A New Model for the Organizational Structure of Medical Record Departments in Hospitals in Iran

PubMed Central

Moghaddasi, Hamid; Hosseini, Azamossadat; Sheikhtaheri, Abbas

2006-01-01

The organizational structure of medical record departments in Iran is not appropriate for the efficient management of healthcare information. In addition, there is no strong information management division to provide comprehensive information management services in hospitals in Iran. Therefore, a suggested model was designed based on four main axes: 1) specifications of a Health Information Management Division, 2) specifications of a Healthcare Information Management Department, 3) the functions of the Healthcare Information Management Department, and 4) the units of the Healthcare Information Management Department. The validity of the model was determined through use of the Delphi technique. The results of the validation process show that the majority of experts agree with the model and consider it to be appropriate and applicable for hospitals in Iran. The model is therefore recommended for hospitals in Iran. PMID:18066362

Homology‐based hydrogen bond information improves crystallographic structures in the PDB

PubMed Central

van Beusekom, Bart; Touw, Wouter G.; Tatineni, Mahidhar; Somani, Sandeep; Rajagopal, Gunaretnam; Luo, Jinquan; Gilliland, Gary L.; Perrakis, Anastassis

2017-01-01

Abstract The Protein Data Bank (PDB) is the global archive for structural information on macromolecules, and a popular resource for researchers, teachers, and students, amassing more than one million unique users each year. Crystallographic structure models in the PDB (more than 100,000 entries) are optimized against the crystal diffraction data and geometrical restraints. This process of crystallographic refinement typically ignored hydrogen bond (H‐bond) distances as a source of information. However, H‐bond restraints can improve structures at low resolution where diffraction data are limited. To improve low‐resolution structure refinement, we present methods for deriving H‐bond information either globally from well‐refined high‐resolution structures from the PDB‐REDO databank, or specifically from on‐the‐fly constructed sets of homologous high‐resolution structures. Refinement incorporating HOmology DErived Restraints (HODER), improves geometrical quality and the fit to the diffraction data for many low‐resolution structures. To make these improvements readily available to the general public, we applied our new algorithms to all crystallographic structures in the PDB: using massively parallel computing, we constructed a new instance of the PDB‐REDO databank (https://pdb-redo.eu). This resource is useful for researchers to gain insight on individual structures, on specific protein families (as we demonstrate with examples), and on general features of protein structure using data mining approaches on a uniformly treated dataset. PMID:29168245

Homology-based hydrogen bond information improves crystallographic structures in the PDB.

PubMed

van Beusekom, Bart; Touw, Wouter G; Tatineni, Mahidhar; Somani, Sandeep; Rajagopal, Gunaretnam; Luo, Jinquan; Gilliland, Gary L; Perrakis, Anastassis; Joosten, Robbie P

2018-03-01

The Protein Data Bank (PDB) is the global archive for structural information on macromolecules, and a popular resource for researchers, teachers, and students, amassing more than one million unique users each year. Crystallographic structure models in the PDB (more than 100,000 entries) are optimized against the crystal diffraction data and geometrical restraints. This process of crystallographic refinement typically ignored hydrogen bond (H-bond) distances as a source of information. However, H-bond restraints can improve structures at low resolution where diffraction data are limited. To improve low-resolution structure refinement, we present methods for deriving H-bond information either globally from well-refined high-resolution structures from the PDB-REDO databank, or specifically from on-the-fly constructed sets of homologous high-resolution structures. Refinement incorporating HOmology DErived Restraints (HODER), improves geometrical quality and the fit to the diffraction data for many low-resolution structures. To make these improvements readily available to the general public, we applied our new algorithms to all crystallographic structures in the PDB: using massively parallel computing, we constructed a new instance of the PDB-REDO databank (https://pdb-redo.eu). This resource is useful for researchers to gain insight on individual structures, on specific protein families (as we demonstrate with examples), and on general features of protein structure using data mining approaches on a uniformly treated dataset. © 2017 The Protein Society.

Information object definition-based unified modeling language representation of DICOM structured reporting: a case study of transcoding DICOM to XML.

PubMed

Tirado-Ramos, Alfredo; Hu, Jingkun; Lee, K P

2002-01-01

Supplement 23 to DICOM (Digital Imaging and Communications for Medicine), Structured Reporting, is a specification that supports a semantically rich representation of image and waveform content, enabling experts to share image and related patient information. DICOM SR supports the representation of textual and coded data linked to images and waveforms. Nevertheless, the medical information technology community needs models that work as bridges between the DICOM relational model and open object-oriented technologies. The authors assert that representations of the DICOM Structured Reporting standard, using object-oriented modeling languages such as the Unified Modeling Language, can provide a high-level reference view of the semantically rich framework of DICOM and its complex structures. They have produced an object-oriented model to represent the DICOM SR standard and have derived XML-exchangeable representations of this model using World Wide Web Consortium specifications. They expect the model to benefit developers and system architects who are interested in developing applications that are compliant with the DICOM SR specification.

Trait Distinctiveness and Age Specificity in Self-Referent Information Processing.

ERIC Educational Resources Information Center

Mueller, John H.; Johnson, W. Calvin

Research has indicated that certain orienting activities help integrate new experiences with pre-existing cognitive structures. The content specificity hypothesis proposes that if the self-concept is distorted so that certain information is missing, then self-referencing that type of material will be ineffective. This notion of content specificity…

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.

Developing transboundary river basin monitoring programmes using the DPSIR indicator framework.

PubMed

Timmerman, J G; Beinat, E; Termeer, C J A M; Cofino, W P

2011-10-01

Policymakers are often dissatisfied by the lack of what they consider useful information to support water management. Analysis of this 'water information gap' shows that this is caused by a lack of proper communication between information users and information producers. To improve this communication the process of specification of information needs has been structured. Earlier experiences showed that this not only entailed developing a structure to manage the process, but also developing a structure to guide the breakdown of policy objectives into information needs. Such a structure to organise the problem supports policy makers and monitoring specialists in their communication. This paper describes three pilot projects where the DPSIR indicator framework was used to organise the problem. It is concluded that the DPSIR framework is useful for improving the communication between information users and information producers and is helpful in breaking down policy objectives into information needs in a structured way. The structured approach in this way assists in narrowing the water information gap. Use of the DPSIR framework however leads to a bias towards water management problems and does not provide for all the relevant information needs.

Information visualization: Beyond traditional engineering

NASA Technical Reports Server (NTRS)

Thomas, James J.

1995-01-01

This presentation addresses a different aspect of the human-computer interface; specifically the human-information interface. This interface will be dominated by an emerging technology called Information Visualization (IV). IV goes beyond the traditional views of computer graphics, CADS, and enables new approaches for engineering. IV specifically must visualize text, documents, sound, images, and video in such a way that the human can rapidly interact with and understand the content structure of information entities. IV is the interactive visual interface between humans and their information resources.

RNACompress: Grammar-based compression and informational complexity measurement of RNA secondary structure.

PubMed

Liu, Qi; Yang, Yu; Chen, Chun; Bu, Jiajun; Zhang, Yin; Ye, Xiuzi

2008-03-31

With the rapid emergence of RNA databases and newly identified non-coding RNAs, an efficient compression algorithm for RNA sequence and structural information is needed for the storage and analysis of such data. Although several algorithms for compressing DNA sequences have been proposed, none of them are suitable for the compression of RNA sequences with their secondary structures simultaneously. This kind of compression not only facilitates the maintenance of RNA data, but also supplies a novel way to measure the informational complexity of RNA structural data, raising the possibility of studying the relationship between the functional activities of RNA structures and their complexities, as well as various structural properties of RNA based on compression. RNACompress employs an efficient grammar-based model to compress RNA sequences and their secondary structures. The main goals of this algorithm are two fold: (1) present a robust and effective way for RNA structural data compression; (2) design a suitable model to represent RNA secondary structure as well as derive the informational complexity of the structural data based on compression. Our extensive tests have shown that RNACompress achieves a universally better compression ratio compared with other sequence-specific or common text-specific compression algorithms, such as Gencompress, winrar and gzip. Moreover, a test of the activities of distinct GTP-binding RNAs (aptamers) compared with their structural complexity shows that our defined informational complexity can be used to describe how complexity varies with activity. These results lead to an objective means of comparing the functional properties of heteropolymers from the information perspective. A universal algorithm for the compression of RNA secondary structure as well as the evaluation of its informational complexity is discussed in this paper. We have developed RNACompress, as a useful tool for academic users. Extensive tests have shown that RNACompress is a universally efficient algorithm for the compression of RNA sequences with their secondary structures. RNACompress also serves as a good measurement of the informational complexity of RNA secondary structure, which can be used to study the functional activities of RNA molecules.

RNACompress: Grammar-based compression and informational complexity measurement of RNA secondary structure

PubMed Central

Liu, Qi; Yang, Yu; Chen, Chun; Bu, Jiajun; Zhang, Yin; Ye, Xiuzi

2008-01-01

Background With the rapid emergence of RNA databases and newly identified non-coding RNAs, an efficient compression algorithm for RNA sequence and structural information is needed for the storage and analysis of such data. Although several algorithms for compressing DNA sequences have been proposed, none of them are suitable for the compression of RNA sequences with their secondary structures simultaneously. This kind of compression not only facilitates the maintenance of RNA data, but also supplies a novel way to measure the informational complexity of RNA structural data, raising the possibility of studying the relationship between the functional activities of RNA structures and their complexities, as well as various structural properties of RNA based on compression. Results RNACompress employs an efficient grammar-based model to compress RNA sequences and their secondary structures. The main goals of this algorithm are two fold: (1) present a robust and effective way for RNA structural data compression; (2) design a suitable model to represent RNA secondary structure as well as derive the informational complexity of the structural data based on compression. Our extensive tests have shown that RNACompress achieves a universally better compression ratio compared with other sequence-specific or common text-specific compression algorithms, such as Gencompress, winrar and gzip. Moreover, a test of the activities of distinct GTP-binding RNAs (aptamers) compared with their structural complexity shows that our defined informational complexity can be used to describe how complexity varies with activity. These results lead to an objective means of comparing the functional properties of heteropolymers from the information perspective. Conclusion A universal algorithm for the compression of RNA secondary structure as well as the evaluation of its informational complexity is discussed in this paper. We have developed RNACompress, as a useful tool for academic users. Extensive tests have shown that RNACompress is a universally efficient algorithm for the compression of RNA sequences with their secondary structures. RNACompress also serves as a good measurement of the informational complexity of RNA secondary structure, which can be used to study the functional activities of RNA molecules. PMID:18373878

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

NASA Technical Reports Server (NTRS)

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

1999-01-01

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

Deconstructing thermodynamic parameters of a coupled system from site-specific observables.

PubMed

Chowdhury, Sandipan; Chanda, Baron

2010-11-02

Cooperative interactions mediate information transfer between structural domains of a protein molecule and are major determinants of protein function and modulation. The prevalent theories to understand the thermodynamic origins of cooperativity have been developed to reproduce the complex behavior of a global thermodynamic observable such as ligand binding or enzyme activity. However, in most cases the measurement of a single global observable cannot uniquely define all the terms that fully describe the energetics of the system. Here we establish a theoretical groundwork for analyzing protein thermodynamics using site-specific information. Our treatment involves extracting a site-specific parameter (defined as χ value) associated with a structural unit. We demonstrate that, under limiting conditions, the χ value is related to the direct interaction terms associated with the structural unit under observation and its intrinsic activation energy. We also introduce a site-specific interaction energy term (χ(diff)) that is a function of the direct interaction energy of that site with every other site in the system. When combined with site-directed mutagenesis and other molecular level perturbations, analyses of χ values of site-specific observables may provide valuable insights into protein thermodynamics and structure.

Targeted Information Dissemination

DTIC Science & Technology

2008-03-01

SETUP, RESULTS AND PERFORMANCE ANALYSIS .......................................... 36 APPENDIX C: TID API SPECIFICATION...are developed using FreePastry1. FreePastry provides an API for a structured P2P overlay network. Information Routing and address resolution is...the TID architecture to demonstrate its key features. TID interface API specifications are described in Appendix C. RSS feeds were used to obtain

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.

Prediction of TF target sites based on atomistic models of protein-DNA complexes

PubMed Central

Angarica, Vladimir Espinosa; Pérez, Abel González; Vasconcelos, Ana T; Collado-Vides, Julio; Contreras-Moreira, Bruno

2008-01-01

Background The specific recognition of genomic cis-regulatory elements by transcription factors (TFs) plays an essential role in the regulation of coordinated gene expression. Studying the mechanisms determining binding specificity in protein-DNA interactions is thus an important goal. Most current approaches for modeling TF specific recognition rely on the knowledge of large sets of cognate target sites and consider only the information contained in their primary sequence. Results Here we describe a structure-based methodology for predicting sequence motifs starting from the coordinates of a TF-DNA complex. Our algorithm combines information regarding the direct and indirect readout of DNA into an atomistic statistical model, which is used to estimate the interaction potential. We first measure the ability of our method to correctly estimate the binding specificities of eight prokaryotic and eukaryotic TFs that belong to different structural superfamilies. Secondly, the method is applied to two homology models, finding that sampling of interface side-chain rotamers remarkably improves the results. Thirdly, the algorithm is compared with a reference structural method based on contact counts, obtaining comparable predictions for the experimental complexes and more accurate sequence motifs for the homology models. Conclusion Our results demonstrate that atomic-detail structural information can be feasibly used to predict TF binding sites. The computational method presented here is universal and might be applied to other systems involving protein-DNA recognition. PMID:18922190

Elements of the cellular metabolic structure

PubMed Central

De la Fuente, Ildefonso M.

2015-01-01

A large number of studies have demonstrated the existence of metabolic covalent modifications in different molecular structures, which are able to store biochemical information that is not encoded by DNA. Some of these covalent mark patterns can be transmitted across generations (epigenetic changes). Recently, the emergence of Hopfield-like attractor dynamics has been observed in self-organized enzymatic networks, which have the capacity to store functional catalytic patterns that can be correctly recovered by specific input stimuli. Hopfield-like metabolic dynamics are stable and can be maintained as a long-term biochemical memory. In addition, specific molecular information can be transferred from the functional dynamics of the metabolic networks to the enzymatic activity involved in covalent post-translational modulation, so that determined functional memory can be embedded in multiple stable molecular marks. The metabolic dynamics governed by Hopfield-type attractors (functional processes), as well as the enzymatic covalent modifications of specific molecules (structural dynamic processes) seem to represent the two stages of the dynamical memory of cellular metabolism (metabolic memory). Epigenetic processes appear to be the structural manifestation of this cellular metabolic memory. Here, a new framework for molecular information storage in the cell is presented, which is characterized by two functionally and molecularly interrelated systems: a dynamic, flexible and adaptive system (metabolic memory) and an essentially conservative system (genetic memory). The molecular information of both systems seems to coordinate the physiological development of the whole cell. PMID:25988183

How electrostatic networks modulate specificity and stability of collagen.

PubMed

Zheng, Hongning; Lu, Cheng; Lan, Jun; Fan, Shilong; Nanda, Vikas; Xu, Fei

2018-06-12

One-quarter of the 28 types of natural collagen exist as heterotrimers. The oligomerization state of collagen affects the structure and mechanics of the extracellular matrix, providing essential cues to modulate biological and pathological processes. A lack of high-resolution structural information limits our mechanistic understanding of collagen heterospecific self-assembly. Here, the 1.77-Å resolution structure of a synthetic heterotrimer demonstrates the balance of intermolecular electrostatics and hydrogen bonding that affects collagen stability and heterospecificity of assembly. Atomistic simulations and mutagenesis based on the solved structure are used to explore the contributions of specific interactions to energetics. A predictive model of collagen stability and specificity is developed for engineering novel collagen structures.

Time-Varying, Multi-Scale Adaptive System Reliability Analysis of Lifeline Infrastructure Networks

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

Gearhart, Jared Lee; Kurtz, Nolan Scot

2014-09-01

The majority of current societal and economic needs world-wide are met by the existing networked, civil infrastructure. Because the cost of managing such infrastructure is high and increases with time, risk-informed decision making is essential for those with management responsibilities for these systems. To address such concerns, a methodology that accounts for new information, deterioration, component models, component importance, group importance, network reliability, hierarchical structure organization, and efficiency concerns has been developed. This methodology analyzes the use of new information through the lens of adaptive Importance Sampling for structural reliability problems. Deterioration, multi-scale bridge models, and time-variant component importance aremore » investigated for a specific network. Furthermore, both bridge and pipeline networks are studied for group and component importance, as well as for hierarchical structures in the context of specific networks. Efficiency is the primary driver throughout this study. With this risk-informed approach, those responsible for management can address deteriorating infrastructure networks in an organized manner.« less

Information Book Read-Alouds as Models for Second-Grade Authors

ERIC Educational Resources Information Center

Bradley, Linda Golson; Donovan, Carol A.

2010-01-01

This article discusses the instructional practice of supporting second graders' information book writing with focused read-alouds that include discussions of information book genre elements, features, and organizational structure. The authors present specific examples of instruction and discuss the resulting information book compositions by…

Learners' Perceptions on the Structure and Usefulness of E-Resources for the Thesis Courses

ERIC Educational Resources Information Center

Aghaee, Naghmeh; Hansson, Henrik; Tedre, Matti; Drougge, Ulrika

2014-01-01

The use of information and communication technology (ICT) in education is a way to facilitate interaction and accessing information for learning in higher education. However, finding a set of structured e-resources to facilitate learning within specific courses is still a big challenge in most higher education institutions. This includes the…

Genetic subpopulation structuring and its implications in a mature eastern white pine stand

Treesearch

Samuel E. Nijensohn; Paul G. Schaberg; Gary J. Hawley; Donald H. DeHayes; Donald H. DeHayes

2005-01-01

We examined patterns of genetic structuring within a mature eastern white pine (Pinus strobus L.) forest, using geographic information system (GIS)-based data and maps that combined genetic (isozyme analysis of 46 loci) and other tree-specific information (e.g., size, growth, age, and location) for 220 trees in Jericho, Vermont. Interconnections between genotypic...

49 CFR 172.704 - Training requirements.

Code of Federal Regulations, 2010 CFR

2010-10-01

... PROVISIONS, HAZARDOUS MATERIALS COMMUNICATIONS, EMERGENCY RESPONSE INFORMATION, TRAINING REQUIREMENTS, AND... communication standards of this subchapter. (2) Function-specific training. (i) Each hazmat employee must be... must include company security objectives, organizational security structure, specific security...

[Influence of "prehistory" of sequential movements of the right and the left hand on reproduction: coding of positions, movements and sequence structure].

PubMed

Bobrova, E V; Liakhovetskiĭ, V A; Borshchevskaia, E R

2011-01-01

The dependence of errors during reproduction of a sequence of hand movements without visual feedback on the previous right- and left-hand performance ("prehistory") and on positions in space of sequence elements (random or ordered by the explicit rule) was analyzed. It was shown that the preceding information about the ordered positions of the sequence elements was used during right-hand movements, whereas left-hand movements were performed with involvement of the information about the random sequence. The data testify to a central mechanism of the analysis of spatial structure of sequence elements. This mechanism activates movement coding specific for the left hemisphere (vector coding) in case of an ordered sequence structure and positional coding specific for the right hemisphere in case of a random sequence structure.

NASA Operational Environment Team (NOET) - NASA's key to environmental technology

NASA Technical Reports Server (NTRS)

Cook, Beth

1993-01-01

NOET is a NASA-wide team which supports the research and development community by sharing information both in person and via a computerized network, assisting in specification and standard revisions, developing cleaner propulsion systems, and exploring environmentally compliant alternatives to current processes. NOET's structure, dissemination of materials, electronic information, EPA compliance, specifications and standards, and environmental research and development are discussed.

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

ERIC Educational Resources Information Center

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

2016-01-01

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

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

YAdumper: extracting and translating large information volumes from relational databases to structured flat files.

PubMed

Fernández, José M; Valencia, Alfonso

2004-10-12

Downloading the information stored in relational databases into XML and other flat formats is a common task in bioinformatics. This periodical dumping of information requires considerable CPU time, disk and memory resources. YAdumper has been developed as a purpose-specific tool to deal with the integral structured information download of relational databases. YAdumper is a Java application that organizes database extraction following an XML template based on an external Document Type Declaration. Compared with other non-native alternatives, YAdumper substantially reduces memory requirements and considerably improves writing performance.

Human errors and violations in computer and information security: the viewpoint of network administrators and security specialists.

PubMed

Kraemer, Sara; Carayon, Pascale

2007-03-01

This paper describes human errors and violations of end users and network administration in computer and information security. This information is summarized in a conceptual framework for examining the human and organizational factors contributing to computer and information security. This framework includes human error taxonomies to describe the work conditions that contribute adversely to computer and information security, i.e. to security vulnerabilities and breaches. The issue of human error and violation in computer and information security was explored through a series of 16 interviews with network administrators and security specialists. The interviews were audio taped, transcribed, and analyzed by coding specific themes in a node structure. The result is an expanded framework that classifies types of human error and identifies specific human and organizational factors that contribute to computer and information security. Network administrators tended to view errors created by end users as more intentional than unintentional, while errors created by network administrators as more unintentional than intentional. Organizational factors, such as communication, security culture, policy, and organizational structure, were the most frequently cited factors associated with computer and information security.

Distillation tray structural parameter study: Phase 1

NASA Technical Reports Server (NTRS)

Winter, J. Ronald

1991-01-01

The purpose here is to identify the structural parameters (plate thickness, liquid level, beam size, number of beams, tray diameter, etc.) that affect the structural integrity of distillation trays in distillation columns. Once the sensitivity of the trays' dynamic response to these parameters has been established, the designer will be able to use this information to prepare more accurate specifications for the construction of new trays. Information is given on both static and dynamic analysis, modal response, and tray failure details.

The Distribution of the Informative Intensity of the Text in Terms of its Structure (On Materials of the English Texts in the Mining Sphere)

NASA Astrophysics Data System (ADS)

Znikina, Ludmila; Rozhneva, Elena

2017-11-01

The article deals with the distribution of informative intensity of the English-language scientific text based on its structural features contributing to the process of formalization of the scientific text and the preservation of the adequacy of the text with derived semantic information in relation to the primary. Discourse analysis is built on specific compositional and meaningful examples of scientific texts taken from the mining field. It also analyzes the adequacy of the translation of foreign texts into another language, the relationships between elements of linguistic systems, the degree of a formal conformance, translation with the specific objectives and information needs of the recipient. Some key words and ideas are emphasized in the paragraphs of the English-language mining scientific texts. The article gives the characteristic features of the structure of paragraphs of technical text and examples of constructions in English scientific texts based on a mining theme with the aim to explain the possible ways of their adequate translation.

A framework for the etiology of running-related injuries.

PubMed

Bertelsen, M L; Hulme, A; Petersen, J; Brund, R K; Sørensen, H; Finch, C F; Parner, E T; Nielsen, R O

2017-11-01

The etiology of running-related injury is important to consider as the effectiveness of a given running-related injury prevention intervention is dependent on whether etiologic factors are readily modifiable and consistent with a biologically plausible causal mechanism. Therefore, the purpose of the present article was to present an evidence-informed conceptual framework outlining the multifactorial nature of running-related injury etiology. In the framework, four mutually exclusive parts are presented: (a) Structure-specific capacity when entering a running session; (b) structure-specific cumulative load per running session; (c) reduction in the structure-specific capacity during a running session; and (d) exceeding the structure-specific capacity. The framework can then be used to inform the design of future running-related injury prevention studies, including the formation of research questions and hypotheses, as well as the monitoring of participation-related and non-participation-related exposures. In addition, future research applications should focus on addressing how changes in one or more exposures influence the risk of running-related injury. This necessitates the investigation of how different factors affect the structure-specific load and/or the load capacity, and the dose-response relationship between running participation and injury risk. Ultimately, this direction allows researchers to move beyond traditional risk factor identification to produce research findings that are not only reliably reported in terms of the observed cause-effect association, but also translatable in practice. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Tools reference manual for a Requirements Specification Language (RSL), version 2.0

NASA Technical Reports Server (NTRS)

Fisher, Gene L.; Cohen, Gerald C.

1993-01-01

This report describes a general-purpose Requirements Specification Language, RSL. The purpose of RSL is to specify precisely the external structure of a mechanized system and to define requirements that the system must meet. A system can be comprised of a mixture of hardware, software, and human processing elements. RSL is a hybrid of features found in several popular requirements specification languages, such as SADT (Structured Analysis and Design Technique), PSL (Problem Statement Language), and RMF (Requirements Modeling Framework). While languages such as these have useful features for structuring a specification, they generally lack formality. To overcome the deficiencies of informal requirements languages, RSL has constructs for formal mathematical specification. These constructs are similar to those found in formal specification languages such as EHDM (Enhanced Hierarchical Development Methodology), Larch, and OBJ3.

A SOA-Based Solution to Monitor Vaccination Coverage Among HIV-Infected Patients in Liguria.

PubMed

Giannini, Barbara; Gazzarata, Roberta; Sticchi, Laura; Giacomini, Mauro

2016-01-01

Vaccination in HIV-infected patients constitutes an essential tool in the prevention of the most common infectious diseases. The Ligurian Vaccination in HIV Program is a proposed vaccination schedule specifically dedicated to this risk group. Selective strategies are proposed within this program, employing ICT (Information and Communication) tools to identify this susceptible target group, to monitor immunization coverage over time and to manage failures and defaulting. The proposal is to connect an immunization registry system to an existing regional platform that allows clinical data re-use among several medical structures, to completely manage the vaccination process. This architecture will adopt a Service Oriented Architecture (SOA) approach and standard HSSP (Health Services Specification Program) interfaces to support interoperability. According to the presented solution, vaccination administration information retrieved from the immunization registry will be structured according to the specifications within the immunization section of the HL7 (Health Level 7) CCD (Continuity of Care Document) document. Immunization coverage will be evaluated through the continuous monitoring of serology and antibody titers gathered from the hospital LIS (Laboratory Information System) structured into a HL7 Version 3 (v3) Clinical Document Architecture Release 2 (CDA R2).

Integrating prior information into microwave tomography Part 1: Impact of detail on image quality.

PubMed

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

2017-12-01

The authors investigate the impact that incremental increases in the level of detail of patient-specific prior information have on image quality and the convergence behavior of an inversion algorithm in the context of near-field microwave breast imaging. A methodology is presented that uses image quality measures to characterize the ability of the algorithm to reconstruct both internal structures and lesions embedded in fibroglandular tissue. The approach permits key aspects that impact the quality of reconstruction of these structures to be identified and quantified. This provides insight into opportunities to improve image reconstruction performance. Patient-specific information is acquired using radar-based methods that form a regional map of the breast. This map is then incorporated into a microwave tomography algorithm. Previous investigations have demonstrated the effectiveness of this approach to improve image quality when applied to data generated with two-dimensional (2D) numerical models. The present study extends this work by generating prior information that is customized to vary the degree of structural detail to facilitate the investigation of the role of prior information in image formation. Numerical 2D breast models constructed from magnetic resonance (MR) scans, and reconstructions formed with a three-dimensional (3D) numerical breast model are used to assess if trends observed for the 2D results can be extended to 3D scenarios. For the blind reconstruction scenario (i.e., no prior information), the breast surface is not accurately identified and internal structures are not clearly resolved. A substantial improvement in image quality is achieved by incorporating the skin surface map and constraining the imaging domain to the breast. Internal features within the breast appear in the reconstructed image. However, it is challenging to discriminate between adipose and glandular regions and there are inaccuracies in both the structural properties of the glandular region and the dielectric properties reconstructed within this structure. Using a regional map with a skin layer only marginally improves this situation. Increasing the structural detail in the prior information to include internal features leads to reconstructions for which the interface that delineates the fat and gland regions can be inferred. Different features within the glandular region corresponding to tissues with varying relative permittivity values, such as a lesion embedded within glandular structure, emerge in the reconstructed images. Including knowledge of the breast surface and skin layer leads to a substantial improvement in image quality compared to the blind case, but the images have limited diagnostic utility for applications such as tumor response tracking. The diagnostic utility of the reconstruction technique is improved considerably when patient-specific structural information is used. This qualitative observation is supported quantitatively with image metrics. © 2017 American Association of Physicists in Medicine.

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.

Comments on the use of network structures to analyse commercial companies’ evolution and their impact on economic behaviour

NASA Astrophysics Data System (ADS)

Costea, Carmen

2006-10-01

Network analysis studies the development of the social structure of relationships around a group or an institutional body, and how it affects beliefs and behaviours. Causal constraints require a special and deeper attention to the social structure. The purpose of this paper is to give a new approach to the idea that this reality should be primarily conceived and investigated from the perspective of the properties of relations between and within units, instead of the properties of these units themselves. The relationship may refer to the exchange of products, labour, information and money. By mapping these relationships, network analysis can help to uncover the emergent and informal communication patterns of commercial companies that may be compared to the formal communication structures. These emergent patterns can be used to explain institutional and individuals’ behaviours. Network analysis techniques focus on the communication structure of an organization that can be subdivided and handled with different approaches. Structural features that can be analysed through the use of network analysis techniques are, for example, the (formal and informal) communication patterns in an organization or the identification of specific groups within an organization. Special attention may be given to specific aspects of communication patterns.

Application of linear array imaging techniques to the real-time inspection of airframe structures and substructures

NASA Technical Reports Server (NTRS)

Miller, James G.

1995-01-01

Development and application of linear array imaging technologies to address specific aging-aircraft inspection issues is described. Real-time video-taped images were obtained from an unmodified commercial linear-array medical scanner of specimens constructed to simulate typical types of flaws encountered in the inspection of aircraft structures. Results suggest that information regarding the characteristics, location, and interface properties of specific types of flaws in materials and structures may be obtained from the images acquired with a linear array. Furthermore, linear array imaging may offer the advantage of being able to compare 'good' regions with 'flawed' regions simultaneously, and in real time. Real-time imaging permits the inspector to obtain image information from various views and provides the opportunity for observing the effects of introducing specific interventions. Observation of an image in real-time can offer the operator the ability to 'interact' with the inspection process, thus providing new capabilities, and perhaps, new approaches to nondestructive inspections.

Personalized Guideline-Based Treatment Recommendations Using Natural Language Processing Techniques.

PubMed

Becker, Matthias; Böckmann, Britta

2017-01-01

Clinical guidelines and clinical pathways are accepted and proven instruments for quality assurance and process optimization. Today, electronic representation of clinical guidelines exists as unstructured text, but is not well-integrated with patient-specific information from electronic health records. Consequently, generic content of the clinical guidelines is accessible, but it is not possible to visualize the position of the patient on the clinical pathway, decision support cannot be provided by personalized guidelines for the next treatment step. The Systematized Nomenclature of Medicine - Clinical Terms (SNOMED CT) provides common reference terminology as well as the semantic link for combining the pathways and the patient-specific information. This paper proposes a model-based approach to support the development of guideline-compliant pathways combined with patient-specific structured and unstructured information using SNOMED CT. To identify SNOMED CT concepts, a software was developed to extract SNOMED CT codes out of structured and unstructured German data to map these with clinical pathways annotated in accordance with the systematized nomenclature.

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.

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.

ASSESSING HIPPOCAMPAL CHANGES INDICATIVE OF NEUROTOXIC EFFECTS.

EPA Science Inventory

Subtle changes in cognitive function are often the earliest indication of neurotoxic effects in humans. The hippocampus is a large forebrain structure subserving specific kinds of information encoding and consolidation in humans and other animals. Because of it laminar structur...

The Design Log: A New Informational Tool

ERIC Educational Resources Information Center

Spivak, Mayer

1978-01-01

The design log is a record of observations, diagnoses, prescriptions, and performance specifications for each space in a structure. It is a systematic approach to design that integrates information about user needs with traditional architectural programming and design. (Author/MLF)

Improving Performance in Constructing specific Web Directory using Focused Crawler: An Experiment on Botany Domain

NASA Astrophysics Data System (ADS)

Khalilian, Madjid; Boroujeni, Farsad Zamani; Mustapha, Norwati

Nowadays the growth of the web causes some difficulties to search and browse useful information especially in specific domains. However, some portion of the web remains largely underdeveloped, as shown in lack of high quality contents. An example is the botany specific web directory, in which lack of well-structured web directories have limited user's ability to browse required information. In this research we propose an improved framework for constructing a specific web directory. In this framework we use an anchor directory as a foundation for primary web directory. This web directory is completed by information which is gathered with automatic component and filtered by experts. We conduct an experiment for evaluating effectiveness, efficiency and satisfaction.

An improved 13C-tracer method for the study of lignin structure and reactions : differential 13C-NMR

Treesearch

Noritsugu Terashima; Dmitry Evtuguin; Carlos Pascoal Neto; Jim Parkas; Magnus Paulsson; Ulla Westermark; Sally Ralph; John Ralph

2003-01-01

The technique of selective 13C-enrichment of specific carbons in lignin combined with 13C-NMR differential spectrometry between spectra of 13C-enriched and unenriched lignins (Ä13C-NMR) provides definitive information on the structure of the lignin macromolecule. Improvements were made on, (1) specific 13C-enrichment of almost all carbons involved in inter-unit bonds...

Characterization and visualization of RNA secondary structure Boltzmann ensemble via information theory.

PubMed

Lin, Luan; McKerrow, Wilson H; Richards, Bryce; Phonsom, Chukiat; Lawrence, Charles E

2018-03-05

The nearest neighbor model and associated dynamic programming algorithms allow for the efficient estimation of the RNA secondary structure Boltzmann ensemble. However because a given RNA secondary structure only contains a fraction of the possible helices that could form from a given sequence, the Boltzmann ensemble is multimodal. Several methods exist for clustering structures and finding those modes. However less focus is given to exploring the underlying reasons for this multimodality: the presence of conflicting basepairs. Information theory, or more specifically mutual information, provides a method to identify those basepairs that are key to the secondary structure. To this end we find most informative basepairs and visualize the effect of these basepairs on the secondary structure. Knowing whether a most informative basepair is present tells us not only the status of the particular pair but also provides a large amount of information about which other pairs are present or not present. We find that a few basepairs account for a large amount of the structural uncertainty. The identification of these pairs indicates small changes to sequence or stability that will have a large effect on structure. We provide a novel algorithm that uses mutual information to identify the key basepairs that lead to a multimodal Boltzmann distribution. We then visualize the effect of these pairs on the overall Boltzmann ensemble.

Automated generation of individually customized visualizations of diagnosis-specific medical information using novel techniques of information extraction

NASA Astrophysics Data System (ADS)

Chen, Andrew A.; Meng, Frank; Morioka, Craig A.; Churchill, Bernard M.; Kangarloo, Hooshang

2005-04-01

Managing pediatric patients with neurogenic bladder (NGB) involves regular laboratory, imaging, and physiologic testing. Using input from domain experts and current literature, we identified specific data points from these tests to develop the concept of an electronic disease vector for NGB. An information extraction engine was used to extract the desired data elements from free-text and semi-structured documents retrieved from the patient"s medical record. Finally, a Java-based presentation engine created graphical visualizations of the extracted data. After precision, recall, and timing evaluation, we conclude that these tools may enable clinically useful, automatically generated, and diagnosis-specific visualizations of patient data, potentially improving compliance and ultimately, outcomes.

Positional information in axolotl and mouse limb extracellular matrix is mediated via heparan sulfate and fibroblast growth factor during limb regeneration in the axolotl (Ambystoma mexicanum).

PubMed

Phan, Anne Q; Lee, Jangwoo; Oei, Michelle; Flath, Craig; Hwe, Caitlyn; Mariano, Rachele; Vu, Tiffany; Shu, Cynthia; Dinh, Andrew; Simkin, Jennifer; Muneoka, Ken; Bryant, Susan V; Gardiner, David M

2015-08-01

Urodele amphibians are unique among adult vertebrates in their ability to regenerate complex body structures after traumatic injury. In salamander regeneration, the cells maintain a memory of their original position and use this positional information to recreate the missing pattern. We used an in vivo gain-of-function assay to determine whether components of the extracellular matrix (ECM) have positional information required to induce formation of new limb pattern during regeneration. We discovered that salamander limb ECM has a position-specific ability to either inhibit regeneration or induce de novo limb structure, and that this difference is dependent on heparan sulfates that are associated with differential expression of heparan sulfate sulfotransferases. We also discovered that an artificial ECM containing only heparan sulfate was sufficient to induce de novo limb pattern in salamander limb regeneration. Finally, ECM from mouse limbs is capable of inducing limb pattern in axolotl blastemas in a position-specific, developmental-stage-specific, and heparan sulfate-dependent manner. This study demonstrates a mechanism for positional information in regeneration and establishes a crucial functional link between salamander regeneration and mammals.

Positional information in axolotl and mouse limb extracellular matrix is mediated via heparan sulfate and fibroblast growth factor during limb regeneration in the axolotl (Ambystoma mexicanum)

PubMed Central

Phan, Anne Q.; Lee, Jangwoo; Oei, Michelle; Flath, Craig; Hwe, Caitlyn; Mariano, Rachele; Vu, Tiffany; Shu, Cynthia; Dinh, Andrew; Simkin, Jennifer; Muneoka, Ken; Bryant, Susan V.

2015-01-01

Abstract Urodele amphibians are unique among adult vertebrates in their ability to regenerate complex body structures after traumatic injury. In salamander regeneration, the cells maintain a memory of their original position and use this positional information to recreate the missing pattern. We used an in vivo gain‐of‐function assay to determine whether components of the extracellular matrix (ECM) have positional information required to induce formation of new limb pattern during regeneration. We discovered that salamander limb ECM has a position‐specific ability to either inhibit regeneration or induce de novo limb structure, and that this difference is dependent on heparan sulfates that are associated with differential expression of heparan sulfate sulfotransferases. We also discovered that an artificial ECM containing only heparan sulfate was sufficient to induce de novo limb pattern in salamander limb regeneration. Finally, ECM from mouse limbs is capable of inducing limb pattern in axolotl blastemas in a position‐specific, developmental‐stage‐specific, and heparan sulfate‐dependent manner. This study demonstrates a mechanism for positional information in regeneration and establishes a crucial functional link between salamander regeneration and mammals. PMID:27499874

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.

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.

Deformation and Failure of Protein Materials in Physiologically Extreme Conditions and Disease

DTIC Science & Technology

2009-03-01

resonance (NMR) spectroscopy and X- ray crystallography have advanced our ability to identify 3D protein structures57. Site-specific studies using NMR, a... ray crystallography, providing structural and temporal information about mechanisms of deformation and assembly (for example in intermediate...tens of thousands of 3D atomistic protein structures, identifying the structure of numerous proteins from varying species sources60. X- ray

Disruption of Information Technology Projects: The Reactive Decoupling of Project Management Methodologies

ERIC Educational Resources Information Center

Schmitz, Kurt W.

2013-01-01

Information Technology projects have migrated toward two dominant Project Management (PM) methodologies. Plan-driven practices provide organizational control through highly structured plans, schedules, and specifications that facilitate oversight by hierarchical bureaucracies. In contrast, agile practices emphasize empowered teams using flexible…

Data Mining of Macromolecular Structures.

PubMed

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

2016-01-01

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

Conceptual Structure within and between Modalities

PubMed Central

Dilkina, Katia; Lambon Ralph, Matthew A.

2012-01-01

Current views of semantic memory share the assumption that conceptual representations are based on multimodal experience, which activates distinct modality-specific brain regions. This proposition is widely accepted, yet little is known about how each modality contributes to conceptual knowledge and how the structure of this contribution varies across these multiple information sources. We used verbal feature lists, features from drawings, and verbal co-occurrence statistics from latent semantic analysis to examine the informational structure in four domains of knowledge: perceptual, functional, encyclopedic, and verbal. The goals of the analysis were three-fold: (1) to assess the structure within individual modalities; (2) to compare structures between modalities; and (3) to assess the degree to which concepts organize categorically or randomly. Our results indicated significant and unique structure in all four modalities: perceptually, concepts organize based on prominent features such as shape, size, color, and parts; functionally, they group based on use and interaction; encyclopedically, they arrange based on commonality in location or behavior; and verbally, they group associatively or relationally. Visual/perceptual knowledge gives rise to the strongest hierarchical organization and is closest to classic taxonomic structure. Information is organized somewhat similarly in the perceptual and encyclopedic domains, which differs significantly from the structure in the functional and verbal domains. Notably, the verbal modality has the most unique organization, which is not at all categorical but also not random. The idiosyncrasy and complexity of conceptual structure across modalities raise the question of how all of these modality-specific experiences are fused together into coherent, multifaceted yet unified concepts. Accordingly, both methodological and theoretical implications of the present findings are discussed. PMID:23293593

Measuring changes in chemistry, composition, and molecular structure within hair fibers by infrared and Raman spectroscopic imaging.

PubMed

Zhang, Guojin; Senak, Laurence; Moore, David J

2011-05-01

Spatially resolved infrared (IR) and Raman images are acquired from human hair cross sections or intact hair fibers. The full informational content of these spectra are spatially correlated to hair chemistry, anatomy, and structural organization through univariate and multivariate data analysis. Specific IR and Raman images from untreated human hair describing the spatial dependence of lipid and protein distribution, protein secondary structure, lipid chain conformational order, and distribution of disulfide cross-links in hair protein are presented in this study. Factor analysis of the image plane acquired with IR microscopy in hair sections, permits delineation of specific micro-regions within the hair. These data indicate that both IR and Raman imaging of molecular structural changes in a specific region of hair will prove to be valuable tools in the understanding of hair structure, physiology, and the effect of various stresses upon its integrity.

Structure-Specific Ribonucleases for MS-Based Elucidation of Higher-Order RNA Structure

NASA Astrophysics Data System (ADS)

Scalabrin, Matteo; Siu, Yik; Asare-Okai, Papa Nii; Fabris, Daniele

2014-07-01

Supported by high-throughput sequencing technologies, structure-specific nucleases are experiencing a renaissance as biochemical probes for genome-wide mapping of nucleic acid structure. This report explores the benefits and pitfalls of the application of Mung bean (Mb) and V1 nuclease, which attack specifically single- and double-stranded regions of nucleic acids, as possible structural probes to be employed in combination with MS detection. Both enzymes were found capable of operating in ammonium-based solutions that are preferred for high-resolution analysis by direct infusion electrospray ionization (ESI). Sequence analysis by tandem mass spectrometry (MS/MS) was performed to confirm mapping assignments and to resolve possible ambiguities arising from the concomitant formation of isobaric products with identical base composition and different sequences. The observed products grouped together into ladder-type series that facilitated their assignment to unique regions of the substrate, but revealed also a certain level of uncertainty in identifying the boundaries between paired and unpaired regions. Various experimental factors that are known to stabilize nucleic acid structure, such as higher ionic strength, presence of Mg(II), etc., increased the accuracy of cleavage information, but did not completely eliminate deviations from expected results. These observations suggest extreme caution in interpreting the results afforded by these types of reagents. Regardless of the analytical platform of choice, the results highlighted the need to repeat probing experiments under the most diverse possible conditions to recognize potential artifacts and to increase the level of confidence in the observed structural information.

Ontology of fractures

NASA Astrophysics Data System (ADS)

Zhong, Jian; Aydina, Atilla; McGuinness, Deborah L.

2009-03-01

Fractures are fundamental structures in the Earth's crust and they can impact many societal and industrial activities including oil and gas exploration and production, aquifer management, CO 2 sequestration, waste isolation, the stabilization of engineering structures, and assessing natural hazards (earthquakes, volcanoes, and landslides). Therefore, an ontology which organizes the concepts of fractures could help facilitate a sound education within, and communication among, the highly diverse professional and academic community interested in the problems cited above. We developed a process-based ontology that makes explicit specifications about fractures, their properties, and the deformation mechanisms which lead to their formation and evolution. Our ontology emphasizes the relationships among concepts such as the factors that influence the mechanism(s) responsible for the formation and evolution of specific fracture types. Our ontology is a valuable resource with a potential to applications in a number of fields utilizing recent advances in Information Technology, specifically for digital data and information in computers, grids, and Web services.

Plasma Membrane Calcium ATPases as Novel Candidates for Therapeutic Agent Development

PubMed Central

Strehler, Emanuel E.

2013-01-01

Plasma membrane Ca2+ ATPases (PMCAs) are highly regulated transporters responsible for Ca2+ extrusion from all eukaryotic cells. Different PMCA isoforms are implicated in various tasks of Ca2+ regulation including bulk Ca2+ transport and localized Ca2+ signaling in specific membrane microdomains. Accumulating evidence shows that loss, mutation or inappropriate expression of different PMCAs is associated with pathologies ranging from hypertension, low bone density and male infertility to hearing loss and cerebellar ataxia. Compared to Ca2+ influx channels, PMCAs have lagged far behind as targets for drug development, mainly due to the lack of detailed understanding of their structure and specific function. This is rapidly changing thanks to integrated efforts combining biochemical, structural, cellular and physiological studies suggesting that selective modulation of PMCA isoforms may be of therapeutic value in the management of different and complex diseases. Both structurally informed rational design and high-throughput small molecule library screenings are promising strategies that are expected to lead to specific and isoform-selective modulators of PMCA function. This short review will provide an overview of the diverse roles played by PMCA isoforms in different cells and tissues and their emerging involvement in pathophysiological processes, summarize recent progress in obtaining structural information on the PMCAs, and discuss current and future strategies to develop specific PMCA inhibitors and activators for potential therapeutic applications. PMID:23958189

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.

Cognitive representations and cognitive processing of team-specific tactics in soccer.

PubMed

Lex, Heiko; Essig, Kai; Knoblauch, Andreas; Schack, Thomas

2015-01-01

Two core elements for the coordination of different actions in sport are tactical information and knowledge about tactical situations. The current study describes two experiments to learn about the memory structure and the cognitive processing of tactical information. Experiment 1 investigated the storage and structuring of team-specific tactics in humans' long-term memory with regard to different expertise levels. Experiment 2 investigated tactical decision-making skills and the corresponding gaze behavior, in presenting participants the identical match situations in a reaction time task. The results showed that more experienced soccer players, in contrast to less experienced soccer players, possess a functionally organized cognitive representation of team-specific tactics in soccer. Moreover, the more experienced soccer players reacted faster in tactical decisions, because they needed less fixations of similar duration as compared to less experienced soccer players. Combined, these experiments offer evidence that a functionally organized memory structure leads to a reaction time and a perceptual advantage in tactical decision-making in soccer. The discussion emphasizes theoretical and applied implications of the current results of the study.

Cognitive Representations and Cognitive Processing of Team-Specific Tactics in Soccer

PubMed Central

Lex, Heiko; Essig, Kai; Knoblauch, Andreas; Schack, Thomas

2015-01-01

Two core elements for the coordination of different actions in sport are tactical information and knowledge about tactical situations. The current study describes two experiments to learn about the memory structure and the cognitive processing of tactical information. Experiment 1 investigated the storage and structuring of team-specific tactics in humans’ long-term memory with regard to different expertise levels. Experiment 2 investigated tactical decision-making skills and the corresponding gaze behavior, in presenting participants the identical match situations in a reaction time task. The results showed that more experienced soccer players, in contrast to less experienced soccer players, possess a functionally organized cognitive representation of team-specific tactics in soccer. Moreover, the more experienced soccer players reacted faster in tactical decisions, because they needed less fixations of similar duration as compared to less experienced soccer players. Combined, these experiments offer evidence that a functionally organized memory structure leads to a reaction time and a perceptual advantage in tactical decision-making in soccer. The discussion emphasizes theoretical and applied implications of the current results of the study. PMID:25714486

Sources of Information on HIV and Sexual and Reproductive Health for Couples Living with HIV in Rural Southern Malawi

PubMed Central

Gombachika, Belinda Chimphamba; Chirwa, Ellen; Malata, Address; Maluwa, Alfred

2013-01-01

With wider access to antiretroviral therapy, people living with HIV are reconsidering their reproductive decisions: remarrying and having children. The purpose of the paper is to explore sources of information for reproductive decision used by couples living with HIV in patrilineal and matrilineal districts of Malawi. Data were collected from forty couples from July to December 2010. Our results illuminate five specific issues: some of the informants (1) remarry after divorce/death of a spouse, (2) establish new marriage relationship with spouses living with HIV, and (3) have children hence the need for information to base their decisions. There are (4) shared and interactive couple decisions, and (5) informal networks of people living with HIV are the main sources of information. In addition, in matrilineal community, cultural practices about remarriage set up structures that constrained information availability unlike in patrilineal community where information on sexual and reproductive health, HIV, and AIDS was disseminated during remarriage counselling. However, both sources are not able to provide comprehensive information due to complexity and lack of up to date information. Therefore, health workers should, offer people living with HIV comprehensive information that takes into consideration the cultural specificity of groups, and empower already existing and accepted local structures with sexual and reproductive health, HIV, and AIDS knowledge. PMID:23662206

Pollen structure visualization using high-resolution laboratory-based hard X-ray tomography

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

Li, Qiong; Gluch, Jürgen; Krüger, Peter

A laboratory-based X-ray microscope is used to investigate the 3D structure of unstained whole pollen grains. For the first time, high-resolution laboratory-based hard X-ray microscopy is applied to study pollen grains. Based on the efficient acquisition of statistically relevant information-rich images using Zernike phase contrast, both surface- and internal structures of pine pollen - including exine, intine and cellular structures - are clearly visualized. The specific volumes of these structures are calculated from the tomographic data. The systematic three-dimensional study of pollen grains provides morphological and structural information about taxonomic characters that are essential in palynology. Such studies have amore » direct impact on disciplines such as forestry, agriculture, horticulture, plant breeding and biodiversity. - Highlights: • The unstained whole pine pollen was visualized by high-resolution laboratory-based HXRM for the first time. • The comparison study of pollen grains by LM, SEM and high-resolution laboratory-based HXRM. • Phase contrast imaging provides significantly higher contrast of the raw images compared to absorption contrast imaging. • Surface and internal structure of the pine pollen including exine, intine and cellular structures are clearly visualized. • 3D volume data of unstained whole pollen grains are acquired and the specific volumes of the different layer are calculated.« less

DbPTM 3.0: an informative resource for investigating substrate site specificity and functional association of protein post-translational modifications.

PubMed

Lu, Cheng-Tsung; Huang, Kai-Yao; Su, Min-Gang; Lee, Tzong-Yi; Bretaña, Neil Arvin; Chang, Wen-Chi; Chen, Yi-Ju; Chen, Yu-Ju; Huang, Hsien-Da

2013-01-01

Protein modification is an extremely important post-translational regulation that adjusts the physical and chemical properties, conformation, stability and activity of a protein; thus altering protein function. Due to the high throughput of mass spectrometry (MS)-based methods in identifying site-specific post-translational modifications (PTMs), dbPTM (http://dbPTM.mbc.nctu.edu.tw/) is updated to integrate experimental PTMs obtained from public resources as well as manually curated MS/MS peptides associated with PTMs from research articles. Version 3.0 of dbPTM aims to be an informative resource for investigating the substrate specificity of PTM sites and functional association of PTMs between substrates and their interacting proteins. In order to investigate the substrate specificity for modification sites, a newly developed statistical method has been applied to identify the significant substrate motifs for each type of PTMs containing sufficient experimental data. According to the data statistics in dbPTM, >60% of PTM sites are located in the functional domains of proteins. It is known that most PTMs can create binding sites for specific protein-interaction domains that work together for cellular function. Thus, this update integrates protein-protein interaction and domain-domain interaction to determine the functional association of PTM sites located in protein-interacting domains. Additionally, the information of structural topologies on transmembrane (TM) proteins is integrated in dbPTM in order to delineate the structural correlation between the reported PTM sites and TM topologies. To facilitate the investigation of PTMs on TM proteins, the PTM substrate sites and the structural topology are graphically represented. Also, literature information related to PTMs, orthologous conservations and substrate motifs of PTMs are also provided in the resource. Finally, this version features an improved web interface to facilitate convenient access to the resource.

Tweeting in the Agora: An Historical Documentary of Educational Structures and Discourse in Ancient Greece and in Modern Social Media

ERIC Educational Resources Information Center

Maraldo, Jill

2014-01-01

This dissertation focuses on the systems and structures of formal and informal education in Ancient Greece under the leadership of Socrates, Plato and Aristotle and the systems and structures of education and discourse on social media, specifically on blogs and Twitter. Using historical documentary research methodology of primary and secondary…

You Need to Know: There Is a Causal Relationship between Structural Knowledge and Control Performance in Complex Problem Solving Tasks

ERIC Educational Resources Information Center

Goode, Natassia; Beckmann, Jens F.

2010-01-01

This study investigates the relationships between structural knowledge, control performance and fluid intelligence in a complex problem solving (CPS) task. 75 participants received either complete, partial or no information regarding the underlying structure of a complex problem solving task, and controlled the task to reach specific goals.…

Identification of GATC- and CCGG- recognizing Type II REases and their putative specificity-determining positions using Scan2S—a novel motif scan algorithm with optional secondary structure constraints

PubMed Central

Niv, Masha Y.; Skrabanek, Lucy; Roberts, Richard J.; Scheraga, Harold A.; Weinstein, Harel

2008-01-01

Restriction endonucleases (REases) are DNA-cleaving enzymes that have become indispensable tools in molecular biology. Type II REases are highly divergent in sequence despite their common structural core, function and, in some cases, common specificities towards DNA sequences. This makes it difficult to identify and classify them functionally based on sequence, and has hampered the efforts of specificity-engineering. Here, we define novel REase sequence motifs, which extend beyond the PD-(D/E)XK hallmark, and incorporate secondary structure information. The automated search using these motifs is carried out with a newly developed fast regular expression matching algorithm that accommodates long patterns with optional secondary structure constraints. Using this new tool, named Scan2S, motifs derived from REases with specificity towards GATC- and CGGG-containing DNA sequences successfully identify REases of the same specificity. Notably, some of these sequences are not identified by standard sequence detection tools. The new motifs highlight potential specificity-determining positions that do not fully overlap for the GATC- and the CCGG-recognizing REases and are candidates for specificity re-engineering. PMID:17972284

Identification of GATC- and CCGG-recognizing Type II REases and their putative specificity-determining positions using Scan2S--a novel motif scan algorithm with optional secondary structure constraints.

PubMed

Niv, Masha Y; Skrabanek, Lucy; Roberts, Richard J; Scheraga, Harold A; Weinstein, Harel

2008-05-01

Restriction endonucleases (REases) are DNA-cleaving enzymes that have become indispensable tools in molecular biology. Type II REases are highly divergent in sequence despite their common structural core, function and, in some cases, common specificities towards DNA sequences. This makes it difficult to identify and classify them functionally based on sequence, and has hampered the efforts of specificity-engineering. Here, we define novel REase sequence motifs, which extend beyond the PD-(D/E)XK hallmark, and incorporate secondary structure information. The automated search using these motifs is carried out with a newly developed fast regular expression matching algorithm that accommodates long patterns with optional secondary structure constraints. Using this new tool, named Scan2S, motifs derived from REases with specificity towards GATC- and CGGG-containing DNA sequences successfully identify REases of the same specificity. Notably, some of these sequences are not identified by standard sequence detection tools. The new motifs highlight potential specificity-determining positions that do not fully overlap for the GATC- and the CCGG-recognizing REases and are candidates for specificity re-engineering.

