac, Don; Shea, Gabrielle; Kumar, Kiran; Hayden, Julia D.; Harper, Angela F.; Brown, Shoshana D.; Morris, John H.; Ferrin, Thomas E.; Babbitt, Patricia C.

2017-01-01

Abstract Protein function identification remains a significant problem. Solving this problem at the molecular functional level would allow mechanistic determinant identification—amino acids that distinguish details between functional families within a superfamily. Active site profiling was developed to identify mechanistic determinants. DASP and DASP2 were developed as tools to search sequence databases using active site profiling. Here, TuLIP (Two‐Level Iterative clustering Process) is introduced as an iterative, divisive clustering process that utilizes active site profiling to separate structurally characterized superfamily members into functionally relevant clusters. Underlying TuLIP is the observation that functionally relevant families (curated by Structure‐Function Linkage Database, SFLD) self‐identify in DASP2 searches; clusters containing multiple functional families do not. Each TuLIP iteration produces candidate clusters, each evaluated to determine if it self‐identifies using DASP2. If so, it is deemed a functionally relevant group. Divisive clustering continues until each structure is either a functionally relevant group member or a singlet. TuLIP is validated on enolase and glutathione transferase structures, superfamilies well‐curated by SFLD. Correlation is strong; small numbers of structures prevent statistically significant analysis. TuLIP‐identified enolase clusters are used in DASP2 GenBank searches to identify sequences sharing functional site features. Analysis shows a true positive rate of 96%, false negative rate of 4%, and maximum false positive rate of 4%. F‐measure and performance analysis on the enolase search results and comparison to GEMMA and SCI‐PHY demonstrate that TuLIP avoids the over‐division problem of these methods. Mechanistic determinants for enolase families are evaluated and shown to correlate well with literature results. PMID:28054422

The mode of inhibitor binding to peptidyl-tRNA hydrolase: binding studies and structure determination of unbound and bound peptidyl-tRNA hydrolase from Acinetobacter baumannii.

PubMed

Kaushik, Sanket; Singh, Nagendra; Yamini, Shavait; Singh, Avinash; Sinha, Mau; Arora, Ashish; Kaur, Punit; Sharma, Sujata; Singh, Tej P

2013-01-01

The incidences of infections caused by an aerobic Gram-negative bacterium, Acinetobacter baumannii are very common in hospital environments. It usually causes soft tissue infections including urinary tract infections and pneumonia. It is difficult to treat due to acquired resistance to available antibiotics is well known. In order to design specific inhibitors against one of the important enzymes, peptidyl-tRNA hydrolase from Acinetobacter baumannii, we have determined its three-dimensional structure. Peptidyl-tRNA hydrolase (AbPth) is involved in recycling of peptidyl-tRNAs which are produced in the cell as a result of premature termination of translation process. We have also determined the structures of two complexes of AbPth with cytidine and uridine. AbPth was cloned, expressed and crystallized in unbound and in two bound states with cytidine and uridine. The binding studies carried out using fluorescence spectroscopic and surface plasmon resonance techniques revealed that both cytidine and uridine bound to AbPth at nanomolar concentrations. The structure determinations of the complexes revealed that both ligands were located in the active site cleft of AbPth. The introduction of ligands to AbPth caused a significant widening of the entrance gate to the active site region and in the process of binding, it expelled several water molecules from the active site. As a result of interactions with protein atoms, the ligands caused conformational changes in several residues to attain the induced tight fittings. Such a binding capability of this protein makes it a versatile molecule for hydrolysis of peptidyl-tRNAs having variable peptide sequences. These are the first studies that revealed the mode of inhibitor binding in Peptidyl-tRNA hydrolases which will facilitate the structure based ligand design.

Wholeness and primary and secondary food structure effects on in vitro digestion patterns determine nutritionally distinct carbohydrate fractions in cereal foods.

PubMed

Mishra, Suman; Monro, John

2012-12-01

Starchy foods of differing structure, including bakery products, breakfast cereals, pastas, and pulses were digested in vitro. Bakery products and processed breakfast cereals with little resilient structure yielded large amounts of rapidly available carbohydrate (RAC), less slowly digested starch (SDS) and little inaccessible digestible starch (IDS) (70:22:8%). Partially processed grains, such as rolled oats contained an increased proportion of SDS (55:38:7%). Pastas, being dense starch structures digested more gradually to completion by superficial erosion, yielding approximately equal proportions of RAC and SDS but little IDS (43:52:4%). Pulses, which retained their cellular morphology, digested more linearly yielding a lower proportion of RAC, a larger proportion of SDS and more IDS (9:69:22%). Preservation of native "primary" structure, and use of processing to create "secondary" structure, are both means by which wholeness, in the sense of intactness, can be used to influence carbohydrate digestion to make foods of lower glycaemic impact. Copyright © 2012 Elsevier Ltd. All rights reserved.

Porous Ceramic Spheres From Cation Exchange Beads

NASA Technical Reports Server (NTRS)

Dynys, Fred

2005-01-01

This document is a slide presentation that examines the use of a simple templating process to produce hollow ceramic spheres with a pore size of 1 to 10 microns. Using ion exchange process it was determined that the method produces porous ceramic spheres with a unique structure: (i.e., inner sphere surrounded by an outer sphere.)

Impact of food processing on rye product properties and their in vitro digestion.

PubMed

Johansson, Daniel P; Gutiérrez, José L Vázquez; Landberg, Rikard; Alminger, Marie; Langton, Maud

2018-06-01

Rye products have been reported to elicit postprandial insulin and glucose responses which may be beneficial for prevention of type-2 diabetes. However, mechanisms underlying variations in responses related to processing techniques are not fully understood. Five differently processed rye products (sourdough-fermented bread, fermented and unfermented crispbread, extrusion-cooked rye, and porridge) and refined wheat bread were characterised. Two in vitro methods, a dynamic method simulating digestion in the stomach and small intestine and a static method, simulating conditions in the stomach were used to determine viscosity development, structural changes and release of glucose during digestion. Structural and compositional differences induced by processing influenced product digestion. Gastric disintegration and digesta particle size were related to characteristics of the starch/protein matrix, while digesta viscosity was reduced due to fibre degradation during fermentation. More cohesive boluses were associated with slower glucose release. Sourdough fermentation increased amylose leakage and appeared to inhibit starch hydrolysis despite low digesta viscosity and rapid disintegration. The net release of glucose during digestion of foods is determined by several factors which may vary in their importance depending on product specific properties.

Structure of synaptophysin: a hexameric MARVEL-domain channel protein.

PubMed

Arthur, Christopher P; Stowell, Michael H B

2007-06-01

Synaptophysin I (SypI) is an archetypal member of the MARVEL-domain family of integral membrane proteins and one of the first synaptic vesicle proteins to be identified and cloned. Most all MARVEL-domain proteins are involved in membrane apposition and vesicle-trafficking events, but their precise role in these processes is unclear. We have purified mammalian SypI and determined its three-dimensional (3D) structure by using electron microscopy and single-particle 3D reconstruction. The hexameric structure resembles an open basket with a large pore and tenuous interactions within the cytosolic domain. The structure suggests a model for Synaptophysin's role in fusion and recycling that is regulated by known interactions with the SNARE machinery. This 3D structure of a MARVEL-domain protein provides a structural foundation for understanding the role of these important proteins in a variety of biological processes.

Growth Control and Disease Mechanisms in Computational Embryogeny

NASA Technical Reports Server (NTRS)

Shapiro, Andrew A.; Yogev, Or; Antonsson, Erik K.

2008-01-01

This paper presents novel approach to applying growth control and diseases mechanisms in computational embryogeny. Our method, which mimics fundamental processes from biology, enables individuals to reach maturity in a controlled process through a stochastic environment. Three different mechanisms were implemented; disease mechanisms, gene suppression, and thermodynamic balancing. This approach was integrated as part of a structural evolutionary model. The model evolved continuum 3-D structures which support an external load. By using these mechanisms we were able to evolve individuals that reached a fixed size limit through the growth process. The growth process was an integral part of the complete development process. The size of the individuals was determined purely by the evolutionary process where different individuals matured to different sizes. Individuals which evolved with these characteristics have been found to be very robust for supporting a wide range of external loads.

Lightweight Concrete Produced Using a Two-Stage Casting Process.

PubMed

Yoon, Jin Young; Kim, Jae Hong; Hwang, Yoon Yi; Shin, Dong Kyu

2015-03-25

The type of lightweight aggregate and its volume fraction in a mix determine the density of lightweight concrete. Minimizing the density obviously requires a higher volume fraction, but this usually causes aggregates segregation in a conventional mixing process. This paper proposes a two-stage casting process to produce a lightweight concrete. This process involves placing lightweight aggregates in a frame and then filling in the remaining interstitial voids with cementitious grout. The casting process results in the lowest density of lightweight concrete, which consequently has low compressive strength. The irregularly shaped aggregates compensate for the weak point in terms of strength while the round-shape aggregates provide a strength of 20 MPa. Therefore, the proposed casting process can be applied for manufacturing non-structural elements and structural composites requiring a very low density and a strength of at most 20 MPa.

Deducing chemical structure from crystallographically determined atomic coordinates

PubMed Central

Bruno, Ian J.; Shields, Gregory P.; Taylor, Robin

2011-01-01

An improved algorithm has been developed for assigning chemical structures to incoming entries to the Cambridge Structural Database, using only the information available in the deposited CIF. Steps in the algorithm include detection of bonds, selection of polymer unit, resolution of disorder, and assignment of bond types and formal charges. The chief difficulty is posed by the large number of metallo-organic crystal structures that must be processed, given our aspiration that assigned chemical structures should accurately reflect properties such as the oxidation states of metals and redox-active ligands, metal coordination numbers and hapticities, and the aromaticity or otherwise of metal ligands. Other complications arise from disorder, especially when it is symmetry imposed or modelled with the SQUEEZE algorithm. Each assigned structure is accompanied by an estimate of reliability and, where necessary, diagnostic information indicating probable points of error. Although the algorithm was written to aid building of the Cambridge Structural Database, it has the potential to develop into a general-purpose tool for adding chemical information to newly determined crystal structures. PMID:21775812

Stories and Gossip in English: The Macro-Structure of Casual Talk.

ERIC Educational Resources Information Center

Slade, Diana

1997-01-01

A discussion of two text-types commonly occurring in casual conversation, stories and gossip, (1) details four kinds of stories told in casual talk, (2) demonstrates that gossip is a culturally-determined process with a distinctive structure, and (3) considers implications for teaching English-as-a- Second-Language. Analysis is based on over three…

Determination of the season-acclimation of photosynthetic apparatus by heat-induced changes in chlorophyll fluorescence

Treesearch

Nicolay Alexandrovich Gaevsky

2002-01-01

Resistance to damage from freezing temperatures is one of the most adaptive properties of "evergreen" (shoot bark, felloderma, needles) woody and bush plant tissues. Species-specific processes accompanying transition of chloroplasts to a frost resistant state (reduction of photochemical activity, the change of chemical structure and structural organization of...

Analytical calculation on the determination of steep side wall angles from far field measurements

NASA Astrophysics Data System (ADS)

Cisotto, Luca; Pereira, Silvania F.; Urbach, H. Paul

2018-06-01

In the semiconductor industry, the performance and capabilities of the lithographic process are evaluated by measuring specific structures. These structures are often gratings of which the shape is described by a few parameters such as period, middle critical dimension, height, and side wall angle (SWA). Upon direct measurement or retrieval of these parameters, the determination of the SWA suffers from considerable inaccuracies. Although the scattering effects that steep SWAs have on the illumination can be obtained with rigorous numerical simulations, analytical models constitute a very useful tool to get insights into the problem we are treating. In this paper, we develop an approach based on analytical calculations to describe the scattering of a cliff and a ridge with steep SWAs. We also propose a detection system to determine the SWAs of the structures.

Calorimetric Studies and Structural Aspects of Ionic Liquids in Designing Sorption Materials for Thermal Energy Storage.

PubMed

Brünig, Thorge; Krekić, Kristijan; Bruhn, Clemens; Pietschnig, Rudolf

2016-11-02

The thermal properties of a series of twenty-four ionic liquids (ILs) have been determined by isothermal titration calorimetry (ITC) with the aim of simulating processes involving water sorption. For eleven water-free ILs, the molecular structures have been determined by X-ray crystallography in the solid state, which have been used to derive the molecular volumes of the ionic components of the ILs. Moreover, the structures reveal a high prevalence of hydrogen bonding in these compounds. A relationship between the molecular volumes and the experimentally determined energies of dilution could be established. The highest energies of dilution observed in this series were obtained for the acetate-based ILs, which underlines their potential as working fluids in sorption-based thermal energy storage systems. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Application of remote sensors in coastal zone observations

NASA Technical Reports Server (NTRS)

Caillat, J. M.; Elachi, C.; Brown, W. E., Jr.

1975-01-01

A review of processes taking place along coastlines and their biological consideration led to the determination of the elements which are required in the study of coastal structures and which are needed for better utilization of the resources from the oceans. The processes considered include waves, currents, and their influence on the erosion of coastal structures. Biological considerations include coastal fisheries, estuaries, and tidal marshes. Various remote sensors were analyzed for the information which they can provide and sites were proposed where a general ocean-observation plan could be tested.

[Determinants of the rural exodus: the importance of place of origin factors, Chile, 1965-1970].

PubMed

Raczynski, D

1982-07-01

Trends in rural-urban migration in Chile during the period 1965-1970 are analyzed, with a focus on the impact of the combination of structural factors and socioeconomic processes in rural areas. Factors of population retention and expulsion are examined in terms of agrarian structure, the process of agrarian reform, urbanization of the countryside, and the availability of basic social services. Rural-urban migration rates in the central and southern areas of the country are compared, and migration rates of males and females are examined.

Sequencing of Dust Filter Production Process Using Design Structure Matrix (DSM)

NASA Astrophysics Data System (ADS)

Sari, R. M.; Matondang, A. R.; Syahputri, K.; Anizar; Siregar, I.; Rizkya, I.; Ursula, C.

2018-01-01

Metal casting company produces machinery spare part for manufactures. One of the product produced is dust filter. Most of palm oil mill used this product. Since it is used in most of palm oil mill, company often have problems to address this product. One of problem is the disordered of production process. It carried out by the job sequencing. The important job that should be solved first, least implement, while less important job and could be completed later, implemented first. Design Structure Matrix (DSM) used to analyse and determine priorities in the production process. DSM analysis is sort of production process through dependency sequencing. The result of dependency sequences shows the sequence process according to the inter-process linkage considering before and after activities. Finally, it demonstrates their activities to the coupled activities for metal smelting, refining, grinding, cutting container castings, metal expenditure of molds, metal casting, coating processes, and manufacture of molds of sand.

Determination of the structure and heating mechanisms of coronal loops from soft X-ray observations with the solar probe. [grazing incidence telescope

NASA Technical Reports Server (NTRS)

Davis, J. M.; Krieger, A. S.

1978-01-01

High resolution soft X-ray imaging from the solar probe is justified in terms of the expected scientific returns which include the determination of the temperature and density structure of a coronal loop. The advantages of the grazing incidence telescope over the multiple pinhole camera are discussed. An instrument package is described which includes a grazing incidence mirror, a thermal prefilter, a three position filter wheel and a focal plane detector baselined as an 800 by 800 back-illuminated charge coupled device. The structural assembly together with the data processing equipment would draw heavily on the designs being developed for the Solar Polar Mission.

Advanced composites structural concepts and materials technologies for primary aircraft structures: Design/manufacturing concept assessment

NASA Technical Reports Server (NTRS)

Chu, Robert L.; Bayha, Tom D.; Davis, HU; Ingram, J. ED; Shukla, Jay G.

1992-01-01

Composite Wing and Fuselage Structural Design/Manufacturing Concepts have been developed and evaluated. Trade studies were performed to determine how well the concepts satisfy the program goals of 25 percent cost savings, 40 percent weight savings with aircraft resizing, and 50 percent part count reduction as compared to the aluminum Lockheed L-1011 baseline. The concepts developed using emerging technologies such as large scale resin transfer molding (RTM), automatic tow placed (ATP), braiding, out-of-autoclave and automated manufacturing processes for both thermoset and thermoplastic materials were evaluated for possible application in the design concepts. Trade studies were used to determine which concepts carry into the detailed design development subtask.

Multifactorial genetic divergence processes drive the onset of speciation in an Amazonian fish

PubMed Central

Torrente-Vilara, Gislene; Quilodran, Claudio; Rodrigues da Costa Doria, Carolina; Montoya-Burgos, Juan I.

2017-01-01

Understanding the processes that drive population genetic divergence in the Amazon is challenging because of the vast scale, the environmental richness and the outstanding biodiversity of the region. We addressed this issue by determining the genetic structure of the widespread Amazonian common sardine fish Triportheus albus (Characidae). We then examined the influence, on this species, of all previously proposed population-structuring factors, including isolation-by-distance, isolation-by-barrier (the Teotônio Falls) and isolation-by-environment using variables that describe floodplain and water characteristics. The population genetics analyses revealed an unusually strong structure with three geographical groups: Negro/Tapajós rivers, Lower Madeira/Central Amazon, and Upper Madeira. Distance-based redundancy analyses showed that the optimal model for explaining the extreme genetic structure contains all proposed structuring factors and accounts for up to 70% of the genetic structure. We further quantified the contribution of each factor via a variance-partitioning analysis. Our results demonstrate that multiple factors, often proposed as individual drivers of population divergence, have acted in conjunction to divide T. albus into three genetic lineages. Because the conjunction of multiple long-standing population-structuring processes may lead to population reproductive isolation, that is, the onset of speciation, we suggest that the multifactorial population-structuring processes highlighted in this study could account for the high speciation rate characterising the Amazon Basin. PMID:29261722

Low-carbon martensitic steels. Alloying and properties

NASA Astrophysics Data System (ADS)

Kleiner, L. M.; Shatsov, A. A.; Larinin, D. M.

2011-03-01

Requirements on the structure of a steel with structural strength and a set of characteristics higher than those of medium-carbon steels with a structure of tempered sorbite are formulated. Principles for choosing compositions for process-adaptable low-carbon martensitic steels are presented. The combination of carbon and alloying elements providing high stability of austenite in the ranges of normal and intermediate transformations is determined, which makes it possible to obtain lath martensite in slow cooling.

Distributed ice accretion sensor for smart aircraft structures

NASA Technical Reports Server (NTRS)

Gerardi, J. J.; Hickman, G. A.

1989-01-01

A distributed ice accretion sensor is presented, based on the concept of smart structures. Ice accretion is determined using spectral techniques to process signals from piezoelectric sensors integral to the airfoil skin. Frequency shifts in the leading edge structural skin modes are correlated to ice thickness. It is suggested that this method may be used to detect ice over large areas with minimal hardware. Results are presented from preliminary tests to measure simulated ice growth.

Effect of supercritical fluid density on nanoencapsulated drug particle size using the supercritical antisolvent method.

PubMed

Kalani, Mahshid; Yunus, Robiah

2012-01-01

The reported work demonstrates and discusses the effect of supercritical fluid density (pressure and temperature of supercritical fluid carbon dioxide) on particle size and distribution using the supercritical antisolvent (SAS) method in the purpose of drug encapsulation. In this study, paracetamol was encapsulated inside L-polylactic acid, a semicrystalline polymer, with different process parameters, including pressure and temperature, using the SAS process. The morphology and particle size of the prepared nanoparticles were determined by scanning electron microscopy and transmission electron microscopy. The results revealed that increasing temperature enhanced mean particle size due to the plasticizing effect. Furthermore, increasing pressure enhanced molecular interaction and solubility; thus, particle size was reduced. Transmission electron microscopy images defined the internal structure of nanoparticles. Thermal characteristics of nanoparticles were also investigated via differential scanning calorimetry. Furthermore, X-ray diffraction pattern revealed the changes in crystallinity structure during the SAS process. In vitro drug release analysis determined the sustained release of paracetamol in over 4 weeks.

Effect of supercritical fluid density on nanoencapsulated drug particle size using the supercritical antisolvent method

PubMed Central

Kalani, Mahshid; Yunus, Robiah

2012-01-01

The reported work demonstrates and discusses the effect of supercritical fluid density (pressure and temperature of supercritical fluid carbon dioxide) on particle size and distribution using the supercritical antisolvent (SAS) method in the purpose of drug encapsulation. In this study, paracetamol was encapsulated inside L-polylactic acid, a semicrystalline polymer, with different process parameters, including pressure and temperature, using the SAS process. The morphology and particle size of the prepared nanoparticles were determined by scanning electron microscopy and transmission electron microscopy. The results revealed that increasing temperature enhanced mean particle size due to the plasticizing effect. Furthermore, increasing pressure enhanced molecular interaction and solubility; thus, particle size was reduced. Transmission electron microscopy images defined the internal structure of nanoparticles. Thermal characteristics of nanoparticles were also investigated via differential scanning calorimetry. Furthermore, X-ray diffraction pattern revealed the changes in crystallinity structure during the SAS process. In vitro drug release analysis determined the sustained release of paracetamol in over 4 weeks. PMID:22619552

3D structure of the influenza virus polymerase complex: Localization of subunit domains

PubMed Central

Area, Estela; Martín-Benito, Jaime; Gastaminza, Pablo; Torreira, Eva; Valpuesta, José M.; Carrascosa, José L.; Ortín, Juan

2004-01-01

The 3D structure of the influenza virus polymerase complex was determined by electron microscopy and image processing of recombinant ribonucleoproteins (RNPs). The RNPs were generated by in vivo amplification using cDNAs of the three polymerase subunits, the nucleoprotein, and a model virus-associated RNA containing 248 nt. The polymerase structure obtained is very compact, with no apparent boundaries among subunits. The position of specific regions of the PB1, PB2, and PA subunits was determined by 3D reconstruction of either RNP–mAb complexes or tagged RNPs. This structural model is available for the polymerase of a negative-stranded RNA virus and provides a general delineation of the complex and its interaction with the template-associated nucleoprotein monomers in the RNP. PMID:14691253

CCP4i2: the new graphical user interface to the CCP4 program suite

PubMed Central

Potterton, Liz; Ballard, Charles; Dodson, Eleanor; Evans, Phil R.; Keegan, Ronan; Krissinel, Eugene; Stevenson, Kyle; Lebedev, Andrey; McNicholas, Stuart J.; Noble, Martin; Pannu, Navraj S.; Roth, Christian; Sheldrick, George; Skubak, Pavol; Uski, Ville

2018-01-01

The CCP4 (Collaborative Computational Project, Number 4) software suite for macromolecular structure determination by X-ray crystallography groups brings together many programs and libraries that, by means of well established conventions, interoperate effectively without adhering to strict design guidelines. Because of this inherent flexibility, users are often presented with diverse, even divergent, choices for solving every type of problem. Recently, CCP4 introduced CCP4i2, a modern graphical interface designed to help structural biologists to navigate the process of structure determination, with an emphasis on pipelining and the streamlined presentation of results. In addition, CCP4i2 provides a framework for writing structure-solution scripts that can be built up incrementally to create increasingly automatic procedures. PMID:29533233

The young person's guide to the PDB.

PubMed

Minor, Wladek; Dauter, Zbigniew; Jaskolski, Mariusz

The Protein Data Bank (PDB), created in 1971 when merely seven protein crystal structures were known, today holds over 120, 000 experimentally-determined three-dimensional models of macromolecules, including gigantic structures comprised of hundreds of thousands of atoms, such as ribosomes and viruses. Most of the deposits come from X-ray crystallography experiments, with important contributions also made by NMR spectroscopy and, recently, by the fast growing Cryo-Electron Microscopy. Although the determination of a macromolecular crystal structure is now facilitated by advanced experimental tools and by sophisticated software, it is still a highly complicated research process requiring specialized training, skill, experience and a bit of luck. Understanding the plethora of structural information provided by the PDB requires that its users (consumers) have at least a rudimentary initiation. This is the purpose of this educational overview.

Long term pavement performance computed parameter : frost penetration

DOT National Transportation Integrated Search

2008-11-01

As the pavement design process moves toward mechanistic-empirical techniques, knowledge of seasonal changes in pavement structural characteristics becomes critical. Specifically, frost penetration information is necessary for determining the effect o...

Promoting and Protecting Against Stigma in Assisted Living and Nursing Homes

PubMed Central

Zimmerman, Sheryl; Dobbs, Debra; Roth, Erin G.; Goldman, Susan; Peeples, Amanda D.; Wallace, Brandy

2016-01-01

Purpose of the Study: To determine the extent to which structures and processes of care in multilevel settings (independent living, assisted living, and nursing homes) result in stigma in assisted living and nursing homes. Design and Methods: Ethnographic in-depth interviews were conducted in 5 multilevel settings with 256 residents, families, and staff members. Qualitative analyses identified the themes that resulted when examining text describing either structures of care or processes of care in relation to 7 codes associated with stigma. Results: Four themes related to structures of care and stigma were identified, including the physical environment, case mix, staff training, and multilevel settings; five themes related to processes of care and stigma, including dining, independence, respect, privacy, and care provision. For each theme, examples were identified illustrating how structures and processes of care can potentially promote or protect against stigma. Implications: In no instance were examples or themes identified that suggested the staff intentionally promoted stigma; on the other hand, there was indication that some structures and processes were intentionally in place to protect against stigma. Perhaps the most important theme is the stigma related to multilevel settings, as it has the potential to reduce individuals’ likelihood to seek and accept necessary care. Results suggest specific recommendations to modify care and reduce stigma. PMID:24928555

Insoluble Coatings for Stirling Engine Heat Pipe Condenser Surfaces

NASA Technical Reports Server (NTRS)

Dussinger, Peter M.; Lindemuth, James E.

1997-01-01

The principal objective of this Phase 2 SBIR program was to develop and demonstrate a practically insoluble coating for nickel-based superalloys for Stirling engine heat pipe applications. Specific technical objectives of the program were: (1) Determine the solubility corrosion rates for Nickel 200, Inconel 718, and Udimet 72OLI in a simulated Stirling engine heat pipe environment, (2) Develop coating processes and techniques for capillary groove and screen wick structures, (3) Evaluate the durability and solubility corrosion rates for capillary groove and screen wick structures coated with an insoluble coating in cylindrical heat pipes operating under Stirling engine conditions, and (4) Design and fabricate a coated full-scale, partial segment of the current Stirling engine heat pipe for the Stirling Space Power Convertor program. The work effort successfully demonstrated a two-step nickel aluminide coating process for groove wick structures and interior wall surfaces in contact with liquid metals; demonstrated a one-step nickel aluminide coating process for nickel screen wick structures; and developed and demonstrated a two-step aluminum-to-nickel aluminide coating process for nickel screen wick structures. In addition, the full-scale, partial segment was fabricated and the interior surfaces and wick structures were coated. The heat pipe was charged with sodium, processed, and scheduled to be life tested for up to ten years as a Phase 3 effort.

Crystal Structure of the HEAT Domain from the Pre-mRNA Processing Factor Symplekin

PubMed Central

Kennedy, Sarah A.; Frazier, Monica L.; Steiniger, Mindy; Mast, Ann M.; Marzluff, William F.; Redinbo, Matthew R.

2009-01-01

The majority of eukaryotic pre-mRNAs are processed by 3′-end cleavage and polyadenylation, although in metazoa the replication-dependant histone mRNAs are processed by 3′-end cleavage but not polyadenylation. The macromolecular complex responsible for processing both canonical and histone pre-mRNAs contains the ~1,160-residue protein Symplekin. Secondary structural prediction algorithms identified putative HEAT domains in the 300 N-terminal residues of all Symplekins of known sequence. The structure and dynamics of this domain were investigated to begin elucidating the role Symplekin plays in mRNA maturation. The crystal structure of the Drosophila melanogaster Symplekin HEAT domain was determined to 2.4 Å resolution using SAD phasing methods. The structure exhibits 5 canonical HEAT repeats along with an extended 31 amino acid loop (loop 8) between the fourth and fifth repeat that is conserved within closely related Symplekin sequences. Molecular dynamics simulations of this domain show that the presence of loop 8 dampens correlated and anticorrelated motion in the HEAT domain, therefore providing a neutral surface for potential protein-protein interactions. HEAT domains are often employed for such macromolecular contacts. The Symplekin HEAT region not only structurally aligns with several established scaffolding proteins, but also has been reported to contact proteins essential for regulating 3′-end processing. Taken together, these data support the conclusion that the Symplekin HEAT domain serves as a scaffold for protein-protein interactions essential to the mRNA maturation process. PMID:19576221

Programmable assembly of pressure sensors using pattern-forming bacteria

PubMed Central

Cao, Yangxiaolu; Feng, Yaying; Ryser, Marc D.; Zhu, Kui; Herschlag, Gregory; Cao, Changyong; Marusak, Katherine; Zauscher, Stefan; You, Lingchong

2017-01-01

Biological systems can generate microstructured materials that combine organic and inorganic components and possess diverse physical and chemical properties. However, these natural processes in materials fabrication are not readily programmable. Here, we use a synthetic-biology approach to mimic such natural processes to assemble patterned materials.. We demonstrate programmable fabrication of three-dimensional (3D) materials by printing engineered self-patterning bacteria on permeable membranes that serve as a structural scaffold. Application of gold nanoparticles to the colonies creates hybrid organic-inorganic dome structures. The dynamics of the dome structures' response to pressure is determined by their geometry (colony size, dome height and pattern), which is easily modified by varying the properties of the membrane (e.g., pore size and hydrophobicity). We generate resettable pressure sensors that process signals in response to varying pressure intensity and duration. PMID:28991268

Rapid condition assessment of structural condition after a blast using state-space identification

NASA Astrophysics Data System (ADS)

Eskew, Edward; Jang, Shinae

2015-04-01

After a blast event, it is important to quickly quantify the structural damage for emergency operations. In order improve the speed, accuracy, and efficiency of condition assessments after a blast, the authors have previously performed work to develop a methodology for rapid assessment of the structural condition of a building after a blast. The method involved determining a post-event equivalent stiffness matrix using vibration measurements and a finite element (FE) model. A structural model was built for the damaged structure based on the equivalent stiffness, and inter-story drifts from the blast are determined using numerical simulations, with forces determined from the blast parameters. The inter-story drifts are then compared to blast design conditions to assess the structures damage. This method still involved engineering judgment in terms of determining significant frequencies, which can lead to error, especially with noisy measurements. In an effort to improve accuracy and automate the process, this paper will look into a similar method of rapid condition assessment using subspace state-space identification. The accuracy of the method will be tested using a benchmark structural model, as well as experimental testing. The blast damage assessments will be validated using pressure-impulse (P-I) diagrams, which present the condition limits across blast parameters. Comparisons between P-I diagrams generated using the true system parameters and equivalent parameters will show the accuracy of the rapid condition based blast assessments.

The Influence of Friction Stir Weld Tool Form and Welding Parameters on Weld Structure and Properties: Nugget Bulge in Self-Reacting Friction Stir Welds

NASA Technical Reports Server (NTRS)

Schneider, Judy; Nunes, Arthur C., Jr.; Brendel, Michael S.

2010-01-01

Although friction stir welding (FSW) was patented in 1991, process development has been based upon trial and error and the literature still exhibits little understanding of the mechanisms determining weld structure and properties. New concepts emerging from a better understanding of these mechanisms enhance the ability of FSW engineers to think about the FSW process in new ways, inevitably leading to advances in the technology. A kinematic approach in which the FSW flow process is decomposed into several simple flow components has been found to explain the basic structural features of FSW welds and to relate them to tool geometry and process parameters. Using this modelling approach, this study reports on a correlation between the features of the weld nugget, process parameters, weld tool geometry, and weld strength. This correlation presents a way to select process parameters for a given tool geometry so as to optimize weld strength. It also provides clues that may ultimately explain why the weld strength varies within the sample population.

Localization of wood floor structure by infrared thermography

NASA Astrophysics Data System (ADS)

Cochior Plescanu, C.; Klein, M.; Ibarra-Castanedo, C.; Bendada, A.; Maldague, X.

2008-03-01

One of our industrial partners, Assek Technologie, is interested in developing a technique that would improve the drying process of wood floor in basements after flooding. In order to optimize the procedure, the floor structure and the damaged (wet) area extent must first be determined with minimum intrusion (minimum or no dismantling). The present study presents the use of infrared thermography to reveal the structure of (flooded) wood floors. The procedure involves opening holes in the floor. Injecting some hot air through those holes reveals the framing structure even if the floor is covered by vinyl or ceramic tiles. This study indicates that thermal imaging can also be used as a tool to validate the decontamination process after drying. Thermal images were obtained on small-scale models and in a demonstration room.

Chemical computing with reaction-diffusion processes.

PubMed

Gorecki, J; Gizynski, K; Guzowski, J; Gorecka, J N; Garstecki, P; Gruenert, G; Dittrich, P

2015-07-28

Chemical reactions are responsible for information processing in living organisms. It is believed that the basic features of biological computing activity are reflected by a reaction-diffusion medium. We illustrate the ideas of chemical information processing considering the Belousov-Zhabotinsky (BZ) reaction and its photosensitive variant. The computational universality of information processing is demonstrated. For different methods of information coding constructions of the simplest signal processing devices are described. The function performed by a particular device is determined by the geometrical structure of oscillatory (or of excitable) and non-excitable regions of the medium. In a living organism, the brain is created as a self-grown structure of interacting nonlinear elements and reaches its functionality as the result of learning. We discuss whether such a strategy can be adopted for generation of chemical information processing devices. Recent studies have shown that lipid-covered droplets containing solution of reagents of BZ reaction can be transported by a flowing oil. Therefore, structures of droplets can be spontaneously formed at specific non-equilibrium conditions, for example forced by flows in a microfluidic reactor. We describe how to introduce information to a droplet structure, track the information flow inside it and optimize medium evolution to achieve the maximum reliability. Applications of droplet structures for classification tasks are discussed. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

Neighbor-Dependent Ramachandran Probability Distributions of Amino Acids Developed from a Hierarchical Dirichlet Process Model

PubMed Central

Mitra, Rajib; Jordan, Michael I.; Dunbrack, Roland L.

