Information flows in hierarchical networks and the capability of organizations to successfully respond to failures, crises, and disasters

NASA Astrophysics Data System (ADS)

Helbing, Dirk; Ammoser, Hendrik; Kühnert, Christian

2006-04-01

In this paper we discuss the problem of information losses in organizations and how they depend on the organization network structure. Hierarchical networks are an optimal organization structure only when the failure rate of nodes or links is negligible. Otherwise, redundant information links are important to reduce the risk of information losses and the related costs. However, as redundant information links are expensive, the optimal organization structure is not a fully connected one. It rather depends on the failure rate. We suggest that sidelinks and temporary, adaptive shortcuts can improve the information flows considerably by generating small-world effects. This calls for modified organization structures to cope with today's challenges of businesses and administrations, in particular, to successfully respond to crises or disasters.

Electromigration and the structure of metallic nanocontacts

NASA Astrophysics Data System (ADS)

Hoffmann-Vogel, R.

2017-09-01

This article reviews efforts to structurally characterize metallic nanocontacts. While the electronic characterization of such junctions is relatively straight forward, usually it is technically challenging to study the nanocontact's structure at small length scales. However, knowing that the structure is the basis for understanding the electronic properties of the nanocontact, for example, it is necessary to explain the electronic properties by calculations based on structural models. Besides using a gate electrode, controlling the structure is an important way of understanding how the electronic transport properties can be influenced. A key to make structural information directly accessible is to choose a fabrication method that is adapted to the structural characterization method. Special emphasis is given to transmission electron microscopy fabrication and to thermally assisted electromigration methods due to their potential for obtaining information on both electrodes of the forming nanocontact. Controlled electromigration aims at studying the contact at constant temperature of the contact during electromigration compared to studies at constant temperature of the environment as done previously. We review efforts to calculate electromigration forces. We describe how hot spots are formed during electromigration. We summarize implications for the structure obtained from studies of the ballistic transport regime, tunneling, and Coulomb-blockade. We review the structure of the nanocontacts known from direct structural characterization. Single-crystalline wires allow suppressing grain boundary electromigration. In thin films, the substrate plays an important role in influencing the defect and temperature distribution. Hot-spot formation and recrystallization are observed. We add information on the local temperature and current density and on alloys important for microelectronic interconnects.

Computational Methods in Drug Discovery

PubMed Central

Sliwoski, Gregory; Kothiwale, Sandeepkumar; Meiler, Jens

2014-01-01

Computer-aided drug discovery/design methods have played a major role in the development of therapeutically important small molecules for over three decades. These methods are broadly classified as either structure-based or ligand-based methods. Structure-based methods are in principle analogous to high-throughput screening in that both target and ligand structure information is imperative. Structure-based approaches include ligand docking, pharmacophore, and ligand design methods. The article discusses theory behind the most important methods and recent successful applications. Ligand-based methods use only ligand information for predicting activity depending on its similarity/dissimilarity to previously known active ligands. We review widely used ligand-based methods such as ligand-based pharmacophores, molecular descriptors, and quantitative structure-activity relationships. In addition, important tools such as target/ligand data bases, homology modeling, ligand fingerprint methods, etc., necessary for successful implementation of various computer-aided drug discovery/design methods in a drug discovery campaign are discussed. Finally, computational methods for toxicity prediction and optimization for favorable physiologic properties are discussed with successful examples from literature. PMID:24381236

Organizational Factors that Affect the Implementation of Information Technology: Perspectives of Middle Managers in Iran

PubMed Central

Barzekar, Hosein; Karami, Mahtab

2014-01-01

ABSTRACT Objective: to examine the organizational factors affecting the application of information technology in hospitals. Since the organizational factors are one of the most important determinants of successful projects, by understanding their impact and identifying them it can help planning a systematic IT implementation. Methods: In this cross-sectional descriptive study 110 middle managers were chosen from teaching hospitals. Structured questionnaire was used for the data collection. Results: There was a significant relationship between organization resource, organizational knowledge, process, management structure and values and goals with implementation of information technology. Conclusion: Findings showed that organizational factors had a considerable impact on implementation of information technology. Top managers must consider the important aspects of effective organizational factors. PMID:25568582

Structural Refinement of Proteins by Restrained Molecular Dynamics Simulations with Non-interacting Molecular Fragments.

PubMed

Shen, Rong; Han, Wei; Fiorin, Giacomo; Islam, Shahidul M; Schulten, Klaus; Roux, Benoît

2015-10-01

The knowledge of multiple conformational states is a prerequisite to understand the function of membrane transport proteins. Unfortunately, the determination of detailed atomic structures for all these functionally important conformational states with conventional high-resolution approaches is often difficult and unsuccessful. In some cases, biophysical and biochemical approaches can provide important complementary structural information that can be exploited with the help of advanced computational methods to derive structural models of specific conformational states. In particular, functional and spectroscopic measurements in combination with site-directed mutations constitute one important source of information to obtain these mixed-resolution structural models. A very common problem with this strategy, however, is the difficulty to simultaneously integrate all the information from multiple independent experiments involving different mutations or chemical labels to derive a unique structural model consistent with the data. To resolve this issue, a novel restrained molecular dynamics structural refinement method is developed to simultaneously incorporate multiple experimentally determined constraints (e.g., engineered metal bridges or spin-labels), each treated as an individual molecular fragment with all atomic details. The internal structure of each of the molecular fragments is treated realistically, while there is no interaction between different molecular fragments to avoid unphysical steric clashes. The information from all the molecular fragments is exploited simultaneously to constrain the backbone to refine a three-dimensional model of the conformational state of the protein. The method is illustrated by refining the structure of the voltage-sensing domain (VSD) of the Kv1.2 potassium channel in the resting state and by exploring the distance histograms between spin-labels attached to T4 lysozyme. The resulting VSD structures are in good agreement with the consensus model of the resting state VSD and the spin-spin distance histograms from ESR/DEER experiments on T4 lysozyme are accurately reproduced.

Development of pair distribution function analysis

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

Vondreele, R.; Billinge, S.; Kwei, G.

1996-09-01

This is the final report of a 3-year LDRD project at LANL. It has become more and more evident that structural coherence in the CuO{sub 2} planes of high-{Tc} superconducting materials over some intermediate length scale (nm range) is important to superconductivity. In recent years, the pair distribution function (PDF) analysis of powder diffraction data has been developed for extracting structural information on these length scales. This project sought to expand and develop this technique, use it to analyze neutron powder diffraction data, and apply it to problems. In particular, interest is in the area of high-{Tc} superconductors, although wemore » planned to extend the study to the closely related perovskite ferroelectric materials andother materials where the local structure affects the properties where detailed knowledge of the local and intermediate range structure is important. In addition, we planned to carry out single crystal experiments to look for diffuse scattering. This information augments the information from the PDF.« less

New methodologies for multi-scale time-variant reliability analysis of complex lifeline networks

NASA Astrophysics Data System (ADS)

Kurtz, Nolan Scot

The cost of maintaining existing civil infrastructure is enormous. Since the livelihood of the public depends on such infrastructure, its state must be managed appropriately using quantitative approaches. Practitioners must consider not only which components are most fragile to hazard, e.g. seismicity, storm surge, hurricane winds, etc., but also how they participate on a network level using network analysis. Focusing on particularly damaged components does not necessarily increase network functionality, which is most important to the people that depend on such infrastructure. Several network analyses, e.g. S-RDA, LP-bounds, and crude-MCS, and performance metrics, e.g. disconnection bounds and component importance, are available for such purposes. Since these networks are existing, the time state is also important. If networks are close to chloride sources, deterioration may be a major issue. Information from field inspections may also have large impacts on quantitative models. To address such issues, hazard risk analysis methodologies for deteriorating networks subjected to seismicity, i.e. earthquakes, have been created from analytics. A bridge component model has been constructed for these methodologies. The bridge fragilities, which were constructed from data, required a deeper level of analysis as these were relevant for specific structures. Furthermore, chloride-induced deterioration network effects were investigated. Depending on how mathematical models incorporate new information, many approaches are available, such as Bayesian model updating. To make such procedures more flexible, an adaptive importance sampling scheme was created for structural reliability problems. Additionally, such a method handles many kinds of system and component problems with singular or multiple important regions of the limit state function. These and previously developed analysis methodologies were found to be strongly sensitive to the network size. Special network topologies may be more or less computationally difficult, while the resolution of the network also has large affects. To take advantage of some types of topologies, network hierarchical structures with super-link representation have been used in the literature to increase the computational efficiency by analyzing smaller, densely connected networks; however, such structures were based on user input and subjective at times. To address this, algorithms must be automated and reliable. These hierarchical structures may indicate the structure of the network itself. This risk analysis methodology has been expanded to larger networks using such automated hierarchical structures. Component importance is the most important objective from such network analysis; however, this may only provide the information of which bridges to inspect/repair earliest and little else. High correlations influence such component importance measures in a negative manner. Additionally, a regional approach is not appropriately modelled. To investigate a more regional view, group importance measures based on hierarchical structures have been created. Such structures may also be used to create regional inspection/repair approaches. Using these analytical, quantitative risk approaches, the next generation of decision makers may make both component and regional-based optimal decisions using information from both network function and further effects of infrastructure deterioration.

A Monumental Lesson: What Historical Structures Can Tell Us

ERIC Educational Resources Information Center

Craven, Jacqueline S.; Sumrall, William J.; Moore, Jerilou J.; Logan, Kellie

2011-01-01

Historical structures have connected civilization across time as a representation of important events, famous people, or experiences of diverse cultures. The value systems of a society are reflected in these structures and convey political and historical information. Knowledge about historical structures provides understanding of cultures of…

Student perception and conceptual development as represented by student mental models of atomic structure

NASA Astrophysics Data System (ADS)

Park, Eun Jung

The nature of matter based upon atomic theory is a principal concept in science; hence, how to teach and how to learn about atoms is an important subject for science education. To this end, this study explored student perceptions of atomic structure and how students learn about this concept by analyzing student mental models of atomic structure. Changes in student mental models serve as a valuable resource for comprehending student conceptual development. Data was collected from students who were taking the introductory chemistry course. Responses to course examinations, pre- and post-questionnaires, and pre- and post-interviews were used to analyze student mental models of atomic structure. First, this study reveals that conceptual development can be achieved, either by elevating mental models toward higher levels of understanding or by developing a single mental model. This study reinforces the importance of higher-order thinking skills to enable students to relate concepts in order to construct a target model of atomic structure. Second, Bohr's orbital structure seems to have had a strong influence on student perceptions of atomic structure. With regard to this finding, this study suggests that it is instructionally important to teach the concept of "orbitals" related to "quantum theory." Third, there were relatively few students who had developed understanding at the level of the target model, which required student understanding of the basic ideas of quantum theory. This study suggests that the understanding of atomic structure based on the idea of quantum theory is both important and difficult. Fourth, this study included different student assessments comprised of course examinations, questionnaires, and interviews. Each assessment can be used to gather information to map out student mental models. Fifth, in the comparison of the pre- and post-interview responses, this study showed that high achieving students moved toward more improved models or to advanced levels of understanding. The analysis of mental models in this study has provided information describing student understanding of the nature and structure of an atom. In addition to an assessment of student cognition, information produced from this study can serve as an important resource for curriculum development, teacher education, and instruction.

Relative importance of current and past landscape structure and local habitat conditions for plant species richness in dry grassland-like forest openings.

PubMed

Husáková, Iveta; Münzbergová, Zuzana

2014-01-01

In fragmented landscapes, plant species richness may depend not only on local habitat conditions but also on landscape structure. In addition, both present and past landscape structure may be important for species richness. There are, however, only a few studies that have investigated the relative importance of all of these factors. The aim of this study was to examine the effect of current and past landscape structures and habitat conditions on species richness at dry grassland-like forest openings in a forested landscape and to assess their relative importance for species richness. We analyzed information on past and present landscape structures using aerial photographs from 1938, 1973, 1988, 2000 and 2007. We calculated the area of each locality and its isolation in the present and in the past and the continuity of localities in GIS. At each locality, we recorded all vascular plant species (296 species in 110 forest openings) and information on abiotic conditions of the localities. We found that the current species richness of the forest openings was significantly determined by local habitat conditions as well as by landscape structure in the present and in the past. The highest species richness was observed on larger and more heterogeneous localities with rocks and shallow soils, which were already large and well connected to other localities in 1938. The changes in the landscape structure in the past can thus have strong effects on current species richness. Future studies attempting to understand determinants of species diversity in fragmented landscapes should also include data on past landscape structure, as it may in fact be more important than the present structure.

Data to knowledge: how to get meaning from your result.

PubMed

Berman, Helen M; Gabanyi, Margaret J; Groom, Colin R; Johnson, John E; Murshudov, Garib N; Nicholls, Robert A; Reddy, Vijay; Schwede, Torsten; Zimmerman, Matthew D; Westbrook, John; Minor, Wladek

2015-01-01

Structural and functional studies require the development of sophisticated 'Big Data' technologies and software to increase the knowledge derived and ensure reproducibility of the data. This paper presents summaries of the Structural Biology Knowledge Base, the VIPERdb Virus Structure Database, evaluation of homology modeling by the Protein Model Portal, the ProSMART tool for conformation-independent structure comparison, the LabDB 'super' laboratory information management system and the Cambridge Structural Database. These techniques and technologies represent important tools for the transformation of crystallographic data into knowledge and information, in an effort to address the problem of non-reproducibility of experimental results.

Rare variation facilitates inferences of fine-scale population structure in humans.

PubMed

O'Connor, Timothy D; Fu, Wenqing; Mychaleckyj, Josyf C; Logsdon, Benjamin; Auer, Paul; Carlson, Christopher S; Leal, Suzanne M; Smith, Joshua D; Rieder, Mark J; Bamshad, Michael J; Nickerson, Deborah A; Akey, Joshua M

2015-03-01

Understanding the genetic structure of human populations has important implications for the design and interpretation of disease mapping studies and reconstructing human evolutionary history. To date, inferences of human population structure have primarily been made with common variants. However, recent large-scale resequencing studies have shown an abundance of rare variation in humans, which may be particularly useful for making inferences of fine-scale population structure. To this end, we used an information theory framework and extensive coalescent simulations to rigorously quantify the informativeness of rare and common variation to detect signatures of fine-scale population structure. We show that rare variation affords unique insights into patterns of recent population structure. Furthermore, to empirically assess our theoretical findings, we analyzed high-coverage exome sequences in 6,515 European and African American individuals. As predicted, rare variants are more informative than common polymorphisms in revealing a distinct cluster of European-American individuals, and subsequent analyses demonstrate that these individuals are likely of Ashkenazi Jewish ancestry. Our results provide new insights into the population structure using rare variation, which will be an important factor to account for in rare variant association studies. © The Author 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

QSAR modeling based on structure-information for properties of interest in human health.

PubMed

Hall, L H; Hall, L M

2005-01-01

The development of QSAR models based on topological structure description is presented for problems in human health. These models are based on the structure-information approach to quantitative biological modeling and prediction, in contrast to the mechanism-based approach. The structure-information approach is outlined, starting with basic structure information developed from the chemical graph (connection table). Information explicit in the connection table (element identity and skeletal connections) leads to significant (implicit) structure information that is useful for establishing sound models of a wide range of properties of interest in drug design. Valence state definition leads to relationships for valence state electronegativity and atom/group molar volume. Based on these important aspects of molecules, together with skeletal branching patterns, both the electrotopological state (E-state) and molecular connectivity (chi indices) structure descriptors are developed and described. A summary of four QSAR models indicates the wide range of applicability of these structure descriptors and the predictive quality of QSAR models based on them: aqueous solubility (5535 chemically diverse compounds, 938 in external validation), percent oral absorption (%OA, 417 therapeutic drugs, 195 drugs in external validation testing), AMES mutagenicity (2963 compounds including 290 therapeutic drugs, 400 in external validation), fish toxicity (92 substituted phenols, anilines and substituted aromatics). These models are established independent of explicit three-dimensional (3-D) structure information and are directly interpretable in terms of the implicit structure information useful to the drug design process.

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 ...

District nurses' prescribing practice and its link to structural conditions.

PubMed

Blanck, Susanne; Engström, Maria

2015-10-01

To describe district nurses' (DNs') prescribing practice and examine associations between DNs' self-reported prescribing frequency, opinions about prescribing, and structural conditions/empowerment. A cross-sectional and correlational design was employed. Data were collected during 2012 using questionnaires and a prescribing register. A random sample of 150 DNs from 32 primary care centers in Sweden was invited. DNs' ability to prescribe is used to a relatively small extent and access to "opportunities" and "informal power" seems to be the most important structural empowerment conditions for increased prescribing frequency and positive opinions about prescribing. The results support Kanter's theory of structural empowerment. This article regarding restricted prescribing shows how important structural conditions/empowerment is to DNs' prescribing and employers have to enhance nurses' access to especially the structures "opportunities" and "informal power" to increase nurse prescribing. More targeted support and training are needed in different prescribing areas to make use of DNs' prescription qualification to a greater extent. ©2015 American Association of Nurse Practitioners.

Mixture models for protein structure ensembles.

PubMed

Hirsch, Michael; Habeck, Michael

2008-10-01

Protein structure ensembles provide important insight into the dynamics and function of a protein and contain information that is not captured with a single static structure. However, it is not clear a priori to what extent the variability within an ensemble is caused by internal structural changes. Additional variability results from overall translations and rotations of the molecule. And most experimental data do not provide information to relate the structures to a common reference frame. To report meaningful values of intrinsic dynamics, structural precision, conformational entropy, etc., it is therefore important to disentangle local from global conformational heterogeneity. We consider the task of disentangling local from global heterogeneity as an inference problem. We use probabilistic methods to infer from the protein ensemble missing information on reference frames and stable conformational sub-states. To this end, we model a protein ensemble as a mixture of Gaussian probability distributions of either entire conformations or structural segments. We learn these models from a protein ensemble using the expectation-maximization algorithm. Our first model can be used to find multiple conformers in a structure ensemble. The second model partitions the protein chain into locally stable structural segments or core elements and less structured regions typically found in loops. Both models are simple to implement and contain only a single free parameter: the number of conformers or structural segments. Our models can be used to analyse experimental ensembles, molecular dynamics trajectories and conformational change in proteins. The Python source code for protein ensemble analysis is available from the authors upon request.

Comprehensible Presentation of Topological Information

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

Weber, Gunther H.; Beketayev, Kenes; Bremer, Peer-Timo

2012-03-05

Topological information has proven very valuable in the analysis of scientific data. An important challenge that remains is presenting this highly abstract information in a way that it is comprehensible even if one does not have an in-depth background in topology. Furthermore, it is often desirable to combine the structural insight gained by topological analysis with complementary information, such as geometric information. We present an overview over methods that use metaphors to make topological information more accessible to non-expert users, and we demonstrate their applicability to a range of scientific data sets. With the increasingly complex output of exascale simulations,more » the importance of having effective means of providing a comprehensible, abstract overview over data will grow. The techniques that we present will serve as an important foundation for this purpose.« less

Automated analysis of information processing, kinetic independence and modular architecture in biochemical networks using MIDIA.

PubMed

Bowsher, Clive G

2011-02-15

Understanding the encoding and propagation of information by biochemical reaction networks and the relationship of such information processing properties to modular network structure is of fundamental importance in the study of cell signalling and regulation. However, a rigorous, automated approach for general biochemical networks has not been available, and high-throughput analysis has therefore been out of reach. Modularization Identification by Dynamic Independence Algorithms (MIDIA) is a user-friendly, extensible R package that performs automated analysis of how information is processed by biochemical networks. An important component is the algorithm's ability to identify exact network decompositions based on both the mass action kinetics and informational properties of the network. These modularizations are visualized using a tree structure from which important dynamic conditional independence properties can be directly read. Only partial stoichiometric information needs to be used as input to MIDIA, and neither simulations nor knowledge of rate parameters are required. When applied to a signalling network, for example, the method identifies the routes and species involved in the sequential propagation of information between its multiple inputs and outputs. These routes correspond to the relevant paths in the tree structure and may be further visualized using the Input-Output Path Matrix tool. MIDIA remains computationally feasible for the largest network reconstructions currently available and is straightforward to use with models written in Systems Biology Markup Language (SBML). The package is distributed under the GNU General Public License and is available, together with a link to browsable Supplementary Material, at http://code.google.com/p/midia. Further information is at www.maths.bris.ac.uk/~macgb/Software.html.

Does similarity in call structure or foraging ecology explain interspecific information transfer in wild Myotis bats?

PubMed

Hügel, Theresa; van Meir, Vincent; Muñoz-Meneses, Amanda; Clarin, B-Markus; Siemers, Björn M; Goerlitz, Holger R

2017-01-01

Animals can gain important information by attending to the signals and cues of other animals in their environment, with acoustic information playing a major role in many taxa. Echolocation call sequences of bats contain information about the identity and behaviour of the sender which is perceptible to close-by receivers. Increasing evidence supports the communicative function of echolocation within species, yet data about its role for interspecific information transfer is scarce. Here, we asked which information bats extract from heterospecific echolocation calls during foraging. In three linked playback experiments, we tested in the flight room and field if foraging Myotis bats approached the foraging call sequences of conspecifics and four heterospecifics that were similar in acoustic call structure only (acoustic similarity hypothesis), in foraging ecology only (foraging similarity hypothesis), both, or none. Compared to the natural prey capture rate of 1.3 buzzes per minute of bat activity, our playbacks of foraging sequences with 23-40 buzzes/min simulated foraging patches with significantly higher profitability. In the flight room, M. capaccinii only approached call sequences of conspecifics and of the heterospecific M. daubentonii with similar acoustics and foraging ecology. In the field, M. capaccinii and M. daubentonii only showed a weak positive response to those two species. Our results confirm information transfer across species boundaries and highlight the importance of context on the studied behaviour, but cannot resolve whether information transfer in trawling Myotis is based on acoustic similarity only or on a combination of similarity in acoustics and foraging ecology. Animals transfer information, both voluntarily and inadvertently, and within and across species boundaries. In echolocating bats, acoustic call structure and foraging ecology are linked, making echolocation calls a rich source of information about species identity, ecology and activity of the sender, which receivers might exploit to find profitable foraging grounds. We tested in three lab and field experiments if information transfer occurs between bat species and if bats obtain information about ecology from echolocation calls. Myotis capaccinii/daubentonii bats approached call playbacks, but only those from con- and heterospecifics with similar call structure and foraging ecology, confirming interspecific information transfer. Reactions differed between lab and field, emphasising situation-dependent differences in animal behaviour, the importance of field research, and the need for further studies on the underlying mechanism of information transfer and the relative contributions of acoustic and ecological similarity.

Representing nested semantic information in a linear string of text using XML.

PubMed

Krauthammer, Michael; Johnson, Stephen B; Hripcsak, George; Campbell, David A; Friedman, Carol

2002-01-01

XML has been widely adopted as an important data interchange language. The structure of XML enables sharing of data elements with variable degrees of nesting as long as the elements are grouped in a strict tree-like fashion. This requirement potentially restricts the usefulness of XML for marking up written text, which often includes features that do not properly nest within other features. We encountered this problem while marking up medical text with structured semantic information from a Natural Language Processor. Traditional approaches to this problem separate the structured information from the actual text mark up. This paper introduces an alternative solution, which tightly integrates the semantic structure with the text. The resulting XML markup preserves the linearity of the medical texts and can therefore be easily expanded with additional types of information.

Representing nested semantic information in a linear string of text using XML.

PubMed Central

Krauthammer, Michael; Johnson, Stephen B.; Hripcsak, George; Campbell, David A.; Friedman, Carol

2002-01-01

XML has been widely adopted as an important data interchange language. The structure of XML enables sharing of data elements with variable degrees of nesting as long as the elements are grouped in a strict tree-like fashion. This requirement potentially restricts the usefulness of XML for marking up written text, which often includes features that do not properly nest within other features. We encountered this problem while marking up medical text with structured semantic information from a Natural Language Processor. Traditional approaches to this problem separate the structured information from the actual text mark up. This paper introduces an alternative solution, which tightly integrates the semantic structure with the text. The resulting XML markup preserves the linearity of the medical texts and can therefore be easily expanded with additional types of information. PMID:12463856

An exponentiation method for XML element retrieval.

PubMed

Wichaiwong, Tanakorn

2014-01-01

XML document is now widely used for modelling and storing structured documents. The structure is very rich and carries important information about contents and their relationships, for example, e-Commerce. XML data-centric collections require query terms allowing users to specify constraints on the document structure; mapping structure queries and assigning the weight are significant for the set of possibly relevant documents with respect to structural conditions. In this paper, we present an extension to the MEXIR search system that supports the combination of structural and content queries in the form of content-and-structure queries, which we call the Exponentiation function. It has been shown the structural information improve the effectiveness of the search system up to 52.60% over the baseline BM25 at MAP.

Natural language processing systems for capturing and standardizing unstructured clinical information: A systematic review.

PubMed

Kreimeyer, Kory; Foster, Matthew; Pandey, Abhishek; Arya, Nina; Halford, Gwendolyn; Jones, Sandra F; Forshee, Richard; Walderhaug, Mark; Botsis, Taxiarchis

2017-09-01

We followed a systematic approach based on the Preferred Reporting Items for Systematic Reviews and Meta-Analyses to identify existing clinical natural language processing (NLP) systems that generate structured information from unstructured free text. Seven literature databases were searched with a query combining the concepts of natural language processing and structured data capture. Two reviewers screened all records for relevance during two screening phases, and information about clinical NLP systems was collected from the final set of papers. A total of 7149 records (after removing duplicates) were retrieved and screened, and 86 were determined to fit the review criteria. These papers contained information about 71 different clinical NLP systems, which were then analyzed. The NLP systems address a wide variety of important clinical and research tasks. Certain tasks are well addressed by the existing systems, while others remain as open challenges that only a small number of systems attempt, such as extraction of temporal information or normalization of concepts to standard terminologies. This review has identified many NLP systems capable of processing clinical free text and generating structured output, and the information collected and evaluated here will be important for prioritizing development of new approaches for clinical NLP. Copyright © 2017 Elsevier Inc. All rights reserved.

Analysis of defect structure in silicon. Characterization of samples from UCP ingot 5848-13C

NASA Technical Reports Server (NTRS)

Natesh, R.; Guyer, T.; Stringfellow, G. B.

1982-01-01

Statistically significant quantitative structural imperfection measurements were made on samples from ubiquitous crystalline process (UCP) Ingot 5848 - 13 C. Important trends were noticed between the measured data, cell efficiency, and diffusion length. Grain boundary substructure appears to have an important effect on the conversion efficiency of solar cells from Semix material. Quantitative microscopy measurements give statistically significant information compared to other microanalytical techniques. A surface preparation technique to obtain proper contrast of structural defects suitable for QTM analysis was perfected.

Selecting SNPs informative for African, American Indian and European Ancestry: application to the Family Investigation of Nephropathy and Diabetes (FIND).

PubMed

Williams, Robert C; Elston, Robert C; Kumar, Pankaj; Knowler, William C; Abboud, Hanna E; Adler, Sharon; Bowden, Donald W; Divers, Jasmin; Freedman, Barry I; Igo, Robert P; Ipp, Eli; Iyengar, Sudha K; Kimmel, Paul L; Klag, Michael J; Kohn, Orly; Langefeld, Carl D; Leehey, David J; Nelson, Robert G; Nicholas, Susanne B; Pahl, Madeleine V; Parekh, Rulan S; Rotter, Jerome I; Schelling, Jeffrey R; Sedor, John R; Shah, Vallabh O; Smith, Michael W; Taylor, Kent D; Thameem, Farook; Thornley-Brown, Denyse; Winkler, Cheryl A; Guo, Xiuqing; Zager, Phillip; Hanson, Robert L

2016-05-04

The presence of population structure in a sample may confound the search for important genetic loci associated with disease. Our four samples in the Family Investigation of Nephropathy and Diabetes (FIND), European Americans, Mexican Americans, African Americans, and American Indians are part of a genome- wide association study in which population structure might be particularly important. We therefore decided to study in detail one component of this, individual genetic ancestry (IGA). From SNPs present on the Affymetrix 6.0 Human SNP array, we identified 3 sets of ancestry informative markers (AIMs), each maximized for the information in one the three contrasts among ancestral populations: Europeans (HAPMAP, CEU), Africans (HAPMAP, YRI and LWK), and Native Americans (full heritage Pima Indians). We estimate IGA and present an algorithm for their standard errors, compare IGA to principal components, emphasize the importance of balancing information in the ancestry informative markers (AIMs), and test the association of IGA with diabetic nephropathy in the combined sample. A fixed parental allele maximum likelihood algorithm was applied to the FIND to estimate IGA in four samples: 869 American Indians; 1385 African Americans; 1451 Mexican Americans; and 826 European Americans. When the information in the AIMs is unbalanced, the estimates are incorrect with large error. Individual genetic admixture is highly correlated with principle components for capturing population structure. It takes ~700 SNPs to reduce the average standard error of individual admixture below 0.01. When the samples are combined, the resulting population structure creates associations between IGA and diabetic nephropathy. The identified set of AIMs, which include American Indian parental allele frequencies, may be particularly useful for estimating genetic admixture in populations from the Americas. Failure to balance information in maximum likelihood, poly-ancestry models creates biased estimates of individual admixture with large error. This also occurs when estimating IGA using the Bayesian clustering method as implemented in the program STRUCTURE. Odds ratios for the associations of IGA with disease are consistent with what is known about the incidence and prevalence of diabetic nephropathy in these populations.

Data to knowledge: how to get meaning from your result

PubMed Central

Berman, Helen M.; Gabanyi, Margaret J.; Groom, Colin R.; Johnson, John E.; Murshudov, Garib N.; Nicholls, Robert A.; Reddy, Vijay; Schwede, Torsten; Zimmerman, Matthew D.; Westbrook, John; Minor, Wladek

2015-01-01

Structural and functional studies require the development of sophisticated ‘Big Data’ technologies and software to increase the knowledge derived and ensure reproducibility of the data. This paper presents summaries of the Structural Biology Knowledge Base, the VIPERdb Virus Structure Database, evaluation of homology modeling by the Protein Model Portal, the ProSMART tool for conformation-independent structure comparison, the LabDB ‘super’ laboratory information management system and the Cambridge Structural Database. These techniques and technologies represent important tools for the transformation of crystallographic data into knowledge and information, in an effort to address the problem of non-reproducibility of experimental results. PMID:25610627

A Generalized Information Theoretical Model for Quantum Secret Sharing

NASA Astrophysics Data System (ADS)

Bai, Chen-Ming; Li, Zhi-Hui; Xu, Ting-Ting; Li, Yong-Ming

2016-11-01

An information theoretical model for quantum secret sharing was introduced by H. Imai et al. (Quantum Inf. Comput. 5(1), 69-80 2005), which was analyzed by quantum information theory. In this paper, we analyze this information theoretical model using the properties of the quantum access structure. By the analysis we propose a generalized model definition for the quantum secret sharing schemes. In our model, there are more quantum access structures which can be realized by our generalized quantum secret sharing schemes than those of the previous one. In addition, we also analyse two kinds of important quantum access structures to illustrate the existence and rationality for the generalized quantum secret sharing schemes and consider the security of the scheme by simple examples.

Incorporating profile information in community detection for online social networks

NASA Astrophysics Data System (ADS)

Fan, W.; Yeung, K. H.

2014-07-01

Community structure is an important feature in the study of complex networks. It is because nodes of the same community may have similar properties. In this paper we extend two popular community detection methods to partition online social networks. In our extended methods, the profile information of users is used for partitioning. We apply the extended methods in several sample networks of Facebook. Compared with the original methods, the community structures we obtain have higher modularity. Our results indicate that users' profile information is consistent with the community structure of their friendship network to some extent. To the best of our knowledge, this paper is the first to discuss how profile information can be used to improve community detection in online social networks.

Structures data collection for The National Map using volunteered geographic information

USGS Publications Warehouse

Poore, Barbara S.; Wolf, Eric B.; Korris, Erin M.; Walter, Jennifer L.; Matthews, Greg D.

2012-01-01

The U.S. Geological Survey (USGS) has historically sponsored volunteered data collection projects to enhance its topographic paper and digital map products. This report describes one phase of an ongoing project to encourage volunteers to contribute data to The National Map using online editing tools. The USGS recruited students studying geographic information systems (GIS) at the University of Colorado Denver and the University of Denver in the spring of 2011 to add data on structures - manmade features such as schools, hospitals, and libraries - to four quadrangles covering metropolitan Denver. The USGS customized a version of the online Potlatch editor created by the OpenStreetMap project and populated it with 30 structure types drawn from the Geographic Names Information System (GNIS), a USGS database of geographic features. The students corrected the location and attributes of these points and added information on structures that were missing. There were two rounds of quality control. Student volunteers reviewed each point, and an in-house review of each point by the USGS followed. Nine-hundred and thirty-eight structure points were initially downloaded from the USGS database. Editing and quality control resulted in 1,214 structure points that were subsequently added to The National Map. A post-project analysis of the data shows that after student edit and peer review, 92 percent of the points contributed by volunteers met National Map Accuracy Standards for horizontal accuracy. Lessons from this project will be applied to later phases. These include: simplifying editing tasks and the user interfaces, stressing to volunteers the importance of adding structures that are missing, and emphasizing the importance of conforming to editorial guidelines for formatting names and addresses of structures. The next phase of the project will encompass the entire State of Colorado and will allow any citizen to contribute structures data. Volunteers will benefit from this project by engaging with their local geography and contributing to a national resource of topographic information that remains in the public domain for anyone to download.

The Acquisition Strategy: A Roadmap to Program Management Success

DTIC Science & Technology

2012-06-01

of the positions taken in the AS. Remember , the PM is the spokesperson and storyteller for his/her program. Potential Pitfalls There are just as...them clearly and precisely • Gathers and assesses relevant information , using abstract ideas to interpret it effectively • Comes to well...incen- tive structure informs the contractor what is important and where to focus. The incentive structure can emphasize performance, cost, or

CMsearch: simultaneous exploration of protein sequence space and structure space improves not only protein homology detection but also protein structure prediction.

PubMed

Cui, Xuefeng; Lu, Zhiwu; Wang, Sheng; Jing-Yan Wang, Jim; Gao, Xin

2016-06-15

Protein homology detection, a fundamental problem in computational biology, is an indispensable step toward predicting protein structures and understanding protein functions. Despite the advances in recent decades on sequence alignment, threading and alignment-free methods, protein homology detection remains a challenging open problem. Recently, network methods that try to find transitive paths in the protein structure space demonstrate the importance of incorporating network information of the structure space. Yet, current methods merge the sequence space and the structure space into a single space, and thus introduce inconsistency in combining different sources of information. We present a novel network-based protein homology detection method, CMsearch, based on cross-modal learning. Instead of exploring a single network built from the mixture of sequence and structure space information, CMsearch builds two separate networks to represent the sequence space and the structure space. It then learns sequence-structure correlation by simultaneously taking sequence information, structure information, sequence space information and structure space information into consideration. We tested CMsearch on two challenging tasks, protein homology detection and protein structure prediction, by querying all 8332 PDB40 proteins. Our results demonstrate that CMsearch is insensitive to the similarity metrics used to define the sequence and the structure spaces. By using HMM-HMM alignment as the sequence similarity metric, CMsearch clearly outperforms state-of-the-art homology detection methods and the CASP-winning template-based protein structure prediction methods. Our program is freely available for download from http://sfb.kaust.edu.sa/Pages/Software.aspx : xin.gao@kaust.edu.sa Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

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

Hunter, Mark S.; Yoon, Chun Hong; DeMirci, Hasan

Structural information about biological macromolecules near the atomic scale provides important insight into the functions of these molecules. To date, X-ray crystallography has been the predominant method used for macromolecular structure determination. However, challenges exist when solving structures with X-rays, including the phase problem and radiation damage. X-ray-free electron lasers (X-ray FELs) have enabled collection of diffraction information before the onset of radiation damage, yet the majority of structures solved at X-ray FELs have been phased using external information via molecular replacement. De novo phasing at X-ray FELs has proven challenging due in part to per-pulse variations in intensity andmore » wavelength. Here we report the solution of a selenobiotinyl-streptavidin structure using phases obtained by the anomalous diffraction of selenium measured at a single wavelength (Se-SAD) at the Linac Coherent Light Source. Finally, our results demonstrate Se-SAD, routinely employed at synchrotrons for novel structure determination, is now possible at X-ray FELs.« less

Bayesian comparison of protein structures using partial Procrustes distance.

PubMed

Ejlali, Nasim; Faghihi, Mohammad Reza; Sadeghi, Mehdi

2017-09-26

An important topic in bioinformatics is the protein structure alignment. Some statistical methods have been proposed for this problem, but most of them align two protein structures based on the global geometric information without considering the effect of neighbourhood in the structures. In this paper, we provide a Bayesian model to align protein structures, by considering the effect of both local and global geometric information of protein structures. Local geometric information is incorporated to the model through the partial Procrustes distance of small substructures. These substructures are composed of β-carbon atoms from the side chains. Parameters are estimated using a Markov chain Monte Carlo (MCMC) approach. We evaluate the performance of our model through some simulation studies. Furthermore, we apply our model to a real dataset and assess the accuracy and convergence rate. Results show that our model is much more efficient than previous approaches.

Immediate use of prosody and context in predicting a syntactic structure.

PubMed

Nakamura, Chie; Arai, Manabu; Mazuka, Reiko

2012-11-01

Numerous studies have reported an effect of prosodic information on parsing but whether prosody can impact even the initial parsing decision is still not evident. In a visual world eye-tracking experiment, we investigated the influence of contrastive intonation and visual context on processing temporarily ambiguous relative clause sentences in Japanese. Our results showed that listeners used the prosodic cue to make a structural prediction before hearing disambiguating information. Importantly, the effect was limited to cases where the visual scene provided an appropriate context for the prosodic cue, thus eliminating the explanation that listeners have simply associated marked prosodic information with a less frequent structure. Furthermore, the influence of the prosodic information was also evident following disambiguating information, in a way that reflected the initial analysis. The current study demonstrates that prosody, when provided with an appropriate context, influences the initial syntactic analysis and also the subsequent cost at disambiguating information. The results also provide first evidence for pre-head structural prediction driven by prosodic and contextual information with a head-final construction. Copyright © 2012 Elsevier B.V. All rights reserved.

Molecular markers for genetic diversity, gene flow and genetic population structure of freshwater mussel species.

PubMed

Choupina, A B; Martins, I M

2014-08-01

Freshwater mussel species are in global decline. Anthropogenic changes of river channels and the decrease of autochthonous fish population, the natural hosts of mussels larval stages (glochidia), are the main causes. Therefore, the conservation of mussel species depends not only on habitat conservation, but also on the availability of the fish host. In Portugal, information concerning most of the mussel species is remarkably scarce. One of the most known species, Unio pictorum is also in decline however, in the basins of the rivers Tua and Sabor (Northeast of Portugal), there is some indication of relatively large populations. The aforementioned rivers can be extremely important for this species conservation not only in Portugal, but also in the remaining Iberian Peninsula. Thus, it is important to obtain data concerning Unio pictorum bioecology (distribution, habitat requirements, population structure, genetic variability, reproductive cycle and recruitment rates), as well as the genetic variability and structure of the population. Concomitantly, information concerning fish population structure, the importance of the different fish species as "glochidia" hosts and their appropriate density to allow effective mussel recruitment, will also be assessed. The achieved data is crucial to obtain information to develop effective management measures in order to promote the conservation of this bivalve species, the conservation of autochthonous fish populations, and consequently the integrity of the river habitats.

Bioinformatics approaches for structural and functional analysis of proteins in secondary metabolism in Withania somnifera.

PubMed

Sanchita; Singh, Swati; Sharma, Ashok

2014-11-01

Withania somnifera (Ashwagandha) is an affluent storehouse of large number of pharmacologically active secondary metabolites known as withanolides. These secondary metabolites are produced by withanolide biosynthetic pathway. Very less information is available on structural and functional aspects of enzymes involved in withanolides biosynthetic pathways of Withiana somnifera. We therefore performed a bioinformatics analysis to look at functional and structural properties of these important enzymes. The pathway enzymes taken for this study were 3-Hydroxy-3-methylglutaryl coenzyme A reductase, 1-Deoxy-D-xylulose-5-phosphate synthase, 1-Deoxy-D-xylulose-5-phosphate reductase, farnesyl pyrophosphate synthase, squalene synthase, squalene epoxidase, and cycloartenol synthase. The prediction of secondary structure was performed for basic structural information. Three-dimensional structures for these enzymes were predicted. The physico-chemical properties such as pI, AI, GRAVY and instability index were also studied. The current information will provide a platform to know the structural attributes responsible for the function of these protein until experimental structures become available.

Multilevel Multi-Informant Structure of the Authoritative School Climate Survey

ERIC Educational Resources Information Center

Konold, Timothy; Cornell, Dewey; Huang, Francis; Meyer, Patrick; Lacey, Anna; Nekvasil, Erin; Heilbrun, Anna; Shukla, Kathan

2014-01-01

The Authoritative School Climate Survey was designed to provide schools with a brief assessment of 2 key characteristics of school climate--disciplinary structure and student support--that are hypothesized to influence 2 important school climate outcomes--student engagement and prevalence of teasing and bullying in school. The factor structure of…

Tagline: Information Extraction for Semi-Structured Text Elements in Medical Progress Notes

ERIC Educational Resources Information Center

Finch, Dezon Kile

2012-01-01

Text analysis has become an important research activity in the Department of Veterans Affairs (VA). Statistical text mining and natural language processing have been shown to be very effective for extracting useful information from medical documents. However, neither of these techniques is effective at extracting the information stored in…

The Stammering Information Programme: A Delphi Study

ERIC Educational Resources Information Center

Berquez, Ali E.; Cook, Frances M.; Millard, Sharon K.; Jarvis, Effie

2011-01-01

Purpose: To find out what information children, parents and education staff feel would be important to know to support a child who stutters in the educational environment, in order to develop appropriate resources. Method: A Delphi study was carried out to seek the opinions of experts about the information to include. A structured six stage…

Using building information modeling to track and assess the structural condition of bridges.

DOT National Transportation Integrated Search

2016-08-01

National Bridge Inspection Standards do not require documenting damage locations during an inspection, but bridge evaluation provisions highlight the importance of it. When determining a safe load-carrying capacity of a bridge, damage location inform...

An Exponentiation Method for XML Element Retrieval

PubMed Central

2014-01-01

XML document is now widely used for modelling and storing structured documents. The structure is very rich and carries important information about contents and their relationships, for example, e-Commerce. XML data-centric collections require query terms allowing users to specify constraints on the document structure; mapping structure queries and assigning the weight are significant for the set of possibly relevant documents with respect to structural conditions. In this paper, we present an extension to the MEXIR search system that supports the combination of structural and content queries in the form of content-and-structure queries, which we call the Exponentiation function. It has been shown the structural information improve the effectiveness of the search system up to 52.60% over the baseline BM25 at MAP. PMID:24696643

Perceiving environmental structure from optical motion

NASA Technical Reports Server (NTRS)

Lappin, Joseph S.

1991-01-01

Generally speaking, one of the most important sources of optical information about environmental structure is known to be the deforming optical patterns produced by the movements of the observer (pilot) or environmental objects. As an observer moves through a rigid environment, the projected optical patterns of environmental objects are systematically transformed according to their orientations and positions in 3D space relative to those of the observer. The detailed characteristics of these deforming optical patterns carry information about the 3D structure of the objects and about their locations and orientations relative to those of the observer. The specific geometrical properties of moving images that may constitute visually detected information about the shapes and locations of environmental objects is examined.

Context Oriented Information Integration

NASA Astrophysics Data System (ADS)

Mohania, Mukesh; Bhide, Manish; Roy, Prasan; Chakaravarthy, Venkatesan T.; Gupta, Himanshu

Faced with growing knowledge management needs, enterprises are increasingly realizing the importance of seamlessly integrating critical business information distributed across both structured and unstructured data sources. Academicians have focused on this problem but there still remain a lot of obstacles for its widespread use in practice. One of the key problems is the absence of schema in unstructured text. In this paper we present a new paradigm for integrating information which overcomes this problem - that of Context Oriented Information Integration. The goal is to integrate unstructured data with the structured data present in the enterprise and use the extracted information to generate actionable insights for the enterprise. We present two techniques which enable context oriented information integration and show how they can be used for solving real world problems.

Cognitive Flexibility through Metastable Neural Dynamics Is Disrupted by Damage to the Structural Connectome.

PubMed

Hellyer, Peter J; Scott, Gregory; Shanahan, Murray; Sharp, David J; Leech, Robert

2015-06-17

Current theory proposes that healthy neural dynamics operate in a metastable regime, where brain regions interact to simultaneously maximize integration and segregation. Metastability may confer important behavioral properties, such as cognitive flexibility. It is increasingly recognized that neural dynamics are constrained by the underlying structural connections between brain regions. An important challenge is, therefore, to relate structural connectivity, neural dynamics, and behavior. Traumatic brain injury (TBI) is a pre-eminent structural disconnection disorder whereby traumatic axonal injury damages large-scale connectivity, producing characteristic cognitive impairments, including slowed information processing speed and reduced cognitive flexibility, that may be a result of disrupted metastable dynamics. Therefore, TBI provides an experimental and theoretical model to examine how metastable dynamics relate to structural connectivity and cognition. Here, we use complementary empirical and computational approaches to investigate how metastability arises from the healthy structural connectome and relates to cognitive performance. We found reduced metastability in large-scale neural dynamics after TBI, measured with resting-state functional MRI. This reduction in metastability was associated with damage to the connectome, measured using diffusion MRI. Furthermore, decreased metastability was associated with reduced cognitive flexibility and information processing. A computational model, defined by empirically derived connectivity data, demonstrates how behaviorally relevant changes in neural dynamics result from structural disconnection. Our findings suggest how metastable dynamics are important for normal brain function and contingent on the structure of the human connectome. Copyright © 2015 the authors 0270-6474/15/359050-14$15.00/0.

What Matters in Scientific Explanations: Effects of Elaboration and Content

PubMed Central

Rottman, Benjamin M.; Keil, Frank C.

2011-01-01

Given the breadth and depth of available information, determining which components of an explanation are most important is a crucial process for simplifying learning. Three experiments tested whether people believe that components of an explanation with more elaboration are more important. In Experiment 1, participants read separate and unstructured components that comprised explanations of real-world scientific phenomena, rated the components on their importance for understanding the explanations, and drew graphs depicting which components elaborated on which other components. Participants gave higher importance scores for components that they judged to be elaborated upon by other components. Experiment 2 demonstrated that experimentally increasing the amount of elaboration of a component increased the perceived importance of the elaborated component. Furthermore, Experiment 3 demonstrated that elaboration increases the importance of the elaborated information by providing insight into understanding the elaborated information; information that was too technical to provide insight into the elaborated component did not increase the importance of the elaborated component. While learning an explanation, people piece together the structure of elaboration relationships between components and use the insight provided by elaboration to identify important components. PMID:21924709

Structure of complexes between aluminum chloride and other chlorides, 2: Alkali-(chloroaluminates). Gaseous complexes

NASA Technical Reports Server (NTRS)

Hargittai, M.

1980-01-01

The structural chemistry of complexes between aluminum chloride and other metal chlorides is important both for practice and theory. Condensed-phase as well as vapor-phase complexes are of interest. Structural information on such complexes is reviewed. The first emphasis is given to the molten state because of its practical importance. Aluminum chloride forms volatile complexes with other metal chlorides and these vapor-phase complexes are dealt with in the second part. Finally, the variations in molecular shape and geometrical parameters are summarized.

Experimental correlation of melt structures, nucleation rates, and thermal histories of silicate melts

NASA Technical Reports Server (NTRS)

Boynton, W. V.; DRAKE; HILDEBRAND; JONES; LEWIS; TREIMAN; WARK

1987-01-01

The theory and measurement of the structure of liquids is an important aspect of modern metallurgy and igneous petrology. Liquid structure exerts strong controls on both the types of crystals that may precipitate from melts and on the chemical composition of those crystals. An interesting aspect of melt structure studies is the problem of melt memories; that is, a melt can retain a memory of previous thermal history. This memory can influence both nucleation behavior and crystal composition. This melt memory may be characterized quantitatively with techniques such as Raman, infrared and NMR spectroscopy to provide information on short-range structure. Melt structure studies at high temperature will take advantage of the microgravity conditions of the Space Station to perform containerless experiments. Melt structure determinations at high temperature (experiments that are greatly facilitated by containerless technology) will provide invaluable information for materials science, glass technology, and geochemistry. In conjunction with studies of nucleation behavior and nucleation rates, information relevant to nucleation in magma chambers in terrestrial planets will be acquired.

Cross-Linking/Mass Spectrometry for Studying Protein Structures and Protein-Protein Interactions: Where Are We Now and Where Should We Go from Here?

PubMed

Sinz, Andrea

2018-05-28

Structural mass spectrometry (MS) is gaining increasing importance for deriving valuable three-dimensional structural information on proteins and protein complexes, and it complements existing techniques, such as NMR spectroscopy and X-ray crystallography. Structural MS unites different MS-based techniques, such as hydrogen/deuterium exchange, native MS, ion-mobility MS, protein footprinting, and chemical cross-linking/MS, and it allows fundamental questions in structural biology to be addressed. In this Minireview, I will focus on the cross-linking/MS strategy. This method not only delivers tertiary structural information on proteins, but is also increasingly being used to decipher protein interaction networks, both in vitro and in vivo. Cross-linking/MS is currently one of the most promising MS-based approaches to derive structural information on very large and transient protein assemblies and intrinsically disordered proteins. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Automated Quantification of Arbitrary Arm-Segment Structure in Spiral Galaxies

NASA Astrophysics Data System (ADS)

Davis, Darren Robert

This thesis describes a system that, given approximately-centered images of spiral galaxies, produces quantitative descriptions of spiral galaxy structure without the need for per-image human input. This structure information consists of a list of spiral arm segments, each associated with a fitted logarithmic spiral arc and a pixel region. This list-of-arcs representation allows description of arbitrary spiral galaxy structure: the arms do not need to be symmetric, may have forks or bends, and, more generally, may be arranged in any manner with a consistent spiral-pattern center (non-merging galaxies have a sufficiently well-defined center). Such flexibility is important in order to accommodate the myriad structure variations observed in spiral galaxies. From the arcs produced from our method it is possible to calculate measures of spiral galaxy structure such as winding direction, winding tightness, arm counts, asymmetry, or other values of interest (including user-defined measures). In addition to providing information about the spiral arm "skeleton" of each galaxy, our method can enable analyses of brightness within individual spiral arms, since we provide the pixel regions associated with each spiral arm segment. For winding direction, arm tightness, and arm count, comparable information is available (to various extents) from previous efforts; to the extent that such information is available, we find strong correspondence with our output. We also characterize the changes to (and invariances in) our output as a function of modifications to important algorithm parameters. By enabling generation of extensive data about spiral galaxy structure from large-scale sky surveys, our method will enable new discoveries and tests regarding the nature of galaxies and the universe, and will facilitate subsequent work to automatically fit detailed brightness models of spiral galaxies.

University Students' Knowledge Structures and Informal Reasoning on the Use of Genetically Modified Foods: Multidimensional Analyses

NASA Astrophysics Data System (ADS)

Wu, Ying-Tien

2013-10-01

This study aims to provide insights into the role of learners' knowledge structures about a socio-scientific issue (SSI) in their informal reasoning on the issue. A total of 42 non-science major university students' knowledge structures and informal reasoning were assessed with multidimensional analyses. With both qualitative and quantitative analyses, this study revealed that those students with more extended and better-organized knowledge structures, as well as those who more frequently used higher-order information processing modes, were more oriented towards achieving a higher-level informal reasoning quality. The regression analyses further showed that the "richness" of the students' knowledge structures explained 25 % of the variation in their rebuttal construction, an important indicator of reasoning quality, indicating the significance of the role of students' sophisticated knowledge structure in SSI reasoning. Besides, this study also provides some initial evidence for the significant role of the "core" concept within one's knowledge structure in one's SSI reasoning. The findings in this study suggest that, in SSI-based instruction, science instructors should try to identify students' core concepts within their prior knowledge regarding the SSI, and then they should try to guide students to construct and structure relevant concepts or ideas regarding the SSI based on their core concepts. Thus, students could obtain extended and well-organized knowledge structures, which would then help them achieve better learning transfer in dealing with SSIs.

Sequence-similar, structure-dissimilar protein pairs in the PDB.

PubMed

Kosloff, Mickey; Kolodny, Rachel

2008-05-01

It is often assumed that in the Protein Data Bank (PDB), two proteins with similar sequences will also have similar structures. Accordingly, it has proved useful to develop subsets of the PDB from which "redundant" structures have been removed, based on a sequence-based criterion for similarity. Similarly, when predicting protein structure using homology modeling, if a template structure for modeling a target sequence is selected by sequence alone, this implicitly assumes that all sequence-similar templates are equivalent. Here, we show that this assumption is often not correct and that standard approaches to create subsets of the PDB can lead to the loss of structurally and functionally important information. We have carried out sequence-based structural superpositions and geometry-based structural alignments of a large number of protein pairs to determine the extent to which sequence similarity ensures structural similarity. We find many examples where two proteins that are similar in sequence have structures that differ significantly from one another. The source of the structural differences usually has a functional basis. The number of such proteins pairs that are identified and the magnitude of the dissimilarity depend on the approach that is used to calculate the differences; in particular sequence-based structure superpositioning will identify a larger number of structurally dissimilar pairs than geometry-based structural alignments. When two sequences can be aligned in a statistically meaningful way, sequence-based structural superpositioning provides a meaningful measure of structural differences. This approach and geometry-based structure alignments reveal somewhat different information and one or the other might be preferable in a given application. Our results suggest that in some cases, notably homology modeling, the common use of nonredundant datasets, culled from the PDB based on sequence, may mask important structural and functional information. We have established a data base of sequence-similar, structurally dissimilar protein pairs that will help address this problem (http://luna.bioc.columbia.edu/rachel/seqsimstrdiff.htm).

CHEMICAL STRUCTURE INDEXING OF TOXICITY DATA ON THE INTERNET: MOVING TOWARDS A FLAT WORLD

EPA Science Inventory

Standardized chemical structure annotation of public toxicity databases and information resources is playing an increasingly important role in the 'flattening' and integration of diverse sets of biological activity data on the Internet. This review discusses public initiatives th...

The contribution of visual information to the perception of speech in noise with and without informative temporal fine structure

PubMed Central

Stacey, Paula C.; Kitterick, Pádraig T.; Morris, Saffron D.; Sumner, Christian J.

2017-01-01

Understanding what is said in demanding listening situations is assisted greatly by looking at the face of a talker. Previous studies have observed that normal-hearing listeners can benefit from this visual information when a talker's voice is presented in background noise. These benefits have also been observed in quiet listening conditions in cochlear-implant users, whose device does not convey the informative temporal fine structure cues in speech, and when normal-hearing individuals listen to speech processed to remove these informative temporal fine structure cues. The current study (1) characterised the benefits of visual information when listening in background noise; and (2) used sine-wave vocoding to compare the size of the visual benefit when speech is presented with or without informative temporal fine structure. The accuracy with which normal-hearing individuals reported words in spoken sentences was assessed across three experiments. The availability of visual information and informative temporal fine structure cues was varied within and across the experiments. The results showed that visual benefit was observed using open- and closed-set tests of speech perception. The size of the benefit increased when informative temporal fine structure cues were removed. This finding suggests that visual information may play an important role in the ability of cochlear-implant users to understand speech in many everyday situations. Models of audio-visual integration were able to account for the additional benefit of visual information when speech was degraded and suggested that auditory and visual information was being integrated in a similar way in all conditions. The modelling results were consistent with the notion that audio-visual benefit is derived from the optimal combination of auditory and visual sensory cues. PMID:27085797

Plant structure predicts leaf litter capture in the tropical montane bromeliad Tillandsia turneri.

PubMed

Ospina-Bautista, F; Estévez Varón, J V

2016-05-03

Leaves intercepted by bromeliads become an important energy and matter resource for invertebrate communities, bacteria, fungi, and the plant itself. The relationship between bromeliad structure, defined as its size and complexity, and accumulated leaf litter was studied in 55 bromeliads of Tillandsia turneri through multiple regression and the Akaike information criterion. Leaf litter accumulation in bromeliads was best explained by size and complexity variables such as plant cover, sheath length, and leaf number. In conclusion, plant structure determines the amount of litter that enters bromeliads, and changes in its structure could affect important processes within ecosystem functioning or species richness.

bcl::Cluster : A method for clustering biological molecules coupled with visualization in the Pymol Molecular Graphics System.

PubMed

Alexander, Nathan; Woetzel, Nils; Meiler, Jens

2011-02-01

Clustering algorithms are used as data analysis tools in a wide variety of applications in Biology. Clustering has become especially important in protein structure prediction and virtual high throughput screening methods. In protein structure prediction, clustering is used to structure the conformational space of thousands of protein models. In virtual high throughput screening, databases with millions of drug-like molecules are organized by structural similarity, e.g. common scaffolds. The tree-like dendrogram structure obtained from hierarchical clustering can provide a qualitative overview of the results, which is important for focusing detailed analysis. However, in practice it is difficult to relate specific components of the dendrogram directly back to the objects of which it is comprised and to display all desired information within the two dimensions of the dendrogram. The current work presents a hierarchical agglomerative clustering method termed bcl::Cluster. bcl::Cluster utilizes the Pymol Molecular Graphics System to graphically depict dendrograms in three dimensions. This allows simultaneous display of relevant biological molecules as well as additional information about the clusters and the members comprising them.

Evaluation of Ultrasonic Fiber Structure Extraction Technique Using Autopsy Specimens of Liver

NASA Astrophysics Data System (ADS)

Yamaguchi, Tadashi; Hirai, Kazuki; Yamada, Hiroyuki; Ebara, Masaaki; Hachiya, Hiroyuki

2005-06-01

It is very important to diagnose liver cirrhosis noninvasively and correctly. In our previous studies, we proposed a processing technique to detect changes in liver tissue in vivo. In this paper, we propose the evaluation of the relationship between liver disease and echo information using autopsy specimens of a human liver in vitro. It is possible to verify the function of a processing parameter clearly and to compare the processing result and the actual human liver tissue structure by in vitro experiment. In the results of our processing technique, information that did not obey a Rayleigh distribution from the echo signal of the autopsy liver specimens was extracted depending on changes in a particular processing parameter. The fiber tissue structure of the same specimen was extracted from a number of histological images of stained tissue. We constructed 3D structures using the information extracted from the echo signal and the fiber structure of the stained tissue and compared the two. By comparing the 3D structures, it is possible to evaluate the relationship between the information that does not obey a Rayleigh distribution of the echo signal and the fibrosis structure.

ICON: 3D reconstruction with 'missing-information' restoration in biological electron tomography.

PubMed

Deng, Yuchen; Chen, Yu; Zhang, Yan; Wang, Shengliu; Zhang, Fa; Sun, Fei

2016-07-01

Electron tomography (ET) plays an important role in revealing biological structures, ranging from macromolecular to subcellular scale. Due to limited tilt angles, ET reconstruction always suffers from the 'missing wedge' artifacts, thus severely weakens the further biological interpretation. In this work, we developed an algorithm called Iterative Compressed-sensing Optimized Non-uniform fast Fourier transform reconstruction (ICON) based on the theory of compressed-sensing and the assumption of sparsity of biological specimens. ICON can significantly restore the missing information in comparison with other reconstruction algorithms. More importantly, we used the leave-one-out method to verify the validity of restored information for both simulated and experimental data. The significant improvement in sub-tomogram averaging by ICON indicates its great potential in the future application of high-resolution structural determination of macromolecules in situ. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

Informational technologies in modern educational structure

NASA Astrophysics Data System (ADS)

Fedyanin, A. B.