Comparison of Three Information Sources for Smoking Information in Electronic Health Records

PubMed Central

Wang, Liwei; Ruan, Xiaoyang; Yang, Ping; Liu, Hongfang

2016-01-01

OBJECTIVE The primary aim was to compare independent and joint performance of retrieving smoking status through different sources, including narrative text processed by natural language processing (NLP), patient-provided information (PPI), and diagnosis codes (ie, International Classification of Diseases, Ninth Revision [ICD-9]). We also compared the performance of retrieving smoking strength information (ie, heavy/light smoker) from narrative text and PPI. MATERIALS AND METHODS Our study leveraged an existing lung cancer cohort for smoking status, amount, and strength information, which was manually chart-reviewed. On the NLP side, smoking-related electronic medical record (EMR) data were retrieved first. A pattern-based smoking information extraction module was then implemented to extract smoking-related information. After that, heuristic rules were used to obtain smoking status-related information. Smoking information was also obtained from structured data sources based on diagnosis codes and PPI. Sensitivity, specificity, and accuracy were measured using patients with coverage (ie, the proportion of patients whose smoking status/strength can be effectively determined). RESULTS NLP alone has the best overall performance for smoking status extraction (patient coverage: 0.88; sensitivity: 0.97; specificity: 0.70; accuracy: 0.88); combining PPI with NLP further improved patient coverage to 0.96. ICD-9 does not provide additional improvement to NLP and its combination with PPI. For smoking strength, combining NLP with PPI has slight improvement over NLP alone. CONCLUSION These findings suggest that narrative text could serve as a more reliable and comprehensive source for obtaining smoking-related information than structured data sources. PPI, the readily available structured data, could be used as a complementary source for more comprehensive patient coverage. PMID:27980387

History of early bridge specifications : a reprint of a paper by J. N. Clary.

DOT National Transportation Integrated Search

2006-01-01

This report is a reprint of an informed review of the specifications for iron and steel bridges, both railroad and highway structures, dating from the mid-19th through the early 20th centuries. It is reprinted with only minor editing as a companion t...

Integrated information theory of consciousness: an updated account.

PubMed

Tononi, G

2012-01-01

This article presents an updated account of integrated information theory of consciousness (IIT) and some of its implications. IIT stems from thought experiments that lead to phenomenological axioms and ontological postulates. The information axiom asserts that every experience is one out of many, i.e. specific - it is what it is by differing in its particular way from a large repertoire of alternatives. The integration axiom asserts that each experience is one, i.e. unified - it cannot be reduced to independent components. The exclusion axiom asserts that every experience is definite - it is limited to particular things and not others and flows at a particular speed and resolution. IIT formalizes these intuitions with three postulates. The information postulate states that only "differences that make a difference" from the intrinsic perspective of a system matter: a mechanism generates cause-effect information if its present state has specific past causes and specific future effects within a system. The integration postulate states that only information that is irreducible matters: mechanisms generate integrated information only to the extent that the information they generate cannot be partitioned into that generated within independent components. The exclusion postulate states that only maxima of integrated information matter: a mechanism specifies only one maximally irreducible set of past causes and future effects - a concept. A complex is a set of elements specifying a maximally irreducible constellation of concepts, where the maximum is evaluated at the optimal spatio-temporal scale. Its concepts specify a maximally integrated conceptual information structure or quale, which is identical with an experience. Finally, changes in information integration upon exposure to the environment reflect a system's ability to match the causal structure of the world. After introducing an updated definition of information integration and related quantities, the article presents some theoretical considerations about the relationship between information and causation and about the relational structure of concepts within a quale. It also explores the relationship between the temporal grain size of information integration and the dynamic of metastable states in the corticothalamic complex. Finally, it summarizes how IIT accounts for empirical findings about the neural substrate of consciousness, and how various aspects of phenomenology may in principle be addressed in terms of the geometry of information integration.

An information extraction framework for cohort identification using electronic health records.

PubMed

Liu, Hongfang; Bielinski, Suzette J; Sohn, Sunghwan; Murphy, Sean; Wagholikar, Kavishwar B; Jonnalagadda, Siddhartha R; Ravikumar, K E; Wu, Stephen T; Kullo, Iftikhar J; Chute, Christopher G

2013-01-01

Information extraction (IE), a natural language processing (NLP) task that automatically extracts structured or semi-structured information from free text, has become popular in the clinical domain for supporting automated systems at point-of-care and enabling secondary use of electronic health records (EHRs) for clinical and translational research. However, a high performance IE system can be very challenging to construct due to the complexity and dynamic nature of human language. In this paper, we report an IE framework for cohort identification using EHRs that is a knowledge-driven framework developed under the Unstructured Information Management Architecture (UIMA). A system to extract specific information can be developed by subject matter experts through expert knowledge engineering of the externalized knowledge resources used in the framework.

10 CFR 52.47 - Contents of applications; technical information.

Code of Federal Regulations, 2013 CFR

2013-01-01

... accidents, e.g., challenges to containment integrity caused by core-concrete interaction, steam explosion... such as the service water intake structure and the ultimate heat sink; (2) An application for... design except for site-specific elements such as the service water intake structure and the ultimate heat...

10 CFR 52.47 - Contents of applications; technical information.

Code of Federal Regulations, 2010 CFR

2010-01-01

... accidents, e.g., challenges to containment integrity caused by core-concrete interaction, steam explosion... such as the service water intake structure and the ultimate heat sink; (2) An application for... design except for site-specific elements such as the service water intake structure and the ultimate heat...

10 CFR 52.47 - Contents of applications; technical information.

Code of Federal Regulations, 2011 CFR

2011-01-01

... accidents, e.g., challenges to containment integrity caused by core-concrete interaction, steam explosion... such as the service water intake structure and the ultimate heat sink; (2) An application for... design except for site-specific elements such as the service water intake structure and the ultimate heat...

10 CFR 52.47 - Contents of applications; technical information.

Code of Federal Regulations, 2014 CFR

2014-01-01

... accidents, e.g., challenges to containment integrity caused by core-concrete interaction, steam explosion... such as the service water intake structure and the ultimate heat sink; (2) An application for... design except for site-specific elements such as the service water intake structure and the ultimate heat...

10 CFR 52.47 - Contents of applications; technical information.

Code of Federal Regulations, 2012 CFR

2012-01-01

... accidents, e.g., challenges to containment integrity caused by core-concrete interaction, steam explosion... such as the service water intake structure and the ultimate heat sink; (2) An application for... design except for site-specific elements such as the service water intake structure and the ultimate heat...

Structured-illumination reflectance imaging for enhanced detection of subsurface tissue bruising in apples

USDA-ARS?s Scientific Manuscript database

In this research, a novel method of fresh bruise detection was developed using a structured illumination reflectance imaging (SIRI) system. The SIRI system projects sinusoidal patterns of illumination onto samples, and image demodulation is then used to recover depth-specific information through var...

Understanding Crisis Information Needs in Context: The Case of Intimate Partner Violence Survivors

ERIC Educational Resources Information Center

Westbrook, Lynn

2008-01-01

The pervasive, personal crisis of intimate partner violence (IPV) demands community information resources in workforce, health care, mental health, public housing, criminal justice, and social service arenas. Although generally underutilized, public libraries have a pivotal role to play as the only public institution specifically structured to…

Noneconomic Analysis Considerations for Management and Information System for Occupational Education.

ERIC Educational Resources Information Center

Creager, John A.

As the first of two papers delineating the design of Massachusetts' Management and Information System for Occupational Education (MISOE), these specific dimensions of MISOE structure and function are considered: (1) the distinction between economic and noneconomic analysis, (2) distinctions among census, sample, and other data, (3) the distinction…

Sample Size and Correlational Inference

ERIC Educational Resources Information Center

Anderson, Richard B.; Doherty, Michael E.; Friedrich, Jeff C.

2008-01-01

In 4 studies, the authors examined the hypothesis that the structure of the informational environment makes small samples more informative than large ones for drawing inferences about population correlations. The specific purpose of the studies was to test predictions arising from the signal detection simulations of R. B. Anderson, M. E. Doherty,…

Research on Higher Education: A U.S. Perspective.

ERIC Educational Resources Information Center

Toombs, William

Characteristics of U.S. higher education are identified, along with the structural features that influence the nature of research, specific research topics, and the locations of research activities. This information was obtained from several sources, including the Educational Resources Information Center database for the years 1981 and 1982, the…

A homecare application based on the ASTM E2369-05 Standard Specification for Continuity of Care Record.

PubMed

Botsivaly, M; Spyropoulos, B; Koutsourakis, K; Mertika, K

2006-01-01

The purpose of this study is the presentation of a system appropriate to be used upon the transition of a patient from hospital to homecare. The developed system is structured according to the ASTM E2369-05 Standard Specification for Continuity of Care Record and its function is based upon the creation of a structured subset of data, containing the patient's most relevant clinical information, enabling simultaneously the planning and the optimal documentation of the provided homecare.

Enriching the annotation of Mycobacterium tuberculosis H37Rv proteome using remote homology detection approaches: insights into structure and function.

PubMed

Ramakrishnan, Gayatri; Ochoa-Montaño, Bernardo; Raghavender, Upadhyayula S; Mudgal, Richa; Joshi, Adwait G; Chandra, Nagasuma R; Sowdhamini, Ramanathan; Blundell, Tom L; Srinivasan, Narayanaswamy

2015-01-01

The availability of the genome sequence of Mycobacterium tuberculosis H37Rv has encouraged determination of large numbers of protein structures and detailed definition of the biological information encoded therein; yet, the functions of many proteins in M. tuberculosis remain unknown. The emergence of multidrug resistant strains makes it a priority to exploit recent advances in homology recognition and structure prediction to re-analyse its gene products. Here we report the structural and functional characterization of gene products encoded in the M. tuberculosis genome, with the help of sensitive profile-based remote homology search and fold recognition algorithms resulting in an enhanced annotation of the proteome where 95% of the M. tuberculosis proteins were identified wholly or partly with information on structure or function. New information includes association of 244 proteins with 205 domain families and a separate set of new association of folds to 64 proteins. Extending structural information across uncharacterized protein families represented in the M. tuberculosis proteome, by determining superfamily relationships between families of known and unknown structures, has contributed to an enhancement in the knowledge of structural content. In retrospect, such superfamily relationships have facilitated recognition of probable structure and/or function for several uncharacterized protein families, eventually aiding recognition of probable functions for homologous proteins corresponding to such families. Gene products unique to mycobacteria for which no functions could be identified are 183. Of these 18 were determined to be M. tuberculosis specific. Such pathogen-specific proteins are speculated to harbour virulence factors required for pathogenesis. A re-annotated proteome of M. tuberculosis, with greater completeness of annotated proteins and domain assigned regions, provides a valuable basis for experimental endeavours designed to obtain a better understanding of pathogenesis and to accelerate the process of drug target discovery. Copyright © 2014 Elsevier Ltd. All rights reserved.

Pollen structure visualization using high-resolution laboratory-based hard X-ray tomography.

PubMed

Li, Qiong; Gluch, Jürgen; Krüger, Peter; Gall, Martin; Neinhuis, Christoph; Zschech, Ehrenfried

2016-10-14

A laboratory-based X-ray microscope is used to investigate the 3D structure of unstained whole pollen grains. For the first time, high-resolution laboratory-based hard X-ray microscopy is applied to study pollen grains. Based on the efficient acquisition of statistically relevant information-rich images using Zernike phase contrast, both surface- and internal structures of pine pollen - including exine, intine and cellular structures - are clearly visualized. The specific volumes of these structures are calculated from the tomographic data. The systematic three-dimensional study of pollen grains provides morphological and structural information about taxonomic characters that are essential in palynology. Such studies have a direct impact on disciplines such as forestry, agriculture, horticulture, plant breeding and biodiversity. Copyright © 2016 Elsevier Inc. All rights reserved.

Live CLEM imaging to analyze nuclear structures at high resolution.

PubMed

Haraguchi, Tokuko; Osakada, Hiroko; Koujin, Takako

2015-01-01

Fluorescence microscopy (FM) and electron microscopy (EM) are powerful tools for observing molecular components in cells. FM can provide temporal information about cellular proteins and structures in living cells. EM provides nanometer resolution images of cellular structures in fixed cells. We have combined FM and EM to develop a new method of correlative light and electron microscopy (CLEM), called "Live CLEM." In this method, the dynamic behavior of specific molecules of interest is first observed in living cells using fluorescence microscopy (FM) and then cellular structures in the same cell are observed using electron microscopy (EM). Following image acquisition, FM and EM images are compared to enable the fluorescent images to be correlated with the high-resolution images of cellular structures obtained using EM. As this method enables analysis of dynamic events involving specific molecules of interest in the context of specific cellular structures at high resolution, it is useful for the study of nuclear structures including nuclear bodies. Here we describe Live CLEM that can be applied to the study of nuclear structures in mammalian cells.

24 CFR 35.105 - Effective dates.

Code of Federal Regulations, 2010 CFR

2010-04-01

... LEAD-BASED PAINT POISONING PREVENTION IN CERTAIN RESIDENTIAL STRUCTURES General Lead-Based Paint... further information on the application of the effective date to specific programs. Before September 15...

Dealing with an information overload of health science data: structured utilisation of libraries, distributed knowledge in databases and Web content.

PubMed

Hoelzer, Simon; Schweiger, Ralf K; Rieger, Joerg; Meyer, Michael

2006-01-01

The organizational structures of web contents and electronic information resources must adapt to the demands of a growing volume of information and user requirements. Otherwise the information society will be threatened by disinformation. The biomedical sciences are especially vulnerable in this regard, since they are strongly oriented toward text-based knowledge sources. Here sustainable improvement can only be achieved by using a comprehensive, integrated approach that not only includes data management but also specifically incorporates the editorial processes, including structuring information sources and publication. The technical resources needed to effectively master these tasks are already available in the form of the data standards and tools of the Semantic Web. They include Rich Site Summaries (RSS), which have become an established means of distributing and syndicating conventional news messages and blogs. They can also provide access to the contents of the previously mentioned information sources, which are conventionally classified as 'deep web' content.

Structure, function, and engineering of enzymes in isoflavonoid biosynthesis.

PubMed

Wang, Xiaoqiang

2011-03-01

Isoflavonoids are a large group of plant natural products and play important roles in plant defense. They also possess valuable health-promoting activities with significant health benefits for animals and humans. The isoflavonoids are identified primarily in leguminous plants and are synthesized through the central phenylpropanoid pathway and the specific isoflavonoid branch pathways in legumes. Structural studies of some key enzymes in the central phenylpropanoid pathway shed light on the early stages of the (iso)flavonoid biosynthetic process. Significant impact has also been made on structural studies of enzymes in the isoflavonoid branch pathways. Structures of isoflavonoid-specific NADPH-dependent reductases revealed how the (iso)flavonoid backbones are modified by reduction reactions and how enzymes specifically recognize isoflavonoids and catalyze stereo-specific reductions. Structural studies of isoflavonoid methyltransferases and glycosyltransferases revealed how isoflavonoids are further decorated with methyl group and sugars in different methylation and glycosylation patterns that determine their bioactivities and functions. In combination with mutagenesis and biochemical studies, the detailed structural information of these enzymes provides a basis for understanding the complex biosynthetic process, enzyme catalytic mechanisms, and substrate specificities. Structure-based homology modeling facilitates the functional characterization of these large groups of biosynthetic enzymes and their homologs. Structure-based enzyme engineering is becoming a new strategy for synthesis of bioactive isoflavonoids and also facilitates plant metabolic engineering towards improvement of quality and production of crop plants.

Predictive Bcl-2 Family Binding Models Rooted in Experiment or Structure

PubMed Central

DeBartolo, Joe; Dutta, Sanjib; Reich, Lothar; Keating, Amy E.

2013-01-01

Proteins of the Bcl-2 family either enhance or suppress programmed cell death and are centrally involved in cancer development and resistance to chemotherapy. BH3 (Bcl-2 homology 3)-only Bcl-2 proteins promote cell death by docking an α-helix into a hydrophobic groove on the surface of one or more of five pro-survival Bcl-2 receptor proteins. There is high structural homology within the pro-death and pro-survival families, yet a high degree of interaction specificity is nevertheless encoded, posing an interesting and important molecular recognition problem. Understanding protein features that dictate Bcl-2 interaction specificity is critical for designing peptide-based cancer therapeutics and diagnostics. In this study, we present peptide SPOT arrays and deep sequencing data from yeast display screening experiments that significantly expand the BH3 sequence space that has been experimentally tested for interaction with five human anti-apoptotic receptors. These data provide rich information about the determinants of Bcl-2 family specificity. To interpret and use the information, we constructed two simple data-based models that can predict affinity and specificity when evaluated on independent data sets within a limited sequence space. We also constructed a novel structure-based statistical potential, called STATIUM, which is remarkably good at predicting Bcl-2 affinity and specificity, especially considering it is not trained on experimental data. We compare the performance of our three models to each other and to alternative structure-based methods and discuss how such tools can guide prediction and design of new Bcl-2 family complexes. PMID:22617328

Strengthening institutional and organizational capacity for social health protection of the informal sector in lesser-developed countries: a study of policy barriers and opportunities in Cambodia.

PubMed

Annear, Peter Leslie; Ahmed, Shakil; Ros, Chhun Eang; Ir, Por

2013-11-01

Reaching out to the poor and the informal sector is a major challenge for achieving universal coverage in lesser-developed countries. In Cambodia, extensive coverage by health equity funds for the poor has created the opportunity to consolidate various non-government health financing schemes under the government's proposed social health protection structure. This paper identifies the main policy and operational challenges to strengthening existing arrangements for the poor and the informal sector, and considers policy options to address these barriers. Conducted in conjunction with the Cambodian Ministry of Health in 2011-12, the study reviewed policy documents and collected qualitative data through 18 semi-structured key informant interviews with government, non-government and donor officials. Data were analysed using the Organizational Assessment for Improving and Strengthening Health Financing conceptual framework. We found that a significant shortfall related to institutional, organisational and health financing issues resulted in fragmentation and constrained the implementation of social health protection schemes, including health equity funds, community-based health insurance, vouchers and others. Key documents proposed the establishment of a national structure for the unification of the informal-sector schemes but left unresolved issues related to structure, institutional capacity and the third-party status of the national agency. This study adds to the evidence base on appropriate and effective institutional and organizational arrangements for social health protection in the informal sector in developing countries. Among the key lessons are: the need to expand the fiscal space for health care; a commitment to equity; specific measures to protect the poor; building national capacity for administration of universal coverage; and working within the specific national context. Copyright © 2013 Elsevier Ltd. All rights reserved.

Bio-AIMS Collection of Chemoinformatics Web Tools based on Molecular Graph Information and Artificial Intelligence Models.

PubMed

Munteanu, Cristian R; Gonzalez-Diaz, Humberto; Garcia, Rafael; Loza, Mabel; Pazos, Alejandro

2015-01-01

The molecular information encoding into molecular descriptors is the first step into in silico Chemoinformatics methods in Drug Design. The Machine Learning methods are a complex solution to find prediction models for specific biological properties of molecules. These models connect the molecular structure information such as atom connectivity (molecular graphs) or physical-chemical properties of an atom/group of atoms to the molecular activity (Quantitative Structure - Activity Relationship, QSAR). Due to the complexity of the proteins, the prediction of their activity is a complicated task and the interpretation of the models is more difficult. The current review presents a series of 11 prediction models for proteins, implemented as free Web tools on an Artificial Intelligence Model Server in Biosciences, Bio-AIMS (http://bio-aims.udc.es/TargetPred.php). Six tools predict protein activity, two models evaluate drug - protein target interactions and the other three calculate protein - protein interactions. The input information is based on the protein 3D structure for nine models, 1D peptide amino acid sequence for three tools and drug SMILES formulas for two servers. The molecular graph descriptor-based Machine Learning models could be useful tools for in silico screening of new peptides/proteins as future drug targets for specific treatments.

Accurate prediction of interfacial residues in two-domain proteins using evolutionary information: implications for three-dimensional modeling.

PubMed

Bhaskara, Ramachandra M; Padhi, Amrita; Srinivasan, Narayanaswamy

2014-07-01

With the preponderance of multidomain proteins in eukaryotic genomes, it is essential to recognize the constituent domains and their functions. Often function involves communications across the domain interfaces, and the knowledge of the interacting sites is essential to our understanding of the structure-function relationship. Using evolutionary information extracted from homologous domains in at least two diverse domain architectures (single and multidomain), we predict the interface residues corresponding to domains from the two-domain proteins. We also use information from the three-dimensional structures of individual domains of two-domain proteins to train naïve Bayes classifier model to predict the interfacial residues. Our predictions are highly accurate (∼85%) and specific (∼95%) to the domain-domain interfaces. This method is specific to multidomain proteins which contain domains in at least more than one protein architectural context. Using predicted residues to constrain domain-domain interaction, rigid-body docking was able to provide us with accurate full-length protein structures with correct orientation of domains. We believe that these results can be of considerable interest toward rational protein and interaction design, apart from providing us with valuable information on the nature of interactions. © 2013 Wiley Periodicals, Inc.

Egg Yolk Lecithin: A Biochemical Laboratory Project

ERIC Educational Resources Information Center

White, Bernard J.; And Others

1974-01-01

Describes an undergraduate laboratory project involving lecithin which integrates two general aspects of lipid methodology: chromatographic techniques and use of enzymes specificity to obtain structural information. (Author/SLH)

Language translation, doman specific languages and ANTLR

NASA Technical Reports Server (NTRS)

Craymer, Loring; Parr, Terence

2002-01-01

We will discuss the features of ANTLR that make it an attractive tool for rapid developement of domain specific language translators and present some practical examples of its use: extraction of information from the Cassini Command Language specification, the processing of structured binary data, and IVL--an English-like language for generating VRML scene graph, which is used in configuring the jGuru.com server.

Specific Non-Local Interactions Are Not Necessary for Recovering Native Protein Dynamics

PubMed Central

Dasgupta, Bhaskar; Kasahara, Kota; Kamiya, Narutoshi; Nakamura, Haruki; Kinjo, Akira R.

2014-01-01

The elastic network model (ENM) is a widely used method to study native protein dynamics by normal mode analysis (NMA). In ENM we need information about all pairwise distances, and the distance between contacting atoms is restrained to the native value. Therefore ENM requires O(N2) information to realize its dynamics for a protein consisting of N amino acid residues. To see if (or to what extent) such a large amount of specific structural information is required to realize native protein dynamics, here we introduce a novel model based on only O(N) restraints. This model, named the ‘contact number diffusion’ model (CND), includes specific distance restraints for only local (along the amino acid sequence) atom pairs, and semi-specific non-local restraints imposed on each atom, rather than atom pairs. The semi-specific non-local restraints are defined in terms of the non-local contact numbers of atoms. The CND model exhibits the dynamic characteristics comparable to ENM and more correlated with the explicit-solvent molecular dynamics simulation than ENM. Moreover, unrealistic surface fluctuations often observed in ENM were suppressed in CND. On the other hand, in some ligand-bound structures CND showed larger fluctuations of buried protein atoms interacting with the ligand compared to ENM. In addition, fluctuations from CND and ENM show comparable correlations with the experimental B-factor. Although there are some indications of the importance of some specific non-local interactions, the semi-specific non-local interactions are mostly sufficient for reproducing the native protein dynamics. PMID:24625758

SMARTIV: combined sequence and structure de-novo motif discovery for in-vivo RNA binding data.

PubMed

Polishchuk, Maya; Paz, Inbal; Yakhini, Zohar; Mandel-Gutfreund, Yael

2018-05-25

Gene expression regulation is highly dependent on binding of RNA-binding proteins (RBPs) to their RNA targets. Growing evidence supports the notion that both RNA primary sequence and its local secondary structure play a role in specific Protein-RNA recognition and binding. Despite the great advance in high-throughput experimental methods for identifying sequence targets of RBPs, predicting the specific sequence and structure binding preferences of RBPs remains a major challenge. We present a novel webserver, SMARTIV, designed for discovering and visualizing combined RNA sequence and structure motifs from high-throughput RNA-binding data, generated from in-vivo experiments. The uniqueness of SMARTIV is that it predicts motifs from enriched k-mers that combine information from ranked RNA sequences and their predicted secondary structure, obtained using various folding methods. Consequently, SMARTIV generates Position Weight Matrices (PWMs) in a combined sequence and structure alphabet with assigned P-values. SMARTIV concisely represents the sequence and structure motif content as a single graphical logo, which is informative and easy for visual perception. SMARTIV was examined extensively on a variety of high-throughput binding experiments for RBPs from different families, generated from different technologies, showing consistent and accurate results. Finally, SMARTIV is a user-friendly webserver, highly efficient in run-time and freely accessible via http://smartiv.technion.ac.il/.

Conveying Movement in Music and Prosody

PubMed Central

Hedger, Stephen C.; Nusbaum, Howard C.; Hoeckner, Berthold

2013-01-01

We investigated whether acoustic variation of musical properties can analogically convey descriptive information about an object. Specifically, we tested whether information from the temporal structure in music interacts with perception of a visual image to form an analog perceptual representation as a natural part of music perception. In Experiment 1, listeners heard music with an accelerating or decelerating temporal pattern, and then saw a picture of a still or moving object and decided whether it was animate or inanimate – a task unrelated to the patterning of the music. Object classification was faster when musical motion matched visually depicted motion. In Experiment 2, participants heard spoken sentences that were accompanied by accelerating or decelerating music, and then were presented with a picture of a still or moving object. When motion information in the music matched motion information in the picture, participants were similarly faster to respond. Fast and slow temporal patterns without acceleration and deceleration, however, did not make participants faster when they saw a picture depicting congruent motion information (Experiment 3), suggesting that understanding temporal structure information in music may depend on specific metaphors about motion in music. Taken together, these results suggest that visuo-spatial referential information can be analogically conveyed and represented by music and can be integrated with speech or influence the understanding of speech. PMID:24146920

The Association between Tax Structure and Cigarette Price Variability: Findings from the International Tobacco Control Policy Evaluation (ITC) Project

PubMed Central

Shang, Ce; Chaloupka, Frank J.; Fong, Geoffrey T; Thompson, Mary; O’Connor, Richard J

2015-01-01

Background Recent studies have shown that more opportunities exist for tax avoidance when cigarette excise tax structure departs from a uniform specific structure. However, the association between tax structure and cigarette price variability has not been thoroughly studied in the existing literature. Objective To examine how cigarette tax structure is associated with price variability. The variability of self-reported prices is measured using the ratios of differences between higher and lower prices to the median price such as the IQR-to-median ratio. Methods We used survey data taken from the International Tobacco Control Policy Evaluation (ITC) Project in 17 countries to conduct the analysis. Cigarette prices were derived using individual purchase information and aggregated to price variability measures for each surveyed country and wave. The effect of tax structures on price variability was estimated using Generalised Estimating Equations after adjusting for year and country attributes. Findings Our study provides empirical evidence of a relationship between tax structure and cigarette price variability. We find that, compared to the specific uniform tax structure, mixed uniform and tiered (specific, ad valorem or mixed) structures are associated with greater price variability (p≤0.01). Moreover, while a greater share of the specific component in total excise taxes is associated with lower price variability (p≤0.05), a tiered tax structure is associated with greater price variability (p≤0.01). The results suggest that a uniform and specific tax structure is the most effective tax structure for reducing tobacco consumption and prevalence by limiting price variability and decreasing opportunities for tax avoidance. PMID:25855641

Structure and DNA-Binding Sites of the SWI1 AT-rich Interaction Domain (ARID) Suggest Determinants for Sequence-Specific DNA Recognition

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

Kim, Suhkmann; Zhang, Ziming; Upchurch, Sean

2004-04-16

2 ARID is a homologous family of DNA-binding domains that occur in DNA binding proteins from a wide variety of species, ranging from yeast to nematodes, insects, mammals and plants. SWI1, a member of the SWI/SNF protein complex that is involved in chromatin remodeling during transcription, contains the ARID motif. The ARID domain of human SWI1 (also known as p270) does not select for a specific DNA sequence from a random sequence pool. The lack of sequence specificity shown by the SWI1 ARID domain stands in contrast to the other characterized ARID domains, which recognize specific AT-rich sequences. We havemore » solved the three-dimensional structure of human SWI1 ARID using solution NMR methods. In addition, we have characterized non-specific DNA-binding by the SWI1 ARID domain. Results from this study indicate that a flexible long internal loop in ARID motif is likely to be important for sequence specific DNA-recognition. The structure of human SWI1 ARID domain also represents a distinct structural subfamily. Studies of ARID indicate that boundary of the DNA binding structural and functional domains can extend beyond the sequence homologous region in a homologous family of proteins. Structural studies of homologous domains such as ARID family of DNA-binding domains should provide information to better predict the boundary of structural and functional domains in structural genomic studies. Key Words: ARID, SWI1, NMR, structural genomics, protein-DNA interaction.« less

An Approach and Instrumentation for Management System Analysis

DTIC Science & Technology

1974-10-01

Benefit Analysis Systems Analysis Manpower Planning Resource Planning Information Theory 20. ABSTRACT (Conlliwa on ravaraa alda It nacaaaary...participants the data necessary to trace both formal and informal information flows and make cost- benefit judgments about specific communications. The...network within a manage- ment structure and to provide a basis tor preliminary cost- benefit evaluations. This objective was in response to Phase I of the

Issue of Building Information Modelling Implementation into the Czech Republic’s Legislation using the Level of Development

NASA Astrophysics Data System (ADS)

Prušková, Kristýna; Nývlt, Vladimír

2017-10-01

The object of this paper is the issue of links between the Level of Development of particular project in Building Information Modeling environment and the projects of certain stages of project documentation within the existing Czech Republic’s Legislation. This research article uses the experiences from the initiative of active working group „WG#03: BIM & Realization“, which is the part of the Czech BIM Council, especially the document called “Draft of unified data structure for Building Information Modeling in the Czech Republic”. The findings of this paper are in the defining specific Level of Development of relative parameters, mentioned in this document, connected to the specific level of information and details requested by the Czech Republic’s Legislation. These findings could be used as an underlay to create document called “Level of Development draft assignment to the individual stages of project documentation in the Czech Republic”. The Level of Development is the most useful way of the information visualization, which leads to the most effortless way of exact stated implementation of Building Information Modeling into the practice of designing structures and buildings in the Czech Republic. The Implementation of using Building Information Modeling technology in designing structures and buildings will lead to the enhanced quality of the project documentation and generally to more effective cost savings during whole life cycle of buildings. Moreover, the all over using of the BIM technology in the Czech Republic will be very useful in the Facility Management area, especially in the facility management and maintenance of state buildings.

Origin of life. Primordial genetics: Information transfer in a pre-RNA world based on self-replicating beta-sheet amyloid conformers.

PubMed

Maury, Carl Peter J

2015-10-07

The question of the origin of life on Earth can largely be reduced to the question of what was the first molecular replicator system that was able to replicate and evolve under the presumably very harsh conditions on the early Earth. It is unlikely that a functional RNA could have existed under such conditions and it is generally assumed that some other kind of information system preceded the RNA world. Here, I present an informational molecular system that is stable, self-replicative, environmentally responsive, and evolvable under conditions characterized by high temperatures, ultraviolet and cosmic radiation. This postulated pregenetic system is based on the amyloid fold, a functionally unique polypeptide fold characterized by a cross beta-sheet structure in which the beta strands are arranged perpendicular to the fiber axis. Beside an extraordinary structural robustness, the amyloid fold possesses a unique ability to transmit information by a three-dimensional templating mechanism. In amyloidogenesis short peptide monomers are added one by one to the growing end of the fiber. From the same monomeric subunits several structural variants of amyloid may be formed. Then, in a self-replicative mode, a specific amyloid conformer can act as a template and confer its spatially encoded information to daughter molecular entities in a repetitive way. In this process, the specific conformational information, the spatially changed organization, is transmitted; the coding element is the steric zipper structure, and recognition occurs by amino acid side chain complementarity. The amyloid information system fulfills several basic requirements of a primordial evolvable replicator system: (i) it is stable under the presumed primitive Earth conditions, (ii) the monomeric building blocks of the informational polymer can be formed from available prebiotic compounds, (iii) the system is self-assembling and self-replicative and (iv) it is adaptive to changes in the environment and evolvable. Copyright © 2015 The Author. Published by Elsevier Ltd.. All rights reserved.

Site-Specific Infrared Probes of Proteins

PubMed Central

Ma, Jianqiang; Pazos, Ileana M.; Zhang, Wenkai; Culik, Robert M.; Gai, Feng

2015-01-01

Infrared spectroscopy has played an instrumental role in studying a wide variety of biological questions. However, in many cases it is impossible or difficult to rely on the intrinsic vibrational modes of biological molecules of interest, such as proteins, to reveal structural and/or environmental information in a site-specific manner. To overcome this limitation, many recent efforts have been dedicated to the development and application of various extrinsic vibrational probes that can be incorporated into biological molecules and used to site-specifically interrogate their structural and/or environmental properties. In this Review, we highlight some recent advancements of this rapidly growing research area. PMID:25580624

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.

Information retrieval system utilizing wavelet transform

DOEpatents

Brewster, Mary E.; Miller, Nancy E.

2000-01-01

A method for automatically partitioning an unstructured electronically formatted natural language document into its sub-topic structure. Specifically, the document is converted to an electronic signal and a wavelet transform is then performed on the signal. The resultant signal may then be used to graphically display and interact with the sub-topic structure of the document.

Bayesian Structural Equation Modeling: A More Flexible Representation of Substantive Theory

ERIC Educational Resources Information Center

Muthen, Bengt; Asparouhov, Tihomir

2012-01-01

This article proposes a new approach to factor analysis and structural equation modeling using Bayesian analysis. The new approach replaces parameter specifications of exact zeros with approximate zeros based on informative, small-variance priors. It is argued that this produces an analysis that better reflects substantive theories. The proposed…

Future networking and cooperation summary of discussion

Treesearch

Roger R. Bay

1993-01-01

At the end of the workshop, I led a lightly structured and informal discussion concerning methods of continuing and improving communications and cooperation among workshop participants. The group specifically ad-dressed three areas: maintaining informal one-on-one direct contacts, improving the use of the ADAP computer system for mail, and the desirability of starting...

Non-Agricultural Databases and Thesauri: Retrieval of Subject Headings and Non-Controlled Terms in Relation to Agriculture

ERIC Educational Resources Information Center

Bartol, Tomaz

2012-01-01

Purpose: The paper aims to assess the utility of non-agriculture-specific information systems, databases, and respective controlled vocabularies (thesauri) in organising and retrieving agricultural information. The purpose is to identify thesaurus-linked tree structures, controlled subject headings/terms (heading words, descriptors), and principal…

A Study of Information Systems Programs Accredited by ABET in Relation to IS 2010

ERIC Educational Resources Information Center

Feinstein, David; Longenecker, Herbert E., Jr.; Shrestha, Dina

2014-01-01

This article examines the relationship between ABET CAC standards for undergraduate programs of information systems and IS 2010 curriculum specifications. We have reviewed current institution described course work that identifies course structures from accredited IS programs. The accredited programs all matched the expectations expressed in ABET…

Management Information System for ESD Program Offices.

DTIC Science & Technology

1978-03-01

Management Information System (MIS) functional requirements for the ESD Program Office are defined in terms of the Computer-Aided Design and Specification Tool. The development of the computer data base and a description of the MIS structure is included in the report. This report addresses management areas such as cost/budgeting, scheduling, tracking capabilities, and ECP

Evaluation in the Older Blind Independent Living Program: Advantages of a Structural Equation Modeling Approach. Research Report

ERIC Educational Resources Information Center

Giesen, Martin J.; Cavenaugh, Brenda S.

2006-01-01

Rehabilitation Services Administration (RSA) requires that independent living programs annually report demographic information on consumers receiving services and the numbers receiving specific types of services. Although some states collect information on consumer outcomes (for example, improvement in daily living skills), RSA does not request…

Databases and Associated Tools for Glycomics and Glycoproteomics.

PubMed

Lisacek, Frederique; Mariethoz, Julien; Alocci, Davide; Rudd, Pauline M; Abrahams, Jodie L; Campbell, Matthew P; Packer, Nicolle H; Ståhle, Jonas; Widmalm, Göran; Mullen, Elaine; Adamczyk, Barbara; Rojas-Macias, Miguel A; Jin, Chunsheng; Karlsson, Niclas G

2017-01-01

The access to biodatabases for glycomics and glycoproteomics has proven to be essential for current glycobiological research. This chapter presents available databases that are devoted to different aspects of glycobioinformatics. This includes oligosaccharide sequence databases, experimental databases, 3D structure databases (of both glycans and glycorelated proteins) and association of glycans with tissue, disease, and proteins. Specific search protocols are also provided using tools associated with experimental databases for converting primary glycoanalytical data to glycan structural information. In particular, researchers using glycoanalysis methods by U/HPLC (GlycoBase), MS (GlycoWorkbench, UniCarb-DB, GlycoDigest), and NMR (CASPER) will benefit from this chapter. In addition we also include information on how to utilize glycan structural information to query databases that associate glycans with proteins (UniCarbKB) and with interactions with pathogens (SugarBind).

Multidisciplinary analysis of actively controlled large flexible spacecraft

NASA Technical Reports Server (NTRS)

Cooper, Paul A.; Young, John W.; Sutter, Thomas R.

1986-01-01

The control of Flexible Structures (COFS) program has supported the development of an analysis capability at the Langley Research Center called the Integrated Multidisciplinary Analysis Tool (IMAT) which provides an efficient data storage and transfer capability among commercial computer codes to aid in the dynamic analysis of actively controlled structures. IMAT is a system of computer programs which transfers Computer-Aided-Design (CAD) configurations, structural finite element models, material property and stress information, structural and rigid-body dynamic model information, and linear system matrices for control law formulation among various commercial applications programs through a common database. Although general in its formulation, IMAT was developed specifically to aid in the evaluation of the structures. A description of the IMAT system and results of an application of the system are given.

An Information Extraction Framework for Cohort Identification Using Electronic Health Records

PubMed Central

Liu, Hongfang; Bielinski, Suzette J.; Sohn, Sunghwan; Murphy, Sean; Wagholikar, Kavishwar B.; Jonnalagadda, Siddhartha R.; Ravikumar, K.E.; Wu, Stephen T.; Kullo, Iftikhar J.; Chute, Christopher G

Information extraction (IE), a natural language processing (NLP) task that automatically extracts structured or semi-structured information from free text, has become popular in the clinical domain for supporting automated systems at point-of-care and enabling secondary use of electronic health records (EHRs) for clinical and translational research. However, a high performance IE system can be very challenging to construct due to the complexity and dynamic nature of human language. In this paper, we report an IE framework for cohort identification using EHRs that is a knowledge-driven framework developed under the Unstructured Information Management Architecture (UIMA). A system to extract specific information can be developed by subject matter experts through expert knowledge engineering of the externalized knowledge resources used in the framework. PMID:24303255

C-ME: A 3D Community-Based, Real-Time Collaboration Tool for Scientific Research and Training

PubMed Central

Kolatkar, Anand; Kennedy, Kevin; Halabuk, Dan; Kunken, Josh; Marrinucci, Dena; Bethel, Kelly; Guzman, Rodney; Huckaby, Tim; Kuhn, Peter

2008-01-01

The need for effective collaboration tools is growing as multidisciplinary proteome-wide projects and distributed research teams become more common. The resulting data is often quite disparate, stored in separate locations, and not contextually related. Collaborative Molecular Modeling Environment (C-ME) is an interactive community-based collaboration system that allows researchers to organize information, visualize data on a two-dimensional (2-D) or three-dimensional (3-D) basis, and share and manage that information with collaborators in real time. C-ME stores the information in industry-standard databases that are immediately accessible by appropriate permission within the computer network directory service or anonymously across the internet through the C-ME application or through a web browser. The system addresses two important aspects of collaboration: context and information management. C-ME allows a researcher to use a 3-D atomic structure model or a 2-D image as a contextual basis on which to attach and share annotations to specific atoms or molecules or to specific regions of a 2-D image. These annotations provide additional information about the atomic structure or image data that can then be evaluated, amended or added to by other project members. PMID:18286178

Structured sparse linear graph embedding.

PubMed

Wang, Haixian

2012-03-01

Subspace learning is a core issue in pattern recognition and machine learning. Linear graph embedding (LGE) is a general framework for subspace learning. In this paper, we propose a structured sparse extension to LGE (SSLGE) by introducing a structured sparsity-inducing norm into LGE. Specifically, SSLGE casts the projection bases learning into a regression-type optimization problem, and then the structured sparsity regularization is applied to the regression coefficients. The regularization selects a subset of features and meanwhile encodes high-order information reflecting a priori structure information of the data. The SSLGE technique provides a unified framework for discovering structured sparse subspace. Computationally, by using a variational equality and the Procrustes transformation, SSLGE is efficiently solved with closed-form updates. Experimental results on face image show the effectiveness of the proposed method. Copyright © 2011 Elsevier Ltd. All rights reserved.

Information entropy of humpback whale songs.

PubMed

Suzuki, Ryuji; Buck, John R; Tyack, Peter L

2006-03-01

The structure of humpback whale (Megaptera novaeangliae) songs was examined using information theory techniques. The song is an ordered sequence of individual sound elements separated by gaps of silence. Song samples were converted into sequences of discrete symbols by both human and automated classifiers. This paper analyzes the song structure in these symbol sequences using information entropy estimators and autocorrelation estimators. Both parametric and nonparametric entropy estimators are applied to the symbol sequences representing the songs. The results provide quantitative evidence consistent with the hierarchical structure proposed for these songs by Payne and McVay [Science 173, 587-597 (1971)]. Specifically, this analysis demonstrates that: (1) There is a strong structural constraint, or syntax, in the generation of the songs, and (2) the structural constraints exhibit periodicities with periods of 6-8 and 180-400 units. This implies that no empirical Markov model is capable of representing the songs' structure. The results are robust to the choice of either human or automated song-to-symbol classifiers. In addition, the entropy estimates indicate that the maximum amount of information that could be communicated by the sequence of sounds made is less than 1 bit per second.

A Method for WD40 Repeat Detection and Secondary Structure Prediction

PubMed Central

Wang, Yang; Jiang, Fan; Zhuo, Zhu; Wu, Xian-Hui; Wu, Yun-Dong

2013-01-01

WD40-repeat proteins (WD40s), as one of the largest protein families in eukaryotes, play vital roles in assembling protein-protein/DNA/RNA complexes. WD40s fold into similar β-propeller structures despite diversified sequences. A program WDSP (WD40 repeat protein Structure Predictor) has been developed to accurately identify WD40 repeats and predict their secondary structures. The method is designed specifically for WD40 proteins by incorporating both local residue information and non-local family-specific structural features. It overcomes the problem of highly diversified protein sequences and variable loops. In addition, WDSP achieves a better prediction in identifying multiple WD40-domain proteins by taking the global combination of repeats into consideration. In secondary structure prediction, the average Q3 accuracy of WDSP in jack-knife test reaches 93.7%. A disease related protein LRRK2 was used as a representive example to demonstrate the structure prediction. PMID:23776530

Chemical computing with reaction-diffusion processes.

PubMed

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

2015-07-28

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

The helpfulness of category labels in semi-supervised learning depends on category structure.

PubMed

Vong, Wai Keen; Navarro, Daniel J; Perfors, Amy

2016-02-01

The study of semi-supervised category learning has generally focused on how additional unlabeled information with given labeled information might benefit category learning. The literature is also somewhat contradictory, sometimes appearing to show a benefit to unlabeled information and sometimes not. In this paper, we frame the problem differently, focusing on when labels might be helpful to a learner who has access to lots of unlabeled information. Using an unconstrained free-sorting categorization experiment, we show that labels are useful to participants only when the category structure is ambiguous and that people's responses are driven by the specific set of labels they see. We present an extension of Anderson's Rational Model of Categorization that captures this effect.

Scanning superlens microscopy for non-invasive large field-of-view visible light nanoscale imaging

NASA Astrophysics Data System (ADS)

Wang, Feifei; Liu, Lianqing; Yu, Haibo; Wen, Yangdong; Yu, Peng; Liu, Zhu; Wang, Yuechao; Li, Wen Jung

2016-12-01

Nanoscale correlation of structural information acquisition with specific-molecule identification provides new insight for studying rare subcellular events. To achieve this correlation, scanning electron microscopy has been combined with super-resolution fluorescent microscopy, despite its destructivity when acquiring biological structure information. Here we propose time-efficient non-invasive microsphere-based scanning superlens microscopy that enables the large-area observation of live-cell morphology or sub-membrane structures with sub-diffraction-limited resolution and is demonstrated by observing biological and non-biological objects. This microscopy operates in both non-invasive and contact modes with ~200 times the acquisition efficiency of atomic force microscopy, which is achieved by replacing the point of an atomic force microscope tip with an imaging area of microspheres and stitching the areas recorded during scanning, enabling sub-diffraction-limited resolution. Our method marks a possible path to non-invasive cell imaging and simultaneous tracking of specific molecules with nanoscale resolution, facilitating the study of subcellular events over a total cell period.

Structure-Templated Predictions of Novel Protein Interactions from Sequence Information

PubMed Central

Betel, Doron; Breitkreuz, Kevin E; Isserlin, Ruth; Dewar-Darch, Danielle; Tyers, Mike; Hogue, Christopher W. V

2007-01-01

The multitude of functions performed in the cell are largely controlled by a set of carefully orchestrated protein interactions often facilitated by specific binding of conserved domains in the interacting proteins. Interacting domains commonly exhibit distinct binding specificity to short and conserved recognition peptides called binding profiles. Although many conserved domains are known in nature, only a few have well-characterized binding profiles. Here, we describe a novel predictive method known as domain–motif interactions from structural topology (D-MIST) for elucidating the binding profiles of interacting domains. A set of domains and their corresponding binding profiles were derived from extant protein structures and protein interaction data and then used to predict novel protein interactions in yeast. A number of the predicted interactions were verified experimentally, including new interactions of the mitotic exit network, RNA polymerases, nucleotide metabolism enzymes, and the chaperone complex. These results demonstrate that new protein interactions can be predicted exclusively from sequence information. PMID:17892321

Revealing the planar chemistry of two-dimensional heterostructures at the atomic level.

PubMed

Chou, Harry; Ismach, Ariel; Ghosh, Rudresh; Ruoff, Rodney S; Dolocan, Andrei

2015-06-23

Two-dimensional (2D) atomic crystals and their heterostructures are an intense area of study owing to their unique properties that result from structural planar confinement. Intrinsically, the performance of a planar vertical device is linked to the quality of its 2D components and their interfaces, therefore requiring characterization tools that can reveal both its planar chemistry and morphology. Here, we propose a characterization methodology combining (micro-) Raman spectroscopy, atomic force microscopy and time-of-flight secondary ion mass spectrometry to provide structural information, morphology and planar chemical composition at virtually the atomic level, aimed specifically at studying 2D vertical heterostructures. As an example system, a graphene-on-h-BN heterostructure is analysed to reveal, with an unprecedented level of detail, the subtle chemistry and interactions within its layer structure that can be assigned to specific fabrication steps. Such detailed chemical information is of crucial importance for the complete integration of 2D heterostructures into functional devices.

Structured output-feedback controller synthesis with design specifications

NASA Astrophysics Data System (ADS)

Hao, Yuqing; Duan, Zhisheng

2017-03-01

This paper considers the problem of structured output-feedback controller synthesis with finite frequency specifications. Based on the orthogonal space information of input matrix, an improved parameter-dependent Lyapunov function method is first proposed. Then, a two-stage construction method is designed, which depends on an initial centralised controller. Corresponding design conditions for three types of output-feedback controllers are presented in terms of unified representations. Moreover, heuristic algorithms are provided to explore the desirable controllers. Finally, the effectiveness of these proposed methods is illustrated via some practical examples.

A Homecare Application based on the ASTM E2369-05 Standard Specification for Continuity of Care Record

PubMed Central

Botsivaly, M.; Spyropoulos, B.; Koutsourakis, K.; Mertika, K.

2006-01-01

The purpose of this study is the presentation of a system appropriate to be used upon the transition of a patient from hospital to homecare. The developed system is structured according to the ASTM E2369-05 Standard Specification for Continuity of Care Record and its function is based upon the creation of a structured subset of data, containing the patient’s most relevant clinical information, enabling simultaneously the planning and the optimal documentation of the provided homecare. PMID:17238479

Distributed Compression in Camera Sensor Networks

DTIC Science & Technology

2006-02-13

complicated in this context. This effort will make use of the correlation structure of the data given by the plenoptic function n the case of multi-camera...systems. In many cases the structure of the plenoptic function can be estimated without requiring inter-sensor communications, but by using some a...priori global geometrical information. Once the structure of the plenoptic function has been predicted, it is possible to develop specific distributed

Electronic structure of the organic semiconductor copper phthalocyanine: experiment and theory.

PubMed

Aristov, V Yu; Molodtsova, O V; Maslyuk, V V; Vyalikh, D V; Zhilin, V M; Ossipyan, Yu A; Bredow, T; Mertig, I; Knupfer, M

2008-01-21

The electronic structure of the organic semiconductor copper-phthalocyanine (CuPc) has been determined by a combination of conventional and resonant photoemission, near-edge x-ray absorption, as well as by the first-principles calculations. The experimentally obtained electronic valence band structure of CuPc is in very good agreement with the calculated density of states results, allowing the derivation of detailed site specific information.

Long term pavement performance computed parameter : frost penetration

DOT National Transportation Integrated Search

2008-11-01

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

43 CFR 10005.15 - Planning and management techniques applicable to the plan.

Code of Federal Regulations, 2013 CFR

2013-10-01

... facilities, instream spawning facilities, water control structures, and fencing that aid in the conservation... biological resources. (g) Applied research that targets specific biological information or management needs...

43 CFR 10005.15 - Planning and management techniques applicable to the plan.

Code of Federal Regulations, 2014 CFR

2014-10-01

... facilities, instream spawning facilities, water control structures, and fencing that aid in the conservation... biological resources. (g) Applied research that targets specific biological information or management needs...

Structural and Biochemical Characterization of Cinnamoyl-CoA Reductases1

PubMed Central

Walker, Alexander M.

2017-01-01

Cinnamoyl-coenzyme A reductase (CCR) catalyzes the reduction of hydroxycinnamoyl-coenzyme A (CoA) esters using NADPH to produce hydroxycinnamyl aldehyde precursors in lignin synthesis. The catalytic mechanism and substrate specificity of cinnamoyl-CoA reductases from sorghum (Sorghum bicolor), a strategic plant for bioenergy production, were deduced from crystal structures, site-directed mutagenesis, and kinetic and thermodynamic analyses. Although SbCCR1 displayed higher affinity for caffeoyl-CoA or p-coumaroyl-CoA than for feruloyl-CoA, the enzyme showed significantly higher activity for the latter substrate. Through molecular docking and comparisons between the crystal structures of the Vitis vinifera dihydroflavonol reductase and SbCCR1, residues threonine-154 and tyrosine-310 were pinpointed as being involved in binding CoA-conjugated phenylpropanoids. Threonine-154 of SbCCR1 and other CCRs likely confers strong substrate specificity for feruloyl-CoA over other cinnamoyl-CoA thioesters, and the T154Y mutation in SbCCR1 led to broader substrate specificity and faster turnover. Through data mining using our structural and biochemical information, four additional putative CCR genes were discovered from sorghum genomic data. One of these, SbCCR2, displayed greater activity toward p-coumaroyl-CoA than did SbCCR1, which could imply a role in the synthesis of defense-related lignin. Taken together, these findings provide knowledge about critical residues and substrate preference among CCRs and provide, to our knowledge, the first three-dimensional structure information for a CCR from a monocot species. PMID:27956488

The association between tax structure and cigarette price variability: findings from the ITC Project.

PubMed

Shang, Ce; Chaloupka, Frank J; Fong, Geoffrey T; Thompson, Mary; O'Connor, Richard J

2015-07-01

Recent studies have shown that more opportunities exist for tax avoidance when cigarette excise tax structure departs from a uniform specific structure. However, the association between tax structure and cigarette price variability has not been thoroughly studied in the existing literature. To examine how cigarette tax structure is associated with price variability. The variability of self-reported prices is measured using the ratios of differences between higher and lower prices to the median price such as the IQR-to-median ratio. We used survey data taken from the International Tobacco Control Policy Evaluation (ITC) Project in 17 countries to conduct the analysis. Cigarette prices were derived using individual purchase information and aggregated to price variability measures for each surveyed country and wave. The effect of tax structures on price variability was estimated using Generalised Estimating Equations after adjusting for year and country attributes. Our study provides empirical evidence of a relationship between tax structure and cigarette price variability. We find that, compared to the specific uniform tax structure, mixed uniform and tiered (specific, ad valorem or mixed) structures are associated with greater price variability (p≤0.01). Moreover, while a greater share of the specific component in total excise taxes is associated with lower price variability (p≤0.05), a tiered tax structure is associated with greater price variability (p≤0.01). The results suggest that a uniform and specific tax structure is the most effective tax structure for reducing tobacco consumption and prevalence by limiting price variability and decreasing opportunities for tax avoidance. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

Pointwise Partial Information Decomposition Using the Specificity and Ambiguity Lattices

NASA Astrophysics Data System (ADS)

Finn, Conor; Lizier, Joseph

2018-04-01

What are the distinct ways in which a set of predictor variables can provide information about a target variable? When does a variable provide unique information, when do variables share redundant information, and when do variables combine synergistically to provide complementary information? The redundancy lattice from the partial information decomposition of Williams and Beer provided a promising glimpse at the answer to these questions. However, this structure was constructed using a much criticised measure of redundant information, and despite sustained research, no completely satisfactory replacement measure has been proposed. In this paper, we take a different approach, applying the axiomatic derivation of the redundancy lattice to a single realisation from a set of discrete variables. To overcome the difficulty associated with signed pointwise mutual information, we apply this decomposition separately to the unsigned entropic components of pointwise mutual information which we refer to as the specificity and ambiguity. This yields a separate redundancy lattice for each component. Then based upon an operational interpretation of redundancy, we define measures of redundant specificity and ambiguity enabling us to evaluate the partial information atoms in each lattice. These atoms can be recombined to yield the sought-after multivariate information decomposition. We apply this framework to canonical examples from the literature and discuss the results and the various properties of the decomposition. In particular, the pointwise decomposition using specificity and ambiguity satisfies a chain rule over target variables, which provides new insights into the so-called two-bit-copy example.

