Elements of Regolith Simulant's Cost Structure

NASA Technical Reports Server (NTRS)

Rickman, Douglas L.

2009-01-01

The cost of lunar regolith simulants is much higher than many users anticipate. After all, it is nothing more than broken rock. This class will discuss the elements which make up the cost structure for simulants. It will also consider which elements can be avoided under certain circumstances and which elements might be altered by the application of additional research and development.

Analysis of random structure-acoustic interaction problems using coupled boundary element and finite element methods

NASA Technical Reports Server (NTRS)

Mei, Chuh; Pates, Carl S., III

1994-01-01

A coupled boundary element (BEM)-finite element (FEM) approach is presented to accurately model structure-acoustic interaction systems. The boundary element method is first applied to interior, two and three-dimensional acoustic domains with complex geometry configurations. Boundary element results are very accurate when compared with limited exact solutions. Structure-interaction problems are then analyzed with the coupled FEM-BEM method, where the finite element method models the structure and the boundary element method models the interior acoustic domain. The coupled analysis is compared with exact and experimental results for a simplistic model. Composite panels are analyzed and compared with isotropic results. The coupled method is then extended for random excitation. Random excitation results are compared with uncoupled results for isotropic and composite panels.

Finite Element Model Development For Aircraft Fuselage Structures

NASA Technical Reports Server (NTRS)

Buehrle, Ralph D.; Fleming, Gary A.; Pappa, Richard S.; Grosveld, Ferdinand W.

2000-01-01

The ability to extend the valid frequency range for finite element based structural dynamic predictions using detailed models of the structural components and attachment interfaces is examined for several stiffened aircraft fuselage structures. This extended dynamic prediction capability is needed for the integration of mid-frequency noise control technology. Beam, plate and solid element models of the stiffener components are evaluated. Attachment models between the stiffener and panel skin range from a line along the rivets of the physical structure to a constraint over the entire contact surface. The finite element models are validated using experimental modal analysis results.

Using support vector machines to improve elemental ion identification in macromolecular crystal structures

DOE PAGES

Morshed, Nader; Echols, Nathaniel; Adams, Paul D.

2015-04-25

In the process of macromolecular model building, crystallographers must examine electron density for isolated atoms and differentiate sites containing structured solvent molecules from those containing elemental ions. This task requires specific knowledge of metal-binding chemistry and scattering properties and is prone to error. A method has previously been described to identify ions based on manually chosen criteria for a number of elements. Here, the use of support vector machines (SVMs) to automatically classify isolated atoms as either solvent or one of various ions is described. Two data sets of protein crystal structures, one containing manually curated structures deposited with anomalousmore » diffraction data and another with automatically filtered, high-resolution structures, were constructed. On the manually curated data set, an SVM classifier was able to distinguish calcium from manganese, zinc, iron and nickel, as well as all five of these ions from water molecules, with a high degree of accuracy. Additionally, SVMs trained on the automatically curated set of high-resolution structures were able to successfully classify most common elemental ions in an independent validation test set. This method is readily extensible to other elemental ions and can also be used in conjunction with previous methods based on a priori expectations of the chemical environment and X-ray scattering.« less

Open-Section Composite Structural Elements

NASA Technical Reports Server (NTRS)

Loftin, T. A.; Smith, C. A.; Raheb, S. J.; Nowitzky, A. M.

1991-01-01

Report describes investigation of manufacture and mechanical properties of graphite-fiber/aluminum-matrix open-section structural elements; e.g., channels and angle bars. Conducted with view toward using such elements to build lightweight, thermally stable truss structures in outer space. Other applications transport to, and assembly at, remote or otherwise uninviting locations. Advantages include shapes permitting high packing density during shipment, convenient paths for routing tubes, hoses, and cables; accessibility of both inner and outer surfaces for repair; and ease of attachment of additional hardware. Easier and require less equipment to fabricate, and more amenable to automated fabrication and assembly at remote site. Disadvantages, not as resistant to some kinds of deformation under load.

A quantitative metric to identify critical elements within seafood supply networks.

PubMed

Plagányi, Éva E; van Putten, Ingrid; Thébaud, Olivier; Hobday, Alistair J; Innes, James; Lim-Camacho, Lilly; Norman-López, Ana; Bustamante, Rodrigo H; Farmery, Anna; Fleming, Aysha; Frusher, Stewart; Green, Bridget; Hoshino, Eriko; Jennings, Sarah; Pecl, Gretta; Pascoe, Sean; Schrobback, Peggy; Thomas, Linda

2014-01-01

A theoretical basis is required for comparing key features and critical elements in wild fisheries and aquaculture supply chains under a changing climate. Here we develop a new quantitative metric that is analogous to indices used to analyse food-webs and identify key species. The Supply Chain Index (SCI) identifies critical elements as those elements with large throughput rates, as well as greater connectivity. The sum of the scores for a supply chain provides a single metric that roughly captures both the resilience and connectedness of a supply chain. Standardised scores can facilitate cross-comparisons both under current conditions as well as under a changing climate. Identification of key elements along the supply chain may assist in informing adaptation strategies to reduce anticipated future risks posed by climate change. The SCI also provides information on the relative stability of different supply chains based on whether there is a fairly even spread in the individual scores of the top few key elements, compared with a more critical dependence on a few key individual supply chain elements. We use as a case study the Australian southern rock lobster Jasus edwardsii fishery, which is challenged by a number of climate change drivers such as impacts on recruitment and growth due to changes in large-scale and local oceanographic features. The SCI identifies airports, processors and Chinese consumers as the key elements in the lobster supply chain that merit attention to enhance stability and potentially enable growth. We also apply the index to an additional four real-world Australian commercial fishery and two aquaculture industry supply chains to highlight the utility of a systematic method for describing supply chains. Overall, our simple methodological approach to empirically-based supply chain research provides an objective method for comparing the resilience of supply chains and highlighting components that may be critical.

A Quantitative Metric to Identify Critical Elements within Seafood Supply Networks

PubMed Central

Plagányi, Éva E.; van Putten, Ingrid; Thébaud, Olivier; Hobday, Alistair J.; Innes, James; Lim-Camacho, Lilly; Norman-López, Ana; Bustamante, Rodrigo H.; Farmery, Anna; Fleming, Aysha; Frusher, Stewart; Green, Bridget; Hoshino, Eriko; Jennings, Sarah; Pecl, Gretta; Pascoe, Sean; Schrobback, Peggy; Thomas, Linda

2014-01-01

A theoretical basis is required for comparing key features and critical elements in wild fisheries and aquaculture supply chains under a changing climate. Here we develop a new quantitative metric that is analogous to indices used to analyse food-webs and identify key species. The Supply Chain Index (SCI) identifies critical elements as those elements with large throughput rates, as well as greater connectivity. The sum of the scores for a supply chain provides a single metric that roughly captures both the resilience and connectedness of a supply chain. Standardised scores can facilitate cross-comparisons both under current conditions as well as under a changing climate. Identification of key elements along the supply chain may assist in informing adaptation strategies to reduce anticipated future risks posed by climate change. The SCI also provides information on the relative stability of different supply chains based on whether there is a fairly even spread in the individual scores of the top few key elements, compared with a more critical dependence on a few key individual supply chain elements. We use as a case study the Australian southern rock lobster Jasus edwardsii fishery, which is challenged by a number of climate change drivers such as impacts on recruitment and growth due to changes in large-scale and local oceanographic features. The SCI identifies airports, processors and Chinese consumers as the key elements in the lobster supply chain that merit attention to enhance stability and potentially enable growth. We also apply the index to an additional four real-world Australian commercial fishery and two aquaculture industry supply chains to highlight the utility of a systematic method for describing supply chains. Overall, our simple methodological approach to empirically-based supply chain research provides an objective method for comparing the resilience of supply chains and highlighting components that may be critical. PMID:24633147

Structural Truss Elements and Forces

ERIC Educational Resources Information Center

Troyer, Steve; Griffis, Kurt; Shackelford, Ray

2005-01-01

In the field of construction, most structures are supported by several groups of truss systems working together synergistically. A "truss" is a group of centered and balanced elements combined to carry a common load (Warner, 2003). Trusses provide strength against loads and forces within a structure. Though a complex field of study, structural…

Diversity and structure of PIF/Harbinger-like elements in the genome of Medicago truncatula

PubMed Central

Grzebelus, Dariusz; Lasota, Slawomir; Gambin, Tomasz; Kucherov, Gregory; Gambin, Anna

2007-01-01

Background Transposable elements constitute a significant fraction of plant genomes. The PIF/Harbinger superfamily includes DNA transposons (class II elements) carrying terminal inverted repeats and producing a 3 bp target site duplication upon insertion. The presence of an ORF coding for the DDE/DDD transposase, required for transposition, is characteristic for the autonomous PIF/Harbinger-like elements. Based on the above features, PIF/Harbinger-like elements were identified in several plant genomes and divided into several evolutionary lineages. Availability of a significant portion of Medicago truncatula genomic sequence allowed for mining PIF/Harbinger-like elements, starting from a single previously described element MtMaster. Results Twenty two putative autonomous, i.e. carrying an ORF coding for TPase and complete terminal inverted repeats, and 67 non-autonomous PIF/Harbinger-like elements were found in the genome of M. truncatula. They were divided into five families, MtPH-A5, MtPH-A6, MtPH-D,MtPH-E, and MtPH-M, corresponding to three previously identified and two new lineages. The largest families, MtPH-A6 and MtPH-M were further divided into four and three subfamilies, respectively. Non-autonomous elements were usually direct deletion derivatives of the putative autonomous element, however other types of rearrangements, including inversions and nested insertions were also observed. An interesting structural characteristic – the presence of 60 bp tandem repeats – was observed in a group of elements of subfamily MtPH-A6-4. Some families could be related to miniature inverted repeat elements (MITEs). The presence of empty loci (RESites), paralogous to those flanking the identified transposable elements, both autonomous and non-autonomous, as well as the presence of transposon insertion related size polymorphisms, confirmed that some of the mined elements were capable for transposition. Conclusion The population of PIF/Harbinger-like elements in the

Potential and Limitations of the Modal Characterization of a Spacecraft Bus Structure by Means of Active Structure Elements

NASA Technical Reports Server (NTRS)

Grillenbeck, Anton M.; Dillinger, Stephan A.; Elliott, Kenny B.