2017-01-01

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

Selenium single-wavelength anomalous diffraction de novo phasing using an X-ray-free electron laser

DOE PAGES

Hunter, Mark S.; Yoon, Chun Hong; DeMirci, Hasan; ...

2016-11-04

Structural information about biological macromolecules near the atomic scale provides important insight into the functions of these molecules. To date, X-ray crystallography has been the predominant method used for macromolecular structure determination. However, challenges exist when solving structures with X-rays, including the phase problem and radiation damage. X-ray-free electron lasers (X-ray FELs) have enabled collection of diffraction information before the onset of radiation damage, yet the majority of structures solved at X-ray FELs have been phased using external information via molecular replacement. De novo phasing at X-ray FELs has proven challenging due in part to per-pulse variations in intensity andmore » wavelength. Here we report the solution of a selenobiotinyl-streptavidin structure using phases obtained by the anomalous diffraction of selenium measured at a single wavelength (Se-SAD) at the Linac Coherent Light Source. Finally, our results demonstrate Se-SAD, routinely employed at synchrotrons for novel structure determination, is now possible at X-ray FELs.« less

[Study on Information Extraction of Clinic Expert Information from Hospital Portals].

PubMed

Zhang, Yuanpeng; Dong, Jiancheng; Qian, Danmin; Geng, Xingyun; Wu, Huiqun; Wang, Li

2015-12-01

Clinic expert information provides important references for residents in need of hospital care. Usually, such information is hidden in the deep web and cannot be directly indexed by search engines. To extract clinic expert information from the deep web, the first challenge is to make a judgment on forms. This paper proposes a novel method based on a domain model, which is a tree structure constructed by the attributes of search interfaces. With this model, search interfaces can be classified to a domain and filled in with domain keywords. Another challenge is to extract information from the returned web pages indexed by search interfaces. To filter the noise information on a web page, a block importance model is proposed. The experiment results indicated that the domain model yielded a precision 10.83% higher than that of the rule-based method, whereas the block importance model yielded an F₁ measure 10.5% higher than that of the XPath method.

Structural analysis of pyrolytic lignins isolated from switchgrass fast pyrolysis oil

USDA-ARS?s Scientific Manuscript database

Structural characterization of lignin extracted from the bio-oil produced by fast pyrolysis of switchgrass (Panicum virgatum) is reported. This new information is important to understanding the utility of lignin as a chemical feedstock in a pyrolysis based biorefinery. Pyrolysis induces a variety of...

The Structure of Habilitation.

ERIC Educational Resources Information Center

Gibson, David; And Others

1987-01-01

Biographic and program information were related to placement outcomes for 75 mentally retarded adults who had completed a three-year training program and up to three years of subsequent community vocational placement. Results suggested an important role for cognitive variables (symbol management and basic concepts) in the overall structure of…

Marketing of Online and CD-ROM Databases.

ERIC Educational Resources Information Center

King, Carol; Oppenheim, Charles

1994-01-01

A survey of 20 British electronic information vendors found that 95% considered marketing important and suggested that it is likely to become more intensive and aggressive as competition increases in the information industry. Analyzed advertisements from professional journals and direct mail literature for readability, structure, and information…

Porcine reproductive and respiratory syndrome virus (PRRSV): pathogenesis and interaction with the immune System

USDA-ARS?s Scientific Manuscript database

This review addresses important issues of porcine reproductive and respiratory syndrome virus (PRRSV) infection, immunity, pathogenesis and control. Worldwide PRRS is the most economically important infectious disease of pigs. We highlight the latest information on viral genome structure, pathogenic...

Statistical inference of protein structural alignments using information and compression.

PubMed

Collier, James H; Allison, Lloyd; Lesk, Arthur M; Stuckey, Peter J; Garcia de la Banda, Maria; Konagurthu, Arun S

2017-04-01

Structural molecular biology depends crucially on computational techniques that compare protein three-dimensional structures and generate structural alignments (the assignment of one-to-one correspondences between subsets of amino acids based on atomic coordinates). Despite its importance, the structural alignment problem has not been formulated, much less solved, in a consistent and reliable way. To overcome these difficulties, we present here a statistical framework for the precise inference of structural alignments, built on the Bayesian and information-theoretic principle of Minimum Message Length (MML). The quality of any alignment is measured by its explanatory power-the amount of lossless compression achieved to explain the protein coordinates using that alignment. We have implemented this approach in MMLigner , the first program able to infer statistically significant structural alignments. We also demonstrate the reliability of MMLigner 's alignment results when compared with the state of the art. Importantly, MMLigner can also discover different structural alignments of comparable quality, a challenging problem for oligomers and protein complexes. Source code, binaries and an interactive web version are available at http://lcb.infotech.monash.edu.au/mmligner . arun.konagurthu@monash.edu. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Molecular Dynamics Methodologies for Probing Cannabinoid Ligand/Receptor Interaction

PubMed Central

Lynch, Diane L.; Hurst, Dow P.; Shore, Derek M.; Pitman, Mike C.; Reggio, Patricia H.

2018-01-01

The cannabinoid type 1 and 2 G-protein-coupled receptors are currently important pharmacological targets with significant drug discovery potential. These receptors have been shown to display functional selectivity or biased agonism, a property currently thought to have substantial therapeutic potential. Although recent advances in crystallization techniques have provided a wealth of structural information about this important class of membrane-embedded proteins, these structures lack dynamical information. In order to fully understand the interplay of structure and function for this important class of proteins, complementary techniques that address the dynamical aspects of their function are required such as NMR as well as a variety of other spectroscopies. Complimentary to these experimental approaches is molecular dynamics, which has been effectively used to help unravel, at the atomic level, the dynamics of ligand binding and activation of these membrane-bound receptors. Here, we discuss and present several representative examples of the application of molecular dynamics simulations to the understanding of the signatures of ligand-binding and -biased signaling at the cannabinoid type 1 and 2 receptors. PMID:28750815

Biofouling community composition across a range of environmental conditions and geographical locations suitable for floating marine renewable energy generation.

PubMed

Macleod, Adrian K; Stanley, Michele S; Day, John G; Cook, Elizabeth J

2016-01-01

Knowledge of biofouling typical of marine structures is essential for engineers to define appropriate loading criteria in addition to informing other stakeholders about the ecological implications of creating novel artificial environments. There is a lack of information regarding biofouling community composition (including weight and density characteristics) on floating structures associated with future marine renewable energy generation technologies. A network of navigation buoys were identified across a range of geographical areas, environmental conditions (tidal flow speed, temperature and salinity), and deployment durations suitable for future developments. Despite the perceived importance of environmental and temporal factors, geographical location explained the greatest proportion of the observed variation in community composition, emphasising the importance of considering geography when assessing the impact of biofouling on device functioning and associated ecology. The principal taxa associated with variation in biofouling community composition were mussels (Mytilus edulis), which were also important when determining loading criteria.

The Role of Human Error in Design, Construction, and Reliability of Marine Structures.

DTIC Science & Technology

1994-10-01

The 1979 Three Mile Island nuclear plant accident was largely a result of a failure to properly sort out and recognize critically important information...determinating the goals and objectives of the program and by evaluating and interpreting the results in terms of structural design, construction, and...67 Checking Models in Structural Design ....................................... 69 Nuclear Power Plants

Using FT-IR Spectroscopy to Elucidate the Structures of Ablative Polymers

NASA Technical Reports Server (NTRS)

Fan, Wendy

2011-01-01

The composition and structure of an ablative polymer has a multifaceted influence on its thermal, mechanical and ablative properties. Understanding the molecular level information is critical to the optimization of material performance because it helps to establish correlations with the macroscopic properties of the material, the so-called structure-property relationship. Moreover, accurate information of molecular structures is also essential to predict the thermal decomposition pathways as well as to identify decomposition species that are fundamentally important to modeling work. In this presentation, I will describe the use of infrared transmission spectroscopy (FT-IR) as a convenient tool to aid the discovery and development of thermal protection system materials.

Approaches to ab initio molecular replacement of α-helical transmembrane proteins.

PubMed

Thomas, Jens M H; Simkovic, Felix; Keegan, Ronan; Mayans, Olga; Zhang, Chengxin; Zhang, Yang; Rigden, Daniel J

2017-12-01

α-Helical transmembrane proteins are a ubiquitous and important class of proteins, but present difficulties for crystallographic structure solution. Here, the effectiveness of the AMPLE molecular replacement pipeline in solving α-helical transmembrane-protein structures is assessed using a small library of eight ideal helices, as well as search models derived from ab initio models generated both with and without evolutionary contact information. The ideal helices prove to be surprisingly effective at solving higher resolution structures, but ab initio-derived search models are able to solve structures that could not be solved with the ideal helices. The addition of evolutionary contact information results in a marked improvement in the modelling and makes additional solutions possible.

Quantification of network structural dissimilarities.

PubMed

Schieber, Tiago A; Carpi, Laura; Díaz-Guilera, Albert; Pardalos, Panos M; Masoller, Cristina; Ravetti, Martín G

2017-01-09

Identifying and quantifying dissimilarities among graphs is a fundamental and challenging problem of practical importance in many fields of science. Current methods of network comparison are limited to extract only partial information or are computationally very demanding. Here we propose an efficient and precise measure for network comparison, which is based on quantifying differences among distance probability distributions extracted from the networks. Extensive experiments on synthetic and real-world networks show that this measure returns non-zero values only when the graphs are non-isomorphic. Most importantly, the measure proposed here can identify and quantify structural topological differences that have a practical impact on the information flow through the network, such as the presence or absence of critical links that connect or disconnect connected components.

Analysis and Visualization of Nerve Vessel Contacts for Neurovascular Decompression

NASA Astrophysics Data System (ADS)

Süßmuth, Jochen; Piazza, Alexander; Enders, Frank; Naraghi, Ramin; Greiner, Günther; Hastreiter, Peter

Neurovascular compression syndromes are caused by a pathological contact between cranial nerves and vascular structures at the surface of the brainstem. Aiming at improved pre-operative analysis of the target structures, we propose calculating distance fields to provide quantitative information of the important nerve-vessel contacts. Furthermore, we suggest reconstructing polygonal models for the nerves and vessels. Color-coding with the respective distance information is used for enhanced visualization. Overall, our new strategy contributes to a significantly improved clinical understanding.

Pilots' Information Needs and Strategies for Operating in Icing Conditions

NASA Technical Reports Server (NTRS)

Vigeant-Langlois, Laurence N.; Hansman, R. John

2003-01-01

Pilot current use of icing information, pilot encounters and strategies for dealing with in-flight aircraft structural icing situations, and desired attributes of new icing information systems were investigated through a survey of pilots of several operational categories. The survey identified important information elements and fiequently used information paths for obtaining icing-related information. Free- response questions solicited descriptions of significant , icing encounters, and probed key icing-related decision and information criteria. Results indicated the information needs for the horizontal and vertical location of icing conditions and the identification of icing-free zones.

Discovering perturbation of modular structure in HIV progression by integrating multiple data sources through non-negative matrix factorization.

PubMed

Ray, Sumanta; Maulik, Ujjwal

2016-12-20

Detecting perturbation in modular structure during HIV-1 disease progression is an important step to understand stage specific infection pattern of HIV-1 virus in human cell. In this article, we proposed a novel methodology on integration of multiple biological information to identify such disruption in human gene module during different stages of HIV-1 infection. We integrate three different biological information: gene expression information, protein-protein interaction information and gene ontology information in single gene meta-module, through non negative matrix factorization (NMF). As the identified metamodules inherit those information so, detecting perturbation of these, reflects the changes in expression pattern, in PPI structure and in functional similarity of genes during the infection progression. To integrate modules of different data sources into strong meta-modules, NMF based clustering is utilized here. Perturbation in meta-modular structure is identified by investigating the topological and intramodular properties and putting rank to those meta-modules using a rank aggregation algorithm. We have also analyzed the preservation structure of significant GO terms in which the human proteins of the meta-modules participate. Moreover, we have performed an analysis to show the change of coregulation pattern of identified transcription factors (TFs) over the HIV progression stages.

Typography, Color, and Information Structure.

ERIC Educational Resources Information Center

Keyes, Elizabeth

1993-01-01

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

Multilingual Thesauri for the Modern World - No Ideal Solution?

ERIC Educational Resources Information Center

Jorna, Kerstin; Davies, Sylvie

2001-01-01

Discusses thesauri as tools for multilingual information retrieval and cross-cultural communication. Considers the need for multilingual thesauri and the importance of explicit conceptual structures, and introduces a pilot thesaurus, InfoDEFT (Information Deutsch-English-Francais Thesaurus), as a possible model for new online thesauri which are…

Specification Theory, Patterns, and Models in Information Systems Domains: An Exploratory Investigation

ERIC Educational Resources Information Center

Woolridge, Richard William

2010-01-01

Application and project domain specifications are an important aspect of Information Systems (IS) development. Observations of over thirty IS projects suggest dimly perceived structural patterns in specifications that are unaccounted for in research and practice. This investigation utilizes a theory building with case studies methodology to…

Reliable structural interpretation of small-angle scattering data from bio-molecules in solution--the importance of quality control and a standard reporting framework.

PubMed

Jacques, David A; Guss, Jules Mitchell; Trewhella, Jill

2012-05-17

Small-angle scattering is becoming an increasingly popular tool for the study of bio-molecular structures in solution. The large number of publications with 3D-structural models generated from small-angle solution scattering data has led to a growing consensus for the need to establish a standard reporting framework for their publication. The International Union of Crystallography recently established a set of guidelines for the necessary information required for the publication of such structural models. Here we describe the rationale for these guidelines and the importance of standardising the way in which small-angle scattering data from bio-molecules and associated structural interpretations are reported.

Professional Help-Seeking for Adolescent Dating Violence in the Rural South: The Role of Social Support and Informal Help-Seeking

PubMed Central

Hedge, Jasmine M.; Sianko, Natallia; McDonell, James R.

2016-01-01

Structural equation modeling with three waves of data was used to assess a mediation model investigating the relationship between perceived social support, informal help-seeking intentions, and professional help-seeking intentions in the context of adolescent dating violence. The sample included 589 adolescents from a rural, southern county who participated in a longitudinal study of teen dating violence victimization and perpetration. Results suggest that informal help-seeking intentions are an important link between perceived social support and professional help-seeking intentions. Findings highlight the importance of informal help-seeking and informal help-giving in fostering professional help-seeking for adolescent victims and perpetrators of dating violence. PMID:27580981

Targeting functional motifs of a protein family

NASA Astrophysics Data System (ADS)

Bhadola, Pradeep; Deo, Nivedita

2016-10-01

The structural organization of a protein family is investigated by devising a method based on the random matrix theory (RMT), which uses the physiochemical properties of the amino acid with multiple sequence alignment. A graphical method to represent protein sequences using physiochemical properties is devised that gives a fast, easy, and informative way of comparing the evolutionary distances between protein sequences. A correlation matrix associated with each property is calculated, where the noise reduction and information filtering is done using RMT involving an ensemble of Wishart matrices. The analysis of the eigenvalue statistics of the correlation matrix for the β -lactamase family shows the universal features as observed in the Gaussian orthogonal ensemble (GOE). The property-based approach captures the short- as well as the long-range correlation (approximately following GOE) between the eigenvalues, whereas the previous approach (treating amino acids as characters) gives the usual short-range correlations, while the long-range correlations are the same as that of an uncorrelated series. The distribution of the eigenvector components for the eigenvalues outside the bulk (RMT bound) deviates significantly from RMT observations and contains important information about the system. The information content of each eigenvector of the correlation matrix is quantified by introducing an entropic estimate, which shows that for the β -lactamase family the smallest eigenvectors (low eigenmodes) are highly localized as well as informative. These small eigenvectors when processed gives clusters involving positions that have well-defined biological and structural importance matching with experiments. The approach is crucial for the recognition of structural motifs as shown in β -lactamase (and other families) and selectively identifies the important positions for targets to deactivate (activate) the enzymatic actions.

DISTRIBUTED STRUCTURE-SEARCHABLE TOXICITY ...

EPA Pesticide Factsheets

The ability to assess the potential genotoxicity, carcinogenicity, or other toxicity of pharmaceutical or industrial chemicals based on chemical structure information is a highly coveted and shared goal of varied academic, commercial, and government regulatory groups. These diverse interests often employ different approaches and have different criteria and use for toxicity assessments, but they share a need for unrestricted access to existing public toxicity data linked with chemical structure information. Currently, there exists no central repository of toxicity information, commercial or public, that adequately meets the data requirements for flexible analogue searching, SAR model development, or building of chemical relational databases (CRD). The Distributed Structure-Searchable Toxicity (DSSTox) Public Database Network is being proposed as a community-supported, web-based effort to address these shared needs of the SAR and toxicology communities. The DSSTox project has the following major elements: 1) to adopt and encourage the use of a common standard file format (SDF) for public toxicity databases that includes chemical structure, text and property information, and that can easily be imported into available CRD applications; 2) to implement a distributed source approach, managed by a DSSTox Central Website, that will enable decentralized, free public access to structure-toxicity data files, and that will effectively link knowledgeable toxicity data s

Genetic diversity and structure of elite cotton germplasm (Gossypium hirsutum L.) using genome-wide SNP data.

PubMed

Ai, XianTao; Liang, YaJun; Wang, JunDuo; Zheng, JuYun; Gong, ZhaoLong; Guo, JiangPing; Li, XueYuan; Qu, YanYing

2017-10-01

Cotton (Gossypium spp.) is the most important natural textile fiber crop, and Gossypium hirsutum L. is responsible for 90% of the annual cotton crop in the world. Information on cotton genetic diversity and population structure is essential for new breeding lines. In this study, we analyzed population structure and genetic diversity of 288 elite Gossypium hirsutum cultivar accessions collected from around the world, and especially from China, using genome-wide single nucleotide polymorphisms (SNP) markers. The average polymorphsim information content (PIC) was 0.25, indicating a relatively low degree of genetic diversity. Population structure analysis revealed extensive admixture and identified three subgroups. Phylogenetic analysis supported the subgroups identified by STRUCTURE. The results from both population structure and phylogenetic analysis were, for the most part, in agreement with pedigree information. Analysis of molecular variance revealed a larger amount of variation was due to diversity within the groups. Establishment of genetic diversity and population structure from this study could be useful for genetic and genomic analysis and systematic utilization of the standing genetic variation in upland cotton.

Using directed information for influence discovery in interconnected dynamical systems

NASA Astrophysics Data System (ADS)

Rao, Arvind; Hero, Alfred O.; States, David J.; Engel, James Douglas

2008-08-01

Structure discovery in non-linear dynamical systems is an important and challenging problem that arises in various applications such as computational neuroscience, econometrics, and biological network discovery. Each of these systems have multiple interacting variables and the key problem is the inference of the underlying structure of the systems (which variables are connected to which others) based on the output observations (such as multiple time trajectories of the variables). Since such applications demand the inference of directed relationships among variables in these non-linear systems, current methods that have a linear assumption on structure or yield undirected variable dependencies are insufficient. Hence, in this work, we present a methodology for structure discovery using an information-theoretic metric called directed time information (DTI). Using both synthetic dynamical systems as well as true biological datasets (kidney development and T-cell data), we demonstrate the utility of DTI in such problems.

Probing hydrogen positions in hydrous compounds: information from parametric neutron powder diffraction studies.

PubMed

Ting, Valeska P; Henry, Paul F; Schmidtmann, Marc; Wilson, Chick C; Weller, Mark T

2012-05-21

We demonstrate the extent to which modern detector technology, coupled with a high flux constant wavelength neutron source, can be used to obtain high quality diffraction data from short data collections, allowing the refinement of the full structures (including hydrogen positions) of hydrous compounds from in situ neutron powder diffraction measurements. The in situ thermodiffractometry and controlled humidity studies reported here reveal that important information on the reorientations of structural water molecules with changing conditions can be easily extracted, providing insight into the effects of hydrogen bonding on bulk physical properties. Using crystalline BaCl2·2H2O as an example system, we analyse the structural changes in the compound and its dehydration intermediates with changing temperature and humidity levels to demonstrate the quality of the dynamic structural information on the hydrogen atoms and associated hydrogen bonding that can be obtained without resorting to sample deuteration.

Antenatal education for childbirth-epidural analgesia.

PubMed

Cutajar, Lisa; Cyna, Allan M

2018-05-07

The language structures used by antenatal educators have not been previously researched in the context of antenatal childbirth classes. Epidural analgesia for labour is a common, and a frequently asked about, component of antenatal education for parents in hospitals providing maternity care. We aimed to identify the way information is described and presented by childbirth educators to assess content and determine which language structures such as metaphor, suggestion, information and storytelling are utilized. This observational study of antenatal education was conducted at a single tertiary referral center for maternity care in Western Sydney, Australia. All three childbirth educators agreed to be video recorded whilst providing information to parents during antenatal classes. Audio data was subsequently transcribed and then analysed by two researchers, independently categorising the various language structures and types of information provided. For the purposes of the current study, data concerning a single topic was used for the analysis-'epidural analgesia for labour'. Language structures used were highly variable between educators, as was the content and time taken for the information being provided. Our findings represent a first attempt to identify baseline information used in the clinical setting of antenatal education in order to categories communication structures used. This study has identified areas for further improvements and consistency in the way educators provide information to parents and has important implications for future midwifery practice, education and research. Copyright © 2018 Elsevier Ltd. All rights reserved.

Bayesian Network Structure Learning for Urban Land Use Classification from Landsat ETM+ and Ancillary Data

NASA Astrophysics Data System (ADS)

Park, M.; Stenstrom, M. K.

2004-12-01

Recognizing urban information from the satellite imagery is problematic due to the diverse features and dynamic changes of urban landuse. The use of Landsat imagery for urban land use classification involves inherent uncertainty due to its spatial resolution and the low separability among land uses. To resolve the uncertainty problem, we investigated the performance of Bayesian networks to classify urban land use since Bayesian networks provide a quantitative way of handling uncertainty and have been successfully used in many areas. In this study, we developed the optimized networks for urban land use classification from Landsat ETM+ images of Marina del Rey area based on USGS land cover/use classification level III. The networks started from a tree structure based on mutual information between variables and added the links to improve accuracy. This methodology offers several advantages: (1) The network structure shows the dependency relationships between variables. The class node value can be predicted even with particular band information missing due to sensor system error. The missing information can be inferred from other dependent bands. (2) The network structure provides information of variables that are important for the classification, which is not available from conventional classification methods such as neural networks and maximum likelihood classification. In our case, for example, bands 1, 5 and 6 are the most important inputs in determining the land use of each pixel. (3) The networks can be reduced with those input variables important for classification. This minimizes the problem without considering all possible variables. We also examined the effect of incorporating ancillary data: geospatial information such as X and Y coordinate values of each pixel and DEM data, and vegetation indices such as NDVI and Tasseled Cap transformation. The results showed that the locational information improved overall accuracy (81%) and kappa coefficient (76%), and lowered the omission and commission errors compared with using only spectral data (accuracy 71%, kappa coefficient 62%). Incorporating DEM data did not significantly improve overall accuracy (74%) and kappa coefficient (66%) but lowered the omission and commission errors. Incorporating NDVI did not much improve the overall accuracy (72%) and k coefficient (65%). Including Tasseled Cap transformation reduced the accuracy (accuracy 70%, kappa 61%). Therefore, additional information from the DEM and vegetation indices was not useful as locational ancillary data.

Annotating Protein Functional Residues by Coupling High-Throughput Fitness Profile and Homologous-Structure Analysis

PubMed Central

Du, Yushen; Wu, Nicholas C.; Jiang, Lin; Zhang, Tianhao; Gong, Danyang; Shu, Sara; Wu, Ting-Ting

2016-01-01

ABSTRACT Identification and annotation of functional residues are fundamental questions in protein sequence analysis. Sequence and structure conservation provides valuable information to tackle these questions. It is, however, limited by the incomplete sampling of sequence space in natural evolution. Moreover, proteins often have multiple functions, with overlapping sequences that present challenges to accurate annotation of the exact functions of individual residues by conservation-based methods. Using the influenza A virus PB1 protein as an example, we developed a method to systematically identify and annotate functional residues. We used saturation mutagenesis and high-throughput sequencing to measure the replication capacity of single nucleotide mutations across the entire PB1 protein. After predicting protein stability upon mutations, we identified functional PB1 residues that are essential for viral replication. To further annotate the functional residues important to the canonical or noncanonical functions of viral RNA-dependent RNA polymerase (vRdRp), we performed a homologous-structure analysis with 16 different vRdRp structures. We achieved high sensitivity in annotating the known canonical polymerase functional residues. Moreover, we identified a cluster of noncanonical functional residues located in the loop region of the PB1 β-ribbon. We further demonstrated that these residues were important for PB1 protein nuclear import through the interaction with Ran-binding protein 5. In summary, we developed a systematic and sensitive method to identify and annotate functional residues that are not restrained by sequence conservation. Importantly, this method is generally applicable to other proteins about which homologous-structure information is available. PMID:27803181

Informal Institutional Responses to Government Interventions: Lessons from Madhupur National Park, Bangladesh

NASA Astrophysics Data System (ADS)

Rahman, H. M. Tuihedur; Sarker, Swapan Kumar; Hickey, Gordon M.; Mohasinul Haque, M.; Das, Niamjit

2014-11-01

Madhupur National Park is renowned for severe resource ownership conflicts between ethnic communities and government authorities in Bangladesh. In this study, we applied the Institutional Analysis and Development framework to identify: (i) past and present informal institutional structures within the ethnic Garo community for land resource management; (ii) the origin of the land ownership dispute; (iii) interaction mechanisms between formal and informal institutions; and (iv) change in land management authority and informal governance structures. We identify that the informal institutions of the traditional community have undergone radical change due to government interventions with implications for the regulation of land use, informal institutional functions, and joint-decision-making. Importantly, the government's persistent denial of the role of existing informal institutions is widening the gap between government and community actors, and driving land ownership conflicts in a cyclic way with associated natural resource degradation.

Informal institutional responses to government interventions: lessons from Madhupur National Park, Bangladesh.

PubMed

Rahman, H M Tuihedur; Sarker, Swapan Kumar; Hickey, Gordon M; Mohasinul Haque, M; Das, Niamjit

2014-11-01

Madhupur National Park is renowned for severe resource ownership conflicts between ethnic communities and government authorities in Bangladesh. In this study, we applied the Institutional Analysis and Development framework to identify: (i) past and present informal institutional structures within the ethnic Garo community for land resource management; (ii) the origin of the land ownership dispute; (iii) interaction mechanisms between formal and informal institutions; and (iv) change in land management authority and informal governance structures. We identify that the informal institutions of the traditional community have undergone radical change due to government interventions with implications for the regulation of land use, informal institutional functions, and joint-decision-making. Importantly, the government's persistent denial of the role of existing informal institutions is widening the gap between government and community actors, and driving land ownership conflicts in a cyclic way with associated natural resource degradation.

Comparing ICD9-encoded diagnoses and NLP-processed discharge summaries for clinical trials pre-screening: a case study.

PubMed

Li, Li; Chase, Herbert S; Patel, Chintan O; Friedman, Carol; Weng, Chunhua

2008-11-06

The prevalence of electronic medical record (EMR) systems has made mass-screening for clinical trials viable through secondary uses of clinical data, which often exist in both structured and free text formats. The tradeoffs of using information in either data format for clinical trials screening are understudied. This paper compares the results of clinical trial eligibility queries over ICD9-encoded diagnoses and NLP-processed textual discharge summaries. The strengths and weaknesses of both data sources are summarized along the following dimensions: information completeness, expressiveness, code granularity, and accuracy of temporal information. We conclude that NLP-processed patient reports supplement important information for eligibility screening and should be used in combination with structured data.

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

Treesearch

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

2014-01-01

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

Development and Assessment of a Molecular Structure and Properties Learning Progression

ERIC Educational Resources Information Center

Cooper, Melanie M.; Underwood, Sonia M.; Hilley, Caleb Z.; Klymkowsky, Michael W.

2012-01-01

Previously, we found that: (i) many students were unable to construct representations of simple molecular structures; (ii) a majority of students fail to make the important connection between these representations and macroscopic properties of the material; and (iii) they were unable to decode the information contained in such representations.…

The Willingness to Change to Formalized Child Care Arrangements: Parental Considerations of Cost and Quality.

ERIC Educational Resources Information Center

Camasso, Michael J.; Roche, Susan E.

1991-01-01

Data from 1988 sample of 1,058 state employees provided evidence that family structure, price, and quality were important determinants of parent's willingness to change from informal to formal child care arrangements. Measured 43 facets of program structure, curriculum, and child development goals. (Author/NB)

Can Thematic Roles Leave Traces of Their Places?

ERIC Educational Resources Information Center

Chang, Franklin; Bock, Kathryn; Goldberg, Adele E.

2003-01-01

An important question in the study of language production is the nature of the semantic information that speakers use to create syntactic structures. A common answer to this question assumes that thematic roles help to mediate the mapping from messages to syntax. However, research using structural priming has suggested that the construction of…

A Structural Equation Model to Analyse the Antecedents to Students' Web-Based Problem-Solving Performance

ERIC Educational Resources Information Center

Hwang, Gwo-Jen; Kuo, Fan-Ray

2015-01-01

Web-based problem-solving, a compound ability of critical thinking, creative thinking, reasoning thinking and information-searching abilities, has been recognised as an important competence for elementary school students. Some researchers have reported the possible correlations between problem-solving competence and information searching ability;…

Appendix B: Fisher, lynx, wolverine summary of distribution information

Treesearch

Mary Maj

1994-01-01

We present maps depicting distributions of fisher, lynx, and wolverine in the western United States since 1961. Comparison of past and current distributions of species can shed light on population persistence, periods of population isolation, meta-population structure, and important connecting landscapes. Information on the distribution of the American marten is not...

Organizational Leadership through Information Technology.

ERIC Educational Resources Information Center

Anderson, John A.

The role of information technology (IT) is changing, and is becoming more important for the overall success of colleges today. The structure of IT has not changed much through the years, but a greater amount of institutions exist where multiple areas of technology are being merged back into a single IT organization. The model of IT explored in…

Eros in Stereo

NASA Image and Video Library

2000-05-07

Stereo imaging, an important tool on NASA NEAR Shoemaker for geologic analysis of Eros, provides three-dimensional information on the asteroid landforms and structures. 3D glasses are necessary to view this image.

CCProf: exploring conformational change profile of proteins

PubMed Central

Chang, Che-Wei; Chou, Chai-Wei; Chang, Darby Tien-Hao

2016-01-01

In many biological processes, proteins have important interactions with various molecules such as proteins, ions or ligands. Many proteins undergo conformational changes upon these interactions, where regions with large conformational changes are critical to the interactions. This work presents the CCProf platform, which provides conformational changes of entire proteins, named conformational change profile (CCP) in the context. CCProf aims to be a platform where users can study potential causes of novel conformational changes. It provides 10 biological features, including conformational change, potential binding target site, secondary structure, conservation, disorder propensity, hydropathy propensity, sequence domain, structural domain, phosphorylation site and catalytic site. All these information are integrated into a well-aligned view, so that researchers can capture important relevance between different biological features visually. The CCProf contains 986 187 protein structure pairs for 3123 proteins. In addition, CCProf provides a 3D view in which users can see the protein structures before and after conformational changes as well as binding targets that induce conformational changes. All information (e.g. CCP, binding targets and protein structures) shown in CCProf, including intermediate data are available for download to expedite further analyses. Database URL: http://zoro.ee.ncku.edu.tw/ccprof/ PMID:27016699

Information-theoretic decomposition of embodied and situated systems.

PubMed

Da Rold, Federico

2018-07-01

The embodied and situated view of cognition stresses the importance of real-time and nonlinear bodily interaction with the environment for developing concepts and structuring knowledge. In this article, populations of robots controlled by an artificial neural network learn a wall-following task through artificial evolution. At the end of the evolutionary process, time series are recorded from perceptual and motor neurons of selected robots. Information-theoretic measures are estimated on pairings of variables to unveil nonlinear interactions that structure the agent-environment system. Specifically, the mutual information is utilized to quantify the degree of dependence and the transfer entropy to detect the direction of the information flow. Furthermore, the system is analyzed with the local form of such measures, thus capturing the underlying dynamics of information. Results show that different measures are interdependent and complementary in uncovering aspects of the robots' interaction with the environment, as well as characteristics of the functional neural structure. Therefore, the set of information-theoretic measures provides a decomposition of the system, capturing the intricacy of nonlinear relationships that characterize robots' behavior and neural dynamics. Copyright © 2018 Elsevier Ltd. All rights reserved.

Clinic expert information extraction based on domain model and block importance model.

PubMed

Zhang, Yuanpeng; Wang, Li; Qian, Danmin; Geng, Xingyun; Yao, Dengfu; Dong, Jiancheng

2015-11-01

To extract expert clinic information from the Deep Web, there are two challenges to face. The first one is to make a judgment on forms. A novel method based on a domain model, which is a tree structure constructed by the attributes of query interfaces is proposed. With this model, query interfaces can be classified to a domain and filled in with domain keywords. Another challenge is to extract information from response Web pages indexed by query interfaces. To filter the noisy information on a Web page, a block importance model is proposed, both content and spatial features are taken into account in this model. The experimental results indicate that the domain model yields a precision 4.89% higher than that of the rule-based method, whereas the block importance model yields an F1 measure 10.5% higher than that of the XPath method. Copyright © 2015 Elsevier Ltd. All rights reserved.

Superposed ruptile deformational events revealed by field and VOM structural analysis

NASA Astrophysics Data System (ADS)

Kumaira, Sissa; Guadagnin, Felipe; Keller Lautert, Maiara

2017-04-01

Virtual outcrop models (VOM) is becoming an important application in the analysis of geological structures due to the possibility of obtaining the geometry and in some cases kinematic aspects of analyzed structures in a tridimensional photorealistic space. These data are used to gain quantitative information on the deformational features which coupled with numeric models can assist in understands deformational processes. Old basement units commonly register superposed deformational events either ductile or ruptile along its evolution. The Porongos Belt, located at southern Brazil, have a complex deformational history registering at least five ductile and ruptile deformational events. In this study, we presents a structural analysis of a quarry in the Porongos Belt, coupling field and VOM structural information to understand process involved in the last two deformational events. Field information was acquired using traditional structural methods for analysis of ruptile structures, such as the descriptions, drawings, acquisition of orientation vectors and kinematic analysis. VOM was created from the image-based modeling method through photogrammetric data acquisition and orthorectification. Photogrammetric data acquisition was acquired using Sony a3500 camera and a total of 128 photographs were taken from ca. 10-20 m from the outcrop in different orientations. Thirty two control point coordinates were acquired using a combination of RTK dGPS surveying and total station work, providing a precision of few millimeters for x, y and z. Photographs were imported into the Photo Scan software to create a 3D dense point cloud from structure from-motion algorithm, which were triangulated and textured to generate the VOM. VOM was georreferenced (oriented and scaled) using the ground control points, and later analyzed in OpenPlot software to extract structural information. Data was imported in Wintensor software to obtain tensor orientations, and Move software to process and interpret geometrical and kinematic data. Planar and linear structural orientations and kinematic indicators revealed superposition of three deformational events: i) compressive, ii) transtensional, and iii) extensional paleostress regimes. The compressive regime was related to a radial to pure compression with N-S horizontal maximum compression vector. This stress regime corresponds mainly to the development of dextral tension fractures and NE-SW reverse faults. The transtensional regime has NW-SE sub-horizontal extension, NE-SW horizontal compressional, and sub-vertical intermediate tensors, generating mainly shear fractures by reactivation of the metamorphic foliation (anisotropy), NE-SW reverse faults and NE-vertical veins and gashes. The extensional regime of strike-slip type presents a NE-SW sub-horizontal extension and NW-SE trending sub-vertical maximum compression vector. Structures related to this regime are sub-vertical tension gashes, conjugate fractures and NW-SE normal faults. Cross-cutting relations show that compression was followed by transtension, which reactivate the ductile foliation, and in the last stage, extension dominated. Most important findings show that: i) local stress fields can modify expected geometry and ii) anisotropy developed by previous structures control the nucleation of new fractures and reactivations. Use of field data integrated in a VOM has great potential as analogues for structured reservoirs.

Corpus callosum segmentation using deep neural networks with prior information from multi-atlas images

NASA Astrophysics Data System (ADS)

Park, Gilsoon; Hong, Jinwoo; Lee, Jong-Min

2018-03-01

In human brain, Corpus Callosum (CC) is the largest white matter structure, connecting between right and left hemispheres. Structural features such as shape and size of CC in midsagittal plane are of great significance for analyzing various neurological diseases, for example Alzheimer's disease, autism and epilepsy. For quantitative and qualitative studies of CC in brain MR images, robust segmentation of CC is important. In this paper, we present a novel method for CC segmentation. Our approach is based on deep neural networks and the prior information generated from multi-atlas images. Deep neural networks have recently shown good performance in various image processing field. Convolutional neural networks (CNN) have shown outstanding performance for classification and segmentation in medical image fields. We used convolutional neural networks for CC segmentation. Multi-atlas based segmentation model have been widely used in medical image segmentation because atlas has powerful information about the target structure we want to segment, consisting of MR images and corresponding manual segmentation of the target structure. We combined the prior information, such as location and intensity distribution of target structure (i.e. CC), made from multi-atlas images in CNN training process for more improving training. The CNN with prior information showed better segmentation performance than without.

Cation Selectivity in Biological Cation Channels Using Experimental Structural Information and Statistical Mechanical Simulation.

PubMed

Finnerty, Justin John; Peyser, Alexander; Carloni, Paolo

2015-01-01

Cation selective channels constitute the gate for ion currents through the cell membrane. Here we present an improved statistical mechanical model based on atomistic structural information, cation hydration state and without tuned parameters that reproduces the selectivity of biological Na+ and Ca2+ ion channels. The importance of the inclusion of step-wise cation hydration in these results confirms the essential role partial dehydration plays in the bacterial Na+ channels. The model, proven reliable against experimental data, could be straightforwardly used for designing Na+ and Ca2+ selective nanopores.

Mass Determination of Entire Amyloid Fibrils by Using Mass Spectrometry.

PubMed

Doussineau, Tristan; Mathevon, Carole; Altamura, Lucie; Vendrely, Charlotte; Dugourd, Philippe; Forge, Vincent; Antoine, Rodolphe

2016-02-12

Amyloid fibrils are self-assembled protein structures with important roles in biology (either pathogenic or physiological), and are attracting increasing interest in nanotechnology. However, because of their high aspect ratio and the presence of some polymorphism, that is, the possibility to adopt various structures, their characterization is challenging and basic information such as their mass is unknown. Here we show that charge-detection mass spectrometry, recently developed for large self-assembled systems such as viruses, provides such information in a straightforward manner. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Adoption of Clinical Information Systems in Health Services Organizations

PubMed Central

Austin, Charles J.; Holland, Gloria J.

1988-01-01

This paper presents a conceptual model of factors which influence organizational decisions to invest in the installation of clinical information systems. Using results of previous research as a framework, the relative influence of clinical, fiscal, and strategic-institutional decision structures are examined. These adoption decisions are important in health services organizations because clinical information is essential for managing demand and allocating resources, managing quality of care, and controlling costs.

Phytoestrogens and Mycoestrogens Induce Signature Structure Dynamics Changes on Estrogen Receptor α

PubMed Central

Chen, Xueyan; Uzuner, Ugur; Li, Man; Shi, Weibing; Yuan, Joshua S.; Dai, Susie Y.

2016-01-01

Endocrine disrupters include a broad spectrum of chemicals such as industrial chemicals, natural estrogens and androgens, synthetic estrogens and androgens. Phytoestrogens are widely present in diet and food supplements; mycoestrogens are frequently found in grains. As human beings and animals are commonly exposed to phytoestrogens and mycoestrogens in diet and environment, it is important to understand the potential beneficial or hazardous effects of estrogenic compounds. Many bioassays have been established to study the binding of estrogenic compounds with estrogen receptor (ER) and provided rich data in the literature. However, limited assays can offer structure information with regard to the ligand/ER complex. Our current study surveys the global structure dynamics changes for ERα ligand binding domain (LBD) when phytoestrogens and mycoestrogens bind. The assay is based on the structure dynamics information probed by hydrogen deuterium exchange mass spectrometry and offers a unique viewpoint to elucidate the mechanism how phytoestrogens and mycoestrogens interact with estrogen receptor. The cluster analysis based on the hydrogen deuterium exchange (HDX) assay data reveals a unique pattern when phytoestrogens and mycoestrogens bind with ERα LBD compared to that of estradiol and synthetic estrogen modulators. Our study highlights that structure dynamics could play an important role in the structure function relationship when endocrine disrupters interact with estrogen receptors. PMID:27589781

MAGDM linear-programming models with distinct uncertain preference structures.

PubMed

Xu, Zeshui S; Chen, Jian

2008-10-01

Group decision making with preference information on alternatives is an interesting and important research topic which has been receiving more and more attention in recent years. The purpose of this paper is to investigate multiple-attribute group decision-making (MAGDM) problems with distinct uncertain preference structures. We develop some linear-programming models for dealing with the MAGDM problems, where the information about attribute weights is incomplete, and the decision makers have their preferences on alternatives. The provided preference information can be represented in the following three distinct uncertain preference structures: 1) interval utility values; 2) interval fuzzy preference relations; and 3) interval multiplicative preference relations. We first establish some linear-programming models based on decision matrix and each of the distinct uncertain preference structures and, then, develop some linear-programming models to integrate all three structures of subjective uncertain preference information provided by the decision makers and the objective information depicted in the decision matrix. Furthermore, we propose a simple and straightforward approach in ranking and selecting the given alternatives. It is worth pointing out that the developed models can also be used to deal with the situations where the three distinct uncertain preference structures are reduced to the traditional ones, i.e., utility values, fuzzy preference relations, and multiplicative preference relations. Finally, we use a practical example to illustrate in detail the calculation process of the developed approach.

Structure-based Markov random field model for representing evolutionary constraints on functional sites.

PubMed

Jeong, Chan-Seok; Kim, Dongsup

2016-02-24

Elucidating the cooperative mechanism of interconnected residues is an important component toward understanding the biological function of a protein. Coevolution analysis has been developed to model the coevolutionary information reflecting structural and functional constraints. Recently, several methods have been developed based on a probabilistic graphical model called the Markov random field (MRF), which have led to significant improvements for coevolution analysis; however, thus far, the performance of these models has mainly been assessed by focusing on the aspect of protein structure. In this study, we built an MRF model whose graphical topology is determined by the residue proximity in the protein structure, and derived a novel positional coevolution estimate utilizing the node weight of the MRF model. This structure-based MRF method was evaluated for three data sets, each of which annotates catalytic site, allosteric site, and comprehensively determined functional site information. We demonstrate that the structure-based MRF architecture can encode the evolutionary information associated with biological function. Furthermore, we show that the node weight can more accurately represent positional coevolution information compared to the edge weight. Lastly, we demonstrate that the structure-based MRF model can be reliably built with only a few aligned sequences in linear time. The results show that adoption of a structure-based architecture could be an acceptable approximation for coevolution modeling with efficient computation complexity.

Image classification using multiscale information fusion based on saliency driven nonlinear diffusion filtering.

PubMed

Hu, Weiming; Hu, Ruiguang; Xie, Nianhua; Ling, Haibin; Maybank, Stephen

2014-04-01

In this paper, we propose saliency driven image multiscale nonlinear diffusion filtering. The resulting scale space in general preserves or even enhances semantically important structures such as edges, lines, or flow-like structures in the foreground, and inhibits and smoothes clutter in the background. The image is classified using multiscale information fusion based on the original image, the image at the final scale at which the diffusion process converges, and the image at a midscale. Our algorithm emphasizes the foreground features, which are important for image classification. The background image regions, whether considered as contexts of the foreground or noise to the foreground, can be globally handled by fusing information from different scales. Experimental tests of the effectiveness of the multiscale space for the image classification are conducted on the following publicly available datasets: 1) the PASCAL 2005 dataset; 2) the Oxford 102 flowers dataset; and 3) the Oxford 17 flowers dataset, with high classification rates.

Active learning for semi-supervised clustering based on locally linear propagation reconstruction.

PubMed

Chang, Chin-Chun; Lin, Po-Yi

2015-03-01

The success of semi-supervised clustering relies on the effectiveness of side information. To get effective side information, a new active learner learning pairwise constraints known as must-link and cannot-link constraints is proposed in this paper. Three novel techniques are developed for learning effective pairwise constraints. The first technique is used to identify samples less important to cluster structures. This technique makes use of a kernel version of locally linear embedding for manifold learning. Samples neither important to locally linear propagation reconstructions of other samples nor on flat patches in the learned manifold are regarded as unimportant samples. The second is a novel criterion for query selection. This criterion considers not only the importance of a sample to expanding the space coverage of the learned samples but also the expected number of queries needed to learn the sample. To facilitate semi-supervised clustering, the third technique yields inferred must-links for passing information about flat patches in the learned manifold to semi-supervised clustering algorithms. Experimental results have shown that the learned pairwise constraints can capture the underlying cluster structures and proven the feasibility of the proposed approach. Copyright © 2014 Elsevier Ltd. All rights reserved.

Information-theoretical noninvasive damage detection in bridge structures

NASA Astrophysics Data System (ADS)

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

2016-11-01

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

A general strategy to solve the phase problem in RNA crystallography

PubMed Central

Keel, Amanda Y.; Rambo, Robert P.; Batey, Robert T.; Kieft, Jeffrey S.

2007-01-01

SUMMARY X-ray crystallography of biologically important RNA molecules has been hampered by technical challenges, including finding a heavy-atom derivative to obtain high-quality experimental phase information. Existing techniques have drawbacks, severely limiting the rate at which important new structures are solved. To address this need, we have developed a reliable means to localize heavy atoms specifically to virtually any RNA. By solving the crystal structures of thirteen variants of the G·U wobble pair cation binding motif we have identified an optimal version that when inserted into an RNA helix introduces a high-occupancy cation binding site suitable for phasing. This “directed soaking” strategy can be integrated fully into existing RNA and crystallography methods, potentially increasing the rate at which important structures are solved and facilitating routine solving of structures using Cu-Kα radiation. The success of this method has been proven in that it has already been used to solve several novel crystal structures. PMID:17637337

Integrated System of Structural Health Monitoring and Intelligent Management for a Cable-Stayed Bridge

PubMed Central

Chen, Bin; Wang, Xu; Sun, Dezhang; Xie, Xu

2014-01-01

It is essential to construct structural health monitoring systems for large important bridges. Zhijiang Bridge is a cable-stayed bridge that was built recently over the Hangzhou Qiantang River (the largest river in Zhejiang Province). The length of Zhijiang Bridge is 478 m, which comprises an arched twin-tower space and a twin-cable plane structure. As an example, the present study describes the integrated system of structural health monitoring and intelligent management for Zhijiang Bridge, which comprises an information acquisition system, data management system, evaluation and decision-making system, and application service system. The monitoring components include the working environment of the bridge and various factors that affect bridge safety, such as the stress and strain of the main bridge structure, vibration, cable force, temperature, and wind speed. In addition, the integrated system includes a forecasting and decision-making module for real-time online evaluation, which provides warnings and makes decisions based on the monitoring information. From this, the monitoring information, evaluation results, maintenance decisions, and warning information can be input simultaneously into the bridge monitoring center and traffic emergency center to share the monitoring data, thereby facilitating evaluations and decision making using the system. PMID:25140342

Integrated system of structural health monitoring and intelligent management for a cable-stayed bridge.

PubMed

Chen, Bin; Wang, Xu; Sun, Dezhang; Xie, Xu

2014-01-01

It is essential to construct structural health monitoring systems for large important bridges. Zhijiang Bridge is a cable-stayed bridge that was built recently over the Hangzhou Qiantang River (the largest river in Zhejiang Province). The length of Zhijiang Bridge is 478 m, which comprises an arched twin-tower space and a twin-cable plane structure. As an example, the present study describes the integrated system of structural health monitoring and intelligent management for Zhijiang Bridge, which comprises an information acquisition system, data management system, evaluation and decision-making system, and application service system. The monitoring components include the working environment of the bridge and various factors that affect bridge safety, such as the stress and strain of the main bridge structure, vibration, cable force, temperature, and wind speed. In addition, the integrated system includes a forecasting and decision-making module for real-time online evaluation, which provides warnings and makes decisions based on the monitoring information. From this, the monitoring information, evaluation results, maintenance decisions, and warning information can be input simultaneously into the bridge monitoring center and traffic emergency center to share the monitoring data, thereby facilitating evaluations and decision making using the system.

Community health information sources--a survey in three disparate communities.

PubMed

Dart, Jared; Gallois, Cindy; Yellowlees, Peter

2008-02-01

To determine the current utilisation, importance, trust and future preference for contemporary sources of health information in three different socioeconomic groups. A pilot study including key informant interviews and direct observation was conducted in a low socioeconomic community. From this work a survey questionnaire was designed and implemented across three different communities. Semi-structured key informant interviews and focus groups capturing 52 respondents. Paper-based surveys were left in community organisations and local health practices in a low socioeconomic (LSE) community on the outskirts of Ipswich, Queensland, a mid-high socioeconomic (MSE) community in the western suburbs of Brisbane, and at a local university. Rank of current and preferred future sources of health information, importance and trustworthiness of health information sources. Across all three communities the local doctor was the most currently used, important, trusted and preferred future source of health information. The most striking difference between the three communities related to the current use and preferred future use of the internet. The internet was a more currently used source of health information and more important source in the university population than the LSE or MSE populations. It was also a less preferred source of future health information in the LSE population than the MSE or university populations. Importantly, currently used sources of health information did not reflect community members' preferred sources of health information. People in different socioeconomic communities obtain health information from various sources. This may reflect access issues, education and awareness of the internet as a source of health information, less health information seeking as well as a reluctance by the e-health community to address the specific needs of this group.

Space Transportation Materials and Structures Technology Workshop. Volume 1: Executive summary

NASA Technical Reports Server (NTRS)

Cazier, F. W., Jr. (Compiler); Gardner, J. E. (Compiler)

1992-01-01

The workshop was held to provide a forum for communication within the space materials and structures technology developer and user communities. Workshop participants were organized into a Vehicle Technology Requirements session and three working panels: Materials and Structures Technologies for Vehicle Systems; Propulsion Systems; and Entry Systems. The goals accomplished were (1) to develop important strategic planning information necessary to transition materials and structures technologies from lab research programs into robust and affordable operational systems; (2) to provide a forum for the exchange of information and ideas between technology developers and users; and (3) to provide senior NASA management with a review of current space transportation programs, related subjects, and specific technology needs. The workshop thus provided a foundation on which a NASA and industry effort to address space transportation materials and structures technologies can grow.

A combination of feature extraction methods with an ensemble of different classifiers for protein structural class prediction problem.

PubMed

Dehzangi, Abdollah; Paliwal, Kuldip; Sharma, Alok; Dehzangi, Omid; Sattar, Abdul

2013-01-01

Better understanding of structural class of a given protein reveals important information about its overall folding type and its domain. It can also be directly used to provide critical information on general tertiary structure of a protein which has a profound impact on protein function determination and drug design. Despite tremendous enhancements made by pattern recognition-based approaches to solve this problem, it still remains as an unsolved issue for bioinformatics that demands more attention and exploration. In this study, we propose a novel feature extraction model that incorporates physicochemical and evolutionary-based information simultaneously. We also propose overlapped segmented distribution and autocorrelation-based feature extraction methods to provide more local and global discriminatory information. The proposed feature extraction methods are explored for 15 most promising attributes that are selected from a wide range of physicochemical-based attributes. Finally, by applying an ensemble of different classifiers namely, Adaboost.M1, LogitBoost, naive Bayes, multilayer perceptron (MLP), and support vector machine (SVM) we show enhancement of the protein structural class prediction accuracy for four popular benchmarks.

Structural Studies of Fucosylated N-Glycans by Ion Mobility Mass Spectrometry and Collision-Induced Fragmentation of Negative Ions

NASA Astrophysics Data System (ADS)

Harvey, David J.; Struwe, Weston B.

2018-05-01

There is considerable potential for the use of ion mobility mass spectrometry in structural glycobiology due in large part to the gas-phase separation attributes not typically observed by orthogonal methods. Here, we evaluate the capability of traveling wave ion mobility combined with negative ion collision-induced dissociation to provide structural information on N-linked glycans containing multiple fucose residues forming the Lewisx and Lewisy epitopes. These epitopes are involved in processes such as cell-cell recognition and are important as cancer biomarkers. Specific information that could be obtained from the intact N-glycans by negative ion CID included the general topology of the glycan such as the presence or absence of a bisecting GlcNAc residue and the branching pattern of the triantennary glycans. Information on the location of the fucose residues was also readily obtainable from ions specific to each antenna. Some isobaric fragment ions produced prior to ion mobility could subsequently be separated and, in some cases, provided additional valuable structural information that was missing from the CID spectra alone.

Organizational structure and operation of defense/aerospace information centers in the United States of America

NASA Technical Reports Server (NTRS)

Sauter, H. E.; Lushina, L. N.

1983-01-01

U.S. Government aerospace and defense information centers are addressed. DTIC and NASA are described in terms of their history, operational authority, information services provided, user community, sources of information collected, efforts under way to improve services, and external agreements regarding the exchange of documents and/or data bases. Contents show how DTIC and NASA provide aerospace/defense information services in support of U.S. research and development efforts. In a general introduction, the importance of scientific and technical information and the need for information centers to acquire, handle, and disseminate it are stressed.

Atomic-resolution 3D structure of amyloid β fibrils: The Osaka mutation

DOE PAGES

Schutz, Anne K.; Wall, Joseph; Vagt, Toni; ...

2014-11-13

Despite its central importance for understanding the molecular basis of Alzheimer's disease (AD), high-resolution structural information on amyloid β-peptide (Aβ) fibrils, which are intimately linked with AD, is scarce. We report an atomic-resolution fibril structure of the Aβ 1-40 peptide with the Osaka mutation (E22Δ), associated with early-onset AD. The structure, which differs substantially from all previously proposed models, is based on a large number of unambiguous intra- and intermolecular solid-state NMR distance restraints

ProCarDB: a database of bacterial carotenoids.

PubMed

Nupur, L N U; Vats, Asheema; Dhanda, Sandeep Kumar; Raghava, Gajendra P S; Pinnaka, Anil Kumar; Kumar, Ashwani

2016-05-26

Carotenoids have important functions in bacteria, ranging from harvesting light energy to neutralizing oxidants and acting as virulence factors. However, information pertaining to the carotenoids is scattered throughout the literature. Furthermore, information about the genes/proteins involved in the biosynthesis of carotenoids has tremendously increased in the post-genomic era. A web server providing the information about microbial carotenoids in a structured manner is required and will be a valuable resource for the scientific community working with microbial carotenoids. Here, we have created a manually curated, open access, comprehensive compilation of bacterial carotenoids named as ProCarDB- Prokaryotic Carotenoid Database. ProCarDB includes 304 unique carotenoids arising from 50 biosynthetic pathways distributed among 611 prokaryotes. ProCarDB provides important information on carotenoids, such as 2D and 3D structures, molecular weight, molecular formula, SMILES, InChI, InChIKey, IUPAC name, KEGG Id, PubChem Id, and ChEBI Id. The database also provides NMR data, UV-vis absorption data, IR data, MS data and HPLC data that play key roles in the identification of carotenoids. An important feature of this database is the extension of biosynthetic pathways from the literature and through the presence of the genes/enzymes in different organisms. The information contained in the database was mined from published literature and databases such as KEGG, PubChem, ChEBI, LipidBank, LPSN, and Uniprot. The database integrates user-friendly browsing and searching with carotenoid analysis tools to help the user. We believe that this database will serve as a major information centre for researchers working on bacterial carotenoids.

Effects of model complexity and priors on estimation using sequential importance sampling/resampling for species conservation

USGS Publications Warehouse

Dunham, Kylee; Grand, James B.

2016-01-01

We examined the effects of complexity and priors on the accuracy of models used to estimate ecological and observational processes, and to make predictions regarding population size and structure. State-space models are useful for estimating complex, unobservable population processes and making predictions about future populations based on limited data. To better understand the utility of state space models in evaluating population dynamics, we used them in a Bayesian framework and compared the accuracy of models with differing complexity, with and without informative priors using sequential importance sampling/resampling (SISR). Count data were simulated for 25 years using known parameters and observation process for each model. We used kernel smoothing to reduce the effect of particle depletion, which is common when estimating both states and parameters with SISR. Models using informative priors estimated parameter values and population size with greater accuracy than their non-informative counterparts. While the estimates of population size and trend did not suffer greatly in models using non-informative priors, the algorithm was unable to accurately estimate demographic parameters. This model framework provides reasonable estimates of population size when little to no information is available; however, when information on some vital rates is available, SISR can be used to obtain more precise estimates of population size and process. Incorporating model complexity such as that required by structured populations with stage-specific vital rates affects precision and accuracy when estimating latent population variables and predicting population dynamics. These results are important to consider when designing monitoring programs and conservation efforts requiring management of specific population segments.

Midcanopy growth following thinning in young-growth conifer forests on the Olympic Peninsula, western Washington

Treesearch

Emily J. Comfort; Scott D. Roberts; Constance A. Harrington

2010-01-01

Midcanopy layers are essential structures in "old-growth" forests on the Olympic Peninsula. Little is known about which stand and tree factors influence the ability of midcanopy trees in young-growth forests to respond to release; however, this information is important to managers interested in accelerating development of late-successional structural...

Genetic diversity and population structure of elite foxtail millet [Setaria italica (L.) P. Beauv.] germplasm in China

USDA-ARS?s Scientific Manuscript database

China is among the countries that have the most severe water deficiency. Due to its excellent drought tolerance, foxtail millet [Setaria italica (L.) P. Beauv.] has become one of the important cereal crops in China. Information on genetic diversity and population structure of foxtail millet may faci...

Abundance of birds in the oak savannas of the southwestern United States

Treesearch

Wendy D. Jones; Carlton M. Jones; Peter F. Ffolliott; Gerald J. Gottfried

2005-01-01

Oak ecosystems of the Southwestern United States are important habitats for a variety of wildlife species. Information is available on the abundance and habitat preferences of some species inhabiting the more densely structured oak woodlands, but little information is available on these topics for the comparatively open oak savannas. Studies are underway to alleviate...

Incorporating remotely sensed tree canopy cover data into broad scale assessments of wildlife habitat distribution and conservation

Treesearch

Sebastian Martinuzzi; Lee A. Vierling; William A. Gould; Kerri T. Vierling; Andrew T. Hudak

2009-01-01

Remote sensing provides critical information for broad scale assessments of wildlife habitat distribution and conservation. However, such efforts have been typically unable to incorporate information about vegetation structure, a variable important for explaining the distribution of many wildlife species. We evaluated the consequences of incorporating remotely sensed...

Encouraging Cognitive Connections and Creativity in the Music Classroom

ERIC Educational Resources Information Center

Peterson, Christopher W.; Madsen, Clifford K.

2010-01-01

The ability to apply knowledge rests at the core of the educational experience and is an important aspect of all teaching. In music education, many experiences are structured so information gained can be related to another activity, but such transfer can be difficult. When students learn to transfer information and knowledge to new situations,…

Interpreting Pitch Accents in Online Comprehension: H* vs. L+H*

ERIC Educational Resources Information Center

Watson, Duane G.; Tanenhaus, Michael K.; Gunlogson, Christine A.

2008-01-01

Although the presence or absence of a pitch accent clearly can play an important role in signaling the discourse and information structure of an utterance, whether the form of an accent determines the type of information it conveys is more controversial. We used an eye-tracking paradigm to investigate whether H*, which has been argued to signal…

Validation of the DeLone and McLean Information Systems Success Model.