Complementary molecular information changes our perception of food web structure

PubMed Central

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

2014-01-01

How networks of ecological interactions are structured has a major impact on their functioning. However, accurately resolving both the nodes of the webs and the links between them is fraught with difficulties. We ask whether the new resolution conferred by molecular information changes perceptions of network structure. To probe a network of antagonistic interactions in the High Arctic, we use two complementary sources of molecular data: parasitoid DNA sequenced from the tissues of their hosts and host DNA sequenced from the gut of adult parasitoids. The information added by molecular analysis radically changes the properties of interaction structure. Overall, three times as many interaction types were revealed by combining molecular information from parasitoids and hosts with rearing data, versus rearing data alone. At the species level, our results alter the perceived host specificity of parasitoids, the parasitoid load of host species, and the web-wide role of predators with a cryptic lifestyle. As the northernmost network of host–parasitoid interactions quantified, our data point exerts high leverage on global comparisons of food web structure. However, how we view its structure will depend on what information we use: compared with variation among networks quantified at other sites, the properties of our web vary as much or much more depending on the techniques used to reconstruct it. We thus urge ecologists to combine multiple pieces of evidence in assessing the structure of interaction webs, and suggest that current perceptions of interaction structure may be strongly affected by the methods used to construct them. PMID:24449902

Lexical Retrieval Constrained by Sound Structure: The Role of the Left Inferior Frontal Gyrus

ERIC Educational Resources Information Center

Sharp, David J.; Scott, Sophie K.; Cutler, Anne; Wise, Richard J. S.

2005-01-01

Positron emission tomography was used to investigate two competing hypotheses about the role of the left inferior frontal gyrus (IFG) in word generation. One proposes a domain-specific organization, with neural activation dependent on the type of information being processed, i.e., surface sound structure or semantic. The other proposes a…

Social Structure of the Contact Situation: Rural Appalachia and Urban America. Appalachian Center Information Report 1.

ERIC Educational Resources Information Center

Schwarzweller, Harry K.; Brown, James S.

An investigation of the characteristic structuring of rural communities in Appalachia and the institutional channels for change which exist within such communities comprise this revised version of a paper read at the Extension Leaders Conference, Morgantown, West Virginia, 1968. Specifically, this essay discusses how education, the mass media,…

Information retrieval system utilizing wavelet transform

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

Brewster, M.E.; Miller, N.E.

A method is disclosed for automatically partitioning an unstructured electronically formatted natural language document into its sub-topic structure. Specifically, the document is converted to an electronic signal and a wavelet transform is then performed on the signal. The resultant signal may then be used to graphically display and interact with the sub-topic structure of the document.

Brain Structure-function Couplings (FY11)

DTIC Science & Technology

2012-01-01

influence time-evolving models of global brain function and dynamic changes in cognitive performance. Both structural and functional connections change on...Artifact Resistant Measure to Detect Cognitive EEG Activity During Locomotion. Journal of NeuroEngineering and Rehabilitation, submitted. 10...Specifically, identifying the communication between brain regions that occurs during tasks may provide information regarding the cognitive processes involved in

Diagnostic efficiency of Mueller-matrix polarization reconstruction system of the phase structure of liver tissue

NASA Astrophysics Data System (ADS)

Zabolotna, Natalia I.; Pavlov, Sergii V.; Radchenko, Kostiantyn O.; Stasenko, Vladyslav A.; Wójcik, Waldemar; Kussambayeva, Nazym

2015-12-01

The application field of using the Mueller-matrix polarizing reconstruction system of phase structure of biological layer for optical-anisotropic parameters differentiation of histological sections of healthy and rat's liver with hepatitis were investigated. Comparison of system informativity with known systems on indexes of sensitivity, specificity and balanced accuracy were performed.

Outcome-Based Practice: Disclosure Rates of Child Sexual Abuse Comparing Allegation Blind and Allegation Informed Structured Interviews.

ERIC Educational Resources Information Center

Cantlon, Julie; And Others

1996-01-01

This study evaluated the use of "allegation blind" interviews (in which interviewers did not know the specific allegation involved) with children (n=1535) suspected of being victims of child sexual abuse. The "allegation blind" interview technique yielded a statistically higher disclosure rate than the "allegation informed" interviews. (Author/DB)

Designing Place-Based Interventions for Sustainability and Replicability: The Case of GO! Austin/VAMOS! Austin

PubMed Central

Hussaini, Aliya; Pulido, Carmen Llanes; Basu, Semonti; Ranjit, Nalini

2018-01-01

Place-based health efforts account for the role of the community environment in shaping decisions and circumstances that affect population well-being. Such efforts, rooted as they are in the theory that health is socially determined, mobilize resources for health promotion that are not typically used, and offer a more informed and robust way of promoting health outcomes within a community. Common criticisms of place-based work include the difficulty of replication, since engagement is so specific to a place, and limited sustainability of the work, in the absence of continued institutional structures, both within the community and supporting structures outside the community, to keep these initiatives resilient. This paper describes a place-based initiative, GO! Austin/VAMOS! Austin (GAVA), which was designed to harness the strengths of place-based work—namely, its specificity to place and community. From the start, the project was designed to balance this specificity with a focus on developing and utilizing a standardized set of evidence-informed implementation and evaluation approaches and tools that were flexible enough to be modified for specific settings. This was accompanied by an emphasis on leadership and capacity building within resident leaders, which provided for informed intervention and demand building capacity, but also for longevity as partners, philanthropic, and otherwise, moved in and out of the work. PMID:29623272

Designing Place-Based Interventions for Sustainability and Replicability: The Case of GO! Austin/VAMOS! Austin.

PubMed

Hussaini, Aliya; Pulido, Carmen Llanes; Basu, Semonti; Ranjit, Nalini

2018-01-01

Place-based health efforts account for the role of the community environment in shaping decisions and circumstances that affect population well-being. Such efforts, rooted as they are in the theory that health is socially determined, mobilize resources for health promotion that are not typically used, and offer a more informed and robust way of promoting health outcomes within a community. Common criticisms of place-based work include the difficulty of replication , since engagement is so specific to a place, and limited sustainability of the work, in the absence of continued institutional structures, both within the community and supporting structures outside the community, to keep these initiatives resilient. This paper describes a place-based initiative, GO! Austin/VAMOS! Austin (GAVA), which was designed to harness the strengths of place-based work-namely, its specificity to place and community. From the start, the project was designed to balance this specificity with a focus on developing and utilizing a standardized set of evidence-informed implementation and evaluation approaches and tools that were flexible enough to be modified for specific settings. This was accompanied by an emphasis on leadership and capacity building within resident leaders, which provided for informed intervention and demand building capacity, but also for longevity as partners, philanthropic, and otherwise, moved in and out of the work.

49 CFR 238.201 - Scope/alternative compliance.

Code of Federal Regulations, 2012 CFR

2012-10-01

... structural standards of this subpart (§ 238.203—static end strength; § 238.205—anti-climbing mechanism; § 238... by § 238.21(c); (ii) Information, including detailed drawings and materials specifications...

49 CFR 238.201 - Scope/alternative compliance.

Code of Federal Regulations, 2013 CFR

2013-10-01

... structural standards of this subpart (§ 238.203—static end strength; § 238.205—anti-climbing mechanism; § 238... by § 238.21(c); (ii) Information, including detailed drawings and materials specifications...

49 CFR 238.201 - Scope/alternative compliance.

Code of Federal Regulations, 2014 CFR

2014-10-01

... structural standards of this subpart (§ 238.203—static end strength; § 238.205—anti-climbing mechanism; § 238... by § 238.21(c); (ii) Information, including detailed drawings and materials specifications...

49 CFR 238.201 - Scope/alternative compliance.

Code of Federal Regulations, 2011 CFR

2011-10-01

... structural standards of this subpart (§ 238.203—static end strength; § 238.205—anti-climbing mechanism; § 238... by § 238.21(c); (ii) Information, including detailed drawings and materials specifications...

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.

ADO: a disease ontology representing the domain knowledge specific to Alzheimer's disease.

PubMed

Malhotra, Ashutosh; Younesi, Erfan; Gündel, Michaela; Müller, Bernd; Heneka, Michael T; Hofmann-Apitius, Martin

2014-03-01

Biomedical ontologies offer the capability to structure and represent domain-specific knowledge semantically. Disease-specific ontologies can facilitate knowledge exchange across multiple disciplines, and ontology-driven mining approaches can generate great value for modeling disease mechanisms. However, in the case of neurodegenerative diseases such as Alzheimer's disease, there is a lack of formal representation of the relevant knowledge domain. Alzheimer's disease ontology (ADO) is constructed in accordance to the ontology building life cycle. The Protégé OWL editor was used as a tool for building ADO in Ontology Web Language format. ADO was developed with the purpose of containing information relevant to four main biological views-preclinical, clinical, etiological, and molecular/cellular mechanisms-and was enriched by adding synonyms and references. Validation of the lexicalized ontology by means of named entity recognition-based methods showed a satisfactory performance (F score = 72%). In addition to structural and functional evaluation, a clinical expert in the field performed a manual evaluation and curation of ADO. Through integration of ADO into an information retrieval environment, we show that the ontology supports semantic search in scientific text. The usefulness of ADO is authenticated by dedicated use case scenarios. Development of ADO as an open ADO is a first attempt to organize information related to Alzheimer's disease in a formalized, structured manner. We demonstrate that ADO is able to capture both established and scattered knowledge existing in scientific text. Copyright © 2014 The Alzheimer's Association. Published by Elsevier Inc. All rights reserved.

The cost of concreteness: the effect of nonessential information on analogical transfer.

PubMed

Kaminski, Jennifer A; Sloutsky, Vladimir M; Heckler, Andrew F

2013-03-01

Most theories of analogical transfer focus on similarities between the learning and transfer domains, where transfer is more likely between domains that share common surface features, similar elements, or common interpretations of structure. We suggest that characteristics of the learning instantiation alone can give rise to different levels of transfer. We propose that concreteness of the learning instantiation can hinder analogical transfer of well-defined structured concepts, such as mathematical concepts. We operationalize the term concreteness as the amount of information communicated through a specific instantiation of a concept. The 5 reported experiments with undergraduate students tested the hypothesis by presenting participants with the concept of a commutative mathematical group of order 3. The experiments varied the level of concreteness of the training instantiation and measured transfer of learning to a new instantiation. The results support the hypothesis, demonstrating better transfer from more generic instantiations (i.e., ones that communicate minimal extraneous information) than from more concrete instantiations. Specifically, concreteness was found to create an obstacle to successful structural alignment across domains, whereas generic instantiations led to spontaneous structural alignment. These findings have important implications for the theory of learning and transfer and practical implications for the design of educational material. Although some concreteness may activate prior knowledge and perhaps offer a leg up in the learning process, this benefit may come at the cost of transfer.

Harnessing glycomics technologies: integrating structure with function for glycan characterization

PubMed Central

Robinson, Luke N.; Artpradit, Charlermchai; Raman, Rahul; Shriver, Zachary H.; Ruchirawat, Mathuros; Sasisekharan, Ram

2013-01-01

Glycans, or complex carbohydrates, are a ubiquitous class of biological molecules which impinge on a variety of physiological processes ranging from signal transduction to tissue development and microbial pathogenesis. In comparison to DNA and proteins, glycans present unique challenges to the study of their structure and function owing to their complex and heterogeneous structures and the dominant role played by multivalency in their sequence-specific biological interactions. Arising from these challenges, there is a need to integrate information from multiple complementary methods to decode structure-function relationships. Focusing on acidic glycans, we describe here key glycomics technologies for characterizing their structural attributes, including linkage, modifications, and topology, as well as for elucidating their role in biological processes. Two cases studies, one involving sialylated branched glycans and the other sulfated glycosaminoglycans, are used to highlight how integration of orthogonal information from diverse datasets enables rapid convergence of glycan characterization for development of robust structure-function relationships. PMID:22522536

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.

Experiences in extraction of contact parameters from process-evaluation test-structures

NASA Technical Reports Server (NTRS)

Lieneweg, Udo

1988-01-01

Six-terminal-contact test structures are introduced for characterizing ohmic contacts between a metal and a heavily doped semiconductor layer. Specifically, the six-terminal test structure supplies the additional information needed in order to calculate the transmission length and eventual corrections to the characteristic resistance per unit width due to finite contact length. The essential feature of this test structure is a square contact with four taps in the lower (semiconductor) layer. Every other one of these taps is used for current injection ('front'). From the voltage drop at the opposite tap and the side taps, the 'end' resistance and the 'side' resistances are calculated. The test structures are shown to give valuable information complementary to the common front resistance measurements. The interfacial resistivity is obtained directly after proper correction for flange effects.

Building an automated SOAP classifier for emergency department reports.

PubMed

Mowery, Danielle; Wiebe, Janyce; Visweswaran, Shyam; Harkema, Henk; Chapman, Wendy W

2012-02-01

Information extraction applications that extract structured event and entity information from unstructured text can leverage knowledge of clinical report structure to improve performance. The Subjective, Objective, Assessment, Plan (SOAP) framework, used to structure progress notes to facilitate problem-specific, clinical decision making by physicians, is one example of a well-known, canonical structure in the medical domain. Although its applicability to structuring data is understood, its contribution to information extraction tasks has not yet been determined. The first step to evaluating the SOAP framework's usefulness for clinical information extraction is to apply the model to clinical narratives and develop an automated SOAP classifier that classifies sentences from clinical reports. In this quantitative study, we applied the SOAP framework to sentences from emergency department reports, and trained and evaluated SOAP classifiers built with various linguistic features. We found the SOAP framework can be applied manually to emergency department reports with high agreement (Cohen's kappa coefficients over 0.70). Using a variety of features, we found classifiers for each SOAP class can be created with moderate to outstanding performance with F(1) scores of 93.9 (subjective), 94.5 (objective), 75.7 (assessment), and 77.0 (plan). We look forward to expanding the framework and applying the SOAP classification to clinical information extraction tasks. Copyright © 2011. Published by Elsevier Inc.

Probing Protein Structure and Folding in the Gas Phase by Electron Capture Dissociation

NASA Astrophysics Data System (ADS)

Schennach, Moritz; Breuker, Kathrin

2015-07-01

The established methods for the study of atom-detailed protein structure in the condensed phases, X-ray crystallography and nuclear magnetic resonance spectroscopy, have recently been complemented by new techniques by which nearly or fully desolvated protein structures are probed in gas-phase experiments. Electron capture dissociation (ECD) is unique among these as it provides residue-specific, although indirect, structural information. In this Critical Insight article, we discuss the development of ECD for the structural probing of gaseous protein ions, its potential, and limitations.

Molecular graph convolutions: moving beyond fingerprints

NASA Astrophysics Data System (ADS)

Kearnes, Steven; McCloskey, Kevin; Berndl, Marc; Pande, Vijay; Riley, Patrick

2016-08-01

Molecular "fingerprints" encoding structural information are the workhorse of cheminformatics and machine learning in drug discovery applications. However, fingerprint representations necessarily emphasize particular aspects of the molecular structure while ignoring others, rather than allowing the model to make data-driven decisions. We describe molecular graph convolutions, a machine learning architecture for learning from undirected graphs, specifically small molecules. Graph convolutions use a simple encoding of the molecular graph—atoms, bonds, distances, etc.—which allows the model to take greater advantage of information in the graph structure. Although graph convolutions do not outperform all fingerprint-based methods, they (along with other graph-based methods) represent a new paradigm in ligand-based virtual screening with exciting opportunities for future improvement.

Molecular graph convolutions: moving beyond fingerprints.

PubMed

Kearnes, Steven; McCloskey, Kevin; Berndl, Marc; Pande, Vijay; Riley, Patrick

2016-08-01

Molecular "fingerprints" encoding structural information are the workhorse of cheminformatics and machine learning in drug discovery applications. However, fingerprint representations necessarily emphasize particular aspects of the molecular structure while ignoring others, rather than allowing the model to make data-driven decisions. We describe molecular graph convolutions, a machine learning architecture for learning from undirected graphs, specifically small molecules. Graph convolutions use a simple encoding of the molecular graph-atoms, bonds, distances, etc.-which allows the model to take greater advantage of information in the graph structure. Although graph convolutions do not outperform all fingerprint-based methods, they (along with other graph-based methods) represent a new paradigm in ligand-based virtual screening with exciting opportunities for future improvement.

Drilling and completion specifications for CA series multilevel piezometers

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

Clawson, T.S.

1986-08-01

CX Series multilevel piezometer boreholes will provide information on hydraulic heads in the Rosalia, Sentinel Gap, Ginkgo, Rocky Coulee, Cohassett, Birkett, and Umtanum flow tops. The borehole sites will be located adjacent to the reference repository location. In addition, information from the boreholes will provide input data used to determine horizontal and vertical flow rates, and identify possible geologic structures. This specification includes details for drilling, piezometer design, hydrologic testing, and hydrochemical sampling of the boreholes. It includes drilling requirements, design, and installation procedures for the series piezometer nests, intervals selected for head monitoring and schedules for drilling and piezometermore » installation. Specific drilling and piezometer installation specifications for boreholes DC-24CX and DC-25CX are also included. 27 refs., 5 figs., 3 tabs.« less

Modelling non-Euclidean movement and landscape connectivity in highly structured ecological networks

USGS Publications Warehouse

Sutherland, Christopher; Fuller, Angela K.; Royle, J. Andrew

2015-01-01

The ecological distance SCR model uses spatially indexed capture-recapture data to estimate how activity patterns are influenced by landscape structure. As well as reducing bias in estimates of abundance, this approach provides biologically realistic representations of home range geometry, and direct information about species-landscape interactions. The incorporation of both structural (landscape) and functional (movement) components of connectivity provides a direct measure of species-specific landscape connectivity.

Designing quantum information processing via structural physical approximation.

PubMed

Bae, Joonwoo

2017-10-01

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

Designing quantum information processing via structural physical approximation

NASA Astrophysics Data System (ADS)

Bae, Joonwoo

2017-10-01

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

Longitudinal Validation of General and Specific Structural Features of Personality Pathology

PubMed Central

Wright, Aidan G.C.; Hopwood, Christopher J.; Skodol, Andrew E.; Morey, Leslie C.

2016-01-01

Theorists have long argued that personality disorder (PD) is best understood in terms of general impairments shared across the disorders as well as more specific instantiations of pathology. A model based on this theoretical structure was proposed as part of the DSM-5 revision process. However, only recently has this structure been subjected to formal quantitative evaluation, with little in the way of validation efforts via external correlates or prospective longitudinal prediction. We used the Collaborative Longitudinal Study of Personality Disorders dataset to: (1) estimate structural models that parse general from specific variance in personality disorder features, (2) examine patterns of growth in general and specific features over the course of 10 years, and (3) establish concurrent and dynamic longitudinal associations in PD features and a host of external validators including basic personality traits and psychosocial functioning scales. We found that general PD exhibited much lower absolute stability and was most strongly related to broad markers of psychosocial functioning, concurrently and longitudinally, whereas specific features had much higher mean stability and exhibited more circumscribed associations with functioning. However, both general and specific factors showed recognizable associations with normative and pathological traits. These results can inform efforts to refine the conceptualization and diagnosis of personality pathology. PMID:27819472

A Novel Information-Theoretic Approach for Variable Clustering and Predictive Modeling Using Dirichlet Process Mixtures

PubMed Central

Chen, Yun; Yang, Hui

2016-01-01

In the era of big data, there are increasing interests on clustering variables for the minimization of data redundancy and the maximization of variable relevancy. Existing clustering methods, however, depend on nontrivial assumptions about the data structure. Note that nonlinear interdependence among variables poses significant challenges on the traditional framework of predictive modeling. In the present work, we reformulate the problem of variable clustering from an information theoretic perspective that does not require the assumption of data structure for the identification of nonlinear interdependence among variables. Specifically, we propose the use of mutual information to characterize and measure nonlinear correlation structures among variables. Further, we develop Dirichlet process (DP) models to cluster variables based on the mutual-information measures among variables. Finally, orthonormalized variables in each cluster are integrated with group elastic-net model to improve the performance of predictive modeling. Both simulation and real-world case studies showed that the proposed methodology not only effectively reveals the nonlinear interdependence structures among variables but also outperforms traditional variable clustering algorithms such as hierarchical clustering. PMID:27966581

A Novel Information-Theoretic Approach for Variable Clustering and Predictive Modeling Using Dirichlet Process Mixtures.

PubMed

Chen, Yun; Yang, Hui

2016-12-14

In the era of big data, there are increasing interests on clustering variables for the minimization of data redundancy and the maximization of variable relevancy. Existing clustering methods, however, depend on nontrivial assumptions about the data structure. Note that nonlinear interdependence among variables poses significant challenges on the traditional framework of predictive modeling. In the present work, we reformulate the problem of variable clustering from an information theoretic perspective that does not require the assumption of data structure for the identification of nonlinear interdependence among variables. Specifically, we propose the use of mutual information to characterize and measure nonlinear correlation structures among variables. Further, we develop Dirichlet process (DP) models to cluster variables based on the mutual-information measures among variables. Finally, orthonormalized variables in each cluster are integrated with group elastic-net model to improve the performance of predictive modeling. Both simulation and real-world case studies showed that the proposed methodology not only effectively reveals the nonlinear interdependence structures among variables but also outperforms traditional variable clustering algorithms such as hierarchical clustering.

Recent advances in standards for collaborative Digital Anatomic Pathology

PubMed Central

2011-01-01

Context Collaborative Digital Anatomic Pathology refers to the use of information technology that supports the creation and sharing or exchange of information, including data and images, during the complex workflow performed in an Anatomic Pathology department from specimen reception to report transmission and exploitation. Collaborative Digital Anatomic Pathology can only be fully achieved using medical informatics standards. The goal of the international integrating the Healthcare Enterprise (IHE) initiative is precisely specifying how medical informatics standards should be implemented to meet specific health care needs and making systems integration more efficient and less expensive. Objective To define the best use of medical informatics standards in order to share and exchange machine-readable structured reports and their evidences (including whole slide images) within hospitals and across healthcare facilities. Methods Specific working groups dedicated to Anatomy Pathology within multiple standards organizations defined standard-based data structures for Anatomic Pathology reports and images as well as informatic transactions in order to integrate Anatomic Pathology information into the electronic healthcare enterprise. Results The DICOM supplements 122 and 145 provide flexible object information definitions dedicated respectively to specimen description and Whole Slide Image acquisition, storage and display. The content profile “Anatomic Pathology Structured Report” (APSR) provides standard templates for structured reports in which textual observations may be bound to digital images or regions of interest. Anatomic Pathology observations are encoded using an international controlled vocabulary defined by the IHE Anatomic Pathology domain that is currently being mapped to SNOMED CT concepts. Conclusion Recent advances in standards for Collaborative Digital Anatomic Pathology are a unique opportunity to share or exchange Anatomic Pathology structured reports that are interoperable at an international level. The use of machine-readable format of APSR supports the development of decision support as well as secondary use of Anatomic Pathology information for epidemiology or clinical research. PMID:21489187

Requirements Specification Language (RSL) and supporting tools

NASA Technical Reports Server (NTRS)

Frincke, Deborah; Wolber, Dave; Fisher, Gene; Cohen, Gerald C.

1992-01-01

This document describes a general purpose Requirement Specification Language (RSL). RSL is a hybrid of features found in several popular requirement specification languages. The purpose of RSL is to describe precisely the external structure of a system comprised of hardware, software, and human processing elements. To overcome the deficiencies of informal specification languages, RSL includes facilities for mathematical specification. Two RSL interface tools are described. The Browser view contains a complete document with all details of the objects and operations. The Dataflow view is a specialized, operation-centered depiction of a specification that shows how specified operations relate in terms of inputs and outputs.

Alzheimer's and Dementia Testing for Earlier Diagnosis

MedlinePlus

... focused on early detection of Alzheimer's disease. Imaging technologies used in Alzheimer's research Structural imaging provides information ... chemical changes linked to specific diseases. Molecular imaging technologies include PET, fMRI and single photon emission computed ...

What Can Interfacial Water Molecules Tell Us About Solute Structure?

NASA Astrophysics Data System (ADS)

Willard, Adam

The molecular structure of bulk liquid water reflects a molecular tendency to engage in tetrahedrally coordinated hydrogen bonding. At a solute interface waters preferred three-dimensional hydrogen bonding network must conform to a locally anisotropy interfacial environment. Interfacial water molecules adopt configurations that balance water-solute and water-water interactions. The arrangements of interfacial water molecules, therefore encode information about the effective solute-water interactions. This solute-specific information is difficult to extract, however, because interfacial structure also reflects waters collective response to an anisotropic hydrogen bonding environment. Here I present a methodology for characterizing the molecular-level structure of liquid water interface from simulation data. This method can be used to explore waters static and/or dynamic response to a wide range of chemically and topologically heterogeneous solutes such as proteins.

An EHR Prototype Using Structured ISO/EN 13606 Documents to Respond to Identified Clinical Information Needs of Diabetes Specialists: A Controlled Study on Feasibility and Impact

PubMed Central

Huebner-Bloder, Gudrun; Duftschmid, Georg; Kohler, Michael; Rinner, Christoph; Saboor, Samrend; Ammenwerth, Elske

2012-01-01

Cross-institutional longitudinal Electronic Health Records (EHR), as introduced in Austria at the moment, increase the challenge of information overload of healthcare professionals. We developed an innovative cross-institutional EHR query prototype that offers extended query options, including searching for specific information items or sets of information items. The available query options were derived from a systematic analysis of information needs of diabetes specialists during patient encounters. The prototype operates in an IHE-XDS-based environment where ISO/EN 13606-structured documents are available. We conducted a controlled study with seven diabetes specialists to assess the feasibility and impact of this EHR query prototype on efficient retrieving of patient information to answer typical clinical questions. The controlled study showed that the specialists were quicker and more successful (measured in percentage of expected information items found) in finding patient information compared to the standard full-document search options. The participants also appreciated the extended query options. PMID:23304308

Structuring Legacy Pathology Reports by openEHR Archetypes to Enable Semantic Querying.

PubMed

Kropf, Stefan; Krücken, Peter; Mueller, Wolf; Denecke, Kerstin

2017-05-18

Clinical information is often stored as free text, e.g. in discharge summaries or pathology reports. These documents are semi-structured using section headers, numbered lists, items and classification strings. However, it is still challenging to retrieve relevant documents since keyword searches applied on complete unstructured documents result in many false positive retrieval results. We are concentrating on the processing of pathology reports as an example for unstructured clinical documents. The objective is to transform reports semi-automatically into an information structure that enables an improved access and retrieval of relevant data. The data is expected to be stored in a standardized, structured way to make it accessible for queries that are applied to specific sections of a document (section-sensitive queries) and for information reuse. Our processing pipeline comprises information modelling, section boundary detection and section-sensitive queries. For enabling a focused search in unstructured data, documents are automatically structured and transformed into a patient information model specified through openEHR archetypes. The resulting XML-based pathology electronic health records (PEHRs) are queried by XQuery and visualized by XSLT in HTML. Pathology reports (PRs) can be reliably structured into sections by a keyword-based approach. The information modelling using openEHR allows saving time in the modelling process since many archetypes can be reused. The resulting standardized, structured PEHRs allow accessing relevant data by retrieving data matching user queries. Mapping unstructured reports into a standardized information model is a practical solution for a better access to data. Archetype-based XML enables section-sensitive retrieval and visualisation by well-established XML techniques. Focussing the retrieval to particular sections has the potential of saving retrieval time and improving the accuracy of the retrieval.

Analysis of genetic population structure in Acacia caven (Leguminosae, Mimosoideae), comparing one exploratory and two Bayesian-model-based methods.

PubMed

Pometti, Carolina L; Bessega, Cecilia F; Saidman, Beatriz O; Vilardi, Juan C

2014-03-01

Bayesian clustering as implemented in STRUCTURE or GENELAND software is widely used to form genetic groups of populations or individuals. On the other hand, in order to satisfy the need for less computer-intensive approaches, multivariate analyses are specifically devoted to extracting information from large datasets. In this paper, we report the use of a dataset of AFLP markers belonging to 15 sampling sites of Acacia caven for studying the genetic structure and comparing the consistency of three methods: STRUCTURE, GENELAND and DAPC. Of these methods, DAPC was the fastest one and showed accuracy in inferring the K number of populations (K = 12 using the find.clusters option and K = 15 with a priori information of populations). GENELAND in turn, provides information on the area of membership probabilities for individuals or populations in the space, when coordinates are specified (K = 12). STRUCTURE also inferred the number of K populations and the membership probabilities of individuals based on ancestry, presenting the result K = 11 without prior information of populations and K = 15 using the LOCPRIOR option. Finally, in this work all three methods showed high consistency in estimating the population structure, inferring similar numbers of populations and the membership probabilities of individuals to each group, with a high correlation between each other.

Computational approaches to define a human milk metaglycome

PubMed Central

Agravat, Sanjay B.; Song, Xuezheng; Rojsajjakul, Teerapat; Cummings, Richard D.; Smith, David F.

2016-01-01

Motivation: The goal of deciphering the human glycome has been hindered by the lack of high-throughput sequencing methods for glycans. Although mass spectrometry (MS) is a key technology in glycan sequencing, MS alone provides limited information about the identification of monosaccharide constituents, their anomericity and their linkages. These features of individual, purified glycans can be partly identified using well-defined glycan-binding proteins, such as lectins and antibodies that recognize specific determinants within glycan structures. Results: We present a novel computational approach to automate the sequencing of glycans using metadata-assisted glycan sequencing, which combines MS analyses with glycan structural information from glycan microarray technology. Success in this approach was aided by the generation of a ‘virtual glycome’ to represent all potential glycan structures that might exist within a metaglycomes based on a set of biosynthetic assumptions using known structural information. We exploited this approach to deduce the structures of soluble glycans within the human milk glycome by matching predicted structures based on experimental data against the virtual glycome. This represents the first meta-glycome to be defined using this method and we provide a publically available web-based application to aid in sequencing milk glycans. Availability and implementation: http://glycomeseq.emory.edu Contact: sagravat@bidmc.harvard.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:26803164

Deriving high-resolution protein backbone structure propensities from all crystal data using the information maximization device.

PubMed

Solis, Armando D

2014-01-01

The most informative probability distribution functions (PDFs) describing the Ramachandran phi-psi dihedral angle pair, a fundamental descriptor of backbone conformation of protein molecules, are derived from high-resolution X-ray crystal structures using an information-theoretic approach. The Information Maximization Device (IMD) is established, based on fundamental information-theoretic concepts, and then applied specifically to derive highly resolved phi-psi maps for all 20 single amino acid and all 8000 triplet sequences at an optimal resolution determined by the volume of current data. The paper shows that utilizing the latent information contained in all viable high-resolution crystal structures found in the Protein Data Bank (PDB), totaling more than 77,000 chains, permits the derivation of a large number of optimized sequence-dependent PDFs. This work demonstrates the effectiveness of the IMD and the superiority of the resulting PDFs by extensive fold recognition experiments and rigorous comparisons with previously published triplet PDFs. Because it automatically optimizes PDFs, IMD results in improved performance of knowledge-based potentials, which rely on such PDFs. Furthermore, it provides an easy computational recipe for empirically deriving other kinds of sequence-dependent structural PDFs with greater detail and precision. The high-resolution phi-psi maps derived in this work are available for download.

Sex-specific habitat suitability models for Panthera tigris in Chitwan National Park, Nepal

NASA Astrophysics Data System (ADS)

Battle, Curtis Scott

Although research on wildlife species across taxa has shown that males and females differentially select habitat, sex-specific models of habitat suitability for endangered species are uncommon. Here, we developed such models for Bengal Tigers (Panthera tigris) based on camera trap data collected from 20 January to 22 March, 2010, within Chitwan National Park, Nepal, and its buffer zone. We compared these to a sex-indiscriminate habitat suitability model in order to identify information that is lost when occurrence data for both sexes are included in the same model, as well as to assess the benefits of a sex-specific approach to habitat suitability modelling. Our sex-specific models allowed us to produce more informative and detailed habitat suitability maps, highlighting key differences in the distribution of suitable habitats for males and females, preferences in vegetation structure, and habitat use near human settlements. In the context of global tiger conservation, such information is essential to fulfilling established conservation goals and population recovery targets.

MyDas, an Extensible Java DAS Server

PubMed Central

Jimenez, Rafael C.; Quinn, Antony F.; Jenkinson, Andrew M.; Mulder, Nicola; Martin, Maria; Hunter, Sarah; Hermjakob, Henning

2012-01-01

A large number of diverse, complex, and distributed data resources are currently available in the Bioinformatics domain. The pace of discovery and the diversity of information means that centralised reference databases like UniProt and Ensembl cannot integrate all potentially relevant information sources. From a user perspective however, centralised access to all relevant information concerning a specific query is essential. The Distributed Annotation System (DAS) defines a communication protocol to exchange annotations on genomic and protein sequences; this standardisation enables clients to retrieve data from a myriad of sources, thus offering centralised access to end-users. We introduce MyDas, a web server that facilitates the publishing of biological annotations according to the DAS specification. It deals with the common functionality requirements of making data available, while also providing an extension mechanism in order to implement the specifics of data store interaction. MyDas allows the user to define where the required information is located along with its structure, and is then responsible for the communication protocol details. PMID:23028496

MyDas, an extensible Java DAS server.

PubMed

Salazar, Gustavo A; García, Leyla J; Jones, Philip; Jimenez, Rafael C; Quinn, Antony F; Jenkinson, Andrew M; Mulder, Nicola; Martin, Maria; Hunter, Sarah; Hermjakob, Henning

2012-01-01

A large number of diverse, complex, and distributed data resources are currently available in the Bioinformatics domain. The pace of discovery and the diversity of information means that centralised reference databases like UniProt and Ensembl cannot integrate all potentially relevant information sources. From a user perspective however, centralised access to all relevant information concerning a specific query is essential. The Distributed Annotation System (DAS) defines a communication protocol to exchange annotations on genomic and protein sequences; this standardisation enables clients to retrieve data from a myriad of sources, thus offering centralised access to end-users.We introduce MyDas, a web server that facilitates the publishing of biological annotations according to the DAS specification. It deals with the common functionality requirements of making data available, while also providing an extension mechanism in order to implement the specifics of data store interaction. MyDas allows the user to define where the required information is located along with its structure, and is then responsible for the communication protocol details.

Apply Pesticides Correctly, A Guide for Commercial Applicators: Industrial, Institutional, Structural and Health Related Pest Control.

ERIC Educational Resources Information Center

Wamsley, Mary Ann, Ed.; Vermeire, Donna M., Ed.

This guide contains basic information to meet the specific standards for pesticide applicators. The thrust of this document is the recognition and control of common pests. Included are those which directly affect man such as bees, roaches, mites, and mosquitoes; and those which destroy food products and wooden structures. Both mechanical and…

Scaled Tank Test Design and Results for the Aquantis 2.5 MW Ocean Current Generation Device

DOE Data Explorer

Swales, Henry; Kils, Ole; Coakley, David B.; Sites, Eric; Mayer, Tyler

2015-06-03

Aquantis 2.5 MW Ocean Current Generation Device, Tow Tank Dynamic Rig Structural Analysis Results. This is the detailed documentation for scaled device testing in a tow tank, including models, drawings, presentations, cost of energy analysis, and structural analysis. This dataset also includes specific information on drivetrain, roller bearing, blade fabrication, mooring, and rotor characteristics.

Detection of Q-Matrix Misspecification Using Two Criteria for Validation of Cognitive Structures under the Least Squares Distance Model

ERIC Educational Resources Information Center

Romero, Sonia J.; Ordoñez, Xavier G.; Ponsoda, Vincente; Revuelta, Javier

2014-01-01

Cognitive Diagnostic Models (CDMs) aim to provide information about the degree to which individuals have mastered specific attributes that underlie the success of these individuals on test items. The Q-matrix is a key element in the application of CDMs, because contains links item-attributes representing the cognitive structure proposed for solve…

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…

Description and Use of the Data Files on Military Careers. Information System for Vocational Decisions.

ERIC Educational Resources Information Center

Yee, Patricia; Seltzer, Joanna

This paper summarizes the contents, structure and possible uses of the Information System for Vocational Decisions (ISVD) data file on military jobs in the 3 major services. In all, 170 specific career fields for enlisted men and 34 for officers are included in the data file, which also provides for converting the inquirer's personal…

High-performance liquid chromatography-mass spectrometry for mapping and sequencing glycosaminoglycan-derived oligosaccharides

PubMed Central

Volpi, Nicola; Linhardt, Robert J

2012-01-01

Glycosaminoglycans (GAGs) have proven to be very difficult to analyze and characterize because of their high negative charge density, polydispersity and sequence heterogeneity. As the specificity of the interactions between GAGs and proteins results from the structure of these polysaccharides, an understanding of GAG structure is essential for developing a structure–activity relationship. Electrospray ionization (ESI) mass spectrometry (MS) is particularly promising for the analysis of oligosaccharides chemically or enzymatically generated by GAGs because of its relatively soft ionization capacity. Furthermore, on-line high-performance liquid chromatography (HPLC)-MS greatly enhances the characterization of complex mixtures of GAG-derived oligosaccharides, providing important structural information and affording their disaccharide composition. A detailed protocol for producing oligosaccharides from various GAGs, using controlled, specific enzymatic or chemical depolymerization, is presented, together with their HPLC separation, using volatile reversed-phase ion-pairing reagents and on-line ESI-MS structural identification. This analysis provides an oligosaccharide map together with sequence information from a reading frame beginning at the nonreducing end of the GAG chains. The preparation of oligosaccharides can be carried out in 10 h, with subsequent HPLC analysis in 1–2 h and HPLC-MS analysis taking another 2 h. PMID:20448545

Do pattern recognition skills transfer across sports? A preliminary analysis.

PubMed

Smeeton, Nicholas J; Ward, Paul; Williams, A Mark

2004-02-01

The ability to recognize patterns of play is fundamental to performance in team sports. While typically assumed to be domain-specific, pattern recognition skills may transfer from one sport to another if similarities exist in the perceptual features and their relations and/or the strategies used to encode and retrieve relevant information. A transfer paradigm was employed to compare skilled and less skilled soccer, field hockey and volleyball players' pattern recognition skills. Participants viewed structured and unstructured action sequences from each sport, half of which were randomly represented with clips not previously seen. The task was to identify previously viewed action sequences quickly and accurately. Transfer of pattern recognition skill was dependent on the participant's skill, sport practised, nature of the task and degree of structure. The skilled soccer and hockey players were quicker than the skilled volleyball players at recognizing structured soccer and hockey action sequences. Performance differences were not observed on the structured volleyball trials between the skilled soccer, field hockey and volleyball players. The skilled field hockey and soccer players were able to transfer perceptual information or strategies between their respective sports. The less skilled participants' results were less clear. Implications for domain-specific expertise, transfer and diversity across domains are discussed.

Porous hollow Co3O4 with rhombic dodecahedral structures for high-performance supercapacitors

NASA Astrophysics Data System (ADS)

Zhang, Yi-Zhou; Wang, Yang; Xie, Ye-Lei; Cheng, Tao; Lai, Wen-Yong; Pang, Huan; Huang, Wei

2014-11-01

Porous hollow Co3O4 with rhombic dodecahedral structures were prepared by the calcination of ZIF-67 ([Co(mim)2; mim = 2-methylimidazolate]) rhombic dodecahedral microcrystals. A supercapacitor was successfully constructed by adopting the resulting porous hollow Co3O4 rhombic dodecahedral structure as the electrode material, which showed a large specific capacitance of 1100 F g-1 and retained more than 95.1% of the specific capacitance after 6000 continuous charge-discharge cycles. The excellent capacitive properties and stability mark the porous hollow Co3O4 with the rhombic dodecahedral structure as one of the most promising electrode materials for high-performance supercapacitors.Porous hollow Co3O4 with rhombic dodecahedral structures were prepared by the calcination of ZIF-67 ([Co(mim)2; mim = 2-methylimidazolate]) rhombic dodecahedral microcrystals. A supercapacitor was successfully constructed by adopting the resulting porous hollow Co3O4 rhombic dodecahedral structure as the electrode material, which showed a large specific capacitance of 1100 F g-1 and retained more than 95.1% of the specific capacitance after 6000 continuous charge-discharge cycles. The excellent capacitive properties and stability mark the porous hollow Co3O4 with the rhombic dodecahedral structure as one of the most promising electrode materials for high-performance supercapacitors. Electronic supplementary information (ESI) available. See DOI: 10.1039/c4nr04782f

[Evaluation of an educational website on First Aid].

PubMed

Mori, Satomi; Whitaker, Iveth Yamaguchi; Marin, Heimar de Fátima

2013-08-01

The aim of this study was to evaluate the structure, quality of information and usability of a website on First Aid. The evaluation was performed by information technology (IT) and health care professionals and by students, using specific and validated instruments. The kappa method was used to evaluate the agreement of the answers, and Cronbach's α coefficient was used to assess the reliability of the instrument. There was no agreement (0.047) among the answers obtained from the IT professionals, indicating that the structure of the website must be reviewed. There was also no agreement in the evaluation by the health care professionals (-0.062); however, the overall positive scores suggest that the quality of the information of the website is adequate. The assessment of reliability of the instrument to evaluate the navigability rendered a value of α=0.974. Although improvement of the website structure is recommended, the quality of the information is good, and its use has contributed to the apprenticeship of students.

Estimating survival rates with time series of standing age‐structure data

USGS Publications Warehouse

Udevitz, Mark S.; Gogan, Peter J.

2012-01-01

It has long been recognized that age‐structure data contain useful information for assessing the status and dynamics of wildlife populations. For example, age‐specific survival rates can be estimated with just a single sample from the age distribution of a stable, stationary population. For a population that is not stable, age‐specific survival rates can be estimated using techniques such as inverse methods that combine time series of age‐structure data with other demographic data. However, estimation of survival rates using these methods typically requires numerical optimization, a relatively long time series of data, and smoothing or other constraints to provide useful estimates. We developed general models for possibly unstable populations that combine time series of age‐structure data with other demographic data to provide explicit maximum likelihood estimators of age‐specific survival rates with as few as two years of data. As an example, we applied these methods to estimate survival rates for female bison (Bison bison) in Yellowstone National Park, USA. This approach provides a simple tool for monitoring survival rates based on age‐structure data.

Structural mechanism underlying capsaicin binding and activation of TRPV1 ion channel

PubMed Central

Cheng, Wei; Yang, Wei; Yu, Peilin; Song, Zhenzhen; Yarov-Yarovoy, Vladimir; Zheng, Jie

2015-01-01

Capsaicin bestows spiciness by activating TRPV1 channel with exquisite potency and selectivity. Capsaicin-bound channel structure was previously resolved by cryo-EM at 4.2-to-4.5 Å resolution, however important details required for mechanistic understandings are unavailable: capsaicin was registered as a small electron density, reflecting neither its chemical structure nor specific ligand-channel interactions. We obtained the missing atomic-level details by iterative computation, which were confirmed by systematic site-specific functional tests. We observed that the bound capsaicin takes “tail-up, head-down” configurations. The vanillyl and amide groups form specific interactions to anchor its bound position, while the aliphatic tail may sample a range of conformations, making it invisible in cryo-EM images. Capsaicin stabilizes the open state by “pull-and-contact” interactions between the vanillyl group and the S4-S5 linker. Our study provided a structural mechanism for the agonistic function of capsaicin and its analogs, and demonstrated an effective approach to obtain atomic level information from cryo-EM structures. PMID:26053297

Some neuroanatomical insights to impulsive aggression in schizophrenia.

PubMed

Leclerc, Marcel P; Regenbogen, Christina; Hamilton, Roy H; Habel, Ute

2018-06-13

Patients with schizophrenia are at increased risk of engaging in violence towards others, compared to both the general population and most other patient groups. We have here explored the role of cortico-limbic impairments in schizophrenia, and have considered these brain regions specifically within the framework of a popular neuroanatomical model of impulsive aggression. In line with this model, evidence in patients with aggressive schizophrenia implicated structural deficits associated with impaired decision-making, emotional control and evaluation, and social information processing, especially in the orbitofrontal and ventrolateral prefrontal cortex. Given the pivotal role of the orbitofrontal and ventrolateral cortex in emotion control and evaluation, structural deficits may result in inappropriate use of socially relevant information and improper recognition of impulses that are in need for regulation. Furthermore, we have extended the original model and incorporated the striatum, important for the generation of aggressive impulses, as well as the hippocampus, a region critical for decision-making, into the model. Lastly, we discuss the question whether structural impairments are specific to aggressive schizophrenia. Our results suggest, that similar findings can be observed in other aggressive patient populations, making the observed impairments non-specific to aggressive schizophrenia. This points towards a shared condition, across pathologies, a potential common denominator being impulsive aggression. Copyright © 2018. Published by Elsevier B.V.

Revisiting the European sovereign bonds with a permutation-information-theory approach

NASA Astrophysics Data System (ADS)

Fernández Bariviera, Aurelio; Zunino, Luciano; Guercio, María Belén; Martinez, Lisana B.; Rosso, Osvaldo A.

2013-12-01

In this paper we study the evolution of the informational efficiency in its weak form for seventeen European sovereign bonds time series. We aim to assess the impact of two specific economic situations in the hypothetical random behavior of these time series: the establishment of a common currency and a wide and deep financial crisis. In order to evaluate the informational efficiency we use permutation quantifiers derived from information theory. Specifically, time series are ranked according to two metrics that measure the intrinsic structure of their correlations: permutation entropy and permutation statistical complexity. These measures provide the rectangular coordinates of the complexity-entropy causality plane; the planar location of the time series in this representation space reveals the degree of informational efficiency. According to our results, the currency union contributed to homogenize the stochastic characteristics of the time series and produced synchronization in the random behavior of them. Additionally, the 2008 financial crisis uncovered differences within the apparently homogeneous European sovereign markets and revealed country-specific characteristics that were partially hidden during the monetary union heyday.

RExPrimer: an integrated primer designing tool increases PCR effectiveness by avoiding 3' SNP-in-primer and mis-priming from structural variation

PubMed Central

2009-01-01

Background Polymerase chain reaction (PCR) is very useful in many areas of molecular biology research. It is commonly observed that PCR success is critically dependent on design of an effective primer pair. Current tools for primer design do not adequately address the problem of PCR failure due to mis-priming on target-related sequences and structural variations in the genome. Methods We have developed an integrated graphical web-based application for primer design, called RExPrimer, which was written in Python language. The software uses Primer3 as the primer designing core algorithm. Locally stored sequence information and genomic variant information were hosted on MySQLv5.0 and were incorporated into RExPrimer. Results RExPrimer provides many functionalities for improved PCR primer design. Several databases, namely annotated human SNP databases, insertion/deletion (indel) polymorphisms database, pseudogene database, and structural genomic variation databases were integrated into RExPrimer, enabling an effective without-leaving-the-website validation of the resulting primers. By incorporating these databases, the primers reported by RExPrimer avoid mis-priming to related sequences (e.g. pseudogene, segmental duplication) as well as possible PCR failure because of structural polymorphisms (SNP, indel, and copy number variation (CNV)). To prevent mismatching caused by unexpected SNPs in the designed primers, in particular the 3' end (SNP-in-Primer), several SNP databases covering the broad range of population-specific SNP information are utilized to report SNPs present in the primer sequences. Population-specific SNP information also helps customize primer design for a specific population. Furthermore, RExPrimer offers a graphical user-friendly interface through the use of scalable vector graphic image that intuitively presents resulting primers along with the corresponding gene structure. In this study, we demonstrated the program effectiveness in successfully generating primers for strong homologous sequences. Conclusion The improvements for primer design incorporated into RExPrimer were demonstrated to be effective in designing primers for challenging PCR experiments. Integration of SNP and structural variation databases allows for robust primer design for a variety of PCR applications, irrespective of the sequence complexity in the region of interest. This software is freely available at http://www4a.biotec.or.th/rexprimer. PMID:19958502

Mapping of Proteomic Composition on the Surfaces of Bacillus spores by Atomic Force Microscopy-based Immunolabeling

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

Plomp, M; Malkin, A J

2008-06-02

Atomic force microscopy provides a unique capability to image high-resolution architecture and structural dynamics of pathogens (e.g. viruses, bacteria and bacterial spores) at near molecular resolution in native conditions. Further development of atomic force microscopy in order to enable the correlation of pathogen protein surface structures with specific gene products is essential to understand the mechanisms of the pathogen life cycle. We have applied an AFM-based immunolabeling technique for the proteomic mapping of macromolecular structures through the visualization of the binding of antibodies, conjugated with nanogold particles, to specific epitopes on Bacillus spore surfaces. This information is generated while simultaneouslymore » acquiring the surface morphology of the pathogen. The immunospecificity of this labeling method was established through the utilization of specific polyclonal and monoclonal antibodies that target spore coat and exosporium epitopes of Bacillus atrophaeus and Bacillus anthracis spores.« less

Synthesizing information-update functions using off-line symbolic processing

NASA Technical Reports Server (NTRS)

Rosenschein, Stanley J.

1990-01-01

This paper explores the synthesis of programs that track dynamic conditions in their environment. An approach is proposed in which the designer specifies, in a declarative language, aspects of the environment in which the program will be embedded. This specification is then automatically compiled into a program that, when executed, updates internal data structures so as to maintain as an invariant a desired correspondence between internal data structures and states of the external environment. This approach retains much of the flexibility of declarative programming while guaranteeing a hard bound on the execution time of information-update functions.

An Ontology Based Approach to Information Security

NASA Astrophysics Data System (ADS)

Pereira, Teresa; Santos, Henrique

The semantically structure of knowledge, based on ontology approaches have been increasingly adopted by several expertise from diverse domains. Recently ontologies have been moved from the philosophical and metaphysics disciplines to be used in the construction of models to describe a specific theory of a domain. The development and the use of ontologies promote the creation of a unique standard to represent concepts within a specific knowledge domain. In the scope of information security systems the use of an ontology to formalize and represent the concepts of security information challenge the mechanisms and techniques currently used. This paper intends to present a conceptual implementation model of an ontology defined in the security domain. The model presented contains the semantic concepts based on the information security standard ISO/IEC_JTC1, and their relationships to other concepts, defined in a subset of the information security domain.

Generalized Information Architecture for Managing Requirements in IBM?s Rational DOORS(r) Application.

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

Aragon, Kathryn M.; Eaton, Shelley M.; McCornack, Marjorie Turner

When a requirements engineering effort fails to meet expectations, often times the requirements management tool is blamed. Working with numerous project teams at Sandia National Laboratories over the last fifteen years has shown us that the tool is rarely the culprit; usually it is the lack of a viable information architecture with well- designed processes to support requirements engineering. This document illustrates design concepts with rationale, as well as a proven information architecture to structure and manage information in support of requirements engineering activities for any size or type of project. This generalized information architecture is specific to IBM's Rationalmore » DOORS (Dynamic Object Oriented Requirements System) software application, which is the requirements management tool in Sandia's CEE (Common Engineering Environment). This generalized information architecture can be used as presented or as a foundation for designing a tailored information architecture for project-specific needs. It may also be tailored for another software tool. Version 1.0 4 November 201« less

Dynamic structure of stock communities: a comparative study between stock returns and turnover rates

NASA Astrophysics Data System (ADS)

Su, Li-Ling; Jiang, Xiong-Fei; Li, Sai-Ping; Zhong, Li-Xin; Ren, Fei

2017-07-01

The detection of community structure in stock market is of theoretical and practical significance for the study of financial dynamics and portfolio risk estimation. We here study the community structures in Chinese stock markets from the aspects of both price returns and turnover rates, by using a combination of the PMFG and infomap methods based on a distance matrix. An empirical study using the overall data set shows that for both returns and turnover rates the largest communities are composed of specific industrial or conceptional sectors and the correlation inside a sector is generally larger than the correlation between different sectors. However, the community structure for turnover rates is more complex than that for returns, which indicates that the interactions between stocks revealed by turnover rates may contain more information. This conclusion is further confirmed by the analysis of the changes in the dynamics of community structures over five sub-periods. Sectors like banks, real estate, health care and New Shanghai take turns to comprise a few of the largest communities in different sub-periods, and more interestingly several specific sectors appear in the communities with different rank orders for returns and turnover rates even in the same sub-period. To better understand their differences, a comparison between the evolution of the returns and turnover rates of the stocks from these sectors is conducted. We find that stock prices only had large changes around important events while turnover rates surged after each of these events relevant to specific sectors, which shows strong evidence that the turnover rates are more susceptible to exogenous shocks than returns and its measurement for community detection may contain more useful information about market structure.

Integration of Department of Defense and State Department Efforts to Continue the Global Pursuit of Violent Extremist Organizations

DTIC Science & Technology

2012-12-14

structure to take on intelligence collection and fusion, the State Department has historically not been a collector of intelligence as a matter of...Government, specifically the CIA and NSA, but their mission, structure and capability will not be addressed in this thesis. It is understood, though...provided firsthand accounts of aspects of DoD and State Department coordination or provided the necessary information about current structure and

FUNCTIONAL NETWORK ARCHITECTURE OF READING-RELATED REGIONS ACROSS DEVELOPMENT

PubMed Central

Vogel, Alecia C.; Church, Jessica A.; Power, Jonathan D.; Miezin, Fran M.; Petersen, Steven E.; Schlaggar, Bradley L.

2013-01-01

Reading requires coordinated neural processing across a large number of brain regions. Studying relationships between reading-related regions informs the specificity of information processing performed in each region. Here, regions of interest were defined from a meta-analysis of reading studies, including a developmental study. Relationships between regions were defined as temporal correlations in spontaneous fMRI signal; i.e., resting state functional connectivity MRI (RSFC). Graph theory based network analysis defined the community structure of the “reading-related” regions. Regions sorted into previously defined communities, such as the fronto-parietal and cingulo-opercular control networks, and the default mode network. This structure was similar in children, and no apparent “reading” community was defined in any age group. These results argue against regions, or sets of regions, being specific or preferential for reading, instead indicating that regions used in reading are also used in a number of other tasks. PMID:23506969

A discrete control model of PLANT

NASA Technical Reports Server (NTRS)

Mitchell, C. M.

1985-01-01

A model of the PLANT system using the discrete control modeling techniques developed by Miller is described. Discrete control models attempt to represent in a mathematical form how a human operator might decompose a complex system into simpler parts and how the control actions and system configuration are coordinated so that acceptable overall system performance is achieved. Basic questions include knowledge representation, information flow, and decision making in complex systems. The structure of the model is a general hierarchical/heterarchical scheme which structurally accounts for coordination and dynamic focus of attention. Mathematically, the discrete control model is defined in terms of a network of finite state systems. Specifically, the discrete control model accounts for how specific control actions are selected from information about the controlled system, the environment, and the context of the situation. The objective is to provide a plausible and empirically testable accounting and, if possible, explanation of control behavior.