1998-01-01

Theoretical and experimental studies have been performed to investigate the potential and limitations of the modal characterization of a typical spacecraft bus structure by means of active structure elements. The aim of these studies has been test and advance tools for performing an accurate on-orbit modal identification which may be characterized by the availability of a generally very limited test instrumentation, autonomous excitation capabilities by active structure elements and a zero-g environment. The NASA LARC CSI Evolutionary Testbed provided an excellent object for the experimental part of this study program. The main subjects of investigation were: (1) the selection of optimum excitation and measurement to unambiguously identify modes of interest; (2) the applicability of different types of excitation means with focus on active structure elements; and (3) the assessment of the modal identification potential of different types of excitation functions and modal analysis tools. Conventional as well as dedicated modal analysis tools were applied to determine modal parameters and mode shapes. The results will be presented and discussed based on orthogonality checks as well as on suitable indicators for the quality of the acquired modes with respect to modal purity. In particular, the suitability for modal analysis of the acquired frequency response functions as obtained by excitation with active structure elements will be demonstrated with the help of reciprocity checks. Finally, the results will be summarized in a procedure to perform an on-orbit modal identification, including an indication of limitation to be observed.

Identifying the Essential Elements of Effective Science Communication: What Do the Experts Say?

ERIC Educational Resources Information Center

Bray, Belinda; France, Bev; Gilbert, John K.

2012-01-01

Experts in science communication were asked to identify the essential elements of a science communication course for post-graduate students. A Delphi methodology provided a framework for a research design that accessed their opinions and allowed them to contribute to, reflect on and identify 10 essential elements. There was a high level of…

Finite element structural redesign by large admissible perturbations

NASA Technical Reports Server (NTRS)

Bernitsas, Michael M.; Beyko, E.; Rim, C. W.; Alzahabi, B.

1991-01-01

In structural redesign, two structural states are involved; the baseline (known) State S1 with unacceptable performance, and the objective (unknown) State S2 with given performance specifications. The difference between the two states in performance and design variables may be as high as 100 percent or more depending on the scale of the structure. A Perturbation Approach to Redesign (PAR) is presented to relate any two structural states S1 and S2 that are modeled by the same finite element model and represented by different values of the design variables. General perturbation equations are derived expressing implicitly the natural frequencies, dynamic modes, static deflections, static stresses, Euler buckling loads, and buckling modes of the objective S2 in terms of its performance specifications, and S1 data and Finite Element Analysis (FEA) results. Large Admissible Perturbation (LEAP) algorithms are implemented in code RESTRUCT to define the objective S2 incrementally without trial and error by postprocessing FEA results of S1 with no additional FEAs. Systematic numerical applications in redesign of a 10 element 48 degree of freedom (dof) beam, a 104 element 192 dof offshore tower, a 64 element 216 dof plate, and a 144 element 896 dof cylindrical shell show the accuracy, efficiency, and potential of PAR to find an objective state that may differ 100 percent from the baseline design.

47 CFR 51.509 - Rate structure standards for specific elements.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 47 Telecommunication 3 2014-10-01 2014-10-01 false Rate structure standards for specific elements... SERVICES (CONTINUED) INTERCONNECTION Pricing of Elements § 51.509 Rate structure standards for specific elements. In addition to the general rules set forth in § 51.507, rates for specific elements shall comply...

47 CFR 51.509 - Rate structure standards for specific elements.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 47 Telecommunication 3 2012-10-01 2012-10-01 false Rate structure standards for specific elements... SERVICES (CONTINUED) INTERCONNECTION Pricing of Elements § 51.509 Rate structure standards for specific elements. In addition to the general rules set forth in § 51.507, rates for specific elements shall comply...

47 CFR 51.509 - Rate structure standards for specific elements.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 47 Telecommunication 3 2010-10-01 2010-10-01 false Rate structure standards for specific elements... SERVICES (CONTINUED) INTERCONNECTION Pricing of Elements § 51.509 Rate structure standards for specific elements. In addition to the general rules set forth in § 51.507, rates for specific elements shall comply...

47 CFR 51.509 - Rate structure standards for specific elements.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 47 Telecommunication 3 2011-10-01 2011-10-01 false Rate structure standards for specific elements... SERVICES (CONTINUED) INTERCONNECTION Pricing of Elements § 51.509 Rate structure standards for specific elements. In addition to the general rules set forth in § 51.507, rates for specific elements shall comply...

47 CFR 51.509 - Rate structure standards for specific elements.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 47 Telecommunication 3 2013-10-01 2013-10-01 false Rate structure standards for specific elements... SERVICES (CONTINUED) INTERCONNECTION Pricing of Elements § 51.509 Rate structure standards for specific elements. In addition to the general rules set forth in § 51.507, rates for specific elements shall comply...

Analysis of secondary structural elements in human microRNA hairpin precursors.

PubMed

Liu, Biao; Childs-Disney, Jessica L; Znosko, Brent M; Wang, Dan; Fallahi, Mohammad; Gallo, Steven M; Disney, Matthew D

2016-03-01

MicroRNAs (miRNAs) regulate gene expression by targeting complementary mRNAs for destruction or translational repression. Aberrant expression of miRNAs has been associated with various diseases including cancer, thus making them interesting therapeutic targets. The composite of secondary structural elements that comprise miRNAs could aid the design of small molecules that modulate their function. We analyzed the secondary structural elements, or motifs, present in all human miRNA hairpin precursors and compared them to highly expressed human RNAs with known structures and other RNAs from various organisms. Amongst human miRNAs, there are 3808 are unique motifs, many residing in processing sites. Further, we identified motifs in miRNAs that are not present in other highly expressed human RNAs, desirable targets for small molecules. MiRNA motifs were incorporated into a searchable database that is freely available. We also analyzed the most frequently occurring bulges and internal loops for each RNA class and found that the smallest loops possible prevail. However, the distribution of loops and the preferred closing base pairs were unique to each class. Collectively, we have completed a broad survey of motifs found in human miRNA precursors, highly expressed human RNAs, and RNAs from other organisms. Interestingly, unique motifs were identified in human miRNA processing sites, binding to which could inhibit miRNA maturation and hence function.

Modular structural elements in the replication origin region of Tetrahymena rDNA.

PubMed Central

Du, C; Sanzgiri, R P; Shaiu, W L; Choi, J K; Hou, Z; Benbow, R M; Dobbs, D L

1995-01-01

Computer analyses of the DNA replication origin region in the amplified rRNA genes of Tetrahymena thermophila identified a potential initiation zone in the 5'NTS [Dobbs, Shaiu and Benbow (1994), Nucleic Acids Res. 22, 2479-2489]. This region consists of a putative DNA unwinding element (DUE) aligned with predicted bent DNA segments, nuclear matrix or scaffold associated region (MAR/SAR) consensus sequences, and other common modular sequence elements previously shown to be clustered in eukaryotic chromosomal origin regions. In this study, two mung bean nuclease-hypersensitive sites in super-coiled plasmid DNA were localized within the major DUE-like element predicted by thermodynamic analyses. Three restriction fragments of the 5'NTS region predicted to contain bent DNA segments exhibited anomalous migration characteristic of bent DNA during electrophoresis on polyacrylamide gels. Restriction fragments containing the 5'NTS region bound Tetrahymena nuclear matrices in an in vitro binding assay, consistent with an association of the replication origin region with the nuclear matrix in vivo. The direct demonstration in a protozoan origin region of elements previously identified in Drosophila, chick and mammalian origin regions suggests that clusters of modular structural elements may be a conserved feature of eukaryotic chromosomal origins of replication. Images PMID:7784181

Compilation of mRNA Polyadenylation Signals in Arabidopsis Revealed a New Signal Element and Potential Secondary Structures1[w

PubMed Central

Loke, Johnny C.; Stahlberg, Eric A.; Strenski, David G.; Haas, Brian J.; Wood, Paul Chris; Li, Qingshun Quinn