PubMed

Ojo, Adebowale I

2017-01-01

This study is an adaptation of the widely used DeLone and McLean information system success model in the context of hospital information systems in a developing country. A survey research design was adopted in the study. A structured questionnaire was used to collect data from 442 health information management personnel in five Nigerian teaching hospitals. A structural equation modeling technique was used to validate the model's constructs. It was revealed that system quality significantly influenced use (β = 0.53, p < 0.001) and user satisfaction (β = 0.17, p < 0.001). Information quality significantly influenced use (β = 0.24, p < 0.001) and user satisfaction (β = 0.17, p < 0.001). Also, service quality significantly influenced use (β = 0.22, p < 0.001) and user satisfaction (β = 0.51, p < 0.001). However, use did not significantly influence user satisfaction (β = 0.00, p > 0.05), but it significantly influenced perceived net benefits (β = 0.21, p < 0.001). Furthermore, user satisfaction did not significantly influence perceived net benefits (β = 0.00, p > 0.05). The study validates the DeLone and McLean information system success model in the context of a hospital information system in a developing country. Importantly, system quality and use were found to be important measures of hospital information system success. It is, therefore, imperative that hospital information systems are designed in such ways that are easy to use, flexible, and functional to serve their purpose.

Validation of the DeLone and McLean Information Systems Success Model

PubMed Central

2017-01-01

Objectives This study is an adaptation of the widely used DeLone and McLean information system success model in the context of hospital information systems in a developing country. Methods A survey research design was adopted in the study. A structured questionnaire was used to collect data from 442 health information management personnel in five Nigerian teaching hospitals. A structural equation modeling technique was used to validate the model's constructs. Results It was revealed that system quality significantly influenced use (β = 0.53, p < 0.001) and user satisfaction (β = 0.17, p < 0.001). Information quality significantly influenced use (β = 0.24, p < 0.001) and user satisfaction (β = 0.17, p < 0.001). Also, service quality significantly influenced use (β = 0.22, p < 0.001) and user satisfaction (β = 0.51, p < 0.001). However, use did not significantly influence user satisfaction (β = 0.00, p > 0.05), but it significantly influenced perceived net benefits (β = 0.21, p < 0.001). Furthermore, user satisfaction did not significantly influence perceived net benefits (β = 0.00, p > 0.05). Conclusions The study validates the DeLone and McLean information system success model in the context of a hospital information system in a developing country. Importantly, system quality and use were found to be important measures of hospital information system success. It is, therefore, imperative that hospital information systems are designed in such ways that are easy to use, flexible, and functional to serve their purpose. PMID:28261532

Distributed structure-searchable toxicity (DSSTox) public database network: a proposal.

PubMed

Richard, Ann M; Williams, ClarLynda R

2002-01-29

The ability to assess the potential genotoxicity, carcinogenicity, or other toxicity of pharmaceutical or industrial chemicals based on chemical structure information is a highly coveted and shared goal of varied academic, commercial, and government regulatory groups. These diverse interests often employ different approaches and have different criteria and use for toxicity assessments, but they share a need for unrestricted access to existing public toxicity data linked with chemical structure information. Currently, there exists no central repository of toxicity information, commercial or public, that adequately meets the data requirements for flexible analogue searching, Structure-Activity Relationship (SAR) model development, or building of chemical relational databases (CRD). The distributed structure-searchable toxicity (DSSTox) public database network is being proposed as a community-supported, web-based effort to address these shared needs of the SAR and toxicology communities. The DSSTox project has the following major elements: (1) to adopt and encourage the use of a common standard file format (structure data file (SDF)) for public toxicity databases that includes chemical structure, text and property information, and that can easily be imported into available CRD applications; (2) to implement a distributed source approach, managed by a DSSTox Central Website, that will enable decentralized, free public access to structure-toxicity data files, and that will effectively link knowledgeable toxicity data sources with potential users of these data from other disciplines (such as chemistry, modeling, and computer science); and (3) to engage public/commercial/academic/industry groups in contributing to and expanding this community-wide, public data sharing and distribution effort. The DSSTox project's overall aims are to effect the closer association of chemical structure information with existing toxicity data, and to promote and facilitate structure-based exploration of these data within a common chemistry-based framework that spans toxicological disciplines.

Teaching resources. Protein phosphatases.

PubMed

Salton, Stephen R

2005-03-01

This Teaching Resource provides lecture notes and slides for a class covering the structure and function of protein phosphatases and is part of the course "Cell Signaling Systems: A Course for Graduate Students." The lecture begins with a discussion of the importance of phosphatases in physiology, recognized by the award of a Nobel Prize in 1992, and then proceeds to describe the two types of protein phosphatases: serine/threonine and tyrosine phosphatases. The information covered includes the structure, regulation, and substrate specificity of protein phosphatases, with an emphasis on their importance in disease and clinical settings.

Accounting for epistatic interactions improves the functional analysis of protein structures

PubMed Central

Wilkins, Angela D.; Venner, Eric; Marciano, David C.; Erdin, Serkan; Atri, Benu; Lua, Rhonald C.; Lichtarge, Olivier

2013-01-01

Motivation: The constraints under which sequence, structure and function coevolve are not fully understood. Bringing this mutual relationship to light can reveal the molecular basis of binding, catalysis and allostery, thereby identifying function and rationally guiding protein redesign. Underlying these relationships are the epistatic interactions that occur when the consequences of a mutation to a protein are determined by the genetic background in which it occurs. Based on prior data, we hypothesize that epistatic forces operate most strongly between residues nearby in the structure, resulting in smooth evolutionary importance across the structure. Methods and Results: We find that when residue scores of evolutionary importance are distributed smoothly between nearby residues, functional site prediction accuracy improves. Accordingly, we designed a novel measure of evolutionary importance that focuses on the interaction between pairs of structurally neighboring residues. This measure that we term pair-interaction Evolutionary Trace yields greater functional site overlap and better structure-based proteome-wide functional predictions. Conclusions: Our data show that the structural smoothness of evolutionary importance is a fundamental feature of the coevolution of sequence, structure and function. Mutations operate on individual residues, but selective pressure depends in part on the extent to which a mutation perturbs interactions with neighboring residues. In practice, this principle led us to redefine the importance of a residue in terms of the importance of its epistatic interactions with neighbors, yielding better annotation of functional residues, motivating experimental validation of a novel functional site in LexA and refining protein function prediction. Contact: lichtarge@bcm.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:24021383

Representation and Integration of Scientific Information

NASA Technical Reports Server (NTRS)

1999-01-01

The objective of this Joint Research Interchange with NASA-Ames was to investigate how the Tsimmis technology could be used to represent and integrate scientific information. The funding allowed us to work with researchers within NAS at the NASA Ames Research Center, to understand their information needs, and to work with them on integration strategies. Most organizations have a need to access and integrate information from multiple, disparate information sources that may include both structured as well as semi-structured information. At Stanford we have been working on an information integration project called Tsimmis, supported by DARPA. The main goal of the Tsimmis project is to allow a decision maker to find information of interest from such sources, fuse it, and process it (e.g., summarize it, visualize it, discover trends). Another important goal is the easy incorporation of new sources, as well the ability of deal with sources whose structure or services evolve. During the Interchange we had research meetings approximately every month or two. The participants from NASA included Michael Cox and Peter Vanderbilt. The Stanford PI, and various students and Stanford staff members also participated. NASA researchers also participated in some of our regular Tsimmis meetings. As planned, our meetings discussed problems and solutions to various information integration problems.

Alkamid database: Chemistry, occurrence and functionality of plant N-alkylamides.

PubMed

Boonen, Jente; Bronselaer, Antoon; Nielandt, Joachim; Veryser, Lieselotte; De Tré, Guy; De Spiegeleer, Bart

2012-08-01

N-Alkylamides (NAAs) are a promising group of bioactive compounds, which are anticipated to act as important lead compounds for plant protection and biocidal products, functional food, cosmeceuticals and drugs in the next decennia. These molecules, currently found in more than 25 plant families and with a wide structural diversity, exert a variety of biological-pharmacological effects and are of high ethnopharmacological importance. However, information is scattered in literature, with different, often unstandardized, pharmacological methodologies being used. Therefore, a comprehensive NAA database (acronym: Alkamid) was constructed to collect the available structural and functional NAA data, linked to their occurrence in plants (family, tribe, species, genus). For loading information in the database, literature data was gathered over the period 1950-2010, by using several search engines. In order to represent the collected information about NAAs, the plants in which they occur and the functionalities for which they have been examined, a relational database is constructed and implemented on a MySQL back-end. The database is supported by describing the NAA plant-, functional- and chemical-space. The chemical space includes a NAA classification, according to their fatty acid and amine structures. The Alkamid database (publicly available on the website http://alkamid.ugent.be/) is not only a central information point, but can also function as a useful tool to prioritize the NAA choice in the evaluation of their functionality, to perform data mining leading to quantitative structure-property relationships (QSPRs), functionality comparisons, clustering, plant biochemistry and taxonomic evaluations. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

An Integrated Modeling Study for Coordinated Observations of H, O, OH, and H2O(+) Emissions in the Coma and Ion Tail of the Comet Hale-Bopp

NASA Technical Reports Server (NTRS)

Smyth, William H.

2001-01-01

This project has two overall objectives. One objective is to advance our general understanding of both the comet neutral atmosphere and the cometary plasma in the atmosphere and ion tall. The other objective is to obtain specific key information about comet Hale-Bopp that is generally important for Hale-Bopp studies. The primary emphasis in this project is to analyze, in a self-consistent manner, excellent quality high resolution image and line profile observations obtained by the University of Wisconsin for H, O, OH, and H2O+ emissions from the inner coma, outer coma, and ion tail of Hale-Bopp. The information on the spatial and velocity distributions of H2O neutral and ionized photo-products in the inner coma, outer coma, and in the H2O+ ion tail is of substantial and direct importance in the development of an integrated understanding of the complex structure and dynamics of the neutral and plasma species in the atmosphere of Hale-Bopp in particular and comets in general. The H2O production rate of Hale-Bopp is determined and, together with the other information related to the structure and dynamics of the neutral and plasma atmospheres obtained in this study, provide critical information important for a wide variety of research conducted by other groups.

[Computational chemistry in structure-based drug design].

PubMed

Cao, Ran; Li, Wei; Sun, Han-Zi; Zhou, Yu; Huang, Niu

2013-07-01

Today, the understanding of the sequence and structure of biologically relevant targets is growing rapidly and researchers from many disciplines, physics and computational science in particular, are making significant contributions to modern biology and drug discovery. However, it remains challenging to rationally design small molecular ligands with desired biological characteristics based on the structural information of the drug targets, which demands more accurate calculation of ligand binding free-energy. With the rapid advances in computer power and extensive efforts in algorithm development, physics-based computational chemistry approaches have played more important roles in structure-based drug design. Here we reviewed the newly developed computational chemistry methods in structure-based drug design as well as the elegant applications, including binding-site druggability assessment, large scale virtual screening of chemical database, and lead compound optimization. Importantly, here we address the current bottlenecks and propose practical solutions.

POOL server: machine learning application for functional site prediction in proteins.

PubMed

Somarowthu, Srinivas; Ondrechen, Mary Jo

2012-08-01

We present an automated web server for partial order optimum likelihood (POOL), a machine learning application that combines computed electrostatic and geometric information for high-performance prediction of catalytic residues from 3D structures. Input features consist of THEMATICS electrostatics data and pocket information from ConCavity. THEMATICS measures deviation from typical, sigmoidal titration behavior to identify functionally important residues and ConCavity identifies binding pockets by analyzing the surface geometry of protein structures. Both THEMATICS and ConCavity (structure only) do not require the query protein to have any sequence or structure similarity to other proteins. Hence, POOL is applicable to proteins with novel folds and engineered proteins. As an additional option for cases where sequence homologues are available, users can include evolutionary information from INTREPID for enhanced accuracy in site prediction. The web site is free and open to all users with no login requirements at http://www.pool.neu.edu. m.ondrechen@neu.edu Supplementary data are available at Bioinformatics online.

Using ancestry-informative markers to identify fine structure across 15 populations of European origin.

PubMed

Huckins, Laura M; Boraska, Vesna; Franklin, Christopher S; Floyd, James A B; Southam, Lorraine; Sullivan, Patrick F; Bulik, Cynthia M; Collier, David A; Tyler-Smith, Chris; Zeggini, Eleftheria; Tachmazidou, Ioanna

2014-10-01

The Wellcome Trust Case Control Consortium 3 anorexia nervosa genome-wide association scan includes 2907 cases from 15 different populations of European origin genotyped on the Illumina 670K chip. We compared methods for identifying population stratification, and suggest list of markers that may help to counter this problem. It is usual to identify population structure in such studies using only common variants with minor allele frequency (MAF) >5%; we find that this may result in highly informative SNPs being discarded, and suggest that instead all SNPs with MAF >1% may be used. We established informative axes of variation identified via principal component analysis and highlight important features of the genetic structure of diverse European-descent populations, some studied for the first time at this scale. Finally, we investigated the substructure within each of these 15 populations and identified SNPs that help capture hidden stratification. This work can provide information regarding the designing and interpretation of association results in the International Consortia.

A Low-Storage-Consumption XML Labeling Method for Efficient Structural Information Extraction

NASA Astrophysics Data System (ADS)

Liang, Wenxin; Takahashi, Akihiro; Yokota, Haruo

Recently, labeling methods to extract and reconstruct the structural information of XML data, which are important for many applications such as XPath query and keyword search, are becoming more attractive. To achieve efficient structural information extraction, in this paper we propose C-DO-VLEI code, a novel update-friendly bit-vector encoding scheme, based on register-length bit operations combining with the properties of Dewey Order numbers, which cannot be implemented in other relevant existing schemes such as ORDPATH. Meanwhile, the proposed method also achieves lower storage consumption because it does not require either prefix schema or any reserved codes for node insertion. We performed experiments to evaluate and compare the performance and storage consumption of the proposed method with those of the ORDPATH method. Experimental results show that the execution times for extracting depth information and parent node labels using the C-DO-VLEI code are about 25% and 15% less, respectively, and the average label size using the C-DO-VLEI code is about 24% smaller, comparing with ORDPATH.

Analysis of genetic diversity and population structure of peanut cultivars and breeding lines from China, India and USA

USDA-ARS?s Scientific Manuscript database

Peanut (Arachis hypogaea L.) is an important source for edible oil and protein. It is important to identify genetic diversity of peanut for cultivar development. In this study, 111 SSR markers with high polymorphic information content (PIC) were used to assess the genetic variation of 79 peanut cult...

Structures and physical properties of gaseous metal cationized biological ions.

PubMed

Burt, Michael B; Fridgen, Travis D

2012-01-01

Metal chelation can alter the activity of free biomolecules by modifying their structures or stabilizing higher energy tautomers. In recent years, mass spectrometric techniques have been used to investigate the effects of metal complexation with proteins, nucleobases and nucleotides, where small conformational changes can have significant physiological consequences. In particular, infrared multiple photon dissociation spectroscopy has emerged as an important tool for determining the structure and reactivity of gas-phase ions. Unlike other mass spectrometric approaches, this method is able to directly resolve structural isomers using characteristic vibrational signatures. Other activation and dissociation methods, such as blackbody infrared radiative dissociation or collision-induced dissociation can also reveal information about the thermochemistry and dissociative pathways of these biological ions. This information can then be used to provide information about the structures of the ionic complexes under study. In this article, we review the use of gas-phase techniques in characterizing metal-bound biomolecules. Particular attention will be given to our own contributions, which detail the ability of metal cations to disrupt nucleobase pairs, direct the self-assembly of nucleobase clusters and stabilize non-canonical isomers of amino acids.

Molecular modeling of the AhR structure and interactions can shed light on ligand-dependent activation and transformation mechanisms.

PubMed

Bonati, Laura; Corrada, Dario; Tagliabue, Sara Giani; Motta, Stefano

2017-02-01

Molecular modeling has given important contributions to elucidation of the main stages in the AhR signal transduction pathway. Despite the lack of experimentally determined structures of the AhR functional domains, information derived from homologous systems has been exploited for modeling their structure and interactions. Homology models of the AhR PASB domain have provided information on the binding cavity and contributed to elucidate species-specific differences in ligand binding. Molecular Docking simulations of the ligand binding process have given insights into differences in binding of diverse agonists, antagonists, and selective AhR modulators, and their application to virtual screening of large databases of compounds have allowed identification of novel AhR ligands. Recently available structural information on protein-protein and protein-DNA complexes of other bHLH-PAS systems has opened the way for modeling the AhR:ARNT dimer structure and investigating the mechanisms of AhR transformation and DNA binding. Future research directions should include simulation of the protein dynamics to obtain a more reliable description of intermolecular interactions involved in signal transmission.

Robust information propagation through noisy neural circuits

PubMed Central

Pouget, Alexandre

2017-01-01

Sensory neurons give highly variable responses to stimulation, which can limit the amount of stimulus information available to downstream circuits. Much work has investigated the factors that affect the amount of information encoded in these population responses, leading to insights about the role of covariability among neurons, tuning curve shape, etc. However, the informativeness of neural responses is not the only relevant feature of population codes; of potentially equal importance is how robustly that information propagates to downstream structures. For instance, to quantify the retina’s performance, one must consider not only the informativeness of the optic nerve responses, but also the amount of information that survives the spike-generating nonlinearity and noise corruption in the next stage of processing, the lateral geniculate nucleus. Our study identifies the set of covariance structures for the upstream cells that optimize the ability of information to propagate through noisy, nonlinear circuits. Within this optimal family are covariances with “differential correlations”, which are known to reduce the information encoded in neural population activities. Thus, covariance structures that maximize information in neural population codes, and those that maximize the ability of this information to propagate, can be very different. Moreover, redundancy is neither necessary nor sufficient to make population codes robust against corruption by noise: redundant codes can be very fragile, and synergistic codes can—in some cases—optimize robustness against noise. PMID:28419098

GO(vis), a gene ontology visualization tool based on multi-dimensional values.

PubMed

Ning, Zi; Jiang, Zhenran

2010-05-01

Most of gene product similarity measurements concentrate on the information content of Gene Ontology (GO) terms or use a path-based similarity between GO terms, which may ignore other important information contained in the structure of the ontology. In our study, we integrate different GO similarity measure approaches to analyze the functional relationship of genes and gene products with a new triangle-based visualization tool called GO(Vis). The purpose of this tool is to demonstrate the effect of three important information factors when measuring the similarity between gene products. One advantage of this tool is that its important ratio can be adjusted to meet different measuring requirements according to the biological knowledge of each factor. The experimental results demonstrate that GO(Vis) can display diagrams of the functional relationship for gene products effectively.

The use of geospatial web services for exchanging utilities data

NASA Astrophysics Data System (ADS)

Kuczyńska, Joanna

2013-04-01

Geographic information technologies and related geo-information systems currently play an important role in the management of public administration in Poland. One of these tasks is to maintain and update Geodetic Evidence of Public Utilities (GESUT), part of the National Geodetic and Cartographic Resource, which contains an important for many institutions information of technical infrastructure. It requires an active exchange of data between the Geodesy and Cartography Documentation Centers and institutions, which administrate transmission lines. The administrator of public utilities, is legally obliged to provide information about utilities to GESUT. The aim of the research work was to develop a universal data exchange methodology, which can be implemented on a variety of hardware and software platforms. This methodology use Unified Modeling Language (UML), eXtensible Markup Language (XML), and Geography Markup Language (GML). The proposed methodology is based on the two different strategies: Model Driven Architecture (MDA) and Service Oriented Architecture (SOA). Used solutions are consistent with the INSPIRE Directive and ISO 19100 series standards for geographic information. On the basis of analysis of the input data structures, conceptual models were built for both databases. Models were written in the universal modeling language: UML. Combined model that defines a common data structure was also built. This model was transformed into developed for the exchange of geographic information GML standard. The structure of the document describing the data that may be exchanged is defined in the .xsd file. Network services were selected and implemented in the system designed for data exchange based on open source tools. Methodology was implemented and tested. Data in the agreed data structure and metadata were set up on the server. Data access was provided by geospatial network services: data searching possibilities by Catalog Service for the Web (CSW), data collection by Web Feature Service (WFS). WFS provides also operation for modification data, for example to update them by utility administrator. The proposed solution significantly increases the efficiency of data exchange and facilitates maintenance the National Geodetic and Cartographic Resource.

CHEMICAL STRUCTURE INDEXING OF TOXICITY DATA ON ...

EPA Pesticide Factsheets

Standardized chemical structure annotation of public toxicity databases and information resources is playing an increasingly important role in the 'flattening' and integration of diverse sets of biological activity data on the Internet. This review discusses public initiatives that are accelerating the pace of this transformation, with particular reference to toxicology-related chemical information. Chemical content annotators, structure locator services, large structure/data aggregator web sites, structure browsers, International Union of Pure and Applied Chemistry (IUPAC) International Chemical Identifier (InChI) codes, toxicity data models and public chemical/biological activity profiling initiatives are all playing a role in overcoming barriers to the integration of toxicity data, and are bringing researchers closer to the reality of a mineable chemical Semantic Web. An example of this integration of data is provided by the collaboration among researchers involved with the Distributed Structure-Searchable Toxicity (DSSTox) project, the Carcinogenic Potency Project, projects at the National Cancer Institute and the PubChem database. Standardizing chemical structure annotation of public toxicity databases

Probabilistic Structural Analysis Methods (PSAM) for select space propulsion system structural components

NASA Technical Reports Server (NTRS)

Cruse, T. A.

1987-01-01

The objective is the development of several modular structural analysis packages capable of predicting the probabilistic response distribution for key structural variables such as maximum stress, natural frequencies, transient response, etc. The structural analysis packages are to include stochastic modeling of loads, material properties, geometry (tolerances), and boundary conditions. The solution is to be in terms of the cumulative probability of exceedance distribution (CDF) and confidence bounds. Two methods of probability modeling are to be included as well as three types of structural models - probabilistic finite-element method (PFEM); probabilistic approximate analysis methods (PAAM); and probabilistic boundary element methods (PBEM). The purpose in doing probabilistic structural analysis is to provide the designer with a more realistic ability to assess the importance of uncertainty in the response of a high performance structure. Probabilistic Structural Analysis Method (PSAM) tools will estimate structural safety and reliability, while providing the engineer with information on the confidence that should be given to the predicted behavior. Perhaps most critically, the PSAM results will directly provide information on the sensitivity of the design response to those variables which are seen to be uncertain.

Probabilistic Structural Analysis Methods for select space propulsion system structural components (PSAM)

NASA Technical Reports Server (NTRS)

Cruse, T. A.; Burnside, O. H.; Wu, Y.-T.; Polch, E. Z.; Dias, J. B.

1988-01-01

The objective is the development of several modular structural analysis packages capable of predicting the probabilistic response distribution for key structural variables such as maximum stress, natural frequencies, transient response, etc. The structural analysis packages are to include stochastic modeling of loads, material properties, geometry (tolerances), and boundary conditions. The solution is to be in terms of the cumulative probability of exceedance distribution (CDF) and confidence bounds. Two methods of probability modeling are to be included as well as three types of structural models - probabilistic finite-element method (PFEM); probabilistic approximate analysis methods (PAAM); and probabilistic boundary element methods (PBEM). The purpose in doing probabilistic structural analysis is to provide the designer with a more realistic ability to assess the importance of uncertainty in the response of a high performance structure. Probabilistic Structural Analysis Method (PSAM) tools will estimate structural safety and reliability, while providing the engineer with information on the confidence that should be given to the predicted behavior. Perhaps most critically, the PSAM results will directly provide information on the sensitivity of the design response to those variables which are seen to be uncertain.

From protein sequence to dynamics and disorder with DynaMine.

PubMed

Cilia, Elisa; Pancsa, Rita; Tompa, Peter; Lenaerts, Tom; Vranken, Wim F

2013-01-01

Protein function and dynamics are closely related; however, accurate dynamics information is difficult to obtain. Here based on a carefully assembled data set derived from experimental data for proteins in solution, we quantify backbone dynamics properties on the amino-acid level and develop DynaMine--a fast, high-quality predictor of protein backbone dynamics. DynaMine uses only protein sequence information as input and shows great potential in distinguishing regions of different structural organization, such as folded domains, disordered linkers, molten globules and pre-structured binding motifs of different sizes. It also identifies disordered regions within proteins with an accuracy comparable to the most sophisticated existing predictors, without depending on prior disorder knowledge or three-dimensional structural information. DynaMine provides molecular biologists with an important new method that grasps the dynamical characteristics of any protein of interest, as we show here for human p53 and E1A from human adenovirus 5.

GENETICS AND POPULATION-LEVEL RISK ASSESSMENT

EPA Science Inventory

Genetic variation defines population structure and provides the mechanism for populations to adapt to novel stressors. Despite its fundamental importance in understanding populations, genetic information has been included rarely in models of population dynamics (endangered speci...

Annotating Protein Functional Residues by Coupling High-Throughput Fitness Profile and Homologous-Structure Analysis.

PubMed

Du, Yushen; Wu, Nicholas C; Jiang, Lin; Zhang, Tianhao; Gong, Danyang; Shu, Sara; Wu, Ting-Ting; Sun, Ren

2016-11-01

Identification and annotation of functional residues are fundamental questions in protein sequence analysis. Sequence and structure conservation provides valuable information to tackle these questions. It is, however, limited by the incomplete sampling of sequence space in natural evolution. Moreover, proteins often have multiple functions, with overlapping sequences that present challenges to accurate annotation of the exact functions of individual residues by conservation-based methods. Using the influenza A virus PB1 protein as an example, we developed a method to systematically identify and annotate functional residues. We used saturation mutagenesis and high-throughput sequencing to measure the replication capacity of single nucleotide mutations across the entire PB1 protein. After predicting protein stability upon mutations, we identified functional PB1 residues that are essential for viral replication. To further annotate the functional residues important to the canonical or noncanonical functions of viral RNA-dependent RNA polymerase (vRdRp), we performed a homologous-structure analysis with 16 different vRdRp structures. We achieved high sensitivity in annotating the known canonical polymerase functional residues. Moreover, we identified a cluster of noncanonical functional residues located in the loop region of the PB1 β-ribbon. We further demonstrated that these residues were important for PB1 protein nuclear import through the interaction with Ran-binding protein 5. In summary, we developed a systematic and sensitive method to identify and annotate functional residues that are not restrained by sequence conservation. Importantly, this method is generally applicable to other proteins about which homologous-structure information is available. To fully comprehend the diverse functions of a protein, it is essential to understand the functionality of individual residues. Current methods are highly dependent on evolutionary sequence conservation, which is usually limited by sampling size. Sequence conservation-based methods are further confounded by structural constraints and multifunctionality of proteins. Here we present a method that can systematically identify and annotate functional residues of a given protein. We used a high-throughput functional profiling platform to identify essential residues. Coupling it with homologous-structure comparison, we were able to annotate multiple functions of proteins. We demonstrated the method with the PB1 protein of influenza A virus and identified novel functional residues in addition to its canonical function as an RNA-dependent RNA polymerase. Not limited to virology, this method is generally applicable to other proteins that can be functionally selected and about which homologous-structure information is available. Copyright © 2016 Du et al.

Learning the 3-D structure of objects from 2-D views depends on shape, not format

PubMed Central

Tian, Moqian; Yamins, Daniel; Grill-Spector, Kalanit

2016-01-01

Humans can learn to recognize new objects just from observing example views. However, it is unknown what structural information enables this learning. To address this question, we manipulated the amount of structural information given to subjects during unsupervised learning by varying the format of the trained views. We then tested how format affected participants' ability to discriminate similar objects across views that were rotated 90° apart. We found that, after training, participants' performance increased and generalized to new views in the same format. Surprisingly, the improvement was similar across line drawings, shape from shading, and shape from shading + stereo even though the latter two formats provide richer depth information compared to line drawings. In contrast, participants' improvement was significantly lower when training used silhouettes, suggesting that silhouettes do not have enough information to generate a robust 3-D structure. To test whether the learned object representations were format-specific or format-invariant, we examined if learning novel objects from example views transfers across formats. We found that learning objects from example line drawings transferred to shape from shading and vice versa. These results have important implications for theories of object recognition because they suggest that (a) learning the 3-D structure of objects does not require rich structural cues during training as long as shape information of internal and external features is provided and (b) learning generates shape-based object representations independent of the training format. PMID:27153196

Sequence analysis, structure prediction and functional validation of phaC1/phaC2 genes of Pseudomonas sp. LDC-25 and its importance in polyhydroxyalkanoate accumulation

USDA-ARS?s Scientific Manuscript database

Polyhydroxyalkanoates (PHAs) are attractive biomaterials in both conventional medical devices and tissue engineering. PHA synthase is responsible for catalyzing the formation of polyhydroxyalkanoates (PHA), but its structural information is limited. Hence, the focus of this study is to predict 3D mo...

Effects of a Structured Resource-Based Web Issue-Quest Approach on Students' Learning Performances in Computer Programming Courses

ERIC Educational Resources Information Center

Hsu, Ting-Chia; Hwang, Gwo-Jen

2017-01-01

Programming concepts are important and challenging to novices who are beginning to study computer programming skills. In addition to the textbook content, students usually learn the concepts of programming from the web; however, it could be difficult for novice learners to effectively derive helpful information from such non-structured open…

An Empirical Study on Information Prominence Reflected in Sentence Structures of Chinese College EFL Argumentative Writing

ERIC Educational Resources Information Center

Ningling, Wei

2015-01-01

Prominence, as an important dimension of cognitive construal, refers to the capacity to evoke a certain substructure as the focus of attention, which can be materialized in a variety of semantic and grammatical expressions (Langacker, 1987). Subject of a sentence (Zhang, 2011) and specific sentence structures (Lin, 2013) can bring a substructure…

A ground-based method of assessing urban forest structure and ecosystem services

Treesearch

David J. Nowak; Daniel E. Crane; Jack C. Stevens; Robert E. Hoehn; Jeffrey T. Walton; Jerry Bond

2008-01-01

To properly manage urban forests, it is essential to have data on this important resource. An efficient means to obtain this information is to randomly sample urban areas. To help assess the urban forest structure (e.g., number of trees, species composition, tree sizes, health) and several functions (e.g., air pollution removal, carbon storage and sequestration), the...

Characterization and classification of vegetation canopy structure and distribution within the Great Smoky Mountains National Park using LiDAR

Treesearch

Jitendra Kumar; Jon Weiner; William W. Hargrove; Steve Norman; Forrest M. Hoffman; Doug Newcomb

2016-01-01

Vegetation canopy structure is a critically important habitat characteristic for many threatened and endangered birds and other animal species, and it is key information needed by forest and wildlife managers for monitoring and managing forest resources, conservation planning and fostering biodiversity. Advances in Light Detection and Ranging (LiDAR) technologies have...

Structural and Network-based Methods for Knowledge-Based Systems

DTIC Science & Technology

2011-12-01

depth) provide important information about knowledge gaps in the KB. For example, if SuccessEstimate (causes-EventEvent, Typhoid - Fever , 1, 3) is...equal to 0, it points toward lack of biological knowledge about Typhoid - Fever in our KB. Similar information can also be obtained from the...position of the consequent. ⋃ ( ( ) ) Therefore, if Q does not contain Typhoid - Fever , then obtaining

The Structure of Scientific Evolution

PubMed Central

2013-01-01

Science is the construction and testing of systems that bind symbols to sensations according to rules. Material implication is the primary rule, providing the structure of definition, elaboration, delimitation, prediction, explanation, and control. The goal of science is not to secure truth, which is a binary function of accuracy, but rather to increase the information about data communicated by theory. This process is symmetric and thus entails an increase in the information about theory communicated by data. Important components in this communication are the elevation of data to the status of facts, the descent of models under the guidance of theory, and their close alignment through the evolving retroductive process. The information mutual to theory and data may be measured as the reduction in the entropy, or complexity, of the field of data given the model. It may also be measured as the reduction in the entropy of the field of models given the data. This symmetry explains the important status of parsimony (how thoroughly the data exploit what the model can say) alongside accuracy (how thoroughly the model represents what can be said about the data). Mutual information is increased by increasing model accuracy and parsimony, and by enlarging and refining the data field under purview. PMID:28018043

Cation Selectivity in Biological Cation Channels Using Experimental Structural Information and Statistical Mechanical Simulation

PubMed Central

Finnerty, Justin John

2015-01-01

Cation selective channels constitute the gate for ion currents through the cell membrane. Here we present an improved statistical mechanical model based on atomistic structural information, cation hydration state and without tuned parameters that reproduces the selectivity of biological Na+ and Ca2+ ion channels. The importance of the inclusion of step-wise cation hydration in these results confirms the essential role partial dehydration plays in the bacterial Na+ channels. The model, proven reliable against experimental data, could be straightforwardly used for designing Na+ and Ca2+ selective nanopores. PMID:26460827

SA-Mot: a web server for the identification of motifs of interest extracted from protein loops

PubMed Central

Regad, Leslie; Saladin, Adrien; Maupetit, Julien; Geneix, Colette; Camproux, Anne-Claude

2011-01-01

The detection of functional motifs is an important step for the determination of protein functions. We present here a new web server SA-Mot (Structural Alphabet Motif) for the extraction and location of structural motifs of interest from protein loops. Contrary to other methods, SA-Mot does not focus only on functional motifs, but it extracts recurrent and conserved structural motifs involved in structural redundancy of loops. SA-Mot uses the structural word notion to extract all structural motifs from uni-dimensional sequences corresponding to loop structures. Then, SA-Mot provides a description of these structural motifs using statistics computed in the loop data set and in SCOP superfamily, sequence and structural parameters. SA-Mot results correspond to an interactive table listing all structural motifs extracted from a target structure and their associated descriptors. Using this information, the users can easily locate loop regions that are important for the protein folding and function. The SA-Mot web server is available at http://sa-mot.mti.univ-paris-diderot.fr. PMID:21665924

SA-Mot: a web server for the identification of motifs of interest extracted from protein loops.

PubMed

Regad, Leslie; Saladin, Adrien; Maupetit, Julien; Geneix, Colette; Camproux, Anne-Claude

2011-07-01

The detection of functional motifs is an important step for the determination of protein functions. We present here a new web server SA-Mot (Structural Alphabet Motif) for the extraction and location of structural motifs of interest from protein loops. Contrary to other methods, SA-Mot does not focus only on functional motifs, but it extracts recurrent and conserved structural motifs involved in structural redundancy of loops. SA-Mot uses the structural word notion to extract all structural motifs from uni-dimensional sequences corresponding to loop structures. Then, SA-Mot provides a description of these structural motifs using statistics computed in the loop data set and in SCOP superfamily, sequence and structural parameters. SA-Mot results correspond to an interactive table listing all structural motifs extracted from a target structure and their associated descriptors. Using this information, the users can easily locate loop regions that are important for the protein folding and function. The SA-Mot web server is available at http://sa-mot.mti.univ-paris-diderot.fr.

Temporal variation in bat-fruit interactions: Foraging strategies influence network structure over time

NASA Astrophysics Data System (ADS)

Zapata-Mesa, Natalya; Montoya-Bustamante, Sebastián; Murillo-García, Oscar E.

2017-11-01

Mutualistic interactions, such as seed dispersal, are important for the maintenance of structure and stability of tropical communities. However, there is a lack of information about spatial and temporal variation in plant-animal interaction networks. Thus, our goal was to assess the effect of bat's foraging strategies on temporal variation in the structure and robustness of bat-fruit networks in both a dry and a rain tropical forest. We evaluated monthly variation in bat-fruit networks by using seven structure metrics: network size, average path length, nestedness, modularity, complementary specialization, normalized degree and betweenness centrality. Seed dispersal networks showed variations in size, species composition and modularity; did not present nested structures and their complementary specialization was high compared to other studies. Both networks presented short path lengths, and a constantly high robustness, despite their monthly variations. Sedentary bat species were recorded during all the study periods and occupied more central positions than nomadic species. We conclude that foraging strategies are important structuring factors that affect the dynamic of networks by determining the functional roles of frugivorous bats over time; thus sedentary bats are more important than nomadic species for the maintenance of the network structure, and their conservation is a must.

If walls could talk

NASA Technical Reports Server (NTRS)

Braam, J.; McIntire, L. V. (Principal Investigator)

1999-01-01

The plant cell wall is very complex, both in structure and function. The wall components and the mechanical properties of the wall have been implicated in conveying information that is important for morphogenesis. Proteoglycans, fragments of polysaccharides and the structural integrity of the wall may relay signals that influence cellular differentiation and growth control. Furthering our knowledge of cell wall structure and function is likely to have a profound impact on our understanding of how plant cells communicate with the extracellular environment.

Elucidation of kinematical and dynamical structure of the Galactic bulge

NASA Astrophysics Data System (ADS)

Yano, T.; Gouda, N.; Ueda, H.; Koyama, H.; Kan-ya, Y.; Taruya, A.

2008-07-01

Future space mission of astrometric satellite, GAIA and JASMINE (Japan Astrometry Satellite Mission for Infrared Exploration), will produce astrometric parameter, such as positions, parallaxes, and proper motions of stars in the Galactic bulge. Then kinematical information will be obtained in the future. Accordingly it is expected that our understanding of the dynamical structure will be greatly improved. Therefore it is important to make a method to construct a kinematical and dynamical structure of the Galactic bulge immediately.

Sensitivity of system stability to model structure

USGS Publications Warehouse

Hosack, G.R.; Li, H.W.; Rossignol, P.A.

2009-01-01

A community is stable, and resilient, if the levels of all community variables can return to the original steady state following a perturbation. The stability properties of a community depend on its structure, which is the network of direct effects (interactions) among the variables within the community. These direct effects form feedback cycles (loops) that determine community stability. Although feedback cycles have an intuitive interpretation, identifying how they form the feedback properties of a particular community can be intractable. Furthermore, determining the role that any specific direct effect plays in the stability of a system is even more daunting. Such information, however, would identify important direct effects for targeted experimental and management manipulation even in complex communities for which quantitative information is lacking. We therefore provide a method that determines the sensitivity of community stability to model structure, and identifies the relative role of particular direct effects, indirect effects, and feedback cycles in determining stability. Structural sensitivities summarize the degree to which each direct effect contributes to stabilizing feedback or destabilizing feedback or both. Structural sensitivities prove useful in identifying ecologically important feedback cycles within the community structure and for detecting direct effects that have strong, or weak, influences on community stability. The approach may guide the development of management intervention and research design. We demonstrate its value with two theoretical models and two empirical examples of different levels of complexity. ?? 2009 Elsevier B.V. All rights reserved.

Implementation of mutual information and bayes theorem for classification microarray data

NASA Astrophysics Data System (ADS)

Dwifebri Purbolaksono, Mahendra; Widiastuti, Kurnia C.; Syahrul Mubarok, Mohamad; Adiwijaya; Aminy Ma’ruf, Firda

2018-03-01

Microarray Technology is one of technology which able to read the structure of gen. The analysis is important for this technology. It is for deciding which attribute is more important than the others. Microarray technology is able to get cancer information to diagnose a person’s gen. Preparation of microarray data is a huge problem and takes a long time. That is because microarray data contains high number of insignificant and irrelevant attributes. So, it needs a method to reduce the dimension of microarray data without eliminating important information in every attribute. This research uses Mutual Information to reduce dimension. System is built with Machine Learning approach specifically Bayes Theorem. This theorem uses a statistical and probability approach. By combining both methods, it will be powerful for Microarray Data Classification. The experiment results show that system is good to classify Microarray data with highest F1-score using Bayesian Network by 91.06%, and Naïve Bayes by 88.85%.

Forest Attributes from Radar Interferometric Structure and its Fusion with Optical Remote Sensing

NASA Technical Reports Server (NTRS)

Treuhaft, Robert N.; Law, Beverly E.; Asner, Gregory P.

2004-01-01

The possibility of global, three-dimensional remote sensing of forest structure with interferometric synthetic aperture radar (InSAR) bears on important forest ecological processes, particularly the carbon cycle. InSAR supplements two-dimensional remote sensing with information in the vertical dimension. Its strengths in potential for global coverage complement those of lidar (light detecting and ranging), which has the potential for high-accuracy vertical profiles over small areas. InSAR derives its sensitivity to forest vertical structure from the differences in signals received by two, spatially separate radar receivers. Estimation of parameters describing vertical structure requires multiple-polarization, multiple-frequency, or multiple-baseline InSAR. Combining InSAR with complementary remote sensing techniques, such as hyperspectral optical imaging and lidar, can enhance vertical-structure estimates and consequent biophysical quantities of importance to ecologists, such as biomass. Future InSAR experiments will supplement recent airborne and spaceborne demonstrations, and together with inputs from ecologists regarding structure, they will suggest designs for future spaceborne strategies for measuring global vegetation structure.

Precambrian Basement Structure Map of the Continental United States - An Interpretation of Geologic and Aeromagnetic Data

USGS Publications Warehouse

Sims, Paul K.; Saltus, Richard W.; Anderson, Eric D.

2008-01-01

The Precambrian basement rocks of the continental United States are largely covered by younger sedimentary and volcanic rocks, and the availability of updated aeromagnetic data (NAMAG, 2002) provides a means to infer major regional basement structures and tie together the scattered, but locally abundant, geologic information. Precambrian basement structures in the continental United States have strongly influenced later Proterozoic and Phanerozoic tectonism within the continent, and there is a growing awareness of the utility of these structures in deciphering major younger tectonic and related episodes. Interest in the role of basement structures in the evolution of continents has been recently stimulated, particularly by publications of the Geological Society of London (Holdsworth and others, 1998; Holdsworth and others, 2001). These publications, as well as others, stress the importance of reactivation of basement structures in guiding the subsequent evolution of continents. Knowledge of basement structures is an important key to understanding the geology of continental interiors.

Characterization and Quantification of the Pore Structures of the Shale Oil Reservoir Formations in Multiscale

NASA Astrophysics Data System (ADS)

Liu, K.; Ostadhassan, M.

2016-12-01

Due to the fast development of hydraulic fracturing and horizontal drilling, shale formations now are one important resource of energy in North America. Characterizing the pore structure of these shale formations is of critical importance in understanding the original oil/gas in place and also the flow properties of the rock matrix. Pore with different properties such as pore size and pore shape can impact the physical, mechanical and chemical properties including strength, elastic modulus, permeability and conductivity. Nowadays, image analysis has been a robust method to quantify the pore information from the porous medium.SEM has been one of the most useful tools to study the pore microstructures due to its high depth of focus which can provide detailed topographical information about the surface. The suitable difference between solid matrix and pores due to the different gray level pixels can be used to study the pore structures.In this paper, we characterized and quantified the pore structures of rock samples from Middle Bakken Formation which is a typical unconventional reservoir in North America. High resolution SEM images of five samples we chose based on the gamma logs were derived after sample preparation. After determining the threshold of the images, we extracted the pore spaces. Then we analyzed the pore structures properties such as pore size distributions and pore shape distributions of the five samples and compared based on their mineral compositions. After that, we analyzed their heterogeneity and isotropy properties which have been identified as an important factor affecting reservoir productivity. Finally, we studied the impact of scale effect on the pore structures characterization.

A multiple-dimension liquid chromatography coupled with mass spectrometry data strategy for the rapid discovery and identification of unknown compounds from a Chinese herbal formula (Er-xian decoction).

PubMed

Wang, Caihong; Zhang, Jinlan; Wu, Caisheng; Wang, Zhe

2017-10-06

It is very important to rapidly discover and identify the multiple components of traditional Chinese medicine (TCM) formula. High performance liquid chromatography with high resolution tandem mass spectrometry (HPLC-HRMS/MS) has been widely used to analyze TCM formula and contains multiple-dimension data including retention time (RT), high resolution mass (HRMS), multiple-stage mass spectrometric (MS n ), and isotope intensity distribution (IID) data. So it is very necessary to exploit a useful strategy to utilize multiple-dimension data to rapidly probe structural information and identify chemical compounds. In this study, a new strategy to initiatively use the multiple-dimension LC-MS data has been developed to discover and identify unknown compounds of TCM in many styles. The strategy guarantees the fast discovery of candidate structural information and provides efficient structure clues for identification. The strategy contains four steps in sequence: (1) to discover potential compounds and obtain sub-structure information by the mass spectral tree similarity filter (MTSF) technique, based on HRMS and MS n data; (2) to classify potential compounds into known chemical classes by discriminant analysis (DA) on the basis of RT and HRMS data; (3) to hit the candidate structural information of compounds by intersection sub-structure between MTSF and DA (M,D-INSS); (4) to annotate and confirm candidate structures by IID data. This strategy allowed for the high exclusion efficiency (greater than 41%) of irrelevant ions in er-xian decoction (EXD) while providing accurate structural information of 553 potential compounds and identifying 66 candidates, therefore accelerating and simplifying the discovery and identification of unknown compounds in TCM formula. Copyright © 2017 Elsevier B.V. All rights reserved.

Multicomplex-based pharmacophore-guided 3D-QSAR studies of N-substituted 2'-(aminoaryl)benzothiazoles as Aurora-A inhibitors.

PubMed

He, Gu; Qiu, Minghua; Li, Rui; Ouyang, Liang; Wu, Fengbo; Song, Xiangrong; Cheng, Li; Xiang, Mingli; Yu, Luoting

2012-06-01

Aurora-A has been known as one of the most important targets for cancer therapy, and some Aurora-A inhibitors have entered clinical trails. In this study, combination of the ligand-based and structure-based methods is used to clarify the essential quantitative structure-activity relationship of known Aurora-A inhibitors, and multicomplex-based pharmacophore-guided method has been suggested to generate a comprehensive pharmacophore of Aurora-A kinase based on a collection of crystal structures of Aurora-A-inhibitor complex. This model has been successfully used to identify the bioactive conformation and align 37 structurally diverse N-substituted 2'-(aminoaryl)benzothiazoles derivatives. The quantitative structure-activity relationship analyses have been performed on these Aurora-A inhibitors based on multicomplex-based pharmacophore-guided alignment. These results may provide important information for further design and virtual screening of novel Aurora-A inhibitors. © 2012 John Wiley & Sons A/S.

Quantifying similarity of pore-geometry in nanoporous materials

DOE PAGES

Lee, Yongjin; Barthel, Senja D.; Dłotko, Paweł; ...

2017-05-23

In most applications of nanoporous materials the pore structure is as important as the chemical composition as a determinant of performance. For example, one can alter performance in applications like carbon capture or methane storage by orders of magnitude by only modifying the pore structure. For these applications it is therefore important to identify the optimal pore geometry and use this information to find similar materials. But, the mathematical language and tools to identify materials with similar pore structures, but different composition, has been lacking. We develop a pore recognition approach to quantify similarity of pore structures and classify themmore » using topological data analysis. This then allows us to identify materials with similar pore geometries, and to screen for materials that are similar to given top-performing structures. Using methane storage as a case study, we also show that materials can be divided into topologically distinct classes requiring different optimization strategies.« less

Applications of Mass Spectrometry to Structural Analysis of Marine Oligosaccharides

PubMed Central

Lang, Yinzhi; Zhao, Xia; Liu, Lili; Yu, Guangli

2014-01-01

Marine oligosaccharides have attracted increasing attention recently in developing potential drugs and biomaterials for their particular physical and chemical properties. However, the composition and sequence analysis of marine oligosaccharides are very challenging for their structural complexity and heterogeneity. Mass spectrometry (MS) has become an important technique for carbohydrate analysis by providing more detailed structural information, including molecular mass, sugar constituent, sequence, inter-residue linkage position and substitution pattern. This paper provides an overview of the structural analysis based on MS approaches in marine oligosaccharides, which are derived from some biologically important marine polysaccharides, including agaran, carrageenan, alginate, sulfated fucan, chitosan, glycosaminoglycan (GAG) and GAG-like polysaccharides. Applications of electrospray ionization mass spectrometry (ESI-MS) are mainly presented and the general applications of matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) are also outlined. Some technical challenges in the structural analysis of marine oligosaccharides by MS have also been pointed out. PMID:24983643

Evaluating structural connectomics in relation to different Q-space sampling techniques.

PubMed

Rodrigues, Paulo; Prats-Galino, Alberto; Gallardo-Pujol, David; Villoslada, Pablo; Falcon, Carles; Prckovska, Vesna

2013-01-01

Brain networks are becoming forefront research in neuroscience. Network-based analysis on the functional and structural connectomes can lead to powerful imaging markers for brain diseases. However, constructing the structural connectome can be based upon different acquisition and reconstruction techniques whose information content and mutual differences has not yet been properly studied in a unified framework. The variations of the structural connectome if not properly understood can lead to dangerous conclusions when performing these type of studies. In this work we present evaluation of the structural connectome by analysing and comparing graph-based measures on real data acquired by the three most important Diffusion Weighted Imaging techniques: DTI, HARDI and DSI. We thus come to several important conclusions demonstrating that even though the different techniques demonstrate differences in the anatomy of the reconstructed fibers the respective connectomes show variations of 20%.

Managing Knowledge And Information In The Sustainable Organization

NASA Astrophysics Data System (ADS)

Grecu, Valentin

2015-09-01

Knowledge and information management are essential for the success of organizations and bring significant competitive advantages. There has been significant investments in setting up technological platforms that support business processes and increase the efficiency of operational structure in many organizations through an efficient management of knowledge and information. This research highlights the importance of using knowledge and information management in order to increase the competitiveness of organizations and to foster the transition towards the sustainable organization, as nowadays an organization that wants to be competitive needs to be sustainable.

Use of Library Readings to Augment Conventional Geology Instruction.

ERIC Educational Resources Information Center

Nold, John Lloyd

1989-01-01

Examples of sets of questions on library readings designed to lead students into articles and emphasize important information and associated literature are presented for introductory geology courses, historical geology, structural geology, mineralogy, and petrology. (Author/CW)

Measuring Children's Perceptions of Parental Involvement in Conjoint Behavioral Consultation: Factor Structure and Reliability of the "Parental Support for Learning Scale"

ERIC Educational Resources Information Center

Rogers, Maria; Markel, Clarisa; Midgett, Jonathan D.; Ryan, Bruce A.; Tannock, Rosemary

2014-01-01

Practitioners of Conjoint Behavioral Consultation rely on several sources of information to assist in planning and evaluation of consultation efforts. Parental involvement in the home is an important aspect in Conjoint Behavioral Consultation, yet there are few questionnaires available to practitioners to assess this important construct,…

(Durability of building materials and components)

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

Naus, D.J.

1990-11-27

The traveler participated in the fourth meeting of RILEM 100-TSL, Techniques for Service Life Prediction,'' and The Fifth International Conference on Durability of Building Materials and Components.'' In addition, the traveler met with staff members at Taywood Engineering Ltd., Electricite de France, and AEA Technology. The meeting pertained to performance of concrete materials in nuclear power plant structures, time variation of concrete material properties, methods for evaluating concrete structures, and modeling to predict the effects of degradation factors on concrete materials. As many of the concrete structures in general civil engineering applications as well as nuclear power plant applications inmore » Europe are aging, there is increasing emphasis on assessing the durability of these structures. Information was provided of direct application to the Structural Aging Program which would not have been available without these visits. Of equal, or possibly more importance, was the individual contacts established at the organizations visited. Each organization was extremely interested in both the approach and scope of the Structural Aging Program and requested that they be informed of progress. The initial steps were taken to cooperate with several of these researchers and this should help the Structural Aging Program keep abreast of related European activities. In summary, information obtained during this trip will benefit the ongoing Structural Aging Program by informing Oak Ridge National Laboratory (ORNL) of the extensive European research programs addressing the durability of concrete structures, and also by forming and strengthening acquaintances with counterparts in other countries, thus enhancing the basis for possible international cooperation.« less

Advanced information society (10)

NASA Astrophysics Data System (ADS)

Masuyama, Keiichi

Informationalization in Japan has spread among various fields of industrial and social life in wide and depth by drastic advancement in technology and networking. Looking at the change in industrial structure as well as international trend in information the Japanese Government regards the role of information and communication technology as infrastructure to be important, and is under the way of constructing various measures with ministries and agencies concerned with them. This paper describes how administrative agencies involved in information and communication such as Ministry of Postal Services, Ministry of International Trade and Industry cope with informationalization, and mentions future direction in information policies.

Roogle: an information retrieval engine for clinical data warehouse.

PubMed

Cuggia, Marc; Garcelon, Nicolas; Campillo-Gimenez, Boris; Bernicot, Thomas; Laurent, Jean-François; Garin, Etienne; Happe, André; Duvauferrier, Régis

2011-01-01

High amount of relevant information is contained in reports stored in the electronic patient records and associated metadata. R-oogle is a project aiming at developing information retrieval engines adapted to these reports and designed for clinicians. The system consists in a data warehouse (full-text reports and structured data) imported from two different hospital information systems. Information retrieval is performed using metadata-based semantic and full-text search methods (as Google). Applications may be biomarkers identification in a translational approach, search of specific cases, and constitution of cohorts, professional practice evaluation, and quality control assessment.

Geographic Information System (GIS) capabilities in traffic accident information management: a qualitative approach.

PubMed

Ahmadi, Maryam; Valinejadi, Ali; Goodarzi, Afshin; Safari, Ameneh; Hemmat, Morteza; Majdabadi, Hesamedin Askari; Mohammadi, Ali

2017-06-01

Traffic accidents are one of the more important national and international issues, and their consequences are important for the political, economical, and social level in a country. Management of traffic accident information requires information systems with analytical and accessibility capabilities to spatial and descriptive data. The aim of this study was to determine the capabilities of a Geographic Information System (GIS) in management of traffic accident information. This qualitative cross-sectional study was performed in 2016. In the first step, GIS capabilities were identified via literature retrieved from the Internet and based on the included criteria. Review of the literature was performed until data saturation was reached; a form was used to extract the capabilities. In the second step, study population were hospital managers, police, emergency, statisticians, and IT experts in trauma, emergency and police centers. Sampling was purposive. Data was collected using a questionnaire based on the first step data; validity and reliability were determined by content validity and Cronbach's alpha of 75%. Data was analyzed using the decision Delphi technique. GIS capabilities were identified in ten categories and 64 sub-categories. Import and process of spatial and descriptive data and so, analysis of this data were the most important capabilities of GIS in traffic accident information management. Storing and retrieving of descriptive and spatial data, providing statistical analysis in table, chart and zoning format, management of bad structure issues, determining the cost effectiveness of the decisions and prioritizing their implementation were the most important capabilities of GIS which can be efficient in the management of traffic accident information.

Ensemble-based evaluation for protein structure models

PubMed Central

Jamroz, Michal; Kolinski, Andrzej; Kihara, Daisuke

2016-01-01

Motivation: Comparing protein tertiary structures is a fundamental procedure in structural biology and protein bioinformatics. Structure comparison is important particularly for evaluating computational protein structure models. Most of the model structure evaluation methods perform rigid body superimposition of a structure model to its crystal structure and measure the difference of the corresponding residue or atom positions between them. However, these methods neglect intrinsic flexibility of proteins by treating the native structure as a rigid molecule. Because different parts of proteins have different levels of flexibility, for example, exposed loop regions are usually more flexible than the core region of a protein structure, disagreement of a model to the native needs to be evaluated differently depending on the flexibility of residues in a protein. Results: We propose a score named FlexScore for comparing protein structures that consider flexibility of each residue in the native state of proteins. Flexibility information may be extracted from experiments such as NMR or molecular dynamics simulation. FlexScore considers an ensemble of conformations of a protein described as a multivariate Gaussian distribution of atomic displacements and compares a query computational model with the ensemble. We compare FlexScore with other commonly used structure similarity scores over various examples. FlexScore agrees with experts’ intuitive assessment of computational models and provides information of practical usefulness of models. Availability and implementation: https://bitbucket.org/mjamroz/flexscore Contact: dkihara@purdue.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27307633

Collecting Information for Rating Global Assessment of Functioning (GAF): Sources of Information and Methods for Information Collection.

PubMed

I H, Monrad Aas

2014-11-01

Global Assessment of Functioning (GAF) is an assessment instrument that is known worldwide. It is widely used for rating the severity of illness. Results from evaluations in psychiatry should characterize the patients. Rating of GAF is based on collected information. The aim of the study is to identify the factors involved in collecting information that is relevant for rating GAF, and gaps in knowledge where it is likely that further development would play a role for improved scoring. A literature search was conducted with a combination of thorough hand search and search in the bibliographic databases PubMed, PsycINFO, Google Scholar, and Campbell Collaboration Library of Systematic Reviews. Collection of information for rating GAF depends on two fundamental factors: the sources of information and the methods for information collection. Sources of information are patients, informants, health personnel, medical records, letters of referral and police records about violence and substance abuse. Methods for information collection include the many different types of interview - unstructured, semi-structured, structured, interviews for Axis I and II disorders, semistructured interviews for rating GAF, and interviews of informants - as well as instruments for rating symptoms and functioning, and observation. The different sources of information, and methods for collection, frequently result in inconsistencies in the information collected. The variation in collected information, and lack of a generally accepted algorithm for combining collected information, is likely to be important for rated GAF values, but there is a fundamental lack of knowledge about the degree of importance. Research to improve GAF has not reached a high level. Rated GAF values are likely to be influenced by both the sources of information used and the methods employed for information collection, but the lack of research-based information about these influences is fundamental. Further development of GAF is feasible and proposals for this are presented.

The HADDOCK2.2 Web Server: User-Friendly Integrative Modeling of Biomolecular Complexes.

PubMed

van Zundert, G C P; Rodrigues, J P G L M; Trellet, M; Schmitz, C; Kastritis, P L; Karaca, E; Melquiond, A S J; van Dijk, M; de Vries, S J; Bonvin, A M J J

2016-02-22

The prediction of the quaternary structure of biomolecular macromolecules is of paramount importance for fundamental understanding of cellular processes and drug design. In the era of integrative structural biology, one way of increasing the accuracy of modeling methods used to predict the structure of biomolecular complexes is to include as much experimental or predictive information as possible in the process. This has been at the core of our information-driven docking approach HADDOCK. We present here the updated version 2.2 of the HADDOCK portal, which offers new features such as support for mixed molecule types, additional experimental restraints and improved protocols, all of this in a user-friendly interface. With well over 6000 registered users and 108,000 jobs served, an increasing fraction of which on grid resources, we hope that this timely upgrade will help the community to solve important biological questions and further advance the field. The HADDOCK2.2 Web server is freely accessible to non-profit users at http://haddock.science.uu.nl/services/HADDOCK2.2. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

Molecular Basis of Ligand Dissociation from G Protein-Coupled Receptors and Predicting Residence Time.

PubMed

Guo, Dong; IJzerman, Adriaan P

2018-01-01

G protein-coupled receptors (GPCRs) are integral membrane proteins and represent the largest class of drug targets. During the past decades progress in structural biology has enabled the crystallographic elucidation of the architecture of these important macromolecules. It also provided atomic-level visualization of ligand-receptor interactions, dramatically boosting the impact of structure-based approaches in drug discovery. However, knowledge obtained through crystallography is limited to static structural information. Less information is available showing how a ligand associates with or dissociates from a given receptor, whose importance is in fact increasingly recognized by the drug research community. Owing to recent advances in computer power and algorithms, molecular dynamics stimulations have become feasible that help in analyzing the kinetics of the ligand binding process. Here, we review what is currently known about the dynamics of GPCRs in the context of ligand association and dissociation, as determined through both crystallography and computer simulations. We particularly focus on the molecular basis of ligand dissociation from GPCRs and provide case studies that predict ligand dissociation pathways and residence time.

Biological structure and dynamics of fish assemblages in tributaries of eastern Lake Ontario

USGS Publications Warehouse

McKenna, James E.; Munawar, M.