Learning, memory, and the role of neural network architecture.

PubMed

Hermundstad, Ann M; Brown, Kevin S; Bassett, Danielle S; Carlson, Jean M

2011-06-01

The performance of information processing systems, from artificial neural networks to natural neuronal ensembles, depends heavily on the underlying system architecture. In this study, we compare the performance of parallel and layered network architectures during sequential tasks that require both acquisition and retention of information, thereby identifying tradeoffs between learning and memory processes. During the task of supervised, sequential function approximation, networks produce and adapt representations of external information. Performance is evaluated by statistically analyzing the error in these representations while varying the initial network state, the structure of the external information, and the time given to learn the information. We link performance to complexity in network architecture by characterizing local error landscape curvature. We find that variations in error landscape structure give rise to tradeoffs in performance; these include the ability of the network to maximize accuracy versus minimize inaccuracy and produce specific versus generalizable representations of information. Parallel networks generate smooth error landscapes with deep, narrow minima, enabling them to find highly specific representations given sufficient time. While accurate, however, these representations are difficult to generalize. In contrast, layered networks generate rough error landscapes with a variety of local minima, allowing them to quickly find coarse representations. Although less accurate, these representations are easily adaptable. The presence of measurable performance tradeoffs in both layered and parallel networks has implications for understanding the behavior of a wide variety of natural and artificial learning systems.

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.

Automatic prediction of facial trait judgments: appearance vs. structural models.

PubMed

Rojas, Mario; Masip, David; Todorov, Alexander; Vitria, Jordi

2011-01-01

Evaluating other individuals with respect to personality characteristics plays a crucial role in human relations and it is the focus of attention for research in diverse fields such as psychology and interactive computer systems. In psychology, face perception has been recognized as a key component of this evaluation system. Multiple studies suggest that observers use face information to infer personality characteristics. Interactive computer systems are trying to take advantage of these findings and apply them to increase the natural aspect of interaction and to improve the performance of interactive computer systems. Here, we experimentally test whether the automatic prediction of facial trait judgments (e.g. dominance) can be made by using the full appearance information of the face and whether a reduced representation of its structure is sufficient. We evaluate two separate approaches: a holistic representation model using the facial appearance information and a structural model constructed from the relations among facial salient points. State of the art machine learning methods are applied to a) derive a facial trait judgment model from training data and b) predict a facial trait value for any face. Furthermore, we address the issue of whether there are specific structural relations among facial points that predict perception of facial traits. Experimental results over a set of labeled data (9 different trait evaluations) and classification rules (4 rules) suggest that a) prediction of perception of facial traits is learnable by both holistic and structural approaches; b) the most reliable prediction of facial trait judgments is obtained by certain type of holistic descriptions of the face appearance; and c) for some traits such as attractiveness and extroversion, there are relationships between specific structural features and social perceptions.

New type of standalone gas sensors based on dye, thin films, and subwavelength structures

NASA Astrophysics Data System (ADS)

Schnieper, Marc; Davoine, Laurent; Holgado, Miguel; Casquel del Campo, Rafael; Barranco, Angel

2009-02-01

A new gas sensor was developed to enable visual indication of a contamination by specific gases like NO2, SO2, UV, etc. The sensor works with a combination of subwavelength structures and specific active dye thin film layers. The objective is to use the optical changes of the dye thin films after exposure and a custom designed subwavelength structure, a suited combination of both will produce a strong color change. The indication should be visible for the human eye. To enhance this visual aspect, we used a reference sensor sealed into a non-contaminated atmosphere. This work was realized within the PHODYE STREP Project, a collaboration of the 6th Framework Program Priority Information Society Technologies.

Synthetic genetic polymers capable of heredity and evolution.

PubMed

Pinheiro, Vitor B; Taylor, Alexander I; Cozens, Christopher; Abramov, Mikhail; Renders, Marleen; Zhang, Su; Chaput, John C; Wengel, Jesper; Peak-Chew, Sew-Yeu; McLaughlin, Stephen H; Herdewijn, Piet; Holliger, Philipp

2012-04-20

Genetic information storage and processing rely on just two polymers, DNA and RNA, yet whether their role reflects evolutionary history or fundamental functional constraints is currently unknown. With the use of polymerase evolution and design, we show that genetic information can be stored in and recovered from six alternative genetic polymers based on simple nucleic acid architectures not found in nature [xeno-nucleic acids (XNAs)]. We also select XNA aptamers, which bind their targets with high affinity and specificity, demonstrating that beyond heredity, specific XNAs have the capacity for Darwinian evolution and folding into defined structures. Thus, heredity and evolution, two hallmarks of life, are not limited to DNA and RNA but are likely to be emergent properties of polymers capable of information storage.

Capturing structured, pulmonary disease-specific data elements in electronic health records.

PubMed

Gronkiewicz, Cynthia; Diamond, Edward J; French, Kim D; Christodouleas, John; Gabriel, Peter E

2015-04-01

Electronic health records (EHRs) have the potential to improve health-care quality by allowing providers to make better decisions at the point of care based on electronically aggregated data and by facilitating clinical research. These goals are easier to achieve when key, disease-specific clinical information is documented as structured data elements (SDEs) that computers can understand and process, rather than as free-text/natural-language narrative. This article reviews the benefits of capturing disease-specific SDEs. It highlights several design and implementation considerations, including the impact on efficiency and expressivity of clinical documentation and the importance of adhering to data standards when available. Pulmonary disease-specific examples of collection instruments are provided from two commonly used commercial EHRs. Future developments that can leverage SDEs to improve clinical quality and research are discussed.

[Construction of chemical information database based on optical structure recognition technique].

PubMed

Lv, C Y; Li, M N; Zhang, L R; Liu, Z M

2018-04-18

To create a protocol that could be used to construct chemical information database from scientific literature quickly and automatically. Scientific literature, patents and technical reports from different chemical disciplines were collected and stored in PDF format as fundamental datasets. Chemical structures were transformed from published documents and images to machine-readable data by using the name conversion technology and optical structure recognition tool CLiDE. In the process of molecular structure information extraction, Markush structures were enumerated into well-defined monomer molecules by means of QueryTools in molecule editor ChemDraw. Document management software EndNote X8 was applied to acquire bibliographical references involving title, author, journal and year of publication. Text mining toolkit ChemDataExtractor was adopted to retrieve information that could be used to populate structured chemical database from figures, tables, and textual paragraphs. After this step, detailed manual revision and annotation were conducted in order to ensure the accuracy and completeness of the data. In addition to the literature data, computing simulation platform Pipeline Pilot 7.5 was utilized to calculate the physical and chemical properties and predict molecular attributes. Furthermore, open database ChEMBL was linked to fetch known bioactivities, such as indications and targets. After information extraction and data expansion, five separate metadata files were generated, including molecular structure data file, molecular information, bibliographical references, predictable attributes and known bioactivities. Canonical simplified molecular input line entry specification as primary key, metadata files were associated through common key nodes including molecular number and PDF number to construct an integrated chemical information database. A reasonable construction protocol of chemical information database was created successfully. A total of 174 research articles and 25 reviews published in Marine Drugs from January 2015 to June 2016 collected as essential data source, and an elementary marine natural product database named PKU-MNPD was built in accordance with this protocol, which contained 3 262 molecules and 19 821 records. This data aggregation protocol is of great help for the chemical information database construction in accuracy, comprehensiveness and efficiency based on original documents. The structured chemical information database can facilitate the access to medical intelligence and accelerate the transformation of scientific research achievements.

Molecular dynamics simulations: advances and applications

PubMed Central

Hospital, Adam; Goñi, Josep Ramon; Orozco, Modesto; Gelpí, Josep L

2015-01-01

Molecular dynamics simulations have evolved into a mature technique that can be used effectively to understand macromolecular structure-to-function relationships. Present simulation times are close to biologically relevant ones. Information gathered about the dynamic properties of macromolecules is rich enough to shift the usual paradigm of structural bioinformatics from studying single structures to analyze conformational ensembles. Here, we describe the foundations of molecular dynamics and the improvements made in the direction of getting such ensemble. Specific application of the technique to three main issues (allosteric regulation, docking, and structure refinement) is discussed. PMID:26604800

Coordinating UAV information for executing national security-oriented collaboration

NASA Astrophysics Data System (ADS)

Isenor, Anthony W.; Allard, Yannick; Lapinski, Anna-Liesa S.; Demers, Hugues; Radulescu, Dan

2014-10-01

Unmanned Aerial Vehicles (UAVs) are being used by numerous nations for defence-related missions. In some cases, the UAV is considered a cost-effective means to acquire data such as imagery over a location or object. Considering Canada's geographic expanse, UAVs are also being suggested as a potential platform for use in surveillance of remote areas, such as northern Canada. However, such activities are typically associated with security as opposed to defence. The use of a defence platform for security activities introduces the issue of information exchange between the defence and security communities and their software applications. This paper explores the flow of information from the system used by the UAVs employed by the Royal Canadian Navy. Multiple computers are setup, each with the information system used by the UAVs, including appropriate communication between the systems. Simulated data that may be expected from a typical maritime UAV mission is then fed into the information system. The information structures common to the Canadian security community are then used to store and transfer the simulated data. The resulting data flow from the defence-oriented UAV system to the security-oriented information structure is then displayed using an open source geospatial application. Use of the information structures and applications relevant to the security community avoids the distribution restrictions often associated with defence-specific applications.

Molecular graph convolutions: moving beyond fingerprints

PubMed Central

Kearnes, Steven; McCloskey, Kevin; Berndl, Marc; Pande, Vijay; Riley, Patrick

2016-01-01

Molecular “fingerprints” encoding structural information are the workhorse of cheminformatics and machine learning in drug discovery applications. However, fingerprint representations necessarily emphasize particular aspects of the molecular structure while ignoring others, rather than allowing the model to make data-driven decisions. We describe molecular graph convolutions, a machine learning architecture for learning from undirected graphs, specifically small molecules. Graph convolutions use a simple encoding of the molecular graph—atoms, bonds, distances, etc.—which allows the model to take greater advantage of information in the graph structure. Although graph convolutions do not outperform all fingerprint-based methods, they (along with other graph-based methods) represent a new paradigm in ligand-based virtual screening with exciting opportunities for future improvement. PMID:27558503

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.

The NIFSTD and BIRNLex Vocabularies: Building Comprehensive Ontologies for Neuroscience

PubMed Central

Bug, William J.; Ascoli, Giorgio A.; Grethe, Jeffrey S.; Gupta, Amarnath; Fennema-Notestine, Christine; Laird, Angela R.; Larson, Stephen D.; Rubin, Daniel; Shepherd, Gordon M.; Turner, Jessica A.; Martone, Maryann E.

2009-01-01

A critical component of the Neuroscience Information Framework (NIF) project is a consistent, flexible terminology for describing and retrieving neuroscience-relevant resources. Although the original NIF specification called for a loosely structured controlled vocabulary for describing neuroscience resources, as the NIF system evolved, the requirement for a formally structured ontology for neuroscience with sufficient granularity to describe and access a diverse collection of information became obvious. This requirement led to the NIF standardized (NIFSTD) ontology, a comprehensive collection of common neuroscience domain terminologies woven into an ontologically consistent, unified representation of the biomedical domains typically used to describe neuroscience data (e.g., anatomy, cell types, techniques), as well as digital resources (tools, databases) being created throughout the neuroscience community. NIFSTD builds upon a structure established by the BIRNLex, a lexicon of concepts covering clinical neuroimaging research developed by the Biomedical Informatics Research Network (BIRN) project. Each distinct domain module is represented using the Web Ontology Language (OWL). As much as has been practical, NIFSTD reuses existing community ontologies that cover the required biomedical domains, building the more specific concepts required to annotate NIF resources. By following this principle, an extensive vocabulary was assembled in a relatively short period of time for NIF information annotation, organization, and retrieval, in a form that promotes easy extension and modification. We report here on the structure of the NIFSTD, and its predecessor BIRNLex, the principles followed in its construction and provide examples of its use within NIF. PMID:18975148

The NIFSTD and BIRNLex vocabularies: building comprehensive ontologies for neuroscience.

PubMed

Bug, William J; Ascoli, Giorgio A; Grethe, Jeffrey S; Gupta, Amarnath; Fennema-Notestine, Christine; Laird, Angela R; Larson, Stephen D; Rubin, Daniel; Shepherd, Gordon M; Turner, Jessica A; Martone, Maryann E

2008-09-01

A critical component of the Neuroscience Information Framework (NIF) project is a consistent, flexible terminology for describing and retrieving neuroscience-relevant resources. Although the original NIF specification called for a loosely structured controlled vocabulary for describing neuroscience resources, as the NIF system evolved, the requirement for a formally structured ontology for neuroscience with sufficient granularity to describe and access a diverse collection of information became obvious. This requirement led to the NIF standardized (NIFSTD) ontology, a comprehensive collection of common neuroscience domain terminologies woven into an ontologically consistent, unified representation of the biomedical domains typically used to describe neuroscience data (e.g., anatomy, cell types, techniques), as well as digital resources (tools, databases) being created throughout the neuroscience community. NIFSTD builds upon a structure established by the BIRNLex, a lexicon of concepts covering clinical neuroimaging research developed by the Biomedical Informatics Research Network (BIRN) project. Each distinct domain module is represented using the Web Ontology Language (OWL). As much as has been practical, NIFSTD reuses existing community ontologies that cover the required biomedical domains, building the more specific concepts required to annotate NIF resources. By following this principle, an extensive vocabulary was assembled in a relatively short period of time for NIF information annotation, organization, and retrieval, in a form that promotes easy extension and modification. We report here on the structure of the NIFSTD, and its predecessor BIRNLex, the principles followed in its construction and provide examples of its use within NIF.

Internationally educated nurses' descriptions of their access to structural empowerment while working in another country's health care context.

PubMed

Eriksson, Elisabet; Engström, Maria

2018-03-12

To examine internationally educated nurses' experiences of empowerment structures using Kanter's theory of structural empowerment. There has been an increase in the number of nurses working in other countries worldwide and concerns have been raised regarding their working conditions. Semi-structured interviews were conducted with a purposive sample of 11 internationally educated nurses. Directed content analysis was used to analyse the data and Kanter's theory of empowerment was used as a framework. Access to information was generally good. Access to support for their relationship with their managers varied. Regarding access to resources, nurses unfamiliar with clinical leadership found team leadership challenging. Access to in-house learning opportunities were reported as good. Access to informal power was more common than access to formal power. The findings support Kanter's theory and demonstrate that internationally experienced nurses encountered varying degrees of access to empowering structures. Access to information and formal power was more general and related to the unit. Access to resources, support, opportunities and informal power were related to both the unit and the informants' specific situation as IENs. Managers need to support IENs when having a team leadership role, facilitate encounters between IENs and ordinary staff, and establishing mentorship for IENs. © 2018 The Authors. Journal of Nursing Management Published by John Wiley & Sons Ltd.

The Protein Information Management System (PiMS): a generic tool for any structural biology research laboratory

PubMed Central

Morris, Chris; Pajon, Anne; Griffiths, Susanne L.; Daniel, Ed; Savitsky, Marc; Lin, Bill; Diprose, Jonathan M.; Wilter da Silva, Alan; Pilicheva, Katya; Troshin, Peter; van Niekerk, Johannes; Isaacs, Neil; Naismith, James; Nave, Colin; Blake, Richard; Wilson, Keith S.; Stuart, David I.; Henrick, Kim; Esnouf, Robert M.

2011-01-01

The techniques used in protein production and structural biology have been developing rapidly, but techniques for recording the laboratory information produced have not kept pace. One approach is the development of laboratory information-management systems (LIMS), which typically use a relational database schema to model and store results from a laboratory workflow. The underlying philosophy and implementation of the Protein Information Management System (PiMS), a LIMS development specifically targeted at the flexible and unpredictable workflows of protein-production research laboratories of all scales, is described. PiMS is a web-based Java application that uses either Postgres or Oracle as the underlying relational database-management system. PiMS is available under a free licence to all academic laboratories either for local installation or for use as a managed service. PMID:21460443

The Protein Information Management System (PiMS): a generic tool for any structural biology research laboratory.

PubMed

Morris, Chris; Pajon, Anne; Griffiths, Susanne L; Daniel, Ed; Savitsky, Marc; Lin, Bill; Diprose, Jonathan M; da Silva, Alan Wilter; Pilicheva, Katya; Troshin, Peter; van Niekerk, Johannes; Isaacs, Neil; Naismith, James; Nave, Colin; Blake, Richard; Wilson, Keith S; Stuart, David I; Henrick, Kim; Esnouf, Robert M

2011-04-01

The techniques used in protein production and structural biology have been developing rapidly, but techniques for recording the laboratory information produced have not kept pace. One approach is the development of laboratory information-management systems (LIMS), which typically use a relational database schema to model and store results from a laboratory workflow. The underlying philosophy and implementation of the Protein Information Management System (PiMS), a LIMS development specifically targeted at the flexible and unpredictable workflows of protein-production research laboratories of all scales, is described. PiMS is a web-based Java application that uses either Postgres or Oracle as the underlying relational database-management system. PiMS is available under a free licence to all academic laboratories either for local installation or for use as a managed service.

To improve the flame resistance of spandex elastic elastomeric fiber

NASA Technical Reports Server (NTRS)

1972-01-01

Strength characteristics of fibers were improved to pass the 70% oxygen/30% nitrogen specification. Spinning techniques and information about incorporating these fibers in fabric structures using wrapping materials of Beta Fiberglas, Nomex, and PBI were developed.

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

Tactical Unit Data and Decision Requirements for Urban Operations

DTIC Science & Technology

2008-10-01

maneuverability, sensor optimization, weapon effects, terrain), and develop rich but lightweight information structures and architecture . Specifically, the goal...tion structure and systemic architecture that enable sharing common data in near real-time, and mission planning and analysis software for U-BE...Building Function Verify mosque and identify possi- ble schools or meeting places Identify types of cinema (stage/theatre) or other similar nearby

Hybrid knowledge systems

NASA Technical Reports Server (NTRS)

Subrahmanian, V. S.

1994-01-01

An architecture called hybrid knowledge system (HKS) is described that can be used to interoperate between a specification of the control laws describing a physical system, a collection of databases, knowledge bases and/or other data structures reflecting information about the world in which the physical system controlled resides, observations (e.g. sensor information) from the external world, and actions that must be taken in response to external observations.

Visual Analysis of Social Networks in a Counter-Insurgency Context

DTIC Science & Technology

2011-06-01

Batagelj and Mrvar 2003] specifically focus on the analysis and visualisation of extremely large networks. Moreover, on top of these data about the...and behavioral components of a complex conflict ecosystem, SpringSim: 23. Batagelj , V. & Mrvar , A., (2003), Pajek - analysis and visualisation of...information regarding network patterns and structures, no spatial information is usually encoded. This is despite the fact that already Wellman [ 1996

Text Mining for Protein Docking

PubMed Central

Badal, Varsha D.; Kundrotas, Petras J.; Vakser, Ilya A.

2015-01-01

The rapidly growing amount of publicly available information from biomedical research is readily accessible on the Internet, providing a powerful resource for predictive biomolecular modeling. The accumulated data on experimentally determined structures transformed structure prediction of proteins and protein complexes. Instead of exploring the enormous search space, predictive tools can simply proceed to the solution based on similarity to the existing, previously determined structures. A similar major paradigm shift is emerging due to the rapidly expanding amount of information, other than experimentally determined structures, which still can be used as constraints in biomolecular structure prediction. Automated text mining has been widely used in recreating protein interaction networks, as well as in detecting small ligand binding sites on protein structures. Combining and expanding these two well-developed areas of research, we applied the text mining to structural modeling of protein-protein complexes (protein docking). Protein docking can be significantly improved when constraints on the docking mode are available. We developed a procedure that retrieves published abstracts on a specific protein-protein interaction and extracts information relevant to docking. The procedure was assessed on protein complexes from Dockground (http://dockground.compbio.ku.edu). The results show that correct information on binding residues can be extracted for about half of the complexes. The amount of irrelevant information was reduced by conceptual analysis of a subset of the retrieved abstracts, based on the bag-of-words (features) approach. Support Vector Machine models were trained and validated on the subset. The remaining abstracts were filtered by the best-performing models, which decreased the irrelevant information for ~ 25% complexes in the dataset. The extracted constraints were incorporated in the docking protocol and tested on the Dockground unbound benchmark set, significantly increasing the docking success rate. PMID:26650466

A deep learning framework for modeling structural features of RNA-binding protein targets

PubMed Central

Zhang, Sai; Zhou, Jingtian; Hu, Hailin; Gong, Haipeng; Chen, Ligong; Cheng, Chao; Zeng, Jianyang

2016-01-01

RNA-binding proteins (RBPs) play important roles in the post-transcriptional control of RNAs. Identifying RBP binding sites and characterizing RBP binding preferences are key steps toward understanding the basic mechanisms of the post-transcriptional gene regulation. Though numerous computational methods have been developed for modeling RBP binding preferences, discovering a complete structural representation of the RBP targets by integrating their available structural features in all three dimensions is still a challenging task. In this paper, we develop a general and flexible deep learning framework for modeling structural binding preferences and predicting binding sites of RBPs, which takes (predicted) RNA tertiary structural information into account for the first time. Our framework constructs a unified representation that characterizes the structural specificities of RBP targets in all three dimensions, which can be further used to predict novel candidate binding sites and discover potential binding motifs. Through testing on the real CLIP-seq datasets, we have demonstrated that our deep learning framework can automatically extract effective hidden structural features from the encoded raw sequence and structural profiles, and predict accurate RBP binding sites. In addition, we have conducted the first study to show that integrating the additional RNA tertiary structural features can improve the model performance in predicting RBP binding sites, especially for the polypyrimidine tract-binding protein (PTB), which also provides a new evidence to support the view that RBPs may own specific tertiary structural binding preferences. In particular, the tests on the internal ribosome entry site (IRES) segments yield satisfiable results with experimental support from the literature and further demonstrate the necessity of incorporating RNA tertiary structural information into the prediction model. The source code of our approach can be found in https://github.com/thucombio/deepnet-rbp. PMID:26467480

In silico local structure approach: a case study on outer membrane proteins.

PubMed

Martin, Juliette; de Brevern, Alexandre G; Camproux, Anne-Claude

2008-04-01

The detection of Outer Membrane Proteins (OMP) in whole genomes is an actual question, their sequence characteristics have thus been intensively studied. This class of protein displays a common beta-barrel architecture, formed by adjacent antiparallel strands. However, due to the lack of available structures, few structural studies have been made on this class of proteins. Here we propose a novel OMP local structure investigation, based on a structural alphabet approach, i.e., the decomposition of 3D structures using a library of four-residue protein fragments. The optimal decomposition of structures using hidden Markov model results in a specific structural alphabet of 20 fragments, six of them dedicated to the decomposition of beta-strands. This optimal alphabet, called SA20-OMP, is analyzed in details, in terms of local structures and transitions between fragments. It highlights a particular and strong organization of beta-strands as series of regular canonical structural fragments. The comparison with alphabets learned on globular structures indicates that the internal organization of OMP structures is more constrained than in globular structures. The analysis of OMP structures using SA20-OMP reveals some recurrent structural patterns. The preferred location of fragments in the distinct regions of the membrane is investigated. The study of pairwise specificity of fragments reveals that some contacts between structural fragments in beta-sheets are clearly favored whereas others are avoided. This contact specificity is stronger in OMP than in globular structures. Moreover, SA20-OMP also captured sequential information. This can be integrated in a scoring function for structural model ranking with very promising results. (c) 2007 Wiley-Liss, Inc.

Function-specific and Enhanced Brain Structural Connectivity Mapping via Joint Modeling of Diffusion and Functional MRI.

PubMed

Chu, Shu-Hsien; Parhi, Keshab K; Lenglet, Christophe

2018-03-16

A joint structural-functional brain network model is presented, which enables the discovery of function-specific brain circuits, and recovers structural connections that are under-estimated by diffusion MRI (dMRI). Incorporating information from functional MRI (fMRI) into diffusion MRI to estimate brain circuits is a challenging task. Usually, seed regions for tractography are selected from fMRI activation maps to extract the white matter pathways of interest. The proposed method jointly analyzes whole brain dMRI and fMRI data, allowing the estimation of complete function-specific structural networks instead of interactively investigating the connectivity of individual cortical/sub-cortical areas. Additionally, tractography techniques are prone to limitations, which can result in erroneous pathways. The proposed framework explicitly models the interactions between structural and functional connectivity measures thereby improving anatomical circuit estimation. Results on Human Connectome Project (HCP) data demonstrate the benefits of the approach by successfully identifying function-specific anatomical circuits, such as the language and resting-state networks. In contrast to correlation-based or independent component analysis (ICA) functional connectivity mapping, detailed anatomical connectivity patterns are revealed for each functional module. Results on a phantom (Fibercup) also indicate improvements in structural connectivity mapping by rejecting false-positive connections with insufficient support from fMRI, and enhancing under-estimated connectivity with strong functional correlation.

System requirements specification for SMART structures mode

NASA Technical Reports Server (NTRS)

1992-01-01

Specified here are the functional and informational requirements for software modules which address the geometric and data modeling needs of the aerospace structural engineer. The modules are to be included as part of the Solid Modeling Aerospace Research Tool (SMART) package developed for the Vehicle Analysis Branch (VAB) at the NASA Langley Research Center (LaRC). The purpose is to precisely state what the SMART Structures modules will do, without consideration of how it will be done. Each requirement is numbered for reference in development and testing.

Structural insights into 5‧ flap DNA unwinding and incision by the human FAN1 dimer

NASA Astrophysics Data System (ADS)

Zhao, Qi; Xue, Xiaoyu; Longerich, Simonne; Sung, Patrick; Xiong, Yong

2014-12-01

Human FANCD2-associated nuclease 1 (FAN1) is a DNA structure-specific nuclease involved in the processing of DNA interstrand crosslinks (ICLs). FAN1 maintains genomic stability and prevents tissue decline in multiple organs, yet it confers ICL-induced anti-cancer drug resistance in several cancer subtypes. Here we report three crystal structures of human FAN1 in complex with a 5‧ flap DNA substrate, showing that two FAN1 molecules form a head-to-tail dimer to locate the lesion, orient the DNA and unwind a 5‧ flap for subsequent incision. Biochemical experiments further validate our model for FAN1 action, as structure-informed mutations that disrupt protein dimerization, substrate orientation or flap unwinding impair the structure-specific nuclease activity. Our work elucidates essential aspects of FAN1-DNA lesion recognition and a unique mechanism of incision. These structural insights shed light on the cellular mechanisms underlying organ degeneration protection and cancer drug resistance mediated by FAN1.

Wireless structural monitoring for homeland security applications

NASA Astrophysics Data System (ADS)

Kiremidjian, Garo K.; Kiremidjian, Anne S.; Lynch, Jerome P.

2004-07-01

This paper addresses the development of a robust, low-cost, low power, and high performance autonomous wireless monitoring system for civil assets such as large facilities, new construction, bridges, dams, commercial buildings, etc. The role of the system is to identify the onset, development, location and severity of structural vulnerability and damage. The proposed system represents an enabling infrastructure for addressing structural vulnerabilities specifically associated with homeland security. The system concept is based on dense networks of "intelligent" wireless sensing units. The fundamental properties of a wireless sensing unit include: (a) interfaces to multiple sensors for measuring structural and environmental data (such as acceleration, displacements, pressure, strain, material degradation, temperature, gas agents, biological agents, humidity, corrosion, etc.); (b) processing of sensor data with embedded algorithms for assessing damage and environmental conditions; (c) peer-to-peer wireless communications for information exchange among units(thus enabling joint "intelligent" processing coordination) and storage of data and processed information in servers for information fusion; (d) ultra low power operation; (e) cost-effectiveness and compact size through the use of low-cost small-size off-the-shelf components. An integral component of the overall system concept is a decision support environment for interpretation and dissemination of information to various decision makers.

Murine Leukemia Virus Reverse Transcriptase: Structural Comparison with HIV-1 Reverse Transcriptase

PubMed Central

Coté, Marie L.; Roth, Monica J.

2008-01-01

Recent X-ray crystal structure determinations of Moloney murine leukemia virus reverse transcriptase (MoMLV RT) have allowed for more accurate structure/function comparisons to HIV-1 RT than were formerly possible. Previous biochemical studies of MoMLV RT in conjunction with knowledge of sequence homologies to HIV-1 RT and overall fold similarities to RTs in general, provided a foundation upon which to build. In addition, numerous crystal structures of the MoMLV RT fingers/palm subdomain had also shed light on one of the critical functions of the enzyme, specifically polymerization. Now in the advent of new structural information, more intricate examination of MoMLV RT in its entirety can be realized, and thus the comparisons with HIV-1 RT may be more critically elucidated. Here, we will review the similarities and differences between MoMLV RT and HIV-1 RT via structural analysis, and propose working models for the MoMLV RT based upon that information. PMID:18294720

Homology modeling of parasite histone deacetylases to guide the structure-based design of selective inhibitors.

PubMed

Melesina, Jelena; Robaa, Dina; Pierce, Raymond J; Romier, Christophe; Sippl, Wolfgang

2015-11-01

Histone deacetylases (HDACs) are promising epigenetic targets for the treatment of various diseases, including cancer and neurodegenerative disorders. There is evidence that they can also be addressed to treat parasitic infections. Recently, the first X-ray structure of a parasite HDAC was published, Schistosoma mansoni HDAC8, giving structural insights into its inhibition. However, most of the targets from parasites of interest still lack this structural information. Therefore, we prepared homology models of relevant parasitic HDACs and compared them to human and S. mansoni HDACs. The information about known S. mansoni HDAC8 inhibitors and compounds that affect the growth of Trypanosoma, Leishmania and Plasmodium species was used to validate the models by docking and molecular dynamics studies. Our results provide analysis of structural features of parasitic HDACs and should be helpful for selecting promising candidates for biological testing and for structure-based optimisation of parasite-specific inhibitors. Copyright © 2015 Elsevier Inc. All rights reserved.

Design and application of a tool for structuring, capitalizing and making more accessible information and lessons learned from accidents involving machinery.

PubMed

Sadeghi, Samira; Sadeghi, Leyla; Tricot, Nicolas; Mathieu, Luc

2017-12-01

Accident reports are published in order to communicate the information and lessons learned from accidents. An efficient accident recording and analysis system is a necessary step towards improvement of safety. However, currently there is a shortage of efficient tools to support such recording and analysis. In this study we introduce a flexible and customizable tool that allows structuring and analysis of this information. This tool has been implemented under TEEXMA®. We named our prototype TEEXMA®SAFETY. This tool provides an information management system to facilitate data collection, organization, query, analysis and reporting of accidents. A predefined information retrieval module provides ready access to data which allows the user to quickly identify the possible hazards for specific machines and provides information on the source of hazards. The main target audience for this tool includes safety personnel, accident reporters and designers. The proposed data model has been developed by analyzing different accident reports.

Structural polymorphism at LCR and its role in beta-globin gene regulation.

PubMed

Kukreti, Shrikant; Kaur, Harpreet; Kaushik, Mahima; Bansal, Aparna; Saxena, Sarika; Kaushik, Shikha; Kukreti, Ritushree

2010-09-01

Information on the secondary structures and conformational manifestations of eukaryotic DNA and their biological significance with reference to gene regulation and expression is limited. The human beta-globin gene Locus Control Region (LCR), a dominant regulator of globin gene expression, is a contiguous piece of DNA with five tissue-specific DNase I-hypersensitive sites (HSs). Since these HSs have a high density of transcription factor binding sites, structural interdependencies between HSs and different promoters may directly or indirectly regulate LCR functions. Mutations and SNPs may stabilize or destabilize the local secondary structures, affecting the gene expression by changes in the protein-DNA recognition patterns. Various palindromic or quasi-palindromic segments within LCR, could cause structural polymorphism and geometrical switching of DNA. This emphasizes the importance of understanding of the sequence-dependent variations of the DNA structure. Such structural motifs might act as regulatory elements. The local conformational variability of a DNA segment or action of a DNA specific protein is key to create and maintain active chromatin domains and affect transcription of various tissue specific beta-globin genes. We, summarize here the current status of beta-globin LCR structure and function. Further structural studies at molecular level and functional genomics might solve the regulatory puzzles that control the beta-globin gene locus. Copyright (c) 2010 Elsevier Masson SAS. All rights reserved.

Analysis of genetic population structure in Acacia caven (Leguminosae, Mimosoideae), comparing one exploratory and two Bayesian-model-based methods

PubMed Central

Pometti, Carolina L.; Bessega, Cecilia F.; Saidman, Beatriz O.; Vilardi, Juan C.

2014-01-01

Bayesian clustering as implemented in STRUCTURE or GENELAND software is widely used to form genetic groups of populations or individuals. On the other hand, in order to satisfy the need for less computer-intensive approaches, multivariate analyses are specifically devoted to extracting information from large datasets. In this paper, we report the use of a dataset of AFLP markers belonging to 15 sampling sites of Acacia caven for studying the genetic structure and comparing the consistency of three methods: STRUCTURE, GENELAND and DAPC. Of these methods, DAPC was the fastest one and showed accuracy in inferring the K number of populations (K = 12 using the find.clusters option and K = 15 with a priori information of populations). GENELAND in turn, provides information on the area of membership probabilities for individuals or populations in the space, when coordinates are specified (K = 12). STRUCTURE also inferred the number of K populations and the membership probabilities of individuals based on ancestry, presenting the result K = 11 without prior information of populations and K = 15 using the LOCPRIOR option. Finally, in this work all three methods showed high consistency in estimating the population structure, inferring similar numbers of populations and the membership probabilities of individuals to each group, with a high correlation between each other. PMID:24688293

SInCRe—structural interactome computational resource for Mycobacterium tuberculosis

PubMed Central

Metri, Rahul; Hariharaputran, Sridhar; Ramakrishnan, Gayatri; Anand, Praveen; Raghavender, Upadhyayula S.; Ochoa-Montaño, Bernardo; Higueruelo, Alicia P.; Sowdhamini, Ramanathan; Chandra, Nagasuma R.; Blundell, Tom L.; Srinivasan, Narayanaswamy

2015-01-01

We have developed an integrated database for Mycobacterium tuberculosis H37Rv (Mtb) that collates information on protein sequences, domain assignments, functional annotation and 3D structural information along with protein–protein and protein–small molecule interactions. SInCRe (Structural Interactome Computational Resource) is developed out of CamBan (Cambridge and Bangalore) collaboration. The motivation for development of this database is to provide an integrated platform to allow easily access and interpretation of data and results obtained by all the groups in CamBan in the field of Mtb informatics. In-house algorithms and databases developed independently by various academic groups in CamBan are used to generate Mtb-specific datasets and are integrated in this database to provide a structural dimension to studies on tuberculosis. The SInCRe database readily provides information on identification of functional domains, genome-scale modelling of structures of Mtb proteins and characterization of the small-molecule binding sites within Mtb. The resource also provides structure-based function annotation, information on small-molecule binders including FDA (Food and Drug Administration)-approved drugs, protein–protein interactions (PPIs) and natural compounds that bind to pathogen proteins potentially and result in weakening or elimination of host–pathogen protein–protein interactions. Together they provide prerequisites for identification of off-target binding. Database URL: http://proline.biochem.iisc.ernet.in/sincre PMID:26130660

21 CFR 99.3 - Definitions.

Code of Federal Regulations, 2011 CFR

2011-04-01

... the purpose of affecting any structure or function of the body; (2) Amounts paid for transportation... AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES GENERAL DISSEMINATION OF INFORMATION... clinical investigation is an investigation in humans that tests a specific clinical hypothesis. (c) Group...

21 CFR 99.3 - Definitions.

Code of Federal Regulations, 2012 CFR

2012-04-01

... the purpose of affecting any structure or function of the body; (2) Amounts paid for transportation... AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES GENERAL DISSEMINATION OF INFORMATION... clinical investigation is an investigation in humans that tests a specific clinical hypothesis. (c) Group...

21 CFR 99.3 - Definitions.

Code of Federal Regulations, 2014 CFR

2014-04-01

... the purpose of affecting any structure or function of the body; (2) Amounts paid for transportation... AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES GENERAL DISSEMINATION OF INFORMATION... clinical investigation is an investigation in humans that tests a specific clinical hypothesis. (c) Group...

21 CFR 99.3 - Definitions.

Code of Federal Regulations, 2013 CFR

2013-04-01

... the purpose of affecting any structure or function of the body; (2) Amounts paid for transportation... AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES GENERAL DISSEMINATION OF INFORMATION... clinical investigation is an investigation in humans that tests a specific clinical hypothesis. (c) Group...

South Florida Freight Advanced Traveler Information System : architecture and implementation options summary report.

DOT National Transportation Integrated Search

2013-07-01

This Final Architecture and Design report has been prepared to describe the structure and design of all the system components for the South Florida FRATIS Demonstration Project. More specifically, this document provides: Detailed descriptions of ...

DORS: DDC Online Retrieval System.

ERIC Educational Resources Information Center

Liu, Songqiao; Svenonius, Elaine

1991-01-01

Describes the Dewey Online Retrieval System (DORS), which was developed at the University of California, Los Angeles (UCLA), to experiment with classification-based search strategies in online catalogs. Classification structures in automated information retrieval are discussed; and specifications for a classification retrieval interface are…

Reliability Technology to Achieve Insertion of Advanced Packaging (RELTECH) program

NASA Astrophysics Data System (ADS)

Fayette, Daniel F.; Speicher, Patricia; Stoklosa, Mark J.; Evans, Jillian V.; Evans, John W.; Gentile, Mike; Pagel, Chuck A.; Hakim, Edward

1993-08-01

A joint military-commercial effort to evaluate multichip module (MCM) structures is discussed. The program, Reliability Technology to Achieve Insertion of Advanced Packaging (RELTECH), has been designed to identify the failure mechanisms that are possible in MCM structures. The RELTECH test vehicles, technical assessment task, product evaluation plan, reliability modeling task, accelerated and environmental testing, and post-test physical analysis and failure analysis are described. The information obtained through RELTECH can be used to address standardization issues, through development of cost effective qualification and appropriate screening criteria, for inclusion into a commercial specification and the MIL-H-38534 general specification for hybrid microcircuits.

Reliability Technology to Achieve Insertion of Advanced Packaging (RELTECH) program

NASA Technical Reports Server (NTRS)

Fayette, Daniel F.; Speicher, Patricia; Stoklosa, Mark J.; Evans, Jillian V.; Evans, John W.; Gentile, Mike; Pagel, Chuck A.; Hakim, Edward

1993-01-01

A joint military-commercial effort to evaluate multichip module (MCM) structures is discussed. The program, Reliability Technology to Achieve Insertion of Advanced Packaging (RELTECH), has been designed to identify the failure mechanisms that are possible in MCM structures. The RELTECH test vehicles, technical assessment task, product evaluation plan, reliability modeling task, accelerated and environmental testing, and post-test physical analysis and failure analysis are described. The information obtained through RELTECH can be used to address standardization issues, through development of cost effective qualification and appropriate screening criteria, for inclusion into a commercial specification and the MIL-H-38534 general specification for hybrid microcircuits.

Processing Information about Support Exchanges in Close Relationships: The Role of a Knowledge Structure.

PubMed

Turan, Bulent

2016-01-01

People develop knowledge of interpersonal interaction patterns (e.g., prototypes and schemas), which shape how they process incoming information. One such knowledge structure based on attachment theory was examined: the secure base script (the prototypic sequence of events when an attachment figure comforts a close relationship partner in distress). In two studies (N = 53 and N = 119), participants were shown animated film clips in which geometric figures depicted the secure base script and asked to describe the animations. Both studies found that many people readily recognize the secure-base script from these minimal cues quite well, suggesting that this script is not only available in the context of specific relationships (i.e., a relationship-specific knowledge): The generalized (abstract) structure of the script is also readily accessible, which would make it possible to apply it to any relationship (including new relationships). Regression analyses suggested that participants who recognized the script were more likely to (a) include more animation elements when describing the animations, (b) see a common theme in different animations, (c) create better organized stories, and (d) later recall more details of the animations. These findings suggest that access to this knowledge structure helps a person organize and remember relevant incoming information. Furthermore, in both Study 1 and Study 2, individual differences in the ready recognition of the script were associated with individual differences in having access to another related knowledge: indicators suggesting that a potential relationship partner can be trusted to be supportive and responsive at times of stress. Results of Study 2 also suggest that recognizing the script is associated with those items of an attachment measure that concern giving and receiving support. Thus, these knowledge structures may shape how people process support-relevant information in their everyday lives, potentially affecting relationship outcomes and mental and physical health.

Processing Information about Support Exchanges in Close Relationships: The Role of a Knowledge Structure

PubMed Central

Turan, Bulent

2016-01-01

People develop knowledge of interpersonal interaction patterns (e.g., prototypes and schemas), which shape how they process incoming information. One such knowledge structure based on attachment theory was examined: the secure base script (the prototypic sequence of events when an attachment figure comforts a close relationship partner in distress). In two studies (N = 53 and N = 119), participants were shown animated film clips in which geometric figures depicted the secure base script and asked to describe the animations. Both studies found that many people readily recognize the secure-base script from these minimal cues quite well, suggesting that this script is not only available in the context of specific relationships (i.e., a relationship-specific knowledge): The generalized (abstract) structure of the script is also readily accessible, which would make it possible to apply it to any relationship (including new relationships). Regression analyses suggested that participants who recognized the script were more likely to (a) include more animation elements when describing the animations, (b) see a common theme in different animations, (c) create better organized stories, and (d) later recall more details of the animations. These findings suggest that access to this knowledge structure helps a person organize and remember relevant incoming information. Furthermore, in both Study 1 and Study 2, individual differences in the ready recognition of the script were associated with individual differences in having access to another related knowledge: indicators suggesting that a potential relationship partner can be trusted to be supportive and responsive at times of stress. Results of Study 2 also suggest that recognizing the script is associated with those items of an attachment measure that concern giving and receiving support. Thus, these knowledge structures may shape how people process support-relevant information in their everyday lives, potentially affecting relationship outcomes and mental and physical health. PMID:26973562

Transcriptome analysis by strand-specific sequencing of complementary DNA

PubMed Central

Parkhomchuk, Dmitri; Borodina, Tatiana; Amstislavskiy, Vyacheslav; Banaru, Maria; Hallen, Linda; Krobitsch, Sylvia; Lehrach, Hans; Soldatov, Alexey

2009-01-01

High-throughput complementary DNA sequencing (RNA-Seq) is a powerful tool for whole-transcriptome analysis, supplying information about a transcript's expression level and structure. However, it is difficult to determine the polarity of transcripts, and therefore identify which strand is transcribed. Here, we present a simple cDNA sequencing protocol that preserves information about a transcript's direction. Using Saccharomyces cerevisiae and mouse brain transcriptomes as models, we demonstrate that knowing the transcript's orientation allows more accurate determination of the structure and expression of genes. It also helps to identify new genes and enables studying promoter-associated and antisense transcription. The transcriptional landscapes we obtained are available online. PMID:19620212

Transcriptome analysis by strand-specific sequencing of complementary DNA.

PubMed

Parkhomchuk, Dmitri; Borodina, Tatiana; Amstislavskiy, Vyacheslav; Banaru, Maria; Hallen, Linda; Krobitsch, Sylvia; Lehrach, Hans; Soldatov, Alexey

2009-10-01

High-throughput complementary DNA sequencing (RNA-Seq) is a powerful tool for whole-transcriptome analysis, supplying information about a transcript's expression level and structure. However, it is difficult to determine the polarity of transcripts, and therefore identify which strand is transcribed. Here, we present a simple cDNA sequencing protocol that preserves information about a transcript's direction. Using Saccharomyces cerevisiae and mouse brain transcriptomes as models, we demonstrate that knowing the transcript's orientation allows more accurate determination of the structure and expression of genes. It also helps to identify new genes and enables studying promoter-associated and antisense transcription. The transcriptional landscapes we obtained are available online.

Sequence harmony: detecting functional specificity from alignments

PubMed Central

Feenstra, K. Anton; Pirovano, Walter; Krab, Klaas; Heringa, Jaap

2007-01-01

Multiple sequence alignments are often used for the identification of key specificity-determining residues within protein families. We present a web server implementation of the Sequence Harmony (SH) method previously introduced. SH accurately detects subfamily specific positions from a multiple alignment by scoring compositional differences between subfamilies, without imposing conservation. The SH web server allows a quick selection of subtype specific sites from a multiple alignment given a subfamily grouping. In addition, it allows the predicted sites to be directly mapped onto a protein structure and displayed. We demonstrate the use of the SH server using the family of plant mitochondrial alternative oxidases (AOX). In addition, we illustrate the usefulness of combining sequence and structural information by showing that the predicted sites are clustered into a few distinct regions in an AOX homology model. The SH web server can be accessed at www.ibi.vu.nl/programs/seqharmwww. PMID:17584793

Optimal Multi-Type Sensor Placement for Structural Identification by Static-Load Testing

PubMed Central

Papadopoulou, Maria; Vernay, Didier; Smith, Ian F. C.

2017-01-01

Assessing ageing infrastructure is a critical challenge for civil engineers due to the difficulty in the estimation and integration of uncertainties in structural models. Field measurements are increasingly used to improve knowledge of the real behavior of a structure; this activity is called structural identification. Error-domain model falsification (EDMF) is an easy-to-use model-based structural-identification methodology which robustly accommodates systematic uncertainties originating from sources such as boundary conditions, numerical modelling and model fidelity, as well as aleatory uncertainties from sources such as measurement error and material parameter-value estimations. In most practical applications of structural identification, sensors are placed using engineering judgment and experience. However, since sensor placement is fundamental to the success of structural identification, a more rational and systematic method is justified. This study presents a measurement system design methodology to identify the best sensor locations and sensor types using information from static-load tests. More specifically, three static-load tests were studied for the sensor system design using three types of sensors for a performance evaluation of a full-scale bridge in Singapore. Several sensor placement strategies are compared using joint entropy as an information-gain metric. A modified version of the hierarchical algorithm for sensor placement is proposed to take into account mutual information between load tests. It is shown that a carefully-configured measurement strategy that includes multiple sensor types and several load tests maximizes information gain. PMID:29240684

Frequency response of electrochemical cells

NASA Technical Reports Server (NTRS)

Thomas, Daniel L.

1989-01-01

Impedance concepts can be applied to the analysis of battery electrodes, yielding information about the structure of the electrode and the processes occurring in the electrode. Structural parameters such as the specific area (surface area per gram of electrode) can be estimated. Electrode variables such as surface overpotential, ohmic losses, and diffusion limitations may be studied. Nickel and cadmium electrodes were studied by measuring the ac impedance as a function of frequency, and the specific areas that were determined were well within the range of specific areas determined from BET measurements. Impedance spectra were measured for the nickel and cadmium electrodes, and for a 20 A-hr NiCd battery as functions of the state of charge. More work is needed to determine the feasibility of using frequency response as a nondestructive testing technique for batteries.

Multi-model inference for incorporating trophic and climate uncertainty into stock assessments

NASA Astrophysics Data System (ADS)

Ianelli, James; Holsman, Kirstin K.; Punt, André E.; Aydin, Kerim

2016-12-01

Ecosystem-based fisheries management (EBFM) approaches allow a broader and more extensive consideration of objectives than is typically possible with conventional single-species approaches. Ecosystem linkages may include trophic interactions and climate change effects on productivity for the relevant species within the system. Presently, models are evolving to include a comprehensive set of fishery and ecosystem information to address these broader management considerations. The increased scope of EBFM approaches is accompanied with a greater number of plausible models to describe the systems. This can lead to harvest recommendations and biological reference points that differ considerably among models. Model selection for projections (and specific catch recommendations) often occurs through a process that tends to adopt familiar, often simpler, models without considering those that incorporate more complex ecosystem information. Multi-model inference provides a framework that resolves this dilemma by providing a means of including information from alternative, often divergent models to inform biological reference points and possible catch consequences. We apply an example of this approach to data for three species of groundfish in the Bering Sea: walleye pollock, Pacific cod, and arrowtooth flounder using three models: 1) an age-structured "conventional" single-species model, 2) an age-structured single-species model with temperature-specific weight at age, and 3) a temperature-specific multi-species stock assessment model. The latter two approaches also include consideration of alternative future climate scenarios, adding another dimension to evaluate model projection uncertainty. We show how Bayesian model-averaging methods can be used to incorporate such trophic and climate information to broaden single-species stock assessments by using an EBFM approach that may better characterize uncertainty.

A comparative study of internally and externally capped balloons using small scale test balloons

NASA Technical Reports Server (NTRS)

Bell, Douglas P.

1994-01-01

Caps have been used to structurally reinforce scientific research balloons since the late 1950's. The scientific research balloons used by the National Aeronautics and Space Administration (NASA) use internal caps. A NASA cap placement specification does not exist since no empirical information exisits concerning cap placement. To develop a cap placement specification, NASA has completed two in-hangar inflation tests comparing the structural contributions of internal caps and external caps. The tests used small scale test balloons designed to develop the highest possible stresses within the constraints of the hangar and balloon materials. An externally capped test balloon and an internally capped test balloon were designed, built, inflated and simulated to determine the structural contributions and benefits of each. The results of the tests and simulations are presented.

Exploring context and content links in social media: a latent space method.

PubMed

Qi, Guo-Jun; Aggarwal, Charu; Tian, Qi; Ji, Heng; Huang, Thomas S

2012-05-01

Social media networks contain both content and context-specific information. Most existing methods work with either of the two for the purpose of multimedia mining and retrieval. In reality, both content and context information are rich sources of information for mining, and the full power of mining and processing algorithms can be realized only with the use of a combination of the two. This paper proposes a new algorithm which mines both context and content links in social media networks to discover the underlying latent semantic space. This mapping of the multimedia objects into latent feature vectors enables the use of any off-the-shelf multimedia retrieval algorithms. Compared to the state-of-the-art latent methods in multimedia analysis, this algorithm effectively solves the problem of sparse context links by mining the geometric structure underlying the content links between multimedia objects. Specifically for multimedia annotation, we show that an effective algorithm can be developed to directly construct annotation models by simultaneously leveraging both context and content information based on latent structure between correlated semantic concepts. We conduct experiments on the Flickr data set, which contains user tags linked with images. We illustrate the advantages of our approach over the state-of-the-art multimedia retrieval techniques.

Everyday bat vocalizations contain information about emitter, addressee, context, and behavior

PubMed Central

Prat, Yosef; Taub, Mor; Yovel, Yossi

2016-01-01

Animal vocal communication is often diverse and structured. Yet, the information concealed in animal vocalizations remains elusive. Several studies have shown that animal calls convey information about their emitter and the context. Often, these studies focus on specific types of calls, as it is rarely possible to probe an entire vocal repertoire at once. In this study, we continuously monitored Egyptian fruit bats for months, recording audio and video around-the-clock. We analyzed almost 15,000 vocalizations, which accompanied the everyday interactions of the bats, and were all directed toward specific individuals, rather than broadcast. We found that bat vocalizations carry ample information about the identity of the emitter, the context of the call, the behavioral response to the call, and even the call’s addressee. Our results underline the importance of studying the mundane, pairwise, directed, vocal interactions of animals. PMID:28005079

Objectivity in a Noisy Photonic Environment through Quantum State Information Broadcasting

NASA Astrophysics Data System (ADS)

Korbicz, J. K.; Horodecki, P.; Horodecki, R.

2014-03-01

Recently, the emergence of classical objectivity as a property of a quantum state has been explicitly derived for a small object embedded in a photonic environment in terms of a spectrum broadcast form—a specific classically correlated state, redundantly encoding information about the preferred states of the object in the environment. However, the environment was in a pure state and the fundamental problem was how generic and robust is the conclusion. Here, we prove that despite the initial environmental noise, the emergence of the broadcast structure still holds, leading to the perceived objectivity of the state of the object. We also show how this leads to a quantum Darwinism-type condition, reflecting the classicality of proliferated information in terms of a limit behavior of the mutual information. Quite surprisingly, we find "singular points" of the decoherence, which can be used to faithfully broadcast a specific classical message through the noisy environment.

Structural Brain Atlases: Design, Rationale, and Applications in Normal and Pathological Cohorts

PubMed Central

Mandal, Pravat K.; Mahajan, Rashima; Dinov, Ivo D.

2015-01-01

Structural magnetic resonance imaging (MRI) provides anatomical information about the brain in healthy as well as in diseased conditions. On the other hand, functional MRI (fMRI) provides information on the brain activity during performance of a specific task. Analysis of fMRI data requires the registration of the data to a reference brain template in order to identify the activated brain regions. Brain templates also find application in other neuroimaging modalities, such as diffusion tensor imaging and multi-voxel spectroscopy. Further, there are certain differences (e.g., brain shape and size) in the brains of populations of different origin and during diseased conditions like in Alzheimer’s disease (AD), population and disease-specific brain templates may be considered crucial for accurate registration and subsequent analysis of fMRI as well as other neuroimaging data. This manuscript provides a comprehensive review of the history, construction and application of brain atlases. A chronological outline of the development of brain template design, starting from the Talairach and Tournoux atlas to the Chinese brain template (to date), along with their respective detailed construction protocols provides the backdrop to this manuscript. The manuscript also provides the automated workflow-based protocol for designing a population-specific brain atlas from structural MRI data using LONI Pipeline graphical workflow environment. We conclude by discussing the scope of brain templates as a research tool and their application in various neuroimaging modalities. PMID:22647262

GIS-based analysis of drinking-water supply structures: a module for microbial risk assessment.

PubMed

Kistemann, T; Herbst, S; Dangendorf, F; Exner, M

2001-05-01

Water-related infections constitute an important health impact world-wide. A set of tools serving for Microbial Risk Assessment (MRA) of waterborne diseases should comprise the entire drinking-water management system and take into account the Hazard Analysis and Critical Control Point (HACCP) concept which provides specific Critical Control Points (CCPs) reflecting each step of drinking-water provision. A Geographical Information System (GIS) study concerning water-supply structure (WSS) was conducted in the Rhein-Berg District (North Rhine-Westphalia, Germany). As a result, suitability of the existing water databases HYGRIS (hydrological basis geo-information system) and TEIS (drinking-water recording and information system) for the development of a WSS-GIS module could be demonstrated. Spatial patterns within the integrated raw and drinking-water data can easily be uncovered by GIS-specific options. The application of WSS-GIS allows a rapid visualization and analysis of drinking-water supply structure and offers huge advantages concerning microbial monitoring of raw and drinking water as well as recognition and investigation of incidents and outbreaks. Increasing requests regarding health protection and health reporting, demands for a better outbreak management and water-related health impacts of global climate change are major challenges of future water management to be tackled with methods including spatial analysis. GIS is assumed to be a very useful tool to meet these requirements.