2005-01-01

Using a novel program, SignalSleuth, and a database containing authenticated polyadenylation [poly(A)] sites, we analyzed the composition of mRNA poly(A) signals in Arabidopsis (Arabidopsis thaliana), and reevaluated previously described cis-elements within the 3′-untranslated (UTR) regions, including near upstream elements and far upstream elements. As predicted, there are absences of high-consensus signal patterns. The AAUAAA signal topped the near upstream elements patterns and was found within the predicted location to only approximately 10% of 3′-UTRs. More importantly, we identified a new set, named cleavage elements, of poly(A) signals flanking both sides of the cleavage site. These cis-elements were not previously revealed by conventional mutagenesis and are contemplated as a cluster of signals for cleavage site recognition. Moreover, a single-nucleotide profile scan on the 3′-UTR regions unveiled a distinct arrangement of alternate stretches of U and A nucleotides, which led to a prediction of the formation of secondary structures. Using an RNA secondary structure prediction program, mFold, we identified three main types of secondary structures on the sequences analyzed. Surprisingly, these observed secondary structures were all interrupted in previously constructed mutations in these regions. These results will enable us to revise the current model of plant poly(A) signals and to develop tools to predict 3′-ends for gene annotation. PMID:15965016

Detection of Earthquake-Induced Damage in a Framed Structure Using a Finite Element Model Updating Procedure

PubMed Central

Kim, Seung-Nam; Park, Taewon; Lee, Sang-Hyun

2014-01-01

Damage of a 5-story framed structure was identified from two types of measured data, which are frequency response functions (FRF) and natural frequencies, using a finite element (FE) model updating procedure. In this study, a procedure to determine the appropriate weightings for different groups of observations was proposed. In addition, a modified frame element which included rotational springs was used to construct the FE model for updating to represent concentrated damage at the member ends (a formulation for plastic hinges in framed structures subjected to strong earthquakes). The results of the model updating and subsequent damage detection when the rotational springs (RS model) were used were compared with those obtained using the conventional frame elements (FS model). Comparisons indicated that the RS model gave more accurate results than the FS model. That is, the errors in the natural frequencies of the updated models were smaller, and the identified damage showed clearer distinctions between damaged and undamaged members and was more consistent with observed damage. PMID:24574888

Computational Approaches to Identify Promoters and cis-Regulatory Elements in Plant Genomes1

PubMed Central

Rombauts, Stephane; Florquin, Kobe; Lescot, Magali; Marchal, Kathleen; Rouzé, Pierre; Van de Peer, Yves

2003-01-01

The identification of promoters and their regulatory elements is one of the major challenges in bioinformatics and integrates comparative, structural, and functional genomics. Many different approaches have been developed to detect conserved motifs in a set of genes that are either coregulated or orthologous. However, although recent approaches seem promising, in general, unambiguous identification of regulatory elements is not straightforward. The delineation of promoters is even harder, due to its complex nature, and in silico promoter prediction is still in its infancy. Here, we review the different approaches that have been developed for identifying promoters and their regulatory elements. We discuss the detection of cis-acting regulatory elements using word-counting or probabilistic methods (so-called “search by signal” methods) and the delineation of promoters by considering both sequence content and structural features (“search by content” methods). As an example of search by content, we explored in greater detail the association of promoters with CpG islands. However, due to differences in sequence content, the parameters used to detect CpG islands in humans and other vertebrates cannot be used for plants. Therefore, a preliminary attempt was made to define parameters that could possibly define CpG and CpNpG islands in Arabidopsis, by exploring the compositional landscape around the transcriptional start site. To this end, a data set of more than 5,000 gene sequences was built, including the promoter region, the 5′-untranslated region, and the first introns and coding exons. Preliminary analysis shows that promoter location based on the detection of potential CpG/CpNpG islands in the Arabidopsis genome is not straightforward. Nevertheless, because the landscape of CpG/CpNpG islands differs considerably between promoters and introns on the one side and exons (whether coding or not) on the other, more sophisticated approaches can probably be

Method for analyzing soil structure according to the size of structural elements

NASA Astrophysics Data System (ADS)

Wieland, Ralf; Rogasik, Helmut

2015-02-01

The soil structure in situ is the result of cropping history and soil development over time. It can be assessed by the size distribution of soil structural elements such as air-filled macro-pores, aggregates and stones, which are responsible for important water and solute transport processes, gas exchange, and the stability of the soil against compacting and shearing forces exerted by agricultural machinery. A method was developed to detect structural elements of the soil in selected horizontal slices of soil core samples with different soil structures in order for them to be implemented accordingly. In the second step, a fitting tool (Eureqa) based on artificial programming was used to find a general function to describe ordered sets of detected structural elements. It was shown that all the samples obey a hyperbolic function: Y(k) = A /(B + k) , k ∈ { 0 , 1 , 2 , … }. This general behavior can be used to develop a classification method based on parameters {A and B}. An open source software program in Python was developed, which can be downloaded together with a selection of soil samples.

The node-weighted Steiner tree approach to identify elements of cancer-related signaling pathways.

PubMed

Sun, Yahui; Ma, Chenkai; Halgamuge, Saman

2017-12-28

Cancer constitutes a momentous health burden in our society. Critical information on cancer may be hidden in its signaling pathways. However, even though a large amount of money has been spent on cancer research, some critical information on cancer-related signaling pathways still remains elusive. Hence, new works towards a complete understanding of cancer-related signaling pathways will greatly benefit the prevention, diagnosis, and treatment of cancer. We propose the node-weighted Steiner tree approach to identify important elements of cancer-related signaling pathways at the level of proteins. This new approach has advantages over previous approaches since it is fast in processing large protein-protein interaction networks. We apply this new approach to identify important elements of two well-known cancer-related signaling pathways: PI3K/Akt and MAPK. First, we generate a node-weighted protein-protein interaction network using protein and signaling pathway data. Second, we modify and use two preprocessing techniques and a state-of-the-art Steiner tree algorithm to identify a subnetwork in the generated network. Third, we propose two new metrics to select important elements from this subnetwork. On a commonly used personal computer, this new approach takes less than 2 s to identify the important elements of PI3K/Akt and MAPK signaling pathways in a large node-weighted protein-protein interaction network with 16,843 vertices and 1,736,922 edges. We further analyze and demonstrate the significance of these identified elements to cancer signal transduction by exploring previously reported experimental evidences. Our node-weighted Steiner tree approach is shown to be both fast and effective to identify important elements of cancer-related signaling pathways. Furthermore, it may provide new perspectives into the identification of signaling pathways for other human diseases.

Insights into Structural and Mechanistic Features of Viral IRES Elements

PubMed Central

Martinez-Salas, Encarnacion; Francisco-Velilla, Rosario; Fernandez-Chamorro, Javier; Embarek, Azman M.

2018-01-01

Internal ribosome entry site (IRES) elements are cis-acting RNA regions that promote internal initiation of protein synthesis using cap-independent mechanisms. However, distinct types of IRES elements present in the genome of various RNA viruses perform the same function despite lacking conservation of sequence and secondary RNA structure. Likewise, IRES elements differ in host factor requirement to recruit the ribosomal subunits. In spite of this diversity, evolutionarily conserved motifs in each family of RNA viruses preserve sequences impacting on RNA structure and RNA–protein interactions important for IRES activity. Indeed, IRES elements adopting remarkable different structural organizations contain RNA structural motifs that play an essential role in recruiting ribosomes, initiation factors and/or RNA-binding proteins using different mechanisms. Therefore, given that a universal IRES motif remains elusive, it is critical to understand how diverse structural motifs deliver functions relevant for IRES activity. This will be useful for understanding the molecular mechanisms beyond cap-independent translation, as well as the evolutionary history of these regulatory elements. Moreover, it could improve the accuracy to predict IRES-like motifs hidden in genome sequences. This review summarizes recent advances on the diversity and biological relevance of RNA structural motifs for viral IRES elements. PMID:29354113

An interactive graphics system to facilitate finite element structural analysis

NASA Technical Reports Server (NTRS)

Burk, R. C.; Held, F. H.

1973-01-01

The characteristics of an interactive graphics systems to facilitate the finite element method of structural analysis are described. The finite element model analysis consists of three phases: (1) preprocessing (model generation), (2) problem solution, and (3) postprocessing (interpretation of results). The advantages of interactive graphics to finite element structural analysis are defined.

SPAR data set contents. [finite element structural analysis system

NASA Technical Reports Server (NTRS)

Cunningham, S. W.

1981-01-01

The contents of the stored data sets of the SPAR (space processing applications rocket) finite element structural analysis system are documented. The data generated by each of the system's processors are stored in a data file organized as a library. Each data set, containing a two-dimensional table or matrix, is identified by a four-word name listed in a table of contents. The creating SPAR processor, number of rows and columns, and definitions of each of the data items are listed for each data set. An example SPAR problem using these data sets is also presented.

Elemental sulfur identified in urine of cheetah, Acinonyx jubatus.

PubMed

Burger, Ben V; Visser, Runine; Moses, Alvira; Le Roux, Maritha

2006-06-01

The urine of the cheetah, Acinonyx jubatus, is almost odorless, and probably for this reason, it has not attracted much attention from scientists. Using gas chromatography-mass spectrometry, we identified 27 and 37 constituents in the headspace vapor of the urine of male and female cheetah, respectively. These constituents, composed of hydrocarbons, short-chain ethers, aldehydes, saturated and unsaturated cyclic and acyclic ketones, 2-acetylfuran, dimethyl disulfide, dimethyl sulfone, phenol, myristic acid (tetradecanoic acid), urea, and elemental sulfur, are all present in the headspace vapor in very small quantities; dimethyl disulfide is present in such a low concentration that it cannot be detected by the human nose. This is only the second example of elemental sulfur being secreted or excreted by an animal. It is hypothesized that the conversion of sulfur-containing compounds in the cheetah's diet to elemental sulfur and to practically odorless dimethyl sulfone enables this carnivore to operate as if "invisible" to the olfactory world of its predators as well as its prey, which would increase its chances of survival.

