Expediting Combinatorial Data Set Analysis by Combining Human and Algorithmic Analysis.

PubMed

Stein, Helge Sören; Jiao, Sally; Ludwig, Alfred

2017-01-09

A challenge in combinatorial materials science remains the efficient analysis of X-ray diffraction (XRD) data and its correlation to functional properties. Rapid identification of phase-regions and proper assignment of corresponding crystal structures is necessary to keep pace with the improved methods for synthesizing and characterizing materials libraries. Therefore, a new modular software called htAx (high-throughput analysis of X-ray and functional properties data) is presented that couples human intelligence tasks used for "ground-truth" phase-region identification with subsequent unbiased verification by an algorithm to efficiently analyze which phases are present in a materials library. Identified phases and phase-regions may then be correlated to functional properties in an expedited manner. For the functionality of htAx to be proven, two previously published XRD benchmark data sets of the materials systems Al-Cr-Fe-O and Ni-Ti-Cu are analyzed by htAx. The analysis of ∼1000 XRD patterns takes less than 1 day with htAx. The proposed method reliably identifies phase-region boundaries and robustly identifies multiphase structures. The method also addresses the problem of identifying regions with previously unpublished crystal structures using a special daisy ternary plot.

Structure identification methods for atomistic simulations of crystalline materials

DOE PAGES

Stukowski, Alexander

2012-05-28

Here, we discuss existing and new computational analysis techniques to classify local atomic arrangements in large-scale atomistic computer simulations of crystalline solids. This article includes a performance comparison of typical analysis algorithms such as common neighbor analysis (CNA), centrosymmetry analysis, bond angle analysis, bond order analysis and Voronoi analysis. In addition we propose a simple extension to the CNA method that makes it suitable for multi-phase systems. Finally, we introduce a new structure identification algorithm, the neighbor distance analysis, which is designed to identify atomic structure units in grain boundaries.

Singularities in Optimal Structural Design

NASA Technical Reports Server (NTRS)

Patnaik, S. N.; Guptill, J. D.; Berke, L.

1992-01-01

Singularity conditions that arise during structural optimization can seriously degrade the performance of the optimizer. The singularities are intrinsic to the formulation of the structural optimization problem and are not associated with the method of analysis. Certain conditions that give rise to singularities have been identified in earlier papers, encompassing the entire structure. Further examination revealed more complex sets of conditions in which singularities occur. Some of these singularities are local in nature, being associated with only a segment of the structure. Moreover, the likelihood that one of these local singularities may arise during an optimization procedure can be much greater than that of the global singularity identified earlier. Examples are provided of these additional forms of singularities. A framework is also given in which these singularities can be recognized. In particular, the singularities can be identified by examination of the stress displacement relations along with the compatibility conditions and/or the displacement stress relations derived in the integrated force method of structural analysis.

Singularities in optimal structural design

NASA Technical Reports Server (NTRS)

Patnaik, S. N.; Guptill, J. D.; Berke, L.

1992-01-01

Singularity conditions that arise during structural optimization can seriously degrade the performance of the optimizer. The singularities are intrinsic to the formulation of the structural optimization problem and are not associated with the method of analysis. Certain conditions that give rise to singularities have been identified in earlier papers, encompassing the entire structure. Further examination revealed more complex sets of conditions in which singularities occur. Some of these singularities are local in nature, being associated with only a segment of the structure. Moreover, the likelihood that one of these local singularities may arise during an optimization procedure can be much greater than that of the global singularity identified earlier. Examples are provided of these additional forms of singularities. A framework is also given in which these singularities can be recognized. In particular, the singularities can be identified by examination of the stress displacement relations along with the compatibility conditions and/or the displacement stress relations derived in the integrated force method of structural analysis.

Domain Hierarchy and closed Loops (DHcL): a server for exploring hierarchy of protein domain structure

PubMed Central

Koczyk, Grzegorz; Berezovsky, Igor N.

2008-01-01

Domain hierarchy and closed loops (DHcL) (http://sitron.bccs.uib.no/dhcl/) is a web server that delineates energy hierarchy of protein domain structure and detects domains at different levels of this hierarchy. The server also identifies closed loops and van der Waals locks, which constitute a structural basis for the protein domain hierarchy. The DHcL can be a useful tool for an express analysis of protein structures and their alternative domain decompositions. The user submits a PDB identifier(s) or uploads a 3D protein structure in a PDB format. The results of the analysis are the location of domains at different levels of hierarchy, closed loops, van der Waals locks and their interactive visualization. The server maintains a regularly updated database of domains, closed loop and van der Waals locks for all X-ray structures in PDB. DHcL server is available at: http://sitron.bccs.uib.no/dhcl. PMID:18502776

BDA: A novel method for identifying defects in body-centered cubic crystals.

PubMed

Möller, Johannes J; Bitzek, Erik

2016-01-01

The accurate and fast identification of crystallographic defects plays a key role for the analysis of atomistic simulation output data. For face-centered cubic (fcc) metals, most existing structure analysis tools allow for the direct distinction of common defects, such as stacking faults or certain low-index surfaces. For body-centered cubic (bcc) metals, on the other hand, a robust way to identify such defects is currently not easily available. We therefore introduce a new method for analyzing atomistic configurations of bcc metals, the BCC Defect Analysis (BDA). It uses existing structure analysis algorithms and combines their results to uniquely distinguish between typical defects in bcc metals. In essence, the BDA method offers the following features:•Identification of typical defect structures in bcc metals.•Reduction of erroneously identified defects by iterative comparison to the defects in the atom's neighborhood.•Availability as ready-to-use Python script for the widespread visualization tool OVITO [http://ovito.org].

Identifying influential factors of business process performance using dependency analysis

NASA Astrophysics Data System (ADS)

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

2011-02-01

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

Joint source based analysis of multiple brain structures in studying major depressive disorder

NASA Astrophysics Data System (ADS)

Ramezani, Mahdi; Rasoulian, Abtin; Hollenstein, Tom; Harkness, Kate; Johnsrude, Ingrid; Abolmaesumi, Purang

2014-03-01

We propose a joint Source-Based Analysis (jSBA) framework to identify brain structural variations in patients with Major Depressive Disorder (MDD). In this framework, features representing position, orientation and size (i.e. pose), shape, and local tissue composition are extracted. Subsequently, simultaneous analysis of these features within a joint analysis method is performed to generate the basis sources that show signi cant di erences between subjects with MDD and those in healthy control. Moreover, in a cross-validation leave- one-out experiment, we use a Fisher Linear Discriminant (FLD) classi er to identify individuals within the MDD group. Results show that we can classify the MDD subjects with an accuracy of 76% solely based on the information gathered from the joint analysis of pose, shape, and tissue composition in multiple brain structures.

The impact of structural uncertainty on cost-effectiveness models for adjuvant endocrine breast cancer treatments: the need for disease-specific model standardization and improved guidance.

PubMed

Frederix, Gerardus W J; van Hasselt, Johan G C; Schellens, Jan H M; Hövels, Anke M; Raaijmakers, Jan A M; Huitema, Alwin D R; Severens, Johan L

2014-01-01

Structural uncertainty relates to differences in model structure and parameterization. For many published health economic analyses in oncology, substantial differences in model structure exist, leading to differences in analysis outcomes and potentially impacting decision-making processes. The objectives of this analysis were (1) to identify differences in model structure and parameterization for cost-effectiveness analyses (CEAs) comparing tamoxifen and anastrazole for adjuvant breast cancer (ABC) treatment; and (2) to quantify the impact of these differences on analysis outcome metrics. The analysis consisted of four steps: (1) review of the literature for identification of eligible CEAs; (2) definition and implementation of a base model structure, which included the core structural components for all identified CEAs; (3) definition and implementation of changes or additions in the base model structure or parameterization; and (4) quantification of the impact of changes in model structure or parameterizations on the analysis outcome metrics life-years gained (LYG), incremental costs (IC) and the incremental cost-effectiveness ratio (ICER). Eleven CEA analyses comparing anastrazole and tamoxifen as ABC treatment were identified. The base model consisted of the following health states: (1) on treatment; (2) off treatment; (3) local recurrence; (4) metastatic disease; (5) death due to breast cancer; and (6) death due to other causes. The base model estimates of anastrazole versus tamoxifen for the LYG, IC and ICER were 0.263 years, €3,647 and €13,868/LYG, respectively. In the published models that were evaluated, differences in model structure included the addition of different recurrence health states, and associated transition rates were identified. Differences in parameterization were related to the incidences of recurrence, local recurrence to metastatic disease, and metastatic disease to death. The separate impact of these model components on the LYG ranged from 0.207 to 0.356 years, while incremental costs ranged from €3,490 to €3,714 and ICERs ranged from €9,804/LYG to €17,966/LYG. When we re-analyzed the published CEAs in our framework by including their respective model properties, the LYG ranged from 0.207 to 0.383 years, IC ranged from €3,556 to €3,731 and ICERs ranged from €9,683/LYG to €17,570/LYG. Differences in model structure and parameterization lead to substantial differences in analysis outcome metrics. This analysis supports the need for more guidance regarding structural uncertainty and the use of standardized disease-specific models for health economic analyses of adjuvant endocrine breast cancer therapies. The developed approach in the current analysis could potentially serve as a template for further evaluations of structural uncertainty and development of disease-specific models.

New families of human regulatory RNA structures identified by comparative analysis of vertebrate genomes.

PubMed

Parker, Brian J; Moltke, Ida; Roth, Adam; Washietl, Stefan; Wen, Jiayu; Kellis, Manolis; Breaker, Ronald; Pedersen, Jakob Skou

2011-11-01

Regulatory RNA structures are often members of families with multiple paralogous instances across the genome. Family members share functional and structural properties, which allow them to be studied as a whole, facilitating both bioinformatic and experimental characterization. We have developed a comparative method, EvoFam, for genome-wide identification of families of regulatory RNA structures, based on primary sequence and secondary structure similarity. We apply EvoFam to a 41-way genomic vertebrate alignment. Genome-wide, we identify 220 human, high-confidence families outside protein-coding regions comprising 725 individual structures, including 48 families with known structural RNA elements. Known families identified include both noncoding RNAs, e.g., miRNAs and the recently identified MALAT1/MEN β lincRNA family; and cis-regulatory structures, e.g., iron-responsive elements. We also identify tens of new families supported by strong evolutionary evidence and other statistical evidence, such as GO term enrichments. For some of these, detailed analysis has led to the formulation of specific functional hypotheses. Examples include two hypothesized auto-regulatory feedback mechanisms: one involving six long hairpins in the 3'-UTR of MAT2A, a key metabolic gene that produces the primary human methyl donor S-adenosylmethionine; the other involving a tRNA-like structure in the intron of the tRNA maturation gene POP1. We experimentally validate the predicted MAT2A structures. Finally, we identify potential new regulatory networks, including large families of short hairpins enriched in immunity-related genes, e.g., TNF, FOS, and CTLA4, which include known transcript destabilizing elements. Our findings exemplify the diversity of post-transcriptional regulation and provide a resource for further characterization of new regulatory mechanisms and families of noncoding RNAs.

Tertiary structure prediction and identification of druggable pocket in the cancer biomarker – Osteopontin-c

PubMed Central

2014-01-01

Background Osteopontin (Eta, secreted sialoprotein 1, opn) is secreted from different cell types including cancer cells. Three splice variant forms namely osteopontin-a, osteopontin-b and osteopontin-c have been identified. The main astonishing feature is that osteopontin-c is found to be elevated in almost all types of cancer cells. This was the vital point to consider it for sequence analysis and structure predictions which provide ample chances for prognostic, therapeutic and preventive cancer research. Methods Osteopontin-c gene sequence was determined from Breast Cancer sample and was translated to protein sequence. It was then analyzed using various software and web tools for binding pockets, docking and druggability analysis. Due to the lack of homological templates, tertiary structure was predicted using ab-initio method server – I-TASSER and was evaluated after refinement using web tools. Refined structure was compared with known bone sialoprotein electron microscopic structure and docked with CD44 for binding analysis and binding pockets were identified for drug designing. Results Signal sequence of about sixteen amino acid residues was identified using signal sequence prediction servers. Due to the absence of known structures of similar proteins, three dimensional structure of osteopontin-c was predicted using I-TASSER server. The predicted structure was refined with the help of SUMMA server and was validated using SAVES server. Molecular dynamic analysis was carried out using GROMACS software. The final model was built and was used for docking with CD44. Druggable pockets were identified using pocket energies. Conclusions The tertiary structure of osteopontin-c was predicted successfully using the ab-initio method and the predictions showed that osteopontin-c is of fibrous nature comparable to firbronectin. Docking studies showed the significant similarities of QSAET motif in the interaction of CD44 and osteopontins between the normal and splice variant forms of osteopontins and binding pockets analyses revealed several pockets which paved the way to the identification of a druggable pocket. PMID:24401206

Failure Mode and Effects Analysis: views of hospital staff in the UK.

PubMed

Shebl, Nada; Franklin, Bryony; Barber, Nick; Burnett, Susan; Parand, Anam

2012-01-01

To explore health care professionals' experiences and perceptions of Failure Mode and Effects Analysis (FMEA), a team-based, prospective risk analysis technique. Semi-structured interviews were conducted with 21 operational leads (20 pharmacists, one nurse) in medicines management teams of hospitals participating in a national quality improvement programme. Interviews were transcribed, coded and emergent themes identified using framework analysis. Themes identified included perceptions and experiences of participants with FMEA, validity and reliability issues, and FMEA's use in practice. FMEA was considered to be a structured but subjective process that helps health care professionals get together to identify high risk areas of care. Both positive and negative opinions were expressed, with the majority of interviewees expressing positive views towards FMEA in relation to its structured nature and the use of a multidisciplinary team. Other participants criticised FMEA for being subjective and lacking validity. Most likely to restrict its widespread use were its time consuming nature and its perceived lack of validity and reliability. FMEA is a subjective but systematic tool that helps identify high risk areas, but its time consuming nature, difficulty with the scores and perceived lack of validity and reliability may limit its widespread use.

Identifying Impacts Using Adaptive Fiber Bragg Grating Demodulator for Structural Health Monitoring Applications

NASA Astrophysics Data System (ADS)

Kirikera, G. R.; Balogun, O.; Krishnaswamy, S.

2008-02-01

A network of Fiber-Bragg Grating (FBG) sensors is developed as part of a Structural Health Monitoring system to identify impact damage. The sensor signals are adaptively demodulated using two-wave mixing (TWM) technology. The signals from multiple FBG sensors are multiplexed into a single TWM demodulator. The FBG sensor network is mounted on a plate, and the structure is subjected to impacts generated by dropping small ball bearings. Impact locations are identified based on time frequency analysis.

PDB2Graph: A toolbox for identifying critical amino acids map in proteins based on graph theory.

PubMed

Niknam, Niloofar; Khakzad, Hamed; Arab, Seyed Shahriar; Naderi-Manesh, Hossein

2016-05-01

The integrative and cooperative nature of protein structure involves the assessment of topological and global features of constituent parts. Network concept takes complete advantage of both of these properties in the analysis concomitantly. High compatibility to structural concepts or physicochemical properties in addition to exploiting a remarkable simplification in the system has made network an ideal tool to explore biological systems. There are numerous examples in which different protein structural and functional characteristics have been clarified by the network approach. Here, we present an interactive and user-friendly Matlab-based toolbox, PDB2Graph, devoted to protein structure network construction, visualization, and analysis. Moreover, PDB2Graph is an appropriate tool for identifying critical nodes involved in protein structural robustness and function based on centrality indices. It maps critical amino acids in protein networks and can greatly aid structural biologists in selecting proper amino acid candidates for manipulating protein structures in a more reasonable and rational manner. To introduce the capability and efficiency of PDB2Graph in detail, the structural modification of Calmodulin through allosteric binding of Ca(2+) is considered. In addition, a mutational analysis for three well-identified model proteins including Phage T4 lysozyme, Barnase and Ribonuclease HI, was performed to inspect the influence of mutating important central residues on protein activity. Copyright © 2016 Elsevier Ltd. All rights reserved.

Failure Analysis and Mechanisms of Failure of Fibrous Composite Structures

NASA Technical Reports Server (NTRS)

Noor, A. K. (Compiler); Shuart, M. J. (Compiler); Starnes, J. H., Jr. (Compiler); Williams, J. G. (Compiler)

1983-01-01

The state of the art of failure analysis and current design practices, especially as applied to the use of fibrous composite materials in aircraft structures is discussed. Deficiencies in these technologies are identified, as are directions for future research.

Effects of Expository Text Structure Interventions on Comprehension: A Meta-Analysis

ERIC Educational Resources Information Center

Pyle, Nicole; Vasquez, Ariana C.; Lignugaris/Kraft, Benjamin; Gillam, Sandra L.; Reutzel, D. Ray; Olszewski, Abbie; Segura, Hugo; Hartzheim, Daphne; Laing, Woodrow; Pyle, Daniel

2017-01-01

This meta-analysis synthesizes results from expository text structure interventions designed to increase comprehension for students in kindergarten to grade 12 published between 1970 and 2013. Twenty-one studies were identified, 19 of which met criteria for a meta-analysis, including 48 studywise effect sizes that were meta-analyzed to determine…

Structure of the alexithymic brain: A parametric coordinate-based meta-analysis.

PubMed

Xu, Pengfei; Opmeer, Esther M; van Tol, Marie-José; Goerlich, Katharina S; Aleman, André

2018-04-01

Alexithymia refers to deficiencies in identifying and expressing emotions. This might be related to changes in structural brain volumes, but its neuroanatomical basis remains uncertain as studies have shown heterogeneous findings. Therefore, we conducted a parametric coordinate-based meta-analysis. We identified seventeen structural neuroimaging studies (including a total of 2586 individuals with different levels of alexithymia) investigating the association between gray matter volume and alexithymia. Volumes of the left insula, left amygdala, orbital frontal cortex and striatum were consistently smaller in people with high levels of alexithymia. These areas are important for emotion perception and emotional experience. Smaller volumes in these areas might lead to deficiencies in appropriately identifying and expressing emotions. These findings provide the first quantitative integration of results pertaining to the structural neuroanatomical basis of alexithymia. Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.

Structural-Vibration-Response Data Analysis

NASA Technical Reports Server (NTRS)

Smith, W. R.; Hechenlaible, R. N.; Perez, R. C.

1983-01-01

Computer program developed as structural-vibration-response data analysis tool for use in dynamic testing of Space Shuttle. Program provides fast and efficient time-domain least-squares curve-fitting procedure for reducing transient response data to obtain structural model frequencies and dampings from free-decay records. Procedure simultaneously identifies frequencies, damping values, and participation factors for noisy multiple-response records.

Identifying Psychopathy Subtypes on the Basis of Personality Structure

ERIC Educational Resources Information Center

Hicks, Brian M.; Markon, Kristian E.; Patrick, Christopher J.; Krueger, Robert F.; Newman, Joseph P.

2004-01-01

The authors used model-based cluster analysis to identify subtypes of criminal psychopaths on the basis of differences in personality structure. Participants included 96 male prisoners diagnosed as psychopathic, using the Psychopathy Checklist Revised (PCL-R; R. D. Hare, 1991). Personality was assessed using the brief form of the Multidimensional…

Liquid chromatography-diode array detection-mass spectrometry for compositional analysis of low molecular weight heparins.

PubMed

Wang, Zhangjie; Li, Daoyuan; Sun, Xiaojun; Bai, Xue; Jin, Lan; Chi, Lianli

2014-04-15

Low molecular weight heparins (LMWHs) are important artificial preparations from heparin polysaccharide and are widely used as anticoagulant drugs. To analyze the structure and composition of LMWHs, identification and quantitation of their natural and modified building blocks are indispensable. We have established a novel reversed-phase high-performance liquid chromatography-diode array detection-electrospray ionization-mass spectrometry approach for compositional analysis of LMWHs. After being exhaustively digested and labeled with 2-aminoacridone, the structural motifs constructing LMWHs, including 17 components from dalteparin and 15 components from enoxaparin, were well separated, identified, and quantified. Besides the eight natural heparin disaccharides, many characteristic structures from dalteparin and enoxaparin, such as modified structures from the reducing end and nonreducing end, 3-O-sulfated tetrasaccharides, and trisaccharides, have been unambiguously identified based on their retention time and mass spectra. Compared with the traditional heparin compositional analysis methods, the approach described here is not only robust but also comprehensive because it is capable of identifying and quantifying nearly all components from lyase digests of LMWHs. Copyright © 2014 Elsevier Inc. All rights reserved.

Structural analysis consultation using artificial intelligence

NASA Technical Reports Server (NTRS)

Melosh, R. J.; Marcal, P. V.; Berke, L.

1978-01-01

The primary goal of consultation is definition of the best strategy to deal with a structural engineering analysis objective. The knowledge base to meet the need is designed to identify the type of numerical analysis, the needed modeling detail, and specific analysis data required. Decisions are constructed on the basis of the data in the knowledge base - material behavior, relations between geometry and structural behavior, measures of the importance of time and temperature changes - and user supplied specifics characteristics of the spectrum of analysis types, the relation between accuracy and model detail on the structure, its mechanical loadings, and its temperature states. Existing software demonstrated the feasibility of the approach, encompassing the 36 analysis classes spanning nonlinear, temperature affected, incremental analyses which track the behavior of structural systems.

Enabling Rapid and Robust Structural Analysis During Conceptual Design

NASA Technical Reports Server (NTRS)

Eldred, Lloyd B.; Padula, Sharon L.; Li, Wu

2015-01-01

This paper describes a multi-year effort to add a structural analysis subprocess to a supersonic aircraft conceptual design process. The desired capabilities include parametric geometry, automatic finite element mesh generation, static and aeroelastic analysis, and structural sizing. The paper discusses implementation details of the new subprocess, captures lessons learned, and suggests future improvements. The subprocess quickly compares concepts and robustly handles large changes in wing or fuselage geometry. The subprocess can rank concepts with regard to their structural feasibility and can identify promising regions of the design space. The automated structural analysis subprocess is deemed robust and rapid enough to be included in multidisciplinary conceptual design and optimization studies.

Chromosomal Microarray versus Karyotyping for Prenatal Diagnosis

PubMed Central

Wapner, Ronald J.; Martin, Christa Lese; Levy, Brynn; Ballif, Blake C.; Eng, Christine M.; Zachary, Julia M.; Savage, Melissa; Platt, Lawrence D.; Saltzman, Daniel; Grobman, William A.; Klugman, Susan; Scholl, Thomas; Simpson, Joe Leigh; McCall, Kimberly; Aggarwal, Vimla S.; Bunke, Brian; Nahum, Odelia; Patel, Ankita; Lamb, Allen N.; Thom, Elizabeth A.; Beaudet, Arthur L.; Ledbetter, David H.; Shaffer, Lisa G.; Jackson, Laird

2013-01-01

Background Chromosomal microarray analysis has emerged as a primary diagnostic tool for the evaluation of developmental delay and structural malformations in children. We aimed to evaluate the accuracy, efficacy, and incremental yield of chromosomal microarray analysis as compared with karyotyping for routine prenatal diagnosis. Methods Samples from women undergoing prenatal diagnosis at 29 centers were sent to a central karyotyping laboratory. Each sample was split in two; standard karyotyping was performed on one portion and the other was sent to one of four laboratories for chromosomal microarray. Results We enrolled a total of 4406 women. Indications for prenatal diagnosis were advanced maternal age (46.6%), abnormal result on Down’s syndrome screening (18.8%), structural anomalies on ultrasonography (25.2%), and other indications (9.4%). In 4340 (98.8%) of the fetal samples, microarray analysis was successful; 87.9% of samples could be used without tissue culture. Microarray analysis of the 4282 nonmosaic samples identified all the aneuploidies and unbalanced rearrangements identified on karyotyping but did not identify balanced translocations and fetal triploidy. In samples with a normal karyotype, microarray analysis revealed clinically relevant deletions or duplications in 6.0% with a structural anomaly and in 1.7% of those whose indications were advanced maternal age or positive screening results. Conclusions In the context of prenatal diagnostic testing, chromosomal microarray analysis identified additional, clinically significant cytogenetic information as compared with karyotyping and was equally efficacious in identifying aneuploidies and unbalanced rearrangements but did not identify balanced translocations and triploidies. (Funded by the Eunice Kennedy Shriver National Institute of Child Health and Human Development and others; ClinicalTrials.gov number, NCT01279733.) PMID:23215555

Direct Duplex Detection: An Emerging Tool in the RNA Structure Analysis Toolbox.

PubMed

Weidmann, Chase A; Mustoe, Anthony M; Weeks, Kevin M

2016-09-01

While a variety of powerful tools exists for analyzing RNA structure, identifying long-range and intermolecular base-pairing interactions has remained challenging. Recently, three groups introduced a high-throughput strategy that uses psoralen-mediated crosslinking to directly identify RNA-RNA duplexes in cells. Initial application of these methods highlights the preponderance of long-range structures within and between RNA molecules and their widespread structural dynamics. Copyright © 2016 Elsevier Ltd. All rights reserved.

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

PubMed

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

2017-04-01

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

Understanding identifiability as a crucial step in uncertainty assessment

NASA Astrophysics Data System (ADS)

Jakeman, A. J.; Guillaume, J. H. A.; Hill, M. C.; Seo, L.

2016-12-01

The topic of identifiability analysis offers concepts and approaches to identify why unique model parameter values cannot be identified, and can suggest possible responses that either increase uniqueness or help to understand the effect of non-uniqueness on predictions. Identifiability analysis typically involves evaluation of the model equations and the parameter estimation process. Non-identifiability can have a number of undesirable effects. In terms of model parameters these effects include: parameters not being estimated uniquely even with ideal data; wildly different values being returned for different initialisations of a parameter optimisation algorithm; and parameters not being physically meaningful in a model attempting to represent a process. This presentation illustrates some of the drastic consequences of ignoring model identifiability analysis. It argues for a more cogent framework and use of identifiability analysis as a way of understanding model limitations and systematically learning about sources of uncertainty and their importance. The presentation specifically distinguishes between five sources of parameter non-uniqueness (and hence uncertainty) within the modelling process, pragmatically capturing key distinctions within existing identifiability literature. It enumerates many of the various approaches discussed in the literature. Admittedly, improving identifiability is often non-trivial. It requires thorough understanding of the cause of non-identifiability, and the time, knowledge and resources to collect or select new data, modify model structures or objective functions, or improve conditioning. But ignoring these problems is not a viable solution. Even simple approaches such as fixing parameter values or naively using a different model structure may have significant impacts on results which are too often overlooked because identifiability analysis is neglected.

Classroom Dialogue and Science Achievement.

ERIC Educational Resources Information Center

Clarke, John A.

This study reports the application to classroom dialogue of the Thematic and Structural Analysis (TSA) Technique which has been used previously in the analysis of text materials. The TSA Technique identifies themes (word clusters) and their structural relationship throughout sequentially organized material. Dialogues from four Year 8 science…

Microbiome Networks: A Systems Framework for Identifying Candidate Microbial Assemblages for Disease Management.

PubMed

Poudel, R; Jumpponen, A; Schlatter, D C; Paulitz, T C; Gardener, B B McSpadden; Kinkel, L L; Garrett, K A

2016-10-01

Network models of soil and plant microbiomes provide new opportunities for enhancing disease management, but also challenges for interpretation. We present a framework for interpreting microbiome networks, illustrating how observed network structures can be used to generate testable hypotheses about candidate microbes affecting plant health. The framework includes four types of network analyses. "General network analysis" identifies candidate taxa for maintaining an existing microbial community. "Host-focused analysis" includes a node representing a plant response such as yield, identifying taxa with direct or indirect associations with that node. "Pathogen-focused analysis" identifies taxa with direct or indirect associations with taxa known a priori as pathogens. "Disease-focused analysis" identifies taxa associated with disease. Positive direct or indirect associations with desirable outcomes, or negative associations with undesirable outcomes, indicate candidate taxa. Network analysis provides characterization not only of taxa with direct associations with important outcomes such as disease suppression, biofertilization, or expression of plant host resistance, but also taxa with indirect associations via their association with other key taxa. We illustrate the interpretation of network structure with analyses of microbiomes in the oak phyllosphere, and in wheat rhizosphere and bulk soil associated with the presence or absence of infection by Rhizoctonia solani.

The impact of distributed computing on education

NASA Technical Reports Server (NTRS)

Utku, S.; Lestingi, J.; Salama, M.

1982-01-01

In this paper, developments in digital computer technology since the early Fifties are reviewed briefly, and the parallelism which exists between these developments and developments in analysis and design procedures of structural engineering is identified. The recent trends in digital computer technology are examined in order to establish the fact that distributed processing is now an accepted philosophy for further developments. The impact of this on the analysis and design practices of structural engineering is assessed by first examining these practices from a data processing standpoint to identify the key operations and data bases, and then fitting them to the characteristics of distributed processing. The merits and drawbacks of the present philosophy in educating structural engineers are discussed and projections are made for the industry-academia relations in the distributed processing environment of structural analysis and design. An ongoing experiment of distributed computing in a university environment is described.

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

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

Hura, Greg L.; Menon, Angeli L.; Hammel, Michal

2009-07-20

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

A confidence building exercise in data and identifiability: Modeling cancer chemotherapy as a case study.

PubMed

Eisenberg, Marisa C; Jain, Harsh V

2017-10-27

Mathematical modeling has a long history in the field of cancer therapeutics, and there is increasing recognition that it can help uncover the mechanisms that underlie tumor response to treatment. However, making quantitative predictions with such models often requires parameter estimation from data, raising questions of parameter identifiability and estimability. Even in the case of structural (theoretical) identifiability, imperfect data and the resulting practical unidentifiability of model parameters can make it difficult to infer the desired information, and in some cases, to yield biologically correct inferences and predictions. Here, we examine parameter identifiability and estimability using a case study of two compartmental, ordinary differential equation models of cancer treatment with drugs that are cell cycle-specific (taxol) as well as non-specific (oxaliplatin). We proceed through model building, structural identifiability analysis, parameter estimation, practical identifiability analysis and its biological implications, as well as alternative data collection protocols and experimental designs that render the model identifiable. We use the differential algebra/input-output relationship approach for structural identifiability, and primarily the profile likelihood approach for practical identifiability. Despite the models being structurally identifiable, we show that without consideration of practical identifiability, incorrect cell cycle distributions can be inferred, that would result in suboptimal therapeutic choices. We illustrate the usefulness of estimating practically identifiable combinations (in addition to the more typically considered structurally identifiable combinations) in generating biologically meaningful insights. We also use simulated data to evaluate how the practical identifiability of the model would change under alternative experimental designs. These results highlight the importance of understanding the underlying mechanisms rather than purely using parsimony or information criteria/goodness-of-fit to decide model selection questions. The overall roadmap for identifiability testing laid out here can be used to help provide mechanistic insight into complex biological phenomena, reduce experimental costs, and optimize model-driven experimentation. Copyright © 2017. Published by Elsevier Ltd.

A factor analysis of landscape pattern and structure metrics

Treesearch

Kurt H. Riitters; R.V. O' Neill; C.T. Hunsaker; James D. Wickham; D.H. Yankee; S.P. Timmins; K.B. Jones; B.L. Jackson

1995-01-01

Fifty-five metrics of landscape pattern and structure were calculated for 85 maps of land use and land cover. A multivariate factor analysis was used to identify the common axes (or dimensions) of pattern and structure which were measured by a reduced set of 26 metrics. The first six factors explained about 87% of the variation in the 26 landscape metrics. These...

Analysis of Malay Word Structure by Pre-Service Special Education Teachers: Foundation-Level Knowledge for Remedial Instruction

ERIC Educational Resources Information Center

Lee, Lay Wah; Low, Hui Min

2014-01-01

Pre-service special educators' Malay word structure knowledge was assessed through their analysis of words. A total of 69 participants analysed a vocabulary list based on a set of criteria formulated from the Malay language word structure. Results indicated that they were able to count syllables and phonemes, and identify types of affixations;…

A systematic review of nurse-related social network analysis studies.

PubMed

Benton, D C; Pérez-Raya, F; Fernández-Fernández, M P; González-Jurado, M A

2015-09-01

Nurses frequently work as part of both uni- and multidisciplinary teams. Communication between team members is critical in the delivery of quality care. Social network analysis is increasingly being used to explore such communication. To explore the use of social network analysis involving nurses either as subjects of the study or as researchers. Standard systematic review procedures were applied to identify nurse-related studies that utilize social network analysis. A comparative thematic approach to synthesis was used. Both published and grey literature written in English, Spanish and Portuguese between January 1965 and December 2013 were identified via a structured search of CINAHL, SciELO and PubMed. In addition, Google and Yahoo search engines were used to identify additional grey literature using the same search strategy. Forty-three primary studies were identified with literature from North America dominating the published work. So far it would appear that no author or group of authors have developed a programme of research in the nursing field using the social network analysis approach although several authors may be in the process of doing so. The dominance of literature from North America may be viewed as problematic as the underlying structures and themes may be an artefact of cultural communication norms from this region. The use of social network analysis in relation to nursing and by nurse researchers has increased rapidly over the past two decades. The lack of longitudinal studies and the absence of replication across multiple sites should be seen as an opportunity for further research. This analytical approach is relatively new in the field of nursing but does show considerable promise in offering insights into the way information flows between individuals, teams, institutions and other structures. An understanding of these structures provides a means of improving communication. © 2014 International Council of Nurses.

23 CFR 973.210 - Indian lands bridge management system (BMS).

Code of Federal Regulations, 2013 CFR

2013-04-01

... analysis (as appropriate, considering size of structure, traffic volume, and structural condition). The investment analysis may include the ability to: (1) Identify alternative strategies to improve bridge... analyzing data for all bridges in the inventory or any subset. The minimum analyses shall include: (i) A...

Report of the NASA Ad Hoc Committee on failure of high strength structural materials

NASA Technical Reports Server (NTRS)

Brown, W. F., Jr. (Editor)

1972-01-01

An analysis of structural failures that have occurred in NASA programs was conducted. Reports of 231 examples of structural failure were reviewed. Attempts were made to identify those factors which contributed to the failures, and recommendations were formulated for actions which would minimize their effects on future NASA programs. Two classes of factors were identified: (1) those associated with deficiencies in existing materials and structures technology and (2) those attributable to inadequate documentation or communication of that technology.

Decision-making in irrigation networks: Selecting appropriate canal structures using multi-attribute decision analysis.

PubMed

Hosseinzade, Zeinab; Pagsuyoin, Sheree A; Ponnambalam, Kumaraswamy; Monem, Mohammad J

2017-12-01

The stiff competition for water between agriculture and non-agricultural production sectors makes it necessary to have effective management of irrigation networks in farms. However, the process of selecting flow control structures in irrigation networks is highly complex and involves different levels of decision makers. In this paper, we apply multi-attribute decision making (MADM) methodology to develop a decision analysis (DA) framework for evaluating, ranking and selecting check and intake structures for irrigation canals. The DA framework consists of identifying relevant attributes for canal structures, developing a robust scoring system for alternatives, identifying a procedure for data quality control, and identifying a MADM model for the decision analysis. An application is illustrated through an analysis for automation purposes of the Qazvin irrigation network, one of the oldest and most complex irrigation networks in Iran. A survey questionnaire designed based on the decision framework was distributed to experts, managers, and operators of the Qazvin network and to experts from the Ministry of Power in Iran. Five check structures and four intake structures were evaluated. A decision matrix was generated from the average scores collected from the survey, and was subsequently solved using TOPSIS (Technique for Order of Preference by Similarity to Ideal Solution) method. To identify the most critical structure attributes for the selection process, optimal attribute weights were calculated using Entropy method. For check structures, results show that the duckbill weir is the preferred structure while the pivot weir is the least preferred. Use of the duckbill weir can potentially address the problem with existing Amil gates where manual intervention is required to regulate water levels during periods of flow extremes. For intake structures, the Neyrpic® gate and constant head orifice are the most and least preferred alternatives, respectively. Some advantages of the Neyrpic® gate are ease of operation and capacity to measure discharge flows. Overall, the application to the Qazvin irrigation network demonstrates the utility of the proposed DA framework in selecting appropriate structures for regulating water flows in irrigation canals. This framework systematically aids the decision process by capturing decisions made at various levels (individual farmers to high-level management). It can be applied to other cases where a new irrigation network is being designed, or where changes in irrigation structures need to be identified to improve flow control in existing networks. Copyright © 2017 Elsevier B.V. All rights reserved.

A 2-year study of Gram stain competency assessment in 40 clinical laboratories.

PubMed

Goodyear, Nancy; Kim, Sara; Reeves, Mary; Astion, Michael L

2006-01-01

We used a computer-based competency assessment tool for Gram stain interpretation to assess the performance of 278 laboratory staff from 40 laboratories on 40 multiple-choice questions. We report test reliability, mean scores, median, item difficulty, discrimination, and analysis of the highest- and lowest-scoring questions. The questions were reliable (KR-20 coefficient, 0.80). Overall mean score was 88% (range, 63%-98%). When categorized by cell type, the means were host cells, 93%; other cells (eg, yeast), 92%; gram-positive, 90%; and gram-negative, 88%. When categorized by type of interpretation, the means were other (eg, underdecolorization), 92%; identify by structure (eg, bacterial morphologic features), 91%; and identify by name (eg, genus and species), 87%. Of the 6 highest-scoring questions (mean scores, > or = 99%) 5 were identify by structure and 1 was identify by name. Of the 6 lowest-scoring questions (mean scores, < 75%) 5 were gram-negative and 1 was host cells. By type of interpretation, 2 were identify by structure and 4 were identify by name. Computer-based Gram stain competency assessment examinations are reliable. Our analysis helps laboratories identify areas for continuing education in Gram stain interpretation and will direct future revisions of the tests.

Research Update: Spatially resolved mapping of electronic structure on atomic level by multivariate statistical analysis

NASA Astrophysics Data System (ADS)

Belianinov, Alex; Ganesh, Panchapakesan; Lin, Wenzhi; Sales, Brian C.; Sefat, Athena S.; Jesse, Stephen; Pan, Minghu; Kalinin, Sergei V.

2014-12-01

Atomic level spatial variability of electronic structure in Fe-based superconductor FeTe0.55Se0.45 (Tc = 15 K) is explored using current-imaging tunneling-spectroscopy. Multivariate statistical analysis of the data differentiates regions of dissimilar electronic behavior that can be identified with the segregation of chalcogen atoms, as well as boundaries between terminations and near neighbor interactions. Subsequent clustering analysis allows identification of the spatial localization of these dissimilar regions. Similar statistical analysis of modeled calculated density of states of chemically inhomogeneous FeTe1-xSex structures further confirms that the two types of chalcogens, i.e., Te and Se, can be identified by their electronic signature and differentiated by their local chemical environment. This approach allows detailed chemical discrimination of the scanning tunneling microscopy data including separation of atomic identities, proximity, and local configuration effects and can be universally applicable to chemically and electronically inhomogeneous surfaces.

An exploration of the structure of mentors' behavior in nursing education using exploratory factor analysis and Mokken scale analysis.

PubMed

Chen, Yanhua; Watson, Roger; Hilton, Andrea

2016-05-01

To understand nursing students' expectation from their mentors and assess mentors' performance, a scale of mentors' behavior was developed based on literature review and focus group in China. This study aims to explore the structure of mentors' behavior. A cross-sectional survey. Data were collected from nursing students in three hospitals in southwest China in 2014. A total of 669 pre-registered nursing students in their final year clinical learning participated in this study. Exploratory factor analysis and Mokken scale analysis was employed to explore the structure and hierarchical property of mentors' behavior. Three dimensions (professional development, facilitating learning and psychosocial support) were identified by factor analysis and confirmed by Mokken scaling analysis. The three sub-scales showed internal consistency reliability from 87% to 91%, and moderate to strong precision in ordering students' expectation about mentors' behavior and a small Mokken scale showing hierarchy was identified. Some insight into the structure of mentoring in nursing education has been obtained and a scale which could be used in the study of mentoring and in the preparation of mentors has been developed. Copyright © 2016 Elsevier Ltd. All rights reserved.

Web-ware bioinformatical analysis and structure modelling of N-terminus of human multisynthetase complex auxiliary component protein p43.

PubMed

Deineko, Viktor

2006-01-01

Human multisynthetase complex auxiliary component, protein p43 is an endothelial monocyte-activating polypeptide II precursor. In this study, comprehensive sequence analysis of N-terminus has been performed to identify structural domains, motifs, sites of post-translation modification and other functionally important parameters. The spatial structure model of full-chain protein p43 is obtained.

Non-Price Competition and the Structure of the Online Information Industry: Q-Analysis of Medical Databases and Hosts.

ERIC Educational Resources Information Center

Davies, Roy

1987-01-01

Discussion of the online information industry emphasizes the effects of non-price competition on its structure and the firms involved. Q-analysis is applied to data on medical databases and hosts, changes over a three-year period are identified, and an optimum structure for the industry based on economic theory is considered. (Author/LRW)

Opportunities Seized and Squandered: An Analysis of Joint Union and Confederate Operations at New Madrid and Island Number Ten

DTIC Science & Technology

2016-06-10

install a command structure , and identify strategies for their geographic commanders. In the Western Theater of the war, both Northern and Southern...Federal and Confederate militaries had to mobilize forces, install a command structure , and identify strategies for their geographic commanders. In...Navy officers avoided these operations with their intermittent periods of importance. The lack of an enduring force structure and a consistent

Composition analysis of a polymer electrolyte membrane fuel cell microporous layer using scanning transmission X-ray microscopy and near edge X-ray absorption fine structure analysis

NASA Astrophysics Data System (ADS)

George, Michael G.; Wang, Jian; Banerjee, Rupak; Bazylak, Aimy

2016-03-01

The novel application of scanning transmission X-ray microscopy (STXM) to the microporous layer (MPL) of a polymer electrolyte membrane fuel cell is investigated. A spatially resolved chemical component distribution map is obtained for the MPL of a commercially available SGL 25 BC sample. This is achieved with near edge X-ray absorption fine structure spectroscopic analysis. Prior to analysis the sample is embedded in non-reactive epoxy and ultra-microtomed to a thickness of 100 nm. Polytetrafluoroethylene (PTFE), carbon particle agglomerates, and supporting epoxy resin distributions are identified and reconstructed for a scanning area of 6 μm × 6 μm. It is observed that the spatial distribution of PTFE is strongly correlated to the carbon particle agglomerations. Additionally, agglomerate structures of PTFE are identified, possibly indicating the presence of a unique mesostructure in the MPL. STXM analysis is presented as a useful technique for the investigation of chemical species distributions in the MPL.

Fracture trends identified by ERTS-1 imagery in Utah and Nevada

NASA Technical Reports Server (NTRS)

Jensen, M. L. (Principal Investigator); Erickson, M. P.; Smith, M. R.

1973-01-01

The author has identified the following significant results. In the Utah-Nevada area, linear structural trends recorded on ERTS-1 imagery conform in part to previously recognized structures. In addition, the ERTS-1 imagery reveals cryptic structures not previously identified and not readily apparent in other imagery. These structures are illustrated by prominent east-west trending structures which appear to be concentrated in pre-volcanic rocks. This suggests that the structures are older than many of those with other trends which are equally prominent in volcanic and non-volcanic terrain. Since the older east-west structures may have controlled early Tertiary emplacement of magma or the ascent of mineralizing fluids, their recognition is important in minerial exploration. Soil-gas sampling and analysis for mercury content is being continued over structures, and projected trends of buried structures which appear, from studies of ERTS-1 imagery, to be favorable to mineralization. Comparison of ERTS-1 and Skylab imagery indicated that ERTS-1 imagery records more previously unrecognized linear structures than the Skylab imagery. In differentiating and identifying different rock types, the Skylab imagery appears to be more effective.

Genome-Wide Analysis of Oleosin Gene Family in 22 Tree Species: An Accelerator for Metabolic Engineering of BioFuel Crops and Agrigenomics Industrial Applications?

PubMed Central

2015-01-01

Abstract Trees contribute to enormous plant oil reserves because many trees contain 50%–80% of oil (triacylglycerols, TAGs) in the fruits and kernels. TAGs accumulate in subcellular structures called oil bodies/droplets, in which TAGs are covered by low-molecular-mass hydrophobic proteins called oleosins (OLEs). The OLEs/TAGs ratio determines the size and shape of intracellular oil bodies. There is a lack of comprehensive sequence analysis and structural information of OLEs among diverse trees. The objectives of this study were to identify OLEs from 22 tree species (e.g., tung tree, tea-oil tree, castor bean), perform genome-wide analysis of OLEs, classify OLEs, identify conserved sequence motifs and amino acid residues, and predict secondary and three-dimensional structures in tree OLEs and OLE subfamilies. Data mining identified 65 OLEs with perfect conservation of the “proline knot” motif (PX5SPX3P) from 19 trees. These OLEs contained >40% hydrophobic amino acid residues. They displayed similar properties and amino acid composition. Genome-wide phylogenetic analysis and multiple sequence alignment demonstrated that these proteins could be classified into five OLE subfamilies. There were distinct patterns of sequence conservation among the OLE subfamilies and within individual tree species. Computational modeling indicated that OLEs were composed of at least three α-helixes connected with short coils without any β-strand and that they exhibited distinct 3D structures and ligand binding sites. These analyses provide fundamental information in the similarity and specificity of diverse OLE isoforms within the same subfamily and among the different species, which should facilitate studying the structure-function relationship and identify critical amino acid residues in OLEs for metabolic engineering of tree TAGs. PMID:26258573

Genome-Wide Analysis of Oleosin Gene Family in 22 Tree Species: An Accelerator for Metabolic Engineering of BioFuel Crops and Agrigenomics Industrial Applications?

PubMed

Cao, Heping

2015-09-01

Trees contribute to enormous plant oil reserves because many trees contain 50%-80% of oil (triacylglycerols, TAGs) in the fruits and kernels. TAGs accumulate in subcellular structures called oil bodies/droplets, in which TAGs are covered by low-molecular-mass hydrophobic proteins called oleosins (OLEs). The OLEs/TAGs ratio determines the size and shape of intracellular oil bodies. There is a lack of comprehensive sequence analysis and structural information of OLEs among diverse trees. The objectives of this study were to identify OLEs from 22 tree species (e.g., tung tree, tea-oil tree, castor bean), perform genome-wide analysis of OLEs, classify OLEs, identify conserved sequence motifs and amino acid residues, and predict secondary and three-dimensional structures in tree OLEs and OLE subfamilies. Data mining identified 65 OLEs with perfect conservation of the "proline knot" motif (PX5SPX3P) from 19 trees. These OLEs contained >40% hydrophobic amino acid residues. They displayed similar properties and amino acid composition. Genome-wide phylogenetic analysis and multiple sequence alignment demonstrated that these proteins could be classified into five OLE subfamilies. There were distinct patterns of sequence conservation among the OLE subfamilies and within individual tree species. Computational modeling indicated that OLEs were composed of at least three α-helixes connected with short coils without any β-strand and that they exhibited distinct 3D structures and ligand binding sites. These analyses provide fundamental information in the similarity and specificity of diverse OLE isoforms within the same subfamily and among the different species, which should facilitate studying the structure-function relationship and identify critical amino acid residues in OLEs for metabolic engineering of tree TAGs.

ON IDENTIFIABILITY OF NONLINEAR ODE MODELS AND APPLICATIONS IN VIRAL DYNAMICS

PubMed Central

MIAO, HONGYU; XIA, XIAOHUA; PERELSON, ALAN S.; WU, HULIN

2011-01-01

Ordinary differential equations (ODE) are a powerful tool for modeling dynamic processes with wide applications in a variety of scientific fields. Over the last 2 decades, ODEs have also emerged as a prevailing tool in various biomedical research fields, especially in infectious disease modeling. In practice, it is important and necessary to determine unknown parameters in ODE models based on experimental data. Identifiability analysis is the first step in determing unknown parameters in ODE models and such analysis techniques for nonlinear ODE models are still under development. In this article, we review identifiability analysis methodologies for nonlinear ODE models developed in the past one to two decades, including structural identifiability analysis, practical identifiability analysis and sensitivity-based identifiability analysis. Some advanced topics and ongoing research are also briefly reviewed. Finally, some examples from modeling viral dynamics of HIV, influenza and hepatitis viruses are given to illustrate how to apply these identifiability analysis methods in practice. PMID:21785515

Automated podosome identification and characterization in fluorescence microscopy images.

PubMed

Meddens, Marjolein B M; Rieger, Bernd; Figdor, Carl G; Cambi, Alessandra; van den Dries, Koen

2013-02-01

Podosomes are cellular adhesion structures involved in matrix degradation and invasion that comprise an actin core and a ring of cytoskeletal adaptor proteins. They are most often identified by staining with phalloidin, which binds F-actin and therefore visualizes the core. However, not only podosomes, but also many other cytoskeletal structures contain actin, which makes podosome segmentation by automated image processing difficult. Here, we have developed a quantitative image analysis algorithm that is optimized to identify podosome cores within a typical sample stained with phalloidin. By sequential local and global thresholding, our analysis identifies up to 76% of podosome cores excluding other F-actin-based structures. Based on the overlap in podosome identifications and quantification of podosome numbers, our algorithm performs equally well compared to three experts. Using our algorithm we show effects of actin polymerization and myosin II inhibition on the actin intensity in both podosome core and associated actin network. Furthermore, by expanding the core segmentations, we reveal a previously unappreciated differential distribution of cytoskeletal adaptor proteins within the podosome ring. These applications illustrate that our algorithm is a valuable tool for rapid and accurate large-scale analysis of podosomes to increase our understanding of these characteristic adhesion structures.

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

PubMed

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

2011-11-01

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

Organizational Structure and Teacher Behavior.

ERIC Educational Resources Information Center

Miklos, Erwin

Two major approaches to the analysis of the organizational structure of schools are described. The rational approach focuses on characteristics that are bureaucratic and relate to the hierarchical exercise of authority. The natural-system approach focuses on the social structure and attempts to identify the power structure through analyses of…

Spatial Guilds in the Serengeti Food Web Revealed by a Bayesian Group Model

PubMed Central

Baskerville, Edward B.; Dobson, Andy P.; Bedford, Trevor; Allesina, Stefano; Anderson, T. Michael; Pascual, Mercedes

2011-01-01

Food webs, networks of feeding relationships in an ecosystem, provide fundamental insights into mechanisms that determine ecosystem stability and persistence. A standard approach in food-web analysis, and network analysis in general, has been to identify compartments, or modules, defined by many links within compartments and few links between them. This approach can identify large habitat boundaries in the network but may fail to identify other important structures. Empirical analyses of food webs have been further limited by low-resolution data for primary producers. In this paper, we present a Bayesian computational method for identifying group structure using a flexible definition that can describe both functional trophic roles and standard compartments. We apply this method to a newly compiled plant-mammal food web from the Serengeti ecosystem that includes high taxonomic resolution at the plant level, allowing a simultaneous examination of the signature of both habitat and trophic roles in network structure. We find that groups at the plant level reflect habitat structure, coupled at higher trophic levels by groups of herbivores, which are in turn coupled by carnivore groups. Thus the group structure of the Serengeti web represents a mixture of trophic guild structure and spatial pattern, in contrast to the standard compartments typically identified. The network topology supports recent ideas on spatial coupling and energy channels in ecosystems that have been proposed as important for persistence. Furthermore, our Bayesian approach provides a powerful, flexible framework for the study of network structure, and we believe it will prove instrumental in a variety of biological contexts. PMID:22219719

Automation method to identify the geological structure of seabed using spatial statistic analysis of echo sounding data

NASA Astrophysics Data System (ADS)

Kwon, O.; Kim, W.; Kim, J.

2017-12-01

Recently construction of subsea tunnel has been increased globally. For safe construction of subsea tunnel, identifying the geological structure including fault at design and construction stage is more than important. Then unlike the tunnel in land, it's very difficult to obtain the data on geological structure because of the limit in geological survey. This study is intended to challenge such difficulties in a way of developing the technology to identify the geological structure of seabed automatically by using echo sounding data. When investigation a potential site for a deep subsea tunnel, there is the technical and economical limit with borehole of geophysical investigation. On the contrary, echo sounding data is easily obtainable while information reliability is higher comparing to above approaches. This study is aimed at developing the algorithm that identifies the large scale of geological structure of seabed using geostatic approach. This study is based on theory of structural geology that topographic features indicate geological structure. Basic concept of algorithm is outlined as follows; (1) convert the seabed topography to the grid data using echo sounding data, (2) apply the moving window in optimal size to the grid data, (3) estimate the spatial statistics of the grid data in the window area, (4) set the percentile standard of spatial statistics, (5) display the values satisfying the standard on the map, (6) visualize the geological structure on the map. The important elements in this study include optimal size of moving window, kinds of optimal spatial statistics and determination of optimal percentile standard. To determine such optimal elements, a numerous simulations were implemented. Eventually, user program based on R was developed using optimal analysis algorithm. The user program was designed to identify the variations of various spatial statistics. It leads to easy analysis of geological structure depending on variation of spatial statistics by arranging to easily designate the type of spatial statistics and percentile standard. This research was supported by the Korea Agency for Infrastructure Technology Advancement under the Ministry of Land, Infrastructure and Transport of the Korean government. (Project Number: 13 Construction Research T01)

Online interactive analysis of protein structure ensembles with Bio3D-web.

PubMed

Skjærven, Lars; Jariwala, Shashank; Yao, Xin-Qiu; Grant, Barry J

2016-11-15

Bio3D-web is an online application for analyzing the sequence, structure and conformational heterogeneity of protein families. Major functionality is provided for identifying protein structure sets for analysis, their alignment and refined structure superposition, sequence and structure conservation analysis, mapping and clustering of conformations and the quantitative comparison of their predicted structural dynamics. Bio3D-web is based on the Bio3D and Shiny R packages. All major browsers are supported and full source code is available under a GPL2 license from http://thegrantlab.org/bio3d-web CONTACT: bjgrant@umich.edu or lars.skjarven@uib.no. © The Author 2016. Published by Oxford University Press.

Advances and trends in computational structural mechanics

NASA Technical Reports Server (NTRS)

Noor, A. K.

1986-01-01

Recent developments in computational structural mechanics are reviewed with reference to computational needs for future structures technology, advances in computational models for material behavior, discrete element technology, assessment and control of numerical simulations of structural response, hybrid analysis, and techniques for large-scale optimization. Research areas in computational structural mechanics which have high potential for meeting future technological needs are identified. These include prediction and analysis of the failure of structural components made of new materials, development of computational strategies and solution methodologies for large-scale structural calculations, and assessment of reliability and adaptive improvement of response predictions.

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

PubMed Central

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

2017-01-01

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

Probabilistic Structural Evaluation of Uncertainties in Radiator Sandwich Panel Design

NASA Technical Reports Server (NTRS)

Kuguoglu, Latife; Ludwiczak, Damian

2006-01-01

The Jupiter Icy Moons Orbiter (JIMO) Space System is part of the NASA's Prometheus Program. As part of the JIMO engineering team at NASA Glenn Research Center, the structural design of the JIMO Heat Rejection Subsystem (HRS) is evaluated. An initial goal of this study was to perform sensitivity analyses to determine the relative importance of the input variables on the structural responses of the radiator panel. The desire was to let the sensitivity analysis information identify the important parameters. The probabilistic analysis methods illustrated here support this objective. The probabilistic structural performance evaluation of a HRS radiator sandwich panel was performed. The radiator panel structural performance was assessed in the presence of uncertainties in the loading, fabrication process variables, and material properties. The stress and displacement contours of the deterministic structural analysis at mean probability was performed and results presented. It is followed by a probabilistic evaluation to determine the effect of the primitive variables on the radiator panel structural performance. Based on uncertainties in material properties, structural geometry and loading, the results of the displacement and stress analysis are used as an input file for the probabilistic analysis of the panel. The sensitivity of the structural responses, such as maximum displacement and maximum tensile and compressive stresses of the facesheet in x and y directions and maximum VonMises stresses of the tube, to the loading and design variables is determined under the boundary condition where all edges of the radiator panel are pinned. Based on this study, design critical material and geometric parameters of the considered sandwich panel are identified.

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

Caliandro, Rocco; Sibillano, Teresa; Belviso, B. Danilo

In this study, we have developed a general X-ray powder diffraction (XPD) methodology for the simultaneous structural and compositional characterization of inorganic nanomaterials. The approach is validated on colloidal tungsten oxide nanocrystals (WO 3-x NCs), as a model polymorphic nanoscale material system. Rod-shaped WO 3-x NCs with different crystal structure and stoichiometry are comparatively investigated under an inert atmosphere and after prolonged air exposure. An initial structural model for the as-synthesized NCs is preliminarily identified by means of Rietveld analysis against several reference crystal phases, followed by atomic pair distribution function (PDF) refinement of the best-matching candidates (static analysis). Subtlemore » stoichiometry deviations from the corresponding bulk standards are revealed. NCs exposed to air at room temperature are monitored by XPD measurements at scheduled time intervals. The static PDF analysis is complemented with an investigation into the evolution of the WO 3-x NC structure, performed by applying the modulation enhanced diffraction technique to the whole time series of XPD profiles (dynamical analysis). Prolonged contact with ambient air is found to cause an appreciable increase in the static disorder of the O atoms in the WO 3-x NC lattice, rather than a variation in stoichiometry. Finally, the time behavior of such structural change is identified on the basis of multivariate analysis.« less

Static and Dynamical Structural Investigations of Metal-Oxide Nanocrystals by Powder X-ray Diffraction: Colloidal Tungsten Oxide as a Case Study

DOE PAGES

Caliandro, Rocco; Sibillano, Teresa; Belviso, B. Danilo; ...

2016-02-02

In this study, we have developed a general X-ray powder diffraction (XPD) methodology for the simultaneous structural and compositional characterization of inorganic nanomaterials. The approach is validated on colloidal tungsten oxide nanocrystals (WO 3-x NCs), as a model polymorphic nanoscale material system. Rod-shaped WO 3-x NCs with different crystal structure and stoichiometry are comparatively investigated under an inert atmosphere and after prolonged air exposure. An initial structural model for the as-synthesized NCs is preliminarily identified by means of Rietveld analysis against several reference crystal phases, followed by atomic pair distribution function (PDF) refinement of the best-matching candidates (static analysis). Subtlemore » stoichiometry deviations from the corresponding bulk standards are revealed. NCs exposed to air at room temperature are monitored by XPD measurements at scheduled time intervals. The static PDF analysis is complemented with an investigation into the evolution of the WO 3-x NC structure, performed by applying the modulation enhanced diffraction technique to the whole time series of XPD profiles (dynamical analysis). Prolonged contact with ambient air is found to cause an appreciable increase in the static disorder of the O atoms in the WO 3-x NC lattice, rather than a variation in stoichiometry. Finally, the time behavior of such structural change is identified on the basis of multivariate analysis.« less

Structural arrangement trade study. Volume 3: Reusable Hydrogen Composite Tank System (RHCTS) and Graphite Composite Primary Structures (GCPS). Addendum

NASA Astrophysics Data System (ADS)

1995-03-01

This volume is the third of a 3 volume set that addresses the structural trade study plan that will identify the most suitable structural configuration for an SSTO winged vehicle capable of delivering 25,000 lbs to a 220 nm circular orbit at 51.6 deg inclination. The most suitable Reusable Hydrogen Composite Tank System (RHCTS), and Graphite Composite Tank System (GCPS) composite materials for intertank, wing and thrust structures are identified. Vehicle resizing charts, selection criteria and back-up charts, parametric costing approach and the finite element method analysis are discussed.

Structural arrangement trade study. Volume 3: Reusable Hydrogen Composite Tank System (RHCTS) and Graphite Composite Primary Structures (GCPS). Addendum

NASA Technical Reports Server (NTRS)

1995-01-01

This volume is the third of a 3 volume set that addresses the structural trade study plan that will identify the most suitable structural configuration for an SSTO winged vehicle capable of delivering 25,000 lbs to a 220 nm circular orbit at 51.6 deg inclination. The most suitable Reusable Hydrogen Composite Tank System (RHCTS), and Graphite Composite Tank System (GCPS) composite materials for intertank, wing and thrust structures are identified. Vehicle resizing charts, selection criteria and back-up charts, parametric costing approach and the finite element method analysis are discussed.

Trade study plan for Graphite Composite Primary Structure (GCPS)

NASA Technical Reports Server (NTRS)

Greenberg, H. S.

1994-01-01

This TA 2 document (with support from TA 1) describes the trade study plan that will identify the most suitable structural configuration for an SSTO winged vehicle capable of delivering 25,000 lbs to a 220 nm circular orbit at 51.6 degree inclination For this most suitable configuration the structural attachment of the wing, and the most suitable GCPS composite materials for intertank, wing, tail and thrust structure are identified. This trade study analysis uses extensive information derived in the TA 1 trade study plan and is identified within the study plan. In view of this, for convenience, the TA 1 study plan is included as an appendix to this document.

Using Structural Equation Models with Latent Variables to Study Student Growth and Development.

ERIC Educational Resources Information Center

Pike, Gary R.

1991-01-01

Analysis of data on freshman-to-senior developmental gains in 722 University of Tennessee-Knoxville students provides evidence of the advantages of structural equation modeling with latent variables and suggests that the group differences identified by traditional analysis of variance and covariance techniques may be an artifact of measurement…

The Factor Structure of the English Language Development Assessment: A Confirmatory Factor Analysis

ERIC Educational Resources Information Center

Kuriakose, Anju

2011-01-01

This study investigated the internal factor structure of the English language development Assessment (ELDA) using confirmatory factor analysis. ELDA is an English language proficiency test developed by a consortium of multiple states and is used to identify and reclassify English language learners in kindergarten to grade 12. Scores on item…

Dynamical compensation and structural identifiability of biological models: Analysis, implications, and reconciliation.

PubMed

Villaverde, Alejandro F; Banga, Julio R

2017-11-01

The concept of dynamical compensation has been recently introduced to describe the ability of a biological system to keep its output dynamics unchanged in the face of varying parameters. However, the original definition of dynamical compensation amounts to lack of structural identifiability. This is relevant if model parameters need to be estimated, as is often the case in biological modelling. Care should we taken when using an unidentifiable model to extract biological insight: the estimated values of structurally unidentifiable parameters are meaningless, and model predictions about unmeasured state variables can be wrong. Taking this into account, we explore alternative definitions of dynamical compensation that do not necessarily imply structural unidentifiability. Accordingly, we show different ways in which a model can be made identifiable while exhibiting dynamical compensation. Our analyses enable the use of the new concept of dynamical compensation in the context of parameter identification, and reconcile it with the desirable property of structural identifiability.