Microelectronics and nanotechnology, and the fractal-like structure of information, knowledge, and science

NASA Astrophysics Data System (ADS)

Nutu, Catalin Silviu; Axinte, Tiberiu

2016-12-01

The article is centralizing and is concentrating the information from a considerable amount of papers related to the field of microelectronics and nanotechnology and also provides an approach to science and to the future evolution of science, based on the theory of the fractals. The new science of microelectronics and nanotechnology is one of the best examples of how the science of future will look like, namely at the confluence of increasingly more other sciences, where increasingly more sciences are to be added in the structure of the new science and the role of the multidisciplinary and interdisciplinary is becoming more and more important. Although not giving explicit details (e.g. specific formulas) the theory of fractals is used in the paper to explain the way of generation of new science for the specific case of microelectronics and nanotechnology, but is also used in the paper to outline a different way to approach new science and eventually to approach new sciences to come. There are mainly two motivations for the present article, namely: on the one hand, the position of the microelectronics and nanotechnologies in the fractal-like structure of science, and, on the other hand, that much of the communication, information, knowledge and science transfer, dissemination and advancement in sciences are taking place using the new technologies related to microelectronics and nanotechnologies.

Risk Classification with an Adaptive Naive Bayes Kernel Machine Model.

PubMed

Minnier, Jessica; Yuan, Ming; Liu, Jun S; Cai, Tianxi

2015-04-22

Genetic studies of complex traits have uncovered only a small number of risk markers explaining a small fraction of heritability and adding little improvement to disease risk prediction. Standard single marker methods may lack power in selecting informative markers or estimating effects. Most existing methods also typically do not account for non-linearity. Identifying markers with weak signals and estimating their joint effects among many non-informative markers remains challenging. One potential approach is to group markers based on biological knowledge such as gene structure. If markers in a group tend to have similar effects, proper usage of the group structure could improve power and efficiency in estimation. We propose a two-stage method relating markers to disease risk by taking advantage of known gene-set structures. Imposing a naive bayes kernel machine (KM) model, we estimate gene-set specific risk models that relate each gene-set to the outcome in stage I. The KM framework efficiently models potentially non-linear effects of predictors without requiring explicit specification of functional forms. In stage II, we aggregate information across gene-sets via a regularization procedure. Estimation and computational efficiency is further improved with kernel principle component analysis. Asymptotic results for model estimation and gene set selection are derived and numerical studies suggest that the proposed procedure could outperform existing procedures for constructing genetic risk models.

Natively Inhibited Trypanosoma brucei Cathepsin B Structure Determined by Using an X-ray Laser

PubMed Central

DePonte, Daniel P.; White, Thomas A.; Rehders, Dirk; Barty, Anton; Stellato, Francesco; Liang, Mengning; Barends, Thomas R.M.; Boutet, Sébastien; Williams, Garth J.; Messerschmidt, Marc; Seibert, M. Marvin; Aquila, Andrew; Arnlund, David; Bajt, Sasa; Barth, Torsten; Bogan, Michael J.; Caleman, Carl; Chao, Tzu-Chiao; Doak, R. Bruce; Fleckenstein, Holger; Frank, Matthias; Fromme, Raimund; Galli, Lorenzo; Grotjohann, Ingo; Hunter, Mark S.; Johansson, Linda C.; Kassemeyer, Stephan; Katona, Gergely; Kirian, Richard A.; Koopmann, Rudolf; Kupitz, Chris; Lomb, Lukas; Martin, Andrew V.; Mogk, Stefan; Neutze, Richard; Shoeman, Robert L.; Steinbrener, Jan; Timneanu, Nicusor; Wang, Dingjie; Weierstall, Uwe; Zatsepin, Nadia A.; Spence, John C. H.; Fromme, Petra; Schlichting, Ilme; Duszenko, Michael; Betzel, Christian; Chapman, Henry N.

2013-01-01

The Trypanosoma brucei cysteine protease cathepsin B (TbCatB), which is involved in host protein degradation, is a promising target to develop new treatments against sleeping sickness, a fatal disease caused by this protozoan parasite. The structure of the mature, active form of TbCatB has so far not provided sufficient information for the design of a safe and specific drug against T. brucei. By combining two recent innovations, in vivo crystallization and serial femtosecond crystallography, we obtained the room-temperature 2.1 angstrom resolution structure of the fully glycosylated precursor complex of TbCatB. The structure reveals the mechanism of native TbCatB inhibition and demonstrates that new biomolecular information can be obtained by the “diffraction-before-destruction” approach of x-ray free-electron lasers from hundreds of thousands of individual microcrystals. PMID:23196907

Exploration Planetary Surface Structural Systems: Design Requirements and Compliance

NASA Technical Reports Server (NTRS)

Dorsey, John T.

2011-01-01

The Lunar Surface Systems Project developed system concepts that would be necessary to establish and maintain a permanent human presence on the Lunar surface. A variety of specific system implementations were generated as a part of the scenarios, some level of system definition was completed, and masses estimated for each system. Because the architecture studies generally spawned a large number of system concepts and the studies were executed in a short amount of time, the resulting system definitions had very low design fidelity. This paper describes the development sequence required to field a particular structural system: 1) Define Requirements, 2) Develop the Design and 3) Demonstrate Compliance of the Design to all Requirements. This paper also outlines and describes in detail the information and data that are required to establish structural design requirements and outlines the information that would comprise a planetary surface system Structures Requirements document.

Advanced composites structural concepts and materials technologies for primary aircraft structures. Structural response and failure analysis: ISPAN modules users manual

NASA Technical Reports Server (NTRS)

Hairr, John W.; Huang, Jui-Ten; Ingram, J. Edward; Shah, Bharat M.

1992-01-01

The ISPAN Program (Interactive Stiffened Panel Analysis) is an interactive design tool that is intended to provide a means of performing simple and self contained preliminary analysis of aircraft primary structures made of composite materials. The program combines a series of modules with the finite element code DIAL as its backbone. Four ISPAN Modules were developed and are documented. These include: (1) flat stiffened panel; (2) curved stiffened panel; (3) flat tubular panel; and (4) curved geodesic panel. Users are instructed to input geometric and material properties, load information and types of analysis (linear, bifurcation buckling, or post-buckling) interactively. The program utilizing this information will generate finite element mesh and perform analysis. The output in the form of summary tables of stress or margins of safety, contour plots of loads or stress, and deflected shape plots may be generalized and used to evaluate specific design.

Inhibition of Monometalated Methionine Aminopeptidase: Inhibitor Discovery and Crystallographic Analysis†

PubMed Central

Huang, Min; Xie, Sheng-Xue; Ma, Ze-Qiang; Huang, Qing-Qing; Nan, Fa-Jun; Ye, Qi-Zhuang

2008-01-01

Two divalent metal ions are commonly seen in the active site cavity of methionine aminopeptidase, and at least one of the metal ions is directly involved in catalysis. Although ample structural and functional information is available for dimetalated enzyme, methionine aminopeptidase likely functions as a monometalated enzyme under physiological conditions. Information on structure, as well as catalysis and inhibition, of the monometalated enzyme is lacking. By improving conditions of high throughput screening, we identified a unique inhibitor with specificity toward the monometalated enzyme. Kinetic characterization indicates a mutual exclusivity in binding between the inhibitor and the second metal ion at the active site. This is confirmed by X-ray structure, and this inhibitor coordinates with the first metal ion and occupies the space normally occupied by the second metal ion. Kinetic and structural analyses of the inhibition by this and other inhibitors provide insight in designing effective inhibitors of methionine aminopeptidase. PMID:17948983

Exposing Latent Information in Folksonomies for Reasoning

DTIC Science & Technology

2010-01-14

publicly available sites such as Flickr (photos), YouTube (video) and Blogger (blogs) and demonstrates the ability to perform higher order ... processing using the induced structure. Specifically, the technology being developed will allow the system to identify photos, videos or blog posts about the

10 CFR 61.12 - Specific technical information.

Code of Federal Regulations, 2010 CFR

2010-01-01

... NUCLEAR REGULATORY COMMISSION (CONTINUED) LICENSING REQUIREMENTS FOR LAND DISPOSAL OF RADIOACTIVE WASTE... of the land disposal facility and the disposal units. For near-surface disposal, the description must...; structural stability of backfill, wastes, and covers; contact of wastes with standing water; disposal site...

10 CFR 61.12 - Specific technical information.

Code of Federal Regulations, 2014 CFR

2014-01-01

... NUCLEAR REGULATORY COMMISSION (CONTINUED) LICENSING REQUIREMENTS FOR LAND DISPOSAL OF RADIOACTIVE WASTE... of the land disposal facility and the disposal units. For near-surface disposal, the description must...; structural stability of backfill, wastes, and covers; contact of wastes with standing water; disposal site...

10 CFR 61.12 - Specific technical information.

Code of Federal Regulations, 2012 CFR

2012-01-01

... NUCLEAR REGULATORY COMMISSION (CONTINUED) LICENSING REQUIREMENTS FOR LAND DISPOSAL OF RADIOACTIVE WASTE... of the land disposal facility and the disposal units. For near-surface disposal, the description must...; structural stability of backfill, wastes, and covers; contact of wastes with standing water; disposal site...

10 CFR 61.12 - Specific technical information.

Code of Federal Regulations, 2013 CFR

2013-01-01

... NUCLEAR REGULATORY COMMISSION (CONTINUED) LICENSING REQUIREMENTS FOR LAND DISPOSAL OF RADIOACTIVE WASTE... of the land disposal facility and the disposal units. For near-surface disposal, the description must...; structural stability of backfill, wastes, and covers; contact of wastes with standing water; disposal site...

10 CFR 61.12 - Specific technical information.

Code of Federal Regulations, 2011 CFR

2011-01-01

... NUCLEAR REGULATORY COMMISSION (CONTINUED) LICENSING REQUIREMENTS FOR LAND DISPOSAL OF RADIOACTIVE WASTE... of the land disposal facility and the disposal units. For near-surface disposal, the description must...; structural stability of backfill, wastes, and covers; contact of wastes with standing water; disposal site...

MultiLIS: A Description of the System Design and Operational Features.

ERIC Educational Resources Information Center

Kelly, Glen J.; And Others

1988-01-01

Describes development, hardware requirements, and features of the MultiLIS integrated library software package. A system profile provides pricing information, operational characteristics, and technical specifications. Sidebars discuss MultiLIS integration structure, incremental architecture, and NCR Tower Computers. (4 references) (MES)

Structures and Materials Experimental Facilities and Capabilities Catalog

NASA Technical Reports Server (NTRS)

Horta, Lucas G. (Compiler); Kurtz-Husch, Jeanette D. (Compiler)

2000-01-01

The NASA Center of Excellent for Structures and Materials at Langley Research Center is responsible for conducting research and developing useable technology in the areas of advanced materials and processing technologies, durability, damage tolerance, structural concepts, advanced sensors, intelligent systems, aircraft ground operations, reliability, prediction tools, performance validation, aeroelastic response, and structural dynamics behavior for aerospace vehicles. Supporting the research activities is a complementary set of facilities and capabilities documented in this report. Because of the volume of information, the information collected was restricted in most cases to one page. Specific questions from potential customers or partners should be directed to the points of contacts provided with the various capabilities. Grouping of the equipment is by location as opposed to function. Geographical information of the various buildings housing the equipment is also provided. Since this is the first time that such an inventory is ever collected at Langley it is by no means complete. It is estimated that over 90 percent of the equipment capabilities at hand are included but equipment is continuously being updated and will be reported in the future.

Integrated structural health monitoring

NASA Astrophysics Data System (ADS)

Farrar, Charles R.; Sohn, Hoon; Fugate, Michael L.; Czarnecki, Jerry J.

2001-07-01

Structural health monitoring is the implementation of a damage detection strategy for aerospace, civil and mechanical engineering infrastructure. Typical damage experienced by this infrastructure might be the development of fatigue cracks, degradation of structural connections, or bearing wear in rotating machinery. The goal of the research effort reported herein is to develop a robust and cost-effective structural health monitoring solution by integrating and extending technologies from various engineering and information technology disciplines. It is the author's opinion that all structural health monitoring systems must be application specific. Therefore, a specific application, monitoring welded moment resisting steel frame connections in structures subjected to seismic excitation, is described along with the motivation for choosing this application. The structural health monitoring solution for this application will integrate structural dynamics, wireless data acquisition, local actuation, micro-electromechanical systems (MEMS) technology, and statistical pattern recognition algorithms. The proposed system is based on an assessment of the deficiencies associated with many current structural health monitoring technologies including past efforts by the authors. This paper provides an example of the integrated approach to structural health monitoring being undertaken at Los Alamos National Laboratory and summarizes progress to date on various aspects of the technology development.

Family history assessment of personality disorders: I. Concordance with direct interview and between pairs of informants.

PubMed

Ferro, T; Klein, D N

1997-01-01

The present study examined the concordance of the Family History Interview for Personality Disorders (FHIPD) with diagnoses based on direct interviews and between pairs of informants. Subjects were 224 probands participating in a series of studies of the familial transmission of mood and personality disorders and their first-degree relatives. Proband informants and relatives provided information about themselves on the Structured Clinical Interview for DSM-III-R (SCID), Personality Disorder Examination (PDE), and Eysenck Personality Questionnaire (EPQ). Information from informants about relatives was collected with the FHIPD. All assessments were made blindly and independently. Using Kappa, concordance between proband informants' family histories and relative direct reports on specific personality disorders was low, ranging from -.01 to .28, with a median of .10. Kappa for a diagnosis of any personality disorder was .16. When two independent informant reports were compared, Kappas for specific Axis II disorders ranged from .10 to .72, with a median of .28. Kappa for a diagnosis of any personality disorder was .36. These data suggest that subjects and informants provide different perspectives on Axis II psychopathology, and support the use of both sources of information whenever possible.

Meso-Mechanics and Meso-Structures: A Matter of Scale

NASA Technical Reports Server (NTRS)

Chamis, Christos C.; Gotsis, P. K.; Mital, S. K.

1998-01-01

Meso-mechanics and meso-structures are described in terms of the scales at which they are observed and formulated. Select composite examples are presented to illustrate that meso-mechanics and/or meso-structures are meaningful only when they refer to a specific scale in a hierarchical scale observation/simulation. These examples include different types of composite unit cells, woven fabric unit cells, and progressive fracture as a composite enhanced infrastructure made from reinforced concrete. The results from the select examples indicate that meso-mechanics and meso-structures are elusive terms and depend mainly on the investigators' knowledge and available information.

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.

Electrostatic and structural similarity of classical and non-classical lactam compounds

NASA Astrophysics Data System (ADS)

Coll, Miguel; Frau, Juan; Vilanova, Bartolomé; Donoso, Josefa; Muñoz, Francisco

2001-09-01

Various electrostatic and structural parameters for a series of classical and non-classical β-lactams were determined and compared in order to ascertain whether some specific β-lactams possess antibacterial or β-lactamase inhibitory properties. The electrostatic parameters obtained, based on the Distributed Multipole Analysis (DMA) of high-quality wavefunctions for the studied structures, suggest that some non-classical β-lactams effectively inhibit the action of β-lactamases. As shown in this work, such electrostatic parameters provide much more reliable information about the antibacterial and inhibitory properties of β-lactams than do structural parameters.

[Technology and progress in the use of information systems in the dental office].

PubMed

Walther, K

1989-09-01

The numerous DP systems used in dental offices are designed for administrative work. Data storage and management is limited to accountancy applications, and the advantages of the flow of information are restricted to operational purposes. Data of medical use are available only to a moderate extent. It should be possible, however, to use these information systems for processing purely medical data, for the structured input of comprehensive diagnostic information, and to have these data available for specific decisions. The use of a "decision-supporting system" has been tested in the documentation of dental diagnostic findings.

Specificity profiling of protein-binding domains using one-bead-one-compound Peptide libraries.

PubMed

Kunys, Andrew R; Lian, Wenlong; Pei, Dehua

2012-12-01

One-bead-one-compound (OBOC) libraries consist of structurally related compounds (e.g., peptides) covalently attached to a solid support, with each resin bead carrying a unique compound. OBOC libraries of high structural diversity can be rapidly synthesized and screened without the need for any special equipment, and therefore can be employed in any chemical or biochemical laboratory. OBOC peptide libraries have been widely used to map the ligand specificity of proteins, to determine the substrate specificity of enzymes, and to develop inhibitors against macromolecular targets. They have proven particularly useful in profiling the binding specificity of protein modular domains (e.g., SH2 domains, BIR domains, and PDZ domains); subsequently, the specificity information can be used to predict the protein targets of these domains. The protocols outlined in this article describe the methodologies for synthesizing and screening OBOC peptide libraries against SH2 and PDZ domains, and the related data analysis. Curr. Protoc. Chem. Biol. 4:331-355 © 2012 by John Wiley & Sons, Inc.

Self-Referencing Enhances Memory Specificity with Age

PubMed Central

Hamami, Ayala; Serbun, Sarah J.; Gutchess, Angela H.

2011-01-01

Self-referencing has been identified as an advantageous mnemonic strategy for young and older adults. However, little research has investigated the ways in which self-referencing may influence older adults’ memory for details, which is typically impaired with age, beyond memory for the item itself. Experiment 1 assessed the effects of self- and other-referencing on memory for visually detailed pictures of objects in thirty-two young and thirty-two older adults. Results indicate that self- and close other-referencing similarly enhance general (item) and specific (detail) recognition for both young and older adults relative to the distant other condition. Experiment 2 extended these findings to source memory, with young and older adults encoding verbal information in self-referent, semantic, and structural conditions. Findings suggest that self-referencing provides an age-equivalent boost in general memory and specific memory for specific source details. We conclude that the mnemonic benefits of referencing the self extend to specific memory for visual and verbal information across the lifespan. PMID:21480719

Structural and Kinetic Properties of the Aldehyde Dehydrogenase NahF, a Broad Substrate Specificity Enzyme for Aldehyde Oxidation.

PubMed

Coitinho, Juliana B; Pereira, Mozart S; Costa, Débora M A; Guimarães, Samuel L; Araújo, Simara S; Hengge, Alvan C; Brandão, Tiago A S; Nagem, Ronaldo A P

2016-09-27

The salicylaldehyde dehydrogenase (NahF) catalyzes the oxidation of salicylaldehyde to salicylate using NAD(+) as a cofactor, the last reaction of the upper degradation pathway of naphthalene in Pseudomonas putida G7. The naphthalene is an abundant and toxic compound in oil and has been used as a model for bioremediation studies. The steady-state kinetic parameters for oxidation of aliphatic or aromatic aldehydes catalyzed by 6xHis-NahF are presented. The 6xHis-NahF catalyzes the oxidation of aromatic aldehydes with large kcat/Km values close to 10(6) M(-1) s(-1). The active site of NahF is highly hydrophobic, and the enzyme shows higher specificity for less polar substrates than for polar substrates, e.g., acetaldehyde. The enzyme shows α/β folding with three well-defined domains: the oligomerization domain, which is responsible for the interlacement between the two monomers; the Rossmann-like fold domain, essential for nucleotide binding; and the catalytic domain. A salicylaldehyde molecule was observed in a deep pocket in the crystal structure of NahF where the catalytic C284 and E250 are present. Moreover, the residues G150, R157, W96, F99, F274, F279, and Y446 were thought to be important for catalysis and specificity for aromatic aldehydes. Understanding the molecular features responsible for NahF activity allows for comparisons with other aldehyde dehydrogenases and, together with structural information, provides the information needed for future mutational studies aimed to enhance its stability and specificity and further its use in biotechnological processes.

Monitoring Data-Structure Evolution in Distributed Message-Passing Programs

NASA Technical Reports Server (NTRS)

Sarukkai, Sekhar R.; Beers, Andrew; Woodrow, Thomas S. (Technical Monitor)

1996-01-01

Monitoring the evolution of data structures in parallel and distributed programs, is critical for debugging its semantics and performance. However, the current state-of-art in tracking and presenting data-structure information on parallel and distributed environments is cumbersome and does not scale. In this paper we present a methodology that automatically tracks memory bindings (not the actual contents) of static and dynamic data-structures of message-passing C programs, using PVM. With the help of a number of examples we show that in addition to determining the impact of memory allocation overheads on program performance, graphical views can help in debugging the semantics of program execution. Scalable animations of virtual address bindings of source-level data-structures are used for debugging the semantics of parallel programs across all processors. In conjunction with light-weight core-files, this technique can be used to complement traditional debuggers on single processors. Detailed information (such as data-structure contents), on specific nodes, can be determined using traditional debuggers after the data structure evolution leading to the semantic error is observed graphically.

TRENCADIS--a WSRF grid MiddleWare for managing DICOM structured reporting objects.

PubMed

Blanquer, Ignacio; Hernandez, Vicente; Segrelles, Damià

2006-01-01

The adoption of the digital processing of medical data, especially on radiology, has leaded to the availability of millions of records (images and reports). However, this information is mainly used at patient level, being the extraction of information, organised according to administrative criteria, which make the extraction of knowledge difficult. Moreover, legal constraints make the direct integration of information systems complex or even impossible. On the other side, the widespread of the DICOM format has leaded to the inclusion of other information different from just radiological images. The possibility of coding radiology reports in a structured form, adding semantic information about the data contained in the DICOM objects, eases the process of structuring images according to content. DICOM Structured Reporting (DICOM-SR) is a specification of tags and sections to code and integrate radiology reports, with seamless references to findings and regions of interests of the associated images, movies, waveforms, signals, etc. The work presented in this paper aims at developing of a framework to efficiently and securely share medical images and radiology reports, as well as to provide high throughput processing services. This system is based on a previously developed architecture in the framework of the TRENCADIS project, and uses other components such as the security system and the Grid processing service developed in previous activities. The work presented here introduces a semantic structuring and an ontology framework, to organise medical images considering standard terminology and disease coding formats (SNOMED, ICD9, LOINC..).

Partial information decomposition as a unified approach to the specification of neural goal functions.

PubMed

Wibral, Michael; Priesemann, Viola; Kay, Jim W; Lizier, Joseph T; Phillips, William A

2017-03-01

In many neural systems anatomical motifs are present repeatedly, but despite their structural similarity they can serve very different tasks. A prime example for such a motif is the canonical microcircuit of six-layered neo-cortex, which is repeated across cortical areas, and is involved in a number of different tasks (e.g. sensory, cognitive, or motor tasks). This observation has spawned interest in finding a common underlying principle, a 'goal function', of information processing implemented in this structure. By definition such a goal function, if universal, cannot be cast in processing-domain specific language (e.g. 'edge filtering', 'working memory'). Thus, to formulate such a principle, we have to use a domain-independent framework. Information theory offers such a framework. However, while the classical framework of information theory focuses on the relation between one input and one output (Shannon's mutual information), we argue that neural information processing crucially depends on the combination of multiple inputs to create the output of a processor. To account for this, we use a very recent extension of Shannon Information theory, called partial information decomposition (PID). PID allows to quantify the information that several inputs provide individually (unique information), redundantly (shared information) or only jointly (synergistic information) about the output. First, we review the framework of PID. Then we apply it to reevaluate and analyze several earlier proposals of information theoretic neural goal functions (predictive coding, infomax and coherent infomax, efficient coding). We find that PID allows to compare these goal functions in a common framework, and also provides a versatile approach to design new goal functions from first principles. Building on this, we design and analyze a novel goal function, called 'coding with synergy', which builds on combining external input and prior knowledge in a synergistic manner. We suggest that this novel goal function may be highly useful in neural information processing. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

Use of reduction rate as a quantitative knob for controlling the twin structure and shape of palladium nanocrystals.

PubMed

Wang, Yi; Peng, Hsin-Chieh; Liu, Jingyue; Huang, Cheng Zhi; Xia, Younan

2015-02-11

Kinetic control is a powerful means for maneuvering the twin structure and shape of metal nanocrystals and thus optimizing their performance in a variety of applications. However, there is only a vague understanding of the explicit roles played by reaction kinetics due to the lack of quantitative information about the kinetic parameters. With Pd as an example, here we demonstrate that kinetic parameters, including rate constant and activation energy, can be derived from spectroscopic measurements and then used to calculate the initial reduction rate and further have this parameter quantitatively correlated with the twin structure of a seed and nanocrystal. On a quantitative basis, we were able to determine the ranges of initial reduction rates required for the formation of nanocrystals with a specific twin structure, including single-crystal, multiply twinned, and stacking fault-lined. This work represents a major step forward toward the deterministic syntheses of colloidal noble-metal nanocrystals with specific twin structures and shapes.

Crystal Structure of the 3.8-MDa Respiratory Supermolecule Hemocyanin at 3.0 Å Resolution.

PubMed

Gai, Zuoqi; Matsuno, Asuka; Kato, Koji; Kato, Sanae; Khan, Md Rafiqul Islam; Shimizu, Takeshi; Yoshioka, Takeya; Kato, Yuki; Kishimura, Hideki; Kanno, Gaku; Miyabe, Yoshikatsu; Terada, Tohru; Tanaka, Yoshikazu; Yao, Min

2015-12-01

Molluscan hemocyanin, a copper-containing oxygen transporter, is one of the largest known proteins. Although molluscan hemocyanins are currently applied as immunotherapeutic agents, their precise structure has not been determined because of their enormous size. Here, we have determined the first X-ray crystal structure of intact molluscan hemocyanin. The structure unveiled the architecture of the 3.8-MDa supermolecule composed of homologous functional units (FUs), wherein the dimers of FUs hierarchically associated to form the entire cylindrical decamer. Most of the specific inter-FU interactions were localized at narrow regions in the FU dimers, suggesting that rigid FU dimers formed by specific interactions assemble with flexibility. Furthermore, the roles of carbohydrates in assembly and allosteric effect, and conserved sulfur-containing residues in copper incorporation, were revealed. The precise structural information obtained in this study will accelerate our understanding of the molecular basis of hemocyanin and its future applications. Copyright © 2015 Elsevier Ltd. All rights reserved.

An automated distinction of DICOM images for lung cancer CAD system

NASA Astrophysics Data System (ADS)

Suzuki, H.; Saita, S.; Kubo, M.; Kawata, Y.; Niki, N.; Nishitani, H.; Ohmatsu, H.; Eguchi, K.; Kaneko, M.; Moriyama, N.

2009-02-01

Automated distinction of medical images is an important preprocessing in Computer-Aided Diagnosis (CAD) systems. The CAD systems have been developed using medical image sets with specific scan conditions and body parts. However, varied examinations are performed in medical sites. The specification of the examination is contained into DICOM textual meta information. Most DICOM textual meta information can be considered reliable, however the body part information cannot always be considered reliable. In this paper, we describe an automated distinction of DICOM images as a preprocessing for lung cancer CAD system. Our approach uses DICOM textual meta information and low cost image processing. Firstly, the textual meta information such as scan conditions of DICOM image is distinguished. Secondly, the DICOM image is set to distinguish the body parts which are identified by image processing. The identification of body parts is based on anatomical structure which is represented by features of three regions, body tissue, bone, and air. The method is effective to the practical use of lung cancer CAD system in medical sites.

The biophysical basis of Benveniste experiments: Entropy, structure, and information in water

NASA Astrophysics Data System (ADS)

Widom, Allan; Srivastava, Yogendra; Valenzi, Vincenzo

Benveniste had observed that highly dilute (and even in the absence of physical molecules) biological agents still triggered relevant biological systems. Some of these experiments were reproduced in three other laboratories who cosigned the article, (Davenas et al., Nature 1988, 333, 816). Further works, [(Medical Hypotheses 2000, 54, 33), (Rivista di Biologia/Biology Forum 97, 2004, 169)], showed that molecular activity in more than 50 biochemical systems and even in bacteria could be induced by electromagnetic signals transferred through water solutes. The sources of the electromagnetic signals were recordings of specific biological activities. These results suggest that electromagnetic transmission of biochemical information can be stored in the electric dipole moments of water in close analogy to the manner in which magnetic moments store information on a computer disk. The electromagnetic transmission would enable in vivo transmissions of the specific molecular information between two functional biomolecules. In the present work, the physical nature of such biological information storage and retrieval in ordered quantum electromagnetic domains of water will be discussed.

Neuronal Representation of Social Information in the Medial Amygdala of Awake Behaving Mice.

PubMed

Li, Ying; Mathis, Alexander; Grewe, Benjamin F; Osterhout, Jessica A; Ahanonu, Biafra; Schnitzer, Mark J; Murthy, Venkatesh N; Dulac, Catherine

2017-11-16

The medial amygdala (MeA) plays a critical role in processing species- and sex-specific signals that trigger social and defensive behaviors. However, the principles by which this deep brain structure encodes social information is poorly understood. We used a miniature microscope to image the Ca 2+ dynamics of large neural ensembles in awake behaving mice and tracked the responses of MeA neurons over several months. These recordings revealed spatially intermingled subsets of MeA neurons with distinct temporal dynamics. The encoding of social information in the MeA differed between males and females and relied on information from both individual cells and neuronal populations. By performing long-term Ca 2+ imaging across different social contexts, we found that sexual experience triggers lasting and sex-specific changes in MeA activity, which, in males, involve signaling by oxytocin. These findings reveal basic principles underlying the brain's representation of social information and its modulation by intrinsic and extrinsic factors. Copyright © 2017 Elsevier Inc. All rights reserved.

Photo-CIDNP NMR spectroscopy of amino acids and proteins.

PubMed

Kuhn, Lars T

2013-01-01

Photo-chemically induced dynamic nuclear polarization (CIDNP) is a nuclear magnetic resonance (NMR) phenomenon which, among other things, is exploited to extract information on biomolecular structure via probing solvent-accessibilities of tryptophan (Trp), tyrosine (Tyr), and histidine (His) amino acid side chains both in polypeptides and proteins in solution. The effect, normally triggered by a (laser) light-induced photochemical reaction in situ, yields both positive and/or negative signal enhancements in the resulting NMR spectra which reflect the solvent exposure of these residues both in equilibrium and during structural transformations in "real time". As such, the method can offer - qualitatively and, to a certain extent, quantitatively - residue-specific structural and kinetic information on both the native and, in particular, the non-native states of proteins which, often, is not readily available from more routine NMR techniques. In this review, basic experimental procedures of the photo-CIDNP technique as applied to amino acids and proteins are discussed, recent improvements to the method highlighted, and future perspectives presented. First, the basic principles of the phenomenon based on the theory of the radical pair mechanism (RPM) are outlined. Second, a description of standard photo-CIDNP applications is given and it is shown how the effect can be exploited to extract residue-specific structural information on the conformational space sampled by unfolded or partially folded proteins on their "path" to the natively folded form. Last, recent methodological advances in the field are highlighted, modern applications of photo-CIDNP in the context of biological NMR evaluated, and an outlook into future perspectives of the method is given.

Assistance to neurosurgical planning: using a fuzzy spatial graph model of the brain for locating anatomical targets in MRI

NASA Astrophysics Data System (ADS)

Villéger, Alice; Ouchchane, Lemlih; Lemaire, Jean-Jacques; Boire, Jean-Yves

2007-03-01

Symptoms of neurodegenerative pathologies such as Parkinson's disease can be relieved through Deep Brain Stimulation. This neurosurgical technique relies on high precision positioning of electrodes in specific areas of the basal ganglia and the thalamus. These subcortical anatomical targets must be located at pre-operative stage, from a set of MRI acquired under stereotactic conditions. In order to assist surgical planning, we designed a semi-automated image analysis process for extracting anatomical areas of interest. Complementary information, provided by both patient's data and expert knowledge, is represented as fuzzy membership maps, which are then fused by means of suitable possibilistic operators in order to achieve the segmentation of targets. More specifically, theoretical prior knowledge on brain anatomy is modelled within a 'virtual atlas' organised as a spatial graph: a list of vertices linked by edges, where each vertex represents an anatomical structure of interest and contains relevant information such as tissue composition, whereas each edge represents a spatial relationship between two structures, such as their relative directions. The model is built using heterogeneous sources of information such as qualitative descriptions from the expert, or quantitative information from prelabelled images. For each patient, tissue membership maps are extracted from MR data through a classification step. Prior model and patient's data are then matched by using a research algorithm (or 'strategy') which simultaneously computes an estimation of the location of every structures. The method was tested on 10 clinical images, with promising results. Location and segmentation results were statistically assessed, opening perspectives for enhancements.

Quality of life and satisfaction with information after radical prostatectomy, radical external beam radiotherapy and postoperative radiotherapy: a long-term follow-up study.

PubMed

Nicolaisen, Marianne; Müller, Stig; Patel, Hitendra R H; Hanssen, Tove Aminda

2014-12-01

To assess patients' symptoms, quality of life and satisfaction with information three to four years after radical prostatectomy, radical external beam radiotherapy and postoperative radiotherapy and to analyse differences between treatment groups and the relationship between disease-specific, health-related and overall quality of life and satisfaction with information. Radical prostate cancer treatments are associated with changes in quality of life. Differences between patients undergoing different treatments in symptoms and quality of life have been reported, but there are limited long-term data comparing radical prostatectomy with radical external beam radiotherapy and postoperative radiotherapy. A cross-sectional survey design was used. The study sample included 143 men treated with radical prostatectomy and/or radical external beam radiotherapy. Quality of life was measured using the 12-item Short Form Health Survey and the 50-item Expanded Prostate Cancer Index Composite Instrument. Questions assessing overall Quality of life and satisfaction with information were included. Descriptive statistics and interference statistical methods were applied to analyse the data. Radical external beam radiotherapy was associated with less urinary incontinence and better urinary function. There were no differences between the groups for disease-specific quality of life sum scores. Sexual quality of life was reported very low in all groups. Disease-specific quality of life and health-related quality of life were associated with overall quality of life. Patients having undergone surgery were more satisfied with information, and there was a positive correlation between quality of life and patient satisfaction. Pretreatment information and patient education lead to better quality of life and satisfaction. This study indicates a need for structured, pretreatment information and follow-up for all men going through radical prostate cancer treatment. Long-term quality of life effects should be considered when planning follow-up and information for men after radical prostate cancer treatment. Structured and organised information/education may increase preparedness for symptoms and bother after the treatment, improve symptom management strategies and result in improved quality of life. © 2014 John Wiley & Sons Ltd.

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

Structure and navigation for electronic publishing

NASA Astrophysics Data System (ADS)

Tillinghast, John; Beretta, Giordano B.

1998-01-01

The sudden explosion of the World Wide Web as a new publication medium has given a dramatic boost to the electronic publishing industry, which previously was a limited market centered around CD-ROMs and on-line databases. While the phenomenon has parallels to the advent of the tabloid press in the middle of last century, the electronic nature of the medium brings with it the typical characteristic of 4th wave media, namely the acceleration in its propagation speed and the volume of information. Consequently, e-publications are even flatter than print media; Shakespeare's Romeo and Juliet share the same computer screen with a home-made plagiarized copy of Deep Throat. The most touted tool for locating useful information on the World Wide Web is the search engine. However, due to the medium's flatness, sought information is drowned in a sea of useless information. A better solution is to build tools that allow authors to structure information so that it can easily be navigated. We experimented with the use of ontologies as a tool to formulate structures for information about a specific topic, so that related concepts are placed in adjacent locations and can easily be navigated using simple and ergonomic user models. We describe our effort in building a World Wide Web based photo album that is shared among a small network of people.

Sentence comprehension in specific language impairment: a task designed to distinguish between cognitive capacity and syntactic complexity.

PubMed

Leonard, Laurence B; Deevy, Patricia; Fey, Marc E; Bredin-Oja, Shelley L

2013-04-01

This study examined sentence comprehension in children with specific language impairment (SLI) in a manner designed to separate the contribution of cognitive capacity from the effects of syntactic structure. Nineteen children with SLI, 19 typically developing children matched for age (TD-A), and 19 younger typically developing children (TD-Y) matched according to sentence comprehension test scores responded to sentence comprehension items that varied in either length or their demands on cognitive capacity, based on the nature of the foils competing with the target picture. The TD-A children were accurate across all item types. The SLI and TD-Y groups were less accurate than the TD-A group on items with greater length and, especially, on items with the greatest demands on cognitive capacity. The types of errors were consistent with failure to retain details of the sentence apart from syntactic structure. The difficulty in the more demanding conditions seemed attributable to interference. Specifically, the children with SLI and the TD-Y children appeared to have difficulty retaining details of the target sentence when the information reflected in the foils closely resembled the information in the target sentence.

Line-scan Raman microscopy complements optical coherence tomography for tumor boundary detection

NASA Astrophysics Data System (ADS)

Sudheendran, Narendran; Qi, Ji; Young, Eric D.; Lazar, Alexander J.; Lev, Dina C.; Pollock, Raphael E.; Larin, Kirill V.; Shih, Wei-Chuan

2014-10-01

Current technique for tumor resection requires biopsy of the tumor region and histological confirmation before the surgeon can be certain that the entire tumor has been resected. This confirmation process is time consuming both for the surgeon and the patient and also requires sacrifice of healthy tissue, motivating the development of novel technologies which can enable real-time detection of tumor-healthy tissue boundary for faster and more efficient surgeries. In this study, the potential of combining structural information from optical coherence tomography (OCT) and molecular information from line-scan Raman microscopy (LSRM) for such an application is presented. The results show a clear presence of boundary between myxoid liposarcoma and normal fat which is easily identifiable both from structural and molecular information. In cases where structural images are indistinguishable, for example, in normal fat and well differentiated liposarcoma (WDLS) or gastrointestinal sarcoma tumor (GIST) and myxoma, distinct molecular spectra have been obtained. The results suggest LSRM can effectively complement OCT to tumor boundary demarcation with high specificity.

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

Los Angeles-Gateway Freight Advanced Traveler Information System : final system design and architecture for FRATIS prototype.

DOT National Transportation Integrated Search

2013-05-01

This Final Architecture and Design report has been prepared to describe the structure and design of all the system components for the LA-Gateway FRATIS Demonstration Project. More specifically, this document provides: Detailed descriptions of the...

Combined X-ray CT and mass spectrometry for biomedical imaging applications

NASA Astrophysics Data System (ADS)

Schioppa, E., Jr.; Ellis, S.; Bruinen, A. L.; Visser, J.; Heeren, R. M. A.; Uher, J.; Koffeman, E.

2014-04-01

Imaging technologies play a key role in many branches of science, especially in biology and medicine. They provide an invaluable insight into both internal structure and processes within a broad range of samples. There are many techniques that allow one to obtain images of an object. Different techniques are based on the analysis of a particular sample property by means of a dedicated imaging system, and as such, each imaging modality provides the researcher with different information. The use of multimodal imaging (imaging with several different techniques) can provide additional and complementary information that is not possible when employing a single imaging technique alone. In this study, we present for the first time a multi-modal imaging technique where X-ray computerized tomography (CT) is combined with mass spectrometry imaging (MSI). While X-ray CT provides 3-dimensional information regarding the internal structure of the sample based on X-ray absorption coefficients, MSI of thin sections acquired from the same sample allows the spatial distribution of many elements/molecules, each distinguished by its unique mass-to-charge ratio (m/z), to be determined within a single measurement and with a spatial resolution as low as 1 μm or even less. The aim of the work is to demonstrate how molecular information from MSI can be spatially correlated with 3D structural information acquired from X-ray CT. In these experiments, frozen samples are imaged in an X-ray CT setup using Medipix based detectors equipped with a CO2 cooled sample holder. Single projections are pre-processed before tomographic reconstruction using a signal-to-thickness calibration. In the second step, the object is sliced into thin sections (circa 20 μm) that are then imaged using both matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) and secondary ion (SIMS) mass spectrometry, where the spatial distribution of specific molecules within the sample is determined. The combination of two vastly different imaging approaches provides complementary information (i.e., anatomical and molecular distributions) that allows the correlation of distinct structural features with specific molecules distributions leading to unique insights in disease development.

Glycoform-independent prion conversion by highly efficient, cell-based, protein misfolding cyclic amplification

PubMed Central

Moudjou, Mohammed; Chapuis, Jérôme; Mekrouti, Mériem; Reine, Fabienne; Herzog, Laetitia; Sibille, Pierre; Laude, Hubert; Vilette, Didier; Andréoletti, Olivier; Rezaei, Human; Dron, Michel; Béringue, Vincent

2016-01-01

Prions are formed of misfolded assemblies (PrPSc) of the variably N-glycosylated cellular prion protein (PrPC). In infected species, prions replicate by seeding the conversion and polymerization of host PrPC. Distinct prion strains can be recognized, exhibiting defined PrPSc biochemical properties such as the glycotype and specific biological traits. While strain information is encoded within the conformation of PrPSc assemblies, the storage of the structural information and the molecular requirements for self-perpetuation remain uncertain. Here, we investigated the specific role of PrPC glycosylation status. First, we developed an efficient protein misfolding cyclic amplification method using cells expressing the PrPC species of interest as substrate. Applying the technique to PrPC glycosylation mutants expressing cells revealed that neither PrPC nor PrPSc glycoform stoichiometry was instrumental to PrPSc formation and strainness perpetuation. Our study supports the view that strain properties, including PrPSc glycotype are enciphered within PrPSc structural backbone, not in the attached glycans. PMID:27384922

Recent progress in automatically extracting information from the pharmacogenomic literature

PubMed Central

Garten, Yael; Coulet, Adrien; Altman, Russ B

2011-01-01

The biomedical literature holds our understanding of pharmacogenomics, but it is dispersed across many journals. In order to integrate our knowledge, connect important facts across publications and generate new hypotheses we must organize and encode the contents of the literature. By creating databases of structured pharmocogenomic knowledge, we can make the value of the literature much greater than the sum of the individual reports. We can, for example, generate candidate gene lists or interpret surprising hits in genome-wide association studies. Text mining automatically adds structure to the unstructured knowledge embedded in millions of publications, and recent years have seen a surge in work on biomedical text mining, some specific to pharmacogenomics literature. These methods enable extraction of specific types of information and can also provide answers to general, systemic queries. In this article, we describe the main tasks of text mining in the context of pharmacogenomics, summarize recent applications and anticipate the next phase of text mining applications. PMID:21047206

A general intermolecular force field based on tight-binding quantum chemical calculations

NASA Astrophysics Data System (ADS)

Grimme, Stefan; Bannwarth, Christoph; Caldeweyher, Eike; Pisarek, Jana; Hansen, Andreas

2017-10-01

A black-box type procedure is presented for the generation of a molecule-specific, intermolecular potential energy function. The method uses quantum chemical (QC) information from our recently published extended tight-binding semi-empirical scheme (GFN-xTB) and can treat non-covalently bound complexes and aggregates with almost arbitrary chemical structure. The necessary QC information consists of the equilibrium structure, Mulliken atomic charges, charge centers of localized molecular orbitals, and also of frontier orbitals and orbital energies. The molecular pair potential includes model density dependent Pauli repulsion, penetration, as well as point charge electrostatics, the newly developed D4 dispersion energy model, Drude oscillators for polarization, and a charge-transfer term. Only one element-specific and about 20 global empirical parameters are needed to cover systems with nuclear charges up to radon (Z = 86). The method is tested for standard small molecule interaction energy benchmark sets where it provides accurate intermolecular energies and equilibrium distances. Examples for structures with a few hundred atoms including charged systems demonstrate the versatility of the approach. The method is implemented in a stand-alone computer code which enables rigid-body, global minimum energy searches for molecular aggregation or alignment.

Tools for Protecting the Privacy of Specific Individuals in Video

NASA Astrophysics Data System (ADS)

Chen, Datong; Chang, Yi; Yan, Rong; Yang, Jie

2007-12-01

This paper presents a system for protecting the privacy of specific individuals in video recordings. We address the following two problems: automatic people identification with limited labeled data, and human body obscuring with preserved structure and motion information. In order to address the first problem, we propose a new discriminative learning algorithm to improve people identification accuracy using limited training data labeled from the original video and imperfect pairwise constraints labeled from face obscured video data. We employ a robust face detection and tracking algorithm to obscure human faces in the video. Our experiments in a nursing home environment show that the system can obtain a high accuracy of people identification using limited labeled data and noisy pairwise constraints. The study result indicates that human subjects can perform reasonably well in labeling pairwise constraints with the face masked data. For the second problem, we propose a novel method of body obscuring, which removes the appearance information of the people while preserving rich structure and motion information. The proposed approach provides a way to minimize the risk of exposing the identities of the protected people while maximizing the use of the captured data for activity/behavior analysis.

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.

Information persistence using XML database technology

NASA Astrophysics Data System (ADS)

Clark, Thomas A.; Lipa, Brian E. G.; Macera, Anthony R.; Staskevich, Gennady R.

2005-05-01

The Joint Battlespace Infosphere (JBI) Information Management (IM) services provide information exchange and persistence capabilities that support tailored, dynamic, and timely access to required information, enabling near real-time planning, control, and execution for DoD decision making. JBI IM services will be built on a substrate of network centric core enterprise services and when transitioned, will establish an interoperable information space that aggregates, integrates, fuses, and intelligently disseminates relevant information to support effective warfighter business processes. This virtual information space provides individual users with information tailored to their specific functional responsibilities and provides a highly tailored repository of, or access to, information that is designed to support a specific Community of Interest (COI), geographic area or mission. Critical to effective operation of JBI IM services is the implementation of repositories, where data, represented as information, is represented and persisted for quick and easy retrieval. This paper will address information representation, persistence and retrieval using existing database technologies to manage structured data in Extensible Markup Language (XML) format as well as unstructured data in an IM services-oriented environment. Three basic categories of database technologies will be compared and contrasted: Relational, XML-Enabled, and Native XML. These technologies have diverse properties such as maturity, performance, query language specifications, indexing, and retrieval methods. We will describe our application of these evolving technologies within the context of a JBI Reference Implementation (RI) by providing some hopefully insightful anecdotes and lessons learned along the way. This paper will also outline future directions, promising technologies and emerging COTS products that can offer more powerful information management representations, better persistence mechanisms and improved retrieval techniques.

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.

Neurobiological correlates of cognitions in fear and anxiety: a cognitive-neurobiological information-processing model.

PubMed

Hofmann, Stefan G; Ellard, Kristen K; Siegle, Greg J

2012-01-01

We review likely neurobiological substrates of cognitions related to fear and anxiety. Cognitive processes are linked to abnormal early activity reflecting hypervigilance in subcortical networks involving the amygdala, hippocampus, and insular cortex, and later recruitment of cortical regulatory resources, including activation of the anterior cingulate cortex and prefrontal cortex to implement avoidant response strategies. Based on this evidence, we present a cognitive-neurobiological information-processing model of fear and anxiety, linking distinct brain structures to specific stages of information processing of perceived threat.

Design of high entropy alloys based on the experience from commercial superalloys

NASA Astrophysics Data System (ADS)

Wang, Z.; Huang, Y.; Wang, J.; Liu, C. T.

2015-01-01

High entropy alloys (HEAs) have been drawing increasing attention recently and gratifying results have been obtained. However, the existing metallurgic rules of HEAs could not provide specific information of selecting candidate alloys for structural applications. Our brief survey reveals that many commercial superalloys have medium and even to high configurational entropies. The experience of commercial superalloys provides a clue for helping us in the development of HEAs for structural applications.

A Combined EOF/Variational Approach for Mapping Radar-Derived Sea Surface Currents

DTIC Science & Technology

2011-01-13

characterized by specific structure of the artificial gaps introduced into the simulated data set assess the benefits of the gap-filling technique. These...15 minutes and 1-2 km respectively. However, the back-scattered HFR signals suffer from to numerous distortions of artificial and natural origin. As a...data because information on the spatial structure of the velocity field within the gap is implicitly drawn from the idealized covariance function

The Forensic Potential of Flash Memory

DTIC Science & Technology

2009-09-01

limit range of 10 to 100 years before data is lost [12]. 5. Flash Memory Logical Structure The logical structure of flash memory from least to...area is not standardized and is manufacturer specific. This information will be used by the wear leveling algorithms and as such will be proprietary...memory cells, the manufacturers of the flash implement a wear leveling algorithm . In contrast, a magnetic disk in an overwrite operation will reuse the

Information storage media and method

DOEpatents

Miller, Steven D.; Endres, George W.

1999-01-01

Disclosed is a method for storing and retrieving information. More specifically, the present invention is a method for forming predetermined patterns, or data structures, using materials which exhibit enhanced absorption of light at certain wavelengths or, when interrogated with a light having a first wavelength, provide a luminescent response at a second wavelength. These materials may exhibit this response to light inherently, or may be made to exhibit this response by treating the materials with ionizing radiation.

VITAL NMR: Using Chemical Shift Derived Secondary Structure Information for a Limited Set of Amino Acids to Assess Homology Model Accuracy

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

Brothers, Michael C; Nesbitt, Anna E; Hallock, Michael J

2011-01-01

Homology modeling is a powerful tool for predicting protein structures, whose success depends on obtaining a reasonable alignment between a given structural template and the protein sequence being analyzed. In order to leverage greater predictive power for proteins with few structural templates, we have developed a method to rank homology models based upon their compliance to secondary structure derived from experimental solid-state NMR (SSNMR) data. Such data is obtainable in a rapid manner by simple SSNMR experiments (e.g., (13)C-(13)C 2D correlation spectra). To test our homology model scoring procedure for various amino acid labeling schemes, we generated a library ofmore » 7,474 homology models for 22 protein targets culled from the TALOS+/SPARTA+ training set of protein structures. Using subsets of amino acids that are plausibly assigned by SSNMR, we discovered that pairs of the residues Val, Ile, Thr, Ala and Leu (VITAL) emulate an ideal dataset where all residues are site specifically assigned. Scoring the models with a predicted VITAL site-specific dataset and calculating secondary structure with the Chemical Shift Index resulted in a Pearson correlation coefficient (-0.75) commensurate to the control (-0.77), where secondary structure was scored site specifically for all amino acids (ALL 20) using STRIDE. This method promises to accelerate structure procurement by SSNMR for proteins with unknown folds through guiding the selection of remotely homologous protein templates and assessing model quality.« less

Quantifying structural alterations in Alzheimer's disease brains using quantitative phase imaging (Conference Presentation)

NASA Astrophysics Data System (ADS)

Lee, Moosung; Lee, Eeksung; Jung, JaeHwang; Yu, Hyeonseung; Kim, Kyoohyun; Yoon, Jonghee; Lee, Shinhwa; Jeong, Yong; Park, YongKeun

2017-02-01

Imaging brain tissues is an essential part of neuroscience because understanding brain structure provides relevant information about brain functions and alterations associated with diseases. Magnetic resonance imaging and positron emission tomography exemplify conventional brain imaging tools, but these techniques suffer from low spatial resolution around 100 μm. As a complementary method, histopathology has been utilized with the development of optical microscopy. The traditional method provides the structural information about biological tissues to cellular scales, but relies on labor-intensive staining procedures. With the advances of illumination sources, label-free imaging techniques based on nonlinear interactions, such as multiphoton excitations and Raman scattering, have been applied to molecule-specific histopathology. Nevertheless, these techniques provide limited qualitative information and require a pulsed laser, which is difficult to use for pathologists with no laser training. Here, we present a label-free optical imaging of mouse brain tissues for addressing structural alteration in Alzheimer's disease. To achieve the mesoscopic, unlabeled tissue images with high contrast and sub-micrometer lateral resolution, we employed holographic microscopy and an automated scanning platform. From the acquired hologram of the brain tissues, we could retrieve scattering coefficients and anisotropies according to the modified scattering-phase theorem. This label-free imaging technique enabled direct access to structural information throughout the tissues with a sub-micrometer lateral resolution and presented a unique means to investigate the structural changes in the optical properties of biological tissues.

Structure and function of seed storage proteins in faba bean (Vicia faba L.).

PubMed

Liu, Yujiao; Wu, Xuexia; Hou, Wanwei; Li, Ping; Sha, Weichao; Tian, Yingying

2017-05-01

The protein subunit is the most important basic unit of protein, and its study can unravel the structure and function of seed storage proteins in faba bean. In this study, we identified six specific protein subunits in Faba bean (cv. Qinghai 13) combining liquid chromatography (LC), liquid chromatography-electronic spray ionization mass (LC-ESI-MS/MS) and bio-information technology. The results suggested a diversity of seed storage proteins in faba bean, and a total of 16 proteins (four GroEL molecular chaperones and 12 plant-specific proteins) were identified from 97-, 96-, 64-, 47-, 42-, and 38-kD-specific protein subunits in faba bean based on the peptide sequence. We also analyzed the composition and abundance of the amino acids, the physicochemical characteristics, secondary structure, three-dimensional structure, transmembrane domain, and possible subcellular localization of these identified proteins in faba bean seed, and finally predicted function and structure. The three-dimensional structures were generated based on homologous modeling, and the protein function was analyzed based on the annotation from the non-redundant protein database (NR database, NCBI) and function analysis of optimal modeling. The objective of this study was to identify the seed storage proteins in faba bean and confirm the structure and function of these proteins. Our results can be useful for the study of protein nutrition and achieve breeding goals for optimal protein quality in faba bean.

Structural Analysis Methods for Structural Health Management of Future Aerospace Vehicles

NASA Technical Reports Server (NTRS)

Tessler, Alexander

2007-01-01

Two finite element based computational methods, Smoothing Element Analysis (SEA) and the inverse Finite Element Method (iFEM), are reviewed, and examples of their use for structural health monitoring are discussed. Due to their versatility, robustness, and computational efficiency, the methods are well suited for real-time structural health monitoring of future space vehicles, large space structures, and habitats. The methods may be effectively employed to enable real-time processing of sensing information, specifically for identifying three-dimensional deformed structural shapes as well as the internal loads. In addition, they may be used in conjunction with evolutionary algorithms to design optimally distributed sensors. These computational tools have demonstrated substantial promise for utilization in future Structural Health Management (SHM) systems.

A preliminary geodetic data model for geographic information systems

NASA Astrophysics Data System (ADS)

Kelly, K. M.