Structural Elements Regulating AAA+ Protein Quality Control Machines.

PubMed

Chang, Chiung-Wen; Lee, Sukyeong; Tsai, Francis T F

2017-01-01

Members of the ATPases Associated with various cellular Activities (AAA+) superfamily participate in essential and diverse cellular pathways in all kingdoms of life by harnessing the energy of ATP binding and hydrolysis to drive their biological functions. Although most AAA+ proteins share a ring-shaped architecture, AAA+ proteins have evolved distinct structural elements that are fine-tuned to their specific functions. A central question in the field is how ATP binding and hydrolysis are coupled to substrate translocation through the central channel of ring-forming AAA+ proteins. In this mini-review, we will discuss structural elements present in AAA+ proteins involved in protein quality control, drawing similarities to their known role in substrate interaction by AAA+ proteins involved in DNA translocation. Elements to be discussed include the pore loop-1, the Inter-Subunit Signaling (ISS) motif, and the Pre-Sensor I insert (PS-I) motif. Lastly, we will summarize our current understanding on the inter-relationship of those structural elements and propose a model how ATP binding and hydrolysis might be coupled to polypeptide translocation in protein quality control machines.

Identification, display, and use of symmetry elements in atomic and electronic structure models.

PubMed

Khosrovani, N; Kung, P W; Freeman, C M; Gorman, A M; Kölmel, C M; Levine, S M; Newsam, J M

1999-01-01

Crystallographic symmetry plays an important role in structure determination from diffraction or scattering data, in spectroscopy and in simulations. It is convenient and insightful to integrate the display and use of such symmetry data with data analysis and modeling methods. We outline the integration of a suite of crystallographic algorithms, closely coupled with interactive graphical displays. These include techniques for identifying the unit cell of a solid, for automatically determining space and point group symmetries, for generalized displays of symmetry elements overlaid on structural models, and for construction, editing, and transformation of models subject to symmetry constraints. In addition, electron densities derived from periodic density functional calculations can be symmetrized and displayed with the corresponding symmetry elements. Applications of these various capabilities in crystallographic research are illustrated by topical examples.

Manufacturing processes for fabricating graphite/PMR 15 polyimide structural elements

NASA Technical Reports Server (NTRS)

Sheppard, C. H.; Hoggatt, J. T.; Symonds, W. A.

1979-01-01

Investigations were conducted to obtain commercially available graphite/PMR-15 polyimide prepreg, develop an autoclave manufacturing process, and demonstrate the process by manufacturing structural elements. Controls were established on polymer, prepreg, composite fabrication, and quality assurance, Successful material quality control and processes were demonstrated by fabricating major structural elements including flat laminates, hat sections, I beam sections, honeycomb sandwich structures, and molded graphite reinforced fittings. Successful fabrication of structural elements and simulated section of the space shuttle aft body flap shows that the graphite/PMR-15 polyimide system and the developed processes are ready for further evaluation in flight test hardware.

Street as Sustainable City Structural Element

NASA Astrophysics Data System (ADS)

Leyzerova, A. V.; Bagina, E. J.

2017-11-01

Sustainability in architecture is nowadays of particular significance in the course of globalization and information density. The technospehere spontaneous development poses a threat to the sustainability of traditional urban forms where a street is one of the essential forming elements in the urban structure. The article proposes to consider formally compositional street features in relation to one of the traditional streets in the historic center of Ekaterinburg. The study examines the street-planning structure, the development of its skeleton elements, silhouette and fabric elevation characteristics as well as the scale characteristics and visual complexity of objects. The study provided architectural and artistic aspects of street sustainability, and limits of the appropriate scale and composition consistency under which the compatibility of alternative compositional forms existing at different times is possible.

Finite Element Model Development and Validation for Aircraft Fuselage Structures

NASA Technical Reports Server (NTRS)

Buehrle, Ralph D.; Fleming, Gary A.; Pappa, Richard S.; Grosveld, Ferdinand W.

2000-01-01

The ability to extend the valid frequency range for finite element based structural dynamic predictions using detailed models of the structural components and attachment interfaces is examined for several stiffened aircraft fuselage structures. This extended dynamic prediction capability is needed for the integration of mid-frequency noise control technology. Beam, plate and solid element models of the stiffener components are evaluated. Attachment models between the stiffener and panel skin range from a line along the rivets of the physical structure to a constraint over the entire contact surface. The finite element models are validated using experimental modal analysis results. The increased frequency range results in a corresponding increase in the number of modes, modal density and spatial resolution requirements. In this study, conventional modal tests using accelerometers are complemented with Scanning Laser Doppler Velocimetry and Electro-Optic Holography measurements to further resolve the spatial response characteristics. Whenever possible, component and subassembly modal tests are used to validate the finite element models at lower levels of assembly. Normal mode predictions for different finite element representations of components and assemblies are compared with experimental results to assess the most accurate techniques for modeling aircraft fuselage type structures.

Galerkin finite element scheme for magnetostrictive structures and composites

NASA Astrophysics Data System (ADS)

Kannan, Kidambi Srinivasan

The ever increasing-role of magnetostrictives in actuation and sensing applications is an indication of their importance in the emerging field of smart structures technology. As newer, and more complex, applications are developed, there is a growing need for a reliable computational tool that can effectively address the magneto-mechanical interactions and other nonlinearities in these materials and in structures incorporating them. This thesis presents a continuum level quasi-static, three-dimensional finite element computational scheme for modeling the nonlinear behavior of bulk magnetostrictive materials and particulate magnetostrictive composites. Models for magnetostriction must deal with two sources of nonlinearities-nonlinear body forces/moments in equilibrium equations governing magneto-mechanical interactions in deformable and magnetized bodies; and nonlinear coupled magneto-mechanical constitutive models for the material of interest. In the present work, classical differential formulations for nonlinear magneto-mechanical interactions are recast in integral form using the weighted-residual method. A discretized finite element form is obtained by applying the Galerkin technique. The finite element formulation is based upon three dimensional eight-noded (isoparametric) brick element interpolation functions and magnetostatic infinite elements at the boundary. Two alternative possibilities are explored for establishing the nonlinear incremental constitutive model-characterization in terms of magnetic field or in terms of magnetization. The former methodology is the one most commonly used in the literature. In this work, a detailed comparative study of both methodologies is carried out. The computational scheme is validated, qualitatively and quantitatively, against experimental measurements published in the literature on structures incorporating the magnetostrictive material Terfenol-D. The influence of nonlinear body forces and body moments of magnetic origin

Structural Elements Recognized by Abacavir-Induced T Cells.

PubMed

Yerly, Daniel; Pompeu, Yuri Andreiw; Schutte, Ryan J; Eriksson, Klara K; Strhyn, Anette; Bracey, Austin W; Buus, Soren; Ostrov, David A

2017-07-07

Adverse drug reactions are one of the leading causes of morbidity and mortality in health care worldwide. Human leukocyte antigen (HLA) alleles have been strongly associated with drug hypersensitivities, and the causative drugs have been shown to stimulate specific T cells at the sites of autoimmune destruction. The structural elements recognized by drug-specific T cell receptors (TCRs) in vivo are poorly defined. Drug-stimulated T cells express TCRs specific for peptide/HLA complexes, but the characteristics of peptides (sequence, or endogenous or exogenous origin) presented in the context of small molecule drugs are not well studied. Using HLA-B*57:01 mediated hypersensitivity to abacavir as a model system, this study examines structural similarities of HLA presented peptides recognized by drug-specific TCRs. Using the crystal structure of HLA-B*57:01 complexed with abacavir and an immunogenic self peptide, VTTDIQVKV SPT5a 976-984, peptide side chains exhibiting flexibility and solvent exposure were identified as potential drug-specific T cell recognition motifs. Viral sequences with structural motifs similar to the immunogenic self peptide were identified. Abacavir-specific T cell clones were used to determine if virus peptides presented in the context of abacavir stimulate T cell responsiveness. An abacavir-specific T cell clone was stimulated by VTQQAQVRL, corresponding to HSV1/2 230-238, in the context of HLA-B*57:01. These data suggest the T cell polyclonal response to abacavir consists of multiple subsets, including T cells that recognize self peptide/HLA-B*57:01 complexes and crossreact with viral peptide/HLA-B*57:01 complexes due to similarity in TCR contact residues.

Structural Elements Recognized by Abacavir-Induced T Cells

PubMed Central

Yerly, Daniel; Pompeu, Yuri Andreiw; Schutte, Ryan J.; Eriksson, Klara. K.; Strhyn, Anette; Bracey, Austin. W.; Buus, Soren; Ostrov, David A.