2010-01-01

Distributions of the backbone dihedral angles of proteins have been studied for over 40 years. While many statistical analyses have been presented, only a handful of probability densities are publicly available for use in structure validation and structure prediction methods. The available distributions differ in a number of important ways, which determine their usefulness for various purposes. These include: 1) input data size and criteria for structure inclusion (resolution, R-factor, etc.); 2) filtering of suspect conformations and outliers using B-factors or other features; 3) secondary structure of input data (e.g., whether helix and sheet are included; whether beta turns are included); 4) the method used for determining probability densities ranging from simple histograms to modern nonparametric density estimation; and 5) whether they include nearest neighbor effects on the distribution of conformations in different regions of the Ramachandran map. In this work, Ramachandran probability distributions are presented for residues in protein loops from a high-resolution data set with filtering based on calculated electron densities. Distributions for all 20 amino acids (with cis and trans proline treated separately) have been determined, as well as 420 left-neighbor and 420 right-neighbor dependent distributions. The neighbor-independent and neighbor-dependent probability densities have been accurately estimated using Bayesian nonparametric statistical analysis based on the Dirichlet process. In particular, we used hierarchical Dirichlet process priors, which allow sharing of information between densities for a particular residue type and different neighbor residue types. The resulting distributions are tested in a loop modeling benchmark with the program Rosetta, and are shown to improve protein loop conformation prediction significantly. The distributions are available at http://dunbrack.fccc.edu/hdp. PMID:20442867

Teaching and Learning the Interplay between Chance and Determinism in Nonlinear Systems

ERIC Educational Resources Information Center

Stavrou, Dimitrios; Duit, Reinders

2014-01-01

That the interplay of random and deterministic processes may result in both the limited predictability of nonlinear systems and the formation of structures seems to be a most valuable general insight into the nature of science. This study investigates the possibility of teaching and learning the interplay of chance and determinism in nonlinear…

Data Mining of Macromolecular Structures.

PubMed

van Beusekom, Bart; Perrakis, Anastassis; Joosten, Robbie P

2016-01-01

The use of macromolecular structures is widespread for a variety of applications, from teaching protein structure principles all the way to ligand optimization in drug development. Applying data mining techniques on these experimentally determined structures requires a highly uniform, standardized structural data source. The Protein Data Bank (PDB) has evolved over the years toward becoming the standard resource for macromolecular structures. However, the process selecting the data most suitable for specific applications is still very much based on personal preferences and understanding of the experimental techniques used to obtain these models. In this chapter, we will first explain the challenges with data standardization, annotation, and uniformity in the PDB entries determined by X-ray crystallography. We then discuss the specific effect that crystallographic data quality and model optimization methods have on structural models and how validation tools can be used to make informed choices. We also discuss specific advantages of using the PDB_REDO databank as a resource for structural data. Finally, we will provide guidelines on how to select the most suitable protein structure models for detailed analysis and how to select a set of structure models suitable for data mining.

Modern Observational Techniques for Comets

NASA Technical Reports Server (NTRS)

Brandt, J. C. (Editor); Greenberg, J. M. (Editor); Donn, B. (Editor); Rahe, J. (Editor)

1981-01-01

Techniques are discussed in the following areas: astrometry, photometry, infrared observations, radio observations, spectroscopy, imaging of coma and tail, image processing of observation. The determination of the chemical composition and physical structure of comets is highlighted.

The Influence of Information Structure on the Depth of Semantic Processing: How Focus and Pitch Accent Determine the Size of the N400 Effect

ERIC Educational Resources Information Center

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

2011-01-01

To highlight relevant information in dialogues, both wh-question context and pitch accent in answers can be used, such that focused information gains more attention and is processed more elaborately. To evaluate the relative influence of context and pitch accent on the depth of semantic processing, we measured event-related potentials (ERPs) to…

Processing of Archaebacterial Intron-Containing tRNA Gene Transcripts.

DTIC Science & Technology

1987-07-31

1{ 1. Project Goals: A. To determine the mechanism of tRNA intron processing in the halophilic archaebacteria. B. Characterize and compare the...enzyme(s) responsible for the removal of 5’-flanking sequences from halophilic and sulfur-dependent tRNA gene transcripts. C. Examine the structure and...distribution of tRNA introns in the halophilic archaebacteria. 2. Accomplishments: A. Intron processing mechanism We have succeeded in our primary

An evaluation of GTAW-P versus GTA welding of alloy 718

NASA Technical Reports Server (NTRS)

Gamwell, W. R.; Kurgan, C.; Malone, T. W.

1991-01-01

Mechanical properties were evaluated to determine statistically whether the pulsed current gas tungsten arc welding (GTAW-P) process produces welds in alloy 718 with room temperature structural performance equivalent to current Space Shuttle Main Engine (SSME) welds manufactured by the constant current GTAW-P process. Evaluations were conducted on two base metal lots, two filler metal lots, two heat input levels, and two welding processes. The material form was 0.125-inch (3.175-mm) alloy 718 sheet. Prior to welding, sheets were treated to either the ST or STA-1 condition. After welding, panels were left as welded or heat treated to the STA-1 condition, and weld beads were left intact or machined flush. Statistical analyses were performed on yield strength, ultimate tensile strength (UTS), and high cycle fatigue (HCF) properties for all the post welded material conditions. Analyses of variance were performed on the data to determine if there were any significant effects on UTS or HCF life due to variations in base metal, filler metal, heat input level, or welding process. Statistical analyses showed that the GTAW-P process does produce welds with room temperature structural performance equivalent to current SSME welds manufactured by the GTAW process, regardless of prior material condition or post welding condition.

Summary and recommendations. [reduced gravitational effects on materials manufactured in space

NASA Technical Reports Server (NTRS)

1975-01-01

An economic analysis using econometric and cost benefit analysis techniques was performed to determine the feasibility of space processing of certain products. The overall objectives of the analysis were (1) to determine specific products or processes uniquely connected with space manufacturing, (2) to select a specific product or process from each of the areas of semiconductors, metals, and biochemicals, and (3) to determine the overall price/cost structure of each product or process considered. The economic elements of the analysis involved a generalized decision making format for analyzing space manufacturing, a comparative cost study of the selected processes in space vs. earth manufacturing, and a supply and demand study of the economic relationships of one of the manufacturing processes. Space processing concepts were explored. The first involved the use of the shuttle as the factory with all operations performed during individual flights. The second concept involved a permanent unmanned space factory which would be launched separately. The shuttle in this case would be used only for maintenance and refurbishment. Finally, some consideration was given to a permanent manned space factory.

HalX: an open-source LIMS (Laboratory Information Management System) for small- to large-scale laboratories.

PubMed

Prilusky, Jaime; Oueillet, Eric; Ulryck, Nathalie; Pajon, Anne; Bernauer, Julie; Krimm, Isabelle; Quevillon-Cheruel, Sophie; Leulliot, Nicolas; Graille, Marc; Liger, Dominique; Trésaugues, Lionel; Sussman, Joel L; Janin, Joël; van Tilbeurgh, Herman; Poupon, Anne

2005-06-01

Structural genomics aims at the establishment of a universal protein-fold dictionary through systematic structure determination either by NMR or X-ray crystallography. In order to catch up with the explosive amount of protein sequence data, the structural biology laboratories are spurred to increase the speed of the structure-determination process. To achieve this goal, high-throughput robotic approaches are increasingly used in all the steps leading from cloning to data collection and even structure interpretation is becoming more and more automatic. The progress made in these areas has begun to have a significant impact on the more 'classical' structural biology laboratories, dramatically increasing the number of individual experiments. This automation creates the need for efficient data management. Here, a new piece of software, HalX, designed as an 'electronic lab book' that aims at (i) storage and (ii) easy access and use of all experimental data is presented. This should lead to much improved management and tracking of structural genomics experimental data.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Makino, Debora Lika, E-mail: dmakino@biochem.mpg.de; Conti, Elena

The crystallographic steps towards the structure determination of a complete eukaryotic exosome complex bound to RNA are presented. Phasing of this 11-protein subunit complex was carried out via molecular replacement. The RNA exosome is an evolutionarily conserved multi-protein complex involved in the 3′ degradation of a variety of RNA transcripts. In the nucleus, the exosome participates in the maturation of structured RNAs, in the surveillance of pre-mRNAs and in the decay of a variety of noncoding transcripts. In the cytoplasm, the exosome degrades mRNAs in constitutive and regulated turnover pathways. Several structures of subcomplexes of eukaryotic exosomes or related prokaryoticmore » exosome-like complexes are known, but how the complete assembly is organized to fulfil processive RNA degradation has been unclear. An atomic snapshot of a Saccharomyces cerevisiae 420 kDa exosome complex bound to an RNA substrate in the pre-cleavage state of a hydrolytic reaction has been determined. Here, the crystallographic steps towards the structural elucidation, which was carried out by molecular replacement, are presented.« less

A semi-supervised learning approach for RNA secondary structure prediction.

PubMed

Yonemoto, Haruka; Asai, Kiyoshi; Hamada, Michiaki

2015-08-01

RNA secondary structure prediction is a key technology in RNA bioinformatics. Most algorithms for RNA secondary structure prediction use probabilistic models, in which the model parameters are trained with reliable RNA secondary structures. Because of the difficulty of determining RNA secondary structures by experimental procedures, such as NMR or X-ray crystal structural analyses, there are still many RNA sequences that could be useful for training whose secondary structures have not been experimentally determined. In this paper, we introduce a novel semi-supervised learning approach for training parameters in a probabilistic model of RNA secondary structures in which we employ not only RNA sequences with annotated secondary structures but also ones with unknown secondary structures. Our model is based on a hybrid of generative (stochastic context-free grammars) and discriminative models (conditional random fields) that has been successfully applied to natural language processing. Computational experiments indicate that the accuracy of secondary structure prediction is improved by incorporating RNA sequences with unknown secondary structures into training. To our knowledge, this is the first study of a semi-supervised learning approach for RNA secondary structure prediction. This technique will be useful when the number of reliable structures is limited. Copyright © 2015 Elsevier Ltd. All rights reserved.

Quantum many-body effects in x-ray spectra efficiently computed using a basic graph algorithm

NASA Astrophysics Data System (ADS)

Liang, Yufeng; Prendergast, David

2018-05-01

The growing interest in using x-ray spectroscopy for refined materials characterization calls for an accurate electronic-structure theory to interpret the x-ray near-edge fine structure. In this work, we propose an efficient and unified framework to describe all the many-electron processes in a Fermi liquid after a sudden perturbation (such as a core hole). This problem has been visited by the Mahan-Noziéres-De Dominicis (MND) theory, but it is intractable to implement various Feynman diagrams within first-principles calculations. Here, we adopt a nondiagrammatic approach and treat all the many-electron processes in the MND theory on an equal footing. Starting from a recently introduced determinant formalism [Phys. Rev. Lett. 118, 096402 (2017), 10.1103/PhysRevLett.118.096402], we exploit the linear dependence of determinants describing different final states involved in the spectral calculations. An elementary graph algorithm, breadth-first search, can be used to quickly identify the important determinants for shaping the spectrum, which avoids the need to evaluate a great number of vanishingly small terms. This search algorithm is performed over the tree-structure of the many-body expansion, which mimics a path-finding process. We demonstrate that the determinantal approach is computationally inexpensive even for obtaining x-ray spectra of extended systems. Using Kohn-Sham orbitals from two self-consistent fields (ground and core-excited state) as input for constructing the determinants, the calculated x-ray spectra for a number of transition metal oxides are in good agreement with experiments. Many-electron aspects beyond the Bethe-Salpeter equation, as captured by this approach, are also discussed, such as shakeup excitations and many-body wave function overlap considered in Anderson's orthogonality catastrophe.

Comparative studies of industrial grade carbon black powders

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chawla, Komal, E-mail: komalchawla.rs@gmail.com; Chauhan, Alok P. S., E-mail: chauhan.alok@gmail.com, E-mail: alok.chauhan@alumni.stonybrook.edu

Comparative studies of two dissimilar industrial grade Carbon Black (CB) powders (N375 and N405) were conducted. The structure, surface area and particle size are the three important characteristics of CB powder that determine their processability and application as filler in preparing rubber compounds. The powders were characterized for their structure using dibutyl phthalate absorption (DBPA), particle size via laser particle size analyzer and surface area by nitrogen adsorption method. The structural characterization showed that N405 had lower DBPA in comparison to N375, confirming low structure of N405 grade CB powder. It was observed from the particle size analysis that N375more » was coarser than N405 grade CB. The total surface area values were determined by the BET method based on the cross sectional area of the nitrogen molecule. N375, a coarse grade CB powder with high structure, depicted less surface area as compared to N405.« less

Hybrid Molecular Structure of the Giant Protease Tripeptidyl Peptidase II

PubMed Central

Chuang, Crystal K.; Rockel, Beate; Seyit, Gönül; Walian, Peter J.; Schönegge, Anne–Marie; Peters, Jürgen; Zwart, Petrus H.; Baumeister, Wolfgang; Jap, Bing K.

2010-01-01

Tripeptidyl peptidase II (TPP II) is the largest known eukaryotic protease (6MDa). It is believed to act downstream of the 26S proteasome cleaving tripeptides from the N– termini of longer peptides and it is implicated in numerous cellular processes. Here we report the structure of Drosophila TPP II determined by a hybrid approach: The structure of the dimer was solved by x–ray crystallography and docked into the three– dimensional map of the holocomplex obtained by single-particle cryo-electron microscopy. The resulting structure reveals the compartmentalization of the active sites inside a system of chambers and suggests the existence of a molecular ruler determining the size of the cleavage products. Furthermore, the structure suggests a model for activation of TPP II involving the relocation of a flexible loop and a repositioning of the active–site serine, coupling it to holocomplex assembly and active site sequestration. PMID:20676100

A Multiscale Approach to Characterize the Early Aggregation Steps of the Amyloid-Forming Peptide GNNQQNY from the Yeast Prion Sup-35

PubMed Central

Nasica-Labouze, Jessica; Meli, Massimiliano; Derreumaux, Philippe; Colombo, Giorgio; Mousseau, Normand

2011-01-01

The self-organization of peptides into amyloidogenic oligomers is one of the key events for a wide range of molecular and degenerative diseases. Atomic-resolution characterization of the mechanisms responsible for the aggregation process and the resulting structures is thus a necessary step to improve our understanding of the determinants of these pathologies. To address this issue, we combine the accelerated sampling properties of replica exchange molecular dynamics simulations based on the OPEP coarse-grained potential with the atomic resolution description of interactions provided by all-atom MD simulations, and investigate the oligomerization process of the GNNQQNY for three system sizes: 3-mers, 12-mers and 20-mers. Results for our integrated simulations show a rich variety of structural arrangements for aggregates of all sizes. Elongated fibril-like structures can form transiently in the 20-mer case, but they are not stable and easily interconvert in more globular and disordered forms. Our extensive characterization of the intermediate structures and their physico-chemical determinants points to a high degree of polymorphism for the GNNQQNY sequence that can be reflected at the macroscopic scale. Detailed mechanisms and structures that underlie amyloid aggregation are also provided. PMID:21625573

The network organization of protein interactions in the spliceosome is reproduced by the simple rules of food-web models

PubMed Central

Pires, Mathias M.; Cantor, Maurício; Guimarães, Paulo R.; de Aguiar, Marcus A. M.; dos Reis, Sérgio F.; Coltri, Patricia P.

2015-01-01

The network structure of biological systems provides information on the underlying processes shaping their organization and dynamics. Here we examined the structure of the network depicting protein interactions within the spliceosome, the macromolecular complex responsible for splicing in eukaryotic cells. We show the interactions of less connected spliceosome proteins are nested subsets of the connections of the highly connected proteins. At the same time, the network has a modular structure with groups of proteins sharing similar interaction patterns. We then investigated the role of affinity and specificity in shaping the spliceosome network by adapting a probabilistic model originally designed to reproduce food webs. This food-web model was as successful in reproducing the structure of protein interactions as it is in reproducing interactions among species. The good performance of the model suggests affinity and specificity, partially determined by protein size and the timing of association to the complex, may be determining network structure. Moreover, because network models allow building ensembles of realistic networks while encompassing uncertainty they can be useful to examine the dynamics and vulnerability of intracelullar processes. Unraveling the mechanisms organizing the spliceosome interactions is important to characterize the role of individual proteins on splicing catalysis and regulation. PMID:26443080

A Latent Variable Analysis of Working Memory Capacity, Short-Term Memory Capacity, Processing Speed, and General Fluid Intelligence.

ERIC Educational Resources Information Center

Conway, Andrew R. A.; Cowan, Nelsin; Bunting, Michael F.; Therriault, David J.; Minkoff, Scott R. B.

2002-01-01

Studied the interrelationships among general fluid intelligence, short-term memory capacity, working memory capacity, and processing speed in 120 young adults and used structural equation modeling to determine the best predictor of general fluid intelligence. Results suggest that working memory capacity, but not short-term memory capacity or…

Phrase Units as Determinants of Visual Processing in Music Reading

ERIC Educational Resources Information Center

Sloboda, John A.

1977-01-01

Keyboard musicians sight-read passages of music in which the amount of information about the presence of phrase units was systematically varied. Results suggest a clear analogy between the cognition of music and language, in that knowledge of abstract structure is of importance in the organization of immediate visual processing of text. (Editor/RK)

The Difficulties of Female Primary School Administrators in the Administration Process and Solution Suggestions

ERIC Educational Resources Information Center

Kosar, Didem; Altunay, Esen; Yalçinkaya, Mu¨nevver

2014-01-01

The aim of this research is to determine the administration experiences of female administrators, find out the troubles they have had during their administration process, and suggest some solutions according to these experiences. The qualitative method was used in this research and data was collected via the semi-structured interview form…

Applying Schema Theory to Mass Media Information Processing: Moving toward a Formal Model.

ERIC Educational Resources Information Center

Wicks, Robert H.

Schema theory may be significant in determining if and how news audiences process information. For any given news topic, people have from none to many schemata (cognitive structures that represent organized knowledge about a given concept or type of stimulus abstracted from prior experience) upon which to draw. Models of how schemata are used…

Photogrammetry Toolbox Reference Manual

NASA Technical Reports Server (NTRS)

Liu, Tianshu; Burner, Alpheus W.

2014-01-01

Specialized photogrammetric and image processing MATLAB functions useful for wind tunnel and other ground-based testing of aerospace structures are described. These functions include single view and multi-view photogrammetric solutions, basic image processing to determine image coordinates, 2D and 3D coordinate transformations and least squares solutions, spatial and radiometric camera calibration, epipolar relations, and various supporting utility functions.

Modernizing the Management of the Educational System. The Fundamentals of Educational Planning: Lecture-Discussion Series No. 35.

ERIC Educational Resources Information Center

Lyons, Raymond F.

One of the main inadequacies in educational management is that planning is not firmly integrated within administration. Five basic processes may be distinguished in administration. The first is planning, or determining what shall be done. The second element of the administrative process is organizing, or defining the administrative structures and…

Ethical considerations for a better collaboration between architects and structural engineers: design of buildings with reinforced concrete frame systems in earthquake zones.

PubMed

Hurol, Yonca

2014-06-01

Architects design building structures, although structural design is the profession of structural engineers. Thus, it is better for architects and structural engineers to collaborate starting from the initial phases of the architectural design. However, this is not very common because of the contradictory design processes and value systems held within the two professions. This article provides a platform upon which architects and structural engineers can resolve the value conflicts between them by analysing phases of the structural design of reinforced concrete frame systems in architecture, the criteria of the structural design for each phase and determining the conflicting values for each criterion. The results shown in the article demonstrate that the architectural design of structures is a complex process, which is based on contradictory values and value systems. Finally, the article suggests to architects and structural engineers to use Value Sensitive Design and to choose an appropriate team leader in order to resolve the unethical conflict between them and to avoid any unreasonable decision making.

Understanding the structure of chocolate

NASA Astrophysics Data System (ADS)

Schenk, H.; Peschar, R.

2004-10-01

Crystallization of cocoa-butter in the β phase from the melt under static conditions is only possible using the memory effect of cocoa-butter. Under all other conditions polymorphs with lower melting temperatures develop, whereas the β phase is the preferred one in chocolate. SAXS experiments proved 1,3-distearoyl-2-oleoylglycerol seeds with triple chain-length packing initiate the β-crystallization. Models for the different phases may be based on the crystal structure determinations of triacylglycerols. A new, patented, way of chocolate making is in development in which the traditional tempering process is replaced by another pre-crystallization process. The process is based on the use of seed crystals in the liquid phase and driven by a feedback system.

Structural Basis for Antigenic Peptide Recognition and Processing by Endoplasmic Reticulum (ER) Aminopeptidase 2.

PubMed

Mpakali, Anastasia; Giastas, Petros; Mathioudakis, Nikolas; Mavridis, Irene M; Saridakis, Emmanuel; Stratikos, Efstratios

2015-10-23

Endoplasmic reticulum (ER) aminopeptidases process antigenic peptide precursors to generate epitopes for presentation by MHC class I molecules and help shape the antigenic peptide repertoire and cytotoxic T-cell responses. To perform this function, ER aminopeptidases have to recognize and process a vast variety of peptide sequences. To understand how these enzymes recognize substrates, we determined crystal structures of ER aminopeptidase 2 (ERAP2) in complex with a substrate analogue and a peptidic product to 2.5 and 2.7 Å, respectively, and compared them to the apo-form structure determined to 3.0 Å. The peptides were found within the internal cavity of the enzyme with no direct access to the outside solvent. The substrate analogue extends away from the catalytic center toward the distal end of the internal cavity, making interactions with several shallow pockets along the path. A similar configuration was evident for the peptidic product, although decreasing electron density toward its C terminus indicated progressive disorder. Enzymatic analysis confirmed that visualized interactions can either positively or negatively impact in vitro trimming rates. Opportunistic side-chain interactions and lack of deep specificity pockets support a limited-selectivity model for antigenic peptide processing by ERAP2. In contrast to proposed models for the homologous ERAP1, no specific recognition of the peptide C terminus by ERAP2 was evident, consistent with functional differences in length selection and self-activation between these two enzymes. Our results suggest that ERAP2 selects substrates by sequestering them in its internal cavity and allowing opportunistic interactions to determine trimming rates, thus combining substrate permissiveness with sequence bias. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Intra-tidal variability of the vertical current structure in the western Dutch Wadden Sea

NASA Astrophysics Data System (ADS)

de Vries, Jurre; Ridderinkhof, Herman; van Aken, Hendrik

2014-05-01

Long-term velocity measurements are presented which were collected during three different seasons at one single location in an estuarine basin of the western Dutch Wadden Sea. These data are used to investigate the processes that determine the variability of the vertical current structure in the western Dutch Wadden Sea, in combination with simplified model runs using the one-dimensional water column model GETM (http://www.getm.eu/). Jay and Musiak [1996] were the first to suggest that intra-tidal variations in the vertical current might be important in determining the residual circulation patterns. More research [e.g. Stacey et al., 2001; Burchard and Hetland, 2010] has supported this hypothesis. Recently, lateral processes have been shown to influence the vertical current structure of alongstream velocity and hence the residual circulation [e.g. Lerczak and Geyer, 2004; Burchard and Schuttelaars, 2012]. Therefore to better understand the tidal dynamics in the western Dutch Wadden Sea, it is crucial to understand the processes that determine the vertical current structure. The two main findings of this study are that the complex bathymetry at the study site seems to produce an intra-tidal asymmetry in near-bed velocities and secondly that cross-stream processes strongly modify the current structure during late flood. Near-bed velocity and the bed roughness are greater during ebb than during flood. The GETM simulations suggest that vertical mixing during ebb is sufficient to destroy vertical stratification generated by classical tidal straining. The cross-stream current during late flood generate vertical stratification and drive an early reversal of the flood current near the surface. Therefore, it is hypothesized that this processes might increase the residual estuarine circulation at the study site. References - Burchard, H., Hetland, R.D. (2010), Quantifying the contributions of tidal straining and gravitational circulation to residual circulation in periodically stratified tidal estuaries, Journal of Physical Oceanography, 40(6), 1243-1262 - Burchard, H., Schuttelaars, H.M. (2012), Analysis of tidal straining as driver for estuarine circulation in well-mixed estuaries, Journal of Physical Oceanography, 42(2), 261-271 - Jay, D.A., Musiak, J.D. (1996), Internal tidal asymmetry in channel flows' origins and consequences, Coastal and Estuarine Studies, 50, 211-249 - Stacey, M.T., Burau J.R., Monismith, S.G. (2001), Creation of residual flows in a partially stratified estuary, Journal of Physical Oceanography, 34, 1410-1428

SPARX, a new environment for Cryo-EM image processing.

PubMed

Hohn, Michael; Tang, Grant; Goodyear, Grant; Baldwin, P R; Huang, Zhong; Penczek, Pawel A; Yang, Chao; Glaeser, Robert M; Adams, Paul D; Ludtke, Steven J

2007-01-01

SPARX (single particle analysis for resolution extension) is a new image processing environment with a particular emphasis on transmission electron microscopy (TEM) structure determination. It includes a graphical user interface that provides a complete graphical programming environment with a novel data/process-flow infrastructure, an extensive library of Python scripts that perform specific TEM-related computational tasks, and a core library of fundamental C++ image processing functions. In addition, SPARX relies on the EMAN2 library and cctbx, the open-source computational crystallography library from PHENIX. The design of the system is such that future inclusion of other image processing libraries is a straightforward task. The SPARX infrastructure intelligently handles retention of intermediate values, even those inside programming structures such as loops and function calls. SPARX and all dependencies are free for academic use and available with complete source.

Computer system for definition of the quantitative geometry of musculature from CT images.

PubMed

Daniel, Matej; Iglic, Ales; Kralj-Iglic, Veronika; Konvicková, Svatava

2005-02-01

The computer system for quantitative determination of musculoskeletal geometry from computer tomography (CT) images has been developed. The computer system processes series of CT images to obtain three-dimensional (3D) model of bony structures where the effective muscle fibres can be interactively defined. Presented computer system has flexible modular structure and is suitable also for educational purposes.

Lightweight Concrete Produced Using a Two-Stage Casting Process

PubMed Central

Yoon, Jin Young; Kim, Jae Hong; Hwang, Yoon Yi; Shin, Dong Kyu

2015-01-01

The type of lightweight aggregate and its volume fraction in a mix determine the density of lightweight concrete. Minimizing the density obviously requires a higher volume fraction, but this usually causes aggregates segregation in a conventional mixing process. This paper proposes a two-stage casting process to produce a lightweight concrete. This process involves placing lightweight aggregates in a frame and then filling in the remaining interstitial voids with cementitious grout. The casting process results in the lowest density of lightweight concrete, which consequently has low compressive strength. The irregularly shaped aggregates compensate for the weak point in terms of strength while the round-shape aggregates provide a strength of 20 MPa. Therefore, the proposed casting process can be applied for manufacturing non-structural elements and structural composites requiring a very low density and a strength of at most 20 MPa. PMID:28788007

Evaluating the solution from MrBUMP and BALBES

PubMed Central

Keegan, Ronan M.; Long, Fei; Fazio, Vincent J.; Winn, Martyn D.; Murshudov, Garib N.; Vagin, Alexei A.

2011-01-01

Molecular replacement is one of the key methods used to solve the problem of determining the phases of structure factors in protein structure solution from X-ray image diffraction data. Its success rate has been steadily improving with the development of improved software methods and the increasing number of structures available in the PDB for use as search models. Despite this, in cases where there is low sequence identity between the target-structure sequence and that of its set of possible homologues it can be a difficult and time-consuming chore to isolate and prepare the best search model for molecular replacement. MrBUMP and BALBES are two recent developments from CCP4 that have been designed to automate and speed up the process of determining and preparing the best search models and putting them through molecular replacement. Their intention is to provide the user with a broad set of results using many search models and to highlight the best of these for further processing. An overview of both programs is presented along with a description of how best to use them, citing case studies and the results of large-scale testing of the software. PMID:21460449

Two Growth Modes of Graphitic Carbon Nanofibers with Herring-Bone Structure

DOE Office of Scientific and Technical Information (OSTI.GOV)

Merkulov, Igor A; Melechko, Anatoli Vasilievich; Wells, Jack C

2005-01-01

A simple mathematical model of the carbon nanofiber catalytic growth process is presented. Two major types of the fiber-catalyst interface shapes have been identified and described having qualitatively different structure in the center of a nanofiber. Presently, we discuss that the appearance of the irregular structure in the nanofiber central area is a result of curved-interface-growth kinematics. We suggest the method to determine the phenomenological parameters of the developed model from experimental data.

Two growth modes of graphitic carbon nanofibers with herring-bone structure

NASA Astrophysics Data System (ADS)

Merkulov, I. A.; Meleshko, A. V.; Wells, J. C.; Cui, H.; Merkulov, V. I.; Simpson, M. L.; Lowndes, D. H.

2005-07-01

A simple mathematical model of the carbon nanofiber catalytic growth process is presented. Two major types of the fiber-catalyst interface shapes have been identified and described having qualitatively different structure in the center of a nanofiber. Presently, we discuss that the appearance of the irregular structure in the nanofiber central area is a result of curved-interface-growth kinematics. We suggest the method to determine the phenomenological parameters of the developed model from experimental data.

Life Prediction/Reliability Data of Glass-Ceramic Material Determined for Radome Applications

NASA Technical Reports Server (NTRS)

Choi, Sung R.; Gyekenyesi, John P.

2002-01-01

Brittle materials, ceramics, are candidate materials for a variety of structural applications for a wide range of temperatures. However, the process of slow crack growth, occurring in any loading configuration, limits the service life of structural components. Therefore, it is important to accurately determine the slow crack growth parameters required for component life prediction using an appropriate test methodology. This test methodology also should be useful in determining the influence of component processing and composition variables on the slow crack growth behavior of newly developed or existing materials, thereby allowing the component processing and composition to be tailored and optimized to specific needs. Through the American Society for Testing and Materials (ASTM), the authors recently developed two test methods to determine the life prediction parameters of ceramics. The two test standards, ASTM 1368 for room temperature and ASTM C 1465 for elevated temperatures, were published in the 2001 Annual Book of ASTM Standards, Vol. 15.01. Briefly, the test method employs constant stress-rate (or dynamic fatigue) testing to determine flexural strengths as a function of the applied stress rate. The merit of this test method lies in its simplicity: strengths are measured in a routine manner in flexure at four or more applied stress rates with an appropriate number of test specimens at each applied stress rate. The slow crack growth parameters necessary for life prediction are then determined from a simple relationship between the strength and the applied stress rate. Extensive life prediction testing was conducted at the NASA Glenn Research Center using the developed ASTM C 1368 test method to determine the life prediction parameters of a glass-ceramic material that the Navy will use for radome applications.

Individual movement behavior, matrix heterogeneity, and the dynamics of spatially structured populations.

PubMed

Revilla, Eloy; Wiegand, Thorsten

2008-12-09

The dynamics of spatially structured populations is characterized by within- and between-patch processes. The available theory describes the latter with simple distance-dependent functions that depend on landscape properties such as interpatch distance or patch size. Despite its potential role, we lack a good mechanistic understanding of how the movement of individuals between patches affects the dynamics of these populations. We used the theoretical framework provided by movement ecology to make a direct representation of the processes determining how individuals connect local populations in a spatially structured population of Iberian lynx. Interpatch processes depended on the heterogeneity of the matrix where patches are embedded and the parameters defining individual movement behavior. They were also very sensitive to the dynamic demographic variables limiting the time moving, the within-patch dynamics of available settlement sites (both spatiotemporally heterogeneous) and the response of individuals to the perceived risk while moving. These context-dependent dynamic factors are an inherent part of the movement process, producing connectivities and dispersal kernels whose variability is affected by other demographic processes. Mechanistic representations of interpatch movements, such as the one provided by the movement-ecology framework, permit the dynamic interaction of birth-death processes and individual movement behavior, thus improving our understanding of stochastic spatially structured populations.

Microstructure evolution and tensile properties of Zr-2.5wt%Nb pressure tubes processed from billets with different microstructures

NASA Astrophysics Data System (ADS)

Kapoor, K.; Saratchandran, N.; Muralidharan, K.

1999-02-01

Starting with identical ingots, billets having different microstructures were obtained by three different processing methods for fabrication of Zr-2.5wt%Nb pressure tubes. The billets were further processed by hot extrusion and cold Pilger tube reducing to the finished product. Microstructural characterization was done at each stage of processing. The effects of the initial billet microstructure on the intermediate and final microstructure and mechanical property results were determined. It was found that the structure at each stage and the final mechanical properties depend strongly on the initial billet microstructure. The structure at the final stage consists of elongated alpha zirconium grains with a network of metastable beta zirconium phase. Some of this metastable phase transforms into stable beta niobium during thermomechanical processing. Billets with quenched structure resulted in less beta niobium at the final stage. The air cooled billets resulted in a large amount of beta niobium. The tensile properties, especially the percentage elongation, were found to vary for the different methods. Higher percentage elongation was observed for billets having quenched structure. Extrusion and forging did not produce any characteristic differences in the properties. The results were used to select a process flow sheet which yields the desired mechanical properties with suitable microstructure in the final product.

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

NASA Technical Reports Server (NTRS)

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

2003-01-01

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

Preparation of mesoporous carbon nitride structure by the dealloying of Ni/a-CN nanocomposite films

NASA Astrophysics Data System (ADS)

Zhou, Han; Shen, Yongqing; Huang, Jie; Liao, Bin; Wu, Xianying; Zhang, Xu

2018-05-01

The preparation of mesoporous carbon nitride (p-CN) structure by the selective dealloying process of Ni/a-CN nanocomposite films is investigated. The composition and structure of the Ni/a-CN nanocomposite films and porous carbon nitride (p-CN) films are determined by scan electron microscopy (SEM), transmission electron microscopy (TEM), X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS) and Raman spectroscopy. Phase separated structure including nickel carbide phase and the surrounding amorphous carbon nitride (a-CN) matrix are detected for the as-deposited films. Though the bulk diffusion is introduced in the film during the annealing process, the grain sizes for the post-annealed films are around 10 nm and change little comparing with the ones of the as-deposited films, which is associated with the thermostability of the CN surrounding in the film. The p-CN skeleton with its pore size around 12.5 nm is formed by etching the post-annealed films, indicative of the stability of the phase separated structure during the annealing process.

Ordering Traces Logically to Identify Lateness in Message Passing Programs

DOE PAGES

Isaacs, Katherine E.; Gamblin, Todd; Bhatele, Abhinav; ...

2015-03-30

Event traces are valuable for understanding the behavior of parallel programs. However, automatically analyzing a large parallel trace is difficult, especially without a specific objective. We aid this endeavor by extracting a trace's logical structure, an ordering of trace events derived from happened-before relationships, while taking into account developer intent. Using this structure, we can calculate an operation's delay relative to its peers on other processes. The logical structure also serves as a platform for comparing and clustering processes as well as highlighting communication patterns in a trace visualization. We present an algorithm for determining this idealized logical structure frommore » traces of message passing programs, and we develop metrics to quantify delays and differences among processes. We implement our techniques in Ravel, a parallel trace visualization tool that displays both logical and physical timelines. Rather than showing the duration of each operation, we display where delays begin and end, and how they propagate. As a result, we apply our approach to the traces of several message passing applications, demonstrating the accuracy of our extracted structure and its utility in analyzing these codes.« less

Ground vibration test results for Drones for Aerodynamic and Structural Testing (DAST)/Aeroelastic Research Wing (ARW-1R) aircraft

NASA Technical Reports Server (NTRS)

Cox, T. H.; Gilyard, G. B.