2009-12-01

Our ability to gather and assimilate integrated data collections from multiple disciplines is important for earth system studies. Moreover, geosciences data collection has increased dramatically, with pervasive networks of observational stations on the ground, in the oceans, in the atmosphere and in space. Contemporary geodetic observations from several space and terrestrial technologies contribute to our knowledge of earth system processes and thus are a valuable source of high accuracy information for many global change studies. Assimilation of these geodetic observations and numerical models into models of weather, climate, oceans, hydrology, ice, and solid Earth processes is an important contribution geodesists can make to the earth science community. Clearly, the geodetic observations and models are fundamental to these contributions. ESRI wishes to provide leadership in the geodetic community to collaboratively build an open, freely available content specification that can be used by anyone to structure and manage geodetic data. This Geodetic Data Model will provide important context for all geographic information. The production of a task-specific geodetic data model involves several steps. The goal of the data model is to provide useful data structures and best practices for each step, making it easier for geodesists to organize their data and metadata in a way that will be useful in their data analyses and to their customers. Built on concepts from the successful Arc Marine data model, we introduce common geodetic data types and summarize the main thematic layers of the Geodetic Data Model. These provide a general framework for envisioning the core feature classes required to represent geodetic data in a geographic information system. Like Arc Marine, the framework is generic to allow users to build workflow or product specific geodetic data models tailored to the specific task(s) at hand. This approach allows integration of the data with other existing geophysical datasets, thus facilitating creation of multi-tiered models. The Geodetic Data Model encourages data assimilation and analysis and facilitates data interoperability, coordination and integration in earth system modeling. It offers a basic set of data structures organized in a simple and homogeneous way and can streamline access to and processing of geodetic data. It can aid knowledge discovery through the use of GIS technology to enable identification and understanding of relationships and provide well-established tools and methods to communicate complex technical knowledge with non-specialist audiences. The Geodetic Data Model comprise the base classes for using workflow driven ontology (WDO) techniques for specifying the computation of complex geodetic products along with the ability to capture provenance information. While we do not specify WDO for any given geodetic product, we recognize that structured geodetic data is essential for generating any geodetic WDO, a task that can be streamlined in some GIS software.

The Semantic Environment: Heuristics for a Cross-Context Human-Information Interaction Model

NASA Astrophysics Data System (ADS)

Resmini, Andrea; Rosati, Luca

This chapter introduces a multidisciplinary holistic approach for the general design of successful bridge experiences as a cross-context human-information interaction model. Nowadays it is common to interact through a number of different domains in order to communicate successfully, complete a task, or elicit a desired response: Users visit a reseller’s web site to find a specific item, book it, then drive to the closest store to complete their purchase. As such, one of the crucial challenges user experience design will face in the near future is how to structure and provide bridge experiences seamlessly spanning multiple communication channels or media formats for a specific purpose.

Divergence of Structure and Function in the Haloacid Dehalogenase Enzyme Superfamily: Bacteroides thetaiotaomicron BT2127 is an Inorganic Pyrophosphatase+

PubMed Central

Huang, Hua; Yury, Patskovsky; Toro, Rafael; Farelli, Jeremiah D.; Pandya, Chetanya; Almo, Steven C.; Allen, Karen N.; Dunaway-Mariano, Debra

2012-01-01

The explosion of protein sequence information requires that current strategies for function assignment must evolve to complement experimental approaches with computationally-based function prediction. This necessitates the development of strategies based on the identification of sequence markers in the form of specificity determinants and a more informed definition of orthologues. Herein, we have undertaken the function assignment of the unknown Haloalkanoate Dehalogenase superfamily member BT2127 (Uniprot accession # Q8A5V9) from Bacteroides thetaiotaomicron using an integrated bioinformatics/structure/mechanism approach. The substrate specificity profile and steady-state rate constants of BT2127 (with kcat/Km value for pyrophosphate of ∼1 × 105 M−1 s−1), together with the gene context, supports the assigned in vivo function as an inorganic pyrophosphatase. The X-ray structural analysis of the wild-type BT2127 and several variants generated by site-directed mutagenesis shows that substrate discrimination is based, in part, on active site space restrictions imposed by the cap domain (specifically by residues Tyr76 and Glu47). Structure guided site directed mutagenesis coupled with kinetic analysis of the mutant enzymes identified the residues required for catalysis, substrate binding, and domain-domain association. Based on this structure-function analysis, the catalytic residues Asp11, Asp13, Thr113, and Lys147 as well the metal binding residues Asp171, Asn172 and Glu47 were used as markers to confirm BT2127 orthologues identified via sequence searches. This bioinformatic analysis demonstrated that the biological range of BT2127 orthologue is restricted to the phylum Bacteroidetes/Chlorobi. The key structural determinants in the divergence of BT2127 and its closest homologue β-phosphoglucomutase control the leaving group size (phosphate vs. glucose-phosphate) and the position of the Asp acid/base in the open vs. closed conformations. HADSF pyrophosphatases represent a third mechanistic and fold type for bacterial pyrophosphatases. PMID:21894910

Identification of the centromere-specific histone H3 variant in Lotus japonicus.

PubMed

Tek, Ahmet L; Kashihara, Kazunari; Murata, Minoru; Nagaki, Kiyotaka

2014-03-15

The centromere is a structurally and functionally specialized region present on every eukaryotic chromosome. Lotus japonicus is a model legume species for which there is very limited information on the centromere structure. Here we cloned and characterized the L. japonicus homolog of the centromere-specific histone H3 gene (LjCenH3) encoding a 159-amino acid protein. Using an Agrobacterium-based transformation system, LjCenH3 tagged with a green fluorescent protein was transferred into L. japonicus cells. The centromeric position of LjCENH3 protein was revealed on L. japonicus metaphase chromosomes by an immunofluorescence assay. The identification of LjCenH3 as a critical centromere landmark could pave the way for a better understanding of centromere structure in this model and other agriculturally important legume species. Published by Elsevier B.V.

Automatic generation of Web mining environments

NASA Astrophysics Data System (ADS)

Cibelli, Maurizio; Costagliola, Gennaro

1999-02-01

The main problem related to the retrieval of information from the world wide web is the enormous number of unstructured documents and resources, i.e., the difficulty of locating and tracking appropriate sources. This paper presents a web mining environment (WME), which is capable of finding, extracting and structuring information related to a particular domain from web documents, using general purpose indices. The WME architecture includes a web engine filter (WEF), to sort and reduce the answer set returned by a web engine, a data source pre-processor (DSP), which processes html layout cues in order to collect and qualify page segments, and a heuristic-based information extraction system (HIES), to finally retrieve the required data. Furthermore, we present a web mining environment generator, WMEG, that allows naive users to generate a WME specific to a given domain by providing a set of specifications.

ABAEnrichment: an R package to test for gene set expression enrichment in the adult and developing human brain.

PubMed

Grote, Steffi; Prüfer, Kay; Kelso, Janet; Dannemann, Michael

2016-10-15

We present ABAEnrichment, an R package that tests for expression enrichment in specific brain regions at different developmental stages using expression information gathered from multiple regions of the adult and developing human brain, together with ontologically organized structural information about the brain, both provided by the Allen Brain Atlas. We validate ABAEnrichment by successfully recovering the origin of gene sets identified in specific brain cell-types and developmental stages. ABAEnrichment was implemented as an R package and is available under GPL (≥ 2) from the Bioconductor website (http://bioconductor.org/packages/3.3/bioc/html/ABAEnrichment.html). steffi_grote@eva.mpg.de, kelso@eva.mpg.de or michael_dannemann@eva.mpg.deSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

Structural health monitoring to detect the presence, location and magnitude of structural damage in cadaveric porcine spines.

PubMed

Kawchuk, Gregory Neil; Decker, Colleen; Dolan, Ryan; Carey, Jason

2009-01-19

Structural health monitoring has been used successfully to identify defects in civil infrastructure and aerospace applications. Given that the majority of low back pain is thought to be mechanical in nature, our objective was to determine if structural health monitoring techniques could be employed successfully to identify the presence, location and magnitude of structural alterations within the spine. In six eviscerated cadaveric pigs, bone screws were drilled into the anterior bodies of L1-L5 and tri-axial accelerometers fixed to each spinous process. Vibration was then applied to the L3 spinous and frequency response functions obtained from each sensor axis before and after specific alterations of spinal structure. These alterations were produced at four unique locations and included (1) use of a cable tie to link anterior bone pins together and (2) progressive disc sectioning. Eighty percent of all data were used to train a neural network while the remaining data were used to test the network's ability to distinguish between structural states. The presence, location and magnitude of structural change within the spine was identified correctly in 5030/5040 possible neural network decisions. The diagnostic sensitivity and specificity of this technique ranged from 0.994 to 1.000. These results indicate that there is sufficient information embedded in frequency response data to identify the presence, location and magnitude of specific structural changes in the spine. If these techniques can be evolved for human use, structural health monitoring may provide a new approach toward understanding the underlying relations between spinal structure and function.

Time, Language, and Autobiographical Memory

ERIC Educational Resources Information Center

Burt, Christopher D. B.

2008-01-01

Life themes, general events, and event-specific episodes, together with autobiographical knowledge, form autobiographical memory. Each of these memory structures is described, and research that has investigated the storage and retrieval of temporal information for life events, such as place in time, duration, and order, is examined. The general…

Basis of Accreditation for Educational Programs in Designated Health Science Professions.

ERIC Educational Resources Information Center

Canadian Medical Association, Ottawa (Ontario).

Designed as a guide to accreditation for educational programs in designated health science professions in Canada, this report provides educators with guidelines, general requirements, and requirements for specific programs. Following information on the organization, structure, goals, mission, values, philosophy, and terminology of accreditation of…

SOILSOLN: A Program for Teaching Equilibria Modeling of Soil Solution Composition.

ERIC Educational Resources Information Center

Wolt, Jeffrey D.

1989-01-01

Presents a computer program for use in teaching ion speciation in soil solutions. Provides information on the structure of the program, execution, and software specifications. The program estimates concentrations of ion pairs, hydrolytic species, metal-organic complexes, and free ions in solutions. (Author/RT)

Dissociation free-energy profiles of specific and nonspecific DNA-protein complexes.

PubMed

Yonetani, Yoshiteru; Kono, Hidetoshi

2013-06-27

DNA-binding proteins recognize DNA sequences with at least two different binding modes: specific and nonspecific. Experimental structures of such complexes provide us a static view of the bindings. However, it is difficult to reveal further mechanisms of their target-site search and recognition only from static information because the transition process between the bound and unbound states is not clarified by static information. What is the difference between specific and nonspecific bindings? Here we performed adaptive biasing force molecular dynamics simulations with the specific and nonspecific structures of DNA-Lac repressor complexes to investigate the dissociation process. The resultant free-energy profiles showed that the specific complex has a sharp, deep well consistent with tight binding, whereas the nonspecific complex has a broad, shallow well consistent with loose binding. The difference in the well depth, ~5 kcal/mol, was in fair agreement with the experimentally obtained value and was found to mainly come from the protein conformational difference, particularly in the C-terminal tail. Also, the free-energy profiles were found to be correlated with changes in the number of protein-DNA contacts and that of surface water molecules. The derived protein spatial distributions around the DNA indicate that any large dissociation occurs rarely, regardless of the specific and nonspecific sites. Comparison of the free-energy barrier for sliding [~8.7 kcal/mol; Furini J. Phys. Chem. B 2010, 114, 2238] and that for dissociation (at least ~16 kcal/mol) calculated in this study suggests that sliding is much preferred to dissociation.

Identifiability of large-scale non-linear dynamic network models applied to the ADM1-case study.

PubMed

Nimmegeers, Philippe; Lauwers, Joost; Telen, Dries; Logist, Filip; Impe, Jan Van

2017-06-01

In this work, both the structural and practical identifiability of the Anaerobic Digestion Model no. 1 (ADM1) is investigated, which serves as a relevant case study of large non-linear dynamic network models. The structural identifiability is investigated using the probabilistic algorithm, adapted to deal with the specifics of the case study (i.e., a large-scale non-linear dynamic system of differential and algebraic equations). The practical identifiability is analyzed using a Monte Carlo parameter estimation procedure for a 'non-informative' and 'informative' experiment, which are heuristically designed. The model structure of ADM1 has been modified by replacing parameters by parameter combinations, to provide a generally locally structurally identifiable version of ADM1. This means that in an idealized theoretical situation, the parameters can be estimated accurately. Furthermore, the generally positive structural identifiability results can be explained from the large number of interconnections between the states in the network structure. This interconnectivity, however, is also observed in the parameter estimates, making uncorrelated parameter estimations in practice difficult. Copyright © 2017. Published by Elsevier Inc.

Remediation of information processing following traumatic brain injury: a community-based rehabilitation approach.

PubMed

Ashley, Mark J; Ashley, Jessica; Kreber, Lisa

2012-01-01

Traumatic brain injury (TBI) results in disruption of information processing via damage to primary, secondary, and tertiary cortical regions, as well as, subcortical pathways supporting information flow within and between cortical structures. TBI predominantly affects the anterior frontal poles, anterior temporal poles, white matter tracts and medial temporal structures. Fundamental information processing skills such as attention, perceptual processing, categorization and cognitive distance are concentrated within these same regions and are frequently disrupted following injury. Information processing skills improve in accordance with the extent to which residual frontal and temporal neurons can be encouraged to recruit and bias neuronal networks or the degree to which the functional connectivity of neural networks can be re-established and result in re-emergence or regeneration of specific cognitive skills. Higher-order cognitive processes, i.e., memory, reasoning, problem solving and other executive functions, are dependent upon the integrity of attention, perceptual processing, categorization, and cognitive distance. A therapeutic construct for treatment of attention, perceptual processing, categorization and cognitive distance deficits is presented along with an interventional model for encouragement of re-emergence or regeneration of these fundamental information processing skills.

Perceived threat and corroboration: key factors that improve a predictive model of trust in internet-based health information and advice.

PubMed

Harris, Peter R; Sillence, Elizabeth; Briggs, Pam

2011-07-27

How do people decide which sites to use when seeking health advice online? We can assume, from related work in e-commerce, that general design factors known to affect trust in the site are important, but in this paper we also address the impact of factors specific to the health domain. The current study aimed to (1) assess the factorial structure of a general measure of Web trust, (2) model how the resultant factors predicted trust in, and readiness to act on, the advice found on health-related websites, and (3) test whether adding variables from social cognition models to capture elements of the response to threatening, online health-risk information enhanced the prediction of these outcomes. Participants were asked to recall a site they had used to search for health-related information and to think of that site when answering an online questionnaire. The questionnaire consisted of a general Web trust questionnaire plus items assessing appraisals of the site, including threat appraisals, information checking, and corroboration. It was promoted on the hungersite.com website. The URL was distributed via Yahoo and local print media. We assessed the factorial structure of the measures using principal components analysis and modeled how well they predicted the outcome measures using structural equation modeling (SEM) with EQS software. We report an analysis of the responses of participants who searched for health advice for themselves (N = 561). Analysis of the general Web trust questionnaire revealed 4 factors: information quality, personalization, impartiality, and credible design. In the final SEM model, information quality and impartiality were direct predictors of trust. However, variables specific to eHealth (perceived threat, coping, and corroboration) added substantially to the ability of the model to predict variance in trust and readiness to act on advice on the site. The final model achieved a satisfactory fit: χ(2) (5) = 10.8 (P = .21), comparative fit index = .99, root mean square error of approximation = .052. The model accounted for 66% of the variance in trust and 49% of the variance in readiness to act on the advice. Adding variables specific to eHealth enhanced the ability of a model of trust to predict trust and readiness to act on advice.

Perceived Threat and Corroboration: Key Factors That Improve a Predictive Model of Trust in Internet-based Health Information and Advice

PubMed Central

Harris, Peter R; Briggs, Pam

2011-01-01

Background How do people decide which sites to use when seeking health advice online? We can assume, from related work in e-commerce, that general design factors known to affect trust in the site are important, but in this paper we also address the impact of factors specific to the health domain. Objective The current study aimed to (1) assess the factorial structure of a general measure of Web trust, (2) model how the resultant factors predicted trust in, and readiness to act on, the advice found on health-related websites, and (3) test whether adding variables from social cognition models to capture elements of the response to threatening, online health-risk information enhanced the prediction of these outcomes. Methods Participants were asked to recall a site they had used to search for health-related information and to think of that site when answering an online questionnaire. The questionnaire consisted of a general Web trust questionnaire plus items assessing appraisals of the site, including threat appraisals, information checking, and corroboration. It was promoted on the hungersite.com website. The URL was distributed via Yahoo and local print media. We assessed the factorial structure of the measures using principal components analysis and modeled how well they predicted the outcome measures using structural equation modeling (SEM) with EQS software. Results We report an analysis of the responses of participants who searched for health advice for themselves (N = 561). Analysis of the general Web trust questionnaire revealed 4 factors: information quality, personalization, impartiality, and credible design. In the final SEM model, information quality and impartiality were direct predictors of trust. However, variables specific to eHealth (perceived threat, coping, and corroboration) added substantially to the ability of the model to predict variance in trust and readiness to act on advice on the site. The final model achieved a satisfactory fit: χ2 5 = 10.8 (P = .21), comparative fit index = .99, root mean square error of approximation = .052. The model accounted for 66% of the variance in trust and 49% of the variance in readiness to act on the advice. Conclusions Adding variables specific to eHealth enhanced the ability of a model of trust to predict trust and readiness to act on advice. PMID:21795237

SORTEZ: a relational translator for NCBI's ASN.1 database.

PubMed

Hart, K W; Searls, D B; Overton, G C

1994-07-01

The National Center for Biotechnology Information (NCBI) has created a database collection that includes several protein and nucleic acid sequence databases, a biosequence-specific subset of MEDLINE, as well as value-added information such as links between similar sequences. Information in the NCBI database is modeled in Abstract Syntax Notation 1 (ASN.1) an Open Systems Interconnection protocol designed for the purpose of exchanging structured data between software applications rather than as a data model for database systems. While the NCBI database is distributed with an easy-to-use information retrieval system, ENTREZ, the ASN.1 data model currently lacks an ad hoc query language for general-purpose data access. For that reason, we have developed a software package, SORTEZ, that transforms the ASN.1 database (or other databases with nested data structures) to a relational data model and subsequently to a relational database management system (Sybase) where information can be accessed through the relational query language, SQL. Because the need to transform data from one data model and schema to another arises naturally in several important contexts, including efficient execution of specific applications, access to multiple databases and adaptation to database evolution this work also serves as a practical study of the issues involved in the various stages of database transformation. We show that transformation from the ASN.1 data model to a relational data model can be largely automated, but that schema transformation and data conversion require considerable domain expertise and would greatly benefit from additional support tools.

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.

A genetic code Boolean structure. II. The genetic information system as a Boolean information system.

PubMed

Sanchez, Robersy; Grau, Ricardo

2005-09-01

A Boolean structure of the genetic code where Boolean deductions have biological and physicochemical meanings was discussed in a previous paper. Now, from these Boolean deductions we propose to define the value of amino acid information in order to consider the genetic information system as a communication system and to introduce the semantic content of information ignored by the conventional information theory. In this proposal, the value of amino acid information is proportional to the molecular weight of amino acids with a proportional constant of about 1.96 x 10(25) bits per kg. In addition to this, for the experimental estimations of the minimum energy dissipation in genetic logic operations, we present two postulates: (1) the energy Ei (i=1,2,...,20) of amino acids in the messages conveyed by proteins is proportional to the value of information, and (2) amino acids are distributed according to their energy Ei so the amino acid population in proteins follows a Boltzmann distribution. Specifically, in the genetic message carried by the DNA from the genomes of living organisms, we found that the minimum energy dissipation in genetic logic operations was close to kTLn(2) joules per bit.

Systems biology of the structural proteome.

PubMed

Brunk, Elizabeth; Mih, Nathan; Monk, Jonathan; Zhang, Zhen; O'Brien, Edward J; Bliven, Spencer E; Chen, Ke; Chang, Roger L; Bourne, Philip E; Palsson, Bernhard O

2016-03-11

The success of genome-scale models (GEMs) can be attributed to the high-quality, bottom-up reconstructions of metabolic, protein synthesis, and transcriptional regulatory networks on an organism-specific basis. Such reconstructions are biochemically, genetically, and genomically structured knowledge bases that can be converted into a mathematical format to enable a myriad of computational biological studies. In recent years, genome-scale reconstructions have been extended to include protein structural information, which has opened up new vistas in systems biology research and empowered applications in structural systems biology and systems pharmacology. Here, we present the generation, application, and dissemination of genome-scale models with protein structures (GEM-PRO) for Escherichia coli and Thermotoga maritima. We show the utility of integrating molecular scale analyses with systems biology approaches by discussing several comparative analyses on the temperature dependence of growth, the distribution of protein fold families, substrate specificity, and characteristic features of whole cell proteomes. Finally, to aid in the grand challenge of big data to knowledge, we provide several explicit tutorials of how protein-related information can be linked to genome-scale models in a public GitHub repository ( https://github.com/SBRG/GEMPro/tree/master/GEMPro_recon/). Translating genome-scale, protein-related information to structured data in the format of a GEM provides a direct mapping of gene to gene-product to protein structure to biochemical reaction to network states to phenotypic function. Integration of molecular-level details of individual proteins, such as their physical, chemical, and structural properties, further expands the description of biochemical network-level properties, and can ultimately influence how to model and predict whole cell phenotypes as well as perform comparative systems biology approaches to study differences between organisms. GEM-PRO offers insight into the physical embodiment of an organism's genotype, and its use in this comparative framework enables exploration of adaptive strategies for these organisms, opening the door to many new lines of research. With these provided tools, tutorials, and background, the reader will be in a position to run GEM-PRO for their own purposes.

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.

Deacylation transition states of a bacterial DD-peptidase.

PubMed

Adediran, S A; Kumar, I; Pratt, R F

2006-10-31

Beta-lactam antibiotics restrict bacterial growth by inhibiting DD-peptidases. These enzymes catalyze the final transpeptidation step in bacterial cell wall biosynthesis. Although much structural information is now available for these enzymes, the mechanism of the actual transpeptidation reaction has not been studied in detail. The reaction is known to involve a double-displacement mechanism with an acyl-enzyme intermediate, which can be attacked by water, specific amino acids, peptides, and other acyl acceptors. We describe in this paper an investigation of acyl acceptor specificity and assess the need for general base catalysis in the deacylation transition state of the Streptomyces R61 DD-peptidase. We show, by the criterion of solvent deuterium kinetic isotope effect measurements and proton inventories, that the transition states of specific and nonspecific substrates are very similar, at least with respect to proton motion. The transition states for attack (tetrahedral intermediate formation) by d-amino acids and Gly-l-Xaa dipeptides do not include a general base catalyst, while such catalysis is essential for reaction with water and d-alpha-hydroxy acids. D-Alpha-hydroxy acids act as acyl acceptors for glycyl substrates but not for more specific d-alanyl substrates; hydroxy acids actually behave, more generally, as mixed inhibitors of the DD-peptidase. The structural and mechanistic bases of these observations are discussed; they should inform transition state analogue design.

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.

TFBSshape: a motif database for DNA shape features of transcription factor binding sites.

PubMed

Yang, Lin; Zhou, Tianyin; Dror, Iris; Mathelier, Anthony; Wasserman, Wyeth W; Gordân, Raluca; Rohs, Remo

2014-01-01

Transcription factor binding sites (TFBSs) are most commonly characterized by the nucleotide preferences at each position of the DNA target. Whereas these sequence motifs are quite accurate descriptions of DNA binding specificities of transcription factors (TFs), proteins recognize DNA as a three-dimensional object. DNA structural features refine the description of TF binding specificities and provide mechanistic insights into protein-DNA recognition. Existing motif databases contain extensive nucleotide sequences identified in binding experiments based on their selection by a TF. To utilize DNA shape information when analysing the DNA binding specificities of TFs, we developed a new tool, the TFBSshape database (available at http://rohslab.cmb.usc.edu/TFBSshape/), for calculating DNA structural features from nucleotide sequences provided by motif databases. The TFBSshape database can be used to generate heat maps and quantitative data for DNA structural features (i.e., minor groove width, roll, propeller twist and helix twist) for 739 TF datasets from 23 different species derived from the motif databases JASPAR and UniPROBE. As demonstrated for the basic helix-loop-helix and homeodomain TF families, our TFBSshape database can be used to compare, qualitatively and quantitatively, the DNA binding specificities of closely related TFs and, thus, uncover differential DNA binding specificities that are not apparent from nucleotide sequence alone.

TFBSshape: a motif database for DNA shape features of transcription factor binding sites

PubMed Central

Yang, Lin; Zhou, Tianyin; Dror, Iris; Mathelier, Anthony; Wasserman, Wyeth W.; Gordân, Raluca; Rohs, Remo

2014-01-01

Transcription factor binding sites (TFBSs) are most commonly characterized by the nucleotide preferences at each position of the DNA target. Whereas these sequence motifs are quite accurate descriptions of DNA binding specificities of transcription factors (TFs), proteins recognize DNA as a three-dimensional object. DNA structural features refine the description of TF binding specificities and provide mechanistic insights into protein–DNA recognition. Existing motif databases contain extensive nucleotide sequences identified in binding experiments based on their selection by a TF. To utilize DNA shape information when analysing the DNA binding specificities of TFs, we developed a new tool, the TFBSshape database (available at http://rohslab.cmb.usc.edu/TFBSshape/), for calculating DNA structural features from nucleotide sequences provided by motif databases. The TFBSshape database can be used to generate heat maps and quantitative data for DNA structural features (i.e., minor groove width, roll, propeller twist and helix twist) for 739 TF datasets from 23 different species derived from the motif databases JASPAR and UniPROBE. As demonstrated for the basic helix-loop-helix and homeodomain TF families, our TFBSshape database can be used to compare, qualitatively and quantitatively, the DNA binding specificities of closely related TFs and, thus, uncover differential DNA binding specificities that are not apparent from nucleotide sequence alone. PMID:24214955

How can clinical practice guidelines be adapted to facilitate shared decision making? A qualitative key-informant study.

PubMed

van der Weijden, Trudy; Pieterse, Arwen H; Koelewijn-van Loon, Marije S; Knaapen, Loes; Légaré, France; Boivin, Antoine; Burgers, Jako S; Stiggelbout, Anne M; Faber, Marjan; Elwyn, Glyn

2013-10-01

To explore how clinical practice guidelines can be adapted to facilitate shared decision making. This was a qualitative key-informant study with group discussions and semi-structured interviews. First, 75 experts in guideline development or shared decision making participated in group discussions at two international conferences. Next, health professionals known as experts in depression or breast cancer, experts on clinical practice guidelines and/or shared decision making, and patient representatives were interviewed (N=20). Using illustrative treatment decisions on depression or breast cancer, we asked the interviewees to indicate as specifically as they could how guidelines could be used to facilitate shared decision making. Interviewees suggested some generic strategies, namely to include a separate chapter on the importance of shared decision making, to use language that encourages patient involvement, and to develop patient versions of guidelines. Recommendation-specific strategies, related to specific decision points in the guideline, were also suggested: These include structuring the presentation of healthcare options to increase professionals' option awareness; structuring the deliberation process between professionals and patients; and providing relevant patient support tools embedded at important decision points in the guideline. This study resulted in an overview of strategies to adapt clinical practice guidelines to facilitate shared decision making. Some strategies seemed more contentious than others. Future research should assess the feasibility and impact of these strategies to make clinical practice guidelines more conducive to facilitate shared decision making.

1993 Fiscal Year Water Resources Division Information Guide

USGS Publications Warehouse

,

1992-01-01

This Guide briefly describes the Water Resources Division's mission, program, and organizational structure, and where and how to obtain specific types of hydrologic information. The Guide also contains a listing of addresses, telephone numbers, and office hours for Headquarters, Regional, District, and State offices. For some offices, two addresses are given: the mailing address of the office to which correspondence should be sent and the street address of the office. The map shows the location of the offices.

Mesoporous silica obtained with methyltriethoxysilane as co-precursor in alkaline medium

NASA Astrophysics Data System (ADS)

Putz, Ana-Maria; Wang, Kunzhou; Len, Adél; Plocek, Jiri; Bezdicka, Petr; Kopitsa, Gennady P.; Khamova, Tamara V.; Ianăşi, Cătălin; Săcărescu, Liviu; Mitróová, Zuzana; Savii, Cecilia; Yan, Minhao; Almásy, László

2017-12-01

Mesoporous silica particles have been synthesized by sol-gel method from tetraethoxysilane (tetraethylorthosilicate, TEOS) and methyltriethoxysilane (MTES), in ethanol and water mixture, at different ratios of the of the silica precursors. Ammonia was used as catalyst at room temperature and hexadecyltrimethylammonium bromide (cetyltrimethylammonium bromide, CTAB) as the structure directing agent. Nitrogen sorption, X-ray diffraction and small-angle neutron scattering gave information on the evolution of the gel structure and pore morphologies in the function of MTES/TEOS molar ratio. Thermogravimetric and differential thermal analysis showed that with addition of MTES the exothermic peak indicating the oxidation of the low molecular weight organic fragments shift to higher temperature. A room-temperature, one-pot synthesis of MCM-41 type materials is presented, in which the variation of the MTES concentration allows to change the hydrophobicity, preserving the specific properties materials, like the ordered pore structure, large specific surface area and high porosity. Specifically, the obtained materials had cylindrical pores, specific surface areas up to 1101 m2/g and total pore volumes up to 0.473 cm3/g. The obtained mesoporous materials are susceptible for further functionalization to improve their selective uptake of guest species in drug delivery applications.

Profiles of Asians in Sacramento. Final Report.

ERIC Educational Resources Information Center

Lee, Ivy

This project was undertaken to provide more information on the condition of Asians. More specifically, it sought to: (1) obtain descriptive and demographic data on Asians; (2) determine the extent of usage of existing social services. Structural and attitudinal factors which facilitate or inhibit usage were examined; (3) identify what Asians…

Inequality across Consonantal Contrasts in Speech Perception: Evidence from Mismatch Negativity

ERIC Educational Resources Information Center

Cornell, Sonia A.; Lahiri, Aditi; Eulitz, Carsten

2013-01-01

The precise structure of speech sound representations is still a matter of debate. In the present neurobiological study, we compared predictions about differential sensitivity to speech contrasts between models that assume full specification of all phonological information in the mental lexicon with those assuming sparse representations (only…

Toward a Semantic Forum for Active Collaborative Learning

ERIC Educational Resources Information Center

Li, Yanyan; Dong, Mingkai; Huang, Ronghuai

2009-01-01

Online discussion forums provide open workspace allowing learners to share information, exchange ideas, address problems and discuss on specific themes. But the substantial impediment to its promotion as effective e-learning facility lies in the continuously increasing messages but with discrete and incoherent structure as well as the loosely-tied…

Basis of Accreditation for Educational Programs in Allied Medical Disciplines.

ERIC Educational Resources Information Center

Canadian Medical Association, Ottawa (Ontario).

Designed as a guide to accreditation for educational programs in the allied medical disciplines in Canada, this report provides educators with guidelines, general requirements and requirements for specific programs. Following information on the organization, structure, goals and terminology of accreditation of allied medical programs in Canada,…

Managing Your Reading Program--A Total System.

ERIC Educational Resources Information Center

Hales, Carma M.; Jones, Maurine E.

This guide provides specific information on designing and implementing a reading program. The guide is divided into the following six parts: (1) "Planning for Instruction," including sections on setting ideal goals, establishing a "reality base," and organizing a work flow; (2) "Content Organization," including sections on the structure of…

Gene flow between divergent cereal - and grass-specific lineages of the rice blast fungus Magnaporthe oryzae

USDA-ARS?s Scientific Manuscript database

Delineating species and epidemic lineages in fungal plant pathogens is critical to our understanding of disease emergence and the structure of fungal biodiversity, and also informs international regulatory decisions. Pyricularia oryzae (syn. Magnaporthe oryzae) is a multi-host pathogen that infects ...

Using Writing Tasks to Elicit Adolescents' Historical Reasoning

ERIC Educational Resources Information Center

Monte-Sano, Chauncey; De La Paz, Susan

2012-01-01

One path to improving adolescents' literacy skills is to integrate reading and writing into the content areas in which such work occurs. Although argumentative writing has been found to help students understand historical content and transform information, scholars do not know the influence of specific task structures on students' writing or…

The Constructs of Identity or the Art of Disregarding Differences.

ERIC Educational Resources Information Center

Von Glasersfeld, Ernst

The information processing terms "content" and "address" are used to describe structural differences between the constructs of individual identity and identity in the equivalence sense. In both cases a sameness relation is established in spite of specific differences. The resulting constructs of identity are known to be…

Flaws in Commercial Reading Materials.

ERIC Educational Resources Information Center

Axelrod, Jerome

Three flaws found in commercial reading materials, such as workbooks and kits, are discussed in this paper, and examples of the flaws are taken from specific materials. The first problem noted is that illustrations frequently provide the information that the learner is supposed to supply through phonetic or structural analysis; the illustrations…

Skill Development: How Brain Research Can Inform Music Teaching

ERIC Educational Resources Information Center

Walter, Donald J.; Walter, Jennifer S.

2015-01-01

Practice is a major element in cultivating musical skill. Some psychologists have proposed that deliberate practice, a specific framework for structuring practice activities, creates the kind of practice necessary to increase skill and develop expertise. While psychologists have been observing behavior, neurologists have studied how the brain…

Martens, sables, and fishers: new synthesis informs management and conservation

Treesearch

Keith B. Aubry; Martin G. Raphael; Marie Oliver

2014-01-01

Martens, sables, and fishers are midsized carnivores belonging to the genus Martes. Their silky coats have been valued in the fur trade for centuries, which has contributed to a marked decline in their numbers. Pacific Northwest Martes species depend on structurally complex forested ecosystems and specific climatic conditions...

Asphalt in Pavement Maintenance.

ERIC Educational Resources Information Center

Asphalt Inst., College Park, MD.

Maintenance methods that can be used equally well in all regions of the country have been developed for the use of asphalt in pavement maintenance. Specific information covering methods, equipment and terminology that applies to the use of asphalt in the maintenance of all types of pavement structures, including shoulders, is provided. In many…

NABIC marker database: A molecular markers information network of agricultural crops.

PubMed

Kim, Chang-Kug; Seol, Young-Joo; Lee, Dong-Jun; Jeong, In-Seon; Yoon, Ung-Han; Lee, Gang-Seob; Hahn, Jang-Ho; Park, Dong-Suk

2013-01-01

In 2013, National Agricultural Biotechnology Information Center (NABIC) reconstructs a molecular marker database for useful genetic resources. The web-based marker database consists of three major functional categories: map viewer, RSN marker and gene annotation. It provides 7250 marker locations, 3301 RSN marker property, 3280 molecular marker annotation information in agricultural plants. The individual molecular marker provides information such as marker name, expressed sequence tag number, gene definition and general marker information. This updated marker-based database provides useful information through a user-friendly web interface that assisted in tracing any new structures of the chromosomes and gene positional functions using specific molecular markers. The database is available for free at http://nabic.rda.go.kr/gere/rice/molecularMarkers/

Nucleotide-dependent bisANS binding to tubulin.

PubMed

Chakraborty, S; Sarkar, N; Bhattacharyya, B

1999-07-13

Non-covalent hydrophobic probes such as 5, 5'-bis(8-anilino-1-naphthalenesulfonate) (bisANS) have become increasingly popular to gain information about protein structure and conformation. However, there are limitations as bisANS binds non-specifically at multiple sites of many proteins. Successful use of this probe depends upon the development of binding conditions where only specific dye-protein interaction will occur. In this report, we have shown that the binding of bisANS to tubulin occurs instantaneously, specifically at one high affinity site when 1 mM guanosine 5'-triphosphate (GTP) is included in the reaction medium. Substantial portions of protein secondary structure and colchicine binding activity of tubulin are lost upon bisANS binding in absence of GTP. BisANS binding increases with time and occurs at multiple sites in the absence of GTP. Like GTP, other analogs, guanosine 5'-diphosphate, guanosine 5'-monophosphate and adenosine 5'-triphosphate, also displace bisANS from the lower affinity sites of tubulin. We believe that these multiple binding sites are generated due to the bisANS-induced structural changes on tubulin and the presence of GTP and other nucleotides protect those structural changes.

Molecular property diagnostic suite (MPDS): Development of disease-specific open source web portals for drug discovery.

PubMed

Nagamani, S; Gaur, A S; Tanneeru, K; Muneeswaran, G; Madugula, S S; Consortium, Mpds; Druzhilovskiy, D; Poroikov, V V; Sastry, G N

2017-11-01

Molecular property diagnostic suite (MPDS) is a Galaxy-based open source drug discovery and development platform. MPDS web portals are designed for several diseases, such as tuberculosis, diabetes mellitus, and other metabolic disorders, specifically aimed to evaluate and estimate the drug-likeness of a given molecule. MPDS consists of three modules, namely data libraries, data processing, and data analysis tools which are configured and interconnected to assist drug discovery for specific diseases. The data library module encompasses vast information on chemical space, wherein the MPDS compound library comprises 110.31 million unique molecules generated from public domain databases. Every molecule is assigned with a unique ID and card, which provides complete information for the molecule. Some of the modules in the MPDS are specific to the diseases, while others are non-specific. Importantly, a suitably altered protocol can be effectively generated for another disease-specific MPDS web portal by modifying some of the modules. Thus, the MPDS suite of web portals shows great promise to emerge as disease-specific portals of great value, integrating chemoinformatics, bioinformatics, molecular modelling, and structure- and analogue-based drug discovery approaches.

Crystallization and preliminary X-ray crystallographic analysis of a highly specific serpin from the beetle Tenebrio molitor

PubMed Central

Park, Sun Hee; Piao, Shunfu; Kwon, Hyun-Mi; Kim, Eun-Hye; Lee, Bok Luel; Ha, Nam-Chul

2010-01-01

The Toll signalling pathway, which is crucial for innate immunity, is transduced in insect haemolymph via a proteolytic cascade consisting of three serine proteases. The proteolytic cascade is downregulated by a specific serine protease inhibitor (serpin). Recently, the serpin SPN48 was found to show an unusual specific reactivity towards the terminal serine protease, Spätzle-processing enzyme, in the beetle Tenebrio molitor. In this study, the mature form of SPN48 was overexpressed in Escherichia coli and purified. The purified SPN48 protein was crystallized using 14% polyethylene glycol 8000 and 0.1 M 2-(N-morpho­lino)ethanesulfonic acid pH 6.0 as the precipitant. The crystals diffracted X-rays to 2.1 Å resolution and were suitable for structure determination. The crystals belonged to space group P21. The crystal structure will provide information regarding how SPN48 achieves its unusual specificity for its target protease. PMID:20124722

Flood type specific construction of synthetic design hydrographs

NASA Astrophysics Data System (ADS)

Brunner, Manuela I.; Viviroli, Daniel; Sikorska, Anna E.; Vannier, Olivier; Favre, Anne-Catherine; Seibert, Jan

2017-02-01

Accurate estimates of flood peaks, corresponding volumes, and hydrographs are required to design safe and cost-effective hydraulic structures. In this paper, we propose a statistical approach for the estimation of the design variables peak and volume by constructing synthetic design hydrographs for different flood types such as flash-floods, short-rain floods, long-rain floods, and rain-on-snow floods. Our approach relies on the fitting of probability density functions to observed flood hydrographs of a certain flood type and accounts for the dependence between peak discharge and flood volume. It makes use of the statistical information contained in the data and retains the process information of the flood type. The method was tested based on data from 39 mesoscale catchments in Switzerland and provides catchment specific and flood type specific synthetic design hydrographs for all of these catchments. We demonstrate that flood type specific synthetic design hydrographs are meaningful in flood-risk management when combined with knowledge on the seasonality and the frequency of different flood types.

Universal Entropy of Word Ordering Across Linguistic Families

PubMed Central

Montemurro, Marcelo A.; Zanette, Damián H.

2011-01-01

Background The language faculty is probably the most distinctive feature of our species, and endows us with a unique ability to exchange highly structured information. In written language, information is encoded by the concatenation of basic symbols under grammatical and semantic constraints. As is also the case in other natural information carriers, the resulting symbolic sequences show a delicate balance between order and disorder. That balance is determined by the interplay between the diversity of symbols and by their specific ordering in the sequences. Here we used entropy to quantify the contribution of different organizational levels to the overall statistical structure of language. Methodology/Principal Findings We computed a relative entropy measure to quantify the degree of ordering in word sequences from languages belonging to several linguistic families. While a direct estimation of the overall entropy of language yielded values that varied for the different families considered, the relative entropy quantifying word ordering presented an almost constant value for all those families. Conclusions/Significance Our results indicate that despite the differences in the structure and vocabulary of the languages analyzed, the impact of word ordering in the structure of language is a statistical linguistic universal. PMID:21603637

Representation of Serendipitous Scientific Data

NASA Technical Reports Server (NTRS)

James, Mark

2006-01-01

A computer program defines and implements an innovative kind of data structure than can be used for representing information derived from serendipitous discoveries made via collection of scientific data on long exploratory spacecraft missions. Data structures capable of collecting any kind of data can easily be implemented in advance, but the task of designing a fixed and efficient data structure suitable for processing raw data into useful information and taking advantage of serendipitous scientific discovery is becoming increasingly difficult as missions go deeper into space. The present software eases the task by enabling definition of arbitrarily complex data structures that can adapt at run time as raw data are transformed into other types of information. This software runs on a variety of computers, and can be distributed in either source code or binary code form. It must be run in conjunction with any one of a number of Lisp compilers that are available commercially or as shareware. It has no specific memory requirements and depends upon the other software with which it is used. This program is implemented as a library that is called by, and becomes folded into, the other software with which it is used.

How individual traces and interactive timelines could support outage execution - Toward an outage historian concept

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

Parfouru, S.; De-Beler, N.

2012-07-01

In the context of a project that is designing innovative ICT-based solutions for the organizational concept of outage management, we focus on the informational process of the OCR (Outage Control Room) underlying the execution of the outages. Informational process are based on structured and unstructured documents that have a key role in the collaborative processes and management of the outage. We especially track the structured and unstructured documents, electronically or not, from creation to sharing. Our analysis allows us to consider that the individual traces produced by an individual participant with a specific role could be multi-purpose and support sharingmore » between participants without creating duplication of work. The ultimate goal is to be able to generate an outage historian, that is not just focused on highly structured information, which could be useful to improve the continuity of information between participants. We study the implementation of this approach through web technologies and social media tools to address this issue. We also investigate the issue of data access through interactive visualization timelines coupled with other modality's to assist users in the navigation and exploration of the proposed historian. (authors)« less

Bim Automation: Advanced Modeling Generative Process for Complex Structures

NASA Astrophysics Data System (ADS)

Banfi, F.; Fai, S.; Brumana, R.

2017-08-01

The new paradigm of the complexity of modern and historic structures, which are characterised by complex forms, morphological and typological variables, is one of the greatest challenges for building information modelling (BIM). Generation of complex parametric models needs new scientific knowledge concerning new digital technologies. These elements are helpful to store a vast quantity of information during the life cycle of buildings (LCB). The latest developments of parametric applications do not provide advanced tools, resulting in time-consuming work for the generation of models. This paper presents a method capable of processing and creating complex parametric Building Information Models (BIM) with Non-Uniform to NURBS) with multiple levels of details (Mixed and ReverseLoD) based on accurate 3D photogrammetric and laser scanning surveys. Complex 3D elements are converted into parametric BIM software and finite element applications (BIM to FEA) using specific exchange formats and new modelling tools. The proposed approach has been applied to different case studies: the BIM of modern structure for the courtyard of West Block on Parliament Hill in Ottawa (Ontario) and the BIM of Masegra Castel in Sondrio (Italy), encouraging the dissemination and interaction of scientific results without losing information during the generative process.

Aging management program of the reactor building concrete at Point Lepreau Generating Station

NASA Astrophysics Data System (ADS)

Aldea, C.-M.; Shenton, B.; Demerchant, M. M.; Gendron, T.

2011-04-01

In order for New Brunswick Power Nuclear (NBPN) to control the risks of degradation of the concrete reactor building at the Point Lepreau Generating Station (PLGS) the development of an aging management plan (AMP) was initiated. The intention of this plan was to determine the requirements for specific structural components of concrete of the reactor building that require regular inspection and maintenance to ensure the safe and reliable operation of the plant. The document is currently in draft form and presents an integrated methodology for the application of an AMP for the concrete of the reactor building. The current AMP addresses the reactor building structure and various components, such as joint sealant and liners that are integral to the structure. It does not include internal components housed within the structure. This paper provides background information regarding the document developed and the strategy developed to manage potential degradation of the concrete of the reactor building, as well as specific programs and preventive and corrective maintenance activities initiated.

AFM Imaging of Hybridization Chain Reaction Mediated Signal Transmission between Two DNA Origami Structures.

PubMed

Helmig, Sarah; Gothelf, Kurt Vesterager

2017-10-23

Signal transfer is central to the controlled exchange of information in biology and advanced technologies. Therefore, the development of reliable, long-range signal transfer systems for artificial nanoscale assemblies is of great scientific interest. We have designed such a system for the signal transfer between two connected DNA nanostructures, using the hybridization chain reaction (HCR). Two sets of metastable DNA hairpins, one of which is immobilized at specific points along tracks on DNA origami structures, are polymerized to form a continuous DNA duplex, which is visible using atomic force microscopy (AFM). Upon addition of a designed initiator, the initiation signal is efficiently transferred more than 200 nm from a specific location on one origami structure to an end point on another origami structure. The system shows no significant loss of signal when crossing from one nanostructure to another and, therefore, has the potential to be applied to larger multi-component DNA assemblies. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Brain white matter structure and information processing speed in healthy older age.

PubMed

Kuznetsova, Ksenia A; Maniega, Susana Muñoz; Ritchie, Stuart J; Cox, Simon R; Storkey, Amos J; Starr, John M; Wardlaw, Joanna M; Deary, Ian J; Bastin, Mark E

2016-07-01

Cognitive decline, especially the slowing of information processing speed, is associated with normal ageing. This decline may be due to brain cortico-cortical disconnection caused by age-related white matter deterioration. We present results from a large, narrow age range cohort of generally healthy, community-dwelling subjects in their seventies who also had their cognitive ability tested in youth (age 11 years). We investigate associations between older age brain white matter structure, several measures of information processing speed and childhood cognitive ability in 581 subjects. Analysis of diffusion tensor MRI data using Tract-based Spatial Statistics (TBSS) showed that all measures of information processing speed, as well as a general speed factor composed from these tests (g speed), were significantly associated with fractional anisotropy (FA) across the white matter skeleton rather than in specific tracts. Cognitive ability measured at age 11 years was not associated with older age white matter FA, except for the g speed-independent components of several individual processing speed tests. These results indicate that quicker and more efficient information processing requires global connectivity in older age, and that associations between white matter FA and information processing speed (both individual test scores and g speed), unlike some other aspects of later life brain structure, are generally not accounted for by cognitive ability measured in youth.

[Studies on the structure-activity relationship of retinoids--Hansch analysis and 3D-OSAR studies on specific ligands of retinoid x receptor].

PubMed

Huang, N; Chu, F; Guo, Z

1998-06-01

Retinoids (Vitamin A, its metabolites and synthetic analogues) play important roles in a variety of biological processes, including cellular differentiation, proliferation and apoptosis. The many diverse actions of retinoids attribute to the ability of regulating transcription of different target genes through activation of multiple retinoid nuclear receptors (RAR of RXR). So, retinoids with selective binding ability to specific receptor may not only have improved therapeutic indices, but may also be invaluable for elucidating the molecular mechanism of retinoidal transcriptional activation. Based on the two dimensional and three dimensional quantitative structure-activity relationships of specific ligands of RXR, we carried out mimesis of environment of ligands interacting with their receptor and, to some extent, mapping the topological and physico-chemical characteristics of receptor. The knowledge of the QSAR study will offer detailed molecular information for design, synthesis and biological evaluation in drug research and development.

General approach to reversing ketol-acid reductoisomerase cofactor dependence from NADPH to NADH

DOE PAGES

Brinkmann-Chen, Sabine; Flock, Tilman; Cahn, Jackson K. B.; ...

2013-06-17

To date, efforts to switch the cofactor specificity of oxidoreductases from nicotinamide adenine dinucleotide phosphate (NADPH) to nicotinamide adenine dinucleotide (NADH) have been made on a case-by-case basis with varying degrees of success. Here we present a straightforward recipe for altering the cofactor specificity of a class of NADPH-dependent oxidoreductases, the ketol-acid reductoisomerases (KARIs). Combining previous results for an engineered NADH-dependent variant of Escherichia coli KARI with available KARI crystal structures and a comprehensive KARI-sequence alignment, we identified key cofactor specificity determinants and used this information to construct five KARIs with reversed cofactor preference. Additional directed evolution generated two enzymesmore » having NADH-dependent catalytic efficiencies that are greater than the wild-type enzymes with NADPH. As a result, high-resolution structures of a wild-type/variant pair reveal the molecular basis of the cofactor switch.« less

DICOM static and dynamic representation through unified modeling language

NASA Astrophysics Data System (ADS)

Martinez-Martinez, Alfonso; Jimenez-Alaniz, Juan R.; Gonzalez-Marquez, A.; Chavez-Avelar, N.

2004-04-01

The DICOM standard, as all standards, specifies in generic way the management in network and storage media environments of digital medical images and their related information. However, understanding the specifications for particular implementation is not a trivial work. Thus, this work is about understanding and modelling parts of the DICOM standard using Object Oriented methodologies, as part of software development processes. This has offered different static and dynamic views, according with the standard specifications, and the resultant models have been represented through the Unified Modelling Language (UML). The modelled parts are related to network conformance claim: Network Communication Support for Message Exchange, Message Exchange, Information Object Definitions, Service Class Specifications, Data Structures and Encoding, and Data Dictionary. The resultant models have given a better understanding about DICOM parts and have opened the possibility of create a software library to develop DICOM conformable PACS applications.

Structural Characterization of Mannan Cell Wall Polysaccharides in Plants Using PACE

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

Pidatala, Venkataramana R.; Mahboubi, Amir; Mortimer, Jenny C.

Plant cell wall polysaccharides are notoriously difficult to analyze, and most methods require expensive equipment, skilled operators, and large amounts of purified material. Here, we describe a simple method for gaining detailed polysaccharide structural information, including resolution of structural isomers. For polysaccharide analysis by gel electrophoresis (PACE), plant cell wall material is hydrolyzed with glycosyl hydrolases specific to the polysaccharide of interest (e.g., mannanases for mannan). Large format polyacrylamide gels are then used to separate the released oligosaccharides, which have been fluorescently labeled. Gels can be visualized with a modified gel imaging system (see Table of Materials). The resulting oligosaccharidemore » fingerprint can either be compared qualitatively or, with replication, quantitatively. Linkage and branching information can be established using additional glycosyl hydrolases (e.g., mannosidases and galactosidases). Whilst this protocol describes a method for analyzing glucomannan structure, it can be applied to any polysaccharide for which characterized glycosyl hydrolases exist. Alternatively, it can be used to characterize novel glycosyl hydrolases using defined polysaccharide substrates.« less

Structural Characterization of Mannan Cell Wall Polysaccharides in Plants Using PACE.

PubMed

Pidatala, Venkataramana R; Mahboubi, Amir; Mortimer, Jenny C

2017-10-16

Plant cell wall polysaccharides are notoriously difficult to analyze, and most methods require expensive equipment, skilled operators, and large amounts of purified material. Here, we describe a simple method for gaining detailed polysaccharide structural information, including resolution of structural isomers. For polysaccharide analysis by gel electrophoresis (PACE), plant cell wall material is hydrolyzed with glycosyl hydrolases specific to the polysaccharide of interest (e.g., mannanases for mannan). Large format polyacrylamide gels are then used to separate the released oligosaccharides, which have been fluorescently labeled. Gels can be visualized with a modified gel imaging system (see Table of Materials). The resulting oligosaccharide fingerprint can either be compared qualitatively or, with replication, quantitatively. Linkage and branching information can be established using additional glycosyl hydrolases (e.g., mannosidases and galactosidases). Whilst this protocol describes a method for analyzing glucomannan structure, it can be applied to any polysaccharide for which characterized glycosyl hydrolases exist. Alternatively, it can be used to characterize novel glycosyl hydrolases using defined polysaccharide substrates.

Structural Characterization of Mannan Cell Wall Polysaccharides in Plants Using PACE

DOE PAGES

Pidatala, Venkataramana R.; Mahboubi, Amir; Mortimer, Jenny C.

2017-10-16

Plant cell wall polysaccharides are notoriously difficult to analyze, and most methods require expensive equipment, skilled operators, and large amounts of purified material. Here, we describe a simple method for gaining detailed polysaccharide structural information, including resolution of structural isomers. For polysaccharide analysis by gel electrophoresis (PACE), plant cell wall material is hydrolyzed with glycosyl hydrolases specific to the polysaccharide of interest (e.g., mannanases for mannan). Large format polyacrylamide gels are then used to separate the released oligosaccharides, which have been fluorescently labeled. Gels can be visualized with a modified gel imaging system (see Table of Materials). The resulting oligosaccharidemore » fingerprint can either be compared qualitatively or, with replication, quantitatively. Linkage and branching information can be established using additional glycosyl hydrolases (e.g., mannosidases and galactosidases). Whilst this protocol describes a method for analyzing glucomannan structure, it can be applied to any polysaccharide for which characterized glycosyl hydrolases exist. Alternatively, it can be used to characterize novel glycosyl hydrolases using defined polysaccharide substrates.« less

Structural health monitoring of civil infrastructure.

PubMed

Brownjohn, J M W

2007-02-15

Structural health monitoring (SHM) is a term increasingly used in the last decade to describe a range of systems implemented on full-scale civil infrastructures and whose purposes are to assist and inform operators about continued 'fitness for purpose' of structures under gradual or sudden changes to their state, to learn about either or both of the load and response mechanisms. Arguably, various forms of SHM have been employed in civil infrastructure for at least half a century, but it is only in the last decade or two that computer-based systems are being designed for the purpose of assisting owners/operators of ageing infrastructure with timely information for their continued safe and economic operation. This paper describes the motivations for and recent history of SHM applications to various forms of civil infrastructure and provides case studies on specific types of structure. It ends with a discussion of the present state-of-the-art and future developments in terms of instrumentation, data acquisition, communication systems and data mining and presentation procedures for diagnosis of infrastructural 'health'.

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.

Normal Science Education and its Dangers: The Case of School Chemistry

NASA Astrophysics Data System (ADS)

Van Berkel, Berry; De Vos, Wobbe; Verdonk, Adri H.; Pilot, Albert

We started the Conceptual Structure of School Chemistry research project, a part of which is reported on here, with an attempt to solve the problem of the hidden structure in school chemistry. In order to solve that problem, and informed by previous research, we performed a content analysis of school chemistry textbooks and syllabi. This led us to the hypothesis that school chemistry curricula are based on an underlying, coherent structure of chemical concepts that students are supposed to learn for the purpose of explaining and predicting chemical phenomena. The elicited comments and criticisms of an International Forum of twenty-eight researchers of chemical education, though, refuted the central claims of this hypothesis. This led to a descriptive theory of the currently dominant school chemistry curriculum in terms of a rigid combination of a specific substantive structure, based on corpuscular theory, a specific philosophical structure, educational positivism, and a specific pedagogical structure, involving initiatory and preparatory training of future chemists. Secondly, it led to an explanatory theory of the structure of school chemistry - based on Kuhn's theory of normal science and scientific training - in which dominant school chemistry is interpreted as a form of normal science education. Since the former has almost all characteristics in common with the latter, dominant school chemistry must be regarded as normal chemistry education. Forum members also formulated a number of normative criticisms on dominant school chemistry, which we interpret as specific dangers of normal chemistry education, complementing Popper's discussion of the general dangers of normal science and its teaching. On the basis of these criticisms, it is argued that normal chemistry education is isolated from common sense, everyday life and society, history and philosophy of science, technology, school physics, and from chemical research.