2017-01-01

Adverse drug reactions are one of the leading causes of morbidity and mortality in health care worldwide. Human leukocyte antigen (HLA) alleles have been strongly associated with drug hypersensitivities, and the causative drugs have been shown to stimulate specific T cells at the sites of autoimmune destruction. The structural elements recognized by drug-specific T cell receptors (TCRs) in vivo are poorly defined. Drug-stimulated T cells express TCRs specific for peptide/HLA complexes, but the characteristics of peptides (sequence, or endogenous or exogenous origin) presented in the context of small molecule drugs are not well studied. Using HLA-B*57:01 mediated hypersensitivity to abacavir as a model system, this study examines structural similarities of HLA presented peptides recognized by drug-specific TCRs. Using the crystal structure of HLA-B*57:01 complexed with abacavir and an immunogenic self peptide, VTTDIQVKV SPT5a 976–984, peptide side chains exhibiting flexibility and solvent exposure were identified as potential drug-specific T cell recognition motifs. Viral sequences with structural motifs similar to the immunogenic self peptide were identified. Abacavir-specific T cell clones were used to determine if virus peptides presented in the context of abacavir stimulate T cell responsiveness. An abacavir-specific T cell clone was stimulated by VTQQAQVRL, corresponding to HSV1/2 230–238, in the context of HLA-B*57:01. These data suggest the T cell polyclonal response to abacavir consists of multiple subsets, including T cells that recognize self peptide/HLA-B*57:01 complexes and crossreact with viral peptide/HLA-B*57:01 complexes due to similarity in TCR contact residues. PMID:28686208

Penalty-Based Finite Element Interface Technology for Analysis of Homogeneous and Composite Structures

NASA Technical Reports Server (NTRS)

Averill, Ronald C.

2002-01-01

An effective and robust interface element technology able to connect independently modeled finite element subdomains has been developed. This method is based on the use of penalty constraints and allows coupling of finite element models whose nodes do not coincide along their common interface. Additionally, the present formulation leads to a computational approach that is very efficient and completely compatible with existing commercial software. A significant effort has been directed toward identifying those model characteristics (element geometric properties, material properties, and loads) that most strongly affect the required penalty parameter, and subsequently to developing simple 'formulae' for automatically calculating the proper penalty parameter for each interface constraint. This task is especially critical in composite materials and structures, where adjacent sub-regions may be composed of significantly different materials or laminates. This approach has been validated by investigating a variety of two-dimensional problems, including composite laminates.

Integration of system identification and finite element modelling of nonlinear vibrating structures

NASA Astrophysics Data System (ADS)

Cooper, Samson B.; DiMaio, Dario; Ewins, David J.

2018-03-01

The Finite Element Method (FEM), Experimental modal analysis (EMA) and other linear analysis techniques have been established as reliable tools for the dynamic analysis of engineering structures. They are often used to provide solutions to small and large structures and other variety of cases in structural dynamics, even those exhibiting a certain degree of nonlinearity. Unfortunately, when the nonlinear effects are substantial or the accuracy of the predicted response is of vital importance, a linear finite element model will generally prove to be unsatisfactory. As a result, the validated linear FE model requires further enhancement so that it can represent and predict the nonlinear behaviour exhibited by the structure. In this paper, a pragmatic approach to integrating test-based system identification and FE modelling of a nonlinear structure is presented. This integration is based on three different phases: the first phase involves the derivation of an Underlying Linear Model (ULM) of the structure, the second phase includes experiment-based nonlinear identification using measured time series and the third phase covers augmenting the linear FE model and experimental validation of the nonlinear FE model. The proposed case study is demonstrated on a twin cantilever beam assembly coupled with a flexible arch shaped beam. In this case, polynomial-type nonlinearities are identified and validated with force-controlled stepped-sine test data at several excitation levels.

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.

Ionomic screening of field-grown soybeans identifies mutants with altered seed elemental composition

USDA-ARS?s Scientific Manuscript database

Soybean seeds contain high levels of mineral nutrients essential for human and animal nutrition. High throughput elemental profiling (ionomics) has identified mutants in model plant species grown in controlled environments. Here, we describe a method for identifying potential soybean ionomics mutant...

Electronic structures of elements according to ionization energies.

PubMed

Zadeh, Dariush H

2017-11-28

The electronic structures of elements in the periodic table were analyzed using available experimental ionization energies. Two new parameters were defined to carry out the study. The first parameter-apparent nuclear charge (ANC)-quantified the overall charge of the nucleus and inner electrons observed by an outer electron during the ionization process. This parameter was utilized to define a second parameter, which presented the shielding ability of an electron against the nuclear charge. This second parameter-electron shielding effect (ESE)-provided an insight into the electronic structure of atoms. This article avoids any sort of approximation, interpolation or extrapolation. First experimental ionization energies were used to obtain the two aforementioned parameters. The second parameter (ESE) was then graphed against the electron number of each element, and was used to read the corresponding electronic structure. The ESE showed spikes/peaks at the end of each electronic shell, providing insight into when an electronic shell closes and a new one starts. The electronic structures of elements in the periodic table were mapped using this methodology. These graphs did not show complete agreement with the previously known "Aufbau" filling rule. A new filling rule was suggested based on the present observations. Finally, a new way to organize elements in the periodic table is suggested. Two earlier topics of effective nuclear charge, and shielding factor were also briefly discussed and compared numerically to demonstrate the capability of the new approach.

Curved Thermopiezoelectric Shell Structures Modeled by Finite Element Analysis

NASA Technical Reports Server (NTRS)

Lee, Ho-Jun

2000-01-01

"Smart" structures composed of piezoelectric materials may significantly improve the performance of aeropropulsion systems through a variety of vibration, noise, and shape-control applications. The development of analytical models for piezoelectric smart structures is an ongoing, in-house activity at the NASA Glenn Research Center at Lewis Field focused toward the experimental characterization of these materials. Research efforts have been directed toward developing analytical models that account for the coupled mechanical, electrical, and thermal response of piezoelectric composite materials. Current work revolves around implementing thermal effects into a curvilinear-shell finite element code. This enhances capabilities to analyze curved structures and to account for coupling effects arising from thermal effects and the curved geometry. The current analytical model implements a unique mixed multi-field laminate theory to improve computational efficiency without sacrificing accuracy. The mechanics can model both the sensory and active behavior of piezoelectric composite shell structures. Finite element equations are being implemented for an eight-node curvilinear shell element, and numerical studies are being conducted to demonstrate capabilities to model the response of curved piezoelectric composite structures (see the figure).

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.

An ant colony optimization based algorithm for identifying gene regulatory elements.

PubMed

Liu, Wei; Chen, Hanwu; Chen, Ling

2013-08-01

It is one of the most important tasks in bioinformatics to identify the regulatory elements in gene sequences. Most of the existing algorithms for identifying regulatory elements are inclined to converge into a local optimum, and have high time complexity. Ant Colony Optimization (ACO) is a meta-heuristic method based on swarm intelligence and is derived from a model inspired by the collective foraging behavior of real ants. Taking advantage of the ACO in traits such as self-organization and robustness, this paper designs and implements an ACO based algorithm named ACRI (ant-colony-regulatory-identification) for identifying all possible binding sites of transcription factor from the upstream of co-expressed genes. To accelerate the ants' searching process, a strategy of local optimization is presented to adjust the ants' start positions on the searched sequences. By exploiting the powerful optimization ability of ACO, the algorithm ACRI can not only improve precision of the results, but also achieve a very high speed. Experimental results on real world datasets show that ACRI can outperform other traditional algorithms in the respects of speed and quality of solutions. Copyright © 2013 Elsevier Ltd. All rights reserved.

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

PubMed Central

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

2016-01-01

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

Identifying structural variation in haploid microbial genomes from short-read resequencing data using breseq.

PubMed

Barrick, Jeffrey E; Colburn, Geoffrey; Deatherage, Daniel E; Traverse, Charles C; Strand, Matthew D; Borges, Jordan J; Knoester, David B; Reba, Aaron; Meyer, Austin G

2014-11-29

Mutations that alter chromosomal structure play critical roles in evolution and disease, including in the origin of new lifestyles and pathogenic traits in microbes. Large-scale rearrangements in genomes are often mediated by recombination events involving new or existing copies of mobile genetic elements, recently duplicated genes, or other repetitive sequences. Most current software programs for predicting structural variation from short-read DNA resequencing data are intended primarily for use on human genomes. They typically disregard information in reads mapping to repeat sequences, and significant post-processing and manual examination of their output is often required to rule out false-positive predictions and precisely describe mutational events. We have implemented an algorithm for identifying structural variation from DNA resequencing data as part of the breseq computational pipeline for predicting mutations in haploid microbial genomes. Our method evaluates the support for new sequence junctions present in a clonal sample from split-read alignments to a reference genome, including matches to repeat sequences. Then, it uses a statistical model of read coverage evenness to accept or reject these predictions. Finally, breseq combines predictions of new junctions and deleted chromosomal regions to output biologically relevant descriptions of mutations and their effects on genes. We demonstrate the performance of breseq on simulated Escherichia coli genomes with deletions generating unique breakpoint sequences, new insertions of mobile genetic elements, and deletions mediated by mobile elements. Then, we reanalyze data from an E. coli K-12 mutation accumulation evolution experiment in which structural variation was not previously identified. Transposon insertions and large-scale chromosomal changes detected by breseq account for ~25% of spontaneous mutations in this strain. In all cases, we find that breseq is able to reliably predict structural variation

An efficient structural finite element for inextensible flexible risers

NASA Astrophysics Data System (ADS)

Papathanasiou, T. K.; Markolefas, S.; Khazaeinejad, P.; Bahai, H.

2017-12-01

A core part of all numerical models used for flexible riser analysis is the structural component representing the main body of the riser as a slender beam. Loads acting on this structural element are self-weight, buoyant and hydrodynamic forces, internal pressure and others. A structural finite element for an inextensible riser with a point-wise enforcement of the inextensibility constrain is presented. In particular, the inextensibility constraint is applied only at the nodes of the meshed arc length parameter. Among the virtues of the proposed approach is the flexibility in the application of boundary conditions and the easy incorporation of dissipative forces. Several attributes of the proposed finite element scheme are analysed and computation times for the solution of some simplified examples are discussed. Future developments aim at the appropriate implementation of material and geometric parameters for the beam model, i.e. flexural and torsional rigidity.