Comprehensive Structural Dynamic Analysis of the SSME/AT Fuel Pump First-Stage Turbine Blade

NASA Technical Reports Server (NTRS)

Brown, A. M.

1998-01-01

A detailed structural dynamic analysis of the Pratt & Whitney high-pressure fuel pump first-stage turbine blades has been performed to identify the cause of the tip cracking found in the turbomachinery in November 1997. The analysis was also used to help evaluate potential fixes for the problem. Many of the methods available in structural dynamics were applied, including modal displacement and stress analysis, frequency and transient response to tip loading from the first-stage Blade Outer Gas Seals (BOGS), fourier analysis, and shock spectra analysis of the transient response. The primary findings were that the BOGS tip loading is impulsive in nature, thereby exciting many modes of the blade that exhibit high stress at the tip cracking location. Therefore, a proposed BOGS count change would not help the situation because a clearly identifiable resonance situation does not exist. The recommendations for the resolution of the problem are to maintain the existing BOGS count, eliminate the stress concentration in the blade due to its geometric design, and reduce the applied load on the blade by adding shiplaps in the BOGS.

Atomistic cluster alignment method for local order mining in liquids and glasses

NASA Astrophysics Data System (ADS)

Fang, X. W.; Wang, C. Z.; Yao, Y. X.; Ding, Z. J.; Ho, K. M.

2010-11-01

An atomistic cluster alignment method is developed to identify and characterize the local atomic structural order in liquids and glasses. With the “order mining” idea for structurally disordered systems, the method can detect the presence of any type of local order in the system and can quantify the structural similarity between a given set of templates and the aligned clusters in a systematic and unbiased manner. Moreover, population analysis can also be carried out for various types of clusters in the system. The advantages of the method in comparison with other previously developed analysis methods are illustrated by performing the structural analysis for four prototype systems (i.e., pure Al, pure Zr, Zr35Cu65 , and Zr36Ni64 ). The results show that the cluster alignment method can identify various types of short-range orders (SROs) in these systems correctly while some of these SROs are difficult to capture by most of the currently available analysis methods (e.g., Voronoi tessellation method). Such a full three-dimensional atomistic analysis method is generic and can be applied to describe the magnitude and nature of noncrystalline ordering in many disordered systems.

Space construction system analysis. Part 2: Space construction experiments concepts

NASA Technical Reports Server (NTRS)

Boddy, J. A.; Wiley, L. F.; Gimlich, G. W.; Greenberg, H. S.; Hart, R. J.; Lefever, A. E.; Lillenas, A. N.; Totah, R. S.

1980-01-01

Technology areas in the orbital assembly of large space structures are addressed. The areas included structures, remotely operated assembly techniques, and control and stabilization. Various large space structure design concepts are reviewed and their construction procedures and requirements are identified.

Segmenting the Stream of Consciousness: The Psychological Correlates of Temporal Structures in the Time Series Data of a Continuous Performance Task

ERIC Educational Resources Information Center

Smallwood, Jonathan; McSpadden, Merrill; Luus, Bryan; Schooler, Joanthan

2008-01-01

Using principal component analysis, we examined whether structural properties in the time series of response time would identify different mental states during a continuous performance task. We examined whether it was possible to identify regular patterns which were present in blocks classified as lacking controlled processing, either…

Dimensional Structure of the Autism Phenotype: Relations between Early Development and Current Presentation

ERIC Educational Resources Information Center

Kamp-Becker, Inge; Ghahreman, Mardjan; Smidt, Judith; Remschmidt, Helmut

2009-01-01

The dimensional structure of higher functioning autism phenotype was investigated by factor analysis. The goal of this study was to identify the degree to which early symptoms of autism (measured using the ADI-R) could be predictive of the current symptoms of autism as identified using the ADOS, the adaptive behavior scales, IQ scores and theory…

The wavelet transform as an analysis tool for structure identification in molecular clouds

NASA Astrophysics Data System (ADS)

Gill, Arnold Gerald

1993-01-01

Of the many methods used to attempt to understand the complex structure of giant molecular clouds, perhaps the most commonly used are the autocorrelation functions (ACF), the structure function, and the power spectrum. However, these do not give unique interpretations of structure, as is shown by explicit examples compared to the Taurus Molecular Complex. Thus, another, independent method of analysis is indicated. Here, the wavelet transform is presented, a relatively new technique less than 10 years old. It can be thought of as a band-pass filter that identifies structures of specific sizes. In addition, its mathematical properties allow it to be used to identify fractal structures and accurately identify the scaling exponent. This is shown by the wavelet transform identifying the fractal dimension of a hierarchical rain cloud model first proposed by Frisch et al. (1978). A wavelet analysis is then carried out for a range of astronomical CO data, including the clouds Orion A and B and NGC 7538 (in (12)CO) and Orion A and B, Mon R2, and L1551 (in (13)CO). The data analyzed consists of the velocities of the fitted Gaussians to the individual spectra, the halfwidths and amplitude of these Gaussians, and the total area of the spectral line. For most of the clouds investigated, each of these data types showed a very high degree of scaling coherence over a wide range of scales, from down at the beam spacing up to the full size of the cloud. The analysis carried out uses both the scaling and structure identification strengths of the wavelet transform The fragmentation parameters used by Scalo (1985) and the parameters of the geometric molecular cloud description introduced by Henriksen (1986) are calculated for each cloud. These results are all consistent with previous observations of these and other molecular clouds, though they are obtained individually for each cloud investigated. It is found that the uncertainties are of a magnitude that the differentiation of various theories of molecular cloud structure is not possible. It is noted that the effects of projection and superposition strongly affect the values of some of these parameters, thus hampering a thorough understanding of the underlying physics. The strengths and weaknesses of the wavelet transform in the analysis of molecular cloud data are presented, as well as directions for future work.

Verification of nonlinear dynamic structural test results by combined image processing and acoustic analysis

NASA Astrophysics Data System (ADS)

Tene, Yair; Tene, Noam; Tene, G.

1993-08-01

An interactive data fusion methodology of video, audio, and nonlinear structural dynamic analysis for potential application in forensic engineering is presented. The methodology was developed and successfully demonstrated in the analysis of heavy transportable bridge collapse during preparation for testing. Multiple bridge elements failures were identified after the collapse, including fracture, cracks and rupture of high performance structural materials. Videotape recording by hand held camcorder was the only source of information about the collapse sequence. The interactive data fusion methodology resulted in extracting relevant information form the videotape and from dynamic nonlinear structural analysis, leading to full account of the sequence of events during the bridge collapse.

Software analysis handbook: Software complexity analysis and software reliability estimation and prediction

NASA Technical Reports Server (NTRS)

Lee, Alice T.; Gunn, Todd; Pham, Tuan; Ricaldi, Ron

1994-01-01

This handbook documents the three software analysis processes the Space Station Software Analysis team uses to assess space station software, including their backgrounds, theories, tools, and analysis procedures. Potential applications of these analysis results are also presented. The first section describes how software complexity analysis provides quantitative information on code, such as code structure and risk areas, throughout the software life cycle. Software complexity analysis allows an analyst to understand the software structure, identify critical software components, assess risk areas within a software system, identify testing deficiencies, and recommend program improvements. Performing this type of analysis during the early design phases of software development can positively affect the process, and may prevent later, much larger, difficulties. The second section describes how software reliability estimation and prediction analysis, or software reliability, provides a quantitative means to measure the probability of failure-free operation of a computer program, and describes the two tools used by JSC to determine failure rates and design tradeoffs between reliability, costs, performance, and schedule.

The Green Bank Ammonia Survey: Observations of Hierarchical Dense Gas Structures in Cepheus-L1251

NASA Astrophysics Data System (ADS)

Keown, Jared; Di Francesco, James; Kirk, Helen; Friesen, Rachel K.; Pineda, Jaime E.; Rosolowsky, Erik; Ginsburg, Adam; Offner, Stella S. R.; Caselli, Paola; Alves, Felipe; Chacón-Tanarro, Ana; Punanova, Anna; Redaelli, Elena; Seo, Young Min; Matzner, Christopher D.; Chun-Yuan Chen, Michael; Goodman, Alyssa A.; Chen, How-Huan; Shirley, Yancy; Singh, Ayushi; Arce, Hector G.; Martin, Peter; Myers, Philip C.

2017-11-01

We use Green Bank Ammonia Survey observations of NH3 (1, 1) and (2, 2) emission with 32″ FWHM resolution from a ˜10 pc2 portion of the Cepheus-L1251 molecular cloud to identify hierarchical dense gas structures. Our dendrogram analysis of the NH3 data results in 22 top-level structures, which reside within 13 lower-level parent structures. The structures are compact (0.01 {pc}≲ {R}{eff}≲ 0.1 {pc}) and are spatially correlated with the highest H2 column density portions of the cloud. We also compare the ammonia data to a catalog of dense cores identified by higher-resolution (18.″2 FWHM) Herschel Space Observatory observations of dust continuum emission from Cepheus-L1251. Maps of kinetic gas temperature, velocity dispersion, and NH3 column density, derived from detailed modeling of the NH3 data, are used to investigate the stability and chemistry of the ammonia-identified and Herschel-identified structures. We show that the dust and dense gas in the structures have similar temperatures, with median T dust and T K measurements of 11.7 ± 1.1 K and 10.3 ± 2.0 K, respectively. Based on a virial analysis, we find that the ammonia-identified structures are gravitationally dominated, yet may be in or near a state of virial equilibrium. Meanwhile, the majority of the Herschel-identified dense cores appear to be not bound by their own gravity and instead confined by external pressure. CCS (20 - 10) and HC5N (9-8) emission from the region reveal broader line widths and centroid velocity offsets when compared to the NH3 (1, 1) emission in some cases, likely due to these carbon-based molecules tracing the turbulent outer layers of the dense cores.

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

PubMed Central

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

2016-01-01

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

Commuter rail seat testing and analysis.

DOT National Transportation Integrated Search

2002-07-31

The need to determine the structural integrity and passenger safety provided by existing commuter rail seats was identified by the Construction/Structural Subgroup of the American Public Transportation Association's (APTA) Passenger Rail Equipment Sa...

Remote geologic structural analysis of Yucca Flat

NASA Astrophysics Data System (ADS)

Foley, M. G.; Heasler, P. G.; Hoover, K. A.; Rynes, N. J.; Thiessen, R. L.; Alfaro, J. L.

1991-12-01

The Remote Geologic Analysis (RGA) system was developed by Pacific Northwest Laboratory (PNL) to identify crustal structures that may affect seismic wave propagation from nuclear tests. Using automated methods, the RGA system identifies all valleys in a digital elevation model (DEM), fits three-dimensional vectors to valley bottoms, and catalogs all potential fracture or fault planes defined by coplanar pairs of valley vectors. The system generates a cluster hierarchy of planar features having greater-than-random density that may represent areas of anomalous topography manifesting structural control of erosional drainage development. Because RGA uses computer methods to identify zones of hypothesized control of topography, ground truth using a well-characterized test site was critical in our evaluation of RGA's characterization of inaccessible test sites for seismic verification studies. Therefore, we applied RGA to a study area centered on Yucca Flat at the Nevada Test Site (NTS) and compared our results with both mapped geology and geologic structures and with seismic yield-magnitude models. This is the final report of PNL's RGA development project for peer review within the U.S. Department of Energy Office of Arms Control (OAC) seismic-verification community. In this report, we discuss the Yucca Flat study area, the analytical basis of the RGA system and its application to Yucca Flat, the results of the analysis, and the relation of the analytical results to known topography, geology, and geologic structures.

LCS-TA to identify similar fragments in RNA 3D structures.

PubMed

Wiedemann, Jakub; Zok, Tomasz; Milostan, Maciej; Szachniuk, Marta

2017-10-23

In modern structural bioinformatics, comparison of molecular structures aimed to identify and assess similarities and differences between them is one of the most commonly performed procedures. It gives the basis for evaluation of in silico predicted models. It constitutes the preliminary step in searching for structural motifs. In particular, it supports tracing the molecular evolution. Faced with an ever-increasing amount of available structural data, researchers need a range of methods enabling comparative analysis of the structures from either global or local perspective. Herein, we present a new, superposition-independent method which processes pairs of RNA 3D structures to identify their local similarities. The similarity is considered in the context of structure bending and bonds' rotation which are described by torsion angles. In the analyzed RNA structures, the method finds the longest continuous segments that show similar torsion within a user-defined threshold. The length of the segment is provided as local similarity measure. The method has been implemented as LCS-TA algorithm (Longest Continuous Segments in Torsion Angle space) and is incorporated into our MCQ4Structures application, freely available for download from http://www.cs.put.poznan.pl/tzok/mcq/ . The presented approach ties torsion-angle-based method of structure analysis with the idea of local similarity identification by handling continuous 3D structure segments. The first method, implemented in MCQ4Structures, has been successfully utilized in RNA-Puzzles initiative. The second one, originally applied in Euclidean space, is a component of LGA (Local-Global Alignment) algorithm commonly used in assessing protein models submitted to CASP. This unique combination of concepts implemented in LCS-TA provides a new perspective on structure quality assessment in local and quantitative aspect. A series of computational experiments show the first results of applying our method to comparison of RNA 3D models. LCS-TA can be used for identifying strengths and weaknesses in the prediction of RNA tertiary structures.

Structural dynamic analysis of the Space Shuttle Main Engine

NASA Technical Reports Server (NTRS)

Scott, L. P.; Jamison, G. T.; Mccutcheon, W. A.; Price, J. M.

1981-01-01

This structural dynamic analysis supports development of the SSME by evaluating components subjected to critical dynamic loads, identifying significant parameters, and evaluating solution methods. Engine operating parameters at both rated and full power levels are considered. Detailed structural dynamic analyses of operationally critical and life limited components support the assessment of engine design modifications and environmental changes. Engine system test results are utilized to verify analytic model simulations. The SSME main chamber injector assembly is an assembly of 600 injector elements which are called LOX posts. The overall LOX post analysis procedure is shown.

Ole e 13 is the unique food allergen in olive: Structure-functional, substrates docking, and molecular allergenicity comparative analysis.

PubMed

Jimenez-Lopez, J C; Robles-Bolivar, P; Lopez-Valverde, F J; Lima-Cabello, E; Kotchoni, S O; Alché, J D

2016-05-01

Thaumatin-like proteins (TLPs) are enzymes with important functions in pathogens defense and in the response to biotic and abiotic stresses. Last identified olive allergen (Ole e 13) is a TLP, which may also importantly contribute to food allergy and cross-allergenicity to pollen allergen proteins. The goals of this study are the characterization of the structural-functionality of Ole e 13 with a focus in its catalytic mechanism, and its molecular allergenicity by extensive analysis using different molecular computer-aided approaches covering a) functional-regulatory motifs, b) comparative study of linear sequence, 2-D and 3D structural homology modeling, c) molecular docking with two different β-D-glucans, d) conservational and evolutionary analysis, e) catalytic mechanism modeling, and f) IgE-binding, B- and T-cell epitopes identification and comparison to other allergenic TLPs. Sequence comparison, structure-based features, and phylogenetic analysis identified Ole e 13 as a thaumatin-like protein. 3D structural characterization revealed a conserved overall folding among plants TLPs, with mayor differences in the acidic (catalytic) cleft. Molecular docking analysis using two β-(1,3)-glucans allowed to identify fundamental residues involved in the endo-1,3-β-glucanase activity, and defining E84 as one of the conserved residues of the TLPs responsible of the nucleophilic attack to initiate the enzymatic reaction and D107 as proton donor, thus proposing a catalytic mechanism for Ole e 13. Identification of IgE-binding, B- and T-cell epitopes may help designing strategies to improve diagnosis and immunotherapy to food allergy and cross-allergenic pollen TLPs. Copyright © 2016 Elsevier Inc. All rights reserved.

Comparative analysis of structural concrete Quality Assurance practices on nine nuclear and three fossil fuel power plant construction projects. Final summary report

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

Willenbrock, J.H.; Thomas, H.R. Jr.; Burati, J.J. Jr.

1978-12-01

A summary of two reports, COO/4120-1 and COO/4120-2, is given. A comparative analysis was made of the Quality Assurance practices related to the structural concrete phase on nine nuclear and three fossil fuel power plant projects which are (or have been) under construction in the United States in the past ten years. For the nuclear projects the analysis identified the response of each Quality Assurance program to the applicable criteria of 10 CFR Part 50, Appendix B as well as to the pertinent regulatory requirements and industry standards. For the fossil projects the analysis identified the response of each Qualitymore » Assurance program to criteria similar to those which were applicable in the nuclear situation. The major emphasis was placed on the construction aspects of the structural concrete phase of each project. The engineering and design aspects were examined whenever they interfaced with the construction aspects.« less

Accurate airway centerline extraction based on topological thinning using graph-theoretic analysis.

PubMed

Bian, Zijian; Tan, Wenjun; Yang, Jinzhu; Liu, Jiren; Zhao, Dazhe

2014-01-01

The quantitative analysis of the airway tree is of critical importance in the CT-based diagnosis and treatment of popular pulmonary diseases. The extraction of airway centerline is a precursor to identify airway hierarchical structure, measure geometrical parameters, and guide visualized detection. Traditional methods suffer from extra branches and circles due to incomplete segmentation results, which induce false analysis in applications. This paper proposed an automatic and robust centerline extraction method for airway tree. First, the centerline is located based on the topological thinning method; border voxels are deleted symmetrically to preserve topological and geometrical properties iteratively. Second, the structural information is generated using graph-theoretic analysis. Then inaccurate circles are removed with a distance weighting strategy, and extra branches are pruned according to clinical anatomic knowledge. The centerline region without false appendices is eventually determined after the described phases. Experimental results show that the proposed method identifies more than 96% branches and keep consistency across different cases and achieves superior circle-free structure and centrality.

Research Update: Spatially resolved mapping of electronic structure on atomic level by multivariate statistical analysis

DOE PAGES

Belianinov, Alex; Panchapakesan, G.; Lin, Wenzhi; ...

2014-12-02

Atomic level spatial variability of electronic structure in Fe-based superconductor FeTe0.55Se0.45 (Tc = 15 K) is explored using current-imaging tunneling-spectroscopy. Multivariate statistical analysis of the data differentiates regions of dissimilar electronic behavior that can be identified with the segregation of chalcogen atoms, as well as boundaries between terminations and near neighbor interactions. Subsequent clustering analysis allows identification of the spatial localization of these dissimilar regions. Similar statistical analysis of modeled calculated density of states of chemically inhomogeneous FeTe1 x Sex structures further confirms that the two types of chalcogens, i.e., Te and Se, can be identified by their electronic signaturemore » and differentiated by their local chemical environment. This approach allows detailed chemical discrimination of the scanning tunneling microscopy data including separation of atomic identities, proximity, and local configuration effects and can be universally applicable to chemically and electronically inhomogeneous surfaces.« less

Research Update: Spatially resolved mapping of electronic structure on atomic level by multivariate statistical analysis

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

Belianinov, Alex, E-mail: belianinova@ornl.gov; Ganesh, Panchapakesan; Lin, Wenzhi

2014-12-01

Atomic level spatial variability of electronic structure in Fe-based superconductor FeTe{sub 0.55}Se{sub 0.45} (T{sub c} = 15 K) is explored using current-imaging tunneling-spectroscopy. Multivariate statistical analysis of the data differentiates regions of dissimilar electronic behavior that can be identified with the segregation of chalcogen atoms, as well as boundaries between terminations and near neighbor interactions. Subsequent clustering analysis allows identification of the spatial localization of these dissimilar regions. Similar statistical analysis of modeled calculated density of states of chemically inhomogeneous FeTe{sub 1−x}Se{sub x} structures further confirms that the two types of chalcogens, i.e., Te and Se, can be identified bymore » their electronic signature and differentiated by their local chemical environment. This approach allows detailed chemical discrimination of the scanning tunneling microscopy data including separation of atomic identities, proximity, and local configuration effects and can be universally applicable to chemically and electronically inhomogeneous surfaces.« less

PDBFlex: exploring flexibility in protein structures

PubMed Central

Hrabe, Thomas; Li, Zhanwen; Sedova, Mayya; Rotkiewicz, Piotr; Jaroszewski, Lukasz; Godzik, Adam

2016-01-01

The PDBFlex database, available freely and with no login requirements at http://pdbflex.org, provides information on flexibility of protein structures as revealed by the analysis of variations between depositions of different structural models of the same protein in the Protein Data Bank (PDB). PDBFlex collects information on all instances of such depositions, identifying them by a 95% sequence identity threshold, performs analysis of their structural differences and clusters them according to their structural similarities for easy analysis. The PDBFlex contains tools and viewers enabling in-depth examination of structural variability including: 2D-scaling visualization of RMSD distances between structures of the same protein, graphs of average local RMSD in the aligned structures of protein chains, graphical presentation of differences in secondary structure and observed structural disorder (unresolved residues), difference distance maps between all sets of coordinates and 3D views of individual structures and simulated transitions between different conformations, the latter displayed using JSMol visualization software. PMID:26615193

Improving the Dynamic Characteristics of Body-in-White Structure Using Structural Optimization

PubMed Central

Yahaya Rashid, Aizzat S.; Mohamed Haris, Sallehuddin; Alias, Anuar

2014-01-01

The dynamic behavior of a body-in-white (BIW) structure has significant influence on the noise, vibration, and harshness (NVH) and crashworthiness of a car. Therefore, by improving the dynamic characteristics of BIW, problems and failures associated with resonance and fatigue can be prevented. The design objectives attempt to improve the existing torsion and bending modes by using structural optimization subjected to dynamic load without compromising other factors such as mass and stiffness of the structure. The natural frequency of the design was modified by identifying and reinforcing the structure at critical locations. These crucial points are first identified by topology optimization using mass and natural frequencies as the design variables. The individual components obtained from the analysis go through a size optimization step to find their target thickness of the structure. The thickness of affected regions of the components will be modified according to the analysis. The results of both optimization steps suggest several design modifications to achieve the target vibration specifications without compromising the stiffness of the structure. A method of combining both optimization approaches is proposed to improve the design modification process. PMID:25101312

Synthesis, structural, thermal and Hirshfeld surface analysis of novel [1,2,4]triazolo[3,4-b][1,3,4] thiadiazine carrying 1,4-benzothiazine-3-one moiety

NASA Astrophysics Data System (ADS)

Shruthi, C.; Ravindrachary, V.; Guruswamy, B.; Lokanath, N. K.; Kumara, Karthik; Goveas, Janet

2018-05-01

Needle shaped single crystal of the title compound was grown by slow evaporation solution growth technique using ethanol as solvent. The grown single crystal was characterized using FT-IR, Single crystal XRD and Thermal analysis. The FT-IR spectrum confirms the molecular structure and identifies the different functional groups present in the compound. Single crystal XRD study reveals that the crystallized compound belongs to the monoclinic crystal system with P21/c space group and the corresponding cell parameters were identified. The thermal stability of the material was determined using both TGA and DTA analysis. The intermolecular interaction of each individual atom in the crystal lattice was estimated using Hirshfeld surface and finger print analysis.

Stress Analysis of B-52B and B-52H Air-Launching Systems Failure-Critical Structural Components

NASA Technical Reports Server (NTRS)

Ko, William L.

2005-01-01

The operational life analysis of any airborne failure-critical structural component requires the stress-load equation, which relates the applied load to the maximum tangential tensile stress at the critical stress point. The failure-critical structural components identified are the B-52B Pegasus pylon adapter shackles, B-52B Pegasus pylon hooks, B-52H airplane pylon hooks, B-52H airplane front fittings, B-52H airplane rear pylon fitting, and the B-52H airplane pylon lower sway brace. Finite-element stress analysis was performed on the said structural components, and the critical stress point was located and the stress-load equation was established for each failure-critical structural component. The ultimate load, yield load, and proof load needed for operational life analysis were established for each failure-critical structural component.

Analysis of copy number variations in Holstein cows identify potential mechanisms contributing to differences in residual feed intake

USDA-ARS?s Scientific Manuscript database

Genomic structural variation is an important and abundant source of genetic and phenotypic variation. In this study, we performed an initial analysis of CNVs using BovineHD SNP genotyping data from 147 Holstein cows identified as having high or low feed efficiency as estimated by residual feed intak...

Genetic diversity and population structure analysis of spinach by single-nucleotide polymorphisms identified through genotyping-by-sequencing

USDA-ARS?s Scientific Manuscript database

Spinach (Spinacia oleracea L., 2n=2x=12) is an economically important vegetable crop worldwide and one of the healthiest vegetables due to its high concentrations of nutrients and mineral compounds. The objective of this research is to conduct genetic diversity and population structure analysis of w...

In silico identification and analysis of phytoene synthase genes in plants.

PubMed

Han, Y; Zheng, Q S; Wei, Y P; Chen, J; Liu, R; Wan, H J

2015-08-14

In this study, we examined phytoene synthetase (PSY), the first key limiting enzyme in the synthesis of carotenoids and catalyzing the formation of geranylgeranyl pyrophosphate in terpenoid biosynthesis. We used known amino acid sequences of the PSY gene in tomato plants to conduct a genome-wide search and identify putative candidates in 34 sequenced plants. A total of 101 homologous genes were identified. Phylogenetic analysis revealed that PSY evolved independently in algae as well as monocotyledonous and dicotyledonous plants. Our results showed that the amino acid structures exhibited 5 motifs (motifs 1 to 5) in algae and those in higher plants were highly conserved. The PSY gene structures showed that the number of intron in algae varied widely, while the number of introns in higher plants was 4 to 5. Identification of PSY genes in plants and the analysis of the gene structure may provide a theoretical basis for studying evolutionary relationships in future analyses.

Transcriptome mining and in silico structural and functional analysis of ascorbic acid and tartaric acid biosynthesis pathway enzymes in rose-scanted geranium.

PubMed

Narnoliya, Lokesh K; Sangwan, Rajender S; Singh, Sudhir P

2018-06-01

Rose-scented geranium (Pelargonium sp.) is widely known as aromatic and medicinal herb, accumulating specialized metabolites of high economic importance, such as essential oils, ascorbic acid, and tartaric acid. Ascorbic acid and tartaric acid are multifunctional metabolites of human value to be used as vital antioxidants and flavor enhancing agents in food products. No information is available related to the structural and functional properties of the enzymes involved in ascorbic acid and tartaric acid biosynthesis in rose-scented geranium. In the present study, transcriptome mining was done to identify full-length genes, followed by their bioinformatic and molecular modeling investigations and understanding of in silico structural and functional properties of these enzymes. Evolutionary conserved domains were identified in the pathway enzymes. In silico physicochemical characterization of the catalytic enzymes revealed isoelectric point (pI), instability index, aliphatic index, and grand average hydropathy (GRAVY) values of the enzymes. Secondary structural prediction revealed abundant proportion of alpha helix and random coil confirmations in the pathway enzymes. Three-dimensional homology models were developed for these enzymes. The predicted structures showed significant structural similarity with their respective templates in root mean square deviation analysis. Ramachandran plot analysis of the modeled enzymes revealed that more than 84% of the amino acid residues were within the favored regions. Further, functionally important residues were identified corresponding to catalytic sites located in the enzymes. To, our best knowledge, this is the first report which provides a foundation on functional annotation and structural determination of ascorbic acid and tartaric acid pathway enzymes in rose-scanted geranium.

Programming Probabilistic Structural Analysis for Parallel Processing Computer

NASA Technical Reports Server (NTRS)

Sues, Robert H.; Chen, Heh-Chyun; Twisdale, Lawrence A.; Chamis, Christos C.; Murthy, Pappu L. N.

1991-01-01

The ultimate goal of this research program is to make Probabilistic Structural Analysis (PSA) computationally efficient and hence practical for the design environment by achieving large scale parallelism. The paper identifies the multiple levels of parallelism in PSA, identifies methodologies for exploiting this parallelism, describes the development of a parallel stochastic finite element code, and presents results of two example applications. It is demonstrated that speeds within five percent of those theoretically possible can be achieved. A special-purpose numerical technique, the stochastic preconditioned conjugate gradient method, is also presented and demonstrated to be extremely efficient for certain classes of PSA problems.

Structural genomics analysis of uncharacterized protein families overrepresented in human gut bacteria identifies a novel glycoside hydrolase

PubMed Central

2014-01-01

Background Bacteroides spp. form a significant part of our gut microbiome and are well known for optimized metabolism of diverse polysaccharides. Initial analysis of the archetypal Bacteroides thetaiotaomicron genome identified 172 glycosyl hydrolases and a large number of uncharacterized proteins associated with polysaccharide metabolism. Results BT_1012 from Bacteroides thetaiotaomicron VPI-5482 is a protein of unknown function and a member of a large protein family consisting entirely of uncharacterized proteins. Initial sequence analysis predicted that this protein has two domains, one on the N- and one on the C-terminal. A PSI-BLAST search found over 150 full length and over 90 half size homologs consisting only of the N-terminal domain. The experimentally determined three-dimensional structure of the BT_1012 protein confirms its two-domain architecture and structural analysis of both domains suggests their specific functions. The N-terminal domain is a putative catalytic domain with significant similarity to known glycoside hydrolases, the C-terminal domain has a beta-sandwich fold typically found in C-terminal domains of other glycosyl hydrolases, however these domains are typically involved in substrate binding. We describe the structure of the BT_1012 protein and discuss its sequence-structure relationship and their possible functional implications. Conclusions Structural and sequence analyses of the BT_1012 protein identifies it as a glycosyl hydrolase, expanding an already impressive catalog of enzymes involved in polysaccharide metabolism in Bacteroides spp. Based on this we have renamed the Pfam families representing the two domains found in the BT_1012 protein, PF13204 and PF12904, as putative glycoside hydrolase and glycoside hydrolase-associated C-terminal domain respectively. PMID:24742328

Chiral Analysis of Isopulegol by Fourier Transform Molecular Rotational Spectroscopy

NASA Astrophysics Data System (ADS)

Evangelisti, Luca; Seifert, Nathan A.; Spada, Lorenzo; Pate, Brooks

2016-06-01

Chiral analysis on molecules with multiple chiral centers can be performed using pulsed-jet Fourier transform rotational spectroscopy. This analysis includes quantitative measurement of diastereomer products and, with the three wave mixing methods developed by Patterson, Schnell, and Doyle (Nature 497, 475-477 (2013)), quantitative determination of the enantiomeric excess of each diastereomer. The high resolution features enable to perform the analysis directly on complex samples without the need for chromatographic separation. Isopulegol has been chosen to show the capabilities of Fourier transform rotational spectroscopy for chiral analysis. Broadband rotational spectroscopy produces spectra with signal-to-noise ratio exceeding 1000:1. The ability to identify low-abundance (0.1-1%) diastereomers in the sample will be described. Methods to rapidly identify rotational spectra from isotopologues at natural abundance will be shown and the molecular structures obtained from this analysis will be compared to theory. The role that quantum chemistry calculations play in identifying structural minima and estimating their spectroscopic properties to aid spectral analysis will be described. Finally, the implementation of three wave mixing techniques to measure the enantiomeric excess of each diastereomer and determine the absolute configuration of the enantiomer in excess will be described.

Structure-based analysis of catalysis and substrate definition in the HIT protein family.

PubMed

Lima, C D; Klein, M G; Hendrickson, W A

1997-10-10

The histidine triad (HIT) protein family is among the most ubiquitous and highly conserved in nature, but a biological activity has not yet been identified for any member of the HIT family. Fragile histidine triad protein (FHIT) and protein kinase C interacting protein (PKCI) were used in a structure-based approach to elucidate characteristics of in vivo ligands and reactions. Crystallographic structures of apo, substrate analog, pentacovalent transition-state analog, and product states of both enzymes reveal a catalytic mechanism and define substrate characteristics required for catalysis, thus unifying the HIT family as nucleotidyl hydrolases, transferases, or both. The approach described here may be useful in identifying structure-function relations between protein families identified through genomics.

Structural analysis of photosystem I polypeptides using chemical crosslinking

NASA Technical Reports Server (NTRS)

Armbrust, T. S.; Odom, W. R.; Guikema, J. A.; Spooner, B. S. (Principal Investigator)

1994-01-01

Thylakoid membranes, obtained from leaves of 14 d soybean (Glycine max L. cv. Williams) plants, were treated with the chemical crosslinkers glutaraldehyde or 1-ethyl-3-(3-dimethylaminopropyl)-carbodiimide (EDC) to investigate the structural organization of photosystem I. Polypeptides were resolved using lithium dodecyl sulfate polyacrylamide gel electrophoresis, and were identified by western blot analysis using a library of polyclonal antibodies specific for photosystem I subunits. An electrophoretic examination of crosslinked thylakoids revealed numerous crosslinked products, using either glutaraldehyde or EDC. However, only a few of these could be identified by western blot analysis using subunit-specific polyclonal antibodies. Several glutaraldehyde dependent crosslinked species were identified. A single band was identified minimally composed of PsaC and PsaD, documenting the close interaction between these two subunits. The most interesting aspect of these studies was a crosslinked species composed of the PsaB subunit observed following EDC treatment of thylakoids. This is either an internally crosslinked species, which will provide structural information concerning the topology of the complex PsaB protein, a linkage with a polypeptide for which we do not yet have an immunological probe, or a masking of epitopes by the EDC linkage at critical locations in the peptide which is linked to PsaB.

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

An optimized color transformation for the analysis of digital images of hematoxylin & eosin stained slides.

PubMed

Zarella, Mark D; Breen, David E; Plagov, Andrei; Garcia, Fernando U

2015-01-01

Hematoxylin and eosin (H&E) staining is ubiquitous in pathology practice and research. As digital pathology has evolved, the reliance of quantitative methods that make use of H&E images has similarly expanded. For example, cell counting and nuclear morphometry rely on the accurate demarcation of nuclei from other structures and each other. One of the major obstacles to quantitative analysis of H&E images is the high degree of variability observed between different samples and different laboratories. In an effort to characterize this variability, as well as to provide a substrate that can potentially mitigate this factor in quantitative image analysis, we developed a technique to project H&E images into an optimized space more appropriate for many image analysis procedures. We used a decision tree-based support vector machine learning algorithm to classify 44 H&E stained whole slide images of resected breast tumors according to the histological structures that are present. This procedure takes an H&E image as an input and produces a classification map of the image that predicts the likelihood of a pixel belonging to any one of a set of user-defined structures (e.g., cytoplasm, stroma). By reducing these maps into their constituent pixels in color space, an optimal reference vector is obtained for each structure, which identifies the color attributes that maximally distinguish one structure from other elements in the image. We show that tissue structures can be identified using this semi-automated technique. By comparing structure centroids across different images, we obtained a quantitative depiction of H&E variability for each structure. This measurement can potentially be utilized in the laboratory to help calibrate daily staining or identify troublesome slides. Moreover, by aligning reference vectors derived from this technique, images can be transformed in a way that standardizes their color properties and makes them more amenable to image processing.

Structural Arrangement Trade Study. Volume 1: Reusable Hydrogen Composite Tank System (RHCTS) and Graphite Composite Primary Structures (GCPS). Executive summary

NASA Astrophysics Data System (ADS)

1995-03-01

This volume is the first of a three volume set that discusses the structural arrangement trade study plan that will identify the most suitable configuration for an SSTO winged vehicle capable of delivering 25,000 lbs to a 220 nm circular orbit at 51.6 deg inclination. The Reusable Hydrogen Composite Tank System (RHCTS), and Graphite Composite Primary Structures most suitable for intertank, wing and thrust structures are identified. This executive summary presents the trade study process, the selection process, requirements used, analysis performed and data generated. Conclusions and recommendations are also presented.

Structural Arrangement Trade Study. Volume 1: Reusable Hydrogen Composite Tank System (RHCTS) and Graphite Composite Primary Structures (GCPS). Executive summary

NASA Technical Reports Server (NTRS)

1995-01-01

This volume is the first of a three volume set that discusses the structural arrangement trade study plan that will identify the most suitable configuration for an SSTO winged vehicle capable of delivering 25,000 lbs to a 220 nm circular orbit at 51.6 deg inclination. The Reusable Hydrogen Composite Tank System (RHCTS), and Graphite Composite Primary Structures most suitable for intertank, wing and thrust structures are identified. This executive summary presents the trade study process, the selection process, requirements used, analysis performed and data generated. Conclusions and recommendations are also presented.

A Thematic Analysis of Online Discussion Boards for Vasectomy.

PubMed

Samplaski, Mary K

2018-01-01

To examine posts on Internet discussion groups related to vasectomies, and identify common ideas through a structured theme analysis. Internet discussion boards were identified using the search term "vasectomy." Three discussion boards were identified as having the most posts and were chosen for analysis. Using an iterative and structured analysis process, each post was analyzed using thematic analysis in 3 steps (open coding, axial coding, and selective coding) to determine common themes. A total of 129 posts were analyzed. The most common posts related to changes in sexual function after vasectomy. The second most common theme was pain after vasectomy. There were also posts about considerations before vasectomy, planning for postvasectomy care, what to expect after vasectomy, potential issues after vasectomy and how to manage these, and feelings about vasectomy. Some of the information present did not have a factual basis. Posts dedicated to postvasectomy pain and sexual dysfunction were of the highest quantity. There was no medical provider input to these discussion boards. Educational efforts should be targeted to these areas and should include a health-care professional. Copyright © 2017 Elsevier Inc. All rights reserved.

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

PubMed

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

2016-11-01

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

Transition in Pulsatile Pipe Flow

NASA Astrophysics Data System (ADS)

Vlachos, Pavlos; Brindise, Melissa

2016-11-01

Transition has been observed to occur in the aorta, and stenotic vessels, where pulsatile flow exists. However, few studies have investigated the characteristics and effects of transition in oscillating or pulsatile flow and none have utilized a physiological waveform. In this work, we explore transition in pipe flow using three pulsatile waveforms which all maintain the same mean and maximum flow rates and range to zero flow, as is physiologically typical. Velocity fields were obtained using planar particle image velocimetry for each pulsatile waveform at six mean Reynolds numbers ranging between 500 and 4000. Turbulent statistics including turbulent kinetic energy (TKE) and Reynolds stresses were computed. Quadrant analysis was used to identify characteristics of the production and dissipation of turbulence. Coherent structures were identified using the λci method. We developed a wavelet-Hilbert time-frequency analysis method to identify high frequency structures and compared these to the coherent structures. The results of this study demonstrate that the different pulsatile waveforms induce different levels of TKE and high frequency structures, suggesting that the rates of acceleration and deceleration influence the onset and development of transition.

Effective constitutive relations for large repetitive frame-like structures

NASA Technical Reports Server (NTRS)

Nayfeh, A. H.; Hefzy, M. S.

1981-01-01

Effective mechanical properties for large repetitive framelike structures are derived using combinations of strength of material and orthogonal transformation techniques. Symmetry considerations are used in order to identify independent property constants. The actual values of these constants are constructed according to a building block format which is carried out in the three consecutive steps: (1) all basic planar lattices are identified; (2) effective continuum properties are derived for each of these planar basic grids using matrix structural analysis methods; and (3) orthogonal transformations are used to determine the contribution of each basic set to the overall effective continuum properties of the structure.

Cross Flow Parameter Calculation for Aerodynamic Analysis

NASA Technical Reports Server (NTRS)

Norman, David, Jr. (Inventor)

2014-01-01

A system and method for determining a cross flow angle for a feature on a structure. A processor unit receives location information identifying a location of the feature on the structure, determines an angle of the feature, identifies flow information for the location, determines a flow angle using the flow information, and determines the cross flow angle for the feature using the flow angle and the angle of the feature. The flow information describes a flow of fluid across the structure. The flow angle comprises an angle of the flow of fluid across the structure for the location of the feature.

Identification of key genes associated with the effect of estrogen on ovarian cancer using microarray analysis.

PubMed

Zhang, Shi-tao; Zuo, Chao; Li, Wan-nan; Fu, Xue-qi; Xing, Shu; Zhang, Xiao-ping

2016-02-01

To identify key genes related to the effect of estrogen on ovarian cancer. Microarray data (GSE22600) were downloaded from Gene Expression Omnibus. Eight estrogen and seven placebo treatment samples were obtained using a 2 × 2 factorial designs, which contained 2 cell lines (PEO4 and 2008) and 2 treatments (estrogen and placebo). Differentially expressed genes were identified by Bayesian methods, and the genes with P < 0.05 and |log2FC (fold change)| ≥0.5 were chosen as cut-off criterion. Differentially co-expressed genes (DCGs) and differentially regulated genes (DRGs) were, respectively, identified by DCe function and DRsort function in DCGL package. Topological structure analysis was performed on the important transcriptional factors (TFs) and genes in transcriptional regulatory network using tYNA. Functional enrichment analysis was, respectively, performed for DEGs and the important genes using Gene Ontology and KEGG databases. In total, 465 DEGs were identified. Functional enrichment analysis of DEGs indicated that ACVR2B, LTBP1, BMP7 and MYC involved in TGF-beta signaling pathway. The 2285 DCG pairs and 357 DRGs were identified. Topological structure analysis showed that 52 important TFs and 65 important genes were identified. Functional enrichment analysis of the important genes showed that TP53 and MLH1 participated in DNA damage response and the genes (ACVR2B, LTBP1, BMP7 and MYC) involved in TGF-beta signaling pathway. TP53, MLH1, ACVR2B, LTBP1 and BMP7 might participate in the pathogenesis of ovarian cancer.

Systematic analysis of mutation distribution in three dimensional protein structures identifies cancer driver genes.

PubMed

Fujimoto, Akihiro; Okada, Yukinori; Boroevich, Keith A; Tsunoda, Tatsuhiko; Taniguchi, Hiroaki; Nakagawa, Hidewaki

2016-05-26

Protein tertiary structure determines molecular function, interaction, and stability of the protein, therefore distribution of mutation in the tertiary structure can facilitate the identification of new driver genes in cancer. To analyze mutation distribution in protein tertiary structures, we applied a novel three dimensional permutation test to the mutation positions. We analyzed somatic mutation datasets of 21 types of cancers obtained from exome sequencing conducted by the TCGA project. Of the 3,622 genes that had ≥3 mutations in the regions with tertiary structure data, 106 genes showed significant skew in mutation distribution. Known tumor suppressors and oncogenes were significantly enriched in these identified cancer gene sets. Physical distances between mutations in known oncogenes were significantly smaller than those of tumor suppressors. Twenty-three genes were detected in multiple cancers. Candidate genes with significant skew of the 3D mutation distribution included kinases (MAPK1, EPHA5, ERBB3, and ERBB4), an apoptosis related gene (APP), an RNA splicing factor (SF1), a miRNA processing factor (DICER1), an E3 ubiquitin ligase (CUL1) and transcription factors (KLF5 and EEF1B2). Our study suggests that systematic analysis of mutation distribution in the tertiary protein structure can help identify cancer driver genes.

Systematic analysis of mutation distribution in three dimensional protein structures identifies cancer driver genes

PubMed Central

Fujimoto, Akihiro; Okada, Yukinori; Boroevich, Keith A.; Tsunoda, Tatsuhiko; Taniguchi, Hiroaki; Nakagawa, Hidewaki

2016-01-01

Protein tertiary structure determines molecular function, interaction, and stability of the protein, therefore distribution of mutation in the tertiary structure can facilitate the identification of new driver genes in cancer. To analyze mutation distribution in protein tertiary structures, we applied a novel three dimensional permutation test to the mutation positions. We analyzed somatic mutation datasets of 21 types of cancers obtained from exome sequencing conducted by the TCGA project. Of the 3,622 genes that had ≥3 mutations in the regions with tertiary structure data, 106 genes showed significant skew in mutation distribution. Known tumor suppressors and oncogenes were significantly enriched in these identified cancer gene sets. Physical distances between mutations in known oncogenes were significantly smaller than those of tumor suppressors. Twenty-three genes were detected in multiple cancers. Candidate genes with significant skew of the 3D mutation distribution included kinases (MAPK1, EPHA5, ERBB3, and ERBB4), an apoptosis related gene (APP), an RNA splicing factor (SF1), a miRNA processing factor (DICER1), an E3 ubiquitin ligase (CUL1) and transcription factors (KLF5 and EEF1B2). Our study suggests that systematic analysis of mutation distribution in the tertiary protein structure can help identify cancer driver genes. PMID:27225414

Genetic Structure of Bluefin Tuna in the Mediterranean Sea Correlates with Environmental Variables

PubMed Central

Riccioni, Giulia; Stagioni, Marco; Landi, Monica; Ferrara, Giorgia; Barbujani, Guido; Tinti, Fausto

2013-01-01

Background Atlantic Bluefin Tuna (ABFT) shows complex demography and ecological variation in the Mediterranean Sea. Genetic surveys have detected significant, although weak, signals of population structuring; catch series analyses and tagging programs identified complex ABFT spatial dynamics and migration patterns. Here, we tested the hypothesis that the genetic structure of the ABFT in the Mediterranean is correlated with mean surface temperature and salinity. Methodology We used six samples collected from Western and Central Mediterranean integrated with a new sample collected from the recently identified easternmost reproductive area of Levantine Sea. To assess population structure in the Mediterranean we used a multidisciplinary framework combining classical population genetics, spatial and Bayesian clustering methods and a multivariate approach based on factor analysis. Conclusions FST analysis and Bayesian clustering methods detected several subpopulations in the Mediterranean, a result also supported by multivariate analyses. In addition, we identified significant correlations of genetic diversity with mean salinity and surface temperature values revealing that ABFT is genetically structured along two environmental gradients. These results suggest that a preference for some spawning habitat conditions could contribute to shape ABFT genetic structuring in the Mediterranean. However, further studies should be performed to assess to what extent ABFT spawning behaviour in the Mediterranean Sea can be affected by environmental variation. PMID:24260341

Singularity in structural optimization

NASA Technical Reports Server (NTRS)

Patnaik, S. N.; Guptill, J. D.; Berke, L.

1993-01-01

The conditions under which global and local singularities may arise in structural optimization are examined. Examples of these singularities are presented, and a framework is given within which the singularities can be recognized. It is shown, in particular, that singularities can be identified through the analysis of stress-displacement relations together with compatibility conditions or the displacement-stress relations derived by the integrated force method of structural analysis. Methods of eliminating the effects of singularities are suggested and illustrated numerically.

Macromolecular structure of coals. 6. Mass spectroscopic analysis of coal-derived liquids

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

Hooker, D.T.; Lucht, L.M.; Peppas, N.A.

1986-02-01

The macromolecular structure of coal networks was analyzed by depolymerizing coal samples using the Sternberg reductive alkylation and the Miyake alkylation techniques. Electron impact mass spectra showed peaks of greater abundance of 125-132, 252-260, 383-391, and 511-520 m/z ratios. Based on analysis of the patterns of the spectra, the cluster size of the cross-linked structure of bituminous coals was determined as 126-130. Various chemical species were identified.

Monitoring of Students' Interaction in Online Learning Settings by Structural Network Analysis and Indicators.

PubMed

Ammenwerth, Elske; Hackl, Werner O

2017-01-01

Learning as a constructive process works best in interaction with other learners. Support of social interaction processes is a particular challenge within online learning settings due to the spatial and temporal distribution of participants. It should thus be carefully monitored. We present structural network analysis and related indicators to analyse and visualize interaction patterns of participants in online learning settings. We validate this approach in two online courses and show how the visualization helps to monitor interaction and to identify activity profiles of learners. Structural network analysis is a feasible approach for an analysis of the intensity and direction of interaction in online learning settings.

Investigation of progressive failure robustness and alternate load paths for damage tolerant structures

NASA Astrophysics Data System (ADS)

Marhadi, Kun Saptohartyadi

Structural optimization for damage tolerance under various unforeseen damage scenarios is computationally challenging. It couples non-linear progressive failure analysis with sampling-based stochastic analysis of random damage. The goal of this research was to understand the relationship between alternate load paths available in a structure and its damage tolerance, and to use this information to develop computationally efficient methods for designing damage tolerant structures. Progressive failure of a redundant truss structure subjected to small random variability was investigated to identify features that correlate with robustness and predictability of the structure's progressive failure. The identified features were used to develop numerical surrogate measures that permit computationally efficient deterministic optimization to achieve robustness and predictability of progressive failure. Analysis of damage tolerance on designs with robust progressive failure indicated that robustness and predictability of progressive failure do not guarantee damage tolerance. Damage tolerance requires a structure to redistribute its load to alternate load paths. In order to investigate the load distribution characteristics that lead to damage tolerance in structures, designs with varying degrees of damage tolerance were generated using brute force stochastic optimization. A method based on principal component analysis was used to describe load distributions (alternate load paths) in the structures. Results indicate that a structure that can develop alternate paths is not necessarily damage tolerant. The alternate load paths must have a required minimum load capability. Robustness analysis of damage tolerant optimum designs indicates that designs are tailored to specified damage. A design Optimized under one damage specification can be sensitive to other damages not considered. Effectiveness of existing load path definitions and characterizations were investigated for continuum structures. A load path definition using a relative compliance change measure (U* field) was demonstrated to be the most useful measure of load path. This measure provides quantitative information on load path trajectories and qualitative information on the effectiveness of the load path. The use of the U* description of load paths in optimizing structures for effective load paths was investigated.

Analysis of Challenges for Management Education in India Using Total Interpretive Structural Modelling

ERIC Educational Resources Information Center

Mahajan, Ritika; Agrawal, Rajat; Sharma, Vinay; Nangia, Vinay

2016-01-01

Purpose: The purpose of this paper is to identify challenges for management education in India and explain their nature, significance and interrelations using total interpretive structural modelling (TISM), an innovative version of Warfield's interpretive structural modelling (ISM). Design/methodology/approach: The challenges have been drawn from…

Structures performance, benefit, cost-study

NASA Technical Reports Server (NTRS)

Woike, O. G.; Salemme, C.; Stearns, E.; Oritz, P.; Roberts, M. L.; Baughman, J. L.; Johnston, R. P.; Demel, H. F.; Stabrylla, R. G.; Coffinberry, G. A.

1981-01-01

New technology concepts and structural analysis development needs which could lead to improved life cycle cost for future high-bypass turbofans were studied. The NASA-GE energy efficient engine technology is used as a base to assess the concept benefits. Recommended programs are identified for attaining these generic structural and other beneficial technologies.

Identifying and Measuring Dimensions of Urban Deprivation in Montreal: An Analysis of the 1996 Census Data.

ERIC Educational Resources Information Center

Langlois, Andre; Kitchen, Peter

2001-01-01

Used 1996 Canadian census data to examine the spatial structure and intensity of urban deprivation in Montreal. Analysis of 20 indicators of urban deprivation identified 6 main types of deprivation in the city and found that they were most visible on the Island of Montreal. Urban deprivation was not confined to the inner city. (SM)

Money-center structures in dynamic banking systems

NASA Astrophysics Data System (ADS)

Li, Shouwei; Zhang, Minghui

2016-10-01

In this paper, we propose a dynamic model for banking systems based on the description of balance sheets. It generates some features identified through empirical analysis. Through simulation analysis of the model, we find that banking systems have the feature of money-center structures, that bank asset distributions are power-law distributions, and that contract size distributions are log-normal distributions.

Thermostructural analysis of a scramjet fuel-injection strut

NASA Technical Reports Server (NTRS)

Wieting, A. R.; Thornton, E. A.

1978-01-01

Results of a thermal/structural design analysis study of a fuel injection strut for an airframe integrated hydrogen cooled scramjet are presented. It is indicated that a feasible thermal/structural concept has been identified for the static load conditions and that thermal stresses dominate the response. It is suggested that the response of the concept to dynamic loads be investigated.

Extending existing structural identifiability analysis methods to mixed-effects models.

PubMed

Janzén, David L I; Jirstrand, Mats; Chappell, Michael J; Evans, Neil D

2018-01-01

The concept of structural identifiability for state-space models is expanded to cover mixed-effects state-space models. Two methods applicable for the analytical study of the structural identifiability of mixed-effects models are presented. The two methods are based on previously established techniques for non-mixed-effects models; namely the Taylor series expansion and the input-output form approach. By generating an exhaustive summary, and by assuming an infinite number of subjects, functions of random variables can be derived which in turn determine the distribution of the system's observation function(s). By considering the uniqueness of the analytical statistical moments of the derived functions of the random variables, the structural identifiability of the corresponding mixed-effects model can be determined. The two methods are applied to a set of examples of mixed-effects models to illustrate how they work in practice. Copyright © 2017 Elsevier Inc. All rights reserved.

Dynamical compensation and structural identifiability of biological models: Analysis, implications, and reconciliation

PubMed Central

2017-01-01

The concept of dynamical compensation has been recently introduced to describe the ability of a biological system to keep its output dynamics unchanged in the face of varying parameters. However, the original definition of dynamical compensation amounts to lack of structural identifiability. This is relevant if model parameters need to be estimated, as is often the case in biological modelling. Care should we taken when using an unidentifiable model to extract biological insight: the estimated values of structurally unidentifiable parameters are meaningless, and model predictions about unmeasured state variables can be wrong. Taking this into account, we explore alternative definitions of dynamical compensation that do not necessarily imply structural unidentifiability. Accordingly, we show different ways in which a model can be made identifiable while exhibiting dynamical compensation. Our analyses enable the use of the new concept of dynamical compensation in the context of parameter identification, and reconcile it with the desirable property of structural identifiability. PMID:29186132

Is scaffold hopping a reliable indicator for the ability of computational methods to identify structurally diverse active compounds?

NASA Astrophysics Data System (ADS)

Dimova, Dilyana; Bajorath, Jürgen

2017-07-01

Computational scaffold hopping aims to identify core structure replacements in active compounds. To evaluate scaffold hopping potential from a principal point of view, regardless of the computational methods that are applied, a global analysis of conventional scaffolds in analog series from compound activity classes was carried out. The majority of analog series was found to contain multiple scaffolds, thus enabling the detection of intra-series scaffold hops among closely related compounds. More than 1000 activity classes were found to contain increasing proportions of multi-scaffold analog series. Thus, using such activity classes for scaffold hopping analysis is likely to overestimate the scaffold hopping (core structure replacement) potential of computational methods, due to an abundance of artificial scaffold hops that are possible within analog series.

System review: a method for investigating medical errors in healthcare settings.

PubMed

Alexander, G L; Stone, T T

2000-01-01

System analysis is a process of evaluating objectives, resources, structure, and design of businesses. System analysis can be used by leaders to collaboratively identify breakthrough opportunities to improve system processes. In healthcare systems, system analysis can be used to review medical errors (system occurrences) that may place patients at risk for injury, disability, and/or death. This study utilizes a case management approach to identify medical errors. Utilizing an interdisciplinary approach, a System Review Team was developed to identify trends in system occurrences, facilitate communication, and enhance the quality of patient care by reducing medical errors.

Comparing direct and iterative equation solvers in a large structural analysis software system

NASA Technical Reports Server (NTRS)

Poole, E. L.

1991-01-01

Two direct Choleski equation solvers and two iterative preconditioned conjugate gradient (PCG) equation solvers used in a large structural analysis software system are described. The two direct solvers are implementations of the Choleski method for variable-band matrix storage and sparse matrix storage. The two iterative PCG solvers include the Jacobi conjugate gradient method and an incomplete Choleski conjugate gradient method. The performance of the direct and iterative solvers is compared by solving several representative structural analysis problems. Some key factors affecting the performance of the iterative solvers relative to the direct solvers are identified.

Computerized structural mechanics for 1990's: Advanced aircraft needs

NASA Technical Reports Server (NTRS)

Viswanathan, A. V.; Backman, B. F.

1989-01-01

The needs for computerized structural mechanics (CSM) as seen from the standpoint of the aircraft industry are discussed. These needs are projected into the 1990's with special focus on the new advanced materials. Preliminary design/analysis, research, and detail design/analysis are identified as major areas. The role of local/global analyses in these different areas is discussed. The lessons learned in the past are used as a basis for the design of a CSM framework that could modify and consolidate existing technology and include future developments in a rational and useful way. A philosophy is stated, and a set of analyses needs driven by the emerging advanced composites is enumerated. The roles of NASA, the universities, and the industry are identified. Finally, a set of rational research targets is recommended based on both the new types of computers and the increased complexity the industry faces. Computerized structural mechanics should be more than new methods in structural mechanics and numerical analyses. It should be a set of engineering applications software products that combines innovations in structural mechanics, numerical analysis, data processing, search and display features, and recent hardware advances and is organized in a framework that directly supports the design process.

Gas Chromatography-Tandem Mass Spectrometry of Lignin Pyrolyzates with Dopant-Assisted Atmospheric Pressure Chemical Ionization and Molecular Structure Search with CSI:FingerID

NASA Astrophysics Data System (ADS)

Larson, Evan A.; Hutchinson, Carolyn P.; Lee, Young Jin

2018-06-01

Dopant-assisted atmospheric pressure chemical ionization (dAPCI) is a soft ionization method rarely used for gas chromatography-mass spectrometry (GC-MS). The current study combines GC-dAPCI with tandem mass spectrometry (MS/MS) for analysis of a complex mixture such as lignin pyrolysis analysis. To identify the structures of volatile lignin pyrolysis products, collision-induced dissociation (CID) MS/MS using a quadrupole time-of-flight mass spectrometer (QTOFMS) and pseudo MS/MS through in-source collision-induced dissociation (ISCID) using a single stage TOFMS are utilized. To overcome the lack of MS/MS database, Compound Structure Identification (CSI):FingerID is used to interpret CID spectra and predict best matched structures from PubChem library. With this approach, a total of 59 compounds were positively identified in comparison to only 22 in NIST database search of GC-EI-MS dataset. This study demonstrates the effectiveness of GC-dAPCI-MS/MS to overcome the limitations of traditional GC-EI-MS analysis when EI-MS database is not sufficient. [Figure not available: see fulltext.

TRPC Channel Structure and Properties.

PubMed

Feng, Shengjie

2017-01-01

TRPC channels are the first identified members in the TRP family. They function as either homo- or heterotetramers regulating intracellular Ca 2+ concentration in response to numerous physiological or pathological stimuli. TRPC channels are nonselective cation channels permeable to Ca 2+ . The properties and the functional domains of TRPC channels have been identified by electrophysiological and biochemical methods. However, due to the large size, instability, and flexibility of their complexes, the structures of the members in TRPC family remain unrevealed. More efforts should be made on structure analysis and generating good tools, including specific antibodies, agonist, and antagonist.

49 CFR 236.923 - Task analysis and basic requirements.

Code of Federal Regulations, 2011 CFR

2011-10-01

... classroom, simulator, computer-based, hands-on, or other formally structured training and testing, except... for Processor-Based Signal and Train Control Systems § 236.923 Task analysis and basic requirements...) Based on a formal task analysis, identify the installation, maintenance, repair, modification...

Modeling corrosion inhibition efficacy of small organic molecules as non-toxic chromate alternatives using comparative molecular surface analysis (CoMSA).

PubMed

Fernandez, Michael; Breedon, Michael; Cole, Ivan S; Barnard, Amanda S

2016-10-01

Traditionally many structural alloys are protected by primer coatings loaded with corrosion inhibiting additives. Strontium Chromate (or other chromates) have been shown to be extremely effectively inhibitors, and find extensive use in protective primer formulations. Unfortunately, hexavalent chromium which imbues these coatings with their corrosion inhibiting properties is also highly toxic, and their use is being increasingly restricted by legislation. In this work we explore a novel tridimensional Quantitative-Structure Property Relationship (3D-QSPR) approach, comparative molecular surface analysis (CoMSA), which was developed to recognize "high-performing" corrosion inhibitor candidates from the distributions of electronegativity, polarizability and van der Waals volume on the molecular surfaces of 28 small organic molecules. Multivariate statistical analysis identified five prototypes molecules, which are capable of explaining 71% of the variance within the inhibitor data set; whilst a further five molecules were also identified as archetypes, describing 75% of data variance. All active corrosion inhibitors, at a 80% threshold, were successfully recognized by the CoMSA model with adequate specificity and precision higher than 70% and 60%, respectively. The model was also capable of identifying structural patterns, that revealed reasonable starting points for where structural changes may augment corrosion inhibition efficacy. The presented methodology can be applied to other functional molecules and extended to cover structure-activity studies in a diverse range of areas such as drug design and novel material discovery. Copyright © 2016 Elsevier Ltd. All rights reserved.

Correlations between brain structure and symptom dimensions of psychosis in schizophrenia, schizoaffective, and psychotic bipolar I disorders.

PubMed

Padmanabhan, Jaya L; Tandon, Neeraj; Haller, Chiara S; Mathew, Ian T; Eack, Shaun M; Clementz, Brett A; Pearlson, Godfrey D; Sweeney, John A; Tamminga, Carol A; Keshavan, Matcheri S

2015-01-01

Structural alterations may correlate with symptom severity in psychotic disorders, but the existing literature on this issue is heterogeneous. In addition, it is not known how cortical thickness and cortical surface area correlate with symptom dimensions of psychosis. Subjects included 455 individuals with schizophrenia, schizoaffective, or bipolar I disorders. Data were obtained as part of the Bipolar Schizophrenia Network for Intermediate Phenotypes study. Diagnosis was made through the Structured Clinical Interview for DSM-IV. Positive and negative symptom subscales were assessed using the Positive and Negative Syndrome Scale. Structural brain measurements were extracted from T1-weight structural MRIs using FreeSurfer v5.1 and were correlated with symptom subscales using partial correlations. Exploratory factor analysis was also used to identify factors among those regions correlating with symptom subscales. The positive symptom subscale correlated inversely with gray matter volume (GMV) and cortical thickness in frontal and temporal regions, whereas the negative symptom subscale correlated inversely with right frontal cortical surface area. Among regions correlating with the positive subscale, factor analysis identified four factors, including a temporal cortical thickness factor and frontal GMV factor. Among regions correlating with the negative subscale, factor analysis identified a frontal GMV-cortical surface area factor. There was no significant diagnosis by structure interactions with symptom severity. Structural measures correlate with positive and negative symptom severity in psychotic disorders. Cortical thickness demonstrated more associations with psychopathology than cortical surface area. © The Author 2014. Published by Oxford University Press on behalf of the Maryland Psychiatric Research Center. All rights reserved. For permissions, please email: journals.permissions@oup.com.

In Search of Rationality: The Purposes behind the Use of Formal Analysis in Organizations.

ERIC Educational Resources Information Center

Langley, Ann

1989-01-01

Examines how formal analysis is actually practiced in 3 different organizations. Identifies 4 main groups of purposes for formal analysis and relates them to various hierarchical relationships. Formal analysis and social interaction seem inextricably linked in organizational decision-making. Different structural configurations may generate…

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.