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.

Interfacing modules for integrating discipline specific structural mechanics codes

NASA Technical Reports Server (NTRS)

Endres, Ned M.

1989-01-01

An outline of the organization and capabilities of the Engine Structures Computational Simulator (Simulator) at NASA Lewis Research Center is given. One of the goals of the research at Lewis is to integrate various discipline specific structural mechanics codes into a software system which can be brought to bear effectively on a wide range of engineering problems. This system must possess the qualities of being effective and efficient while still remaining user friendly. The simulator was initially designed for the finite element simulation of gas jet engine components. Currently, the simulator has been restricted to only the analysis of high pressure turbine blades and the accompanying rotor assembly, although the current installation can be expanded for other applications. The simulator presently assists the user throughout its procedures by performing information management tasks, executing external support tasks, organizing analysis modules and executing these modules in the user defined order while maintaining processing continuity.

The development of structural complexity in the child's concept of family: the effect of cognitive stage, sex, and intactness of family.

PubMed

Wedemeyer, N V; Bickhard, M H; Cooper, R G

1989-12-01

Twenty-eight boys and 28 girls at each of the Piagetian preoperational, concrete operational, and formal operational cognitive stages were given an interview focusing on their concepts of family. Half of each group were from intact families, and half were from divorced families. Interviews were scored for two structural aspects of the concept of family: conceptual level, and use of dimensions that structure the concept. The complexity of children's concepts was strongly related to cognitive stage and, to a lesser degree, to sex. Frequency of use of concept dimensions was strongly affected by general developmental level, though not specifically cognitive stage, and by intactness of family, but to a lesser degree by sex. Specific information is provided on the effect of these factors on perceptions of family composition, parental roles, and breadth of family activities.

Effects of using structured templates for recalling chemistry experiments.

PubMed

Willoughby, Cerys; Logothetis, Thomas A; Frey, Jeremy G

2016-01-01

The way that we recall information is dependent upon both the knowledge in our memories and the conditions under which we recall the information. Electronic Laboratory Notebooks can provide a structured interface for the capture of experiment records through the use of forms and templates. These templates can be useful by providing cues to help researchers to remember to record particular aspects of their experiment, but they may also constrain the information that is recorded by encouraging them to record only what is asked for. It is therefore unknown whether using structured templates for capturing experiment records will have positive or negative effects on the quality and usefulness of the records for assessment and future use. In this paper we report on the results of a set of studies investigating the effects of different template designs on the recording of experiments by undergraduate students and academic researchers. The results indicate that using structured templates to write up experiments does make a significant difference to the information that is recalled and recorded. These differences have both positive and negative effects, with templates prompting the capture of specific information that is otherwise forgotten, but also apparently losing some of the personal elements of the experiment experience such as observations and explanations. Other unexpected effects were seen with templates that can change the information that is captured, but also interfere with the way an experiment is conducted. Our results showed that using structured templates can improve the completeness of the experiment context information captured but can also cause a loss of personal elements of the experiment experience when compared with allowing the researcher to structure their own record. The results suggest that interfaces for recording information about chemistry experiments, whether paper-based questionnaires or templates in Electronic Laboratory Notebooks, can be an effective way to improve the quality of experiment write-ups, but that care needs to be taken to ensure that the correct cues are provided.Graphical abstractScientists have traditionally recorded their research in paper notebooks, a format that provides great flexibility for capturing information. In contrast, Electronic Laboratory Notebooks frequently make use of forms or structured templates for capturing experiment records. Structured templates can provide cues that can improve record quality by increasing the amount of information captured and encouraging consistency. However, using the wrong cues can lead to a loss of personal elements of the experiment experience and frustrate users. This image shows two participants from one of our studies recording their experiment using a computer-based template.

General specifications for the development of a PC-based simulator of the NASA RECON system

NASA Technical Reports Server (NTRS)

Dominick, Wayne D. (Editor); Triantafyllopoulos, Spiros

1984-01-01

The general specifications for the design and implementation of an IBM PC/XT-based simulator of the NASA RECON system, including record designs, file structure designs, command language analysis, program design issues, error recovery considerations, and usage monitoring facilities are discussed. Once implemented, such a simulator will be utilized to evaluate the effectiveness of simulated information system access in addition to actual system usage as part of the total educational programs being developed within the NASA contract.

On the modal characteristics of damaging structures subjected to earthquakes

NASA Astrophysics Data System (ADS)

Carlo Ponzo, Felice; Ditommaso, Rocco; Auletta, Gianluca; Iacovino, Chiara; Mossucca, Antonello; Nigro, Antonella; Nigro, Domenico

2015-04-01

Structural Health Monitoring, especially for structures located in seismic prone areas, has assumed a meaning of great importance in last years, for the possibility to make a more objective and more rapid estimation of the damage occurred on buildings after a seismic event. In the last years many researchers are working to set-up new methodologies for Non-destructive Damage Evaluation based on the variation of the dynamic behaviour of structures under seismic loads. The NDE methods for damage detection and evaluation can be classified into four levels, according to the specific criteria provided by the Rytter. Each level of identification is correlated with specific information related to monitored structure. In fact, by increasing the level it is possible to obtain more information about the state of the health of the structures, to know if damage occurred on the structures, to quantify and localize the damage and to evaluate its impact on the monitored structure. Several authors discussed on the possibility to use the mode shape curvature to localize damage on structural elements, for example, by applying the curvature-based method to frequency response function instead of mode shape, and demonstrated the potential of this approach by considering real data. Damage detection approach based on dynamic monitoring of structural properties over time has received a considerable attention in recent scientific literature. In earthquake engineering field, the recourse to experimental research is necessary to understand the mechanical behaviour of the various structural and non-structural components. In this paper a new methodology to detect and localize a possible damage occurred on a framed structure after an earthquake is presented and discussed. The main outcomes retrieved from many numerical non linear dynamic models of reinforced concrete framed structures characterized by 3, 5 and 8 floors with different geometric configurations and designed for gravity loads only are here presented. In addition, the main results of experimental shaking table tests carried out on a steel framed model are also showed to confirm the effectiveness of the proposed procedure. Acknowledgements This study was partially funded by the Italian Civil Protection Department within the project DPC-RELUIS 2014 - RS4 ''Seismic observatory of structures and health monitoring''.

Specificity in the interaction of natural products with their target proteins--a biochemical and structural insight.

PubMed

Venkatraman, Prasanna

2010-06-01

Natural products are an abundant source of anti cancer agents. They act as cytotoxic drugs, and inhibitors of apoptosis, transcription, cell proliferation and angiogenesis. While pathways targeted by natural products have been well studied, there is paucity of information about the in vivo molecular target/s of these compounds. This review summarizes some of the natural compounds for which the molecular targets, mechanism of action and structural basis of specificity have been well documented. These examples illustrate that 'off target' binding can be explained on the basis of diversity inherent to biomolecular interactions. There is enough evidence to suggest that natural compounds are potent and versatile warheads that can be optimized for a multi targeted therapeutic intervention in cancer.

Tool for Constructing Data Albums for Significant Weather Events

NASA Astrophysics Data System (ADS)

Kulkarni, A.; Ramachandran, R.; Conover, H.; McEniry, M.; Goodman, H.; Zavodsky, B. T.; Braun, S. A.; Wilson, B. D.

2012-12-01

Case study analysis and climatology studies are common approaches used in Atmospheric Science research. Research based on case studies involves a detailed description of specific weather events using data from different sources, to characterize physical processes in play for a given event. Climatology-based research tends to focus on the representativeness of a given event, by studying the characteristics and distribution of a large number of events. To gather relevant data and information for case studies and climatology analysis is tedious and time consuming; current Earth Science data systems are not suited to assemble multi-instrument, multi mission datasets around specific events. For example, in hurricane science, finding airborne or satellite data relevant to a given storm requires searching through web pages and data archives. Background information related to damages, deaths, and injuries requires extensive online searches for news reports and official storm summaries. We will present a knowledge synthesis engine to create curated "Data Albums" to support case study analysis and climatology studies. The technological challenges in building such a reusable and scalable knowledge synthesis engine are several. First, how to encode domain knowledge in a machine usable form? This knowledge must capture what information and data resources are relevant and the semantic relationships between the various fragments of information and data. Second, how to extract semantic information from various heterogeneous sources including unstructured texts using the encoded knowledge? Finally, how to design a structured database from the encoded knowledge to store all information and to support querying? The structured database must allow both knowledge overviews of an event as well as drill down capability needed for detailed analysis. An application ontology driven framework is being used to design the knowledge synthesis engine. The knowledge synthesis engine is being applied to build a portal for hurricane case studies at the Global Hydrology and Resource Center (GHRC), a NASA Data Center. This portal will auto-generate Data Albums for specific hurricane events, compiling information from distributed resources such as NASA field campaign collections, relevant data sets, storm reports, pictures, videos and other useful sources.

Crystal Structure of Human Dual-Specificity Tyrosine-Regulated Kinase 3 Reveals New Structural Features and Insights into its Auto-phosphorylation.

PubMed

Kim, Kuglae; Cha, Jeong Seok; Cho, Yong-Soon; Kim, Hoyoung; Chang, Nienping; Kim, Hye-Jung; Cho, Hyun-Soo

2018-05-11

Dual-specificity tyrosine-regulated kinases (DYRKs) auto-phosphorylate a critical tyrosine residue in their activation loop and phosphorylate their substrate on serine and threonine residues. The auto-phosphorylation occurs intramolecularly and is a one-off event. DYRK3 is selectively expressed at a high level in hematopoietic cells and attenuates erythroblast development, leading to anemia. In the present study, we determined the crystal structure of the mature form of human DYRK3 in complex with harmine, an ATP competitive inhibitor. The crystal structure revealed a phosphorylation site, residue S350, whose phosphorylation increases the stability of DYRK3 and enhances its kinase activity. In addition, our structural and biochemical assays suggest that the N-terminal auto-phosphorylation accessory domain stabilizes the DYRK3 protein, followed by auto-phosphorylation of the tyrosine of the activation loop, which is important for kinase activity. Finally, our docking analysis provides information for the design of novel and potent therapeutics to treat anemia. Copyright © 2018 Elsevier Ltd. All rights reserved.

First principles examination of electronic structure and optical features of 4H-GaN1-xPx polytype alloys

NASA Astrophysics Data System (ADS)

Laref, A.; Hussain, Z.; Laref, S.; Yang, J. T.; Xiong, Y. C.; Luo, S. J.

2018-04-01

By using first-principles calculations, we compute the electronic band structures and typical aspects of the optical spectra of hexagonally structured GaN1-xPx alloys. Although a type III-V semiconductor, GaP commonly possesses a zinc-blende structure with an indirect band gap; as such, it may additionally form hexagonal polytypes under specific growth conditions. The electronic structures and optical properties are calculated by combining a non-nitride III-V semiconductor and a nitride III-V semiconductor, as GaP and GaN crystallizing in a 4H polytype, with the N composition ranging between x = 0-1. For all studied materials, the energy gap is found to be direct. The optical properties of the hexagonal materials may illustrate the strong polarization dependence owing to the crystalline anisotropy. This investigation for GaN1-xPx alloys is anticipated to supply paramount information for applications in the visible/ultraviolet spectral regions. At a specific concentration, x, these alloys would be exclusively appealing candidates for solar-cell applications.

Unzippers, Resolvers and Sensors: A Structural and Functional Biochemistry Tale of RNA Helicases

PubMed Central

Leitão, Ana Lúcia; Costa, Marina C.; Enguita, Francisco J.

2015-01-01

The centrality of RNA within the biological world is an irrefutable fact that currently attracts increasing attention from the scientific community. The panoply of functional RNAs requires the existence of specific biological caretakers, RNA helicases, devoted to maintain the proper folding of those molecules, resolving unstable structures. However, evolution has taken advantage of the specific position and characteristics of RNA helicases to develop new functions for these proteins, which are at the interface of the basic processes for transference of information from DNA to proteins. RNA helicases are involved in many biologically relevant processes, not only as RNA chaperones, but also as signal transducers, scaffolds of molecular complexes, and regulatory elements. Structural biology studies during the last decade, founded in X-ray crystallography, have characterized in detail several RNA-helicases. This comprehensive review summarizes the structural knowledge accumulated in the last two decades within this family of proteins, with special emphasis on the structure-function relationships of the most widely-studied families of RNA helicases: the DEAD-box, RIG-I-like and viral NS3 classes. PMID:25622248

Functional Classification of Immune Regulatory Proteins

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

Rubinstein, Rotem; Ramagopal, Udupi A.; Nathenson, Stanley G.

2013-05-01

Members of the immunoglobulin superfamily (IgSF) control innate and adaptive immunity and are prime targets for the treatment of autoimmune diseases, infectious diseases, and malignancies. We describe a computational method, termed the Brotherhood algorithm, which utilizes intermediate sequence information to classify proteins into functionally related families. This approach identifies functional relationships within the IgSF and predicts additional receptor-ligand interactions. As a specific example, we examine the nectin/nectin-like family of cell adhesion and signaling proteins and propose receptor-ligand interactions within this family. We were guided by the Brotherhood approach and present the high-resolution structural characterization of a homophilic interaction involving themore » class-I MHC-restricted T-cell-associated molecule, which we now classify as a nectin-like family member. The Brotherhood algorithm is likely to have a significant impact on structural immunology by identifying those proteins and complexes for which structural characterization will be particularly informative.« less

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.

Chemical and protein structural basis for biological crosstalk between PPAR α and COX enzymes

NASA Astrophysics Data System (ADS)

Cleves, Ann E.; Jain, Ajay N.

2015-02-01

We have previously validated a probabilistic framework that combined computational approaches for predicting the biological activities of small molecule drugs. Molecule comparison methods included molecular structural similarity metrics and similarity computed from lexical analysis of text in drug package inserts. Here we present an analysis of novel drug/target predictions, focusing on those that were not obvious based on known pharmacological crosstalk. Considering those cases where the predicted target was an enzyme with known 3D structure allowed incorporation of information from molecular docking and protein binding pocket similarity in addition to ligand-based comparisons. Taken together, the combination of orthogonal information sources led to investigation of a surprising predicted relationship between a transcription factor and an enzyme, specifically, PPAR α and the cyclooxygenase enzymes. These predictions were confirmed by direct biochemical experiments which validate the approach and show for the first time that PPAR α agonists are cyclooxygenase inhibitors.

Three-dimensional compound comparison methods and their application in drug discovery.

PubMed

Shin, Woong-Hee; Zhu, Xiaolei; Bures, Mark Gregory; Kihara, Daisuke

2015-07-16

Virtual screening has been widely used in the drug discovery process. Ligand-based virtual screening (LBVS) methods compare a library of compounds with a known active ligand. Two notable advantages of LBVS methods are that they do not require structural information of a target receptor and that they are faster than structure-based methods. LBVS methods can be classified based on the complexity of ligand structure information utilized: one-dimensional (1D), two-dimensional (2D), and three-dimensional (3D). Unlike 1D and 2D methods, 3D methods can have enhanced performance since they treat the conformational flexibility of compounds. In this paper, a number of 3D methods will be reviewed. In addition, four representative 3D methods were benchmarked to understand their performance in virtual screening. Specifically, we tested overall performance in key aspects including the ability to find dissimilar active compounds, and computational speed.

Extending Data Worth Analyses to Select Multiple Observations Targeting Multiple Forecasts.

PubMed

Vilhelmsen, Troels N; Ferré, Ty P A

2018-05-01

Hydrological models are often set up to provide specific forecasts of interest. Owing to the inherent uncertainty in data used to derive model structure and used to constrain parameter variations, the model forecasts will be uncertain. Additional data collection is often performed to minimize this forecast uncertainty. Given our common financial restrictions, it is critical that we identify data with maximal information content with respect to forecast of interest. In practice, this often devolves to qualitative decisions based on expert opinion. However, there is no assurance that this will lead to optimal design, especially for complex hydrogeological problems. Specifically, these complexities include considerations of multiple forecasts, shared information among potential observations, information content of existing data, and the assumptions and simplifications underlying model construction. In the present study, we extend previous data worth analyses to include: simultaneous selection of multiple new measurements and consideration of multiple forecasts of interest. We show how the suggested approach can be used to optimize data collection. This can be used in a manner that suggests specific measurement sets or that produces probability maps indicating areas likely to be informative for specific forecasts. Moreover, we provide examples documenting that sequential measurement election approaches often lead to suboptimal designs and that estimates of data covariance should be included when selecting future measurement sets. © 2017, National Ground Water Association.

A general way for quantitative magnetic measurement by transmitted electrons

NASA Astrophysics Data System (ADS)

Song, Dongsheng; Li, Gen; Cai, Jianwang; Zhu, Jing

2016-01-01

EMCD (electron magnetic circular dichroism) technique opens a new door to explore magnetic properties by transmitted electrons. The recently developed site-specific EMCD technique makes it possible to obtain rich magnetic information from the Fe atoms sited at nonequivalent crystallographic planes in NiFe2O4, however it is based on a critical demand for the crystallographic structure of the testing sample. Here, we have further improved and tested the method for quantitative site-specific magnetic measurement applicable for more complex crystallographic structure by using the effective dynamical diffraction effects (general routine for selecting proper diffraction conditions, making use of the asymmetry of dynamical diffraction for design of experimental geometry and quantitative measurement, etc), and taken yttrium iron garnet (Y3Fe5O12, YIG) with more complex crystallographic structure as an example to demonstrate its applicability. As a result, the intrinsic magnetic circular dichroism signals, spin and orbital magnetic moment of iron with site-specific are quantitatively determined. The method will further promote the development of quantitative magnetic measurement with high spatial resolution by transmitted electrons.

Compound-Specific Isotopic Analysis of Meteoritic Amino Acids as a Tool for Evaluating Potential Formation Pathways

NASA Technical Reports Server (NTRS)

Elsila, Jamie E.; Burton, Aaron S.; Callahan, Michael C.; Charnley, Steven B.; Glavin, Daniel P.; Dworkin, Jason P.

2012-01-01

Measurements of stable hydrogen, carbon, and nitrogen isotopic ratios (delta D, delta C-13, delta N-15) of organic compounds can reveal information about their origin and formation pathways. Several formation mechanisms and environments have been postulated for the amino acids detected in carbonaceous chondrites. As each proposed mechanism utilizes different precursor molecules, the isotopic signatures of the resulting amino acids may point towards the most likely of these proposed pathways. The technique of gas chromatography coupled with mass spectrometry and isotope ratio mass spectrometry provides compound-specific structural and isotopic information from a single splitless injection, enhancing the amount of information gained from small amounts of precious samples such as carbonaceous chondrites. We have applied this technique to measure the compound-specific C, N, and H isotopic ratios of amino acids from seven CM and CR carbonaceous chondrites. We are using these measurements to evaluate predictions of expected isotopic enrichments from potential formation pathways and environments, leading to a better understanding of the origin of these compounds.

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.

O' Connell bridge inspection by means of Ground Penetrating Radar

NASA Astrophysics Data System (ADS)

Santos Assuncao, Sonia, ,, Dr

2016-04-01

Ground Penetrating Radar (GPR) is a well-known technique successfully applied in different areas. In structural inspection the methodology may expose information about structural arrangement and pathologies. GPR emits high frequency electromagnetic impulses allowing to detect changes on the electromagnetic properties: electrical conductivity, dielectric constant and magnetic permeability. The central frequency of the each antenna is characterized by a specific resolution and penetration depth. Therefore, different scales of structures can be analysed. High frequency antennas output high resolution images/signals about the shallowest elements such as rebar and the thickness of the first layer. On the other hand, intermediate or lower frequency antennas locate deeper structures, such as the thickness of the arch. The compilation of distinct frequencies gives a better understanding and a more accurate detection of elements in the inner structure. O'Connell Bridge (1877) is one of 24 bridges along River Liffey and one the most famous historical structures in Dublin. It is composed by sandstones and granite and covered by asphalt which represents a suitable structure to evaluate by means of GPR. The lack of inner structural information, especially the thickness of the layer, presence of reinforcement or other metallic elements of support required, at least, a dual frequency analysis of the bridge. In this case, it was applied the (200 MHz and 600 MHz) Multi-Channel Stream EM combined with 1.6 GHz GSSI high frequency antenna. The inspection of bridges by means of GPR may provide not exclusively interesting structural data but historical information and the state of conservation.

Data-directed RNA secondary structure prediction using probabilistic modeling

PubMed Central

Deng, Fei; Ledda, Mirko; Vaziri, Sana; Aviran, Sharon

2016-01-01

Structure dictates the function of many RNAs, but secondary RNA structure analysis is either labor intensive and costly or relies on computational predictions that are often inaccurate. These limitations are alleviated by integration of structure probing data into prediction algorithms. However, existing algorithms are optimized for a specific type of probing data. Recently, new chemistries combined with advances in sequencing have facilitated structure probing at unprecedented scale and sensitivity. These novel technologies and anticipated wealth of data highlight a need for algorithms that readily accommodate more complex and diverse input sources. We implemented and investigated a recently outlined probabilistic framework for RNA secondary structure prediction and extended it to accommodate further refinement of structural information. This framework utilizes direct likelihood-based calculations of pseudo-energy terms per considered structural context and can readily accommodate diverse data types and complex data dependencies. We use real data in conjunction with simulations to evaluate performances of several implementations and to show that proper integration of structural contexts can lead to improvements. Our tests also reveal discrepancies between real data and simulations, which we show can be alleviated by refined modeling. We then propose statistical preprocessing approaches to standardize data interpretation and integration into such a generic framework. We further systematically quantify the information content of data subsets, demonstrating that high reactivities are major drivers of SHAPE-directed predictions and that better understanding of less informative reactivities is key to further improvements. Finally, we provide evidence for the adaptive capability of our framework using mock probe simulations. PMID:27251549

Semantic Web Services with Web Ontology Language (OWL-S) - Specification of Agent-Services for DARPA Agent Markup Language (DAML)

DTIC Science & Technology

2006-08-01

effective for describing taxonomic categories and properties of things, the structures found in SWRL and SPARQL are better suited to describing conditions...up the query processing time, which may occur many times and furthermore it is time critical. In order to maintain information about the...that time spent during this phase does not depend linearly on the number of concepts present in the data structure , but in the order of log of concepts

A Cultural Resources Survey of the Whitlow Ranch Dam and Reservoir Area, Eastern Pinal County, Arizona,

DTIC Science & Technology

1986-01-01

Superstition foothills. What was not expected was the high proportion of sites which show evidence of structures, and the equally high proportion which can be...to look at an attempt to hit paydirt that ultimately failed. Specifically, we can ask: what is the structure of a mining effort at this early stage...badly disturbed by looting but (as has been learned in recent years) even highly disturbed pueblo sites can be made to yield significant new information

Evolution of an Intelligent Information Fusion System

NASA Technical Reports Server (NTRS)

Campbell, William J.; Cromp, Robert F.

1990-01-01

Consideration is given to the hardware and software needed to manage the enormous amount and complexity of data that the next generation of space-borne sensors will provide. An anthology is presented illustrating the evolution of artificial intelligence, science data processing, and management from the 1960s to the near future. Problems and limitations of technologies, data structures, data standards, and conceptual thinking are addressed. The development of an end-to-end Intelligent Information Fusion System that embodies knowledge of the user's domain-specific goals is proposed.

Modelling and Decision Support of Clinical Pathways

NASA Astrophysics Data System (ADS)

Gabriel, Roland; Lux, Thomas

The German health care market is under a rapid rate of change, forcing especially hospitals to provide high-quality services at low costs. Appropriate measures for more effective and efficient service provision are process orientation and decision support by information technology of clinical pathway of a patient. The essential requirements are adequate modelling of clinical pathways as well as usage of adequate systems, which are capable of assisting the complete path of a patient within a hospital, and preferably also outside of it, in a digital way. To fulfil these specifications the authors present a suitable concept, which meets the challenges of well-structured clinical pathways as well as rather poorly structured diagnostic and therapeutic decisions, by interplay of process-oriented and knowledge-based hospital information systems.

Metocean Data Needs Assessment for U.S. Offshore Wind Energy

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

Bailey, Bruce H.; Filippelli, Matthew; Baker, Matthew

2015-01-01

A potential barrier to developing offshore wind energy in the United States is the general lack of accurate information in most offshore areas about the wind resource characteristics and external metocean design conditions at the heights and depths relevant to wind turbines and their associated structures and components. Knowledge of these conditions enables specification of the appropriate design basis for wind turbine structures and components so they can withstand the loads expected over a project’s lifetime. Human safety, vessel navigation, and project construction and maintenance activities are equally tied to the metocean environment. Currently, metocean data is sparse in potentialmore » development areas and even when available, does not include the detail or quality required to make informed decisions.« less

Automatically updating predictive modeling workflows support decision-making in drug design.

PubMed

Muegge, Ingo; Bentzien, Jörg; Mukherjee, Prasenjit; Hughes, Robert O

2016-09-01

Using predictive models for early decision-making in drug discovery has become standard practice. We suggest that model building needs to be automated with minimum input and low technical maintenance requirements. Models perform best when tailored to answering specific compound optimization related questions. If qualitative answers are required, 2-bin classification models are preferred. Integrating predictive modeling results with structural information stimulates better decision making. For in silico models supporting rapid structure-activity relationship cycles the performance deteriorates within weeks. Frequent automated updates of predictive models ensure best predictions. Consensus between multiple modeling approaches increases the prediction confidence. Combining qualified and nonqualified data optimally uses all available information. Dose predictions provide a holistic alternative to multiple individual property predictions for reaching complex decisions.

Using Multispectral False Color Imaging to Characterize Tropical Cyclone Structure and Environment

NASA Astrophysics Data System (ADS)

Cossuth, J.; Bankert, R.; Richardson, K.; Surratt, M. L.

2016-12-01

The Naval Research Laboratory's (NRL) tropical cyclone (TC) web page (http://www.nrlmry.navy.mil/TC.html) has provided nearly two decades of near real-time access to TC-centric images and products by TC forecasters and enthusiasts around the world. Particularly, microwave imager and sounder information that is featured on this site provides crucial internal storm structure information by allowing users to perceive hydrometeor structure, providing key details beyond cloud top information provided by visible and infrared channels. Towards improving TC analysis techniques and helping advance the utility of the NRL TC webpage resource, new research efforts are presented. This work demonstrates results as well as the methodology used to develop new automated, objective satellite-based TC structure and intensity guidance and enhanced data fusion imagery products that aim to bolster and streamline TC forecast operations. This presentation focuses on the creation and interpretation of false color RGB composite imagery that leverages the different emissive and scattering properties of atmospheric ice, liquid, and vapor water as well as ocean surface roughness as seen by microwave radiometers. Specifically, a combination of near-realtime data and a standardized digital database of global TCs in microwave imagery from 1987-2012 is employed as a climatology of TC structures. The broad range of TC structures, from pinhole eyes through multiple eyewall configurations, is characterized as resolved by passive microwave sensors. The extraction of these characteristic features from historical data also lends itself to statistical analysis. For example, histograms of brightness temperature distributions allows a rigorous examination of how structural features are conveyed in image products, allowing a better representation of colors and breakpoints as they relate to physical features. Such climatological work also suggests steps to better inform the near-real time application of upcoming satellite datasets to TC analyses.

Structural basis for inhibition of DNA replication by aphidicolin

DOE PAGES

Baranovskiy, A. G.; Babayeva, N. D.; Suwa, Y.; ...

2014-11-27

Natural tetracyclic diterpenoid aphidicolin is a potent and specific inhibitor of B-family DNA polymerases, haltering replication and possessing a strong antimitotic activity in human cancer cell lines. Clinical trials revealed limitations of aphidicolin as an antitumor drug because of its low solubility and fast clearance from human plasma. The absence of structural information hampered the improvement of aphidicolin-like inhibitors: more than 50 modifications have been generated so far, but all have lost the inhibitory and antitumor properties. Here we report the crystal structure of the catalytic core of human DNA polymerase α (Pol α) in the ternary complex with anmore » RNA-primed DNA template and aphidicolin. The inhibitor blocks binding of dCTP by docking at the Pol α active site and by rotating the template guanine. The structure provides a plausible mechanism for the selectivity of aphidicolin incorporation opposite template guanine and explains why previous modifications of aphidicolin failed to improve its affinity for Pol α. With new structural information, aphidicolin becomes an attractive lead compound for the design of novel derivatives with enhanced inhibitory properties for B-family DNA polymerases.« less

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.

Correlative nanoscale imaging of actin filaments and their complexes

NASA Astrophysics Data System (ADS)

Sharma, Shivani; Zhu, Huanqi; Grintsevich, Elena E.; Reisler, Emil; Gimzewski, James K.

2013-06-01

Actin remodeling is an area of interest in biology in which correlative microscopy can bring a new way to analyze protein complexes at the nanoscale. Advances in EM, X-ray diffraction, fluorescence, and single molecule techniques have provided a wealth of information about the modulation of the F-actin structure and its regulation by actin binding proteins (ABPs). Yet, there are technological limitations of these approaches to achieving quantitative molecular level information on the structural and biophysical changes resulting from ABPs interaction with F-actin. Fundamental questions about the actin structure and dynamics and how these determine the function of ABPs remain unanswered. Specifically, how local and long-range structural and conformational changes result in ABPs induced remodeling of F-actin needs to be addressed at the single filament level. Advanced, sensitive and accurate experimental tools for detailed understanding of ABP-actin interactions are much needed. This article discusses the current understanding of nanoscale structural and mechanical modulation of F-actin by ABPs at the single filament level using several correlative microscopic techniques, focusing mainly on results obtained by Atomic Force Microscopy (AFM) analysis of ABP-actin complexes.

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

Parenting around child snacking: development of a theoretically-guided, empirically informed conceptual model.

PubMed

Davison, Kirsten K; Blake, Christine E; Blaine, Rachel E; Younginer, Nicholas A; Orloski, Alexandria; Hamtil, Heather A; Ganter, Claudia; Bruton, Yasmeen P; Vaughn, Amber E; Fisher, Jennifer O

2015-09-17

Snacking contributes to excessive energy intakes in children. Yet factors shaping child snacking are virtually unstudied. This study examines food parenting practices specific to child snacking among low-income caregivers. Semi-structured interviews were conducted in English or Spanish with 60 low-income caregivers of preschool-aged children (18 non-Hispanic white, 22 African American/Black, 20 Hispanic; 92% mothers). A structured interview guide was used to solicit caregivers' definitions of snacking and strategies they use to decide what, when and how much snack their child eats. Interviews were audio-recorded, transcribed verbatim and analyzed using an iterative theory-based and grounded approach. A conceptual model of food parenting specific to child snacking was developed to summarize the findings and inform future research. Caregivers' descriptions of food parenting practices specific to child snacking were consistent with previous models of food parenting developed based on expert opinion [1, 2]. A few noteworthy differences however emerged. More than half of participants mentioned permissive feeding approaches (e.g., my child is the boss when it comes to snacks). As a result, permissive feeding was included as a higher order feeding dimension in the resulting model. In addition, a number of novel feeding approaches specific to child snacking emerged including child-centered provision of snacks (i.e., responding to a child's hunger cues when making decisions about snacks), parent unilateral decision making (i.e., making decisions about a child's snacks without any input from the child), and excessive monitoring of snacks (i.e., monitoring all snacks provided to and consumed by the child). The resulting conceptual model includes four higher order feeding dimensions including autonomy support, coercive control, structure and permissiveness and 20 sub-dimensions. This study formulates a language around food parenting practices specific to child snacking, identifies dominant constructs, and proposes a conceptual framework to guide future research.

NOTE: MMCTP: a radiotherapy research environment for Monte Carlo and patient-specific treatment planning

NASA Astrophysics Data System (ADS)

Alexander, A.; DeBlois, F.; Stroian, G.; Al-Yahya, K.; Heath, E.; Seuntjens, J.

2007-07-01

Radiotherapy research lacks a flexible computational research environment for Monte Carlo (MC) and patient-specific treatment planning. The purpose of this study was to develop a flexible software package on low-cost hardware with the aim of integrating new patient-specific treatment planning with MC dose calculations suitable for large-scale prospective and retrospective treatment planning studies. We designed the software package 'McGill Monte Carlo treatment planning' (MMCTP) for the research development of MC and patient-specific treatment planning. The MMCTP design consists of a graphical user interface (GUI), which runs on a simple workstation connected through standard secure-shell protocol to a cluster for lengthy MC calculations. Treatment planning information (e.g., images, structures, beam geometry properties and dose distributions) is converted into a convenient MMCTP local file storage format designated, the McGill RT format. MMCTP features include (a) DICOM_RT, RTOG and CADPlan CART format imports; (b) 2D and 3D visualization views for images, structure contours, and dose distributions; (c) contouring tools; (d) DVH analysis, and dose matrix comparison tools; (e) external beam editing; (f) MC transport calculation from beam source to patient geometry for photon and electron beams. The MC input files, which are prepared from the beam geometry properties and patient information (e.g., images and structure contours), are uploaded and run on a cluster using shell commands controlled from the MMCTP GUI. The visualization, dose matrix operation and DVH tools offer extensive options for plan analysis and comparison between MC plans and plans imported from commercial treatment planning systems. The MMCTP GUI provides a flexible research platform for the development of patient-specific MC treatment planning for photon and electron external beam radiation therapy. The impact of this tool lies in the fact that it allows for systematic, platform-independent, large-scale MC treatment planning for different treatment sites. Patient recalculations were performed to validate the software and ensure proper functionality.

A healthcare management system for Turkey based on a service-oriented architecture.

PubMed

Herand, Deniz; Gürder, Filiz; Taşkin, Harun; Yuksel, Emre Nuri

2013-09-01

The current Turkish healthcare management system has a structure that is extremely inordinate, cumbersome and inflexible. Furthermore, this structure has no common point of view and thus has no interoperability and responds slowly to innovations. The purpose of this study is to show that using which methods can the Turkish healthcare management system provide a structure that could be more modern, more flexible and more quick to respond to innovations and changes taking advantage of the benefits given by a service-oriented architecture (SOA). In this paper, the Turkish healthcare management system is chosen to be examined since Turkey is considered as one of the Third World countries and the information architecture of the existing healthcare management system of Turkey has not yet been configured with SOA, which is a contemporary innovative approach and should provide the base architecture of the new solution. The innovation of this study is the symbiosis of two main integration approaches, SOA and Health Level 7 (HL7), for integrating divergent healthcare information systems. A model is developed which is based on SOA and enables obtaining a healthcare management system having the SSF standards (HSSP Service Specification Framework) developed by the framework of the HSSP (Healthcare Services Specification Project) under the leadership of HL7 and the Object Management Group.

Composite materials and structures: Science, technology and applications. A compendium of books, review papers, and other sources of information

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

Bogdanovich, A.E.; Sierakowski, R.L.

A fast growing volume of literature in various fields of composite materials and structures has inspired the authors to attempt to assemble all major books and review papers in a concise compendium presented here. This could give researchers, engineers, designers, and graduate students a rapid access to the vast volume of references on any specific topic in the field of composites and thereby satisfy their research requirements. The compendium includes encyclopedias, handbooks, design guides, textbooks, reference books, review papers and also a few collections of papers. The topics span theory, modeling and analysis of composite materials, processing and manufacturing, propertiesmore » and characterization, theory and analysis of composite structures, joints and connections, designing with composites, and composites applications. The compendium includes over 400 references, which are arranged in alphabetical order within each topic under consideration. Additionally, the reader can find, in this compendium, the lists of major conferences, journals, and ASTM STP publications on composites. The major objective of this work is not critically reviewing or discussing specific research approaches and results. The authors have rather intended to provide extensive bibliographic information that may help the reader to get familiar with the primary literature and, in necessary, undertake further literature search on any particular problem of interest.« less

A framework for scalable parameter estimation of gene circuit models using structural information.

PubMed

Kuwahara, Hiroyuki; Fan, Ming; Wang, Suojin; Gao, Xin

2013-07-01

Systematic and scalable parameter estimation is a key to construct complex gene regulatory models and to ultimately facilitate an integrative systems biology approach to quantitatively understand the molecular mechanisms underpinning gene regulation. Here, we report a novel framework for efficient and scalable parameter estimation that focuses specifically on modeling of gene circuits. Exploiting the structure commonly found in gene circuit models, this framework decomposes a system of coupled rate equations into individual ones and efficiently integrates them separately to reconstruct the mean time evolution of the gene products. The accuracy of the parameter estimates is refined by iteratively increasing the accuracy of numerical integration using the model structure. As a case study, we applied our framework to four gene circuit models with complex dynamics based on three synthetic datasets and one time series microarray data set. We compared our framework to three state-of-the-art parameter estimation methods and found that our approach consistently generated higher quality parameter solutions efficiently. Although many general-purpose parameter estimation methods have been applied for modeling of gene circuits, our results suggest that the use of more tailored approaches to use domain-specific information may be a key to reverse engineering of complex biological systems. http://sfb.kaust.edu.sa/Pages/Software.aspx. Supplementary data are available at Bioinformatics online.

New optomechanical approach to quantitative characterization of fatigue behavior of dynamically loaded structures

NASA Astrophysics Data System (ADS)

Furlong, Cosme; Pryputniewicz, Ryszard J.

1995-06-01

The basic relationships between stress and strain under cyclic conditions of loading are not at present well understood. It would seem that information of this type is vital for a fundamental approach to understand the fatigue behavior of dynamically loaded structures. In this paper, experimental and computational methods are utilized to study the fatigue behavior of a thin aluminum cantilever plate subjected to dynamic loading. The studies are performed by combining optomechanical and finite element methods. The cantilever plate is loaded periodically by excitation set at a fixed amplitude and at a specific resonance frequency of the plate. By continuously applying this type of loading and using holographic interferometry, the behavior of the plate during a specific period of time is investigated. Quantitative information is obtained from laser vibrometry data which are utilized by a finite element program to calculate strains and stresses assuming a homogeneous and isotropic material and constant strain elements. It is shown that the use of experimental and computational hybrid methodologies allows identification of different zones of the plate that are fatigue critical. This optomechanical approach proves to be a viable tool for understanding of fatigue behavior of mechanical components and for performing optimization of structures subjected to fatigue conditions.

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.

Stages and transitions in medical education around the world: clarifying structures and terminology.

PubMed

Wijnen-Meijer, Marjo; Burdick, William; Alofs, Lonneke; Burgers, Chantalle; ten Cate, Olle

2013-04-01

In a world that increasingly serves the international exchange of information on medical training, many students, physicians and educators encounter numerous variations in curricula, degrees, point of licensing and terminology. The aim of this study was to shed some light for those trying to compare medical training formats across countries. We surveyed a sample of key informants from 40 countries. Survey questions included: structure of medical education, moment that unrestricted practice is allowed, various options after general medical licensing, nomenclature of degrees granted and relevant terminology related to the medical education system. In addition, we searched the literature for description of country-specific information. Based on the results, we described the six models of current medical training around the world, supplemented with a list of degrees granted after medical school and an explanation of frequently used terminology. The results of this questionnaire study lead to the conclusion that while there are many differences between countries, there appear to be six dominant models. The models vary in structure and length of medical training, point of full registration and degrees that are granted.

Integrated structural biology to unravel molecular mechanisms of protein-RNA recognition.

PubMed

Schlundt, Andreas; Tants, Jan-Niklas; Sattler, Michael

2017-04-15

Recent advances in RNA sequencing technologies have greatly expanded our knowledge of the RNA landscape in cells, often with spatiotemporal resolution. These techniques identified many new (often non-coding) RNA molecules. Large-scale studies have also discovered novel RNA binding proteins (RBPs), which exhibit single or multiple RNA binding domains (RBDs) for recognition of specific sequence or structured motifs in RNA. Starting from these large-scale approaches it is crucial to unravel the molecular principles of protein-RNA recognition in ribonucleoprotein complexes (RNPs) to understand the underlying mechanisms of gene regulation. Structural biology and biophysical studies at highest possible resolution are key to elucidate molecular mechanisms of RNA recognition by RBPs and how conformational dynamics, weak interactions and cooperative binding contribute to the formation of specific, context-dependent RNPs. While large compact RNPs can be well studied by X-ray crystallography and cryo-EM, analysis of dynamics and weak interaction necessitates the use of solution methods to capture these properties. Here, we illustrate methods to study the structure and conformational dynamics of protein-RNA complexes in solution starting from the identification of interaction partners in a given RNP. Biophysical and biochemical techniques support the characterization of a protein-RNA complex and identify regions relevant in structural analysis. Nuclear magnetic resonance (NMR) is a powerful tool to gain information on folding, stability and dynamics of RNAs and characterize RNPs in solution. It provides crucial information that is complementary to the static pictures derived from other techniques. NMR can be readily combined with other solution techniques, such as small angle X-ray and/or neutron scattering (SAXS/SANS), electron paramagnetic resonance (EPR), and Förster resonance energy transfer (FRET), which provide information about overall shapes, internal domain arrangements and dynamics. Principles of protein-RNA recognition and current approaches are reviewed and illustrated with recent studies. Copyright © 2017 Elsevier Inc. All rights reserved.

[Needs-based offers and gender-specific aspects in nursing homes : Results of a representative survey among directors of nursing homes].

PubMed

Teubner, Christian; Sulmann, Daniela; Lahmann, Nils; Suhr, Ralf

2016-12-01

Nursing and care that consider individual and biographically shaped impressions requires, among other things sensitivity for the specific needs of persons in need of care. A representative survey was conducted among directors of nursing homes to provide information about the importance of gender-specific aspects in nursing. In a written survey 516 directors of German resident care facilities were interviewed about their attitudes and perceptions regarding the subject, about information on general and gender-specific offers and about demographic information on the management of nursing homes. Activities specifically considering the needs of men and women (gender-specific 43.1 %) are not widespread in the nursing homes surveyed. Most respondents reasoned that there was no demand for such offers (57.1 %) or that they are dispensable due to the composition of residents (47.6 %). Of the respondents 36.4 % saw specific needs more with women than with men (18.4 %). Nevertheless, the need for male-specific activities is given a relatively high priority. The consideration of gender aspects in the planning of care processes (57.0 %) and the regular reflection of gender issues (20.7 %) are strongly correlated with the existence of gender-specific offers, while structural factors, such as the institution size and the education of nursing home directors are not. Currently, gender-specific activity offers in nursing facilities are not widespread. Existing offers are mostly based on traditional gender stereotypes; therefore, it would be desirable if the diversity in the reality of life and the individual needs of women and men would be recognized.

Technical and management information system: The tool for professional productivity on the space station program

NASA Technical Reports Server (NTRS)

Montoya, G.; Boldon, P.

1985-01-01

The Space Station Program is highly complex not only in its technological goals and requirements but also in its organizational structure. Eight Contractor teams supporting four NASA centers plus Headquarters must depend on effective exchange of information--the lifeblood of the program. The Technical and Management Information System (TMIS) is the means by which this exchange can take place. Value of the TMIS in increasing productivity comes primarily from its ability to make the right information available to whomever needs it when it is needed. Productivity of the aerospace professional and how it can be enhanced by the use of specifically recommended techniques and procedures for information management using the TMIS are discussed.

Integrating medical and research information: a big data approach.

PubMed

Tilve Álvarez, Carlos M; Ayora Pais, Alberto; Ruíz Romero, Cristina; Llamas Gómez, Daniel; Carrajo García, Lino; Blanco García, Francisco J; Vázquez González, Guillermo

2015-01-01

Most of the information collected in different fields by Instituto de Investigación Biomédica de A Coruña (INIBIC) is classified as unstructured due to its high volume and heterogeneity. This situation, linked to the recent requirement of integrating it to the medical information, makes it necessary to implant specific architectures to collect and organize it before it can be analysed. The purpose of this article is to present the Hadoop framework as a solution to the problem of integrating research information in the Business Intelligence field. This framework can collect, explore, process and structure the aforementioned information, which allow us to develop an equivalent function to a data mart in an Intelligence Business system.

Stand dynamics in 60-year-old Allegheny hardwoods after thinning

Treesearch

Gary W. Miller

1997-01-01

Stand dynamics and tree growth in even-aged hardwood stands can be influenced by manipulating relative stand density, species composition, and stand structure. Land managers need quantitative information on the effect of vegetation manipulation to prescribe stand treatments that are appropriate for specific management objectives. Sixty-year-old stands composed of black...

Correlates of Mental Health among Latino Farmworkers in North Carolina

ERIC Educational Resources Information Center

Crain, Rebecca; Grzywacz, Joseph G.; Schwantes, Melody; Isom, Scott; Quandt, Sara A.; Arcury, Thomas A.

2012-01-01

Purpose: Latino farmworkers are a vulnerable population who confront multiple threats to their mental health. Informed by the stress-process model of psychiatric disorder, the goal of this paper is to determine primary and context-specific stressors of poor mental health among Latino farmworkers. Methods: Structured interview data were obtained…

Talking the Talk, Not Walking the Walk: Expressions from Underrepresented Students about Their Counselor Education Doctoral Programs

ERIC Educational Resources Information Center

Baker, Caroline Ann

2010-01-01

This qualitative study explored the perceptions of self-identified racial or ethnic minorities about their counselor education doctoral programs in relation to multicultural competence. More specifically, semi-structured interview questions were used to obtain information about their doctoral experiences related to faculty and peer relationships,…

The Dawn of Development: A Guide for Educating Visually Impaired Young Children. Volume I: Assessment.

ERIC Educational Resources Information Center

Umansky, Warren; And Others

The guide offers a means for evaluating specific learning characteristics of visually impaired children at three levels: prereadiness (prekindergarten), readiness (kindergarten), and academic (primary grades). Items are designed to be administered by informal observation and structured testing. Score sheets contain space for reporting two testing…

Development of an Observational Procedure for Assessment of Parent-Child Interaction.

ERIC Educational Resources Information Center

Cunningham, Jo Lynn; Boger, Robert P.

The feasibility of using an observational rating schedule to elicit information about parent-child interaction was studied. The Parent-Child Interaction Rating Procedure (P-CIRP), focusing specifically on parent-child interaction with a structured teaching task, was developed for this purpose. The interaction setting is teaching the child simple…

76 FR 14662 - Notice of Public Information Collection(s) Being Reviewed by the Federal Communications...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-03-17

... (STS) based on the Multi-state Average Rate Structure (MARS) plan proposed by Hamilton Relay, Inc., (2... intrastate Internet-Protocol (IP) Captioned Telephone Service (IP CTS) based on the MARS plan, (3) a cost... with the MARS plan cost recovery methodology for compensation from the Fund. Specifically, TRS...

Hopes & Hurdles: California Foster Youth and College Financial Aid

ERIC Educational Resources Information Center

Cochrane, Deborah Frankle; Szabo-Kubitz, Laura

2009-01-01

This report examines why former foster youth in California are not receiving the aid they are likely eligible for, from inadequate or poorly targeted information about college costs and financial aid to structural obstacles within the aid process and programs. While many of this report's findings and recommendations are specific to foster youth,…

Early Childhood Preservice Teachers' Use of Verbal and Non-Verbal Guidance Strategies across Classroom Contexts

ERIC Educational Resources Information Center

Caudle, Lori A.; Jung, Min-Jung; Fouts, Hillary N.; Wallace, Heather S.

2014-01-01

Observations of preservice teachers often lack information about specific strategies they use when guiding children's behavior. This study investigated how preservice teachers used verbal and non-verbal behavior modification techniques within structured and transition classroom contexts. Using an on-the-mark 20- second observe and 10-second record…

Statistical Indicators for Religious Studies: Indicators of Level and Structure

ERIC Educational Resources Information Center

Herteliu, Claudiu; Isaic-Maniu, Alexandru

2009-01-01

Using statistic indicators as vectors of information relative to the operational status of a phenomenon, including a religious one, is unanimously accepted. By introducing a system of statistic indicators we can also analyze the interfacing areas of a phenomenon. In this context, we have elaborated a system of statistic indicators specific to the…

Knowledge Cultures and the Shaping of Work-Based Learning: The Case of Computer Engineering

ERIC Educational Resources Information Center

Nerland, Monika

2008-01-01

This paper examines how the knowledge culture of computer engineering--that is, the ways in which knowledge is produced, distributed, accumulated and collectively approached within this profession--serve to construct work-based learning in specific ways. Typically, the epistemic infrastructures take the form of information structures with a global…

Family-Centered Early Intervention for Communication Disorders: Prevention and Treatment. Excellence in Practice Series.

ERIC Educational Resources Information Center

Donahue-Kilburg, Gail

This book is designed to provide a broad range of information on family structure and function in an increasingly multicultural society, family system characteristics and the implications for intervention, communication development in the family context, the nature and delivery of family centered-services, specific requirements of Public Law…

Preparing Teachers to Support Struggling First-Grade Readers

ERIC Educational Resources Information Center

Baker, Bettina

2007-01-01

The purpose of this report is to provide education professors teaching early literacy methods courses with information for beginning teachers to support struggling first-grade readers. This analysis identifies the specific word structures children are expected to know by the end of first grade, and shows the actual learning rates of these…

Math Problems for Water Quality Control Personnel, Instructor's Manual. Second Edition.

ERIC Educational Resources Information Center

Delvecchio, Fred; Brutsch, Gloria

This document is the instructor's manual for a course in mathematics for water quality control personnel. It is designed so a program may be designed for a specific facility. The problem structures are arranged alphabetically by treatment process. Charts, graphs and/or drawings representing familiar data forms contain the necessary information to…

47 CFR 1.1311 - Environmental information to be included in the environmental assessment (EA).

Code of Federal Regulations, 2014 CFR

2014-10-01

... earth stations, a description of the facilities as well as supporting structures and appurtenances, and..., the applicant's analysis must utilize the best scientific and commercial data available, see 50 CFR...'s environmental impact, if any. The EA shall deal specifically with any feature of the site which...

47 CFR 1.1311 - Environmental information to be included in the environmental assessment (EA).

Code of Federal Regulations, 2013 CFR

2013-10-01

... earth stations, a description of the facilities as well as supporting structures and appurtenances, and..., the applicant's analysis must utilize the best scientific and commercial data available, see 50 CFR...'s environmental impact, if any. The EA shall deal specifically with any feature of the site which...

47 CFR 1.1311 - Environmental information to be included in the environmental assessment (EA).

Code of Federal Regulations, 2012 CFR

2012-10-01

... earth stations, a description of the facilities as well as supporting structures and appurtenances, and..., the applicant's analysis must utilize the best scientific and commercial data available, see 50 CFR...'s environmental impact, if any. The EA shall deal specifically with any feature of the site which...

Glycoform-independent prion conversion by highly efficient, cell-based, protein misfolding cyclic amplification.

PubMed

Moudjou, Mohammed; Chapuis, Jérôme; Mekrouti, Mériem; Reine, Fabienne; Herzog, Laetitia; Sibille, Pierre; Laude, Hubert; Vilette, Didier; Andréoletti, Olivier; Rezaei, Human; Dron, Michel; Béringue, Vincent

2016-07-07

Prions are formed of misfolded assemblies (PrP(Sc)) of the variably N-glycosylated cellular prion protein (PrP(C)). In infected species, prions replicate by seeding the conversion and polymerization of host PrP(C). Distinct prion strains can be recognized, exhibiting defined PrP(Sc) biochemical properties such as the glycotype and specific biological traits. While strain information is encoded within the conformation of PrP(Sc) assemblies, the storage of the structural information and the molecular requirements for self-perpetuation remain uncertain. Here, we investigated the specific role of PrP(C) glycosylation status. First, we developed an efficient protein misfolding cyclic amplification method using cells expressing the PrP(C) species of interest as substrate. Applying the technique to PrP(C) glycosylation mutants expressing cells revealed that neither PrP(C) nor PrP(Sc) glycoform stoichiometry was instrumental to PrP(Sc) formation and strainness perpetuation. Our study supports the view that strain properties, including PrP(Sc) glycotype are enciphered within PrP(Sc) structural backbone, not in the attached glycans.

Predicting the melting temperature of ice-Ih with only electronic structure information as input.

PubMed

Pinnick, Eric R; Erramilli, Shyamsunder; Wang, Feng

2012-07-07

The melting temperature of ice-Ih was calculated with only electronic structure information as input by creating a problem-specific force field. The force field, Water model by AFM for Ice and Liquid (WAIL), was developed with the adaptive force matching (AFM) method by fitting to post-Hartree-Fock quality forces obtained in quantum mechanics∕molecular mechanics calculations. WAIL predicts the ice-Ih melting temperature to be 270 K. The model also predicts the densities of ice and water, the temperature of maximum density of water, the heat of vaporizations, and the radial distribution functions for both ice and water in good agreement with experimental measurements. The non-dissociative WAIL model is very similar to a flexible version of the popular TIP4P potential and has comparable computational cost. By customizing to problem-specific configurations with the AFM approach, the resulting model is remarkably more accurate than any variants of TIP4P for simulating ice-Ih and water in the temperature range from 253 K and 293 K under ambient pressure.

Modelling road accidents: An approach using structural time series

NASA Astrophysics Data System (ADS)

Junus, Noor Wahida Md; Ismail, Mohd Tahir

2014-09-01

In this paper, the trend of road accidents in Malaysia for the years 2001 until 2012 was modelled using a structural time series approach. The structural time series model was identified using a stepwise method, and the residuals for each model were tested. The best-fitted model was chosen based on the smallest Akaike Information Criterion (AIC) and prediction error variance. In order to check the quality of the model, a data validation procedure was performed by predicting the monthly number of road accidents for the year 2012. Results indicate that the best specification of the structural time series model to represent road accidents is the local level with a seasonal model.

The music of morality and logic.

PubMed

Mesz, Bruno; Rodriguez Zivic, Pablo H; Cecchi, Guillermo A; Sigman, Mariano; Trevisan, Marcos A

2015-01-01

Musical theory has built on the premise that musical structures can refer to something different from themselves (Nattiez and Abbate, 1990). The aim of this work is to statistically corroborate the intuitions of musical thinkers and practitioners starting at least with Plato, that music can express complex human concepts beyond merely "happy" and "sad" (Mattheson and Lenneberg, 1958). To do so, we ask whether musical improvisations can be used to classify the semantic category of the word that triggers them. We investigated two specific domains of semantics: morality and logic. While morality has been historically associated with music, logic concepts, which involve more abstract forms of thought, are more rarely associated with music. We examined musical improvisations inspired by positive and negative morality (e.g., good and evil) and logic concepts (true and false), analyzing the associations between these words and their musical representations in terms of acoustic and perceptual features. We found that music conveys information about valence (good and true vs. evil and false) with remarkable consistency across individuals. This information is carried by several musical dimensions which act in synergy to achieve very high classification accuracy. Positive concepts are represented by music with more ordered pitch structure and lower harmonic and sensorial dissonance than negative concepts. Music also conveys information indicating whether the word which triggered it belongs to the domains of logic or morality (true vs. good), principally through musical articulation. In summary, improvisations consistently map logic and morality information to specific musical dimensions, testifying the capacity of music to accurately convey semantic information in domains related to abstract forms of thought.