2003-01-01

Interest in effective management of Great Lakes natural resources and restoration of native populations has stimulated interest in the conditions and ecological role of tributaries in the Great Lakes ecosystem. Rivers of Lake Ontario's eastern basin provide an excellent opportunity to examine important tributaries and their relationship to Lake Ontario. This paper reports on the results of an investigation of fish assemblage structure in lower reaches of the Salmon and Oswego Rivers and at their interfaces with Lake Ontario. These two systems represent conditions near the end points on a continuum from highly disturbed to pristine. They are also of great interest to resource managers for their important fisheries and other economic values. The objective was to identify distinct fish assemblages within these systems and relate their characteristics to biotic and abiotic conditions in an attempt to determine factors responsible for structuring and maintaining those species assemblages. This information is intended to provide baseline information for monitoring the status of these rivers and coastal systems and to aid in the development of models of ecological health.

The PubChem chemical structure sketcher

PubMed Central

2009-01-01

PubChem is an important public, Web-based information source for chemical and bioactivity information. In order to provide convenient structure search methods on compounds stored in this database, one mandatory component is a Web-based drawing tool for interactive sketching of chemical query structures. Web-enabled chemical structure sketchers are not new, being in existence for years; however, solutions available rely on complex technology like Java applets or platform-dependent plug-ins. Due to general policy and support incident rate considerations, Java-based or platform-specific sketchers cannot be deployed as a part of public NCBI Web services. Our solution: a chemical structure sketching tool based exclusively on CGI server processing, client-side JavaScript functions, and image sequence streaming. The PubChem structure editor does not require the presence of any specific runtime support libraries or browser configurations on the client. It is completely platform-independent and verified to work on all major Web browsers, including older ones without support for Web2.0 JavaScript objects. PMID:20298522

Informational laws of genome structures

PubMed Central

Bonnici, Vincenzo; Manca, Vincenzo

2016-01-01

In recent years, the analysis of genomes by means of strings of length k occurring in the genomes, called k-mers, has provided important insights into the basic mechanisms and design principles of genome structures. In the present study, we focus on the proper choice of the value of k for applying information theoretic concepts that express intrinsic aspects of genomes. The value k = lg2(n), where n is the genome length, is determined to be the best choice in the definition of some genomic informational indexes that are studied and computed for seventy genomes. These indexes, which are based on information entropies and on suitable comparisons with random genomes, suggest five informational laws, to which all of the considered genomes obey. Moreover, an informational genome complexity measure is proposed, which is a generalized logistic map that balances entropic and anti-entropic components of genomes and is related to their evolutionary dynamics. Finally, applications to computational synthetic biology are briefly outlined. PMID:27354155

Informational laws of genome structures

NASA Astrophysics Data System (ADS)

Bonnici, Vincenzo; Manca, Vincenzo

2016-06-01

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

Stakeholder perceptions of communication about vaccination in two regions of Cameroon: A qualitative case study

PubMed Central

Njang, Diangha Mabel; Glenton, Claire; Fretheim, Atle; Kaufman, Jessica; Hill, Sophie; Oku, Afiong; Cliff, Julie; Cartier, Yuri; Bosch-Capblanch, Xavier; Rada, Gabriel; Muloliwa, Artur Manuel; Oyo-Ita, Angela; Kum, Awah Paschal; Lewin, Simon

2017-01-01

Background Understanding stakeholders’ (parents’, communities’ and health workers’) perspectives of communication about childhood vaccination, including their preferences for its format, delivery and content, is an important step towards designing better communication strategies and ensuring more informed parents. Our objectives were to explore stakeholders’ views, experiences and preferences for childhood vaccination communication in Cameroon. Methods In 2014, in the Central and North West Regions of Cameron, we gathered qualitative data for our case study using the following methods: semi structured interviews; observations and informal conversations during routine immunization clinics and three rounds of the National Polio Immunization Campaign; document analysis of reports and mass media communications about vaccination; and a survey of parents. We conducted a thematic analysis of the qualitative data to identify themes relating to views, experiences and perceptions of vaccination information and its delivery. Survey data were analysed using simple descriptive statistics. Results All of the parents interviewed felt that vaccinating their child was important, and trusted the information provided by health workers. However, many parents wanted more information. Parents did not always feel that they could ask questions during vaccination appointments. All participants felt that health workers and vaccination clinics were important sources of information. Social mobilisation activities such as door-to-door visits and announcements during religious services were important and accepted ways of communicating information, especially during vaccination campaigns. Information communicated through mass media and text messages was also seen as important. In general, stakeholders believed that more consistent messaging about routine vaccination through community channels would be helpful to remind parents of the importance of routine vaccination during ongoing rounds of vaccination campaigns against polio. Conclusions This study confirms that parents regard information about childhood vaccination as important, but that health services need to be organized in ways that prioritize and facilitate communication, particularly about routine vaccination. PMID:28859101

A Decade of Experience in Creating and Maintaining Data Elements for Structured Clinical Documentation in EHRs

PubMed Central

Zhou, Li; Collins, Sarah; Morgan, Stephen J.; Zafar, Neelam; Gesner, Emily J.; Fehrenbach, Martin; Rocha, Roberto A.

2016-01-01

Structured clinical documentation is an important component of electronic health records (EHRs) and plays an important role in clinical care, administrative functions, and research activities. Clinical data elements serve as basic building blocks for composing the templates used for generating clinical documents (such as notes and forms). We present our experience in creating and maintaining data elements for three different EHRs (one home-grown and two commercial systems) across different clinical settings, using flowsheet data elements as examples in our case studies. We identified basic but important challenges (including naming convention, links to standard terminologies, and versioning and change management) and possible solutions to address them. We also discussed more complicated challenges regarding governance, documentation vs. structured data capture, pre-coordination vs. post-coordination, reference information models, as well as monitoring, communication and training. PMID:28269927

An exploration of health beliefs, lifestyle behaviours, and health needs of the London-based Greek Cypriot community.

PubMed

Papadopoulos, I

2000-07-01

This article reports selected results of the qualitative phase of a multimethod study into an investigation of the health beliefs, lifestyle behaviours, and health status of Greek Cypriots living in London. Data for this phase, which involved 79 informants, were collected through group and individual semistructured interviews. Six major themes were identified. These detail the informants' health and illness beliefs and use of folk remedies. The importance of the family as both a force for health and a cause for health problems is discussed. The informants' experiences as health users are also reported. The article concludes that culture is an important mediator for the health of this ethnic group. Culturally competent care depends on the nurses' understanding of the cultural background of their patients. The article recommends that nurses must be aware of the importance of societal and institutional structures that may discriminate against people from minority ethnic groups.

Quantum coupled mutation finder: predicting functionally or structurally important sites in proteins using quantum Jensen-Shannon divergence and CUDA programming.

PubMed

Gültas, Mehmet; Düzgün, Güncel; Herzog, Sebastian; Jäger, Sven Joachim; Meckbach, Cornelia; Wingender, Edgar; Waack, Stephan

2014-04-03

The identification of functionally or structurally important non-conserved residue sites in protein MSAs is an important challenge for understanding the structural basis and molecular mechanism of protein functions. Despite the rich literature on compensatory mutations as well as sequence conservation analysis for the detection of those important residues, previous methods often rely on classical information-theoretic measures. However, these measures usually do not take into account dis/similarities of amino acids which are likely to be crucial for those residues. In this study, we present a new method, the Quantum Coupled Mutation Finder (QCMF) that incorporates significant dis/similar amino acid pair signals in the prediction of functionally or structurally important sites. The result of this study is twofold. First, using the essential sites of two human proteins, namely epidermal growth factor receptor (EGFR) and glucokinase (GCK), we tested the QCMF-method. The QCMF includes two metrics based on quantum Jensen-Shannon divergence to measure both sequence conservation and compensatory mutations. We found that the QCMF reaches an improved performance in identifying essential sites from MSAs of both proteins with a significantly higher Matthews correlation coefficient (MCC) value in comparison to previous methods. Second, using a data set of 153 proteins, we made a pairwise comparison between QCMF and three conventional methods. This comparison study strongly suggests that QCMF complements the conventional methods for the identification of correlated mutations in MSAs. QCMF utilizes the notion of entanglement, which is a major resource of quantum information, to model significant dissimilar and similar amino acid pair signals in the detection of functionally or structurally important sites. Our results suggest that on the one hand QCMF significantly outperforms the previous method, which mainly focuses on dissimilar amino acid signals, to detect essential sites in proteins. On the other hand, it is complementary to the existing methods for the identification of correlated mutations. The method of QCMF is computationally intensive. To ensure a feasible computation time of the QCMF's algorithm, we leveraged Compute Unified Device Architecture (CUDA).The QCMF server is freely accessible at http://qcmf.informatik.uni-goettingen.de/.

X-ray absorption spectroscopy: EXAFS (Extended X-ray Absorption Fine Structure) and XANES (X-ray Absorption Near Edge Structure)

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

Alp, E.E.; Mini, S.M.; Ramanathan, M.

1990-04-01

The x-ray absorption spectroscopy (XAS) had been an essential tool to gather spectroscopic information about atomic energy level structure in the early decades of this century. It has also played an important role in the discovery and systematization of rare-earth elements. The discovery of synchrotron radiation in 1952, and later the availability of broadly tunable synchrotron based x-ray sources have revitalized this technique since the 1970's. The correct interpretation of the oscillatory structure in the x-ray absorption cross-section above the absorption edge by Sayers et. al. has transformed XAS from a spectroscopic tool to a structural technique. EXAFS (Extended X-raymore » Absorption Fine Structure) yields information about the interatomic distances, near neighbor coordination numbers, and lattice dynamics. An excellent description of the principles and data analysis techniques of EXAFS is given by Teo. XANES (X-ray Absorption Near Edge Structure), on the other hand, gives information about the valence state, energy bandwidth and bond angles. Today, there are about 50 experimental stations in various synchrotrons around the world dedicated to collecting x-ray absorption data from the bulk and surfaces of solids and liquids. In this chapter, we will give the basic principles of XAS, explain the information content of essentially two different aspects of the absorption process leading to EXAFS and XANES, and discuss the source and samples limitations.« less

Altered structural development and accelerated succession from intermediate-scale wind disturbance in Quercus stands on the Cumberland Plateau, USA

Treesearch

Stephen D White; Justin L. Hart; Callie J. Schweitzer; Daniel C. Dey

2015-01-01

Natural disturbances play important roles in shaping the structure and composition of all forest ecosystems and can be used to inform silvicultural practices. Canopy disturbances are often classified along a gradient ranging from highly localized, gap-scale events to stand-replacing events. Wind storms such as downbursts, derechos, and low intensity tornadoes typically...

Structural integrity of materials in nuclear service: a bibliography

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

Heddleson, F.A.

This report contains 679 abstracts from the Nuclear Safety Information Center (NSIC) computer file dated 1973 through 1976 covering material properties with respect to structural integrity. All materials important to the nuclear industry (except concrete) are covered for mechanical properties, chemical properties, corrosion, fracture or failure, radiation damage, creep, cracking, and swelling. Keyword, author, and permuted-title indexes are included for the convenience of the user.

Structural Genomics of Bacterial Virulence Factors

DTIC Science & Technology

2006-05-01

positioned in the unit cell by Molecular Replacement (Protein Data Bank ( PDB ) ID code 1acc)6 using MOLREP, and refined with REFMAC version 5.0 (ref. 24...increase our understanding of the molecular mechanisms of pathogenicity, putting us in a stronger position to anticipate and react to emerging...term, the accumulated structural information will generate important and testable hypotheses that will increase our understanding of the molecular

Congressional Oversight of Intelligence: Current Structure and Alternatives

DTIC Science & Technology

2012-03-14

Intelligence Information, by Richard A. Best Jr.; CRS Report RL33639, Sources of Systemic Risk in Large Value Interbank Payment Systems, by Edward V. Murphy...Numerous initiatives to change Congress’s oversight structure have materialized in the meantime, including, most importantly, the creation of parallel... Risk : Report, available at http://www.preventionwmd.gov/report, p. 9. 12 Kay King, Congress and National Security, Council on Foreign Relations

Cognitive representations of flight-deck information attributes

NASA Technical Reports Server (NTRS)

Ricks, Wendell R.; Jonsson, Jon E.; Rogers, William H.

1994-01-01

A large number of aviation issues are generically being called fligh-deck information management issues, underscoring the need for an organization or classification structure. One objective of this study was to empirically determine how pilots organize flight-deck information attributes and -- based upon that data -- develop a useful taxonomy (in terms of better understanding the problems and directing solutions) for classifying flight-deck information management issues. This study also empirically determined how pilots model the importance of flight-deck information attributes for managing information. The results of this analysis suggest areas in which flight-deck researchers and designers may wish to consider focusing their efforts.

The "SIMCLAS" Model: Simultaneous Analysis of Coupled Binary Data Matrices with Noise Heterogeneity between and within Data Blocks

ERIC Educational Resources Information Center

Wilderjans, Tom F.; Ceulemans, E.; Van Mechelen, I.

2012-01-01

In many research domains different pieces of information are collected regarding the same set of objects. Each piece of information constitutes a data block, and all these (coupled) blocks have the object mode in common. When analyzing such data, an important aim is to obtain an overall picture of the structure underlying the whole set of coupled…

The Interaction of Knowledge and Text Structure on the Ability to Identify Main Ideas in Texts. Content Knowledge and Reading Comprehension.

ERIC Educational Resources Information Center

Day, Jeanne D.; Engelhardt, Jean

Two studies examined how the factors of content-relevant knowledge and text organization influence students' abilities to study and to remember text information. The first experiment examined the effect of prior content knowledge on students' ability to identify important information in the text. Forty 7th- and forty 11th-grade students, experts…

Sub-Millimeter Heterodyne Focal-Plane Arrays for High-Resolution Astronomical Spectroscopy

NASA Astrophysics Data System (ADS)

Goldsmith, Paul F.

2017-09-01

Spectral lines are vital tools for astronomy, particularly for studying the interstellar medium, which is widely distributed throughout the volume of our Milky Way and of other galaxies. Broadband emissions, including synchrotron, free-free, and thermal dust emissions give astronomers important information. However, they do not give information about the motions of, for example, interstellar clouds, the filamentary structures found within them, star-forming dense cores, and photon-dominated regions energized by massive young stars. For study of the interstellar medium, spectral lines at sub-millimeter wavelengths are particularly important, for two reasons. First, they offer the unique ability to observe a variety of important molecules, atoms, and ions, which are the most important gas coolants (fine-structure lines of ionized and neutral carbon, neutral oxygen), probes of physical conditions (high-J transitions of CO, HF, fine-structure lines of ionized nitrogen), and of obvious biogenic importance (H2O). In addition, high-resolution observations of spectral lines offer the unique ability to disentangle the complex motions within these regions and, in some cases, to determine their arrangement along the line of sight. To accomplish this, spectral resolution high enough to resolve the spectral lines of interest is required. We can measure the resolution of the spectrometer in terms of its resolution, R = f/δf, where f is the rest frequency of the line, and δJ is the frequency resolution of the spectrometer. More-active sources can be advantageously studied with R = 3 × 10^5, while more quiescent sources require R as high as 10^7.

Mode of action and the assessment of chemical hazards in the presence of limited data: use of structure-activity relationships (SAR) under TSCA, Section 5.

PubMed Central

Auer, C M; Nabholz, J V; Baetcke, K P

1990-01-01

Section 5 of the Toxic Substances Control Act (TSCA) requires that manufacturers and importers of new chemicals must submit a Premanufacture Notification (PMN) to the U.S. Environmental Protection Agency 90 days before they intend to commence manufacture or import. Certain information such as chemical identity, uses, etc., must be included in the notification. The submission of test data on the new substance, however, is not required, although any available health and environmental information must be provided. Nonetheless, over half of all PMNs submitted to the agency do not contain any test data; because PMN chemicals are new, no test data is generally available in the scientific literature. Given this situation, EPA has had to develop techniques for hazard assessment that can be used in the presence of limited test data. EPA's approach has been termed "structure-activity relationships" (SAR) and involves three major components: the first is critical evaluation and interpretation of available toxicity data on the chemical; the second component involves evaluation of test data available on analogous substances and/or potential metabolites; and the third component involves the use of mathematical expressions for biological activity known as "quantitative structure-activity relationships" (QSARs). At present, the use of QSARs is limited to estimating physical chemical properties, environmental toxicity, and bioconcentration factors. An important overarching element in EPA's approach is the experience and judgment of scientific assessors in interpreting and integrating the available data and information. Examples are provided that illustrate EPA's approach to hazard assessment for PMN chemicals. PMID:2269224

Functional Insights from Structural Genomics

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

Forouhar,F.; Kuzin, A.; Seetharaman, J.

2007-01-01

Structural genomics efforts have produced structural information, either directly or by modeling, for thousands of proteins over the past few years. While many of these proteins have known functions, a large percentage of them have not been characterized at the functional level. The structural information has provided valuable functional insights on some of these proteins, through careful structural analyses, serendipity, and structure-guided functional screening. Some of the success stories based on structures solved at the Northeast Structural Genomics Consortium (NESG) are reported here. These include a novel methyl salicylate esterase with important role in plant innate immunity, a novel RNAmore » methyltransferase (H. influenzae yggJ (HI0303)), a novel spermidine/spermine N-acetyltransferase (B. subtilis PaiA), a novel methyltransferase or AdoMet binding protein (A. fulgidus AF{_}0241), an ATP:cob(I)alamin adenosyltransferase (B. subtilis YvqK), a novel carboxysome pore (E. coli EutN), a proline racemase homolog with a disrupted active site (B. melitensis BME11586), an FMN-dependent enzyme (S. pneumoniae SP{_}1951), and a 12-stranded {beta}-barrel with a novel fold (V. parahaemolyticus VPA1032).« less

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

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.

Online Information Sharing About Risks: The Case of Organic Food.

PubMed

Hilverda, Femke; Kuttschreuter, Margôt

2018-03-23

Individuals have to make sense of an abundance of information to decide whether or not to purchase certain food products. One of the means to sense-making is information sharing. This article reports on a quantitative study examining online information sharing behavior regarding the risks of organic food products. An online survey among 535 respondents was conducted in the Netherlands to examine the determinants of information sharing behavior, and their relationships. Structural equation modeling was applied to test both the measurement model and the structural model. Results showed that the intention to share information online about the risks of organic food was low. Conversations and email were the preferred channels to share information; of the social media Facebook stood out. The developed model was found to provide an adequate description of the data. It explained 41% of the variance in information sharing. Injunctive norms and outcome expectancies were most important in predicting online information sharing, followed by information-related determinants. Risk-perception-related determinants showed a significant, but weak, positive relationship with online information sharing. Implications for authorities communicating on risks associated with food are addressed. © 2018 The Authors Risk Analysis published by Wiley Periodicals, Inc. on behalf of Society for Risk Analysis.

Genetic structure of the threatened Phaedranassa schizantha (Amaryllidaceae)

USDA-ARS?s Scientific Manuscript database

Population genetic analysis can provide important information for the conservation of endangered species. Phaedranassa schizantha Baker (Amaryllidaceae) is an endangered species endemic to Ecuador. Taxonomically P. schizantha was described as two varieties: P. schizantha var. schizantha and P. schiz...

The Rest of the Story: A Qualitative Study of Complementing Standardized Assessment Data with Informal Interviews with Older Patients and Families.

PubMed

Lafortune, Claire; Elliott, Jacobi; Egan, Mary Y; Stolee, Paul

2017-04-01

While standardized health assessments capture valuable information on patients' demographic and diagnostic characteristics, health conditions, and physical and mental functioning, they may not capture information of most relevance to individual patients and their families. Given that patients and their informal caregivers are the experts on that patient's unique context, it is important to ensure they are able to convey all relevant personal information to formal healthcare providers so that high-quality, patient-centered care may be delivered. This study aims to identify information that older patients and families consider important but that might not be included in standardized assessments. Transcripts were analyzed from 29 interviews relating to eight patients with hip fractures from three sites (large urban, smaller urban, rural) in two provinces in Canada. These interviews were conducted as part of a larger ethnographic study. Each transcript was analyzed by two researchers using content analysis. Results were reviewed in two focus group interviews with older adults and family caregivers. Identified themes were compared with items from two standardized assessments used in healthcare settings. Three broad themes emerged from the qualitative analysis that were not covered in the standardized assessments: informal caregiver and family considerations, insider healthcare knowledge, and patients' healthcare attitudes and experiences. The importance of these themes was confirmed through focus group interviews. Focus group participants also emphasized the importance of conducting assessments in a patient-centered way and the importance of open-ended questions. A less structured interview approach may yield information that would otherwise be missed in standardized assessments. Combining both sources could yield better-informed healthcare planning and quality-improvement efforts.

Low Resolution Refinement of Atomic Models Against Crystallographic Data.

PubMed

Nicholls, Robert A; Kovalevskiy, Oleg; Murshudov, Garib N

2017-01-01

This review describes some of the problems encountered during low-resolution refinement and map calculation. Refinement is considered as an application of Bayes' theorem, allowing combination of information from various sources including crystallographic experimental data and prior chemical and structural knowledge. The sources of prior knowledge relevant to macromolecules include basic chemical information such as bonds and angles, structural information from reference models of known homologs, knowledge about secondary structures, hydrogen bonding patterns, and similarity of non-crystallographically related copies of a molecule. Additionally, prior information encapsulating local conformational conservation is exploited, keeping local interatomic distances similar to those in the starting atomic model. The importance of designing an accurate likelihood function-the only link between model parameters and observed data-is emphasized. The review also reemphasizes the importance of phases, and describes how the use of raw observed amplitudes could give a better correlation between the calculated and "true" maps. It is shown that very noisy or absent observations can be replaced by calculated structure factors, weighted according to the accuracy of the atomic model. This approach helps to smoothen the map. However, such replacement should be used sparingly, as the bias toward errors in the model could be too much to avoid. It is in general recommended that, whenever a new map is calculated, map quality should be judged by inspection of the parts of the map where there is no atomic model. It is also noted that it is advisable to work with multiple blurred and sharpened maps, as different parts of a crystal may exhibit different degrees of mobility. Doing so can allow accurate building of atomic models, accounting for overall shape as well as finer structural details. Some of the results described in this review have been implemented in the programs REFMAC5, ProSMART and LORESTR, which are available as part of the CCP4 software suite.

Meta-Generalis: A Novel Method for Structuring Information from Radiology Reports

PubMed Central

Barbosa, Flavio; Traina, Agma Jucci

2016-01-01

Summary Background A structured report for imaging exams aims at increasing the precision in information retrieval and communication between physicians. However, it is more concise than free text and may limit specialists’ descriptions of important findings not covered by pre-defined structures. A computational ontological structure derived from free texts designed by specialists may be a solution for this problem. Therefore, the goal of our study was to develop a methodology for structuring information in radiology reports covering specifications required for the Brazilian Portuguese language, including the terminology to be used. Methods We gathered 1,701 radiological reports of magnetic resonance imaging (MRI) studies of the lumbosacral spine from three different institutions. Techniques of text mining and ontological conceptualization of lexical units extracted were used to structure information. Ten radiologists, specialists in lumbosacral MRI, evaluated the textual superstructure and terminology extracted using an electronic questionnaire. Results The established methodology consists of six steps: 1) collection of radiology reports of a specific MRI examination; 2) textual decomposition; 3) normalization of lexical units; 4) identification of textual superstructures; 5) conceptualization of candidate-terms; and 6) evaluation of superstructures and extracted terminology by experts using an electronic questionnaire. Three different textual superstructures were identified, with terminological variations in the names of their textual categories. The number of candidate-terms conceptualized was 4,183, yielding 727 concepts. There were a total of 13,963 relationships between candidate-terms and concepts and 789 relationships among concepts. Conclusions The proposed methodology allowed structuring information in a more intuitive and practical way. Indications of three textual superstructures, extraction of lexicon units and the normalization and ontologically conceptualization were achieved while maintaining references to their respective categories and free text radiology reports. PMID:27580980

Meta-generalis: A novel method for structuring information from radiology reports.

PubMed

Barbosa, Flavio; Traina, Agma Jucci; Muglia, Valdair Francisco

2016-08-24

A structured report for imaging exams aims at increasing the precision in information retrieval and communication between physicians. However, it is more concise than free text and may limit specialists' descriptions of important findings not covered by pre-defined structures. A computational ontological structure derived from free texts designed by specialists may be a solution for this problem. Therefore, the goal of our study was to develop a methodology for structuring information in radiology reports covering specifications required for the Brazilian Portuguese language, including the terminology to be used. We gathered 1,701 radiological reports of magnetic resonance imaging (MRI) studies of the lumbosacral spine from three different institutions. Techniques of text mining and ontological conceptualization of lexical units extracted were used to structure information. Ten radiologists, specialists in lumbosacral MRI, evaluated the textual superstructure and terminology extracted using an electronic questionnaire. The established methodology consists of six steps: 1) collection of radiology reports of a specific MRI examination; 2) textual decomposition; 3) normalization of lexical units; 4) identification of textual superstructures; 5) conceptualization of candidate-terms; and 6) evaluation of superstructures and extracted terminology by experts using an electronic questionnaire. Three different textual superstructures were identified, with terminological variations in the names of their textual categories. The number of candidate-terms conceptualized was 4,183, yielding 727 concepts. There were a total of 13,963 relationships between candidate-terms and concepts and 789 relationships among concepts. The proposed methodology allowed structuring information in a more intuitive and practical way. Indications of three textual superstructures, extraction of lexicon units and the normalization and ontologically conceptualization were achieved while maintaining references to their respective categories and free text radiology reports.

Image understanding systems based on the unifying representation of perceptual and conceptual information and the solution of mid-level and high-level vision problems

NASA Astrophysics Data System (ADS)

Kuvychko, Igor

2001-10-01

Vision is a part of a larger information system that converts visual information into knowledge structures. These structures drive vision process, resolving ambiguity and uncertainty via feedback, and provide image understanding, that is an interpretation of visual information in terms of such knowledge models. A computer vision system based on such principles requires unifying representation of perceptual and conceptual information. Computer simulation models are built on the basis of graphs/networks. The ability of human brain to emulate similar graph/networks models is found. That means a very important shift of paradigm in our knowledge about brain from neural networks to the cortical software. Starting from the primary visual areas, brain analyzes an image as a graph-type spatial structure. Primary areas provide active fusion of image features on a spatial grid-like structure, where nodes are cortical columns. The spatial combination of different neighbor features cannot be described as a statistical/integral characteristic of the analyzed region, but uniquely characterizes such region itself. Spatial logic and topology naturally present in such structures. Mid-level vision processes like clustering, perceptual grouping, multilevel hierarchical compression, separation of figure from ground, etc. are special kinds of graph/network transformations. They convert low-level image structure into the set of more abstract ones, which represent objects and visual scene, making them easy for analysis by higher-level knowledge structures. Higher-level vision phenomena like shape from shading, occlusion, etc. are results of such analysis. Such approach gives opportunity not only to explain frequently unexplainable results of the cognitive science, but also to create intelligent computer vision systems that simulate perceptional processes in both what and where visual pathways. Such systems can open new horizons for robotic and computer vision industries.

Redundant unbalance compensation of an active magnetic bearing system

NASA Astrophysics Data System (ADS)

Hutterer, Markus; Kalteis, Gerald; Schrödl, Manfred

2017-09-01

To achieve a good running behavior of a magnetic levitated rotor, a well-developed position controller and different compensation methods are required. Two very important structures in this context are the reduction of the gyroscopic effect and the unbalance vibration. Both structures have in common that they need the angular velocity information for calculation. For industrial applications this information is normally provided by an angle sensor which is fixed on the rotor. The angle information is also necessary for the field oriented control of the electrical drive. The main drawback of external position sensors are the case of a breakdown or an error of the motor controller. Therefore, the magnetic bearing can get unstable, because no angular velocity information is provided. To overcome this problem the presented paper describes the development of a selfsensing unbalance rejection in combination with a selfsensing speed control of the motor controller. Selfsensing means in this context that no angle sensor is required for the unbalance or torque control. With such structures two redundant speed and angle information sources are available and can be used for the magnetic bearing and the motor controller without the usage of an angle sensor.

Structural Bioinformatics of the Interactome

PubMed Central

Petrey, Donald; Honig, Barry

2014-01-01

The last decade has seen a dramatic expansion in the number and range of techniques available to obtain genome-wide information, and to analyze this information so as to infer both the function of individual molecules and how they interact to modulate the behavior of biological systems. Here we review these techniques, focusing on the construction of physical protein-protein interaction networks, and highlighting approaches that incorporate protein structure which is becoming an increasingly important component of systems-level computational techniques. We also discuss how network analyses are being applied to enhance the basic understanding of biological systems and their disregulation, and how they are being applied in drug development. PMID:24895853

A top-down approach to crystal engineering of a racemic Δ2-isoxazoline.

PubMed

Lombardo, Giuseppe M; Rescifina, Antonio; Chiacchio, Ugo; Bacchi, Alessia; Punzo, Francesco

2014-02-01

The crystal structure of racemic dimethyl (4RS,5RS)-3-(4-nitrophenyl)-4,5-dihydroisoxazole-4,5-dicarboxylate, C13H12N2O7, has been determined by single-crystal X-ray diffraction. By analysing the degree of growth of the morphologically important crystal faces, a ranking of the most relevant non-covalent interactions determining the crystal structure can be inferred. The morphological information is considered with an approach opposite to the conventional one: instead of searching inside the structure for the potential key interactions and using them to calculate the crystal habit, the observed crystal morphology is used to define the preferential lines of growth of the crystal, and then this information is interpreted by means of density functional theory (DFT) calculations. Comparison with the X-ray structure confirms the validity of the strategy, thus suggesting this top-down approach to be a useful tool for crystal engineering.

A project management system for the X-29A flight test program

NASA Technical Reports Server (NTRS)

Stewart, J. F.; Bauer, C. A.

1983-01-01

The project-management system developed for NASA's participation in the X-29A aircraft development program is characterized from a theoretical perspective, as an example of a system appropriate to advanced, highly integrated technology projects. System-control theory is applied to the analysis of classical project-management techniques and structures, which are found to be of closed-loop multivariable type; and the effects of increasing project complexity and integration are evaluated. The importance of information flow, sampling frequency, information holding, and delays is stressed. The X-29A system is developed in four stages: establishment of overall objectives and requirements, determination of information processes (block diagrams) definition of personnel functional roles and relationships, and development of a detailed work-breakdown structure. The resulting system is shown to require a greater information flow to management than conventional methods. Sample block diagrams are provided.

Terminology model discovery using natural language processing and visualization techniques.

PubMed

Zhou, Li; Tao, Ying; Cimino, James J; Chen, Elizabeth S; Liu, Hongfang; Lussier, Yves A; Hripcsak, George; Friedman, Carol

2006-12-01

Medical terminologies are important for unambiguous encoding and exchange of clinical information. The traditional manual method of developing terminology models is time-consuming and limited in the number of phrases that a human developer can examine. In this paper, we present an automated method for developing medical terminology models based on natural language processing (NLP) and information visualization techniques. Surgical pathology reports were selected as the testing corpus for developing a pathology procedure terminology model. The use of a general NLP processor for the medical domain, MedLEE, provides an automated method for acquiring semantic structures from a free text corpus and sheds light on a new high-throughput method of medical terminology model development. The use of an information visualization technique supports the summarization and visualization of the large quantity of semantic structures generated from medical documents. We believe that a general method based on NLP and information visualization will facilitate the modeling of medical terminologies.

[NASA/DOD Aerospace Knowledge Diffusion Research Project. Paper 18:] Scientific and Technical Information (STI) policy and the competitive position of the US aerospace industry

NASA Technical Reports Server (NTRS)

Hernon, Peter; Pinelli, Thomas E.

1992-01-01

With its contribution to trade, its coupling with national security, and its symbolism of U.S. technological strength, the U.S. aerospace industry holds a unique position in the Nation's industrial structure. Federal science and technology policy and Federal scientific and technical information (STI) policy loom important as strategic contributions to the U.S. aerospace industry's leading competitive position. However, three fundamental policy problems exist. First, the United States lacks a coherent STI policy and a unified approach to the development of such a policy. Second, policymakers fail to understand the relationship of STI to science and technology policy. Third, STI is treated as a part of general information policy, without any recognition of its uniqueness. This paper provides an overview of the Federal information policy structure as it relates to STI and frames the policy issues that require resolution.

Experimental demonstration of graph-state quantum secret sharing.

PubMed

Bell, B A; Markham, D; Herrera-Martí, D A; Marin, A; Wadsworth, W J; Rarity, J G; Tame, M S

2014-11-21

Quantum communication and computing offer many new opportunities for information processing in a connected world. Networks using quantum resources with tailor-made entanglement structures have been proposed for a variety of tasks, including distributing, sharing and processing information. Recently, a class of states known as graph states has emerged, providing versatile quantum resources for such networking tasks. Here we report an experimental demonstration of graph state-based quantum secret sharing--an important primitive for a quantum network with applications ranging from secure money transfer to multiparty quantum computation. We use an all-optical setup, encoding quantum information into photons representing a five-qubit graph state. We find that one can reliably encode, distribute and share quantum information amongst four parties, with various access structures based on the complex connectivity of the graph. Our results show that graph states are a promising approach for realising sophisticated multi-layered communication protocols in quantum networks.

NASA/DOD Aerospace Knowledge Diffusion Research Project. Paper 18: Scientific and Technical Information (STI) policy and the competitive position of the US aerospace industry

NASA Technical Reports Server (NTRS)

Hernon, Peter; Pinelli, Thomas E.

1992-01-01

With its contribution to trade, its coupling with national security, and its symbolism of U.S. technological strength, the U.S. aerospace industry holds a unique position in the Nation's industrial structure. Federal science and technology policy and Federal scientific and technical information (STI) policy loom important as strategic contributions to the U.S. aerospace industry's leading competitive position. However, three fundamental policy problems exist. First, the United States lacks a coherent STI policy and a unified approach to the development of such a policy. Second, policymakers fail to understand the relationship of STI to science and technology policy. Third, STI is treated as a part of general information policy, without any recognition of its uniqueness. This paper provides an overview of the Federal information policy structure as it relates to STI and frames the policy issues that require resolution.

Limited role of spectra in dynamo theory: coherent versus random dynamos.

PubMed

Tobias, Steven M; Cattaneo, Fausto

2008-09-19

We discuss the importance of phase information and coherence times in determining the dynamo properties of turbulent flows. We compare the kinematic dynamo properties of three flows with the same energy spectrum. The first flow is dominated by coherent structures with nontrivial phase information and long eddy coherence times, the second has random phases and long-coherence time, the third has nontrivial phase information, but short coherence time. We demonstrate that the first flow is the most efficient kinematic dynamo, owing to the presence of sustained stretching and constructive folding. We argue that these results place limitations on the possible inferences of the dynamo properties of flows from the use of spectra alone, and that the role of coherent structures must always be accounted for.

Effects of Sample Selection Bias on the Accuracy of Population Structure and Ancestry Inference

PubMed Central

Shringarpure, Suyash; Xing, Eric P.

2014-01-01

Population stratification is an important task in genetic analyses. It provides information about the ancestry of individuals and can be an important confounder in genome-wide association studies. Public genotyping projects have made a large number of datasets available for study. However, practical constraints dictate that of a geographical/ethnic population, only a small number of individuals are genotyped. The resulting data are a sample from the entire population. If the distribution of sample sizes is not representative of the populations being sampled, the accuracy of population stratification analyses of the data could be affected. We attempt to understand the effect of biased sampling on the accuracy of population structure analysis and individual ancestry recovery. We examined two commonly used methods for analyses of such datasets, ADMIXTURE and EIGENSOFT, and found that the accuracy of recovery of population structure is affected to a large extent by the sample used for analysis and how representative it is of the underlying populations. Using simulated data and real genotype data from cattle, we show that sample selection bias can affect the results of population structure analyses. We develop a mathematical framework for sample selection bias in models for population structure and also proposed a correction for sample selection bias using auxiliary information about the sample. We demonstrate that such a correction is effective in practice using simulated and real data. PMID:24637351

Gust prediction via artificial hair sensor array and neural network

NASA Astrophysics Data System (ADS)

Pankonien, Alexander M.; Thapa Magar, Kaman S.; Beblo, Richard V.; Reich, Gregory W.

2017-04-01

Gust Load Alleviation (GLA) is an important aspect of flight dynamics and control that reduces structural loadings and enhances ride quality. In conventional GLA systems, the structural response to aerodynamic excitation informs the control scheme. A phase lag, imposed by inertia, between the excitation and the measurement inherently limits the effectiveness of these systems. Hence, direct measurement of the aerodynamic loading can eliminate this lag, providing valuable information for effective GLA system design. Distributed arrays of Artificial Hair Sensors (AHS) are ideal for surface flow measurements that can be used to predict other necessary parameters such as aerodynamic forces, moments, and turbulence. In previous work, the spatially distributed surface flow velocities obtained from an array of artificial hair sensors using a Single-State (or feedforward) Neural Network were found to be effective in estimating the steady aerodynamic parameters such as air speed, angle of attack, lift and moment coefficient. This paper extends the investigation of the same configuration to unsteady force and moment estimation, which is important for active GLA control design. Implementing a Recurrent Neural Network that includes previous-timestep sensor information, the hair sensor array is shown to be capable of capturing gust disturbances with a wide range of periods, reducing predictive error in lift and moment by 68% and 52% respectively. The L2 norms of the first layer of the weight matrices were compared showing a 23% emphasis on prior versus current information. The Recurrent architecture also improves robustness, exhibiting only a 30% increase in predictive error when undertrained as compared to a 170% increase by the Single-State NN. This diverse, localized information can thus be directly implemented into a control scheme that alleviates the gusts without waiting for a structural response or requiring user-intensive sensor calibration.

The Fundamentals of Community College Fund Raising.

ERIC Educational Resources Information Center

Brumbach, Mary A.; Bumphus, Walter G.

1993-01-01

Presents a guide for community college fund raising. Discusses organizational principles and structural models; operational concerns such as stewardship of funds, information dissemination, and donor research; and the importance of presidential support, institutional reputation and environment, and experienced grants managers. Includes practical…

Quantum chemical studies of estrogenic compounds

USDA-ARS?s Scientific Manuscript database

Quantum chemical methods are potent tools to provide information on the chemical structure and electronic properties of organic molecules. Modern computational chemistry methods have provided a great deal of insight into the binding of estrogenic compounds to estrogenic receptors (ER), an important ...

Chemistry from Issues.

ERIC Educational Resources Information Center

Harding, Jan; Donaldson, Jim

1986-01-01

Describes the "Chemistry from Issues" project at Chelsea College. Provides the background information, rationale, and overall structure of a proposed course about the importance of chemistry to common culture. Outlines one module about the British steel industry that has been taught at King's College. (TW)

Structure solution of network materials by solid-state NMR without knowledge of the crystallographic space group.

PubMed

Brouwer, Darren H

2013-01-01

An algorithm is presented for solving the structures of silicate network materials such as zeolites or layered silicates from solid-state (29)Si double-quantum NMR data for situations in which the crystallographic space group is not known. The algorithm is explained and illustrated in detail using a hypothetical two-dimensional network structure as a working example. The algorithm involves an atom-by-atom structure building process in which candidate partial structures are evaluated according to their agreement with Si-O-Si connectivity information, symmetry restraints, and fits to (29)Si double quantum NMR curves followed by minimization of a cost function that incorporates connectivity, symmetry, and quality of fit to the double quantum curves. The two-dimensional network material is successfully reconstructed from hypothetical NMR data that can be reasonably expected to be obtained for real samples. This advance in "NMR crystallography" is expected to be important for structure determination of partially ordered silicate materials for which diffraction provides very limited structural information. Copyright © 2013 Elsevier Inc. All rights reserved.

Crystal structure of a putative exo-β-1,3-galactanase from Bifidobacterium bifidum S17

PubMed Central

Godoy, Andre S.; de Lima, Mariana Z. T.; Camilo, Cesar M.; Polikarpov, Igor

2016-01-01

Given the current interest in second-generation biofuels, carbohydrate-active enzymes have become the most important tool to overcome the structural recalcitrance of the plant cell wall. While some glycoside hydrolase families have been exhaustively described, others remain poorly characterized, especially with regard to structural information. The family 43 glycoside hydrolases are a diverse group of inverting enzymes; the available structure information on these enzymes is mainly from xylosidases and arabinofuranosidase. Currently, only one structure of an exo-β-1,3-galactanase is available. Here, the production, crystallization and structure determination of a putative exo-β-1,3-galactanase from Bifidobacterium bifidum S17 (BbGal43A) are described. BbGal43A was successfully produced and showed activity towards synthetic galactosides. BbGal43A was subsequently crystallized and data were collected to 1.4 Å resolution. The structure shows a single-domain molecule, differing from known homologues, and crystal contact analysis predicts the formation of a dimer in solution. Further biochemical studies are necessary to elucidate the differences between BbGal43A and its characterized homologues. PMID:27050262

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

Datta, Kaustuv; Neder, Reinhard B.; Chen, Jun

Revelation of unequivocal structural information at the atomic level for complex systems is uniquely important for deeper and generic understanding of the structure property connections and a key challenge in materials science. Here in this paper we report an experimental study of the local structure by applying total elastic scattering and Raman scattering analyses to an important non-relaxor ferroelectric solid solution exhibiting the so-called composition-induced morphotropic phase boundary (MPB), where concomitant enhancement of physical properties have been detected. The powerful combination of static and dynamic structural probes enabled us to derive direct correspondence between the atomic-level structural correlations and reportedmore » properties. The atomic pair distribution functions obtained from the neutron total scattering experiments were analysed through big-box atom-modelling implementing reverse Monte Carlo method, from which distributions of magnitudes and directions of off-centred cationic displacements were extracted. We found that an enhanced randomness of the displacement-directions for all ferroelectrically active cations combined with a strong dynamical coupling between the A- and B-site cations of the perovskite structure, can explain the abrupt amplification of piezoelectric response of the system near MPB. Finally, altogether this provides a more fundamental basis in inferring structure-property connections in similar systems including important implications in designing novel and bespoke materials.« less

Toward a patient-centered ambulatory after-visit summary: Identifying primary care patients' information needs.

PubMed

Clarke, Martina A; Moore, Joi L; Steege, Linsey M; Koopman, Richelle J; Belden, Jeffery L; Canfield, Shannon M; Kim, Min S

2018-09-01

The purpose of this study was to determine the information needs of primary care patients as they review clinic visit notes to inform information that should be contained in an after-visit summary (AVS). We collected data from 15 patients with an acute illness and 14 patients with a chronic disease using semi-structured interviews. The acute patients reviewed seven major sections, and chronic patients reviewed eight major sections of a simulated, but realistic visit note to identify relevant information needs for their AVS. Patients in the acute illness group identified the Plan, Assessment and History of Present Illness the most as important note sections, while patients in the chronic care group identified Significant Lab Data, Plan, and Assessment the most as important note sections. This study was able to identify primary care patients' information needs after clinic visit. Primary care patients have information needs pertaining to diagnosis and treatment, which may be the reason why both patient groups identified Plan and Assessment as important note sections. Future research should also develop and assess an AVS based on the information gathered in this study and evaluate its usefulness among primary care patients. The results of this study can be used to inform the development of an after-visit summary that assists patients to fully understand their treatment plan, which may improve treatment adherence.

Facilitators on networks reveal optimal interplay between information exchange and reciprocity.

PubMed

Szolnoki, Attila; Perc, Matjaž; Mobilia, Mauro

2014-04-01

Reciprocity is firmly established as an important mechanism that promotes cooperation. An efficient information exchange is likewise important, especially on structured populations, where interactions between players are limited. Motivated by these two facts, we explore the role of facilitators in social dilemmas on networks. Facilitators are here mirrors to their neighbors-they cooperate with cooperators and defect with defectors-but they do not participate in the exchange of strategies. As such, in addition to introducing direct reciprocity, they also obstruct information exchange. In well-mixed populations, facilitators favor the replacement and invasion of defection by cooperation as long as their number exceeds a critical value. In structured populations, on the other hand, there exists a delicate balance between the benefits of reciprocity and the deterioration of information exchange. Extensive Monte Carlo simulations of social dilemmas on various interaction networks reveal that there exists an optimal interplay between reciprocity and information exchange, which sets in only when a small number of facilitators occupy the main hubs of the scale-free network. The drawbacks of missing cooperative hubs are more than compensated for by reciprocity and, at the same time, the compromised information exchange is routed via the auxiliary hubs with only marginal losses in effectivity. These results indicate that it is not always optimal for the main hubs to become leaders of the masses, but rather to exploit their highly connected state to promote tit-for-tat-like behavior.

Automatically Recognizing Medication and Adverse Event Information From Food and Drug Administration’s Adverse Event Reporting System Narratives

PubMed Central

Polepalli Ramesh, Balaji; Belknap, Steven M; Li, Zuofeng; Frid, Nadya; West, Dennis P

2014-01-01

Background The Food and Drug Administration’s (FDA) Adverse Event Reporting System (FAERS) is a repository of spontaneously-reported adverse drug events (ADEs) for FDA-approved prescription drugs. FAERS reports include both structured reports and unstructured narratives. The narratives often include essential information for evaluation of the severity, causality, and description of ADEs that are not present in the structured data. The timely identification of unknown toxicities of prescription drugs is an important, unsolved problem. Objective The objective of this study was to develop an annotated corpus of FAERS narratives and biomedical named entity tagger to automatically identify ADE related information in the FAERS narratives. Methods We developed an annotation guideline and annotate medication information and adverse event related entities on 122 FAERS narratives comprising approximately 23,000 word tokens. A named entity tagger using supervised machine learning approaches was built for detecting medication information and adverse event entities using various categories of features. Results The annotated corpus had an agreement of over .9 Cohen’s kappa for medication and adverse event entities. The best performing tagger achieves an overall performance of 0.73 F1 score for detection of medication, adverse event and other named entities. Conclusions In this study, we developed an annotated corpus of FAERS narratives and machine learning based models for automatically extracting medication and adverse event information from the FAERS narratives. Our study is an important step towards enriching the FAERS data for postmarketing pharmacovigilance. PMID:25600332

Polarization Remote Sensing Physical Mechanism, Key Methods and Application

NASA Astrophysics Data System (ADS)

Yang, B.; Wu, T.; Chen, W.; Li, Y.; Knjazihhin, J.; Asundi, A.; Yan, L.

2017-09-01

China's long-term planning major projects "high-resolution earth observation system" has been invested nearly 100 billion and the satellites will reach 100 to 2020. As to 2/3 of China's area covered by mountains it has a higher demand for remote sensing. In addition to light intensity, frequency, phase, polarization is also the main physical characteristics of remote sensing electromagnetic waves. Polarization is an important component of the reflected information from the surface and the atmospheric information, and the polarization effect of the ground object reflection is the basis of the observation of polarization remote sensing. Therefore, the effect of eliminating the polarization effect is very important for remote sensing applications. The main innovations of this paper is as follows: (1) Remote sensing observation method. It is theoretically deduced and verified that the polarization can weaken the light in the strong light region, and then provide the polarization effective information. In turn, the polarization in the low light region can strengthen the weak light, the same can be obtained polarization effective information. (2) Polarization effect of vegetation. By analyzing the structure characteristics of vegetation, polarization information is obtained, then the vegetation structure information directly affects the absorption of biochemical components of leaves. (3) Atmospheric polarization neutral point observation method. It is proved to be effective to achieve the ground-gas separation, which can achieve the effect of eliminating the atmospheric polarization effect and enhancing the polarization effect of the object.

Facilitators on networks reveal optimal interplay between information exchange and reciprocity

NASA Astrophysics Data System (ADS)

Szolnoki, Attila; Perc, Matjaž; Mobilia, Mauro

2014-04-01

Reciprocity is firmly established as an important mechanism that promotes cooperation. An efficient information exchange is likewise important, especially on structured populations, where interactions between players are limited. Motivated by these two facts, we explore the role of facilitators in social dilemmas on networks. Facilitators are here mirrors to their neighbors—they cooperate with cooperators and defect with defectors—but they do not participate in the exchange of strategies. As such, in addition to introducing direct reciprocity, they also obstruct information exchange. In well-mixed populations, facilitators favor the replacement and invasion of defection by cooperation as long as their number exceeds a critical value. In structured populations, on the other hand, there exists a delicate balance between the benefits of reciprocity and the deterioration of information exchange. Extensive Monte Carlo simulations of social dilemmas on various interaction networks reveal that there exists an optimal interplay between reciprocity and information exchange, which sets in only when a small number of facilitators occupy the main hubs of the scale-free network. The drawbacks of missing cooperative hubs are more than compensated for by reciprocity and, at the same time, the compromised information exchange is routed via the auxiliary hubs with only marginal losses in effectivity. These results indicate that it is not always optimal for the main hubs to become leaders of the masses, but rather to exploit their highly connected state to promote tit-for-tat-like behavior.

Student Views about the Public Spot Advertisement Signs in the Context of Lifelong Learning (The Example of Reading Culture Themed Public Spot Advertisement)

ERIC Educational Resources Information Center

Tanca, H. Altug; Ünal, Fatma

2018-01-01

It's important that the messages and information in the public spot advertisements that is wanted to be conveyed to the individuals to be reached at the desired level and an asymmetric structure existing between the message prepared with a fictional structure and the perception between the message and the receiving party. Because, a decent…

Geological Mapping Uses Landsat 4-5TM Satellite Data in Manlai Soum of Omnogovi Aimag

NASA Astrophysics Data System (ADS)

Norovsuren, B.

2014-12-01

Author: Bayanmonkh N1, Undram.G1, Tsolmon.R2, Ariunzul.Ya1, Bayartungalag B31 Environmental Research Information and Study Center 2NUM-ITC-UNESCO Space Science and Remote Sensing International Laboratory, National University of Mongolia 3Geology and Hydrology School, Korea University KEY WORDS: geology, mineral resources, fracture, structure, lithologyABSTRACTGeologic map is the most important map for mining when it does exploration job. In Mongolia geological map completed by Russian geologists which is done by earlier technology. Those maps doesn't satisfy for present requirements. Thus we want to study improve geological map which includes fracture, structural map and lithology use Landsat TM4-5 satellite data. If we can produce a geological map from satellite data with more specification then geologist can explain or read mineralogy very easily. We searched all methodology and researches of every single element of geological mapping. Then we used 3 different remote sensing methodologies to produce structural and lithology and fracture map based on geographic information system's softwares. There can be found a visible lithology border improvement and understandable structural map and we found fracture of the Russian geological map has a lot of distortion. The result of research geologist can read mineralogy elements very easy and discovered 3 unfound important elements from satellite image.

Institutional change to support regime transformation: Lessons from Australia's water sector

NASA Astrophysics Data System (ADS)

Werbeloff, Lara; Brown, Rebekah; Cocklin, Chris

2017-07-01

Institutional change is fundamental to regime transformation, and a necessary part of moving toward integrated water management. However, insight into the role of institutional change processes in such transitions is currently limited. A more nuanced understanding of institutional frameworks is necessary, both to advance understanding of institutional change in the context of transitions toward improved water management and to inform strategies for guiding such processes. To this end, we examine two contemporary cases of transformative change in Australia's urban water sector, exploring the evolution of institutional change in each city. This paper offers insights into regime transformation, providing guidance on types of institutional structures and the ways structure-change initiatives can be sequenced to support a transition. The results reveal the importance of regulation in embedding regime change and suggest that engagement with structural frameworks should begin early in transition processes to ensure the timely introduction of supporting regulation. Our findings also highlight the inextricable link between culture-based and structure-based change initiatives, and the importance of using a diverse range of institutional change mechanisms in a mutually reinforcing way to provide a strong foundation for change. These findings provide a foundation for further scholarly examination of institutional change mechanisms, while also serving to inform the strategic activities of transition-oriented organizations and actors.

Geographic Information System (GIS) capabilities in traffic accident information management: a qualitative approach

PubMed Central

Ahmadi, Maryam; Valinejadi, Ali; Goodarzi, Afshin; Safari, Ameneh; Hemmat, Morteza; Majdabadi, Hesamedin Askari; Mohammadi, Ali

2017-01-01

Background Traffic accidents are one of the more important national and international issues, and their consequences are important for the political, economical, and social level in a country. Management of traffic accident information requires information systems with analytical and accessibility capabilities to spatial and descriptive data. Objective The aim of this study was to determine the capabilities of a Geographic Information System (GIS) in management of traffic accident information. Methods This qualitative cross-sectional study was performed in 2016. In the first step, GIS capabilities were identified via literature retrieved from the Internet and based on the included criteria. Review of the literature was performed until data saturation was reached; a form was used to extract the capabilities. In the second step, study population were hospital managers, police, emergency, statisticians, and IT experts in trauma, emergency and police centers. Sampling was purposive. Data was collected using a questionnaire based on the first step data; validity and reliability were determined by content validity and Cronbach’s alpha of 75%. Data was analyzed using the decision Delphi technique. Results GIS capabilities were identified in ten categories and 64 sub-categories. Import and process of spatial and descriptive data and so, analysis of this data were the most important capabilities of GIS in traffic accident information management. Conclusion Storing and retrieving of descriptive and spatial data, providing statistical analysis in table, chart and zoning format, management of bad structure issues, determining the cost effectiveness of the decisions and prioritizing their implementation were the most important capabilities of GIS which can be efficient in the management of traffic accident information. PMID:28848627

On the role of spatial phase and phase correlation in vision, illusion, and cognition

PubMed Central

Gladilin, Evgeny; Eils, Roland

2015-01-01

Numerous findings indicate that spatial phase bears an important cognitive information. Distortion of phase affects topology of edge structures and makes images unrecognizable. In turn, appropriately phase-structured patterns give rise to various illusions of virtual image content and apparent motion. Despite a large body of phenomenological evidence not much is known yet about the role of phase information in neural mechanisms of visual perception and cognition. Here, we are concerned with analysis of the role of spatial phase in computational and biological vision, emergence of visual illusions and pattern recognition. We hypothesize that fundamental importance of phase information for invariant retrieval of structural image features and motion detection promoted development of phase-based mechanisms of neural image processing in course of evolution of biological vision. Using an extension of Fourier phase correlation technique, we show that the core functions of visual system such as motion detection and pattern recognition can be facilitated by the same basic mechanism. Our analysis suggests that emergence of visual illusions can be attributed to presence of coherently phase-shifted repetitive patterns as well as the effects of acuity compensation by saccadic eye movements. We speculate that biological vision relies on perceptual mechanisms effectively similar to phase correlation, and predict neural features of visual pattern (dis)similarity that can be used for experimental validation of our hypothesis of “cognition by phase correlation.” PMID:25954190

Synchrotron Radiation Circular Dichroism (SRCD) Spectroscopy - An Enhanced Method for Examining Protein Conformations and Protein Interactions

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

B Wallace; R Janes

CD (circular dichroism) spectroscopy is a well-established technique in structural biology. SRCD (synchrotron radiation circular dichroism) spectroscopy extends the utility and applications of conventional CD spectroscopy (using laboratory-based instruments) because the high flux of a synchrotron enables collection of data at lower wavelengths (resulting in higher information content), detection of spectra with higher signal-to-noise levels and measurements in the presence of absorbing components (buffers, salts, lipids and detergents). SRCD spectroscopy can provide important static and dynamic structural information on proteins in solution, including secondary structures of intact proteins and their domains, protein stability, the differences between wild-type and mutant proteins,more » the identification of natively disordered regions in proteins, and the dynamic processes of protein folding and membrane insertion and the kinetics of enzyme reactions. It has also been used to effectively study protein interactions, including protein-protein complex formation involving either induced-fit or rigid-body mechanisms, and protein-lipid complexes. A new web-based bioinformatics resource, the Protein Circular Dichroism Data Bank (PCDDB), has been created which enables archiving, access and analyses of CD and SRCD spectra and supporting metadata, now making this information publicly available. To summarize, the developing method of SRCD spectroscopy has the potential for playing an important role in new types of studies of protein conformations and their complexes.« less

On the role of spatial phase and phase correlation in vision, illusion, and cognition.

PubMed

Gladilin, Evgeny; Eils, Roland

2015-01-01

Numerous findings indicate that spatial phase bears an important cognitive information. Distortion of phase affects topology of edge structures and makes images unrecognizable. In turn, appropriately phase-structured patterns give rise to various illusions of virtual image content and apparent motion. Despite a large body of phenomenological evidence not much is known yet about the role of phase information in neural mechanisms of visual perception and cognition. Here, we are concerned with analysis of the role of spatial phase in computational and biological vision, emergence of visual illusions and pattern recognition. We hypothesize that fundamental importance of phase information for invariant retrieval of structural image features and motion detection promoted development of phase-based mechanisms of neural image processing in course of evolution of biological vision. Using an extension of Fourier phase correlation technique, we show that the core functions of visual system such as motion detection and pattern recognition can be facilitated by the same basic mechanism. Our analysis suggests that emergence of visual illusions can be attributed to presence of coherently phase-shifted repetitive patterns as well as the effects of acuity compensation by saccadic eye movements. We speculate that biological vision relies on perceptual mechanisms effectively similar to phase correlation, and predict neural features of visual pattern (dis)similarity that can be used for experimental validation of our hypothesis of "cognition by phase correlation."

Use of New Commercial, Off-the-Shelf, High-Definition Structure Scanning Fathometer/Depth Finder For Coastal Current Survey Operations

NASA Astrophysics Data System (ADS)

Roggenstein, E. B.; Gray, G.

2013-12-01

The National Oceanic and Atmospheric Administration (NOAA) National Ocean Service (NOS) Center for Operational Oceanographic Products and Services (COOPS) manages three national observing system programs. These are the National Water level Observation Network (NWLON) (210 stations), the 23 NOAA/Physical Oceanographic Real-Time Systems (PORTS), and National Currents Observing Program (NCOP) (approximately 70 deployments/year). In support of its mission COOPS operates and maintains a number of small boats. During vessel operations, side-scan sonar data are at times needed to provide information about bottom structure for future work in the area. For example, potential hazards, obstructions, or bottom morphology features that have not been identified on localized charts for a given area could be used to inform decisions on planned installations. Side-scan sonar capability is also important when attempting to reacquire bottom mounts that fail to surface at the conclusion of a current meter survey. Structure mapping and side-scan capabilities have been added to recent consumer-level, commercial, off-the-shelf fathometers, generally intended for recreational, commercial fishing, and diving applications. We are proposing to investigate these systems' viability for meeting survey requirements. We assess their ability to provide a flexible alternative to research/commercial oceanographic level side-scan system at a significant cost savings. Such systems could provide important information to support scientific missions that require qualitative seafloor imagery.

[Osteosarcoma: reliability and quality of the information in the internet].

PubMed

Schippinger, Michael; Ruckenstuhl, Paul; Friesenbichler, Jörg; Leithner, Andreas

2014-09-01

The World Wide Web has grown during the last years to a considerable source of medical information for experts as well as for laymen and patients. The quality of this information is subjected to some limitation linked with the structure of the Internet and the management of Internet pages. The cross- sectional study presented evaluates and compares quality and reliability of information with respect of osteosarcoma in the most common German-language Internet pages for medical information. As both, one of the most common primary malignant bone tumors and its peak of incidence at the age of childhood and youth, osteosarcoma is considered of significant importance in orthopedic oncology.

Information systems - Issues in global habitability

NASA Technical Reports Server (NTRS)

Norman, S. D.; Brass, J. A.; Jones, H.; Morse, D. R.

1984-01-01

The present investigation is concerned with fundamental issues, related to information considerations, which arise in an interdisciplinary approach to questions of global habitability. Information system problems and issues are illustrated with the aid of an example involving biochemical cycling and biochemical productivity. The estimation of net primary production (NPP) as an important consideration in the overall global habitability issue is discussed. The NPP model requires three types of data, related to meteorological information, a land surface inventory, and the vegetation structure. Approaches for obtaining and processing these data are discussed. Attention is given to user requirements, information system requirements, workstations, network communications, hardware/software access, and data management.