A network model of the interbank market

NASA Astrophysics Data System (ADS)

Li, Shouwei; He, Jianmin; Zhuang, Yaming

2010-12-01

This work introduces a network model of an interbank market based on interbank credit lending relationships. It generates some network features identified through empirical analysis. The critical issue to construct an interbank network is to decide the edges among banks, which is realized in this paper based on the interbank’s degree of trust. Through simulation analysis of the interbank network model, some typical structural features are identified in our interbank network, which are also proved to exist in real interbank networks. They are namely, a low clustering coefficient and a relatively short average path length, community structures, and a two-power-law distribution of out-degree and in-degree.

Identifying protein domains by global analysis of soluble fragment data.

PubMed

Bulloch, Esther M M; Kingston, Richard L

2014-11-15

The production and analysis of individual structural domains is a common strategy for studying large or complex proteins, which may be experimentally intractable in their full-length form. However, identifying domain boundaries is challenging if there is little structural information concerning the protein target. One experimental procedure for mapping domains is to screen a library of random protein fragments for solubility, since truncation of a domain will typically expose hydrophobic groups, leading to poor fragment solubility. We have coupled fragment solubility screening with global data analysis to develop an effective method for identifying structural domains within a protein. A gene fragment library is generated using mechanical shearing, or by uracil doping of the gene and a uracil-specific enzymatic digest. A split green fluorescent protein (GFP) assay is used to screen the corresponding protein fragments for solubility when expressed in Escherichia coli. The soluble fragment data are then analyzed using two complementary approaches. Fragmentation "hotspots" indicate possible interdomain regions. Clustering algorithms are used to group related fragments, and concomitantly predict domain location. The effectiveness of this Domain Seeking procedure is demonstrated by application to the well-characterized human protein p85α. Copyright © 2014 Elsevier Inc. All rights reserved.

Influence of pH and fuels on the combustion synthesis, structural, morphological, electrical and magnetic properties of CoFe{sub 2}O{sub 4} nanoparticles

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

Shanmugavani, A.; Selvan, R.Kalai, E-mail: selvankram@buc.edu.in; Layek, Samar

2015-11-15

Nanocrystalline spinel cobalt ferrite particles are synthesized by simple combustion method using aspartic acid and glycine as fuels. The single phase cubic structure of CoFe{sub 2}O{sub 4} is revealed through X-ray diffraction analysis (XRD). Further the Rietveld refinement confirms the formation of inverse spinel structure of CoFe{sub 2}O{sub 4}. The characteristic functional groups of Co–O and Fe–O are identified from Fourier Transform Infrared (FT-IR) analysis. Uniform distribution of of nearly spherical particles with the size range of 40–80 nm is identified through field emission scanning electron microscope (FESEM) images. The calculated DC conductivity is 1.469 × 10{sup −7} and 2.214more » × 10{sup −8} S cm{sup −1}, for CoFe{sub 2}O{sub 4} synthesized using aspartic acid and glycine, respectively. The dielectric behavior obeys the Maxwell–Wagner interfacial polarization. The ferromagnetic behavior of CoFe{sub 2}O{sub 4} is identified using VSM analysis and the calculated coercivity is 27 Oe and saturation magnetization is 68 emu/g.« less

DISTING: A web application for fast algorithmic computation of alternative indistinguishable linear compartmental models.

PubMed

Davidson, Natalie R; Godfrey, Keith R; Alquaddoomi, Faisal; Nola, David; DiStefano, Joseph J

2017-05-01

We describe and illustrate use of DISTING, a novel web application for computing alternative structurally identifiable linear compartmental models that are input-output indistinguishable from a postulated linear compartmental model. Several computer packages are available for analysing the structural identifiability of such models, but DISTING is the first to be made available for assessing indistinguishability. The computational algorithms embedded in DISTING are based on advanced versions of established geometric and algebraic properties of linear compartmental models, embedded in a user-friendly graphic model user interface. Novel computational tools greatly speed up the overall procedure. These include algorithms for Jacobian matrix reduction, submatrix rank reduction, and parallelization of candidate rank computations in symbolic matrix analysis. The application of DISTING to three postulated models with respectively two, three and four compartments is given. The 2-compartment example is used to illustrate the indistinguishability problem; the original (unidentifiable) model is found to have two structurally identifiable models that are indistinguishable from it. The 3-compartment example has three structurally identifiable indistinguishable models. It is found from DISTING that the four-compartment example has five structurally identifiable models indistinguishable from the original postulated model. This example shows that care is needed when dealing with models that have two or more compartments which are neither perturbed nor observed, because the numbering of these compartments may be arbitrary. DISTING is universally and freely available via the Internet. It is easy to use and circumvents tedious and complicated algebraic analysis previously done by hand. Copyright © 2017 Elsevier B.V. All rights reserved.

Identification and Assessment of Taiwanese Children's Conceptions of Learning Mathematics

ERIC Educational Resources Information Center

Chiu, Mei-Shiu

2012-01-01

The aim of the present study was to identify children's conceptions of learning mathematics and to assess the identified conceptions. Children's conceptions are identified by interviewing 73 grade 5 students in Taiwan. The interviews are analyzed using qualitative data analysis methods, which results in a structure of 5 major conceptions, each…

Identifying and Assessing Self-Images in Drawings by Delinquent Adolescents (in 2 Parts).

ERIC Educational Resources Information Center

Silver, Rawley; Ellison, JoAnne

1995-01-01

Examines assumption that art therapists can objectively identify self-images in drawings by troubled adolescents without talking to these youth. Findings suggest that discussion, though preferable, is not required for identifying self-images. Analysis of adolescents' drawings indicates that structured art assessment can be useful in evaluating…

Quantifying similarity of pore-geometry in nanoporous materials

DOE PAGES

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

2017-05-23

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

FLUT - A program for aeroelastic stability analysis. [of aircraft structures in subsonic flow

NASA Technical Reports Server (NTRS)

Johnson, E. H.

1977-01-01

A computer program (FLUT) that can be used to evaluate the aeroelastic stability of aircraft structures in subsonic flow is described. The algorithm synthesizes data from a structural vibration analysis with an unsteady aerodynamics analysis and then performs a complex eigenvalue analysis to assess the system stability. The theoretical basis of the program is discussed with special emphasis placed on some innovative techniques which improve the efficiency of the analysis. User information needed to efficiently and successfully utilize the program is provided. In addition to identifying the required input, the flow of the program execution and some possible sources of difficulty are included. The use of the program is demonstrated with a listing of the input and output for a simple example.

Stochastic subspace identification for operational modal analysis of an arch bridge

NASA Astrophysics Data System (ADS)

Loh, Chin-Hsiung; Chen, Ming-Che; Chao, Shu-Hsien

2012-04-01

In this paer the application of output-only system identification technique, known as Stochastic Subspace Identification (SSI) algorithms, for civil infrastructures is carried out. The ability of covariance driven stochastic subspace identification (SSI-COV) was proved through the analysis of the ambient data of an arch bridge under operational condition. A newly developed signal processing technique, Singular Spectrum analysis (SSA), capable to smooth noisy signals, is adopted for pre-processing the recorded data before the SSI. The conjunction of SSA and SSICOV provides a useful criterion for the system order determination. With the aim of estimating accurate modal parameters of the structure in off-line analysis, a stabilization diagram is constructed by plotting the identified poles of the system with increasing the size of data Hankel matrix. Identification task of a real structure, Guandu Bridge, is carried out to identify the system natural frequencies and mode shapes. The uncertainty of the identified model parameters from output-only measurement of the bridge under operation condition, such as temperature and traffic loading conditions, is discussed.

Principal component similarity analysis of Raman spectra to study the effects of pH, heating, and kappa-carrageenan on whey protein structure.

PubMed

Alizadeh-Pasdar, Nooshin; Nakai, Shuryo; Li-Chan, Eunice C Y

2002-10-09

Raman spectroscopy was used to elucidate structural changes of beta-lactoglobulin (BLG), whey protein isolate (WPI), and bovine serum albumin (BSA), at 15% concentration, as a function of pH (5.0, 7.0, and 9.0), heating (80 degrees C, 30 min), and presence of 0.24% kappa-carrageenan. Three data-processing techniques were used to assist in identifying significant changes in Raman spectral data. Analysis of variance showed that of 12 characteristics examined in the Raman spectra, only a few were significantly affected by pH, heating, kappa-carrageenan, and their interactions. These included amide I (1658 cm(-1)) for WPI and BLG, alpha-helix for BLG and BSA, beta-sheet for BSA, CH stretching (2880 cm(-1)) for BLG and BSA, and CH stretching (2930 cm(-1)) for BSA. Principal component analysis reduced dimensionality of the characteristics. Heating and its interaction with kappa-carrageenan were identified as the most influential in overall structure of the whey proteins, using principal component similarity analysis.

Enterprising health: creating the conditions for entrepreneurial behaviour as a strategy for effective and sustainable change in health services.

PubMed

Exton, Rosemary

2010-01-01

This paper seeks to investigate conditions under which entrepreneurs emerge as agents of effective and sustainable change in UK National Health Service Trusts. The research synthesises literature on changing regulatory structures ("post-bureaucracy") and entrepreneurial behaviour to understand how individual identity construction is informed both by context and by individual attributes. Thematic analysis of interview data involving managers from 11 NHS Trusts, including detailed analysis of six transcripts, focuses on regulatory processes, the emergence of entrepreneurial behaviour and outcome variations in workplace innovation and improvement. This study identifies co-existing modes of regulation, which interact with individual behaviour, generating strategies differentiated as entrepreneurial or conformist. Four ideal types are identified: organisational entrepreneurship, resisted or dissonant entrepreneurship, conformity, and symbolic entrepreneurship. Analysis reinforces those literature findings, which suggest that the interaction of regulatory structures and the identity work of individuals influence the emergence of entrepreneurial behaviour and the effectiveness of change. The ability to achieve effective and sustainable outcomes varies considerably even between NHS Trusts faced with comparable challenges in implementing nationally prescribed targets. This variance is explained in terms of the organisation's ability to generate the structures, processes, individual competence and motivation which enable employees at all levels to act entrepreneurially with the ability and legitimacy to achieve strategic goals by working creatively in the spaces between formal organisational structures. The study identifies specific conditions, which stimulate the emergence of entrepreneurs as agents of effective and sustainable change in the NHS, identifying factors that policymakers should consider when implementing change.

Taxonomy of Caribbean Tourism Alcohol Venues: Implications for HIV Transmission*

PubMed Central

GUILAMO-RAMOS, Vincent; JACCARD, James; MCCARTHY, Katharine; QUIÑONES, Zahira; LUSHIN, Viktor; SKINNER-DAY, Molly; PADILLA, Mark; MEISTERLIN, Leah

2013-01-01

Background Tourism areas represent ecologies of heightened HIV vulnerability characterized by a disproportionate concentration of alcohol venues. Limited research has explored how alcohol venues facilitate HIV transmission. Methods We spatially mapped locations of alcohol venues in a Dominican tourism town and conducted a venue-based survey of key informants (n=135) focused on three facets of alcohol venues: structural features, type of patrons, and HIV risk behaviors. Using latent class analysis, we identified evidence-based typologies of alcohol venues for each of the three facets. Focused contrasts identified the co-occurrence of classes of structural features, classes of types of patrons, and classes of HIV risk behavior, thus elaborating the nature of high risk venues. Results We identified three categories of venue structural features, three for venue patrons, and five for HIV risk behaviors. Analysis revealed that alcohol venues with the greatest structural risks (e.g., sex work on site with lack of HIV prevention services) were most likely frequented by the venue patron category characterized by high population-mixing between locals and foreign tourists, who were in turn most likely to engage in the riskiest behaviors. Conclusion Our results highlight the stratification of venue patrons into groups who engage in behaviors of varying risk in structural settings that vary in risk. The convergence of high-risk patron groups in alcohol venues with the greatest structural risk suggests these locations have potential for HIV transmission. Policymakers and prevention scientists can use these methods and data to target HIV prevention resources to identified priority areas. PMID:23478154

Taxonomy of Caribbean tourism alcohol venues: implications for HIV transmission.

PubMed

Guilamo-Ramos, Vincent; Jaccard, James; McCarthy, Katharine; Quiñones, Zahira; Lushin, Viktor; Skinner-Day, Molly; Padilla, Mark; Meisterlin, Leah

2013-09-01

Tourism areas represent ecologies of heightened HIV vulnerability characterized by a disproportionate concentration of alcohol venues. Limited research has explored how alcohol venues facilitate HIV transmission. We spatially mapped locations of alcohol venues in a Dominican tourism town and conducted a venue-based survey of key informants (n=135) focused on three facets of alcohol venues: structural features, type of patrons, and HIV risk behaviors. Using latent class analysis, we identified evidence-based typologies of alcohol venues for each of the three facets. Focused contrasts identified the co-occurrence of classes of structural features, classes of types of patrons, and classes of HIV risk behavior, thus elaborating the nature of high risk venues. We identified three categories of venue structural features, three for venue patrons, and five for HIV risk behaviors. Analysis revealed that alcohol venues with the greatest structural risks (e.g. sex work on-site with lack of HIV prevention services) were most likely frequented by the venue patron category characterized by high population-mixing between locals and foreign tourists, who were in turn most likely to engage in the riskiest behaviors. Our results highlight the stratification of venue patrons into groups who engage in behaviors of varying risk in structural settings that vary in risk. The convergence of high-risk patron groups in alcohol venues with the greatest structural risk suggests these locations have potential for HIV transmission. Policymakers and prevention scientists can use these methods and data to target HIV prevention resources to identified priority areas. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

A general model-based design of experiments approach to achieve practical identifiability of pharmacokinetic and pharmacodynamic models.

PubMed

Galvanin, Federico; Ballan, Carlo C; Barolo, Massimiliano; Bezzo, Fabrizio

2013-08-01

The use of pharmacokinetic (PK) and pharmacodynamic (PD) models is a common and widespread practice in the preliminary stages of drug development. However, PK-PD models may be affected by structural identifiability issues intrinsically related to their mathematical formulation. A preliminary structural identifiability analysis is usually carried out to check if the set of model parameters can be uniquely determined from experimental observations under the ideal assumptions of noise-free data and no model uncertainty. However, even for structurally identifiable models, real-life experimental conditions and model uncertainty may strongly affect the practical possibility to estimate the model parameters in a statistically sound way. A systematic procedure coupling the numerical assessment of structural identifiability with advanced model-based design of experiments formulations is presented in this paper. The objective is to propose a general approach to design experiments in an optimal way, detecting a proper set of experimental settings that ensure the practical identifiability of PK-PD models. Two simulated case studies based on in vitro bacterial growth and killing models are presented to demonstrate the applicability and generality of the methodology to tackle model identifiability issues effectively, through the design of feasible and highly informative experiments.

Structural health monitoring (vibration) as a tool for identifying structural alterations of the lumbar spine: a twin control study.

PubMed

Kawchuk, Gregory N; Hartvigsen, Jan; Edgecombe, Tiffany; Prasad, Narasimha; van Dieen, Jaap H

2016-03-11

Structural health monitoring (SHM) is an engineering technique used to identify mechanical abnormalities not readily apparent through other means. Recently, SHM has been adapted for use in biological systems, but its invasive nature limits its clinical application. As such, the purpose of this project was to determine if a non-invasive form of SHM could identify structural alterations in the spines of living human subjects. Lumbar spines of 10 twin pairs were visualized by magnetic resonance imaging then assessed by a blinded radiologist to determine whether twin pairs were structurally concordant or discordant. Vibration was then applied to each subject's spine and the resulting response recorded from sensors overlying lumbar spinous processes. The peak frequency, area under the curve and the root mean square were computed from the frequency response function of each sensor. Statistical analysis demonstrated that in twins whose structural appearance was discordant, peak frequency was significantly different between twin pairs while in concordant twins, no outcomes were significantly different. From these results, we conclude that structural changes within the spine can alter its vibration response. As such, further investigation of SHM to identify spinal abnormalities in larger human populations is warranted.

Probabilistic Structural Analysis Methods for select space propulsion system components (PSAM). Volume 3: Literature surveys and technical reports

NASA Technical Reports Server (NTRS)

1992-01-01

The technical effort and computer code developed during the first year are summarized. Several formulations for Probabilistic Finite Element Analysis (PFEA) are described with emphasis on the selected formulation. The strategies being implemented in the first-version computer code to perform linear, elastic PFEA is described. The results of a series of select Space Shuttle Main Engine (SSME) component surveys are presented. These results identify the critical components and provide the information necessary for probabilistic structural analysis.

A Comprehensive Analysis in Terms of Molecule-Intrinsic, Quasi-Atomic Orbitals. III. The Covalent Bonding Structure of Urea.

PubMed

West, Aaron C; Schmidt, Michael W; Gordon, Mark S; Ruedenberg, Klaus

2015-10-15

The analysis of molecular electron density matrices in terms of quasi-atomic orbitals, which was developed in previous investigations, is quantitatively exemplified by a detailed application to the urea molecule. The analysis is found to identify strong and weak covalent bonding interactions as well as intramolecular charge transfers. It yields a qualitative as well as quantitative ab initio description of the bonding structure of this molecule, which raises questions regarding some traditional rationalizations.

Proteomic analysis reveals diverse proline hydroxylation-mediated oxygen-sensing cellular pathways in cancer cells

PubMed Central

Liu, Bing; Gao, Yankun; Ruan, Hai-Bin; Chen, Yue

2016-01-01

Proline hydroxylation is a critical cellular mechanism regulating oxygen-response pathways in tumor initiation and progression. Yet, its substrate diversity and functions remain largely unknown. Here, we report a system-wide analysis to characterize proline hydroxylation substrates in cancer cells using an immunoaffinity-purification assisted proteomics strategy. We identified 562 sites from 272 proteins in HeLa cells. Bioinformatic analysis revealed that proline hydroxylation substrates are significantly enriched with mRNA processing and stress-response cellular pathways with canonical and diverse flanking sequence motifs. Structural analysis indicates a significant enrichment of proline hydroxylation participating in the secondary structure of substrate proteins. Our study identified and validated Brd4, a key transcription factor, as a novel proline hydroxylation substrate. Functional analysis showed that the inhibition of proline hydroxylation pathway significantly reduced the proline hydroxylation abundance on Brd4 and affected Brd4-mediated transcriptional activity as well as cell proliferation in AML leukemia cells. Taken together, our study identified a broad regulatory role of proline hydroxylation in cellular oxygen-sensing pathways and revealed potentially new targets that dynamically respond to hypoxia microenvironment in tumor cells. PMID:27764789

Multivariate Analysis of Two-Dimensional 1H, 13C Methyl NMR Spectra of Monoclonal Antibody Therapeutics To Facilitate Assessment of Higher Order Structure.

PubMed

Arbogast, Luke W; Delaglio, Frank; Schiel, John E; Marino, John P

2017-11-07

Two-dimensional (2D) 1 H- 13 C methyl NMR provides a powerful tool to probe the higher order structure (HOS) of monoclonal antibodies (mAbs), since spectra can readily be acquired on intact mAbs at natural isotopic abundance, and small changes in chemical environment and structure give rise to observable changes in corresponding spectra, which can be interpreted at atomic resolution. This makes it possible to apply 2D NMR spectral fingerprinting approaches directly to drug products in order to systematically characterize structure and excipient effects. Systematic collections of NMR spectra are often analyzed in terms of the changes in specifically identified peak positions, as well as changes in peak height and line widths. A complementary approach is to apply principal component analysis (PCA) directly to the matrix of spectral data, correlating spectra according to similarities and differences in their overall shapes, rather than according to parameters of individually identified peaks. This is particularly well-suited for spectra of mAbs, where some of the individual peaks might not be well resolved. Here we demonstrate the performance of the PCA method for discriminating structural variation among systematic sets of 2D NMR fingerprint spectra using the NISTmAb and illustrate how spectral variability identified by PCA may be correlated to structure.

A spatial cluster analysis of tractor overturns in Kentucky from 1960 to 2002

USGS Publications Warehouse

Saman, D.M.; Cole, H.P.; Odoi, A.; Myers, M.L.; Carey, D.I.; Westneat, S.C.

2012-01-01

Background: Agricultural tractor overturns without rollover protective structures are the leading cause of farm fatalities in the United States. To our knowledge, no studies have incorporated the spatial scan statistic in identifying high-risk areas for tractor overturns. The aim of this study was to determine whether tractor overturns cluster in certain parts of Kentucky and identify factors associated with tractor overturns. Methods: A spatial statistical analysis using Kulldorff's spatial scan statistic was performed to identify county clusters at greatest risk for tractor overturns. A regression analysis was then performed to identify factors associated with tractor overturns. Results: The spatial analysis revealed a cluster of higher than expected tractor overturns in four counties in northern Kentucky (RR = 2.55) and 10 counties in eastern Kentucky (RR = 1.97). Higher rates of tractor overturns were associated with steeper average percent slope of pasture land by county (p = 0.0002) and a greater percent of total tractors with less than 40 horsepower by county (p<0.0001). Conclusions: This study reveals that geographic hotspots of tractor overturns exist in Kentucky and identifies factors associated with overturns. This study provides policymakers a guide to targeted county-level interventions (e.g., roll-over protective structures promotion interventions) with the intention of reducing tractor overturns in the highest risk counties in Kentucky. ?? 2012 Saman et al.

Synthesis and structure identification of 2-amino-4, 6- dimethyl pyrimidine with gallic acid and pimelic acid

NASA Astrophysics Data System (ADS)

Mekala, R.; Jagdish, P.; Mathammal, R.

2018-07-01

Reaction of 2-amino-4, 6- dimethyl pyrimidine with carboxylic acid such as gallic acid and pimelic acid, yielded a salt and co-crystal, respectively. The new crystal forms were obtained from slow evaporation technique. The crystal structure and hydrogen bond interaction of the two crystals were determined by single X-ray diffraction analysis. Inter molecular interactions of the compounds were investigated using the 3D Hirshfeld surfaces and the associated 2D fingerprint plots. The functional groups were identified by the FTIR, FT-Raman spectral studies. The presence of carbon and hydrogen in the two samples were identified by the 1H and 13C NMR analysis. The excited energy was observed using UV-Visible spectral analysis. The fluorescence spectra revealed the emission state of the two samples. The thermal behaviour and stability of the two compounds were evaluated by the TGA-DSC analysis.

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.

Distribution of resistive and conductive structures in Nankai accretionary wedge reveals contrasting stress paths

NASA Astrophysics Data System (ADS)

Conin, Marianne; Bourlange, Sylvain; Henry, Pierre; Boiselet, Aurelien; Gaillot, Philippe

2014-01-01

In this article, we study the characteristics and spatial distribution of the deformation structures along the Kumano transect of the Nankai accretionary wedge, and use this information to interpret the stress path followed by the sediments. Deformation structures are identified from logging while drilling (LWD) resistivity images of the materials surrounding the drill hole and from 3-dimensional X-ray CT-images of cores acquired during the IODP NanTroSEIZE project. The relative resistivity of the structures identified on logs and the strike, dip, and density of structures identified on CT scan images are measured. The analysis of dip and strike of structures indicates that most of the resistive structures identified on logging data correspond to compactive shear bands. Results also indicate that conductive structures predominate at the toe of the prism and above the main out of sequence thrust, in locations where past and recent erosion occurred. We propose several mechanisms that could explain the relation between erosion and the absence of compactive shear bands. We conclude that sediments followed different stress paths depending on their location within the wedge, and that those differences explain the distribution of deformation structures within the wedge. We also show the coexistence of dilatant and compactant structures in fault zones including the frontal thrust and mega splay fault, and we interpret the coexistence of these structures as a possible consequence of a transient fluid pressure.

Moving Toward Improved Acquisition Outcomes: The Interrelationships Between Culture, Commitment, and Leadership

DTIC Science & Technology

2011-04-01

structure modeling . Psychological Methods, 1, 130–149. Mowday, R. T., Porter , L. W., & Steers, R. M. (1982). Organizational linkages: The psychology of...Leadership, Structural Equation Modeling , Analysis of Moment Structures (AMOS), Organizational Productivity MOVING TOWARD IMPROVED ACQUISITION OUTCOMES...greater than the sum of their individual elements. A conceptual model was identified and used as the foundation for building hypotheses. Structural

Advanced Technology Composite Fuselage-Structural Performance

NASA Technical Reports Server (NTRS)

Walker, T. H.; Minguet, P. J.; Flynn, B. W.; Carbery, D. J.; Swanson, G. D.; Ilcewicz, L. B.

1997-01-01

Boeing is studying the technologies associated with the application of composite materials to commercial transport fuselage structure under the NASA-sponsored contracts for Advanced Technology Composite Aircraft Structures (ATCAS) and Materials Development Omnibus Contract (MDOC). This report addresses the program activities related to structural performance of the selected concepts, including both the design development and subsequent detailed evaluation. Design criteria were developed to ensure compliance with regulatory requirements and typical company objectives. Accurate analysis methods were selected and/or developed where practical, and conservative approaches were used where significant approximations were necessary. Design sizing activities supported subsequent development by providing representative design configurations for structural evaluation and by identifying the critical performance issues. Significant program efforts were directed towards assessing structural performance predictive capability. The structural database collected to perform this assessment was intimately linked to the manufacturing scale-up activities to ensure inclusion of manufacturing-induced performance traits. Mechanical tests were conducted to support the development and critical evaluation of analysis methods addressing internal loads, stability, ultimate strength, attachment and splice strength, and damage tolerance. Unresolved aspects of these performance issues were identified as part of the assessments, providing direction for future development.

Sc20C60: a volleyballene

NASA Astrophysics Data System (ADS)

Wang, Jing; Ma, Hong-Man; Liu, Ying

2016-06-01

An exceptionally stable hollow cage containing 20 scandium atoms and 60 carbon atoms has been identified. This Sc20C60 molecular cluster has a Th point group symmetry and a volleyball-like shape that we refer to below as ``Volleyballene''. Electronic structure analysis shows that the formation of delocalized π bonds between Sc atoms and the neighboring pentagonal rings made of carbon atoms is crucial for stabilizing the cage structure. A relatively large HOMO-LUMO gap (~1.4 eV) was found. The results of vibrational frequency analysis and molecular dynamics simulations both demonstrate that this Volleyballene molecule is exceptionally stable.An exceptionally stable hollow cage containing 20 scandium atoms and 60 carbon atoms has been identified. This Sc20C60 molecular cluster has a Th point group symmetry and a volleyball-like shape that we refer to below as ``Volleyballene''. Electronic structure analysis shows that the formation of delocalized π bonds between Sc atoms and the neighboring pentagonal rings made of carbon atoms is crucial for stabilizing the cage structure. A relatively large HOMO-LUMO gap (~1.4 eV) was found. The results of vibrational frequency analysis and molecular dynamics simulations both demonstrate that this Volleyballene molecule is exceptionally stable. Electronic supplementary information (ESI) available: Sc20C60: a Volleyballene_SI. See DOI: 10.1039/c5nr07784b

Exaggeration and suppression of iridescence: the evolution of two-dimensional butterfly structural colours

PubMed Central

Wickham, Shelley; Large, Maryanne C.J; Poladian, Leon; Jermiin, Lars S

2005-01-01

Many butterfly species possess ‘structural’ colour, where colour is due to optical microstructures found in the wing scales. A number of such structures have been identified in butterfly scales, including three variations on a simple multi-layer structure. In this study, we optically characterize examples of all three types of multi-layer structure, as found in 10 species. The optical mechanism of the suppression and exaggeration of the angle-dependent optical properties (iridescence) of these structures is described. In addition, we consider the phylogeny of the butterflies, and are thus able to relate the optical properties of the structures to their evolutionary development. By applying two different types of analysis, the mechanism of adaptation is addressed. A simple parsimony analysis, in which all evolutionary changes are given an equal weighting, suggests convergent evolution of one structure. A Dollo parsimony analysis, in which the evolutionary ‘cost’ of losing a structure is less than that of gaining it, implies that ‘latent’ structures can be reused. PMID:16849221

A GIS approach to identifying the distribution and structure of coast redwood across its range

Treesearch

Peter Cowan; Emily E. Burns; Richard Campbell

2017-01-01

To better understand the distribution and current structure of coast redwood (Sequoia sempervirens (D.Don) Endl.) forests throughout the range and how it varies by land ownerships, the Save the Redwoods League has conducted a redwood specific analysis of a high resolution forest structure database encompassing the entire natural coast redwood range...

CSI 3.0: a web server for identifying secondary and super-secondary structure in proteins using NMR chemical shifts

PubMed Central

Hafsa, Noor E.; Arndt, David; Wishart, David S.

2015-01-01

The Chemical Shift Index or CSI 3.0 (http://csi3.wishartlab.com) is a web server designed to accurately identify the location of secondary and super-secondary structures in protein chains using only nuclear magnetic resonance (NMR) backbone chemical shifts and their corresponding protein sequence data. Unlike earlier versions of CSI, which only identified three types of secondary structure (helix, β-strand and coil), CSI 3.0 now identifies total of 11 types of secondary and super-secondary structures, including helices, β-strands, coil regions, five common β-turns (type I, II, I′, II′ and VIII), β hairpins as well as interior and edge β-strands. CSI 3.0 accepts experimental NMR chemical shift data in multiple formats (NMR Star 2.1, NMR Star 3.1 and SHIFTY) and generates colorful CSI plots (bar graphs) and secondary/super-secondary structure assignments. The output can be readily used as constraints for structure determination and refinement or the images may be used for presentations and publications. CSI 3.0 uses a pipeline of several well-tested, previously published programs to identify the secondary and super-secondary structures in protein chains. Comparisons with secondary and super-secondary structure assignments made via standard coordinate analysis programs such as DSSP, STRIDE and VADAR on high-resolution protein structures solved by X-ray and NMR show >90% agreement between those made with CSI 3.0. PMID:25979265

Hekate: Software Suite for the Mass Spectrometric Analysis and Three-Dimensional Visualization of Cross-Linked Protein Samples

PubMed Central

2013-01-01

Chemical cross-linking of proteins combined with mass spectrometry provides an attractive and novel method for the analysis of native protein structures and protein complexes. Analysis of the data however is complex. Only a small number of cross-linked peptides are produced during sample preparation and must be identified against a background of more abundant native peptides. To facilitate the search and identification of cross-linked peptides, we have developed a novel software suite, named Hekate. Hekate is a suite of tools that address the challenges involved in analyzing protein cross-linking experiments when combined with mass spectrometry. The software is an integrated pipeline for the automation of the data analysis workflow and provides a novel scoring system based on principles of linear peptide analysis. In addition, it provides a tool for the visualization of identified cross-links using three-dimensional models, which is particularly useful when combining chemical cross-linking with other structural techniques. Hekate was validated by the comparative analysis of cytochrome c (bovine heart) against previously reported data.1 Further validation was carried out on known structural elements of DNA polymerase III, the catalytic α-subunit of the Escherichia coli DNA replisome along with new insight into the previously uncharacterized C-terminal domain of the protein. PMID:24010795

Electrochemical Characterization of Carbon Nanotubes for Fuel Cell MEA's

NASA Technical Reports Server (NTRS)

Panagaris, Jael; Loyselle, Patricia

2004-01-01

Single-walled and multi-walled carbon nanotubes from different sources have been evaluated before and after sonication to identify structural differences and evaluate electrochemical performance. Raman spectral analysis and cyclic voltammetry in situ with QCM were the principle means of evaluating the tubes. The raman data indicates that sonication in toluene modifies the structural properties of the nanotubes. Sonication also affects the electrochemical performance of single-walled nanotubes and the multi-walled tubes differently. The characterization of different types of carbon nanotubes leads up to identifying a potential candidate for incorporating carbon nanotubes for fuel cell MEA structures.

Pharmacophore modeling, docking, and principal component analysis based clustering: combined computer-assisted approaches to identify new inhibitors of the human rhinovirus coat protein.

PubMed

Steindl, Theodora M; Crump, Carolyn E; Hayden, Frederick G; Langer, Thierry

2005-10-06

The development and application of a sophisticated virtual screening and selection protocol to identify potential, novel inhibitors of the human rhinovirus coat protein employing various computer-assisted strategies are described. A large commercially available database of compounds was screened using a highly selective, structure-based pharmacophore model generated with the program Catalyst. A docking study and a principal component analysis were carried out within the software package Cerius and served to validate and further refine the obtained results. These combined efforts led to the selection of six candidate structures, for which in vitro anti-rhinoviral activity could be shown in a biological assay.

One Hundred False-Positive Amphetamine Specimens Characterized by Liquid Chromatography Time-of-Flight Mass Spectrometry.

PubMed

Marin, Stephanie J; Doyle, Kelly; Chang, Annie; Concheiro-Guisan, Marta; Huestis, Marilyn A; Johnson-Davis, Kamisha L

2016-01-01

Some amphetamine (AMP) and ecstacy (MDMA) urine immunoassay (IA) kits are prone to false-positive results due to poor specificity of the antibody. We employed two techniques, high-resolution mass spectrometry (HRMS) and an in silico structure search, to identify compounds likely to cause false-positive results. Hundred false-positive IA specimens for AMP and/or MDMA were analyzed by an Agilent 6230 time-of-flight (TOF) mass spectrometer. Separately, SciFinder (Chemical Abstracts) was used as an in silico structure search to generate a library of compounds that are known to cross-react with AMP/MDMA IAs. Chemical formulas and exact masses of 145 structures were then compared against masses identified by TOF. Compounds known to have cross-reactivity with the IAs were identified in the structure-based search. The chemical formulas and exact masses of 145 structures (of 20 chemical formulas) were compared against masses identified by TOF. Urine analysis by HRMS correlates accurate mass with chemical formulae, but provides little information regarding compound structure. Structural data of targeted antigens can be utilized to correlate HRMS-derived chemical formulas with structural analogs. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Dissecting the Genetic Basis for Seed Coat Mucilage Heteroxylan Biosynthesis in Plantago ovata Using Gamma Irradiation and Infrared Spectroscopy

PubMed Central

Tucker, Matthew R.; Ma, Chao; Phan, Jana; Neumann, Kylie; Shirley, Neil J.; Hahn, Michael G.; Cozzolino, Daniel; Burton, Rachel A.

2017-01-01

Seeds from the myxospermous species Plantago ovata release a polysaccharide-rich mucilage upon contact with water. This seed coat derived mucilage is composed predominantly of heteroxylan (HX) and is utilized as a gluten-free dietary fiber supplement to promote human colorectal health. In this study, a gamma-irradiated P. ovata population was generated and screened using histological stains and Fourier Transform Mid Infrared (FTMIR) spectroscopy to identify putative mutants showing defects in seed coat mucilage HX composition and/or structure. FTMIR analysis of dry seed revealed variation in regions of the IR spectra previously linked to xylan structure in Secale cereale (rye). Subsequent absorbance ratio and PCA multivariate analysis identified 22 putative mutant families with differences in the HX IR fingerprint region. Many of these showed distinct changes in the amount and subtle changes in structure of HX after mucilage extrusion, while 20% of the putative HX mutants identified by FTMIR showed no difference in staining patterns of extruded mucilage compared to wild-type. Transcriptional screening analysis of two putative reduced xylan in mucilage (rxm) mutants, rxm1 and rxm3, revealed that changes in HX levels in rxm1 correlate with reduced transcription of known and novel genes associated with xylan synthesis, possibly indicative of specific co-regulatory units within the xylan biosynthetic pathway. These results confirm that FTMIR is a suitable method for identifying putative mutants with altered mucilage HX composition in P. ovata, and therefore forms a resource to identify novel genes involved in xylan biosynthesis. PMID:28377777

Using argument notation to engineer biological simulations with increased confidence

PubMed Central

Alden, Kieran; Andrews, Paul S.; Polack, Fiona A. C.; Veiga-Fernandes, Henrique; Coles, Mark C.; Timmis, Jon

2015-01-01

The application of computational and mathematical modelling to explore the mechanics of biological systems is becoming prevalent. To significantly impact biological research, notably in developing novel therapeutics, it is critical that the model adequately represents the captured system. Confidence in adopting in silico approaches can be improved by applying a structured argumentation approach, alongside model development and results analysis. We propose an approach based on argumentation from safety-critical systems engineering, where a system is subjected to a stringent analysis of compliance against identified criteria. We show its use in examining the biological information upon which a model is based, identifying model strengths, highlighting areas requiring additional biological experimentation and providing documentation to support model publication. We demonstrate our use of structured argumentation in the development of a model of lymphoid tissue formation, specifically Peyer's Patches. The argumentation structure is captured using Artoo (www.york.ac.uk/ycil/software/artoo), our Web-based tool for constructing fitness-for-purpose arguments, using a notation based on the safety-critical goal structuring notation. We show how argumentation helps in making the design and structured analysis of a model transparent, capturing the reasoning behind the inclusion or exclusion of each biological feature and recording assumptions, as well as pointing to evidence supporting model-derived conclusions. PMID:25589574

Using argument notation to engineer biological simulations with increased confidence.

PubMed

Alden, Kieran; Andrews, Paul S; Polack, Fiona A C; Veiga-Fernandes, Henrique; Coles, Mark C; Timmis, Jon

2015-03-06

The application of computational and mathematical modelling to explore the mechanics of biological systems is becoming prevalent. To significantly impact biological research, notably in developing novel therapeutics, it is critical that the model adequately represents the captured system. Confidence in adopting in silico approaches can be improved by applying a structured argumentation approach, alongside model development and results analysis. We propose an approach based on argumentation from safety-critical systems engineering, where a system is subjected to a stringent analysis of compliance against identified criteria. We show its use in examining the biological information upon which a model is based, identifying model strengths, highlighting areas requiring additional biological experimentation and providing documentation to support model publication. We demonstrate our use of structured argumentation in the development of a model of lymphoid tissue formation, specifically Peyer's Patches. The argumentation structure is captured using Artoo (www.york.ac.uk/ycil/software/artoo), our Web-based tool for constructing fitness-for-purpose arguments, using a notation based on the safety-critical goal structuring notation. We show how argumentation helps in making the design and structured analysis of a model transparent, capturing the reasoning behind the inclusion or exclusion of each biological feature and recording assumptions, as well as pointing to evidence supporting model-derived conclusions.

Molecular Diversity and Population Structure of a Worldwide Collection of Cultivated Tetraploid Alfalfa (Medicago sativa subsp. sativa L.) Germplasm as Revealed by Microsatellite Markers.

PubMed

Qiang, Haiping; Chen, Zhihong; Zhang, Zhengli; Wang, Xuemin; Gao, Hongwen; Wang, Zan

2015-01-01

Information on genetic diversity and population structure of a tetraploid alfalfa collection might be valuable in effective use of the genetic resources. A set of 336 worldwide genotypes of tetraploid alfalfa (Medicago sativa subsp. sativa L.) was genotyped using 85 genome-wide distributed SSR markers to reveal the genetic diversity and population structure in the alfalfa. Genetic diversity analysis identified a total of 1056 alleles across 85 marker loci. The average expected heterozygosity and polymorphism information content values were 0.677 and 0.638, respectively, showing high levels of genetic diversity in the cultivated tetraploid alfalfa germplasm. Comparison of genetic characteristics across chromosomes indicated regions of chromosomes 2 and 3 had the highest genetic diversity. A higher genetic diversity was detected in alfalfa landraces than that of wild materials and cultivars. Two populations were identified by the model-based population structure, principal coordinate and neighbor-joining analyses, corresponding to China and other parts of the world. However, lack of strictly correlation between clustering and geographic origins suggested extensive germplasm exchanges of alfalfa germplasm across diverse geographic regions. The quantitative analysis of the genetic diversity and population structure in this study could be useful for genetic and genomic analysis and utilization of the genetic variation in alfalfa breeding.

Immunoinformatic Analysis of Crimean Congo Hemorrhagic Fever Virus Glycoproteins and Epitope Prediction for Synthetic Peptide Vaccine.

PubMed

Tipu, Hamid Nawaz

2016-02-01

To determine the Crimean Congo Hemorrhagic Fever (CCHF) virus M segement glycoprotein's immunoinformatic parameters, and identify Human Leukocyte Antigen (HLA) class I binders as candidates for synthetic peptide vaccines. Cross-sectional study. Combined Military Hospital, Khuzdar Cantt, in May 2015. Data acquisition, antigenicity prediction, secondary and tertiary structure prediction, residue analysis were done using immunoinformatics tools. HLAclass I binders in glycoprotein's sequence were identified at nanomer length using NetMHC 3.4 and mapped onto tertiary structure. Docking was done for strongest binder against its corresponding allele with CABS-dock. HLAA*0101, 0201, 0301, 2402, 2601 and B*0702, 0801, 2705, 3901, 4001, 5801, 1501 were analyzed against two glycoprotein components of the virus. Atotal of 35 nanomers from GP1, and 3 from GP2 were identified. HLAB*0702 bound maximum number of peptides (6), while HLAB*4001 showed strongest binding affinity. HLAspecific glycoproteins epitope prediction can help identify synthetic peptide vaccine candidates.

Covariant Evolutionary Event Analysis for Base Interaction Prediction Using a Relational Database Management System for RNA.

PubMed

Xu, Weijia; Ozer, Stuart; Gutell, Robin R

2009-01-01

With an increasingly large amount of sequences properly aligned, comparative sequence analysis can accurately identify not only common structures formed by standard base pairing but also new types of structural elements and constraints. However, traditional methods are too computationally expensive to perform well on large scale alignment and less effective with the sequences from diversified phylogenetic classifications. We propose a new approach that utilizes coevolutional rates among pairs of nucleotide positions using phylogenetic and evolutionary relationships of the organisms of aligned sequences. With a novel data schema to manage relevant information within a relational database, our method, implemented with a Microsoft SQL Server 2005, showed 90% sensitivity in identifying base pair interactions among 16S ribosomal RNA sequences from Bacteria, at a scale 40 times bigger and 50% better sensitivity than a previous study. The results also indicated covariation signals for a few sets of cross-strand base stacking pairs in secondary structure helices, and other subtle constraints in the RNA structure.

Covariant Evolutionary Event Analysis for Base Interaction Prediction Using a Relational Database Management System for RNA

PubMed Central

Xu, Weijia; Ozer, Stuart; Gutell, Robin R.

2010-01-01

With an increasingly large amount of sequences properly aligned, comparative sequence analysis can accurately identify not only common structures formed by standard base pairing but also new types of structural elements and constraints. However, traditional methods are too computationally expensive to perform well on large scale alignment and less effective with the sequences from diversified phylogenetic classifications. We propose a new approach that utilizes coevolutional rates among pairs of nucleotide positions using phylogenetic and evolutionary relationships of the organisms of aligned sequences. With a novel data schema to manage relevant information within a relational database, our method, implemented with a Microsoft SQL Server 2005, showed 90% sensitivity in identifying base pair interactions among 16S ribosomal RNA sequences from Bacteria, at a scale 40 times bigger and 50% better sensitivity than a previous study. The results also indicated covariation signals for a few sets of cross-strand base stacking pairs in secondary structure helices, and other subtle constraints in the RNA structure. PMID:20502534

Preconditioned conjugate gradient technique for the analysis of symmetric anisotropic structures

NASA Technical Reports Server (NTRS)

Noor, Ahmed K.; Peters, Jeanne M.

1987-01-01

An efficient preconditioned conjugate gradient (PCG) technique and a computational procedure are presented for the analysis of symmetric anisotropic structures. The technique is based on selecting the preconditioning matrix as the orthotropic part of the global stiffness matrix of the structure, with all the nonorthotropic terms set equal to zero. This particular choice of the preconditioning matrix results in reducing the size of the analysis model of the anisotropic structure to that of the corresponding orthotropic structure. The similarities between the proposed PCG technique and a reduction technique previously presented by the authors are identified and exploited to generate from the PCG technique direct measures for the sensitivity of the different response quantities to the nonorthotropic (anisotropic) material coefficients of the structure. The effectiveness of the PCG technique is demonstrated by means of a numerical example of an anisotropic cylindrical panel.

Benefits of Matching Domain Structure for Planning Software: The Right Stuff

NASA Technical Reports Server (NTRS)

Billman, Dorrit Owen; Arsintescu, Lucica; Feary, Michael S.; Lee, Jessica Chia-Rong; Smith, Asha Halima; Tiwary, Rachna

2011-01-01

We investigated the role of domain structure in software design. We compared 2 planning applications, for a Mission Control group (International Space Station), and measured users speed and accuracy. Based on our needs analysis, we identified domain structure and used this to develop new prototype software that matched domain structure better than the legacy system. We took a high-fidelity analog of the natural task into the laboratory and found (large) periformance differences, favoring the system that matched domain structure. Our task design enabled us to attribute better periormance to better match of domain structure. We ran through the whole development cycle, in miniature, from needs analysis through design, development, and evaluation. Doing so enabled inferences not just about the particular systems compared, but also provided evidence for the viability of the design process (particularly needs analysis) that we are exploring.

Accurate Identification of Unknown and Known Metabolic Mixture Components by Combining 3D NMR with Fourier Transform Ion Cyclotron Resonance Tandem Mass Spectrometry.

PubMed

Wang, Cheng; He, Lidong; Li, Da-Wei; Bruschweiler-Li, Lei; Marshall, Alan G; Brüschweiler, Rafael

2017-10-06

Metabolite identification in metabolomics samples is a key step that critically impacts downstream analysis. We recently introduced the SUMMIT NMR/mass spectrometry (MS) hybrid approach for the identification of the molecular structure of unknown metabolites based on the combination of NMR, MS, and combinatorial cheminformatics. Here, we demonstrate the feasibility of the approach for an untargeted analysis of both a model mixture and E. coli cell lysate based on 2D/3D NMR experiments in combination with Fourier transform ion cyclotron resonance MS and MS/MS data. For 19 of the 25 model metabolites, SUMMIT yielded complete structures that matched those in the mixture independent of database information. Of those, seven top-ranked structures matched those in the mixture, and four of those were further validated by positive ion MS/MS. For five metabolites, not part of the 19 metabolites, correct molecular structural motifs could be identified. For E. coli, SUMMIT MS/NMR identified 20 previously known metabolites with three or more 1 H spins independent of database information. Moreover, for 15 unknown metabolites, molecular structural fragments were determined consistent with their spin systems and chemical shifts. By providing structural information for entire metabolites or molecular fragments, SUMMIT MS/NMR greatly assists the targeted or untargeted analysis of complex mixtures of unknown compounds.

Genetic diversity, linkage disequilibrium, population structure and construction of a core collection of Prunus avium L. landraces and bred cultivars.

PubMed

Campoy, José Antonio; Lerigoleur-Balsemin, Emilie; Christmann, Hélène; Beauvieux, Rémi; Girollet, Nabil; Quero-García, José; Dirlewanger, Elisabeth; Barreneche, Teresa

2016-02-24

Depiction of the genetic diversity, linkage disequilibrium (LD) and population structure is essential for the efficient organization and exploitation of genetic resources. The objectives of this study were to (i) to evaluate the genetic diversity and to detect the patterns of LD, (ii) to estimate the levels of population structure and (iii) to identify a 'core collection' suitable for association genetic studies in sweet cherry. A total of 210 genotypes including modern cultivars and landraces from 16 countries were genotyped using the RosBREED cherry 6 K SNP array v1. Two groups, mainly bred cultivars and landraces, respectively, were first detected using STRUCTURE software and confirmed by Principal Coordinate Analysis (PCoA). Further analyses identified nine subgroups using STRUCTURE and Discriminant Analysis of Principal Components (DAPC). Several sub-groups correspond to different eco-geographic regions of landraces distribution. Linkage disequilibrium was evaluated showing lower values than in peach, the reference Prunus species. A 'core collection' containing 156 accessions was selected using the maximum length sub tree method. The present study constitutes the first population genetics analysis in cultivated sweet cherry using a medium-density SNP (single nucleotide polymorphism) marker array. We provided estimations of linkage disequilibrium, genetic structure and the definition of a first INRA's Sweet Cherry core collection useful for breeding programs, germplasm management and association genetics studies.

Likelihood analysis of spatial capture-recapture models for stratified or class structured populations

USGS Publications Warehouse

Royle, J. Andrew; Sutherland, Christopher S.; Fuller, Angela K.; Sun, Catherine C.

2015-01-01

We develop a likelihood analysis framework for fitting spatial capture-recapture (SCR) models to data collected on class structured or stratified populations. Our interest is motivated by the necessity of accommodating the problem of missing observations of individual class membership. This is particularly problematic in SCR data arising from DNA analysis of scat, hair or other material, which frequently yields individual identity but fails to identify the sex. Moreover, this can represent a large fraction of the data and, given the typically small sample sizes of many capture-recapture studies based on DNA information, utilization of the data with missing sex information is necessary. We develop the class structured likelihood for the case of missing covariate values, and then we address the scaling of the likelihood so that models with and without class structured parameters can be formally compared regardless of missing values. We apply our class structured model to black bear data collected in New York in which sex could be determined for only 62 of 169 uniquely identified individuals. The models containing sex-specificity of both the intercept of the SCR encounter probability model and the distance coefficient, and including a behavioral response are strongly favored by log-likelihood. Estimated population sex ratio is strongly influenced by sex structure in model parameters illustrating the importance of rigorous modeling of sex differences in capture-recapture models.

Pleomorphic Structures in Human Blood Are Red Blood Cell-Derived Microparticles, Not Bacteria.

PubMed

Mitchell, Adam J; Gray, Warren D; Schroeder, Max; Yi, Hong; Taylor, Jeannette V; Dillard, Rebecca S; Ke, Zunlong; Wright, Elizabeth R; Stephens, David; Roback, John D; Searles, Charles D

2016-01-01

Red blood cell (RBC) transfusions are a common, life-saving therapy for many patients, but they have also been associated with poor clinical outcomes. We identified unusual, pleomorphic structures in human RBC transfusion units by negative-stain electron microscopy that appeared identical to those previously reported to be bacteria in healthy human blood samples. The presence of viable, replicating bacteria in stored blood could explain poor outcomes in transfusion recipients and have major implications for transfusion medicine. Here, we investigated the possibility that these structures were bacteria. Flow cytometry, miRNA analysis, protein analysis, and additional electron microscopy studies strongly indicated that the pleomorphic structures in the supernatant of stored RBCs were RBC-derived microparticles (RMPs). Bacterial 16S rDNA PCR amplified from these samples were sequenced and was found to be highly similar to species that are known to commonly contaminate laboratory reagents. These studies suggest that pleomorphic structures identified in human blood are RMPs and not bacteria, and they provide an example in which laboratory contaminants may can mislead investigators.

Structure-Based Annotation of a Novel Sugar Isomerase from the Pathogenic E. coli O157:H7

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

van Staalduinen, L.; Park, C; Yeom, S

2010-01-01

Prokaryotes can use a variety of sugars as carbon sources in order to provide a selective survival advantage. The gene z5688 found in the pathogenic Escherichia coli O157:H7 encodes a 'hypothetical' protein of unknown function. Sequence analysis identified the gene product as a putative member of the cupin superfamily of proteins, but no other functional information was known. We have determined the crystal structure of the Z5688 protein at 1.6 {angstrom} resolution and identified the protein as a novel E. coli sugar isomerase (EcSI) through overall fold analysis and secondary-structure matching. Extensive substrate screening revealed that EcSI is capable ofmore » acting on D-lyxose and D-mannose. The complex structure of EcSI with fructose allowed the identification of key active-site residues, and mutagenesis confirmed their importance. The structure of EcSI also suggested a novel mechanism for substrate binding and product release in a cupin sugar isomerase. Supplementation of a nonpathogenic E. coli strain with EcSI enabled cell growth on the rare pentose d-lyxose.« less

Advances in the REDCAT software package

PubMed Central

2013-01-01

Background Residual Dipolar Couplings (RDCs) have emerged in the past two decades as an informative source of experimental restraints for the study of structure and dynamics of biological macromolecules and complexes. The REDCAT software package was previously introduced for the analysis of molecular structures using RDC data. Here we report additional features that have been included in this software package in order to expand the scope of its analyses. We first discuss the features that enhance REDCATs user-friendly nature, such as the integration of a number of analyses into one single operation and enabling convenient examination of a structural ensemble in order to identify the most suitable structure. We then describe the new features which expand the scope of RDC analyses, performing exercises that utilize both synthetic and experimental data to illustrate and evaluate different features with regard to structure refinement and structure validation. Results We establish the seamless interaction that takes place between REDCAT, VMD, and Xplor-NIH in demonstrations that utilize our newly developed REDCAT-VMD and XplorGUI interfaces. These modules enable visualization of RDC analysis results on the molecular structure displayed in VMD and refinement of structures with Xplor-NIH, respectively. We also highlight REDCAT’s Error-Analysis feature in reporting the localized fitness of a structure to RDC data, which provides a more effective means of recognizing local structural anomalies. This allows for structurally sound regions of a molecule to be identified, and for any refinement efforts to be focused solely on locally distorted regions. Conclusions The newly engineered REDCAT software package, which is available for download via the WWW from http://ifestos.cse.sc.edu, has been developed in the Object Oriented C++ environment. Our most recent enhancements to REDCAT serve to provide a more complete RDC analysis suite, while also accommodating a more user-friendly experience, and will be of great interest to the community of researchers and developers since it hides the complications of software development. PMID:24098943

UPLC-MSE Profiling of Phytoplankton Metabolites: Application to the Identification of Pigments and Structural Analysis of Metabolites in Porphyridium purpureum

PubMed Central

Juin, Camille; Bonnet, Antoine; Nicolau, Elodie; Bérard, Jean-Baptiste; Devillers, Romain; Thiéry, Valérie; Cadoret, Jean-Paul; Picot, Laurent

2015-01-01

A fast and high-resolution UPLC-MSE analysis was used to identify phytoplankton pigments in an ethanol extract of Porphyridium purpureum (Pp) devoid of phycobiliproteins. In a first step, 22 standard pigments were analyzed by UPLC-MSE to build a database including retention time and accurate masses of parent and fragment ions. Using this database, seven pigments or derivatives previously reported in Pp were unequivocally identified: β,β-carotene, chlorophyll a, zeaxanthin, chlorophyllide a, pheophorbide a, pheophytin a, and cryptoxanthin. Minor amounts of Divinyl chlorophyll a, a chemotaxonomic pigment marker for prochlorophytes, were also unequivocally identified using the database. Additional analysis of ionization and fragmentation patterns indicated the presence of ions that could correspond to hydroxylated derivatives of chlorophyll a and pheophytin a, produced during the ethanolic extraction, as well as previously described galactosyldiacylglycerols, the thylakoid coenzyme plastoquinone, and gracilamide B, a molecule previously reported in the red seaweed Gracillaria asiatica. These data point to UPLC-MSE as an efficient technique to identify phytoplankton pigments for which standards are available, and demonstrate its major interest as a complementary method for the structural elucidation of ionizable marine molecules. PMID:25913708

76 FR 72493 - ITS Joint Program Office Webinar on Alternative Organizational Structures for a Certificate...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-11-23

... over time. (This study is an institutional analysis only, not a technical analysis, and it is not... Adam Hopps at (202) 680-0091. The ITS JPO will present results from an early analysis of organizational models. This analysis will describe the functions that need to be performed by a CME; identify key...

Structural Analysis of the Redesigned Ice/Frost Ramp Bracket

NASA Technical Reports Server (NTRS)

Phillips, D. R.; Dawicke, D. S.; Gentz, S. J.; Roberts, P. W.; Raju, I. S.

2007-01-01

This paper describes the interim structural analysis of a redesigned Ice/Frost Ramp bracket for the Space Shuttle External Tank (ET). The proposed redesigned bracket consists of mounts for attachment to the ET wall, supports for the electronic/instrument cables and propellant repressurization lines that run along the ET, an upper plate, a lower plate, and complex bolted connections. The eight nominal bolted connections are considered critical in the summarized structural analysis. Each bolted connection contains a bolt, a nut, four washers, and a non-metallic spacer and block that are designed for thermal insulation. A three-dimensional (3D) finite element model of the bracket is developed using solid 10-node tetrahedral elements. The loading provided by the ET Project is used in the analysis. Because of the complexities associated with accurately modeling the bolted connections in the bracket, the analysis is performed using a global/local analysis procedure. The finite element analysis of the bracket identifies one of the eight bolted connections as having high stress concentrations. A local area of the bracket surrounding this bolted connection is extracted from the global model and used as a local model. Within the local model, the various components of the bolted connection are refined, and contact is introduced along the appropriate interfaces determined by the analysts. The deformations from the global model are applied as boundary conditions to the local model. The results from the global/local analysis show that while the stresses in the bolts are well within yield, the spacers fail due to compression. The primary objective of the interim structural analysis is to show concept viability for static thermal testing. The proposed design concept would undergo continued design optimization to address the identified analytical assumptions and concept shortcomings, assuming successful thermal testing.

Analysis of structural dynamic data from Skylab. Volume 1: Technical discussion

NASA Technical Reports Server (NTRS)

Demchak, L.; Harcrow, H.

1976-01-01

A compendium of Skylab structural dynamics analytical and test programs is presented. These programs are assessed to identify lessons learned from the structural dynamic prediction effort and to provide guidelines for future analysts and program managers of complex spacecraft systems. It is a synopsis of the structural dynamic effort performed under the Skylab Integration contract and specifically covers the development, utilization, and correlation of Skylab Dynamic Orbital Models.

Structural, functional and evolutionary characterization of major drought transcription factors families in maize

NASA Astrophysics Data System (ADS)

Mittal, Shikha; Banduni, Pooja; Mallikarjuna, Mallana G.; Rao, Atmakuri R.; Jain, Prashant A.; Dash, Prasanta K.; Thirunavukkarasu, Nepolean

2018-05-01

Drought is one of the major threats to maize production. In order to improve the production and to breed tolerant hybrids, understanding the genes and regulatory mechanisms during drought stress is important. Transcription factors (TFs) play a major role in gene regulation and many TFs have been identified in response to drought stress. In our experiment, a set of 15 major TF families comprising 1436 genes was structurally and functionally characterized using in-silico tools and a gene expression assay. All 1436 genes were mapped on 10 chromosome of maize. The functional annotation indicated the involvement of these genes in ABA signaling, ROS scavenging, photosynthesis, stomatal regulation, and sucrose metabolism. Duplication was identified as the primary force in divergence and expansion of TF families. Phylogenetic relationship was developed individually for each TF family as well as combined TF families. Phylogenetic analysis grouped the TF family of genes into TF-specific and mixed groups. Phylogenetic analysis of genes belonging to various TF families suggested that the origin of TFs occurred in the lineage of maize evolution. Gene structure analysis revealed that more number of genes were intron-rich as compared to intronless genes. Drought-responsive CRE’s such as ABREA, ABREB, DRE1 and DRECRTCOREAT have been identified. Expression and interaction analyses identified leaf-specific bZIP TF, GRMZM2G140355, as a potential contributor toward drought tolerance in maize. We also analyzed protein-protein interaction network of 269 drought-responsive genes belonging to different drought-related TFs. The information generated on structural and functional characteristics, expression and interaction of the drought-related TF families will be useful to decipher the drought tolerance mechanisms and to derive drought-tolerant genotypes in maize.

A novel structure of gel grown strontium cyanurate crystal and its structural, optical, electrical characterization

NASA Astrophysics Data System (ADS)

Divya, R.; Nair, Lekshmi P.; Bijini, B. R.; Nair, C. M. K.; Gopakumar, N.; Babu, K. Rajendra

2017-12-01

Strontium cyanurate crystals with novel structure and unique optical property like mechanoluminescence have been grown by conventional gel method. Transparent crystals were obtained. The single crystal X-ray diffraction analysis reveals the exquisite structure of the grown crystal. The crystal is centrosymmetric and has a three dimensional polymeric structure. The powder X ray diffraction analysis confirms its crystalline nature. The functional groups present in the crystal were identified by Fourier transform infrared spectroscopy. Elemental analysis confirmed the composition of the complex. A study of thermal properties was done by thermo gravimetric analysis and differential thermal analysis. The optical properties like band gap, refractive index and extinction coefficient were evaluated from the UV visible spectral analysis. The etching study was done to reveal the dislocations in the crystal which in turn explains mechanoluminescence emission. The mechanoluminescence property exhibited by the crystal makes it suitable for stress sensing applications. Besides being a centrosymmetric crystal, it also exhibits NLO behavior. Dielectric properties were studied and theoretical calculations of Fermi energy, valence electron plasma energy, penn gap and polarisability have been done.

Automating Structural Analysis of Spacecraft Vehicles

NASA Technical Reports Server (NTRS)

Hrinda, Glenn A.

2004-01-01

A major effort within NASA's vehicle analysis discipline has been to automate structural analysis and sizing optimization during conceptual design studies of advanced spacecraft. Traditional spacecraft structural sizing has involved detailed finite element analysis (FEA) requiring large degree-of-freedom (DOF) finite element models (FEM). Creation and analysis of these models can be time consuming and limit model size during conceptual designs. The goal is to find an optimal design that meets the mission requirements but produces the lightest structure. A structural sizing tool called HyperSizer has been successfully used in the conceptual design phase of a reusable launch vehicle and planetary exploration spacecraft. The program couples with FEA to enable system level performance assessments and weight predictions including design optimization of material selections and sizing of spacecraft members. The software's analysis capabilities are based on established aerospace structural methods for strength, stability and stiffness that produce adequately sized members and reliable structural weight estimates. The software also helps to identify potential structural deficiencies early in the conceptual design so changes can be made without wasted time. HyperSizer's automated analysis and sizing optimization increases productivity and brings standardization to a systems study. These benefits will be illustrated in examining two different types of conceptual spacecraft designed using the software. A hypersonic air breathing, single stage to orbit (SSTO), reusable launch vehicle (RLV) will be highlighted as well as an aeroshell for a planetary exploration vehicle used for aerocapture at Mars. By showing the two different types of vehicles, the software's flexibility will be demonstrated with an emphasis on reducing aeroshell structural weight. Member sizes, concepts and material selections will be discussed as well as analysis methods used in optimizing the structure. Analysis based on the HyperSizer structural sizing software will be discussed. Design trades required to optimize structural weight will be presented.