1986-01-01

The drones for aerodynamic and structural testing (DAST) project was designed to control flutter actively at high subsonic speeds. Accurate knowledge of the structural model was critical for the successful design of the control system. A ground vibration test was conducted on the DAST vehicle to determine the structural model characteristics. This report presents and discusses the vibration and test equipment, the test setup and procedures, and the antisymmetric and symmetric mode shape results. The modal characteristics were subsequently used to update the structural model employed in the control law design process.

Ab initio phasing by molecular averaging in real space with new criteria: application to structure determination of a betanodavirus.

PubMed

Yoshimura, Masato; Chen, Nai Chi; Guan, Hong Hsiang; Chuankhayan, Phimonphan; Lin, Chien Chih; Nakagawa, Atsushi; Chen, Chun Jung

2016-07-01

Molecular averaging, including noncrystallographic symmetry (NCS) averaging, is a powerful method for ab initio phase determination and phase improvement. Applications of the cross-crystal averaging (CCA) method have been shown to be effective for phase improvement after initial phasing by molecular replacement, isomorphous replacement, anomalous dispersion or combinations of these methods. Here, a two-step process for phase determination in the X-ray structural analysis of a new coat protein from a betanodavirus, Grouper nervous necrosis virus, is described in detail. The first step is ab initio structure determination of the T = 3 icosahedral virus-like particle using NCS averaging (NCSA). The second step involves structure determination of the protrusion domain of the viral molecule using cross-crystal averaging. In this method, molecular averaging and solvent flattening constrain the electron density in real space. To quantify these constraints, a new, simple and general indicator, free fraction (ff), is introduced, where ff is defined as the ratio of the volume of the electron density that is freely changed to the total volume of the crystal unit cell. This indicator is useful and effective to evaluate the strengths of both NCSA and CCA. Under the condition that a mask (envelope) covers the target molecule well, an ff value of less than 0.1, as a new rule of thumb, gives sufficient phasing power for the successful construction of new structures.

Prototyping of Dental Structures Using Laser Milling

NASA Astrophysics Data System (ADS)

Andreev, A. O.; Kosenko, M. S.; Petrovskiy, V. N.; Mironov, V. D.

2016-02-01

The results of experimental studies of the effect of an ytterbium fiber laser radiation parameters on processing efficiency and quality of ZrO2 ceramics widely used in stomatology are presented. Laser operating conditions with optimum characteristics for obtaining high quality final surfaces and rapid material removal of dental structures are determined. The ability of forming thin-walled ceramic structures by laser milling technology (a minimum wall thickness of 50 μm) is demonstrated. The examples of three-dimensional dental structures created in computer 3D-models of human teeth using laser milling are shown.

Microscopic Evaluation of Friction Plug Welds- Correlation to a Processing Analysis

NASA Technical Reports Server (NTRS)

Rabenberg, Ellen M.; Chen, Poshou; Gorti, Sridhar

2017-01-01

Recently an analysis of dynamic forge load data from the friction plug weld (FPW) process and the corresponding tensile test results showed that good plug welds fit well within an analytically determined processing parameter box. There were, however, some outliers that compromised the predictions. Here the microstructure of the plug weld material is presented in view of the load analysis with the intent of further understanding the FPW process and how it is affected by the grain structure and subsequent mechanical properties.

ASSET: Analysis of Sequences of Synchronous Events in Massively Parallel Spike Trains

PubMed Central

Canova, Carlos; Denker, Michael; Gerstein, George; Helias, Moritz

2016-01-01

With the ability to observe the activity from large numbers of neurons simultaneously using modern recording technologies, the chance to identify sub-networks involved in coordinated processing increases. Sequences of synchronous spike events (SSEs) constitute one type of such coordinated spiking that propagates activity in a temporally precise manner. The synfire chain was proposed as one potential model for such network processing. Previous work introduced a method for visualization of SSEs in massively parallel spike trains, based on an intersection matrix that contains in each entry the degree of overlap of active neurons in two corresponding time bins. Repeated SSEs are reflected in the matrix as diagonal structures of high overlap values. The method as such, however, leaves the task of identifying these diagonal structures to visual inspection rather than to a quantitative analysis. Here we present ASSET (Analysis of Sequences of Synchronous EvenTs), an improved, fully automated method which determines diagonal structures in the intersection matrix by a robust mathematical procedure. The method consists of a sequence of steps that i) assess which entries in the matrix potentially belong to a diagonal structure, ii) cluster these entries into individual diagonal structures and iii) determine the neurons composing the associated SSEs. We employ parallel point processes generated by stochastic simulations as test data to demonstrate the performance of the method under a wide range of realistic scenarios, including different types of non-stationarity of the spiking activity and different correlation structures. Finally, the ability of the method to discover SSEs is demonstrated on complex data from large network simulations with embedded synfire chains. Thus, ASSET represents an effective and efficient tool to analyze massively parallel spike data for temporal sequences of synchronous activity. PMID:27420734

Hygrothermal effects on the mechanical behaviour of graphite fibre-reinforced epoxy laminates beyond initial failure

NASA Technical Reports Server (NTRS)

Ishai, O.; Garg, A.; Nelson, H. G.

1986-01-01

The critical load levels and associated cracking beyond which a multidirectional laminate can be considered as structurally failed has been determined by loading graphite fiber-reinforced epoxy laminates to different strain levels up to ultimate failure. Transverse matrix cracking was monitored by acoustic and optical methods. The residual stiffness and strength parallel and perpendicular to the cracks were determined and related to the environmental/loading history. Within the range of experimental conditions studied, it is concluded that the transverse cracking process does not have a crucial effect on the structural performance of multidirectional composite laminates.

Screening programme to select a resin for Gravity Probe-B composites

NASA Technical Reports Server (NTRS)

Will, E. T.

1992-01-01

The Gravity Probe-B (GP-B) program undertook a screening program to select a possible replacement resin for the E-787 resin currently used in composite neck tubes and support struts. The goal was to find a resin with good cryogenic and structural properties, low-helium permeation and an easily repeatable fabrication process. Cycom 92, SCI REZ 081 and RS-3 were selected for comparison with E-787. Identical composite tubes made from each resin and gamma-alumina fiber (85 percent Al2O3, 15 percent SiO2) were evaluated for cryogenic and structural performance and for processability. Cryogenic performance was evaluated by measuring low-temperature permeation and leaks to determine cryogenic strain behavior. Structural performance was evaluated by comparing the resin-dominated shear strength of the composites. Processability was evaluated from fabrication comments and GP-B's own experience. SCI REZ 081 was selected as the best overall resin with superior strength and cryogenic performance and consistent processability.

The Stress-Strain State of Recent Structures in the Northeastern Sector of the Russian Arctic Region

NASA Astrophysics Data System (ADS)

Imaeva, L. P.; Imaev, V. S.; Mel'nikova, V. I.

2018-03-01

Complex research to determine the stress-strain state of the Earth's crust and the types of seismotectonic destruction for the northeastern sector of the Russian Arctic was conducted. The principles of regional ranking of neotectonic structures were developed according to the activity of geodynamic processes, and argumentation for their class differentiation is presented. The structural-tectonic position, the parameters of the deep structure, the system of active faults, and the tectonic stress fields, calculated on the basis of both tectonophysical analysis of discontinuous and folded late Cenozoic deformations and seismological data, were analyzed. This complex of investigations made it possible to determine the directions of the main axes of deformations of the stress-strain state of the Earth's crust and to reveal the regularity in the change of tectonic regimes.

The young person’s guide to the PDB*

PubMed Central

Minor, Wladek; Dauter, Zbigniew; Jaskolski, Mariusz

2017-01-01

The Protein Data Bank (PDB), created in 1971 when merely seven protein crystal structures were known, today holds over 120,000 experimentally-determined three-dimensional models of macromolecules, including gigantic structures comprised of hundreds of thousands of atoms, such as ribosomes and viruses. Most of the deposits come from X-ray crystallography experiments, with important contributions also made by NMR spectroscopy and, recently, by the fast growing Cryo-Electron Microscopy. Although the determination of a macromolecular crystal structure is now facilitated by advanced experimental tools and by sophisticated software, it is still a highly complicated research process requiring specialized training, skill, experience and a bit of luck. Understanding the plethora of structural information provided by the PDB requires that its users (consumers) have at least a rudimentary initiation. This is the purpose of this educational overview. PMID:28132477

Development of a Novel Method for Determination of Residual Stresses in a Friction Stir Weld

NASA Technical Reports Server (NTRS)

Reynolds, Anthony P.

2001-01-01

Material constitutive properties, which describe the mechanical behavior of a material under loading, are vital to the design and implementation of engineering materials. For homogeneous materials, the standard process for determining these properties is the tensile test, which is used to measure the material stress-strain response. However, a majority of the applications for engineering materials involve the use of heterogeneous materials and structures (i.e. alloys, welded components) that exhibit heterogeneity on a global or local level. Regardless of the scale of heterogeneity, the overall response of the material or structure is dependent on the response of each of the constituents. Therefore, in order to produce materials and structures that perform in the best possible manner, the properties of the constituents that make up the heterogeneous material must be thoroughly examined. When materials exhibit heterogeneity on a local level, such as in alloys or particle/matrix composites, they are often treated as statistically homogenous and the resulting 'effective' properties may be determined through homogenization techniques. In the case of globally heterogeneous materials, such as weldments, the standard tensile test provides the global response but no information on what is Occurring locally within the different constituents. This information is necessary to improve the material processing as well as the end product.

Research on the middle-of-receiver-spread assumption of the MASW method

USGS Publications Warehouse

Luo, Y.; Xia, J.; Liu, J.; Xu, Y.; Liu, Q.

2009-01-01

The multichannel analysis of surface wave (MASW) method has been effectively used to determine near-surface shear- (S-) wave velocity. Estimating the S-wave velocity profile from Rayleigh-wave measurements is straightforward. A three-step process is required to obtain S-wave velocity profiles: acquisition of a multiple number of multichannel records along a linear survey line by use of the roll-along mode, extraction of dispersion curves of Rayleigh waves, and inversion of dispersion curves for an S-wave velocity profile for each shot gather. A pseudo-2D S-wave velocity section can be generated by aligning 1D S-wave velocity models. In this process, it is very important to understand where the inverted 1D S-wave velocity profile should be located: the midpoint of each spread (a middle-of-receiver-spread assumption) or somewhere between the source and the last receiver. In other words, the extracted dispersion curve is determined by the geophysical structure within the geophone spread or strongly affected by the source geophysical structure. In this paper, dispersion curves of synthetic datasets and a real-world example are calculated by fixing the receiver spread and changing the source location. Results demonstrate that the dispersion curves are mainly determined by structures within a receiver spread. ?? 2008 Elsevier Ltd. All rights reserved.

Processing of Archaebacterial Intron-Containing tRNA Gene Transcripts

DTIC Science & Technology

1988-07-27

number) The overall goal of this project is to develop an understanding of tRNA gene structure and transcript processing in the halophilic Archaebacteria...containing precursor tRNAs in the halophilic Archaebecteria suggest that tRNATr p may be the only interrupted tR?4A gene in these organisms...1 August 1986 RESEARCH OBJECTIVE: To determine the mechanism of tRNA intron processing in the halophilic archaebacteria; characterize the enzyme

Kinetics of Structural Changes on GaSb(001) Singular and Vicinal Surfaces During the UHV Annealing

NASA Astrophysics Data System (ADS)

Vasev, A. V.; Putyato, M. A.; Preobrazhenskii, V. V.; Bakarov, A. K.; Toropov, A. I.

2018-05-01

The dynamics of processes of antimony desorption was investigated on the singular and vicinal GaSb(001) surface by RHEED method. The role of the terraces edges was determined during antimony evaporation in Langmuir desorption mode. It is shown that the structural transition (2x5) -> (1x3) is a complex of two transitions - order -> disorder and disorder -> order. The influence of the degree of surface miscut from the singular face on the dimension of the transition (2x5) -> DO was studied. The activation energies of structural transitions ex(2x5) -> (2x5), (2x5) -> DO and DO -> (1x3) on singular and vicinal faces GaSb(001) were determined.

Physiological Implications of Myocardial Scar Structure

PubMed Central

Richardson, WJ; Clarke, SA; Quinn, TA; Holmes, JW

2016-01-01

Once myocardium dies during a heart attack, it is replaced by scar tissue over the course of several weeks. The size, location, composition, structure and mechanical properties of the healing scar are all critical determinants of the fate of patients who survive the initial infarction. While the central importance of scar structure in determining pump function and remodeling has long been recognized, it has proven remarkably difficult to design therapies that improve heart function or limit remodeling by modifying scar structure. Many exciting new therapies are under development, but predicting their long-term effects requires a detailed understanding of how infarct scar forms, how its properties impact left ventricular function and remodeling, and how changes in scar structure and properties feed back to affect not only heart mechanics but also electrical conduction, reflex hemodynamic compensations, and the ongoing process of scar formation itself. In this article, we outline the scar formation process following an MI, discuss interpretation of standard measures of heart function in the setting of a healing infarct, then present implications of infarct scar geometry and structure for both mechanical and electrical function of the heart and summarize experiences to date with therapeutic interventions that aim to modify scar geometry and structure. One important conclusion that emerges from the studies reviewed here is that computational modeling is an essential tool for integrating the wealth of information required to understand this complex system and predict the impact of novel therapies on scar healing, heart function, and remodeling following myocardial infarction. PMID:26426470

Research on criticality analysis method of CNC machine tools components under fault rate correlation

NASA Astrophysics Data System (ADS)

Gui-xiang, Shen; Xian-zhuo, Zhao; Zhang, Ying-zhi; Chen-yu, Han

2018-02-01

In order to determine the key components of CNC machine tools under fault rate correlation, a system component criticality analysis method is proposed. Based on the fault mechanism analysis, the component fault relation is determined, and the adjacency matrix is introduced to describe it. Then, the fault structure relation is hierarchical by using the interpretive structure model (ISM). Assuming that the impact of the fault obeys the Markov process, the fault association matrix is described and transformed, and the Pagerank algorithm is used to determine the relative influence values, combined component fault rate under time correlation can obtain comprehensive fault rate. Based on the fault mode frequency and fault influence, the criticality of the components under the fault rate correlation is determined, and the key components are determined to provide the correct basis for equationting the reliability assurance measures. Finally, taking machining centers as an example, the effectiveness of the method is verified.

Chromatin Structure and Replication Origins: Determinants Of Chromosome Replication And Nuclear Organization

PubMed Central

Smith, Owen K.; Aladjem, Mirit I.

2014-01-01

The DNA replication program is, in part, determined by the epigenetic landscape that governs local chromosome architecture and directs chromosome duplication. Replication must coordinate with other biochemical processes occurring concomitantly on chromatin, such as transcription and remodeling, to insure accurate duplication of both genetic and epigenetic features and to preserve genomic stability. The importance of genome architecture and chromatin looping in coordinating cellular processes on chromatin is illustrated by two recent sets of discoveries. First, chromatin-associated proteins that are not part of the core replication machinery were shown to affect the timing of DNA replication. These chromatin-associated proteins could be working in concert, or perhaps in competition, with the transcriptional machinery and with chromatin modifiers to determine the spatial and temporal organization of replication initiation events. Second, epigenetic interactions are mediated by DNA sequences that determine chromosomal replication. In this review we summarize recent findings and current models linking spatial and temporal regulation of the replication program with epigenetic signaling. We discuss these issues in the context of the genome’s three-dimensional structure with an emphasis on events occurring during the initiation of DNA replication. PMID:24905010

Analytical Models of Exoplanetary Atmospheres. V. Non-gray Thermal Structure with Coherent Scattering

NASA Astrophysics Data System (ADS)

Mohandas, Gopakumar; Pessah, Martin E.; Heng, Kevin

2018-05-01

We apply the picket fence treatment to model the effects brought about by spectral lines on the thermal structure of irradiated atmospheres. The lines may be due to pure absorption processes, pure coherent scattering processes, or some combination of absorption and scattering. If the lines arise as a pure absorption process, the surface layers of the atmosphere are cooler, whereas this surface cooling is completely absent if the lines are due to pure coherent isotropic scattering. The lines also lead to a warming of the deeper atmosphere. The warming of the deeper layers is, however, independent of the nature of line formation. Accounting for coherent isotropic scattering in the shortwave and longwave continuum results in anti-greenhouse cooling and greenhouse warming on an atmosphere-wide scale. The effects of coherent isotropic scattering in the line and continuum operate in tandem to determine the resulting thermal structure of the irradiated atmosphere.

Structure formation in pH-sensitive hydrogels composed of sodium caseinate and N,O-carboxymethyl chitosan.

PubMed

Wei, Yanxia; Xie, Rui; Lin, Yanbin; Xu, Yunfei; Wang, Fengxia; Liang, Wanfu; Zhang, Ji

2016-08-01

The pH-sensitive hydrogels composed of sodium caseinate (SC) and N,O-carboxymethyl chitosan (NOCC) were prepared and a new method to characterize the gelation process was presented in this work. Reological tests suggested that RSC/NOCC=3/7 (the weight ratio of SC and NOCC) was the best ratio of hydrogel. The well-developed three-dimensional network structures in the hydrogel were confirmed by AFM. Two structural parameters, tIS and tCS, denoted as the initial and critical structure formation time, respectively, were used to provide an exact determination of the start of structure formation and description of gelation process. The gelation process strongly depended on temperature changes, a high temperature resulted in an early start of gelation. The non-kinetic model suggested the higher activation energy in the higher temperatures was disadvantageous to structure formation, and vice versa. Due to the smart gel reported here was very stable at room temperature, we believed that the gel is required for applications in drug delivery or could be exploited in the development of potential application as molecular switches in the future. Copyright © 2016 Elsevier B.V. All rights reserved.

Structural and functional diversity in Listeria cell wall teichoic acids.

PubMed

Shen, Yang; Boulos, Samy; Sumrall, Eric; Gerber, Benjamin; Julian-Rodero, Alicia; Eugster, Marcel R; Fieseler, Lars; Nyström, Laura; Ebert, Marc-Olivier; Loessner, Martin J

2017-10-27

Wall teichoic acids (WTAs) are the most abundant glycopolymers found on the cell wall of many Gram-positive bacteria, whose diverse surface structures play key roles in multiple biological processes. Despite recent technological advances in glycan analysis, structural elucidation of WTAs remains challenging due to their complex nature. Here, we employed a combination of ultra-performance liquid chromatography-coupled electrospray ionization tandem-MS/MS and NMR to determine the structural complexity of WTAs from Listeria species. We unveiled more than 10 different types of WTA polymers that vary in their linkage and repeating units. Disparity in GlcNAc to ribitol connectivity, as well as variable O -acetylation and glycosylation of GlcNAc contribute to the structural diversity of WTAs. Notably, SPR analysis indicated that constitution of WTA determines the recognition by bacteriophage endolysins. Collectively, these findings provide detailed insight into Listeria cell wall-associated carbohydrates, and will guide further studies on the structure-function relationship of WTAs. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

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

PubMed

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

2011-06-15

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

Use of a structured functional evaluation process for independent medical evaluations of claimants presenting with disabling mental illness: rationale and design for a multi-center reliability study.

PubMed

Bachmann, Monica; de Boer, Wout; Schandelmaier, Stefan; Leibold, Andrea; Marelli, Renato; Jeger, Joerg; Hoffmann-Richter, Ulrike; Mager, Ralph; Schaad, Heinz; Zumbrunn, Thomas; Vogel, Nicole; Bänziger, Oskar; Busse, Jason W; Fischer, Katrin; Kunz, Regina

2016-07-29

Work capacity evaluations by independent medical experts are widely used to inform insurers whether injured or ill workers are capable of engaging in competitive employment. In many countries, evaluation processes lack a clearly structured approach, standardized instruments, and an explicit focus on claimants' functional abilities. Evaluation of subjective complaints, such as mental illness, present additional challenges in the determination of work capacity. We have therefore developed a process for functional evaluation of claimants with mental disorders which complements usual psychiatric evaluation. Here we report the design of a study to measure the reliability of our approach in determining work capacity among patients with mental illness applying for disability benefits. We will conduct a multi-center reliability study, in which 20 psychiatrists trained in our functional evaluation process will assess 30 claimants presenting with mental illness for eligibility to receive disability benefits [Reliability of Functional Evaluation in Psychiatry, RELY-study]. The functional evaluation process entails a five-step structured interview and a reporting instrument (Instrument of Functional Assessment in Psychiatry [IFAP]) to document the severity of work-related functional limitations. We will videotape all evaluations which will be viewed by three psychiatrists who will independently rate claimants' functional limitations. Our primary outcome measure is the evaluation of claimant's work capacity as a percentage (0 to 100 %), and our secondary outcomes are the 12 mental functions and 13 functional capacities assessed by the IFAP-instrument. Inter-rater reliability of four psychiatric experts will be explored using multilevel models to estimate the intraclass correlation coefficient (ICC). Additional analyses include subgroups according to mental disorder, the typicality of claimants, and claimant perceived fairness of the assessment process. We hypothesize that a structured functional approach will show moderate reliability (ICC ≥ 0.6) of psychiatric evaluation of work capacity. Enrollment of actual claimants with mental disorders referred for evaluation by disability/accident insurers will increase the external validity of our findings. Finding moderate levels of reliability, we will continue with a randomized trial to test the reliability of a structured functional approach versus evaluation-as-usual.

The loop structure and the RNA helicase p72/DDX17 influence the processing efficiency of the mice miR-132

PubMed Central

Remenyi, Judit; Bajan, Sarah; Fuller-Pace, Frances V.; Arthur, J. Simon C.; Hutvagner, Gyorgy

2016-01-01

miRNAs are small RNAs that are key regulators of gene expression in eukaryotic organisms. The processing of miRNAs is regulated by structural characteristics of the RNA and is also tightly controlled by auxiliary protein factors. Among them, RNA binding proteins play crucial roles to facilitate or inhibit miRNA maturation and can be controlled in a cell, tissue and species-specific manners or in response to environmental stimuli. In this study we dissect the molecular mechanism that promotes the overexpression of miR-132 in mice over its related, co-transcribed and co-regulated miRNA, miR-212. We have shown that the loop structure of miR-132 is a key determinant for its efficient processing in cells. We have also identified a range of RNA binding proteins that recognize the loop of miR-132 and influence both miR-132 and miR-212 processing. The DEAD box helicase p72/DDX17 was identified as a factor that facilitates the specific processing of miR-132. PMID:26947125

A technique for determining the deuterium/hydrogen contrast map in neutron macromolecular crystallography.

PubMed

Chatake, Toshiyuki; Fujiwara, Satoru

2016-01-01

A difference in the neutron scattering length between hydrogen and deuterium leads to a high density contrast in neutron Fourier maps. In this study, a technique for determining the deuterium/hydrogen (D/H) contrast map in neutron macromolecular crystallography is developed and evaluated using ribonuclease A. The contrast map between the D2O-solvent and H2O-solvent crystals is calculated in real space, rather than in reciprocal space as performed in previous neutron D/H contrast crystallography. The present technique can thus utilize all of the amplitudes of the neutron structure factors for both D2O-solvent and H2O-solvent crystals. The neutron D/H contrast maps clearly demonstrate the powerful detectability of H/D exchange in proteins. In fact, alternative protonation states and alternative conformations of hydroxyl groups are observed at medium resolution (1.8 Å). Moreover, water molecules can be categorized into three types according to their tendency towards rotational disorder. These results directly indicate improvement in the neutron crystal structure analysis. This technique is suitable for incorporation into the standard structure-determination process used in neutron protein crystallography; consequently, more precise and efficient determination of the D-atom positions is possible using a combination of this D/H contrast technique and standard neutron structure-determination protocols.

Analysis of Dependence of the Properties of Alloy V95 on the Pressure Applied to Crystallizing Metal

NASA Astrophysics Data System (ADS)

Korostelev, V. F.; Khromova, L. P.; Denisov, M. S.

2017-05-01

Results of a study aimed at formation of a single-phase fine-grained structure in pistons from aluminum alloy V95 in the process of their fabrication, which involves isostatic pressing of liquid metal before the start of crystallization, application of pressure to the crystallizing metal, and holding under pressure in the process of cooling to the shop temperature, are presented. The ultimate strength and the structure of alloy V95 after casting with imposition of pressure are determined. An example of application of the method suggested for fabricating cast billets ∅ 82 × 70 mm in size with a uniform dense structure without gas shrinkage defects, volume and dendritic segregation is considered.

Structured decision making as a conceptual framework to identify thresholds for conservation and management

USGS Publications Warehouse

Martin, J.; Runge, M.C.; Nichols, J.D.; Lubow, B.C.; Kendall, W.L.

2009-01-01

Thresholds and their relevance to conservation have become a major topic of discussion in the ecological literature. Unfortunately, in many cases the lack of a clear conceptual framework for thinking about thresholds may have led to confusion in attempts to apply the concept of thresholds to conservation decisions. Here, we advocate a framework for thinking about thresholds in terms of a structured decision making process. The purpose of this framework is to promote a logical and transparent process for making informed decisions for conservation. Specification of such a framework leads naturally to consideration of definitions and roles of different kinds of thresholds in the process. We distinguish among three categories of thresholds. Ecological thresholds are values of system state variables at which small changes bring about substantial changes in system dynamics. Utility thresholds are components of management objectives (determined by human values) and are values of state or performance variables at which small changes yield substantial changes in the value of the management outcome. Decision thresholds are values of system state variables at which small changes prompt changes in management actions in order to reach specified management objectives. The approach that we present focuses directly on the objectives of management, with an aim to providing decisions that are optimal with respect to those objectives. This approach clearly distinguishes the components of the decision process that are inherently subjective (management objectives, potential management actions) from those that are more objective (system models, estimates of system state). Optimization based on these components then leads to decision matrices specifying optimal actions to be taken at various values of system state variables. Values of state variables separating different actions in such matrices are viewed as decision thresholds. Utility thresholds are included in the objectives component, and ecological thresholds may be embedded in models projecting consequences of management actions. Decision thresholds are determined by the above-listed components of a structured decision process. These components may themselves vary over time, inducing variation in the decision thresholds inherited from them. These dynamic decision thresholds can then be determined using adaptive management. We provide numerical examples (that are based on patch occupancy models) of structured decision processes that include all three kinds of thresholds. ?? 2009 by the Ecological Society of America.

Protein crystallography for non-crystallographers, or how to get the best (but not more) from published macromolecular structures

PubMed Central

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

2015-01-01

The number of macromolecular structures deposited in the Protein Data Bank now exceeds 45 000, with the vast majority determined using crystallographic methods. Thousands of studies describing such structures have been published in the scientific literature, and 14 Nobel prizes in chemistry or medicine have been awarded to protein crystallographers. As important as these structures are for understanding the processes that take place in living organisms and also for practical applications such as drug design, many non-crystallographers still have problems with critical evaluation of the structural literature data. This review attempts to provide a brief outline of technical aspects of crystallography and to explain the meaning of some parameters that should be evaluated by users of macromolecular structures in order to interpret, but not over-interpret, the information present in the coordinate files and in their description. A discussion of the extent of the information that can be gleaned from the coordinates of structures solved at different resolution, as well as problems and pitfalls encountered in structure determination and interpretation are also covered. PMID:18034855

NDI method for quantification of weak bonding strength of composite structures. Final report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Johnson, R.F.

This Phase 1 Final Report is for a Small Business Innovation Research program conducted for the Navy under Federal Contract N00189-96-M-JT09. The purpose was to investigate ways to determine the overall strength of a composite structure by using a nondestructive evaluative (NDE) optical technique, shearography. The purpose of the research was to determine if there is an effective way to assess the strength of composite components on in-service aircraft rather than in the front end of the composite manufacturing process. The goal was to determine the overall feasibility of such an NDE method, and to investigate various means of probingmore » the material under test.« less

Rheological changes of polyamide 12 under oscillatory shear

NASA Astrophysics Data System (ADS)

Mielicki, C.; Gronhoff, B.; Wortberg, J.

2014-05-01

Changes in material properties as well as process deviation prevent Laser Sintering (LS) technology from manufacturing of quality assured parts in a series production. In this context, the viscosity of Polyamide 12 (PA12) is assumed to possess the most significant influence, as it determines the sintering velocity, the resistance towards melt formation and the bonding strength of sintered layers. Moreover, the viscosity is directly related to the structure of the molten polymer. In particular, it has been recently reported that LS process conditions lead to structural changes of PA12 affecting viscosity and coalescence of adjacent polymer particles, i.e. melt formation significantly. Structural change of PA12 was understood as a post condensation. Its influence on viscosity was described by a time and temperature depending rheological model whereas time dependence was considered by a novel structural change shift factor which was derived from melt volume rate data. In combination with process data that was recorded using online thermal imaging, the model is suitable to control the viscosity (processability of the material) as result of material and process properties. However, as soon as laser energy is exposed to the powder bed PA12 undergoes a phase transition from solid to molten state. Above the melting point, structural change is expected to occur faster due to a higher kinetic energy and free volume of the molten polymer. Oscillatory shear results were used to study the influence of aging time and for validation of the novel structural change shift factor and its model parameters which were calibrated based on LS processing condition.

The SPRING Nanoenergetics Hub at UTD

DTIC Science & Technology

2008-12-01

synthesis and processing of advanced nanostructured materials, the structure and property characterization needed for materials optimization, the...nano-particles into hexane solvent a deposited films. Here we are modeling that processes to see how the droplet evaporation progresses in time. What...nanofibers was determined by powder X-ray diffraction (XRD) (Scintag XDS 2000 X-ray diffractometer with Cu Ka radiation). The fiber morphology was

Experimental study of copper-alkali ion exchange in glass

NASA Astrophysics Data System (ADS)

Gonella, F.; Caccavale, F.; Bogomolova, L. D.; D'Acapito, F.; Quaranta, A.

1998-02-01

Copper-alkali ion exchange was performed by immersing different silicate glasses (soda-lime and BK7) in different molten eutectic salt baths (CuSO4:Na2SO4 and CuSO4:K2SO4). The obtained optical waveguides were characterized by m-lines spectroscopy for the determination of refractive index profiles, and by secondary ion mass spectrometry for the concentration profiles of the ion species involved in the exchange process. The different oxidation states of copper inside the glass structure were studied by electron paramagnetic resonance and x-ray absorption techniques. Interdiffusion copper coefficients were also determined. The Cu-alkali exchange was observed to give rise to local structural rearrangement of the atoms in the glass matrix. The Cu+ ion was found to mainly govern the exchange process, while competition between Cu-Na and K-Na exchanges occurred when a potassium sulfate bath was used. In this case, significant waveguide modal birefringence was observed.

Determining average path length and average trapping time on generalized dual dendrimer

NASA Astrophysics Data System (ADS)

Li, Ling; Guan, Jihong

2015-03-01

Dendrimer has wide number of important applications in various fields. In some cases during transport or diffusion process, it transforms into its dual structure named Husimi cactus. In this paper, we study the structure properties and trapping problem on a family of generalized dual dendrimer with arbitrary coordination numbers. We first calculate exactly the average path length (APL) of the networks. The APL increases logarithmically with the network size, indicating that the networks exhibit a small-world effect. Then we determine the average trapping time (ATT) of the trapping process in two cases, i.e., the trap placed on a central node and the trap is uniformly distributed in all the nodes of the network. In both case, we obtain explicit solutions of ATT and show how they vary with the networks size. Besides, we also discuss the influence of the coordination number on trapping efficiency.

Iterative Development of an Application to Support Nuclear Magnetic Resonance Data Analysis of Proteins.

PubMed

Ellis, Heidi J C; Nowling, Ronald J; Vyas, Jay; Martyn, Timothy O; Gryk, Michael R

2011-04-11

The CONNecticut Joint University Research (CONNJUR) team is a group of biochemical and software engineering researchers at multiple institutions. The vision of the team is to develop a comprehensive application that integrates a variety of existing analysis tools with workflow and data management to support the process of protein structure determination using Nuclear Magnetic Resonance (NMR). The use of multiple disparate tools and lack of data management, currently the norm in NMR data processing, provides strong motivation for such an integrated environment. This manuscript briefly describes the domain of NMR as used for protein structure determination and explains the formation of the CONNJUR team and its operation in developing the CONNJUR application. The manuscript also describes the evolution of the CONNJUR application through four prototypes and describes the challenges faced while developing the CONNJUR application and how those challenges were met.

Solar Wind Access to Lunar Polar Craters: Feedback Between Surface Charging and Plasma Expansion

NASA Technical Reports Server (NTRS)

Zimmerman, M. I.; Farrell, W. M.; Stubbs, T. J.; Halekas, J. S.; Jackson, T. L.

2011-01-01

Determining the plasma environment within permanently shadowed lunar craters is critical to understanding local processes such as surface charging, electrostatic dust transport, volatile sequestration, and space weathering. In order to investigate the nature of this plasma environment, the first two-dimensional kinetic simulations of solar wind expansion into a lunar crater with a self-consistent plasma-surface interaction have been undertaken. The present results reveal how the plasma expansion into a crater couples with the electrically-charged lunar surface to produce a quasi-steady wake structure. In particular, there is a negative feedback between surface charging and ambipolar wake potential that allows an equilibrium to be achieved, with secondary electron emission strongly moderating the process. A range of secondary electron yields is explored, and two distinct limits are highlighted in which either surface charging or ambipoiar expansion is responsible for determining the overall wake structure.

Pattern recognition of concrete surface cracks and defects using integrated image processing algorithms

NASA Astrophysics Data System (ADS)

Balbin, Jessie R.; Hortinela, Carlos C.; Garcia, Ramon G.; Baylon, Sunnycille; Ignacio, Alexander Joshua; Rivera, Marco Antonio; Sebastian, Jaimie

2017-06-01

Pattern recognition of concrete surface crack defects is very important in determining stability of structure like building, roads or bridges. Surface crack is one of the subjects in inspection, diagnosis, and maintenance as well as life prediction for the safety of the structures. Traditionally determining defects and cracks on concrete surfaces are done manually by inspection. Moreover, any internal defects on the concrete would require destructive testing for detection. The researchers created an automated surface crack detection for concrete using image processing techniques including Hough transform, LoG weighted, Dilation, Grayscale, Canny Edge Detection and Haar Wavelet Transform. An automatic surface crack detection robot is designed to capture the concrete surface by sectoring method. Surface crack classification was done with the use of Haar trained cascade object detector that uses both positive samples and negative samples which proved that it is possible to effectively identify the surface crack defects.

Integrated unaligned resonant modulator tuning

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zortman, William A.; Lentine, Anthony L.