Remote Sensing of plant functional types: Relative importance of biochemical and structural plant traits

NASA Astrophysics Data System (ADS)

Kattenborn, Teja; Schmidtlein, Sebastian

2017-04-01

Monitoring ecosystems is a key priority in order to understand vegetation patterns, underlying resource cycles and changes their off. Driven by biotic and abiotic factors, plant species within an ecosystem are likely to share similar structural, physiological or phenological traits and can therefore be grouped into plant functional types (PFT). It can be assumed that plants which share similar traits also share similar optical characteristics. Therefore optical remote sensing was identified as a valuable tool for differentiating PFT. Although several authors list structural and biochemical plant traits which are important for differentiating PFT using hyperspectral remote sensing, there is no quantitative or qualitative information on the relative importance of these traits. Thus, little is known about the explicit role of plant traits for an optical discrimination of PFT. One of the main reasons for this is that various optical traits affect the same wavelength regions and it is therefore difficult to isolate the discriminative power of a single trait. A way to determine the effect of single plant traits on the optical reflectance of plant canopies is given by radiative transfer models. The most established radiative transfer model is PROSAIL, which incorporates biochemical and structural plant traits, such as pigment contents or leaf area index. In the present study 25 grassland species of different PFT were cultivated and traits relevant for PROSAIL were measured for the entire vegetation season of 2016. The information content of each trait for differentiating PFTs was determined by applying a Multi-response Permutation Procedure on the actual traits, as well as on simulated canopy spectra derived from PROSAIL. According to our results some traits, especially biochemical traits, show a weaker separability of PFT on a spectral level than compared to the actual trait measurements. Overall structural traits (leaf angle and leaf area index) are more important for differentiating PFT than biochemical traits.

The Structural Basis of Cryptosporidium-Specific IMP Dehydrogenase Inhibitor Selectivity

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

MacPherson, Iain S.; Kirubakaran, Sivapriya; Gorla, Suresh Kumar

2010-03-29

Cryptosporidium parvum is a potential biowarfare agent, an important AIDS pathogen, and a major cause of diarrhea and malnutrition. No vaccines or effective drug treatment exist to combat Cryptosporidium infection. This parasite relies on inosine 5{prime}-monophosphate dehydrogenase (IMPDH) to obtain guanine nucleotides, and inhibition of this enzyme blocks parasite proliferation. Here, we report the first crystal structures of CpIMPDH. These structures reveal the structural basis of inhibitor selectivity and suggest a strategy for further optimization. Using this information, we have synthesized low-nanomolar inhibitors that display 10{sup 3} selectivity for the parasite enzyme over human IMPDH2.

Structure-function insights of membrane and soluble proteins revealed by electron crystallography.

PubMed

Dreaden, Tina M; Devarajan, Bharanidharan; Barry, Bridgette A; Schmidt-Krey, Ingeborg

2013-01-01

Electron crystallography is emerging as an important method in solving protein structures. While it has found extensive applications in the understanding of membrane protein structure and function at a wide range of resolutions, from revealing oligomeric arrangements to atomic models, electron crystallography has also provided invaluable information on the soluble α/β-tubulin which could not be obtained by any other method to date. Examples of critical insights from selected structures of membrane proteins as well as α/β-tubulin are described here, demonstrating the vast potential of electron crystallography that is first beginning to unfold.

Design of Student Information Management Database Application System for Office and Departmental Target Responsibility System

NASA Astrophysics Data System (ADS)

Zhou, Hui

It is the inevitable outcome of higher education reform to carry out office and departmental target responsibility system, in which statistical processing of student's information is an important part of student's performance review. On the basis of the analysis of the student's evaluation, the student information management database application system is designed by using relational database management system software in this paper. In order to implement the function of student information management, the functional requirement, overall structure, data sheets and fields, data sheet Association and software codes are designed in details.

CASTp 3.0: computed atlas of surface topography of proteins.

PubMed

Tian, Wei; Chen, Chang; Lei, Xue; Zhao, Jieling; Liang, Jie

2018-06-01

Geometric and topological properties of protein structures, including surface pockets, interior cavities and cross channels, are of fundamental importance for proteins to carry out their functions. Computed Atlas of Surface Topography of proteins (CASTp) is a web server that provides online services for locating, delineating and measuring these geometric and topological properties of protein structures. It has been widely used since its inception in 2003. In this article, we present the latest version of the web server, CASTp 3.0. CASTp 3.0 continues to provide reliable and comprehensive identifications and quantifications of protein topography. In addition, it now provides: (i) imprints of the negative volumes of pockets, cavities and channels, (ii) topographic features of biological assemblies in the Protein Data Bank, (iii) improved visualization of protein structures and pockets, and (iv) more intuitive structural and annotated information, including information of secondary structure, functional sites, variant sites and other annotations of protein residues. The CASTp 3.0 web server is freely accessible at http://sts.bioe.uic.edu/castp/.

Estimating and Identifying Unspecified Correlation Structure for Longitudinal Data

PubMed Central

Hu, Jianhua; Wang, Peng; Qu, Annie

2014-01-01

Identifying correlation structure is important to achieving estimation efficiency in analyzing longitudinal data, and is also crucial for drawing valid statistical inference for large size clustered data. In this paper, we propose a nonparametric method to estimate the correlation structure, which is applicable for discrete longitudinal data. We utilize eigenvector-based basis matrices to approximate the inverse of the empirical correlation matrix and determine the number of basis matrices via model selection. A penalized objective function based on the difference between the empirical and model approximation of the correlation matrices is adopted to select an informative structure for the correlation matrix. The eigenvector representation of the correlation estimation is capable of reducing the risk of model misspecification, and also provides useful information on the specific within-cluster correlation pattern of the data. We show that the proposed method possesses the oracle property and selects the true correlation structure consistently. The proposed method is illustrated through simulations and two data examples on air pollution and sonar signal studies. PMID:26361433

Worldwide Protein Data Bank validation information: usage and trends.

PubMed

Smart, Oliver S; Horský, Vladimír; Gore, Swanand; Svobodová Vařeková, Radka; Bendová, Veronika; Kleywegt, Gerard J; Velankar, Sameer

2018-03-01

Realising the importance of assessing the quality of the biomolecular structures deposited in the Protein Data Bank (PDB), the Worldwide Protein Data Bank (wwPDB) partners established Validation Task Forces to obtain advice on the methods and standards to be used to validate structures determined by X-ray crystallography, nuclear magnetic resonance spectroscopy and three-dimensional electron cryo-microscopy. The resulting wwPDB validation pipeline is an integral part of the wwPDB OneDep deposition, biocuration and validation system. The wwPDB Validation Service webserver (https://validate.wwpdb.org) can be used to perform checks prior to deposition. Here, it is shown how validation metrics can be combined to produce an overall score that allows the ranking of macromolecular structures and domains in search results. The ValTrends DB database provides users with a convenient way to access and analyse validation information and other properties of X-ray crystal structures in the PDB, including investigating trends in and correlations between different structure properties and validation metrics.

Worldwide Protein Data Bank validation information: usage and trends

PubMed Central

Horský, Vladimír; Gore, Swanand; Svobodová Vařeková, Radka; Bendová, Veronika

2018-01-01

Realising the importance of assessing the quality of the biomolecular structures deposited in the Protein Data Bank (PDB), the Worldwide Protein Data Bank (wwPDB) partners established Validation Task Forces to obtain advice on the methods and standards to be used to validate structures determined by X-ray crystallography, nuclear magnetic resonance spectroscopy and three-dimensional electron cryo-microscopy. The resulting wwPDB validation pipeline is an integral part of the wwPDB OneDep deposition, biocuration and validation system. The wwPDB Validation Service webserver (https://validate.wwpdb.org) can be used to perform checks prior to deposition. Here, it is shown how validation metrics can be combined to produce an overall score that allows the ranking of macromolecular structures and domains in search results. The ValTrendsDB database provides users with a convenient way to access and analyse validation information and other properties of X-ray crystal structures in the PDB, including investigating trends in and correlations between different structure properties and validation metrics. PMID:29533231

Can thematic roles leave traces of their places?

PubMed

Chang, Franklin; Bock, Kathryn; Goldberg, Adele E

2003-11-01

An important question in the study of language production is the nature of the semantic information that speakers use to create syntactic structures. A common answer to this question assumes that thematic roles help to mediate the mapping from messages to syntax. However, research using structural priming has suggested that the construction of syntactic frames may be insensitive to variations in thematic roles within messages (Cognition 35 (1990) 1; Psychological Review 99 (1992) 150). Because these studies involved structural alternations whose syntax covaries with the order of thematic roles, it is difficult to assess any independent contribution that role information may make to the positioning of phrases. In this study, we primed the order of the roles without changing the syntactic structure of the sentences produced, and found that the order of the roles was influenced by the priming manipulation. This implies that thematic roles or the features that differentiate them are active within the mapping between messages and sentence structures.

Optimal physiological structure of small neurons to guarantee stable information processing

NASA Astrophysics Data System (ADS)

Zeng, S. Y.; Zhang, Z. Z.; Wei, D. Q.; Luo, X. S.; Tang, W. Y.; Zeng, S. W.; Wang, R. F.

2013-02-01

Spike is the basic element for neuronal information processing and the spontaneous spiking frequency should be less than 1 Hz for stable information processing. If the neuronal membrane area is small, the frequency of neuronal spontaneous spiking caused by ion channel noise may be high. Therefore, it is important to suppress the deleterious spontaneous spiking of the small neurons. We find by simulation of stochastic neurons with Hodgkin-Huxley-type channels that the leakage system is critical and extremely efficient to suppress the spontaneous spiking and guarantee stable information processing of the small neurons. However, within the physiological limit the potassium system cannot do so. The suppression effect of the leakage system is super-exponential, but that of the potassium system is quasi-linear. With the minor physiological cost and the minimal consumption of metabolic energy, a slightly lower reversal potential and a relatively larger conductance of the leakage system give the optimal physiological structure to suppress the deleterious spontaneous spiking and guarantee stable information processing of small neurons, dendrites and axons.

Structuring Broadcast Audio for Information Access

NASA Astrophysics Data System (ADS)

Gauvain, Jean-Luc; Lamel, Lori

2003-12-01

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

Genome scale enzyme–metabolite and drug–target interaction predictions using the signature molecular descriptor

DOE PAGES

Faulon, Jean-Loup; Misra, Milind; Martin, Shawn; ...

2007-11-23

Motivation: Identifying protein enzymatic or pharmacological activities are important areas of research in biology and chemistry. Biological and chemical databases are increasingly being populated with linkages between protein sequences and chemical structures. Additionally, there is now sufficient information to apply machine-learning techniques to predict interactions between chemicals and proteins at a genome scale. Current machine-learning techniques use as input either protein sequences and structures or chemical information. We propose here a method to infer protein–chemical interactions using heterogeneous input consisting of both protein sequence and chemical information. Results: Our method relies on expressing proteins and chemicals with a common cheminformaticsmore » representation. We demonstrate our approach by predicting whether proteins can catalyze reactions not present in training sets. We also predict whether a given drug can bind a target, in the absence of prior binding information for that drug and target. Lastly, such predictions cannot be made with current machine-learning techniques requiring binding information for individual reactions or individual targets.« less

If you watch it move, you'll recognize it in 3D: Transfer of depth cues between encoding and retrieval.

PubMed

Papenmeier, Frank; Schwan, Stephan

2016-02-01

Viewing objects with stereoscopic displays provides additional depth cues through binocular disparity supporting object recognition. So far, it was unknown whether this results from the representation of specific stereoscopic information in memory or a more general representation of an object's depth structure. Therefore, we investigated whether continuous object rotation acting as depth cue during encoding results in a memory representation that can subsequently be accessed by stereoscopic information during retrieval. In Experiment 1, we found such transfer effects from continuous object rotation during encoding to stereoscopic presentations during retrieval. In Experiments 2a and 2b, we found that the continuity of object rotation is important because only continuous rotation and/or stereoscopic depth but not multiple static snapshots presented without stereoscopic information caused the extraction of an object's depth structure into memory. We conclude that an object's depth structure and not specific depth cues are represented in memory. Copyright © 2015 Elsevier B.V. All rights reserved.

A novel optical system design of light field camera

NASA Astrophysics Data System (ADS)

Wang, Ye; Li, Wenhua; Hao, Chenyang

2016-01-01

The structure of main lens - Micro Lens Array (MLA) - imaging sensor is usually adopted in optical system of light field camera, and the MLA is the most important part in the optical system, which has the function of collecting and recording the amplitude and phase information of the field light. In this paper, a novel optical system structure is proposed. The novel optical system is based on the 4f optical structure, and the micro-aperture array (MAA) is used to instead of the MLA for realizing the information acquisition of the 4D light field. We analyze the principle that the novel optical system could realize the information acquisition of the light field. At the same time, a simple MAA, line grating optical system, is designed by ZEMAX software in this paper. The novel optical system is simulated by a line grating optical system, and multiple images are obtained in the image plane. The imaging quality of the novel optical system is analyzed.

Protein complex prediction in large ontology attributed protein-protein interaction networks.

PubMed

Zhang, Yijia; Lin, Hongfei; Yang, Zhihao; Wang, Jian; Li, Yanpeng; Xu, Bo

2013-01-01

Protein complexes are important for unraveling the secrets of cellular organization and function. Many computational approaches have been developed to predict protein complexes in protein-protein interaction (PPI) networks. However, most existing approaches focus mainly on the topological structure of PPI networks, and largely ignore the gene ontology (GO) annotation information. In this paper, we constructed ontology attributed PPI networks with PPI data and GO resource. After constructing ontology attributed networks, we proposed a novel approach called CSO (clustering based on network structure and ontology attribute similarity). Structural information and GO attribute information are complementary in ontology attributed networks. CSO can effectively take advantage of the correlation between frequent GO annotation sets and the dense subgraph for protein complex prediction. Our proposed CSO approach was applied to four different yeast PPI data sets and predicted many well-known protein complexes. The experimental results showed that CSO was valuable in predicting protein complexes and achieved state-of-the-art performance.

Driving with roadmaps and dashboards: using information resources to structure the decision models in service organizations.

PubMed

Chorpita, Bruce F; Bernstein, Adam; Daleiden, Eric L

2008-03-01

This paper illustrates the application of design principles for tools that structure clinical decision-making. If the effort to implement evidence-based practices in community services organizations is to be effective, attention must be paid to the decision-making context in which such treatments are delivered. Clinical research trials commonly occur in an environment characterized by structured decision making and expert supports. Technology has great potential to serve mental health organizations by supporting these potentially important contextual features of the research environment, through organization and reporting of clinical data into interpretable information to support decisions and anchor decision-making procedures. This article describes one example of a behavioral health reporting system designed to facilitate clinical and administrative use of evidence-based practices. The design processes underlying this system-mapping of decision points and distillation of performance information at the individual, caseload, and organizational levels-can be implemented to support clinical practice in a wide variety of settings.

NMR Spectroscopy in Glass Science: A Review of the Elements

PubMed Central

2018-01-01

The study of inorganic glass structure is critically important for basic glass science and especially the commercial development of glasses for a variety of technological uses. One of the best means by which to achieve this understanding is through application of solid-state nuclear magnetic resonance (NMR) spectroscopy, which has a long and interesting history. This technique is element specific, but highly complex, and thus, one of the many inquiries made by non-NMR specialists working in glass science is what type of information and which elements can be studied by this method. This review presents a summary of the different elements that are amenable to the study of glasses by NMR spectroscopy and provides examples of the type of atomic level structural information that can be achieved. It serves to inform the non-specialist working in glass science and technology about some of the benefits and challenges involved in the study of inorganic glass structure using modern, readily-available NMR methods. PMID:29565328

A hierarchical structure for representing and learning fuzzy rules

NASA Technical Reports Server (NTRS)

Yager, Ronald R.

1993-01-01

Yager provides an example in which the flat representation of fuzzy if-then rules leads to unsatisfactory results. Consider a rule base consisting to two rules: if U is 12 the V is 29; if U is (10-15) the V is (25-30). If U = 12 we would get V is G where G = (25-30). The application of the defuzzification process leads to a selection of V = 27.5. Thus we see that the very specific instruction was not followed. The problem with the technique used is that the most specific information was swamped by the less specific information. In this paper we shall provide for a new structure for the representation of fuzzy if-then rules. The representational form introduced here is called a Hierarchical Prioritized Structure (HPS) representation. Most importantly in addition to overcoming the problem illustrated in the previous example this HPS representation has an inherent capability to emulate the learning of general rules and provides a reasonable accurate cognitive mapping of how human beings store information.

Organisational capacity and chronic disease care: an Australian general practice perspective.

PubMed

Proudfoot, Judith; Infante, Fernando; Holton, Christine; Powell-Davies, Gawaine; Bubner, Tanya; Beilby, Justin; Harris, Mark

2007-04-01

Although we are rapidly improving our understanding of how to manage patients with chronic illness in Australian general practice, many patients are still receiving suboptimal care. General practices have limited organisational capacity to provide the structured care that is required for managing chronic conditions: regular monitoring, decision support, patient recall, supporting patient self management, team work, and information management. This requires a shift away from episodic, acute models. Overseas research has shown that areas such as team work, clinical information systems, decision support, linkages and leadership are also important in managing chronic illness, but we do not know which of these are most important in Australia.

Distributed digital signal processors for multi-body flexible structures

NASA Technical Reports Server (NTRS)

Lee, Gordon K. F.

1992-01-01

Multi-body flexible structures, such as those currently under investigation in spacecraft design, are large scale (high-order) dimensional systems. Controlling and filtering such structures is a computationally complex problem. This is particularly important when many sensors and actuators are located along the structure and need to be processed in real time. This report summarizes research activity focused on solving the signal processing (that is, information processing) issues of multi-body structures. A distributed architecture is developed in which single loop processors are employed for local filtering and control. By implementing such a philosophy with an embedded controller configuration, a supervising controller may be used to process global data and make global decisions as the local devices are processing local information. A hardware testbed, a position controller system for a servo motor, is employed to illustrate the capabilities of the embedded controller structure. Several filtering and control structures which can be modeled as rational functions can be implemented on the system developed in this research effort. Thus the results of the study provide a support tool for many Control/Structure Interaction (CSI) NASA testbeds such as the Evolutionary model and the nine-bay truss structure.

Consume, Modify, Share (CMS): The Interplay between Individual Decisions and Structural Network Properties in the Diffusion of Information

PubMed Central

Koren, Hila; Kaminer, Ido

2016-01-01

Widely used information diffusion models such as Independent Cascade Model, Susceptible Infected Recovered (SIR) and others fail to acknowledge that information is constantly subject to modification. Some aspects of information diffusion are best explained by network structural characteristics while in some cases strong influence comes from individual decisions. We introduce reinvention, the ability to modify information, as an individual level decision that affects the diffusion process as a whole. Based on a combination of constructs from the Diffusion of Innovations and the Critical Mass Theories, the present study advances the CMS (consume, modify, share) model which accounts for the interplay between network structure and human behavior and interactions. The model's building blocks include processes leading up to and following the formation of a critical mass of information adopters and disseminators. We examine the formation of an inflection point, information reach, sustainability of the diffusion process and collective value creation. The CMS model is tested on two directed networks and one undirected network, assuming weak or strong ties and applying constant and relative modification schemes. While all three networks are designed for disseminating new knowledge they differ in structural properties. Our findings suggest that modification enhances the diffusion of information in networks that support undirected connections and carries the biggest effect when information is shared via weak ties. Rogers' diffusion model and traditional information contagion models are fine tuned. Our results show that modifications not only contribute to a sustainable diffusion process, but also aid information in reaching remote areas of the network. The results point to the importance of cultivating weak ties, allowing reciprocal interaction among nodes and supporting the modification of information in promoting diffusion processes. These results have theoretical and practical implications for designing networks aimed at accelerating the creation and diffusion of information. PMID:27798636

Consume, Modify, Share (CMS): The Interplay between Individual Decisions and Structural Network Properties in the Diffusion of Information.

PubMed

Koren, Hila; Kaminer, Ido; Raban, Daphne Ruth

2016-01-01

Widely used information diffusion models such as Independent Cascade Model, Susceptible Infected Recovered (SIR) and others fail to acknowledge that information is constantly subject to modification. Some aspects of information diffusion are best explained by network structural characteristics while in some cases strong influence comes from individual decisions. We introduce reinvention, the ability to modify information, as an individual level decision that affects the diffusion process as a whole. Based on a combination of constructs from the Diffusion of Innovations and the Critical Mass Theories, the present study advances the CMS (consume, modify, share) model which accounts for the interplay between network structure and human behavior and interactions. The model's building blocks include processes leading up to and following the formation of a critical mass of information adopters and disseminators. We examine the formation of an inflection point, information reach, sustainability of the diffusion process and collective value creation. The CMS model is tested on two directed networks and one undirected network, assuming weak or strong ties and applying constant and relative modification schemes. While all three networks are designed for disseminating new knowledge they differ in structural properties. Our findings suggest that modification enhances the diffusion of information in networks that support undirected connections and carries the biggest effect when information is shared via weak ties. Rogers' diffusion model and traditional information contagion models are fine tuned. Our results show that modifications not only contribute to a sustainable diffusion process, but also aid information in reaching remote areas of the network. The results point to the importance of cultivating weak ties, allowing reciprocal interaction among nodes and supporting the modification of information in promoting diffusion processes. These results have theoretical and practical implications for designing networks aimed at accelerating the creation and diffusion of information.

Structural characterization/correlation of calorimetric properties of coal fluids: Final report, September 1, 1985--August 31, 1988

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

Starling, K.E.; Mallinson, R.G.; Li, M.H.

The objective of this research is to examine the relationship between the calorimetric properties of coal fluids and their molecular functional group composition. Coal fluid samples which have had their calorimetric properties measured are characterized using proton NMR, IR, and elemental analysis. These characterizations are then used in a chemical structural model to determine the composition of the coal fluid in terms of the important molecular functional groups. These functional groups are particularly important in determining the intramolecular based properties of a fluid, such as ideal gas heat capacities. Correlational frameworks for ideal gas heat capacities are then examined withinmore » an existing equation of state methodology to determine an optimal correlation. The optimal correlation for obtaining the characterization/chemical structure information and the sensitivity of the correlation to the characterization and structural model is examined. 8 refs.« less

Structural characterization/correlation of calorimetric properties of coal fluids: Second annual report, September 1, 1986-August 31, 1987

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

Starling, K.E.; Mallinson, R.G.; Li, M.H.

The objective of this research is to examine the relationship between the calorimetric properties of coal fluids and their molecular functional group composition. Coal fluid samples which have had their calorimetric properties measured are characterized using proton NMR, ir, and elemental analysis. These characterizations are then used in a chemical structural model to determine the composition of the coal fluid in terms of the important molecular functional groups. These functional groups are particularly important in determining the intramolecular based properties of a fluid, such as ideal gas heat capacities. Correlational frameworks for ideal gas heat capacities are then examined withinmore » an existing equation of state methodology to determine an optimal correlation. The optimal correlation for obtaining the characterization/chemical structure information and the sensitivity of the correlation to the characterization and structural model is examined.« less

Structural characterization/correlation of calorimetric properties of coal fluids. First annual report, September 1, 1985-August 31, 1986

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

Starling, K.E.; Mallinson, R.G.; Li, M.H.

The objective of this research is to examine the relationship between the calorimetric properties of coal liquids and their molecular functional group composition. Coal liquid samples which have had their calorimetric properties measured are characterized using proton NMR, ir and elemental analysis. These characterizations are then used in a chemical structural model to determine the composition of the coal liquid in terms of the important molecular functional groups. These functional groups are particularly important in determining the intramolecular based properties of a fluid, such as ideal gas heat capacities. Correlational frameworks for heat capacities will then be examined within anmore » existing equation of state methodology to determine an optimal correlation. Also, the optimal recipe for obtaining the characterization/chemical structure information and the sensitivity of the correlation to the characterization and structural model will be examined and determined. 7 refs.« less

Langley's CSI evolutionary model: Phase 2

NASA Technical Reports Server (NTRS)

Horta, Lucas G.; Reaves, Mercedes C.; Elliott, Kenny B.; Belvin, W. Keith; Teter, John E.

1995-01-01

Phase 2 testbed is part of a sequence of laboratory models, developed at NASA Langley Research Center, to enhance our understanding on how to model, control, and design structures for space applications. A key problem with structures that must perform in space is the appearance of unwanted vibrations during operations. Instruments, design independently by different scientists, must share the same vehicle causing them to interact with each other. Once in space, these problems are difficult to correct and therefore, prediction via analysis design, and experiments is very important. Phase 2 laboratory model and its predecessors are designed to fill a gap between theory and practice and to aid in understanding important aspects in modeling, sensor and actuator technology, ground testing techniques, and control design issues. This document provides detailed information on the truss structure and its main components, control computer architecture, and structural models generated along with corresponding experimental results.

A computational prediction of structure and function of novel homologue of Arabidopsis thaliana Vps51/Vps67 subunit in Corchorus olitorius.

PubMed

Zaman, Aubhishek; Fancy, Nurun Nahar

2012-12-01

Vps mediated vesicular transport is important for transferring macromolecules trapped inside a vesicle. Although highly abundant, Vps shows tremendous sequence variation among diverse array of species. However, this difference in sequence, which seems to also translate into substantial functional variation, is hardly characterized in Corchorus spp. Here, our computational study investigates structural and functional features of one of the Vps subunit namely Vps51/Vps67 in C. olitorius. Broad scale structural characterization revealed novel information about the overall Vps structure and binding sites. Moreover, functional analyses indicate interaction partners which were unexplored to date. Since membrane trafficking is essentially associated with nutrient uptake and chemical de-toxification, characterization of the Vps subunit can well provide us with better insight into important agronomic traits such as stress response, immune response and phytoremediation capacity.

Revisiting place and temporal theories of pitch

PubMed Central

2014-01-01

The nature of pitch and its neural coding have been studied for over a century. A popular debate has revolved around the question of whether pitch is coded via “place” cues in the cochlea, or via timing cues in the auditory nerve. In the most recent incarnation of this debate, the role of temporal fine structure has been emphasized in conveying important pitch and speech information, particularly because the lack of temporal fine structure coding in cochlear implants might explain some of the difficulties faced by cochlear implant users in perceiving music and pitch contours in speech. In addition, some studies have postulated that hearing-impaired listeners may have a specific deficit related to processing temporal fine structure. This article reviews some of the recent literature surrounding the debate, and argues that much of the recent evidence suggesting the importance of temporal fine structure processing can also be accounted for using spectral (place) or temporal-envelope cues. PMID:25364292

Active vision and image/video understanding with decision structures based on the network-symbolic models

NASA Astrophysics Data System (ADS)

Kuvich, Gary

2003-08-01

Vision is a part of a larger information system that converts visual information into knowledge structures. These structures drive vision process, resolve ambiguity and uncertainty via feedback projections, and provide image understanding that is an interpretation of visual information in terms of such knowledge models. The ability of human brain to emulate knowledge structures in the form of networks-symbolic models is found. And that means an important shift of paradigm in our knowledge about brain from neural networks to "cortical software". Symbols, predicates and grammars naturally emerge in such active multilevel hierarchical networks, and logic is simply a way of restructuring such models. Brain analyzes an image as a graph-type decision structure created via multilevel hierarchical compression of visual information. Mid-level vision processes like clustering, perceptual grouping, separation of figure from ground, are special kinds of graph/network transformations. They convert low-level image structure into the set of more abstract ones, which represent objects and visual scene, making them easy for analysis by higher-level knowledge structures. Higher-level vision phenomena are results of such analysis. Composition of network-symbolic models works similar to frames and agents, combines learning, classification, analogy together with higher-level model-based reasoning into a single framework. Such models do not require supercomputers. Based on such principles, and using methods of Computational intelligence, an Image Understanding system can convert images into the network-symbolic knowledge models, and effectively resolve uncertainty and ambiguity, providing unifying representation for perception and cognition. That allows creating new intelligent computer vision systems for robotic and defense industries.

CLINICALLY RELEVANT IGE-CROSS-REACTIVITY OF NUT ALLERGENS

EPA Science Inventory

All data resulting from this study will be catalogued in SDAP .This work will generate important information relating the structure/ physicochemical properties of cross-reactive IgE epitopes to clinical response, and model factors that underlie allergen recognition by the immu...

Explanation and Categorization: How "Why?" Informs "What?"

ERIC Educational Resources Information Center

Lombrozo, Tania

2009-01-01

Recent theoretical and empirical work suggests that explanation and categorization are intimately related. This paper explores the hypothesis that explanations can help structure conceptual representations, and thereby influence the relative importance of features in categorization decisions. In particular, features may be differentially important…

An improved spatial contour tree constructed method

NASA Astrophysics Data System (ADS)

Zheng, Yi; Zhang, Ling; Guilbert, Eric; Long, Yi

2018-05-01

Contours are important data to delineate the landform on a map. A contour tree provides an object-oriented description of landforms and can be used to enrich the topological information. The traditional contour tree is used to store topological relationships between contours in a hierarchical structure and allows for the identification of eminences and depressions as sets of nested contours. This research proposes an improved contour tree so-called spatial contour tree that contains not only the topological but also the geometric information. It can be regarded as a terrain skeleton in 3-dimention, and it is established based on the spatial nodes of contours which have the latitude, longitude and elevation information. The spatial contour tree is built by connecting spatial nodes from low to high elevation for a positive landform, and from high to low elevation for a negative landform to form a hierarchical structure. The connection between two spatial nodes can provide the real distance and direction as a Euclidean vector in 3-dimention. In this paper, the construction method is tested in the experiment, and the results are discussed. The proposed hierarchical structure is in 3-demintion and can show the skeleton inside a terrain. The structure, where all nodes have geo-information, can be used to distinguish different landforms and applied for contour generalization with consideration of geographic characteristics.

Consumers' Preferences for Electronic Nicotine Delivery System Product Features: A Structured Content Analysis.

PubMed

Kistler, Christine E; Crutchfield, Trisha M; Sutfin, Erin L; Ranney, Leah M; Berman, Micah L; Zarkin, Gary A; Goldstein, Adam O

2017-06-07

To inform potential governmental regulations, we aimed to develop a list of electronic nicotine delivery system (ENDS) product features important to U.S. consumers by age and gender. We employed qualitative data methods. Participants were eligible if they had used an ENDS at least once. Groups were selected by age and gender (young adult group aged 18-25, n = 11; middle-age group aged 26-64, n = 9; and women's group aged 26-64, n = 9). We conducted five individual older adult interviews (aged 68-80). Participants discussed important ENDS features. We conducted a structured content analysis of the group and interview responses. Of 34 participants, 68% were white and 56% were female. Participants mentioned 12 important ENDS features, including: (1) user experience; (2) social acceptability; (3) cost; (4) health risks/benefits; (5) ease of use; (6) flavors; (7) smoking cessation aid; (8) nicotine content; (9) modifiability; (10) ENDS regulation; (11) bridge between tobacco cigarettes; (12) collectability. The most frequently mentioned ENDS feature was modifiability for young adults, user experience for middle-age and older adults, and flavor for the women's group. This study identified multiple features important to ENDS consumers. Groups differed in how they viewed various features by age and gender. These results can inform ongoing regulatory efforts.

Consumers’ Preferences for Electronic Nicotine Delivery System Product Features: A Structured Content Analysis

PubMed Central

Kistler, Christine E.; Crutchfield, Trisha M.; Sutfin, Erin L.; Ranney, Leah M.; Berman, Micah L.; Zarkin, Gary A.; Goldstein, Adam O.

2017-01-01

To inform potential governmental regulations, we aimed to develop a list of electronic nicotine delivery system (ENDS) product features important to U.S. consumers by age and gender. We employed qualitative data methods. Participants were eligible if they had used an ENDS at least once. Groups were selected by age and gender (young adult group aged 18–25, n = 11; middle-age group aged 26–64, n = 9; and women’s group aged 26–64, n = 9). We conducted five individual older adult interviews (aged 68–80). Participants discussed important ENDS features. We conducted a structured content analysis of the group and interview responses. Of 34 participants, 68% were white and 56% were female. Participants mentioned 12 important ENDS features, including: (1) user experience; (2) social acceptability; (3) cost; (4) health risks/benefits; (5) ease of use; (6) flavors; (7) smoking cessation aid; (8) nicotine content; (9) modifiability; (10) ENDS regulation; (11) bridge between tobacco cigarettes; (12) collectability. The most frequently mentioned ENDS feature was modifiability for young adults, user experience for middle-age and older adults, and flavor for the women’s group. This study identified multiple features important to ENDS consumers. Groups differed in how they viewed various features by age and gender. These results can inform ongoing regulatory efforts. PMID:28590444

Genetic diversity and population structure of bocachico Prochilodus magdalenae (Pisces, Prochilodontidae) in the Magdalena River basin and its tributaries, Colombia

PubMed Central

Berdugo, Gilberto Orozco; Narváez Barandica, Juan C.

2014-01-01

Prochilodus magdalenae is an endemic freshwater fish that occurs in the Magdalena, Sinú and Atrato hydrographic basins. It has an important economic role and is a food resource for the artisanal fishing communities. Its socioeconomic importance contrasts with the current status of its fisheries, where stocks are being depleted. Considering its importance and lack of information on its genetic structure, we used seven microsatellite markers to assess the genetic structure of wild populations of P. magdalenae. The genetic diversity was assessed and the population genetic structure was estimated through Fst, analysis of molecular variance and Bayesian analysis. A total of 290 alleles were found in all loci throughout all population. The high polymorphism contrasts with the levels of observed heterozygosity (Ho = 0.276), which are the lowest values recorded for the family. We found three populations of bocachico coexisting throughout the studied system, contradicting the hypothesis that freshwater migratory fish form panmictic populations. These results on the genetic structure of P. magdalenae constitute tools for a better understanding of the behavior and biology of this species, contributing to fish management and conservation programs. PMID:24688289

Engaging, Recruiting, and Retaining Black Men Who Have Sex With Men in Research Studies: Don’t Underestimate the Importance of Staffing—Lessons Learned From HPTN 061, the BROTHERS Study

PubMed Central

Magnus, Manya; Franks, Julie; Griffith, Sam; Arnold, Michael P.; Goodman, Krista; Wheeler, Darrell P.

2014-01-01

Context HIV/AIDS in the United States continues to primarily impact men who have sex with men (MSM), with disproportionately high rates among black MSM. Objective The purpose of this study was to identify factors that may influence engagement and retention of black MSM in HIV research. Design and Participants This was a qualitative evaluation of study implementation within a multisite, prospective, observational study (HIV Prevention Trials Network 061, BROTHERS) that enrolled 1553 black MSM in 6 cities throughout the United States. Data collection for this evaluation included a written, structured survey collected from each of the sites describing site characteristics including staff and organizational structure, reviews of site standard operating procedures, and work plans; semistructured key informant interviews were conducted with site coordinators to characterize staffing, site-level factors facilitating or impeding effective community engagement, study recruitment, and retention. Data from completed surveys and site standard operating procedures were collated, and notes from key informant interviews were thematically coded for content by 2 independent reviewers. Results Several key themes emerged from the data, including the importance of inclusion of members of the community being studied as staff, institutional hiring practices that support inclusive staffing, cultivating a supportive working environment for study implementation, and ongoing relationships between research institutions and community. Conclusions This study underscores the importance of staffing in implementing research with black MSM. Investigators should consider how staffing and organizational structures affect implementation during study design and when preparing to initiate study activities. Ongoing monitoring of community engagement can inform and improve methods for engagement and ensure cultural relevance while removing barriers for participation. PMID:24406940

Engaging, recruiting, and retaining black men who have sex with men in research studies: don't underestimate the importance of staffing--lessons learned from HPTN 061, the BROTHERS study.

PubMed

Magnus, Manya; Franks, Julie; Griffith, Sam; Arnold, Michael P; Goodman, Krista; Wheeler, Darrell P

2014-01-01

HIV/AIDS in the United States continues to primarily impact men who have sex with men (MSM), with disproportionately high rates among black MSM. The purpose of this study was to identify factors that may influence engagement and retention of black MSM in HIV research. This was a qualitative evaluation of study implementation within a multisite, prospective, observational study (HIV Prevention Trials Network 061, BROTHERS) that enrolled 1553 black MSM in 6 cities throughout the United States. Data collection for this evaluation included a written, structured survey collected from each of the sites describing site characteristics including staff and organizational structure, reviews of site standard operating procedures, and work plans; semistructured key informant interviews were conducted with site coordinators to characterize staffing, site-level factors facilitating or impeding effective community engagement, study recruitment, and retention. Data from completed surveys and site standard operating procedures were collated, and notes from key informant interviews were thematically coded for content by 2 independent reviewers. Several key themes emerged from the data, including the importance of inclusion of members of the community being studied as staff, institutional hiring practices that support inclusive staffing, cultivating a supportive working environment for study implementation, and ongoing relationships between research institutions and community. This study underscores the importance of staffing in implementing research with black MSM. Investigators should consider how staffing and organizational structures affect implementation during study design and when preparing to initiate study activities. Ongoing monitoring of community engagement can inform and improve methods for engagement and ensure cultural relevance while removing barriers for participation.

A systematization of spectral data on the methanol molecule

NASA Astrophysics Data System (ADS)

Akhlyostin, A. Yu.; Voronina, S. S.; Lavrentiev, N. A.; Privezentsev, A. I.; Rodimova, O. B.; Fazliev, A. Z.

2015-11-01

Problems underlying a systematization of spectral data on the methanol molecule are formulated. Data on the energy levels and vacuum wavenumbers acquired from the published literature are presented in the form of information sources imported into the W@DIS information system. Sets of quantum numbers and labels used to describe the CH3OH molecular states are analyzed. The set of labels is different from universally accepted sets. A system of importing the data sources into W@DIS is outlined. The structure of databases characterizing transitions in an isolated CH3OH molecule is introduced and a digital library of the relevant published literature is discussed. A brief description is given of an imported data quality analysis and representation of the results obtained in the form of ontologies for subsequent computer processing.

Unusual monosaccharides: components of O-antigenic polysaccharides of microorganisms

NASA Astrophysics Data System (ADS)

Kochetkov, Nikolai K.

1996-09-01

The data on new monosaccharides detected in O-antigenic polysaccharides of Gram-negative bacteria have been surveyed. The results of isolation and structure determination of these unusual monosaccharides have been arranged and described systematically. The NMR spectroscopy techniques are shown to be promising for the O-antigenic polysaccharides structure determination. The information about fine structure of monosaccharides which constitute the base of important class of microbial polysaccharides, is of great significance for applied studies, first of all, the design and synthesis of biologically active substances. The bibliography includes 216 references.

Internet: a new concept of antenatal education.

PubMed

Nikolova, Gergana

2015-02-01

Historically antenatal education has been seen as an important part of antenatal care and a mechanism to provide women with close to realistic interpretations of childbirth and motherhood. Through the years, the main themes and emphases of parenting education have changed, sometimes to reflect the new socio-economic structure and sometimes forced by the women themselves seeking specific information and knowledge. Yet again, this time the invasion of online information and social media is about to change the perception and the philosophy of antenatal education from an informative opportunity to a powerful and effective intervention.

RNA structural constraints in the evolution of the influenza A virus genome NP segment

PubMed Central

Gultyaev, Alexander P; Tsyganov-Bodounov, Anton; Spronken, Monique IJ; van der Kooij, Sander; Fouchier, Ron AM; Olsthoorn, René CL

2014-01-01

Conserved RNA secondary structures were predicted in the nucleoprotein (NP) segment of the influenza A virus genome using comparative sequence and structure analysis. A number of structural elements exhibiting nucleotide covariations were identified over the whole segment length, including protein-coding regions. Calculations of mutual information values at the paired nucleotide positions demonstrate that these structures impose considerable constraints on the virus genome evolution. Functional importance of a pseudoknot structure, predicted in the NP packaging signal region, was confirmed by plaque assays of the mutant viruses with disrupted structure and those with restored folding using compensatory substitutions. Possible functions of the conserved RNA folding patterns in the influenza A virus genome are discussed. PMID:25180940

Information seeking by parents of children with physical disabilities: An exploratory qualitative study.

PubMed

Alsem, M W; Ausems, F; Verhoef, M; Jongmans, M J; Meily-Visser, J M A; Ketelaar, M

2017-01-01

Evidence suggests that parents of children with disabilities feel that not all their information needs are being met, but it remains unclear how parents try to fill these information gaps. The aim of this study is to describe how parents of children with physical disabilities search for and evaluate information. Qualitative semi-structured interviews were conducted with 15 parents of children with a disability, aged 1.5-21 years. Data were analysed using thematic analysis. There was much variation in information needs between parents. Parents used different sources, depending on the type of information needed, the most important being healthcare professionals, peers, and websites. Peers played an important role in information provision and were the preferred source of experience-based knowledge and support. The Internet is a widely used medium to search for information and to access various sources. There was a general preference for closed Internet communities for peer contact. Information was commonly evaluated by comparing sources. Parents use different sources for different information needs, and evaluate information by comparing them. Healthcare professionals and parents can support each other in locating and evaluating information including experience-based knowledge. Healthcare professionals should guide parents in their search for information and experience-based knowledge from peers. Copyright © 2016 Elsevier Ltd. All rights reserved.

An improved label propagation algorithm based on node importance and random walk for community detection

NASA Astrophysics Data System (ADS)

Ma, Tianren; Xia, Zhengyou

2017-05-01

Currently, with the rapid development of information technology, the electronic media for social communication is becoming more and more popular. Discovery of communities is a very effective way to understand the properties of complex networks. However, traditional community detection algorithms consider the structural characteristics of a social organization only, with more information about nodes and edges wasted. In the meanwhile, these algorithms do not consider each node on its merits. Label propagation algorithm (LPA) is a near linear time algorithm which aims to find the community in the network. It attracts many scholars owing to its high efficiency. In recent years, there are more improved algorithms that were put forward based on LPA. In this paper, an improved LPA based on random walk and node importance (NILPA) is proposed. Firstly, a list of node importance is obtained through calculation. The nodes in the network are sorted in descending order of importance. On the basis of random walk, a matrix is constructed to measure the similarity of nodes and it avoids the random choice in the LPA. Secondly, a new metric IAS (importance and similarity) is calculated by node importance and similarity matrix, which we can use to avoid the random selection in the original LPA and improve the algorithm stability. Finally, a test in real-world and synthetic networks is given. The result shows that this algorithm has better performance than existing methods in finding community structure.

Smartphone based hemispherical photography for canopy structure measurement

NASA Astrophysics Data System (ADS)

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

2018-01-01

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

Quality assessment of protein model-structures using evolutionary conservation.

PubMed

Kalman, Matan; Ben-Tal, Nir

2010-05-15

Programs that evaluate the quality of a protein structural model are important both for validating the structure determination procedure and for guiding the model-building process. Such programs are based on properties of native structures that are generally not expected for faulty models. One such property, which is rarely used for automatic structure quality assessment, is the tendency for conserved residues to be located at the structural core and for variable residues to be located at the surface. We present ConQuass, a novel quality assessment program based on the consistency between the model structure and the protein's conservation pattern. We show that it can identify problematic structural models, and that the scores it assigns to the server models in CASP8 correlate with the similarity of the models to the native structure. We also show that when the conservation information is reliable, the method's performance is comparable and complementary to that of the other single-structure quality assessment methods that participated in CASP8 and that do not use additional structural information from homologs. A perl implementation of the method, as well as the various perl and R scripts used for the analysis are available at http://bental.tau.ac.il/ConQuass/. nirb@tauex.tau.ac.il Supplementary data are available at Bioinformatics online.

In-Depth View of the Structure and Growth of SnO2 Nanowires and Nanobrushes.

PubMed

Stuckert, Erin P; Geiss, Roy H; Miller, Christopher J; Fisher, Ellen R

2016-08-31

Strategic application of an array of complementary imaging and diffraction techniques is critical to determine accurate structural information on nanomaterials, especially when also seeking to elucidate structure-property relationships and their effects on gas sensors. In this work, SnO2 nanowires and nanobrushes grown via chemical vapor deposition (CVD) displayed the same tetragonal SnO2 structure as revealed via powder X-ray diffraction bulk crystallinity data. Additional characterization using a range of electron microscopy imaging and diffraction techniques, however, revealed important structure and morphology distinctions between the nanomaterials. Tailoring scanning transmission electron microscopy (STEM) modes combined with transmission electron backscatter diffraction (t-EBSD) techniques afforded a more detailed view of the SnO2 nanostructures. Indeed, upon deeper analysis of individual wires and brushes, we discovered that, despite a similar bulk structure, wires and brushes grew with different crystal faces and lattice spacings. Had we not utilized multiple STEM diffraction modes in conjunction with t-EBSD, differences in orientation related to bristle density would have been overlooked. Thus, it is only through a methodical combination of several structural analysis techniques that precise structural information can be reliably obtained.

Fishing and temperature effects on the size structure of exploited fish stocks.

PubMed

Tu, Chen-Yi; Chen, Kuan-Ting; Hsieh, Chih-Hao

2018-05-08

Size structure of fish stock plays an important role in maintaining sustainability of the population. Size distribution of an exploited stock is predicted to shift toward small individuals caused by size-selective fishing and/or warming; however, their relative contribution remains relatively unexplored. In addition, existing analyses on size structure have focused on univariate size-based indicators (SBIs), such as mean length, evenness of size classes, or the upper 95-percentile of the length frequency distribution; these approaches may not capture full information of size structure. To bridge the gap, we used the variation partitioning approach to examine how the size structure (composition of size classes) responded to fishing, warming and the interaction. We analyzed 28 exploited stocks in the West US, Alaska and North Sea. Our result shows fishing has the most prominent effect on the size structure of the exploited stocks. In addition, the fish stocks experienced higher variability in fishing is more responsive to the temperature effect in their size structure, suggesting that fishing may elevate the sensitivity of exploited stocks in responding to environmental effects. The variation partitioning approach provides complementary information to univariate SBIs in analyzing size structure.

Binocular stereo matching method based on structure tensor

NASA Astrophysics Data System (ADS)

Song, Xiaowei; Yang, Manyi; Fan, Yubo; Yang, Lei

2016-10-01

In a binocular visual system, to recover the three-dimensional information of the object, the most important step is to acquire matching points. Structure tensor is the vector representation of each point in its local neighborhood. Therefore, structure tensor performs well in region detection of local structure, and it is very suitable for detecting specific graphics such as pedestrians, cars and road signs in the image. In this paper, the structure tensor is combined with the luminance information to form the extended structure tensor. The directional derivatives of luminance in x and y directions are calculated, so that the local structure of the image is more prominent. Meanwhile, the Euclidean distance between the eigenvectors of key points is used as the similarity determination metric of key points in the two images. By matching, the coordinates of the matching points in the detected target are precisely acquired. In this paper, experiments were performed on the captured left and right images. After the binocular calibration, image matching was done to acquire the matching points, and then the target depth was calculated according to these matching points. By comparison, it is proved that the structure tensor can accurately acquire the matching points in binocular stereo matching.

X-Ray Crystallographic Studies on Acetylcholinesterase and Related Enzymes.

DTIC Science & Technology

1999-10-01

nerve gas intoxication, as well as of insecticide poisoning. Such structures can yield direct information concerning the functional groups and steric...Glyll7His mutant (48). Recent solution of the 3D structures of conjugates of the nerve agents , sarin, soman, DFP and VX with 7cAChE (49, 50) has revealed... pesticides and chemical warfare agents is a topic of considerable environmental and toxicological importance. Hence, a substantial research effort is being

Fiber Optic Chemical Sensors

DTIC Science & Technology

1993-10-01

patent rights. A major problem was identification of the property of ST&E vs LLNL ST&E was formed to manage the activities of Dr. Hirschfeld and Dr...positions of the fields defined in a fixed format to allow its importation into file management programs both in the microcomputer and the minicomputer...Systems Inc., Perry, Florida. askSam is a free-form information manager . A few basic elements of structure can be used to create a highly structured

Skeleton of weighted social network

NASA Astrophysics Data System (ADS)

Zhang, X.; Zhu, J.

2013-03-01

In the literature of social networks, understanding topological structure is an important scientific issue. In this paper, we construct a network from mobile phone call records and use the cumulative number of calls as a measure of the weight of a social tie. We extract skeletons from the weighted social network on the basis of the weights of ties, and we study their properties. We find that strong ties can support the skeleton in the network by studying the percolation characters. We explore the centrality of w-skeletons based on the correlation between some centrality measures and the skeleton index w of a vertex, and we find that the average centrality of a w-skeleton increases as w increases. We also study the cumulative degree distribution of the successive w-skeletons and find that as w increases, the w-skeleton tends to become more self-similar. Furthermore, fractal characteristics appear in higher w-skeletons. We also explore the global information diffusion efficiency of w-skeletons using simulations, from which we can see that the ties in the high w-skeletons play important roles in information diffusion. Identifying such a simple structure of a w-skeleton is a step forward toward understanding and representing the topological structure of weighted social networks.

The structure of social exchange in self-help support groups: development of a measure.

PubMed

Brown, Louis D; Tang, Xiaohui; Hollman, Ruth L

2014-03-01

Self-help support groups are indigenous community resources designed to help people manage a variety of personal challenges, from alcohol abuse to xeroderma pigmentosum. The social exchanges that occur during group meetings are central to understanding how people benefit from participation. This paper examines the different types of social exchange behaviors that occur during meetings, using two studies to develop empirically distinct scales that reliably measure theoretically important types of exchange. Resource theory informed the initial measurement development efforts. Exploratory factor analyses from the first study led to revisions in the factor structure of the social exchange scales. The revised measure captured the exchange of emotional support, experiential information, humor, unwanted behaviors, and exchanges outside meetings. Confirmatory factor analyses from a follow-up study with a different sample of self-help support groups provided good model fit, suggesting the revised structure accurately represented the data. Further, the scales demonstrated good convergent and discriminant validity with related constructs. Future research can use the scales to identify aspects of social exchange that are most important in improving health outcomes among self-help support group participants. Groups can use the scales in practice to celebrate strengths and address weaknesses in their social exchange dynamics.

Processing convexity and concavity along a 2-D contour: figure-ground, structural shape, and attention.

PubMed

Bertamini, Marco; Wagemans, Johan

2013-04-01

Interest in convexity has a long history in vision science. For smooth contours in an image, it is possible to code regions of positive (convex) and negative (concave) curvature, and this provides useful information about solid shape. We review a large body of evidence on the role of this information in perception of shape and in attention. This includes evidence from behavioral, neurophysiological, imaging, and developmental studies. A review is necessary to analyze the evidence on how convexity affects (1) separation between figure and ground, (2) part structure, and (3) attention allocation. Despite some broad agreement on the importance of convexity in these areas, there is a lack of consensus on the interpretation of specific claims--for example, on the contribution of convexity to metric depth and on the automatic directing of attention to convexities or to concavities. The focus is on convexity and concavity along a 2-D contour, not convexity and concavity in 3-D, but the important link between the two is discussed. We conclude that there is good evidence for the role of convexity information in figure-ground organization and in parsing, but other, more specific claims are not (yet) well supported.

Adaptive Correction from Virtually Complex Dynamic Libraries: The Role of Noncovalent Interactions in Structural Selection and Folding.

PubMed

Lafuente, Maria; Atcher, Joan; Solà, Jordi; Alfonso, Ignacio

2015-11-16

The hierarchical self-assembling of complex molecular systems is dictated by the chemical and structural information stored in their components. This information can be expressed through an adaptive process that determines the structurally fittest assembly under given environmental conditions. We have set up complex disulfide-based dynamic covalent libraries of chemically and topologically diverse pseudopeptidic compounds. We show how the reaction evolves from very complex mixtures at short reaction times to the almost exclusive formation of a major compound, through the establishment of intramolecular noncovalent interactions. Our experiments demonstrate that the systems evolve through error-check and error-correction processes. The nature of these interactions, the importance of the folding and the effects of the environment are also discussed. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Explaining the effects of a point-of-purchase nutrition-information intervention in university canteens: a structural equation modelling analysis

PubMed Central

2012-01-01

Background The importance of canteen meals in the diet of many university students makes the provision of simple point-of-purchase (POP) nutrition information in university canteens a potentially effective way to promote healthier diets in an important group of young adults. However, modifications to environments such as the posting of POP nutrition information in canteens may not cause an immediate change in meal choices and nutrient intakes. The present study aimed at understanding the process by which the POP nutrition information achieved its effects on the meal choice and energy intake, and whether the information was more effective in changing the meal choice of subgroups of university canteen customers. Methods The POP nutrition-information intervention used a one-group pretest-posttest design. A sample of 224 customers of two university canteens completed the baseline and 6-months follow-up surveys. A multi-group structural equation modelling analysis was used to test mediation effects of individual difference variables (liking, understanding and use of the information, subjective knowledge and attitude) on the energy intake from canteen meals, moderated by the objective nutrition knowledge and motivation to change diet. Results Significant relations were identified between liking of the information and its use on one hand and a positive effect in attitude towards healthy canteen meals on the other hand. Motivation to change diet and sufficient objective nutrition knowledge were required to maintain a recommended energy intake from canteen meals or to lead to a decrease in energy intake. Participants with greater objective nutrition knowledge had a greater understanding of the POP nutrition information which also resulted in a more effective use of the information. Conclusions The results suggest that nutrition-information interventions may be more effective when using nutrition information that is generally liked by the target population in combination with an educational intervention to increase objective nutrition knowledge. Trial registration NCT01249508 PMID:22967195

Explaining the effects of a point-of-purchase nutrition-information intervention in university canteens: a structural equation modelling analysis.

PubMed

Hoefkens, Christine; Pieniak, Zuzanna; Van Camp, John; Verbeke, Wim

2012-09-11

The importance of canteen meals in the diet of many university students makes the provision of simple point-of-purchase (POP) nutrition information in university canteens a potentially effective way to promote healthier diets in an important group of young adults. However, modifications to environments such as the posting of POP nutrition information in canteens may not cause an immediate change in meal choices and nutrient intakes. The present study aimed at understanding the process by which the POP nutrition information achieved its effects on the meal choice and energy intake, and whether the information was more effective in changing the meal choice of subgroups of university canteen customers. The POP nutrition-information intervention used a one-group pretest-posttest design. A sample of 224 customers of two university canteens completed the baseline and 6-months follow-up surveys. A multi-group structural equation modelling analysis was used to test mediation effects of individual difference variables (liking, understanding and use of the information, subjective knowledge and attitude) on the energy intake from canteen meals, moderated by the objective nutrition knowledge and motivation to change diet. Significant relations were identified between liking of the information and its use on one hand and a positive effect in attitude towards healthy canteen meals on the other hand. Motivation to change diet and sufficient objective nutrition knowledge were required to maintain a recommended energy intake from canteen meals or to lead to a decrease in energy intake. Participants with greater objective nutrition knowledge had a greater understanding of the POP nutrition information which also resulted in a more effective use of the information. The results suggest that nutrition-information interventions may be more effective when using nutrition information that is generally liked by the target population in combination with an educational intervention to increase objective nutrition knowledge.

BUREAUCRATIC STRUCTURE AND DECISIONMAKING.

ERIC Educational Resources Information Center

DOWNS, ANTHONY

ASPECTS OF ORGANIZATION THEORY ARE REVIEWED ANALYTICALLY TO DEVELOP THE IMPLICATIONS OF THREE MAJOR HYPOTHESES DEFINING THE RELATIONSHIP OF BUREAUS AND BUREAUCRATIC OFFICIALS TO THE DECISIONMAKING PROCESS IN A REALISTIC WORLD WHERE INFORMATION IS COSTLY AND UNCERTAINTY IS AN IMPORTANT FACTOR IN MAKING DECISIONS--(1) BUREAUCRATIC OFFICIALS SEEK TO…

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.

Building on Florida's strength in space : a plan for action

DOT National Transportation Integrated Search

1999-12-01

The report is structured as follows: : 1) Section II provides background information on the role of the space sector : in Florida. It is presented to help the reader understand: : 2) Why space is important to the current and future economy of Florida...

Network Learning for Educational Change. Professional Learning

ERIC Educational Resources Information Center

Veugelers, Wiel, Ed.; O'Hair, Mary John, Ed.

2005-01-01

School-university networks are becoming an important method to enhance educational renewal and student achievement. Networks go beyond tensions of top-down versus bottom-up, school development and professional development of individuals, theory and practice, and formal and informal organizational structures. The theoretical base of networking…

10 CFR 1.19 - Other committees, boards, and panels.

Code of Federal Regulations, 2011 CFR

2011-01-01

... of Nuclear Regulatory Research on important management matters in the direction of the Commission's... science, waste disposal and seismic and structural engineering. In performing its activities, the... information science and in managing records of the Commission's licensing process for the HLW repository. [52...

10 CFR 1.19 - Other committees, boards, and panels.

Code of Federal Regulations, 2013 CFR

2013-01-01

... of Nuclear Regulatory Research on important management matters in the direction of the Commission's... science, waste disposal and seismic and structural engineering. In performing its activities, the... information science and in managing records of the Commission's licensing process for the HLW repository. [52...

10 CFR 1.19 - Other committees, boards, and panels.

Code of Federal Regulations, 2010 CFR

2010-01-01

... of Nuclear Regulatory Research on important management matters in the direction of the Commission's... science, waste disposal and seismic and structural engineering. In performing its activities, the... information science and in managing records of the Commission's licensing process for the HLW repository. [52...

10 CFR 1.19 - Other committees, boards, and panels.

Code of Federal Regulations, 2012 CFR

2012-01-01

... of Nuclear Regulatory Research on important management matters in the direction of the Commission's... science, waste disposal and seismic and structural engineering. In performing its activities, the... information science and in managing records of the Commission's licensing process for the HLW repository. [52...

10 CFR 1.19 - Other committees, boards, and panels.

Code of Federal Regulations, 2014 CFR

2014-01-01

... of Nuclear Regulatory Research on important management matters in the direction of the Commission's... science, waste disposal and seismic and structural engineering. In performing its activities, the... information science and in managing records of the Commission's licensing process for the HLW repository. [52...

Structural bases for neurophysiological investigations of amygdaloid complex of the brain

NASA Astrophysics Data System (ADS)

Kalimullina, Liliya B.; Kalkamanov, Kh. A.; Akhmadeev, Azat V.; Zakharov, Vadim P.; Sharafullin, Ildus F.

2015-11-01

Amygdala (Am) as a part of limbic system of the brain defines such important functions as adaptive behavior of animals, formation of emotions and memory, regulation of endocrine and visceral functions. We worked out, with the help of mathematic modelling of the pattern recognition theory, principles for organization of neurophysiological and neuromorphological studies of Am nuclei, which take into account the existing heterogeneity of its formations and optimize, to a great extent, the protocol for carrying out of such investigations. The given scheme of studies of Am’s structural-functional organization at its highly-informative sections can be used as a guide for precise placement of electrodes’, cannulae’s and microsensors into particular Am nucleus in the brain with the registration not only the nucleus itself, but also its extensions. This information is also important for defining the number of slices covering specific Am nuclei which must be investigated to reveal the physiological role of a particular part of amygdaloid complex.

Magnetic resonance imaging based functional imaging in paediatric oncology.

PubMed

Manias, Karen A; Gill, Simrandip K; MacPherson, Lesley; Foster, Katharine; Oates, Adam; Peet, Andrew C

2017-02-01

Imaging is central to management of solid tumours in children. Conventional magnetic resonance imaging (MRI) is the standard imaging modality for tumours of the central nervous system (CNS) and limbs and is increasingly used in the abdomen. It provides excellent structural detail, but imparts limited information about tumour type, aggressiveness, metastatic potential or early treatment response. MRI based functional imaging techniques, such as magnetic resonance spectroscopy, diffusion and perfusion weighted imaging, probe tissue properties to provide clinically important information about metabolites, structure and blood flow. This review describes the role of and evidence behind these functional imaging techniques in paediatric oncology and implications for integrating them into routine clinical practice. Copyright © 2016 Elsevier Ltd. All rights reserved.