Multiscale Feature Analysis of Salivary Gland Branching Morphogenesis

PubMed Central

Baydil, Banu; Daley, William P.; Larsen, Melinda; Yener, Bülent

2012-01-01

Pattern formation in developing tissues involves dynamic spatio-temporal changes in cellular organization and subsequent evolution of functional adult structures. Branching morphogenesis is a developmental mechanism by which patterns are generated in many developing organs, which is controlled by underlying molecular pathways. Understanding the relationship between molecular signaling, cellular behavior and resulting morphological change requires quantification and categorization of the cellular behavior. In this study, tissue-level and cellular changes in developing salivary gland in response to disruption of ROCK-mediated signaling by are modeled by building cell-graphs to compute mathematical features capturing structural properties at multiple scales. These features were used to generate multiscale cell-graph signatures of untreated and ROCK signaling disrupted salivary gland organ explants. From confocal images of mouse submandibular salivary gland organ explants in which epithelial and mesenchymal nuclei were marked, a multiscale feature set capturing global structural properties, local structural properties, spectral, and morphological properties of the tissues was derived. Six feature selection algorithms and multiway modeling of the data was performed to identify distinct subsets of cell graph features that can uniquely classify and differentiate between different cell populations. Multiscale cell-graph analysis was most effective in classification of the tissue state. Cellular and tissue organization, as defined by a multiscale subset of cell-graph features, are both quantitatively distinct in epithelial and mesenchymal cell types both in the presence and absence of ROCK inhibitors. Whereas tensor analysis demonstrate that epithelial tissue was affected the most by inhibition of ROCK signaling, significant multiscale changes in mesenchymal tissue organization were identified with this analysis that were not identified in previous biological studies. We here show how to define and calculate a multiscale feature set as an effective computational approach to identify and quantify changes at multiple biological scales and to distinguish between different states in developing tissues. PMID:22403724

Determination of the crystalline structure of scale solids from the 16H evaporator gravity drain line to tank 38H

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

Oji, L. N.

2015-10-01

August 2015, scale solids from the 16H Evaporator Gravity Drain Line (GDL) to the Tank 38H were delivered to SRNL for analysis. The desired analytical goal was to identify and confirm the crystalline structure of the scale material and determine if the form of the aluminosilicate mineral was consistent with previous analysis of the scale material from the GDL.

Structure Line Detection from LIDAR Point Clouds Using Topological Elevation Analysis

NASA Astrophysics Data System (ADS)

Lo, C. Y.; Chen, L. C.

2012-07-01

Airborne LIDAR point clouds, which have considerable points on object surfaces, are essential to building modeling. In the last two decades, studies have developed different approaches to identify structure lines using two main approaches, data-driven and modeldriven. These studies have shown that automatic modeling processes depend on certain considerations, such as used thresholds, initial value, designed formulas, and predefined cues. Following the development of laser scanning systems, scanning rates have increased and can provide point clouds with higher point density. Therefore, this study proposes using topological elevation analysis (TEA) to detect structure lines instead of threshold-dependent concepts and predefined constraints. This analysis contains two parts: data pre-processing and structure line detection. To preserve the original elevation information, a pseudo-grid for generating digital surface models is produced during the first part. The highest point in each grid is set as the elevation value, and its original threedimensional position is preserved. In the second part, using TEA, the structure lines are identified based on the topology of local elevation changes in two directions. Because structure lines can contain certain geometric properties, their locations have small relieves in the radial direction and steep elevation changes in the circular direction. Following the proposed approach, TEA can be used to determine 3D line information without selecting thresholds. For validation, the TEA results are compared with those of the region growing approach. The results indicate that the proposed method can produce structure lines using dense point clouds.

JSEM: A Framework for Identifying and Evaluating Indicators.

ERIC Educational Resources Information Center

Hyman, Jeffrey B.; Leibowitz, Scott G.

2001-01-01

Presents an approach to identifying and evaluating combinations of indicators when the mathematical relationships between the indicators and an endpoint may not be quantified, a limitation common to many ecological assessments. Uses the framework of Structural Equation Modeling (SEM), which combines path analysis with measurement model, to…

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

Rohrbaugh, Wayne Joseph

Results are reported from an investigation of correlations between molecular structural parameters of selected organophosphorus insecticides and their corresponding toxic effectiveness. The crystal and molecular structures of azinphos-methyl, emidithion, and tetrachlorvinphos were determined via three-dimensional x-ray analysis. Acetylcholinesterase (AChE) in nerve cells was identified as the target for organophosphorus insecticides.

PACM: A Two-Stage Procedure for Analyzing Structural Models.

ERIC Educational Resources Information Center

Lehmann, Donald R.; Gupta, Sunil

1989-01-01

Path Analysis of Covariance Matrix (PACM) is described as a way to separately estimate measurement and structural models using standard least squares procedures. PACM was empirically compared to simultaneous maximum likelihood estimation and use of the LISREL computer program, and its advantages are identified. (SLD)

Structural Validation of the Holistic Wellness Assessment

ERIC Educational Resources Information Center

Brown, Charlene; Applegate, E. Brooks; Yildiz, Mustafa

2015-01-01

The Holistic Wellness Assessment (HWA) is a relatively new assessment instrument based on an emergent transdisciplinary model of wellness. This study validated the factor structure identified via exploratory factor analysis (EFA), assessed test-retest reliability, and investigated concurrent validity of the HWA in three separate samples. The…

An investigation of the factor structure of the beck depression inventory-II in anorexia nervosa.

PubMed

Fuss, Samantha; Trottier, Kathryn; Carter, Jacqueline

2015-01-01

Symptoms of depression frequently co-occur with eating disorders and have been associated with negative outcomes. Self-report measures such as the Beck Depression Inventory-II (BDI-II) are commonly used to assess for the presence of depressive symptoms in eating disorders, but the instrument's factor structure in this population has not been examined. The purposes of this study were to explore the factor structure of the BDI-II in a sample of individuals (N = 437) with anorexia nervosa undergoing inpatient treatment and to examine changes in depressive symptoms on each of the identified factors following a course of treatment for anorexia nervosa in order to provide evidence supporting the construct validity of the measure. Exploratory factor analysis revealed that a three-factor model reflected the best fit for the data. Confirmatory factor analysis was used to validate this model against competing models and the three-factor model exhibited strong model fit characteristics. BDI-II scores were significantly reduced on all three factors following inpatient treatment, which supported the construct validity of the scale. The BDI-II appears to be reliable in this population, and the factor structure identified through this analysis may offer predictive utility for identifying individuals who may have more difficulty achieving weight restoration in the context of inpatient treatment. Copyright © 2014 John Wiley & Sons, Ltd and Eating Disorders Association. Copyright © 2014 John Wiley & Sons, Ltd and Eating Disorders Association.

Genetic structure of lake whitefish, Coregonus clupeaformis, populations in the northern main basin of Lake Huron

USGS Publications Warehouse

Stott, Wendylee; Ebener, Mark P.; Mohr, Lloyd; Schaeffer, Jeff; Roseman, Edward F.; Harford, William J.; Johnson, James E.; Fietsch, Cherie-Lee

2012-01-01

Genetic analysis of spawning lake whitefish (Coregonus clupeaformis) from six sites in the main basin of Lake Huron was conducted to determine population structure. Samples from fisheryindependent assessment surveys in the northwest main basin were analyzed to determine the relative contributions of lake whitefish genetic populations. Genetic population structure was identified using data from seven microsatellite DNA loci. One population was identified at Manitoulin Island, one to two were observed in the east-central main basin (Fishing Island and Douglas Point), and one to two populations were found in the northwest (Thunder Bay and Duncan Bay). The genetic identity of collections from Duncan Bay and Thunder Bay was not consistent among methods used to analyze population structure. Low genetic distances suggested that they comprised one population, but genic differences indicated that they may constitute separate populations. Simulated data indicated that the genetic origins of samples from a mixed-fishery could be accurately identified, but accuracy could be improved by incorporating additional microsatellite loci. Mixture analysis and individual assignment tests performed on mixed-stock samples collected from the western main basin suggested that genetic populations from the east-central main basin contributed less than those from the western main basin and that the proportional contribution of each baseline population was similar in each assessment sample. Analysis of additional microsatellite DNA loci may be useful to help improve the precision of the estimates, thus increasing our ability to manage and protect this valuable resource.

Structural Monitoring and Field Test for Kao Ping Hsi Cable-Stayed Bridge in Taiwan

NASA Astrophysics Data System (ADS)

Chen, Chern-Hwa

2010-05-01

This work applies system identification techniques to analyze the measured data from structural monitoring system and field test for Kao Ping Hsi cable-stayed bridge in Taiwan. The continuous wavelet transform algorithm can be used to identify the dynamic characteristics of the cable-stayed bridge under environmental vibration. The identified results with traffic flow were compared with those obtained from ambient vibration test. The excellent agreement both the identified results from different traffic conditions indicates that the traffic flow would not significantly change the natural frequencies of the cable-stayed bridge. The modal parameters identified from the field vibration test will be compared with those used in the finite element analysis. The results obtained herein will be used as the damage detection for monitoring the long-term safety of the Kao Ping Hsi cable-stayed bridge by using structural monitoring system.

Development of a data independent acquisition mass spectrometry workflow to enable glycopeptide analysis without predefined glycan compositional knowledge.

PubMed

Lin, Chi-Hung; Krisp, Christoph; Packer, Nicolle H; Molloy, Mark P

2018-02-10

Glycoproteomics investigates glycan moieties in a site specific manner to reveal the functional roles of protein glycosylation. Identification of glycopeptides from data-dependent acquisition (DDA) relies on high quality MS/MS spectra of glycopeptide precursors and often requires manual validation to ensure confident assignments. In this study, we investigated pseudo-MRM (MRM-HR) and data-independent acquisition (DIA) as alternative acquisition strategies for glycopeptide analysis. These approaches allow data acquisition over the full MS/MS scan range allowing data re-analysis post-acquisition, without data re-acquisition. The advantage of MRM-HR over DDA for N-glycopeptide detection was demonstrated from targeted analysis of bovine fetuin where all three N-glycosylation sites were detected, which was not the case with DDA. To overcome the duty cycle limitation of MRM-HR acquisition needed for analysis of complex samples such as plasma we trialed DIA. This allowed development of a targeted DIA method to identify N-glycopeptides without pre-defined knowledge of the glycan composition, thus providing the potential to identify N-glycopeptides with unexpected structures. This workflow was demonstrated by detection of 59 N-glycosylation sites from 41 glycoproteins from a HILIC enriched human plasma tryptic digest. 21 glycoforms of IgG1 glycopeptides were identified including two truncated structures that are rarely reported. We developed a data-independent mass spectrometry workflow to identify specific glycopeptides from complex biological mixtures. The novelty is that this approach does not require glycan composition to be pre-defined, thereby allowing glycopeptides carrying unexpected glycans to be identified. This is demonstrated through the analysis of immunoglobulins in human plasma where we detected two IgG1 glycoforms that are rarely observed. Copyright © 2017 Elsevier B.V. All rights reserved.

Structure of Science Popularizations: A Genre-Analysis Approach to the Schema of Popularized Medical Texts.

ERIC Educational Resources Information Center

Nwogu, Kevin N.

1991-01-01

Attempts to characterize one discourse type of science popularization, the Journalistic Reported Version (JRV) of research articles in science magazines and newspapers. Results indicate that the JRV has an identifiable schema by which the information it contains is structured, and a typical JRV text may have as many as nine schematic structures.…

Program Calculates Forces in Bolted Structural Joints

NASA Technical Reports Server (NTRS)

Buder, Daniel A.

2005-01-01

FORTRAN 77 computer program calculates forces in bolts in the joints of structures. This program is used in conjunction with the NASTRAN finite-element structural-analysis program. A mathematical model of a structure is first created by approximating its load-bearing members with representative finite elements, then NASTRAN calculates the forces and moments that each finite element contributes to grid points located throughout the structure. The user selects the finite elements that correspond to structural members that contribute loads to the joints of interest, and identifies the grid point nearest to each such joint. This program reads the pertinent NASTRAN output, combines the forces and moments from the contributing elements to determine the resultant force and moment acting at each proximate grid point, then transforms the forces and moments from these grid points to the centroids of the affected joints. Then the program uses these joint loads to obtain the axial and shear forces in the individual bolts. The program identifies which bolts bear the greatest axial and/or shear loads. The program also performs a fail-safe analysis in which the foregoing calculations are repeated for a sequence of cases in which each fastener, in turn, is assumed not to transmit an axial force.

Free-energy landscape, principal component analysis, and structural clustering to identify representative conformations from molecular dynamics simulations: the myoglobin case.

PubMed

Papaleo, Elena; Mereghetti, Paolo; Fantucci, Piercarlo; Grandori, Rita; De Gioia, Luca

2009-01-01

Several molecular dynamics (MD) simulations were used to sample conformations in the neighborhood of the native structure of holo-myoglobin (holo-Mb), collecting trajectories spanning 0.22 micros at 300 K. Principal component (PCA) and free-energy landscape (FEL) analyses, integrated by cluster analysis, which was performed considering the position and structures of the individual helices of the globin fold, were carried out. The coherence between the different structural clusters and the basins of the FEL, together with the convergence of parameters derived by PCA indicates that an accurate description of the Mb conformational space around the native state was achieved by multiple MD trajectories spanning at least 0.14 micros. The integration of FEL, PCA, and structural clustering was shown to be a very useful approach to gain an overall view of the conformational landscape accessible to a protein and to identify representative protein substates. This method could be also used to investigate the conformational and dynamical properties of Mb apo-, mutant, or delete versions, in which greater conformational variability is expected and, therefore identification of representative substates from the simulations is relevant to disclose structure-function relationship.

Using machine learning to identify structural breaks in single-group interrupted time series designs.

PubMed

Linden, Ariel; Yarnold, Paul R

2016-12-01

Single-group interrupted time series analysis (ITSA) is a popular evaluation methodology in which a single unit of observation is being studied, the outcome variable is serially ordered as a time series and the intervention is expected to 'interrupt' the level and/or trend of the time series, subsequent to its introduction. Given that the internal validity of the design rests on the premise that the interruption in the time series is associated with the introduction of the treatment, treatment effects may seem less plausible if a parallel trend already exists in the time series prior to the actual intervention. Thus, sensitivity analyses should focus on detecting structural breaks in the time series before the intervention. In this paper, we introduce a machine-learning algorithm called optimal discriminant analysis (ODA) as an approach to determine if structural breaks can be identified in years prior to the initiation of the intervention, using data from California's 1988 voter-initiated Proposition 99 to reduce smoking rates. The ODA analysis indicates that numerous structural breaks occurred prior to the actual initiation of Proposition 99 in 1989, including perfect structural breaks in 1983 and 1985, thereby casting doubt on the validity of treatment effects estimated for the actual intervention when using a single-group ITSA design. Given the widespread use of ITSA for evaluating observational data and the increasing use of machine-learning techniques in traditional research, we recommend that structural break sensitivity analysis is routinely incorporated in all research using the single-group ITSA design. © 2016 John Wiley & Sons, Ltd.

Reduced structural connectivity within a prefrontal-motor-subcortical network in amyotrophic lateral sclerosis.

PubMed

Buchanan, Colin R; Pettit, Lewis D; Storkey, Amos J; Abrahams, Sharon; Bastin, Mark E

2015-05-01

To investigate white matter structural connectivity changes associated with amyotrophic lateral sclerosis (ALS) using network analysis and compare the results with those obtained using standard voxel-based methods, specifically Tract-based Spatial Statistics (TBSS). MRI data were acquired from 30 patients with ALS and 30 age-matched healthy controls. For each subject, 85 grey matter regions (network nodes) were identified from high resolution structural MRI, and network connections formed from the white matter tracts generated by diffusion MRI and probabilistic tractography. Whole-brain networks were constructed using strong constraints on anatomical plausibility and a weighting reflecting tract-averaged fractional anisotropy (FA). Analysis using Network-based Statistics (NBS), without a priori selected regions, identified an impaired motor-frontal-subcortical subnetwork (10 nodes and 12 bidirectional connections), consistent with upper motor neuron pathology, in the ALS group compared with the controls (P = 0.020). Reduced FA in three of the impaired network connections, which involved fibers of the corticospinal tract, correlated with rate of disease progression (P ≤ 0.024). A novel network-tract comparison revealed that the connections involved in the affected network had a strong correspondence (mean overlap of 86.2%) with white matter tracts identified as having reduced FA compared with the control group using TBSS. These findings suggest that white matter degeneration in ALS is strongly linked to the motor cortex, and that impaired structural networks identified using NBS have a strong correspondence to affected white matter tracts identified using more conventional voxel-based methods. © 2014 Wiley Periodicals, Inc.

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

PubMed

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

2014-10-01

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

Identification of G-quadruplex forming sequences in three manatee papillomaviruses

PubMed Central

Zahin, Maryam; Dean, William L.; Ghim, Shin-je; Joh, Joongho; Gray, Robert D.; Khanal, Sujita; Bossart, Gregory D.; Mignucci-Giannoni, Antonio A.; Rouchka, Eric C.; Jenson, Alfred B.; Trent, John O.; Chaires, Jonathan B.

2018-01-01

The Florida manatee (Trichechus manatus latirotris) is a threatened aquatic mammal in United States coastal waters. Over the past decade, the appearance of papillomavirus-induced lesions and viral papillomatosis in manatees has been a concern for those involved in the management and rehabilitation of this species. To date, three manatee papillomaviruses (TmPVs) have been identified in Florida manatees, one forming cutaneous lesions (TmPV1) and two forming genital lesions (TmPV3 and TmPV4). We identified DNA sequences with the potential to form G-quadruplex structures (G4) across the three genomes. G4 were located on both DNA strands and across coding and non-coding regions on all TmPVs, offering multiple targets for viral control. Although G4 have been identified in several viral genomes, including human PVs, most research has focused on canonical structures comprised of three G-tetrads. In contrast, the vast majority of sequences we identified would allow the formation of non-canonical structures with only two G-tetrads. Our biophysical analysis confirmed the formation of G4 with parallel topology in three such sequences from the E2 region. Two of the structures appear comprised of multiple stacked two G-tetrad structures, perhaps serving to increase structural stability. Computational analysis demonstrated enrichment of G4 sequences on all TmPVs on the reverse strand in the E2/E4 region and on both strands in the L2 region. Several G4 sequences occurred at similar regional locations on all PVs, most notably on the reverse strand in the E2 region. In other cases, G4 were identified at similar regional locations only on PVs forming genital lesions. On all TmPVs, G4 sequences were located in the non-coding region near putative E2 binding sites. Together, these findings suggest that G4 are possible regulatory elements in TmPVs. PMID:29630682

Tripartite community structure in social bookmarking data

NASA Astrophysics Data System (ADS)

Neubauer, Nicolas; Obermayer, Klaus

2011-12-01

Community detection is a branch of network analysis concerned with identifying strongly connected subnetworks. Social bookmarking sites aggregate datasets of often hundreds of millions of triples (document, user, and tag), which, when interpreted as edges of a graph, give rise to special networks called 3-partite, 3-uniform hypergraphs. We identify challenges and opportunities of generalizing community detection and in particular modularity optimization to these structures. Two methods for community detection are introduced that preserve the hypergraph's special structure to different degrees. Their performance is compared on synthetic datasets, showing the benefits of structure preservation. Furthermore, a tool for interactive exploration of the community detection results is introduced and applied to examples from real datasets. We find additional evidence for the importance of structure preservation and, more generally, demonstrate how tripartite community detection can help understand the structure of social bookmarking data.

Neural network system and methods for analysis of organic materials and structures using spectral data

DOEpatents

Meyer, Bernd J.; Sellers, Jeffrey P.; Thomsen, Jan U.

1993-01-01

Apparatus and processes for recognizing and identifying materials. Characteristic spectra are obtained for the materials via spectroscopy techniques including nuclear magnetic resonance spectroscopy, infrared absorption analysis, x-ray analysis, mass spectroscopy and gas chromatography. Desired portions of the spectra may be selected and then placed in proper form and format for presentation to a number of input layer neurons in an offline neural network. The network is first trained according to a predetermined training process; it may then be employed to identify particular materials. Such apparatus and processes are particularly useful for recognizing and identifying organic compounds such as complex carbohydrates, whose spectra conventionally require a high level of training and many hours of hard work to identify, and are frequently indistinguishable from one another by human interpretation.

QSAR and 3D QSAR of inhibitors of the epidermal growth factor receptor

NASA Astrophysics Data System (ADS)

Pinto-Bazurco, Mariano; Tsakovska, Ivanka; Pajeva, Ilza

This article reports quantitative structure-activity relationships (QSAR) and 3D QSAR models of 134 structurally diverse inhibitors of the epidermal growth factor receptor (EGFR) tyrosine kinase. Free-Wilson analysis was used to derive the QSAR model. It identified the substituents in aniline, the polycyclic system, and the substituents at the 6- and 7-positions of the polycyclic system as the most important structural features. Comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) were used in the 3D QSAR modeling. The steric and electrostatic interactions proved the most important for the inhibitory effect. Both QSAR and 3D QSAR models led to consistent results. On the basis of the statistically significant models, new structures were proposed and their inhibitory activities were predicted.

Sensitivity analysis for axis rotation diagrid structural systems according to brace angle changes

NASA Astrophysics Data System (ADS)

Yang, Jae-Kwang; Li, Long-Yang; Park, Sung-Soo

2017-10-01

General regular shaped diagrid structures can express diverse shapes because braces are installed along the exterior faces of the structures and the structures have no columns. However, since irregular shaped structures have diverse variables, studies to assess behaviors resulting from various variables are continuously required to supplement the imperfections related to such variables. In the present study, materials elastic modulus and yield strength were selected as variables for strength that would be applied to diagrid structural systems in the form of Twisters among the irregular shaped buildings classified by Vollers and that affect the structural design of these structural systems. The purpose of this study is to conduct sensitivity analysis for axial rotation diagrid structural systems according to changes in brace angles in order to identify the design variables that have relatively larger effects and the tendencies of the sensitivity of the structures according to changes in brace angles and axial rotation angles.

Noise elimination algorithm for modal analysis

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

Bao, X. X., E-mail: baoxingxian@upc.edu.cn; Li, C. L.; Xiong, C. B.

2015-07-27

Modal analysis is an ongoing interdisciplinary physical issue. Modal parameters estimation is applied to determine the dynamic characteristics of structures under vibration excitation. Modal analysis is more challenging for the measured vibration response signals are contaminated with noise. This study develops a mathematical algorithm of structured low rank approximation combined with the complex exponential method to estimate the modal parameters. Physical experiments using a steel cantilever beam with ten accelerometers mounted, excited by an impulse load, demonstrate that this method can significantly eliminate noise from measured signals and accurately identify the modal frequencies and damping ratios. This study provides amore » fundamental mechanism of noise elimination using structured low rank approximation in physical fields.« less

Realist identification of group-level latent variables for perinatal social epidemiology theory building.

PubMed

Eastwood, John Graeme; Jalaludin, Bin Badrudin; Kemp, Lynn Ann; Phung, Hai Ngoc

2014-01-01

We have previously reported in this journal on an ecological study of perinatal depressive symptoms in South Western Sydney. In that article, we briefly reported on a factor analysis that was utilized to identify empirical indicators for analysis. In this article, we report on the mixed method approach that was used to identify those latent variables. Social epidemiology has been slow to embrace a latent variable approach to the study of social, political, economic, and cultural structures and mechanisms, partly for philosophical reasons. Critical realist ontology and epistemology have been advocated as an appropriate methodological approach to both theory building and theory testing in the health sciences. We describe here an emergent mixed method approach that uses qualitative methods to identify latent constructs followed by factor analysis using empirical indicators chosen to measure identified qualitative codes. Comparative analysis of the findings is reported together with a limited description of realist approaches to abstract reasoning.

More powerful virus inhibitors from structure-based analysis of HEV71 capsid-binding molecules

PubMed Central

Spyrou, John A. B.; Kelly, James; Ren, Jingshan; Grimes, Jonathan; Puerstinger, Gerhard; Stonehouse, Nicola; Walter, Thomas S.; Hu, Zhongyu; Wang, Junzhi; Li, Xuemei; Peng, Wei; Rowlands, David; Fry, Elizabeth E.; Rao, Zihe; Stuart, David I.

2014-01-01

Enterovirus 71 (HEV71) epidemics amongst children and infants result mainly in mild symptoms, however, especially in the Asia-Pacific region, infection can be fatal. At present no therapies are available. We have used structural analysis of the complete virus to guide the design of HEV71 inhibitors. Analysis of complexes with four 3-(-4-pyridyl)-2-imidazolidinone derivatives with varying anti-HEV71 activities, pinpointed key structure-activity correlates. We then identified additional potentially beneficial substitutions, developed methods to reliably triage compounds by quantum mechanics-enhanced ligand docking, and synthesized two candidates. Structural analysis and in vitro assays confirmed the predicted binding modes and their ability to block viral infection. One ligand (IC50 = 25 pM) is an order of magnitude more potent than the best previously reported inhibitor, and is also more soluble. Our approach may be useful in the design of effective drugs for enterovirus infections. PMID:24509833

Proteomic analysis of plasma-purified VLDL, LDL, and HDL fractions from atherosclerotic patients undergoing carotid endarterectomy: identification of serum amyloid A as a potential marker.

PubMed

Lepedda, Antonio J; Nieddu, Gabriele; Zinellu, Elisabetta; De Muro, Pierina; Piredda, Franco; Guarino, Anna; Spirito, Rita; Carta, Franco; Turrini, Francesco; Formato, Marilena

2013-01-01

Apolipoproteins are very heterogeneous protein family, implicated in plasma lipoprotein structural stabilization, lipid metabolism, inflammation, or immunity. Obtaining detailed information on apolipoprotein composition and structure may contribute to elucidating lipoprotein roles in atherogenesis and to developing new therapeutic strategies for the treatment of lipoprotein-associated disorders. This study aimed at developing a comprehensive method for characterizing the apolipoprotein component of plasma VLDL, LDL, and HDL fractions from patients undergoing carotid endarterectomy, by means of two-dimensional electrophoresis (2-DE) coupled with Mass Spectrometry analysis, useful for identifying potential markers of plaque presence and vulnerability. The adopted method allowed obtaining reproducible 2-DE maps of exchangeable apolipoproteins from VLDL, LDL, and HDL. Twenty-three protein isoforms were identified by peptide mass fingerprinting analysis. Differential proteomic analysis allowed for identifying increased levels of acute-phase serum amyloid A protein (AP SAA) in all lipoprotein fractions, especially in LDL from atherosclerotic patients. Results have been confirmed by western blotting analysis on each lipoprotein fraction using apo AI levels for data normalization. The higher levels of AP SAA found in patients suggest a role of LDL as AP SAA carrier into the subendothelial space of artery wall, where AP SAA accumulates and may exert noxious effects.

Fast neutron induced structural rearrangements at a soybean NAP1 locus result in gnarled trichomes

USDA-ARS?s Scientific Manuscript database

A soybean (Glycine max (L.) Merr.) gnarled trichome mutant, exhibiting stunted trichomes compared to wild-type, was identified in a fast neutron mutant population. Genetic mapping using whole genome sequence-based bulked segregant analysis identified a 26.6 megabase interval on chromosome 20 that ...

CSI 3.0: a web server for identifying secondary and super-secondary structure in proteins using NMR chemical shifts.

PubMed

Hafsa, Noor E; Arndt, David; Wishart, David S

2015-07-01

The Chemical Shift Index or CSI 3.0 (http://csi3.wishartlab.com) is a web server designed to accurately identify the location of secondary and super-secondary structures in protein chains using only nuclear magnetic resonance (NMR) backbone chemical shifts and their corresponding protein sequence data. Unlike earlier versions of CSI, which only identified three types of secondary structure (helix, β-strand and coil), CSI 3.0 now identifies total of 11 types of secondary and super-secondary structures, including helices, β-strands, coil regions, five common β-turns (type I, II, I', II' and VIII), β hairpins as well as interior and edge β-strands. CSI 3.0 accepts experimental NMR chemical shift data in multiple formats (NMR Star 2.1, NMR Star 3.1 and SHIFTY) and generates colorful CSI plots (bar graphs) and secondary/super-secondary structure assignments. The output can be readily used as constraints for structure determination and refinement or the images may be used for presentations and publications. CSI 3.0 uses a pipeline of several well-tested, previously published programs to identify the secondary and super-secondary structures in protein chains. Comparisons with secondary and super-secondary structure assignments made via standard coordinate analysis programs such as DSSP, STRIDE and VADAR on high-resolution protein structures solved by X-ray and NMR show >90% agreement between those made with CSI 3.0. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

10 CFR 63.112 - Requirements for preclosure safety analysis of the geologic repository operations area.

Code of Federal Regulations, 2014 CFR

2014-01-01

... emergency power to instruments, utility service systems, and operating systems important to safety if there... include: (a) A general description of the structures, systems, components, equipment, and process... of the performance of the structures, systems, and components to identify those that are important to...

10 CFR 63.112 - Requirements for preclosure safety analysis of the geologic repository operations area.

Code of Federal Regulations, 2013 CFR

2013-01-01

... emergency power to instruments, utility service systems, and operating systems important to safety if there... include: (a) A general description of the structures, systems, components, equipment, and process... of the performance of the structures, systems, and components to identify those that are important to...

10 CFR 63.112 - Requirements for preclosure safety analysis of the geologic repository operations area.

Code of Federal Regulations, 2012 CFR

2012-01-01

... emergency power to instruments, utility service systems, and operating systems important to safety if there... include: (a) A general description of the structures, systems, components, equipment, and process... of the performance of the structures, systems, and components to identify those that are important to...

10 CFR 63.112 - Requirements for preclosure safety analysis of the geologic repository operations area.

Code of Federal Regulations, 2011 CFR

2011-01-01

... emergency power to instruments, utility service systems, and operating systems important to safety if there... include: (a) A general description of the structures, systems, components, equipment, and process... of the performance of the structures, systems, and components to identify those that are important to...

Analysis of the Tail Structures of Comet 1P/Halley 1910 II

NASA Astrophysics Data System (ADS)

Voelzke, Marcos Rincon

2013-11-01

For the purpose of identifying, measuring, and correlating the morphological structures along the plasma tail of 1P/Halley, 886 images from September 1909 to May 1911 are analysed. These images are from the Atlas of Comet Halley 1910 II (DONN; RAHE; BRANDT, 1986).

High Throughput Light Absorber Discovery, Part 2: Establishing Structure-Band Gap Energy Relationships.

PubMed

Suram, Santosh K; Newhouse, Paul F; Zhou, Lan; Van Campen, Douglas G; Mehta, Apurva; Gregoire, John M

2016-11-14

Combinatorial materials science strategies have accelerated materials development in a variety of fields, and we extend these strategies to enable structure-property mapping for light absorber materials, particularly in high order composition spaces. High throughput optical spectroscopy and synchrotron X-ray diffraction are combined to identify the optical properties of Bi-V-Fe oxides, leading to the identification of Bi 4 V 1.5 Fe 0.5 O 10.5 as a light absorber with direct band gap near 2.7 eV. The strategic combination of experimental and data analysis techniques includes automated Tauc analysis to estimate band gap energies from the high throughput spectroscopy data, providing an automated platform for identifying new optical materials.

The structural identifiability and parameter estimation of a multispecies model for the transmission of mastitis in dairy cows with postmilking teat disinfection.

PubMed

White, L J; Evans, N D; Lam, T J G M; Schukken, Y H; Medley, G F; Godfrey, K R; Chappell, M J

2002-01-01

A mathematical model for the transmission of two interacting classes of mastitis causing bacterial pathogens in a herd of dairy cows is presented and applied to a specific data set. The data were derived from a field trial of a specific measure used in the control of these pathogens, where half the individuals were subjected to the control and in the others the treatment was discontinued. The resultant mathematical model (eight non-linear simultaneous ordinary differential equations) therefore incorporates heterogeneity in the host as well as the infectious agent and consequently the effects of control are intrinsic in the model structure. A structural identifiability analysis of the model is presented demonstrating that the scope of the novel method used allows application to high order non-linear systems. The results of a simultaneous estimation of six unknown system parameters are presented. Previous work has only estimated a subset of these either simultaneously or individually. Therefore not only are new estimates provided for the parameters relating to the transmission and control of the classes of pathogens under study, but also information about the relationships between them. We exploit the close link between mathematical modelling, structural identifiability analysis, and parameter estimation to obtain biological insights into the system modelled.

Evidential Reasoning in Expert Systems for Image Analysis.

DTIC Science & Technology

1985-02-01

techniques to image analysis (IA). There is growing evidence that these techniques offer significant improvements in image analysis , particularly in the...2) to provide a common framework for analysis, (3) to structure the ER process for major expert-system tasks in image analysis , and (4) to identify...approaches to three important tasks for expert systems in the domain of image analysis . This segment concluded with an assessment of the strengths

PAT: predictor for structured units and its application for the optimization of target molecules for the generation of synthetic antibodies.

PubMed

Jeon, Jouhyun; Arnold, Roland; Singh, Fateh; Teyra, Joan; Braun, Tatjana; Kim, Philip M

2016-04-01

The identification of structured units in a protein sequence is an important first step for most biochemical studies. Importantly for this study, the identification of stable structured region is a crucial first step to generate novel synthetic antibodies. While many approaches to find domains or predict structured regions exist, important limitations remain, such as the optimization of domain boundaries and the lack of identification of non-domain structured units. Moreover, no integrated tool exists to find and optimize structural domains within protein sequences. Here, we describe a new tool, PAT ( http://www.kimlab.org/software/pat ) that can efficiently identify both domains (with optimized boundaries) and non-domain putative structured units. PAT automatically analyzes various structural properties, evaluates the folding stability, and reports possible structural domains in a given protein sequence. For reliability evaluation of PAT, we applied PAT to identify antibody target molecules based on the notion that soluble and well-defined protein secondary and tertiary structures are appropriate target molecules for synthetic antibodies. PAT is an efficient and sensitive tool to identify structured units. A performance analysis shows that PAT can characterize structurally well-defined regions in a given sequence and outperforms other efforts to define reliable boundaries of domains. Specially, PAT successfully identifies experimentally confirmed target molecules for antibody generation. PAT also offers the pre-calculated results of 20,210 human proteins to accelerate common queries. PAT can therefore help to investigate large-scale structured domains and improve the success rate for synthetic antibody generation.

Measuring System Value in the Ares 1 Rocket Using an Uncertainty-Based Coupling Analysis Approach

NASA Astrophysics Data System (ADS)

Wenger, Christopher

Coupling of physics in large-scale complex engineering systems must be correctly accounted for during the systems engineering process to ensure no unanticipated behaviors or unintended consequences arise in the system during operation. Structural vibration of large segmented solid rocket motors, known as thrust oscillation, is a well-documented problem that can affect the health and safety of any crew onboard. Within the Ares 1 rocket, larger than anticipated vibrations were recorded during late stage flight that propagated from the engine chamber to the Orion crew module. Upon investigation engineers found the root cause to be the structure of the rockets feedback onto fluid flow within the engine. The goal of this paper is to showcase a coupling strength analysis from the field of Multidisciplinary Design Optimization to identify the major impacts that caused the Thrust Oscillation event in the Ares 1. Once identified an uncertainty analysis of the coupled system using an uncertainty based optimization technique is used to identify the likelihood of occurrence for these strong or weak interactions to take place.

Proteomic analysis of skeletal organic matrix from the stony coral Stylophora pistillata

PubMed Central

Drake, Jeana L.; Mass, Tali; Haramaty, Liti; Zelzion, Ehud; Bhattacharya, Debashish; Falkowski, Paul G.

2013-01-01

It has long been recognized that a suite of proteins exists in coral skeletons that is critical for the oriented precipitation of calcium carbonate crystals, yet these proteins remain poorly characterized. Using liquid chromatography-tandem mass spectrometry analysis of proteins extracted from the cell-free skeleton of the hermatypic coral, Stylophora pistillata, combined with a draft genome assembly from the cnidarian host cells of the same species, we identified 36 coral skeletal organic matrix proteins. The proteome of the coral skeleton contains an assemblage of adhesion and structural proteins as well as two highly acidic proteins that may constitute a unique coral skeletal organic matrix protein subfamily. We compared the 36 skeletal organic matrix protein sequences to genome and transcriptome data from three other corals, three additional invertebrates, one vertebrate, and three single-celled organisms. This work represents a unique extensive proteomic analysis of biomineralization-related proteins in corals from which we identify a biomineralization “toolkit,” an organic scaffold upon which aragonite crystals can be deposited in specific orientations to form a phenotypically identifiable structure. PMID:23431140

MSSA de-noising of horizon time structure to improve the curvature attribute analysis

NASA Astrophysics Data System (ADS)

Tiwari, R. K.; Rekapalli, R.; Vedanti, N.

2017-12-01

Although the seismic attributes are useful for identifying sub-surface structural features like faults, fractures, lineaments and sharp stratigraphy etc., the different kinds of noises arising from unknown physical sources during the data acquisition and processing creates acute problems in physical interpretation of complex crustal structures. Hence, we propose to study effect of noise on curvature attribute analysis of seismic time structure data. We propose here Multichannel Singular Spectrum Analysis (MSSA) de-noising algorithm as a pre filtering scheme to reduce effect of noise. To demonstrate the procedure, first, we compute the most positive and negative curvature on a synthetic time structure with surface features resembling anticlines, synclines and faults and then adding the known percentage of noise. We noticed that the curvatures estimated from the noisy data reveal considerable deviations from the curvature of pure synthetic data. This suggests that there is a strong impact of noise on the curvature estimates. Further, we have employed 2D median filter and MSSA methods to filter the noisy time structure and then computed the curvatures. The comparisons of curvatures estimated from de-noised data suggest that the results obtained from MSSA de-noised data match well with the curvatures of pure synthetic data. Finally, we present an example of real data analysis from Utsira Top (UT) horizon of Southern Viking Graben, Norway to identify the time-lapse changes in UT horizon after CO2 injection. We applied the MSSA de-noising algorithm on UT horizon time structure and amplitude data of pre and post CO2 injection. Our analyses suggest modest but clearly visible, structural changes in the UT horizon after CO2 injection at a few locations, which seem to be associated with the locations of change in seismic amplitudes. Thus, the results from both the synthetic and real field data suggest that the MSSA based de-noising algorithm is robust for filtering the horizon time structures for accurate curvature attributes analysis and better interpretation of structural changes in geological features. Key Words: Curvature attributes, MSSA, Seismic Horizon, 2D-median filter, Utsira Horizon.

Automatic identification of mobile and rigid substructures in molecular dynamics simulations and fractional structural fluctuation analysis.

PubMed

Martínez, Leandro

2015-01-01

The analysis of structural mobility in molecular dynamics plays a key role in data interpretation, particularly in the simulation of biomolecules. The most common mobility measures computed from simulations are the Root Mean Square Deviation (RMSD) and Root Mean Square Fluctuations (RMSF) of the structures. These are computed after the alignment of atomic coordinates in each trajectory step to a reference structure. This rigid-body alignment is not robust, in the sense that if a small portion of the structure is highly mobile, the RMSD and RMSF increase for all atoms, resulting possibly in poor quantification of the structural fluctuations and, often, to overlooking important fluctuations associated to biological function. The motivation of this work is to provide a robust measure of structural mobility that is practical, and easy to interpret. We propose a Low-Order-Value-Optimization (LOVO) strategy for the robust alignment of the least mobile substructures in a simulation. These substructures are automatically identified by the method. The algorithm consists of the iterative superposition of the fraction of structure displaying the smallest displacements. Therefore, the least mobile substructures are identified, providing a clearer picture of the overall structural fluctuations. Examples are given to illustrate the interpretative advantages of this strategy. The software for performing the alignments was named MDLovoFit and it is available as free-software at: http://leandro.iqm.unicamp.br/mdlovofit.

Automatic Identification of Mobile and Rigid Substructures in Molecular Dynamics Simulations and Fractional Structural Fluctuation Analysis

PubMed Central

Martínez, Leandro

2015-01-01

The analysis of structural mobility in molecular dynamics plays a key role in data interpretation, particularly in the simulation of biomolecules. The most common mobility measures computed from simulations are the Root Mean Square Deviation (RMSD) and Root Mean Square Fluctuations (RMSF) of the structures. These are computed after the alignment of atomic coordinates in each trajectory step to a reference structure. This rigid-body alignment is not robust, in the sense that if a small portion of the structure is highly mobile, the RMSD and RMSF increase for all atoms, resulting possibly in poor quantification of the structural fluctuations and, often, to overlooking important fluctuations associated to biological function. The motivation of this work is to provide a robust measure of structural mobility that is practical, and easy to interpret. We propose a Low-Order-Value-Optimization (LOVO) strategy for the robust alignment of the least mobile substructures in a simulation. These substructures are automatically identified by the method. The algorithm consists of the iterative superposition of the fraction of structure displaying the smallest displacements. Therefore, the least mobile substructures are identified, providing a clearer picture of the overall structural fluctuations. Examples are given to illustrate the interpretative advantages of this strategy. The software for performing the alignments was named MDLovoFit and it is available as free-software at: http://leandro.iqm.unicamp.br/mdlovofit PMID:25816325

Global-local methodologies and their application to nonlinear analysis. [for structural postbuckling study

NASA Technical Reports Server (NTRS)

Noor, Ahmed K.

1986-01-01

An assessment is made of the potential of different global-local analysis strategies for predicting the nonlinear and postbuckling responses of structures. Two postbuckling problems of composite panels are used as benchmarks and the application of different global-local methodologies to these benchmarks is outlined. The key elements of each of the global-local strategies are discussed and future research areas needed to realize the full potential of global-local methodologies are identified.

Microwave power transmission system studies. Volume 3, section 8: Mechanical systems and flight operations

NASA Technical Reports Server (NTRS)

Maynard, O. E.; Brown, W. C.; Edwards, A.; Haley, J. T.; Meltz, G.; Howell, J. M.; Nathan, A.

1975-01-01

The efforts and recommendations associated with preliminary design and concept definition for mechanical systems and flight operations are presented. Technical discussion in the areas of mission analysis, antenna structural concept, configuration analysis, assembly and packaging with associated costs are presented. Technology issues for the control system, structural system, thermal system and assembly including cost and man's role in assembly and maintenance are identified. Background and desired outputs for future efforts are discussed.

Impact of new computing systems on computational mechanics and flight-vehicle structures technology

NASA Technical Reports Server (NTRS)

Noor, A. K.; Storaasli, O. O.; Fulton, R. E.

1984-01-01

Advances in computer technology which may have an impact on computational mechanics and flight vehicle structures technology were reviewed. The characteristics of supersystems, highly parallel systems, and small systems are summarized. The interrelations of numerical algorithms and software with parallel architectures are discussed. A scenario for future hardware/software environment and engineering analysis systems is presented. Research areas with potential for improving the effectiveness of analysis methods in the new environment are identified.

Industrial entrepreneurial network: Structural and functional analysis

NASA Astrophysics Data System (ADS)

Medvedeva, M. A.; Davletbaev, R. H.; Berg, D. B.; Nazarova, J. J.; Parusheva, S. S.

2016-12-01

Structure and functioning of two model industrial entrepreneurial networks are investigated in the present paper. One of these networks is forming when implementing an integrated project and consists of eight agents, which interact with each other and external environment. The other one is obtained from the municipal economy and is based on the set of the 12 real business entities. Analysis of the networks is carried out on the basis of the matrix of mutual payments aggregated over the certain time period. The matrix is created by the methods of experimental economics. Social Network Analysis (SNA) methods and instruments were used in the present research. The set of basic structural characteristics was investigated: set of quantitative parameters such as density, diameter, clustering coefficient, different kinds of centrality, and etc. They were compared with the random Bernoulli graphs of the corresponding size and density. Discovered variations of random and entrepreneurial networks structure are explained by the peculiarities of agents functioning in production network. Separately, were identified the closed exchange circuits (cyclically closed contours of graph) forming an autopoietic (self-replicating) network pattern. The purpose of the functional analysis was to identify the contribution of the autopoietic network pattern in its gross product. It was found that the magnitude of this contribution is more than 20%. Such value allows using of the complementary currency in order to stimulate economic activity of network agents.

Bearing-Load Modeling and Analysis Study for Mechanically Connected Structures

NASA Technical Reports Server (NTRS)

Knight, Norman F., Jr.

2006-01-01

Bearing-load response for a pin-loaded hole is studied within the context of two-dimensional finite element analyses. Pin-loaded-hole configurations are representative of mechanically connected structures, such as a stiffener fastened to a rib of an isogrid panel, that are idealized as part of a larger structural component. Within this context, the larger structural component may be idealized as a two-dimensional shell finite element model to identify load paths and high stress regions. Finite element modeling and analysis aspects of a pin-loaded hole are considered in the present paper including the use of linear and nonlinear springs to simulate the pin-bearing contact condition. Simulating pin-connected structures within a two-dimensional finite element analysis model using nonlinear spring or gap elements provides an effective way for accurate prediction of the local effective stress state and peak forces.

The structural studies of vanadium substituted lithium-bismuth-boro-tellurite glass

NASA Astrophysics Data System (ADS)

Madhu, A.; Eraiah, B.

2018-05-01

The structural studies of vanadium substituted lithium-bismuth-boro-tellurite glass is successfully prepared and certain analysis like XRD,FTIR,DTA/TGA with density, molar volume are done. The amorphous phase has been identified based on X-ray diffraction analysis. The vanadium oxide plays the role as a glass-modifier and influences on BO3 ↔ BO4 conversion. The observed nonlinear variation in Tg with vanadium oxide increase, it reflects structural changes. The nonlinear variation of density and molar volume can be attributed to vanadium oxide incorporation have increased the number of Non-bridging oxygen (NBO'S).

Industrial Instrument Mechanic. Occupational Analyses Series.

ERIC Educational Resources Information Center

Dean, Ann; Zagorac, Mike; Bumbaka, Nick

This analysis covers tasks performed by an industrial instrument mechanic, an occupational title some provinces and territories of Canada have also identified as industrial instrumentation and instrument mechanic. A guide to analysis discusses development, structure, and validation method; scope of the occupation; trends; and safety. To facilitate…

Using Refined Regression Analysis To Assess The Ecological Services Of Restored Wetlands

EPA Science Inventory

A hierarchical approach to regression analysis of wetland water treatment was conducted to determine which factors are the most appropriate for characterizing wetlands of differing structure and function. We used this approach in an effort to identify the types and characteristi...

Farm Equipment Mechanic. Occupational Analyses Series.

ERIC Educational Resources Information Center

Ross, Douglas

This analysis covers tasks performed by a farm equipment mechanic, an occupational title some provinces and territories of Canada have also identified as agricultural machinery technician, agricultural mechanic, and farm equipment service technician. A guide to analysis discusses development, structure, and validation method; scope of the…

Recreation Vehicle Mechanic. Occupational Analyses Series.

ERIC Educational Resources Information Center

Dean, Ann; Embree, Rick

This analysis covers tasks performed by a recreation vehicle mechanic, an occupational title some provinces and territories of Canada have also identified as recreation vehicle technician and recreation vehicle service technician. A guide to analysis discusses development, structure, and validation method; scope of the occupation; trends; and…

An overview of STRUCTURE: applications, parameter settings, and supporting software

PubMed Central

Porras-Hurtado, Liliana; Ruiz, Yarimar; Santos, Carla; Phillips, Christopher; Carracedo, Ángel; Lareu, Maria V.

2013-01-01

Objectives: We present an up-to-date review of STRUCTURE software: one of the most widely used population analysis tools that allows researchers to assess patterns of genetic structure in a set of samples. STRUCTURE can identify subsets of the whole sample by detecting allele frequency differences within the data and can assign individuals to those sub-populations based on analysis of likelihoods. The review covers STRUCTURE's most commonly used ancestry and frequency models, plus an overview of the main applications of the software in human genetics including case-control association studies (CCAS), population genetics, and forensic analysis. The review is accompanied by supplementary material providing a step-by-step guide to running STRUCTURE. Methods: With reference to a worked example, we explore the effects of changing the principal analysis parameters on STRUCTURE results when analyzing a uniform set of human genetic data. Use of the supporting software: CLUMPP and distruct is detailed and we provide an overview and worked example of STRAT software, applicable to CCAS. Conclusion: The guide offers a simplified view of how STRUCTURE, CLUMPP, distruct, and STRAT can be applied to provide researchers with an informed choice of parameter settings and supporting software when analyzing their own genetic data. PMID:23755071

Optimum element density studies for finite-element thermal analysis of hypersonic aircraft structures

NASA Technical Reports Server (NTRS)

Ko, William L.; Olona, Timothy; Muramoto, Kyle M.

1990-01-01

Different finite element models previously set up for thermal analysis of the space shuttle orbiter structure are discussed and their shortcomings identified. Element density criteria are established for the finite element thermal modelings of space shuttle orbiter-type large, hypersonic aircraft structures. These criteria are based on rigorous studies on solution accuracies using different finite element models having different element densities set up for one cell of the orbiter wing. Also, a method for optimization of the transient thermal analysis computer central processing unit (CPU) time is discussed. Based on the newly established element density criteria, the orbiter wing midspan segment was modeled for the examination of thermal analysis solution accuracies and the extent of computation CPU time requirements. The results showed that the distributions of the structural temperatures and the thermal stresses obtained from this wing segment model were satisfactory and the computation CPU time was at the acceptable level. The studies offered the hope that modeling the large, hypersonic aircraft structures using high-density elements for transient thermal analysis is possible if a CPU optimization technique was used.

Phylogeographical analysis of the dominant multidrug-resistant H58 clade of Salmonella Typhi identifies inter- and intracontinental transmission events.

PubMed

Wong, Vanessa K; Baker, Stephen; Pickard, Derek J; Parkhill, Julian; Page, Andrew J; Feasey, Nicholas A; Kingsley, Robert A; Thomson, Nicholas R; Keane, Jacqueline A; Weill, François-Xavier; Edwards, David J; Hawkey, Jane; Harris, Simon R; Mather, Alison E; Cain, Amy K; Hadfield, James; Hart, Peter J; Thieu, Nga Tran Vu; Klemm, Elizabeth J; Glinos, Dafni A; Breiman, Robert F; Watson, Conall H; Kariuki, Samuel; Gordon, Melita A; Heyderman, Robert S; Okoro, Chinyere; Jacobs, Jan; Lunguya, Octavie; Edmunds, W John; Msefula, Chisomo; Chabalgoity, Jose A; Kama, Mike; Jenkins, Kylie; Dutta, Shanta; Marks, Florian; Campos, Josefina; Thompson, Corinne; Obaro, Stephen; MacLennan, Calman A; Dolecek, Christiane; Keddy, Karen H; Smith, Anthony M; Parry, Christopher M; Karkey, Abhilasha; Mulholland, E Kim; Campbell, James I; Dongol, Sabina; Basnyat, Buddha; Dufour, Muriel; Bandaranayake, Don; Naseri, Take Toleafoa; Singh, Shalini Pravin; Hatta, Mochammad; Newton, Paul; Onsare, Robert S; Isaia, Lupeoletalalei; Dance, David; Davong, Viengmon; Thwaites, Guy; Wijedoru, Lalith; Crump, John A; De Pinna, Elizabeth; Nair, Satheesh; Nilles, Eric J; Thanh, Duy Pham; Turner, Paul; Soeng, Sona; Valcanis, Mary; Powling, Joan; Dimovski, Karolina; Hogg, Geoff; Farrar, Jeremy; Holt, Kathryn E; Dougan, Gordon

2015-06-01

The emergence of multidrug-resistant (MDR) typhoid is a major global health threat affecting many countries where the disease is endemic. Here whole-genome sequence analysis of 1,832 Salmonella enterica serovar Typhi (S. Typhi) identifies a single dominant MDR lineage, H58, that has emerged and spread throughout Asia and Africa over the last 30 years. Our analysis identifies numerous transmissions of H58, including multiple transfers from Asia to Africa and an ongoing, unrecognized MDR epidemic within Africa itself. Notably, our analysis indicates that H58 lineages are displacing antibiotic-sensitive isolates, transforming the global population structure of this pathogen. H58 isolates can harbor a complex MDR element residing either on transmissible IncHI1 plasmids or within multiple chromosomal integration sites. We also identify new mutations that define the H58 lineage. This phylogeographical analysis provides a framework to facilitate global management of MDR typhoid and is applicable to similar MDR lineages emerging in other bacterial species.

Phylogeographical analysis of the dominant multidrug-resistant H58 clade of Salmonella Typhi identifies inter- and intracontinental transmission events

PubMed Central

Wong, Vanessa K; Baker, Stephen; Pickard, Derek J; Parkhill, Julian; Page, Andrew J; Feasey, Nicholas A; Kingsley, Robert A; Thomson, Nicholas R; Keane, Jacqueline A; Weill, François-Xavier; Edwards, David J; Hawkey, Jane; Harris, Simon R; Mather, Alison E; Cain, Amy K; Hadfield, James; Hart, Peter J; Thieu, Nga Tran Vu; Klemm, Elizabeth J; Glinos, Dafni A; Breiman, Robert F; Watson, Conall H; Kariuki, Samuel; Gordon, Melita A; Heyderman, Robert S; Okoro, Chinyere; Jacobs, Jan; Lunguya, Octavie; Edmunds, W John; Msefula, Chisomo; Chabalgoity, Jose A; Kama, Mike; Jenkins, Kylie; Dutta, Shanta; Marks, Florian; Campos, Josefina; Thompson, Corinne; Obaro, Stephen; MacLennan, Calman A; Dolecek, Christiane; Keddy, Karen H; Smith, Anthony M; Parry, Christopher M; Karkey, Abhilasha; Mulholland, E Kim; Campbell, James I; Dongol, Sabina; Basnyat, Buddha; Dufour, Muriel; Bandaranayake, Don; Naseri, Take Toleafoa; Singh, Shalini Pravin; Hatta, Mochammad; Newton, Paul; Onsare, Robert S; Isaia, Lupeoletalalei; Dance, David; Davong, Viengmon; Thwaites, Guy; Wijedoru, Lalith; Crump, John A; De Pinna, Elizabeth; Nair, Satheesh; Nilles, Eric J; Thanh, Duy Pham; Turner, Paul; Soeng, Sona; Valcanis, Mary; Powling, Joan; Dimovski, Karolina; Hogg, Geoff; Farrar, Jeremy; Holt, Kathryn E; Dougan, Gordon

2016-01-01

The emergence of multidrug-resistant (MDR) typhoid is a major global health threat affecting many countries where the disease is endemic. Here whole-genome sequence analysis of 1,832 Salmonella enterica serovar Typhi (S. Typhi) identifies a single dominant MDR lineage, H58, that has emerged and spread throughout Asia and Africa over the last 30 years. Our analysis identifies numerous transmissions of H58, including multiple transfers from Asia to Africa and an ongoing, unrecognized MDR epidemic within Africa itself. Notably, our analysis indicates that H58 lineages are displacing antibiotic-sensitive isolates, transforming the global population structure of this pathogen. H58 isolates can harbor a complex MDR element residing either on transmissible IncHI1 plasmids or within multiple chromosomal integration sites. We also identify new mutations that define the H58 lineage. This phylogeographical analysis provides a framework to facilitate global management of MDR typhoid and is applicable to similar MDR lineages emerging in other bacterial species. PMID:25961941

Evidence for cryptic northern refugia in the last glacial period in Cryptomeria japonica

PubMed Central

Kimura, Megumi K.; Uchiyama, Kentaro; Nakao, Katsuhiro; Moriguchi, Yoshinari; San Jose-Maldia, Lerma; Tsumura, Yoshihiko

2014-01-01

Background and Aims Distribution shifts and natural selection during past climatic changes are important factors in determining the genetic structure of forest species. In particular, climatic fluctuations during the Quaternary appear to have caused changes in the distribution ranges of plants, and thus strongly affected their genetic structure. This study was undertaken to identify the responses of the conifer Cryptomeria japonica, endemic to the Japanese Archipelago, to past climatic changes using a combination of phylogeography and species distribution modelling (SDM) methods. Specifically, this study focused on the locations of refugia during the last glacial maximum (LGM). Methods Genetic diversity and structure were examined using 20 microsatellite markers in 37 populations of C. japonica. The locations of glacial refugia were assessed using STRUCTURE analysis, and potential habitats under current and past climate conditions were predicted using SDM. The process of genetic divergence was also examined using the approximate Bayesian computation procedure (ABC) in DIY ABC to test the divergence time between the gene pools detected by the STRUCTURE analysis. Key Results STRUCTURE analysis identified four gene pools: northern Tohoku district; from Chubu to Chugoku district; from Tohoku to Shikoku district on the Pacific Ocean side of the Archipelago; and Yakushima Island. DIY ABC analysis indicated that the four gene pools diverged at the same time before the LGM. SDM also indicated potential northern cryptic refugia. Conclusions The combined evidence from microsatellites and SDM clearly indicates that climatic changes have shaped the genetic structure of C. japonica. The gene pool detected in northern Tohoku district is likely to have been established by cryptic northern refugia on the coast of the Japan Sea to the west of the Archipelago. The gene pool in Yakushima Island can probably be explained simply by long-term isolation from the other gene pools since the LGM. These results are supported by those of SDM and the predicted divergence time determined using ABC analysis. PMID:25355521

AbDb: antibody structure database—a database of PDB-derived antibody structures

PubMed Central

Ferdous, Saba

2018-01-01

Abstract In order to analyse structures of proteins of a particular class, these need to be extracted from Protein Data Bank (PDB) files. In the case of antibodies, there are a number of special considerations: (i) identifying antibodies in the PDB is not trivial, (ii) they may be crystallized with or without antigen, (iii) for analysis purposes, one is normally only interested in the Fv region of the antibody, (iv) structural analysis of epitopes, in particular, requires individual antibody–antigen complexes from a PDB file which may contain multiple copies of the same, or different, antibodies and (v) standard numbering schemes should be applied. Consequently, there is a need for a specialist resource containing pre-numbered non-redundant antibody Fv structures with their cognate antigens. We have created an automatically updated resource, AbDb, which collects the Fv regions from antibody structures using information from our SACS database which summarizes antibody structures from the PDB. PDB files containing multiple structures are split and numbered and each antibody structure is associated with its antigen where available. Antibody structures with only light or heavy chains have also been processed and sequences of antibodies are compared to identify multiple structures of the same antibody. The data may be queried on the basis of PDB code, or the name or species of the antibody or antigen, and the complete datasets may be downloaded. Database URL: www.bioinf.org.uk/abs/abdb/ PMID:29718130

Finite Element Analysis of Wrinkled Membrane Structures for Sunshield Applications

NASA Technical Reports Server (NTRS)

Johnston, John D.; Brodeur, Stephen J. (Technical Monitor)

2002-01-01

The deployable sunshield is an example of a gossamer structure envisioned for use on future space telescopes. The basic structure consists of multiple layers of pretensioned, thin-film membranes supported by deployable booms. The prediction and verification of sunshield dynamics has been identified as an area in need of technology development due to the difficulties inherent in predicting nonlinear structural behavior of the membranes and because of the challenges involved. in ground testing of the full-scale structure. This paper describes a finite element analysis of a subscale sunshield that has been subjected to ground testing in support of the Next Generation Space Telescope (NGST) program. The analysis utilizes a nonlinear material model that accounts for wrinkling of the membranes. Results are presented from a nonlinear static preloading analysis and subsequent dynamics analyses to illustrate baseline sunshield structural characteristics. Studies are then described which provide further insight into the effect of membrane. preload on sunshield dynamics and the performance of different membrane modeling techniques. Lastly, a comparison of analytical predictions and ground test results is presented.

Molecular Diversity and Population Structure of a Worldwide Collection of Cultivated Tetraploid Alfalfa (Medicago sativa subsp. sativa L.) Germplasm as Revealed by Microsatellite Markers

PubMed Central

Qiang, Haiping; Chen, Zhihong; Zhang, Zhengli; Wang, Xuemin; Gao, Hongwen; Wang, Zan

2015-01-01

Information on genetic diversity and population structure of a tetraploid alfalfa collection might be valuable in effective use of the genetic resources. A set of 336 worldwide genotypes of tetraploid alfalfa (Medicago sativa subsp. sativa L.) was genotyped using 85 genome-wide distributed SSR markers to reveal the genetic diversity and population structure in the alfalfa. Genetic diversity analysis identified a total of 1056 alleles across 85 marker loci. The average expected heterozygosity and polymorphism information content values were 0.677 and 0.638, respectively, showing high levels of genetic diversity in the cultivated tetraploid alfalfa germplasm. Comparison of genetic characteristics across chromosomes indicated regions of chromosomes 2 and 3 had the highest genetic diversity. A higher genetic diversity was detected in alfalfa landraces than that of wild materials and cultivars. Two populations were identified by the model-based population structure, principal coordinate and neighbor-joining analyses, corresponding to China and other parts of the world. However, lack of strictly correlation between clustering and geographic origins suggested extensive germplasm exchanges of alfalfa germplasm across diverse geographic regions. The quantitative analysis of the genetic diversity and population structure in this study could be useful for genetic and genomic analysis and utilization of the genetic variation in alfalfa breeding. PMID:25901573

Functional and Structural Analysis of the Conserved EFhd2 Protein

PubMed Central

Acosta, Yancy Ferrer; Rodríguez Cruz, Eva N.; Vaquer, Ana del C.; Vega, Irving E.

2013-01-01

EFhd2 is a novel protein conserved from C. elegans to H. sapiens. This novel protein was originally identified in cells of the immune and central nervous systems. However, it is most abundant in the central nervous system, where it has been found associated with pathological forms of the microtubule-associated protein tau. The physiological or pathological roles of EFhd2 are poorly understood. In this study, a functional and structural analysis was carried to characterize the molecular requirements for EFhd2’s calcium binding activity. The results showed that mutations of a conserved aspartate on either EF-hand motif disrupted the calcium binding activity, indicating that these motifs work in pair as a functional calcium binding domain. Furthermore, characterization of an identified single-nucleotide polymorphisms (SNP) that introduced a missense mutation indicates the importance of a conserved phenylalanine on EFhd2 calcium binding activity. Structural analysis revealed that EFhd2 is predominantly composed of alpha helix and random coil structures and that this novel protein is thermostable. EFhd2’s thermo stability depends on its N-terminus. In the absence of the N-terminus, calcium binding restored EFhd2’s thermal stability. Overall, these studies contribute to our understanding on EFhd2 functional and structural properties, and introduce it into the family of canonical EF-hand domain containing proteins. PMID:22973849

Functional and structural analysis of a highly-expressed Yersinia pestis small RNA following infection of cultured macrophages

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

Li, Nan; Hennelly, Scott P.; Stubben, Chris J.