Methods and systems for tuning a resonant modulator are disclosed. One method includes receiving a carrier signal modulated by the resonant modulator with a stream of data having an approximately equal number of high and low bits, determining an average power of the modulated carrier signal, comparing the average power to a predetermined threshold, and operating a tuning device coupled to the resonant modulator based on the comparison of the average power and the predetermined threshold. One system includes an input structure, a plurality of processing elements, and a digital control element. The input structure is configured to receive, frommore » the resonant modulator, a modulated carrier signal. The plurality of processing elements are configured to determine an average power of the modulated carrier signal. The digital control element is configured to operate a tuning device coupled to the resonant modulator based on the average power of the modulated carrier signal.« less

Interactions of Kraft lignin and wheat gluten during biomaterial processing: evidence for the role of phenolic groups.

PubMed

Kaewtatip, Kaewta; Menut, Paul; Auvergne, Remi; Tanrattanakul, Varaporn; Morel, Marie-Helene; Guilbert, Stephane

2010-04-14

The chemical interactions between Kraft lignin and wheat gluten under processing conditions were investigated by determining the extent of the protein network formation. To clarify the role of different chemical functions found in lignin, the effect of Kraft lignin was compared with that of an esterified lignin, in which hydroxyl groups had been suppressed by esterification, and with a series of simple aromatics and phenolic structures with different functionalities (conjugated double bonds, hydroxyl, carboxylic acid, and aldehyde). The protein solubility was determined by using the Kjeldahl method. The role of the hydroxyl function was assessed by the significantly lower effect of esterified lignin. The importance of the phenolic radical scavenging structure is evidenced by the effect of guaiacol, which results in a behavior similar to that of the Kraft lignin. In addition, the significant effect of conjugated double bonds on gluten reactivity, through nucleophilic addition, was demonstrated.

Acquiring and processing verb argument structure: distributional learning in a miniature language.

PubMed

Wonnacott, Elizabeth; Newport, Elissa L; Tanenhaus, Michael K

2008-05-01

Adult knowledge of a language involves correctly balancing lexically-based and more language-general patterns. For example, verb argument structures may sometimes readily generalize to new verbs, yet with particular verbs may resist generalization. From the perspective of acquisition, this creates significant learnability problems, with some researchers claiming a crucial role for verb semantics in the determination of when generalization may and may not occur. Similarly, there has been debate regarding how verb-specific and more generalized constraints interact in sentence processing and on the role of semantics in this process. The current work explores these issues using artificial language learning. In three experiments using languages without semantic cues to verb distribution, we demonstrate that learners can acquire both verb-specific and verb-general patterns, based on distributional information in the linguistic input regarding each of the verbs as well as across the language as a whole. As with natural languages, these factors are shown to affect production, judgments and real-time processing. We demonstrate that learners apply a rational procedure in determining their usage of these different input statistics and conclude by suggesting that a Bayesian perspective on statistical learning may be an appropriate framework for capturing our findings.

Analysis of offshore platforms lifting with fixed pile structure type (fixed platform) based on ASD89

NASA Astrophysics Data System (ADS)

Sugianto, Agus; Indriani, Andi Marini

2017-11-01

Platform construction GTS (Gathering Testing Sattelite) is offshore construction platform with fix pile structure type/fixed platform functioning to support the mining of petroleum exploitation. After construction fabrication process platform was moved to barges, then shipped to the installation site. Moving process is generally done by pull or push based on construction design determined when planning. But at the time of lifting equipment/cranes available in the work area then the moving process can be done by lifting so that moving activity can be implemented more quickly of work. This analysis moving process of GTS platform in a different way that is generally done to GTS platform types by lifting using problem is construction reinforcement required, so the construction can be moved by lifting with analyzing and checking structure working stress that occurs due to construction moving process by lifting AISC code standard and analysis using the SAP2000 structure analysis program. The analysis result showed that existing condition cannot be moved by lifting because stress ratio is above maximum allowable value that is 0.950 (AISC-ASD89). Overstress occurs on the member 295 and 324 with stress ratio value 0.97 and 0.95 so that it is required structural reinforcement. Box plate aplication at both members so that it produces stress ratio values 0.78 at the member 295 and stress ratio of 0.77 at the member 324. These results indicate that the construction have qualified structural reinforcement for being moved by lifting.

Seeing tobacco mosaic virus through direct electron detectors

PubMed Central

Fromm, Simon A.; Bharat, Tanmay A.M.; Jakobi, Arjen J.; Hagen, Wim J.H.; Sachse, Carsten

2015-01-01

With the introduction of direct electron detectors (DED) to the field of electron cryo-microscopy, a wave of atomic-resolution structures has become available. As the new detectors still require comparative characterization, we have used tobacco mosaic virus (TMV) as a test specimen to study the quality of 3D image reconstructions from data recorded on the two direct electron detector cameras, K2 Summit and Falcon II. Using DED movie frames, we explored related image-processing aspects and compared the performance of micrograph-based and segment-based motion correction approaches. In addition, we investigated the effect of dose deposition on the atomic-resolution structure of TMV and show that radiation damage affects negative carboxyl chains first in a side-chain specific manner. Finally, using 450,000 asymmetric units and limiting the effects of radiation damage, we determined a high-resolution cryo-EM map at 3.35 Å resolution. Here, we provide a comparative case study of highly ordered TMV recorded on different direct electron detectors to establish recording and processing conditions that enable structure determination up to 3.2 Å in resolution using cryo-EM. PMID:25528571

Three-Dimensional Molecular Modeling of a Diverse Range of SC Clan Serine Proteases

PubMed Central

Laskar, Aparna; Chatterjee, Aniruddha; Chatterjee, Somnath; Rodger, Euan J.

2012-01-01

Serine proteases are involved in a variety of biological processes and are classified into clans sharing structural homology. Although various three-dimensional structures of SC clan proteases have been experimentally determined, they are mostly bacterial and animal proteases, with some from archaea, plants, and fungi, and as yet no structures have been determined for protozoa. To bridge this gap, we have used molecular modeling techniques to investigate the structural properties of different SC clan serine proteases from a diverse range of taxa. Either SWISS-MODEL was used for homology-based structure prediction or the LOOPP server was used for threading-based structure prediction. The predicted models were refined using Insight II and SCRWL and validated against experimental structures. Investigation of secondary structures and electrostatic surface potential was performed using MOLMOL. The structural geometry of the catalytic core shows clear deviations between taxa, but the relative positions of the catalytic triad residues were conserved. Evolutionary divergence was also exhibited by large variation in secondary structure features outside the core, differences in overall amino acid distribution, and unique surface electrostatic potential patterns between species. Encompassing a wide range of taxa, our structural analysis provides an evolutionary perspective on SC clan serine proteases. PMID:23213528

Hot topics: Signal processing in acoustics

NASA Astrophysics Data System (ADS)

Gaumond, Charles F.

2005-09-01

Signal processing in acoustics is a multidisciplinary group of people that work in many areas of acoustics. We have chosen two areas that have shown exciting new applications of signal processing to acoustics or have shown exciting and important results from the use of signal processing. In this session, two hot topics are shown: the use of noiselike acoustic fields to determine sound propagation structure and the use of localization to determine animal behaviors. The first topic shows the application of correlation on geo-acoustic fields to determine the Greens function for propagation through the Earth. These results can then be further used to solve geo-acoustic inverse problems. The first topic also shows the application of correlation using oceanic noise fields to determine the Greens function through the ocean. These results also have utility for oceanic inverse problems. The second topic shows exciting results from the detection, localization, and tracking of marine mammals by two different groups. Results from detection and localization of bullfrogs are shown, too. Each of these studies contributed to the knowledge of animal behavior. [Work supported by ONR.

Failure mechanisms in energy-absorbing composite structures

NASA Astrophysics Data System (ADS)

Johnson, Alastair F.; David, Matthew

2010-11-01

Quasi-static tests are described for determination of the energy-absorption properties of composite crash energy-absorbing segment elements under axial loads. Detailed computer tomography scans of failed specimens were used to identify local compression crush failure mechanisms at the crush front. These mechanisms are important for selecting composite materials for energy-absorbing structures, such as helicopter and aircraft sub-floors. Finite element models of the failure processes are described that could be the basis for materials selection and future design procedures for crashworthy structures.

The Diamond Light Source and the challenges ahead for structural biology: some informal remarks.

PubMed

Ramakrishnan, V

2015-03-06

The remarkable advances in structural biology in the past three decades have led to the determination of increasingly complex structures that lie at the heart of many important biological processes. Many of these advances have been made possible by the use of X-ray crystallography using synchrotron radiation. In this short article, some of the challenges and prospects that lie ahead will be summarized. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

The Participation to The All Japan College of Technology Design Competition and The Trial of Art and Design Education

NASA Astrophysics Data System (ADS)

Kato, Kenji; Takeshita, Junji

The works of Toyota national college of technology gets excellent result on structural design competition (bridge contest) of national college design competition. This paper reports planning and making process of these works. As increase strength of the structures, it is important point the determination of structural type by numerical analysis and test, and precision of production and idea of joining. Second, it reports the curriculum of special items connection with excellent works.

Sequence and structure-specific elements of HERG mRNA determine channel synthesis and trafficking efficiency

PubMed Central

Sroubek, Jakub; Krishnan, Yamini; McDonald, Thomas V.

2013-01-01

Human ether-á-gogo-related gene (HERG) encodes a potassium channel that is highly susceptible to deleterious mutations resulting in susceptibility to fatal cardiac arrhythmias. Most mutations adversely affect HERG channel assembly and trafficking. Why the channel is so vulnerable to missense mutations is not well understood. Since nothing is known of how mRNA structural elements factor in channel processing, we synthesized a codon-modified HERG cDNA (HERG-CM) where the codons were synonymously changed to reduce GC content, secondary structure, and rare codon usage. HERG-CM produced typical IKr-like currents; however, channel synthesis and processing were markedly different. Translation efficiency was reduced for HERG-CM, as determined by heterologous expression, in vitro translation, and polysomal profiling. Trafficking efficiency to the cell surface was greatly enhanced, as assayed by immunofluorescence, subcellular fractionation, and surface labeling. Chimeras of HERG-NT/CM indicated that trafficking efficiency was largely dependent on 5′ sequences, while translation efficiency involved multiple areas. These results suggest that HERG translation and trafficking rates are independently governed by noncoding information in various regions of the mRNA molecule. Noncoding information embedded within the mRNA may play a role in the pathogenesis of hereditary arrhythmia syndromes and could provide an avenue for targeted therapeutics.—Sroubek, J., Krishnan, Y., McDonald, T V. Sequence- and structure-specific elements of HERG mRNA determine channel synthesis and trafficking efficiency. PMID:23608144

Indistinguishability and identifiability of kinetic models for the MurC reaction in peptidoglycan biosynthesis.

PubMed

Hattersley, J G; Pérez-Velázquez, J; Chappell, M J; Bearup, D; Roper, D; Dowson, C; Bugg, T; Evans, N D

2011-11-01

An important question in Systems Biology is the design of experiments that enable discrimination between two (or more) competing chemical pathway models or biological mechanisms. In this paper analysis is performed between two different models describing the kinetic mechanism of a three-substrate three-product reaction, namely the MurC reaction in the cytoplasmic phase of peptidoglycan biosynthesis. One model involves ordered substrate binding and ordered release of the three products; the competing model also assumes ordered substrate binding, but with fast release of the three products. The two versions are shown to be distinguishable; however, if standard quasi-steady-state assumptions are made distinguishability cannot be determined. Once model structure uniqueness is ensured the experimenter must determine if it is possible to successfully recover rate constant values given the experiment observations, a process known as structural identifiability. Structural identifiability analysis is carried out for both models to determine which of the unknown reaction parameters can be determined uniquely, or otherwise, from the ideal system outputs. This structural analysis forms an integrated step towards the modelling of the full pathway of the cytoplasmic phase of peptidoglycan biosynthesis. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

Promoting and Protecting Against Stigma in Assisted Living and Nursing Homes.

PubMed

Zimmerman, Sheryl; Dobbs, Debra; Roth, Erin G; Goldman, Susan; Peeples, Amanda D; Wallace, Brandy

2016-06-01

To determine the extent to which structures and processes of care in multilevel settings (independent living, assisted living, and nursing homes) result in stigma in assisted living and nursing homes. Ethnographic in-depth interviews were conducted in 5 multilevel settings with 256 residents, families, and staff members. Qualitative analyses identified the themes that resulted when examining text describing either structures of care or processes of care in relation to 7 codes associated with stigma. Four themes related to structures of care and stigma were identified, including the physical environment, case mix, staff training, and multilevel settings; five themes related to processes of care and stigma, including dining, independence, respect, privacy, and care provision. For each theme, examples were identified illustrating how structures and processes of care can potentially promote or protect against stigma. In no instance were examples or themes identified that suggested the staff intentionally promoted stigma; on the other hand, there was indication that some structures and processes were intentionally in place to protect against stigma. Perhaps the most important theme is the stigma related to multilevel settings, as it has the potential to reduce individuals' likelihood to seek and accept necessary care. Results suggest specific recommendations to modify care and reduce stigma. © The Author 2014. Published by Oxford University Press on behalf of The Gerontological Society of America. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

The Effect of Hole Quality on the Fatigue Life of 2024-T3 Aluminum Alloy Sheet

NASA Technical Reports Server (NTRS)

Everett, Richard A., Jr.

2004-01-01

This paper presents the results of a study whose main objective was to determine which type of fabrication process would least affect the fatigue life of an open-hole structural detail. Since the open-hole detail is often the fundamental building block for determining the stress concentration of built-up structural parts, it is important to understand any factor that can affect the fatigue life of an open hole. A test program of constant-amplitude fatigue tests was conducted on five different sets of test specimens each made using a different hole fabrication process. Three of the sets used different mechanical drilling procedures while a fourth and fifth set were mechanically drilled and then chemically polished. Two sets of specimens were also tested under spectrum loading to aid in understanding the effects of residual compressive stresses on fatigue life. Three conclusions were made from this study. One, the residual compressive stresses caused by the hole-drilling process increased the fatigue life by two to three times over specimens that were chemically polished after the holes were drilled. Second, the chemical polishing process does not appear to adversely affect the fatigue life. Third, the chemical polishing process will produce a stress-state adjacent to the hole that has insignificant machining residual stresses.

Relationship between Mental Models Related to the Particulate Nature of Matter and the Infinite Nature of Geometrical Figures.

ERIC Educational Resources Information Center

Tirosh, Dina; Stavy, Ruth

A study was conducted in Israel to determine effects of external similarity in problem structure on students' responses. Fifty students from each of the 7th, 8th, 10th, and 12th grade levels were presented with three problems involving successive divisions that were similar in structure. The problems asked separately whether the processes of…

Design concepts for a composite door frame system for general automotive applications

NASA Technical Reports Server (NTRS)

Tauber, J. A.

1976-01-01

Conceptual design, manufacturing process, and costs are explored to determine the feasibility of replacing present steel parts in automotive door structures with various composite materials. The problems of conforming to present anti-intrusion specifications with advanced materials are examined and discussed. Modest weight reductions, at competitive costs, were identified for the utilization of specific composite materials in automotive door structures.

Modeling personnel turnover in the parametric organization

NASA Technical Reports Server (NTRS)

Dean, Edwin B.

1991-01-01

A model is developed for simulating the dynamics of a newly formed organization, credible during all phases of organizational development. The model development process is broken down into the activities of determining the tasks required for parametric cost analysis (PCA), determining the skills required for each PCA task, determining the skills available in the applicant marketplace, determining the structure of the model, implementing the model, and testing it. The model, parameterized by the likelihood of job function transition, has demonstrated by the capability to represent the transition of personnel across functional boundaries within a parametric organization using a linear dynamical system, and the ability to predict required staffing profiles to meet functional needs at the desired time. The model can be extended by revisions of the state and transition structure to provide refinements in functional definition for the parametric and extended organization.

In-process, non-destructive multimodal dynamic testing of high-speed composite rotors

NASA Astrophysics Data System (ADS)

Kuschmierz, Robert; Filippatos, Angelos; Langkamp, Albert; Hufenbach, Werner; Czarske, Jürgern W.; Fischer, Andreas

2014-03-01

Fibre reinforced plastic (FRP) rotors are lightweight and offer great perspectives in high-speed applications such as turbo machinery. Currently, novel rotor structures and materials are investigated for the purpose of increasing machine efficiency, lifetime and loading limits. Due to complex rotor structures, high anisotropy and non-linear behavior of FRP under dynamic loads, an in-process measurement system is necessary to monitor and to investigate the evolution of damages under real operation conditions. A non-invasive, optical laser Doppler distance sensor measurement system is applied to determine the biaxial deformation of a bladed FRP rotor with micron uncertainty as well as the tangential blade vibrations at surface speeds above 300 m/s. The laser Doppler distance sensor is applicable under vacuum conditions. Measurements at varying loading conditions are used to determine elastic and plastic deformations. Furthermore they allow to determine hysteresis, fatigue, Eigenfrequency shifts and loading limits. The deformation measurements show a highly anisotropic and nonlinear behavior and offer a deeper understanding of the damage evolution in FRP rotors. The experimental results are used to validate and to calibrate a simulation model of the deformation. The simulation combines finite element analysis and a damage mechanics model. The combination of simulation and measurement system enables the monitoring and prediction of damage evolutions of FRP rotors in process.

Assessment of nutrient remobilization through structural changes of palisade and spongy parenchyma in oilseed rape leaves during senescence.

PubMed

Sorin, Clément; Musse, Maja; Mariette, François; Bouchereau, Alain; Leport, Laurent

2015-02-01

Differential palisade and spongy parenchyma structural changes in oilseed rape leaf were demonstrated. These dismantling processes were linked to early senescence events and associated to remobilization processes. During leaf senescence, an ordered cell dismantling process allows efficient nutrient remobilization. However, in Brassica napus plants, an important amount of nitrogen (N) in fallen leaves is associated with low N remobilization efficiency (NRE). The leaf is a complex organ mainly constituted of palisade and spongy parenchyma characterized by different structures and functions concerning water relations and carbon fixation. The aim of the present study was to demonstrate a specific structural evolution of these parenchyma throughout natural senescence in B. napus, probably linked to differential nutrient remobilization processes. The study was performed on 340 leaves from 32 plants during an 8-week development period under controlled growing conditions. Water distribution and status at the cellular level were investigated by low-field proton nuclear magnetic resonance (NMR), while light and electron microscopy were used to observe cell and plast structure. Physiological parameters were determined on all leaves studied and used as indicators of leaf development and remobilization progress. The results revealed a process of hydration and cell enlargement of leaf tissues associated with senescence. Wide variations were observed in the palisade parenchyma while spongy cells changed only very slightly. The major new functional information revealed was the link between the early senescence events and specific tissue dismantling processes.

The Saturn PRobe Interior and aTmosphere Explorer (SPRITE) Mission Concept

NASA Astrophysics Data System (ADS)

Atkinson, David H.; Simon, Amy; Banfield, Don

2017-04-01

The proposed NASA New Frontiers Saturn PRobe Interior and aTmosphere Explorer (SPRITE) mission would measure the abundance of helium and the other noble gases, elemental and isotopic abundances, the clouds, dynamics, and processes within Saturn's troposphere. In situ measurements of Saturn's atmosphere by SPRITE would provide a significantly improved context for understanding the results from the Galileo Jupiter probe, and the formation and evolution of the gas giant planets, resulting in a paradigm shift in our understanding of the formation, evolution, and ultimately the present day structure of the solar system. The proposed SPRITE concept carries an instrument payload to measure Saturn's atmospheric structure, dynamics, composition, chemistry, and clouds to at least 10 bars. A Quadrupole Mass Spectrometer measures noble gases and noble gas isotopes to accuracies that exceed the Galileo probe measurements at Jupiter and allows for discrimination between competing theories of giant planet formation, evolution, and possible migration. Of particular importance are measurements of helium, key to understanding Saturn's thermal evolution. A Tunable Laser Spectrometer measures molecular abundances and isotope ratios to determine the chemical structure of Saturn's atmosphere, and disequilibrium species such as PH3 and CO which can be used to predict Saturn's deep water abundance. An Atmospheric Structure Instrument provides the pressure/temperature profile of Saturn's atmosphere to determine the altitude profile of static stability, and when combined with cloud measurements from the SPRITE Nephelometer, would elucidate processes that determine the location and structure of Saturn's multiple cloud layers. Coupled with the measurement of atmospheric vertical velocities from the Atmospheric Structure Instrument, a Doppler Wind Experiment provides a measure of the 3-dimensional dynamics of the Saturn atmosphere, including the profile of zonal winds with depth and vertical motions from atmospheric waves. The proposed Science Objectives of the SPRITE mission are to: 1. Constrain competing models of habitable system formation and extent of migration in the early solar system by obtaining a chemical inventory of Saturn's troposphere, 2. Determine if Saturn's in situ atmosphere chemistry agrees with condensation models and remotely observed composition, 3. Constrain Saturn's helium depletion to reconcile observed temperatures with thermal evolution models. 4. Perform in situ characterization of Saturn's tropospheric cloud structure to provide the ground truth basis for cloud retrieval models, and 5. Determine Saturn's in situ 3-dimensional atmospheric dynamics along the probe descent path to inform global circulation and analytical models of the time-variable cloud top motions. To develop an improved understanding of the formation, evolution, and structure of the solar system, it is essential that the role played by the giant planets be well understood, and this cannot be accomplished without in situ measurements of the composition, structure, dynamics, and processes of Saturn's atmosphere. The proposed SPRITE mission would carry a suite of instruments specifically tailored to achieve the science objectives, to provide fundamental ground truth measurements for improved understanding of remote sensing measurements including from Cassini, and to understand the formation, evolution, and structure of the solar system as well as represent key ground truth for understanding exoplanets.

Structure Characterization of Honey-Processed Astragalus Polysaccharides and Its Anti-Inflammatory Activity In Vitro.

PubMed

Liao, Jingzhu; Li, Chanyi; Huang, Jing; Liu, Wuping; Chen, Hongce; Liao, Shuangye; Chen, Hongyuan; Rui, Wen

2018-01-15

Honey-processed Astragalus is a dosage form of Radix Astragalus mixed with honey by a traditional Chinese medicine processing method which strengthens the tonic effect. Astragalus polysaccharide (APS), perform its immunomodulatory effects by relying on the tonic effect of Radix Astragalus , therefore, the improved pharmacological activity of honey-processed Astragalus polysaccharide (HAPS) might be due to structural changes during processing. The molecular weights of HAPS and APS were 1,695,788 Da, 2,047,756 Da, respectively, as determined by high performance gel filtration chromatography combined with evaporative light scattering detection (HPGFC-ELSD). The monosaccharide composition was determined by ultra-performance liquid chromatogram quadrupole time-of-flight mass spectrometry (UPLC/ESI-Q-TOF-MS) after pre-column derivatization with 1-phenyl-3-methyl-5-pyrazolone (PMP). The results showed that the essential components were mannose, glucose, xylose, arabinose, glucuronic acid and rhamnose, is molar ratios of 0.06:28.34:0.58:0.24:0.33:0.21 and 0.27:12.83:1.63:0.71:1.04:0.56, respectively. FT-IR and NMR analysis of HAPS results showed the presence of uronic acid and acetyl groups. The anti-inflammatory activities of HAPS were more effective than those of APS according to the NO contents and the expression of IFN-γ, IL-1β, IL-22 and TNF-α in lipopolysaccharide (LPS)-induced RAW264.7 cells. This findings suggest that the anti-inflammatory and bioactivity improvement might be associated with molecular structure changes, bearing on the potential immunomodulatory action.

Technique for Determination of Rational Boundaries in Combining Construction and Installation Processes Based on Quantitative Estimation of Technological Connections

NASA Astrophysics Data System (ADS)

Gusev, E. V.; Mukhametzyanov, Z. R.; Razyapov, R. V.

2017-11-01

The problems of the existing methods for the determination of combining and technologically interlinked construction processes and activities are considered under the modern construction conditions of various facilities. The necessity to identify common parameters that characterize the interaction nature of all the technology-related construction and installation processes and activities is shown. The research of the technologies of construction and installation processes for buildings and structures with the goal of determining a common parameter for evaluating the relationship between technologically interconnected processes and construction works are conducted. The result of this research was to identify the quantitative evaluation of interaction construction and installation processes and activities in a minimum technologically necessary volume of the previous process allowing one to plan and organize the execution of a subsequent technologically interconnected process. The quantitative evaluation is used as the basis for the calculation of the optimum range of the combination of processes and activities. The calculation method is based on the use of the graph theory. The authors applied a generic characterization parameter to reveal the technological links between construction and installation processes, and the proposed technique has adaptive properties which are key for wide use in organizational decisions forming. The article provides a written practical significance of the developed technique.

A new protocol to accurately determine microtubule lattice seam location

DOE PAGES

Zhang, Rui; Nogales, Eva

2015-09-28

Microtubules (MTs) are cylindrical polymers of αβ-tubulin that display pseudo-helical symmetry due to the presence of a lattice seam of heterologous lateral contacts. The structural similarity between α- and β-tubulin makes it difficult to computationally distinguish them in the noisy cryo-EM images, unless a marker protein for the tubulin dimer, such as kinesin motor domain, is present. We have developed a new data processing protocol that can accurately determine αβ-tubulin register and seam location for MT segments. Our strategy can handle difficult situations, where the marker protein is relatively small or the decoration of marker protein is sparse. Using thismore » new seam-search protocol, combined with movie processing for data from a direct electron detection camera, we were able to determine the cryo-EM structures of MT at 3.5. Å resolution in different functional states. The successful distinction of α- and β-tubulin allowed us to visualize the nucleotide state at the E-site and the configuration of lateral contacts at the seam.« less

Intrinsic thermodynamics of ethoxzolamide inhibitor binding to human carbonic anhydrase XIII

PubMed Central

2012-01-01

Background Human carbonic anhydrases (CAs) play crucial role in various physiological processes including carbon dioxide and hydrocarbon transport, acid homeostasis, biosynthetic reactions, and various pathological processes, especially tumor progression. Therefore, CAs are interesting targets for pharmaceutical research. The structure-activity relationships (SAR) of designed inhibitors require detailed thermodynamic and structural characterization of the binding reaction. Unfortunately, most publications list only the observed thermodynamic parameters that are significantly different from the intrinsic parameters. However, only intrinsic parameters could be used in the rational design and SAR of the novel compounds. Results Intrinsic binding parameters for several inhibitors, including ethoxzolamide, trifluoromethanesulfonamide, and acetazolamide, binding to recombinant human CA XIII isozyme were determined. The parameters were the intrinsic Gibbs free energy, enthalpy, entropy, and the heat capacity. They were determined by titration calorimetry and thermal shift assay in a wide pH and temperature range to dissect all linked protonation reaction contributions. Conclusions Precise determination of the inhibitor binding thermodynamics enabled correct intrinsic affinity and enthalpy ranking of the compounds and provided the means for SAR analysis of other rationally designed CA inhibitors. PMID:22676044

Study of RF breakdown and multipacting in accelerator components

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pande, Manjiri; Singh, P., E-mail: manjiri@barc.gov.in, E-mail: psingh@barc.gov.in

2014-07-01

Radio frequency (RF) structures that are part of accelerators and energy sources, operate with sinusoidally varying electromagnetic fields under high RF energy. Here, RF breakdown and multipacting take place in RF structures and limit their performance. Electron field emission processes in a RF structure are precursors for breakdown processes. RF breakdown is a major phenomena affecting and causing the irreversible damage to RF structures. Breakdown rate and the damage induced by the breakdowns are its important properties. The damage is related to power absorbed during breakdown, while the breakdown rate is determined by the amplitudes of surface electric and magneticmore » fields, geometry, metal surface preparation and conditioning history. It limits working power and produces irreversible surface damage. The breakdown limit depends on the RF circuit, structure geometry, RF frequency, input RF power, pulse width, materials used, surface processing technique and surface electric and magnetic fields. Multipactor (MP) is a low power, electron multiplication based resonance breakdown phenomenon in vacuum and is often observed in RF structures. A multipactor discharge is undesirable, as it can create a reactive component that detunes the resonant cavities and components, generates noise in communication system and induces gas desorption from the conductor surfaces. In RF structures, certain conditions are required to generate multipacting. (author)« less

Elevated intrabolus pressure identifies obstructive processes when integrated relaxation pressure is normal on esophageal high-resolution manometry.

PubMed

Quader, Farhan; Reddy, Chanakyaram; Patel, Amit; Gyawali, C Prakash

2017-07-01

Elevated integrated relaxation pressure (IRP) on esophageal high-resolution manometry (HRM) identifies obstructive processes at the esophagogastric junction (EGJ). Our aim was to determine whether intrabolus pressure (IBP) can identify structural EGJ processes when IRP is normal. In this observational cohort study, adult patients with dysphagia and undergoing HRM were evaluated for endoscopic evidence of structural EGJ processes (strictures, rings, hiatus hernia) in the setting of normal IRP. HRM metrics [IRP, distal contractile integral (DCI), distal latency (DL), IBP, and EGJ contractile integral (EGJ-CI)] were compared among 74 patients with structural EGJ findings (62.8 ± 1.6 yr, 67.6% women), 27 patients with normal EGD (52.9 ± 3.2 yr, 70.3% women), and 21 healthy controls (27.6 ± 0.6 yr, 52.4% women). Findings were validated in 85 consecutive symptomatic patients to address clinical utility. In the primary cohort, mean IBP (18.4 ± 0.9 mmHg) was higher with structural EGJ findings compared with dysphagia with normal EGD (13.5 ± 1.1 mmHg, P = 0.002) and healthy controls (10.9 ± 0.9 mmHg, P < 0.001). However, mean IRP, DCI, DL, and EGJ-CI were similar across groups ( P > 0.05 for each comparison). During multiple rapid swallows, IBP remained higher in the structural findings group compared with controls ( P = 0.02). Similar analysis of the prospective validation cohort confirmed IBP elevation in structural EGJ processes, but correlation with dysphagia could not be demonstrated. We conclude that elevated IBP predicts the presence of structural EGJ processes even when IRP is normal, but correlation with dysphagia is suboptimal. NEW & NOTEWORTHY Integrated relaxation pressure (IRP) above the upper limit of normal defines esophageal outflow obstruction using high-resolution manometry. In patients with normal IRP, elevated intrabolus pressure (IBP) can be a surrogate marker for a structural restrictive or obstructive process at the esophagogastric junction (EGJ). This has the potential to augment the clinical value of esophageal HRM by raising suspicion for a structural EGJ process when IBP is elevated.

Geophysical Analysis of an Urban Region in Southwestern Pennsylvania

DOE Office of Scientific and Technical Information (OSTI.GOV)

Harbert, W.P.; Lipinski, B.A.; Kaminski, V.

2006-12-01

The goal of this project was to categorize the subsurface beneath an urban region of Southwestern Pennsylvania and to determine geological structure and attempt to image pathways for gas migration in this area. Natural gas had been commercially produced from this region at the turn of the century but this field, with more than 100 wells drilled, was closed approximately eighty years ago. There are surface expressions of gas migration visible in the study region. We applied geophysical methods to determine geological structure in this region, which included multi frequency electromagnetic survey performed using Geophex Gem-2 system, portable reflection seismicmore » and a System I/O-based reflection seismic survey. Processing and interpretation of EM data included filtering 10 raw channels (inphase and quadrature components measured at 5 frequencies), inverting the data for apparent conductivity using EM1DFM software by University of British Columbia, Canada and further interpretation in terms of nearsurface features at a maximum depth of up to 20 meters. Analysis of the collected seismic data included standard seismic processing and the use of the SurfSeis software package developed by the Kansas Geological Survey. Standard reflection processing of these data were completed using the LandMark ProMAX 2D/3D and Parallel Geoscience Corporations software. Final stacked sections were then imported into a Seismic Micro Technologies Kingdom Suite+ geodatabase for visualization and analysis. Interpretation of these data was successful in identifying and confirming a region of unmined Freeport coal, determining regional stratigraphic structure and identifying possible S-wave lower velocity anomalies in the shallow subsurface.« less

Effects of low-scale landscape structures on aeolian transport processes on arable land

NASA Astrophysics Data System (ADS)

Siegmund, Nicole; Funk, Roger; Koszinsky, Sylvia; Buschiazzo, Daniel Eduardo; Sommer, Michael

2018-06-01

The landscape of the semiarid Pampa in central Argentina is characterized by late Pleistocene aeolian deposits, covering large plains with sporadic dune structures. Since the current land use changed from extensive livestock production within the Caldenal forest ecosystem to arable land, the wind erosion risk increased distinctly. We measured wind erosion and deposition patterns at the plot scale and investigated the spatial variability of the erosion processes. The wind-induced mass-transport was measured with 18 Modified Wilson and Cooke samplers (MWAC), installed on a 1.44 ha large field in a 20 × 40 m grid. Physical and chemical soil properties from the upper soil as well as a digital elevation model were recorded in a 20 × 20 m grid. In a 5-month measuring campaign data from seven storms with three different wind directions was obtained. Results show very heterogeneous patterns of erosion and deposition for each storm and indicate favoured erosion on windward and deposits on leeward terrain positions. Furthermore, a multiple regression model was build, explaining up to 70% of the spatial variance of erosion by just using four predictors: topsoil thickness, relative elevation, soil organic carbon content and slope direction. Our findings suggest a structure-process-structure complex where the landscape structure determines the effects of recent wind erosion processes which again slowly influence the structure, leading to a gradual increase of soil heterogeneity.

Uncertainty quantification and validation of 3D lattice scaffolds for computer-aided biomedical applications.

PubMed

Gorguluarslan, Recep M; Choi, Seung-Kyum; Saldana, Christopher J

2017-07-01

A methodology is proposed for uncertainty quantification and validation to accurately predict the mechanical response of lattice structures used in the design of scaffolds. Effective structural properties of the scaffolds are characterized using a developed multi-level stochastic upscaling process that propagates the quantified uncertainties at strut level to the lattice structure level. To obtain realistic simulation models for the stochastic upscaling process and minimize the experimental cost, high-resolution finite element models of individual struts were reconstructed from the micro-CT scan images of lattice structures which are fabricated by selective laser melting. The upscaling method facilitates the process of determining homogenized strut properties to reduce the computational cost of the detailed simulation model for the scaffold. Bayesian Information Criterion is utilized to quantify the uncertainties with parametric distributions based on the statistical data obtained from the reconstructed strut models. A systematic validation approach that can minimize the experimental cost is also developed to assess the predictive capability of the stochastic upscaling method used at the strut level and lattice structure level. In comparison with physical compression test results, the proposed methodology of linking the uncertainty quantification with the multi-level stochastic upscaling method enabled an accurate prediction of the elastic behavior of the lattice structure with minimal experimental cost by accounting for the uncertainties induced by the additive manufacturing process. Copyright © 2017 Elsevier Ltd. All rights reserved.

[The catecholamine content of the hypothalamus during the modelling of the ulcer process in the gastroduodenal area].