RNA secondary structure prediction with pseudoknots: Contribution of algorithm versus energy model.

PubMed

Jabbari, Hosna; Wark, Ian; Montemagno, Carlo

2018-01-01

RNA is a biopolymer with various applications inside the cell and in biotechnology. Structure of an RNA molecule mainly determines its function and is essential to guide nanostructure design. Since experimental structure determination is time-consuming and expensive, accurate computational prediction of RNA structure is of great importance. Prediction of RNA secondary structure is relatively simpler than its tertiary structure and provides information about its tertiary structure, therefore, RNA secondary structure prediction has received attention in the past decades. Numerous methods with different folding approaches have been developed for RNA secondary structure prediction. While methods for prediction of RNA pseudoknot-free structure (structures with no crossing base pairs) have greatly improved in terms of their accuracy, methods for prediction of RNA pseudoknotted secondary structure (structures with crossing base pairs) still have room for improvement. A long-standing question for improving the prediction accuracy of RNA pseudoknotted secondary structure is whether to focus on the prediction algorithm or the underlying energy model, as there is a trade-off on computational cost of the prediction algorithm versus the generality of the method. The aim of this work is to argue when comparing different methods for RNA pseudoknotted structure prediction, the combination of algorithm and energy model should be considered and a method should not be considered superior or inferior to others if they do not use the same scoring model. We demonstrate that while the folding approach is important in structure prediction, it is not the only important factor in prediction accuracy of a given method as the underlying energy model is also as of great value. Therefore we encourage researchers to pay particular attention in comparing methods with different energy models.

Conceptualization and Implementation of the Central Information Portal on Rare Diseases: Protocol for a Qualitative Study

PubMed Central

Hartz, Tobias; Göbel, Jens; Storf, Holger; Pauer, Frédéric; Babac, Ana; Lührs, Verena; Bruckner-Tuderman, Leena; Schauer, Franziska; Schmidtke, Jörg; Biehl, Lisa; Wagner, TOF; Graf von der Schulenburg, J-Matthias; Frank, Martin

2018-01-01

Background Recently, public and political interest has focused on people living with rare diseases and their health concerns. Due to the large number of different types of rare diseases and the sizable number of patients, taking action to improve the life of those affected is gaining importance. In 2013, the federal government of Germany adopted a national action plan for rare diseases, including the call to establish a central information portal on rare diseases (Zentrales Informationsportal über seltene Erkrankungen, ZIPSE). Objective The objective of this study, therefore, was to conduct scientific research on how such a portal must be designed to meet the needs of patients, their families, and medical professionals, and to provide high-quality information for information seekers. Methods We chose a 3-step procedure to develop a needs-based prototype of a central information portal. In the first step, we determined the information needs of patients with rare diseases, their relatives, and health care professionals by means of qualitative interviews and their content-analytical evaluation. On the basis of this, we developed the basic structure of the portal. In the second step, we identified quality criteria for websites on rare diseases to ensure that the information linked with ZIPSE meets the quality demands. Therefore, we gathered existing criteria catalogs and discussed them in an expert workshop. In the third step, we implemented and tested the developed prototypical information portal. Results A portal page was configured and made accessible on the Web. The structure of ZIPSE was based on the findings from 108 qualitative interviews with patients, their relatives, and health care professionals, through which numerous information needs were identified. We placed particularly important areas of information, such as symptoms, therapy, research, and advisory services, on the start page. Moreover, we defined 13 quality criteria, referring to factors such as author information, creation date, and privacy, enabling links with high-quality information. Moreover, 19 users tested all the developed routines based on usability and comprehensibility. Subsequently, we improved the visual presentation of search results and other important search functions. Conclusions The implemented information portal, ZIPSE, provides high-quality information on rare diseases from a central point of access. By integrating the targeted groups as well as different experts on medical information during the construction, the website can assure an improved search for information for users. ZIPSE can also serve as a model for other Web-based information systems in the field of rare diseases. Registered Report Identifier RR1-10.2196/7425 PMID:29752252

Integrating prior information into microwave tomography part 2: Impact of errors in prior information on microwave tomography image quality.

PubMed

Kurrant, Douglas; Fear, Elise; Baran, Anastasia; LoVetri, Joe

2017-12-01

The authors have developed a method to combine a patient-specific map of tissue structure and average dielectric properties with microwave tomography. The patient-specific map is acquired with radar-based techniques and serves as prior information for microwave tomography. The impact that the degree of structural detail included in this prior information has on image quality was reported in a previous investigation. The aim of the present study is to extend this previous work by identifying and quantifying the impact that errors in the prior information have on image quality, including the reconstruction of internal structures and lesions embedded in fibroglandular tissue. This study also extends the work of others reported in literature by emulating a clinical setting with a set of experiments that incorporate heterogeneity into both the breast interior and glandular region, as well as prior information related to both fat and glandular structures. Patient-specific structural information is acquired using radar-based methods that form a regional map of the breast. Errors are introduced to create a discrepancy in the geometry and electrical properties between the regional map and the model used to generate the data. This permits the impact that errors in the prior information have on image quality to be evaluated. Image quality is quantitatively assessed by measuring the ability of the algorithm to reconstruct both internal structures and lesions embedded in fibroglandular tissue. The study is conducted using both 2D and 3D numerical breast models constructed from MRI scans. The reconstruction results demonstrate robustness of the method relative to errors in the dielectric properties of the background regional map, and to misalignment errors. These errors do not significantly influence the reconstruction accuracy of the underlying structures, or the ability of the algorithm to reconstruct malignant tissue. Although misalignment errors do not significantly impact the quality of the reconstructed fat and glandular structures for the 3D scenarios, the dielectric properties are reconstructed less accurately within the glandular structure for these cases relative to the 2D cases. However, general agreement between the 2D and 3D results was found. A key contribution of this paper is the detailed analysis of the impact of prior information errors on the reconstruction accuracy and ability to detect tumors. The results support the utility of acquiring patient-specific information with radar-based techniques and incorporating this information into MWT. The method is robust to errors in the dielectric properties of the background regional map, and to misalignment errors. Completion of this analysis is an important step toward developing the method into a practical diagnostic tool. © 2017 American Association of Physicists in Medicine.

Rtools: a web server for various secondary structural analyses on single RNA sequences.

PubMed

Hamada, Michiaki; Ono, Yukiteru; Kiryu, Hisanori; Sato, Kengo; Kato, Yuki; Fukunaga, Tsukasa; Mori, Ryota; Asai, Kiyoshi

2016-07-08

The secondary structures, as well as the nucleotide sequences, are the important features of RNA molecules to characterize their functions. According to the thermodynamic model, however, the probability of any secondary structure is very small. As a consequence, any tool to predict the secondary structures of RNAs has limited accuracy. On the other hand, there are a few tools to compensate the imperfect predictions by calculating and visualizing the secondary structural information from RNA sequences. It is desirable to obtain the rich information from those tools through a friendly interface. We implemented a web server of the tools to predict secondary structures and to calculate various structural features based on the energy models of secondary structures. By just giving an RNA sequence to the web server, the user can get the different types of solutions of the secondary structures, the marginal probabilities such as base-paring probabilities, loop probabilities and accessibilities of the local bases, the energy changes by arbitrary base mutations as well as the measures for validations of the predicted secondary structures. The web server is available at http://rtools.cbrc.jp, which integrates software tools, CentroidFold, CentroidHomfold, IPKnot, CapR, Raccess, Rchange and RintD. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Microscopically derived potential energy surfaces from mostly structural considerations

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

Ermamatov, M.J.; Institute of Nuclear Physics, Ulughbek, Tashkent 100214; Hess, Peter O., E-mail: hess@nucleares.unam.mx

2016-08-15

A simple procedure to estimate the quadrupole Potential-Energy-Surface (PES) is presented, using mainly structural information, namely the content of the shell model space and the Pauli exclusion principle. Further microscopic properties are implicitly contained through the use of results from the Möller and Nix tables or experimental information. A mapping to the geometric potential is performed yielding the PES. The General Collective Model is used in order to obtain an estimate on the spectrum and quadrupole transitions, adjusting only the mass parameter. First, we test the conjecture on known nuclei, deriving the PES and compare them to known data. Wemore » will see that the PES approximates very well the structure expected. Having acquired a certain confidence, we predict the PES of several chain of isotopes of heavy and super-heavy nuclei and at the end we investigate the structure of nuclei in the supposed island of stability. One of the main points to show is that simple assumptions can provide already important information on the structure of nuclei outside known regions and that spectra and electromagnetic transitions can be estimated without using involved calculations and assumptions. The procedure does not allow to calculate binding energies. The method presented can be viewed as a starting point for further improvements.« less

Compound Structure-Independent Activity Prediction in High-Dimensional Target Space.

PubMed

Balfer, Jenny; Hu, Ye; Bajorath, Jürgen

2014-08-01

Profiling of compound libraries against arrays of targets has become an important approach in pharmaceutical research. The prediction of multi-target compound activities also represents an attractive task for machine learning with potential for drug discovery applications. Herein, we have explored activity prediction in high-dimensional target space. Different types of models were derived to predict multi-target activities. The models included naïve Bayesian (NB) and support vector machine (SVM) classifiers based upon compound structure information and NB models derived on the basis of activity profiles, without considering compound structure. Because the latter approach can be applied to incomplete training data and principally depends on the feature independence assumption, SVM modeling was not applicable in this case. Furthermore, iterative hybrid NB models making use of both activity profiles and compound structure information were built. In high-dimensional target space, NB models utilizing activity profile data were found to yield more accurate activity predictions than structure-based NB and SVM models or hybrid models. An in-depth analysis of activity profile-based models revealed the presence of correlation effects across different targets and rationalized prediction accuracy. Taken together, the results indicate that activity profile information can be effectively used to predict the activity of test compounds against novel targets. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Architecture for WSN Nodes Integration in Context Aware Systems Using Semantic Messages

NASA Astrophysics Data System (ADS)

Larizgoitia, Iker; Muguira, Leire; Vazquez, Juan Ignacio

Wireless sensor networks (WSN) are becoming extremely popular in the development of context aware systems. Traditionally WSN have been focused on capturing data, which was later analyzed and interpreted in a server with more computational power. In this kind of scenario the problem of representing the sensor information needs to be addressed. Every node in the network might have different sensors attached; therefore their correspondent packet structures will be different. The server has to be aware of the meaning of every single structure and data in order to be able to interpret them. Multiple sensors, multiple nodes, multiple packet structures (and not following a standard format) is neither scalable nor interoperable. Context aware systems have solved this problem with the use of semantic technologies. They provide a common framework to achieve a standard definition of any domain. Nevertheless, these representations are computationally expensive, so a WSN cannot afford them. The work presented in this paper tries to bridge the gap between the sensor information and its semantic representation, by defining a simple architecture that enables the definition of this information natively in a semantic way, achieving the integration of the semantic information in the network packets. This will have several benefits, the most important being the possibility of promoting every WSN node to a real semantic information source.

Information needs assessment of medical equipment offices based on Critical Success Factors (CSF) and Business System Planning (BSP) methods.

PubMed

Khorrami, F; Ahmadi, M; Alizadeh, A; Roozbeh, N; Mohseni, S

2015-01-01

Introduction: Given the ever-increasing importance and value of information, providing the management with a reliable information system, which can facilitate decision-making regarding planning, organization and control, is vitally important. This study aimed to analyze and evaluate the information needs of medical equipment offices. Methods: This descriptive applied cross-sectional study was carried out in 2010. The population of the study included the managers of statistic and medical records at the offices of vice-chancellor for treatment in 39 medical universities in Iran. Data were collected by using structured questioners. With regard to different kinds of designing information systems, sampling was done by two methods, BSP (based on processes of job description) and CSF method (based on critical success factors). The data were analyzed by SPSS-16. Results: Our study showed that 41% of information needs were found to be critical success factors of managers of office. The first priority of managers was "the number of bed and bed occupancy in hospitals". Of 29 identified information needs, 62% were initial information needs of managers (from the viewpoints of managers). Of all, 4% of the information needs were obtained through the form, 14% through both the form and database, 11% through the web site, and 71% had no sources (forms, databases, web site). Conclusion: Since 71% of the information needs of medical equipment offices managers had no information sources, the development of information system in these offices seems to be necessary. Despite the important role of users in designing the information systems (identifying 62% of information needs), other scientific methods is also needed to be utilized in designing the information systems.

Information needs assessment of medical equipment offices based on Critical Success Factors (CSF) and Business System Planning (BSP) methods

PubMed Central

Khorrami, F; Ahmadi, M; Alizadeh, A; Roozbeh, N; Mohseni, S

2015-01-01

Introduction: Given the ever-increasing importance and value of information, providing the management with a reliable information system, which can facilitate decision-making regarding planning, organization and control, is vitally important. This study aimed to analyze and evaluate the information needs of medical equipment offices. Methods: This descriptive applied cross-sectional study was carried out in 2010. The population of the study included the managers of statistic and medical records at the offices of vice-chancellor for treatment in 39 medical universities in Iran. Data were collected by using structured questioners. With regard to different kinds of designing information systems, sampling was done by two methods, BSP (based on processes of job description) and CSF method (based on critical success factors). The data were analyzed by SPSS-16. Results: Our study showed that 41% of information needs were found to be critical success factors of managers of office. The first priority of managers was “the number of bed and bed occupancy in hospitals”. Of 29 identified information needs, 62% were initial information needs of managers (from the viewpoints of managers). Of all, 4% of the information needs were obtained through the form, 14% through both the form and database, 11% through the web site, and 71% had no sources (forms, databases, web site). Conclusion: Since 71% of the information needs of medical equipment offices managers had no information sources, the development of information system in these offices seems to be necessary. Despite the important role of users in designing the information systems (identifying 62% of information needs), other scientific methods is also needed to be utilized in designing the information systems. PMID:28255389

Multi-service terminal adapter based on IP technology applications in rural area

NASA Astrophysics Data System (ADS)

Gao, Li; Li, Xiaobo; Yan, Juntao; Ren, Xupeng

Take advantage of ample modern existing telecom network resources to rural areas may achieve it's information society gradually. This includes the establishment of integrated rural information service platform, modern remote education center and electronic administration management platform for rural areas. The geographical and economic constraints must be overcome for structuring the rural service support system, in order to provide technical support, information products and information services to modern rural information service system. It is important that development an access platform based IP technology, which supports multi-service access in order to implement a variety of types of mobile terminal equipment adapter access and to reduce restrictions on mobile terminal equipment.

Selected Topics in Light Front Field Theory and Applications to the High Energy Phenomena

NASA Astrophysics Data System (ADS)

Kundu, Rajen

1999-10-01

In this thesis, we have presented some of the aspects of light-front (LF) field theory through their successful application in the Deep Inelastic Scattering (DIS). We have developed a LFQCD Hamiltonian description of the DIS structure functions starting from Bjorken-Johnson-Low limit of virtual forward Compton scattering amplitude and using LF current commutators. We worked in the LF gauge A^+=0 and used the old-fashioned LFQCD perturbation theory in our calculations. The importance of our work are summarized below. Our approach shares the intution of parton model and addresses directly the structure functions, which are experimental objects, instead of its moments as in OPE method. Moreover, it can potentially incorporate the non-perturbative contents of the structure functions as we have demonstrated by introducing a new factorization scheme. In the context of nucleonic helicity structure, the well known gauge fixed LF helicity operator is shown to provide consistent physical information and helps us defining new relevant structure functions. The anomalous dimensions relevant for the Q^2-evolution of such structure functions are calculated. Our study is important in establishing the equivalance of LF field theory and the usual equal-time one through perturbative calculations of the dressed parton structure functions reproducing the well known results. Also the importance of Gallilean boost symmetry in understanding the correctness of any higher order calculation using (x^+)-ordered LFQCD perturbation theory are emphasized.

A Molecular Dynamics Study of the Structure-Dynamics Relationships of Supercooled Liquids and Glasses

NASA Astrophysics Data System (ADS)

Soklaski, Ryan

Central to the field of condensed matter physics is a decades old outstanding problem in the study of glasses -- namely explaining the extreme slowing of dynamics in a liquid as it is supercooled towards the so-called glass transition. Efforts to universally describe the stretched relaxation processes and heterogeneous dynamics that characteristically develop in supercooled liquids remain divided in both their approaches and successes. Towards this end, a consensus on the role that atomic and molecular structures play in the liquid is even more tenuous. However, mounting material science research efforts have culminated to reveal that the vast diversity of metallic glass species and their properties are rooted in an equally-broad set of structural archetypes. Herein lies the motivation of this dissertation: the detailed information available regarding the structure-property relationships of metallic glasses provides a new context in which one can study the evolution of a supercooled liquid by utilizing a structural motif that is known to dominate the glass. Cu64Zr36 is a binary alloy whose good glass-forming ability and simple composition makes it a canonical material to both empirical and numerical studies. Here, we perform classical molecular dynamics simulations and conduct a comprehensive analysis of the dynamical regimes of liquid Cu64Zr36, while focusing on the roles played by atomic icosahedral ordering -- a structural motif which ultimately percolates the glass' structure. Large data analysis techniques are leveraged to obtain uniquely detailed structural and dynamical information in this context. In doing so, we develop the first account of the origin of icosahedral order in this alloy, revealing deep connections between this incipient structural ordering, frustration-limited domain theory, and recent important empirical findings that are relevant to the nature of metallic liquids at large. Furthermore, important dynamical landmarks such as the breakdown of the Stokes-Einstein relationship, the decoupling of particle diffusivities, and the development of general "glassy" relaxation features are found to coincide with successive manifestation of icosahedral ordering that arise as the liquid is supercooled. Remarkably, we detect critical-like features in the growth of the icosahedron network, with signatures that suggest that a liquid-liquid phase transition may occur in the deeply supercooled regime to precede glass formation. Such a transition is predicted to occur in many supercooled liquids, although explicit evidence of this phenomenon in realistic systems is scarce. Ultimately this work concludes that icosahedral order characterizes all dynamical regimes of Cu64Zr 36, demonstrating the importance and utility of studying supercooled liquids in the context of locally-preferred structure. More broadly, it serves to confirm and inform recent theoretical and empirical findings that are central to understanding the physics underlying the glass transition.

Snohomish Estuary Wetlands Study. Volume I. Summary Report

DTIC Science & Technology

1979-05-01

Large marine facilities are structures used for _.. argy development (oil rigs and platforms), raw material pro-cessing, and marine terminals. Such...State) * Wetlands Land Use 20. A9rTlACT (Camthaism revaes ebb N rNeeaa-7 maid Identifr by block number) The study underlines the importance of wetlands...function of a habitat. This study was conducted using information on these and all other subjects. Additional data will provide important refinements

Surface relief model for photopolymers without cover plating.

PubMed

Gallego, S; Márquez, A; Ortuño, M; Francés, J; Marini, S; Beléndez, A; Pascual, I

2011-05-23

Relief surface changes provide interesting possibilities for storing diffractive optical elements on photopolymers and are an important source of information to characterize and understand the material behaviour. In this paper we present a 3-dimensional model based on direct measurements of parameters to predict the relief structures generated on the material. This model is successfully applied to different photopolymers with different values of monomer diffusion. The importance of monomer diffusion in depth is also discussed.

Structure-based drug design: aiming for a perfect fit

PubMed Central

van Montfort, Rob L.M.; Workman, Paul

2017-01-01

Knowledge of the three-dimensional structure of therapeutically relevant targets has informed drug discovery since the first protein structures were determined using X-ray crystallography in the 1950s and 1960s. In this editorial we provide a brief overview of the powerful impact of structure-based drug design (SBDD), which has its roots in computational and structural biology, with major contributions from both academia and industry. We describe advances in the application of SBDD for integral membrane protein targets that have traditionally proved very challenging. We emphasize the major progress made in fragment-based approaches for which success has been exemplified by over 30 clinical drug candidates and importantly three FDA-approved drugs in oncology. We summarize the articles in this issue that provide an excellent snapshot of the current state of the field of SBDD and fragment-based drug design and which offer key insights into exciting new developments, such as the X-ray free-electron laser technology, cryo-electron microscopy, open science approaches and targeted protein degradation. We stress the value of SBDD in the design of high-quality chemical tools that are used to interrogate biology and disease pathology, and to inform target validation. We emphasize the need to maintain the scientific rigour that has been traditionally associated with structural biology and extend this to other methods used in drug discovery. This is particularly important because the quality and robustness of any form of contributory data determines its usefulness in accelerating drug design, and therefore ultimately in providing patient benefit. PMID:29118091

An inverse modeling approach for semilunar heart valve leaflet mechanics: exploitation of tissue structure.

PubMed

Aggarwal, Ankush; Sacks, Michael S

2016-08-01

Determining the biomechanical behavior of heart valve leaflet tissues in a noninvasive manner remains an important clinical goal. While advances in 3D imaging modalities have made in vivo valve geometric data available, optimal methods to exploit such information in order to obtain functional information remain to be established. Herein we present and evaluate a novel leaflet shape-based framework to estimate the biomechanical behavior of heart valves from surface deformations by exploiting tissue structure. We determined accuracy levels using an "ideal" in vitro dataset, in which the leaflet geometry, strains, mechanical behavior, and fibrous structure were known to a high level of precision. By utilizing a simplified structural model for the leaflet mechanical behavior, we were able to limit the number of parameters to be determined per leaflet to only two. This approach allowed us to dramatically reduce the computational time and easily visualize the cost function to guide the minimization process. We determined that the image resolution and the number of available imaging frames were important components in the accuracy of our framework. Furthermore, our results suggest that it is possible to detect differences in fiber structure using our framework, thus allowing an opportunity to diagnose asymptomatic valve diseases and begin treatment at their early stages. Lastly, we observed good agreement of the final resulting stress-strain response when an averaged fiber architecture was used. This suggests that population-averaged fiber structural data may be sufficient for the application of the present framework to in vivo studies, although clearly much work remains to extend the present approach to in vivo problems.

A biopolymer transistor: electrical amplification by microtubules.

PubMed

Priel, Avner; Ramos, Arnolt J; Tuszynski, Jack A; Cantiello, Horacio F

2006-06-15

Microtubules (MTs) are important cytoskeletal structures engaged in a number of specific cellular activities, including vesicular traffic, cell cyto-architecture and motility, cell division, and information processing within neuronal processes. MTs have also been implicated in higher neuronal functions, including memory and the emergence of "consciousness". How MTs handle and process electrical information, however, is heretofore unknown. Here we show new electrodynamic properties of MTs. Isolated, taxol-stabilized MTs behave as biomolecular transistors capable of amplifying electrical information. Electrical amplification by MTs can lead to the enhancement of dynamic information, and processivity in neurons can be conceptualized as an "ionic-based" transistor, which may affect, among other known functions, neuronal computational capabilities.

Robust X-ray angular correlations for the study of meso-structures

DOE PAGES

Lhermitte, Julien R.; Tian, Cheng; Stein, Aaron; ...

2017-05-08

As self-assembling nanomaterials become more sophisticated, it is becoming increasingly important to measure the structural order of finite-sized assemblies of nano-objects. These mesoscale clusters represent an acute challenge to conventional structural probes, owing to the range of implicated size scales (10 nm to several micrometres), the weak scattering signal and the dynamic nature of meso-clusters in native solution environments. The high X-ray flux and coherence of modern synchrotrons present an opportunity to extract structural information from these challenging systems, but conventional ensemble X-ray scattering averages out crucial information about local particle configurations. Conversely, a single meso-cluster scatters too weakly tomore » recover the full diffraction pattern. Using X-ray angular cross-correlation analysis, it is possible to combine multiple noisy measurements to obtain robust structural information. This paper explores the key theoretical limits and experimental challenges that constrain the application of these methods to probing structural order in real nanomaterials. A metric is presented to quantify the signal-to-noise ratio of angular correlations, and it is used to identify several experimental artifacts that arise. In particular, it is found that background scattering, data masking and inter-cluster interference profoundly affect the quality of correlation analyses. A robust workflow is demonstrated for mitigating these effects and extracting reliable angular correlations from realistic experimental data.« less

Exploring the measurement structure of the Gambling Related Cognitions Scale (GRCS) in treatment-seekers: A Bayesian structural equation modelling approach.

PubMed

Smith, David; Woodman, Richard; Drummond, Aaron; Battersby, Malcolm

2016-03-30

Knowledge of a problem gambler's underlying gambling related cognitions plays an important role in treatment planning. The Gambling Related Cognitions Scale (GRCS) is therefore frequently used in clinical settings for screening and evaluation of treatment outcomes. However, GRCS validation studies have generated conflicting results regarding its latent structure using traditional confirmatory factor analyses (CFA). This may partly be due to the rigid constraints imposed on cross-factor loadings with traditional CFA. The aim of this investigation was to determine whether a Bayesian structural equation modelling (BSEM) approach to examination of the GRCS factor structure would better replicate substantive theory and also inform model re-specifications. Participants were 454 treatment-seekers at first presentation to a gambling treatment centre between January 2012 and December 2014. Model fit indices were well below acceptable standards for CFA. In contrast, the BSEM model which included small informative priors for the residual covariance matrix in addition to cross-loadings produced excellent model fit for the original hypothesised factor structure. The results also informed re-specification of the CFA model which provided more reasonable model fit. These conclusions have implications that should be useful to both clinicians and researchers evaluating measurement models relating to gambling related cognitions in treatment-seekers. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Influence maximization based on partial network structure information: A comparative analysis on seed selection heuristics

NASA Astrophysics Data System (ADS)

Erkol, Şirag; Yücel, Gönenç

In this study, the problem of seed selection is investigated. This problem is mainly treated as an optimization problem, which is proved to be NP-hard. There are several heuristic approaches in the literature which mostly use algorithmic heuristics. These approaches mainly focus on the trade-off between computational complexity and accuracy. Although the accuracy of algorithmic heuristics are high, they also have high computational complexity. Furthermore, in the literature, it is generally assumed that complete information on the structure and features of a network is available, which is not the case in most of the times. For the study, a simulation model is constructed, which is capable of creating networks, performing seed selection heuristics, and simulating diffusion models. Novel metric-based seed selection heuristics that rely only on partial information are proposed and tested using the simulation model. These heuristics use local information available from nodes in the synthetically created networks. The performances of heuristics are comparatively analyzed on three different network types. The results clearly show that the performance of a heuristic depends on the structure of a network. A heuristic to be used should be selected after investigating the properties of the network at hand. More importantly, the approach of partial information provided promising results. In certain cases, selection heuristics that rely only on partial network information perform very close to similar heuristics that require complete network data.

Measuring Physicochemical Properties to Inform the Scope of Existing QSAR/QSPR Models (SOT annual meeting)

EPA Science Inventory

Chemical structures and their properties are important for determining their potential toxicological effects, toxicokinetics, and route of exposure. These data are needed to prioritize thousands of environmental chemicals, but are often lacking. In order to fill data gaps, robust...

A population structure and genome-wide association analysis on the USDA soybean germplasm collection

USDA-ARS?s Scientific Manuscript database

Genotype-phenotype associations within the soybean (Glycine max) germplasm collection could provide valuable information on the frequency and distribution of alleles affecting economically important traits. Here we performed a genome-wide association study (GWAS) for seed protein and oil content in ...

The Significance of the Bond Angle in Sulfur Dioxide.

ERIC Educational Resources Information Center

Purser, Gordon H.

1989-01-01

Examined are the illustrations and descriptions of the molecular structure of sulfur dioxide found in selected chemistry textbooks. Inconsistencies and incorrect information are indicated. It is suggested that molecules other than sulfur dioxide be used as examples of molecules for which resonance is important. (CW)

Evaluation of biochars by temperature programmed oxidation/mass spectrometry

Treesearch

Michael Jackson; Thomas Eberhardt; Akwasi Boateng; Charles Mullen; Les Groom

2013-01-01

Biochars produced from thermochemical conversions of biomass were evaluated by temperature programmed oxidation (TPO). This technique, used to characterize carbon deposits on petroleum cracking catalysts, provides information on the oxidative stability of carbonaceous solids, where higher temperature reactivity indicates greater structural order, an important property...

A Handbook of Bright Ideas: Facilitating Giftedness.

ERIC Educational Resources Information Center

Cherry, Betty S., Ed.

Presented is a manual developed by the Manatee, Florida, program for gifted students which includes articles by leading thinkers, information on J. Guilford's structure of the intellect model, the importance of cognitive and affective balance, creative development, checklists, games, and other ideas for teachers of gifted students. Articles…

Argonne News Brief: Two Key Zika Proteins Unlocked at Advanced Photon Source

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

None

The Zika virus is a global health emergency. Now two new studies have revealed the molecular structure of important Zika virus proteins, providing scientists around the globe with new information about how the virus replicates—and potential avenues for antiviral drugs or vaccines.

XML-Based Generator of C++ Code for Integration With GUIs

NASA Technical Reports Server (NTRS)

Hua, Hook; Oyafuso, Fabiano; Klimeck, Gerhard

2003-01-01

An open source computer program has been developed to satisfy a need for simplified organization of structured input data for scientific simulation programs. Typically, such input data are parsed in from a flat American Standard Code for Information Interchange (ASCII) text file into computational data structures. Also typically, when a graphical user interface (GUI) is used, there is a need to completely duplicate the input information while providing it to a user in a more structured form. Heretofore, the duplication of the input information has entailed duplication of software efforts and increases in susceptibility to software errors because of the concomitant need to maintain two independent input-handling mechanisms. The present program implements a method in which the input data for a simulation program are completely specified in an Extensible Markup Language (XML)-based text file. The key benefit for XML is storing input data in a structured manner. More importantly, XML allows not just storing of data but also describing what each of the data items are. That XML file contains information useful for rendering the data by other applications. It also then generates data structures in the C++ language that are to be used in the simulation program. In this method, all input data are specified in one place only, and it is easy to integrate the data structures into both the simulation program and the GUI. XML-to-C is useful in two ways: 1. As an executable, it generates the corresponding C++ classes and 2. As a library, it automatically fills the objects with the input data values.

An overview on benzylisoquinoline derivatives with dopaminergic and serotonergic activities.

PubMed

Cabedo, N; Berenguer, I; Figadère, B; Cortes, D

2009-01-01

Dopamine and serotonin are important neurotransmitters in the mammalian central nervous system (CNS) involved in numerous physiological and behavioural disorders such as schizophrenia, major depression, anxiety, Parkinson's and Huntington's diseases, and attention deficit hyperactivity disorder. Several natural and synthetic benzylisoquinoline derivatives have displayed affinity for dopamine and serotonin receptors in nanomolar or micromolar ranges. This review covers the last three decades of dopaminergic and serotonergic activities, and especially focuses on structure-activity relationships of natural and synthetic benzylisoquinoline derivatives. We have included aporphines, 1-benzyltetrahydroisoquinolines, bis-benzylisoquinolines, protoberberines, cularines and other structural analogues. Further molecular modelling calculations have been considered as important tools to not only obtain structural information of both neurotransmitter receptors, but to also identify their pharmacophore features. The development of selective potential ligands like benzylisoquinoline derivatives may help in the therapy of diseases related to CNS dysfunction.

Microbial biotin protein ligases aid in understanding holocarboxylase synthetase deficiency.

PubMed

Pendini, Nicole R; Bailey, Lisa M; Booker, Grant W; Wilce, Matthew C; Wallace, John C; Polyak, Steven W

2008-01-01

The attachment of biotin onto the biotin-dependent enzymes is catalysed by biotin protein ligase (BPL), also known as holocarboxylase synthase HCS in mammals. Mammals contain five biotin-enzymes that participate in a number of important metabolic pathways such as fatty acid biogenesis, gluconeogenesis and amino acid catabolism. All mammalian biotin-enzymes are post-translationally biotinylated, and therefore activated, through the action of a single HCS. Substrate recognition by BPLs occurs through conserved structural cues that govern the specificity of biotinylation. Defects in biotin metabolism, including HCS, give rise to multiple carboxylase deficiency (MCD). Here we review the literature on this important enzyme. In particular, we focus on the new information that has been learned about BPL's from a number of recently published protein structures. Through molecular modelling studies insights into the structural basis of HCS deficiency in MCD are discussed.

Bounds on the information rate of quantum-secret-sharing schemes

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

Sarvepalli, Pradeep

An important metric of the performance of a quantum-secret-sharing scheme is its information rate. Beyond the fact that the information rate is upper-bounded by one, very little is known in terms of bounds on the information rate of quantum-secret-sharing schemes. Furthermore, not every scheme can be realized with rate one. In this paper we derive upper bounds for the information rates of quantum-secret-sharing schemes. We show that there exist quantum access structures on n players for which the information rate cannot be better than O((log{sub 2}n)/n). These results are the quantum analogues of the bounds for classical-secret-sharing schemes proved bymore » Csirmaz.« less

An important Norwegian contribution to the study of the bursae of the upper and lower extremities.

PubMed

Musil, Vladimir; Selnes, Christoffer V; Falck, Aleksander T; Sandve, Lars; Shekarchi, Siamek; O'Donnell, Bruce; Kachlik, David

2010-10-01

We present a critical analysis of the monograph of A.S.D. Synnestvedt (1869) “En anatomisk beskrivelse af de paa over- og underestremiteterne forekommende Bursae mucosae”. The analysis was completed using anatomical information from the historically oldest publications dealing with the bursae of the extremities: Albinus (1734) , Monro (1788) , Rosenmüller (1799) . We are of the opinion that Synnestvedt's publication is important, not only historically but also as a source of information for recent medical practitioners. Synnestvedt's monograph has a wealth of literary citations, unambiguous opinions of seasoned anatomists regarding the structure and function of the synovial membrane, and detailed descriptions of dissections he performed on fetal and adult cadavers. The information in this publication may enhance the diagnosis of bursopathies and enthesopathies of the extremities.

An important Norwegian contribution to the study of the bursae of the upper and lower extremities

PubMed Central

2010-01-01

We present a critical analysis of the monograph of A.S.D. Synnestvedt (1869) “En anatomisk beskrivelse af de paa over- og underestremiteterne forekommende Bursae mucosae”. The analysis was completed using anatomical information from the historically oldest publications dealing with the bursae of the extremities: Albinus (1734), Monro (1788), Rosenmüller (1799). We are of the opinion that Synnestvedt's publication is important, not only historically but also as a source of information for recent medical practitioners. Synnestvedt's monograph has a wealth of literary citations, unambiguous opinions of seasoned anatomists regarding the structure and function of the synovial membrane, and detailed descriptions of dissections he performed on fetal and adult cadavers. The information in this publication may enhance the diagnosis of bursopathies and enthesopathies of the extremities. PMID:20860444

Metal Transport across Biomembranes: Emerging Models for a Distinct Chemistry*

PubMed Central

Argüello, José M.; Raimunda, Daniel; González-Guerrero, Manuel

2012-01-01

Transition metals are essential components of important biomolecules, and their homeostasis is central to many life processes. Transmembrane transporters are key elements controlling the distribution of metals in various compartments. However, due to their chemical properties, transition elements require transporters with different structural-functional characteristics from those of alkali and alkali earth ions. Emerging structural information and functional studies have revealed distinctive features of metal transport. Among these are the relevance of multifaceted events involving metal transfer among participating proteins, the importance of coordination geometry at transmembrane transport sites, and the presence of the largely irreversible steps associated with vectorial transport. Here, we discuss how these characteristics shape novel transition metal ion transport models. PMID:22389499

Metal transport across biomembranes: emerging models for a distinct chemistry.

PubMed

Argüello, José M; Raimunda, Daniel; González-Guerrero, Manuel

2012-04-20

Transition metals are essential components of important biomolecules, and their homeostasis is central to many life processes. Transmembrane transporters are key elements controlling the distribution of metals in various compartments. However, due to their chemical properties, transition elements require transporters with different structural-functional characteristics from those of alkali and alkali earth ions. Emerging structural information and functional studies have revealed distinctive features of metal transport. Among these are the relevance of multifaceted events involving metal transfer among participating proteins, the importance of coordination geometry at transmembrane transport sites, and the presence of the largely irreversible steps associated with vectorial transport. Here, we discuss how these characteristics shape novel transition metal ion transport models.

Structuration and sensemaking: frameworks for understanding the management of health information systems in the ICU.

PubMed

Ghosh, Tip

2007-01-01

This paper will describe two alternate conceptual frameworks (i.e. Structuration and Sensemaking) that will help to describe and provide insight into how best to implement health information systems in ICUs throughout the globe. Structuration and sensemaking are two competing ways to view the social world within hospitals. To examine the impact of information technology in health care organizations, it is important to explore the dynamic interplay between clinical decisionmaking, outcomes of HIT implementation, and individual characteristics of the organizational setting. The adaptation of information technology within health care organizations is by its very nature quite complex. The recursive pattern of social interactions that shape the implementation of technologies within that setting is key. Structuration theory provides an understanding of human work as social interaction within that organizational culture, mediated by artifacts such as tools, language, rules and procedures, and open to change. The ICU provides multiple opportunities for sensemaking. It involves caring for multiple patients simultaneously; is subject to high levels of uncertainty and is provided under significant time constraints. It is highly interdependent work, necessitating shared sensemaking as well as individual sensemaking. Sensemaking is made partially visible in this context as clinicians communicate to each other what they think is the cause of the patient's symptoms and how to treat them in the form of discussions about patient care, consultation requests, ancillary testing, and the electronic medical record. The collaborative nature of work in the ICU lends itself to the application of sensemaking and structuration theories.

Communicating a diagnosis of Autism Spectrum Disorder - a qualitative study of parents' experiences.

PubMed

Abbott, Mandy; Bernard, Paul; Forge, Jenny

2013-07-01

Not enough is known about parents' experiences of receiving the news that their child warrants a diagnosis of Autism Spectrum Disorder (ASD). Sharing this information with parents is an important and difficult part of Child and Adolescent Mental Health (CAMH) practice. Qualitative methodology was used to explore the experiences of the 'feedback session' with nine sets of parents in a community Child and Adolescent Mental Health Service (CAMHS) in North East England. Parents gave vivid accounts of their experiences and described issues relating to the structure, style and content of the session. The experiences of CAMHS users should inform the development of good practice in this important area.

Paragenesis and Geochronology of the Nopal I Uranium Deposit, Mexico

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

M. Fayek; M. Ren

2007-02-14

Uranium deposits can, by analogy, provide important information on the long-term performance of radioactive waste forms and radioactive waste repositories. Their complex mineralogy and variable elemental and isotopic compositions can provide important information, provided that analyses are obtained on the scale of several micrometers. Here, we present a structural model of the Nopal I deposit as well as petrography at the nanoscale coupled with preliminary U-Th-Pb ages and O isotopic compositions of uranium-rich minerals obtained by Secondary Ion Mass Spectrometry (SIMS). This multi-technique approach promises to provide ''natural system'' data on the corrosion rate of uraninite, the natural analogue ofmore » spent nuclear fuel.« less

The relative importance of different perceptual-cognitive skills during anticipation.

PubMed

North, Jamie S; Hope, Ed; Williams, A Mark

2016-10-01

We examined whether anticipation is underpinned by perceiving structured patterns or postural cues and whether the relative importance of these processes varied as a function of task constraints. Skilled and less-skilled soccer players completed anticipation paradigms in video-film and point light display (PLD) format. Skilled players anticipated more accurately regardless of display condition, indicating that both perception of structured patterns between players and postural cues contribute to anticipation. However, the Skill×Display interaction showed skilled players' advantage was enhanced in the video-film condition, suggesting that they make better use of postural cues when available during anticipation. We also examined anticipation as a function of proximity to the ball. When participants were near the ball, anticipation was more accurate for video-film than PLD clips, whereas when the ball was far away there was no difference between viewing conditions. Perceiving advance postural cues appears more important than structured patterns when the ball is closer to the observer, whereas the reverse is true when the ball is far away. Various perceptual-cognitive skills contribute to anticipation with the relative importance of perceiving structured patterns and advance postural cues being determined by task constraints and the availability of perceptual information. Copyright © 2016 Elsevier B.V. All rights reserved.

Crystal structure of a putative exo-β-1,3-galactanase from Bifidobacterium bifidum S17

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

Godoy, Andre S.; de Lima, Mariana Z. T.; Camilo, Cesar M.

2016-03-16

Given the current interest in second-generation biofuels, carbohydrate-active enzymes have become the most important tool to overcome the structural recalcitrance of the plant cell wall. While some glycoside hydrolase families have been exhaustively described, others remain poorly characterized, especially with regard to structural information. The family 43 glycoside hydrolases are a diverse group of inverting enzymes; the available structure information on these enzymes is mainly from xylosidases and arabinofuranosidase. Currently, only one structure of an exo-β-1,3-galactanase is available. Here, the production, crystallization and structure determination of a putative exo-β-1,3-galactanase fromBifidobacterium bifidumS17 (BbGal43A) are described.BbGal43A was successfully produced and showed activitymore » towards synthetic galactosides.BbGal43A was subsequently crystallized and data were collected to 1.4 Å resolution. The structure shows a single-domain molecule, differing from known homologues, and crystal contact analysis predicts the formation of a dimer in solution. Further biochemical studies are necessary to elucidate the differences betweenBbGal43A and its characterized homologues.« less

Metrics for comparing neuronal tree shapes based on persistent homology.

PubMed

Li, Yanjie; Wang, Dingkang; Ascoli, Giorgio A; Mitra, Partha; Wang, Yusu

2017-01-01

As more and more neuroanatomical data are made available through efforts such as NeuroMorpho.Org and FlyCircuit.org, the need to develop computational tools to facilitate automatic knowledge discovery from such large datasets becomes more urgent. One fundamental question is how best to compare neuron structures, for instance to organize and classify large collection of neurons. We aim to develop a flexible yet powerful framework to support comparison and classification of large collection of neuron structures efficiently. Specifically we propose to use a topological persistence-based feature vectorization framework. Existing methods to vectorize a neuron (i.e, convert a neuron to a feature vector so as to support efficient comparison and/or searching) typically rely on statistics or summaries of morphometric information, such as the average or maximum local torque angle or partition asymmetry. These simple summaries have limited power in encoding global tree structures. Based on the concept of topological persistence recently developed in the field of computational topology, we vectorize each neuron structure into a simple yet informative summary. In particular, each type of information of interest can be represented as a descriptor function defined on the neuron tree, which is then mapped to a simple persistence-signature. Our framework can encode both local and global tree structure, as well as other information of interest (electrophysiological or dynamical measures), by considering multiple descriptor functions on the neuron. The resulting persistence-based signature is potentially more informative than simple statistical summaries (such as average/mean/max) of morphometric quantities-Indeed, we show that using a certain descriptor function will give a persistence-based signature containing strictly more information than the classical Sholl analysis. At the same time, our framework retains the efficiency associated with treating neurons as points in a simple Euclidean feature space, which would be important for constructing efficient searching or indexing structures over them. We present preliminary experimental results to demonstrate the effectiveness of our persistence-based neuronal feature vectorization framework.

Metrics for comparing neuronal tree shapes based on persistent homology

PubMed Central

Li, Yanjie; Wang, Dingkang; Ascoli, Giorgio A.; Mitra, Partha

2017-01-01

As more and more neuroanatomical data are made available through efforts such as NeuroMorpho.Org and FlyCircuit.org, the need to develop computational tools to facilitate automatic knowledge discovery from such large datasets becomes more urgent. One fundamental question is how best to compare neuron structures, for instance to organize and classify large collection of neurons. We aim to develop a flexible yet powerful framework to support comparison and classification of large collection of neuron structures efficiently. Specifically we propose to use a topological persistence-based feature vectorization framework. Existing methods to vectorize a neuron (i.e, convert a neuron to a feature vector so as to support efficient comparison and/or searching) typically rely on statistics or summaries of morphometric information, such as the average or maximum local torque angle or partition asymmetry. These simple summaries have limited power in encoding global tree structures. Based on the concept of topological persistence recently developed in the field of computational topology, we vectorize each neuron structure into a simple yet informative summary. In particular, each type of information of interest can be represented as a descriptor function defined on the neuron tree, which is then mapped to a simple persistence-signature. Our framework can encode both local and global tree structure, as well as other information of interest (electrophysiological or dynamical measures), by considering multiple descriptor functions on the neuron. The resulting persistence-based signature is potentially more informative than simple statistical summaries (such as average/mean/max) of morphometric quantities—Indeed, we show that using a certain descriptor function will give a persistence-based signature containing strictly more information than the classical Sholl analysis. At the same time, our framework retains the efficiency associated with treating neurons as points in a simple Euclidean feature space, which would be important for constructing efficient searching or indexing structures over them. We present preliminary experimental results to demonstrate the effectiveness of our persistence-based neuronal feature vectorization framework. PMID:28809960

Structure and content of chronic kidney disease information on the World Wide Web: barriers to public understanding of a pandemic.

PubMed

Calderón, José Luis; Zadshir, Ashraf; Norris, Keith

2004-10-01

Chronic kidney disease (CKD) is a pandemic and the need to inform those at risk has never been more important. The World Wide Web (WWW) is no w considered a key source of health information, but the quality and utility of this information has been challenged. In this article, we assess structural, content, and linguistic barriers to accessed CKD information and discuss the implications of limited Internet access to communicating health. Technical (number of hyperlinks), content (number of six core CKD and risk factor information domains included), and linguistic (readability and variation in readability) barriers were assessed for websites offered by 12 kidney disease associations. The Flesch Reading Ease Index method was used to estimate readability scores, and variation in the readability of information was assessed. Eleven websites met inclusion criteria. Six of 11 websites provided information in all 6 domains of CKD information. A mean of 4 hyperlinks (range 3-5) was clicked before CKD information was available and a mean of 6 hyperlinks (range 4-12) was clicked to access all available CKD information. Mean readability scores for all six domains of CKD information exceeded national average literacy skills and far exceeded the 5th grade level readability desired for informing vulnerable populations. Information about CKD and diabetes consistently had higher readability scores. The WWW currently has little utility for informing populations at greatest risk for CKD. Barriers to accessing CKD information on the WWW are socioeconomic, technical, and linguistic. Having lower socioeconomic status, less access to computers and the WWW, multiple website hyperlinks, incomplete information, difficult readability, and significant variation in readability of CKD information on the WWW are social, structural, and content barriers to communicating CKD information. This may contribute to the growing epidemics of diminished public understanding about CKD, and disparities in CKD health status experienced by racial/ethnic minority populations globally.

User's guide for the Flight Design System (FDS)

NASA Technical Reports Server (NTRS)

Ramsey, H. R.; Atwood, M. E.; Frisius, W. G.; Turner, A. A.; Willoughby, J. K.

1980-01-01

Information about the Flight Design System (FDS) in the context of flight design is presented. The guide introduces the FDS user to the structure of FDS and to constructs within FDS (such as files of information or the part of FDS which interacts directly with the user). A guide to the commands available to FDS users is presented. A glossary of important terms, an index to terms, and a quick reference to the commands of FDS are included.

Drug Release Kinetics and Transport Mechanisms of Non-degradable and Degradable Polymeric Delivery Systems

PubMed Central

Fu, Yao; Kao, Weiyuan John

2010-01-01

Importance of the field The advancement in material design and engineering has led to the rapid development of novel materials with increasing complexity and functions. Both non-degradable and degradable polymers have found wide applications in the controlled delivery field. Studies on drug release kinetics provide important information into the function of material systems. To elucidate the detailed transport mechanism and the structure-function relationship of a material system, it is critical to bridge the gap between the macroscopic data and the transport behavior at the molecular level. Areas covered in this review The structure and function information of selected non-degradable and degradable polymers have been collected and summarized from literatures published after 1990s. The release kinetics of selected drug compounds from various material systems will be discussed in case studies. Recent progresses in the mathematical models based on different transport mechanisms will be highlighted. What the reader will gain This article aims to provide an overview of structure-function relationships of selected non-degradable and degradable polymers as drug delivery matrices. Take home message Understanding the structure-function relationship of the material system is key to the successful design of a delivery system for a particular application. Moreover, developing complex polymeric matrices requires more robust mathematical models to elucidate the solute transport mechanisms. PMID:20331353

Online Cancer Information Seeking: Applying and Extending the Comprehensive Model of Information Seeking.

PubMed

Van Stee, Stephanie K; Yang, Qinghua

2017-10-30

This study applied the comprehensive model of information seeking (CMIS) to online cancer information and extended the model by incorporating an exogenous variable: interest in online health information exchange with health providers. A nationally representative sample from the Health Information National Trends Survey 4 Cycle 4 was analyzed to examine the extended CMIS in predicting online cancer information seeking. Findings from a structural equation model supported most of the hypotheses derived from the CMIS, as well as the extension of the model related to interest in online health information exchange. In particular, socioeconomic status, beliefs, and interest in online health information exchange predicted utility. Utility, in turn, predicted online cancer information seeking, as did information-carrier characteristics. An unexpected but important finding from the study was the significant, direct relationship between cancer worry and online cancer information seeking. Theoretical and practical implications are discussed.

Adjoint-tomography for a Local Surface Structure: Methodology and a Blind Test

NASA Astrophysics Data System (ADS)

Kubina, Filip; Michlik, Filip; Moczo, Peter; Kristek, Jozef; Stripajova, Svetlana

2017-04-01

We have developed a multiscale full-waveform adjoint-tomography method for local surface sedimentary structures with complicated interference wavefields. The local surface sedimentary basins and valleys are often responsible for anomalous earthquake ground motions and corresponding damage in earthquakes. In many cases only relatively small number of records of a few local earthquakes is available for a site of interest. Consequently, prediction of earthquake ground motion at the site has to include numerical modeling for a realistic model of the local structure. Though limited, the information about the local structure encoded in the records is important and irreplaceable. It is therefore reasonable to have a method capable of using the limited information in records for improving a model of the local structure. A local surface structure and its interference wavefield require a specific multiscale approach. In order to verify our inversion method, we performed a blind test. We obtained synthetic seismograms at 8 receivers for 2 local sources, complete description of the sources, positions of the receivers and material parameters of the bedrock. We considered the simplest possible starting model - a homogeneous halfspace made of the bedrock. Using our inversion method we obtained an inverted model. Given the starting model, synthetic seismograms simulated for the inverted model are surprisingly close to the synthetic seismograms simulated for the true structure in the target frequency range up to 4.5 Hz. We quantify the level of agreement between the true and inverted seismograms using the L2 and time-frequency misfits, and, more importantly for earthquake-engineering applications, also using the goodness-of-fit criteria based on the earthquake-engineering characteristics of earthquake ground motion. We also verified the inverted model for other source-receiver configurations not used in the inversion.

Intergenerational transfers and informal care for disabled elderly persons in China: evidence from CHARLS.

PubMed

Liu, Xiaoting; Lu, Bei; Feng, Zhixin

2017-07-01

Aiming at 'ageing healthier and ageing better', a certain amount of high-quality informal care should be available for elderly persons with physical disability as formal care is barely accessible in China. The demographic transition and family structural changes have dramatically weakened traditional norms of filial piety and the structure of intergenerational transfers. This article employed nationwide representative data from the first wave (2011) of Chinese Health and Retirement Longitudinal Study (CHARLS) in order to identify the duration of informal care provision at home for frail elders (1122 in rural areas and 577 in urban areas, total 1699), measured in monthly hours, before estimating the associations between intergenerational transfers and the received time of informal care with Tobit Model analysis. Results showed that financial support from the younger generation was unexpectedly negatively associated with the monthly hours of care, implying a reduction of caring support along with increasing financial transfers towards older parents. The lack of informal care could not be compensated by having more children, co-residing with children, or increasing the parent-to-child/grandchild transfers. Spouses were shown to replace children as the major caregivers. In addition, the community-based long-term care system needs to be promoted to sustain and develop informal care, as the latter will become increasingly important with changing family dynamics. Finally, the received time of informal care, rather than the severity of physical disability measured by difficulty with ADLs or IADLs, was introduced to identify the actual demand for care by elders. The paper argues that it is important to reconceptualise and re-investigate the duration of care provision in the Chinese context in order to develop standards of payment as part of long-term care policies. © 2017 John Wiley & Sons Ltd.

Characterising protein, salt and water interactions with combined vibrational spectroscopic techniques.

PubMed

Perisic, Nebojsa; Afseth, Nils Kristian; Ofstad, Ragni; Hassani, Sahar; Kohler, Achim

2013-05-01

In this paper a combination of NIR spectroscopy and FTIR and Raman microspectroscopy was used to elucidate the effects of different salts (NaCl, KCl and MgSO(4)) on structural proteins and their hydration in muscle tissue. Multivariate multi-block technique Consensus Principal Component Analysis enabled integration of different vibrational spectroscopic techniques: macroscopic information obtained by NIR spectroscopy is directly related to microscopic information obtained by FTIR and Raman microspectroscopy. Changes in protein secondary structure observed at different concentrations of salts were linked to changes in protein hydration affinity. The evidence for this was given by connecting the underlying FTIR bands of the amide I region (1700-1600 cm(-1)) and the water region (3500-3000 cm(-1)) with water vibrations obtained by NIR spectroscopy. In addition, Raman microspectroscopy demonstrated that different cations affected structures of aromatic amino acid residues differently, which indicates that cation-π interactions play an important role in determination of the final structure of protein molecules. Copyright © 2012 Elsevier Ltd. All rights reserved.

On Cognition, Structured Sequence Processing, and Adaptive Dynamical Systems

NASA Astrophysics Data System (ADS)

Petersson, Karl Magnus

2008-11-01

Cognitive neuroscience approaches the brain as a cognitive system: a system that functionally is conceptualized in terms of information processing. We outline some aspects of this concept and consider a physical system to be an information processing device when a subclass of its physical states can be viewed as representational/cognitive and transitions between these can be conceptualized as a process operating on these states by implementing operations on the corresponding representational structures. We identify a generic and fundamental problem in cognition: sequentially organized structured processing. Structured sequence processing provides the brain, in an essential sense, with its processing logic. In an approach addressing this problem, we illustrate how to integrate levels of analysis within a framework of adaptive dynamical systems. We note that the dynamical system framework lends itself to a description of asynchronous event-driven devices, which is likely to be important in cognition because the brain appears to be an asynchronous processing system. We use the human language faculty and natural language processing as a concrete example through out.

Chemical Proteomics and Structural Biology Define EPHA2 Inhibition by Clinical Kinase Drugs.

PubMed

Heinzlmeir, Stephanie; Kudlinzki, Denis; Sreeramulu, Sridhar; Klaeger, Susan; Gande, Santosh Lakshmi; Linhard, Verena; Wilhelm, Mathias; Qiao, Huichao; Helm, Dominic; Ruprecht, Benjamin; Saxena, Krishna; Médard, Guillaume; Schwalbe, Harald; Kuster, Bernhard

2016-12-16

The receptor tyrosine kinase EPHA2 (Ephrin type-A receptor 2) plays important roles in oncogenesis, metastasis, and treatment resistance, yet therapeutic targeting, drug discovery, or investigation of EPHA2 biology is hampered by the lack of appropriate inhibitors and structural information. Here, we used chemical proteomics to survey 235 clinical kinase inhibitors for their kinase selectivity and identified 24 drugs with submicromolar affinities for EPHA2. NMR-based conformational dynamics together with nine new cocrystal structures delineated drug-EPHA2 interactions in full detail. The combination of selectivity profiling, structure determination, and kinome wide sequence alignment allowed the development of a classification system in which amino acids in the drug binding site of EPHA2 are categorized into key, scaffold, potency, and selectivity residues. This scheme should be generally applicable in kinase drug discovery, and we anticipate that the provided information will greatly facilitate the development of selective EPHA2 inhibitors in particular and the repurposing of clinical kinase inhibitors in general.

MULTISCALE TENSOR ANISOTROPIC FILTERING OF FLUORESCENCE MICROSCOPY FOR DENOISING MICROVASCULATURE.

PubMed

Prasath, V B S; Pelapur, R; Glinskii, O V; Glinsky, V V; Huxley, V H; Palaniappan, K

2015-04-01

Fluorescence microscopy images are contaminated by noise and improving image quality without blurring vascular structures by filtering is an important step in automatic image analysis. The application of interest here is to automatically extract the structural components of the microvascular system with accuracy from images acquired by fluorescence microscopy. A robust denoising process is necessary in order to extract accurate vascular morphology information. For this purpose, we propose a multiscale tensor with anisotropic diffusion model which progressively and adaptively updates the amount of smoothing while preserving vessel boundaries accurately. Based on a coherency enhancing flow with planar confidence measure and fused 3D structure information, our method integrates multiple scales for microvasculature preservation and noise removal membrane structures. Experimental results on simulated synthetic images and epifluorescence images show the advantage of our improvement over other related diffusion filters. We further show that the proposed multiscale integration approach improves denoising accuracy of different tensor diffusion methods to obtain better microvasculature segmentation.

Photogrammetric mapping for cadastral land information systems

NASA Astrophysics Data System (ADS)

Muzakidis, Panagiotis D.

The creation of a "clean" digital database is a most important and complex task, upon which the usefulness of a Parcel-Based Land Information System depends. Capturing data by photogrammetric methods for cadastral purposes necessitates the transformation of data into a computer compatible form. Such input requires the encoding, editing and structuring of data. The research is carried out in two phases, the first is concerned with defining the data modelling schemes and the classification of basic data for a parcel-based land information system together with the photogrammetric methods to be adopted to collect these data. The second deals with data editing and data structuring processes in order to produce "clean" information relevant to such a system. Implementation of the proposed system at both the data collection stage and within the data processing stage itself demands a number of flexible criteria to be defined within the methodology. Development of these criteria will include consideration of the cadastral characteristics peculiar to Greece.

Advance Directives as Support of Autonomy for Persons with Dementia? A Pilot Study among Persons with Dementia and Their Informal Caregivers.

PubMed

Schmidhuber, Martina; Haeupler, Sandra; Marinova-Schmidt, Velislava; Frewer, Andreas; Kolominsky-Rabas, Peter L

2017-01-01

Advance directives could be an important instrument to support a person's will once he/she is not able to consent anymore - if composed competently. A survey was conducted to identify the level of knowledge concerning possibilities and limits of advance directives. The study was conducted as part of the Bavarian Dementia Survey (BayDem). Data were collected from January 2014 to December 2015 by structured face-to-face interviews. Study participants were persons with dementia and their informal caregivers ( n = 74). In total, 66% reported having written an advance directive. Concerning the participants' knowledge about possibilities and limitations of advance directives, a lack of knowledge was noted about the possibility to revoke an advance directive. Furthermore, 70% of informal caregivers and 56% of persons with dementia were not aware of the possibility to include dementia-specific terms in the advance directive. It is necessary to optimize structures for public information and education concerning the topic of advance directives for persons with dementia.

BAYESIAN PROTEIN STRUCTURE ALIGNMENT.

PubMed

Rodriguez, Abel; Schmidler, Scott C

The analysis of the three-dimensional structure of proteins is an important topic in molecular biochemistry. Structure plays a critical role in defining the function of proteins and is more strongly conserved than amino acid sequence over evolutionary timescales. A key challenge is the identification and evaluation of structural similarity between proteins; such analysis can aid in understanding the role of newly discovered proteins and help elucidate evolutionary relationships between organisms. Computational biologists have developed many clever algorithmic techniques for comparing protein structures, however, all are based on heuristic optimization criteria, making statistical interpretation somewhat difficult. Here we present a fully probabilistic framework for pairwise structural alignment of proteins. Our approach has several advantages, including the ability to capture alignment uncertainty and to estimate key "gap" parameters which critically affect the quality of the alignment. We show that several existing alignment methods arise as maximum a posteriori estimates under specific choices of prior distributions and error models. Our probabilistic framework is also easily extended to incorporate additional information, which we demonstrate by including primary sequence information to generate simultaneous sequence-structure alignments that can resolve ambiguities obtained using structure alone. This combined model also provides a natural approach for the difficult task of estimating evolutionary distance based on structural alignments. The model is illustrated by comparison with well-established methods on several challenging protein alignment examples.