Non-coding small RNAs (sRNAs) are found in practically all bacterial genomes and play important roles in regulating gene expression to impact bacterial metabolism, growth, and virulence. We performed transcriptomics analysis to identify sRNAs that are differentially expressed in Yersinia pestis that invaded the human macrophage cell line THP-1, compared to pathogens that remained extracellular in the presence of host. Using ultra high-throughput sequencing, we identified 37 novel and 143 previously known sRNAs in Y. pestis. In particular, the sRNA Ysr170 was highly expressed in intracellular Yersinia and exhibited a log2 fold change ~3.6 higher levels compared to extracellular bacteria. Wemore » found that knock-down of Ysr170 expression attenuated infection efficiency in cell culture and growth rate in response to different stressors. In addition, we applied selective 2’-hydroxyl acylation analyzed by primer extension (SHAPE) analysis to determine the secondary structure of Ysr170 and observed structural changes resulting from interactions with the aminoglycoside antibiotic gentamycin and the RNA chaperone Hfq. Interestingly, gentamicin stabilized helix 4 of Ysr170, which structurally resembles the native gentamicin 16S ribosomal binding site. Lastly, we modeled the tertiary structure of Ysr170 binding to gentamycin using RNA motif modeling. Integration of these experimental and structural methods can provide further insight into the design of small molecules that can inhibit function of sRNAs required for pathogen virulence.« less

Functional and structural analysis of a highly-expressed Yersinia pestis small RNA following infection of cultured macrophages

DOE PAGES

Li, Nan; Hennelly, Scott P.; Stubben, Chris J.; ...

2016-12-28

Non-coding small RNAs (sRNAs) are found in practically all bacterial genomes and play important roles in regulating gene expression to impact bacterial metabolism, growth, and virulence. We performed transcriptomics analysis to identify sRNAs that are differentially expressed in Yersinia pestis that invaded the human macrophage cell line THP-1, compared to pathogens that remained extracellular in the presence of host. Using ultra high-throughput sequencing, we identified 37 novel and 143 previously known sRNAs in Y. pestis. In particular, the sRNA Ysr170 was highly expressed in intracellular Yersinia and exhibited a log2 fold change ~3.6 higher levels compared to extracellular bacteria. Wemore » found that knock-down of Ysr170 expression attenuated infection efficiency in cell culture and growth rate in response to different stressors. In addition, we applied selective 2’-hydroxyl acylation analyzed by primer extension (SHAPE) analysis to determine the secondary structure of Ysr170 and observed structural changes resulting from interactions with the aminoglycoside antibiotic gentamycin and the RNA chaperone Hfq. Interestingly, gentamicin stabilized helix 4 of Ysr170, which structurally resembles the native gentamicin 16S ribosomal binding site. Lastly, we modeled the tertiary structure of Ysr170 binding to gentamycin using RNA motif modeling. Integration of these experimental and structural methods can provide further insight into the design of small molecules that can inhibit function of sRNAs required for pathogen virulence.« less

Structural identifiability analysis of a cardiovascular system model.

PubMed

Pironet, Antoine; Dauby, Pierre C; Chase, J Geoffrey; Docherty, Paul D; Revie, James A; Desaive, Thomas

2016-05-01

The six-chamber cardiovascular system model of Burkhoff and Tyberg has been used in several theoretical and experimental studies. However, this cardiovascular system model (and others derived from it) are not identifiable from any output set. In this work, two such cases of structural non-identifiability are first presented. These cases occur when the model output set only contains a single type of information (pressure or volume). A specific output set is thus chosen, mixing pressure and volume information and containing only a limited number of clinically available measurements. Then, by manipulating the model equations involving these outputs, it is demonstrated that the six-chamber cardiovascular system model is structurally globally identifiable. A further simplification is made, assuming known cardiac valve resistances. Because of the poor practical identifiability of these four parameters, this assumption is usual. Under this hypothesis, the six-chamber cardiovascular system model is structurally identifiable from an even smaller dataset. As a consequence, parameter values computed from limited but well-chosen datasets are theoretically unique. This means that the parameter identification procedure can safely be performed on the model from such a well-chosen dataset. Thus, the model may be considered suitable for use in diagnosis. Copyright © 2016 IPEM. Published by Elsevier Ltd. All rights reserved.

Evaluating the quality of NMR structures by local density of protons.

PubMed

Ban, Yih-En Andrew; Rudolph, Johannes; Zhou, Pei; Edelsbrunner, Herbert

2006-03-01

Evaluating the quality of experimentally determined protein structural models is an essential step toward identifying potential errors and guiding further structural refinement. Herein, we report the use of proton local density as a sensitive measure to assess the quality of nuclear magnetic resonance (NMR) structures. Using 256 high-resolution crystal structures with protons added and optimized, we show that the local density of different proton types display distinct distributions. These distributions can be characterized by statistical moments and are used to establish local density Z-scores for evaluating both global and local packing for individual protons. Analysis of 546 crystal structures at various resolutions shows that the local density Z-scores increase as the structural resolution decreases and correlate well with the ClashScore (Word et al. J Mol Biol 1999;285(4):1711-1733) generated by all atom contact analysis. Local density Z-scores for NMR structures exhibit a significantly wider range of values than for X-ray structures and demonstrate a combination of potentially problematic inflation and compression. Water-refined NMR structures show improved packing quality. Our analysis of a high-quality structural ensemble of ubiquitin refined against order parameters shows proton density distributions that correlate nearly perfectly with our standards derived from crystal structures, further validating our approach. We present an automated analysis and visualization tool for proton packing to evaluate the quality of NMR structures. 2005 Wiley-Liss, Inc.

Correspondence Analysis-Theory and Application in Management Accounting Research

NASA Astrophysics Data System (ADS)

Duller, Christine

2010-09-01

Correspondence analysis is an explanatory data analytic technique and is used to identify systematic relations between categorical variables. It is related to principal component analysis and the results provide information on the structure of categorical variables similar to the results given by a principal component analysis in case of metric variables. Classical correspondence analysis is designed two-dimensional, whereas multiple correspondence analysis is an extension to more than two variables. After an introductory overview of the idea and the implementation in standard software packages (PASW, SAS, R) an example in recent research is presented, which deals with strategic management accounting in family and non-family enterprises in Austria, where 70% to 80% of all enterprises can be classified as family firms. Although there is a growing body of literature focusing on various management issues in family firms, so far the state of the art of strategic management accounting in family firms is an empirically under-researched subject. In relevant literature only the (empirically untested) hypothesis can be found, that family firms tend to have less formalized management accounting systems than non-family enterprises. Creating a correspondence analysis will help to identify the underlying structure, which is responsible for differences in strategic management accounting.

Leaf flavonoids of Albizia lebbeck.

PubMed

el-Mousallamy, A M

1998-06-01

Two new tri-O-glycoside flavonols: kaempferol and quercetin 3-O-alpha-rhamnopyranosyl(1-->6)-beta-glucopyranosyl(1-->6)-beta- galactopyranosides, were identified from the leaves of Albizia lebbeck. Structures were established by conventional methods of analysis and confirmed by ESI-MS, 1H and 13C-NMR spectral analysis.

Lather (Interior Systems Mechanic). Occupational Analyses Series.

ERIC Educational Resources Information Center

Chapman, Mike; Chapman, Carol; MacLean, Margaret

This analysis covers tasks performed by a lather, an occupational title some provinces and territories of Canada have also identified as drywall and acoustical mechanic; interior systems installer; and interior systems mechanic. A guide to analysis discusses development, structure, and validation method; scope of the occupation; trends; and…

Bricklayer. Occupational Analyses Series.

ERIC Educational Resources Information Center

Cap, Orest; Cap, Ihor; Semenovych, Viktor

This analysis covers tasks performed by a bricklayer, an occupational title some provinces and territories of Canada have also identified as bricklayer-mason, brick and stone mason, and mason. A guide to analysis discusses development, structure, and validation method; scope of the occupation; trends; and safety. To facilitate understanding the…

Neural network system and methods for analysis of organic materials and structures using spectral data

DOEpatents

Meyer, B.J.; Sellers, J.P.; Thomsen, J.U.

1993-06-08

Apparatus and processes are described for recognizing and identifying materials. Characteristic spectra are obtained for the materials via spectroscopy techniques including nuclear magnetic resonance spectroscopy, infrared absorption analysis, x-ray analysis, mass spectroscopy and gas chromatography. Desired portions of the spectra may be selected and then placed in proper form and format for presentation to a number of input layer neurons in an offline neural network. The network is first trained according to a predetermined training process; it may then be employed to identify particular materials. Such apparatus and processes are particularly useful for recognizing and identifying organic compounds such as complex carbohydrates, whose spectra conventionally require a high level of training and many hours of hard work to identify, and are frequently indistinguishable from one another by human interpretation.

Patient-centered knowledge sharing in healthcare organizations: Identifying the external barriers.

PubMed

Zhou, Lihong

2017-12-01

This paper reports on a research study, which aims to identify, qualify, and theorize the external barriers that prevent and hinder the exercises and activities of patient-centered knowledge sharing (KS) in healthcare organizations. The project adopted a qualitative secondary analysis approach as the overarching methodology to guide the analysis of data collected in a previously completed research study. Specifically, 46 semi-structured interview data were included and analyzed using a thematic analysis approach. The secondary analysis showed that healthcare KS is strongly influenced and hindered by five external barriers: social belief and preference, cultural values, healthcare education structure, political decisions, and economic environment and constraints. Moreover, the research findings suggest that these external barriers cannot be overlooked in KS implementation and operation in healthcare organizations and should be carefully assessed beginning in the early stages of KS design and strategic planning. Based on the secondary analysis, this paper proposes a conceptual model, which will contribute to the development of hypotheses in the future for building a generalized knowledge. The case study used is Chinese healthcare, but the KS problems studied can be shared across international borders.

Micro-Raman spectroscopy and chemometrical analysis for the distinction of copper phthalocyanine polymorphs in paint layers.

PubMed

Defeyt, C; Van Pevenage, J; Moens, L; Strivay, D; Vandenabeele, P

2013-11-01

In art analysis, copper phthalocyanine (CuPc) is often identified as an important pigment (PB15) in 20th century artworks. Raman spectroscopy is a very valuable technique for the detection of this pigment in paint systems. However, PB15 is used in different polymorphic forms and identification of the polymorph could retrieve information on the production process of the pigment at the moment. Raman spectroscopy, being a molecular spectroscopic method of analysis, is able to discriminate between polymorphs of crystals. However, in the case of PB15, spectral interpretation is not straightforward, and Raman data treatment requires some improvements concerning the PB15 polymorphic discrimination in paints. Here, Raman spectroscopy is combined with chemometrical analysis in order to develop a procedure allowing us to identify the PB15 crystalline structure in painted layers and in artworks. The results obtained by Linear Discriminant Analysis (LDA), using intensity ratios as variables, demonstrate the ability of this procedure to predict the crystalline structure of a PB15 pigment in unknown paint samples. Copyright © 2013 Elsevier B.V. All rights reserved.

Multivariate information-theoretic measures reveal directed information structure and task relevant changes in fMRI connectivity.

PubMed

Lizier, Joseph T; Heinzle, Jakob; Horstmann, Annette; Haynes, John-Dylan; Prokopenko, Mikhail

2011-02-01

The human brain undertakes highly sophisticated information processing facilitated by the interaction between its sub-regions. We present a novel method for interregional connectivity analysis, using multivariate extensions to the mutual information and transfer entropy. The method allows us to identify the underlying directed information structure between brain regions, and how that structure changes according to behavioral conditions. This method is distinguished in using asymmetric, multivariate, information-theoretical analysis, which captures not only directional and non-linear relationships, but also collective interactions. Importantly, the method is able to estimate multivariate information measures with only relatively little data. We demonstrate the method to analyze functional magnetic resonance imaging time series to establish the directed information structure between brain regions involved in a visuo-motor tracking task. Importantly, this results in a tiered structure, with known movement planning regions driving visual and motor control regions. Also, we examine the changes in this structure as the difficulty of the tracking task is increased. We find that task difficulty modulates the coupling strength between regions of a cortical network involved in movement planning and between motor cortex and the cerebellum which is involved in the fine-tuning of motor control. It is likely these methods will find utility in identifying interregional structure (and experimentally induced changes in this structure) in other cognitive tasks and data modalities.

Population genetic structure in a social landscape: barley in a traditional Ethiopian agricultural system

PubMed Central

Samberg, Leah H; Fishman, Lila; Allendorf, Fred W

2013-01-01

Conservation strategies are increasingly driven by our understanding of the processes and patterns of gene flow across complex landscapes. The expansion of population genetic approaches into traditional agricultural systems requires understanding how social factors contribute to that landscape, and thus to gene flow. This study incorporates extensive farmer interviews and population genetic analysis of barley landraces (Hordeum vulgare) to build a holistic picture of farmer-mediated geneflow in an ancient, traditional agricultural system in the highlands of Ethiopia. We analyze barley samples at 14 microsatellite loci across sites at varying elevations and locations across a contiguous mountain range, and across farmer-identified barley types and management strategies. Genetic structure is analyzed using population-based and individual-based methods, including measures of population differentiation and genetic distance, multivariate Principal Coordinate Analysis, and Bayesian assignment tests. Phenotypic analysis links genetic patterns to traits identified by farmers. We find that differential farmer management strategies lead to markedly different patterns of population structure across elevation classes and barley types. The extent to which farmer seed management appears as a stronger determinant of spatial structure than the physical landscape highlights the need for incorporation of social, landscape, and genetic data for the design of conservation strategies in human-influenced landscapes. PMID:24478796

Dynamics explorer: Interface definition study, volume 1

NASA Technical Reports Server (NTRS)

1978-01-01

Work done in response to the work statement wherein a specific deliverable was not identified but where design and analysis tasks were identified is reported. The summary and baseline change list is included along with design notes for the spacecraft system, thermal subsystem, power subsystem, communications subsystem, plasma wave instrument interface definition, and the structure.

Wind erosion in semiarid landscapes: Predictive models and remote sensing methods for the influence of vegetation

NASA Technical Reports Server (NTRS)

Musick, H. Brad

1993-01-01

The objectives of this research are: to develop and test predictive relations for the quantitative influence of vegetation canopy structure on wind erosion of semiarid rangeland soils, and to develop remote sensing methods for measuring the canopy structural parameters that determine sheltering against wind erosion. The influence of canopy structure on wind erosion will be investigated by means of wind-tunnel and field experiments using structural variables identified by the wind-tunnel and field experiments using model roughness elements to simulate plant canopies. The canopy structural variables identified by the wind-tunnel and field experiments as important in determining vegetative sheltering against wind erosion will then be measured at a number of naturally vegetated field sites and compared with estimates of these variables derived from analysis of remotely sensed data.

Theses "Discussion" Sections: A Structural Move Analysis

ERIC Educational Resources Information Center

Nodoushan, Mohammad Ali Salmani; Khakbaz, Nafiseh

2011-01-01

The current study aimed at finding the probable differences between the move structure of Iranian MA graduates' thesis discussion subgenres and those of their non-Iranian counterparts, on the one hand, and those of journal paper authors, on the other. It also aimed at identifying the moves that are considered obligatory, conventional, or optional…

Factor Structure of the Children's Behavior Questionnaire in Children with Williams Syndrome

ERIC Educational Resources Information Center

Leyfer, Ovsanna; John, Angela E.; Woodruff-Borden, Janet; Mervis, Carolyn B.

2012-01-01

To examine the factor structure of temperament in 5-10-year-olds with Williams syndrome, an exploratory factor analysis was conducted on the responses of parents of 192 children on the children's behavior questionnaire. Four factors were identified. Two corresponded to factors reported for typically developing children: effortful control and…

The Relationship of Morphological Analysis and Morphological Decoding to Reading Comprehension

ERIC Educational Resources Information Center

Deacon, S. Hélène; Tong, Xiuli; Francis, Kathryn

2017-01-01

The ultimate goal of children's reading development is the full and fluid understanding of texts. Morphological structure awareness, or children's awareness of the minimal units of meaning in language, has been identified as a key skill influencing reading comprehension. Here, we evaluate the roles of morphological structure awareness and two…

Document boundary determination using structural and lexical analysis

NASA Astrophysics Data System (ADS)

Taghva, Kazem; Cartright, Marc-Allen

2009-01-01

The document boundary determination problem is the process of identifying individual documents in a stack of papers. In this paper, we report on a classification system for automation of this process. The system employs features based on document structure and lexical content. We also report on experimental results to support the effectiveness of this system.

Chinese American Post-Secondary Achievement and Attainment: A Cultural and Structural Analysis

ERIC Educational Resources Information Center

Pearce, Richard R.; Lin, Zeng

2007-01-01

In this article, the authors compare Chinese American post-secondary educational attainment with that of White Americans and, in identifying those factors that most strongly account for success, argue that commonalities exist among social structural factors, while distinct differences are evident among cultural capital factors. The article rejects…

Agonistic reciprocity is associated with reduced male reproductive success within haremic social networks

PubMed Central

Solomon-Lane, Tessa K.; Pradhan, Devaleena S.; Willis, Madelyne C.; Grober, Matthew S.

2015-01-01

While individual variation in social behaviour is ubiquitous and causes social groups to differ in structure, how these structural differences affect fitness remains largely unknown. We used social network analysis of replicate bluebanded goby (Lythrypnus dalli) harems to identify the reproductive correlates of social network structure. In stable groups, we quantified agonistic behaviour, reproduction and steroid hormones, which can both affect and respond to social/reproductive cues. We identified distinct, optimal social structures associated with different reproductive measures. Male hatching success (HS) was negatively associated with agonistic reciprocity, a network structure that describes whether subordinates ‘reciprocated’ agonism received from dominants. Egg laying was associated with the individual network positions of the male and dominant female. Thus, males face a trade-off between promoting structures that facilitate egg laying versus HS. Whether this reproductive conflict is avoidable remains to be determined. We also identified different social and/or reproductive roles for 11-ketotestosterone, 17β-oestradiol and cortisol, suggesting that specific neuroendocrine mechanisms may underlie connections between network structure and fitness. This is one of the first investigations of the reproductive and neuroendocrine correlates of social behaviour and network structure in replicate, naturalistic social groups and supports network structure as an important target for natural selection. PMID:26156769

Non-traditional Infrasound Deployment

NASA Astrophysics Data System (ADS)

McKenna, M. H.; McComas, S.; Simpson, C. P.; Diaz-Alvarez, H.; Costley, R. D.; Hayward, C.; Golden, P.; Endress, A.

2017-12-01

Historically, infrasound arrays have been deployed in rural environments where anthropological noise sources are limited. As interest in monitoring low energy sources at local distances grows in the infrasound community, it will be vital to understand how to monitor infrasound sources in an urban environment. Arrays deployed in urban centers have to overcome the decreased signal-to-noise ratio and reduced amount of real estate available to deploy an array. To advance the understanding of monitoring infrasound sources in urban environments, local and regional infrasound arrays were deployed on building rooftops on the campus at Southern Methodist University (SMU), and data were collected for one seasonal cycle. The data were evaluated for structural source signals (continuous-wave packets), and when a signal was identified, the back azimuth to the source was determined through frequency-wavenumber analysis. This information was used to identify hypothesized structural sources; these sources were verified through direct measurement and dynamic structural analysis modeling. In addition to the rooftop arrays, a camouflaged infrasound sensor was installed on the SMU campus and evaluated to determine its effectiveness for wind noise reduction. Permission to publish was granted by Director, Geotechnical and Structures Laboratory.

MOTIVATION INTERNALIZATION AND SIMPLEX STRUCTURE IN SELF-DETERMINATION THEORY.

PubMed

Ünlü, Ali; Dettweiler, Ulrich

2015-12-01

Self-determination theory, as proposed by Deci and Ryan, postulated different types of motivation regulation. As to the introjected and identified regulation of extrinsic motivation, their internalizations were described as "somewhat external" and "somewhat internal" and remained undetermined in the theory. This paper introduces a constrained regression analysis that allows these vaguely expressed motivations to be estimated in an "optimal" manner, in any given empirical context. The approach was even generalized and applied for simplex structure analysis in self-determination theory. The technique was exemplified with an empirical study comparing science teaching in a classical school class versus an expeditionary outdoor program. Based on a sample of 84 German pupils (43 girls, 41 boys, 10 to 12 years old), data were collected using the German version of the Academic Self-Regulation Questionnaire. The science-teaching format was seen to not influence the pupils' internalization of identified regulation. The internalization of introjected regulation differed and shifted more toward the external pole in the outdoor teaching format. The quantification approach supported the simplex structure of self-determination theory, whereas correlations may disconfirm the simplex structure.

A quadratically regularized functional canonical correlation analysis for identifying the global structure of pleiotropy with NGS data

PubMed Central

Zhu, Yun; Fan, Ruzong; Xiong, Momiao

2017-01-01

Investigating the pleiotropic effects of genetic variants can increase statistical power, provide important information to achieve deep understanding of the complex genetic structures of disease, and offer powerful tools for designing effective treatments with fewer side effects. However, the current multiple phenotype association analysis paradigm lacks breadth (number of phenotypes and genetic variants jointly analyzed at the same time) and depth (hierarchical structure of phenotype and genotypes). A key issue for high dimensional pleiotropic analysis is to effectively extract informative internal representation and features from high dimensional genotype and phenotype data. To explore correlation information of genetic variants, effectively reduce data dimensions, and overcome critical barriers in advancing the development of novel statistical methods and computational algorithms for genetic pleiotropic analysis, we proposed a new statistic method referred to as a quadratically regularized functional CCA (QRFCCA) for association analysis which combines three approaches: (1) quadratically regularized matrix factorization, (2) functional data analysis and (3) canonical correlation analysis (CCA). Large-scale simulations show that the QRFCCA has a much higher power than that of the ten competing statistics while retaining the appropriate type 1 errors. To further evaluate performance, the QRFCCA and ten other statistics are applied to the whole genome sequencing dataset from the TwinsUK study. We identify a total of 79 genes with rare variants and 67 genes with common variants significantly associated with the 46 traits using QRFCCA. The results show that the QRFCCA substantially outperforms the ten other statistics. PMID:29040274

Do anesthetics harm the developing human brain? An integrative analysis of animal and human studies.

PubMed

Lin, Erica P; Lee, Jeong-Rim; Lee, Christopher S; Deng, Meng; Loepke, Andreas W

Anesthetics that permit surgical procedures and stressful interventions have been found to cause structural brain abnormalities and functional impairment in immature animals, generating extensive concerns among clinicians, parents, and government regulators regarding the safe use of these drugs in young children. Critically important questions remain, such as the exact age at which the developing brain is most vulnerable to the effects of anesthetic exposure, whether a particular age exists beyond which anesthetics are devoid of long-term effects on the brain, and whether any specific exposure duration exists that does not lead to deleterious effects. Accordingly, the present analysis attempts to put the growing body of animal studies, which we identified to include >440 laboratory studies to date, into a translational context, by integrating the preclinical data on brain structure and function with clinical results attained from human neurocognitive studies, which currently exceed 30 studies. Our analysis demonstrated no clear exposure duration threshold below which no structural injury or subsequent cognitive abnormalities occurred. Animal data did not clearly identify a specific age beyond which anesthetic exposure did not cause any structural or functional abnormalities. Several potential mitigating strategies were found, however, no general anesthetic was identified that consistently lacked neurodegenerative properties and could be recommended over other anesthetics. It therefore is imperative, to expand efforts to devise safer anesthetic techniques and mitigating strategies, even before long-term alterations in brain development are unequivocally confirmed to occur in millions of young children undergoing anesthesia every year. Copyright © 2016 Elsevier Inc. All rights reserved.

Network Analysis of Protein Adaptation: Modeling the Functional Impact of Multiple Mutations

PubMed Central

Beleva Guthrie, Violeta; Masica, David L; Fraser, Andrew; Federico, Joseph; Fan, Yunfan; Camps, Manel; Karchin, Rachel

2018-01-01

Abstract The evolution of new biochemical activities frequently involves complex dependencies between mutations and rapid evolutionary radiation. Mutation co-occurrence and covariation have previously been used to identify compensating mutations that are the result of physical contacts and preserve protein function and fold. Here, we model pairwise functional dependencies and higher order interactions that enable evolution of new protein functions. We use a network model to find complex dependencies between mutations resulting from evolutionary trade-offs and pleiotropic effects. We present a method to construct these networks and to identify functionally interacting mutations in both extant and reconstructed ancestral sequences (Network Analysis of Protein Adaptation). The time ordering of mutations can be incorporated into the networks through phylogenetic reconstruction. We apply NAPA to three distantly homologous β-lactamase protein clusters (TEM, CTX-M-3, and OXA-51), each of which has experienced recent evolutionary radiation under substantially different selective pressures. By analyzing the network properties of each protein cluster, we identify key adaptive mutations, positive pairwise interactions, different adaptive solutions to the same selective pressure, and complex evolutionary trajectories likely to increase protein fitness. We also present evidence that incorporating information from phylogenetic reconstruction and ancestral sequence inference can reduce the number of spurious links in the network, whereas preserving overall network community structure. The analysis does not require structural or biochemical data. In contrast to function-preserving mutation dependencies, which are frequently from structural contacts, gain-of-function mutation dependencies are most commonly between residues distal in protein structure. PMID:29522102

Lean methodology for performance improvement in the trauma discharge process.

PubMed

O'Mara, Michael Shaymus; Ramaniuk, Aliaksandr; Graymire, Vickie; Rozzell, Monica; Martin, Stacey

2014-07-01

High-volume, complex services such as trauma and acute care surgery are at risk for inefficiency. Lean process improvement can reduce health care waste. Lean allows a structured look at processes not easily amenable to analysis. We applied lean methodology to the current state of communication and discharge planning on an urban trauma service, citing areas for improvement. A lean process mapping event was held. The process map was used to identify areas for immediate analysis and intervention-defining metrics for the stakeholders. After intervention, new performance was assessed by direct data evaluation. The process was completed with an analysis of effect and plans made for addressing future focus areas. The primary area of concern identified was interservice communication. Changes centering on a standardized morning report structure reduced the number of consult questions unanswered from 67% to 34% (p = 0.0021). Physical therapy rework was reduced from 35% to 19% (p = 0.016). Patients admitted to units not designated to the trauma service had 1.6 times longer stays (p < 0.0001). The lean process lasted 8 months, and three areas for new improvement were identified: (1) the off-unit patients; (2) patients with length of stay more than 15 days contribute disproportionately to length of stay; and (3) miscommunication exists around patient education at discharge. Lean process improvement is a viable means of health care analysis. When applied to a trauma service with 4,000 admissions annually, lean identifies areas ripe for improvement. Our inefficiencies surrounded communication and patient localization. Strategies arising from the input of all stakeholders led to real solutions for communication through a face-to-face morning report and identified areas for ongoing improvement. This focuses resource use and identifies areas for improvement of throughput in care delivery.

Structural domains and main-chain flexibility in prion proteins.

PubMed

Blinov, N; Berjanskii, M; Wishart, D S; Stepanova, M

2009-02-24

In this study we describe a novel approach to define structural domains and to characterize the local flexibility in both human and chicken prion proteins. The approach we use is based on a comprehensive theory of collective dynamics in proteins that was recently developed. This method determines the essential collective coordinates, which can be found from molecular dynamics trajectories via principal component analysis. Under this particular framework, we are able to identify the domains where atoms move coherently while at the same time to determine the local main-chain flexibility for each residue. We have verified this approach by comparing our results for the predicted dynamic domain systems with the computed main-chain flexibility profiles and the NMR-derived random coil indexes for human and chicken prion proteins. The three sets of data show excellent agreement. Additionally, we demonstrate that the dynamic domains calculated in this fashion provide a highly sensitive measure of protein collective structure and dynamics. Furthermore, such an analysis is capable of revealing structural and dynamic properties of proteins that are inaccessible to the conventional assessment of secondary structure. Using the collective dynamic simulation approach described here along with a high-temperature simulations of unfolding of human prion protein, we have explored whether locations of relatively low stability could be identified where the unfolding process could potentially be facilitated. According to our analysis, the locations of relatively low stability may be associated with the beta-sheet formed by strands S1 and S2 and the adjacent loops, whereas helix HC appears to be a relatively stable part of the protein. We suggest that this kind of structural analysis may provide a useful background for a more quantitative assessment of potential routes of spontaneous misfolding in prion proteins.

IUTAM Symposium and NATO Advanced Research Workshop on Interpretation of Time Series from Nonlinear Mechanical Systems Held in Coventry, England on 26-30 August 1991. Conference Abstracts

DTIC Science & Technology

1991-08-01

day oscillation in the extratropical atmosphere as identified by multi-channel singular spectrum analysis 10:25 Coffee Break 10:50 Read Chaotic...day oscillation in the extratropical atmosphere as identified by multi-channel singular spectrum analysis M. Kimoto, M. Ghil and K.-C. Mo ABSTRACT...The three-dimensional spatial structure of an oscillatory mode in the Northern Hemisphere (NH) extratropics will be describe.d The oscillation is

Coevolution analysis of Hepatitis C virus genome to identify the structural and functional dependency network of viral proteins

NASA Astrophysics Data System (ADS)

Champeimont, Raphaël; Laine, Elodie; Hu, Shuang-Wei; Penin, Francois; Carbone, Alessandra

2016-05-01

A novel computational approach of coevolution analysis allowed us to reconstruct the protein-protein interaction network of the Hepatitis C Virus (HCV) at the residue resolution. For the first time, coevolution analysis of an entire viral genome was realized, based on a limited set of protein sequences with high sequence identity within genotypes. The identified coevolving residues constitute highly relevant predictions of protein-protein interactions for further experimental identification of HCV protein complexes. The method can be used to analyse other viral genomes and to predict the associated protein interaction networks.

Probabilistic Structural Analysis Methods for select space propulsion system components (PSAM). Volume 2: Literature surveys of critical Space Shuttle main engine components

NASA Technical Reports Server (NTRS)

Rajagopal, K. R.

1992-01-01

The technical effort and computer code development is summarized. Several formulations for Probabilistic Finite Element Analysis (PFEA) are described with emphasis on the selected formulation. The strategies being implemented in the first-version computer code to perform linear, elastic PFEA is described. The results of a series of select Space Shuttle Main Engine (SSME) component surveys are presented. These results identify the critical components and provide the information necessary for probabilistic structural analysis. Volume 2 is a summary of critical SSME components.

Structured Analysis for the Logistic Support Analysis (LSA) Task and the Integrated Logistic Support (ILS) Element. Structured Analysis - ILS Assessment Element E11. Design Influence

DTIC Science & Technology

1989-01-01

format size of this report, the full identifying entry may well be forcibly shortened, thereby introducing the possibility of misunderstanding. Therefore...OF MATERIEL" 3d . "AR 570-9, "MANPOWER AND EQUIPMENT CONTROL - HOST NATION SUPPORT" 2. AR 700-9, "POLICIES OF THE ARMY LOGISTIC SYSTEM" 3. AR 700-82...PERSONNEL 4. TRAINING 5. SYSTEM SAFETY 6. HEALTH HAZARDS. TEE ASSESSMENT Or MANPRINT INFLUENCE ON DESIGNS IS ADDRESSED IN SIX (6) SPECIFIC AREAS IN

RNA-Seq Based Transcriptional Map of Bovine Respiratory Disease Pathogen “Histophilus somni 2336”

PubMed Central

Kumar, Ranjit; Lawrence, Mark L.; Watt, James; Cooksey, Amanda M.; Burgess, Shane C.; Nanduri, Bindu

2012-01-01

Genome structural annotation, i.e., identification and demarcation of the boundaries for all the functional elements in a genome (e.g., genes, non-coding RNAs, proteins and regulatory elements), is a prerequisite for systems level analysis. Current genome annotation programs do not identify all of the functional elements of the genome, especially small non-coding RNAs (sRNAs). Whole genome transcriptome analysis is a complementary method to identify “novel” genes, small RNAs, regulatory regions, and operon structures, thus improving the structural annotation in bacteria. In particular, the identification of non-coding RNAs has revealed their widespread occurrence and functional importance in gene regulation, stress and virulence. However, very little is known about non-coding transcripts in Histophilus somni, one of the causative agents of Bovine Respiratory Disease (BRD) as well as bovine infertility, abortion, septicemia, arthritis, myocarditis, and thrombotic meningoencephalitis. In this study, we report a single nucleotide resolution transcriptome map of H. somni strain 2336 using RNA-Seq method. The RNA-Seq based transcriptome map identified 94 sRNAs in the H. somni genome of which 82 sRNAs were never predicted or reported in earlier studies. We also identified 38 novel potential protein coding open reading frames that were absent in the current genome annotation. The transcriptome map allowed the identification of 278 operon (total 730 genes) structures in the genome. When compared with the genome sequence of a non-virulent strain 129Pt, a disproportionate number of sRNAs (∼30%) were located in genomic region unique to strain 2336 (∼18% of the total genome). This observation suggests that a number of the newly identified sRNAs in strain 2336 may be involved in strain-specific adaptations. PMID:22276113

RNA-seq based transcriptional map of bovine respiratory disease pathogen "Histophilus somni 2336".

PubMed

Kumar, Ranjit; Lawrence, Mark L; Watt, James; Cooksey, Amanda M; Burgess, Shane C; Nanduri, Bindu

2012-01-01

Genome structural annotation, i.e., identification and demarcation of the boundaries for all the functional elements in a genome (e.g., genes, non-coding RNAs, proteins and regulatory elements), is a prerequisite for systems level analysis. Current genome annotation programs do not identify all of the functional elements of the genome, especially small non-coding RNAs (sRNAs). Whole genome transcriptome analysis is a complementary method to identify "novel" genes, small RNAs, regulatory regions, and operon structures, thus improving the structural annotation in bacteria. In particular, the identification of non-coding RNAs has revealed their widespread occurrence and functional importance in gene regulation, stress and virulence. However, very little is known about non-coding transcripts in Histophilus somni, one of the causative agents of Bovine Respiratory Disease (BRD) as well as bovine infertility, abortion, septicemia, arthritis, myocarditis, and thrombotic meningoencephalitis. In this study, we report a single nucleotide resolution transcriptome map of H. somni strain 2336 using RNA-Seq method.The RNA-Seq based transcriptome map identified 94 sRNAs in the H. somni genome of which 82 sRNAs were never predicted or reported in earlier studies. We also identified 38 novel potential protein coding open reading frames that were absent in the current genome annotation. The transcriptome map allowed the identification of 278 operon (total 730 genes) structures in the genome. When compared with the genome sequence of a non-virulent strain 129Pt, a disproportionate number of sRNAs (∼30%) were located in genomic region unique to strain 2336 (∼18% of the total genome). This observation suggests that a number of the newly identified sRNAs in strain 2336 may be involved in strain-specific adaptations.

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.

Application of phyto-indication and radiocesium indicative methods for microrelief mapping

NASA Astrophysics Data System (ADS)

Panidi, E.; Trofimetz, L.; Sokolova, J.

2016-04-01

Remote sensing technologies are widely used for production of Digital Elevation Models (DEMs), and geomorphometry techniques are valuable tools for DEM analysis. One of the broadly used applications of these technologies and techniques is relief mapping. In the simplest case, we can identify relief structures using DEM analysis, and produce a map or map series to show the relief condition. However, traditional techniques might fail when used for mapping microrelief structures (structures below ten meters in size). In this case high microrelief dynamics lead to technological and conceptual difficulties. Moreover, erosion of microrelief structures cannot be detected at the initial evolution stage using DEM modelling and analysis only. In our study, we investigate the possibilities and specific techniques for allocation of erosion microrelief structures, and mapping techniques for the microrelief derivatives (e.g. quantitative parameters of microrelief). Our toolset includes the analysis of spatial redistribution of the soil pollutants and phyto-indication analysis, which complement the common DEM modelling and geomorphometric analysis. We use field surveys produced at the test area, which is arable territory with high erosion risks. Our main conclusion at the current stage is that the indicative methods (i.e. radiocesium and phyto-indication methods) are effective for allocation of the erosion microrelief structures. Also, these methods need to be formalized for convenient use.

Primary and secondary structural analyses of glutathione S-transferase pi from human placenta.

PubMed

Ahmad, H; Wilson, D E; Fritz, R R; Singh, S V; Medh, R D; Nagle, G T; Awasthi, Y C; Kurosky, A

1990-05-01

The primary structure of glutathione S-transferase (GST) pi from a single human placenta was determined. The structure was established by chemical characterization of tryptic and cyanogen bromide peptides as well as automated sequence analysis of the intact enzyme. The structural analysis indicated that the protein is comprised of 209 amino acid residues and gave no evidence of post-translational modifications. The amino acid sequence differed from that of the deduced amino acid sequence determined by nucleotide sequence analysis of a cDNA clone (Kano, T., Sakai, M., and Muramatsu, M., 1987, Cancer Res. 47, 5626-5630) at position 104 which contained both valine and isoleucine whereas the deduced sequence from nucleotide sequence analysis identified only isoleucine at this position. These results demonstrated that in the one individual placenta studied at least two GST pi genes are coexpressed, probably as a result of allelomorphism. Computer assisted consensus sequence evaluation identified a hydrophobic region in GST pi (residues 155-181) that was predicted to be either a buried transmembrane helical region or a signal sequence region. The significance of this hydrophobic region was interpreted in relation to the mode of action of the enzyme especially in regard to the potential involvement of a histidine in the active site mechanism. A comparison of the chemical similarity of five known human GST complete enzyme structures, one of pi, one of mu, two of alpha, and one microsomal, gave evidence that all five enzymes have evolved by a divergent evolutionary process after gene duplication, with the microsomal enzyme representing the most divergent form.

Insights into Bacteriophage T5 Structure from Analysis of Its Morphogenesis Genes and Protein Components

PubMed Central

Zivanovic, Yvan; Confalonieri, Fabrice; Ponchon, Luc; Lurz, Rudi; Chami, Mohamed; Flayhan, Ali; Renouard, Madalena; Huet, Alexis; Decottignies, Paulette; Davidson, Alan R.; Breyton, Cécile

2014-01-01

Bacteriophage T5 represents a large family of lytic Siphoviridae infecting Gram-negative bacteria. The low-resolution structure of T5 showed the T=13 geometry of the capsid and the unusual trimeric organization of the tail tube, and the assembly pathway of the capsid was established. Although major structural proteins of T5 have been identified in these studies, most of the genes encoding the morphogenesis proteins remained to be identified. Here, we combine a proteomic analysis of T5 particles with a bioinformatic study and electron microscopic immunolocalization to assign function to the genes encoding the structural proteins, the packaging proteins, and other nonstructural components required for T5 assembly. A head maturation protease that likely accounts for the cleavage of the different capsid proteins is identified. Two other proteins involved in capsid maturation add originality to the T5 capsid assembly mechanism: the single head-to-tail joining protein, which closes the T5 capsid after DNA packaging, and the nicking endonuclease responsible for the single-strand interruptions in the T5 genome. We localize most of the tail proteins that were hitherto uncharacterized and provide a detailed description of the tail tip composition. Our findings highlight novel variations of viral assembly strategies and of virion particle architecture. They further recommend T5 for exploring phage structure and assembly and for deciphering conformational rearrangements that accompany DNA transfer from the capsid to the host cytoplasm. PMID:24198424

Structural comparison of four different antibodies interacting with human papillomavirus 16 and mechanisms of neutralization

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

Guan, Jian; Bywaters, Stephanie M.; Brendle, Sarah A.

2015-09-15

Cryo-electron microscopy (cryo-EM) was used to solve the structures of human papillomavirus type 16 (HPV16) complexed with fragments of antibody (Fab) from three different neutralizing monoclonals (mAbs): H16.1A, H16.14J, and H263.A2. The structure-function analysis revealed predominantly monovalent binding of each Fab with capsid interactions that involved multiple loops from symmetry related copies of the major capsid protein. The residues identified in each Fab-virus interface map to a conformational groove on the surface of the capsomer. In addition to the known involvement of the FG and HI loops, the DE loop was also found to constitute the core of each epitope.more » Surprisingly, the epitope mapping also identified minor contributions by EF and BC loops. Complementary immunological assays included mAb and Fab neutralization. The specific binding characteristics of mAbs correlated with different neutralizing behaviors in pre- and post-attachment neutralization assays. - Highlights: • We present HPV16-Fab complexes from neutralizing mAbs: H16.1A, H16.14J, and H263.A2. • The structure-function analysis revealed predominantly monovalent binding of each mAb. • Capsid–Fab interactions involved multiple loops from symmetry related L1 proteins. • Besides the known FG and HI loops, epitope mapping also identified DE, EF, and BC loops. • Neutralizing assays complement the structures to show multiple neutralization mechanisms.« less

Matthew Jones House: Recommendations for Treatment

DTIC Science & Technology

2016-04-01

strongly recommend that a structural engineer be contracted to provide in depth analysis and monitoring. The decay of the historic timber top plates...of the structure . This report summarizes the research and findings by the NCPTT. It also includes an engineer’s report and other supplemental in...NEEDED. DO NOT RETURN IT TO THE ORIGINATOR. ERDC/CERL CR-16-1 iii Foreword After identifying a variety of structural issues with the Matthew Jones

Designing a ticket to ride with the Cognitive Work Analysis Design Toolkit.

PubMed

Read, Gemma J M; Salmon, Paul M; Lenné, Michael G; Jenkins, Daniel P

2015-01-01

Cognitive work analysis has been applied in the design of numerous sociotechnical systems. The process used to translate analysis outputs into design concepts, however, is not always clear. Moreover, structured processes for translating the outputs of ergonomics methods into concrete designs are lacking. This paper introduces the Cognitive Work Analysis Design Toolkit (CWA-DT), a design approach which has been developed specifically to provide a structured means of incorporating cognitive work analysis outputs in design using design principles and values derived from sociotechnical systems theory. This paper outlines the CWA-DT and describes its application in a public transport ticketing design case study. Qualitative and quantitative evaluations of the process provide promising early evidence that the toolkit fulfils the evaluation criteria identified for its success, with opportunities for improvement also highlighted. The Cognitive Work Analysis Design Toolkit has been developed to provide ergonomics practitioners with a structured approach for translating the outputs of cognitive work analysis into design solutions. This paper demonstrates an application of the toolkit and provides evaluation findings.

Linguistic methodology for the analysis of aviation accidents

NASA Technical Reports Server (NTRS)

Goguen, J. A.; Linde, C.

1983-01-01

A linguistic method for the analysis of small group discourse, was developed and the use of this method on transcripts of commercial air transpot accidents is demonstrated. The method identifies the discourse types that occur and determine their linguistic structure; it identifies significant linguistic variables based upon these structures or other linguistic concepts such as speech act and topic; it tests hypotheses that support significance and reliability of these variables; and it indicates the implications of the validated hypotheses. These implications fall into three categories: (1) to train crews to use more nearly optimal communication patterns; (2) to use linguistic variables as indices for aspects of crew performance such as attention; and (3) to provide guidelines for the design of aviation procedures and equipment, especially those that involve speech.

Insulator (Heat and Frost). Occupational Analyses Series.

ERIC Educational Resources Information Center

McRory, Aline; Ally, Mohamed

This analysis covers tasks performed by an insulator, an occupational title some provinces and territories of Canada have also identified as heat and frost insulator. A guide to analysis discusses development, structure, and validation method; scope of the occupation; trends; and safety. To facilitate understanding the nature of the occupation,…

Establishing Evidence for Internal Structure Using Exploratory Factor Analysis

ERIC Educational Resources Information Center

Watson, Joshua C.

2017-01-01

Exploratory factor analysis (EFA) is a data reduction technique used to condense data into smaller sets of summary variables by identifying underlying factors potentially accounting for patterns of collinearity among said variables. Using an illustrative example, the 5 general steps of EFA are described with best practices for decision making…

Truck and Transport Mechanic. Occupational Analyses Series.

ERIC Educational Resources Information Center

McRory, Aline; Ally, Mohamed

This analysis covers tasks performed by a truck and transport mechanic, an occupational title some provinces and territories of Canada have also identified as commercial transport vehicle mechanic; transport truck mechanic; truck and coach technician; and truck and transport service technician. A guide to analysis discusses development, structure,…

Fostering Deeper Critical Inquiry with Causal Layered Analysis

ERIC Educational Resources Information Center

Haigh, Martin

2016-01-01

Causal layered analysis (CLA) is a technique that enables deeper critical inquiry through a structured exploration of four layers of causation. CLA's layers reach down from the surface litany of media understanding, through the layer of systemic causes identified by conventional research, to underpinning worldviews, ideologies and philosophies,…

Framing life and death on YouTube: the strategic communication of organ donation messages by organ procurement organizations.

PubMed

VanderKnyff, Jeremy; Friedman, Daniela B; Tanner, Andrea

2015-01-01

Using a sample of YouTube videos posted on the YouTube channels of organ procurement organizations, a content analysis was conducted to identify the frames used to strategically communicate prodonation messages. A total of 377 videos were coded for general characteristics, format, speaker characteristics, organs discussed, structure, problem definition, and treatment. Principal components analysis identified message frames, and k-means cluster analysis established distinct groupings of videos on the basis of the strength of their relationship to message frames. Analysis of these frames and clusters found that organ procurement organizations present multiple, and sometimes competing, video types and message frames on YouTube. This study serves as important formative research that will inform future studies to measure the effectiveness of the distinct message frames and clusters identified.

Patient satisfaction constructs.

PubMed

Rahman, Muhammad Sabbir; Osmangani, Aahad M

2015-01-01

The purpose of this paper is to examine the five-factor structure of patients' satisfaction constructs toward private healthcare service providers. This research is a cross-sectional study. A questionnaire-based survey was conducted with previous and current Bangladeshi patients. Exploratory factor analysis was employed to extract the underlying constructs. Five underlying dimensions that play a significant role in structuring the satisfaction perceived by Bangladeshi private healthcare patients are identified in this study. Practical implications - The main contribution of this study is identifying the dimensions of satisfaction perceived by Bangladeshi patients regarding private healthcare service providers. Healthcare managers adopt the five identified underlying construct items in their business practices to improve their respective healthcare efficiency while ensuring overall customer satisfaction.

Towards fully automated structure-based function prediction in structural genomics: a case study.

PubMed

Watson, James D; Sanderson, Steve; Ezersky, Alexandra; Savchenko, Alexei; Edwards, Aled; Orengo, Christine; Joachimiak, Andrzej; Laskowski, Roman A; Thornton, Janet M

2007-04-13

As the global Structural Genomics projects have picked up pace, the number of structures annotated in the Protein Data Bank as hypothetical protein or unknown function has grown significantly. A major challenge now involves the development of computational methods to assign functions to these proteins accurately and automatically. As part of the Midwest Center for Structural Genomics (MCSG) we have developed a fully automated functional analysis server, ProFunc, which performs a battery of analyses on a submitted structure. The analyses combine a number of sequence-based and structure-based methods to identify functional clues. After the first stage of the Protein Structure Initiative (PSI), we review the success of the pipeline and the importance of structure-based function prediction. As a dataset, we have chosen all structures solved by the MCSG during the 5 years of the first PSI. Our analysis suggests that two of the structure-based methods are particularly successful and provide examples of local similarity that is difficult to identify using current sequence-based methods. No one method is successful in all cases, so, through the use of a number of complementary sequence and structural approaches, the ProFunc server increases the chances that at least one method will find a significant hit that can help elucidate function. Manual assessment of the results is a time-consuming process and subject to individual interpretation and human error. We present a method based on the Gene Ontology (GO) schema using GO-slims that can allow the automated assessment of hits with a success rate approaching that of expert manual assessment.

Accurate Structural Correlations from Maximum Likelihood Superpositions

PubMed Central

Theobald, Douglas L; Wuttke, Deborah S

2008-01-01

The cores of globular proteins are densely packed, resulting in complicated networks of structural interactions. These interactions in turn give rise to dynamic structural correlations over a wide range of time scales. Accurate analysis of these complex correlations is crucial for understanding biomolecular mechanisms and for relating structure to function. Here we report a highly accurate technique for inferring the major modes of structural correlation in macromolecules using likelihood-based statistical analysis of sets of structures. This method is generally applicable to any ensemble of related molecules, including families of nuclear magnetic resonance (NMR) models, different crystal forms of a protein, and structural alignments of homologous proteins, as well as molecular dynamics trajectories. Dominant modes of structural correlation are determined using principal components analysis (PCA) of the maximum likelihood estimate of the correlation matrix. The correlations we identify are inherently independent of the statistical uncertainty and dynamic heterogeneity associated with the structural coordinates. We additionally present an easily interpretable method (“PCA plots”) for displaying these positional correlations by color-coding them onto a macromolecular structure. Maximum likelihood PCA of structural superpositions, and the structural PCA plots that illustrate the results, will facilitate the accurate determination of dynamic structural correlations analyzed in diverse fields of structural biology. PMID:18282091

Structural analysis of commercial ceramides by gas chromatography-mass spectrometry.

PubMed

Bleton, J; Gaudin, K; Chaminade, P; Goursaud, S; Baillet, A; Tchapla, A

2001-05-11

A simple method using gas chromatography-mass spectrometry was applied to analyse structures of ceramides. Identification of trimethylsilylated ceramides were obtained in short analysis times (derivatization of ceramides in 30 min at room temperature and 20 min gas chromatography mass spectrometry run) even for complex mixtures. For example in ceramide Type III, 18 peaks were observed which represent 27 various structures. The coeluted compounds were ceramides containing the same functional groups and the same carbon number but with a different distribution on the two alkyl chains of the molecule. They were accurately differentiated by mass spectrometry. Therefore, 83 structures of trimethylsilylated ceramides were identified in 11 different commercial mixtures. For 52 structures of these, mass spectral data were not described in the literature, neither full mass spectra nor characteristic fragments.

Identifying Turbulent Structures through Topological Segmentation

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

Bremer, Peer-Timo; Gruber, Andrea; Bennett, Janine C.

2016-01-01

A new method of extracting vortical structures from a turbulent flow is proposed whereby topological segmentation of an indicator function scalar field is used to identify the regions of influence of the individual vortices. This addresses a long-standing challenge in vector field topological analysis: indicator functions commonly used produce a scalar field based on the local velocity vector field; reconstructing regions of influence for a particular structure requires selecting a threshold to define vortex extent. In practice, the same threshold is rarely meaningful throughout a given flow. By also considering the topology of the indicator field function, the characteristics ofmore » vortex strength and extent can be separated and the ambiguity in the choice of the threshold reduced. The proposed approach is able to identify several types of vortices observed in a jet in cross-flow configuration simultaneously where no single threshold value for a selection of common indicator functions appears able to identify all of these vortex types.« less

Phylogeography and population structure of the biologically invasive phytopathogen Erwinia amylovora inferred using minisatellites.

PubMed

Bühlmann, Andreas; Dreo, Tanja; Rezzonico, Fabio; Pothier, Joël F; Smits, Theo H M; Ravnikar, Maja; Frey, Jürg E; Duffy, Brion

2014-07-01

Erwinia amylovora causes a major disease of pome fruit trees worldwide, and is regulated as a quarantine organism in many countries. While some diversity of isolates has been observed, molecular epidemiology of this bacterium is hindered by a lack of simple molecular typing techniques with sufficiently high resolution. We report a molecular typing system of E. amylovora based on variable number of tandem repeats (VNTR) analysis. Repeats in the E. amylovora genome were identified with comparative genomic tools, and VNTR markers were developed and validated. A Multiple-Locus VNTR Analysis (MLVA) was applied to E. amylovora isolates from bacterial collections representing global and regional distribution of the pathogen. Based on six repeats, MLVA allowed the distinction of 227 haplotypes among a collection of 833 isolates of worldwide origin. Three geographically separated groups were recognized among global isolates using Bayesian clustering methods. Analysis of regional outbreaks confirmed presence of diverse haplotypes but also high representation of certain haplotypes during outbreaks. MLVA analysis is a practical method for epidemiological studies of E. amylovora, identifying previously unresolved population structure within outbreaks. Knowledge of such structure can increase our understanding on how plant diseases emerge and spread over a given geographical region. © 2013 Society for Applied Microbiology and John Wiley & Sons Ltd.

Trophic structure of a coastal fish community determined with diet and stable isotope analyses.

PubMed

Malek, A J; Collie, J S; Taylor, D L

2016-09-01

A combination of dietary guild analysis and nitrogen (δ(15) N) and carbon (δ(13) C) stable-isotope analysis was used to assess the trophic structure of the fish community in Rhode Island and Block Island Sounds, an area off southern New England identified for offshore wind energy development. In the autumn of 2009, 2010 and 2011, stomach and tissue samples were taken from 20 fish and invertebrate species for analysis of diet composition and δ(15) N and δ(13) C signatures. The food chain in Rhode Island and Block Island Sounds comprises approximately four trophic levels within which the fish community is divided into distinct dietary guilds, including planktivores, benthivores, crustacivores and piscivores. Within these guilds, inter-species isotopic and dietary overlap is high, suggesting that resource partitioning or competitive interactions play a major role in structuring the fish community. Carbon isotopes indicate that most fishes are supported by pelagic phytoplankton, although there is evidence that benthic production also plays a role, particularly for obligate benthivores such as skates Leucoraja spp. This type of analysis is useful for developing an ecosystem-based approach to management, as it identifies species that act as direct links to basal resources as well as species groups that share trophic roles. © 2016 The Fisheries Society of the British Isles.

Comparative analysis of structural concrete quality assurance practices on nine nuclear power plant construction projects. Final report

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

Willenbrock, J.H.; Thomas, H.R. Jr.; Burati, J.L. Jr.

1978-06-01

The basic objective of this research effort was to perform a comparative analysis of the Quality Assurance practices related to the structural concrete phase on nine nuclear power plant projects which are (or have been) under construction in the United States in the past ten years. This analysis identified the response of each Quality Assurance program to the applicable criteria of 10 CFR Part 50, Appendix B as well as to the pertinent regulatory requirements and industry standards. The major emphasis was placed on the construction aspects of the structural concrete phase of each project. The engineering and design aspectsmore » were examined whenever they interfaced with the construction aspects. For those aspects of the Quality Assurance system which can be considered managerial in nature (i.e., organizational relationships, types of Quality Assurance programs, corrective action procedures, etc.) an attempt has been made to present the alternative approaches that were identified. For those aspects of the Quality Assurance system which are technical in nature (i.e., the frequency of testing for slump, compressive strength, etc.) an attempt has been made to present a comparative analysis between projects and in relation to the recommended or mandated practices presented in the appropriate industry codes and standards.« less

Characterization of Isomeric Glycans by Reversed Phase Liquid Chromatography-Electronic Excitation Dissociation Tandem Mass Spectrometry

NASA Astrophysics Data System (ADS)

Tang, Yang; Wei, Juan; Costello, Catherine E.; Lin, Cheng

2018-04-01

The occurrence of numerous structural isomers in glycans from biological sources presents a severe challenge for structural glycomics. The subtle differences among isomeric structures demand analytical methods that can provide structural details while working efficiently with on-line glycan separation methods. Although liquid chromatography-tandem mass spectrometry (LC-MS/MS) is a powerful tool for mixture analysis, the commonly utilized collision-induced dissociation (CID) method often does not generate a sufficient number of fragments at the MS2 level for comprehensive structural characterization. Here, we studied the electronic excitation dissociation (EED) behaviors of metal-adducted, permethylated glycans, and identified key spectral features that could facilitate both topology and linkage determinations. We developed an EED-based, nanoscale, reversed phase (RP)LC-MS/MS platform, and demonstrated its ability to achieve complete structural elucidation of up to five structural isomers in a single LC-MS/MS analysis. [Figure not available: see fulltext.

A Unified Analysis of Structured Sonar-terrain Data using Bayesian Functional Mixed Models.

PubMed

Zhu, Hongxiao; Caspers, Philip; Morris, Jeffrey S; Wu, Xiaowei; Müller, Rolf

2018-01-01

Sonar emits pulses of sound and uses the reflected echoes to gain information about target objects. It offers a low cost, complementary sensing modality for small robotic platforms. While existing analytical approaches often assume independence across echoes, real sonar data can have more complicated structures due to device setup or experimental design. In this paper, we consider sonar echo data collected from multiple terrain substrates with a dual-channel sonar head. Our goals are to identify the differential sonar responses to terrains and study the effectiveness of this dual-channel design in discriminating targets. We describe a unified analytical framework that achieves these goals rigorously, simultaneously, and automatically. The analysis was done by treating the echo envelope signals as functional responses and the terrain/channel information as covariates in a functional regression setting. We adopt functional mixed models that facilitate the estimation of terrain and channel effects while capturing the complex hierarchical structure in data. This unified analytical framework incorporates both Gaussian models and robust models. We fit the models using a full Bayesian approach, which enables us to perform multiple inferential tasks under the same modeling framework, including selecting models, estimating the effects of interest, identifying significant local regions, discriminating terrain types, and describing the discriminatory power of local regions. Our analysis of the sonar-terrain data identifies time regions that reflect differential sonar responses to terrains. The discriminant analysis suggests that a multi- or dual-channel design achieves target identification performance comparable with or better than a single-channel design.

A Unified Analysis of Structured Sonar-terrain Data using Bayesian Functional Mixed Models

PubMed Central

Zhu, Hongxiao; Caspers, Philip; Morris, Jeffrey S.; Wu, Xiaowei; Müller, Rolf

2017-01-01

Sonar emits pulses of sound and uses the reflected echoes to gain information about target objects. It offers a low cost, complementary sensing modality for small robotic platforms. While existing analytical approaches often assume independence across echoes, real sonar data can have more complicated structures due to device setup or experimental design. In this paper, we consider sonar echo data collected from multiple terrain substrates with a dual-channel sonar head. Our goals are to identify the differential sonar responses to terrains and study the effectiveness of this dual-channel design in discriminating targets. We describe a unified analytical framework that achieves these goals rigorously, simultaneously, and automatically. The analysis was done by treating the echo envelope signals as functional responses and the terrain/channel information as covariates in a functional regression setting. We adopt functional mixed models that facilitate the estimation of terrain and channel effects while capturing the complex hierarchical structure in data. This unified analytical framework incorporates both Gaussian models and robust models. We fit the models using a full Bayesian approach, which enables us to perform multiple inferential tasks under the same modeling framework, including selecting models, estimating the effects of interest, identifying significant local regions, discriminating terrain types, and describing the discriminatory power of local regions. Our analysis of the sonar-terrain data identifies time regions that reflect differential sonar responses to terrains. The discriminant analysis suggests that a multi- or dual-channel design achieves target identification performance comparable with or better than a single-channel design. PMID:29749977

Towards Implicational Scales for Use in Chicano English Composition. Papers in Southwest English 1: Research Techniques and Prospects.

ERIC Educational Resources Information Center

Hoffer, Bates

Dialect analysis should follow the procedure for analysis of a new language: collection of a corpus of words, stories, and sentences and identifying structural features of phonology, morphology, syntax, and lexicon. Contrastive analysis between standard English and the native language is used and the ethnic dialect of English is described and…

Development of deployable structures for large space platform systems, volume 1

NASA Technical Reports Server (NTRS)

1982-01-01

Generic deployable spacecraft configurations and deployable platform systems concepts were identified. Sizing, building block concepts, orbiter packaging, thermal analysis, cost analysis, and mass properties analysis as related to platform systems integration are considered. Technology needs are examined and the major criteria used in concept selection are delineated. Requirements for deployable habitat modules, tunnels, and OTV hangars are considered.

The child welfare system: through the eyes of public health nurses.

PubMed

Schneiderman, Janet U

2005-01-01

This qualitative descriptive study investigates how public health nurses working within the child welfare system view the organization and the organization's effect on their case management practice. Semistructured interviews were conducted utilizing the Bolman-Deal Organizational Model. This model identifies four frames of an organization: symbolic, human resources, political, and structural. A purposive sample of nine nurses and one social worker was selected to participate in comprehensive interviews. Data analysis identified two main themes. The first theme was the presence of organizational structural barriers to providing case management. The second theme was the lack of political influence by the nurses to change the structure of the organization; hence, their skills could be more completely utilized. Public health nurses who work in child welfare will need to systematically analyze their role within the organization and understand how to work in "host settings." Nursing educators need to prepare public health nurses to work in non-health care settings by teaching organizational analysis.

Organization in memory and behavior1

PubMed Central

Shimp, Charles P.

1976-01-01

Some common reinforcement contingencies make the delivery of a reinforcer depend on the occurrence of behavior lacking significant temporal structure: a reinforcer may be contingent on nearly instantaneous responses such as a pigeon's key peck, a rat's lever press, a human's button press or brief verbal utterance, and so on. Such a reinforcement contingency conforms much more closely to the functionalist tradition in experimental psychology than to the structuralist tradition. Until recently, the functionalist tradition, in the form of a kind of associationism, typified most research on human learning and memory. Recently, however, research on human memory has focused more on structural issues: now the basic unit of analysis often involves an organized temporal pattern of behavior. A focus on the interrelations between the function and structure of behavior identifies a set of independent and dependent variables different from those identified by certain common kinds of “molar” behavioral analyses. In so doing, such a focus redefines some of the significant issues in the experimental analysis of behavior. PMID:16811925

A psychometric analysis of the reading the mind in the eyes test: toward a brief form for research and applied settings

PubMed Central

Olderbak, Sally; Wilhelm, Oliver; Olaru, Gabriel; Geiger, Mattis; Brenneman, Meghan W.; Roberts, Richard D.

2015-01-01

The Reading the Mind in the Eyes Test is a popular measure of individual differences in Theory of Mind that is often applied in the assessment of particular clinical populations (primarily, individuals on the autism spectrum). However, little is known about the test's psychometric properties, including factor structure, internal consistency, and convergent validity evidence. We present a psychometric analysis of the test followed by an evaluation of other empirically proposed and statistically identified structures. We identified, and cross-validated in a second sample, an adequate short-form solution that is homogeneous with adequate internal consistency, and is moderately related to Cognitive Empathy, Emotion Perception, and strongly related to Vocabulary. We recommend the use of this short-form solution in normal adults as a more precise measure over the original version. Future revisions of the test should seek to reduce the test's reliance on one's vocabulary and evaluate the short-form structure in clinical populations. PMID:26500578

A rapid NMR-based method for discrimination of strain-specific cell wall teichoic acid structures reveals a third backbone type in Lactobacillus plantarum.

PubMed

Tomita, Satoru; Tanaka, Naoto; Okada, Sanae

2017-03-01

The lactic acid bacterium Lactobacillus plantarum is capable of producing strain-specific structures of cell wall teichoic acid (WTA), an anionic polysaccharide found in the Gram-positive bacterial cell wall. In this study, we established a rapid, NMR-based procedure to discriminate WTA structures in this species, and applied it to 94 strains of L. plantarum. Six previously reported glycerol- and ribitol-containing WTA subtypes were successfully identified from 78 strains, suggesting that these were the dominant structures. However, the level of structural variety differed markedly among bacterial sources, possibly reflecting differences in strain-level microbial diversity. WTAs from eight strains were not identified based on NMR spectra and were classified into three groups. Structural analysis of a partial degradation product of an unidentified WTA produced by strain TUA 1496L revealed that the WTA was 1-O-β-d-glucosylglycerol. Two-dimensional NMR analysis of the polymer structure showed phosphodiester bonds between C-3 and C-6 of the glycerol and glucose residues, suggesting a polymer structure of 3,6΄-linked poly(1-O-β-d-glucosyl-sn-glycerol phosphate). This is the third WTA backbone structure in L. plantarum, following 3,6΄-linked poly(1-O-α-d-glucosyl-sn-glycerol phosphate) and 1,5-linked poly(ribitol phosphate). © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Tertiary structural propensities reveal fundamental sequence/structure relationships.