PubMed

Iemel'ianenko, I V; Sultanova, I D; Voronych, N M

1995-01-01

The content of catecholamines in rat hypothalamus in experimental ulcer process in gastroduodenal region has been studied in experiments on rats. It was determined that under these conditions the content of hypothalamus adrenalin increases and the content of noradrenalin decreases. The level of dofamin and DOFA in this brain structure changes in phases. The mentioned shifts depended on the duration and character of the pathological process in the gastroduodenal region.

A dimensional approach to determine common and specific neurofunctional markers for depression and social anxiety during emotional face processing.

PubMed

Luo, Lizhu; Becker, Benjamin; Zheng, Xiaoxiao; Zhao, Zhiying; Xu, Xiaolei; Zhou, Feng; Wang, Jiaojian; Kou, Juan; Dai, Jing; Kendrick, Keith M

2018-02-01

Major depression disorder (MDD) and anxiety disorder are both prevalent and debilitating. High rates of comorbidity between MDD and social anxiety disorder (SAD) suggest common pathological pathways, including aberrant neural processing of interpersonal signals. In patient populations, the determination of common and distinct neurofunctional markers of MDD and SAD is often hampered by confounding factors, such as generally elevated anxiety levels and disorder-specific brain structural alterations. This study employed a dimensional disorder approach to map neurofunctional markers associated with levels of depression and social anxiety symptoms in a cohort of 91 healthy subjects using an emotional face processing paradigm. Examining linear associations between levels of depression and social anxiety, while controlling for trait anxiety revealed that both were associated with exaggerated dorsal striatal reactivity to fearful and sad expression faces respectively. Exploratory analysis revealed that depression scores were positively correlated with dorsal striatal functional connectivity during processing of fearful faces, whereas those of social anxiety showed a negative association during processing of sad faces. No linear relationships between levels of depression and social anxiety were observed during a facial-identity matching task or with brain structure. Together, the present findings indicate that dorsal striatal neurofunctional alterations might underlie aberrant interpersonal processing associated with both increased levels of depression and social anxiety. © 2017 Wiley Periodicals, Inc.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vogt

This report describes a U.S. Department of Energy, (DOE) Chemical and Biological National Security Program project that sought to establish what is known about decontamination of structures, objects, and people following an exposure to chemical or biological materials. Specifically we sought to identify the procedures and protocols used to determine when and how people or buildings are considered ''clean'' following decontamination. To fulfill this objective, the study systematically examined reported decontamination experiences to determine what procedures and protocols are currently employed for decontamination, the timeframe involved to initiate and complete the decontamination process, how the contaminants were identified, the factorsmore » determining when people were (or were not) decontaminated, the problems encountered during the decontamination process, how response efforts of agencies were coordinated, and the perceived social psychological effects on people who were decontaminated or who participated in the decontamination process. Findings and recommendations from the study are intended to aid decision-making and to improve the basis for determining appropriate decontamination protocols for recovery planners and policy makers for responding to chemical and biological events.« less

Sensor yarns for real-time in situ detection of damage behavior for the purpose of structural health monitoring of textile-reinforced thermoset composites: development of a continuous wet-chemical silvering process for high-performance filament yarn

NASA Astrophysics Data System (ADS)

Onggar, T.; Häntzsche, E.; Nocke, A.; Hund, R. D.; Cherif, Ch

2017-04-01

High-performance textile yarns such as glass filament (GF) yarn will be used as the base material for the development of sensor yarns because glass filament yarns offer both high tensile strengths and moduli of elasticity, as well as high melting temperatures and elongation. A new continuous wet-chemical metallization process has been developed for GF yarns on a laboratory scale to achieve special properties such as electrical conductivity. The aim of the work is to develop a continuous wet-chemical silver plating process for the GF-filament yarn in order to achieve electrical conductivity on the GF-surface. The process was carried out continuously in order to metallize the GF, which is sensitive to the shear force. A homogeneous, completely covered and adhered silver layer on the GF yarn surfaces was obtained by the application of this technology. The surface morphology was been determined by light and scanning electron microscopy to assess the silver layer properties such as structure, homogeneity, and cracking. The chemical structure of the surfaces was analyzed by means of energy dispersive x-ray spectroscopy. For structural analysis, GF yarns were investigated using a Fourier transform infrared spectrometer. The dispersive and polar component of the surface energy of the sized and silvered GF yarn was measured by using a single fiber Tensiometer K100. The silver layer thickness and the silver content were determined after the metallization. Textile physical tests of the tensile strength, elasticity modulus, elongation at break, and yarn fineness of the single GF yarns as well as GF bundle were carried out.

Potential role of centrioles in determining the morphogenetic status of animal somatic cells.

PubMed

Tkemaladze, J; Chichinadze, K

2005-05-01

Irreversible differentiation (change of morphogenetic status) and programmed death (apoptosis) are observed only in somatic cells. Cell division is the only way by which the morphogenetic status of the offspring cells may be modified. It is known that there is a fixed limit to the number of possible cell divisions, the so-called 'Hayflick limit'. Existing links between cell division, differentiation and apoptosis make it possible to conclude that all these processes could be controlled by a single self-reproducing structure. Potential candidates for this replicable structure in a somatic cell are chromosomes, mitochondria (both contain DNA), and centrioles. Centrioles (diplosome) are the most likely unit that can fully regulate the processes of irreversible differentiation, determination and modification of the morphogenetic status. It may contain differently encoded RNA molecules stacked in a definite order. During mitosis, these RNA molecules are released one by one into the cytoplasm. In the presence of reverse transcriptase and endonuclease, RNA can be embedded in nuclear DNA. This process presumably changes the status of repressed and potentially active genes and, subsequently, the morphogenetic status of a cell.

Orientation determination of interfacial beta-sheet structures in situ.

PubMed

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

2010-07-01

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

Aggregates, broccoli and cauliflower

NASA Astrophysics Data System (ADS)

Grey, Francois; Kjems, Jørgen K.

1989-09-01

Naturally grown structures with fractal characters like broccoli and cauliflower are discussed and compared with DLA-type aggregates. It is suggested that the branching density can be used to characterize the growth process and an experimental method to determine this parameter is proposed.

Phenylethynyl Terminated Imide (PETI) Composites Made by High Temperature Vartm

NASA Technical Reports Server (NTRS)

Ghose, Sayata; Watson, Kent A.; Cano, Roberto J.; Britton, Sean M.; Jensen, Brian J.; Connell, John W.; Herring, Helen M.; Lineberry, Quentin J.

2010-01-01

The use of composites as primary structures on aerospace vehicles has increased dramatically over the past decade. As these advanced structures increase in size and complexity, their production costs have grown significantly. A major contributor to these manufacturing costs is the requirement of elevated pressures, during high temperature processing, to create fully consolidated composite parts. Recently, NASA Langley has licensed a series of low viscosity Phenyl Ethynyl Terminated Imide, PETI, oligomers that possess a wide processing window to allow for Resin Transfer Molding, RTM, processing. These resins, PETI-8 and PETI-330, demonstrate void fractions of approx.1% under elevated pressure consolidation. However, when used with a standardized thermal curing cycle in a High Temperature Vacuum Assisted RTM (HT-VARTM) process, they display undesirable void contents in excess of 7%. It was determined previously that under the thermal cycles used for laminate fabrication, the phenylethynyl endcap underwent degradation leading to volatile evolution. Modifications to the processing cycle used in the laminate fabrication have reduced the void content significantly (typically less than 3%) for carbon fiber biaxially woven fabric. For carbon fiber uniaxial fabric, void contents of less than 2% have been obtained using both PETI-8 and PETI-330. The resins were infused into carbon fiber preforms at 260 C and cured between 316 C and 371 C. Photomicrographs of the panels were taken and void contents were determined by acid digestion. Mechanical properties of the panels were determined at both room and elevated temperatures. These include short beam shear and flexure tests. The results of this work are presented herein.

Computational modeling of RNA 3D structures, with the aid of experimental restraints

PubMed Central

Magnus, Marcin; Matelska, Dorota; Łach, Grzegorz; Chojnowski, Grzegorz; Boniecki, Michal J; Purta, Elzbieta; Dawson, Wayne; Dunin-Horkawicz, Stanislaw; Bujnicki, Janusz M

2014-01-01

In addition to mRNAs whose primary function is transmission of genetic information from DNA to proteins, numerous other classes of RNA molecules exist, which are involved in a variety of functions, such as catalyzing biochemical reactions or performing regulatory roles. In analogy to proteins, the function of RNAs depends on their structure and dynamics, which are largely determined by the ribonucleotide sequence. Experimental determination of high-resolution RNA structures is both laborious and difficult, and therefore, the majority of known RNAs remain structurally uncharacterized. To address this problem, computational structure prediction methods were developed that simulate either the physical process of RNA structure formation (“Greek science” approach) or utilize information derived from known structures of other RNA molecules (“Babylonian science” approach). All computational methods suffer from various limitations that make them generally unreliable for structure prediction of long RNA sequences. However, in many cases, the limitations of computational and experimental methods can be overcome by combining these two complementary approaches with each other. In this work, we review computational approaches for RNA structure prediction, with emphasis on implementations (particular programs) that can utilize restraints derived from experimental analyses. We also list experimental approaches, whose results can be relatively easily used by computational methods. Finally, we describe case studies where computational and experimental analyses were successfully combined to determine RNA structures that would remain out of reach for each of these approaches applied separately. PMID:24785264

The importance of bulk density determination in gravity data processing for structure interpretation

NASA Astrophysics Data System (ADS)

Wildan, D.; Akbar, A. M.; Novranza, K. M. S.; Sobirin, R.; Permadi, A. N.; Supriyanto

2017-07-01

Gravity method use rock density variation for determining subsurface lithology and geological structure. In the "green area" where measurement of rock density has not been done, an attemp to find density is usually performed by calculating using Parasnis method, or by using using the average of rock density in the earth's crust (2,67 gr/cm3) or by using theoritical value of dominant rock density in the survey area (2,90 gr/cm3). Those three values of densities are applied to gravity data analysis in the hilly "X" area. And we have compared all together in order to observed which value has represented the structure better. The result showed that the higher value of rock density, the more obvious structure in the Bouguer anomaly profile. It is due to the contrast of maximum and minimum value of Bouguer anomaly that will affect the exageration in distance vs Bouguer anomaly graphic.

Protein Data Bank Japan (PDBj): updated user interfaces, resource description framework, analysis tools for large structures

PubMed Central

Kinjo, Akira R.; Bekker, Gert-Jan; Suzuki, Hirofumi; Tsuchiya, Yuko; Kawabata, Takeshi; Ikegawa, Yasuyo; Nakamura, Haruki

2017-01-01

The Protein Data Bank Japan (PDBj, http://pdbj.org), a member of the worldwide Protein Data Bank (wwPDB), accepts and processes the deposited data of experimentally determined macromolecular structures. While maintaining the archive in collaboration with other wwPDB partners, PDBj also provides a wide range of services and tools for analyzing structures and functions of proteins. We herein outline the updated web user interfaces together with RESTful web services and the backend relational database that support the former. To enhance the interoperability of the PDB data, we have previously developed PDB/RDF, PDB data in the Resource Description Framework (RDF) format, which is now a wwPDB standard called wwPDB/RDF. We have enhanced the connectivity of the wwPDB/RDF data by incorporating various external data resources. Services for searching, comparing and analyzing the ever-increasing large structures determined by hybrid methods are also described. PMID:27789697

A cost-effective protocol for the over-expression and purification of fully-functional and more stable Erwinia chrisanthemi ligand-gated ion channel

PubMed Central

Elberson, Benjamin W.; Whisenant, Ty E.; Cortes, D. Marien; Cuello, Luis G.

2017-01-01

The Erwinia chrisanthemi ligand-gated ion channel, ELIC, is considered an excellent structural and functional surrogate for the whole pentameric ligand-gated ion channel family. Despite its simplicity, ELIC is structurally capable of undergoing ligand-dependent activation and a concomitant desensitization process. To determine at the molecular level the structural changes underlying ELIC’s function, it is desirable to produce large quantities of protein. This protein should be properly folded, fully-functional and amenable to structural determinations. In the current paper, we report a completely new protocol for the expression and purification of milligram quantities of fully-functional, more stable and crystallizable ELIC. The use of an autoinduction media and inexpensive detergents during ELIC extraction, in addition to the high-quality and large quantity of the purified channel, are the highlights of this improved biochemical protocol. PMID:28279818

The Mode of Inhibitor Binding to Peptidyl-tRNA Hydrolase: Binding Studies and Structure Determination of Unbound and Bound Peptidyl-tRNA Hydrolase from Acinetobacter baumannii

PubMed Central

Kaushik, Sanket; Singh, Nagendra; Yamini, Shavait; Singh, Avinash; Sinha, Mau; Arora, Ashish; Kaur, Punit; Sharma, Sujata; Singh, Tej P.

2013-01-01

The incidences of infections caused by an aerobic Gram-negative bacterium, Acinetobacter baumannii are very common in hospital environments. It usually causes soft tissue infections including urinary tract infections and pneumonia. It is difficult to treat due to acquired resistance to available antibiotics is well known. In order to design specific inhibitors against one of the important enzymes, peptidyl-tRNA hydrolase from Acinetobacter baumannii, we have determined its three-dimensional structure. Peptidyl-tRNA hydrolase (AbPth) is involved in recycling of peptidyl-tRNAs which are produced in the cell as a result of premature termination of translation process. We have also determined the structures of two complexes of AbPth with cytidine and uridine. AbPth was cloned, expressed and crystallized in unbound and in two bound states with cytidine and uridine. The binding studies carried out using fluorescence spectroscopic and surface plasmon resonance techniques revealed that both cytidine and uridine bound to AbPth at nanomolar concentrations. The structure determinations of the complexes revealed that both ligands were located in the active site cleft of AbPth. The introduction of ligands to AbPth caused a significant widening of the entrance gate to the active site region and in the process of binding, it expelled several water molecules from the active site. As a result of interactions with protein atoms, the ligands caused conformational changes in several residues to attain the induced tight fittings. Such a binding capability of this protein makes it a versatile molecule for hydrolysis of peptidyl-tRNAs having variable peptide sequences. These are the first studies that revealed the mode of inhibitor binding in Peptidyl-tRNA hydrolases which will facilitate the structure based ligand design. PMID:23844024

Sequence Determinants of Compaction in Intrinsically Disordered Proteins

PubMed Central

Marsh, Joseph A.; Forman-Kay, Julie D.

2010-01-01

Abstract Intrinsically disordered proteins (IDPs), which lack folded structure and are disordered under nondenaturing conditions, have been shown to perform important functions in a large number of cellular processes. These proteins have interesting structural properties that deviate from the random-coil-like behavior exhibited by chemically denatured proteins. In particular, IDPs are often observed to exhibit significant compaction. In this study, we have analyzed the hydrodynamic radii of a number of IDPs to investigate the sequence determinants of this compaction. Net charge and proline content are observed to be strongly correlated with increased hydrodynamic radii, suggesting that these are the dominant contributors to compaction. Hydrophobicity and secondary structure, on the other hand, appear to have negligible effects on compaction, which implies that the determinants of structure in folded and intrinsically disordered proteins are profoundly different. Finally, we observe that polyhistidine tags seem to increase IDP compaction, which suggests that these tags have significant perturbing effects and thus should be removed before any structural characterizations of IDPs. Using the relationships observed in this analysis, we have developed a sequence-based predictor of hydrodynamic radius for IDPs that shows substantial improvement over a simple model based upon chain length alone. PMID:20483348

nextPARS: parallel probing of RNA structures in Illumina

PubMed Central

Saus, Ester; Willis, Jesse R.; Pryszcz, Leszek P.; Hafez, Ahmed; Llorens, Carlos; Himmelbauer, Heinz

2018-01-01

RNA molecules play important roles in virtually every cellular process. These functions are often mediated through the adoption of specific structures that enable RNAs to interact with other molecules. Thus, determining the secondary structures of RNAs is central to understanding their function and evolution. In recent years several sequencing-based approaches have been developed that allow probing structural features of thousands of RNA molecules present in a sample. Here, we describe nextPARS, a novel Illumina-based implementation of in vitro parallel probing of RNA structures. Our approach achieves comparable accuracy to previous implementations, while enabling higher throughput and sample multiplexing. PMID:29358234

Structural basis of viral invasion: lessons from paramyxovirus F

PubMed Central

Lamb, Robert A.; Jardetzky, Theodore S.

2007-01-01

Summary The structures of glycoproteins that mediate enveloped virus entry into cells have revealed dramatic structural changes that accompany membrane fusion and provided mechanistic insights into this process. The group of class I viral fusion proteins includes the influenza hemagglutinin, paramyxovirus F, HIV env and other mechanistically related fusogens, but these proteins are unrelated in sequence and exhibit clearly distinct structural features. Recently determined crystal structures of the paramyxovirus F protein in two conformations, representing prefusion and postfusion states, reveal a novel protein architecture that undergoes large-scale, irreversible refolding during membrane fusion, extending our understanding of this diverse group of membrane fusion machines. PMID:17870467

The implementation of the integrated design process in the hole-plan system

NASA Astrophysics Data System (ADS)

Ruy, Won-Sun; Ko, Dae-Eun; Yang, Young-Soon

2012-12-01

All current shipyards are using the customized CAD/CAM programs in order to improve the design quality and increase the design efficiency. Even though the data structures for ship design and construction are almost completed, the implementation related to the ship design processes are still in progress so that it has been the main causes of the bottleneck and delay during the middle of design process. In this study, we thought that the hole-plan system would be a good example which is remained to be improved. The people of outfitting division who don't have direct authority to edit the structural panels, should request the hull design division to install the holes for the outfitting equipment. For acceptance, they should calculate the hole position, determine the hole type, and find the intersected contour of panel. After consideration of the hull people, the requested holes are manually installed on the hull structure. As the above, many processes are needed such as communication and discussion between the divisions, drawings for hole-plan, and the consideration for the structural or production compatibility. However this iterative process takes a lot of working time and requires mental pressure to the related people and cross-division conflict. This paper will handle the hole-plan system in detail to automate the series of process and minimize the human efforts and time-consumption.

Improving fault image by determination of optimum seismic survey parameters using ray-based modeling

NASA Astrophysics Data System (ADS)

Saffarzadeh, Sadegh; Javaherian, Abdolrahim; Hasani, Hossein; Talebi, Mohammad Ali

2018-06-01

In complex structures such as faults, salt domes and reefs, specifying the survey parameters is more challenging and critical owing to the complicated wave field behavior involved in such structures. In the petroleum industry, detecting faults has become crucial for reservoir potential where faults can act as traps for hydrocarbon. In this regard, seismic survey modeling is employed to construct a model close to the real structure, and obtain very realistic synthetic seismic data. Seismic modeling software, the velocity model and parameters pre-determined by conventional methods enable a seismic survey designer to run a shot-by-shot virtual survey operation. A reliable velocity model of structures can be constructed by integrating the 2D seismic data, geological reports and the well information. The effects of various survey designs can be investigated by the analysis of illumination maps and flower plots. Also, seismic processing of the synthetic data output can describe the target image using different survey parameters. Therefore, seismic modeling is one of the most economical ways to establish and test the optimum acquisition parameters to obtain the best image when dealing with complex geological structures. The primary objective of this study is to design a proper 3D seismic survey orientation to achieve fault zone structures through ray-tracing seismic modeling. The results prove that a seismic survey designer can enhance the image of fault planes in a seismic section by utilizing the proposed modeling and processing approach.

Influence of media with different acidity on structure of FeNi nanotubes

NASA Astrophysics Data System (ADS)

Shumskaya, Alena; Kaniukov, Egor; Kutuzau, Maksim; Bundyukova, Victoria; Tulebayeva, Dinara; Kozlovskiy, Artem; Borgekov, Daryn; Kenzhina, Inesh; Zdorovets, Maxim

2018-04-01

A detailed analysis of the structure features of FeNi nanotubes exposed at environment with different acidity is carried out. It is demonstrated that the exposure of the nanostructures in the environment with high acidity causes the structure deformation, leading to sharply increasing of the presents of oxide phases and partial amorphization of nanotubes walls that determined the rate of FeNi nanotubes destruction. It was established that the evolution of the crystal structure parameters concerned with appearance of oxide phases and with formation of disorder regions as a result of oxidation processes.

A glimpse of structural biology through X-ray crystallography.

PubMed

Shi, Yigong

2014-11-20

Since determination of the myoglobin structure in 1957, X-ray crystallography, as the anchoring tool of structural biology, has played an instrumental role in deciphering the secrets of life. Knowledge gained through X-ray crystallography has fundamentally advanced our views on cellular processes and greatly facilitated development of modern medicine. In this brief narrative, I describe my personal understanding of the evolution of structural biology through X-ray crystallography-using as examples mechanistic understanding of protein kinases and integral membrane proteins-and comment on the impact of technological development and outlook of X-ray crystallography.

High-throughput crystal-optimization strategies in the South Paris Yeast Structural Genomics Project: one size fits all?

PubMed

Leulliot, Nicolas; Trésaugues, Lionel; Bremang, Michael; Sorel, Isabelle; Ulryck, Nathalie; Graille, Marc; Aboulfath, Ilham; Poupon, Anne; Liger, Dominique; Quevillon-Cheruel, Sophie; Janin, Joël; van Tilbeurgh, Herman

2005-06-01

Crystallization has long been regarded as one of the major bottlenecks in high-throughput structural determination by X-ray crystallography. Structural genomics projects have addressed this issue by using robots to set up automated crystal screens using nanodrop technology. This has moved the bottleneck from obtaining the first crystal hit to obtaining diffraction-quality crystals, as crystal optimization is a notoriously slow process that is difficult to automatize. This article describes the high-throughput optimization strategies used in the Yeast Structural Genomics project, with selected successful examples.

Determinism and probability in the development of the cell theory.

PubMed

Duchesneau, François

2012-09-01

A return to Claude Bernard's original use of the concept of 'determinism' displays the fact that natural laws were presumed to rule over all natural processes. In a more restricted sense, the term boiled down to a mere presupposition of constant determinant causes for those processes, leaving aside any particular ontological principle, even stochastic. The history of the cell theory until around 1900 was dominated by a twofold conception of determinant causes. Along a reductionist trend, cells' structures and processes were supposed to be accounted for through their analysis into detailed partial mechanisms. But a more holistic approach tended to subsume those analytic means and the mechanism involved under a program of global functional determinations. When mitotic and meiotic sequences in nuclear replication were being unveiled and that neo-Mendelian genetics was being grafted onto cytology and embryology, a conception of strict determinism at the nuclear level, principally represented by Wilhelm Roux and August Weismann, would seem to rule unilaterally over the mosaic interpretation of the cleavage of blastomeres. But, as shown by E.B. Wilson, in developmental processes there occur contingent outcomes of cell division which observations and experiments reveal. This induces the need to admit 'epigenetic' determinants and relativize the presumed 'preformation' of thedevelopmental phases by making room for an emergent order which the accidental circumstances of gene replication would trigger on. Copyright © 2012 Elsevier Ltd. All rights reserved.

Honing process optimization algorithms

NASA Astrophysics Data System (ADS)

Kadyrov, Ramil R.; Charikov, Pavel N.; Pryanichnikova, Valeria V.

2018-03-01

This article considers the relevance of honing processes for creating high-quality mechanical engineering products. The features of the honing process are revealed and such important concepts as the task for optimization of honing operations, the optimal structure of the honing working cycles, stepped and stepless honing cycles, simulation of processing and its purpose are emphasized. It is noted that the reliability of the mathematical model determines the quality parameters of the honing process control. An algorithm for continuous control of the honing process is proposed. The process model reliably describes the machining of a workpiece in a sufficiently wide area and can be used to operate the CNC machine CC743.

Ab initio phasing by molecular averaging in real space with new criteria: application to structure determination of a betanodavirus

PubMed Central

Yoshimura, Masato; Chen, Nai-Chi; Guan, Hong-Hsiang; Chuankhayan, Phimonphan; Lin, Chien-Chih; Nakagawa, Atsushi; Chen, Chun-Jung

2016-01-01

Molecular averaging, including noncrystallographic symmetry (NCS) averaging, is a powerful method for ab initio phase determination and phase improvement. Applications of the cross-crystal averaging (CCA) method have been shown to be effective for phase improvement after initial phasing by molecular replacement, isomorphous replacement, anomalous dispersion or combinations of these methods. Here, a two-step process for phase determination in the X-ray structural analysis of a new coat protein from a betanodavirus, Grouper nervous necrosis virus, is described in detail. The first step is ab initio structure determination of the T = 3 icosahedral virus-like particle using NCS averaging (NCSA). The second step involves structure determination of the protrusion domain of the viral molecule using cross-crystal averaging. In this method, molecular averaging and solvent flattening constrain the electron density in real space. To quantify these constraints, a new, simple and general indicator, free fraction (ff), is introduced, where ff is defined as the ratio of the volume of the electron density that is freely changed to the total volume of the crystal unit cell. This indicator is useful and effective to evaluate the strengths of both NCSA and CCA. Under the condition that a mask (envelope) covers the target molecule well, an ff value of less than 0.1, as a new rule of thumb, gives sufficient phasing power for the successful construction of new structures. PMID:27377380

Fabrication process scale-up and optimization for a boron-aluminum composite radiator

NASA Technical Reports Server (NTRS)

Okelly, K. P.

1973-01-01

Design approaches to a practical utilization of a boron-aluminum radiator for the space shuttle orbiter are presented. The program includes studies of laboratory composite material processes to determine the feasibility of a structural and functional composite radiator panel, and to estimate the cost of its fabrication. The objective is the incorporation of boron-aluminum modulator radiator on the space shuttle.

Progress research of non-Cz silicon material

NASA Technical Reports Server (NTRS)

Campbell, R. B.

1983-01-01

The simultaneous diffusion of liquid boron and liquid phosphorus dopants into N-type dendritic silicon web for solar cells was investigated. It is planned that the diffusion parameters required to achieve the desired P(+)NN(+) cell structure be determined and the resultant cell properties be compared to cells produced in a sequential differential process. A cost analysis of the simultaneous junction formation process is proposed.

Process research of non-Czochralski silicon material

NASA Technical Reports Server (NTRS)

Campbell, R. B.

1986-01-01

Simultaneous diffusion of liquid precursors containing phosphorus and boron into dendritic web silicon to form solar cell structures was investigated. A simultaneous junction formation techniques was developed. It was determined that to produce high quality cells, an annealing cycle (nominal 800 C for 30 min) should follow the diffusion process to anneal quenched-in defects. Two ohm-cm n-base cells were fabricated with efficiencies greater than 15%. A cost analysis indicated that the simultansous diffusion process costs can be as low as 65% of the costs of the sequential diffusion process.

How Can I Describe Social Studies Curriculum in the First Three Years of Primary School? A Case Study

ERIC Educational Resources Information Center

Aktan, Sümer

2016-01-01

The aim of this study is to determine the opinions of a multigrade class teacher on the nature of social studies lesson, the structure of the social studies curriculum, and the teaching process of social studies lesson. The study was structured in line with a holistic single case design which is contained in the tradition of qualitative research.…

Photogrammetric Modeling and Image-Based Rendering for Rapid Virtual Environment Creation

DTIC Science & Technology

2004-12-01

area and different methods have been proposed. Pertinent methods include: Camera Calibration , Structure from Motion, Stereo Correspondence, and Image...Based Rendering 1.1.1 Camera Calibration Determining the 3D structure of a model from multiple views becomes simpler if the intrinsic (or internal...can introduce significant nonlinearities into the image. We have found that camera calibration is a straightforward process which can simplify the

Direct evidence for the gas phase thermal polymerization of styrene. Determination of the initiation mechanism and structures of the early oligomers by ion mobility.

PubMed

Alsharaeh, Edreese H; Ibrahim, Yehia M; El-Shall, M Samy

2005-05-04

We present here direct evidence for the thermal self-initiated polymerization of styrene in the gas phase and establish that the initiation process proceeds via essentially the same mechanism (the Mayo mechanism) as in condensed phase polymerization. Furthermore, we provide structural identifications of the dimers and trimers formed in the gas phase.

From protein structure to function via single crystal optical spectroscopy

PubMed Central

Ronda, Luca; Bruno, Stefano; Bettati, Stefano; Storici, Paola; Mozzarelli, Andrea

2015-01-01

The more than 100,000 protein structures determined by X-ray crystallography provide a wealth of information for the characterization of biological processes at the molecular level. However, several crystallographic “artifacts,” including conformational selection, crystallization conditions and radiation damages, may affect the quality and the interpretation of the electron density maps, thus limiting the relevance of structure determinations. Moreover, for most of these structures, no functional data have been obtained in the crystalline state, thus posing serious questions on their validity in infereing protein mechanisms. In order to solve these issues, spectroscopic methods have been applied for the determination of equilibrium and kinetic properties of proteins in the crystalline state. These methods are UV-vis spectrophotometry, spectrofluorimetry, IR, EPR, Raman, and resonance Raman spectroscopy. Some of these approaches have been implemented with on-line instruments at X-ray synchrotron beamlines. Here, we provide an overview of investigations predominantly carried out in our laboratory by single crystal polarized absorption UV-vis microspectrophotometry, the most applied technique for the functional characterization of proteins in the crystalline state. Studies on hemoglobins, pyridoxal 5′-phosphate dependent enzymes and green fluorescent protein in the crystalline state have addressed key biological issues, leading to either straightforward structure-function correlations or limitations to structure-based mechanisms. PMID:25988179

Introducing double polar heads to highly fluorescent Thiazoles: Influence on supramolecular structures and photonic properties.

PubMed

Kaufmann, M; Hupfer, M L; Sachse, T; Herrmann-Westendorf, F; Weiß, D; Dietzek, B; Beckert, R; Presselt, M

2018-04-30

Supramolecular structures determine properties of optoelectronically active materials and can be tailored via the Langmuir-Blodgett (LB) technique. Interactions between dyes can cause high crystallinities of Langmuir monolayers, thus rendering retaining their integrity during the LB-deposition challenging. However, increasing degrees of freedom exclusively at the polar anchoring moieties of dyes might improve processability without perturbing the dye's optoelectronic properties nor the function-determining crystallinity of the layer. (Amphiphilic) thiazole dyes without, with a mono-polar, and with a double-polar anchor were synthesized, whereas the two constituting polar moieties of the latter derivate are separated by a flexible alkyl chain. The supramolecular structures and crystallinities of Langmuir and LB monolayers were characterized by means of LB isotherms, atomic force microscopy and polarization-resolved fluorescence spectroscopy. As compared to the mono-polar reference the introduction of a flexible double-polar head did not deteriorate UV-vis absorption, emission or electrochemical properties of the thiazole but significantly extended the range of constant compressibility modulus, thus indicating improved processability of the Langmuir monolayers. Indeed, AFM studies revealed that the integrity of the monolayers could be retained during LB-deposition. Additionally, also the underlying supramolecular structure of the chromophore moieties is largely identical to those obtained from the mono-polar reference thiazoles. Copyright © 2018. Published by Elsevier Inc.

High-resolution Single Particle Analysis from Electron Cryo-microscopy Images Using SPHIRE

PubMed Central

Moriya, Toshio; Saur, Michael; Stabrin, Markus; Merino, Felipe; Voicu, Horatiu; Huang, Zhong; Penczek, Pawel A.; Raunser, Stefan; Gatsogiannis, Christos

2017-01-01

SPHIRE (SPARX for High-Resolution Electron Microscopy) is a novel open-source, user-friendly software suite for the semi-automated processing of single particle electron cryo-microscopy (cryo-EM) data. The protocol presented here describes in detail how to obtain a near-atomic resolution structure starting from cryo-EM micrograph movies by guiding users through all steps of the single particle structure determination pipeline. These steps are controlled from the new SPHIRE graphical user interface and require minimum user intervention. Using this protocol, a 3.5 Å structure of TcdA1, a Tc toxin complex from Photorhabdus luminescens, was derived from only 9500 single particles. This streamlined approach will help novice users without extensive processing experience and a priori structural information, to obtain noise-free and unbiased atomic models of their purified macromolecular complexes in their native state. PMID:28570515

Electron crystallography of PhoE porin, an outer membrane, channel- forming protein from E. coli

DOE Office of Scientific and Technical Information (OSTI.GOV)

Walian, P.J.

1989-11-01

One approach to studying the structure of membrane proteins is the use of electron crystallography. Dr. Bing Jap has crystallized PhoE pore-forming protein (porin) from the outer membrane of escherichia coli (E. coli) into monolayer crystals. The findings of this research and those of Jap (1988, 1989) have determined these crystals to be highly ordered, yielding structural information to a resolution of better than 2.8 angstroms. The task of this thesis has been to collect and process the electron diffraction patterns necessary to generate a complete three-dimensional set of high resolution structure factor amplitudes of PhoE porin. Fourier processing ofmore » these amplitudes when combined with the corresponding phase data is expected to yield the three-dimensional structure of PhoE porin at better than 3.5 angstroms resolution. 92 refs., 33 figs., 3 tabs. (CBS)« less

Status quo and future research challenges on organic food quality determination with focus on laboratory methods.

PubMed

Kahl, Johannes; Bodroza-Solarov, Marija; Busscher, Nicolaas; Hajslova, Jana; Kneifel, Wolfgang; Kokornaczyk, Maria Olga; van Ruth, Saskia; Schulzova, Vera; Stolz, Peter

2014-10-01

Organic food quality determination needs multi-dimensional evaluation tools. The main focus is on the authentication as an analytical verification of the certification process. New fingerprinting approaches such as ultra-performance liquid chromatography-mass spectrometry, gas chromatography-mass spectrometry, direct analysis in real time-high-resolution mass spectrometry as well as crystallization with and without the presence of additives seem to be promising methods in terms of time of analysis and detecting organic system-related parameters. For further methodological development, a system approach is recommended, which also takes into account food structure aspects. Furthermore, the authentication of processed organic samples needs more consciousness, hence most of organic food is complex and processed. © 2013 Society of Chemical Industry.

Testing Strategies for Model-Based Development

NASA Technical Reports Server (NTRS)

Heimdahl, Mats P. E.; Whalen, Mike; Rajan, Ajitha; Miller, Steven P.

2006-01-01

This report presents an approach for testing artifacts generated in a model-based development process. This approach divides the traditional testing process into two parts: requirements-based testing (validation testing) which determines whether the model implements the high-level requirements and model-based testing (conformance testing) which determines whether the code generated from a model is behaviorally equivalent to the model. The goals of the two processes differ significantly and this report explores suitable testing metrics and automation strategies for each. To support requirements-based testing, we define novel objective requirements coverage metrics similar to existing specification and code coverage metrics. For model-based testing, we briefly describe automation strategies and examine the fault-finding capability of different structural coverage metrics using tests automatically generated from the model.