The music of morality and logic

PubMed Central

Mesz, Bruno; Rodriguez Zivic, Pablo H.; Cecchi, Guillermo A.; Sigman, Mariano; Trevisan, Marcos A.

2015-01-01

Musical theory has built on the premise that musical structures can refer to something different from themselves (Nattiez and Abbate, 1990). The aim of this work is to statistically corroborate the intuitions of musical thinkers and practitioners starting at least with Plato, that music can express complex human concepts beyond merely “happy” and “sad” (Mattheson and Lenneberg, 1958). To do so, we ask whether musical improvisations can be used to classify the semantic category of the word that triggers them. We investigated two specific domains of semantics: morality and logic. While morality has been historically associated with music, logic concepts, which involve more abstract forms of thought, are more rarely associated with music. We examined musical improvisations inspired by positive and negative morality (e.g., good and evil) and logic concepts (true and false), analyzing the associations between these words and their musical representations in terms of acoustic and perceptual features. We found that music conveys information about valence (good and true vs. evil and false) with remarkable consistency across individuals. This information is carried by several musical dimensions which act in synergy to achieve very high classification accuracy. Positive concepts are represented by music with more ordered pitch structure and lower harmonic and sensorial dissonance than negative concepts. Music also conveys information indicating whether the word which triggered it belongs to the domains of logic or morality (true vs. good), principally through musical articulation. In summary, improvisations consistently map logic and morality information to specific musical dimensions, testifying the capacity of music to accurately convey semantic information in domains related to abstract forms of thought. PMID:26191020

Practical Methods for Including Torsional Anharmonicity in Thermochemical Calculations on Complex Molecules: The Internal-Coordinate Multi-Structural Approximation

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

Zheng, J.; Yu, T.; Papajak, E.

2011-01-01

Many methods for correcting harmonic partition functions for the presence of torsional motions employ some form of one-dimensional torsional treatment to replace the harmonic contribution of a specific normal mode. However, torsions are often strongly coupled to other degrees of freedom, especially other torsions and low-frequency bending motions, and this coupling can make assigning torsions to specific normal modes problematic. Here, we present a new class of methods, called multi-structural (MS) methods, that circumvents the need for such assignments by instead adjusting the harmonic results by torsional correction factors that are determined using internal coordinates. We present three versions ofmore » the MS method: (i) MS-AS based on including all structures (AS), i.e., all conformers generated by internal rotations; (ii) MS-ASCB based on all structures augmented with explicit conformational barrier (CB) information, i.e., including explicit calculations of all barrier heights for internal-rotation barriers between the conformers; and (iii) MS-RS based on including all conformers generated from a reference structure (RS) by independent torsions. In the MS-AS scheme, one has two options for obtaining the local periodicity parameters, one based on consideration of the nearly separable limit and one based on strongly coupled torsions. The latter involves assigning the local periodicities on the basis of Voronoi volumes. The methods are illustrated with calculations for ethanol, 1-butanol, and 1-pentyl radical as well as two one-dimensional torsional potentials. The MS-AS method is particularly interesting because it does not require any information about conformational barriers or about the paths that connect the various structures.« less

Practical methods for including torsional anharmonicity in thermochemical calculations on complex molecules: the internal-coordinate multi-structural approximation.

PubMed

Zheng, Jingjing; Yu, Tao; Papajak, Ewa; Alecu, I M; Mielke, Steven L; Truhlar, Donald G

2011-06-21

Many methods for correcting harmonic partition functions for the presence of torsional motions employ some form of one-dimensional torsional treatment to replace the harmonic contribution of a specific normal mode. However, torsions are often strongly coupled to other degrees of freedom, especially other torsions and low-frequency bending motions, and this coupling can make assigning torsions to specific normal modes problematic. Here, we present a new class of methods, called multi-structural (MS) methods, that circumvents the need for such assignments by instead adjusting the harmonic results by torsional correction factors that are determined using internal coordinates. We present three versions of the MS method: (i) MS-AS based on including all structures (AS), i.e., all conformers generated by internal rotations; (ii) MS-ASCB based on all structures augmented with explicit conformational barrier (CB) information, i.e., including explicit calculations of all barrier heights for internal-rotation barriers between the conformers; and (iii) MS-RS based on including all conformers generated from a reference structure (RS) by independent torsions. In the MS-AS scheme, one has two options for obtaining the local periodicity parameters, one based on consideration of the nearly separable limit and one based on strongly coupled torsions. The latter involves assigning the local periodicities on the basis of Voronoi volumes. The methods are illustrated with calculations for ethanol, 1-butanol, and 1-pentyl radical as well as two one-dimensional torsional potentials. The MS-AS method is particularly interesting because it does not require any information about conformational barriers or about the paths that connect the various structures.

Evaluating Health Information Systems Using Ontologies

PubMed Central

Anderberg, Peter; Larsson, Tobias C; Fricker, Samuel A; Berglund, Johan

2016-01-01

Background There are several frameworks that attempt to address the challenges of evaluation of health information systems by offering models, methods, and guidelines about what to evaluate, how to evaluate, and how to report the evaluation results. Model-based evaluation frameworks usually suggest universally applicable evaluation aspects but do not consider case-specific aspects. On the other hand, evaluation frameworks that are case specific, by eliciting user requirements, limit their output to the evaluation aspects suggested by the users in the early phases of system development. In addition, these case-specific approaches extract different sets of evaluation aspects from each case, making it challenging to collectively compare, unify, or aggregate the evaluation of a set of heterogeneous health information systems. Objectives The aim of this paper is to find a method capable of suggesting evaluation aspects for a set of one or more health information systems—whether similar or heterogeneous—by organizing, unifying, and aggregating the quality attributes extracted from those systems and from an external evaluation framework. Methods On the basis of the available literature in semantic networks and ontologies, a method (called Unified eValuation using Ontology; UVON) was developed that can organize, unify, and aggregate the quality attributes of several health information systems into a tree-style ontology structure. The method was extended to integrate its generated ontology with the evaluation aspects suggested by model-based evaluation frameworks. An approach was developed to extract evaluation aspects from the ontology that also considers evaluation case practicalities such as the maximum number of evaluation aspects to be measured or their required degree of specificity. The method was applied and tested in Future Internet Social and Technological Alignment Research (FI-STAR), a project of 7 cloud-based eHealth applications that were developed and deployed across European Union countries. Results The relevance of the evaluation aspects created by the UVON method for the FI-STAR project was validated by the corresponding stakeholders of each case. These evaluation aspects were extracted from a UVON-generated ontology structure that reflects both the internally declared required quality attributes in the 7 eHealth applications of the FI-STAR project and the evaluation aspects recommended by the Model for ASsessment of Telemedicine applications (MAST) evaluation framework. The extracted evaluation aspects were used to create questionnaires (for the corresponding patients and health professionals) to evaluate each individual case and the whole of the FI-STAR project. Conclusions The UVON method can provide a relevant set of evaluation aspects for a heterogeneous set of health information systems by organizing, unifying, and aggregating the quality attributes through ontological structures. Those quality attributes can be either suggested by evaluation models or elicited from the stakeholders of those systems in the form of system requirements. The method continues to be systematic, context sensitive, and relevant across a heterogeneous set of health information systems. PMID:27311735

Evaluating Health Information Systems Using Ontologies.

PubMed

Eivazzadeh, Shahryar; Anderberg, Peter; Larsson, Tobias C; Fricker, Samuel A; Berglund, Johan

2016-06-16

There are several frameworks that attempt to address the challenges of evaluation of health information systems by offering models, methods, and guidelines about what to evaluate, how to evaluate, and how to report the evaluation results. Model-based evaluation frameworks usually suggest universally applicable evaluation aspects but do not consider case-specific aspects. On the other hand, evaluation frameworks that are case specific, by eliciting user requirements, limit their output to the evaluation aspects suggested by the users in the early phases of system development. In addition, these case-specific approaches extract different sets of evaluation aspects from each case, making it challenging to collectively compare, unify, or aggregate the evaluation of a set of heterogeneous health information systems. The aim of this paper is to find a method capable of suggesting evaluation aspects for a set of one or more health information systems-whether similar or heterogeneous-by organizing, unifying, and aggregating the quality attributes extracted from those systems and from an external evaluation framework. On the basis of the available literature in semantic networks and ontologies, a method (called Unified eValuation using Ontology; UVON) was developed that can organize, unify, and aggregate the quality attributes of several health information systems into a tree-style ontology structure. The method was extended to integrate its generated ontology with the evaluation aspects suggested by model-based evaluation frameworks. An approach was developed to extract evaluation aspects from the ontology that also considers evaluation case practicalities such as the maximum number of evaluation aspects to be measured or their required degree of specificity. The method was applied and tested in Future Internet Social and Technological Alignment Research (FI-STAR), a project of 7 cloud-based eHealth applications that were developed and deployed across European Union countries. The relevance of the evaluation aspects created by the UVON method for the FI-STAR project was validated by the corresponding stakeholders of each case. These evaluation aspects were extracted from a UVON-generated ontology structure that reflects both the internally declared required quality attributes in the 7 eHealth applications of the FI-STAR project and the evaluation aspects recommended by the Model for ASsessment of Telemedicine applications (MAST) evaluation framework. The extracted evaluation aspects were used to create questionnaires (for the corresponding patients and health professionals) to evaluate each individual case and the whole of the FI-STAR project. The UVON method can provide a relevant set of evaluation aspects for a heterogeneous set of health information systems by organizing, unifying, and aggregating the quality attributes through ontological structures. Those quality attributes can be either suggested by evaluation models or elicited from the stakeholders of those systems in the form of system requirements. The method continues to be systematic, context sensitive, and relevant across a heterogeneous set of health information systems.

The evolution of the FIGARO data reduction system

NASA Technical Reports Server (NTRS)

Shortridge, K.

1992-01-01

The Figaro data reduction system originated at Caltech around 1983. It was based on concepts being developed in the U.K. by the Starlink organization, particularly the use of hierarchical self-defining data structures and the abstraction of most user-interaction into a set of 'parameter system' routines. Since 1984 it has continued to be developed at AAO, in collaboration with Starlink and Caltech. It was adopted as Starlink's main spectroscopic data reduction package, although it is by no means limited to spectra; it has operations for images and data cubes and even a few (very specialized) for four-dimensional data hypercubes. It continued to be used at Caltech and will be used at the Keck. It is also in use at a variety of other organizations around the world. Figaro was originally a system for VMS Vaxes. Recently it was ported (at Caltech) to run on SUN's, and work is underway at the University of New South Wales on a DecStation version. It is hoped to coordinate all this work into a unified release, but coordination of the development of a system by organizations covering three continents poses a number of interesting administrative problems. The hierarchical data structures used by Figaro allow it to handle a variety of types of data, and to add new items to data structures. Error and data quality information was added to the basic file format used, error information being particularly useful for infrared data. Cooperating sets of programs can add specific sub-structures to data files to carry information that they understand (polarimetry data containing multiple data arrays, for example), without this affecting the way other programs handle the files. Complex instrument-specific ancillary information can be added to data files written at a telescope and can be used by programs that understand the instrumental details in order to produce properly calibrated data files. Once this preliminary data processing was done the resulting files contain 'ordinary' spectra or images that can be processed by programs that are not instrument-specific. The structures holding the instrumental information can then be discarded from the files. Much effort has gone into trying to make it easy to write Figaro programs; data access subroutines are now available to handle access to all the conventional items found in Figaro files (main data arrays, error information, quality information etc), and programs that only need to access such items can be very simple indeed. A large number of Figaro users do indeed write their own Figaro applications using these routines. The fact that Figaro programs are written as callable subroutines getting information from the user through a small set of parameter routines means that they can be invoked in numerous ways; they are normally linked and run as individual programs (called by a small main routine that is generated automatically), but are also available linked to run under the ADAM data acquisition system and there is an interface that lets them be called as part of a user-written Fortran program. The long-term future of Figaro probably depends to a large extent on how successfully it manages the transition from being a VMS-only system to being a multi-platform system.

Structural insights into the anti-HIV activity of the Oscillatoria agardhii agglutinin homolog lectin family.

PubMed

Koharudin, Leonardus M I; Kollipara, Sireesha; Aiken, Christopher; Gronenborn, Angela M

2012-09-28

Oscillatoria agardhii agglutinin homolog (OAAH) proteins belong to a recently discovered lectin family. All members contain a sequence repeat of ~66 amino acids, with the number of repeats varying among different family members. Apart from data for the founding member OAA, neither three-dimensional structures, information about carbohydrate binding specificities, nor antiviral activity data have been available up to now for any other members of the OAAH family. To elucidate the structural basis for the antiviral mechanism of OAAHs, we determined the crystal structures of Pseudomonas fluorescens and Myxococcus xanthus lectins. Both proteins exhibit the same fold, resembling the founding family member, OAA, with minor differences in loop conformations. Carbohydrate binding studies by NMR and x-ray structures of glycan-lectin complexes reveal that the number of sugar binding sites corresponds to the number of sequence repeats in each protein. As for OAA, tight and specific binding to α3,α6-mannopentaose was observed. All the OAAH proteins described here exhibit potent anti-HIV activity at comparable levels. Altogether, our results provide structural details of the protein-carbohydrate interaction for this novel lectin family and insights into the molecular basis of their HIV inactivation properties.

Influence of secondary structure on in-source decay of protein in matrix-assisted laser desorption/ionization mass spectrometry.

PubMed

Takayama, Mitsuo; Osaka, Issey; Sakakura, Motoshi

2012-01-01

The susceptibility of the N-Cα bond of the peptide backbone to specific cleavage by in-source decay (ISD) in matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) was studied from the standpoint of the secondary structure of three proteins. A naphthalene derivative, 5-amino-1-naphtol (5,1-ANL), was used as the matrix. The resulting c'-ions, which originate from the cleavage at N-Cα bonds in flexible secondary structures such as turn and bend, and are free from intra-molecular hydrogen-bonded α-helix structure, gave relatively intense peaks. Furthermore, ISD spectra of the proteins showed that the N-Cα bonds of specific amino acid residues, namely Gly-Xxx, Xxx-Asp, and Xxx-Asn, were more susceptible to MALDI-ISD than other amino acid residues. This is in agreement with the observation that Gly, Asp and Asn residues usually located in turns, rather than α-helix. The results obtained indicate that protein molecules embedded into the matrix crystal in the MALDI experiments maintain their secondary structures as determined by X-ray crystallography, and that MALDI-ISD has the capability for providing information concerning the secondary structure of protein.

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.

Computational Amide I Spectroscopy for Refinement of Disordered Peptide Ensembles: Maximum Entropy and Related Approaches

NASA Astrophysics Data System (ADS)

Reppert, Michael; Tokmakoff, Andrei

The structural characterization of intrinsically disordered peptides (IDPs) presents a challenging biophysical problem. Extreme heterogeneity and rapid conformational interconversion make traditional methods difficult to interpret. Due to its ultrafast (ps) shutter speed, Amide I vibrational spectroscopy has received considerable interest as a novel technique to probe IDP structure and dynamics. Historically, Amide I spectroscopy has been limited to delivering global secondary structural information. More recently, however, the method has been adapted to study structure at the local level through incorporation of isotope labels into the protein backbone at specific amide bonds. Thanks to the acute sensitivity of Amide I frequencies to local electrostatic interactions-particularly hydrogen bonds-spectroscopic data on isotope labeled residues directly reports on local peptide conformation. Quantitative information can be extracted using electrostatic frequency maps which translate molecular dynamics trajectories into Amide I spectra for comparison with experiment. Here we present our recent efforts in the development of a rigorous approach to incorporating Amide I spectroscopic restraints into refined molecular dynamics structural ensembles using maximum entropy and related approaches. By combining force field predictions with experimental spectroscopic data, we construct refined structural ensembles for a family of short, strongly disordered, elastin-like peptides in aqueous solution.

A Knowledge Discovery framework for Planetary Defense

NASA Astrophysics Data System (ADS)

Jiang, Y.; Yang, C. P.; Li, Y.; Yu, M.; Bambacus, M.; Seery, B.; Barbee, B.

2016-12-01

Planetary Defense, a project funded by NASA Goddard and the NSF, is a multi-faceted effort focused on the mitigation of Near Earth Object (NEO) threats to our planet. Currently, there exists a dispersion of information concerning NEO's amongst different organizations and scientists, leading to a lack of a coherent system of information to be used for efficient NEO mitigation. In this paper, a planetary defense knowledge discovery engine is proposed to better assist the development and integration of a NEO responding system. Specifically, we have implemented an organized information framework by two means: 1) the development of a semantic knowledge base, which provides a structure for relevant information. It has been developed by the implementation of web crawling and natural language processing techniques, which allows us to collect and store the most relevant structured information on a regular basis. 2) the development of a knowledge discovery engine, which allows for the efficient retrieval of information from our knowledge base. The knowledge discovery engine has been built on the top of Elasticsearch, an open source full-text search engine, as well as cutting-edge machine learning ranking and recommendation algorithms. This proposed framework is expected to advance the knowledge discovery and innovation in planetary science domain.

Sensitivity and Specificity of OCT Angiography to Detect Choroidal Neovascularization.

PubMed

Faridi, Ambar; Jia, Yali; Gao, Simon S; Huang, David; Bhavsar, Kavita V; Wilson, David J; Sill, Andrew; Flaxel, Christina J; Hwang, Thomas S; Lauer, Andreas K; Bailey, Steven T

2017-01-01

To determine the sensitivity and specificity of optical coherence tomography angiography (OCTA) in the detection of choroidal neovascularization (CNV) in age-related macular degeneration (AMD). Prospective case series. Prospective series of seventy-two eyes were studied, which included eyes with treatment-naive CNV due to AMD, non-neovascular AMD, and normal controls. All eyes underwent OCTA with a spectral domain (SD) OCT (Optovue, Inc.). The 3D angiogram was segmented into separate en face views including the inner retinal angiogram, outer retinal angiogram, and choriocapillaris angiogram. Detection of abnormal flow in the outer retina served as candidate CNV with OCTA. Masked graders reviewed structural OCT alone, en face OCTA alone, and en face OCTA combined with cross-sectional OCTA for the presence of CNV. The sensitivity and specificity of CNV detection compared to the gold standard of fluorescein angiography (FA) and OCT was determined for structural SD-OCT alone, en face OCTA alone, and with en face OCTA combined with cross-sectional OCTA. Of 32 eyes with CNV, both graders identified 26 true positives with en face OCTA alone, resulting in a sensitivity of 81.3%. Four of the 6 false negatives had large subretinal hemorrhage (SRH) and sensitivity improved to 94% for both graders if eyes with SRH were excluded. The addition of cross-sectional OCTA along with en face OCTA improved the sensitivity to 100% for both graders. Structural OCT alone also had a sensitivity of 100%. The specificity of en face OCTA alone was 92.5% for grader A and 97.5% for grader B. The specificity of structural OCT alone was 97.5% for grader A and 85% for grader B. Cross-sectional OCTA combined with en face OCTA had a specificity of 97.5% for grader A and 100% for grader B. Sensitivity and specificity for CNV detection with en face OCTA combined with cross-sectional OCTA approaches that of the gold standard of FA with OCT, and it is better than en face OCTA alone. Structural OCT alone has excellent sensitivity for CNV detection. False positives from structural OCT can be mitigated with the addition of flow information with OCTA.

CYPSI: a structure-based interface for cytochrome P450s and ligands in Arabidopsis thaliana

PubMed Central

2012-01-01

Background The cytochrome P450 (CYP) superfamily enables terrestrial plants to adapt to harsh environments. CYPs are key enzymes involved in a wide range of metabolic pathways. It is particularly useful to be able to analyse the three-dimensional (3D) structure when investigating the interactions between CYPs and their substrates. However, only two plant CYP structures have been resolved. In addition, no currently available databases contain structural information on plant CYPs and ligands. Fortunately, the 3D structure of CYPs is highly conserved and this has made it possible to obtain structural information from template-based modelling (TBM). Description The CYP Structure Interface (CYPSI) is a platform for CYP studies. CYPSI integrated the 3D structures for 266 A. thaliana CYPs predicted by three TBM methods: BMCD, which we developed specifically for CYP TBM; and two well-known web-servers, MUSTER and I-TASSER. After careful template selection and optimization, the models built by BMCD were accurate enough for practical application, which we demonstrated using a docking example aimed at searching for the CYPs responsible for ABA 8′-hydroxylation. CYPSI also provides extensive resources for A. thaliana CYP structure and function studies, including 400 PDB entries for solved CYPs, 48 metabolic pathways associated with A. thaliana CYPs, 232 reported CYP ligands and 18 A. thaliana CYPs docked with ligands (61 complexes in total). In addition, CYPSI also includes the ability to search for similar sequences and chemicals. Conclusions CYPSI provides comprehensive structure and function information for A. thaliana CYPs, which should facilitate investigations into the interactions between CYPs and their substrates. CYPSI has a user-friendly interface, which is available at http://bioinfo.cau.edu.cn/CYPSI. PMID:23256889

FINDSITE-metal: Integrating evolutionary information and machine learning for structure-based metal binding site prediction at the proteome level

PubMed Central

Brylinski, Michal; Skolnick, Jeffrey

2010-01-01

The rapid accumulation of gene sequences, many of which are hypothetical proteins with unknown function, has stimulated the development of accurate computational tools for protein function prediction with evolution/structure-based approaches showing considerable promise. In this paper, we present FINDSITE-metal, a new threading-based method designed specifically to detect metal binding sites in modeled protein structures. Comprehensive benchmarks using different quality protein structures show that weakly homologous protein models provide sufficient structural information for quite accurate annotation by FINDSITE-metal. Combining structure/evolutionary information with machine learning results in highly accurate metal binding annotations; for protein models constructed by TASSER, whose average Cα RMSD from the native structure is 8.9 Å, 59.5% (71.9%) of the best of top five predicted metal locations are within 4 Å (8 Å) from a bound metal in the crystal structure. For most of the targets, multiple metal binding sites are detected with the best predicted binding site at rank 1 and within the top 2 ranks in 65.6% and 83.1% of the cases, respectively. Furthermore, for iron, copper, zinc, calcium and magnesium ions, the binding metal can be predicted with high, typically 70-90%, accuracy. FINDSITE-metal also provides a set of confidence indexes that help assess the reliability of predictions. Finally, we describe the proteome-wide application of FINDSITE-metal that quantifies the metal binding complement of the human proteome. FINDSITE-metal is freely available to the academic community at http://cssb.biology.gatech.edu/findsite-metal/. PMID:21287609

Flexible and Scalable Data Fusion using Proactive Schemaless Information Services

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

Widener, Patrick

2014-05-01

Exascale data environments are fast approaching, driven by diverse structured and unstructured data such as system and application telemetry streams, open-source information capture, and on-demand simulation output. Storage costs having plummeted, the question is now one of converting vast stores of data to actionable information. Complicating this problem are the low degrees of awareness across domain boundaries about what potentially useful data may exist, and write-once- read-never issues (data generation/collection rates outpacing data analysis and integration rates). Increasingly, technologists and researchers need to correlate previously unrelated data sources and artifacts to produce fused data views for domain-specific purposes. New toolsmore » and approaches for creating such views from vast amounts of data are vitally important to maintaining research and operational momentum. We propose to research and develop tools and services to assist in the creation, refinement, discovery and reuse of fused data views over large, diverse collections of heterogeneously structured data. We innovate in the following ways. First, we enable and encourage end-users to introduce customized index methods selected for local benefit rather than for global interaction (flexible multi-indexing). We envision rich combinations of such views on application data: views that span backing stores with different semantics, that introduce analytic methods of indexing, and that define multiple views on individual data items. We specifically decline to build a big fused database of everything providing a centralized index over all data, or to export a rigid schema to all comers as in federated query approaches. Second, we proactively advertise these application-specific views so that they may be programmatically reused and extended (data proactivity). Through this mechanism, both changes in state (new data in existing view collected) and changes in structure (new or derived view exists) are made known. Lastly, we embrace found data heterogeneity by coupling multi-indexing to backing stores with appropriate semantics (as opposed to a single store or schema).« less

Flexible and Scalable Data Fusion using Proactive, Schemaless Information Services

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

Widener, Patrick M.

2014-05-01

Exascale data environments are fast approaching, driven by diverse structured and unstructured data such as system and application telemetry streams, open-source information capture, and on-demand simulation output. Storage costs having plummeted, the question is now one of converting vast stores of data to actionable information. Complicating this problem are the low degrees of awareness across domain boundaries about what potentially useful data may exist, and write-once-read- never issues (data generation/collection rates outpacing data analysis and integration rates). Increasingly, technologists and researchers need to correlate previously unrelated data sources and artifacts to produce fused data views for domain-specific purposes. New toolsmore » and approaches for creating such views from vast amounts of data are vitally important to maintaining research and operational momentum. We propose to research and develop tools and services to assist in the creation, refinement, discovery and reuse of fused data views over large, diverse collections of heterogeneously structured data. We innovate in the following ways. First, we enable and encourage end-users to introduce customized index methods selected for local benefit rather than for global interaction (flexible multi-indexing). We envision rich combinations of such views on application data: views that span backing stores with different semantics, that introduce analytic methods of indexing, and that define multiple views on individual data items. We specifically decline to build a big fused database of everything providing a centralized index over all data, or to export a rigid schema to all comers as in federated query approaches. Second, we proactively advertise these application-specific views so that they may be programmatically reused and extended (data proactivity). Through this mechanism, both changes in state (new data in existing view collected) and changes in structure (new or derived view exists) are made known. Lastly, we embrace found data heterogeneity by coupling multi-indexing to backing stores with appropriate semantics (as opposed to a single store or schema).« less

Interactions of information transfer along separable causal paths

NASA Astrophysics Data System (ADS)

Jiang, Peishi; Kumar, Praveen

2018-04-01

Complex systems arise as a result of interdependences between multiple variables, whose causal interactions can be visualized in a time-series graph. Transfer entropy and information partitioning approaches have been used to characterize such dependences. However, these approaches capture net information transfer occurring through a multitude of pathways involved in the interaction and as a result mask our ability to discern the causal interaction within a subgraph of interest through specific pathways. We build on recent developments of momentary information transfer along causal paths proposed by Runge [Phys. Rev. E 92, 062829 (2015), 10.1103/PhysRevE.92.062829] to develop a framework for quantifying information partitioning along separable causal paths. Momentary information transfer along causal paths captures the amount of information transfer between any two variables lagged at two specific points in time. Our approach expands this concept to characterize the causal interaction in terms of synergistic, unique, and redundant information transfer through separable causal paths. Through a graphical model, we analyze the impact of the separable and nonseparable causal paths and the causality structure embedded in the graph as well as the noise effect on information partitioning by using synthetic data generated from two coupled logistic equation models. Our approach can provide a valuable reference for an autonomous information partitioning along separable causal paths which form a causal subgraph influencing a target.

Modalities for Visualization of Cortical Bone Remodeling: The Past, Present, and Future

PubMed Central

Harrison, Kimberly D.; Cooper, David M. L.

2015-01-01

Bone’s ability to respond to load-related phenomena and repair microdamage is achieved through the remodeling process, which renews bone by activating groups of cells known as basic multicellular units (BMUs). The products of BMUs, secondary osteons, have been extensively studied via classic two-dimensional techniques, which have provided a wealth of information on how histomorphology relates to skeletal structure and function. Remodeling is critical in maintaining healthy bone tissue; however, in osteoporotic bone, imbalanced resorption results in increased bone fragility and fracture. With increasing life expectancy, such degenerative bone diseases are a growing concern. The three-dimensional (3D) morphology of BMUs and their correlation to function, however, are not well-characterized and little is known about the specific mechanisms that initiate and regulate their activity within cortical bone. We believe a key limitation has been the lack of 3D information about BMU morphology and activity. Thus, this paper reviews methodologies for 3D investigation of cortical bone remodeling and, specifically, structures associated with BMU activity (resorption spaces) and the structures they create (secondary osteons), spanning from histology to modern ex vivo imaging modalities, culminating with the growing potential of in vivo imaging. This collection of papers focuses on the theme of “putting the ‘why’ back into bone architecture.” Remodeling is one of two mechanisms “how” bone structure is dynamically modified and thus an improved 3D understanding of this fundamental process is crucial to ultimately understanding the “why.” PMID:26322017

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

PubMed Central

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

2013-01-01

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

Sensitivity and specificity of cone beam computed tomography in thin bony structures in maxillofacial surgery – A clinical trial.

PubMed

Thönissen, P; Ermer, M A; Schmelzeisen, R; Gutwald, R; Metzger, M C; Bittermann, G

2015-09-01

Cone-Beam Computed Tomography (CBCT) has become widely used in dentistry and maxillofacial surgery. Accuracy, sensitivity and specificity of thin bony structures below 0.5 mm have been subject of some in vitro studies. This prospective in vivo study investigates the correlation between preoperative CBCT-imaging and intraoperative clinical examination of thin bony structures. We hereby present results from daily clinical routine. A total number of 80 sites in 64 patients has been examined to differentiate between preoperative 3D imaging and clinical measurements on cystic lesions in maxilla and mandible. Different CBCT-devices with a voxel size ranging from 0.08 mm to 0.4 mm were used. Overall-specificity found for detecting thin bony structures of the human jaw is 13.89%, overall sensitivity is 100%, positive predictive value (PPV) is 58.67% and negative predictive value (NPV) is 100%. Image quality is the key to make use of additional information CBCT provides and depends on spatial, temporal and contrast resolution. CBCT does not depict reliably thin bony structures of the jaw, even if high voxel resolution is used. In selected cases using high resolution protocols should be considered despite affecting the patient with higher doses of radiation. Copyright © 2015 European Association for Cranio-Maxillo-Facial Surgery. Published by Elsevier Ltd. All rights reserved.

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

Prof. P. Somasundaran

The aim of the project is to develop and evaluate efficient novel surfactant mixtures for enhanced oil recovery. Preliminary ultra-filtration tests suggest that two kinds of micelles may exist in binary surfactant mixtures at different concentrations. Due to the important role played in interfacial processes by micelles as determined by their structures, focus of the current work is on the delineation of the relationship between such aggregate structures and chemical compositions of the surfactants. A novel analytical centrifuge application is explored to generate information on structures of different surfactants aggregates. In this report, optical systems, typical output of the analyticalmore » ultracentrifuge results and four basic experiments are discussed. Initial sedimentation velocity investigations were conducted using nonyl phenol ethoxylated decyl ether (NP-10) to choose the best analytical protocol, calculate the partial specific volume and obtain information on sedimentation coefficient, aggregation mass of micelles. The partial specific volume was calculated to be 0.920. Four softwares: Optima{trademark} XL-A/XL-I data analysis software, DCDT+, Svedberg and SEDFIT, were compared for the analysis of sedimentation velocity experimental data. The sedimentation coefficient and aggregation number of NP-10 micelles obtained using the first three softwares at 25 C are 209, 127, and 111, respectively. The last one is closest to the result from Light Scattering. The reason for the differences in numbers obtained using the three softwares is discussed. Based on these tests, Svedberg and SEDFIT analysis are chosen for further studies. This approach using the analytical ultracentrifugation offers an unprecedented opportunity now to obtain important information on mixed micelles and their role in interfacial processes.« less

Unraveling the unknown areas of the human metabolome: the role of infrared ion spectroscopy.

PubMed

Martens, Jonathan; Berden, Giel; Bentlage, Herman; Coene, Karlien L M; Engelke, Udo F; Wishart, David; van Scherpenzeel, Monique; Kluijtmans, Leo A J; Wevers, Ron A; Oomens, Jos

2018-05-01

The identification of molecular biomarkers is critical for diagnosing and treating patients and for establishing a fundamental understanding of the pathophysiology and underlying biochemistry of inborn errors of metabolism. Currently, liquid chromatography/high-resolution mass spectrometry and nuclear magnetic resonance spectroscopy are the principle methods used for biomarker research and for structural elucidation of small molecules in patient body fluids. While both are powerful techniques, several limitations exist that often make the identification of unknown compounds challenging. Here, we describe how infrared ion spectroscopy has the potential to be a valuable orthogonal technique that provides highly-specific molecular structure information while maintaining ultra-high sensitivity. Here, we characterize and distinguish two well-known biomarkers of inborn errors of metabolism, glutaric acid for glutaric aciduria and ethylmalonic acid for short-chain acyl-CoA dehydrogenase deficiency, using infrared ion spectroscopy. In contrast to tandem mass spectra, in which ion fragments can hardly be predicted, we show that the prediction of an IR spectrum allows reference-free identification in the case that standard compounds are either commercially or synthetically unavailable. Finally, we illustrate how functional group information can be obtained from an IR spectrum for an unknown and how this is valuable information to, for example, narrow down a list of candidate structures resulting from a database query. Early diagnosis in inborn errors of metabolism is crucial for enabling treatment and depends on the identification of biomarkers specific for the disorder. Infrared ion spectroscopy has the potential to play a pivotal role in the identification of challenging biomarkers.

The sound manifesto

NASA Astrophysics Data System (ADS)

O'Donnell, Michael J.; Bisnovatyi, Ilia

2000-11-01

Computing practice today depends on visual output to drive almost all user interaction. Other senses, such as audition, may be totally neglected, or used tangentially, or used in highly restricted specialized ways. We have excellent audio rendering through D-A conversion, but we lack rich general facilities for modeling and manipulating sound comparable in quality and flexibility to graphics. We need coordinated research in several disciplines to improve the use of sound as an interactive information channel. Incremental and separate improvements in synthesis, analysis, speech processing, audiology, acoustics, music, etc. will not alone produce the radical progress that we seek in sonic practice. We also need to create a new central topic of study in digital audio research. The new topic will assimilate the contributions of different disciplines on a common foundation. The key central concept that we lack is sound as a general-purpose information channel. We must investigate the structure of this information channel, which is driven by the cooperative development of auditory perception and physical sound production. Particular audible encodings, such as speech and music, illuminate sonic information by example, but they are no more sufficient for a characterization than typography is sufficient for characterization of visual information. To develop this new conceptual topic of sonic information structure, we need to integrate insights from a number of different disciplines that deal with sound. In particular, we need to coordinate central and foundational studies of the representational models of sound with specific applications that illuminate the good and bad qualities of these models. Each natural or artificial process that generates informative sound, and each perceptual mechanism that derives information from sound, will teach us something about the right structure to attribute to the sound itself. The new Sound topic will combine the work of computer scientists with that of numerical mathematicians studying sonification, psychologists, linguists, bioacousticians, and musicians to illuminate the structure of sound from different angles. Each of these disciplines deals with the use of sound to carry a different sort of information, under different requirements and constraints. By combining their insights, we can learn to understand of the structure of sound in general.

Factor structure and clinical utility of the Beck depression inventory in patients with binge eating disorder and obesity.

PubMed

Udo, Tomoko; McKee, Sherry A; Grilo, Carlos M

2015-01-01

The Beck Depression Inventory (BDI) is often used to assess depression symptoms, but its factor structure and its clinical utility have not been evaluated in patients with binge eating disorder (BED) and obesity. A total of 882 treatment-seeking obese patients with BED were administered structured interviews (Structured Clinical Interview for Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition Axis I Disorders) and completed self-report questionnaires. Exploratory and confirmatory factor analyses supported a brief 16-item BDI version with a three-factor structure (affective, attitudinal and somatic). Both 21- and 16-item versions showed excellent internal consistency (both α=0.89) and had significant correlation patterns with different aspects of eating disorder psychopathology; three factors showed significant but variable associations with eating disorder psychopathology. Area under the curves (AUC) for both BDI versions were significant in predicting major depressive disorder (MDD; AUC=0.773 [16-item], 73.5% sensitivity/70.2% specificity, AUC=0.769 [21-item], 79.5% sensitivity/64.1% specificity) and mood disorders (AUC=0.763 [16-item], 67.1% sensitivity/71.5% specificity, AUC=0.769 [21-item], 84.2% sensitivity/55.7% specificity). The 21-item BDI (cutoff score ≥16) showed higher negative predictive values (94.0% vs. 93.0% [MDD]; 92.4% vs. 88.3% [mood disorders]) than the brief 16-item BDI (cutoff score ≥13). Both BDI versions demonstrated moderate performance as a screening instrument for MDD/mood disorders in obese patients with BED. Advantages and disadvantages for both versions are discussed. A three-factor structure has potential to inform the conceptualization of depression features. Copyright © 2015 Elsevier Inc. All rights reserved.

Eyeing the Cyr61/CTGF/NOV (CCN) group of genes in development and diseases: highlights of their structural likenesses and functional dissimilarities.

PubMed

Krupska, Izabela; Bruford, Elspeth A; Chaqour, Brahim

2015-09-23

"CCN" is an acronym referring to the first letter of each of the first three members of this original group of mammalian functionally and phylogenetically distinct extracellular matrix (ECM) proteins [i.e., cysteine-rich 61 (CYR61), connective tissue growth factor (CTGF), and nephroblastoma-overexpressed (NOV)]. Although "CCN" genes are unlikely to have arisen from a common ancestral gene, their encoded proteins share multimodular structures in which most cysteine residues are strictly conserved in their positions within several structural motifs. The CCN genes can be subdivided into members developmentally indispensable for embryonic viability (e.g., CCN1, 2 and 5), each assuming unique tissue-specific functions, and members not essential for embryonic development (e.g., CCN3, 4 and 6), probably due to a balance of functional redundancy and specialization during evolution. The temporo-spatial regulation of the CCN genes and the structural information contained within the sequences of their encoded proteins reflect diversity in their context and tissue-specific functions. Genetic association studies and experimental anomalies, replicated in various animal models, have shown that altered CCN gene structure or expression is associated with "injury" stimuli--whether mechanical (e.g., trauma, shear stress) or chemical (e.g., ischemia, hyperglycemia, hyperlipidemia, inflammation). Consequently, increased organ-specific susceptibility to structural damages ensues. These data underscore the critical functions of CCN proteins in the dynamics of tissue repair and regeneration and in the compensatory responses preceding organ failure. A better understanding of the regulation and mode of action of each CCN member will be useful in developing specific gain- or loss-of-function strategies for therapeutic purposes.

Structural Basis of Substrate Specificity and Regiochemistry in the MycF/TylF Family of Sugar O -Methyltransferases.

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

Bernard, Steffen M.; Akey, David L.; Tripathi, Ashootosh

Sugar moieties in natural products are frequently modified by O-methylation. In the biosynthesis of the macrolide antibiotic mycinamicin, methylation of a 6'-deoxyallose substituent occurs in a stepwise manner first at the 2'- and then the 3'-hydroxyl groups to produce the mycinose moiety in the final product. The timing and placement of the O-methylations impact final stage C-H functionalization reactions mediated by the P450 monooxygenase MycG. The structural basis of pathway ordering and substrate specificity is unknown. A series of crystal structures of MycF, the 3'-O-methyltransferase, including the free enzyme and complexes with S-adenosyl homocysteine (SAH), substrate, product, and unnatural substrates,more » show that SAM binding induces substantial ordering that creates the binding site for the natural substrate, and a bound metal ion positions the substrate for catalysis. A single amino acid substitution relaxed the 2'-methoxy specificity but retained regiospecificity. The engineered variant produced a new mycinamicin analog, demonstrating the utility of structural information to facilitate bioengineering approaches for the chemoenzymatic synthesis of complex small molecules containing modified sugars. Using the MycF substrate complex and the modeled substrate complex of a 4'-specific homolog, active site residues were identified that correlate with the 3'- or 4'- specificity of MycF family members and define the protein and substrate features that direct the regiochemistry of methyltransfer. Lastly, this classification scheme will be useful in the annotation of new secondary metabolite pathways that utilize this family of enzymes.« less

Structural Basis of Substrate Specificity and Regiochemistry in the MycF/TylF Family of Sugar O -Methyltransferases.

DOE PAGES

Bernard, Steffen M.; Akey, David L.; Tripathi, Ashootosh; ...

2015-02-18

Sugar moieties in natural products are frequently modified by O-methylation. In the biosynthesis of the macrolide antibiotic mycinamicin, methylation of a 6'-deoxyallose substituent occurs in a stepwise manner first at the 2'- and then the 3'-hydroxyl groups to produce the mycinose moiety in the final product. The timing and placement of the O-methylations impact final stage C-H functionalization reactions mediated by the P450 monooxygenase MycG. The structural basis of pathway ordering and substrate specificity is unknown. A series of crystal structures of MycF, the 3'-O-methyltransferase, including the free enzyme and complexes with S-adenosyl homocysteine (SAH), substrate, product, and unnatural substrates,more » show that SAM binding induces substantial ordering that creates the binding site for the natural substrate, and a bound metal ion positions the substrate for catalysis. A single amino acid substitution relaxed the 2'-methoxy specificity but retained regiospecificity. The engineered variant produced a new mycinamicin analog, demonstrating the utility of structural information to facilitate bioengineering approaches for the chemoenzymatic synthesis of complex small molecules containing modified sugars. Using the MycF substrate complex and the modeled substrate complex of a 4'-specific homolog, active site residues were identified that correlate with the 3'- or 4'- specificity of MycF family members and define the protein and substrate features that direct the regiochemistry of methyltransfer. Lastly, this classification scheme will be useful in the annotation of new secondary metabolite pathways that utilize this family of enzymes.« less

A decade and a half of protein intrinsic disorder: Biology still waits for physics

PubMed Central

Uversky, Vladimir N

2013-01-01

The abundant existence of proteins and regions that possess specific functions without being uniquely folded into unique 3D structures has become accepted by a significant number of protein scientists. Sequences of these intrinsically disordered proteins (IDPs) and IDP regions (IDPRs) are characterized by a number of specific features, such as low overall hydrophobicity and high net charge which makes these proteins predictable. IDPs/IDPRs possess large hydrodynamic volumes, low contents of ordered secondary structure, and are characterized by high structural heterogeneity. They are very flexible, but some may undergo disorder to order transitions in the presence of natural ligands. The degree of these structural rearrangements varies over a very wide range. IDPs/IDPRs are tightly controlled under the normal conditions and have numerous specific functions that complement functions of ordered proteins and domains. When lacking proper control, they have multiple roles in pathogenesis of various human diseases. Gaining structural and functional information about these proteins is a challenge, since they do not typically “freeze” while their “pictures are taken.” However, despite or perhaps because of the experimental challenges, these fuzzy objects with fuzzy structures and fuzzy functions are among the most interesting targets for modern protein research. This review briefly summarizes some of the recent advances in this exciting field and considers some of the basic lessons learned from the analysis of physics, chemistry, and biology of IDPs. PMID:23553817

Software requirements: Guidance and control software development specification

NASA Technical Reports Server (NTRS)

Withers, B. Edward; Rich, Don C.; Lowman, Douglas S.; Buckland, R. C.

1990-01-01

The software requirements for an implementation of Guidance and Control Software (GCS) are specified. The purpose of the GCS is to provide guidance and engine control to a planetary landing vehicle during its terminal descent onto a planetary surface and to communicate sensory information about that vehicle and its descent to some receiving device. The specification was developed using the structured analysis for real time system specification methodology by Hatley and Pirbhai and was based on a simulation program used to study the probability of success of the 1976 Viking Lander missions to Mars. Three versions of GCS are being generated for use in software error studies.

Development and evaluation of task-specific NLP framework in China.

PubMed

Ge, Caixia; Zhang, Yinsheng; Huang, Zhenzhen; Jia, Zheng; Ju, Meizhi; Duan, Huilong; Li, Haomin

2015-01-01

Natural language processing (NLP) has been designed to convert narrative text into structured data. Although some general NLP architectures have been developed, a task-specific NLP framework to facilitate the effective use of data is still a challenge in lexical resource limited regions, such as China. The purpose of this study is to design and develop a task-specific NLP framework to extract targeted information from particular documents by adopting dedicated algorithms on current limited lexical resources. In this framework, a shared and evolving ontology mechanism was designed. The result has shown that such a free text driven platform will accelerate the NLP technology acceptance in China.

Information architecture for a patient-specific dashboard in head and neck tumor boards.

PubMed

Oeser, Alexander; Gaebel, Jan; Dietz, Andreas; Wiegand, Susanne; Oeltze-Jafra, Steffen

2018-03-28

Overcoming the flaws of current data management conditions in head and neck oncology could enable integrated information systems specifically tailored to the needs of medical experts in a tumor board meeting. Clinical dashboards are a promising method to assist various aspects of the decision-making process in such cognitively demanding scenarios. However, in order to provide extensive and intuitive assistance to the participating physicians, the design and development of such a system have to be user-centric. To accomplish this task, conceptual methods need to be performed prior to the technical development and integration stages. We have conducted a qualitative survey including eight clinical experts with different levels of expertise in the field of head and neck oncology. According to the principles of information architecture, the survey focused on the identification and causal interconnection of necessary metrics for information assessment in the tumor board. Based on the feedback by the clinical experts, we have constructed a detailed map of the required information items for a tumor board dashboard in head and neck oncology. Furthermore, we have identified three distinct groups of metrics (patient, disease and therapy metrics) as well as specific recommendations for their structural and graphical implementation. By using the information architecture, we were able to gather valuable feedback about the requirements and cognitive processes of the tumor board members. Those insights have helped us to develop a dashboard application that closely adapts to the specified needs and characteristics, and thus is primarily user-centric.

Localized zinc distribution in shark vertebrae suggests differential deposition during ontogeny and across vertebral structures.

PubMed

Raoult, Vincent; Howell, Nicholas; Zahra, David; Peddemors, Victor M; Howard, Daryl L; de Jonge, Martin D; Buchan, Benjamin L; Williamson, Jane E

2018-01-01

The development of shark vertebrae and the possible drivers of inter- and intra-specific differences in vertebral structure are poorly understood. Shark vertebrae are used to examine life-history traits related to trophic ecology, movement patterns, and the management of fisheries; a better understanding of their development would be beneficial to many fields of research that rely on these calcified structures. This study used Scanning X-ray Fluorescence Microscopy to observe zinc distribution within vertebrae of ten shark species from five different orders. Zinc was mostly localised within the intermedialis and was generally detected at levels an order of magnitude lower in the corpus calcareum. In most species, zinc concentrations were higher pre-birth mark, indicating a high rate of pre-natal zinc deposition. These results suggest there are inter-specific differences in elemental deposition within vertebrae. Since the deposition of zinc is physiologically-driven, these differences suggest that the processes of growth and deposition are potentially different in the intermedialis and corpus calcareum, and that caution should be taken when extrapolating information such as annual growth bands from one structure to the other. Together these results suggest that the high inter-specific variation in vertebral zinc deposition and associated physiologies may explain the varying effectiveness of ageing methodologies applied to elasmobranch vertebrae.

Automated global structure extraction for effective local building block processing in XCS.

PubMed

Butz, Martin V; Pelikan, Martin; Llorà, Xavier; Goldberg, David E

2006-01-01

Learning Classifier Systems (LCSs), such as the accuracy-based XCS, evolve distributed problem solutions represented by a population of rules. During evolution, features are specialized, propagated, and recombined to provide increasingly accurate subsolutions. Recently, it was shown that, as in conventional genetic algorithms (GAs), some problems require efficient processing of subsets of features to find problem solutions efficiently. In such problems, standard variation operators of genetic and evolutionary algorithms used in LCSs suffer from potential disruption of groups of interacting features, resulting in poor performance. This paper introduces efficient crossover operators to XCS by incorporating techniques derived from competent GAs: the extended compact GA (ECGA) and the Bayesian optimization algorithm (BOA). Instead of simple crossover operators such as uniform crossover or one-point crossover, ECGA or BOA-derived mechanisms are used to build a probabilistic model of the global population and to generate offspring classifiers locally using the model. Several offspring generation variations are introduced and evaluated. The results show that it is possible to achieve performance similar to runs with an informed crossover operator that is specifically designed to yield ideal problem-dependent exploration, exploiting provided problem structure information. Thus, we create the first competent LCSs, XCS/ECGA and XCS/BOA, that detect dependency structures online and propagate corresponding lower-level dependency structures effectively without any information about these structures given in advance.

InterEvDock: a docking server to predict the structure of protein–protein interactions using evolutionary information

PubMed Central

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

2016-01-01

The structural modeling of protein–protein interactions is key in understanding how cell machineries cross-talk with each other. Molecular docking simulations provide efficient means to explore how two unbound protein structures interact. InterEvDock is a server for protein docking based on a free rigid-body docking strategy. A systematic rigid-body docking search is performed using the FRODOCK program and the resulting models are re-scored with InterEvScore and SOAP-PP statistical potentials. The InterEvScore potential was specifically designed to integrate co-evolutionary information in the docking process. InterEvDock server is thus particularly well suited in case homologous sequences are available for both binding partners. The server returns 10 structures of the most likely consensus models together with 10 predicted residues most likely involved in the interface. In 91% of all complexes tested in the benchmark, at least one residue out of the 10 predicted is involved in the interface, providing useful guidelines for mutagenesis. InterEvDock is able to identify a correct model among the top10 models for 49% of the rigid-body cases with evolutionary information, making it a unique and efficient tool to explore structural interactomes under an evolutionary perspective. The InterEvDock web interface is available at http://bioserv.rpbs.univ-paris-diderot.fr/services/InterEvDock/. PMID:27131368

The macrostructure of informal arguments: a proposed model and analysis.

PubMed

Ricco, Robert B

2003-08-01

Theories of informal reasoning and critical thinking often maintain that everyday, informal arguments can be classified into types based on the specific organization that the premises or reasons enter into in their support for the conclusion (Snoeck Henkemans, 2000; Vorobej, 1995b). Three general types are identified: convergent, coordinately linked, and subordinately linked arguments. There has been no empirical research, however, to determine whether these structural distinctions have any psychological reality. In the first two of four experiments, college students were presented with premise pairs from larger, informal arguments and were asked to judge the nature of the relationship between the premises in a pair. The judgments involved applying "tests" of linkage, subordination, and so on, that have been proposed in the theoretical literature on argument analysis (e.g., Walton, 1996a; Yanal, 1991). Results suggest that adults can effectively distinguish between linked (interdependent) and convergent relationships and can further distinguish between interdependencies that are full and those that are merely partial. Adults also distinguished between subordinate and nonsubordinate relations. Experiments 3 and 4 provide evidence that adults make use of information about argument structure in evaluating argument strength and in categorizing arguments. Experiment 4 further suggests that facility with macrostructure is only modestly related to deductive reasoning competence. Findings are framed in terms of a speculative account of how argument structure is identified and mentally represented.

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.

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

Laboratory Information Systems in Molecular Diagnostics: Why Molecular Diagnostics Data are Different.

PubMed

Lee, Roy E; Henricks, Walter H; Sirintrapun, Sahussapont J

2016-03-01

Molecular diagnostic testing presents new challenges to information management that are yet to be sufficiently addressed by currently available information systems for the molecular laboratory. These challenges relate to unique aspects of molecular genetic testing: molecular test ordering, informed consent issues, diverse specimen types that encompass the full breadth of specimens handled by traditional anatomic and clinical pathology information systems, data structures and data elements specific to molecular testing, varied testing workflows and protocols, diverse instrument outputs, unique needs and requirements of molecular test reporting, and nuances related to the dissemination of molecular pathology test reports. By satisfactorily addressing these needs in molecular test data management, a laboratory information system designed for the unique needs of molecular diagnostics presents a compelling reason to migrate away from the current paper and spreadsheet information management that many molecular laboratories currently use. This paper reviews the issues and challenges of information management in the molecular diagnostics laboratory.

Substrate specificity of bacterial DD-peptidases (penicillin-binding proteins).

PubMed

Pratt, R F

2008-07-01

The DD-peptidase enzymes (penicillin-binding proteins) catalyze the final transpeptidation reaction of bacterial cell wall (peptidoglycan) biosynthesis. Although there is now much structural information available about these enzymes, studies of their activity as enzymes lag. It is now established that representatives of two low-molecular-mass classes of DD-peptidases recognize elements of peptidoglycan structure and rapidly react with substrates and inhibitors incorporating these elements. No members of other DD-peptidase classes, including the high-molecular-mass enzymes, essential for bacterial growth, appear to interact strongly with any particular elements of peptidoglycan structure. Rational design of inhibitors for these enzymes is therefore challenging.

Designing of plant artificial chromosome (PAC) by using the Chlorella smallest chromosome as a model system.

PubMed

Noutoshi, Y; Arai, R; Fujie, M; Yamada, T

1997-01-01

As a model for plant-type chromosomes, we have been characterizing molecular organization of the Chlorella vulgaris C-169 chromosome I. To identify chromosome structural elements including the centromeric region and replication origins, we constructed a chromosome I specific cosmid library and aligned each cosmid clones to generate contigs. So far, more than 80% of the entire chromosome I has been covered. A complete clonal physical reconstitution of chromosome I provides information on the structure and genomic organization of plant genome. We propose our strategy to construct an artificial chromosome by assembling the functional chromosome structural elements identified on Chrorella chromosome I.

Bond graph modelling of multibody dynamics and its symbolic scheme

NASA Astrophysics Data System (ADS)

Kawase, Takehiko; Yoshimura, Hiroaki

A bond graph method of modeling multibody dynamics is demonstrated. Specifically, a symbolic generation scheme which fully utilizes the bond graph information is presented. It is also demonstrated that structural understanding and representation in bond graph theory is quite powerful for the modeling of such large scale systems, and that the nonenergic multiport of junction structure, which is a multiport expression of the system structure, plays an important role, as first suggested by Paynter. The principal part of the proposed symbolic scheme, that is, the elimination of excess variables, is done through tearing and interconnection in the sense of Kron using newly defined causal and causal coefficient arrays.

The role of information and communication technology in the transformation of the healthcare business model: a case study of Slovenia.

PubMed

Stanimirovic, Dalibor; Vintar, Mirko

The Slovenian healthcare business model (BM) has largely failed to integrate information and communication technologies (ICT) into its operational context, instead maintaining its rigid structure and traditional 'way of doing business'wo managers of public clinics). Findings present a roadmap for the redefinition of BM elements and the transformation of the Slovenian healthcare BM. It includes the specific reconfiguration of BM actors and their interactions, and the application of advanced ICT solutions, which could facilitate more effective utilisation of healthcare resources and promote an improved delivery of healthcare services and products. The presented development approach and derived conceptual solution could be transferable to other countries with similar socio-economic characteristics and comparable healthcare systems, subject to certain adjustments and inclusion of national specifics.