PubMed

Zheng, Fan; Zhang, Jian; Grigoryan, Gevorg

2015-05-05

Extracting useful generalizations from the continually growing Protein Data Bank (PDB) is of central importance. We hypothesize that the PDB contains valuable quantitative information on the level of local tertiary structural motifs (TERMs). We show that by breaking a protein structure into its constituent TERMs, and querying the PDB to characterize the natural ensemble matching each, we can estimate the compatibility of the structure with a given amino acid sequence through a metric we term "structure score." Considering submissions from recent Critical Assessment of Structure Prediction (CASP) experiments, we found a strong correlation (R = 0.69) between structure score and model accuracy, with poorly predicted regions readily identifiable. This performance exceeds that of leading atomistic statistical energy functions. Furthermore, TERM-based analysis of two prototypical multi-state proteins rapidly produced structural insights fully consistent with prior extensive experimental studies. We thus find that TERM-based analysis should have considerable utility for protein structural biology. Copyright © 2015 Elsevier Ltd. All rights reserved.

Structuring injustice: partisan politics in the making and unmaking of James Madison University's equal opportunity policy.

PubMed

Robinson, Christine M; Spivey, Sue E

2011-01-01

This analysis contributes to LGBT campus climate research on the quality of campus life in higher education in the United States. We argue that public education institutions in different states face divergent impediments to improving campus climate, and that more research is needed identifying structural factors affecting campus climate. Using a social systems analysis of policymaking at one university as a case study, we illustrate how partisan politics and state regulation make Virginia colleges and universities more vulnerable to political scrutiny and control. Finally, we propose a social justice-oriented policy agenda to address structural inequalities.

Structural and Sequence Stratigraphic Analysis of the Onshore Nile Delta, Egypt.

NASA Astrophysics Data System (ADS)

Barakat, Moataz; Dominik, Wilhelm

2010-05-01

The Nile Delta is considered the earliest known delta in the world. It was already described by Herodotus in the 5th Century AC. Nowadays; the Nile Delta is an emerging giant gas province in the Middle East with proven gas reserves which have more than doubled in size in the last years. The Nile Delta basin contains a thick sedimentary sequence inferred to extend from Jurassic to recent time. Structural styles and depositional environments varied during this period. Facies architecture and sequence stratigraphy of the Nile Delta are resolved using seismic stratigraphy based on (2D seismic lines) including synthetic seismograms and tying in well log data. Synthetic seismograms were constructed using sonic and density logs. The combination of structural interpretation and sequence stratigraphy of the development of the basin was resolved. Seven chrono-stratigraphic boundaries have been identified and correlated on seismic and well log data. Several unconformity boundaries also identified on seismic lines range from angular to disconformity type. Furthermore, time structure maps, velocity maps, depth structure maps as well as Isopach maps were constructed using seismic lines and log data. Several structural features were identified: normal faults, growth faults, listric faults, secondary antithetic faults and large rotated fault blocks of manly Miocene age. In some cases minor rollover structures could be identified. Sedimentary features such as paleo-channels were distinctively recognized. Typical Sequence stratigraphic features such as incised valley, clinoforms, topsets, offlaps and onlaps are identified and traced on the seismic lines allowing a good insight into sequence stratigraphic history of the Nile Delta most especially in the Miocene to Pliocene clastic sedimentary succession.

Identification of the underlying factor structure of the Derriford Appearance Scale 24

PubMed Central

Lawson, Victoria; White, Paul

2015-01-01

Background. The Derriford Appearance Scale24 (DAS24) is a widely used measure of distress and dysfunction in relation to self-consciousness of appearance. It has been used in clinical and research settings, and translated into numerous European and Asian languages. Hitherto, no study has conducted an analysis to determine the underlying factor structure of the scale. Methods. A large (n = 1,265) sample of community and hospital patients with a visible difference were recruited face to face or by post, and completed the DAS24. Results. A two factor solution was generated. An evaluation of the congruence of the factor solutions on each of the the hospital and the community samples using Tucker’s Coefficient of Congruence (rc = .979) and confirmatory factor analysis, which demonstrated a consistent factor structure. A main factor, general self consciousness (GSC), was represented by 18 items. Six items comprised a second factor, sexual and body self-consciousness (SBSC). The SBSC scale demonstrated greater sensitivity and specificity in identifying distress for sexually significant areas of the body. Discussion. The factor structure of the DAS24 facilitates a more nuanced interpretation of scores using this scale. Two conceptually and statistically coherent sub-scales were identified. The SBSC sub-scale offers a means of identifying distress and dysfunction around sexually significant areas of the body not previously possible with this scale. PMID:26157633

Identification of the underlying factor structure of the Derriford Appearance Scale 24.

PubMed

Moss, Timothy P; Lawson, Victoria; White, Paul

2015-01-01

Background. The Derriford Appearance Scale24 (DAS24) is a widely used measure of distress and dysfunction in relation to self-consciousness of appearance. It has been used in clinical and research settings, and translated into numerous European and Asian languages. Hitherto, no study has conducted an analysis to determine the underlying factor structure of the scale. Methods. A large (n = 1,265) sample of community and hospital patients with a visible difference were recruited face to face or by post, and completed the DAS24. Results. A two factor solution was generated. An evaluation of the congruence of the factor solutions on each of the the hospital and the community samples using Tucker's Coefficient of Congruence (rc = .979) and confirmatory factor analysis, which demonstrated a consistent factor structure. A main factor, general self consciousness (GSC), was represented by 18 items. Six items comprised a second factor, sexual and body self-consciousness (SBSC). The SBSC scale demonstrated greater sensitivity and specificity in identifying distress for sexually significant areas of the body. Discussion. The factor structure of the DAS24 facilitates a more nuanced interpretation of scores using this scale. Two conceptually and statistically coherent sub-scales were identified. The SBSC sub-scale offers a means of identifying distress and dysfunction around sexually significant areas of the body not previously possible with this scale.

In vitro and in vivo structure and activity relationship analysis of polymethoxylated flavonoids: identifying sinensetin as a novel antiangiogenesis agent.

PubMed

Lam, In Kei; Alex, Deepa; Wang, You-Hua; Liu, Ping; Liu, Ai-Lin; Du, Guan-Hua; Lee, Simon Ming Yuen

2012-06-01

Polymethoxylated flavonoids are present in citrus fruit in a range of chemical structures and abundance. These compounds have potential for anticarcinogenesis, antitumor, and cardiovascular protective activity, but the effect on angiogenesis has not been well studied. Human umbilical vein endothelial cells (HUVECs) in vitro and zebrafish (Danio rerio) in vivo models were used to screen and identify the antiangiogenesis activity of seven polymethoxylated flavonoids; namely, hesperetin, naringin, neohesperidin, nobiletin, scutellarein, scutellarein tetramethylether, and sinensetin. Five, excluding naringin and neohesperidin, showed different degrees of potency of antiangiogenesis activity. Sinensetin, which had the most potent antiangiogenesis activity and the lowest toxicity, inhibited angiogenesis by inducing cell cycle arrest in the G0/G1 phase in HUVEC culture and downregulating the mRNA expressions of angiogenesis genes flt1, kdrl, and hras in zebrafish. The in vivo structure-activity relationship (SAR) analysis indicated that a flavonoid with a methoxylated group at the C3' position offers a stronger antiangiogenesis activity, whereas the absence of a methoxylated group at the C8 position offers lower lethal toxicity in addition to enhancing the antiangiogenesis activity. This study provides new insight into how modification of the chemical structure of polymethoxylated flavonoids affects this newly identified antiangiogenesis activity. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Factor structure of the Minnesota Satisfaction Questionnaire short form for restaurant employees.

PubMed

Hancer, Mura; George, R Thomas

2004-02-01

The factor structure of the Minnesota Satisfaction Questionnaire short form for nonsupervisory restaurant employees was explored in questions among 2000 employees of three full-service restaurant chains operating in midwestern United States. A total of 2000 surveys were distributed to hourly employees of the three chains. From the mailing, 924 surveys were returned and found useable, a 46.2% response rate. Principal factors analysis identified a four-factor structure for the employees, in contrast to the original two-factor structure, but as in other studies the structure was multifactorial.

Issues in Biomedical Research Data Management and Analysis: Needs and Barriers

PubMed Central

Anderson, Nicholas R.; Lee, E. Sally; Brockenbrough, J. Scott; Minie, Mark E.; Fuller, Sherrilynne; Brinkley, James; Tarczy-Hornoch, Peter

2007-01-01

Objectives A. Identify the current state of data management needs of academic biomedical researchers. B. Explore their anticipated data management and analysis needs. C. Identify barriers to addressing those needs. Design A multimodal needs analysis was conducted using a combination of an online survey and in-depth one-on-one semi-structured interviews. Subjects were recruited via an e-mail list representing a wide range of academic biomedical researchers in the Pacific Northwest. Measurements The results from 286 survey respondents were used to provide triangulation of the qualitative analysis of data gathered from 15 semi-structured in-depth interviews. Results Three major themes were identified: 1) there continues to be widespread use of basic general-purpose applications for core data management; 2) there is broad perceived need for additional support in managing and analyzing large datasets; and 3) the barriers to acquiring currently available tools are most commonly related to financial burdens on small labs and unmet expectations of institutional support. Conclusion Themes identified in this study suggest that at least some common data management needs will best be served by improving access to basic level tools such that researchers can solve their own problems. Additionally, institutions and informaticians should focus on three components: 1) facilitate and encourage the use of modern data exchange models and standards, enabling researchers to leverage a common layer of interoperability and analysis; 2) improve the ability of researchers to maintain provenance of data and models as they evolve over time though tools and the leveraging of standards; and 3) develop and support information management service cores that could assist in these previous components while providing researchers with unique data analysis and information design support within a spectrum of informatics capabilities. PMID:17460139

Secondary structure prediction and structure-specific sequence analysis of single-stranded DNA.

PubMed

Dong, F; Allawi, H T; Anderson, T; Neri, B P; Lyamichev, V I

2001-08-01

DNA sequence analysis by oligonucleotide binding is often affected by interference with the secondary structure of the target DNA. Here we describe an approach that improves DNA secondary structure prediction by combining enzymatic probing of DNA by structure-specific 5'-nucleases with an energy minimization algorithm that utilizes the 5'-nuclease cleavage sites as constraints. The method can identify structural differences between two DNA molecules caused by minor sequence variations such as a single nucleotide mutation. It also demonstrates the existence of long-range interactions between DNA regions separated by >300 nt and the formation of multiple alternative structures by a 244 nt DNA molecule. The differences in the secondary structure of DNA molecules revealed by 5'-nuclease probing were used to design structure-specific probes for mutation discrimination that target the regions of structural, rather than sequence, differences. We also demonstrate the performance of structure-specific 'bridge' probes complementary to non-contiguous regions of the target molecule. The structure-specific probes do not require the high stringency binding conditions necessary for methods based on mismatch formation and permit mutation detection at temperatures from 4 to 37 degrees C. Structure-specific sequence analysis is applied for mutation detection in the Mycobacterium tuberculosis katG gene and for genotyping of the hepatitis C virus.

Training Community Clergy in Serious Illness: Balancing Faith and Medicine.

PubMed

Koss, Sarah E; Weissman, Ross; Chow, Vinca; Smith, Patrick T; Slack, Bethany; Voytenko, Vitaliy; Balboni, Tracy A; Balboni, Michael J

2018-06-06

Community-based clergy are highly engaged in helping seriously ill patients address spiritual concerns at the end of life (EOL). While they desire EOL training, no data exist in guiding how to conceptualize a clergy-training program. The objective of this study was used to identify best practices in an EOL training program for community clergy. As part of the National Clergy Project on End-of-Life Care, the project conducted key informant interviews and focus groups with active clergy in five US states (California, Illinois, Massachusetts, New York, and Texas). A diverse purposive sample of 35 active clergy representing pre-identified racial, educational, theological, and denominational categories hypothesized to be associated with more intensive utilization of medical care at the EOL. We assessed suggested curriculum structure and content for clergy EOL training through interviews and focus groups for the purpose of qualitative analysis. Thematic analysis identified key themes around curriculum structure, curriculum content, and issues of tension. Curriculum structure included ideas for targeting clergy as well as lay congregational leaders and found that clergy were open to combining resources from both religious and health-based institutions. Curriculum content included clergy desires for educational topics such as increasing their medical literacy and reviewing pastoral counseling approaches. Finally, clergy identified challenging barriers to EOL training needing to be openly discussed, including difficulties in collaborating with medical teams, surrounding issues of trust, the role of miracles, and caution of prognostication. Future EOL training is desired and needed for community-based clergy. In partnering together, religious-medical training programs should consider curricula sensitive toward structure, desired content, and perceived clergy tensions.

The Network Structure of Human Personality According to the NEO-PI-R: Matching Network Community Structure to Factor Structure

PubMed Central

Goekoop, Rutger; Goekoop, Jaap G.; Scholte, H. Steven

2012-01-01

Introduction Human personality is described preferentially in terms of factors (dimensions) found using factor analysis. An alternative and highly related method is network analysis, which may have several advantages over factor analytic methods. Aim To directly compare the ability of network community detection (NCD) and principal component factor analysis (PCA) to examine modularity in multidimensional datasets such as the neuroticism-extraversion-openness personality inventory revised (NEO-PI-R). Methods 434 healthy subjects were tested on the NEO-PI-R. PCA was performed to extract factor structures (FS) of the current dataset using both item scores and facet scores. Correlational network graphs were constructed from univariate correlation matrices of interactions between both items and facets. These networks were pruned in a link-by-link fashion while calculating the network community structure (NCS) of each resulting network using the Wakita Tsurumi clustering algorithm. NCSs were matched against FS and networks of best matches were kept for further analysis. Results At facet level, NCS showed a best match (96.2%) with a ‘confirmatory’ 5-FS. At item level, NCS showed a best match (80%) with the standard 5-FS and involved a total of 6 network clusters. Lesser matches were found with ‘confirmatory’ 5-FS and ‘exploratory’ 6-FS of the current dataset. Network analysis did not identify facets as a separate level of organization in between items and clusters. A small-world network structure was found in both item- and facet level networks. Conclusion We present the first optimized network graph of personality traits according to the NEO-PI-R: a ‘Personality Web’. Such a web may represent the possible routes that subjects can take during personality development. NCD outperforms PCA by producing plausible modularity at item level in non-standard datasets, and can identify the key roles of individual items and clusters in the network. PMID:23284713

The network structure of human personality according to the NEO-PI-R: matching network community structure to factor structure.

PubMed

Goekoop, Rutger; Goekoop, Jaap G; Scholte, H Steven

2012-01-01

Human personality is described preferentially in terms of factors (dimensions) found using factor analysis. An alternative and highly related method is network analysis, which may have several advantages over factor analytic methods. To directly compare the ability of network community detection (NCD) and principal component factor analysis (PCA) to examine modularity in multidimensional datasets such as the neuroticism-extraversion-openness personality inventory revised (NEO-PI-R). 434 healthy subjects were tested on the NEO-PI-R. PCA was performed to extract factor structures (FS) of the current dataset using both item scores and facet scores. Correlational network graphs were constructed from univariate correlation matrices of interactions between both items and facets. These networks were pruned in a link-by-link fashion while calculating the network community structure (NCS) of each resulting network using the Wakita Tsurumi clustering algorithm. NCSs were matched against FS and networks of best matches were kept for further analysis. At facet level, NCS showed a best match (96.2%) with a 'confirmatory' 5-FS. At item level, NCS showed a best match (80%) with the standard 5-FS and involved a total of 6 network clusters. Lesser matches were found with 'confirmatory' 5-FS and 'exploratory' 6-FS of the current dataset. Network analysis did not identify facets as a separate level of organization in between items and clusters. A small-world network structure was found in both item- and facet level networks. We present the first optimized network graph of personality traits according to the NEO-PI-R: a 'Personality Web'. Such a web may represent the possible routes that subjects can take during personality development. NCD outperforms PCA by producing plausible modularity at item level in non-standard datasets, and can identify the key roles of individual items and clusters in the network.

De-identifying an EHR database - anonymity, correctness and readability of the medical record.

PubMed

Pantazos, Kostas; Lauesen, Soren; Lippert, Soren

2011-01-01

Electronic health records (EHR) contain a large amount of structured data and free text. Exploring and sharing clinical data can improve healthcare and facilitate the development of medical software. However, revealing confidential information is against ethical principles and laws. We de-identified a Danish EHR database with 437,164 patients. The goal was to generate a version with real medical records, but related to artificial persons. We developed a de-identification algorithm that uses lists of named entities, simple language analysis, and special rules. Our algorithm consists of 3 steps: collect lists of identifiers from the database and external resources, define a replacement for each identifier, and replace identifiers in structured data and free text. Some patient records could not be safely de-identified, so the de-identified database has 323,122 patient records with an acceptable degree of anonymity, readability and correctness (F-measure of 95%). The algorithm has to be adjusted for each culture, language and database.

Identifying Time Periods of Minimal Thermal Gradient for Temperature-Driven Structural Health Monitoring

PubMed Central

Reilly, John; Glisic, Branko

2018-01-01

Temperature changes play a large role in the day to day structural behavior of structures, but a smaller direct role in most contemporary Structural Health Monitoring (SHM) analyses. Temperature-Driven SHM will consider temperature as the principal driving force in SHM, relating a measurable input temperature to measurable output generalized strain (strain, curvature, etc.) and generalized displacement (deflection, rotation, etc.) to create three-dimensional signatures descriptive of the structural behavior. Identifying time periods of minimal thermal gradient provides the foundation for the formulation of the temperature–deformation–displacement model. Thermal gradients in a structure can cause curvature in multiple directions, as well as non-linear strain and stress distributions within the cross-sections, which significantly complicates data analysis and interpretation, distorts the signatures, and may lead to unreliable conclusions regarding structural behavior and condition. These adverse effects can be minimized if the signatures are evaluated at times when thermal gradients in the structure are minimal. This paper proposes two classes of methods based on the following two metrics: (i) the range of raw temperatures on the structure, and (ii) the distribution of the local thermal gradients, for identifying time periods of minimal thermal gradient on a structure with the ability to vary the tolerance of acceptable thermal gradients. The methods are tested and validated with data collected from the Streicker Bridge on campus at Princeton University. PMID:29494496

Identifying Time Periods of Minimal Thermal Gradient for Temperature-Driven Structural Health Monitoring.

PubMed

Reilly, John; Glisic, Branko

2018-03-01

Temperature changes play a large role in the day to day structural behavior of structures, but a smaller direct role in most contemporary Structural Health Monitoring (SHM) analyses. Temperature-Driven SHM will consider temperature as the principal driving force in SHM, relating a measurable input temperature to measurable output generalized strain (strain, curvature, etc.) and generalized displacement (deflection, rotation, etc.) to create three-dimensional signatures descriptive of the structural behavior. Identifying time periods of minimal thermal gradient provides the foundation for the formulation of the temperature-deformation-displacement model. Thermal gradients in a structure can cause curvature in multiple directions, as well as non-linear strain and stress distributions within the cross-sections, which significantly complicates data analysis and interpretation, distorts the signatures, and may lead to unreliable conclusions regarding structural behavior and condition. These adverse effects can be minimized if the signatures are evaluated at times when thermal gradients in the structure are minimal. This paper proposes two classes of methods based on the following two metrics: (i) the range of raw temperatures on the structure, and (ii) the distribution of the local thermal gradients, for identifying time periods of minimal thermal gradient on a structure with the ability to vary the tolerance of acceptable thermal gradients. The methods are tested and validated with data collected from the Streicker Bridge on campus at Princeton University.

Local kernel nonparametric discriminant analysis for adaptive extraction of complex structures

NASA Astrophysics Data System (ADS)

Li, Quanbao; Wei, Fajie; Zhou, Shenghan

2017-05-01

The linear discriminant analysis (LDA) is one of popular means for linear feature extraction. It usually performs well when the global data structure is consistent with the local data structure. Other frequently-used approaches of feature extraction usually require linear, independence, or large sample condition. However, in real world applications, these assumptions are not always satisfied or cannot be tested. In this paper, we introduce an adaptive method, local kernel nonparametric discriminant analysis (LKNDA), which integrates conventional discriminant analysis with nonparametric statistics. LKNDA is adept in identifying both complex nonlinear structures and the ad hoc rule. Six simulation cases demonstrate that LKNDA have both parametric and nonparametric algorithm advantages and higher classification accuracy. Quartic unilateral kernel function may provide better robustness of prediction than other functions. LKNDA gives an alternative solution for discriminant cases of complex nonlinear feature extraction or unknown feature extraction. At last, the application of LKNDA in the complex feature extraction of financial market activities is proposed.

Identification of phases, symmetries and defects through local crystallography

DOE PAGES

Belianinov, Alex; He, Qian; Kravchenko, Mikhail; ...

2015-07-20

Here we report that advances in electron and probe microscopies allow 10 pm or higher precision in measurements of atomic positions. This level of fidelity is sufficient to correlate the length (and hence energy) of bonds, as well as bond angles to functional properties of materials. Traditionally, this relied on mapping locally measured parameters to macroscopic variables, for example, average unit cell. This description effectively ignores the information contained in the microscopic degrees of freedom available in a high-resolution image. Here we introduce an approach for local analysis of material structure based on statistical analysis of individual atomic neighbourhoods. Clusteringmore » and multivariate algorithms such as principal component analysis explore the connectivity of lattice and bond structure, as well as identify minute structural distortions, thus allowing for chemical description and identification of phases. This analysis lays the framework for building image genomes and structure–property libraries, based on conjoining structural and spectral realms through local atomic behaviour.« less

Competencies Required by Special Librarians: An Analysis by Educational Levels

ERIC Educational Resources Information Center

Peyvand Robati, Alireza; Singh, Diljit

2013-01-01

This paper presents the results of a study conducted with the aim of identifying competencies needed by special librarians in Iran at three different levels of library and information science education. A list of competencies was initially identified from the literature and 21 semi-structured interviews with managers of special libraries in Iran.…

All the School's a Stage: A Multimodal Interaction Analysis of a School Administrator's Literate Life as Dramaturgical Metaphor

ERIC Educational Resources Information Center

Tomlin, Dru DeLance

2013-01-01

In "Images of Leadership" (1991), Bolman and Deal identified four "frames" that school administrators use when making decisions: structural, symbolic, human resource and political. They discovered that the latter two frames, which focus on relationships, partnerships, and communication, were most frequently identified as…

Parental Experiences of Caring for a Child with Intellectual Disabilities: A UK Perspective

ERIC Educational Resources Information Center

Willingham-Storr, Gemma Louise

2014-01-01

A structured literature search and thematic analysis of six research articles relating to stress and parenting of a child with an intellectual disability in the United Kingdom identified four key themes: impact upon families, service provision and support networks, coping and transition. The findings identified that parenting a child with an…

A Model Based Analysis of the Role of an Upper-Level Front and Stratospheric Intrusion in the Mack Lake Fire

Treesearch

Tarisa K. Zimet; Jonathan E. Martin

2003-01-01

Meteorological assessment of wildfire risk has traditionally involved identification of several synoptic types empirically determined to influence wildfire spread. Such weather types are characterized by identifiable synoptic-scale structures and processes. Schroeder et. al. (1964) identified four recognizable synoptic-scale patterns that contribute most frequently to...

Fluid-structure interaction analysis of deformation of sail of 30-foot yacht

NASA Astrophysics Data System (ADS)

Bak, Sera; Yoo, Jaehoon; Song, Chang Yong

2013-06-01

Most yacht sails are made of thin fabric, and they have a cambered shape to generate lift force; however, their shape can be easily deformed by wind pressure. Deformation of the sail shape changes the flow characteristics over the sail, which in turn further deforms the sail shape. Therefore, fluid-structure interaction (FSI) analysis is applied for the precise evaluation or optimization of the sail design. In this study, fluid flow analyses are performed for the main sail of a 30-foot yacht, and the results are applied to loading conditions for structural analyses. By applying the supporting forces from the rig, such as the mast and boom-end outhaul, as boundary conditions for structural analysis, the deformed sail shape is identified. Both the flow analyses and the structural analyses are iteratively carried out for the deformed sail shape. A comparison of the flow characteristics and surface pressures over the deformed sail shape with those over the initial shape shows that a considerable difference exists between the two and that FSI analysis is suitable for application to sail design.

Feasibility Analysis of Incorporating In-Vitro Toxicokinetic Data as a Surrogate for In-Vivo Data for Read-across Predictions (ASCCT meeting)

EPA Science Inventory

The underlying principle of read-across is that biological activity is a function of physical and structural properties of chemicals. Analogs are typically identified on the basis of structural similarity and subsequently evaluated for their use in read-across on the basis of the...

Potential ligand-binding residues in rat olfactory receptors identified by correlated mutation analysis

NASA Technical Reports Server (NTRS)

Singer, M. S.; Oliveira, L.; Vriend, G.; Shepherd, G. M.

1995-01-01

A family of G-protein-coupled receptors is believed to mediate the recognition of odor molecules. In order to identify potential ligand-binding residues, we have applied correlated mutation analysis to receptor sequences from the rat. This method identifies pairs of sequence positions where residues remain conserved or mutate in tandem, thereby suggesting structural or functional importance. The analysis supported molecular modeling studies in suggesting several residues in positions that were consistent with ligand-binding function. Two of these positions, dominated by histidine residues, may play important roles in ligand binding and could confer broad specificity to mammalian odor receptors. The presence of positive (overdominant) selection at some of the identified positions provides additional evidence for roles in ligand binding. Higher-order groups of correlated residues were also observed. Each group may interact with an individual ligand determinant, and combinations of these groups may provide a multi-dimensional mechanism for receptor diversity.

Analysis Methods for Progressive Damage of Composite Structures

NASA Technical Reports Server (NTRS)

Rose, Cheryl A.; Davila, Carlos G.; Leone, Frank A.

2013-01-01

This document provides an overview of recent accomplishments and lessons learned in the development of general progressive damage analysis methods for predicting the residual strength and life of composite structures. These developments are described within their State-of-the-Art (SoA) context and the associated technology barriers. The emphasis of the authors is on developing these analysis tools for application at the structural level. Hence, modeling of damage progression is undertaken at the mesoscale, where the plies of a laminate are represented as a homogenous orthotropic continuum. The aim of the present effort is establish the ranges of validity of available models, to identify technology barriers, and to establish the foundations of the future investigation efforts. Such are the necessary steps towards accurate and robust simulations that can replace some of the expensive and time-consuming "building block" tests that are currently required for the design and certification of aerospace structures.

Analysis of post-tensioned girders structural behaviour using continuous temperature and strain monitoring

NASA Astrophysics Data System (ADS)

Bednarski, Ł.; Sieńko, R.; Howiacki, T.

2017-10-01

This article presents the possibility of using structural health monitoring system data for the analysis of structure’s operation during its life cycle. Within the specific case study it was proved, that continuous, automatic and long term monitoring of selected physical quantities such as strains and temperatures, can significantly improve the assessment of technical condition by identifying hazardous phenomena. In this work the analysis of structural behaviour of post-tensioned girders within the roofing of sport halls in Cracow, Poland, was performed based on measurement results and verified by numerical model carried out in SOFiSTiK software. Thanks to the possibility of performing calculations in real time and informing the manager of the object about abnormalities it is possible to manage the structure in effective way by, inter alia, planning the renovations or supporting decisions about snow removal.

Community investment in wind farms: funding structure effects in wind energy infrastructure development.

PubMed

Beery, Joshua A; Day, Jennifer E

2015-03-03

Wind energy development is an increasingly popular form of renewable energy infrastructure in rural areas. Communities generally perceive socioeconomic benefits accrue and that community funding structures are preferable to corporate structures, yet lack supporting quantitative data to inform energy policy. This study uses the Everpower wind development, to be located in Midwestern Ohio, as a hypothetical modeling environment to identify and examine socioeconomic impact trends arising from corporate, community and diversified funding structures. Analysis of five National Renewable Energy Laboratory Jobs and Economic Development Impact models incorporating local economic data and review of relevant literature were conducted. The findings suggest that community and diversified funding structures exhibit 40-100% higher socioeconomic impact levels than corporate structures. Prioritization of funding sources and retention of federal tax incentives were identified as key elements. The incorporation of local shares was found to mitigate the negative effects of foreign private equity, local debt financing increased economic output and opportunities for private equity investment were identified. The results provide the groundwork for energy policies focused to maximize socioeconomic impacts while creating opportunities for inclusive economic participation and improved social acceptance levels fundamental to the deployment of renewable energy technology.

Mediation analysis with time varying exposures and mediators

PubMed Central

VanderWeele, Tyler J.; Tchetgen Tchetgen, Eric J.

2016-01-01

Summary In this paper we consider causal mediation analysis when exposures and mediators vary over time. We give non-parametric identification results, discuss parametric implementation, and also provide a weighting approach to direct and indirect effects based on combining the results of two marginal structural models. We also discuss how our results give rise to a causal interpretation of the effect estimates produced from longitudinal structural equation models. When there are time-varying confounders affected by prior exposure and mediator, natural direct and indirect effects are not identified. However, we define a randomized interventional analogue of natural direct and indirect effects that are identified in this setting. The formula that identifies these effects we refer to as the “mediational g-formula.” When there is no mediation, the mediational g-formula reduces to Robins’ regular g-formula for longitudinal data. When there are no time-varying confounders affected by prior exposure and mediator values, then the mediational g-formula reduces to a longitudinal version of Pearl’s mediation formula. However, the mediational g-formula itself can accommodate both mediation and time-varying confounders and constitutes a general approach to mediation analysis with time-varying exposures and mediators. PMID:28824285

Mediation analysis with time varying exposures and mediators.

PubMed

VanderWeele, Tyler J; Tchetgen Tchetgen, Eric J

2017-06-01

In this paper we consider causal mediation analysis when exposures and mediators vary over time. We give non-parametric identification results, discuss parametric implementation, and also provide a weighting approach to direct and indirect effects based on combining the results of two marginal structural models. We also discuss how our results give rise to a causal interpretation of the effect estimates produced from longitudinal structural equation models. When there are time-varying confounders affected by prior exposure and mediator, natural direct and indirect effects are not identified. However, we define a randomized interventional analogue of natural direct and indirect effects that are identified in this setting. The formula that identifies these effects we refer to as the "mediational g-formula." When there is no mediation, the mediational g-formula reduces to Robins' regular g-formula for longitudinal data. When there are no time-varying confounders affected by prior exposure and mediator values, then the mediational g-formula reduces to a longitudinal version of Pearl's mediation formula. However, the mediational g-formula itself can accommodate both mediation and time-varying confounders and constitutes a general approach to mediation analysis with time-varying exposures and mediators.

A Coupling Analysis Approach to Capture Unexpected Behaviors in Ares 1

NASA Astrophysics Data System (ADS)

Kis, David

Coupling of physics in large-scale complex engineering systems must be correctly accounted for during the systems engineering process. Preliminary corrections ensure no unanticipated behaviors arise during operation. Structural vibration of large segmented solid rocket motors, known as thrust oscillation, is a well-documented problem that can effect solid rocket motors in adverse ways. Within the Ares 1 rocket, unexpected vibrations deemed potentially harmful to future crew were recorded during late stage flight that propagated from the engine chamber to the Orion crew module. This research proposes the use of a coupling strength analysis during the design and development phase to identify potential unanticipated behaviors such as thrust oscillation. Once these behaviors and couplings are identified then a value function, based on research in Value Driven Design, is proposed to evaluate mitigation strategies and their impact on system value. The results from this study showcase a strong coupling interaction from structural displacement back onto the fluid flow of the Ares 1 that was previously deemed inconsequential. These findings show that the use of a coupling strength analysis can aid engineers and managers in identifying unanticipated behaviors and then rank order their importance based on the impact they have on value.

A functional approach to movement analysis and error identification in sports and physical education

PubMed Central

Hossner, Ernst-Joachim; Schiebl, Frank; Göhner, Ulrich

2015-01-01

In a hypothesis-and-theory paper, a functional approach to movement analysis in sports is introduced. In this approach, contrary to classical concepts, it is not anymore the “ideal” movement of elite athletes that is taken as a template for the movements produced by learners. Instead, movements are understood as the means to solve given tasks that in turn, are defined by to-be-achieved task goals. A functional analysis comprises the steps of (1) recognizing constraints that define the functional structure, (2) identifying sub-actions that subserve the achievement of structure-dependent goals, (3) explicating modalities as specifics of the movement execution, and (4) assigning functions to actions, sub-actions and modalities. Regarding motor-control theory, a functional approach can be linked to a dynamical-system framework of behavioral shaping, to cognitive models of modular effect-related motor control as well as to explicit concepts of goal setting and goal achievement. Finally, it is shown that a functional approach is of particular help for sports practice in the context of structuring part practice, recognizing functionally equivalent task solutions, finding innovative technique alternatives, distinguishing errors from style, and identifying root causes of movement errors. PMID:26441717

A study of facilities and fixtures for testing of a high speed civil transport wing component

NASA Technical Reports Server (NTRS)

Cerro, J. A.; Vause, R. F.; Bowman, L. M.; Jensen, J. K.; Martin, C. J., Jr.; Stockwell, A. E.; Waters, W. A., Jr.

1996-01-01

A study was performed to determine the feasibility of testing a large-scale High Speed Civil Transport wing component in the Structures and Materials Testing Laboratory in Building 1148 at NASA Langley Research Center. The report includes a survey of the electrical and hydraulic resources and identifies the backing structure and floor hard points which would be available for reacting the test loads. The backing structure analysis uses a new finite element model of the floor and backstop support system in the Structures Laboratory. Information on the data acquisition system and the thermal power requirements is also presented. The study identified the hardware that would be required to test a typical component, including the number and arrangement of hydraulic actuators required to simulate expected flight loads. Load introduction and reaction structure concepts were analyzed to investigate the effects of experimentally induced boundary conditions.

Structured vs. Unstructured: Factors Affecting Adverse Drug Reaction Documentation in an EMR Repository

PubMed Central

Skentzos, Stephen; Shubina, Maria; Plutzky, Jorge; Turchin, Alexander

2011-01-01

Adverse reactions to medications to which the patient was known to be intolerant are common. Electronic decision support can prevent them but only if history of adverse reactions to medications is recorded in structured format. We have conducted a retrospective study of 31,531 patients with adverse reactions to statins documented in the notes, as identified with natural language processing. The software identified statin adverse reactions with sensitivity of 86.5% and precision of 91.9%. Only 9020 of these patients had an adverse reaction to a statin recorded in structured format. In multivariable analysis the strongest predictor of structured documentation was utilization of EMR functionality that integrated the medication list with the structured medication adverse reaction repository (odds ratio 48.6, p < 0.0001). Integration of information flow between EMR modules can help improve documentation and potentially prevent adverse drug events. PMID:22195188

Shakespearean tragedies dynamics: identifying a generic structure in Shakespeare's four major tragedies

NASA Astrophysics Data System (ADS)

Domínguez-Rué, Emma; Mrotzek, Maximilian

2012-10-01

Many interpretations of Shakespearean tragedy have been conducted, mostly following the principles of interpretation in literary study. In our paper, four tragedies by William Shakespeare - Hamlet, King Lear, Othello, and Macbeth - were analysed systemically to find out whether they inhabit a common structure. Using the plot structure as the basis for our analysis, we identified the most important system elements, their connections, and interactive behaviour using causal loop diagrams (CLDs). Our results revealed that all four tragedies basically conform to Senge's archetypal structure 'shifting the burden', adding the action of the heroine or villain and the characters' boundaries of perception. The results suggest that, even though characters and settings vary highly, these tragedies have similar structures and archetypal solutions exist to overcome the problem. Furthermore, we propose that CLDs and systems archetypes are a reasonable hermeneutic tool to analyse not only Shakespearean tragedies but also other literary works.

Hierarchical super-structure identified by polarized light microscopy, electron microscopy and nanoindentation: Implications for the limits of biological control over the growth mode of abalone sea shells

PubMed Central

2012-01-01

Background Mollusc shells are commonly investigated using high-resolution imaging techniques based on cryo-fixation. Less detailed information is available regarding the light-optical properties. Sea shells of Haliotis pulcherina were embedded for polishing in defined orientations in order to investigate the interface between prismatic calcite and nacreous aragonite by standard materialographic methods. A polished thin section of the interface was prepared with a defined thickness of 60 μm for quantitative birefringence analysis using polarized light and LC-PolScope microscopy. Scanning electron microscopy images were obtained for comparison. In order to study structural-mechanical relationships, nanoindentation experiments were performed. Results Incident light microscopy revealed a super-structure in semi-transparent regions of the polished cross-section under a defined angle. This super-structure is not visible in transmitted birefringence analysis due to the blurred polarization of small nacre platelets and numerous organic interfaces. The relative orientation and homogeneity of calcite prisms was directly identified, some of them with their optical axes exactly normal to the imaging plane. Co-oriented "prism colonies" were identified by polarized light analyses. The nacreous super-structure was also visualized by secondary electron imaging under defined angles. The domains of the super-structure were interpreted to consist of crystallographically aligned platelet stacks. Nanoindentation experiments showed that mechanical properties changed with the same periodicity as the domain size. Conclusions In this study, we have demonstrated that insights into the growth mechanisms of nacre can be obtained by conventional light-optical methods. For example, we observed super-structures formed by co-oriented nacre platelets as previously identified using X-ray Photo-electron Emission Microscopy (X-PEEM) [Gilbert et al., Journal of the American Chemical Society 2008, 130:17519–17527]. Polarized optical microscopy revealed unprecedented super-structures in the calcitic shell part. This bears, in principle, the potential for in vivo studies, which might be useful for investigating the growth modes of nacre and other shell types. PMID:22967319

Integrated Analysis and Visualization of Group Differences in Structural and Functional Brain Connectivity: Applications in Typical Ageing and Schizophrenia.

PubMed

Langen, Carolyn D; White, Tonya; Ikram, M Arfan; Vernooij, Meike W; Niessen, Wiro J

2015-01-01

Structural and functional brain connectivity are increasingly used to identify and analyze group differences in studies of brain disease. This study presents methods to analyze uni- and bi-modal brain connectivity and evaluate their ability to identify differences. Novel visualizations of significantly different connections comparing multiple metrics are presented. On the global level, "bi-modal comparison plots" show the distribution of uni- and bi-modal group differences and the relationship between structure and function. Differences between brain lobes are visualized using "worm plots". Group differences in connections are examined with an existing visualization, the "connectogram". These visualizations were evaluated in two proof-of-concept studies: (1) middle-aged versus elderly subjects; and (2) patients with schizophrenia versus controls. Each included two measures derived from diffusion weighted images and two from functional magnetic resonance images. The structural measures were minimum cost path between two anatomical regions according to the "Statistical Analysis of Minimum cost path based Structural Connectivity" method and the average fractional anisotropy along the fiber. The functional measures were Pearson's correlation and partial correlation of mean regional time series. The relationship between structure and function was similar in both studies. Uni-modal group differences varied greatly between connectivity types. Group differences were identified in both studies globally, within brain lobes and between regions. In the aging study, minimum cost path was highly effective in identifying group differences on all levels; fractional anisotropy and mean correlation showed smaller differences on the brain lobe and regional levels. In the schizophrenia study, minimum cost path and fractional anisotropy showed differences on the global level and within brain lobes; mean correlation showed small differences on the lobe level. Only fractional anisotropy and mean correlation showed regional differences. The presented visualizations were helpful in comparing and evaluating connectivity measures on multiple levels in both studies.

HIV-1 Protease Function and Structure Studies with the Simplicial Neighborhood Analysis of Protein Packing (SNAPP) Method

PubMed Central

Zhang, Shuxing; Kaplan, Andrew H.; Tropsha, Alexander

2009-01-01

The Simplicial Neighborhood Analysis of Protein Packing (SNAPP) method was used to predict the effect of mutagenesis on the enzymatic activity of the HIV-1 protease (HIVP). SNAPP relies on a four-body statistical scoring function derived from the analysis of spatially nearest neighbor residue compositional preferences in a diverse and representative subset of protein structures from the Protein Data Bank. The method was applied to the analysis of HIVP mutants with residue substitutions in the hydrophobic core as well as at the interface between the two protease monomers. Both wild type and tethered structures were employed in the calculations. We obtained a strong correlation, with R2 as high as 0.96, between ΔSNAPP score (i.e., the difference in SNAPP scores between wild type and mutant proteins) and the protease catalytic activity for tethered structures. A weaker but significant correlation was also obtained for non-tethered structures as well. Our analysis identified residues both in the hydrophobic core and at the dimeric interface (DI) that are very important for the protease function. This study demonstrates a potential utility of the SNAPP method for rational design of mutagenesis studies and protein engineering. PMID:18498108

Machine-learned cluster identification in high-dimensional data.

PubMed

Ultsch, Alfred; Lötsch, Jörn

2017-02-01

High-dimensional biomedical data are frequently clustered to identify subgroup structures pointing at distinct disease subtypes. It is crucial that the used cluster algorithm works correctly. However, by imposing a predefined shape on the clusters, classical algorithms occasionally suggest a cluster structure in homogenously distributed data or assign data points to incorrect clusters. We analyzed whether this can be avoided by using emergent self-organizing feature maps (ESOM). Data sets with different degrees of complexity were submitted to ESOM analysis with large numbers of neurons, using an interactive R-based bioinformatics tool. On top of the trained ESOM the distance structure in the high dimensional feature space was visualized in the form of a so-called U-matrix. Clustering results were compared with those provided by classical common cluster algorithms including single linkage, Ward and k-means. Ward clustering imposed cluster structures on cluster-less "golf ball", "cuboid" and "S-shaped" data sets that contained no structure at all (random data). Ward clustering also imposed structures on permuted real world data sets. By contrast, the ESOM/U-matrix approach correctly found that these data contain no cluster structure. However, ESOM/U-matrix was correct in identifying clusters in biomedical data truly containing subgroups. It was always correct in cluster structure identification in further canonical artificial data. Using intentionally simple data sets, it is shown that popular clustering algorithms typically used for biomedical data sets may fail to cluster data correctly, suggesting that they are also likely to perform erroneously on high dimensional biomedical data. The present analyses emphasized that generally established classical hierarchical clustering algorithms carry a considerable tendency to produce erroneous results. By contrast, unsupervised machine-learned analysis of cluster structures, applied using the ESOM/U-matrix method, is a viable, unbiased method to identify true clusters in the high-dimensional space of complex data. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Interrelation of structure and operational states in cascading failure of overloading lines in power grids

NASA Astrophysics Data System (ADS)

Xue, Fei; Bompard, Ettore; Huang, Tao; Jiang, Lin; Lu, Shaofeng; Zhu, Huaiying

2017-09-01

As the modern power system is expected to develop to a more intelligent and efficient version, i.e. the smart grid, or to be the central backbone of energy internet for free energy interactions, security concerns related to cascading failures have been raised with consideration of catastrophic results. The researches of topological analysis based on complex networks have made great contributions in revealing structural vulnerabilities of power grids including cascading failure analysis. However, existing literature with inappropriate assumptions in modeling still cannot distinguish the effects between the structure and operational state to give meaningful guidance for system operation. This paper is to reveal the interrelation between network structure and operational states in cascading failure and give quantitative evaluation by integrating both perspectives. For structure analysis, cascading paths will be identified by extended betweenness and quantitatively described by cascading drop and cascading gradient. Furthermore, the operational state for cascading paths will be described by loading level. Then, the risk of cascading failure along a specific cascading path can be quantitatively evaluated considering these two factors. The maximum cascading gradient of all possible cascading paths can be used as an overall metric to evaluate the entire power grid for its features related to cascading failure. The proposed method is tested and verified on IEEE30-bus system and IEEE118-bus system, simulation evidences presented in this paper suggests that the proposed model can identify the structural causes for cascading failure and is promising to give meaningful guidance for the protection of system operation in the future.

NoFold: RNA structure clustering without folding or alignment.

PubMed

Middleton, Sarah A; Kim, Junhyong

2014-11-01

Structures that recur across multiple different transcripts, called structure motifs, often perform a similar function-for example, recruiting a specific RNA-binding protein that then regulates translation, splicing, or subcellular localization. Identifying common motifs between coregulated transcripts may therefore yield significant insight into their binding partners and mechanism of regulation. However, as most methods for clustering structures are based on folding individual sequences or doing many pairwise alignments, this results in a tradeoff between speed and accuracy that can be problematic for large-scale data sets. Here we describe a novel method for comparing and characterizing RNA secondary structures that does not require folding or pairwise alignment of the input sequences. Our method uses the idea of constructing a distance function between two objects by their respective distances to a collection of empirical examples or models, which in our case consists of 1973 Rfam family covariance models. Using this as a basis for measuring structural similarity, we developed a clustering pipeline called NoFold to automatically identify and annotate structure motifs within large sequence data sets. We demonstrate that NoFold can simultaneously identify multiple structure motifs with an average sensitivity of 0.80 and precision of 0.98 and generally exceeds the performance of existing methods. We also perform a cross-validation analysis of the entire set of Rfam families, achieving an average sensitivity of 0.57. We apply NoFold to identify motifs enriched in dendritically localized transcripts and report 213 enriched motifs, including both known and novel structures. © 2014 Middleton and Kim; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

An Exploratory Study on Using Principal-Component Analysis and Confirmatory Factor Analysis to Identify Bolt-On Dimensions: The EQ-5D Case Study.

PubMed

Finch, Aureliano Paolo; Brazier, John Edward; Mukuria, Clara; Bjorner, Jakob Bue

2017-12-01

Generic preference-based measures such as the EuroQol five-dimensional questionnaire (EQ-5D) are used in economic evaluation, but may not be appropriate for all conditions. When this happens, a possible solution is adding bolt-ons to expand their descriptive systems. Using review-based methods, studies published to date claimed the relevance of bolt-ons in the presence of poor psychometric results. This approach does not identify the specific dimensions missing from the Generic preference-based measure core descriptive system, and is inappropriate for identifying dimensions that might improve the measure generically. This study explores the use of principal-component analysis (PCA) and confirmatory factor analysis (CFA) for bolt-on identification in the EQ-5D. Data were drawn from the international Multi-Instrument Comparison study, which is an online survey on health and well-being measures in five countries. Analysis was based on a pool of 92 items from nine instruments. Initial content analysis provided a theoretical framework for PCA results interpretation and CFA model development. PCA was used to investigate the underlining dimensional structure and whether EQ-5D items were represented in the identified constructs. CFA was used to confirm the structure. CFA was cross-validated in random halves of the sample. PCA suggested a nine-component solution, which was confirmed by CFA. This included psychological symptoms, physical functioning, and pain, which were covered by the EQ-5D, and satisfaction, speech/cognition,relationships, hearing, vision, and energy/sleep which were not. These latter factors may represent relevant candidate bolt-ons. PCA and CFA appear useful methods for identifying potential bolt-ons dimensions for an instrument such as the EQ-5D. Copyright © 2017 International Society for Pharmacoeconomics and Outcomes Research (ISPOR). Published by Elsevier Inc. All rights reserved.

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.

DMS-MaPseq for genome-wide or targeted RNA structure probing in vivo.

PubMed

Zubradt, Meghan; Gupta, Paromita; Persad, Sitara; Lambowitz, Alan M; Weissman, Jonathan S; Rouskin, Silvi

2017-01-01

Coupling of structure-specific in vivo chemical modification to next-generation sequencing is transforming RNA secondary structure studies in living cells. The dominant strategy for detecting in vivo chemical modifications uses reverse transcriptase truncation products, which introduce biases and necessitate population-average assessments of RNA structure. Here we present dimethyl sulfate (DMS) mutational profiling with sequencing (DMS-MaPseq), which encodes DMS modifications as mismatches using a thermostable group II intron reverse transcriptase. DMS-MaPseq yields a high signal-to-noise ratio, can report multiple structural features per molecule, and allows both genome-wide studies and focused in vivo investigations of even low-abundance RNAs. We apply DMS-MaPseq for the first analysis of RNA structure within an animal tissue and to identify a functional structure involved in noncanonical translation initiation. Additionally, we use DMS-MaPseq to compare the in vivo structure of pre-mRNAs with their mature isoforms. These applications illustrate DMS-MaPseq's capacity to dramatically expand in vivo analysis of RNA structure.

Deciphering the shape and deformation of secondary structures through local conformation analysis

PubMed Central

2011-01-01

Background Protein deformation has been extensively analysed through global methods based on RMSD, torsion angles and Principal Components Analysis calculations. Here we use a local approach, able to distinguish among the different backbone conformations within loops, α-helices and β-strands, to address the question of secondary structures' shape variation within proteins and deformation at interface upon complexation. Results Using a structural alphabet, we translated the 3 D structures of large sets of protein-protein complexes into sequences of structural letters. The shape of the secondary structures can be assessed by the structural letters that modeled them in the structural sequences. The distribution analysis of the structural letters in the three protein compartments (surface, core and interface) reveals that secondary structures tend to adopt preferential conformations that differ among the compartments. The local description of secondary structures highlights that curved conformations are preferred on the surface while straight ones are preferred in the core. Interfaces display a mixture of local conformations either preferred in core or surface. The analysis of the structural letters transition occurring between protein-bound and unbound conformations shows that the deformation of secondary structure is tightly linked to the compartment preference of the local conformations. Conclusion The conformation of secondary structures can be further analysed and detailed thanks to a structural alphabet which allows a better description of protein surface, core and interface in terms of secondary structures' shape and deformation. Induced-fit modification tendencies described here should be valuable information to identify and characterize regions under strong structural constraints for functional reasons. PMID:21284872

Deciphering the shape and deformation of secondary structures through local conformation analysis.

PubMed

Baussand, Julie; Camproux, Anne-Claude

2011-02-01

Protein deformation has been extensively analysed through global methods based on RMSD, torsion angles and Principal Components Analysis calculations. Here we use a local approach, able to distinguish among the different backbone conformations within loops, α-helices and β-strands, to address the question of secondary structures' shape variation within proteins and deformation at interface upon complexation. Using a structural alphabet, we translated the 3 D structures of large sets of protein-protein complexes into sequences of structural letters. The shape of the secondary structures can be assessed by the structural letters that modeled them in the structural sequences. The distribution analysis of the structural letters in the three protein compartments (surface, core and interface) reveals that secondary structures tend to adopt preferential conformations that differ among the compartments. The local description of secondary structures highlights that curved conformations are preferred on the surface while straight ones are preferred in the core. Interfaces display a mixture of local conformations either preferred in core or surface. The analysis of the structural letters transition occurring between protein-bound and unbound conformations shows that the deformation of secondary structure is tightly linked to the compartment preference of the local conformations. The conformation of secondary structures can be further analysed and detailed thanks to a structural alphabet which allows a better description of protein surface, core and interface in terms of secondary structures' shape and deformation. Induced-fit modification tendencies described here should be valuable information to identify and characterize regions under strong structural constraints for functional reasons.

Matching biomedical ontologies based on formal concept analysis.

PubMed

Zhao, Mengyi; Zhang, Songmao; Li, Weizhuo; Chen, Guowei

2018-03-19

The goal of ontology matching is to identify correspondences between entities from different yet overlapping ontologies so as to facilitate semantic integration, reuse and interoperability. As a well developed mathematical model for analyzing individuals and structuring concepts, Formal Concept Analysis (FCA) has been applied to ontology matching (OM) tasks since the beginning of OM research, whereas ontological knowledge exploited in FCA-based methods is limited. This motivates the study in this paper, i.e., to empower FCA with as much as ontological knowledge as possible for identifying mappings across ontologies. We propose a method based on Formal Concept Analysis to identify and validate mappings across ontologies, including one-to-one mappings, complex mappings and correspondences between object properties. Our method, called FCA-Map, incrementally generates a total of five types of formal contexts and extracts mappings from the lattices derived. First, the token-based formal context describes how class names, labels and synonyms share lexical tokens, leading to lexical mappings (anchors) across ontologies. Second, the relation-based formal context describes how classes are in taxonomic, partonomic and disjoint relationships with the anchors, leading to positive and negative structural evidence for validating the lexical matching. Third, the positive relation-based context can be used to discover structural mappings. Afterwards, the property-based formal context describes how object properties are used in axioms to connect anchor classes across ontologies, leading to property mappings. Last, the restriction-based formal context describes co-occurrence of classes across ontologies in anonymous ancestors of anchors, from which extended structural mappings and complex mappings can be identified. Evaluation on the Anatomy, the Large Biomedical Ontologies, and the Disease and Phenotype track of the 2016 Ontology Alignment Evaluation Initiative campaign demonstrates the effectiveness of FCA-Map and its competitiveness with the top-ranked systems. FCA-Map can achieve a better balance between precision and recall for large-scale domain ontologies through constructing multiple FCA structures, whereas it performs unsatisfactorily for smaller-sized ontologies with less lexical and semantic expressions. Compared with other FCA-based OM systems, the study in this paper is more comprehensive as an attempt to push the envelope of the Formal Concept Analysis formalism in ontology matching tasks. Five types of formal contexts are constructed incrementally, and their derived concept lattices are used to cluster the commonalities among classes at lexical and structural level, respectively. Experiments on large, real-world domain ontologies show promising results and reveal the power of FCA.

HTA and its legal issues: a framework for identifying legal issues in health technology assessment.

PubMed

Widrig, Daniel; Tag, Brigitte

2014-12-01

Legal analysis can highlight important issues that are relevant when deciding whether a medical technology should be implemented or reimbursed. Literature and studies show that even though the law is an acknowledged part of health technology assessment (HTA), legal issues are rarely considered in practice. One reason for this may be the lack of knowledge about the diversity of legal issues that are relevant for HTA. Therefore, this contribution aims primarily to identify and then explain the relevant legal issues in HTA. This study offers a framework for identifying the legal issues in HTAs in different jurisdictions and provides a basis for further research. After extensive literature search, the authors review Swiss health law to identify legal issues that are relevant to HTA. The authors then categorize these legal issues using a framework with an inside and outside perspective. Finally, they explain a selection of these legal issues with several examples. This study reveals numerous legal issues that are relevant for HTA and underlines the necessity of incorporating legal analysis in HTAs. The suggested perspectival framework in this study provides a basis to structure the legal analysis. The identified legal issues are relevant in other countries and the perspectival framework is transferable to other jurisdictions. The article underlines the importance of in-depth discussion about the role of law in HTA. It provides a structured overview of the legal issues in HTA and suggests a development of more concrete instruments toward a standardized legal technology assessment.

Factor structure of DSM-IV criteria for obsessive compulsive personality disorder in patients with binge eating disorder.

PubMed

Grilo, C M

2004-01-01

To examine the factor structure of DSM-IV criteria for obsessive compulsive personality disorder (OCPD) in patients with binge eating disorder (BED). Two hundred and eleven consecutive out-patients with axis I diagnoses of BED were reliably assessed with semi-structured diagnostic interviews. The eight criteria for the OCPD diagnosis were examined with reliability and correlational analyses. Exploratory factor analysis was performed to identify potential components. Cronbach's coefficient alpha for the OCPD criteria was 0.77. Principal components factor analysis with varimax rotation revealed a three-factor solution (rigidity, perfectionism, and miserliness), which accounted for 65% of variance. The DSM-IV criteria for OCPD showed good internal consistency. Exploratory factor analysis, however, revealed three components that may reflect distinct interpersonal, intrapersonal (cognitive), and behavioral features.

Laboratory ultrasonic pulse velocity logging for determination of elastic properties from rock core

NASA Astrophysics Data System (ADS)

Blacklock, Natalie Erin

During the development of deep underground excavations spalling and rockbursting have been recognized as significant mechanisms of violent brittle failure. In order to predict whether violent brittle failure will occur, it is important to identify the location of stiffness transitions that are associated with geologic structure. One approach to identify the effect of geologic structures is to apply borehole geophysical tools ahead of the tunnel advance. Stiffness transitions can be identified using mechanical property analysis surveys that combine acoustic velocity and density data to calculate acoustic estimates of elastic moduli. However, logistical concerns arise since the approach must be conducted at the advancing tunnel face. As a result, borehole mechanical property analyses are rarely used. Within this context, laboratory ultrasonic pulse velocity testing has been proposed as a potential alternative to borehole mechanical property analysis since moving the analysis to the laboratory would remove logistical constraints and improve safety for the evaluators. In addition to the traditional method of conducting velocity testing along the core axis, two new methodologies for point-focused testing were developed across the core diameter, and indirectly along intact lengths of drill core. The indirect test procedure was implemented in a continuous ultrasonic velocity test program along 573m of drill core to identify key geologic structures that generated transitions in ultrasonic elastic moduli. The test program was successful at identifying the location of geologic contacts, igneous intrusions, faults and shear structures. Ultrasonic values of Young's modulus and bulk modulus were determined at locations of significant velocity transitions to examine the potential for energy storage and energy release. Comparison of results from different ultrasonic velocity test configurations determined that the indirect test configuration provided underestimates for values of Young's modulus. This indicated that the test procedure will require modifications to improve coupling of the transducers to the core surface. In order to assess whether laboratory testing can be an alternative to borehole surveys, laboratory velocity testing must be directly assessed with results from acoustic borehole logging. There is also potential for the laboratory velocity program to be used to assess small scale stiffness changes, differences in mineral composition and the degree of fracturing of drill core.

Heparin/heparan sulfate 6-O-sulfatase from Flavobacterium heparinum: integrated structural and biochemical investigation of enzyme active site and substrate specificity.

PubMed

Myette, James R; Soundararajan, Venkataramanan; Shriver, Zachary; Raman, Rahul; Sasisekharan, Ram

2009-12-11

Heparin and heparan sulfate glycosaminoglycans (HSGAGs) comprise a chemically heterogeneous class of sulfated polysaccharides. The development of structure-activity relationships for this class of polysaccharides requires the identification and characterization of degrading enzymes with defined substrate specificity and enzymatic activity. Toward this end, we report here the molecular cloning and extensive structure-function analysis of a 6-O-sulfatase from the Gram-negative bacterium Flavobacterium heparinum. In addition, we report the recombinant expression of this enzyme in Escherichia coli in a soluble, active form and identify it as a specific HSGAG sulfatase. We further define the mechanism of action of the enzyme through biochemical and structural studies. Through the use of defined substrates, we investigate the kinetic properties of the enzyme. This analysis was complemented by homology-based molecular modeling studies that sought to rationalize the substrate specificity of the enzyme and mode of action through an analysis of the active-site topology of the enzyme including identifying key enzyme-substrate interactions and assigning key amino acids within the active site of the enzyme. Taken together, our structural and biochemical studies indicate that 6-O-sulfatase is a predominantly exolytic enzyme that specifically acts on N-sulfated or N-acetylated 6-O-sulfated glucosamines present at the non-reducing end of HSGAG oligosaccharide substrates. This requirement for the N-acetyl or N-sulfo groups on the glucosamine substrate can be explained through eliciting favorable interactions with key residues within the active site of the enzyme. These findings provide a framework that enables the use of 6-O-sulfatase as a tool for HSGAG structure-activity studies as well as expand our biochemical and structural understanding of this important class of enzymes.

Using active shape modeling based on MRI to study morphologic and pitch-related functional changes affecting vocal structures and the airway.

PubMed

Miller, Nicola A; Gregory, Jennifer S; Aspden, Richard M; Stollery, Peter J; Gilbert, Fiona J

2014-09-01

The shape of the vocal tract and associated structures (eg, tongue and velum) is complicated and varies according to development and function. This variability challenges interpretation of voice experiments. Quantifying differences between shapes and understanding how vocal structures move in relation to each other is difficult using traditional linear and angle measurements. With statistical shape models, shape can be characterized in terms of independent modes of variation. Here, we build an active shape model (ASM) to assess morphologic and pitch-related functional changes affecting vocal structures and the airway. Using a cross-sectional study design, we obtained six midsagittal magnetic resonance images from 10 healthy adults (five men and five women) at rest, while breathing out, and while listening to, and humming low and high notes. Eighty landmark points were chosen to define the shape of interest and an ASM was built using these (60) images. Principal component analysis was used to identify independent modes of variation, and statistical analysis was performed using one-way repeated-measures analysis of variance. Twenty modes of variation were identified with modes 1 and 2 accounting for half the total variance. Modes 1 and 9 were significantly associated with humming low and high notes (P < 0.001) and showed coordinated changes affecting the cervical spine, vocal structures, and airway. Mode 2 highlighted wide structural variations between subjects. This study highlights the potential of active shape modeling to advance understanding of factors underlying morphologic and pitch-related functional variations affecting vocal structures and the airway in health and disease. Copyright © 2014 The Voice Foundation. Published by Elsevier Inc. All rights reserved.

A simple method for identifying parameter correlations in partially observed linear dynamic models.

PubMed

Li, Pu; Vu, Quoc Dong

2015-12-14

Parameter estimation represents one of the most significant challenges in systems biology. This is because biological models commonly contain a large number of parameters among which there may be functional interrelationships, thus leading to the problem of non-identifiability. Although identifiability analysis has been extensively studied by analytical as well as numerical approaches, systematic methods for remedying practically non-identifiable models have rarely been investigated. We propose a simple method for identifying pairwise correlations and higher order interrelationships of parameters in partially observed linear dynamic models. This is made by derivation of the output sensitivity matrix and analysis of the linear dependencies of its columns. Consequently, analytical relations between the identifiability of the model parameters and the initial conditions as well as the input functions can be achieved. In the case of structural non-identifiability, identifiable combinations can be obtained by solving the resulting homogenous linear equations. In the case of practical non-identifiability, experiment conditions (i.e. initial condition and constant control signals) can be provided which are necessary for remedying the non-identifiability and unique parameter estimation. It is noted that the approach does not consider noisy data. In this way, the practical non-identifiability issue, which is popular for linear biological models, can be remedied. Several linear compartment models including an insulin receptor dynamics model are taken to illustrate the application of the proposed approach. Both structural and practical identifiability of partially observed linear dynamic models can be clarified by the proposed method. The result of this method provides important information for experimental design to remedy the practical non-identifiability if applicable. The derivation of the method is straightforward and thus the algorithm can be easily implemented into a software packet.

Attitudes of French-Canadian university students toward use of condoms: a structural analysis.