Nucleation, Growth, and Alignment of Poly(3-hexylthiophene) Nanofibers for High-Performance OFETs.

PubMed

Persson, Nils E; Chu, Ping-Hsun; McBride, Michael; Grover, Martha; Reichmanis, Elsa

2017-04-18

Conjugated semiconducting polymers have been the subject of intense study for over two decades with promising advances toward a printable electronics manufacturing ecosystem. These materials will deliver functional electronic devices that are lightweight, flexible, large-area, and cost-effective, with applications ranging from biomedical sensors to solar cells. Synthesis of novel molecules has led to significant improvements in charge carrier mobility, a defining electrical performance metric for many applications. However, the solution processing and thin film deposition of conjugated polymers must also be properly controlled to obtain reproducible device performance. This has led to an abundance of research on the process-structure-property relationships governing the microstructural evolution of the model semicrystalline poly(3-hexylthiophene) (P3HT) as applied to organic field effect transistor (OFET) fabrication. What followed was the production of an expansive body of work on the crystallization, self-assembly, and charge transport behavior of this semiflexible polymer whose strong π-π stacking interactions allow for highly creative methods of structural control, including the modulation of solvent and solution properties, flow-induced crystallization and alignment techniques, structural templating, and solid-state thermal and mechanical processing. This Account relates recent progress in the microstructural control of P3HT thin films through the nucleation, growth, and alignment of P3HT nanofibers. Solution-based nanofiber formation allows one to develop structural order prior to thin film deposition, mitigating the need for intricate deposition processes and enabling the use of batch and continuous chemical processing steps. Fiber growth is framed as a traditional crystallization problem, with the balance between nucleation and growth rates determining the fiber size and ultimately the distribution of grain boundaries in the solid state. Control of nucleation can be accomplished through a sonication-based seeding procedure, while growth can be modulated through supersaturation control via the tuning of solvent quality, the use of UV irradiation or through aging. These principles carry over to the flow-induced growth of P3HT nanofibers in a continuous microfluidic processing system, leading to thin films with significantly enhanced mobility. Further gains can be made by promoting long-range polymer chain alignment, achieved by depositing nanofibers through shear-based coating methods that promote high fiber packing density and alignment. All of these developments in processing were carried out on a standard OFET platform, enabling us to generalize quantitative structure-property relationships from structural data sources such as UV-vis, AFM, and GIWAXS. It is shown that a linear correlation exists between mobility and the in-plane orientational order of nanofibers, as extracted from AFM images using advanced computer vision software developed by our group. Herein, we discuss data-driven approaches to the determination of process-structure-property relationships, as well as the transferability of structural control strategies for P3HT to other conjugated polymer systems and applications.

High-throughput determination of structural phase diagram and constituent phases using GRENDEL

NASA Astrophysics Data System (ADS)

Kusne, A. G.; Keller, D.; Anderson, A.; Zaban, A.; Takeuchi, I.

2015-11-01

Advances in high-throughput materials fabrication and characterization techniques have resulted in faster rates of data collection and rapidly growing volumes of experimental data. To convert this mass of information into actionable knowledge of material process-structure-property relationships requires high-throughput data analysis techniques. This work explores the use of the Graph-based endmember extraction and labeling (GRENDEL) algorithm as a high-throughput method for analyzing structural data from combinatorial libraries, specifically, to determine phase diagrams and constituent phases from both x-ray diffraction and Raman spectral data. The GRENDEL algorithm utilizes a set of physical constraints to optimize results and provides a framework by which additional physics-based constraints can be easily incorporated. GRENDEL also permits the integration of database data as shown by the use of critically evaluated data from the Inorganic Crystal Structure Database in the x-ray diffraction data analysis. Also the Sunburst radial tree map is demonstrated as a tool to visualize material structure-property relationships found through graph based analysis.

The application of data mining and cloud computing techniques in data-driven models for structural health monitoring

NASA Astrophysics Data System (ADS)

Khazaeli, S.; Ravandi, A. G.; Banerji, S.; Bagchi, A.

2016-04-01

Recently, data-driven models for Structural Health Monitoring (SHM) have been of great interest among many researchers. In data-driven models, the sensed data are processed to determine the structural performance and evaluate the damages of an instrumented structure without necessitating the mathematical modeling of the structure. A framework of data-driven models for online assessment of the condition of a structure has been developed here. The developed framework is intended for automated evaluation of the monitoring data and structural performance by the Internet technology and resources. The main challenges in developing such framework include: (a) utilizing the sensor measurements to estimate and localize the induced damage in a structure by means of signal processing and data mining techniques, and (b) optimizing the computing and storage resources with the aid of cloud services. The main focus in this paper is to demonstrate the efficiency of the proposed framework for real-time damage detection of a multi-story shear-building structure in two damage scenarios (change in mass and stiffness) in various locations. Several features are extracted from the sensed data by signal processing techniques and statistical methods. Machine learning algorithms are deployed to select damage-sensitive features as well as classifying the data to trace the anomaly in the response of the structure. Here, the cloud computing resources from Amazon Web Services (AWS) have been used to implement the proposed framework.

Determination of mechanical properties for cement-treated aggregate base : final report.

DOT National Transportation Integrated Search

2017-06-01

The Virginia Department of Transportation (VDOT) currently follows pavement design procedures for all new and rehabilitated pavements based on the 1993 AASHTO Guide for Design of Pavement Structures. VDOTs Materials Division is in the process of i...

Using Cooperative Learning Structures in Physical Education.

ERIC Educational Resources Information Center

Dyson, Ben; Grineski, Steve

2001-01-01

Research has determined that cooperative learning has positive effects in physical education. This article presents five important components of cooperative learning to help physical educators maximize learning (team formation, positive interdependence, individual accountability, positive social interaction, and group processing), describing five…

The social neuroscience and the theory of integrative levels.

PubMed

Bello-Morales, Raquel; Delgado-García, José María

2015-01-01

The theory of integrative levels provides a general description of the evolution of matter through successive orders of complexity and integration. Along its development, material forms pass through different levels of organization, such as physical, chemical, biological or sociological. The appearance of novel structures and dynamics during this process of development of matter in complex systems has been called emergence. Social neuroscience (SN), an interdisciplinary field that aims to investigate the biological mechanisms that underlie social structures, processes, and behavior and the influences between social and biological levels of organization, has affirmed the necessity for including social context as an essential element to understand the human behavior. To do this, SN proposes a multilevel integrative approach by means of three principles: multiple determinism, nonadditive determinism and reciprocal determinism. These theoretical principles seem to share the basic tenets of the theory of integrative levels but, in this paper, we aim to reveal the differences among both doctrines. First, SN asserts that combination of neural and social variables can produce emergent phenomena that would not be predictable from a neuroscientific or social psychological analysis alone; SN also suggests that to achieve a complete understanding of social structures we should use an integrative analysis that encompasses levels of organization ranging from the genetic level to the social one; finally, SN establishes that there can be mutual influences between biological and social factors in determining behavior, accepting, therefore, a double influence, upward from biology to social level, and downward, from social level to biology. In contrast, following the theory of integrative levels, emergent phenomena are not produced by the combination of variables from two levels, but by the increment of complexity at one level. In addition, the social behavior and structures might be contemplated not as the result of mixing or summing social and biological influences, but as emergent phenomena that should be described with its own laws. Finally, following the integrative levels view, influences upward, from biology to social level, and downward, from social level to biology, might not be equivalent, since the bottom-up processes are emergent and the downward causation (DC) is not.

The social neuroscience and the theory of integrative levels

PubMed Central

Bello-Morales, Raquel; Delgado-García, José María

2015-01-01

The theory of integrative levels provides a general description of the evolution of matter through successive orders of complexity and integration. Along its development, material forms pass through different levels of organization, such as physical, chemical, biological or sociological. The appearance of novel structures and dynamics during this process of development of matter in complex systems has been called emergence. Social neuroscience (SN), an interdisciplinary field that aims to investigate the biological mechanisms that underlie social structures, processes, and behavior and the influences between social and biological levels of organization, has affirmed the necessity for including social context as an essential element to understand the human behavior. To do this, SN proposes a multilevel integrative approach by means of three principles: multiple determinism, nonadditive determinism and reciprocal determinism. These theoretical principles seem to share the basic tenets of the theory of integrative levels but, in this paper, we aim to reveal the differences among both doctrines. First, SN asserts that combination of neural and social variables can produce emergent phenomena that would not be predictable from a neuroscientific or social psychological analysis alone; SN also suggests that to achieve a complete understanding of social structures we should use an integrative analysis that encompasses levels of organization ranging from the genetic level to the social one; finally, SN establishes that there can be mutual influences between biological and social factors in determining behavior, accepting, therefore, a double influence, upward from biology to social level, and downward, from social level to biology. In contrast, following the theory of integrative levels, emergent phenomena are not produced by the combination of variables from two levels, but by the increment of complexity at one level. In addition, the social behavior and structures might be contemplated not as the result of mixing or summing social and biological influences, but as emergent phenomena that should be described with its own laws. Finally, following the integrative levels view, influences upward, from biology to social level, and downward, from social level to biology, might not be equivalent, since the bottom-up processes are emergent and the downward causation (DC) is not. PMID:26578909

Quasi-Static Probabilistic Structural Analyses Process and Criteria

NASA Technical Reports Server (NTRS)

Goldberg, B.; Verderaime, V.

1999-01-01

Current deterministic structural methods are easily applied to substructures and components, and analysts have built great design insights and confidence in them over the years. However, deterministic methods cannot support systems risk analyses, and it was recently reported that deterministic treatment of statistical data is inconsistent with error propagation laws that can result in unevenly conservative structural predictions. Assuming non-nal distributions and using statistical data formats throughout prevailing stress deterministic processes lead to a safety factor in statistical format, which integrated into the safety index, provides a safety factor and first order reliability relationship. The embedded safety factor in the safety index expression allows a historically based risk to be determined and verified over a variety of quasi-static metallic substructures consistent with the traditional safety factor methods and NASA Std. 5001 criteria.

Application of Solid-State NMR to Reveal Structural Differences in Cefazolin Sodium Pentahydrate from Different Manufacturing Processes

NASA Astrophysics Data System (ADS)

Tian, Ye; Wang, Wei D.; Zou, Wen-Bo; Qian, Jian-Qin; Hu, Chang-Qin

2018-04-01

The solid form of an active pharmaceutical ingredient is important when developing a new chemical entity. A solid understanding of the crystal structure and morphology that affect the mechanical and physical characteristics of pharmaceutical powders determines the manufacturing process. Solid-state NMR, thermogravimetric analysis, X-ray diffraction, and Fourier-transform infrared spectroscopy were combined with theoretical calculation to investigate different crystal packings of α-cefazolin sodium from three different vendors and conformational polymorphism was identified to exist in the α-cefazolin sodium. Marginal differences observed among CEZ-Na pentahydrate 1, 2, and 3 were speculated as the proportion of conformation 2. Understanding the differences in the polymorphic structure of α-cefazolin sodium may help with making modifications to incorporate new knowledge with a product’s development.

Single-fluorophore monitoring of DNA hybridization for investigating the effect of secondary structure on the nucleation step.

PubMed

Jo, Joon-Jung; Kim, Min-Ji; Son, Jung-Tae; Kim, Jandi; Shin, Jong-Shik

2009-07-17

Nucleic acid hybridization is one of the essential biological processes involved in storage and transmission of genetic information. Here we quantitatively determined the effect of secondary structure on the hybridization activation energy using structurally defined oligonucleotides. It turned out that activation energy is linearly proportional to the length of a single-stranded region flanking a nucleation site, generating a 0.18 kcal/mol energy barrier per nucleotide. Based on this result, we propose that the presence of single-stranded segments available for non-productive base pairing with a nucleation counterpart extends the searching process for nucleation sites to find a perfect match. This result may provide insights into rational selection of a target mRNA site for siRNA and antisense gene silencing.

Programmable assembly of pressure sensors using pattern-forming bacteria.

PubMed

Cao, Yangxiaolu; Feng, Yaying; Ryser, Marc D; Zhu, Kui; Herschlag, Gregory; Cao, Changyong; Marusak, Katherine; Zauscher, Stefan; You, Lingchong

2017-11-01

Biological systems can generate microstructured materials that combine organic and inorganic components and possess diverse physical and chemical properties. However, these natural processes in materials fabrication are not readily programmable. Here, we use a synthetic-biology approach to assemble patterned materials. We demonstrate programmable fabrication of three-dimensional (3D) materials by printing engineered self-patterning bacteria on permeable membranes that serve as a structural scaffold. Application of gold nanoparticles to the colonies creates hybrid organic-inorganic dome structures. The dynamics of the dome structures' response to pressure is determined by their geometry (colony size, dome height, and pattern), which is easily modified by varying the properties of the membrane (e.g., pore size and hydrophobicity). We generate resettable pressure sensors that process signals in response to varying pressure intensity and duration.

Large 3D direct laser written scaffolds for tissue engineering applications

NASA Astrophysics Data System (ADS)

Trautmann, Anika; Rüth, Marieke; Lemke, Horst-Dieter; Walther, Thomas; Hellmann, Ralf

2018-01-01

We report on the fabrication of three-dimensional direct laser written scaffolds for tissue engineering and the seeding of primary fibroblasts on these structures. Scaffolds are realized by two-photon absorption induced polymerization in the inorganic-organic hybrid polymer OrmoComp using a 515 nm femtosecond laser. A nonstop single-line single-pass writing process is implemented in order to produce periodic reproducible large scaled structures with a dimension in the range of several millimeters and reduce process time to less than one hour. This method allows us to determine optimized process parameters for writing stable structures while achieving pore sizes ranging from 5 μm to 90 μm and a scanning speed of up to 5 mm/s. After a multi-stage post-treatment, normal human dermal fibroblasts are applied to the scaffolds to test if these macroscopic structures with large surface and numerous small gaps between the pores provide nontoxic conditions. Furthermore, we study the cell behavior in this environment and observe both cell growth on as well as ingrowth on the three-dimensional structures. In particular, fibroblasts adhere and grow also on the vertical walls of the scaffolds.

Spying on the neighbors' pool

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xantheas, S. S.

2016-12-01

The structure and properties of the aqueous proton is of fundamental interest in many areas of chemistry and biology. Acids and bases are molecules that are able to transfer (donate / accept) a proton according to Brønsted and Lowry, a process that was further explained by Lewis in terms of changes in their electronic structure in an attempt to offer a generalization of the Arrhenius theory. Simple proton transfers or the ones coupled to an electron transfer determine speciation, valence and reactivity in aqueous media and explain electrochemical processes, while voltage-gated proton channels have severe implications to the function ofmore » a number of tissues and species.« less

Computer simulation of low-temperature composites sintering processes for additive technologies

NASA Astrophysics Data System (ADS)

Tovpinets, A. O.; Leytsin, V. N.; Dmitrieva, M. A.

2017-12-01

This is impact research of mixture raw components characteristics on the low-temperature composites structure formation during the sintering process. The obtained results showed that the structure determination of initial compacts obtained after thermal destruction of the polymer binder lets quantify the concentrations of main components and the refractory crystalline product of thermal destruction. Accounting for the distribution of thermal destruction refractory product allows us to refine the forecast of thermal stresses in the matrix of sintered composite. The presented results can be considered as a basis for optimization of initial compositions of multilayer low-temperature composites obtained by additive technologies.

Influence of dietary fiber on inflammatory bowel disease and colon cancer: importance of fermentation pattern.

PubMed

Rose, Devin J; DeMeo, Mark T; Keshavarzian, Ali; Hamaker, Bruce R

2007-02-01

The benefits of dietary fiber on inflammatory bowel disease may be related to the fermentative production of butyrate in the colon, which appears to decrease the inflammatory response. The benefits of dietary fiber against colon cancer may be related to both fermentative and non-fermentative processes, although poorly fermentable fibers appear more influential. Dietary fiber fermentation profiles are important in determining optimal fibers for colonic health, and may be a function of structure, processing conditions, and other food components. A greater understanding of the relationships between fermentation rate and dietary fiber structure would allow for development of dietary fibers for optimum colonic health.

Frequency response of electrochemical cells

NASA Technical Reports Server (NTRS)

Thomas, Daniel L.

1989-01-01

Impedance concepts can be applied to the analysis of battery electrodes, yielding information about the structure of the electrode and the processes occurring in the electrode. Structural parameters such as the specific area (surface area per gram of electrode) can be estimated. Electrode variables such as surface overpotential, ohmic losses, and diffusion limitations may be studied. Nickel and cadmium electrodes were studied by measuring the ac impedance as a function of frequency, and the specific areas that were determined were well within the range of specific areas determined from BET measurements. Impedance spectra were measured for the nickel and cadmium electrodes, and for a 20 A-hr NiCd battery as functions of the state of charge. More work is needed to determine the feasibility of using frequency response as a nondestructive testing technique for batteries.

Status and directions of modified tribological surfaces by ion processes

NASA Technical Reports Server (NTRS)

Spalvins, Talivaldis

1988-01-01

An overview is presented of recent advances in modifying contacting surfaces in motion by the various ion assisted surface coating/modification processes to reduce and control tribological failures. The ion assisted coating processes and the surface modification processes offer the greatest potential to custom tailor and optimize the tribological performance. Hard, wear resistant and low shear coatings deposited by the ion assisted processes are discussed. Primarily the recent advances of sputtered MoS2 ion plated Au, Ag, Pb lubricating films and sputtered and ion plated hard, wear resistant TiN, HfN, TiC films are described in terms of structural property performance interrelationships which lead to improved adhesion, cohesion, nucleation, morphological growth, density, film thickness as determined by structural and chemical characterization and frictional and wear behavior. Also, the recent tribological advances using the surface modification processes such as ion implantation, ion beam mixing is discussed with emphasis on the development of lubricous high temperature ceramic surfaces.

Behaviors and kinetics of toluene adsorption-desorption on activated carbons with varying pore structure.

PubMed

Yang, Xi; Yi, Honghong; Tang, Xiaolong; Zhao, Shunzheng; Yang, Zhongyu; Ma, Yueqiang; Feng, Tiecheng; Cui, Xiaoxu

2018-05-01

This work was undertaken to investigate the behaviors and kinetics of toluene adsorption and desorption on activated carbons with varying pore structure. Five kinds of activated carbon from different raw materials were selected. Adsorption isotherms and breakthrough curves for toluene were measured. Langmuir and Freundlich equations were fitted to the equilibrium data, and the Freundlich equation was more suitable for simulating toluene adsorption. The process consisted of monolayer, multilayer and partial active site adsorption types. The effect of the pore structure of the activated carbons on toluene adsorption capacity was investigated. The quasi-first-order model was more suitable for describing the process than the quasi-second-order model. The adsorption data was also modeled by the internal particle diffusion model and it was found that the adsorption process could be divided into three stages. In the external surface adsorption process, the rate depended on the specific surface area. During the particle diffusion stage, pore structure and volume were the main factors affecting adsorption rate. In the final equilibrium stage, the rate was determined by the ratio of meso- and macro-pores to total pore volume. The rate over the whole adsorption process was dominated by the toluene concentration. The desorption behavior of toluene on activated carbons was investigated, and the process was divided into heat and mass transfer parts corresponding to emission and diffusion mechanisms, respectively. Physical adsorption played the main role during the adsorption process. Copyright © 2017. Published by Elsevier B.V.

Structural Basis for Guide RNA Processing and Seed-Dependent DNA Targeting by CRISPR-Cas12a.

PubMed

Swarts, Daan C; van der Oost, John; Jinek, Martin

2017-04-20

The CRISPR-associated protein Cas12a (Cpf1), which has been repurposed for genome editing, possesses two distinct nuclease activities: endoribonuclease activity for processing its own guide RNAs and RNA-guided DNase activity for target DNA cleavage. To elucidate the molecular basis of both activities, we determined crystal structures of Francisella novicida Cas12a bound to guide RNA and in complex with an R-loop formed by a non-cleavable guide RNA precursor and a full-length target DNA. Corroborated by biochemical experiments, these structures reveal the mechanisms of guide RNA processing and pre-ordering of the seed sequence in the guide RNA that primes Cas12a for target DNA binding. Furthermore, the R-loop complex structure reveals the strand displacement mechanism that facilitates guide-target hybridization and suggests a mechanism for double-stranded DNA cleavage involving a single active site. Together, these insights advance our mechanistic understanding of Cas12a enzymes and may contribute to further development of genome editing technologies. Copyright © 2017 Elsevier Inc. All rights reserved.

Structure of the transporter associated with antigen processing trapped by herpes simplex virus

PubMed Central

Oldham, Michael L; Grigorieff, Nikolaus; Chen, Jue

2016-01-01

The transporter associated with antigen processing (TAP) is an ATP-binding cassette (ABC) transporter essential to cellular immunity against viral infection. Some persistent viruses have evolved strategies to inhibit TAP so that they may go undetected by the immune system. The herpes simplex virus for example evades immune surveillance by blocking peptide transport with a small viral protein ICP47. In this study, we determined the structure of human TAP bound to ICP47 by electron cryo-microscopy (cryo-EM) to 4.0 Å. The structure shows that ICP47 traps TAP in an inactive conformation distinct from the normal transport cycle. The specificity and potency of ICP47 inhibition result from contacts between the tip of the helical hairpin and the apex of the transmembrane cavity. This work provides a clear molecular description of immune evasion by a persistent virus. It also establishes the molecular structure of TAP to facilitate mechanistic studies of the antigen presentation process. DOI: http://dx.doi.org/10.7554/eLife.21829.001 PMID:27935481

Complex furrows in a 2D epithelial sheet code the 3D structure of a beetle horn.

PubMed

Matsuda, Keisuke; Gotoh, Hiroki; Tajika, Yuki; Sushida, Takamichi; Aonuma, Hitoshi; Niimi, Teruyuki; Akiyama, Masakazu; Inoue, Yasuhiro; Kondo, Shigeru

2017-10-24

The external organs of holometabolous insects are generated through two consecutive processes: the development of imaginal primordia and their subsequent transformation into the adult structures. During the latter process, many different phenomena at the cellular level (e.g. cell shape changes, cell migration, folding and unfolding of epithelial sheets) contribute to the drastic changes observed in size and shape. Because of this complexity, the logic behind the formation of the 3D structure of adult external organs remains largely unknown. In this report, we investigated the metamorphosis of the horn in the Japanese rhinoceros beetle Trypoxylus dichotomus. The horn primordia is essentially a 2D epithelial cell sheet with dense furrows. We experimentally unfolded these furrows using three different methods and found that the furrow pattern solely determines the 3D horn structure, indicating that horn formation in beetles occurs by two distinct processes: formation of the furrows and subsequently unfolding them. We postulate that this developmental simplicity offers an inherent advantage to understanding the principles that guide 3D morphogenesis in insects.

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

PubMed

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

2018-03-01

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

Automation of orbit determination functions for National Aeronautics and Space Administration (NASA)-supported satellite missions

NASA Technical Reports Server (NTRS)

Mardirossian, H.; Beri, A. C.; Doll, C. E.

1990-01-01

The Flight Dynamics Facility (FDF) at Goddard Space Flight Center (GSFC) provides spacecraft trajectory determination for a wide variety of National Aeronautics and Space Administration (NASA)-supported satellite missions, using the Tracking Data Relay Satellite System (TDRSS) and Ground Spaceflight and Tracking Data Network (GSTDN). To take advantage of computerized decision making processes that can be used in spacecraft navigation, the Orbit Determination Automation System (ODAS) was designed, developed, and implemented as a prototype system to automate orbit determination (OD) and orbit quality assurance (QA) functions performed by orbit operations. Based on a machine-resident generic schedule and predetermined mission-dependent QA criteria, ODAS autonomously activates an interface with the existing trajectory determination system using a batch least-squares differential correction algorithm to perform the basic OD functions. The computational parameters determined during the OD are processed to make computerized decisions regarding QA, and a controlled recovery process is activated when the criteria are not satisfied. The complete cycle is autonomous and continuous. ODAS was extensively tested for performance under conditions resembling actual operational conditions and found to be effective and reliable for extended autonomous OD. Details of the system structure and function are discussed, and test results are presented.

Automation of orbit determination functions for National Aeronautics and Space Administration (NASA)-supported satellite missions

NASA Technical Reports Server (NTRS)

Mardirossian, H.; Heuerman, K.; Beri, A.; Samii, M. V.; Doll, C. E.

1989-01-01

The Flight Dynamics Facility (FDF) at Goddard Space Flight Center (GSFC) provides spacecraft trajectory determination for a wide variety of National Aeronautics and Space Administration (NASA)-supported satellite missions, using the Tracking Data Relay Satellite System (TDRSS) and Ground Spaceflight and Tracking Data Network (GSTDN). To take advantage of computerized decision making processes that can be used in spacecraft navigation, the Orbit Determination Automation System (ODAS) was designed, developed, and implemented as a prototype system to automate orbit determination (OD) and orbit quality assurance (QA) functions performed by orbit operations. Based on a machine-resident generic schedule and predetermined mission-dependent QA criteria, ODAS autonomously activates an interface with the existing trajectory determination system using a batch least-squares differential correction algorithm to perform the basic OD functions. The computational parameters determined during the OD are processed to make computerized decisions regarding QA, and a controlled recovery process isactivated when the criteria are not satisfied. The complete cycle is autonomous and continuous. ODAS was extensively tested for performance under conditions resembling actual operational conditions and found to be effective and reliable for extended autonomous OD. Details of the system structure and function are discussed, and test results are presented.

Understanding Business Models in Health Care.

PubMed

Sharan, Alok D; Schroeder, Gregory D; West, Michael E; Vaccaro, Alexander R

2016-05-01

The increasing focus on the costs of care is forcing health care organizations to critically look at their basic set of processes and activities, to determine what type of value they can deliver. A business model describes the resources, processes, and cost assumptions that an organization makes that will lead to the delivery of a unique value proposition to a customer. As health care organizations are beginning to transform their structure in preparation for a value-based delivery system, understanding business model theory can help in the redesign process.

A review on the relationship between food structure, processing, and bioavailability.

PubMed

Sensoy, Ilkay

2014-01-01

This review highlights the effects of processing and food matrix on bioaccessibility and bioavailability of functional components. Human digestive system is reviewed as an element in bioavailability. Methods for bioaccessibility and bioavailability determination are described. Information about the location of functional compounds in the tissue is presented to portray the matrix information. Research data on the effects of food matrix and processing on bioaccessibility and bioavailability are summarized. Finally, trends in the development of functional component delivery systems are included.

Structure-to-property relationships in fuel cell catalyst supports: Correlation of surface chemistry and morphology with oxidation resistance of carbon blacks

NASA Astrophysics Data System (ADS)

Artyushkova, Kateryna; Pylypenko, Svitlana; Dowlapalli, Madhu; Atanassov, Plamen

2012-09-01

Linking durability of carbon blacks, expressed as their oxidation resistance, used in PEMFCs as catalyst supports, with their chemistry and morphology is an important task towards designing carbon blacks with desired properties. Structure-to-property relationship between surface chemistry determined by X-ray photoelectron spectroscopy (XPS), morphological structure determined by digital image processing of scanning electron microscopy (SEM) images, physical properties, and electrochemical corrosion behavior determined in an air-breathing gas-diffusion electrode is studied for several un-altered and several modified carbon blacks. We are showing that surface chemistry, graphitic content and certain physical characteristics such as Brunauer-Emmett-Teller (BET) surface area and pore volume, determined by nitrogen adsorptions are not sufficient to explain high corrosion instability of types of carbon blacks. Inclusion of morphological characteristics, such as roughness, texture and shape parameters provide for more inclusive description and therefore more complete structure-to-property correlations of corrosion behavior of carbon blacks. This paper presents the first direct statistically-derived structure-to-property relationship, developed by multivariate analysis (MVA) that links chemical and physical structural properties of the carbon blacks to their critical properties as supports for PEMFC catalysts. We have found that balance between electrocatalytic activity and high resistance towards oxidation and corrosion is achieved by balance between amount of graphitic content and surface oxide coverage, smaller overall roughness and, finally, larger amount of big elongated and loose, and, hypothetically, more hydrophobic pores.

Update of the equations of the limit state of the structural material with the realization of their deformation

NASA Astrophysics Data System (ADS)

Zenkov, E. V.

2018-01-01

Two methods are given in the article by considering the type of stressed-Deformed state (SDS) based on equations limit condition and analyzing the results of laboratory tests of special specimens for mechanical testing, focus having destruction thereof in the same view of SDS as in focus possible destruction of the structural member. The considered limited use of these methods in terms of considering physically consistent strength criterion type Pisarenko-Lebedev. A revised design-experimental procedure for determining the strength of the material of the structure, combining therein the elements of these two methods, consisting in determining the strength parameters of construction material, entering criterion equation Pisarenko-Lebedev, considering the actual appearance of the region-of-interest SDS structure. The implementation of the procedure is performed on the basis of the selection of the respective experimental laboratory specimens for mechanical testing, plan SDS in working zone coinciding with a SDS: structure whose strength is evaluated. The refinement process limit state equations demonstrated in determining 50CrV4 steel strength parameters, being in a state of biaxial stretching. Design-experimentally determined by, that steel for a given voltage limit value is almost a quarter of its value is reduced compared to the conventional tensile strength. value is reduced compared to the conventional tensile strength.

Climate effects and feedback structure determining weed population dynamics in a long-term experiment.

PubMed

Lima, Mauricio; Navarrete, Luis; González-Andujar, José Luis

2012-01-01

Pest control is one of the areas in which population dynamic theory has been successfully applied to solve practical problems. However, the links between population dynamic theory and model construction have been less emphasized in the management and control of weed populations. Most management models of weed population dynamics have emphasized the role of the endogenous process, but the role of exogenous variables such as climate have been ignored in the study of weed populations and their management. Here, we use long-term data (22 years) on two annual weed species from a locality in Central Spain to determine the importance of endogenous and exogenous processes (local and large-scale climate factors). Our modeling study determined two different feedback structures and climate effects in the two weed species analyzed. While Descurainia sophia exhibited a second-order feedback and low climate influence, Veronica hederifolia was characterized by a first-order feedback structure and important effects from temperature and rainfall. Our results strongly suggest the importance of theoretical population dynamics in understanding plant population systems. Moreover, the use of this approach, discerning between the effect of exogenous and endogenous factors, can be fundamental to applying weed management practices in agricultural systems and to controlling invasive weedy species. This is a radical change from most approaches currently used to guide weed and invasive weedy species managements.

Climate Effects and Feedback Structure Determining Weed Population Dynamics in a Long-Term Experiment

PubMed Central

Lima, Mauricio; Navarrete, Luis; González-Andujar, José Luis

2012-01-01

Pest control is one of the areas in which population dynamic theory has been successfully applied to solve practical problems. However, the links between population dynamic theory and model construction have been less emphasized in the management and control of weed populations. Most management models of weed population dynamics have emphasized the role of the endogenous process, but the role of exogenous variables such as climate have been ignored in the study of weed populations and their management. Here, we use long-term data (22 years) on two annual weed species from a locality in Central Spain to determine the importance of endogenous and exogenous processes (local and large-scale climate factors). Our modeling study determined two different feedback structures and climate effects in the two weed species analyzed. While Descurainia sophia exhibited a second-order feedback and low climate influence, Veronica hederifolia was characterized by a first-order feedback structure and important effects from temperature and rainfall. Our results strongly suggest the importance of theoretical population dynamics in understanding plant population systems. Moreover, the use of this approach, discerning between the effect of exogenous and endogenous factors, can be fundamental to applying weed management practices in agricultural systems and to controlling invasive weedy species. This is a radical change from most approaches currently used to guide weed and invasive weedy species managements. PMID:22272362

DOE Office of Scientific and Technical Information (OSTI.GOV)

Januszyk, Kurt; Liu, Quansheng; Lima, Christopher D.

The eukaryotic RNA exosome is a highly conserved multi-subunit complex that catalyzes degradation and processing of coding and noncoding RNA. A noncatalytic nine-subunit exosome core interacts with Rrp44 and Rrp6, two subunits that possess processive and distributive 3'-to-5' exoribonuclease activity, respectively. While both Rrp6 and Rrp44 are responsible for RNA processing in budding yeast, Rrp6 may play a more prominent role in processing, as it has been demonstrated to be inhibited by stable RNA secondary structure in vitro and because the null allele in budding yeast leads to the buildup of specific structured RNA substrates. Human RRP6, otherwise known asmore » PM/SCL-100 or EXOSC10, shares sequence similarity to budding yeast Rrp6 and is proposed to catalyze 3'-to-5' exoribonuclease activity on a variety of nuclear transcripts including ribosomal RNA subunits, RNA that has been poly-adenylated by TRAMP, as well as other nuclear RNA transcripts destined for processing and/or destruction. To characterize human RRP6, we expressed the full-length enzyme as well as truncation mutants that retain catalytic activity, compared their activities to analogous constructs for Saccharomyces cerevisiae Rrp6, and determined the X-ray structure of a human construct containing the exoribonuclease and HRDC domains that retains catalytic activity. Structural data show that the human active site is more exposed when compared to the yeast structure, and biochemical data suggest that this feature may play a role in the ability of human RRP6 to productively engage and degrade structured RNA substrates more effectively than the analogous budding yeast enzyme.« less

Correlation of lattice defects and thermal processing in the crystallization of titania nanotube arrays

NASA Astrophysics Data System (ADS)

Hosseinpour, Pegah M.; Yung, Daniel; Panaitescu, Eugen; Heiman, Don; Menon, Latika; Budil, David; Lewis, Laura H.

2014-12-01

Titania nanotubes have the potential to be employed in a wide range of energy-related applications such as solar energy-harvesting devices and hydrogen production. As the functionality of titania nanostructures is critically affected by their morphology and crystallinity, it is necessary to understand and control these factors in order to engineer useful materials for green applications. In this study, electrochemically-synthesized titania nanotube arrays were thermally processed in inert and reducing environments to isolate the role of post-synthesis processing conditions on the crystallization behavior, electronic structure and morphology development in titania nanotubes, correlated with the nanotube functionality. Structural and calorimetric studies revealed that as-synthesized amorphous nanotubes crystallize to form the anatase structure in a three-stage process that is facilitated by the creation of structural defects. It is concluded that processing in a reducing gas atmosphere versus in an inert environment provides a larger unit cell volume and a higher concentration of Ti3+ associated with oxygen vacancies, thereby reducing the activation energy of crystallization. Further, post-synthesis annealing in either reducing or inert atmospheres produces pronounced morphological changes, confirming that the nanotube arrays thermally transform into a porous morphology consisting of a fragmented tubular architecture surrounded by a network of connected nanoparticles. This study links explicit data concerning morphology, crystallization and defects, and shows that the annealing gas environment determines the details of the crystal structure, the electronic structure and the morphology of titania nanotubes. These factors, in turn, impact the charge transport and consequently the functionality of these nanotubes as photocatalysts.