The KnowRISK project - Know your city, Reduce seISmic risK through non-structural elements

NASA Astrophysics Data System (ADS)

Sousa Oliveria, Carlos; Amaral Ferreira, Mónica; Lopez, Mário; Sousa Silva, Delta; Musacchio, Gemma; Rupakhety, Rajesh; Falsaperla, Susanna; Meroni, Fabrizio; Langer, Horst

2016-04-01

Historically, there is a tendency to focus on seismic structural performance of buildings, neglecting the potential for damage of non-structural elements. In particular, non-structural elements of buildings are their architectural parts (i.e. partitions, ceilings, cladding), electrical and mechanical components (i.e., distribution panels, piping, plumbing), and contents (e.g., furniture, bookcases, computers and desktop equipment). Damage of these elements often contributes significantly to earthquake impacts. In the 1999 Izmit Earthquake, Turkey, 50% of the injuries and 3% of human losses were caused by non-structural failures. In the 2010-2011 Christchurch Earthquakes (New Zealand), 40% of building damage was induced by non-structural malfunctions. Around 70%-85% of construction cost goes into these elements, and their damage can strongly influence the ability of communities to cope with and recover from earthquakes. The project Know your city, Reduce seISmic risK through non-structural elements (KnowRISK) aims at facilitating local communities' access to expert knowledge on non-structural seismic protection solutions. The project will study seismic scenarios critical for non-structural damage, produce a portfolio of non-structural protection measures and investigate the level of awareness in specific communities. We will implement risk communication strategies that will take into account the social and cultural background and a participatory approach to raise awareness in local communities. The paradox between the progress of scientific knowledge and the ongoing increase of losses from natural disasters worldwide is a well-identified gap in the UN Hyogo Framework for Action 2005-2015, in which one of the main priorities is the investment on "knowledge use, innovation and education to build a culture of safety and resilience". The KnowRISK is well aligned with these priorities and will contribute to participatory action aimed at: i) transferring expert knowledge

LINE-1 Elements in Structural Variation and Disease

PubMed Central

Beck, Christine R.; Garcia-Perez, José Luis; Badge, Richard M.; Moran, John V.

2014-01-01

The completion of the human genome reference sequence ushered in a new era for the study and discovery of human transposable elements. It now is undeniable that transposable elements, historically dismissed as junk DNA, have had an instrumental role in sculpting the structure and function of our genomes. In particular, long interspersed element-1 (LINE-1 or L1) and short interspersed elements (SINEs) continue to affect our genome, and their movement can lead to sporadic cases of disease. Here, we briefly review the types of transposable elements present in the human genome and their mechanisms of mobility. We next highlight how advances in DNA sequencing and genomic technologies have enabled the discovery of novel retrotransposons in individual genomes. Finally, we discuss how L1-mediated retrotransposition events impact human genomes. PMID:21801021

Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity

PubMed Central

Song, Lingyun; Zhang, Zhancheng; Grasfeder, Linda L.; Boyle, Alan P.; Giresi, Paul G.; Lee, Bum-Kyu; Sheffield, Nathan C.; Gräf, Stefan; Huss, Mikael; Keefe, Damian; Liu, Zheng; London, Darin; McDaniell, Ryan M.; Shibata, Yoichiro; Showers, Kimberly A.; Simon, Jeremy M.; Vales, Teresa; Wang, Tianyuan; Winter, Deborah; Zhang, Zhuzhu; Clarke, Neil D.; Birney, Ewan; Iyer, Vishwanath R.; Crawford, Gregory E.; Lieb, Jason D.; Furey, Terrence S.

2011-01-01

The human body contains thousands of unique cell types, each with specialized functions. Cell identity is governed in large part by gene transcription programs, which are determined by regulatory elements encoded in DNA. To identify regulatory elements active in seven cell lines representative of diverse human cell types, we used DNase-seq and FAIRE-seq (Formaldehyde Assisted Isolation of Regulatory Elements) to map “open chromatin.” Over 870,000 DNaseI or FAIRE sites, which correspond tightly to nucleosome-depleted regions, were identified across the seven cell lines, covering nearly 9% of the genome. The combination of DNaseI and FAIRE is more effective than either assay alone in identifying likely regulatory elements, as judged by coincidence with transcription factor binding locations determined in the same cells. Open chromatin common to all seven cell types tended to be at or near transcription start sites and to be coincident with CTCF binding sites, while open chromatin sites found in only one cell type were typically located away from transcription start sites and contained DNA motifs recognized by regulators of cell-type identity. We show that open chromatin regions bound by CTCF are potent insulators. We identified clusters of open regulatory elements (COREs) that were physically near each other and whose appearance was coordinated among one or more cell types. Gene expression and RNA Pol II binding data support the hypothesis that COREs control gene activity required for the maintenance of cell-type identity. This publicly available atlas of regulatory elements may prove valuable in identifying noncoding DNA sequence variants that are causally linked to human disease. PMID:21750106

SSEP: secondary structural elements of proteins

PubMed Central

Shanthi, V.; Selvarani, P.; Kiran Kumar, Ch.; Mohire, C. S.; Sekar, K.

2003-01-01

SSEP is a comprehensive resource for accessing information related to the secondary structural elements present in the 25 and 90% non-redundant protein chains. The database contains 1771 protein chains from 1670 protein structures and 6182 protein chains from 5425 protein structures in 25 and 90% non-redundant protein chains, respectively. The current version provides information about the α-helical segments and β-strand fragments of varying lengths. In addition, it also contains the information about 310-helix, β- and ν-turns and hairpin loops. The free graphics program RASMOL has been interfaced with the search engine to visualize the three-dimensional structures of the user queried secondary structural fragment. The database is updated regularly and is available through Bioinformatics web server at http://cluster.physics.iisc.ernet.in/ssep/ or http://144.16.71.148/ssep/. PMID:12824336

Life assessment of structural components using inelastic finite element analyses

NASA Technical Reports Server (NTRS)

Arya, Vinod K.; Halford, Gary R.

1993-01-01

The need for enhanced and improved performance of structural components subject to severe cyclic thermal/mechanical loadings, such as in the aerospace industry, requires development of appropriate solution technologies involving time-dependent inelastic analyses. Such analyses are mandatory to predict local stress-strain response and to assess more accurately the cyclic life time of structural components. The NASA-Lewis Research Center is cognizant of this need. As a result of concerted efforts at Lewis during the last few years, several such finite element solution technologies (in conjunction with the finite element program MARC) were developed and successfully applied to numerous uniaxial and multiaxial problems. These solution technologies, although developed for use with MARC program, are general in nature and can easily be extended for adaptation with other finite element programs such as ABAQUS, ANSYS, etc. The description and results obtained from two such inelastic finite element solution technologies are presented. The first employs a classical (non-unified) creep-plasticity model. An application of this technology is presented for a hypersonic inlet cowl-lip problem. The second of these technologies uses a unified creep-plasticity model put forth by Freed. The structural component for which this finite element solution technology is illustrated, is a cylindrical rocket engine thrust chamber. The advantages of employing a viscoplastic model for nonlinear time-dependent structural analyses are demonstrated. The life analyses for cowl-lip and cylindrical thrust chambers are presented. These analyses are conducted by using the stress-strain response of these components obtained from the corresponding finite element analyses.

Finite element normal mode analysis of resistance welding jointed of dissimilar plate hat structure

NASA Astrophysics Data System (ADS)

Nazri, N. A.; Sani, M. S. M.

2017-10-01

Structural joints offer connection between structural element (beam, plate, solid etc.) in order to build a whole assembled structure. The complex behaviour of connecting elements plays a valuable role in characteristics of dynamic such as natural frequencies and mode shapes. In automotive structures, the trustworthiness arrangement of the structure extremely depends on joints. In this paper, top hat structure is modelled and designed with spot welding joint using dissimilar materials which is mild steel 1010 and stainless steel 304, using finite element software. Different types of connector elements such as rigid body element (RBE2), welding joint element (CWELD), and bar element (CBAR) are applied to represent real connection between two dissimilar plates. Normal mode analysis is simulated with different types of joining element in order to determine modal properties. Natural frequencies using RBE2, CBAR and CWELD are compared to equivalent rigid body method. Connection that gives the lowest percentage error among these three will be selected as the most reliable joining for resistance spot weld. From the analysis, it is shown that CWELD is better compared to others in term of weld joining among dissimilar plate materials. It is expected that joint modelling of finite element plays significant role in structural dynamics.

Finite element solution of transient fluid-structure interaction problems

NASA Technical Reports Server (NTRS)

Everstine, Gordon C.; Cheng, Raymond S.; Hambric, Stephen A.

1991-01-01

A finite element approach using NASTRAN is developed for solving time-dependent fluid-structure interaction problems, with emphasis on the transient scattering of acoustic waves from submerged elastic structures. Finite elements are used for modeling both structure and fluid domains to facilitate the graphical display of the wave motion through both media. For the liquid, the use of velocity potential as the fundamental unknown results in a symmetric matrix equation. The approach is illustrated for the problem of transient scattering from a submerged elastic spherical shell subjected to an incident tone burst. The use of an analogy between the equations of elasticity and the wave equation of acoustics, a necessary ingredient to the procedure, is summarized.