PubMed

Bernard, J; Hébert, Y; de Man, A; Farrar, D

1989-12-01

164 French-Canadian university students took part in a study analyzing the factorial pattern of attitudes toward the use of condoms. A principal component analysis identified 7 factors, namely, positive general attitude toward use of condoms, contraceptive security, inhibition of sexual pleasure, inconvenience, embarrassment, responsibility, and lessening of physical pleasure.

An Analysis of Culturalism in Latino Mental Health: Folk Medicine as a Case in Point.

ERIC Educational Resources Information Center

De La Cancela, Victor; Martinez, Iris Zavala

1983-01-01

Identifies limitations of culturalist perspective often advocated by Latino mental health workers outlines folk healing practices they favor. Notes that culturalist perspective suffers from ahistorical/asocial/static conceptualization, and lacks analysis of class/sex/structural dimensions of so-called cultural expressions. Calls for recognition of…

Case-Exercises, Diagnosis, and Explanations in a Knowledge Based Tutoring System for Project Planning.

ERIC Educational Resources Information Center

Pulz, Michael; Lusti, Markus

PROJECTTUTOR is an intelligent tutoring system that enhances conventional classroom instruction by teaching problem solving in project planning. The domain knowledge covered by the expert module is divided into three functions. Structural analysis, identifies the activities that make up the project, time analysis, computes the earliest and latest…

Neutral model analysis of landscape patterns from mathematical morphology

Treesearch

Kurt H. Riitters; Peter Vogt; Pierre Soille; Jacek Kozak; Christine Estreguil

2007-01-01

Mathematical morphology encompasses methods for characterizing land-cover patterns in ecological research and biodiversity assessments. This paper reports a neutral model analysis of patterns in the absence of a structuring ecological process, to help set standards for comparing and interpreting patterns identified by mathematical morphology on real land-cover maps. We...

The dynamics of information-driven coordination phenomena: A transfer entropy analysis

PubMed Central

Borge-Holthoefer, Javier; Perra, Nicola; Gonçalves, Bruno; González-Bailón, Sandra; Arenas, Alex; Moreno, Yamir; Vespignani, Alessandro

2016-01-01

Data from social media provide unprecedented opportunities to investigate the processes that govern the dynamics of collective social phenomena. We consider an information theoretical approach to define and measure the temporal and structural signatures typical of collective social events as they arise and gain prominence. We use the symbolic transfer entropy analysis of microblogging time series to extract directed networks of influence among geolocalized subunits in social systems. This methodology captures the emergence of system-level dynamics close to the onset of socially relevant collective phenomena. The framework is validated against a detailed empirical analysis of five case studies. In particular, we identify a change in the characteristic time scale of the information transfer that flags the onset of information-driven collective phenomena. Furthermore, our approach identifies an order-disorder transition in the directed network of influence between social subunits. In the absence of clear exogenous driving, social collective phenomena can be represented as endogenously driven structural transitions of the information transfer network. This study provides results that can help define models and predictive algorithms for the analysis of societal events based on open source data. PMID:27051875

The dynamics of information-driven coordination phenomena: A transfer entropy analysis.

PubMed

Borge-Holthoefer, Javier; Perra, Nicola; Gonçalves, Bruno; González-Bailón, Sandra; Arenas, Alex; Moreno, Yamir; Vespignani, Alessandro

2016-04-01

Data from social media provide unprecedented opportunities to investigate the processes that govern the dynamics of collective social phenomena. We consider an information theoretical approach to define and measure the temporal and structural signatures typical of collective social events as they arise and gain prominence. We use the symbolic transfer entropy analysis of microblogging time series to extract directed networks of influence among geolocalized subunits in social systems. This methodology captures the emergence of system-level dynamics close to the onset of socially relevant collective phenomena. The framework is validated against a detailed empirical analysis of five case studies. In particular, we identify a change in the characteristic time scale of the information transfer that flags the onset of information-driven collective phenomena. Furthermore, our approach identifies an order-disorder transition in the directed network of influence between social subunits. In the absence of clear exogenous driving, social collective phenomena can be represented as endogenously driven structural transitions of the information transfer network. This study provides results that can help define models and predictive algorithms for the analysis of societal events based on open source data.

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

Li, X.J., E-mail: lixj@alum.imr.ac.cn

During the deposition of diamond films on Ti alloy substrates, titanium carbide is a common precipitated phase, preferentially formed at the interfacial region. However, in this case, the precipitation of an ordered structure of titanium carbide has not been reported. In our work, a long periodic ordered structure of TiC has been observed at the deposited diamond film/Ti alloy interface by high resolution transmission electron microscopy (HRTEM). The long periodic ordered structure is identified as 6H-type. The formation mechanism is revealed by comparative studies on the different structures of TiC precipitated under different diamond deposition conditions in terms of depositionmore » time, atmosphere and temperature. A large number of carbon vacancies in the interfacial precipitated TiC phase are verified through electron energy loss spectroscopy (EELS) quantification analysis. However, an ordered arrangement of these carbon vacancies occurs only when the interfacial stress is large enough to induce the precipitation of 6H-type TiC. The supplementary analysis by X-ray diffraction (XRD) further confirms that additional diffraction peaks presented in the XRD patterns are corresponding to the precipitation of 6H-type TiC. - Highlights: •Different structures of TiC are observed during deposited diamond on Ti alloy. •One is common NaCl structure, the other is periodic structure. •The periodic structure is identified as 6H-type by HRTEM. •Carbon vacancies are verified to always exist in the TiC phase. •The precipitation of 6H-type TiC is mainly affected by interfacial stress.« less

Alternative to Ritt's pseudodivision for finding the input-output equations of multi-output models.

PubMed

Meshkat, Nicolette; Anderson, Chris; DiStefano, Joseph J

2012-09-01

Differential algebra approaches to structural identifiability analysis of a dynamic system model in many instances heavily depend upon Ritt's pseudodivision at an early step in analysis. The pseudodivision algorithm is used to find the characteristic set, of which a subset, the input-output equations, is used for identifiability analysis. A simpler algorithm is proposed for this step, using Gröbner Bases, along with a proof of the method that includes a reduced upper bound on derivative requirements. Efficacy of the new algorithm is illustrated with several biosystem model examples. Copyright © 2012 Elsevier Inc. All rights reserved.

Combined sequence and structure analysis of the fungal laccase family.

PubMed

Kumar, S V Suresh; Phale, Prashant S; Durani, S; Wangikar, Pramod P

2003-08-20

Plant and fungal laccases belong to the family of multi-copper oxidases and show much broader substrate specificity than other members of the family. Laccases have consequently been of interest for potential industrial applications. We have analyzed the essential sequence features of fungal laccases based on multiple sequence alignments of more than 100 laccases. This has resulted in identification of a set of four ungapped sequence regions, L1-L4, as the overall signature sequences that can be used to identify the laccases, distinguishing them within the broader class of multi-copper oxidases. The 12 amino acid residues in the enzymes serving as the copper ligands are housed within these four identified conserved regions, of which L2 and L4 conform to the earlier reported copper signature sequences of multi-copper oxidases while L1 and L3 are distinctive to the laccases. The mapping of regions L1-L4 on to the three-dimensional structure of the Coprinus cinerius laccase indicates that many of the non-copper-ligating residues of the conserved regions could be critical in maintaining a specific, more or less C-2 symmetric, protein conformational motif characterizing the active site apparatus of the enzymes. The observed intraprotein homologies between L1 and L3 and between L2 and L4 at both the structure and the sequence levels suggest that the quasi C-2 symmetric active site conformational motif may have arisen from a structural duplication event that neither the sequence homology analysis nor the structure homology analysis alone would have unraveled. Although the sequence and structure homology is not detectable in the rest of the protein, the relative orientation of region L1 with L2 is similar to that of L3 with L4. The structure duplication of first-shell and second-shell residues has become cryptic because the intraprotein sequence homology noticeable for a given laccase becomes significant only after comparing the conservation pattern in several fungal laccases. The identified motifs, L1-L4, can be useful in searching the newly sequenced genomes for putative laccase enzymes. Copyright 2003 Wiley Periodicals, Inc. Biotechnol Bioeng 83: 386-394, 2003.

Initial empirical analysis of nuclear power plant organization and its effect on safety performance

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

Olson, J.; McLaughlin, S.D.; Osborn, R.N.

This report contains an analysis of the relationship between selected aspects of organizational structure and the safety-related performance of nuclear power plants. The report starts by identifying and operationalizing certain key dimensions of organizational structure that may be expected to be related to plant safety performance. Next, indicators of plant safety performance are created by combining existing performance measures into more reliable indicators. Finally, the indicators of plant safety performance using correlational and discriminant analysis. The overall results show that plants with better developed coordination mechanisms, shorter vertical hierarchies, and a greater number of departments tend to perform more safely.

Structural study of Cu(II) complexes with benzo[b]furancarboxylic acids

NASA Astrophysics Data System (ADS)

Kalinowska, Diana; Klepka, Marcin T.; Wolska, Anna; Drzewiecka-Antonik, Aleksandra; Ostrowska, Kinga; Struga, Marta

2017-11-01

Four Cu(II) complexes with 2- and 3-benzo[b]furancarboxylic acids have been synthesized and characterized using combination of two spectroscopic techniques. These techniques were: (i) FTIR and (ii) XAFS. FTIR analysis confirmed that complexes were formed and gave insight into identification of possible coordinating groups to the metallic center. XANES analysis indicated that the oxidation state of Cu is +2. EXAFS analysis allowed to identify that the first coordination sphere is formed by 4-5 oxygen atoms with the Cu-O distances around 2 Å. Combining these techniques it was possible to structurally describe novel Cu(II) complexes with benzo[b]furancarboxylic acids.

Analysing Health Professionals' Learning Interactions in an Online Social Network: A Longitudinal Study.

PubMed

Li, Xin; Verspoor, Karin; Gray, Kathleen; Barnett, Stephen

2016-01-01

This paper summarises a longitudinal analysis of learning interactions occurring over three years among health professionals in an online social network. The study employs the techniques of Social Network Analysis (SNA) and statistical modeling to identify the changes in patterns of interaction over time and test associated structural network effects. SNA results indicate overall low participation in the network, although some participants became active over time and even led discussions. In particular, the analysis has shown that a change of lead contributor results in a change in learning interaction and network structure. The analysis of structural network effects demonstrates that the interaction dynamics slow down over time, indicating that interactions in the network are more stable. The health professionals may be reluctant to share knowledge and collaborate in groups but were interested in building personal learning networks or simply seeking information.

Integrated proteomic and transcriptomic analysis of the Aedes aegypti eggshell

PubMed Central

2014-01-01

Background Mosquito eggshells show remarkable diversity in physical properties and structure consistent with adaptations to the wide variety of environments exploited by these insects. We applied proteomic, transcriptomic, and hybridization in situ techniques to identify gene products and pathways that participate in the assembly of the Aedes aegypti eggshell. Aedes aegypti population density is low during cold and dry seasons and increases immediately after rainfall. The survival of embryos through unfavorable periods is a key factor in the persistence of their populations. The work described here supports integrated vector control approaches that target eggshell formation and result in Ae. aegypti drought-intolerant phenotypes for public health initiatives directed to reduce mosquito-borne diseases. Results A total of 130 proteins were identified from the combined mass spectrometric analyses of eggshell preparations. Conclusions Classification of proteins according to their known and putative functions revealed the complexity of the eggshell structure. Three novel Ae. aegypti vitelline membrane proteins were discovered. Odorant-binding and cysteine-rich proteins that may be structural components of the eggshell were identified. Enzymes with peroxidase, laccase and phenoloxidase activities also were identified, and their likely involvements in cross-linking reactions that stabilize the eggshell structure are discussed. PMID:24707823

Role of DNA secondary structures in fragile site breakage along human chromosome 10

PubMed Central

Dillon, Laura W.; Pierce, Levi C. T.; Ng, Maggie C. Y.; Wang, Yuh-Hwa

2013-01-01

The formation of alternative DNA secondary structures can result in DNA breakage leading to cancer and other diseases. Chromosomal fragile sites, which are regions of the genome that exhibit chromosomal breakage under conditions of mild replication stress, are predicted to form stable DNA secondary structures. DNA breakage at fragile sites is associated with regions that are deleted, amplified or rearranged in cancer. Despite the correlation, unbiased examination of the ability to form secondary structures has not been evaluated in fragile sites. Here, using the Mfold program, we predict potential DNA secondary structure formation on the human chromosome 10 sequence, and utilize this analysis to compare fragile and non-fragile DNA. We found that aphidicolin (APH)-induced common fragile sites contain more sequence segments with potential high secondary structure-forming ability, and these segments clustered more densely than those in non-fragile DNA. Additionally, using a threshold of secondary structure-forming ability, we refined legitimate fragile sites within the cytogenetically defined boundaries, and identified potential fragile regions within non-fragile DNA. In vitro detection of alternative DNA structure formation and a DNA breakage cell assay were used to validate the computational predictions. Many of the regions identified by our analysis coincide with genes mutated in various diseases and regions of copy number alteration in cancer. This study supports the role of DNA secondary structures in common fragile site instability, provides a systematic method for their identification and suggests a mechanism by which DNA secondary structures can lead to human disease. PMID:23297364

Inferring Biological Structures from Super-Resolution Single Molecule Images Using Generative Models

PubMed Central

Maji, Suvrajit; Bruchez, Marcel P.

2012-01-01

Localization-based super resolution imaging is presently limited by sampling requirements for dynamic measurements of biological structures. Generating an image requires serial acquisition of individual molecular positions at sufficient density to define a biological structure, increasing the acquisition time. Efficient analysis of biological structures from sparse localization data could substantially improve the dynamic imaging capabilities of these methods. Using a feature extraction technique called the Hough Transform simple biological structures are identified from both simulated and real localization data. We demonstrate that these generative models can efficiently infer biological structures in the data from far fewer localizations than are required for complete spatial sampling. Analysis at partial data densities revealed efficient recovery of clathrin vesicle size distributions and microtubule orientation angles with as little as 10% of the localization data. This approach significantly increases the temporal resolution for dynamic imaging and provides quantitatively useful biological information. PMID:22629348

Unraveling Appalachian tectonics: domain analysis of topographic lineaments in Pennsylvania

NASA Astrophysics Data System (ADS)

Karimi, B.; Schon, K.; Nussbaum, G. W.; Storer, N. D.; McGuire, J. L.; Hardcastle, K.

2016-12-01

Litho-tectonic provinces provide different components of a regions' tectonic history, and are identified as spatial entities with common structural elements, or a number of contiguous related elements. The province boundaries are easily identified when geomorphic expressions are distinct, or significant rock exposure allows for little uncertainty. When exposures are limited, locations of boundaries between provinces are uncertain. In such instances, satellite imagery can be quite advantageous, as tectonically sourced features (faults, folds, fractures, and joints) may exert a strong control on topographic patterns by creating pathways for weathering and erosion. Lineament analyses of topography often focus on well-pronounced tectonic features to interpret regional tectonics. We suggest that lineament analyses including all topographic features may include more subtle tectonic features, resulting in the identification of minor heterogeneities within litho-tectonic provinces. Our study focuses on Appalachian tectonics, specifically in Pennsylvania (PA), home to the Appalachian Orocline and 5 distinct tectonic provinces. Using hillshades from a digital elevation model (DEM) of PA, we manually pick all topographic lineaments 1 km or greater, discriminating only against man-made structures. The final lineament coverage of the state is subdivided into smaller areas for which rose diagrams were prepared. The dominant lineament trends were compared and associated with known structural features. Peaks with no known source are marked as possible tectonic features requiring further research. A domain analysis is performed on the lineament data to identify the extent and interplay of swarms, followed by an investigation of their azimuthal compatibility. We present the results of our domain analysis of all topographic lineaments in the context of identifying litho-tectonic provinces associated with Appalachian tectonics in Pennsylvania, and possible heterogeneities within them.

Genotyping-By-Sequencing (GBS) Detects Genetic Structure and Confirms Behavioral QTL in Tame and Aggressive Foxes (Vulpes vulpes)

PubMed Central

Johnson, Jennifer L.; Wittgenstein, Helena; Mitchell, Sharon E.; Hyma, Katie E.; Temnykh, Svetlana V.; Kharlamova, Anastasiya V.; Gulevich, Rimma G.; Vladimirova, Anastasiya V.; Fong, Hiu Wa Flora; Acland, Gregory M.; Trut, Lyudmila N.; Kukekova, Anna V.

2015-01-01

The silver fox (Vulpes vulpes) offers a novel model for studying the genetics of social behavior and animal domestication. Selection of foxes, separately, for tame and for aggressive behavior has yielded two strains with markedly different, genetically determined, behavioral phenotypes. Tame strain foxes are eager to establish human contact while foxes from the aggressive strain are aggressive and difficult to handle. These strains have been maintained as separate outbred lines for over 40 generations but their genetic structure has not been previously investigated. We applied a genotyping-by-sequencing (GBS) approach to provide insights into the genetic composition of these fox populations. Sequence analysis of EcoT22I genomic libraries of tame and aggressive foxes identified 48,294 high quality SNPs. Population structure analysis revealed genetic divergence between the two strains and more diversity in the aggressive strain than in the tame one. Significant differences in allele frequency between the strains were identified for 68 SNPs. Three of these SNPs were located on fox chromosome 14 within an interval of a previously identified behavioral QTL, further supporting the importance of this region for behavior. The GBS SNP data confirmed that significant genetic diversity has been preserved in both fox populations despite many years of selective breeding. Analysis of SNP allele frequencies in the two populations identified several regions of genetic divergence between the tame and aggressive foxes, some of which may represent targets of selection for behavior. The GBS protocol used in this study significantly expanded genomic resources for the fox, and can be adapted for SNP discovery and genotyping in other canid species. PMID:26061395

Genotyping-By-Sequencing (GBS) Detects Genetic Structure and Confirms Behavioral QTL in Tame and Aggressive Foxes (Vulpes vulpes).

PubMed

Johnson, Jennifer L; Wittgenstein, Helena; Mitchell, Sharon E; Hyma, Katie E; Temnykh, Svetlana V; Kharlamova, Anastasiya V; Gulevich, Rimma G; Vladimirova, Anastasiya V; Fong, Hiu Wa Flora; Acland, Gregory M; Trut, Lyudmila N; Kukekova, Anna V

2015-01-01

The silver fox (Vulpes vulpes) offers a novel model for studying the genetics of social behavior and animal domestication. Selection of foxes, separately, for tame and for aggressive behavior has yielded two strains with markedly different, genetically determined, behavioral phenotypes. Tame strain foxes are eager to establish human contact while foxes from the aggressive strain are aggressive and difficult to handle. These strains have been maintained as separate outbred lines for over 40 generations but their genetic structure has not been previously investigated. We applied a genotyping-by-sequencing (GBS) approach to provide insights into the genetic composition of these fox populations. Sequence analysis of EcoT22I genomic libraries of tame and aggressive foxes identified 48,294 high quality SNPs. Population structure analysis revealed genetic divergence between the two strains and more diversity in the aggressive strain than in the tame one. Significant differences in allele frequency between the strains were identified for 68 SNPs. Three of these SNPs were located on fox chromosome 14 within an interval of a previously identified behavioral QTL, further supporting the importance of this region for behavior. The GBS SNP data confirmed that significant genetic diversity has been preserved in both fox populations despite many years of selective breeding. Analysis of SNP allele frequencies in the two populations identified several regions of genetic divergence between the tame and aggressive foxes, some of which may represent targets of selection for behavior. The GBS protocol used in this study significantly expanded genomic resources for the fox, and can be adapted for SNP discovery and genotyping in other canid species.

Analysis of mitochondrial genetic diversity of Ustilago maydis in Mexico.

PubMed

Jiménez-Becerril, María F; Hernández-Delgado, Sanjuana; Solís-Oba, Myrna; González Prieto, Juan M

2018-01-01

The current understanding of the genetic diversity of the phytopathogenic fungus Ustilago maydis is limited. To determine the genetic diversity and structure of U. maydis, 48 fungal isolates were analyzed using mitochondrial simple sequence repeats (SSRs). Tumours (corn smut or 'huitlacoche') were collected from different Mexican states with diverse environmental conditions. Using bioinformatic tools, five microsatellites were identified within intergenic regions of the U. maydis mitochondrial genome. SSRMUM4 was the most polymorphic marker. The most common repeats were hexanucleotides. A total of 12 allelic variants were identified, with a mean of 2.4 alleles per locus. An estimate of the genetic diversity using analysis of molecular variance (AMOVA) revealed that the highest variance component is within states (84%), with moderate genetic differentiation between states (16%) (F ST  = 0.158). A dendrogram generated using the unweighted paired-grouping method with arithmetic averages (UPGMA) and the Bayesian analysis of population structure grouped the U. maydis isolates into two subgroups (K = 2) based on their shared SSRs.

[Analysis of barriers to therapeutic adherence for Colombian women with HIV/AIDS: a question of health rights].

PubMed

Arrivillaga-Quintero, Marcela

2010-01-01

To identify and analyze HIV/AIDS treatment adherence among Colombian women. A qualitative, descriptive-interpretative study with content analysis was developed between 2008 and 2009. Sixty six women participated in five focus group discussions. To complement data, semi-structured interviews with seven key informants were conducted. Main barriers are determined structurally by the current Colombian health system, based on insurance market. The right to access to treatment in a timely and continuous manner, the rights to confidentiality and non discrimination, and the right to quality care with gender focus are affected among participant women. Consequently, adherence is negatively affected. The current Colombian health system determines critical processes affecting HIV/AIDS treatment adherence in women. However, further research must be conducted to identify specific associations with non-universal health systems.

Toward a dynamical theory of body movement in musical performance

PubMed Central

Demos, Alexander P.; Chaffin, Roger; Kant, Vivek

2014-01-01

Musicians sway expressively as they play in ways that seem clearly related to the music, but quantifying the relationship has been difficult. We suggest that a complex systems framework and its accompanying tools for analyzing non-linear dynamical systems can help identify the motor synergies involved. Synergies are temporary assemblies of parts that come together to accomplish specific goals. We assume that the goal of the performer is to convey musical structure and expression to the audience and to other performers. We provide examples of how dynamical systems tools, such as recurrence quantification analysis (RQA), can be used to examine performers' movements and relate them to the musical structure and to the musician's expressive intentions. We show how detrended fluctuation analysis (DFA) can be used to identify synergies and discover how they are affected by the performer's expressive intentions. PMID:24904490

[Regression analysis to select native-like structures from decoys of antigen-antibody docking].

PubMed

Chen, Zhengshan; Chi, Xiangyang; Fan, Pengfei; Zhang, Guanying; Wang, Meirong; Yu, Changming; Chen, Wei

2018-06-25

Given the increasing exploitation of antibodies in different contexts such as molecular diagnostics and therapeutics, it would be beneficial to unravel properties of antigen-antibody interaction with modeling of computational protein-protein docking, especially, in the absence of a cocrystal structure. However, obtaining a native-like antigen-antibody structure remains challenging due in part to failing to reliably discriminate accurate from inaccurate structures among tens of thousands of decoys after computational docking with existing scoring function. We hypothesized that some important physicochemical and energetic features could be used to describe antigen-antibody interfaces and identify native-like antigen-antibody structure. We prepared a dataset, a subset of Protein-Protein Docking Benchmark Version 4.0, comprising 37 nonredundant 3D structures of antigen-antibody complexes, and used it to train and test multivariate logistic regression equation which took several important physicochemical and energetic features of decoys as dependent variables. Our results indicate that the ability to identify native-like structures of our method is superior to ZRANK and ZDOCK score for the subset of antigen-antibody complexes. And then, we use our method in workflow of predicting epitope of anti-Ebola glycoprotein monoclonal antibody-4G7 and identify three accurate residues in its epitope.

Farm, household, and farmer characteristics associated with changes in management practices and technology adoption among dairy smallholders.

PubMed

Martínez-García, Carlos Galdino; Ugoretz, Sarah Janes; Arriaga-Jordán, Carlos Manuel; Wattiaux, Michel André

2015-02-01

This study explored whether technology adoption and changes in management practices were associated with farm structure, household, and farmer characteristics and to identify processes that may foster productivity and sustainability of small-scale dairy farming in the central highlands of Mexico. Factor analysis of survey data from 44 smallholders identified three factors-related to farm size, farmer's engagement, and household structure-that explained 70 % of cumulative variance. The subsequent hierarchical cluster analysis yielded three clusters. Cluster 1 included the most senior farmers with fewest years of education but greatest years of experience. Cluster 2 included farmers who reported access to extension, cooperative services, and more management changes. Cluster 2 obtained 25 and 35 % more milk than farmers in clusters 1 and 3, respectively. Cluster 3 included the youngest farmers, with most years of education and greatest availability of family labor. Access to a network and membership in a community of peers appeared as important contributors to success. Smallholders gravitated towards easy to implement technologies that have immediate benefits. Nonusers of high investment technologies found them unaffordable because of cost, insufficient farm size, and lack of knowledge or reliable electricity. Multivariate analysis may be a useful tool in planning extension activities and organizing channels of communication to effectively target farmers with varying needs, constraints, and motivations for change and in identifying farmers who may exemplify models of change for others who manage farms that are structurally similar but performing at a lower level.

A streamlined failure mode and effects analysis.

PubMed

Ford, Eric C; Smith, Koren; Terezakis, Stephanie; Croog, Victoria; Gollamudi, Smitha; Gage, Irene; Keck, Jordie; DeWeese, Theodore; Sibley, Greg

2014-06-01

Explore the feasibility and impact of a streamlined failure mode and effects analysis (FMEA) using a structured process that is designed to minimize staff effort. FMEA for the external beam process was conducted at an affiliate radiation oncology center that treats approximately 60 patients per day. A structured FMEA process was developed which included clearly defined roles and goals for each phase. A core group of seven people was identified and a facilitator was chosen to lead the effort. Failure modes were identified and scored according to the FMEA formalism. A risk priority number,RPN, was calculated and used to rank failure modes. Failure modes with RPN > 150 received safety improvement interventions. Staff effort was carefully tracked throughout the project. Fifty-two failure modes were identified, 22 collected during meetings, and 30 from take-home worksheets. The four top-ranked failure modes were: delay in film check, missing pacemaker protocol/consent, critical structures not contoured, and pregnant patient simulated without the team's knowledge of the pregnancy. These four failure modes had RPN > 150 and received safety interventions. The FMEA was completed in one month in four 1-h meetings. A total of 55 staff hours were required and, additionally, 20 h by the facilitator. Streamlined FMEA provides a means of accomplishing a relatively large-scale analysis with modest effort. One potential value of FMEA is that it potentially provides a means of measuring the impact of quality improvement efforts through a reduction in risk scores. Future study of this possibility is needed.

An Analysis Technique/Automated Tool for Comparing and Tracking Analysis Modes of Different Finite Element Models

NASA Technical Reports Server (NTRS)

Towner, Robert L.; Band, Jonathan L.

2012-01-01

An analysis technique was developed to compare and track mode shapes for different Finite Element Models. The technique may be applied to a variety of structural dynamics analyses, including model reduction validation (comparing unreduced and reduced models), mode tracking for various parametric analyses (e.g., launch vehicle model dispersion analysis to identify sensitivities to modal gain for Guidance, Navigation, and Control), comparing models of different mesh fidelity (e.g., a coarse model for a preliminary analysis compared to a higher-fidelity model for a detailed analysis) and mode tracking for a structure with properties that change over time (e.g., a launch vehicle from liftoff through end-of-burn, with propellant being expended during the flight). Mode shapes for different models are compared and tracked using several numerical indicators, including traditional Cross-Orthogonality and Modal Assurance Criteria approaches, as well as numerical indicators obtained by comparing modal strain energy and kinetic energy distributions. This analysis technique has been used to reliably identify correlated mode shapes for complex Finite Element Models that would otherwise be difficult to compare using traditional techniques. This improved approach also utilizes an adaptive mode tracking algorithm that allows for automated tracking when working with complex models and/or comparing a large group of models.

[Studies on chemical constituents from leaves and stems of Aconitum coreanum].

PubMed

Li, Yan; Liang, Shuai

2009-05-01

To study the chemical constituents in the leaves and stems of Aconitum coreanum. The isolation and purification of chemical constituents were carried out on silica gel and polyamide column chromatographic. Their structures were identified by physico-chemical properties and spectral analysis. Five compounds were obtained and their structures were identified as guan-fu base I (1), guan-fu base R (2), beta-sitosterol (3), D-mannitol (4), daucosterol (5). Compound 2 is a new compound. Compounds 1 and 3, 4 are isolated from the leaves and stems of A. coreanum for the first time.

Computing and visualizing time-varying merge trees for high-dimensional data

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

Oesterling, Patrick; Heine, Christian; Weber, Gunther H.

2017-06-03

We introduce a new method that identifies and tracks features in arbitrary dimensions using the merge tree -- a structure for identifying topological features based on thresholding in scalar fields. This method analyzes the evolution of features of the function by tracking changes in the merge tree and relates features by matching subtrees between consecutive time steps. Using the time-varying merge tree, we present a structural visualization of the changing function that illustrates both features and their temporal evolution. We demonstrate the utility of our approach by applying it to temporal cluster analysis of high-dimensional point clouds.

Analysis of Crushing Response of Composite Crashworthy Structures

NASA Astrophysics Data System (ADS)

David, Matthew; Johnson, Alastair F.; Voggenreiter, H.

2013-10-01

The paper describes quasi-static and dynamic tests to characterise the energy absorption properties of polymer composite crash energy absorbing segment elements under axial loads. Detailed computer tomography scans of failed specimens are used to identify local compression crush failure mechanisms at the crush front. The varied crushing morphology between the compression strain rates identified in this paper is observed to be due to the differences in the response modes and mechanical properties of the strain dependent epoxy matrix. The importance of understanding the role of strain rate effects in composite crash energy absorbing structures is highlighted in this paper.

An Information Transmission Measure for the Analysis of Effective Connectivity among Cortical Neurons

PubMed Central

Law, Andrew J.; Sharma, Gaurav; Schieber, Marc H.

2014-01-01

We present a methodology for detecting effective connections between simultaneously recorded neurons using an information transmission measure to identify the presence and direction of information flow from one neuron to another. Using simulated and experimentally-measured data, we evaluate the performance of our proposed method and compare it to the traditional transfer entropy approach. In simulations, our measure of information transmission outperforms transfer entropy in identifying the effective connectivity structure of a neuron ensemble. For experimentally recorded data, where ground truth is unavailable, the proposed method also yields a more plausible connectivity structure than transfer entropy. PMID:21096617

Total systems design analysis of high performance structures

NASA Technical Reports Server (NTRS)

Verderaime, V.

1993-01-01

Designer-control parameters were identified at interdiscipline interfaces to optimize structural systems performance and downstream development and operations with reliability and least life-cycle cost. Interface tasks and iterations are tracked through a matrix of performance disciplines integration versus manufacturing, verification, and operations interactions for a total system design analysis. Performance integration tasks include shapes, sizes, environments, and materials. Integrity integrating tasks are reliability and recurring structural costs. Significant interface designer control parameters were noted as shapes, dimensions, probability range factors, and cost. Structural failure concept is presented, and first-order reliability and deterministic methods, benefits, and limitations are discussed. A deterministic reliability technique combining benefits of both is proposed for static structures which is also timely and economically verifiable. Though launch vehicle environments were primarily considered, the system design process is applicable to any surface system using its own unique filed environments.

Theoretical analysis of metamaterial-gold auxiliary grating sensing structure for surface plasmon resonance sensing application based on polarization control method

NASA Astrophysics Data System (ADS)

Sun, Yi; Cai, Haoyuan; Wang, Xiaoping

2017-12-01

A metamaterial-gold multilayer sensing structure designed using the particle swarm optimization (PSO) algorithm with an auxiliary grating is proposed for using in a surface plasmon resonance (SPR) sensor system based on the polarization control method. After numerical calculations and simulation analysis, it was found that the metamaterial sensing structure significantly improves the sensitivity of the SPR signal with intensity singularity. The metamaterial sensing structure also increases the penetration depth of evanescent wave, making it possible to detect low-molecular-weight biomolecules and larger cells such as bacteria. The auxiliary grating structure was designed to identify the refractive index of the sensing region on both sides of intensity singularity. The stability of recognition and the electric field intensity of the visible light band were also studied.

Network structure and travel time perception.

PubMed

Parthasarathi, Pavithra; Levinson, David; Hochmair, Hartwig

2013-01-01

The purpose of this research is to test the systematic variation in the perception of travel time among travelers and relate the variation to the underlying street network structure. Travel survey data from the Twin Cities metropolitan area (which includes the cities of Minneapolis and St. Paul) is used for the analysis. Travelers are classified into two groups based on the ratio of perceived and estimated commute travel time. The measures of network structure are estimated using the street network along the identified commute route. T-test comparisons are conducted to identify statistically significant differences in estimated network measures between the two traveler groups. The combined effect of these estimated network measures on travel time is then analyzed using regression models. The results from the t-test and regression analyses confirm the influence of the underlying network structure on the perception of travel time.

Structural modelling and comparative analysis of homologous, analogous and specific proteins from Trypanosoma cruzi versus Homo sapiens: putative drug targets for chagas' disease treatment

PubMed Central

2010-01-01

Background Trypanosoma cruzi is the etiological agent of Chagas' disease, an endemic infection that causes thousands of deaths every year in Latin America. Therapeutic options remain inefficient, demanding the search for new drugs and/or new molecular targets. Such efforts can focus on proteins that are specific to the parasite, but analogous enzymes and enzymes with a three-dimensional (3D) structure sufficiently different from the corresponding host proteins may represent equally interesting targets. In order to find these targets we used the workflows MHOLline and AnEnΠ obtaining 3D models from homologous, analogous and specific proteins of Trypanosoma cruzi versus Homo sapiens. Results We applied genome wide comparative modelling techniques to obtain 3D models for 3,286 predicted proteins of T. cruzi. In combination with comparative genome analysis to Homo sapiens, we were able to identify a subset of 397 enzyme sequences, of which 356 are homologous, 3 analogous and 38 specific to the parasite. Conclusions In this work, we present a set of 397 enzyme models of T. cruzi that can constitute potential structure-based drug targets to be investigated for the development of new strategies to fight Chagas' disease. The strategies presented here support the concept of structural analysis in conjunction with protein functional analysis as an interesting computational methodology to detect potential targets for structure-based rational drug design. For example, 2,4-dienoyl-CoA reductase (EC 1.3.1.34) and triacylglycerol lipase (EC 3.1.1.3), classified as analogous proteins in relation to H. sapiens enzymes, were identified as new potential molecular targets. PMID:21034488

Structural modelling and comparative analysis of homologous, analogous and specific proteins from Trypanosoma cruzi versus Homo sapiens: putative drug targets for chagas' disease treatment.

PubMed

Capriles, Priscila V S Z; Guimarães, Ana C R; Otto, Thomas D; Miranda, Antonio B; Dardenne, Laurent E; Degrave, Wim M

2010-10-29

Trypanosoma cruzi is the etiological agent of Chagas' disease, an endemic infection that causes thousands of deaths every year in Latin America. Therapeutic options remain inefficient, demanding the search for new drugs and/or new molecular targets. Such efforts can focus on proteins that are specific to the parasite, but analogous enzymes and enzymes with a three-dimensional (3D) structure sufficiently different from the corresponding host proteins may represent equally interesting targets. In order to find these targets we used the workflows MHOLline and AnEnΠ obtaining 3D models from homologous, analogous and specific proteins of Trypanosoma cruzi versus Homo sapiens. We applied genome wide comparative modelling techniques to obtain 3D models for 3,286 predicted proteins of T. cruzi. In combination with comparative genome analysis to Homo sapiens, we were able to identify a subset of 397 enzyme sequences, of which 356 are homologous, 3 analogous and 38 specific to the parasite. In this work, we present a set of 397 enzyme models of T. cruzi that can constitute potential structure-based drug targets to be investigated for the development of new strategies to fight Chagas' disease. The strategies presented here support the concept of structural analysis in conjunction with protein functional analysis as an interesting computational methodology to detect potential targets for structure-based rational drug design. For example, 2,4-dienoyl-CoA reductase (EC 1.3.1.34) and triacylglycerol lipase (EC 3.1.1.3), classified as analogous proteins in relation to H. sapiens enzymes, were identified as new potential molecular targets.

Psychometrican analysis and dimensional structure of the Brazilian version of melasma quality of life scale (MELASQoL-BP)*

PubMed Central

Maranzatto, Camila Fernandes Pollo; Miot, Hélio Amante; Miot, Luciane Donida Bartoli; Meneguin, Silmara

2016-01-01

Background Although asymptomatic, melasma inflicts significant impact on quality of life. MELASQoL is the main instrument used to assess quality of life associated with melasma, it has been validated in several languages, but its latent dimensional structure and psychometric properties haven´t been fully explored. Objectives To evaluate psychometric characteristics, information and dimensional structure of the Brazilian version of MELASQoL. Methods Survey with patients with facial melasma through socio-demographic questionnaire, DLQI-BRA, MASI and MELASQoL-BP, exploratory and confirmatory factor analysis, internal consistency of MELASQoL and latent dimensions (Cronbach's alpha). The informativeness of the model and items were investigated by the Rasch model (ordinal data). Results We evaluated 154 patients, 134 (87%) were female, mean age (± SD) of 39 (± 8) years, the onset of melasma at 27 (± 8) years, median (p25-p75) of MASI scores , DLQI and MELASQoL 8 (5-15) 2 (1-6) and 30 (17-44). The correlation (rho) of MELASQoL with DLQI and MASI were: 0.70 and 0.36. Exploratory factor analysis identified two latent dimensions: Q1-Q3 and Q4-Q10, which had significantly more adjusted factor structure than the one-dimensional model: Χ2 / gl = 2.03, CFI = 0.95, AGFI = 0.94, RMSEA = 0.08. Cronbach's coefficient for the one-dimensional model and the factors were: 0.95, 0.92 and 0.93. Rasch analysis demonstrated that the use of seven alternatives per item resulted in no increase in the model informativeness. Conclusions MELASQoL-BP showed good psychometric performance and a latent structure of two dimensions. We also identified an oversizing of item alternatives to characterize the aggregate information to each dimension. PMID:27579735

Methodological flaws introduce strong bias into molecular analysis of microbial populations.

PubMed

Krakat, N; Anjum, R; Demirel, B; Schröder, P

2017-02-01

In this study, we report how different cell disruption methods, PCR primers and in silico analyses can seriously bias results from microbial population studies, with consequences for the credibility and reproducibility of the findings. Our results emphasize the pitfalls of commonly used experimental methods that can seriously weaken the interpretation of results. Four different cell lysis methods, three commonly used primer pairs and various computer-based analyses were applied to investigate the microbial diversity of a fermentation sample composed of chicken dung. The fault-prone, but still frequently used, amplified rRNA gene restriction analysis was chosen to identify common weaknesses. In contrast to other studies, we focused on the complete analytical process, from cell disruption to in silico analysis, and identified potential error rates. This identified a wide disagreement of results between applied experimental approaches leading to very different community structures depending on the chosen approach. The interpretation of microbial diversity data remains a challenge. In order to accurately investigate the taxonomic diversity and structure of prokaryotic communities, we suggest a multi-level approach combining DNA-based and DNA-independent techniques. The identified weaknesses of commonly used methods to study microbial diversity can be overcome by a multi-level approach, which produces more reliable data about the fate and behaviour of microbial communities of engineered habitats such as biogas plants, so that the best performance can be ensured. © 2016 The Society for Applied Microbiology.

Computer-aided drug design of falcipain inhibitors: virtual screening, structure-activity relationships, hydration site thermodynamics, and reactivity analysis.

PubMed

Shah, Falgun; Gut, Jiri; Legac, Jennifer; Shivakumar, Devleena; Sherman, Woody; Rosenthal, Philip J; Avery, Mitchell A

2012-03-26

Falcipains (FPs) are hemoglobinases of Plasmodium falciparum that are validated targets for the development of antimalarial chemotherapy. A combined ligand- and structure-based virtual screening of commercial databases was performed to identify structural analogs of virtual screening hits previously discovered in our laboratory. A total of 28 low micromolar inhibitors of FP-2 and FP-3 were identified and the structure-activity relationship (SAR) in each series was elaborated. The SAR of the compounds was unusually steep in some cases and could not be explained by a traditional analysis of the ligand-protein interactions (van der Waals, electrostatics, and hydrogen bonds). To gain further insights, a statistical thermodynamic analysis of explicit solvent in the ligand binding domains of FP-2 and FP-3 was carried out to understand the roles played by water molecules in binding of these inhibitors. Indeed, the energetics associated with the displacement of water molecules upon ligand binding explained some of the complex trends in the SAR. Furthermore, low potency of a subset of FP-2 inhibitors that could not be understood by the water energetics was explained in the context of poor chemical reactivity of the reactive centers of these compounds. The present study highlights the importance of considering energetic contributors to binding beyond traditional ligand-protein interactions. © 2012 American Chemical Society

Topological framework for local structure analysis in condensed matter

PubMed Central

Lazar, Emanuel A.; Han, Jian; Srolovitz, David J.

2015-01-01

Physical systems are frequently modeled as sets of points in space, each representing the position of an atom, molecule, or mesoscale particle. As many properties of such systems depend on the underlying ordering of their constituent particles, understanding that structure is a primary objective of condensed matter research. Although perfect crystals are fully described by a set of translation and basis vectors, real-world materials are never perfect, as thermal vibrations and defects introduce significant deviation from ideal order. Meanwhile, liquids and glasses present yet more complexity. A complete understanding of structure thus remains a central, open problem. Here we propose a unified mathematical framework, based on the topology of the Voronoi cell of a particle, for classifying local structure in ordered and disordered systems that is powerful and practical. We explain the underlying reason why this topological description of local structure is better suited for structural analysis than continuous descriptions. We demonstrate the connection of this approach to the behavior of physical systems and explore how crystalline structure is compromised at elevated temperatures. We also illustrate potential applications to identifying defects in plastically deformed polycrystals at high temperatures, automating analysis of complex structures, and characterizing general disordered systems. PMID:26460045

Process and assembly plans for low cost commercial fuselage structure

NASA Technical Reports Server (NTRS)

Willden, Kurtis; Metschan, Stephen; Starkey, Val

1991-01-01

Cost and weight reduction for a composite structure is a result of selecting design concepts that can be built using efficient low cost manufacturing and assembly processes. Since design and manufacturing are inherently cost dependent, concurrent engineering in the form of a Design-Build Team (DBT) is essential for low cost designs. Detailed cost analysis from DBT designs and hardware verification must be performed to identify the cost drivers and relationships between design and manufacturing processes. Results from the global evaluation are used to quantitatively rank design, identify cost centers for higher ranking design concepts, define and prioritize a list of technical/economic issues and barriers, and identify parameters that control concept response. These results are then used for final design optimization.

Structural Analysis of Silicic Lavas Reveals the Importance of Endogenous Flow During Emplacement

NASA Astrophysics Data System (ADS)

Andrews, G. D.; Martens, A.; Isom, S.; Maxwell, A.; Brown, S. R.

2017-12-01

Recent observations of silicic lava flows in Chile strongly suggest sustained, endogeneous flow beneath an insulating carapace, where the flow advances through breakouts at the flow margin. New mapping of vertical exposures around the margin of Obsidian Dome, California, has identified discreet lobe structures in cross-section, suggesting that flow-front breakouts occured there during emplacement. The flow lobes are identified through structural measurements of flow-banding orientation and the stretching directions of vesicles. Newly acquired lidar of the Inyo Domes, including Obsidian Dome, is being analyzed to better understand the patterns of folding on the upper surface of the lavas, and to test for fold vergence patterns that may distinguish between endogenous and exogenous flow.

Student generated learning objectives: extent of congruence with faculty set objectives and factors influencing their generation.

PubMed

Abdul Ghaffar Al-Shaibani, Tarik A; Sachs-Robertson, Annette; Al Shazali, Hafiz O; Sequeira, Reginald P; Hamdy, Hosam; Al-Roomi, Khaldoon

2003-07-01

A problem-based learning strategy is used for curriculum planning and implementation at the Arabian Gulf University, Bahrain. Problems are constructed in a way that faculty-set objectives are expected to be identified by students during tutorials. Students in small groups, along with a tutor functioning as a facilitator, identify learning issues and define their learning objectives. We compared objectives identified by student groups with faculty-set objectives to determine extent of congruence, and identified factors that influenced students' ability at identifying faculty-set objectives. Male and female students were segregated and randomly grouped. A faculty tutor was allocated for each group. This study was based on 13 problems given to entry-level medical students. Pooled objectives of these problems were classified into four categories: structural, functional, clinical and psychosocial. Univariate analysis of variance was used for comparison, and a p > 0.05 was considered significant. The mean of overall objectives generated by the students was 54.2%, for each problem. Students identified psychosocial learning objectives more readily than structural ones. Female students identified more psychosocial objectives, whereas male students identified more of structural objectives. Tutor characteristics such as medical/non-medical background, and the years of teaching were correlated with categories of learning issues identified. Students identify part of the faculty-set learning objectives during tutorials with a faculty tutor acting as a facilitator. Students' gender influences types of learning issues identified. Content expertise of tutors does not influence identification of learning needs by students.

Print News Coverage of School-Based HPV Vaccine Mandate

PubMed Central

Casciotti, Dana; Smith, Katherine C.; Andon, Lindsay; Vernick, Jon; Tsui, Amy; Klassen, Ann C.

2015-01-01

BACKGROUND In 2007, legislation was proposed in 24 states and the District of Columbia for school-based HPV vaccine mandates, and mandates were enacted in Texas, Virginia, and the District of Columbia. Media coverage of these events was extensive, and media messages both reflected and contributed to controversy surrounding these legislative activities. Messages communicated through the media are an important influence on adolescent and parent understanding of school-based vaccine mandates. METHODS We conducted structured text analysis of newspaper coverage, including quantitative analysis of 169 articles published in mandate jurisdictions from 2005-2009, and qualitative analysis of 63 articles from 2007. Our structured analysis identified topics, key stakeholders and sources, tone, and the presence of conflict. Qualitative thematic analysis identified key messages and issues. RESULTS Media coverage was often incomplete, providing little context about cervical cancer or screening. Skepticism and autonomy concerns were common. Messages reflected conflict and distrust of government activities, which could negatively impact this and other youth-focused public health initiatives. CONCLUSIONS If school health professionals are aware of the potential issues raised in media coverage of school-based health mandates, they will be more able to convey appropriate health education messages, and promote informed decision-making by parents and students. PMID:25099421

Complete genome analysis of dengue virus type 3 isolated from the 2013 dengue outbreak in Yunnan, China.

PubMed

Wang, Xiaodan; Ma, Dehong; Huang, Xinwei; Li, Lihua; Li, Duo; Zhao, Yujiao; Qiu, Lijuan; Pan, Yue; Chen, Junying; Xi, Juemin; Shan, Xiyun; Sun, Qiangming

2017-06-15

In the past few decades, dengue has spread rapidly and is an emerging disease in China. An unexpected dengue outbreak occurred in Xishuangbanna, Yunnan, China, resulting in 1331 patients in 2013. In order to obtain the complete genome information and perform mutation and evolutionary analysis of causative agent related to this largest outbreak of dengue fever. The viruses were isolated by cell culture and evaluated by genome sequence analysis. Phylogenetic trees were then constructed by Neighbor-Joining methods (MEGA6.0), followed by analysis of nucleotide mutation and amino acid substitution. The analysis of the diversity of secondary structure for E and NS1 protein were also performed. Then selection pressures acting on the coding sequences were estimated by PAML software. The complete genome sequences of two isolated strains (YNSW1, YNSW2) were 10,710 and 10,702 nucleotides in length, respectively. Phylogenetic analysis revealed both strain were classified as genotype II of DENV-3. The results indicated that both isolated strains of Xishuangbanna in 2013 and Laos 2013 stains (KF816161.1, KF816158.1, LC147061.1, LC147059.1, KF816162.1) were most similar to Bangladesh (AY496873.2) in 2002. After comparing with the DENV-3SS (H87) 62 amino acid substitutions were identified in translated regions, and 38 amino acid substitutions were identified in translated regions compared with DENV-3 genotype II stains Bangladesh (AY496873.2). 27(YNSW1) or 28(YNSW2) single nucleotide changes were observed in structural protein sequences with 7(YNSW1) or 8(YNSW2) non-synonymous mutations compared with AY496873.2. Of them, 4 non-synonymous mutations were identified in E protein sequences with (2 in the β-sheet, 2 in the coil). Meanwhile, 117(YNSW1) or 115 (YNSW2) single nucleotide changes were observed in non-structural protein sequences with 31(YNSW1) or 30 (YNSW2) non-synonymous mutations. Particularly, 14 single nucleotide changes were observed in NS1 sequences with 4/14 non-synonymous substitutions (4 in the coil). Selection pressure analysis revealed no positive selection in the amino acid sites of the genes encoding for structural and non-structural proteins. This study may help understand the intrinsic geographical relatedness of dengue virus 3 and contributes further to research on their infectivity, pathogenicity and vaccine development. Copyright © 2017 Elsevier B.V. All rights reserved.

Probabilistic and structural reliability analysis of laminated composite structures based on the IPACS code

NASA Technical Reports Server (NTRS)

Sobel, Larry; Buttitta, Claudio; Suarez, James

1993-01-01

Probabilistic predictions based on the Integrated Probabilistic Assessment of Composite Structures (IPACS) code are presented for the material and structural response of unnotched and notched, 1M6/3501-6 Gr/Ep laminates. Comparisons of predicted and measured modulus and strength distributions are given for unnotched unidirectional, cross-ply, and quasi-isotropic laminates. The predicted modulus distributions were found to correlate well with the test results for all three unnotched laminates. Correlations of strength distributions for the unnotched laminates are judged good for the unidirectional laminate and fair for the cross-ply laminate, whereas the strength correlation for the quasi-isotropic laminate is deficient because IPACS did not yet have a progressive failure capability. The paper also presents probabilistic and structural reliability analysis predictions for the strain concentration factor (SCF) for an open-hole, quasi-isotropic laminate subjected to longitudinal tension. A special procedure was developed to adapt IPACS for the structural reliability analysis. The reliability results show the importance of identifying the most significant random variables upon which the SCF depends, and of having accurate scatter values for these variables.

[Dimensional structure of the Brazilian version of the Scale of Satisfaction with Interpersonal Processes of General Medical Care].

PubMed

Nascimento, Maria Isabel do; Reichenheim, Michael Eduardo; Monteiro, Gina Torres Rego

2011-12-01

The objective of this study was to reassess the dimensional structure of a Brazilian version of the Scale of Satisfaction with Interpersonal Processes of General Medical Care, proposed originally as a one-dimensional instrument. Strict confirmatory factor analysis (CFA) and exploratory factor analysis modeled within a CFA framework (E/CFA) were used to identify the best model. An initial CFA rejected the one-dimensional structure, while an E/CFA suggested a two-dimensional structure. The latter structure was followed by a new CFA, which showed that the model without cross-loading was the most parsimonious, with adequate fit indices (CFI = 0.982 and TLI = 0.988), except for RMSEA (0.062). Although the model achieved convergent validity, discriminant validity was questionable, with the square-root of the mean variance extracted from dimension 1 estimates falling below the respective factor correlation. According to these results, there is not sufficient evidence to recommend the immediate use of the instrument, and further studies are needed for a more in-depth analysis of the postulated structures.

Positioning within a Cultural Context: Using Ricoeur's Preunderstandings as a Heuristic for Narrative Data Analysis in Exploring Identity, Structure, and Agency

ERIC Educational Resources Information Center

Wilson, Rachel E.

2015-01-01

I argue that Ricoeur's "preunderstandings" can be used as a heuristic to aid researchers who collect narratives as data (1) to identify cultural meanings that become resources for participants' positioning work, (2) to ground the identified cultural meanings in participants' experiences, and (3) to understand participants'…

[Studies on alkaloids of Asteropyrum cavaleriei (Lévl. et Vant.) Drumm. et Hutch].

PubMed

Xu, H L

2000-08-01

To investigate the chemical constituents in the plant of Asteropyrum cavaleriei. The Chemical constituents were extracted with cation exchange resin 732 and separated by column chromatography, and the structures were identified by spectral analysis. Four compounds were isolated and identified as berberine, berberrabine, palmatine and magnoflorine. All compounds were separated from A. Cavaleriei for the first time.

Study of Factors Preventing Children from Enrolment in Primary School in the Republic of Honduras: Analysis Using Structural Equation Modelling

ERIC Educational Resources Information Center

Ashida, Akemi

2015-01-01

Studies have investigated factors that impede enrolment in Honduras. However, they have not analysed individual factors as a whole or identified the relationships among them. This study used longitudinal data for 1971 children who entered primary schools from 1986 to 2000, and employed structural equation modelling to examine the factors…

Factors Affecting Higher Order Thinking Skills of Students: A Meta-Analytic Structural Equation Modeling Study

ERIC Educational Resources Information Center

Budsankom, Prayoonsri; Sawangboon, Tatsirin; Damrongpanit, Suntorapot; Chuensirimongkol, Jariya

2015-01-01

The purpose of the research is to develop and identify the validity of factors affecting higher order thinking skills (HOTS) of students. The thinking skills can be divided into three types: analytical, critical, and creative thinking. This analysis is done by applying the meta-analytic structural equation modeling (MASEM) based on a database of…

Large Modal Survey Testing Using the Ibrahim Time Domain Identification Technique

NASA Technical Reports Server (NTRS)

Ibrahim, S. R.; Pappa, R. S.

1985-01-01

The ability of the ITD identification algorithm in identifying a complete set of structural modal parameters using a large number of free-response time histories simultaneously in one analysis, assuming a math model with a high number of degrees-of-freedom, has been studied. Identification results using simulated free responses of a uniform rectangular plate, with 225 measurement stations, and experimental responses from a ground vibration test of the Long Duration Exposure Facility (LDEF) Space Shuttle payload, with 142 measurement stations, are presented. As many as 300 degrees-of-freedom were allowed in analyzing these data. In general, the use of a significantly oversized math model in the identification process was found to maintain or increase identification accuracy and to identify modes of low response level that are not identified with smaller math model sizes. The concept of a Mode Shape Correlation Constant is introduced for use when more than one identification analysis of the same structure are conducted. This constant quantifies the degree of correlation between any two sets of complex mode shapes identified using different excitation conditions, different user-selectable algorithm constants, or overlapping sets of measurements.

Large modal survey testing using the Ibrahim time domain /ITD/ identification technique

NASA Technical Reports Server (NTRS)

Ibrahim, S. R.; Pappa, R. S.

1981-01-01

The ability of the ITD identification algorithm in identifying a complete set of structural modal parameters using a large number of free-response time histories simultaneously in one analysis, assuming a math model with a high number of degrees-of-freedom, has been studied. Identification results using simulated free responses of a uniform rectangular plate, with 225 measurement stations, and experimental responses from a ground vibration test of the Long Duration Exposure Facility (LDEF) Space Shuttle payload, with 142 measurement stations, are presented. As many as 300 degrees-of-freedom were allowed in analyzing these data. In general, the use of a significantly oversized math model in the identification process was found to maintain or increase identification accuracy and to identify modes of low response level that are not identified with smaller math model sizes. The concept of a Mode Shape Correlation Constant is introduced for use when more than one identification analysis of the same structure are conducted. This constant quantifies the degree of correlation between any two sets of complex mode shapes identified using different excitation conditions, different user-selectable algorithm constants, or overlapping sets of measurements.

Maternal Styles of Talking about Child Feeding across Sociodemographic Groups

PubMed Central

Pesch, Megan H.; Harrell, Kristina J.; Kaciroti, Niko; Rosenblum, Kate; Lumeng, Julie C.

2011-01-01

This study sought to identify maternal styles of talking about child feeding from a semi-structured interview and to evaluate associated maternal and child characteristics. Mothers of preschool-aged children (n = 133) of diverse race/ethnicity and socioeconomic status (SES) (45 lower SES black, 29 lower SES white, 32 lower SES Hispanic, 15 middle to upper SES white, 12 middle to upper SES Asian) participated in a semi-structured interview about feeding. Interviews were audio-taped and transcribed. Themes were identified, and individual interviews were coded within these themes: authority (high/low), confidence (confident/conflicted/unopinionated), and investment (deep/mild/removed). Demographic characteristics were collected and a subset of children had measured weights and heights. Cluster analysis was used to identify narrative styles. Participant characteristics were compared across clusters using Fisher’s exact test and analysis of variance. Six narrative styles were identified: Easy-Going, Practical No-Nonsense, Disengaged, Effortful No-Nonsense, Indulgent Worry, and Conflicted Control. Cluster membership differed significantly based on maternal demographic group (P < .001) and child weight status (P < .05). More than half (60%) of children of mothers in the Conflicted Control cluster were obese. Maternal styles of talking about feeding are associated with maternal and child characteristics. PMID:22117662

Dimensional Model for Estimating Factors influencing Childhood Obesity: Path Analysis Based Modeling

PubMed Central

Kheirollahpour, Maryam; Shohaimi, Shamarina

2014-01-01

The main objective of this study is to identify and develop a comprehensive model which estimates and evaluates the overall relations among the factors that lead to weight gain in children by using structural equation modeling. The proposed models in this study explore the connection among the socioeconomic status of the family, parental feeding practice, and physical activity. Six structural models were tested to identify the direct and indirect relationship between the socioeconomic status and parental feeding practice general level of physical activity, and weight status of children. Finally, a comprehensive model was devised to show how these factors relate to each other as well as to the body mass index (BMI) of the children simultaneously. Concerning the methodology of the current study, confirmatory factor analysis (CFA) was applied to reveal the hidden (secondary) effect of socioeconomic factors on feeding practice and ultimately on the weight status of the children and also to determine the degree of model fit. The comprehensive structural model tested in this study suggested that there are significant direct and indirect relationships among variables of interest. Moreover, the results suggest that parental feeding practice and physical activity are mediators in the structural model. PMID:25097878

Method for identifying subsurface fluid migration and drainage pathways in and among oil and gas reservoirs using 3-D and 4-D seismic imaging

DOEpatents

Anderson, R.N.; Boulanger, A.; Bagdonas, E.P.; Xu, L.; He, W.

1996-12-17

The invention utilizes 3-D and 4-D seismic surveys as a means of deriving information useful in petroleum exploration and reservoir management. The methods use both single seismic surveys (3-D) and multiple seismic surveys separated in time (4-D) of a region of interest to determine large scale migration pathways within sedimentary basins, and fine scale drainage structure and oil-water-gas regions within individual petroleum producing reservoirs. Such structure is identified using pattern recognition tools which define the regions of interest. The 4-D seismic data sets may be used for data completion for large scale structure where time intervals between surveys do not allow for dynamic evolution. The 4-D seismic data sets also may be used to find variations over time of small scale structure within individual reservoirs which may be used to identify petroleum drainage pathways, oil-water-gas regions and, hence, attractive drilling targets. After spatial orientation, and amplitude and frequency matching of the multiple seismic data sets, High Amplitude Event (HAE) regions consistent with the presence of petroleum are identified using seismic attribute analysis. High Amplitude Regions are grown and interconnected to establish plumbing networks on the large scale and reservoir structure on the small scale. Small scale variations over time between seismic surveys within individual reservoirs are identified and used to identify drainage patterns and bypassed petroleum to be recovered. The location of such drainage patterns and bypassed petroleum may be used to site wells. 22 figs.

Method for identifying subsurface fluid migration and drainage pathways in and among oil and gas reservoirs using 3-D and 4-D seismic imaging

DOEpatents

Anderson, Roger N.; Boulanger, Albert; Bagdonas, Edward P.; Xu, Liqing; He, Wei

1996-01-01

The invention utilizes 3-D and 4-D seismic surveys as a means of deriving information useful in petroleum exploration and reservoir management. The methods use both single seismic surveys (3-D) and multiple seismic surveys separated in time (4-D) of a region of interest to determine large scale migration pathways within sedimentary basins, and fine scale drainage structure and oil-water-gas regions within individual petroleum producing reservoirs. Such structure is identified using pattern recognition tools which define the regions of interest. The 4-D seismic data sets may be used for data completion for large scale structure where time intervals between surveys do not allow for dynamic evolution. The 4-D seismic data sets also may be used to find variations over time of small scale structure within individual reservoirs which may be used to identify petroleum drainage pathways, oil-water-gas regions and, hence, attractive drilling targets. After spatial orientation, and amplitude and frequency matching of the multiple seismic data sets, High Amplitude Event (HAE) regions consistent with the presence of petroleum are identified using seismic attribute analysis. High Amplitude Regions are grown and interconnected to establish plumbing networks on the large scale and reservoir structure on the small scale. Small scale variations over time between seismic surveys within individual reservoirs are identified and used to identify drainage patterns and bypassed petroleum to be recovered. The location of such drainage patterns and bypassed petroleum may be used to site wells.

Exploring biomedical ontology mappings with graph theory methods.

PubMed

Kocbek, Simon; Kim, Jin-Dong

2017-01-01

In the era of semantic web, life science ontologies play an important role in tasks such as annotating biological objects, linking relevant data pieces, and verifying data consistency. Understanding ontology structures and overlapping ontologies is essential for tasks such as ontology reuse and development. We present an exploratory study where we examine structure and look for patterns in BioPortal, a comprehensive publicly available repository of live science ontologies. We report an analysis of biomedical ontology mapping data over time. We apply graph theory methods such as Modularity Analysis and Betweenness Centrality to analyse data gathered at five different time points. We identify communities, i.e., sets of overlapping ontologies, and define similar and closest communities. We demonstrate evolution of identified communities over time and identify core ontologies of the closest communities. We use BioPortal project and category data to measure community coherence. We also validate identified communities with their mutual mentions in scientific literature. With comparing mapping data gathered at five different time points, we identified similar and closest communities of overlapping ontologies, and demonstrated evolution of communities over time. Results showed that anatomy and health ontologies tend to form more isolated communities compared to other categories. We also showed that communities contain all or the majority of ontologies being used in narrower projects. In addition, we identified major changes in mapping data after migration to BioPortal Version 4.

Tensor-driven extraction of developmental features from varying paediatric EEG datasets.