Weight optimization of large span steel truss structures with genetic algorithm

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mojolic, Cristian; Hulea, Radu; Pârv, Bianca Roxana

2015-03-10

The paper presents the weight optimization process of the main steel truss that supports the Slatina Sport Hall roof. The structure was loaded with self-weight, dead loads, live loads, snow, wind and temperature, grouped in eleven load cases. The optimization of the structure was made using genetic algorithms implemented in a Matlab code. A total number of four different cases were taken into consideration when trying to determine the lowest weight of the structure, depending on the types of connections with the concrete structure ( types of supports, bearing modes), and the possibility of the lower truss chord nodes tomore » change their vertical position. A number of restrictions for tension, maximum displacement and buckling were enforced on the elements, and the cross sections are chosen by the program from a user data base. The results in each of the four cases were analyzed in terms of weight, element tension, element section and displacement. The paper presents the optimization process and the conclusions drawn.« less

Micrometer-scale fabrication of complex three dimensional lattice + basis structures in silicon

DOE PAGES

Burckel, D. Bruce; Resnick, Paul J.; Finnegan, Patrick S.; ...

2015-01-01

A complementary metal oxide semiconductor (CMOS) compatible version of membrane projection lithography (MPL) for fabrication of micrometer-scale three-dimensional structures is presented. The approach uses all inorganic materials and standard CMOS processing equipment. In a single layer, MPL is capable of creating all 5 2D-Bravais lattices. Furthermore, standard semiconductor processing steps can be used in a layer-by-layer approach to create fully three dimensional structures with any of the 14 3D-Bravais lattices. The unit cell basis is determined by the projection of the membrane pattern, with many degrees of freedom for defining functional inclusions. Here we demonstrate several unique structural motifs, andmore » characterize 2D arrays of unit cells with split ring resonators in a silicon matrix. The structures exhibit strong polarization dependent resonances and, for properly oriented split ring resonators (SRRs), coupling to the magnetic field of a normally incident transverse electromagnetic wave, a response unique to 3D inclusions.« less

Geophysical Monitoring Station (GEMS)

NASA Astrophysics Data System (ADS)

Banerdt, B.; Dehant, V. M.; Lognonne, P.; Smrekar, S. E.; Spohn, T.; GEMS Mission Team

2011-12-01

GEMS (GEophysical Monitoring Station) is one of three missions undergoing Phase A development for possible selection by NASA's Discovery Program. If selected, GEMS will perform the first comprehensive surface-based geophysical investigation of Mars, filling a longstanding gap in the scientific exploration of the solar system. It will illuminate the fundamental processes of terrestrial planet formation and evolution, providing unique and critical information about the initial accretion of the planet, the formation and differentiation of the core and crust, and the subsequent evolution of the interior. The scientific goals of GEMS are to understand the formation and evolution of terrestrial planets through investigation of the interior structure and processes of Mars and to determine its present level of tectonic activity and impact flux. A straightforward set of scientific objectives address these goals: 1) Determine the size, composition and physical state of the core; 2) Determine the thickness and structure of the crust; 3) Determine the composition and structure of the mantle; 4) Determine the thermal state of the interior; 5) Measure the rate and distribution of internal seismic activity; and 6) Measure the rate of impacts on the surface. To accomplish these objectives, GEMS carries a tightly-focused payload consisting of 3 investigations: 1) SEIS, a 6-component, very-broad-band seismometer, with careful thermal compensation/control and a sensitivity comparable to the best terrestrial instruments across a frequency range of 1 mHz to 50 Hz; 2) HP3 (Heat Flow and Physical Properties Package), an instrumented self-penetrating mole system that trails a string of temperature sensors to measure the thermal gradient and conductivity of the upper several meters, and thus the planetary heat flux; and 3) RISE (Rotation and Interior Structure Experiment), which would use the spacecraft X-band communication system to provide precision tracking for planetary dynamical studies. The two instruments are moved from the lander deck to the martian surface by an Instrument Deployment Arm, with an appropriate location identified using an Instrument Deployment Camera. In order to ensure low risk within the tight Discovery cost limits, GEMS reuses the successful Lockheed Martin Phoenix spacecraft design, with a cruise and EDL system that has demonstrated capability for safe landing on Mars with well-understood costs. To take full advantage of this approach, all science requirements (such as instrument mass and power, landing site, and downlinked data volume) strictly conform to existing, demonstrated capabilities of the spacecraft and mission system. It is widely believed that multiple landers making simultaneous measurements (a network) are required to address the objectives for understanding terrestrial planet interiors. Nonetheless, comprehensive measurements from a single geophysical station are extremely valuable, because observations constraining the structure and processes of the deep interior of Mars are virtually nonexistent. GEMS would utilize sophisticated analysis techniques specific to single-station measurements to determine crustal thickness, mantle structure, core state and size, and heat flow, providing our first real look deep beneath the surface of Mars.

Protein control of true, gated, and coupled electron transfer reactions.

PubMed

Davidson, Victor L

2008-06-01

Electron transfer (ET) through and between proteins is a fundamental biological process. The rates of ET depend upon the thermodynamic driving force, the reorganization energy, and the degree of electronic coupling between the reactant and product states. The analysis of protein ET reactions is complicated by the fact that non-ET processes might influence the observed ET rate in kinetically complex biological systems. This Account describes studies of the methylamine dehydrogenase-amicyanin-cytochrome c-551i protein ET complex that have revealed the influence of several features of the protein structure on the magnitudes of the physical parameters for true ET reactions and how they dictate the kinetic mechanisms of non-ET processes that sometimes influence protein ET reactions. Kinetic and thermodynamic studies, coupled with structural information and biochemical data, are necessary to fully describe the ET reactions of proteins. Site-directed mutagenesis can be used to elucidate specific structure-function relationships. When mutations selectively alter the electronic coupling, reorganization energy, or driving force for the ET reaction, it becomes possible to use the parameters of the ET process to determine how specific amino acid residues and other features of the protein structure influence the ET rates. When mutations alter the kinetic mechanism for ET, one can determine the mechanisms by which non-ET processes, such as protein conformational changes or proton transfers, control the rates of ET reactions and how specific amino acid residues and certain features of the protein structure influence these non-ET reactions. A complete description of the mechanism of regulation of biological ET reactions enhances our understanding of metabolism, respiration, and photosynthesis at the molecular level. Such information has important medical relevance. Defective protein ET leads to production of the reactive oxygen species and free radicals that are associated with aging and many disease states. Defective ET within the respiratory chain also causes certain mitochondrial myopathies. An understanding of the mechanisms of regulation of protein ET is also of practical value because it provides a logical basis for the design of applications utilizing redox enzymes, such as enzyme-based electrode sensors and fuel cells.

Optimization of digital image processing to determine quantum dots' height and density from atomic force microscopy.

PubMed

Ruiz, J E; Paciornik, S; Pinto, L D; Ptak, F; Pires, M P; Souza, P L

2018-01-01

An optimized method of digital image processing to interpret quantum dots' height measurements obtained by atomic force microscopy is presented. The method was developed by combining well-known digital image processing techniques and particle recognition algorithms. The properties of quantum dot structures strongly depend on dots' height, among other features. Determination of their height is sensitive to small variations in their digital image processing parameters, which can generate misleading results. Comparing the results obtained with two image processing techniques - a conventional method and the new method proposed herein - with the data obtained by determining the height of quantum dots one by one within a fixed area, showed that the optimized method leads to more accurate results. Moreover, the log-normal distribution, which is often used to represent natural processes, shows a better fit to the quantum dots' height histogram obtained with the proposed method. Finally, the quantum dots' height obtained were used to calculate the predicted photoluminescence peak energies which were compared with the experimental data. Again, a better match was observed when using the proposed method to evaluate the quantum dots' height. Copyright © 2017 Elsevier B.V. All rights reserved.

Determination of the nuclear level densities and radiative strength function for 43 nuclei in the mass interval 28≤A≤200

NASA Astrophysics Data System (ADS)

Knezevic, David; Jovancevic, Nikola; Sukhovoj, Anatoly M.; Mitsyna, Ludmila V.; Krmar, Miodrag; Cong, Vu D.; Hambsch, Franz-Josef; Oberstedt, Stephan; Revay, Zsolt; Stieghorst, Christian; Dragic, Aleksandar

2018-03-01

The determination of nuclear level densities and radiative strength functions is one of the most important tasks in low-energy nuclear physics. Accurate experimental values of these parameters are critical for the study of the fundamental properties of nuclear structure. The step-like structure in the dependence of the level densities p on the excitation energy of nuclei Eex is observed in the two-step gamma cascade measurements for nuclei in the 28 ≤ A ≤ 200 mass region. This characteristic structure can be explained only if a co-existence of quasi-particles and phonons, as well as their interaction in a nucleus, are taken into account in the process of gamma-decay. Here we present a new improvement to the Dubna practical model for the determination of nuclear level densities and radiative strength functions. The new practical model guarantees a good description of the available intensities of the two step gamma cascades, comparable to the experimental data accuracy.

Role of structural barriers for carotenoid bioaccessibility upon high pressure homogenization.

PubMed

Palmero, Paola; Panozzo, Agnese; Colle, Ines; Chigwedere, Claire; Hendrickx, Marc; Van Loey, Ann

2016-05-15

A specific approach to investigate the effect of high pressure homogenization on the carotenoid bioaccessibility in tomato-based products was developed. Six different tomato-based model systems were reconstituted in order to target the specific role of the natural structural barriers (chromoplast substructure/cell wall) and of the phases (soluble/insoluble) in determining the carotenoid bioaccessibility and viscosity changes upon high pressure homogenization. Results indicated that in the absence of natural structural barriers (carotenoid enriched oil), the soluble and insoluble phases determined the carotenoid bioaccessibility upon processing whereas, in their presence, these barriers governed the bioaccessibility. Furthermore, it was shown that the increment of the viscosity upon high pressure homogenization is determined by the presence of insoluble phase, however, this result was related to the initial ratio of the soluble:insoluble phases in the system. In addition, no relationship between the changes in viscosity and carotenoid bioaccessibility upon high pressure homogenization was found. Copyright © 2015 Elsevier Ltd. All rights reserved.

Observing the overall rocking motion of a protein in a crystal

NASA Astrophysics Data System (ADS)

Ma, Peixiang; Xue, Yi; Coquelle, Nicolas; Haller, Jens D.; Yuwen, Tairan; Ayala, Isabel; Mikhailovskii, Oleg; Willbold, Dieter; Colletier, Jacques-Philippe; Skrynnikov, Nikolai R.; Schanda, Paul

2015-10-01

The large majority of three-dimensional structures of biological macromolecules have been determined by X-ray diffraction of crystalline samples. High-resolution structure determination crucially depends on the homogeneity of the protein crystal. Overall `rocking' motion of molecules in the crystal is expected to influence diffraction quality, and such motion may therefore affect the process of solving crystal structures. Yet, so far overall molecular motion has not directly been observed in protein crystals, and the timescale of such dynamics remains unclear. Here we use solid-state NMR, X-ray diffraction methods and μs-long molecular dynamics simulations to directly characterize the rigid-body motion of a protein in different crystal forms. For ubiquitin crystals investigated in this study we determine the range of possible correlation times of rocking motion, 0.1-100 μs. The amplitude of rocking varies from one crystal form to another and is correlated with the resolution obtainable in X-ray diffraction experiments.

De facto molecular weight distributions of glucans by size-exclusion chromatography combined with mass/molar-detection of fluorescence labeled terminal hemiacetals.

PubMed

Praznik, Werner; Huber, Anton

2005-09-25

A major capability of polysaccharides in aqueous media is their tendency for aggregation and dynamic formation of supermolecular structures. Even extended dissolution processes will not eliminate these structures which dominate many analytical approaches, in particular absolute molecular weight determinations referring to light scattering data. An alternative approach for determination of de facto molecular weight for glucans with free terminal hemiacetal functionality (reducing end group) has been adjusted from carbohydrates for midrange and high-dp glucans: quantitative and stabilized labeling as aminopyridyl-derivatives (AP-glucans) and subsequent analysis of SEC-separated elution profiles based on simultaneously monitored mass and molar fractions by refractive index and fluorescence detection. SEC-DRI/FL of AP-glucans proved as an appropriate approach for determination of de facto molecular weight of constituting glucan molecules even in the presence of supermolecular structures for non-branched (pullulan), branched (dextran), narrow distributed and broad distributed and for mixes of compact and loose packed polymer coils (starch glucan hydrolizate).

Structure determination of a major facilitator peptide transporter: Inward facing PepTSt from Streptococcus thermophilus crystallized in space group P3121

PubMed Central

Quistgaard, Esben M.; Martinez Molledo, Maria

2017-01-01

Major facilitator superfamily (MFS) peptide transporters (typically referred to as PepT, POT or PTR transporters) mediate the uptake of di- and tripeptides, and so play an important dietary role in many organisms. In recent years, a better understanding of the molecular basis for this process has emerged, which is in large part due to a steep increase in structural information. Yet, the conformational transitions underlying the transport mechanism are still not fully understood, and additional data is therefore needed. Here we report in detail the detergent screening, crystallization, experimental MIRAS phasing, and refinement of the peptide transporter PepTSt from Streptococcus thermophilus. The space group is P3121, and the protein is crystallized in a monomeric inward facing form. The binding site is likely to be somewhat occluded, as the lobe encompassing transmembrane helices 10 and 11 is markedly bent towards the central pore of the protein, but the extent of this potential occlusion could not be determined due to disorder at the apex of the lobe. Based on structural comparisons with the seven previously determined P212121 and C2221 structures of inward facing PepTSt, the structural flexibility as well as the conformational changes mediating transition between the inward open and inward facing occluded states are discussed. In conclusion, this report improves our understanding of the structure and conformational cycle of PepTSt, and can furthermore serve as a case study, which may aid in supporting future structure determinations of additional MFS transporters or other integral membrane proteins. PMID:28264013

Structural Investigation of Alkali Activated Clay Minerals for Application in Water Treatment Systems

NASA Astrophysics Data System (ADS)

Bumanis, G.; Bajare, D.; Dembovska, L.

2015-11-01

Alkali activation technology can be applied for a wide range of alumo-silicates to produce innovative materials with various areas of application. Most researches focuse on the application of alumo-silicate materials in building industry as cement binder replacement to produce mortar and concrete [1]. However, alkali activation technology offers high potential also in biotechnologies [2]. In the processes where certain pH level, especially alkaline environment, must be ensured, alkali activated materials can be applied. One of such fields is water treatment systems where high level pH (up to pH 10.5) ensures efficient removal of water pollutants such as manganese [3]. Previous investigations had shown that alkali activation technology can be applied to calcined clay powder and aluminium scrap recycling waste as a foam forming agent to create porous alkali activated materials. This investigation focuses on the structural investigation of calcined kaolin and illite clay alkali activation processes. Chemical and mineralogical composition of both clays were determined and structural investigation of alkali activated materials was made by using XRD, DTA, FTIR analysis; the microstructure of hardened specimens was observed by SEM. Physical properties of the obtained material were determined. Investigation indicates the essential role of chemical composition of the clay used in the alkali activation process, and potential use of the obtained material in water treatment systems.

Conductive aluminum line formation on aluminum nitride surface by infrared nanosecond laser

NASA Astrophysics Data System (ADS)

Kozioł, Paweł E.; Antończak, Arkadiusz J.; Szymczyk, Patrycja; Stępak, Bogusz; Abramski, Krzysztof M.

2013-12-01

In this paper the fabrication of conductive aluminum paths on AlN ceramic's surface due to the interaction of laser radiation Nd:YAG (1.064 μm) is presented. The metallization process produces an appropriate power value on the ceramics surface to ensure the correct temperature (2200 °C) for which aluminum and nitrogen bonds are broken. Studies have been undertaken on creating low-ohmic structures depending on the parameters such as radiation power, scanning speed, the coverage of subsequent pulses and the environmental impact of the process (air, nitrogen, argon). Furthermore, with regards to the application of this method, it was significant to determine the thickness of the functional layer. A structure of the resistivity of ρ = 0.64 × 10-6 Ω m and aluminum layer thickness of 10 μm was achieved for the process carried out on the inert gas, argon. In addition, a quantitative analysis of nitrogen and aluminum for laser-treated structures was conducted. The performed tests confirmed that the highest amount of aluminum was produced on the surface treated by laser radiation in the environment of the process gas, argon.

Influence of Culture and Personality on Determinants of Cognitive Processes Under Conditions of Uncertainty

DTIC Science & Technology

2004-05-14

Tal , Y., Raviv , A., & Spitzer, A., 1999). Janis and Mann (1977) suggested that situational conditions determine how individuals cope with decision...and ignore contrary information relative to non-stressful conditions, which can have disastrous consequences. Bar- Tal , Raviv , and Spitzer (1999...1176. Bar- Tal , Y., Raviv , A., & Spitzer, A. (1999). The need and ability to achieve cognitive structuring: Individual differences that moderate

Electrochemical Characterization of InP and GaAs Based Structures for Space Solar Cell Applications.

NASA Technical Reports Server (NTRS)

Faur, Maria; Faur, Mircea; Jenkins, Philip P.; Goradia, Manju; Wilt, David M.

1994-01-01

In this paper the emphasis is on accurate majority carrier concentration EC-V profiling of structures based on Indium Phosphide and Gallium Arsenide, using a newly developed electrolyte based on Hydrogen Flouride, Acetic Acid, Phosphoric Acid, 1-phenyl-2-propanamine and Ammonia Diflouride. Some preliminary data on the use of this electrolyte for determining the energy distribution of surface and deep states of these structures, applicable to fabrication process optimization and radiation induced defects studies of solar cells, are also provided.

Structural constraints-based evaluation of immunogenic avirulent toxins from Clostridium botulinum C2 and C3 toxins as subunit vaccines.

PubMed

Prisilla, A; Prathiviraj, R; Sasikala, R; Chellapandi, P

2016-10-01

Clostridium botulinum (group-III) is an anaerobic bacterium producing C2 and C3 toxins in addition to botulinum neurotoxins in avian and mammalian cells. C2 and C3 toxins are members of bacterial ADP-ribosyltransferase superfamily, which modify the eukaryotic cell surface proteins by ADP-ribosylation reaction. Herein, the mutant proteins with lack of catalytic and pore forming function derived from C2 (C2I and C2II) and C3 toxins were computationally evaluated to understand their structure-function integrity. We have chosen many structural constraints including local structural environment, folding process, backbone conformation, conformational dynamic sub-space, NAD-binding specificity and antigenic determinants for screening of suitable avirulent toxins. A total of 20 avirulent mutants were identified out of 23 mutants, which were experimentally produced by site-directed mutagenesis. No changes in secondary structural elements in particular to α-helices and β-sheets and also in fold rate of all-β classes. Structural stability was maintained by reordered hydrophobic and hydrogen bonding patterns. Molecular dynamic studies suggested that coupled mutations may restrain the binding affinity to NAD(+) or protein substrate upon structural destabilization. Avirulent toxins of this study have stable energetic backbone conformation with a common blue print of folding process. Molecular docking studies revealed that avirulent mutants formed more favorable hydrogen bonding with the side-chain of amino acids near to conserved NAD-binding core, despite of restraining NAD-binding specificity. Thus, structural constraints in the avirulent toxins would determine their immunogenic nature for the prioritization of protein-based subunit vaccine/immunogens to avian and veterinary animals infected with C. botulinum. Copyright © 2016 Elsevier B.V. All rights reserved.

Neutral Evolution of Multiple Quantitative Characters: A Genealogical Approach

PubMed Central

Griswold, Cortland K.; Logsdon, Benjamin; Gomulkiewicz, Richard

2007-01-01

The G matrix measures the components of phenotypic variation that are genetically heritable. The structure of G, that is, its principal components and their associated variances, determines, in part, the direction and speed of multivariate trait evolution. In this article we present a framework and results that give the structure of G under the assumption of neutrality. We suggest that a neutral expectation of the structure of G is important because it gives a null expectation for the structure of G from which the unique consequences of selection can be determined. We demonstrate how the processes of mutation, recombination, and drift shape the structure of G. Furthermore, we demonstrate how shared common ancestry between segregating alleles shapes the structure of G. Our results show that shared common ancestry, which manifests itself in the form of a gene genealogy, causes the structure of G to be nonuniform in that the variances associated with the principal components of G decline at an approximately exponential rate. Furthermore we show that the extent of the nonuniformity in the structure of G is enhanced with declines in mutation rates, recombination rates, and numbers of loci and is dependent on the pattern and modality of mutation. PMID:17339224

Nondestructive x-ray Scattering Characterization of High Temperature Superconducting Wires

DOE Office of Scientific and Technical Information (OSTI.GOV)

Thurston, T R

The purpose of this CRADA was to characterize the structural properties of the superconductor material within the wires in order to determine which processing procedures produce the best superconductor texture and phase development, and hence the best ultimate current carrying capacity.

Analysis of damaging process and crack propagation

NASA Astrophysics Data System (ADS)

Semenski, D.; Wolf, H.; Božić, Ž.

2010-06-01

Supervising and health monitoring of structures can assess the actual state of existing structures after initial loading or in the state of operation. Structural life management requires the integration of design and analysis, materials behavior and structural testing, as given for several examples. Procedure of survey of structural elements and criteria for their selection must be strongly defined as it is for the offshore gas platforms. Numerical analysis of dynamic loading is shown for the Aeolian vibrations of overhead transmission line conductors. Since the damper’s efficiency strongly depends on its position, the procedure of determining the optimum position of the damper is described. The optical method of caustics is established in isotropic materials for determination of the stress intensity factors (SIFs) of the cracks in deformed structures and is advantageously improved for the application to fiberreinforced composites. A procedure for simulation of crack propagation for multiple cracks was introduced and SIFs have been calculated by using finite element method. Crack growth of a single crack or a periodical array of cracks initiated at the stiffeners in a stiffened panel has been investigated.

A Study of Vehicle Structural Layouts in Post-WWII Aircraft

NASA Technical Reports Server (NTRS)

Sensmeier, Mark D.; Samareh, Jamshid A.

2004-01-01

In this paper, results of a study of structural layouts of post-WWII aircraft are presented. This study was undertaken to provide the background information necessary to determine typical layouts, design practices, and industry trends in aircraft structural design. Design decisions are often predicated not on performance-related criteria, but rather on such factors as manufacturability, maintenance access, and of course cost. For this reason, a thorough understanding of current best practices in the industry is required as an input for the design optimization process. To determine these best practices and industry trends, a large number of aircraft structural cutaway illustrations were analyzed for five different aircraft categories (commercial transport jets, business jets, combat jet aircraft, single engine propeller aircraft, and twin-engine propeller aircraft). Several aspects of wing design and fuselage design characteristics are presented here for the commercial transport and combat aircraft categories. A great deal of commonality was observed for transport structure designs over a range of eras and manufacturers. A much higher degree of variability in structural designs was observed for the combat aircraft, though some discernable trends were observed as well.

Simplified Protein Models: Predicting Folding Pathways and Structure Using Amino Acid Sequences

NASA Astrophysics Data System (ADS)

Adhikari, Aashish N.; Freed, Karl F.; Sosnick, Tobin R.

2013-07-01

We demonstrate the ability of simultaneously determining a protein’s folding pathway and structure using a properly formulated model without prior knowledge of the native structure. Our model employs a natural coordinate system for describing proteins and a search strategy inspired by the observation that real proteins fold in a sequential fashion by incrementally stabilizing nativelike substructures or “foldons.” Comparable folding pathways and structures are obtained for the twelve proteins recently studied using atomistic molecular dynamics simulations [K. Lindorff-Larsen, S. Piana, R. O. Dror, D. E. Shaw, Science 334, 517 (2011)], with our calculations running several orders of magnitude faster. We find that nativelike propensities in the unfolded state do not necessarily determine the order of structure formation, a departure from a major conclusion of the molecular dynamics study. Instead, our results support a more expansive view wherein intrinsic local structural propensities may be enhanced or overridden in the folding process by environmental context. The success of our search strategy validates it as an expedient mechanism for folding both in silico and in vivo.

What determines direction of asymmetry: genes, environment or chance?

PubMed Central

2016-01-01

Conspicuous asymmetries seen in many animals and plants offer diverse opportunities to test how the development of a similar morphological feature has evolved in wildly different types of organisms. One key question is: do common rules govern how direction of asymmetry is determined (symmetry is broken) during ontogeny to yield an asymmetrical individual? Examples from numerous organisms illustrate how diverse this process is. These examples also provide some surprising answers to related questions. Is direction of asymmetry in an individual determined by genes, environment or chance? Is direction of asymmetry determined locally (structure by structure) or globally (at the level of the whole body)? Does direction of asymmetry persist when an asymmetrical structure regenerates following autotomy? The answers vary greatly for asymmetries as diverse as gastropod coiling direction, flatfish eye side, crossbill finch bill crossing, asymmetrical claws in shrimp, lobsters and crabs, katydid sound-producing structures, earwig penises and various plant asymmetries. Several examples also reveal how stochastic asymmetry in mollusc and crustacean early cleavage, in Drosophila oogenesis, and in Caenorhabditis elegans epidermal blast cell movement, is a normal component of deterministic development. Collectively, these examples shed light on the role of genes as leaders or followers in evolution. This article is part of the themed issue ‘Provocative questions in left–right asymmetry’. PMID:27821528

High-throughput crystallization screening.

PubMed

Skarina, Tatiana; Xu, Xiaohui; Evdokimova, Elena; Savchenko, Alexei

2014-01-01

Protein structure determination by X-ray crystallography is dependent on obtaining a single protein crystal suitable for diffraction data collection. Due to this requirement, protein crystallization represents a key step in protein structure determination. The conditions for protein crystallization have to be determined empirically for each protein, making this step also a bottleneck in the structure determination process. Typical protein crystallization practice involves parallel setup and monitoring of a considerable number of individual protein crystallization experiments (also called crystallization trials). In these trials the aliquots of purified protein are mixed with a range of solutions composed of a precipitating agent, buffer, and sometimes an additive that have been previously successful in prompting protein crystallization. The individual chemical conditions in which a particular protein shows signs of crystallization are used as a starting point for further crystallization experiments. The goal is optimizing the formation of individual protein crystals of sufficient size and quality to make them suitable for diffraction data collection. Thus the composition of the primary crystallization screen is critical for successful crystallization.Systematic analysis of crystallization experiments carried out on several hundred proteins as part of large-scale structural genomics efforts allowed the optimization of the protein crystallization protocol and identification of a minimal set of 96 crystallization solutions (the "TRAP" screen) that, in our experience, led to crystallization of the maximum number of proteins.

Self-Elongation with Sequential Folding of a Filament of Bacterial Cells

NASA Astrophysics Data System (ADS)

Honda, Ryojiro; Wakita, Jun-ichi; Katori, Makoto

2015-11-01

Under hard-agar and nutrient-rich conditions, a cell of Bacillus subtilis grows as a single filament owing to the failure of cell separation after each growth and division cycle. The self-elongating filament of cells shows sequential folding processes, and multifold structures extend over an agar plate. We report that the growth process from the exponential phase to the stationary phase is well described by the time evolution of fractal dimensions of the filament configuration. We propose a method of characterizing filament configurations using a set of lengths of multifold parts of a filament. Systems of differential equations are introduced to describe the folding processes that create multifold structures in the early stage of the growth process. We show that the fitting of experimental data to the solutions of equations is excellent, and the parameters involved in our model systems are determined.

Femtosecond stimulated Raman evidence for charge-transfer character in pentacene singlet fission.

PubMed

Hart, Stephanie M; Silva, W Ruchira; Frontiera, Renee R

2018-02-07

Singlet fission is a spin-allowed process in which an excited singlet state evolves into two triplet states. We use femtosecond stimulated Raman spectroscopy, an ultrafast vibrational technique, to follow the molecular structural evolution during singlet fission in order to determine the mechanism of this process. In crystalline pentacene, we observe the formation of an intermediate characterized by pairs of excited state peaks that are red- and blue-shifted relative to the ground state features. We hypothesize that these features arise from the formation of cationic and anionic species due to partial transfer of electron density from one pentacene molecule to a neighboring molecule. These observations provide experimental evidence for the role of states with significant charge-transfer character which facilitate the singlet fission process in pentacene. Our work both provides new insight into the singlet fission mechanism in pentacene and demonstrates the utility of structurally-sensitive time-resolved spectroscopic techniques in monitoring ultrafast processes.

Influence of low-temperature annealing time on the evolution of the structure and mechanical properties of a titanium Ti-Al-V alloy in the submicrocrystalline state

NASA Astrophysics Data System (ADS)

Ratochka, I. V.; Lykova, O. N.; Naidenkin, E. V.

2015-03-01

The effect of annealing at 673 K for 6-24 h on the structural and phase state and mechanical properties of the titanium alloy of a Ti-Al-V system that was previously subjected to severe plastic deformation by uniform compression deformation, has been studied. It has been established that these annealings lead to a nonmontonic dependence of the mechanical properties of the alloy on the annealing time. It has been shown that the annealing of the Ti-Al-V alloy in a submicrocrystalline state is accompanied by simultaneous hardening processes, i.e., the formation of fine particles during phase transformations and the formation of new nanosized grains, and softening processes, i.e., recovery processes and the growth grains to micron sizes. The prevalence of a given process during annealing determines the deterioration or improvement of the alloy's mechanical properties.

[Structures and processes in outpatient neurorehabilitation].

PubMed

Pöppl, Dominik; Deck, R; Kringler, W; Reuther, P

2014-06-01

Quality of structures, processes and outcome are commonly accepted as dimensions of quality management and quality assurance. Data of structures and processes are not published to date for German outpatient neurorehabilitation. Rehabilitative care and service providers are legally bound to apply concepts of quality management and quality assurance. The service providers pass recommendations, which have to be implemented by outpatient neurorehabilitation centres. Data analysis of existing structures and processes in outpatient neurorehabilitation centres are embedded as a part of a long-term multicentres outcome study. 22 outpatient neurorehabilitation centres participated in an online survey with 227 items using the google tool "Docs" between September and December 2011. Following issues were asked: general information about the centres (e. g. date of establishment, number of therapy places, kind of patients, responsible organization), utility supply contracts with service providers, local cooperation and networking, staff and equipment and appliances, treatment concepts, processes of therapy (e. g. individual and group therapy, frequency, concentration, planning), team processes, goals and team development, quality management and documentation. In the meantime outpatient centres of neurorehabilitation are well-established as care providers and commonly accepted by service providers. However a comprehensive availability does not exist. The results show comparable structures of the centres, what is mostly determined by the service provider audited regulatory framework. Different concepts result in different processes. There are a lot of hints with respect to different concepts in form and content to implement the legally obligated mandate. In general their work with context -factors is still a frequently unused potential. It can be countered by the therapeutic inclusion of the social and environmental living conditions of the patients. © Georg Thieme Verlag KG Stuttgart · New York.

Alteration of biomacromolecule in corn by steam flaking in relation to biodegradation kinetics in ruminant, revealed with vibrational molecular spectroscopy

NASA Astrophysics Data System (ADS)

Xu, Ningning; Liu, Jianxin; Yu, Peiqiang

2018-02-01

Large scale of steam flaked corn has been used in dairy ration to maintain high milk production level. This study aimed to determine effects of steam flaking on processing-induced intrinsic molecular structure changes that were associated with rumen degradation kinetics and nutrients supply. The advanced vibrational molecular spectroscopy was applied to reveal the processing-induced intrinsic structure changes on a molecular basis. The rumen degradation kinetics and nutrient supply were determined using in situ approach in ruminant livestock system. Raw corn grain (RC) and steam flaked corn grain (SFC) were obtained from two different processing plants. The results showed that (1) Compared to RC, SFC had greater truly digestible non-fiber carbohydrate [tdNFC: 86.8 versus 78.0% dry matter (DM)], but lower truly digestible crude protein [tdCP: 7.7 versus 9.0% DM]. (2) The steam flaking increased (P < 0.01) rumen degradable DM (RDDM) and starch (RDSt), but decreased (P < 0.01) rumen degradable protein (RDP). (3) Molecular absorbance intensities of most carbohydrate biopolymers were greater in SFC (P < 0.01), but protein amides associated molecular spectral intensities were lower (P < 0.01) in SFC. (4). The molecular structure and nutrient interactive study showed that carbohydrate spectral intensities were positively (P < 0.10) associated with RDDM and RDSt and protein amide spectral intensities were positively (P < 0.10) associated with RDP. This results indicated that the steam flaking induced molecular structure changes had an interactive relationship with rumen degradation kinetics.

Mechanisms of Current Transfer in Electrodeposited Layers of Submicron Semiconductor Particles

NASA Astrophysics Data System (ADS)

Zhukov, N. D.; Mosiyash, D. S.; Sinev, I. V.; Khazanov, A. A.; Smirnov, A. V.; Lapshin, I. V.

2017-12-01

Current-voltage ( I- V) characteristics of conductance in multigrain layers of submicron particles of silicon, gallium arsenide, indium arsenide, and indium antimonide have been studied. Nanoparticles of all semiconductors were obtained by processing initial single crystals in a ball mill and applied after sedimentation onto substrates by means of electrodeposition. Detailed analysis of the I- V curves of electrodeposited layers shows that their behavior is determined by the mechanism of intergranular tunneling emission from near-surface electron states of submicron particles. Parameters of this emission process have been determined. The proposed multigrain semiconductor structures can be used in gas sensors, optical detectors, IR imagers, etc.

Representation and Analysis of Real-Time Control Structures.

DTIC Science & Technology

1980-08-01

external processes which cannot be forced to cooperate with programmed processes through use of a synchronization primitive such as a semaphore [Dijkstre...amounts to each task, but the time slices are synchronized with program execution. The length of the codestrip is determined by the response time...which might be synchronous or asynchronous with respect to the executing task. The notation can represent total and partial orderings among its tasks, and

An advanced technique for the prediction of decelerator system dynamics.

NASA Technical Reports Server (NTRS)

Talay, T. A.; Morris, W. D.; Whitlock, C. H.

1973-01-01

An advanced two-body six-degree-of-freedom computer model employing an indeterminate structures approach has been developed for the parachute deployment process. The program determines both vehicular and decelerator responses to aerodynamic and physical property inputs. A better insight into the dynamic processes that occur during parachute deployment has been developed. The model is of value in sensitivity studies to isolate important parameters that affect the vehicular response.

Development of an Advanced Continuum Theory for Composite Laminates. Volume 1

DTIC Science & Technology

1993-12-31

defor- mation, degradation, aging, and other processes. These process are "multidisciplinary" in every sense, and the mechanics, chemistry ...3 representation of the strain field in discrete layer laminates and allowing accurate determination of ply level stresses. During the course of this...macro-structures were examined and the rela- ŗ tionship between strain measures at micro- and macro- levels were derived. The field equations for

The Use of Nominal Group Technique to Determine Additional Support Needs for a Group of Victorian TAFE Managers and Senior Educators

ERIC Educational Resources Information Center

Bailey, Anthony

2013-01-01

The nominal group technique (NGT) is a structured process to gather information from a group. The technique was first described in 1975 and has since become a widely-used standard to facilitate working groups. The NGT is effective for generating large numbers of creative new ideas and for group priority setting. This paper describes the process of…

A detailed view of microparticle formation by in-process monitoring of the glass transition temperature.