Structural Identifiability of Dynamic Systems Biology Models

PubMed Central

Villaverde, Alejandro F.

2016-01-01

A powerful way of gaining insight into biological systems is by creating a nonlinear differential equation model, which usually contains many unknown parameters. Such a model is called structurally identifiable if it is possible to determine the values of its parameters from measurements of the model outputs. Structural identifiability is a prerequisite for parameter estimation, and should be assessed before exploiting a model. However, this analysis is seldom performed due to the high computational cost involved in the necessary symbolic calculations, which quickly becomes prohibitive as the problem size increases. In this paper we show how to analyse the structural identifiability of a very general class of nonlinear models by extending methods originally developed for studying observability. We present results about models whose identifiability had not been previously determined, report unidentifiabilities that had not been found before, and show how to modify those unidentifiable models to make them identifiable. This method helps prevent problems caused by lack of identifiability analysis, which can compromise the success of tasks such as experiment design, parameter estimation, and model-based optimization. The procedure is called STRIKE-GOLDD (STRuctural Identifiability taKen as Extended-Generalized Observability with Lie Derivatives and Decomposition), and it is implemented in a MATLAB toolbox which is available as open source software. The broad applicability of this approach facilitates the analysis of the increasingly complex models used in systems biology and other areas. PMID:27792726

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

PubMed

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

2014-09-01

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

Finite element modeling of truss structures with frequency-dependent material damping

NASA Technical Reports Server (NTRS)

Lesieutre, George A.

1991-01-01

A physically motivated modelling technique for structural dynamic analysis that accommodates frequency dependent material damping was developed. Key features of the technique are the introduction of augmenting thermodynamic fields (AFT) to interact with the usual mechanical displacement field, and the treatment of the resulting coupled governing equations using finite element analysis methods. The AFT method is fully compatible with current structural finite element analysis techniques. The method is demonstrated in the dynamic analysis of a 10-bay planar truss structure, a structure representative of those contemplated for use in future space systems.

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

On modelling three-dimensional piezoelectric smart structures with boundary spectral element method

NASA Astrophysics Data System (ADS)

Zou, Fangxin; Aliabadi, M. H.

2017-05-01

The computational efficiency of the boundary element method in elastodynamic analysis can be significantly improved by employing high-order spectral elements for boundary discretisation. In this work, for the first time, the so-called boundary spectral element method is utilised to formulate the piezoelectric smart structures that are widely used in structural health monitoring (SHM) applications. The resultant boundary spectral element formulation has been validated by the finite element method (FEM) and physical experiments. The new formulation has demonstrated a lower demand on computational resources and a higher numerical stability than commercial FEM packages. Comparing to the conventional boundary element formulation, a significant reduction in computational expenses has been achieved. In summary, the boundary spectral element formulation presented in this paper provides a highly efficient and stable mathematical tool for the development of SHM applications.

Comprehensive evaluation of disease- and trait-specific enrichment for eight functional elements among GWAS-identified variants.

PubMed

Markunas, Christina A; Johnson, Eric O; Hancock, Dana B

2017-07-01

Genome-wide association study (GWAS)-identified variants are enriched for functional elements. However, we have limited knowledge of how functional enrichment may differ by disease/trait and tissue type. We tested a broad set of eight functional elements for enrichment among GWAS-identified SNPs (p < 5×10 -8 ) from the NHGRI-EBI Catalog across seven disease/trait categories: cancer, cardiovascular disease, diabetes, autoimmune disease, psychiatric disease, neurological disease, and anthropometric traits. SNPs were annotated using HaploReg for the eight functional elements across any tissue: DNase sites, expression quantitative trait loci (eQTL), sequence conservation, enhancers, promoters, missense variants, sequence motifs, and protein binding sites. In addition, tissue-specific annotations were considered for brain vs. blood. Disease/trait SNPs were compared to a control set of 4809 SNPs matched to the GWAS SNPs (N = 1639) on allele frequency, gene density, distance to nearest gene, and linkage disequilibrium at ~3:1 ratio. Enrichment analyses were conducted using logistic regression, with Bonferroni correction. Overall, a significant enrichment was observed for all functional elements, except sequence motifs. Missense SNPs showed the strongest magnitude of enrichment. eQTLs were the only functional element significantly enriched across all diseases/traits. Magnitudes of enrichment were generally similar across diseases/traits, where enrichment was statistically significant. Blood vs. brain tissue effects on enrichment were dependent on disease/trait and functional element (e.g., cardiovascular disease: eQTLs P TissueDifference  = 1.28 × 10 -6 vs. enhancers P TissueDifference  = 0.94). Identifying disease/trait-relevant functional elements and tissue types could provide new insight into the underlying biology, by guiding a priori GWAS analyses (e.g., brain enhancer elements for psychiatric disease) or facilitating post hoc interpretation.

STARS: A general-purpose finite element computer program for analysis of engineering structures

NASA Technical Reports Server (NTRS)

Gupta, K. K.

1984-01-01

STARS (Structural Analysis Routines) is primarily an interactive, graphics-oriented, finite-element computer program for analyzing the static, stability, free vibration, and dynamic responses of damped and undamped structures, including rotating systems. The element library consists of one-dimensional (1-D) line elements, two-dimensional (2-D) triangular and quadrilateral shell elements, and three-dimensional (3-D) tetrahedral and hexahedral solid elements. These elements enable the solution of structural problems that include truss, beam, space frame, plane, plate, shell, and solid structures, or any combination thereof. Zero, finite, and interdependent deflection boundary conditions can be implemented by the program. The associated dynamic response analysis capability provides for initial deformation and velocity inputs, whereas the transient excitation may be either forces or accelerations. An effective in-core or out-of-core solution strategy is automatically employed by the program, depending on the size of the problem. Data input may be at random within a data set, and the program offers certain automatic data-generation features. Input data are formatted as an optimal combination of free and fixed formats. Interactive graphics capabilities enable convenient display of nodal deformations, mode shapes, and element stresses.

Better Finite-Element Analysis of Composite Shell Structures

NASA Technical Reports Server (NTRS)

Clarke, Gregory

2007-01-01

A computer program implements a finite-element-based method of predicting the deformations of thin aerospace structures made of isotropic materials or anisotropic fiber-reinforced composite materials. The technique and corresponding software are applicable to thin shell structures in general and are particularly useful for analysis of thin beamlike members having open cross-sections (e.g. I-beams and C-channels) in which significant warping can occur.

Fluid-structure interaction simulations of deformable structures with non-linear thin shell elements

NASA Astrophysics Data System (ADS)

Asgharzadeh, Hafez; Hedayat, Mohammadali; Borazjani, Iman; Scientific Computing; Biofluids Laboratory Team

2017-11-01

Large deformation of structures in a fluid is simulated using a strongly coupled partitioned fluid-structure interaction (FSI) approach which is stabilized with under-relaxation and the Aitken acceleration technique. The fluid is simulated using a recently developed implicit Newton-Krylov method with a novel analytical Jacobian. Structures are simulated using a triangular thin-shell finite element formulation, which considers only translational degrees of freedom. The thin-shell method is developed on the top of a previously implemented membrane finite element formulation. A sharp interface immersed boundary method is used to handle structures in the fluid domain. The developed FSI framework is validated against two three-dimensional experiments: (1) a flexible aquatic vegetation in the fluid and (2) a heaving flexible panel in fluid. Furthermore, the developed FSI framework is used to simulate tissue heart valves, which involve large deformations and non-linear material properties. This work was supported by American Heart Association (AHA) Grant 13SDG17220022 and the Center of Computational Research (CCR) of University at Buffalo.

Testing for change in structural elements of forest inventories

Treesearch

Melinda Vokoun; David Wear; Robert Abt

2009-01-01

In this article we develop a methodology to test for changes in the underlying relationships between measures of forest productivity (structural elements) and site characteristics, herein referred to as structural changes, using standard forest inventories. Changes in measures of forest growing stock volume and number of trees for both...

Structural weights analysis of advanced aerospace vehicles using finite element analysis

NASA Technical Reports Server (NTRS)

Bush, Lance B.; Lentz, Christopher A.; Rehder, John J.; Naftel, J. Chris; Cerro, Jeffrey A.

1989-01-01

A conceptual/preliminary level structural design system has been developed for structural integrity analysis and weight estimation of advanced space transportation vehicles. The system includes a three-dimensional interactive geometry modeler, a finite element pre- and post-processor, a finite element analyzer, and a structural sizing program. Inputs to the system include the geometry, surface temperature, material constants, construction methods, and aerodynamic and inertial loads. The results are a sized vehicle structure capable of withstanding the static loads incurred during assembly, transportation, operations, and missions, and a corresponding structural weight. An analysis of the Space Shuttle external tank is included in this paper as a validation and benchmark case of the system.

Safety envelope for load tolerance of structural element design based on multi-stage testing

DOE PAGES

Park, Chanyoung; Kim, Nam H.