Divergent Synthesis of Chondroitin Sulfate Disaccharides and Identification of Sulfate Motifs that Inhibit Triple Negative Breast Cancer

NASA Astrophysics Data System (ADS)

Wei Poh, Zhong; Heng Gan, Chin; Lee, Eric J.; Guo, Suxian; Yip, George W.; Lam, Yulin

2015-09-01

Glycosaminoglycans (GAGs) regulate many important physiological processes. A pertinent issue to address is whether GAGs encode important functional information via introduction of position specific sulfate groups in the GAG structure. However, procurement of pure, homogenous GAG motifs to probe the “sulfation code” is a challenging task due to isolation difficulty and structural complexity. To this end, we devised a versatile synthetic strategy to obtain all the 16 theoretically possible sulfation patterns in the chondroitin sulfate (CS) repeating unit; these include rare but potentially important sulfated motifs which have not been isolated earlier. Biological evaluation indicated that CS sulfation patterns had differing effects for different breast cancer cell types, and the greatest inhibitory effect was observed for the most aggressive, triple negative breast cancer cell line MDA-MB-231.

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

A First Step Toward Understanding Nucleation Processes: in situ High-Temperature X-ray Diffraction and Absorption Investigations

NASA Astrophysics Data System (ADS)

Strukelj, E.; Neuville, D. R.; Cochain, B.; Hennet, L.; Thiaudière, D.; Guillot, B.; Roskosz, M.; Comte, M.; Richet, P.

2009-05-01

Nucleation is the first step of the transition between the amorphous and crystalline states and thus plays a key role in Earth and Materials sciences whenever crystallization takes place. In spite of its considerable importance in igneous petrology and industrial applications (ceramics, glass-ceramics, etc.), nucleation remains known poorly because of the difficulties of investigating the structural rearrangements that take place at a nm scale when an ordered atomic packing begins to develop in a melt. In addition, the structure of amorphous phases is not only difficult to determine, but the wealth of information available for glasses is not necessarily applicable to nucleation because of the existence of temperature-induced structural changes in melts. In view of the basic geological and industrial importance of the SiO2-Al2O3-CaO system, we have investigated a calcium aluminosilicate whose crystallization has already been studied. And because elements such as Ti or Zr can promote rapid nucleation, information can be gained about the structural changes they induce by probing specifically their own environment. In this work we have thus performed a high-temperature study of the very first steps of crystallization in a calcium aluminosilicate with 7 mol percent ZrO2 by X-ray absorption measurements at the Zr K-edge et 1873 K on the homogenous melt and 1173 K on a nucleating supercooled liquid. To complement these results with information on medium range order (MRO) X-Ray diffraction experiments have also been performed under the same conditions. As a reference, the glass has been investigated by both techniques at room temperature.

Entropy and information in flagellar axoneme cybernetics: a radial spokes integrative function.

PubMed

Cibert, Christian

2003-04-01

Radial spokes and the consequences of their relationships with the central apparatus seem to play a very important role in the regulation of axonemal activity. We modeled their behavior and observed that it appears to differ in the cilium and the flagellum with respect to the development of bending as a function of time. Specifically, our calculation raises the question of the real function of the radial spokes in the regulation of the axoneme, because a given curvature of the flagellar axoneme may correspond to two opposite of their tilts. The stable nil/low amplitude shear points that we had characterized along the flagellum allowed us to describe their axoneme as a series of modules [Cibert, 2002: Cell Motil. Cytoskeleton 51:89-111]. We observed that a nil/low shearing point moves along each module during beating when a new bend is created at the base of the flagellum [Cibert, 2001: Cell Motil. Cytoskeleton 49:161-175]. We propose that the structural gradients of isoforms of tubulin could be basic verniers that act as structural references for the axonemal machinery during the beating. This allowed us to interpret the axonemal organization as a segmented structure, that could be analyzed according to the complexion(1) theory and Shannon's information theory, which associate entropy and probability in the creation of information. The important consequence of this interpretation is that regulation of the axonemal machinery appears to be due to the upstream and downstream cross-talk between the axonemal segments that do not involve any dedicated integrative structure but depend on the energy level of the entire length of each module. Copyright 2003 Wiley-Liss, Inc.(1)Complexion was defined by Boltzman in 1877 and used by Planck in 1900 to calculate the energy distribution of a normal spectrum [Morowitz, 1970].

The demographic consequences of growing older and bigger in oyster populations.

PubMed

Moore, Jacob L; Lipcius, Romuald N; Puckett, Brandon; Schreiber, Sebastian J

2016-10-01

Structured population models, particularly size- or age-structured, have a long history of informing conservation and natural resource management. While size is often easier to measure than age and is the focus of many management strategies, age-structure can have important effects on population dynamics that are not captured in size-only models. However, relatively few studies have included the simultaneous effects of both age- and size-structure. To better understand how population structure, particularly that of age and size, impacts restoration and management decisions, we developed and compared a size-structured integral projection model (IPM) and an age- and size-structured IPM, using a population of Crassostrea gigas oysters in the northeastern Pacific Ocean. We analyzed sensitivity of model results across values of local retention that give populations decreasing in size to populations increasing in size. We found that age- and size-structured models yielded the best fit to the demographic data and provided more reliable results about long-term demography. Elasticity analysis showed that population growth rate was most sensitive to changes in the survival of both large (>175 mm shell length) and small (<75 mm shell length) oysters, indicating that a maximum size limit, in addition to a minimum size limit, could be an effective strategy for maintaining a sustainable population. In contrast, the purely size-structured model did not detect the importance of large individuals. Finally, patterns in stable age and stable size distributions differed between populations decreasing in size due to limited local retention and populations increasing in size due to high local retention. These patterns can be used to determine population status and restoration success. The methodology described here provides general insight into the necessity of including both age- and size-structure into modeling frameworks when using population models to inform restoration and management decisions. © 2016 by the Ecological Society of America.

Atomic-level structural correlations across the morphotropic phase boundary of a ferroelectric solid solution: xBiMg 1/2Ti 1/2O 3-(1$-$x)PbTiO 3

DOE PAGES

Datta, Kaustuv; Neder, Reinhard B.; Chen, Jun; ...

2017-03-28

Revelation of unequivocal structural information at the atomic level for complex systems is uniquely important for deeper and generic understanding of the structure property connections and a key challenge in materials science. Here in this paper we report an experimental study of the local structure by applying total elastic scattering and Raman scattering analyses to an important non-relaxor ferroelectric solid solution exhibiting the so-called composition-induced morphotropic phase boundary (MPB), where concomitant enhancement of physical properties have been detected. The powerful combination of static and dynamic structural probes enabled us to derive direct correspondence between the atomic-level structural correlations and reportedmore » properties. The atomic pair distribution functions obtained from the neutron total scattering experiments were analysed through big-box atom-modelling implementing reverse Monte Carlo method, from which distributions of magnitudes and directions of off-centred cationic displacements were extracted. We found that an enhanced randomness of the displacement-directions for all ferroelectrically active cations combined with a strong dynamical coupling between the A- and B-site cations of the perovskite structure, can explain the abrupt amplification of piezoelectric response of the system near MPB. Finally, altogether this provides a more fundamental basis in inferring structure-property connections in similar systems including important implications in designing novel and bespoke materials.« less

Women Empowerment through Health Information Seeking: A Qualitative Study

PubMed Central

Nikbakht Nasrabadi, Alireza; Sabzevari, Sakineh; Negahban Bonabi, Tayebeh

2015-01-01

Background Today, women empowering is an important issue.  Several methods have been introduced to empower women. Health information seeking is one of the most important activities in this regard. A wide range of capabilities have been reported as outcomes of health information seeking in several studies. As health information seeking is developed within personal-social interactions and also the health system context, it seems that the qualitative paradigm is appropriate to use in studies in this regard. This study aimed to explore how women’s empowerment through health information seeking is done. Methods In this qualitative content analysis study, data collection was done with regard to inclusion criteria, through purposive sampling by semi-structured interviews with 17 women and using documentation and field notes until data saturation. Qualitative data analysis was done constantly and simultaneous with data collection. Results Four central themes were emerged to explain women’s empowerment through health information seeking that included: a) Health concerns management with three subcategories of Better coping, Stress management, Control of situation, b) Collaborative care with two subcategories of Effective interaction with health professions and Participation in health decision making c) Individual development d) Self-protection with four sub- categories of Life style modification,  Preventive behaviors promoting, Self-care promoting, and  medication adherence. Conclusion The results of this study indicate the importance of women empowerment through foraging their health information seeking rights and comprehensive health information management. PMID:26005690

The Dams and Monitoring Systems and Case Study: Ataturk and Karakaya Dams

NASA Astrophysics Data System (ADS)

Kalkan, Y.; Bilgi, S.; Gülnerman, A. G.

2017-12-01

Dams are among the most important engineering structures used for flood controls, agricultural purposes as well as drinking and hydroelectric power. Especially after the Second World War, developments on the construction technology, increase the construction of larger capacity dams. There are more than 150.000 dams in the world and almost 1000 dams in Turkey, according to international criteria. Although dams provide benefits to humans, they possess structural risks too. To determine the performance of dams on structural safety, assessing the spatial data is very important. These are movement, water pressure, seepage, reservoir and tail-water elevations, local seismic activities, total pressure, stress and strain, internal concrete temperature, ambient temperature and precipitation. These physical data are measured and monitored by the instruments and equipment. Dams and their surroundings have to be monitored by using essential methods at periodic time intervals in order to determine the possible changes that may occur over the time. Monitoring programs typically consist of; surveillance or visual observation. These programs on dams provide information for evaluating the dam's performance related to the design intent and expected changes that could affect the safety performance of the dam. Additionally, these programs are used for investigating and evaluating the abnormal or degrading performance where any remedial action is necessary. Geodetic and non-geodetic methods are used for monitoring. Monitoring the performance of the dams is critical for producing and maintaining the safe dams. This study provides some general information on dams and their different monitoring systems by taking into account two different dams and their structural specifications with the required information. The case study in this paper depends on a comparison of the monitoring surveys on Atatürk Dam and Karakaya Dam, which are constructed on Firat River with two different structural type in Turkey. In addition, brief information is given about these dams and the methods of geodetic and non-geodetic monitoring measurements applied by various disciplines. The last part of the study focuses on the inference of the geodetic monitoring methods, which depend on a seven years of geodetic monitoring.

A case study of the use of GPR for rehabilitation of a classified Art Deco building: The InovaDomus house

NASA Astrophysics Data System (ADS)

Barraca, Nuno; Almeida, Miguel; Varum, Humberto; Almeida, Fernando; Matias, Manuel Senos

2016-04-01

Ancient buildings in historical town centers can be protected by Cultural Heritage legislation, thus implying that any rehabilitation must respect their main architectural features. These concerns also apply to Modern and Contemporary buildings, in particular if they are important examples of architectural styles from those periods. These extra problems, or motivations, add to the inherent structural delicacy of ancient building restoration that requires detailed knowledge of the building foundations, characteristics and materials, modification history, infrastructure mapping, current pathologies, etc., all relevant information for an informed rehabilitation project. Such knowledge is seldom available before the actual rehabilitation works begin, and the usual invasive preliminary surveys are frequently expensive, time-consuming and likely significantly alter/damage the building's main features or structural integrity. Hence, the current demand for indirect, non-invasive, reliable and high resolution imagery techniques able to produce relevant information at the early stages of a rehabilitation project. The present work demonstrates that Ground Penetrating Radar (GPR or Georadar) surveys can provide a priori knowledge on the structure, construction techniques, materials, history and pathologies in a classified Modern Age building. It is also shown that the use of GPR on these projects requires carefully designed surveys, taking into account the known information, spatial constraints, environmental noise, nature and dimensions of the expected targets and suitable data processing sequences. Thus, if properly applied, GPR produces high-resolution results crucial for sound engineering/architectural interventions aiming to restore and renovate Modern and Contemporary buildings, with (1) focus on the overall quality of the end-result, (2) no damage inflicted to the existing structure, (3) respect of the building's historical coherence and architectural elements and characteristics, that is, its Cultural Heritage value. Most of the findings and applications discussed in this work can be seen as an approximation to model studies, so that, relevant information can be drawn from the different investigated situations. Therefore, owing to the nature and the range of the problems encountered in this case study, it is also expected that the presented GPR data and interpretation will provide important clues and guidance in the planning and investigation of similar projects and problems.

A Weld Position Recognition Method Based on Directional and Structured Light Information Fusion in Multi-Layer/Multi-Pass Welding.

PubMed

Zeng, Jinle; Chang, Baohua; Du, Dong; Wang, Li; Chang, Shuhe; Peng, Guodong; Wang, Wenzhu

2018-01-05

Multi-layer/multi-pass welding (MLMPW) technology is widely used in the energy industry to join thick components. During automatic welding using robots or other actuators, it is very important to recognize the actual weld pass position using visual methods, which can then be used not only to perform reasonable path planning for actuators, but also to correct any deviations between the welding torch and the weld pass position in real time. However, due to the small geometrical differences between adjacent weld passes, existing weld position recognition technologies such as structured light methods are not suitable for weld position detection in MLMPW. This paper proposes a novel method for weld position detection, which fuses various kinds of information in MLMPW. First, a synchronous acquisition method is developed to obtain various kinds of visual information when directional light and structured light sources are on, respectively. Then, interferences are eliminated by fusing adjacent images. Finally, the information from directional and structured light images is fused to obtain the 3D positions of the weld passes. Experiment results show that each process can be done in 30 ms and the deviation is less than 0.6 mm. The proposed method can be used for automatic path planning and seam tracking in the robotic MLMPW process as well as electron beam freeform fabrication process.

Agricultural conservation planning framework: 3. Land use and field boundary database development and structure

USDA-ARS?s Scientific Manuscript database

Conservation planning information is important in identifying options for watershed water quality improvement, and can be developed for use at field, farm, and watershed scales. Translation across scales is a key issue impeding progress at watershed scales because watershed improvement goals must be...

High School Technical Education--High Prerequisite for Getting a Job

ERIC Educational Resources Information Center

Paprokova, Anna

2013-01-01

The paper is theoretically based on the concept of "postindustrial" (information) society (Bell, 1973) where the importance of education is emphasized and caused by changes in the structure of employment rate, growing intellectual labor exigence as well as higher unemployment rate of individuals of the lowest educational category.…

How Design Guides Learning from Matrix Diagrams

ERIC Educational Resources Information Center

van der Meij, Jan; van Amelsvoort, Marije; Anjewierden, Anjo

2017-01-01

Compared to text, diagrams are superior in their ability to structure and summarize information and to show relations between concepts and ideas. Perceptual cues, like arrows, are expected to improve the retention of diagrams by guiding the learner towards important elements or showing a preferred reading sequence. In our experiment, we analyzed…

Phonetics and Phonology of Thematic Contrast in German

ERIC Educational Resources Information Center

Braun, Bettina

2006-01-01

It is acknowledged that contrast plays an important role in understanding discourse and information structure. While it is commonly assumed that contrast can be marked by intonation only, our understanding of the intonational realization of contrast is limited. For German there is mainly introspective evidence that the rising theme accent (or…

Metaphor in Professional Counseling

ERIC Educational Resources Information Center

Wagener, Alwin E.

2017-01-01

Metaphors are linked to how individuals process information and emotions, and they are important to understand and utilize in counseling. A description of the structure of metaphors and metaphor theory is provided. The role of metaphors in emotional processing is explained, and the process of counseling is tied to the therapeutic usage of…

Geography of genetic differentiation in the barley wild relative Hordeum vulgare subsp. spontaneum in Jordan

USDA-ARS?s Scientific Manuscript database

Informed collecting, conservation, monitoring and utilization of genetic diversity require knowledge of the distribution and structure of genetic variation occurring in a species. Hordeum vulgare subsp. spontaneum (K. Koch) Thell., a primary wild relative of barley, is an important source of genetic...

Value of decision analysis in stakeholder interactions for the restoration and recovery from the Gulf of Mexico oil spill

EPA Science Inventory

The importance of stakeholder involvement in the management of watersheds is receiving greater recognition than in the past; however, interacting with stakeholders is frequently accomplished using informal procedures. It is essential to structure elicitations so that they can be ...

The Relationship between Students' Epistemologies and Model-Based Reasoning.

ERIC Educational Resources Information Center

Gobert, Janice; Discenna, Jennifer

Models and modeling are frequently used as instructional tools in science education to convey important information concerning both the explanatory and structural features of topic areas in science. The efficacy of models as such rests almost entirely upon students' ability to conceptualize them as abstracted "representations" of…

Tropical Rainforest Education. ERIC Digest.

ERIC Educational Resources Information Center

Rillero, Peter

This digest provides four guideposts for tropical rainforest education: (1) structure; (2) location and climate; (3) importance; and (4) conservation of resources. Research is cited and background information provided about the layers of life and the adaptations of life within the tropical rain forest. Aspects of life within and near rain forests…

Daybooks: A Book for Your Mind

ERIC Educational Resources Information Center

Keith, Karin J.; Pridemore, Celeste B.

2014-01-01

This article explains how to create and use a daybook in the literacy classroom. Readers learn what a daybook is, how the daybook in one fourth and fifth grade classroom is structured, and how students in this classroom use that daybook during reading instruction to engage, record important information, and discuss a text.

Quantifying extreme precipitation events and their hydrologic response in Southeastern Arizona

USDA-ARS?s Scientific Manuscript database

Design criteria such as rainfall intensities and runoff rates for small watersheds (<200km2) are needed for modeling, sizing and design of drainage and flood control structures. In the Southwest US the need for accurate information about these rates is increasingly important as development of range...

Section summary: Remote sensing

Treesearch

Belinda Arunarwati Margono

2013-01-01

Remote sensing is an important data source for monitoring the change of forest cover, in terms of both total removal of forest cover (deforestation), and change of canopy cover, structure and forest ecosystem services that result in forest degradation. In the context of Intergovernmental Panel on Climate Change (IPCC), forest degradation monitoring requires information...

75 FR 64694 - Second Antidumping Duty Administrative Review of Certain Polyester Staple Fiber From the People's...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-10-20

... Limit for the Final Results Agency: Import Administration, International Trade Administration... significant amount of information pertaining to the respondents' corporate structure and ownership, sales practices and manufacturing methods, as well as the labor wage rate surrogate value. Therefore, given the...

Are Grade Expectations Rational? A Classroom Experiment

ERIC Educational Resources Information Center

Hossain, Belayet; Tsigaris, Panagiotis

2015-01-01

This study examines students' expectations about their final grade. An attempt is made to determine whether students form expectations rationally. Expectations in economics, rational or otherwise, carry valuable information and have important implications in terms of both teaching effectiveness and the role of grades as an incentive structure for…

Using Diagrams as Tools for the Solution of Non-Routine Mathematical Problems

ERIC Educational Resources Information Center

Pantziara, Marilena; Gagatsis, Athanasios; Elia, Iliada

2009-01-01

The Mathematics education community has long recognized the importance of diagrams in the solution of mathematical problems. Particularly, it is stated that diagrams facilitate the solution of mathematical problems because they represent problems' structure and information (Novick & Hurley, 2001; Diezmann, 2005). Novick and Hurley were the first…

Nibbling at the Core.

ERIC Educational Resources Information Center

D'Antonio, William V.

1983-01-01

Outlined is a body of knowledge, the core of sociology, that belongs in the introductory sociology course. How the course is taught is also important. Class sections should be small; students should be required to write a great deal; and an informal, but structured setting should stimulate student- teacher interaction. (Author/RM)

Which information resources are used by general practitioners for updating knowledge regarding diabetes?

PubMed

Tabatabaei-Malazy, Ozra; Nedjat, Saharnaz; Majdzadeh, Reza

2012-04-01

Little is known about the degree of utilization of information resources on diabetes by general practitioners (GPs) and its impact on their clinical behavior in developing countries. Such information is vital if GPs' diabetes knowledge is to be improved. This cross-sectional study recruited 319 GPs in the summer of 2008. Questions were about the updates on diabetes knowledge in the previous two years, utilization of information resources (domestic and foreign journals, congresses, the Internet, reference books, mass media, and peers), attitude toward the importance of each resource, and impact of each resource on clinical behavior. A total of 62% of GPs had used information resources for improving their knowledge on diabetes in the previous two years. Domestic journals accounted for the highest utilization (30%) and the highest importance score (83 points from 100); with the importance score not being affected by sex, years elapsed after graduation, and numbers of diabetic visits. Clinical behavior was not influenced by the information resources listed; whereas knowledge upgrade, irrespective of the sources utilized, had a significantly positive correlation with clinical behavior. Domestic journals constituted the main information resource utilized by the GPs; this resource, however, in tandem with the other information resources on diabetes exerted no significant impact on the GPs' clinical behavior. In contrast to the developed countries, clinical guidelines do not have any place as a source of information and or practice. Indubitably, the improvement of diabetes knowledge transfer requires serious interventions to improve information resources as well as the structure of scientific gatherings and collaborations.

Multiple-wavelength neutron holography with pulsed neutrons

PubMed Central

Hayashi, Kouichi; Ohoyama, Kenji; Happo, Naohisa; Matsushita, Tomohiro; Hosokawa, Shinya; Harada, Masahide; Inamura, Yasuhiro; Nitani, Hiroaki; Shishido, Toetsu; Yubuta, Kunio

2017-01-01

Local structures around impurities in solids provide important information for understanding the mechanisms of material functions, because most of them are controlled by dopants. For this purpose, the x-ray absorption fine structure method, which provides radial distribution functions around specific elements, is most widely used. However, a similar method using neutron techniques has not yet been developed. If one can establish a method of local structural analysis with neutrons, then a new frontier of materials science can be explored owing to the specific nature of neutron scattering—that is, its high sensitivity to light elements and magnetic moments. Multiple-wavelength neutron holography using the time-of-flight technique with pulsed neutrons has great potential to realize this. We demonstrated multiple-wavelength neutron holography using a Eu-doped CaF2 single crystal and obtained a clear three-dimensional atomic image around trivalent Eu substituted for divalent Ca, revealing an interesting feature of the local structure that allows it to maintain charge neutrality. The new holography technique is expected to provide new information on local structures using the neutron technique. PMID:28835917

Multiple-wavelength neutron holography with pulsed neutrons.

PubMed

Hayashi, Kouichi; Ohoyama, Kenji; Happo, Naohisa; Matsushita, Tomohiro; Hosokawa, Shinya; Harada, Masahide; Inamura, Yasuhiro; Nitani, Hiroaki; Shishido, Toetsu; Yubuta, Kunio

2017-08-01

Local structures around impurities in solids provide important information for understanding the mechanisms of material functions, because most of them are controlled by dopants. For this purpose, the x-ray absorption fine structure method, which provides radial distribution functions around specific elements, is most widely used. However, a similar method using neutron techniques has not yet been developed. If one can establish a method of local structural analysis with neutrons, then a new frontier of materials science can be explored owing to the specific nature of neutron scattering-that is, its high sensitivity to light elements and magnetic moments. Multiple-wavelength neutron holography using the time-of-flight technique with pulsed neutrons has great potential to realize this. We demonstrated multiple-wavelength neutron holography using a Eu-doped CaF 2 single crystal and obtained a clear three-dimensional atomic image around trivalent Eu substituted for divalent Ca, revealing an interesting feature of the local structure that allows it to maintain charge neutrality. The new holography technique is expected to provide new information on local structures using the neutron technique.

Structural Chemistry of Human RNA Methyltransferases.

PubMed

Schapira, Matthieu

2016-03-18

RNA methyltransferases (RNMTs) play important roles in RNA stability, splicing, and epigenetic mechanisms. They constitute a promising target class that is underexplored by the medicinal chemistry community. Information of relevance to drug design can be extracted from the rich structural coverage of human RNMTs. In this work, the structural chemistry of this protein family is analyzed in depth. Unlike most methyltransferases, RNMTs generally feature a substrate-binding site that is largely open on the cofactor-binding pocket, favoring the design of bisubstrate inhibitors. Substrate purine or pyrimidines are often sandwiched between hydrophobic walls that can accommodate planar ring systems. When the substrate base is laying on a shallow surface, a 5' flanking base is sometimes anchored in a druggable cavity. The cofactor-binding site is structurally more diverse than in protein methyltransferases and more druggable in SPOUT than in Rossman-fold enzymes. Finally, conformational plasticity observed both at the substrate and cofactor binding sites may be a challenge for structure-based drug design. The landscape drawn here may inform ongoing efforts toward the discovery of the first human RNMT inhibitors.

Spatial vision processes: From the optical image to the symbolic structures of contour information

NASA Technical Reports Server (NTRS)

Jobson, Daniel J.

1988-01-01

The significance of machine and natural vision is discussed together with the need for a general approach to image acquisition and processing aimed at recognition. An exploratory scheme is proposed which encompasses the definition of spatial primitives, intrinsic image properties and sampling, 2-D edge detection at the smallest scale, the construction of spatial primitives from edges, and the isolation of contour information from textural information. Concepts drawn from or suggested by natural vision at both perceptual and physiological levels are relied upon heavily to guide the development of the overall scheme. The scheme is intended to provide a larger context in which to place the emerging technology of detector array focal-plane processors. The approach differs from many recent efforts in edge detection and image coding by emphasizing smallest scale edge detection as a foundation for multi-scale symbolic processing while diminishing somewhat the importance of image convolutions with multi-scale edge operators. Cursory treatments of information theory illustrate that the direct application of this theory to structural information in images could not be realized.

Research on nursing handoffs for medical and surgical settings: an integrative review.

PubMed

Staggers, Nancy; Blaz, Jacquelyn W

2013-02-01

To synthesize outcomes from research on handoffs to guide future computerization of the process on medical and surgical units. Handoffs can create important information gaps, omissions and errors in patient care. Authors call for the computerization of handoffs; however, a synthesis of the literature is not yet available that might guide computerization. PubMed, CINAHL, Cochrane, PsycINFO, Scopus and a handoff database from Cohen and Hilligoss. Integrative literature review. This integrative review included studies from 1980-March 2011 in peer-reviewed journals. Exclusions were studies outside medical and surgical units, handoff education and nurses' perceptions. The search strategy yielded a total of 247 references; 81 were retrieved, read and rated for relevance and research quality. A set of 30 articles met relevance criteria. Studies about handoff functions and rituals are saturated topics. Verbal handoffs serve important functions beyond information transfer and should be retained. Greater consideration is needed on analysing handoffs from a patient-centred perspective. Handoff methods should be highly tailored to nurses and their contextual needs. The current preference for bedside handoffs is not supported by available evidence. The specific handoff structure for all units may be less important than having a structure for contextually based handoffs. Research on pertinent information content for contextually based handoffs is an urgent need. Without it, handoff computerization is not likely to be successful. Researchers need to use more sophisticated experimental research designs, control for individual and unit differences and improve sampling frames. © 2012 Blackwell Publishing Ltd.

Correlation filtering in financial time series (Invited Paper)

NASA Astrophysics Data System (ADS)

Aste, T.; Di Matteo, Tiziana; Tumminello, M.; Mantegna, R. N.

2005-05-01

We apply a method to filter relevant information from the correlation coefficient matrix by extracting a network of relevant interactions. This method succeeds to generate networks with the same hierarchical structure of the Minimum Spanning Tree but containing a larger amount of links resulting in a richer network topology allowing loops and cliques. In Tumminello et al.,1 we have shown that this method, applied to a financial portfolio of 100 stocks in the USA equity markets, is pretty efficient in filtering relevant information about the clustering of the system and its hierarchical structure both on the whole system and within each cluster. In particular, we have found that triangular loops and 4 element cliques have important and significant relations with the market structure and properties. Here we apply this filtering procedure to the analysis of correlation in two different kind of interest rate time series (16 Eurodollars and 34 US interest rates).

Towards Effective Clustering Techniques for the Analysis of Electric Power Grids

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

Hogan, Emilie A.; Cotilla Sanchez, Jose E.; Halappanavar, Mahantesh

2013-11-30

Clustering is an important data analysis technique with numerous applications in the analysis of electric power grids. Standard clustering techniques are oblivious to the rich structural and dynamic information available for power grids. Therefore, by exploiting the inherent topological and electrical structure in the power grid data, we propose new methods for clustering with applications to model reduction, locational marginal pricing, phasor measurement unit (PMU or synchrophasor) placement, and power system protection. We focus our attention on model reduction for analysis based on time-series information from synchrophasor measurement devices, and spectral techniques for clustering. By comparing different clustering techniques onmore » two instances of realistic power grids we show that the solutions are related and therefore one could leverage that relationship for a computational advantage. Thus, by contrasting different clustering techniques we make a case for exploiting structure inherent in the data with implications for several domains including power systems.« less

Evaluation of nonmetallic thermal protection materials for the manned space shuttle. Volume 1, task 1: Assessment of technical risks associated with utilization of nonmetallic thermal protection system

NASA Technical Reports Server (NTRS)

Wilkinson, W. H.; Kirkhart, F. P.; Kistler, C. W.; Duckworth, W. H.; Ungar, E. W.; Foster, E. L.

1970-01-01

Technical problems of design and flight qualification of the proposed classes of surface insulation materials and leading edge materials were reviewed. A screening test plan, a preliminary design data test plan and a design data test plan were outlined. This program defined the apparent critical differences between the surface insulators and the leading edge materials, structuring specialized screening test plans for each of these two classes of materials. Unique testing techniques were shown to be important in evaluating the structural interaction aspects of the surface insulators and a separate task was defined to validate the test plan. In addition, a compilation was made of available information on proposed material (including metallic TPS), previous shuttle programs, pertinent test procedures, and other national programs of merit. This material was collected and summarized in an informally structured workbook.

The way to uncover community structure with core and diversity

NASA Astrophysics Data System (ADS)

Chang, Y. F.; Han, S. K.; Wang, X. D.

2018-07-01

Communities are ubiquitous in nature and society. Individuals that share common properties often self-organize to form communities. Avoiding the shortages of computation complexity, pre-given information and unstable results in different run, in this paper, we propose a simple and efficient method to deepen our understanding of the emergence and diversity of communities in complex systems. By introducing the rational random selection, our method reveals the hidden deterministic and normal diverse community states of community structure. To demonstrate this method, we test it with real-world systems. The results show that our method could not only detect community structure with high sensitivity and reliability, but also provide instructional information about the hidden deterministic community world and the real normal diverse community world by giving out the core-community, the real-community, the tide and the diversity. Thizs is of paramount importance in understanding, predicting, and controlling a variety of collective behaviors in complex systems.

Water oxidation chemistry of photosystem II.

PubMed

Brudvig, Gary W

2008-03-27

Photosystem II (PSII) uses light energy to split water into protons, electrons and O2. In this reaction, nature has solved the difficult chemical problem of efficient four-electron oxidation of water to yield O2 without significant amounts of reactive intermediate species such as superoxide, hydrogen peroxide and hydroxyl radicals. In order to use nature's solution for the design of artificial catalysts that split water, it is important to understand the mechanism of the reaction. The recently published X-ray crystal structures of cyanobacterial PSII complexes provide information on the structure of the Mn and Ca ions, the redox-active tyrosine called YZ and the surrounding amino acids that comprise the O2-evolving complex (OEC). The emerging structure of the OEC provides constraints on the different hypothesized mechanisms for O2 evolution. The water oxidation mechanism of PSII is discussed in the light of biophysical and computational studies, inorganic chemistry and X-ray crystallographic information.

Tackling both the player and the ball: lessons from crystallographic studies on the N-utilization substance B (NusB) from Mycobacterium tuberculosis

NASA Astrophysics Data System (ADS)

Haire, L. F.; Gopal, B.

2001-11-01

The N-utilization substance B (NusB) from Mycobacterium tuberculosis is an important element in a complex assembly of other proteins and ribonucleic acid effecting transcription antitermination in this organism. The cloning and overexpression of the protein in E. coli, followed by the purification, crystallization, and use of selenomethionine samples to obtain phase information by anomalous dispersion techniques, allows us to investigate the fine interplay of sample engineering and modification of crystallization parameters leading to successful structure determination. Knowledge of the crystal structure and the surface properties of the protein allows an analysis of the packing of the NusB dimers in the crystal lattice. This exercise, albeit post facto, helps to demonstrate how biophysical and functional information could help 'rationalize' the course of obtaining protein crystals suitable for structural studies.

Intelligent Access to Sequence and Structure Databases (IASSD) - an interface for accessing information from major web databases.

PubMed

Ganguli, Sayak; Gupta, Manoj Kumar; Basu, Protip; Banik, Rahul; Singh, Pankaj Kumar; Vishal, Vineet; Bera, Abhisek Ranjan; Chakraborty, Hirak Jyoti; Das, Sasti Gopal

2014-01-01

With the advent of age of big data and advances in high throughput technology accessing data has become one of the most important step in the entire knowledge discovery process. Most users are not able to decipher the query result that is obtained when non specific keywords or a combination of keywords are used. Intelligent access to sequence and structure databases (IASSD) is a desktop application for windows operating system. It is written in Java and utilizes the web service description language (wsdl) files and Jar files of E-utilities of various databases such as National Centre for Biotechnology Information (NCBI) and Protein Data Bank (PDB). Apart from that IASSD allows the user to view protein structure using a JMOL application which supports conditional editing. The Jar file is freely available through e-mail from the corresponding author.

An Informationally Structured Room for Robotic Assistance †

PubMed Central

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

2015-01-01

The application of assistive technologies for elderly people is one of the most promising and interesting scenarios for intelligent technologies in the present and near future. Moreover, the improvement of the quality of life for the elderly is one of the first priorities in modern countries and societies. In this work, we present an informationally structured room that is aimed at supporting the daily life activities of elderly people. This room integrates different sensor modalities in a natural and non-invasive way inside the environment. The information gathered by the sensors is processed and sent to a centralized management system, which makes it available to a service robot assisting the people. One important restriction of our intelligent room is reducing as much as possible any interference with daily activities. Finally, this paper presents several experiments and situations using our intelligent environment in cooperation with our service robot. PMID:25912347

Time Allocation in Social Networks: Correlation Between Social Structure and Human Communication Dynamics

NASA Astrophysics Data System (ADS)

Miritello, Giovanna; Lara, Rubén; Moro, Esteban

Recent research has shown the deep impact of the dynamics of human interactions (or temporal social networks) on the spreading of information, opinion formation, etc. In general, the bursty nature of human interactions lowers the interaction between people to the extent that both the speed and reach of information diffusion are diminished. Using a large database of 20 million users of mobile phone calls we show evidence this effect is not homogeneous in the social network but in fact, there is a large correlation between this effect and the social topological structure around a given individual. In particular, we show that social relations of hubs in a network are relatively weaker from the dynamical point than those that are poorer connected in the information diffusion process. Our results show the importance of the temporal patterns of communication when analyzing and modeling dynamical process on social networks.

Statistical discovery of site inter-dependencies in sub-molecular hierarchical protein structuring

PubMed Central

2012-01-01

Background Much progress has been made in understanding the 3D structure of proteins using methods such as NMR and X-ray crystallography. The resulting 3D structures are extremely informative, but do not always reveal which sites and residues within the structure are of special importance. Recently, there are indications that multiple-residue, sub-domain structural relationships within the larger 3D consensus structure of a protein can be inferred from the analysis of the multiple sequence alignment data of a protein family. These intra-dependent clusters of associated sites are used to indicate hierarchical inter-residue relationships within the 3D structure. To reveal the patterns of associations among individual amino acids or sub-domain components within the structure, we apply a k-modes attribute (aligned site) clustering algorithm to the ubiquitin and transthyretin families in order to discover associations among groups of sites within the multiple sequence alignment. We then observe what these associations imply within the 3D structure of these two protein families. Results The k-modes site clustering algorithm we developed maximizes the intra-group interdependencies based on a normalized mutual information measure. The clusters formed correspond to sub-structural components or binding and interface locations. Applying this data-directed method to the ubiquitin and transthyretin protein family multiple sequence alignments as a test bed, we located numerous interesting associations of interdependent sites. These clusters were then arranged into cluster tree diagrams which revealed four structural sub-domains within the single domain structure of ubiquitin and a single large sub-domain within transthyretin associated with the interface among transthyretin monomers. In addition, several clusters of mutually interdependent sites were discovered for each protein family, each of which appear to play an important role in the molecular structure and/or function. Conclusions Our results demonstrate that the method we present here using a k-modes site clustering algorithm based on interdependency evaluation among sites obtained from a sequence alignment of homologous proteins can provide significant insights into the complex, hierarchical inter-residue structural relationships within the 3D structure of a protein family. PMID:22793672

Statistical discovery of site inter-dependencies in sub-molecular hierarchical protein structuring.

PubMed

Durston, Kirk K; Chiu, David Ky; Wong, Andrew Kc; Li, Gary Cl

2012-07-13

Much progress has been made in understanding the 3D structure of proteins using methods such as NMR and X-ray crystallography. The resulting 3D structures are extremely informative, but do not always reveal which sites and residues within the structure are of special importance. Recently, there are indications that multiple-residue, sub-domain structural relationships within the larger 3D consensus structure of a protein can be inferred from the analysis of the multiple sequence alignment data of a protein family. These intra-dependent clusters of associated sites are used to indicate hierarchical inter-residue relationships within the 3D structure. To reveal the patterns of associations among individual amino acids or sub-domain components within the structure, we apply a k-modes attribute (aligned site) clustering algorithm to the ubiquitin and transthyretin families in order to discover associations among groups of sites within the multiple sequence alignment. We then observe what these associations imply within the 3D structure of these two protein families. The k-modes site clustering algorithm we developed maximizes the intra-group interdependencies based on a normalized mutual information measure. The clusters formed correspond to sub-structural components or binding and interface locations. Applying this data-directed method to the ubiquitin and transthyretin protein family multiple sequence alignments as a test bed, we located numerous interesting associations of interdependent sites. These clusters were then arranged into cluster tree diagrams which revealed four structural sub-domains within the single domain structure of ubiquitin and a single large sub-domain within transthyretin associated with the interface among transthyretin monomers. In addition, several clusters of mutually interdependent sites were discovered for each protein family, each of which appear to play an important role in the molecular structure and/or function. Our results demonstrate that the method we present here using a k-modes site clustering algorithm based on interdependency evaluation among sites obtained from a sequence alignment of homologous proteins can provide significant insights into the complex, hierarchical inter-residue structural relationships within the 3D structure of a protein family.

Evolution of Integrated Causal Structures in Animats Exposed to Environments of Increasing Complexity

PubMed Central

Albantakis, Larissa; Hintze, Arend; Koch, Christof; Adami, Christoph; Tononi, Giulio

2014-01-01

Natural selection favors the evolution of brains that can capture fitness-relevant features of the environment's causal structure. We investigated the evolution of small, adaptive logic-gate networks (“animats”) in task environments where falling blocks of different sizes have to be caught or avoided in a ‘Tetris-like’ game. Solving these tasks requires the integration of sensor inputs and memory. Evolved networks were evaluated using measures of information integration, including the number of evolved concepts and the total amount of integrated conceptual information. The results show that, over the course of the animats' adaptation, i) the number of concepts grows; ii) integrated conceptual information increases; iii) this increase depends on the complexity of the environment, especially on the requirement for sequential memory. These results suggest that the need to capture the causal structure of a rich environment, given limited sensors and internal mechanisms, is an important driving force for organisms to develop highly integrated networks (“brains”) with many concepts, leading to an increase in their internal complexity. PMID:25521484

Fan Beam Emission Tomography for Laminar Fires

NASA Technical Reports Server (NTRS)

Sivathanu, Yudaya; Lim, Jongmook; Feikema, Douglas

2003-01-01

Obtaining information on the instantaneous structure of turbulent and transient flames is important in a wide variety of applications such as fire safety, pollution reduction, flame spread studies, and model validation. Durao et al. has reviewed the different methods of obtaining structure information in reacting flows. These include Tunable Laser Absorption Spectroscopy, Fourier Transform Infrared Spectroscopy, and Emission Spectroscopy to mention a few. Most flames emit significant radiation signatures that are used in various applications such as fire detection, light-off detection, flame diagnostics, etc. Radiation signatures can be utilized to maximum advantage for determining structural information in turbulent flows. Emission spectroscopy is most advantageous in the infrared regions of the spectra, principally because these emission lines arise from transitions in the fundamental bands of stable species such as CO2 and H2O. Based on the above, the objective of this work was to develop a fan beam emission tomography system to obtain the local scalar properties such as temperature and mole fractions of major gas species from path integrated multi-wavelength infrared radiation measurements.

Computer-Aided Drug Design Methods.

PubMed

Yu, Wenbo; MacKerell, Alexander D

2017-01-01

Computational approaches are useful tools to interpret and guide experiments to expedite the antibiotic drug design process. Structure-based drug design (SBDD) and ligand-based drug design (LBDD) are the two general types of computer-aided drug design (CADD) approaches in existence. SBDD methods analyze macromolecular target 3-dimensional structural information, typically of proteins or RNA, to identify key sites and interactions that are important for their respective biological functions. Such information can then be utilized to design antibiotic drugs that can compete with essential interactions involving the target and thus interrupt the biological pathways essential for survival of the microorganism(s). LBDD methods focus on known antibiotic ligands for a target to establish a relationship between their physiochemical properties and antibiotic activities, referred to as a structure-activity relationship (SAR), information that can be used for optimization of known drugs or guide the design of new drugs with improved activity. In this chapter, standard CADD protocols for both SBDD and LBDD will be presented with a special focus on methodologies and targets routinely studied in our laboratory for antibiotic drug discoveries.

Testing the importance of family solidarity, community structure, information access, and social capital in predicting nutrition health knowledge and food choices in the Philippines.

PubMed

Moxley, Robert L; Jicha, Karl A; Thompson, Gretchen H

2011-01-01

This study investigates the influence of family solidarity, community structure, information access, social capital, and socioeconomic status on the extent of nutrition and health knowledge (NHK) among primary household meal planners. In turn, we pose the question: does this knowledge influence dietary decision making? Data are taken from a survey determining socioeconomic impacts of vitamin A fortified peanut butter on Philippine households. Questions on the relationships of nutrition to health were selected to construct a knowledge index on which household respondents could be ranked. We then tested hypotheses regarding what types of individual, family-level, and community structural characteristics would predict performance on this index. The results indicate that the strongest predictors of NHK come from sociological theory related to family solidarity and community centrality, in addition to information accessibility and household income. Our findings also indicate that NHK influences dietary choices with regard to the purchase of a vitamin fortified staple food product, which is essential when addressing nutritional deficiency problems in developing countries.

Biological water-oxidizing complex: a nano-sized manganese-calcium oxide in a protein environment.

PubMed

Najafpour, Mohammad Mahdi; Moghaddam, Atefeh Nemati; Yang, Young Nam; Aro, Eva-Mari; Carpentier, Robert; Eaton-Rye, Julian J; Lee, Choon-Hwan; Allakhverdiev, Suleyman I

2012-10-01

The resolution of Photosystem II (PS II) crystals has been improved using isolated PS II from the thermophilic cyanobacterium Thermosynechococcus vulcanus. The new 1.9 Å resolution data have provided detailed information on the structure of the water-oxidizing complex (Umena et al. Nature 473: 55-61, 2011). The atomic level structure of the manganese-calcium cluster is important for understanding the mechanism of water oxidation and to design an efficient catalyst for water oxidation in artificial photosynthetic systems. Here, we have briefly reviewed our knowledge of the structure and function of the cluster.

Aligned and Unaligned Coherence: A New Diagnostic Tool

NASA Technical Reports Server (NTRS)

Miles, Jeffrey Hilton

2006-01-01

The study of combustion noise from turbofan engines has become important again as the noise from other sources like the fan and jet are reduced. A method has been developed to help identify combustion noise spectra using an aligned and unaligned coherence technique. When used with the well known three signal coherent power method and coherent power method it provides new information by separating tonal information from random process information. Examples are presented showing the underlying tonal structure which is buried under broadband noise and jet noise. The method is applied to data from a Pratt and Whitney PW4098 turbofan engine.

Population structure of Aphis spiraecola (Hemiptera: Aphididae) on pear trees in China identified using microsatellites.

PubMed

Cao, Jinjun; Li, Jie; Niu, Jianqun; Liu, Xiaoxia; Zhang, Qingwen

2012-04-01

The spiraea aphid (Aphis spiraecola Patch) is a primary pest of fruit trees, particularly pear trees in China. Despite the economic importance of this pest, little is known about its genetic structure or its patterns of dispersal at local and regional scales; however, knowledge of these characteristics is important for establishing effective control strategies for this pest. The genetic variability of 431 individuals from 21 populations on pear trees in China was investigated using eight polymorphic microsatellite loci. The high polymorphism of these markers was evident from the expected heterozygosity value (He = 0.824) and the Polymorphism Information Content (PIC = 0.805), indicating that the spiraea aphid maintains a high level of genetic diversity. The analysis of molecular variance revealed a middle level of population differentiation (F(ST) = 0.1478) among A. spiraecola populations. This result is consistent with the results of the STRUCTURE analysis (K = 3), the unweighted pair-group method with arithmetic average tree and the Mantel test (r = 0.6392; P < 0.05). Our results indicate high levels of genetic exchange in the spiraea aphid, possibly facilitated by geography and climate. Our findings emphasize the importance of considering regional differences in studies of population structure, even when strong isolation-by-distance influences the genetic population structure of species.

What is What in the Nanoworld: A Handbook on Nanoscience and Nanotechnology

NASA Astrophysics Data System (ADS)

Borisenko, Victor E.; Ossicini, Stefano

2004-10-01

This introductory, reference handbook summarizes the terms and definitions, most important phenomena, and regulations discovered in the physics, chemistry, technology, and application of nanostructures. These nanostructures are typically inorganic and organic structures at the atomic scale. Fast progressing nanoelectronics and optoelectronics, molecular electronics and spintronics, nanotechnology and quantum processing of information, are of strategic importance for the information society of the 21st century. The short form of information taken from textbooks, special encyclopedias, recent original books and papers provides fast support in understanding "old" and new terms of nanoscience and technology widely used in scientific literature on recent developments. Such support is indeed important when one reads a scientific paper presenting new results in nanoscience. A representative collection of fundamental terms and definitions from quantum physics, and quantum chemistry, special mathematics, organic and inorganic chemistry, solid state physics, material science and technology accompanies recommended second sources (books, reviews, websites) for an extended study of a subject. Each entry interprets the term or definition under consideration and briefly presents main features of the phenomena behind it. Additional information in the form of notes ("First described in: ?", "Recognition: ?", "More details in: ?") supplements entries and gives a historical retrospective of the subject with reference to further sources. Ideal for answering questions related to unknown terms and definitions of undergraduate and Ph.D. students studying the physics of low-dimensional structures, nanoelectronics, nanotechnology. The handbook provides fast support, when one likes to know or to remind the essence of a scientific term, especially when it contains a personal name in its title, like in terms "Anderson localization", "Aharonov-Bohm effect", "Bose-Einstein condensate", e.t.c. More than 1000 entries, from a few sentences to a page in length.

Accelerating Exploitation of Low-grade Intelligence through Semantic Text Processing of Social Media

DTIC Science & Technology

2013-06-01

importance as an information source. The brevity of social media content (e.g., 140 characters per tweet) combined with the increasing usage of mobile...platform imports unstructured text from a variety of sources and then maps the text to an existing ontology of frames (FrameNet, https...framenet.icsi.berkeley.edu/fndrupal/) during a process of Semantic Role Labeling ( SRL ). FrameNet is a structured language model grounded in the theory of Frame

MIDAS: Regionally linear multivariate discriminative statistical mapping.

PubMed

Varol, Erdem; Sotiras, Aristeidis; Davatzikos, Christos

2018-07-01

Statistical parametric maps formed via voxel-wise mass-univariate tests, such as the general linear model, are commonly used to test hypotheses about regionally specific effects in neuroimaging cross-sectional studies where each subject is represented by a single image. Despite being informative, these techniques remain limited as they ignore multivariate relationships in the data. Most importantly, the commonly employed local Gaussian smoothing, which is important for accounting for registration errors and making the data follow Gaussian distributions, is usually chosen in an ad hoc fashion. Thus, it is often suboptimal for the task of detecting group differences and correlations with non-imaging variables. Information mapping techniques, such as searchlight, which use pattern classifiers to exploit multivariate information and obtain more powerful statistical maps, have become increasingly popular in recent years. However, existing methods may lead to important interpretation errors in practice (i.e., misidentifying a cluster as informative, or failing to detect truly informative voxels), while often being computationally expensive. To address these issues, we introduce a novel efficient multivariate statistical framework for cross-sectional studies, termed MIDAS, seeking highly sensitive and specific voxel-wise brain maps, while leveraging the power of regional discriminant analysis. In MIDAS, locally linear discriminative learning is applied to estimate the pattern that best discriminates between two groups, or predicts a variable of interest. This pattern is equivalent to local filtering by an optimal kernel whose coefficients are the weights of the linear discriminant. By composing information from all neighborhoods that contain a given voxel, MIDAS produces a statistic that collectively reflects the contribution of the voxel to the regional classifiers as well as the discriminative power of the classifiers. Critically, MIDAS efficiently assesses the statistical significance of the derived statistic by analytically approximating its null distribution without the need for computationally expensive permutation tests. The proposed framework was extensively validated using simulated atrophy in structural magnetic resonance imaging (MRI) and further tested using data from a task-based functional MRI study as well as a structural MRI study of cognitive performance. The performance of the proposed framework was evaluated against standard voxel-wise general linear models and other information mapping methods. The experimental results showed that MIDAS achieves relatively higher sensitivity and specificity in detecting group differences. Together, our results demonstrate the potential of the proposed approach to efficiently map effects of interest in both structural and functional data. Copyright © 2018. Published by Elsevier Inc.

A tool for filtering information in complex systems

PubMed Central

Tumminello, M.; Aste, T.; Di Matteo, T.; Mantegna, R. N.

2005-01-01

We introduce a technique to filter out complex data sets by extracting a subgraph of representative links. Such a filtering can be tuned up to any desired level by controlling the genus of the resulting graph. We show that this technique is especially suitable for correlation-based graphs, giving filtered graphs that preserve the hierarchical organization of the minimum spanning tree but containing a larger amount of information in their internal structure. In particular in the case of planar filtered graphs (genus equal to 0), triangular loops and four-element cliques are formed. The application of this filtering procedure to 100 stocks in the U.S. equity markets shows that such loops and cliques have important and significant relationships with the market structure and properties. PMID:16027373

A tool for filtering information in complex systems.

PubMed

Tumminello, M; Aste, T; Di Matteo, T; Mantegna, R N

2005-07-26

We introduce a technique to filter out complex data sets by extracting a subgraph of representative links. Such a filtering can be tuned up to any desired level by controlling the genus of the resulting graph. We show that this technique is especially suitable for correlation-based graphs, giving filtered graphs that preserve the hierarchical organization of the minimum spanning tree but containing a larger amount of information in their internal structure. In particular in the case of planar filtered graphs (genus equal to 0), triangular loops and four-element cliques are formed. The application of this filtering procedure to 100 stocks in the U.S. equity markets shows that such loops and cliques have important and significant relationships with the market structure and properties.

Gstruct: a system for extracting schemas from GML documents

NASA Astrophysics Data System (ADS)

Chen, Hui; Zhu, Fubao; Guan, Jihong; Zhou, Shuigeng

2008-10-01

Geography Markup Language (GML) becomes the de facto standard for geographic information representation on the internet. GML schema provides a way to define the structure, content, and semantic of GML documents. It contains useful structural information of GML documents and plays an important role in storing, querying and analyzing GML data. However, GML schema is not mandatory, and it is common that a GML document contains no schema. In this paper, we present Gstruct, a tool for GML schema extraction. Gstruct finds the features in the input GML documents, identifies geometry datatypes as well as simple datatypes, then integrates all these features and eliminates improper components to output the optimal schema. Experiments demonstrate that Gstruct is effective in extracting semantically meaningful schemas from GML documents.

Developing a clinical information system: the role of the chief information officer.

PubMed

Glaser, J

1994-11-01

Chief information officers (CIOs) must play a pivotal role in the formation and implementation of a clinical information system, the subset of an organizational information system that deals specifically with support of clinical care activities. Major elements include the applications software, technology and data architecture, databases, and analysis. The organizational structures and processes that manage the development of improvement activities, including the clinical information system itself, are just as vital to the design of an information system as the hardware and software. To develop, sustain, and advance an information infrastructure, the CIO must help establish certain organizational precursors, such as medical staff involvement, experience with quality improvement, and ability to meet data needs. The CIO must then work with the senior administrative and medical leadership in developing a vision for the information system. The CIO must also create new roles and knowledge for information system and medical staff members. Interaction between information services and medical staff is vitally important to the success of a clinical information system. Organizational committees and structures that Brigham and Women's Hospital in Boston put in place to formalize the relationship between information systems and medical staff include the Clinical Initiative Development Program and the Center for Applied Medical Information Systems Research. Improving the clinical management of care and the efficacy of care processes involves complex changes in organizational culture and processes, medical practice and information system applications, technologies, staff, and data.

Structure of the human TRiC/CCT Subunit 5 associated with hereditary sensory neuropathy.

PubMed

Pereira, Jose H; McAndrew, Ryan P; Sergeeva, Oksana A; Ralston, Corie Y; King, Jonathan A; Adams, Paul D

2017-06-16

The human chaperonin TRiC consists of eight non-identical subunits, and its protein-folding activity is critical for cellular health. Misfolded proteins are associated with many human diseases, such as amyloid diseases, cancer, and neuropathies, making TRiC a potential therapeutic target. A detailed structural understanding of its ATP-dependent folding mechanism and substrate recognition is therefore of great importance. Of particular health-related interest is the mutation Histidine 147 to Arginine (H147R) in human TRiC subunit 5 (CCT5), which has been associated with hereditary sensory neuropathy. In this paper, we describe the crystal structures of CCT5 and the CCT5-H147R mutant, which provide important structural information for this vital protein-folding machine in humans. This first X-ray crystallographic study of a single human CCT subunit in the context of a hexadecameric complex can be expanded in the future to the other 7 subunits that form the TRiC complex.

Parametric imaging of collagen structural changes in human osteoarthritic cartilage using optical polarization tractography

NASA Astrophysics Data System (ADS)

Ravanfar, Mohammadreza; Pfeiffer, Ferris M.; Bozynski, Chantelle C.; Wang, Yuanbo; Yao, Gang

2017-12-01

Collagen degeneration is an important pathological feature of osteoarthritis. The purpose of this study is to investigate whether the polarization-sensitive optical coherence tomography (PSOCT)-based optical polarization tractography (OPT) can be useful in imaging collagen structural changes in human osteoarthritic cartilage samples. OPT eliminated the banding artifacts in conventional PSOCT by calculating the depth-resolved local birefringence and fiber orientation. A close comparison between OPT and PSOCT showed that OPT provided improved visualization and characterization of the zonal structure in human cartilage. Experimental results obtained in this study also underlined the importance of knowing the collagen fiber orientation in conventional polarized light microscopy assessment. In addition, parametric OPT imaging was achieved by quantifying the surface roughness, birefringence, and fiber dispersion in the superficial zone of the cartilage. These quantitative parametric images provided complementary information on the structural changes in cartilage, which can be useful for a comprehensive evaluation of collagen damage in osteoarthritic cartilage.

Social roles and the evolution of networks in extreme and isolated environments

NASA Technical Reports Server (NTRS)

Johnson, Jeffrey C.; Boster, James S.; Palinkas, Lawrence A.

2003-01-01

This article reports on the evolution of network structure as it relates to formal and informal social roles in well-bounded, isolated groups. Research was conducted at the Amundsen-Scott South Pole Station. Data were collected on crewmembers' networks of social interaction over each of three winter-over periods, when the station is completely isolated. In addition, data were collected on the informal roles played by crewmembers (e.g., instrumental leadership, expressive leadership). The study found that globally coherent networks in winter-over groups were associated with group consensus on the presence of critically important informal social roles (e.g., expressive leadership) where global coherence is the extent to which a network forms a single group composed of a unitary core and periphery as opposed to being factionalized into two or more subgroups. Conversely, the evolution of multiple subgroups was associated with the absence of consensus on critical informal social roles, above all the critically important role of instrumental leader.

Structural constraints on the three-dimensional geometry of simple viruses: case studies of a new predictive tool

PubMed Central

Keef, Thomas; Wardman, Jessica P.; Ranson, Neil A.; Stockley, Peter G.; Twarock, Reidun

2013-01-01

Understanding the fundamental principles of virus architecture is one of the most important challenges in biology and medicine. Crick and Watson were the first to propose that viruses exhibit symmetry in the organization of their protein containers for reasons of genetic economy. Based on this, Caspar and Klug introduced quasi-equivalence theory to predict the relative locations of the coat proteins within these containers and classified virus structure in terms of T-numbers. Here it is shown that quasi-equivalence is part of a wider set of structural constraints on virus structure. These constraints can be formulated using an extension of the underlying symmetry group and this is demonstrated with a number of case studies. This new concept in virus biology provides for the first time predictive information on the structural constraints on coat protein and genome topography, and reveals a previously unrecognized structural interdependence of the shapes and sizes of different viral components. It opens up the possibility of distinguishing the structures of different viruses with the same T-number, suggesting a refined viral structure classification scheme. It can moreover be used as a basis for models of virus function, e.g. to characterize the start and end configurations of a structural transition important for infection. PMID:23403965

Structural constraints on the three-dimensional geometry of simple viruses: case studies of a new predictive tool.

PubMed

Keef, Thomas; Wardman, Jessica P; Ranson, Neil A; Stockley, Peter G; Twarock, Reidun

2013-03-01

Understanding the fundamental principles of virus architecture is one of the most important challenges in biology and medicine. Crick and Watson were the first to propose that viruses exhibit symmetry in the organization of their protein containers for reasons of genetic economy. Based on this, Caspar and Klug introduced quasi-equivalence theory to predict the relative locations of the coat proteins within these containers and classified virus structure in terms of T-numbers. Here it is shown that quasi-equivalence is part of a wider set of structural constraints on virus structure. These constraints can be formulated using an extension of the underlying symmetry group and this is demonstrated with a number of case studies. This new concept in virus biology provides for the first time predictive information on the structural constraints on coat protein and genome topography, and reveals a previously unrecognized structural interdependence of the shapes and sizes of different viral components. It opens up the possibility of distinguishing the structures of different viruses with the same T-number, suggesting a refined viral structure classification scheme. It can moreover be used as a basis for models of virus function, e.g. to characterize the start and end configurations of a structural transition important for infection.

Redesigning a Ministry of Health's organizational structure: exploring implementation challenges through Botswana's experiences.

PubMed

Seitio-Kgokgwe, Onalenna; Gauld, Robin D C; Hill, Philip C; Barnett, Pauline

2016-04-01

The Botswana's Ministry of Health redesigned and adopted a new organizational structure in 2005, which was poorly implemented. This article explores factors that influenced the implementation of this organizational structure. This article draws from data collected through in-depth interviews with 54 purposively selected key informants comprising policy makers, senior managers and staff of the Ministry of Health (N = 40) and senior officers from various stakeholder organizations (N = 14). Participants generally felt that the review of the Ministry of Health organizational structure was important. The previous structure was considered obsolete with fragmented functions that limited the overall performance of the health system. The new organizational structure was viewed to be aligned to current national priorities with potential to positively influence performance. Some key weaknesses identified included lack of consultation and information sharing with workers during the restructuring process, which affected the understanding of their new roles, failure to mobilize key resources to support implementation of the new structure and inadequate monitoring of the implementation process. Redesigning an organizational structure is a major change. There is a need for effective and sustained leadership to plan, direct, coordinate, monitor and evaluate the implementation phase of the reform. Copyright © 2014 John Wiley & Sons, Ltd. Copyright © 2014 John Wiley & Sons, Ltd.