PubMed

Kinney-Lang, Eli; Spyrou, Loukianos; Ebied, Ahmed; Chin, Richard Fm; Escudero, Javier

2018-05-21

Constant changes in developing children's brains can pose a challenge in EEG dependant technologies. Advancing signal processing methods to identify developmental differences in paediatric populations could help improve function and usability of such technologies. Taking advantage of the multi-dimensional structure of EEG data through tensor analysis may offer a framework for extracting relevant developmental features of paediatric datasets. A proof of concept is demonstrated through identifying latent developmental features in resting-state EEG. Approach. Three paediatric datasets (n = 50, 17, 44) were analyzed using a two-step constrained parallel factor (PARAFAC) tensor decomposition. Subject age was used as a proxy measure of development. Classification used support vector machines (SVM) to test if PARAFAC identified features could predict subject age. The results were cross-validated within each dataset. Classification analysis was complemented by visualization of the high-dimensional feature structures using t-distributed Stochastic Neighbour Embedding (t-SNE) maps. Main Results. Development-related features were successfully identified for the developmental conditions of each dataset. SVM classification showed the identified features could accurately predict subject at a significant level above chance for both healthy and impaired populations. t-SNE maps revealed suitable tensor factorization was key in extracting the developmental features. Significance. The described methods are a promising tool for identifying latent developmental features occurring throughout childhood EEG. © 2018 IOP Publishing Ltd.

UAV-based urban structural damage assessment using object-based image analysis and semantic reasoning

NASA Astrophysics Data System (ADS)

Fernandez Galarreta, J.; Kerle, N.; Gerke, M.

2015-06-01

Structural damage assessment is critical after disasters but remains a challenge. Many studies have explored the potential of remote sensing data, but limitations of vertical data persist. Oblique imagery has been identified as more useful, though the multi-angle imagery also adds a new dimension of complexity. This paper addresses damage assessment based on multi-perspective, overlapping, very high resolution oblique images obtained with unmanned aerial vehicles (UAVs). 3-D point-cloud assessment for the entire building is combined with detailed object-based image analysis (OBIA) of façades and roofs. This research focuses not on automatic damage assessment, but on creating a methodology that supports the often ambiguous classification of intermediate damage levels, aiming at producing comprehensive per-building damage scores. We identify completely damaged structures in the 3-D point cloud, and for all other cases provide the OBIA-based damage indicators to be used as auxiliary information by damage analysts. The results demonstrate the usability of the 3-D point-cloud data to identify major damage features. Also the UAV-derived and OBIA-processed oblique images are shown to be a suitable basis for the identification of detailed damage features on façades and roofs. Finally, we also demonstrate the possibility of aggregating the multi-perspective damage information at building level.

Influence networks among substance abuse treatment clinics: implications for the dissemination of innovations.

PubMed

Johnson, Kimberly; Quanbeck, Andrew; Maus, Adam; Gustafson, David H; Dearing, James W

2015-09-01

Understanding influence networks among substance abuse treatment clinics may speed the diffusion of innovations. The purpose of this study was to describe influence networks in Massachusetts, Michigan, New York, Oregon, and Washington and test two expectations, using social network analysis: (1) Social network measures can identify influential clinics; and (2) Within a network, some weakly connected clinics access out-of-network sources of innovative evidence-based practices and can spread these innovations through the network. A survey of 201 clinics in a parent study on quality improvement provided the data. Network measures and sociograms were obtained from adjacency matrixes created by UCINet. We used regression analysis to determine whether network status relates to clinics' adopting innovations. Findings suggest that influential clinics can be identified and that loosely linked clinics were likely to join the study sooner than more influential clinics but were not more likely to have improved outcomes than other organizations. Findings identify the structure of influence networks for SUD treatment organizations and have mixed results on how those structures impacted diffusion of the intervention under study. Further study is necessary to test whether use of knowledge of the network structure will have an effect on the pace and breadth of dissemination of innovations.

Structural RNAs of known and unknown function identified in malaria parasites by comparative genomics and RNA analysis

PubMed Central

Chakrabarti, Kausik; Pearson, Michael; Grate, Leslie; Sterne-Weiler, Timothy; Deans, Jonathan; Donohue, John Paul; Ares, Manuel

2007-01-01

As the genomes of more eukaryotic pathogens are sequenced, understanding how molecular differences between parasite and host might be exploited to provide new therapies has become a major focus. Central to cell function are RNA-containing complexes involved in gene expression, such as the ribosome, the spliceosome, snoRNAs, RNase P, and telomerase, among others. In this article we identify by comparative genomics and validate by RNA analysis numerous previously unknown structural RNAs encoded by the Plasmodium falciparum genome, including the telomerase RNA, U3, 31 snoRNAs, as well as previously predicted spliceosomal snRNAs, SRP RNA, MRP RNA, and RNAse P RNA. Furthermore, we identify six new RNA coding genes of unknown function. To investigate the relationships of the RNA coding genes to other genomic features in related parasites, we developed a genome browser for P. falciparum (http://areslab.ucsc.edu/cgi-bin/hgGateway). Additional experiments provide evidence supporting the prediction that snoRNAs guide methylation of a specific position on U4 snRNA, as well as predicting an snRNA promoter element particular to Plasmodium sp. These findings should allow detailed structural comparisons between the RNA components of the gene expression machinery of the parasite and its vertebrate hosts. PMID:17901154

Test plan. GCPS task 7, subtask 7.1: IHM development

NASA Technical Reports Server (NTRS)

Greenberg, H. S.

1994-01-01

The overall objective of Task 7 is to identify cost-effective life cycle integrated health management (IHM) approaches for a reusable launch vehicle's primary structure. Acceptable IHM approaches must: eliminate and accommodate faults through robust designs, identify optimum inspection/maintenance periods, automate ground and on-board test and check-out, and accommodate and detect structural faults by providing wide and localized area sensor and test coverage as required. These requirements are elements of our targeted primary structure low cost operations approach using airline-like maintenance by exception philosophies. This development plan will follow an evolutionary path paving the way to the ultimate development of flight-quality production, operations, and vehicle systems. This effort will be focused on maturing the recommended sensor technologies required for localized and wide area health monitoring to a technology readiness level (TRL) of 6 and to establish flight ready system design requirements. The following is a brief list of IHM program objectives: design out faults by analyzing material properties, structural geometry, and load and environment variables and identify failure modes and damage tolerance requirements; design in system robustness while meeting performance objectives (weight limitations) of the reusable launch vehicle primary structure; establish structural integrity margins to preclude the need for test and checkout and predict optimum inspection/maintenance periods through life prediction analysis; identify optimum fault protection system concept definitions combining system robustness and integrity margins established above with cost effective health monitoring technologies; and use coupons, panels, and integrated full scale primary structure test articles to identify, evaluate, and characterize the preferred NDE/NDI/IHM sensor technologies that will be a part of the fault protection system.

Meteorological regimes for the classification of aerospace air quality predictions for NASA-Kennedy Space Center

NASA Technical Reports Server (NTRS)

Stephens, J. B.; Sloan, J. C.

1976-01-01

A method is described for developing a statistical air quality assessment for the launch of an aerospace vehicle from the Kennedy Space Center in terms of existing climatological data sets. The procedure can be refined as developing meteorological conditions are identified for use with the NASA-Marshall Space Flight Center Rocket Exhaust Effluent Diffusion (REED) description. Classical climatological regimes for the long range analysis can be narrowed as the synoptic and mesoscale structure is identified. Only broad synoptic regimes are identified at this stage of analysis. As the statistical data matrix is developed, synoptic regimes will be refined in terms of the resulting eigenvectors as applicable to aerospace air quality predictions.

Genomic Organization and Molecular Analysis of Virulent Bacteriophage 2972 Infecting an Exopolysaccharide-Producing Streptococcus thermophilus Strain

PubMed Central

Lévesque, Céline; Duplessis, Martin; Labonté, Jessica; Labrie, Steve; Fremaux, Christophe; Tremblay, Denise; Moineau, Sylvain

2005-01-01

The Streptococcus thermophilus virulent pac-type phage 2972 was isolated from a yogurt made in France in 1999. It is a representative of several phages that have emerged with the industrial use of the exopolysaccharide-producing S. thermophilus strain RD534. The genome of phage 2972 has 34,704 bp with an overall G+C content of 40.15%, making it the shortest S. thermophilus phage genome analyzed so far. Forty-four open reading frames (ORFs) encoding putative proteins of 40 or more amino acids were identified, and bioinformatic analyses led to the assignment of putative functions to 23 ORFs. Comparative genomic analysis of phage 2972 with the six other sequenced S. thermophilus phage genomes confirmed that the replication module is conserved and that cos- and pac-type phages have distinct structural and packaging genes. Two group I introns were identified in the genome of 2972. They interrupted the genes coding for the putative endolysin and the terminase large subunit. Phage mRNA splicing was demonstrated for both introns, and the secondary structures were predicted. Eight structural proteins were also identified by N-terminal sequencing and/or matrix-assisted laser desorption ionization—time-of-flight mass spectrometry. Detailed analysis of the putative minor tail proteins ORF19 and ORF21 as well as the putative receptor-binding protein ORF20 showed the following interesting features: (i) ORF19 is a hybrid protein, because it displays significant identity with both pac- and cos-type phages; (ii) ORF20 is unique; and (iii) a protein similar to ORF21 of 2972 was also found in the structure of the cos-type phage DT1, indicating that this structural protein is present in both S. thermophilus phage groups. The implications of these findings for phage classification are discussed. PMID:16000821

Classification and Lateralization of Temporal Lobe Epilepsies with and without Hippocampal Atrophy Based on Whole-Brain Automatic MRI Segmentation

PubMed Central

Keihaninejad, Shiva; Heckemann, Rolf A.; Gousias, Ioannis S.; Hajnal, Joseph V.; Duncan, John S.; Aljabar, Paul; Rueckert, Daniel; Hammers, Alexander

2012-01-01

Brain images contain information suitable for automatically sorting subjects into categories such as healthy controls and patients. We sought to identify morphometric criteria for distinguishing controls (n = 28) from patients with unilateral temporal lobe epilepsy (TLE), 60 with and 20 without hippocampal atrophy (TLE-HA and TLE-N, respectively), and for determining the presumed side of seizure onset. The framework employs multi-atlas segmentation to estimate the volumes of 83 brain structures. A kernel-based separability criterion was then used to identify structures whose volumes discriminate between the groups. Next, we applied support vector machines (SVM) to the selected set for classification on the basis of volumes. We also computed pairwise similarities between all subjects and used spectral analysis to convert these into per-subject features. SVM was again applied to these feature data. After training on a subgroup, all TLE-HA patients were correctly distinguished from controls, achieving an accuracy of 96 ± 2% in both classification schemes. For TLE-N patients, the accuracy was 86 ± 2% based on structural volumes and 91 ± 3% using spectral analysis. Structures discriminating between patients and controls were mainly localized ipsilaterally to the presumed seizure focus. For the TLE-HA group, they were mainly in the temporal lobe; for the TLE-N group they included orbitofrontal regions, as well as the ipsilateral substantia nigra. Correct lateralization of the presumed seizure onset zone was achieved using hippocampi and parahippocampal gyri in all TLE-HA patients using either classification scheme; in the TLE-N patients, lateralization was accurate based on structural volumes in 86 ± 4%, and in 94 ± 4% with the spectral analysis approach. Unilateral TLE has imaging features that can be identified automatically, even when they are invisible to human experts. Such morphometric image features may serve as classification and lateralization criteria. The technique also detects unsuspected distinguishing features like the substantia nigra, warranting further study. PMID:22523539

The strength study of the rotating device driver indexing spatial mechanism

NASA Astrophysics Data System (ADS)

Zakharenkov, N. V.; Kvasov, I. N.

2018-04-01

The indexing spatial mechanisms are widely used in automatic machines. The mechanisms maximum load-bearing capacity measurement is possible based on both the physical and numerical models tests results. The paper deals with the driven disk indexing spatial cam mechanism numerical model at the constant angular cam velocity. The presented mechanism kinematics and geometry parameters and finite element model are analyzed in the SolidWorks design environment. The calculation initial data and missing parameters having been found from the structure analysis were identified. The structure and kinematics analysis revealed the mechanism failures possible reasons. The numerical calculations results showing the structure performance at the contact and bending stresses are represented.

Using Social Networking to Understand Social Networks: Analysis of a Mobile Phone Closed User Group Used by a Ghanaian Health Team

PubMed Central

Akosah, Eric; Ohemeng-Dapaah, Seth; Sakyi Baah, Joseph; Kanter, Andrew S

2013-01-01

Background The network structure of an organization influences how well or poorly an organization communicates and manages its resources. In the Millennium Villages Project site in Bonsaaso, Ghana, a mobile phone closed user group has been introduced for use by the Bonsaaso Millennium Villages Project Health Team and other key individuals. No assessment on the benefits or barriers of the use of the closed user group had been carried out. Objective The purpose of this research was to make the case for the use of social network analysis methods to be applied in health systems research—specifically related to mobile health. Methods This study used mobile phone voice records of, conducted interviews with, and reviewed call journals kept by a mobile phone closed user group consisting of the Bonsaaso Millennium Villages Project Health Team. Social network analysis methodology complemented by a qualitative component was used. Monthly voice data of the closed user group from Airtel Bharti Ghana were analyzed using UCINET and visual depictions of the network were created using NetDraw. Interviews and call journals kept by informants were analyzed using NVivo. Results The methodology was successful in helping identify effective organizational structure. Members of the Health Management Team were the more central players in the network, rather than the Community Health Nurses (who might have been expected to be central). Conclusions Social network analysis methodology can be used to determine the most productive structure for an organization or team, identify gaps in communication, identify key actors with greatest influence, and more. In conclusion, this methodology can be a useful analytical tool, especially in the context of mobile health, health services, and operational and managerial research. PMID:23552721

Using social networking to understand social networks: analysis of a mobile phone closed user group used by a Ghanaian health team.

PubMed

Kaonga, Nadi Nina; Labrique, Alain; Mechael, Patricia; Akosah, Eric; Ohemeng-Dapaah, Seth; Sakyi Baah, Joseph; Kodie, Richmond; Kanter, Andrew S; Levine, Orin

2013-04-03

The network structure of an organization influences how well or poorly an organization communicates and manages its resources. In the Millennium Villages Project site in Bonsaaso, Ghana, a mobile phone closed user group has been introduced for use by the Bonsaaso Millennium Villages Project Health Team and other key individuals. No assessment on the benefits or barriers of the use of the closed user group had been carried out. The purpose of this research was to make the case for the use of social network analysis methods to be applied in health systems research--specifically related to mobile health. This study used mobile phone voice records of, conducted interviews with, and reviewed call journals kept by a mobile phone closed user group consisting of the Bonsaaso Millennium Villages Project Health Team. Social network analysis methodology complemented by a qualitative component was used. Monthly voice data of the closed user group from Airtel Bharti Ghana were analyzed using UCINET and visual depictions of the network were created using NetDraw. Interviews and call journals kept by informants were analyzed using NVivo. The methodology was successful in helping identify effective organizational structure. Members of the Health Management Team were the more central players in the network, rather than the Community Health Nurses (who might have been expected to be central). Social network analysis methodology can be used to determine the most productive structure for an organization or team, identify gaps in communication, identify key actors with greatest influence, and more. In conclusion, this methodology can be a useful analytical tool, especially in the context of mobile health, health services, and operational and managerial research.

Structural Test and Analysis of a Hybrid Inflatable Antenna

NASA Technical Reports Server (NTRS)

Gaspar, James L.; Mann, Troy; Sreekantamurthy, Tham; Behun, Vaughn

2007-01-01

NASA is developing ultra-lightweight structures technology for communication antennas for space missions. One of the research goals is to evaluate the structural characteristics of inflatable and rigidizable antennas through test and analysis. Being able to test and analyze the structural characteristics of a full scale antenna is important to enable the simulation of various mission scenarios to determine system performance in space. Recent work completed to evaluate a Hybrid Inflatable Antenna concept will be discussed. Tests were completed on a 2-m prototype to optimize its static shape and identify its modal dynamics that are important for analytical model validation. These test results were used to evaluate a preliminary finite element model of the antenna, and this model development and correlation activity is also described in the paper.

An easily implemented static condensation method for structural sensitivity analysis

NASA Technical Reports Server (NTRS)

Gangadharan, S. N.; Haftka, R. T.; Nikolaidis, E.

1990-01-01

A black-box approach to static condensation for sensitivity analysis is presented with illustrative examples of a cube and a car structure. The sensitivity of the structural response with respect to joint stiffness parameter is calculated using the direct method, forward-difference, and central-difference schemes. The efficiency of the various methods for identifying joint stiffness parameters from measured static deflections of these structures is compared. The results indicate that the use of static condensation can reduce computation times significantly and the black-box approach is only slightly less efficient than the standard implementation of static condensation. The ease of implementation of the black-box approach recommends it for use with general-purpose finite element codes that do not have a built-in facility for static condensation.

Body weight of hypersonic aircraft, part 1

NASA Technical Reports Server (NTRS)

Ardema, Mark D.

1988-01-01

The load bearing body weight of wing-body and all-body hypersonic aircraft is estimated for a wide variety of structural materials and geometries. Variations of weight with key design and configuration parameters are presented and discussed. Both hot and cool structure approaches are considered in isotropic, organic composite, and metal matrix composite materials; structural shells are sandwich or skin-stringer. Conformal and pillow-tank designs are investigated for the all-body shape. The results identify the most promising hypersonic aircraft body structure design approaches and their weight trends. Geometric definition of vehicle shapes and structural analysis methods are presented in appendices.

An example of requirements for Advanced Subsonic Civil Transport (ASCT) flight control system using structured techniques

NASA Technical Reports Server (NTRS)

Mclees, Robert E.; Cohen, Gerald C.

1991-01-01

The requirements are presented for an Advanced Subsonic Civil Transport (ASCT) flight control system generated using structured techniques. The requirements definition starts from initially performing a mission analysis to identify the high level control system requirements and functions necessary to satisfy the mission flight. The result of the study is an example set of control system requirements partially represented using a derivative of Yourdon's structured techniques. Also provided is a research focus for studying structured design methodologies and in particular design-for-validation philosophies.

Co-authorship network analysis in health research: method and potential use.

PubMed

Fonseca, Bruna de Paula Fonseca E; Sampaio, Ricardo Barros; Fonseca, Marcus Vinicius de Araújo; Zicker, Fabio

2016-04-30

Scientific collaboration networks are a hallmark of contemporary academic research. Researchers are no longer independent players, but members of teams that bring together complementary skills and multidisciplinary approaches around common goals. Social network analysis and co-authorship networks are increasingly used as powerful tools to assess collaboration trends and to identify leading scientists and organizations. The analysis reveals the social structure of the networks by identifying actors and their connections. This article reviews the method and potential applications of co-authorship network analysis in health. The basic steps for conducting co-authorship studies in health research are described and common network metrics are presented. The application of the method is exemplified by an overview of the global research network for Chikungunya virus vaccines.

Experimental Modal Analysis and Dynaic Strain Fiber Bragg Gratings for Structural Health Monitoring of Composite Aerospace Structures

NASA Astrophysics Data System (ADS)

Panopoulou, A.; Fransen, S.; Gomez Molinero, V.; Kostopoulos, V.

2012-07-01

The objective of this work is to develop a new structural health monitoring system for composite aerospace structures based on dynamic response strain measurements and experimental modal analysis techniques. Fibre Bragg Grating (FBG) optical sensors were used for monitoring the dynamic response of the composite structure. The structural dynamic behaviour has been numerically simulated and experimentally verified by means of vibration testing. The hypothesis of all vibration tests was that actual damage in composites reduces their stiffness and produces the same result as mass increase produces. Thus, damage was simulated by slightly varying locally the mass of the structure at different zones. Experimental modal analysis based on the strain responses was conducted and the extracted strain mode shapes were the input for the damage detection expert system. A feed-forward back propagation neural network was the core of the damage detection system. The features-input to the neural network consisted of the strain mode shapes, extracted from the experimental modal analysis. Dedicated training and validation activities were carried out based on the experimental results. The system showed high reliability, confirmed by the ability of the neural network to recognize the size and the position of damage on the structure. The experiments were performed on a real structure i.e. a lightweight antenna sub- reflector, manufactured and tested at EADS CASA ESPACIO. An integrated FBG sensor network, based on the advantage of multiplexing, was mounted on the structure with optimum topology. Numerical simulation of both structures was used as a support tool at all the steps of the work. Potential applications for the proposed system are during ground qualification extensive tests of space structures and during the mission as modal analysis tool on board, being able via the FBG responses to identify a potential failure.

Collision-induced dissociative chemical cross-linking reagents and methodology: Applications to protein structural characterization using tandem mass spectrometry analysis.

PubMed

Soderblom, Erik J; Goshe, Michael B

2006-12-01

Chemical cross-linking combined with mass spectrometry is a viable approach to study the low-resolution structure of protein and protein complexes. However, unambiguous identification of the residues involved in a cross-link remains analytically challenging. To enable a more effective analysis across various MS platforms, we have developed a novel set of collision-induced dissociative cross-linking reagents and methodology for chemical cross-linking experiments using tandem mass spectrometry (CID-CXL-MS/MS). These reagents incorporate a single gas-phase cleavable bond within their linker region that can be selectively fragmented within the in-source region of the mass spectrometer, enabling independent MS/MS analysis for each peptide. Initial design concepts were characterized using a synthesized cross-linked peptide complex. Following verification and subsequent optimization of cross-linked peptide complex dissociation, our reagents were applied to homodimeric glutathione S-transferase and monomeric bovine serum albumin. Cross-linked residues identified by our CID-CXL-MS/MS method were in agreement with published crystal structures and previous cross-linking studies using conventional approaches. Common LC/MS/MS acquisition approaches such as data-dependent acquisition experiments using ion trap mass spectrometers and product ion spectral analysis using SEQUEST were shown to be compatible with our CID-CXL-MS/MS reagents, obviating the requirement for high resolution and high mass accuracy measurements to identify both intra- and interpeptide cross-links.

Individual Differences in Dynamic Functional Brain Connectivity across the Human Lifespan.

PubMed

Davison, Elizabeth N; Turner, Benjamin O; Schlesinger, Kimberly J; Miller, Michael B; Grafton, Scott T; Bassett, Danielle S; Carlson, Jean M

2016-11-01

Individual differences in brain functional networks may be related to complex personal identifiers, including health, age, and ability. Dynamic network theory has been used to identify properties of dynamic brain function from fMRI data, but the majority of analyses and findings remain at the level of the group. Here, we apply hypergraph analysis, a method from dynamic network theory, to quantify individual differences in brain functional dynamics. Using a summary metric derived from the hypergraph formalism-hypergraph cardinality-we investigate individual variations in two separate, complementary data sets. The first data set ("multi-task") consists of 77 individuals engaging in four consecutive cognitive tasks. We observe that hypergraph cardinality exhibits variation across individuals while remaining consistent within individuals between tasks; moreover, the analysis of one of the memory tasks revealed a marginally significant correspondence between hypergraph cardinality and age. This finding motivated a similar analysis of the second data set ("age-memory"), in which 95 individuals, aged 18-75, performed a memory task with a similar structure to the multi-task memory task. With the increased age range in the age-memory data set, the correlation between hypergraph cardinality and age correspondence becomes significant. We discuss these results in the context of the well-known finding linking age with network structure, and suggest that hypergraph analysis should serve as a useful tool in furthering our understanding of the dynamic network structure of the brain.

Genome-wide characterization of the Pectate Lyase-like (PLL) genes in Brassica rapa.

PubMed

Jiang, Jingjing; Yao, Lina; Miao, Ying; Cao, Jiashu

2013-11-01

Pectate lyases (PL) depolymerize demethylated pectin (pectate, EC 4.2.2.2) by catalyzing the eliminative cleavage of α-1,4-glycosidic linked galacturonan. Pectate Lyase-like (PLL) genes are one of the largest and most complex families in plants. However, studies on the phylogeny, gene structure, and expression of PLL genes are limited. To understand the potential functions of PLL genes in plants, we characterized their intron-exon structure, phylogenetic relationships, and protein structures, and measured their expression patterns in various tissues, specifically the reproductive tissues in Brassica rapa. Sequence alignments revealed two characteristic motifs in PLL genes. The chromosome location analysis indicated that 18 of the 46 PLL genes were located in the least fractionated sub-genome (LF) of B. rapa, while 16 were located in the medium fractionated sub-genome (MF1) and 12 in the more fractionated sub-genome (MF2). Quantitative RT-PCR analysis showed that BrPLL genes were expressed in various tissues, with most of them being expressed in flowers. Detailed qRT-PCR analysis identified 11 pollen specific PLL genes and several other genes with unique spatial expression patterns. In addition, some duplicated genes showed similar expression patterns. The phylogenetic analysis identified three PLL gene subfamilies in plants, among which subfamily II might have evolved from gene neofunctionalization or subfunctionalization. Therefore, this study opens the possibility for exploring the roles of PLL genes during plant development.

The structure of binding curves and practical identifiability of equilibrium ligand-binding parameters

PubMed Central

Middendorf, Thomas R.

2017-01-01

A critical but often overlooked question in the study of ligands binding to proteins is whether the parameters obtained from analyzing binding data are practically identifiable (PI), i.e., whether the estimates obtained from fitting models to noisy data are accurate and unique. Here we report a general approach to assess and understand binding parameter identifiability, which provides a toolkit to assist experimentalists in the design of binding studies and in the analysis of binding data. The partial fraction (PF) expansion technique is used to decompose binding curves for proteins with n ligand-binding sites exactly and uniquely into n components, each of which has the form of a one-site binding curve. The association constants of the PF component curves, being the roots of an n-th order polynomial, may be real or complex. We demonstrate a fundamental connection between binding parameter identifiability and the nature of these one-site association constants: all binding parameters are identifiable if the constants are all real and distinct; otherwise, at least some of the parameters are not identifiable. The theory is used to construct identifiability maps from which the practical identifiability of binding parameters for any two-, three-, or four-site binding curve can be assessed. Instructions for extending the method to generate identifiability maps for proteins with more than four binding sites are also given. Further analysis of the identifiability maps leads to the simple rule that the maximum number of structurally identifiable binding parameters (shown in the previous paper to be equal to n) will also be PI only if the binding curve line shape contains n resolved components. PMID:27993951

Protein structure similarity from Principle Component Correlation analysis.

PubMed

Zhou, Xiaobo; Chou, James; Wong, Stephen T C

2006-01-25

Owing to rapid expansion of protein structure databases in recent years, methods of structure comparison are becoming increasingly effective and important in revealing novel information on functional properties of proteins and their roles in the grand scheme of evolutionary biology. Currently, the structural similarity between two proteins is measured by the root-mean-square-deviation (RMSD) in their best-superimposed atomic coordinates. RMSD is the golden rule of measuring structural similarity when the structures are nearly identical; it, however, fails to detect the higher order topological similarities in proteins evolved into different shapes. We propose new algorithms for extracting geometrical invariants of proteins that can be effectively used to identify homologous protein structures or topologies in order to quantify both close and remote structural similarities. We measure structural similarity between proteins by correlating the principle components of their secondary structure interaction matrix. In our approach, the Principle Component Correlation (PCC) analysis, a symmetric interaction matrix for a protein structure is constructed with relationship parameters between secondary elements that can take the form of distance, orientation, or other relevant structural invariants. When using a distance-based construction in the presence or absence of encoded N to C terminal sense, there are strong correlations between the principle components of interaction matrices of structurally or topologically similar proteins. The PCC method is extensively tested for protein structures that belong to the same topological class but are significantly different by RMSD measure. The PCC analysis can also differentiate proteins having similar shapes but different topological arrangements. Additionally, we demonstrate that when using two independently defined interaction matrices, comparison of their maximum eigenvalues can be highly effective in clustering structurally or topologically similar proteins. We believe that the PCC analysis of interaction matrix is highly flexible in adopting various structural parameters for protein structure comparison.

DAISY: a new software tool to test global identifiability of biological and physiological systems.

PubMed

Bellu, Giuseppina; Saccomani, Maria Pia; Audoly, Stefania; D'Angiò, Leontina

2007-10-01

A priori global identifiability is a structural property of biological and physiological models. It is considered a prerequisite for well-posed estimation, since it concerns the possibility of recovering uniquely the unknown model parameters from measured input-output data, under ideal conditions (noise-free observations and error-free model structure). Of course, determining if the parameters can be uniquely recovered from observed data is essential before investing resources, time and effort in performing actual biomedical experiments. Many interesting biological models are nonlinear but identifiability analysis for nonlinear system turns out to be a difficult mathematical problem. Different methods have been proposed in the literature to test identifiability of nonlinear models but, to the best of our knowledge, so far no software tools have been proposed for automatically checking identifiability of nonlinear models. In this paper, we describe a software tool implementing a differential algebra algorithm to perform parameter identifiability analysis for (linear and) nonlinear dynamic models described by polynomial or rational equations. Our goal is to provide the biological investigator a completely automatized software, requiring minimum prior knowledge of mathematical modelling and no in-depth understanding of the mathematical tools. The DAISY (Differential Algebra for Identifiability of SYstems) software will potentially be useful in biological modelling studies, especially in physiology and clinical medicine, where research experiments are particularly expensive and/or difficult to perform. Practical examples of use of the software tool DAISY are presented. DAISY is available at the web site http://www.dei.unipd.it/~pia/.

A Polytomous Item Response Theory Analysis of Social Physique Anxiety Scale

ERIC Educational Resources Information Center

Fletcher, Richard B.; Crocker, Peter

2014-01-01

The present study investigated the social physique anxiety scale's factor structure and item properties using confirmatory factor analysis and item response theory. An additional aim was to identify differences in response patterns between groups (gender). A large sample of high school students aged 11-15 years (N = 1,529) consisting of n =…

Multilevel Latent Class Analysis: An Application of Adolescent Smoking Typologies with Individual and Contextual Predictors

ERIC Educational Resources Information Center

Henry, Kimberly L.; Muthen, Bengt

2010-01-01

Latent class analysis (LCA) is a statistical method used to identify subtypes of related cases using a set of categorical or continuous observed variables. Traditional LCA assumes that observations are independent. However, multilevel data structures are common in social and behavioral research and alternative strategies are needed. In this…

A Co-Citation Network of Young Children's Learning with Technology

ERIC Educational Resources Information Center

Tang, Kai-Yu; Li, Ming-Chaun; Hsin, Ching-Ting; Tsai, Chin-Chung

2016-01-01

This paper used a novel literature review approach--co-citation network analysis--to illuminate the latent structure of 87 empirical papers in the field of young children's learning with technology (YCLT). Based on the document co-citation analysis, a total of 206 co-citation relationships among the 87 papers were identified and then graphically…

Conflagration Analysis System II: Bibliography.

DTIC Science & Technology

1985-04-01

Therefore, it is Lmportant to examine both the reinforcement and the supplemental considerations Eor the quantitative methods for conflagration...and the meaningful quantitative factors for conflagration analysis are determined, the relevatn literature will be brought into the nainstream of the... quantitative :hods. Fire Development in Multiple Structures From a purely analytical view, the research identified in the literature fire development in

Method and apparatus for enhanced sequencing of complex molecules using surface-induced dissociation in conjunction with mass spectrometric analysis

DOEpatents

Laskin, Julia [Richland, WA; Futrell, Jean H [Richland, WA

2008-04-29

The invention relates to a method and apparatus for enhanced sequencing of complex molecules using surface-induced dissociation (SID) in conjunction with mass spectrometric analysis. Results demonstrate formation of a wide distribution of structure-specific fragments having wide sequence coverage useful for sequencing and identifying the complex molecules.

Front-End Analysis Methods for the Noncommissioned Officer Education System

DTIC Science & Technology

2013-02-01

The Noncommissioned Officer Education System plays a crucial role in Soldier development by providing both institutional training and structured-self...created challenges with maintaining currency of institutional training . Questions have arisen regarding the optimal placement of tasks as their...relevance changes, especially considering the resources required to update institutional training . An analysis was conducted to identify the

The Transition from a University College to a University: A United Kingdom Study

ERIC Educational Resources Information Center

Hemmings, Brian; Hill, Doug; Sharp, John

2015-01-01

As a result of policy changes, nearly all university colleges in the UK have been redesignated as universities. This transition was studied in one such institution using semi-structured interviews with a representative sample of six academic staff and the transcripts subjected to a thematic analysis. This analysis identified three themes: staying…

An Empirical Analysis of Chinese College Learners' Obstacles to MOOC Learning in an English Context

ERIC Educational Resources Information Center

Liu, Liangxing

2017-01-01

This article reports a study applying an exploratory factor analysis to discovering the underlying factor structure of Chinese college students' obstacles to learning MOOC in an English context. Seven obstacle factors are identified: 1. academic and language skills; 2. internet skills; 3. course instruction/management; 4. learning motivations; 5.…

Remote sensing strategic exploration of large or superlarge gold ore deposits

NASA Astrophysics Data System (ADS)

Yan, Shouxun; Liu, Qingsheng; Wang, Hongmei; Wang, Zhigang; Liu, Suhong

1998-08-01

To prospect large or superlarge gold ore deposits, blending of remote sensing techniques and modern metallogenitic theories is one of the effective measures. The theory of metallogeny plays a director role before and during remote sensing technique applications. The remote sensing data with different platforms and different resolutions can be respectively applied to detect direct or indirect metallogenic information, and to identify the ore-controlling structure, especially, the ore-controlling structural assemblage, which, conversely, usually are the new conditions to study and to modify the metallogenic model, and to further develop the exploration model of large or superlarge ore deposits. Guidance by an academic idea of 'adjustment structure' which is the conceptual model of transverse structure, an obscured ore- controlling transverse structure has been identified on the refined TM imagery in the Hadamengou gold ore deposit, Setai Hyperspectral Geological Remote Sensing Testing Site (SHGRSTS), Wulashan mountains, Inner Mongolia, China. Meanwhile, The MAIS data has been applied to quickly identify the auriferous alteration rocks with Correspondence Analysis method and Spectral Angle Mapping (SAM) technique. The theoretical system and technical method of remote sensing strategic exploration of large or superlarge gold ore deposits have been demonstrated by the practices in the SHGRSTS.

Search-based model identification of smart-structure damage

NASA Technical Reports Server (NTRS)

Glass, B. J.; Macalou, A.

1991-01-01

This paper describes the use of a combined model and parameter identification approach, based on modal analysis and artificial intelligence (AI) techniques, for identifying damage or flaws in a rotating truss structure incorporating embedded piezoceramic sensors. This smart structure example is representative of a class of structures commonly found in aerospace systems and next generation space structures. Artificial intelligence techniques of classification, heuristic search, and an object-oriented knowledge base are used in an AI-based model identification approach. A finite model space is classified into a search tree, over which a variant of best-first search is used to identify the model whose stored response most closely matches that of the input. Newly-encountered models can be incorporated into the model space. This adaptativeness demonstrates the potential for learning control. Following this output-error model identification, numerical parameter identification is used to further refine the identified model. Given the rotating truss example in this paper, noisy data corresponding to various damage configurations are input to both this approach and a conventional parameter identification method. The combination of the AI-based model identification with parameter identification is shown to lead to smaller parameter corrections than required by the use of parameter identification alone.

Combination of volume and perfusion parameters reveals different types of grey matter changes in schizophrenia.

PubMed

Xu, Lixue; Qin, Wen; Zhuo, Chuanjun; Liu, Huaigui; Zhu, Jiajia; Yu, Chunshui

2017-03-27

Diverse brain structural and functional changes have been reported in schizophrenia. Identifying different types of brain changes may help to understand the neural mechanisms and to develop reliable biomarkers in schizophrenia. We aimed to categorize different grey matter changes in schizophrenia based on grey matter volume (GMV) and cerebral blood flow (CBF). Structural and perfusion magnetic resonance imaging data were acquired in 100 schizophrenia patients and 95 healthy comparison subjects. Voxel-based GMV comparison was used to show structural changes, CBF analysis was used to demonstrate functional changes. We identified three types of grey matter changes in schizophrenia: structural and functional impairments in the anterior cingulate cortex and insular cortex, displaying reduction in both GMV and CBF; structural impairment with preserved function in the frontal and temporal cortices, demonstrating decreased GMV with normal CBF; pure functional abnormality in the anterior cingulate cortex and lateral prefrontal cortex and putamen, showing altered CBF with normal GMV. By combination of GMV and CBF, we identified three types of grey matter changes in schizophrenia. These findings may help to understand the complex manifestations and to develop reliable biomarkers in schizophrenia.

Identification of faulty sensor using relative partial decomposition via independent component analysis

NASA Astrophysics Data System (ADS)

Wang, Z.; Quek, S. T.

2015-07-01

Performance of any structural health monitoring algorithm relies heavily on good measurement data. Hence, it is necessary to employ robust faulty sensor detection approaches to isolate sensors with abnormal behaviour and exclude the highly inaccurate data in the subsequent analysis. The independent component analysis (ICA) is implemented to detect the presence of sensors showing abnormal behaviour. A normalized form of the relative partial decomposition contribution (rPDC) is proposed to identify the faulty sensor. Both additive and multiplicative types of faults are addressed and the detectability illustrated using a numerical and an experimental example. An empirical method to establish control limits for detecting and identifying the type of fault is also proposed. The results show the effectiveness of the ICA and rPDC method in identifying faulty sensor assuming that baseline cases are available.

[The registry of home artificial nutrition and ambulatory of the Spanish Society of Parenteral and Enteral Nutrition; SWOT analysis].

PubMed

Wanden-Berghe, C; Pérez de la Cruz, A; Lobo Tamer, G; Calleja Fernández, A; Gómez Candela, C; Zugasti Murillo, A; Apezetxea Celaya, A; Torres Corts, A; Moreno Villarés, J M; de Luis, D; Penacho, Ma Á; Laborda, L; Burgos, R; Irles, J A; Cuerda Compes, C; Virgili Casas, Ma N; Martínez Olmos, M A; García Luna, P P

2012-01-01

To evidence by means of a SWOT-R analysis performed by an expert consensus the most worrying characteristics of the register on Home-based and Outpatient Artificial Nutrition. SWOT-R analysis with expert consensus. We requested the participation of the active members of the NADYA group within the last 5 years with the premise of structuring the SWOT-R based on the characteristics of the NADYA registry from its beginning. 18 experts from hospitals all over Spain have participated. The internal analysis seems to be positive, presenting the registry as having important resources. The external analysis did not show a great number of threats, there are very potent factors, "the voluntariness" of the registry and the "dependence on external financing". The opportunities identified are important. The recommendations are aimed at stabilizing the system by decreasing the threats as one of the main focus of the strategies to develop as well as promoting the items identified as opportunities and strengths. The analysis shows that the NADYA register shows a big potentiality for improvement. The proposed recommendations should be structured in order to stay on the track of development and quality improvement that has characterized the NADYA register from the beginning.

Aerodynamic and structural studies of joined-wing aircraft

NASA Technical Reports Server (NTRS)

Kroo, Ilan; Smith, Stephen; Gallman, John

1991-01-01

A method for rapidly evaluating the structural and aerodynamic characteristics of joined-wing aircraft was developed and used to study the fundamental advantages attributed to this concept. The technique involves a rapid turnaround aerodynamic analysis method for computing minimum trimmed drag combined with a simple structural optimization. A variety of joined-wing designs are compared on the basis of trimmed drag, structural weight, and, finally, trimmed drag with fixed structural weight. The range of joined-wing design parameters resulting in best cruise performance is identified. Structural weight savings and net drag reductions are predicted for certain joined-wing configurations compared with conventional cantilever-wing configurations.

Bacterial Diversity and Community Structure of Supragingival Plaques in Adults with Dental Health or Caries Revealed by 16S Pyrosequencing

PubMed Central

Xiao, Cuicui; Ran, Shujun; Huang, Zhengwei; Liang, Jingping

2016-01-01

Dental caries has a polymicrobial etiology within the complex oral microbial ecosystem. However, the overall diversity and structure of supragingival plaque microbiota in adult dental health and caries are not well understood. Here, 160 supragingival plaque samples from patients with dental health and different severities of dental caries were collected for bacterial genomic DNA extraction, pyrosequencing by amplification of the 16S rDNA V1–V3 hypervariable regions, and bioinformatic analysis. High-quality sequences (2,261,700) clustered into 10,365 operational taxonomic units (OTUs; 97% identity), representing 453 independent species belonging to 122 genera, 66 families, 34 orders, 21 classes, and 12 phyla. All groups shared 7522 OTUs, indicating the presence of a core plaque microbiome. α diversity analysis showed that the microbial diversity in healthy plaques exceeded that of dental caries, with the diversity decreasing gradually with the severity of caries. The dominant phyla of plaque microbiota included Bacteroidetes, Actinobacteria, Proteobacteria, Firmicutes, Fusobacteria, and TM7. The dominant genera included Capnocytophaga, Prevotella, Actinomyces, Corynebacterium, Neisseria, Streptococcus, Rothia, and Leptotrichia. β diversity analysis showed that the plaque microbial community structure was similar in all groups. Using LEfSe analysis, 25 differentially abundant taxa were identified as potential biomarkers. Key genera (27) that potentially contributed to the differential distributions of plaque microbiota between groups were identified by PLS-DA analysis. Finally, co-occurrence network analysis and function predictions were performed. Treatment strategies directed toward modulating microbial interactions and their functional output should be further developed. PMID:27499752

Visual analysis as a method of interpretation of the results of satellite ionospheric measurements for exploratory problems

NASA Astrophysics Data System (ADS)

Korneva, N. N.; Mogilevskii, M. M.; Nazarov, V. N.

2016-05-01

Traditional methods of time series analysis of satellite ionospheric measurements have some limitations and disadvantages that are mainly associated with the complex nonstationary signal structure. In this paper, the possibility of identifying and studying the temporal characteristics of signals via visual analysis is considered. The proposed approach is illustrated by the example of the visual analysis of wave measurements on the DEMETER microsatellite during its passage over the HAARP facility.

The Job Dimensions Underlying the Job Elements of the Position Analysis Questionnaire (PAQ) (Form B).

DTIC Science & Technology

The study was concerned with the identification of the job dimension underlying the job elements of the Position Analysis Questionnaire ( PAQ ), Form B...The PAQ is a structured job analysis instrument consisting of 187 worker-oriented job elements which are divided into six a priori major divisions...The statistical procedure of principal components analysis was used to identify the job dimensions of the PAQ . Forty-five job dimensions were

A holistic approach to determine tree structural complexity based on laser scanning data and fractal analysis.

PubMed

Seidel, Dominik

2018-01-01

The three-dimensional forest structure affects many ecosystem functions and services provided by forests. As forests are made of trees it seems reasonable to approach their structure by investigating individual tree structure. Based on three-dimensional point clouds from laser scanning, a newly developed holistic approach is presented that enables to calculate the box dimension as a measure of structural complexity of individual trees using fractal analysis. It was found that the box dimension of trees was significantly different among the tested species, among trees belonging to the same species but exposed to different growing conditions (at gap vs. forest interior) or to different kinds of competition (intraspecific vs. interspecific). Furthermore, it was shown that the box dimension is positively related to the trees' growth rate. The box dimension was identified as an easy to calculate measure that integrates the effect of several external drivers of tree structure, such as competition strength and type, while simultaneously providing information on structure-related properties, like tree growth.

Identification of the chemical components of Saussurea involucrata by high-resolution mass spectrometry and the mass spectral trees similarity filter technique.

PubMed

Jia, Zhixin; Wu, Caisheng; Jin, Hongtao; Zhang, Jinlan

2014-11-15

Saussurea involucrata is a rare traditional Chinese medicine (TCM) that displays anti-fatigue, anti-inflammatory and anti-tumor effects. In this paper, the different chemical components of Saussurea involucrata were characterized and identified over a wide dynamic range by high-performance liquid chromatography coupled with high-resolution hybrid mass spectrometry (HPLC/HRMS/MS(n)) and the mass spectral trees similarity filter (MTSF) technique. The aerial parts of Saussurea involucrata were extracted with 75% ethanol. The partial extract was separated on a chromatography column to concentrate the low-concentration compounds. Mass data were acquired using full-scan mass analysis (resolving power 50,000) with data-dependent incorporation of dynamic exclusion analysis. The identified compounds were used as templates to construct a database of mass spectral trees. Data for the unknown compounds were matched with those templates and matching candidate structures were obtained. The detected compounds were characterized based on matching to candidate structures by the MTSF technique and were further identified by their accurate mass weight, multiple-stage analysis and fragmentation patterns and through comparison with literature data. A total of 38 compounds were identified including 19 flavones, 11 phenylpropanoids and 8 sphingolipids. Among them, 7 flavonoids, 8 phenylpropanoids and 8 sphingolipids were identified for the first time in Saussurea involucrata. HPLC/HRMS/MS(n) combined with MTSF was successfully used to discover and identify the chemical compounds in Saussurea involucrata. The results indicated that this combined technique was extremely useful for the rapid detection and identification of the chemical components in TCMs. Copyright © 2014 John Wiley & Sons, Ltd.

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

PubMed Central

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

2016-01-01

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

Pore Structure Characterization of Sodium Hydroxide Activated Slag Using Mercury Intrusion Porosimetry, Nitrogen Adsorption, and Image Analysis.

PubMed

Zuo, Yibing; Ye, Guang

2018-06-19

The pore structure of alkali-activated slag has a significant influence on its performance. However, the literature shows insufficient studies regarding the suitability of different techniques for characterizing the pore structure and the influences of Na₂O and curing age on pore structure development. In pursuit of a better understanding, the pore structure of sodium hydroxide activated slag paste was characterized by multiple techniques, e.g., mercury intrusion porosimetry (MIP), nitrogen (N₂) adsorption, and scanning electron microscopy (SEM) image analysis. The sodium hydroxide activated slag pastes were prepared with three different contents of Na₂O (Na₂O/slag = 4, 6, and 8%) and cured for different times up to 360 days. The microstructure observation reveals that outer C⁻(N⁻)A⁻S⁻H and inner C⁻(N⁻)A⁻S⁻H grow successively around the reacting slag grains, along with crystalline reaction products which are formed in the empty coarse pore space. The increase of Na₂O content and curing age lead to a finer pore structure. The MIP measurements show that the total porosity drops about 70% within the first day, and that one peak at most, corresponding to gel pores, was identified in the differential curves of all the investigated samples from 1 to 360 days. On the contrary, only one peak, corresponding to capillary pores, was identified by SEM-image analysis. The differential curves derived from N₂ adsorption generally reveal two peaks, and the trend that the pore diameters of those two peaks vary with curing age depends on the content of Na₂O. Compared to Portland cement, sodium hydroxide activated slag has a higher pore space filling capacity ( χ , V products / V slag-reacted ), while the capacity decreases with increasing Na₂O content and curing age.

Multiple solvent crystal structures of ribonuclease A: An assessment of the method

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

Dechene, Michelle; Wink, Glenna; Smith, Mychal

2010-11-12

The multiple solvent crystal structures (MSCS) method uses organic solvents to map the surfaces of proteins. It identifies binding sites and allows for a more thorough examination of protein plasticity and hydration than could be achieved by a single structure. The crystal structures of bovine pancreatic ribonuclease A (RNAse A) soaked in the following organic solvents are presented: 50% dioxane, 50% dimethylformamide, 70% dimethylsulfoxide, 70% 1,6-hexanediol, 70% isopropanol, 50% R,S,R-bisfuran alcohol, 70% t-butanol, 50% trifluoroethanol, or 1.0M trimethylamine-N-oxide. This set of structures is compared with four sets of crystal structures of RNAse A from the protein data bank (PDB) andmore » with the solution NMR structure to assess the validity of previously untested assumptions associated with MSCS analysis. Plasticity from MSCS is the same as from PDB structures obtained in the same crystal form and deviates only at crystal contacts when compared to structures from a diverse set of crystal environments. Furthermore, there is a good correlation between plasticity as observed by MSCS and the dynamic regions seen by NMR. Conserved water binding sites are identified by MSCS to be those that are conserved in the sets of structures taken from the PDB. Comparison of the MSCS structures with inhibitor-bound crystal structures of RNAse A reveals that the organic solvent molecules identify key interactions made by inhibitor molecules, highlighting ligand binding hot-spots in the active site. The present work firmly establishes the relevance of information obtained by MSCS.« less

Assessment of current state of the art in modeling techniques and analysis methods for large space structures

NASA Technical Reports Server (NTRS)

Noor, A. K.

1983-01-01

Advances in continuum modeling, progress in reduction methods, and analysis and modeling needs for large space structures are covered with specific attention given to repetitive lattice trusses. As far as continuum modeling is concerned, an effective and verified analysis capability exists for linear thermoelastic stress, birfurcation buckling, and free vibration problems of repetitive lattices. However, application of continuum modeling to nonlinear analysis needs more development. Reduction methods are very effective for bifurcation buckling and static (steady-state) nonlinear analysis. However, more work is needed to realize their full potential for nonlinear dynamic and time-dependent problems. As far as analysis and modeling needs are concerned, three areas are identified: loads determination, modeling and nonclassical behavior characteristics, and computational algorithms. The impact of new advances in computer hardware, software, integrated analysis, CAD/CAM stems, and materials technology is also discussed.

Uncertainty quantification in operational modal analysis with stochastic subspace identification: Validation and applications

NASA Astrophysics Data System (ADS)

Reynders, Edwin; Maes, Kristof; Lombaert, Geert; De Roeck, Guido

2016-01-01

Identified modal characteristics are often used as a basis for the calibration and validation of dynamic structural models, for structural control, for structural health monitoring, etc. It is therefore important to know their accuracy. In this article, a method for estimating the (co)variance of modal characteristics that are identified with the stochastic subspace identification method is validated for two civil engineering structures. The first structure is a damaged prestressed concrete bridge for which acceleration and dynamic strain data were measured in 36 different setups. The second structure is a mid-rise building for which acceleration data were measured in 10 different setups. There is a good quantitative agreement between the predicted levels of uncertainty and the observed variability of the eigenfrequencies and damping ratios between the different setups. The method can therefore be used with confidence for quantifying the uncertainty of the identified modal characteristics, also when some or all of them are estimated from a single batch of vibration data. Furthermore, the method is seen to yield valuable insight in the variability of the estimation accuracy from mode to mode and from setup to setup: the more informative a setup is regarding an estimated modal characteristic, the smaller is the estimated variance.

Four structural risk factors identify most fibril-forming kappa light chains.

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

Stevens, F. J.; Biosciences Division

2000-09-01

Antibody light chains (LCs) comprise the most structurally diverse family of proteins involved in amyloidosis. Many antibody LCs incorporate structural features that impair their stability and solubility, leading to their assembly into fibrils and to their subsequent pathological deposition when produced in excess during multiple myeloma and primary amyloidosis. The particular amino acid variations in antibody LCs that account for fibril formation and amyloidogenesis have not been identified. This study focuses on amyloidogenesis within the Kl family of human LCs. Reanalysis of the current database of primary structures of proteins from more than 100 patients who produced Kl LCS, 37more » of which were amyloidogenic, reveals apparent structural features that may contribute to amyloidosis. These features include loss of conserved residues or the gain of particular residues through mutation at sites involving a repertoire of approximately 20% of the amino acid positions in the light chain variable domain (V{sub L}). Moreover, 80% of all K1 amyloidogenic V{sub L}s are identifiable by the presence of at least one of three single-site substitutions or the acquisition of an N-linked glycosylation site through mutations. These findings suggest that it is feasible to predict fibril propensity by analysis of primary structure.« less

Analysis of sulfates on low molecular weight heparin using mass spectrometry: structural characterization of enoxaparin.

PubMed

Gupta, Rohitesh; Ponnusamy, Moorthy P

2018-05-31

Structural characterization of low molecular weight heparin (LMWH) is critical to meet biosimilarity standards. In this context, the review focuses on structural analysis of labile sulfates attached to the side-groups of LMWH using mass spectrometry. A comprehensive review of this topic will help readers to identify key strategies for tackling the problem related to sulfate loss. At the same time, various mass spectrometry techniques are presented to facilitate compositional analysis of LMWH, mainly enoxaparin. Areas covered: This review summarizes findings on mass spectrometry application for LMWH, including modulation of sulfates, using enzymology and sample preparation approaches. Furthermore, popular open-source software packages for automated spectral data interpretation are also discussed. Successful use of LC/MS can decipher structural composition for LMWH and help evaluate their sameness or biosimilarity with the innovator molecule. Overall, the literature has been searched using PubMed by typing various search queries such as 'enoxaparin', 'mass spectrometry', 'low molecular weight heparin', 'structural characterization', etc. Expert commentary: This section highlights clinically relevant areas that need improvement to achieve satisfactory commercialization of LMWHs. It also primarily emphasizes the advancements in instrumentation related to mass spectrometry, and discusses building automated software for data interpretation and analysis.

Hybrid Wing-Body (HWB) Pressurized Fuselage Modeling, Analysis, and Design for Weight Reduction

NASA Technical Reports Server (NTRS)

Mukhopadhyay, Vivek

2012-01-01

This paper describes the interim progress for an in-house study that is directed toward innovative structural analysis and design of next-generation advanced aircraft concepts, such as the Hybrid Wing-Body (HWB) and the Advanced Mobility Concept-X flight vehicles, for structural weight reduction and associated performance enhancement. Unlike the conventional, skin-stringer-frame construction for a cylindrical fuselage, the box-type pressurized fuselage panels in the HWB undergo significant deformation of the outer aerodynamic surfaces, which must be minimized without significant structural weight penalty. Simple beam and orthotropic plate theory is first considered for sizing, analytical verification, and possible equivalent-plate analysis with appropriate simplification. By designing advanced composite stiffened-shell configurations, significant weight reduction may be possible compared with the sandwich and ribbed-shell structural concepts that have been studied previously. The study involves independent analysis of the advanced composite structural concepts that are presently being developed by The Boeing Company for pressurized HWB flight vehicles. High-fidelity parametric finite-element models of test coupons, panels, and multibay fuselage sections, were developed for conducting design studies and identifying critical areas of potential failure. Interim results are discussed to assess the overall weight/strength advantages.

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

A study of structural concepts for ultralightweight spacecraft

NASA Technical Reports Server (NTRS)

Miller, R. K.; Knapp, K.; Hedgepeth, J. M.

1984-01-01

Structural concepts for ultralightweight spacecraft were studied. Concepts for ultralightweight space structures were identified and the validity of heir potential application in advanced spacecraft was assessed. The following topics were investigated: (1) membrane wrinkling under pretensioning; (2) load-carrying capability of pressurized tubes; (3) equilibrium of a precompressed rim; (4) design of an inflated reflector spacecraft; (5) general instability of a rim; and (6) structural analysis of a pressurized isotensoid column. The design approaches for a paraboloidal reflector spacecraft included a spin-stiffened design, both inflated and truss central columns, and to include both deep truss and rim-stiffened geodesic designs. The spinning spacecraft analysis is included, and the two truss designs are covered. The performances of four different approaches to the structural design of a paraboloidal reflector spacecraft are compared. The spinning and inflated configurations result in very low total masses and some concerns about their performance due to unresolved questions about dynamic stability and lifetimes, respectively.

A user exposure based approach for non-structural road network vulnerability analysis

PubMed Central

Jin, Lei; Wang, Haizhong; Yu, Le; Liu, Lin

2017-01-01

Aiming at the dense urban road network vulnerability without structural negative consequences, this paper proposes a novel non-structural road network vulnerability analysis framework. Three aspects of the framework are mainly described: (i) the rationality of non-structural road network vulnerability, (ii) the metrics for negative consequences accounting for variant road conditions, and (iii) the introduction of a new vulnerability index based on user exposure. Based on the proposed methodology, a case study in the Sioux Falls network which was usually threatened by regular heavy snow during wintertime is detailedly discussed. The vulnerability ranking of links of Sioux Falls network with respect to heavy snow scenario is identified. As a result of non-structural consequences accompanied by conceivable degeneration of network, there are significant increases in generalized travel time costs which are measurements for “emotionally hurt” of topological road network. PMID:29176832

Basic as well as detailed neurosonograms can be performed by offline analysis of three-dimensional fetal brain volumes.

PubMed

Bornstein, E; Monteagudo, A; Santos, R; Strock, I; Tsymbal, T; Lenchner, E; Timor-Tritsch, I E

2010-07-01

To evaluate the feasibility and the processing time of offline analysis of three-dimensional (3D) brain volumes to perform a basic, as well as a detailed, targeted, fetal neurosonogram. 3D fetal brain volumes were obtained in 103 consecutive healthy fetuses that underwent routine anatomical survey at 20-23 postmenstrual weeks. Transabdominal gray-scale and power Doppler volumes of the fetal brain were acquired by one of three experienced sonographers (an average of seven volumes per fetus). Acquisition was first attempted in the sagittal and coronal planes. When the fetal position did not enable easy and rapid access to these planes, axial acquisition at the level of the biparietal diameter was performed. Offline analysis of each volume was performed by two of the authors in a blinded manner. A systematic technique of 'volume manipulation' was used to identify a list of 25 brain dimensions/structures comprising a complete basic evaluation, intracranial biometry and a detailed targeted fetal neurosonogram. The feasibility and reproducibility of obtaining diagnostic-quality images of the different structures was evaluated, and processing times were recorded, by the two examiners. Diagnostic-quality visualization was feasible in all of the 25 structures, with an excellent visualization rate (85-100%) reported in 18 structures, a good visualization rate (69-97%) reported in five structures and a low visualization rate (38-54%) reported in two structures, by the two examiners. An average of 4.3 and 5.4 volumes were used to complete the examination by the two examiners, with a mean processing time of 7.2 and 8.8 minutes, respectively. The overall agreement rate for diagnostic visualization of the different brain structures between the two examiners was 89.9%, with a kappa coefficient of 0.5 (P < 0.001). In experienced hands, offline analysis of 3D brain volumes is a reproducible modality that can identify all structures necessary to complete both a basic and a detailed second-trimester fetal neurosonogram. Copyright 2010 ISUOG. Published by John Wiley & Sons, Ltd.

Definitive Mineralogical Analysis of Mars Analog Rocks Using the CheMin XRD/XRF Instrument

NASA Technical Reports Server (NTRS)

Blake, D. F.; Sarrazin, P.; Bish, D. L.; Feldman, S.; Chipera, S. J.; Vaniman, D. T.; Collins, S.

2004-01-01

Mineral identification is a critical component of Mars Astrobiological missions. Chemical or elemental data alone are not definitive because a single elemental or chemical composition or even a single bonding type can represent a range of substances or mineral assemblages. Minerals are defined as unique structural and compositional phases that occur naturally. There are about 15,000 minerals that have been described on Earth, all uniquely identifiable via diffraction methods. There are likely many minerals yet undiscovered on Earth, and likewise on Mars. If an unknown phase is identified on Mars, it can be fully characterized by structural (X-ray Diffraction, XRD) and elemental analysis (X-ray Fluorescence, XRF) without recourse to other data because XRD relies on the principles of atomic arrangement for its determinations. XRD is the principal means of identification and characterization of minerals on Earth.

A STUDY OF THE EFFECTS OF PARENTAL AWARENESS AND EXPERIENCE ON DRINKING WATER POLICIES IN ELEMENTARY SCHOOLS

NASA Astrophysics Data System (ADS)

Yamamura, Sombo; Ohnuki, Maromi; Nagaoka, Hiroshi

Recently increased number of elementary school pupils brings drinks from home for their hydration at school and this phenomenon indicates the change of the role of water supply at schools. In order to investigate the potential causes and the structure of the problem, an online survey targeting mothers of grade-schoolers was carried out, taking account of psychological factors of mothers as well as their decision making process. In the questionnaire preparation, latent variables and observable variables were assumed. The identified results include: difference exists on people's choice of drinking water; more parents in western Japan wish pupils bring drinks and some parents in eastern Japan wish the same. Covariance structure analysis identified a causalmodel; in which parents' frustration to schools associated with decreased reliability to tap water cause parents' advice to pupils take drink from home. Policy makers are expected to make the most of the result of analysis.

Basic research on design analysis methods for rotorcraft vibrations

NASA Technical Reports Server (NTRS)

Hanagud, S.

1991-01-01

The objective of the present work was to develop a method for identifying physically plausible finite element system models of airframe structures from test data. The assumed models were based on linear elastic behavior with general (nonproportional) damping. Physical plausibility of the identified system matrices was insured by restricting the identification process to designated physical parameters only and not simply to the elements of the system matrices themselves. For example, in a large finite element model the identified parameters might be restricted to the moduli for each of the different materials used in the structure. In the case of damping, a restricted set of damping values might be assigned to finite elements based on the material type and on the fabrication processes used. In this case, different damping values might be associated with riveted, bolted and bonded elements. The method itself is developed first, and several approaches are outlined for computing the identified parameter values. The method is applied first to a simple structure for which the 'measured' response is actually synthesized from an assumed model. Both stiffness and damping parameter values are accurately identified. The true test, however, is the application to a full-scale airframe structure. In this case, a NASTRAN model and actual measured modal parameters formed the basis for the identification of a restricted set of physically plausible stiffness and damping parameters.

A Persian version of the parental bonding instrument: factor structure and psychometric properties.

PubMed

Behzadi, Behnaz; Parker, Gordon

2015-02-28

The Parental Bonding Instrument (PBI) is a widely used self-report measure for quantifying key parenting styles as perceived by the child during its first 16 years. While its development study identified two key parental dimensions, subsequent studies have variably confirmed those two or argued for one or more additional parental constructs. We developed a Persian translation of the PBI and administered it to a sample of 340 high school students. The construct validity of the Persian PBI was examined by Exploratory Factor Analysis while Confirmatory Factor Analysis was used to identify the most adequate model. Analyses of the Persian PBI favored a four-factor model for both parental forms. The Persian PBI has a factorial structure consistent with constructs identified in western cultures, as well as high internal consistency and test-retest reliability. Multivariate analyses indicated significant differences between boys and girls across some factors. The PBI appears an acceptable and appropriate measure for quantifying parent-child bonding in Iranian samples. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Potential Alternatives Report for Validation of Alternative Low-Emission Surface PreparationlDepainting Technologies for Structural Steel

NASA Technical Reports Server (NTRS)

Lewis, Pattie

2006-01-01

For this project, particulates and solvents used during the depainting process of steel structures were the identified hazardous material (HazMat) targeted for elimination or reduction. This Potential Alternatives Report (PAR) provides technical analyses of identified alternatives to the current coating removal processes, criteria used to select alternatives for further analysis, and a list of those alternatives recommended for testing. The initial coating removal alternatives list was compiled using literature searches and center participant recommendations. The involved project participants initially considered fifteen (15) alternatives. In late 2004, stakeholders down-selected the list and identified specific processes as potential alternatives to the current depainting methods. The selected alternatives were: 1. Plastic Blast Media 2. Hard Abrasive Media 3. Sponge Blast Media 4. Mechanical Removal with Vacuum Attachment 5. Liquid Nitrogen 6. Laser Coating Removal Available information about these processes was used to analyze the technical merits and the potential environmental, safety, and occupational health (ESOH) impacts of these methods. A preliminary cost benefit analysis will be performed to determine if implementation of alternative technologies is economically justified. NASA AP2