PubMed

Vay, Kerstin; Frieß, Wolfgang; Scheler, Stefan

2012-06-01

Biodegradable poly(D,L-lactide-co-glycolide) microspheres were prepared by a well-controlled emulsion solvent extraction/evaporation process. The objective of this study was to investigate how drug release can be modified by changing the morphology of the polymer matrix. The matrix structure was controlled by the preparation temperature which was varied between 10 and 35 °C, thus changing the 4 weeks release pattern from almost linear kinetics to a sigmoidal profile with a distinct lag phase and furthermore decreasing the encapsulation efficiency. By monitoring the glass transition temperature during the extraction process, it was shown that the preparation temperature determines the particle morphology by influencing the time span in which the polymer chains were mobile and flexible during the extraction process. Further factors determining drug release were found to be the molecular weight of the polymer and the rate of solvent removal. The latter, however, has also influence on the encapsulation efficiency with slow removal causing a higher drug loss. A secondary modification of the outer particle structure could be achieved by ethanolic post-treatment of the particles, which caused an extension of the lag phase and subsequently an accelerated drug release. Copyright © 2012. Published by Elsevier B.V.

Creative brains: designing in the real world†

PubMed Central

Goel, Vinod

2014-01-01

The process of designing artifacts is a creative activity. It is proposed that, at the cognitive level, one key to understanding design creativity is to understand the array of symbol systems designers utilize. These symbol systems range from being vague, imprecise, abstract, ambiguous, and indeterminate (like conceptual sketches), to being very precise, concrete, unambiguous, and determinate (like contract documents). The former types of symbol systems support associative processes that facilitate lateral (or divergent) transformations that broaden the problem space, while the latter types of symbol systems support inference processes facilitating vertical (or convergent) transformations that deepen of the problem space. The process of artifact design requires the judicious application of both lateral and vertical transformations. This leads to a dual mechanism model of design problem-solving comprising of an associative engine and an inference engine. It is further claimed that this dual mechanism model is supported by an interesting hemispheric dissociation in human prefrontal cortex. The associative engine and neural structures that support imprecise, ambiguous, abstract, indeterminate representations are lateralized in the right prefrontal cortex, while the inference engine and neural structures that support precise, unambiguous, determinant representations are lateralized in the left prefrontal cortex. At the brain level, successful design of artifacts requires a delicate balance between the two hemispheres of prefrontal cortex. PMID:24817846

Processing, properties and applications of composites using powder-coated epoxy towpreg technology

NASA Technical Reports Server (NTRS)

Bayha, T. D.; Osborne, P. P.; Thrasher, T. P.; Hartness, J. T.; Johnston, N. J.; Marchello, J. M.; Hugh, M. K.

1993-01-01

Composite manufacturing using the current prepregging technology of impregnating liquid resin into three-dimensionally reinforced textile preforms can be a costly and difficult operation. Alternatively, using polymer in the solid form, grinding it into a powder, and then depositing it onto a carbon fiber tow prior to making a textile preform is a viable method for the production of complex textile shapes. The powder-coated towpreg yarn is stable, needs no refrigeration, contains no solvents and is easy to process into various woven and braided preforms for later consolidation into composite structures. NASA's Advanced Composites Technology (ACT) program has provided an avenue for developing the technology by which advanced resins and their powder-coated preforms may be used in aircraft structures. Two-dimensional braiding and weaving studies using powder-coated towpreg have been conducted to determine the effect of resin content, towpreg size and twist on textile composite properties. Studies have been made to customize the towpreg to reduce friction and bulk factor. Processing parameters have been determined for three epoxy resin systems on eight-harness satin fabric, and on more advanced 3-D preform architectures for the downselected resin system. Processing effects and the resultant mechanical properties of these textile composites will be presented and compared.

Network analysis of corticocortical connections reveals ventral and dorsal processing streams in mouse visual cortex

PubMed Central

Wang, Quanxin; Sporns, Olaf; Burkhalter, Andreas

2012-01-01

Much of the information used for visual perception and visually guided actions is processed in complex networks of connections within the cortex. To understand how this works in the normal brain and to determine the impact of disease, mice are promising models. In primate visual cortex, information is processed in a dorsal stream specialized for visuospatial processing and guided action and a ventral stream for object recognition. Here, we traced the outputs of 10 visual areas and used quantitative graph analytic tools of modern network science to determine, from the projection strengths in 39 cortical targets, the community structure of the network. We found a high density of the cortical graph that exceeded that previously shown in monkey. Each source area showed a unique distribution of projection weights across its targets (i.e. connectivity profile) that was well-fit by a lognormal function. Importantly, the community structure was strongly dependent on the location of the source area: outputs from medial/anterior extrastriate areas were more strongly linked to parietal, motor and limbic cortex, whereas lateral extrastriate areas were preferentially connected to temporal and parahippocampal cortex. These two subnetworks resemble dorsal and ventral cortical streams in primates, demonstrating that the basic layout of cortical networks is conserved across species. PMID:22457489

"Coding" and "Decoding": hypothesis for the regulatory mechanism involved in heparan sulfate biosynthesis.

PubMed

Zhang, Xu; Wang, Fengshan; Sheng, Juzheng

2016-06-16

Heparan sulfate (HS) is widely distributed in mammalian tissues in the form of HS proteoglycans, which play essential roles in various physiological and pathological processes. In contrast to the template-guided processes involved in the synthesis of DNA and proteins, HS biosynthesis is not believed to involve a template. However, it appears that the final structure of HS chains was strictly regulated. Herein, we report research based hypothesis that two major steps, namely "coding" and "decoding" steps, are involved in the biosynthesis of HS, which strictly regulate its chemical structure and biological activity. The "coding" process in this context is based on the distribution of sulfate moieties on the amino groups of the glucosamine residues in the HS chains. The sulfation of these amine groups is catalyzed by N-deacetylase/N-sulfotransferase, which has four isozymes. The composition and distribution of sulfate groups and iduronic acid residues on the glycan chains of HS are determined by several other modification enzymes, which can recognize these coding sequences (i.e., the "decoding" process). The degree and pattern of the sulfation and epimerization in the HS chains determines the extent of their interactions with several different protein factors, which further influences their biological activity. Copyright © 2016 Elsevier Ltd. All rights reserved.

In situ health monitoring of piezoelectric sensors

NASA Technical Reports Server (NTRS)

Drouant, George J. (Inventor); Jensen, Scott L. (Inventor)

2013-01-01

An in situ health monitoring apparatus may include an exciter circuit that applies a pulse to a piezoelectric transducer and a data processing system that determines the piezoelectric transducer's dynamic response to the first pulse. The dynamic response can be used to evaluate the operating range, health, and as-mounted resonance frequency of the transducer, as well as the strength of a coupling between the transducer and a structure and the health of the structure.

Argon-oxygen atmospheric pressure plasma treatment on carbon fiber reinforced polymer for improved bonding

NASA Astrophysics Data System (ADS)

Chartosias, Marios

Acceptance of Carbon Fiber Reinforced Polymer (CFRP) structures requires a robust surface preparation method with improved process controls capable of ensuring high bond quality. Surface preparation in a production clean room environment prior to applying adhesive for bonding would minimize risk of contamination and reduce cost. Plasma treatment is a robust surface preparation process capable of being applied in a production clean room environment with process parameters that are easily controlled and documented. Repeatable and consistent processing is enabled through the development of a process parameter window utilizing techniques such as Design of Experiments (DOE) tailored to specific adhesive and substrate bonding applications. Insight from respective plasma treatment Original Equipment Manufacturers (OEMs) and screening tests determined critical process factors from non-factors and set the associated factor levels prior to execution of the DOE. Results from mode I Double Cantilever Beam (DCB) testing per ASTM D 5528 [1] standard and DOE statistical analysis software are used to produce a regression model and determine appropriate optimum settings for each factor.

Fixation probabilities on superstars, revisited and revised.

PubMed

Jamieson-Lane, Alastair; Hauert, Christoph

2015-10-07

Population structures can be crucial determinants of evolutionary processes. For the Moran process on graphs certain structures suppress selective pressure, while others amplify it (Lieberman et al., 2005). Evolutionary amplifiers suppress random drift and enhance selection. Recently, some results for the most powerful known evolutionary amplifier, the superstar, have been invalidated by a counter example (Díaz et al., 2013). Here we correct the original proof and derive improved upper and lower bounds, which indicate that the fixation probability remains close to 1-1/(r(4)H) for population size N→∞ and structural parameter H⪢1. This correction resolves the differences between the two aforementioned papers. We also confirm that in the limit N,H→∞ superstars remain capable of eliminating random drift and hence of providing arbitrarily strong selective advantages to any beneficial mutation. In addition, we investigate the robustness of amplification in superstars and find that it appears to be a fragile phenomenon with respect to changes in the selection or mutation processes. Copyright © 2015 Elsevier Ltd. All rights reserved.

Impacts of chemical gradients on microbial community structure

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, Jianwei; Hanke, Anna; Tegetmeyer, Halina E.

Succession of redox processes is sometimes assumed to define a basic microbial community structure for ecosystems with oxygen gradients. In this paradigm, aerobic respiration, denitrification, fermentation and sulfate reduction proceed in a thermodynamically determined order, known as the ‘redox tower’. Here, we investigated whether redox sorting of microbial processes explains microbial community structure at low-oxygen concentrations. We subjected a diverse microbial community sampled from a coastal marine sediment to 100 days of tidal cycling in a laboratory chemostat. Oxygen gradients (both in space and time) led to the assembly of a microbial community dominated by populations that each performed aerobicmore » and anaerobic metabolism in parallel. This was shown by metagenomics, transcriptomics, proteomics and stable isotope incubations. Effective oxygen consumption combined with the formation of microaggregates sustained the activity of oxygen-sensitive anaerobic enzymes, leading to braiding of unsorted redox processes, within and between populations. Analyses of available metagenomic data sets indicated that the same ecological strategies might also be successful in some natural ecosystems.« less

MT+, integrating magnetotellurics to determine earth structure, physical state, and processes

USGS Publications Warehouse

Bedrosian, P.A.

2007-01-01

As one of the few deep-earth imaging techniques, magnetotellurics provides information on both the structure and physical state of the crust and upper mantle. Magnetotellurics is sensitive to electrical conductivity, which varies within the earth by many orders of magnitude and is modified by a range of earth processes. As with all geophysical techniques, magnetotellurics has a non-unique inverse problem and has limitations in resolution and sensitivity. As such, an integrated approach, either via the joint interpretation of independent geophysical models, or through the simultaneous inversion of independent data sets is valuable, and at times essential to an accurate interpretation. Magnetotelluric data and models are increasingly integrated with geological, geophysical and geochemical information. This review considers recent studies that illustrate the ways in which such information is combined, from qualitative comparisons to statistical correlation studies to multi-property inversions. Also emphasized are the range of problems addressed by these integrated approaches, and their value in elucidating earth structure, physical state, and processes. ?? Springer Science+Business Media B.V. 2007.

Texture segmentation: do the processing units on the saliency map increase with eccentricity?

PubMed

Schade, Ursula; Meinecke, Cristina

2011-01-01

The saliency map is a computational model and has been constructed for simulating human saliency processing, e.g. pop-out target detection (e.g. Itti & Koch, 2000). In this study the spatial structure on the saliency map was investigated. It is proposed that the saliency map is structured into processing units whose size is increasing with retinal eccentricity. In two experiments the distance between a target in the stimulus and an irrelevant structure in the mask was varied systematically. Our findings had two main points. Firstly, in texture segmentation tasks the saliency signals from two texture irregularities interfere, when these irregularities appear within a critical spatial distance. Second, the critical distances increase with target eccentricity. The eccentricity-dependent critical distances can be interpreted as crowding effects. It is assumed that additionally to the target eccentricity, also the strength of a saliency signal can determine the spatial area of its impairing influence. Copyright © 2010 Elsevier Ltd. All rights reserved.

[Anatomy typological and clinical parallels in case of disturbance of soft tissue formations of shoulder girdle].

PubMed

Volkov, A V; Shutov, Iu M; Shutova, M Z

2012-01-01

The influence of anthropology on topographical anatomical structure peculiarities of soft tissue formations of shoulder girdle has been investigated. The dependence of anatomical structure and topography of muscles, ligaments, tendon sheaths, synovial bursae, rotator cuffs on patient's body constitution type has been examined. The influence of a somatotype on topical damage of soft tissue structures of shoulder girdle has been proved. The so-called "holes" or weak areas, joint capsules, places where ligaments attach to bones and cartilages, where vascular formations also take place have been revealed. It is in these areas that degenerative inflammatory process begins. First of all this process influences hemolymph circulation, then it results in disturbance in production and resorption of synovial fluid and causes destructive processes in ligaments, tendons and osteochondral tissue. Due to research the ability to conduct differential diagnosis has been determined, methods of modality treatment and prevention of periarticular tissue diseases have been optimized.

Impacts of chemical gradients on microbial community structure

DOE PAGES

Chen, Jianwei; Hanke, Anna; Tegetmeyer, Halina E.; ...

2017-01-17

Succession of redox processes is sometimes assumed to define a basic microbial community structure for ecosystems with oxygen gradients. In this paradigm, aerobic respiration, denitrification, fermentation and sulfate reduction proceed in a thermodynamically determined order, known as the ‘redox tower’. Here, we investigated whether redox sorting of microbial processes explains microbial community structure at low-oxygen concentrations. We subjected a diverse microbial community sampled from a coastal marine sediment to 100 days of tidal cycling in a laboratory chemostat. Oxygen gradients (both in space and time) led to the assembly of a microbial community dominated by populations that each performed aerobicmore » and anaerobic metabolism in parallel. This was shown by metagenomics, transcriptomics, proteomics and stable isotope incubations. Effective oxygen consumption combined with the formation of microaggregates sustained the activity of oxygen-sensitive anaerobic enzymes, leading to braiding of unsorted redox processes, within and between populations. Analyses of available metagenomic data sets indicated that the same ecological strategies might also be successful in some natural ecosystems.« less

Neutral Community Dynamics and the Evolution of Species Interactions.

PubMed

Coelho, Marco Túlio P; Rangel, Thiago F

2018-04-01

A contemporary goal in ecology is to determine the ecological and evolutionary processes that generate recurring structural patterns in mutualistic networks. One of the great challenges is testing the capacity of neutral processes to replicate observed patterns in ecological networks, since the original formulation of the neutral theory lacks trophic interactions. Here, we develop a stochastic-simulation neutral model adding trophic interactions to the neutral theory of biodiversity. Without invoking ecological differences among individuals of different species, and assuming that ecological interactions emerge randomly, we demonstrate that a spatially explicit multitrophic neutral model is able to capture the recurrent structural patterns of mutualistic networks (i.e., degree distribution, connectance, nestedness, and phylogenetic signal of species interactions). Nonrandom species distribution, caused by probabilistic events of migration and speciation, create nonrandom network patterns. These findings have broad implications for the interpretation of niche-based processes as drivers of ecological networks, as well as for the integration of network structures with demographic stochasticity.

Impacts of chemical gradients on microbial community structure

PubMed Central

Chen, Jianwei; Hanke, Anna; Tegetmeyer, Halina E; Kattelmann, Ines; Sharma, Ritin; Hamann, Emmo; Hargesheimer, Theresa; Kraft, Beate; Lenk, Sabine; Geelhoed, Jeanine S; Hettich, Robert L; Strous, Marc

2017-01-01

Succession of redox processes is sometimes assumed to define a basic microbial community structure for ecosystems with oxygen gradients. In this paradigm, aerobic respiration, denitrification, fermentation and sulfate reduction proceed in a thermodynamically determined order, known as the ‘redox tower'. Here, we investigated whether redox sorting of microbial processes explains microbial community structure at low-oxygen concentrations. We subjected a diverse microbial community sampled from a coastal marine sediment to 100 days of tidal cycling in a laboratory chemostat. Oxygen gradients (both in space and time) led to the assembly of a microbial community dominated by populations that each performed aerobic and anaerobic metabolism in parallel. This was shown by metagenomics, transcriptomics, proteomics and stable isotope incubations. Effective oxygen consumption combined with the formation of microaggregates sustained the activity of oxygen-sensitive anaerobic enzymes, leading to braiding of unsorted redox processes, within and between populations. Analyses of available metagenomic data sets indicated that the same ecological strategies might also be successful in some natural ecosystems. PMID:28094795

Effects of high-speed homogenization and high-pressure homogenization on structure of tomato residue fibers.

PubMed

Hua, Xiao; Xu, Shanan; Wang, Mingming; Chen, Ying; Yang, Hui; Yang, Ruijin

2017-10-01

Tomato residue fibers obtained after derosination and deproteinization were processed by high-speed homogenization (HSH) and high-pressure homogenization (HPH), and their effects on fiber structure was investigated, respectively. Characterizations including particle size distribution, SEM, TEM and XRD were performed. HSH could break raw fibers to small particles of around 60μm, while HPH could reshape fibers to build network structure. Microfibrils were released and their nanostructure consisting of elementary fibrils was observed by TEM. XRD patterns indicated both HSH and HPH could hardly alter the nanostructure of the fibers. Physicochemical properties including expansibility, WHC and OHC were determined. Both HSH and HPH could increase the soluble fiber content by about 8%, but HSH-HPH combined processing did not show better result. Acid (4mol/L HCl) was used in replacement of water medium and the acidic degradation of fibers could be promoted by high speed shearing or high pressure processing. Copyright © 2017 Elsevier Ltd. All rights reserved.

Impacts of chemical gradients on microbial community structure.

PubMed

Chen, Jianwei; Hanke, Anna; Tegetmeyer, Halina E; Kattelmann, Ines; Sharma, Ritin; Hamann, Emmo; Hargesheimer, Theresa; Kraft, Beate; Lenk, Sabine; Geelhoed, Jeanine S; Hettich, Robert L; Strous, Marc

2017-04-01

Succession of redox processes is sometimes assumed to define a basic microbial community structure for ecosystems with oxygen gradients. In this paradigm, aerobic respiration, denitrification, fermentation and sulfate reduction proceed in a thermodynamically determined order, known as the 'redox tower'. Here, we investigated whether redox sorting of microbial processes explains microbial community structure at low-oxygen concentrations. We subjected a diverse microbial community sampled from a coastal marine sediment to 100 days of tidal cycling in a laboratory chemostat. Oxygen gradients (both in space and time) led to the assembly of a microbial community dominated by populations that each performed aerobic and anaerobic metabolism in parallel. This was shown by metagenomics, transcriptomics, proteomics and stable isotope incubations. Effective oxygen consumption combined with the formation of microaggregates sustained the activity of oxygen-sensitive anaerobic enzymes, leading to braiding of unsorted redox processes, within and between populations. Analyses of available metagenomic data sets indicated that the same ecological strategies might also be successful in some natural ecosystems.

Rate Constants for Fine-Structure Excitations in O - H Collisions with Error Bars Obtained by Machine Learning

NASA Astrophysics Data System (ADS)

Vieira, Daniel; Krems, Roman

2017-04-01

Fine-structure transitions in collisions of O(3Pj) with atomic hydrogen are an important cooling mechanism in the interstellar medium; knowledge of the rate coefficients for these transitions has a wide range of astrophysical applications. The accuracy of the theoretical calculation is limited by inaccuracy in the ab initio interaction potentials used in the coupled-channel quantum scattering calculations from which the rate coefficients can be obtained. In this work we use the latest ab initio results for the O(3Pj) + H interaction potentials to improve on previous calculations of the rate coefficients. We further present a machine-learning technique based on Gaussian Process regression to determine the sensitivity of the rate coefficients to variations of the underlying adiabatic interaction potentials. To account for the inaccuracy inherent in the ab initio calculations we compute error bars for the rate coefficients corresponding to 20% variation in each of the interaction potentials. We obtain these error bars by fitting a Gaussian Process model to a data set of potential curves and rate constants. We use the fitted model to do sensitivity analysis, determining the relative importance of individual adiabatic potential curves to a given fine-structure transition. NSERC.

Conformational changes accompany activation of reovirus RNA-dependent RNA transcription

PubMed Central

Mendez, Israel I.; Weiner, Scott G.; She, Yi-Min; Yeager, Mark; Coombs, Kevin M.

2009-01-01

Many critical biologic processes involve dynamic interactions between proteins and nucleic acids. Such dynamic processes are often difficult to delineate by conventional static methods. For example, while a variety of nucleic acid polymerase structures have been determined at atomic resolution, the details of how some multi-protein transcriptase complexes actively produce mRNA, as well as conformational changes associated with activation of such complexes, remain poorly understood. The mammalian reovirus innermost capsid (core) manifests all enzymatic activities necessary to produce mRNA from each of the 10 encased double-stranded RNA genes. We used rapid freezing and electron cryo-microscopy to trap and visualize transcriptionally active reovirus core particles and compared them to inactive core images. Rod-like density centered within actively transcribing core spike channels was attributed to exiting nascent mRNA. Comparative radial density plots of active and inactive core particles identified several structural changes in both internal and external regions of the icosahedral core capsid. Inactive and transcriptionally active cores were partially digested with trypsin and identities of initial tryptic peptides determined by mass spectrometry. Differentially-digested peptides, which also suggest transcription-associated conformational changes, were placed within the known 3-dimensional structures of major core proteins. PMID:18321727

Detection of free nickel monocarbonyl, NiCO: rotational spectrum and structure.

PubMed

Yamazaki, Emi; Okabayashi, Toshiaki; Tanimoto, Mitsutoshi

2004-02-04

Unsaturated transition metal carbonyls are important in processes such as organometallic synthesis, homogeneous catalysis, and photochemical decomposition of organometallics. In particular, a metal monocarbonyl offers a zeroth-order model for interpreting the chemisorption of a CO molecule on a metal surface in catalytic activation processes. Quite large numbers of theoretical papers have appeared which predict spectroscopic and structural properties of transition metal carbonyls. The nickel monocarbonyl NiCO has been one of the metal carbonyls most extensively studied by the theoretical calculations. At least 50 theoretical studies have been published on this simplest transition metal carbonyl up to the present time. However, experimental evidence of NiCO is much more sparse than theoretical predictions, and the actual structure of NiCO has never been determined by any experimental methods. This Communication reports the first preparation of free nickel monocarbonyl and observation of its rotational transitions. The NiCO molecule was generated by the sputtering reaction of a Ni cathode in the presence of CO. The accurate bond lengths of Ni-C and C-O were experimentally determined from isotopic data and were compared with the theoretical predictions for the first time.

W-waves Explain Gravitropism, Phototropism, Sap Flow, Plant Structure, and other Plant Processes

NASA Astrophysics Data System (ADS)

Wagner, Raymond E.; Wagner, Orvin E.

1996-11-01

Eight years of research here confirm that plants act as wave guides for W-waves: The wavelengths of these longitudinal plant waves depend on the angle with which they are traveling with respect to the gravitational field. A structure grows tuned to a particular angle under the influence of genetics. If a structure is displaced from this angle plant action produces a correction. (2) Light waves produce certain W-wave modes in the W-wave medium and a plant's response to light results. (3) Wave action produces forces in the plant (that cancel gravity in the vertical case), combined with other affects, and sap flow results. (4) Plant structures are determined by genetics and environment from a set of quantized wavelengths available to all plants. The quantized values available to plants and all life provide templates for life to develop. Compare with quantum mechanics as a template for the structure of matter. Life processes suggest that templates also influence the development and stability of all structures in the universe (see www.chatlink.com/ oedphd/ for references).

Local Structure and Anisotropy in the Amorphous Precursor= to Ba-Hexaferrite Thin Films

NASA Astrophysics Data System (ADS)

Snyder, J. E.; Harris, V. G.; Koon, N. C.; Sui, X.; Kryder, M. H.

1996-03-01

Ba-hexaferrite thin-films for recording media applications are commonly fabricated by a two-step process: sputter-deposition of an amorphous precursor, followed by annealing to crystallize the BaFe_12O_19 phase. The magnetic anisotropy of the crystalline films can be either in-plane or perpendicular, depending on the sputtering process used in the first step. However, conventional characterization techniques (x-ray diffraction and TEM) have been unable to observe any structure in the amorphous precursor films. In this study, such films are investigated by PD-EXAFS (polarization-dependent extended x-ray absorption fine structure). An anisotropic local ordered structure is observed around both Fe and Ba atoms in the "amorphous" films. This anisotropic local structure appears to determine the orientation of the fast-growing basal plane directions during crystallization, and thus the directions of the c-axes and the magnetic anisotropy. Results suggest that the structure of the amorphous films consists of networks made up of units of Fe atoms surrounded by their O nearest neighbors, that are connected together. Ba atoms appear to fit into in-between spaces as network-modifiers.

Using Carbon-14 Isotope Tracing to Investigate Molecular Structure Effects of the Oxygenate Dibutyl Maleate on Soot Emissions from a DI Diesel Engine

DOE Office of Scientific and Technical Information (OSTI.GOV)

Buchholz, B A; Mueller, C J; Upatnieks, A

2004-01-07

The effect of oxygenate molecular structure on soot emissions from a DI diesel engine was examined using carbon-14 ({sup 14}C) isotope tracing. Carbon atoms in three distinct chemical structures within the diesel oxygenate dibutyl maleate (DBM) were labeled with {sup 14}C. The {sup 14}C from the labeled DBM was then detected in engine-out particulate matter (PM), in-cylinder deposits, and CO{sub 2} emissions using accelerator mass spectrometry (AMS). The results indicate that molecular structure plays an important role in determining whether a specific carbon atom either does or does not form soot. Chemical-kinetic modeling results indicate that structures that produce CO{submore » 2} directly from the fuel are less effective at reducing soot than structures that produce CO before producing CO{sub 2}. Because they can follow individual carbon atoms through a real combustion process, {sup 14}C isotope tracing studies help strengthen the connection between actual engine emissions and chemical-kinetic models of combustion and soot formation/oxidation processes.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ozkendir, Osman Murat, E-mail: ozkendir@gmail.com

Highlights: • Crystal and electronic structure properties of Nd{sub x}Ti{sub 1−x}BO{sub 2+d} structure were investigated. • New crystal structures for Nd–Ti complexes are determined. • Distortions in the crystal structure were observed as a result of Boron shortage. • Prominent change in electronic properties of the samples with the increasing Nd amount. - Abstract: Neodymium substituted TiBO{sub 3} samples were investigated according to their crystal, electric and electronic properties. Studies were conducted by X-ray absorption fine structure spectroscopy (XAFS) technique for the samples with different substitutions in the preparation processes. To achieve better crystal structure results during the study, XRDmore » pattern results were supported by extended-XAFS (EXAFS) analysis. The electronic structure analysis were studied by X-ray absorption near-edge structure spectroscopy (XANES) measurements at the room temperatures. Due to the substituted Nd atoms, prominent changes in crystal structure, new crystal geometries for Nd-Ti complexes, phase transitions in the crystals structure were detected according to the increasing Nd substitutions in the samples. In the entire stages of the substitutions, Nd atoms were observed as governing the whole phenomena due to their dominant characteristics in Ti geometries. Besides, electrical resistivity decay was determined in the materials with the increasing amount of Nd substitution.« less

Total-energy Assisted Tight-binding Method Based on Local Density Approximation of Density Functional Theory

NASA Astrophysics Data System (ADS)

Fujiwara, Takeo; Nishino, Shinya; Yamamoto, Susumu; Suzuki, Takashi; Ikeda, Minoru; Ohtani, Yasuaki

2018-06-01

A novel tight-binding method is developed, based on the extended Hückel approximation and charge self-consistency, with referring the band structure and the total energy of the local density approximation of the density functional theory. The parameters are so adjusted by computer that the result reproduces the band structure and the total energy, and the algorithm for determining parameters is established. The set of determined parameters is applicable to a variety of crystalline compounds and change of lattice constants, and, in other words, it is transferable. Examples are demonstrated for Si crystals of several crystalline structures varying lattice constants. Since the set of parameters is transferable, the present tight-binding method may be applicable also to molecular dynamics simulations of large-scale systems and long-time dynamical processes.

Empirical evaluation of neutral interactions in host-parasite networks.

PubMed

Canard, E F; Mouquet, N; Mouillot, D; Stanko, M; Miklisova, D; Gravel, D

2014-04-01

While niche-based processes have been invoked extensively to explain the structure of interaction networks, recent studies propose that neutrality could also be of great importance. Under the neutral hypothesis, network structure would simply emerge from random encounters between individuals and thus would be directly linked to species abundance. We investigated the impact of species abundance distributions on qualitative and quantitative metrics of 113 host-parasite networks. We analyzed the concordance between neutral expectations and empirical observations at interaction, species, and network levels. We found that species abundance accurately predicts network metrics at all levels. Despite host-parasite systems being constrained by physiology and immunology, our results suggest that neutrality could also explain, at least partially, their structure. We hypothesize that trait matching would determine potential interactions between species, while abundance would determine their realization.

Profiling and multivariate statistical analysis of Panax ginseng based on ultra-high-performance liquid chromatography coupled with quadrupole-time-of-flight mass spectrometry.

PubMed

Wu, Wei; Sun, Le; Zhang, Zhe; Guo, Yingying; Liu, Shuying

2015-03-25

An ultra-high-performance liquid chromatography coupled with quadrupole-time-of-flight mass spectrometry (UHPLC-Q-TOF-MS) method was developed for the detection and structural analysis of ginsenosides in white ginseng and related processed products (red ginseng). Original neutral, malonyl, and chemically transformed ginsenosides were identified in white and red ginseng samples. The aglycone types of ginsenosides were determined by MS/MS as PPD (m/z 459), PPT (m/z 475), C-24, -25 hydrated-PPD or PPT (m/z 477 or m/z 493), and Δ20(21)-or Δ20(22)-dehydrated-PPD or PPT (m/z 441 or m/z 457). Following the structural determination, the UHPLC-Q-TOF-MS-based chemical profiling coupled with multivariate statistical analysis method was applied for global analysis of white and processed ginseng samples. The chemical markers present between the processed products red ginseng and white ginseng could be assigned. Process-mediated chemical changes were recognized as the hydrolysis of ginsenosides with large molecular weight, chemical transformations of ginsenosides, changes in malonyl-ginsenosides, and generation of 20-(R)-ginsenoside enantiomers. The relative contents of compounds classified as PPD, PPT, malonyl, and transformed ginsenosides were calculated based on peak areas in ginseng before and after processing. This study provides possibility to monitor multiple components for the quality control and global evaluation of ginseng products during processing. Copyright © 2014 Elsevier B.V. All rights reserved.

A geophysical investigation of the northeastern rim of the St. Martin impact structure, Manitoba, Canada

NASA Astrophysics Data System (ADS)

Zivkovic, Vladimir B.

The St. Martin impact structure is a 40 Km diameter structure located in Manitoba, Canada lies in featureless, glaciated terrain lacking any surface expression of an impact structure. The age of the structure has been re-determined to range between 224.3 Ma to 241.4 Ma which nullified a previous hypothesis suggesting this impact was part of a multiple impact event. Within the proposed structural boundary two outcrops of Archean granite are present. The first outcrop is located in what has been identified as the central peak of the impact structure. The second outcrop lies along the northeastern boundary and is known locally as Big Rock. The purpose of this investigation was to determine the relationship of Big Rock, if any, to the impact event and to constrain a more accurate diameter of the structure. To accomplish this I conducted two geophysical surveys and used selected data from a previous survey. The two methods I conducted were: a magnetic survey and seismic reflection profiling. Selected data from a previous gravity survey was used to supplement survey results. The magnetic survey was conducted using the total field G-856 Memory-Mag proton precession magnetometer which measures local or regional field strength. The seismic reflection survey was conducted using three Geometrics Geode exploration seismographs. Due to the complexity of seismic data processing I retained an outside seismic data processing company. Previous gravity anomaly data were acquired using a LaCoste and Romberg Model G gravimeter. The results of this geophysical investigation reveal a shallowing of granitic basement rock with exposure near Big Rock. However, a suggested listric fault near Big Rock was not identified via seismic reflection profiling, but was suggested by both the gravity and magnetic surveys. Listric faults that are genetically related to impact structures are also indicative of the structure's outer boundary and therefore can confirm that the St. Martin impact structure is indeed 40 Km in diameter.

Hydraulic and separation characteristics of an industrial gas centrifuge calculated with neural networks

NASA Astrophysics Data System (ADS)

Butov, Vladimir; Timchenko, Sergey; Ushakov, Ivan; Golovkov, Nikita; Poberezhnikov, Andrey

2018-03-01

Single gas centrifuge (GC) is generally used for the separation of binary mixtures of isotopes. Processes taking place within the centrifuge are complex and non-linear. Their characteristics can change over time with long-term operation due to wear of the main structural elements of the GC construction. The paper is devoted to the determination of basic operation parameters of the centrifuge with the help of neural networks. We have developed a method for determining the parameters of the industrial GC operation by processing statistical data. In this work, we have constructed a neural network that is capable of determining the main hydraulic and separation characteristics of the gas centrifuge, depending on the geometric dimensions of the gas centrifuge, load value, and rotor speed.

Fourier-based classification of protein secondary structures.

PubMed

Shu, Jian-Jun; Yong, Kian Yan

2017-04-15

The correct prediction of protein secondary structures is one of the key issues in predicting the correct protein folded shape, which is used for determining gene function. Existing methods make use of amino acids properties as indices to classify protein secondary structures, but are faced with a significant number of misclassifications. The paper presents a technique for the classification of protein secondary structures based on protein "signal-plotting" and the use of the Fourier technique for digital signal processing. New indices are proposed to classify protein secondary structures by analyzing hydrophobicity profiles. The approach is simple and straightforward. Results show that the more types of protein secondary structures can be classified by means of these newly-proposed indices. Copyright © 2017 Elsevier Inc. All rights reserved.

Determinants of cation transport selectivity: Equilibrium binding and transport kinetics

PubMed Central

2015-01-01

The crystal structures of channels and transporters reveal the chemical nature of ion-binding sites and, thereby, constrain mechanistic models for their transport processes. However, these structures, in and of themselves, do not reveal equilibrium selectivity or transport preferences, which can be discerned only from various functional assays. In this Review, I explore the relationship between cation transport protein structures, equilibrium binding measurements, and ion transport selectivity. The primary focus is on K+-selective channels and nonselective cation channels because they have been extensively studied both functionally and structurally, but the principles discussed are relevant to other transport proteins and molecules. PMID:26078056