A network-based approach for semi-quantitative knowledge mining and its application to yield variability

NASA Astrophysics Data System (ADS)

Schauberger, Bernhard; Rolinski, Susanne; Müller, Christoph

2016-12-01

Variability of crop yields is detrimental for food security. Under climate change its amplitude is likely to increase, thus it is essential to understand the underlying causes and mechanisms. Crop models are the primary tool to project future changes in crop yields under climate change. A systematic overview of drivers and mechanisms of crop yield variability (YV) can thus inform crop model development and facilitate improved understanding of climate change impacts on crop yields. Yet there is a vast body of literature on crop physiology and YV, which makes a prioritization of mechanisms for implementation in models challenging. Therefore this paper takes on a novel approach to systematically mine and organize existing knowledge from the literature. The aim is to identify important mechanisms lacking in models, which can help to set priorities in model improvement. We structure knowledge from the literature in a semi-quantitative network. This network consists of complex interactions between growing conditions, plant physiology and crop yield. We utilize the resulting network structure to assign relative importance to causes of YV and related plant physiological processes. As expected, our findings confirm existing knowledge, in particular on the dominant role of temperature and precipitation, but also highlight other important drivers of YV. More importantly, our method allows for identifying the relevant physiological processes that transmit variability in growing conditions to variability in yield. We can identify explicit targets for the improvement of crop models. The network can additionally guide model development by outlining complex interactions between processes and by easily retrieving quantitative information for each of the 350 interactions. We show the validity of our network method as a structured, consistent and scalable dictionary of literature. The method can easily be applied to many other research fields.

On confidence and consequence: the certainty and importance of self-knowledge.

PubMed

Pelham, B W

1991-04-01

Belief certainty and belief importance represent 2 relatively independent forms of investment in the self-concept. Three studies suggested that whereas certainty is associated with epistemic (i.e., rational or informational) factors, importance is more closely associated with emotive (i.e., emotional and motivational) factors. A 4th study explored the implications of certainty and importance for the temporal stability of people's self-views and revealed that whereas belief certainty was associated with the stability of both positive and negative beliefs, belief importance was associated with the stability of positive beliefs only. The implications of belief investment for the verification-enhancement debate and for the structure and measurement of the self-concept are discussed.

Economic considerations and health in all policies initiatives: evidence from interviews with key informants in Sweden, Quebec and South Australia.

PubMed

Pinto, Andrew D; Molnar, Agnes; Shankardass, Ketan; O'Campo, Patricia J; Bayoumi, Ahmed M

2015-02-18

Health in All Policies (HiAP) is a form of intersectoral action that aims to include the promotion of health in government initiatives across sectors. To date, there has been little study of economic considerations within the implementation of HiAP. As part of an ongoing program of research on the implementation of HiAP around the world, we examined how economic considerations influence the implementation of HiAP. By economic considerations we mean the cost and financial gain (or loss) of implementing a HiAP process or structure within government, or the cost and financial gain (or loss) of the policies that emerge from such a HiAP process or structure. We examined three jurisdictions: Sweden, Quebec and South Australia. Semi-structured telephone interviews were conducted with 12 to 14 key informants in each jurisdiction. Two investigators separately coded transcripts to identify relevant statements. Initial readings of transcripts led to the development of a coding framework for statements related to economic considerations. First, economic evaluations of HiAP are viewed as important for prompting HiAP and many forms of economic evaluation were considered. However, economic evaluations were often absent, informal, or incomplete. Second, funding for HiAP initiatives is important, but is less important than a high-level commitment to intersectoral collaboration. Furthermore, having multiple sources of funding of HiAP can be beneficial, if it increases participation across government, but can also be disadvantageous, if it exposes underlying tensions. Third, HiAP can also highlight the challenge of achieving both economic and social objectives. Our results are useful for elaborating propositions for use in realist multiple explanatory case studies. First, we propose that economic considerations are currently used primarily as a method by health sectors to promote and legitimize HiAP to non-health sectors with the goal of securing resources for HiAP. Second, allocating resources and making funding decisions regarding HiAP are inherently political acts that reflect tensions within government sectors. This study contributes important insights into how intersectoral action works, how economic evaluations of HiAP might be structured, and how economic considerations can be used to both promote HiAP and to present barriers to implementation.

[Technologies for Complex Intelligent Clinical Data Analysis].

PubMed

Baranov, A A; Namazova-Baranova, L S; Smirnov, I V; Devyatkin, D A; Shelmanov, A O; Vishneva, E A; Antonova, E V; Smirnov, V I

2016-01-01

The paper presents the system for intelligent analysis of clinical information. Authors describe methods implemented in the system for clinical information retrieval, intelligent diagnostics of chronic diseases, patient's features importance and for detection of hidden dependencies between features. Results of the experimental evaluation of these methods are also presented. Healthcare facilities generate a large flow of both structured and unstructured data which contain important information about patients. Test results are usually retained as structured data but some data is retained in the form of natural language texts (medical history, the results of physical examination, and the results of other examinations, such as ultrasound, ECG or X-ray studies). Many tasks arising in clinical practice can be automated applying methods for intelligent analysis of accumulated structured array and unstructured data that leads to improvement of the healthcare quality. the creation of the complex system for intelligent data analysis in the multi-disciplinary pediatric center. Authors propose methods for information extraction from clinical texts in Russian. The methods are carried out on the basis of deep linguistic analysis. They retrieve terms of diseases, symptoms, areas of the body and drugs. The methods can recognize additional attributes such as "negation" (indicates that the disease is absent), "no patient" (indicates that the disease refers to the patient's family member, but not to the patient), "severity of illness", disease course", "body region to which the disease refers". Authors use a set of hand-drawn templates and various techniques based on machine learning to retrieve information using a medical thesaurus. The extracted information is used to solve the problem of automatic diagnosis of chronic diseases. A machine learning method for classification of patients with similar nosology and the methodfor determining the most informative patients'features are also proposed. Authors have processed anonymized health records from the pediatric center to estimate the proposed methods. The results show the applicability of the information extracted from the texts for solving practical problems. The records ofpatients with allergic, glomerular and rheumatic diseases were used for experimental assessment of the method of automatic diagnostic. Authors have also determined the most appropriate machine learning methods for classification of patients for each group of diseases, as well as the most informative disease signs. It has been found that using additional information extracted from clinical texts, together with structured data helps to improve the quality of diagnosis of chronic diseases. Authors have also obtained pattern combinations of signs of diseases. The proposed methods have been implemented in the intelligent data processing system for a multidisciplinary pediatric center. The experimental results show the availability of the system to improve the quality of pediatric healthcare.

The Lens Capsule

PubMed Central

Danysh, Brian P.; Duncan, Melinda K.

2009-01-01

The lens capsule is a modified basement membrane that completely surrounds the ocular lens. It is known that this extracellular matrix is important for both the structure and biomechanics of the lens in addition to providing informational cues to maintain lens cell phenotype. This review covers the development and structure of the lens capsule, lens diseases associated with mutations in extracellular matrix genes and the role of the capsule in lens function including those proposed for visual accommodation, selective permeability to infectious agents, and cell signaling. PMID:18773892

Cone beam computed tomography in the diagnosis of dental disease.

PubMed

Tetradis, Sotirios; Anstey, Paul; Graff-Radford, Steven

2011-07-01

Conventional radiographs provide important information for dental disease diagnosis. However, they represent 2-D images of 3-D objects with significant structure superimposition and unpredictable magnification. Cone beam computed tomography, however, allows true 3-D visualization of the dentoalveolar structures, avoiding major limitations of conventional radiographs. Cone beam computed tomography images offer great advantages in disease detection for selected patients. The authors discuss cone beam computed tomography applications in dental disease diagnosis, reviewing the pertinent literature when available.

Mononuclear Cu/O2 Complexes

PubMed Central

Cramer, Christopher J.; Tolman, William B.

2008-01-01

Using interwoven experimental and theoretical methods, detailed studies of several structurally defined 1:1 Cu/O2 complexes have provided important fundamental chemical information useful for understanding the nature of intermediates involved in aerobic oxidations in synthetic and enzymatic copper-mediated catalysis. In particular, these studies have shed new light onto the factors that influence the mode of O2 coordination (end-on vs. side-on) and the electronic structure, which can vary between Cu(II)-superoxo and Cu(III)-peroxo extremes. PMID:17458929

Cartographic generalization of urban street networks based on gravitational field theory

NASA Astrophysics Data System (ADS)

Liu, Gang; Li, Yongshu; Li, Zheng; Guo, Jiawei

2014-05-01

The automatic generalization of urban street networks is a constant and important aspect of geographical information science. Previous studies show that the dual graph for street-street relationships more accurately reflects the overall morphological properties and importance of streets than do other methods. In this study, we construct a dual graph to represent street-street relationship and propose an approach to generalize street networks based on gravitational field theory. We retain the global structural properties and topological connectivity of an original street network and borrow from gravitational field theory to define the gravitational force between nodes. The concept of multi-order neighbors is introduced and the gravitational force is taken as the measure of the importance contribution between nodes. The importance of a node is defined as the result of the interaction between a given node and its multi-order neighbors. Degree distribution is used to evaluate the level of maintaining the global structure and topological characteristics of a street network and to illustrate the efficiency of the suggested method. Experimental results indicate that the proposed approach can be used in generalizing street networks and retaining their density characteristics, connectivity and global structure.

Management issues in systems engineering

NASA Astrophysics Data System (ADS)

Shishko, Robert; Chamberlain, Robert G.; Aster, Robert; Bilardo, Vincent; Forsberg, Kevin; Mooz, Hal; Polaski, Lou; Wade, Ron

When applied to a system, the doctrine of successive refinement is a divide-and-conquer strategy. Complex systems are sucessively divided into pieces that are less complex, until they are simple enough to be conquered. This decomposition results in several structures for describing the product system and the producing system. These structures play important roles in systems engineering and project management. Many of the remaining sections in this chapter are devoted to describing some of these key structures. Structures that describe the product system include, but are not limited to, the requirements tree, system architecture and certain symbolic information such as system drawings, schematics, and data bases. The structures that describe the producing system include the project's work breakdown, schedules, cost accounts and organization.

Management issues in systems engineering

NASA Technical Reports Server (NTRS)

Shishko, Robert; Chamberlain, Robert G.; Aster, Robert; Bilardo, Vincent; Forsberg, Kevin; Mooz, Hal; Polaski, Lou; Wade, Ron

1993-01-01

When applied to a system, the doctrine of successive refinement is a divide-and-conquer strategy. Complex systems are sucessively divided into pieces that are less complex, until they are simple enough to be conquered. This decomposition results in several structures for describing the product system and the producing system. These structures play important roles in systems engineering and project management. Many of the remaining sections in this chapter are devoted to describing some of these key structures. Structures that describe the product system include, but are not limited to, the requirements tree, system architecture and certain symbolic information such as system drawings, schematics, and data bases. The structures that describe the producing system include the project's work breakdown, schedules, cost accounts and organization.

Information sources used by the suicidal to inform choice of method.

PubMed

Biddle, Lucy; Gunnell, David; Owen-Smith, Amanda; Potokar, John; Longson, Damien; Hawton, Keith; Kapur, Nav; Donovan, Jenny

2012-02-01

Choice of suicide method strongly influences the outcome of an attempt. Public knowledge of possible methods is an important but less frequently considered aspect of the accessibility of suicide. This qualitative study explored the sources of information shaping the near-fatal suicide attempts of 22 individuals. Respondents were recruited from nine hospitals in England. Semi-structured interviews were conducted to gain detailed narratives of the planning of the suicide attempt. Interviews were recorded, transcribed, then subjected to thematic analysis utilising constant comparison techniques. Information sources discussed most frequently were television, news stories, the Internet, and previous self-harm. Others were professional resources, personal knowledge of others' attempts and information gleaned from healthcare professionals. Many respondents reported seeing media portrayals or reports of suicide, which had contributed to their awareness of suicide methods. Several provided examples of direct imitation. Some had deliberately sought information about methods when planning their attempt--mostly from the Internet. Past experience was used to identify 'best' methods and perfect implementation. The frequency with which sources of information are 'used' by particular groups and their relative import cannot be inferred from a qualitative sample. Near-fatal cases may differ from completed suicides. The media is an important contributor to the cognitive availability of suicide in society and could be used for prevention through carefully crafted portrayals of suicide designed to generate negative social perceptions of popular methods. Understanding of how sources of information can influence perceptions of suicide could inform the content of clinical conversations with patients. Copyright © 2011 Elsevier B.V. All rights reserved.

Structure of an agonist-bound ionotropic glutamate receptor.

PubMed

Yelshanskaya, Maria V; Li, Minfen; Sobolevsky, Alexander I

2014-08-29

Ionotropic glutamate receptors (iGluRs) mediate most excitatory neurotransmission in the central nervous system and function by opening their ion channel in response to binding of agonist glutamate. Here, we report a structure of a homotetrameric rat GluA2 receptor in complex with partial agonist (S)-5-nitrowillardiine. Comparison of this structure with the closed-state structure in complex with competitive antagonist ZK 200775 suggests conformational changes that occur during iGluR gating. Guided by the structures, we engineered disulfide cross-links to probe domain interactions that are important for iGluR gating events. The combination of structural information, kinetic modeling, and biochemical and electrophysiological experiments provides insight into the mechanism of iGluR gating. Copyright © 2014, American Association for the Advancement of Science.

Evidence For Rapid Spatiotemporal Changes in Genetic Structure of an Alien Whitefly During Initial Invasion

PubMed Central

Chu, Dong; Guo, Dong; Tao, Yunli; Jiang, Defeng; Li, Jie; Zhang, Youjun

2014-01-01

The sweetpotato whitefly Bemisia tabaci Q species is a recent invader and important pest of agricultural crops in China. This research tested the hypothesis that the Q populations that establish in agricultural fields in northern China each year are derived from multiple secondary introductions and/or local populations that overwinter in greenhouses (the pest cannot survive winters in the field in northern China). Here, we report the evidence that the Q populations in agricultural fields mainly derive from multiple secondary introductions. In addition, the common use of greenhouses during the winter in certain locations in northern China helps increase the genetic diversity and the genetic structure of the pest. The genetic structure information generated from this long-term and large-scale field analysis increases our understanding of B. tabaci Q as an invasive pest and has important implications for B. tabaci Q management. PMID:24637851

Uncovering the spatial structure of mobility networks

NASA Astrophysics Data System (ADS)

Louail, Thomas; Lenormand, Maxime; Picornell, Miguel; García Cantú, Oliva; Herranz, Ricardo; Frias-Martinez, Enrique; Ramasco, José J.; Barthelemy, Marc

2015-01-01

The extraction of a clear and simple footprint of the structure of large, weighted and directed networks is a general problem that has relevance for many applications. An important example is seen in origin-destination matrices, which contain the complete information on commuting flows, but are difficult to analyze and compare. We propose here a versatile method, which extracts a coarse-grained signature of mobility networks, under the form of a 2 × 2 matrix that separates the flows into four categories. We apply this method to origin-destination matrices extracted from mobile phone data recorded in 31 Spanish cities. We show that these cities essentially differ by their proportion of two types of flows: integrated (between residential and employment hotspots) and random flows, whose importance increases with city size. Finally, the method allows the determination of categories of networks, and in the mobility case, the classification of cities according to their commuting structure.

Ab initio surface properties of Ag-Sn alloys: implications for lead-free soldering.

PubMed

Saleh, Gabriele; Xu, Chen; Sanvito, Stefano

2018-02-07

Ag and Sn are the major components of solder alloys adopted to assemble printed circuit boards. The qualities that make them the alloys of choice for the modern electronic industry are related to their physical and chemical properties. For corrosion resistance and solderability, surface properties are particularly important. Yet, atomic-level information about the surfaces of these alloys is not known. Here we fill this gap by presenting an extensive ab initio investigation of composition, energetics, structure and reactivity of Ag-Sn alloy surfaces. The structure and stability of various surfaces is evaluated, and the main factors determining the energetics of surface formation are uncovered. Oxygen and sulphur chemisorptions are studied and discussed in the framework of corrosion tendency, an important issue for printed circuit boards. Adsorption energy trends are rationalized based on the analysis of structural and electronic features.

Characterization of Microgravity Effects on Bone Structure and Strength Using Fractal Analysis

NASA Technical Reports Server (NTRS)

Acharya, Raj S.; Shackelford, Linda

1996-01-01

Protecting humans against extreme environmental conditions requires a thorough understanding of the pathophysiological changes resulting from the exposure to those extreme conditions. Knowledge of the degree of medical risk associated with the exposure is of paramount importance in the design of effective prophylactic and therapeutic measures for space exploration. Major health hazards due o musculoskeletal systems include the signs and symptoms of hypercalciuria, lengthy recovery of lost bone tissue after flight, the possibility of irreversible trabecular bone loss, the possible effect of calcification in the soft tissues, and the possible increase in fracture potential. In this research, we characterize the trabecular structure with the aid of fractal analysis. Our research to relate local trabecular structural information to microgravity conditions is an important initial step in understanding the effect of microgravity and countermeasures on bone condition and strength. The proposed research is also closely linked with Osteoporosis and will benefit the general population.

Using Knowledge of Chemical and Structural Defenses of Seaweeds to Develop a Standardized Measure of Herbivory in Tropical and Subtropical Habitats

NASA Astrophysics Data System (ADS)

Paul, V. J.

2016-02-01

Herbivory is an important process determining the structure and function of marine ecosystems, and this is especially true on coral reefs and in associated tropical and subtropical habitats where grazing by fishes can be intense. As reef degradation is occurring on a global scale, and overfishing can contribute to this problem, rates of herbivory can be an important indicator of reef function and resilience. Our goal was to develop a standardized herbivory assay that can be deployed globally to measure the impact of herbivorous fishes across multiple habitat types. Many tropical and subtropical seaweeds contain chemical and structural defenses that can protect them from herbivores, and this information was key to selecting a range of marine plants that are differentially palatable to herbivorous fishes for these assays. We present method development and experimental results from extensive deployment of these herbivory assays at Carrie Bow Cay, Belize.

The Impact of the Security Competency on "Self-Efficacy in Information Security" for Effective Health Information Security in Iran.

PubMed

Shahri, Ahmad Bakhtiyari; Ismail, Zuraini; Mohanna, Shahram

2016-11-01

The security effectiveness based on users' behaviors is becoming a top priority of Health Information System (HIS). In the first step of this study, through the review of previous studies 'Self-efficacy in Information Security' (SEIS) and 'Security Competency' (SCMP) were identified as the important factors to transforming HIS users to the first line of defense in the security. Subsequently, a conceptual model was proposed taking into mentioned factors for HIS security effectiveness. Then, this quantitative study used the structural equation modeling to examine the proposed model based on survey data collected from a sample of 263 HIS users from eight hospitals in Iran. The result shows that SEIS is one of the important factors to cultivate of good end users' behaviors toward HIS security effectiveness. However SCMP appears a feasible alternative to providing SEIS. This study also confirms the mediation effects of SEIS on the relationship between SCMP and HIS security effectiveness. The results of this research paper can be used by HIS and IT managers to implement their information security process more effectively.

Crossing the quality chasm: the role of information technology departments.

PubMed

Weir, Charlene R; Hicken, Bret L; Rappaport, Hank Steven; Nebeker, Jonathan R

2006-01-01

Integrating information technology (IT) into medical settings is considered essential to transforming hospitals into 21st-century health care institutions. Yet the role of IT departments in maximizing the effectiveness of information systems is not well understood. This article reports a 3-round Delphi panel of Veterans Administration personnel experienced with provider order entry electronic systems. In round 1, 35 administrative, clinical, and IT personnel answered 10 open-ended questions about IT strategies and structures that best support successful transformation. In round 2, panelists rated item importance and ranked proposed strategies. In round 3, panelists received aggregate feedback and rerated the items. Four domains emerged from round 1: IT organization, IT performance monitoring, user-support activities, and core IT responsibilities (eg, computer security, training). In rounds 2 and 3, IT performance monitoring was rated the most important, closely followed by clinical support. Strategies associated with each domain are identified and discussed.

Distance matrix-based approach to protein structure prediction.

PubMed

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

2009-03-01

Much structural information is encoded in the internal distances; a distance matrix-based approach can be used to predict protein structure and dynamics, and for structural refinement. Our approach is based on the square distance matrix D = [r(ij)(2)] containing all square distances between residues in proteins. This distance matrix contains more information than the contact matrix C, that has elements of either 0 or 1 depending on whether the distance r (ij) is greater or less than a cutoff value r (cutoff). We have performed spectral decomposition of the distance matrices D = sigma lambda(k)V(k)V(kT), in terms of eigenvalues lambda kappa and the corresponding eigenvectors v kappa and found that it contains at most five nonzero terms. A dominant eigenvector is proportional to r (2)--the square distance of points from the center of mass, with the next three being the principal components of the system of points. By predicting r (2) from the sequence we can approximate a distance matrix of a protein with an expected RMSD value of about 7.3 A, and by combining it with the prediction of the first principal component we can improve this approximation to 4.0 A. We can also explain the role of hydrophobic interactions for the protein structure, because r is highly correlated with the hydrophobic profile of the sequence. Moreover, r is highly correlated with several sequence profiles which are useful in protein structure prediction, such as contact number, the residue-wise contact order (RWCO) or mean square fluctuations (i.e. crystallographic temperature factors). We have also shown that the next three components are related to spatial directionality of the secondary structure elements, and they may be also predicted from the sequence, improving overall structure prediction. We have also shown that the large number of available HIV-1 protease structures provides a remarkable sampling of conformations, which can be viewed as direct structural information about the dynamics. After structure matching, we apply principal component analysis (PCA) to obtain the important apparent motions for both bound and unbound structures. There are significant similarities between the first few key motions and the first few low-frequency normal modes calculated from a static representative structure with an elastic network model (ENM) that is based on the contact matrix C (related to D), strongly suggesting that the variations among the observed structures and the corresponding conformational changes are facilitated by the low-frequency, global motions intrinsic to the structure. Similarities are also found when the approach is applied to an NMR ensemble, as well as to atomic molecular dynamics (MD) trajectories. Thus, a sufficiently large number of experimental structures can directly provide important information about protein dynamics, but ENM can also provide a similar sampling of conformations. Finally, we use distance constraints from databases of known protein structures for structure refinement. We use the distributions of distances of various types in known protein structures to obtain the most probable ranges or the mean-force potentials for the distances. We then impose these constraints on structures to be refined or include the mean-force potentials directly in the energy minimization so that more plausible structural models can be built. This approach has been successfully used by us in 2006 in the CASPR structure refinement (http://predictioncenter.org/caspR).

Uridine Nucleoside Thiation: Gas-Phase Structures and Energetics

NASA Astrophysics Data System (ADS)

Hamlow, Lucas; Lee, Justin; Rodgers, M. T.; Berden, Giel; Oomens, Jos

2016-06-01

The naturally occurring thiated uridine nucleosides, 4-thiouridine (s4Urd) and 2-thiouridine (s2Urd), play important roles in the function and analysis of a variety of RNAs. 2-Thiouridine and its C5 modified analogues are commonly found in tRNAs and are believed to play an important role in codon recognition possibly due to their different structure, which has been shown by NMR to be predominantly C3'-endo. 2-Thiouridine may also play an important role in facilitating nonenzymatic RNA replication and transcription. 4-Thiouridine is a commonly used photoactivatable crosslinker that is often used to study RNA-RNA and RNA-protein cross-linking behavior. Differences in the base pairing between uracil and 4-thiouracil with adenine and guanine are an important factor in their role as a cross linker. The photoactivity of s4Urd may also aid in preventing near-UV lethality in cells. An understanding of their intrinsic structure in the gas-phase may help further elucidate the roles these modified nucleosides play in the regulation of RNAs. In this work, infrared multiple photon dissociation (IRMPD) action spectra of the protonated forms of s2Urd and s4Urd were collected in the IR fingerprint region. Structural information is determined by comparison with theoretical linear IR spectra generated from density functional theory calculations using molecular modeling to generate low-energy candidate structures. Present results are compared with analogous results for the protonated forms of uridine and 2'-deoxyuridine as well as solution phase NMR data and crystal structures.

Determine Age-structure of Gelatinous Zooplankton Using Optical Coherence Tomography

NASA Astrophysics Data System (ADS)

Bi, H.; Shahrestani, S.; He, Y.

2016-02-01

Gelatinous are delicate and transparent by nature, but are conspicuous in many ecosystems when in bloom. Their proliferations are a bothersome and costly nuisance and influencing important food webs and species interactions. More importantly, gelatinous zooplankton respond to climate change rapidly and understanding their upsurge needs information on their recruitment and population dynamics which in turn require their age-structure. However, ageing gelatinous zooplankton is often restricted by the fact that they shrink under unfavorable conditions. In the present study, we examine the potential of using optical coherence tomography (OCT) to age gelatinous zooplankton. OCT is a non-invasive imaging technique that uses light waves to examine 2D or 3D structure of target objects at a resolution of 3-5 µm. We were able to successfully capture both 3D and 2D images of sea nettle muscle fibers. Preliminary results on ctenophores will be discussed. Overall, this non-destructive sampling allows us to scan and capture images of mesoglea from jellyfish cultured in the lab, using the same individual repeatedly through time, documenting its growth which will provide precise measurements to construct an age key that will be applied to gelatinous zooplankton captured in the field. Coupled with information on abundance, we can start to quantify their recruitment timing and success rate.

The Structure of Social Exchange in Self-Help Support Groups: Development of a Measure

PubMed Central

Brown, Louis D.; Tang, Xiaohui; Hollman, Ruth L.

2014-01-01

Self-help support groups are indigenous community resources designed to help people manage a variety of personal challenges, from alcohol abuse to xeroderma pigmentosum. The social exchanges that occur during group meetings are central to understanding how people benefit from participation. This paper examines the different types of social exchange behaviors that occur during meetings, using two studies to develop empirically distinct scales that reliably measure theoretically important types of exchange. Resource theory informed the initial measurement development efforts. Exploratory factor analyses from the first study led to revisions in the factor structure of the social exchange scales. The revised measure captured the exchange of emotional support, experiential information, humor, unwanted behaviors, and exchanges outside meetings. Confirmatory factor analyses from a follow-up study with a different sample of self-help support groups provided good model fit, suggesting the revised structure accurately represented the data. Further, the scales demonstrated good convergent and discriminant validity with related constructs. Future research can use the scales to identify aspects of social exchange that are most important in improving health outcomes among self-help support group participants. Groups can use the scales in practice to celebrate strengths and address weaknesses in their social exchange dynamics. PMID:24398622

Top-down causation and emergence: some comments on mechanisms

PubMed Central

Ellis, George F. R.

2012-01-01

Both bottom-up and top-down causation occur in the hierarchy of structure and causation. A key feature is multiple realizability of higher level functions, and consequent existence of equivalence classes of lower level variables that correspond to the same higher level state. Five essentially different classes of top-down influence can be identified, and their existence demonstrated by many real-world examples. They are: algorithmic top-down causation; top-down causation via non-adaptive information control, top-down causation via adaptive selection, top-down causation via adaptive information control and intelligent top-down causation (the effect of the human mind on the physical world). Through the mind, abstract entities such as mathematical structures have causal power. The causal slack enabling top-down action to take place lies in the structuring of the system so as to attain higher level functions; in the way the nature of lower level elements is changed by context, and in micro-indeterminism combined with adaptive selection. Understanding top-down causation can have important effects on society. Two cases will be mentioned: medical/healthcare issues, and education—in particular, teaching reading and writing. In both cases, an ongoing battle between bottom-up and top-down approaches has important consequences for society. PMID:23386967

Coding Early Naturalists' Accounts into Long-Term Fish Community Changes in the Adriatic Sea (1800–2000)

PubMed Central

Fortibuoni, Tomaso; Libralato, Simone; Raicevich, Saša; Giovanardi, Otello; Solidoro, Cosimo

2010-01-01

The understanding of fish communities' changes over the past centuries has important implications for conservation policy and marine resource management. However, reconstructing these changes is difficult because information on marine communities before the second half of the 20th century is, in most cases, anecdotal and merely qualitative. Therefore, historical qualitative records and modern quantitative data are not directly comparable, and their integration for long-term analyses is not straightforward. We developed a methodology that allows the coding of qualitative information provided by early naturalists into semi-quantitative information through an intercalibration with landing proportions. This approach allowed us to reconstruct and quantitatively analyze a 200-year-long time series of fish community structure indicators in the Northern Adriatic Sea (Mediterranean Sea). Our analysis provides evidence of long-term changes in fish community structure, including the decline of Chondrichthyes, large-sized and late-maturing species. This work highlights the importance of broadening the time-frame through which we look at marine ecosystem changes and provides a methodology to exploit, in a quantitative framework, historical qualitative sources. To the purpose, naturalists' eyewitness accounts proved to be useful for extending the analysis on fish community back in the past, well before the onset of field-based monitoring programs. PMID:21103349

An asset-based approach to vulnerability: the case of small-scale fishing areas in Cameroon and Nigeria.

PubMed

Chiwaula, Levison S; Witt, Rudolf; Waibel, Hermann

2011-01-01

This paper analyses vulnerability to poverty of rural small-scale fishing communities using cross-section data from 295 households in Cameroon and 267 in Nigeria. We propose a vulnerability measure that incorporates the idea of asset poverty into the concept of expected poverty, which allows decomposing expected poverty into expected structural-chronic, structural-transient, and stochastic-transient poverty. The findings show that most households in our study areas are expected to be structurally-chronic and structurally-transient poor. This underlines the importance of asset formation for long-term poverty reduction strategies. Further refinements are possible with longitudinal data and information about future states of nature.

The Evolving Contribution of Mass Spectrometry to Integrative Structural Biology

NASA Astrophysics Data System (ADS)

Faini, Marco; Stengel, Florian; Aebersold, Ruedi

2016-06-01

Protein complexes are key catalysts and regulators for the majority of cellular processes. Unveiling their assembly and structure is essential to understanding their function and mechanism of action. Although conventional structural techniques such as X-ray crystallography and NMR have solved the structure of important protein complexes, they cannot consistently deal with dynamic and heterogeneous assemblies, limiting their applications to small scale experiments. A novel methodological paradigm, integrative structural biology, aims at overcoming such limitations by combining complementary data sources into a comprehensive structural model. Recent applications have shown that a range of mass spectrometry (MS) techniques are able to generate interaction and spatial restraints (cross-linking MS) information on native complexes or to study the stoichiometry and connectivity of entire assemblies (native MS) rapidly, reliably, and from small amounts of substrate. Although these techniques by themselves do not solve structures, they do provide invaluable structural information and are thus ideally suited to contribute to integrative modeling efforts. The group of Brian Chait has made seminal contributions in the use of mass spectrometric techniques to study protein complexes. In this perspective, we honor the contributions of the Chait group and discuss concepts and milestones of integrative structural biology. We also review recent examples of integration of structural MS techniques with an emphasis on cross-linking MS. We then speculate on future MS applications that would unravel the dynamic nature of protein complexes upon diverse cellular states.

StraPep: a structure database of bioactive peptides

PubMed Central

Wang, Jian; Yin, Tailang; Xiao, Xuwen; He, Dan; Xue, Zhidong; Jiang, Xinnong; Wang, Yan

2018-01-01

Abstract Bioactive peptides, with a variety of biological activities and wide distribution in nature, have attracted great research interest in biological and medical fields, especially in pharmaceutical industry. The structural information of bioactive peptide is important for the development of peptide-based drugs. Many databases have been developed cataloguing bioactive peptides. However, to our knowledge, database dedicated to collect all the bioactive peptides with known structure is not available yet. Thus, we developed StraPep, a structure database of bioactive peptides. StraPep holds 3791 bioactive peptide structures, which belong to 1312 unique bioactive peptide sequences. About 905 out of 1312 (68%) bioactive peptides in StraPep contain disulfide bonds, which is significantly higher than that (21%) of PDB. Interestingly, 150 out of 616 (24%) bioactive peptides with three or more disulfide bonds form a structural motif known as cystine knot, which confers considerable structural stability on proteins and is an attractive scaffold for drug design. Detailed information of each peptide, including the experimental structure, the location of disulfide bonds, secondary structure, classification, post-translational modification and so on, has been provided. A wide range of user-friendly tools, such as browsing, sequence and structure-based searching and so on, has been incorporated into StraPep. We hope that this database will be helpful for the research community. Database URL: http://isyslab.info/StraPep PMID:29688386

Global heating distributions for January 1979 calculated from GLA assimilated and simulated model-based datasets

NASA Technical Reports Server (NTRS)

Schaack, Todd K.; Lenzen, Allen J.; Johnson, Donald R.

1991-01-01

This study surveys the large-scale distribution of heating for January 1979 obtained from five sources of information. Through intercomparison of these distributions, with emphasis on satellite-derived information, an investigation is conducted into the global distribution of atmospheric heating and the impact of observations on the diagnostic estimates of heating derived from assimilated datasets. The results indicate a substantial impact of satellite information on diagnostic estimates of heating in regions where there is a scarcity of conventional observations. The addition of satellite data provides information on the atmosphere's temperature and wind structure that is important for estimation of the global distribution of heating and energy exchange.

Brief report: Attention to positive information mediates the relationship between hope and psychosocial well-being of adolescents.

PubMed

Yeung, Dannii Y; Ho, Samuel M Y; Mak, Christine W Y

2015-07-01

This study tested the mediating roles of cognitive reappraisal and attentional preferences in the relationship between hope and psychosocial well-being among 712 adolescents. Results of the structural equation modeling revealed that the beneficial relation of hope to subjective happiness, anxiety, depressive symptoms, and interpersonal difficulties was partially mediated by attention to positive information but not cognitive reappraisal. Findings of this study may inform the design of intervention research by highlighting the importance of hopeful thinking style and attention to positive information in mental health of adolescents. Copyright © 2015 The Foundation for Professionals in Services for Adolescents. Published by Elsevier Ltd. All rights reserved.

Intraoperative virtual brain counseling

NASA Astrophysics Data System (ADS)

Jiang, Zhaowei; Grosky, William I.; Zamorano, Lucia J.; Muzik, Otto; Diaz, Fernando

1997-06-01

Our objective is to offer online real-tim e intelligent guidance to the neurosurgeon. Different from traditional image-guidance technologies that offer intra-operative visualization of medical images or atlas images, virtual brain counseling goes one step further. It can distinguish related brain structures and provide information about them intra-operatively. Virtual brain counseling is the foundation for surgical planing optimization and on-line surgical reference. It can provide a warning system that alerts the neurosurgeon if the chosen trajectory will pass through eloquent brain areas. In order to fulfill this objective, tracking techniques are involved for intra- operativity. Most importantly, a 3D virtual brian environment, different from traditional 3D digitized atlases, is an object-oriented model of the brain that stores information about different brain structures together with their elated information. An object-oriented hierarchical hyper-voxel space (HHVS) is introduced to integrate anatomical and functional structures. Spatial queries based on position of interest, line segment of interest, and volume of interest are introduced in this paper. The virtual brain environment is integrated with existing surgical pre-planning and intra-operative tracking systems to provide information for planning optimization and on-line surgical guidance. The neurosurgeon is alerted automatically if the planned treatment affects any critical structures. Architectures such as HHVS and algorithms, such as spatial querying, normalizing, and warping are presented in the paper. A prototype has shown that the virtual brain is intuitive in its hierarchical 3D appearance. It also showed that HHVS, as the key structure for virtual brain counseling, efficiently integrates multi-scale brain structures based on their spatial relationships.This is a promising development for optimization of treatment plans and online surgical intelligent guidance.

HEDEA: A Python Tool for Extracting and Analysing Semi-structured Information from Medical Records

PubMed Central

Aggarwal, Anshul; Garhwal, Sunita

2018-01-01

Objectives One of the most important functions for a medical practitioner while treating a patient is to study the patient's complete medical history by going through all records, from test results to doctor's notes. With the increasing use of technology in medicine, these records are mostly digital, alleviating the problem of looking through a stack of papers, which are easily misplaced, but some of these are in an unstructured form. Large parts of clinical reports are in written text form and are tedious to use directly without appropriate pre-processing. In medical research, such health records may be a good, convenient source of medical data; however, lack of structure means that the data is unfit for statistical evaluation. In this paper, we introduce a system to extract, store, retrieve, and analyse information from health records, with a focus on the Indian healthcare scene. Methods A Python-based tool, Healthcare Data Extraction and Analysis (HEDEA), has been designed to extract structured information from various medical records using a regular expression-based approach. Results The HEDEA system is working, covering a large set of formats, to extract and analyse health information. Conclusions This tool can be used to generate analysis report and charts using the central database. This information is only provided after prior approval has been received from the patient for medical research purposes. PMID:29770248

Comparing the neural basis of monetary reward and cognitive feedback during information-integration category learning.

PubMed

Daniel, Reka; Pollmann, Stefan

2010-01-06

The dopaminergic system is known to play a central role in reward-based learning (Schultz, 2006), yet it was also observed to be involved when only cognitive feedback is given (Aron et al., 2004). Within the domain of information-integration category learning, in which information from several stimulus dimensions has to be integrated predecisionally (Ashby and Maddox, 2005), the importance of contingent feedback is well established (Maddox et al., 2003). We examined the common neural correlates of reward anticipation and prediction error in this task. Sixteen subjects performed two parallel information-integration tasks within a single event-related functional magnetic resonance imaging session but received a monetary reward only for one of them. Similar functional areas including basal ganglia structures were activated in both task versions. In contrast, a single structure, the nucleus accumbens, showed higher activation during monetary reward anticipation compared with the anticipation of cognitive feedback in information-integration learning. Additionally, this activation was predicted by measures of intrinsic motivation in the cognitive feedback task and by measures of extrinsic motivation in the rewarded task. Our results indicate that, although all other structures implicated in category learning are not significantly affected by altering the type of reward, the nucleus accumbens responds to the positive incentive properties of an expected reward depending on the specific type of the reward.

The role of readability in effective health communication: an experiment using a Japanese health information text on chronic suppurative otitis media.

PubMed

Sakai, Yukiko

2013-09-01

This study identifies the most significant readability factors and examines ways of improving and evaluating Japanese health information text in terms of ease of reading and understanding. Six different Japanese texts were prepared based on an original short text written by a medical doctor for a hospital web site intended for laypersons regarding chronic suppurative otitis media. Four were revised for single readability factor (syntax, vocabulary, or text structure) and two were modified in all three factors. Using a web-based survey, 270 high school students read one of the seven texts, including the original, completed two kinds of comprehension tests, and answered questions on their impressions of the text's readability. Significantly higher comprehension test scores were shown in the true or false test for a mixed text that presented important information first for better text structure. They were also found in the cloze test for a text using common vocabulary and a cohesive mixed text. Vocabulary could be a critical single readability factor when presumably combined with better text structure. Using multiple evaluation methods can help assess comprehensive readability. The findings on improvement and evaluation methods of readability can be applied to support effective health communication. © 2013 The authors. Health Information and Libraries Journal © 2013 Health Libraries Group Health Information and Libraries Journal.

HEDEA: A Python Tool for Extracting and Analysing Semi-structured Information from Medical Records.

PubMed

Aggarwal, Anshul; Garhwal, Sunita; Kumar, Ajay

2018-04-01

One of the most important functions for a medical practitioner while treating a patient is to study the patient's complete medical history by going through all records, from test results to doctor's notes. With the increasing use of technology in medicine, these records are mostly digital, alleviating the problem of looking through a stack of papers, which are easily misplaced, but some of these are in an unstructured form. Large parts of clinical reports are in written text form and are tedious to use directly without appropriate pre-processing. In medical research, such health records may be a good, convenient source of medical data; however, lack of structure means that the data is unfit for statistical evaluation. In this paper, we introduce a system to extract, store, retrieve, and analyse information from health records, with a focus on the Indian healthcare scene. A Python-based tool, Healthcare Data Extraction and Analysis (HEDEA), has been designed to extract structured information from various medical records using a regular expression-based approach. The HEDEA system is working, covering a large set of formats, to extract and analyse health information. This tool can be used to generate analysis report and charts using the central database. This information is only provided after prior approval has been received from the patient for medical research purposes.

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

Sturgeon, J I

This volume relates primarily to Time-of-Day rates standard, PURPA IB(d)3, and deals with the content and methods of providing rate and conservation information to customers when Time-of-Day rates are used. Information to customers in the Demonstration and Pilot Projects fell mainly into four categories: administrative communications; explanations of new rate structures; information and advice on load management; and facts, recommendations and encouragements about energy conservation and end-use improvement. Administrative communications were about such matters as the existence of Projects, their funding, their periods of performance, the selection of their test customers, conditions of participation, procedural changes during the tests, andmore » the time and conditions of ending the tests. These communications were important to good customer cooperation. All Demonstration Projects devoted considerable effort to the crucial task of clearly explaining the rationale of Time-of-Use (TOU) pricing and the test rate structures. The Projects then presented the concept of TOU pricing as a means of (a) fairly charging customers the true cost of their electricity and (b) rewarding them for shifting consumption to times when costs are less. For the most part, Demonstration Projects gave specific information on the individual customer's own rate structure and none on any others that were under test. The information was presented in face-to-face interviews, group presentations, television, radio, and print media, and traveling exhibits. The results are evaluated. (LCL)« less

Structural evolution of nrDNA ITS in Pinaceae and its phylogenetic implications.

PubMed

Kan, Xian-Zhao; Wang, Shan-Shan; Ding, Xin; Wang, Xiao-Quan

2007-08-01

Nuclear ribosomal DNA (nrDNA) has been considered as an important tool for inferring phylogenetic relationships at many taxonomic levels. In comparison with its fast concerted evolution in angiosperms, nrDNA is symbolized by slow concerted evolution and substantial ITS region length variation in gymnosperms, particularly in Pinaceae. Here we studied structure characteristics, including subrepeat composition, size, GC content and secondary structure, of nrDNA ITS regions of all Pinaceae genera. The results showed that the ITS regions of all taxa studied contained subrepeat units, ranging from 2 to 9 in number, and these units could be divided into two types, longer subrepeat (LSR) without the motif (5'-GGCCACCCTAGTC) and shorter subrepeat (SSR) with the motif. Phylogenetic analyses indicate that the homology of some SSRs still can be recognized, providing important informations for the evolutionary history of nrDNA ITS and phylogeny of Pinaceae. In particular, the adjacent tandem SSRs are not more closely related to one another than they are to remote SSRs in some genera, which may imply that multiple structure variations such as recombination have occurred in the ITS1 region of these groups. This study also found that GC content in the ITS1 region is relevant to its sequence length and subrepeat number, and could provide some phylogenetic information, especially supporting the close relationships among Picea, Pinus, and Cathaya. Moreover, several characteristics of the secondary structure of Pinaceae ITS1 were found as follows: (1) the structure is dominated by several extended hairpins; (2) the configuration complexity is positively correlated with subrepeat number; (3) paired subrepeats often partially overlap at the conserved motif (5'-GGCCACCCTAGTC), and form a long stem, while other subrepeats fold onto itself, leaving part of the conserved motif exposed in hairpin loops.

Comparison of topological clustering within protein networks using edge metrics that evaluate full sequence, full structure, and active site microenvironment similarity.

PubMed

Leuthaeuser, Janelle B; Knutson, Stacy T; Kumar, Kiran; Babbitt, Patricia C; Fetrow, Jacquelyn S

2015-09-01

The development of accurate protein function annotation methods has emerged as a major unsolved biological problem. Protein similarity networks, one approach to function annotation via annotation transfer, group proteins into similarity-based clusters. An underlying assumption is that the edge metric used to identify such clusters correlates with functional information. In this contribution, this assumption is evaluated by observing topologies in similarity networks using three different edge metrics: sequence (BLAST), structure (TM-Align), and active site similarity (active site profiling, implemented in DASP). Network topologies for four well-studied protein superfamilies (enolase, peroxiredoxin (Prx), glutathione transferase (GST), and crotonase) were compared with curated functional hierarchies and structure. As expected, network topology differs, depending on edge metric; comparison of topologies provides valuable information on structure/function relationships. Subnetworks based on active site similarity correlate with known functional hierarchies at a single edge threshold more often than sequence- or structure-based networks. Sequence- and structure-based networks are useful for identifying sequence and domain similarities and differences; therefore, it is important to consider the clustering goal before deciding appropriate edge metric. Further, conserved active site residues identified in enolase and GST active site subnetworks correspond with published functionally important residues. Extension of this analysis yields predictions of functionally determinant residues for GST subgroups. These results support the hypothesis that active site similarity-based networks reveal clusters that share functional details and lay the foundation for capturing functionally relevant hierarchies using an approach that is both automatable and can deliver greater precision in function annotation than current similarity-based methods. © 2015 The Authors Protein Science published by Wiley Periodicals, Inc. on behalf of The Protein Society.

Essential Parameters for Structural Analysis and Dereplication by 1H NMR Spectroscopy

PubMed Central

2015-01-01

The present study demonstrates the importance of adequate precision when reporting the δ and J parameters of frequency domain 1H NMR (HNMR) data. Using a variety of structural classes (terpenoids, phenolics, alkaloids) from different taxa (plants, cyanobacteria), this study develops rationales that explain the importance of enhanced precision in NMR spectroscopic analysis and rationalizes the need for reporting Δδ and ΔJ values at the 0.1–1 ppb and 10 mHz level, respectively. Spectral simulations paired with iteration are shown to be essential tools for complete spectral interpretation, adequate precision, and unambiguous HNMR-driven dereplication and metabolomic analysis. The broader applicability of the recommendation relates to the physicochemical properties of hydrogen (1H) and its ubiquity in organic molecules, making HNMR spectra an integral component of structure elucidation and verification. Regardless of origin or molecular weight, the HNMR spectrum of a compound can be very complex and encode a wealth of structural information that is often obscured by limited spectral dispersion and the occurrence of higher order effects. This altogether limits spectral interpretation, confines decoding of the underlying spin parameters, and explains the major challenge associated with the translation of HNMR spectra into tabulated information. On the other hand, the reproducibility of the spectral data set of any (new) chemical entity is essential for its structure elucidation and subsequent dereplication. Handling and documenting HNMR data with adequate precision is critical for establishing unequivocal links between chemical structure, analytical data, metabolomes, and biological activity. Using the full potential of HNMR spectra will facilitate the general reproducibility for future studies of bioactive chemicals, especially of compounds obtained from the diversity of terrestrial and marine organisms. PMID:24895010

Comparison of topological clustering within protein networks using edge metrics that evaluate full sequence, full structure, and active site microenvironment similarity

PubMed Central

Leuthaeuser, Janelle B; Knutson, Stacy T; Kumar, Kiran; Babbitt, Patricia C; Fetrow, Jacquelyn S

2015-01-01

The development of accurate protein function annotation methods has emerged as a major unsolved biological problem. Protein similarity networks, one approach to function annotation via annotation transfer, group proteins into similarity-based clusters. An underlying assumption is that the edge metric used to identify such clusters correlates with functional information. In this contribution, this assumption is evaluated by observing topologies in similarity networks using three different edge metrics: sequence (BLAST), structure (TM-Align), and active site similarity (active site profiling, implemented in DASP). Network topologies for four well-studied protein superfamilies (enolase, peroxiredoxin (Prx), glutathione transferase (GST), and crotonase) were compared with curated functional hierarchies and structure. As expected, network topology differs, depending on edge metric; comparison of topologies provides valuable information on structure/function relationships. Subnetworks based on active site similarity correlate with known functional hierarchies at a single edge threshold more often than sequence- or structure-based networks. Sequence- and structure-based networks are useful for identifying sequence and domain similarities and differences; therefore, it is important to consider the clustering goal before deciding appropriate edge metric. Further, conserved active site residues identified in enolase and GST active site subnetworks correspond with published functionally important residues. Extension of this analysis yields predictions of functionally determinant residues for GST subgroups. These results support the hypothesis that active site similarity-based networks reveal clusters that share functional details and lay the foundation for capturing functionally relevant hierarchies using an approach that is both automatable and can deliver greater precision in function annotation than current similarity-based methods. PMID:26073648

Structural Magnetic Resonance Imaging Markers of Alzheimer's Disease and Its Retranslation to Rodent Models.

PubMed

Kincses, Zsigmond Tamas; Király, András; Veréb, Dániel; Vécsei, László

2015-01-01

The importance of imaging biomarkers has been acknowledged in the diagnosis and in the follow-up of Alzheimer's disease (AD), one of the major causes of dementia. Next to the molecular biomarkers and PET imaging investigations, structural MRI approaches provide important information about the disease progression and about the pathomechanism. Furthermore,a growing body of literature retranslates these imaging biomarkers to various rodent models of the disease. The goal of this review is to provide an overview of the macro- and microstructural imaging biomarkers of AD, concentrating on atrophy measures and diffusion MRI alterations. A survey is also given of the imaging approaches used in rodent models of dementias that can promote drug development.

Large-scale prediction of adverse drug reactions using chemical, biological, and phenotypic properties of drugs.

PubMed

Liu, Mei; Wu, Yonghui; Chen, Yukun; Sun, Jingchun; Zhao, Zhongming; Chen, Xue-wen; Matheny, Michael Edwin; Xu, Hua

2012-06-01

Adverse drug reaction (ADR) is one of the major causes of failure in drug development. Severe ADRs that go undetected until the post-marketing phase of a drug often lead to patient morbidity. Accurate prediction of potential ADRs is required in the entire life cycle of a drug, including early stages of drug design, different phases of clinical trials, and post-marketing surveillance. Many studies have utilized either chemical structures or molecular pathways of the drugs to predict ADRs. Here, the authors propose a machine-learning-based approach for ADR prediction by integrating the phenotypic characteristics of a drug, including indications and other known ADRs, with the drug's chemical structures and biological properties, including protein targets and pathway information. A large-scale study was conducted to predict 1385 known ADRs of 832 approved drugs, and five machine-learning algorithms for this task were compared. This evaluation, based on a fivefold cross-validation, showed that the support vector machine algorithm outperformed the others. Of the three types of information, phenotypic data were the most informative for ADR prediction. When biological and phenotypic features were added to the baseline chemical information, the ADR prediction model achieved significant improvements in area under the curve (from 0.9054 to 0.9524), precision (from 43.37% to 66.17%), and recall (from 49.25% to 63.06%). Most importantly, the proposed model successfully predicted the ADRs associated with withdrawal of rofecoxib and cerivastatin. The results suggest that phenotypic information on drugs is valuable for ADR prediction. Moreover, they demonstrate that different models that combine chemical, biological, or phenotypic information can be built from approved drugs, and they have the potential to detect clinically important ADRs in both preclinical and post-marketing phases.

Challenges to the implementation of the integrated management of childhood illness (IMCI) at community health centres in West Java province, Indonesia.

PubMed

Titaley, C R; Jusril, H; Ariawan, I; Soeharno, N; Setiawan, T; Weber, M W

2014-01-01

The integrated management of childhood illness (IMCI) is a comprehensive approach to child health, which has been adopted in Indonesia since 1997. This study aims to provide an overview of IMCI implementation at community health centres (puskesmas) in West Java province, Indonesia. Data were derived from a cross-sectional study conducted in 10 districts of West Java province, from November to December 2012. Semi-structured interviews were used to obtain information from staff at 80 puskesmas, including the heads (80 informants), pharmacy staff (79 informants) and midwives/nurses trained in IMCI (148 informants), using semi-structured interviews. Quantitative data were analysed using frequency tabulations and qualitative data were analysed by identifying themes that emerged in informants' responses. Almost all (N = 79) puskesmas implemented the IMCI strategy; however, only 64% applied it to all visiting children. Several barriers to IMCI implementation were identified, including shortage of health workers trained in IMCI (only 43% of puskesmas had all health workers in the child care unit trained in IMCI and 40% of puskesmas conducted on-the-job training). Only 19% of puskesmas had all the essential drugs and equipment for IMCI. Nearly all health workers acknowledged the importance of IMCI in their routine services and very few did not perceive its benefits. Lack of supervision from district health office staff and low community awareness regarding the importance of IMCI were reported. Complaints received from patients'families were generally related to the long duration of treatment and no administration of medication after physical examination. Interventions aiming to create local regulations endorsing IMCI implementation; promoting monitoring and supervision; encouraging on-the-job training for health workers; and strengthening training programmes, counselling and other promotional activities are important for promoting IMCI implementation in West Java province, and are also likely to be useful elsewhere in the country.

Fair Shares and Sharing Fairly: A Survey of Public Views on Open Science, Informed Consent and Participatory Research in Biobanking.

PubMed

Joly, Yann; Dalpé, Gratien; So, Derek; Birko, Stanislav

2015-01-01

Biobanks are important resources which enable large-scale genomic research with human samples and data, raising significant ethical concerns about how participants' information is managed and shared. Three previous studies of the Canadian public's opinion about these topics have been conducted. Building on those results, an online survey representing the first study of public perceptions about biobanking spanning all Canadian provinces was conducted. Specifically, this study examined qualitative views about biobank objectives, governance structure, control and ownership of samples and data, benefit sharing, consent practices and data sharing norms, as well as additional questions and ethical concerns expressed by the public. Over half the respondents preferred to give a one-time general consent for the future sharing of their samples among researchers. Most expressed willingness for their data to be shared with the international scientific community rather than used by one or more Canadian institutions. Whereas more respondents indicated a preference for one-time general consent than any other model of consent, they constituted less than half of the total responses, revealing a lack of consensus among survey respondents regarding this question. Respondents identified biobank objectives, governance structure and accountability as the most important information to provide participants. Respondents' concerns about biobanking generally centred around the control and ownership of biological samples and data, especially with respect to potential misuse by insurers, the government and other third parties. Although almost half the respondents suggested that these should be managed by the researchers' institutions, results indicate that the public is interested in being well-informed about these projects and suggest the importance of increased involvement from participants. In conclusion, the study discusses the viability of several proposed models for informed consent, including e-governance, independent trustees and the use of exclusion clauses, in the context of these new findings about the views of the Canadian public.

Fair Shares and Sharing Fairly: A Survey of Public Views on Open Science, Informed Consent and Participatory Research in Biobanking

PubMed Central

Joly, Yann; Dalpé, Gratien; So, Derek; Birko, Stanislav

2015-01-01

Context Biobanks are important resources which enable large-scale genomic research with human samples and data, raising significant ethical concerns about how participants’ information is managed and shared. Three previous studies of the Canadian public’s opinion about these topics have been conducted. Building on those results, an online survey representing the first study of public perceptions about biobanking spanning all Canadian provinces was conducted. Specifically, this study examined qualitative views about biobank objectives, governance structure, control and ownership of samples and data, benefit sharing, consent practices and data sharing norms, as well as additional questions and ethical concerns expressed by the public. Results Over half the respondents preferred to give a one-time general consent for the future sharing of their samples among researchers. Most expressed willingness for their data to be shared with the international scientific community rather than used by one or more Canadian institutions. Whereas more respondents indicated a preference for one-time general consent than any other model of consent, they constituted less than half of the total responses, revealing a lack of consensus among survey respondents regarding this question. Respondents identified biobank objectives, governance structure and accountability as the most important information to provide participants. Respondents’ concerns about biobanking generally centred around the control and ownership of biological samples and data, especially with respect to potential misuse by insurers, the government and other third parties. Although almost half the respondents suggested that these should be managed by the researchers’ institutions, results indicate that the public is interested in being well-informed about these projects and suggest the importance of increased involvement from participants. In conclusion, the study discusses the viability of several proposed models for informed consent, including e-governance, independent trustees and the use of exclusion clauses, in the context of these new findings about the views of the Canadian public. PMID:26154134

Human cell structure-driven model construction for predicting protein subcellular location from biological images.

PubMed

Shao, Wei; Liu, Mingxia; Zhang, Daoqiang

2016-01-01

The systematic study of subcellular location pattern is very important for fully characterizing the human proteome. Nowadays, with the great advances in automated microscopic imaging, accurate bioimage-based classification methods to predict protein subcellular locations are highly desired. All existing models were constructed on the independent parallel hypothesis, where the cellular component classes are positioned independently in a multi-class classification engine. The important structural information of cellular compartments is missed. To deal with this problem for developing more accurate models, we proposed a novel cell structure-driven classifier construction approach (SC-PSorter) by employing the prior biological structural information in the learning model. Specifically, the structural relationship among the cellular components is reflected by a new codeword matrix under the error correcting output coding framework. Then, we construct multiple SC-PSorter-based classifiers corresponding to the columns of the error correcting output coding codeword matrix using a multi-kernel support vector machine classification approach. Finally, we perform the classifier ensemble by combining those multiple SC-PSorter-based classifiers via majority voting. We evaluate our method on a collection of 1636 immunohistochemistry images from the Human Protein Atlas database. The experimental results show that our method achieves an overall accuracy of 89.0%, which is 6.4% higher than the state-of-the-art method. The dataset and code can be downloaded from https://github.com/shaoweinuaa/. dqzhang@nuaa.edu.cn Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

The psychometric properties of the Chinese version of the Conditions of Work Effectiveness Questionnaire-II.

PubMed

Sun, Ning; Li, Qiu-Jie; Lv, Dong-Mei; Lu, Gui-Zhi; Lin, Ping; An, Xue-Mei

2014-10-01

The present study was conducted to evaluate the psychometric properties of a newly adapted Chinese version of an instrument designed to measure structural empowerment among staff nurses. Structural empowerment has been shown to be important to nurses in Western cultures, but its importance in China is unknown. A convenience sample of 650 staff nurses was selected from six hospitals in Harbin, China. After linguistic adaptation using the forward-backward translation method, the 19-item Conditions of Work Effectiveness Questionnaire-II (CWEQ-II-CV) was answered by participants. Content validity, Cronbach's alpha, item-to-total correlation and exploratory factor analysis were used to assess the reliability and validity of the translated instrument. In the factor analysis, a six-factor solution was found to be reasonable with the sub-dimensions of structural empowerment that included support (three items), resources (three items), information (three items), opportunity (three items), formal power (three items) and informal power (four items). Cronbach's alpha coefficient for the total instrument was 0.92 and ranged from 0.68 to 0.86 in the six subscales. The item-to-total correlation coefficients ranged from 0.48 to 0.80. The findings also gave support for content validity. Evidence was found to support the reliability and validity of the CWEQ-II-CV scale that measures the quality of the work environment for nurses from a structural empowerment perspective. The translated version of CWEQ-II-CV can provide an effective evaluation tool for structural empowerment in the Chinese nursing workplace. © 2013 John Wiley & Sons Ltd.

Modulation of individual steps in group I intron catalysis by a peripheral metal ion.

PubMed

Forconi, Marcello; Piccirilli, Joseph A; Herschlag, Daniel

2007-10-01

Enzymes are complex macromolecules that catalyze chemical reactions at their active sites. Important information about catalytic interactions is commonly gathered by perturbation or mutation of active site residues that directly contact substrates. However, active sites are engaged in intricate networks of interactions within the overall structure of the macromolecule, and there is a growing body of evidence about the importance of peripheral interactions in the precise structural organization of the active site. Here, we use functional studies, in conjunction with published structural information, to determine the effect of perturbation of a peripheral metal ion binding site on catalysis in a well-characterized catalytic RNA, the Tetrahymena thermophila group I ribozyme. We perturbed the metal ion binding site by site-specifically introducing a phosphorothioate substitution in the ribozyme's backbone, replacing the native ligands (the pro-R (P) oxygen atoms at positions 307 and 308) with sulfur atoms. Our data reveal that these perturbations affect several reaction steps, including the chemical step, despite the absence of direct contacts of this metal ion with the atoms involved in the chemical transformation. As structural probing with hydroxyl radicals did not reveal significant change in the three-dimensional structure upon phosphorothioate substitution, the effects are likely transmitted through local, rather subtle conformational rearrangements. Addition of Cd(2+), a thiophilic metal ion, rescues some reaction steps but has deleterious effects on other steps. These results suggest that native interactions in the active site may have been aligned by the naturally occurring peripheral residues and interactions to optimize the overall catalytic cycle.