2016-09-06

Structural elements, such as stiffened panels and lap joints, are basic components of aircraft structures. For aircraft structural design, designers select predesigned elements satisfying the design load requirement based on their load-carrying capabilities. Therefore, estimation of safety envelope of structural elements for load tolerances would be a good investment for design purpose. In this article, a method of estimating safety envelope is presented using probabilistic classification, which can estimate a specific level of failure probability under both aleatory and epistemic uncertainties. An important contribution of this article is that the calculation uncertainty is reflected in building a safety envelope usingmore » Gaussian process, and the effect of element test data on reducing the calculation uncertainty is incorporated by updating the Gaussian process model with the element test data. It is shown that even one element test can significantly reduce the calculation uncertainty due to lacking knowledge of actual physics, so that conservativeness in a safety envelope is significantly reduced. The proposed approach was demonstrated with a cantilever beam example, which represents a structural element. The example shows that calculation uncertainty provides about 93% conservativeness against the uncertainty due to a few element tests. As a result, it is shown that even a single element test can increase the load tolerance modeled with the safety envelope by 20%.« less

Identifying Effective Treatments from a Brief Experimental Analysis: Using a Single-Case Design Elements To Aid Decision Making.

ERIC Educational Resources Information Center

Martens, Brian K.; Eckert, Tanya L.; Bradley, Tracy A.; Ardoin, Scott P.

1999-01-01

Discusses the benefits of using brief experimental analysis to aid in treatment selection, identifies the forms of treatment that are most appropriate for this type of analysis, and describes key design elements for comparing treatments. Presents a study demonstrating the use of these design elements to identify an effective intervention for two…

DYCAST: A finite element program for the crash analysis of structures

NASA Technical Reports Server (NTRS)

Pifko, A. B.; Winter, R.; Ogilvie, P.

1987-01-01

DYCAST is a nonlinear structural dynamic finite element computer code developed for crash simulation. The element library contains stringers, beams, membrane skin triangles, plate bending triangles and spring elements. Changing stiffnesses in the structure are accounted for by plasticity and very large deflections. Material nonlinearities are accommodated by one of three options: elastic-perfectly plastic, elastic-linear hardening plastic, or elastic-nonlinear hardening plastic of the Ramberg-Osgood type. Geometric nonlinearities are handled in an updated Lagrangian formulation by reforming the structure into its deformed shape after small time increments while accumulating deformations, strains, and forces. The nonlinearities due to combined loadings are maintained, and stiffness variation due to structural failures are computed. Numerical time integrators available are fixed-step central difference, modified Adams, Newmark-beta, and Wilson-theta. The last three have a variable time step capability, which is controlled internally by a solution convergence error measure. Other features include: multiple time-load history tables to subject the structure to time dependent loading; gravity loading; initial pitch, roll, yaw, and translation of the structural model with respect to the global system; a bandwidth optimizer as a pre-processor; and deformed plots and graphics as post-processors.

Slave finite elements for nonlinear analysis of engine structures, volume 1

NASA Technical Reports Server (NTRS)

Gellin, S.

1991-01-01

A 336 degrees of freedom slave finite element processing capability to analyze engine structures under severe thermomechanical loading is presented. Description of the theoretical development and demonstration of that element is presented in this volume.

A new structure-property connection in the skeletal elements of the marine sponge Tethya aurantia that guards against buckling instability

NASA Astrophysics Data System (ADS)

Monn, Michael A.; Kesari, Haneesh

2017-01-01

We identify a new structure-property connection in the skeletal elements of the marine sponge Tethya aurantia. The skeletal elements, known as spicules, are millimeter-long, axisymmetric, silica rods that are tapered along their lengths. Mechanical designs in other structural biomaterials, such as nacre and bone, have been studied primarily for their benefits to toughness properties. The structure-property connection we identify, however, falls in the entirely new category of buckling resistance. We use computational mechanics calculations and information about the spicules’ arrangement within the sponge to develop a structural mechanics model for the spicules. We use our structural mechanics model along with measurements of the spicules’ shape to estimate the load they can transmit before buckling. Compared to a cylinder with the same length and volume, we predict that the spicules’ shape enhances this critical load by up to 30%. We also find that the spicules’ shape is close to the shape of the column that is optimized to transmit the largest load before buckling. In man-made structures, many strategies are used to prevent buckling. We find, however, that the spicules use a completely new strategy. We hope our discussion will generate a greater appreciation for nature’s ability to produce beneficial designs.

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

Institutional and structural barriers to HIV testing: elements for a theoretical framework.

PubMed

Meyerson, Beth; Barnes, Priscilla; Emetu, Roberta; Bailey, Marlon; Ohmit, Anita; Gillespie, Anthony

2014-01-01

Stigma is a barrier to HIV health seeking, but little is known about institutional and structural expressions of stigma in HIV testing. This study examines evidence of institutional and structural stigma in the HIV testing process. A qualitative, grounded theory study was conducted using secondary data from a 2011 HIV test site evaluation data in a Midwestern, moderate HIV incidence state. Expressions of structural and institutional stigma were found with over half of the testing sites and at three stages of the HIV testing visit. Examples of structural stigma included social geography, organization, and staff behavior at first encounter and reception, and staff behavior when experiencing the actual HIV test. Institutional stigma was socially expressed through staff behavior at entry/reception and when experiencing the HIV test. The emerging elements demonstrate the potential compounding of stigma experiences with deleterious effect. Study findings may inform future development of a theoretical framework. In practice, findings can guide organizations seeking to reduce HIV testing barriers, as they provide a window into how test seekers experience HIV test sites at first encounter, entry/reception, and at testing stages; and can identify how stigma might be intensified by structural and institutional expressions.

Elements of Regolith Simulant's Cost Structure--Why Rock Is NOT Cheap

NASA Technical Reports Server (NTRS)

Rickman, Douglas L.

2009-01-01

The cost of lunar regolith simulants is much higher than many users anticipate. After all, it is nothing more than broken rock. This class will discuss the elements which make up the cost structure for simulants. It will also consider which elements can be avoided under certain circumstances and which elements might be altered by the application of additional research and development.

Transcriptomic analysis of rice aleurone cells identified a novel abscisic acid response element.

PubMed

Watanabe, Kenneth A; Homayouni, Arielle; Gu, Lingkun; Huang, Kuan-Ying; Ho, Tuan-Hua David; Shen, Qingxi J

2017-09-01

Seeds serve as a great model to study plant responses to drought stress, which is largely mediated by abscisic acid (ABA). The ABA responsive element (ABRE) is a key cis-regulatory element in ABA signalling. However, its consensus sequence (ACGTG(G/T)C) is present in the promoters of only about 40% of ABA-induced genes in rice aleurone cells, suggesting other ABREs may exist. To identify novel ABREs, RNA sequencing was performed on aleurone cells of rice seeds treated with 20 μM ABA. Gibbs sampling was used to identify enriched elements, and particle bombardment-mediated transient expression studies were performed to verify the function. Gene ontology analysis was performed to predict the roles of genes containing the novel ABREs. This study revealed 2443 ABA-inducible genes and a novel ABRE, designated as ABREN, which was experimentally verified to mediate ABA signalling in rice aleurone cells. Many of the ABREN-containing genes are predicted to be involved in stress responses and transcription. Analysis of other species suggests that the ABREN may be monocot specific. This study also revealed interesting expression patterns of genes involved in ABA metabolism and signalling. Collectively, this study advanced our understanding of diverse cis-regulatory sequences and the transcriptomes underlying ABA responses in rice aleurone cells. © 2017 John Wiley & Sons Ltd.

Identifying Common Practice Elements to Improve Social, Emotional, and Behavioral Outcomes of Young Children in Early Childhood Classrooms.

PubMed

McLeod, Bryce D; Sutherland, Kevin S; Martinez, Ruben G; Conroy, Maureen A; Snyder, Patricia A; Southam-Gerow, Michael A

2017-02-01

Educators are increasingly being encouraged to implement evidence-based interventions and practices to address the social, emotional, and behavioral needs of young children who exhibit problem behavior in early childhood settings. Given the nature of social-emotional learning during the early childhood years and the lack of a common set of core evidence-based practices within the early childhood literature, selection of instructional practices that foster positive social, emotional, and behavioral outcomes for children in early childhood settings can be difficult. The purpose of this paper is to report findings from a study designed to identify common practice elements found in comprehensive intervention models (i.e., manualized interventions that include a number of components) or discrete practices (i.e., a specific behavior or action) designed to target social, emotional, and behavioral learning of young children who exhibit problem behavior. We conducted a systematic review of early childhood classroom interventions that had been evaluated in randomized group designs, quasi-experimental designs, and single-case experimental designs. A total of 49 published articles were identified, and an iterative process was used to identify common practice elements. The practice elements were subsequently reviewed by experts in social-emotional and behavioral interventions for young children. Twenty-four practice elements were identified and classified into content (the goal or general principle that guides a practice element) and delivery (the way in which a teacher provides instruction to the child) categories. We discuss implications that the identification of these practice elements found in the early childhood literature has for efforts to implement models and practices.

On location of piezoelectric element in a smart-structure: numerical investigation and experiment

NASA Astrophysics Data System (ADS)

Oshmarin, D.; Iurlov, M.

2017-06-01

In this paper, based on some example problems it was demonstrated that in examining the possibilities of smart structure applications, the matter of considerable researchers’ concern is the problem of location of piezoelectric elements in the structure to allow effective realization of its smart functions in the framework of the specified strategy of structure control and target purposes (vibration damping, defectoscopy, etc.) The numerical and experimental investigations have shown that for structures with the elements made of piezoelectric materials, it is more convenient to use as a parameter, specifying the best location of the piezoelectric element for damping the vibrations at the prescribed frequency, the coefficient of electromechanical coupling, which is evaluated by the values of eigenfrequencies of the structure in the short-circuit and open-circuit regimes. The values of eigenfrequencies of vibrations are evaluated by solving the problem of natural vibrations of electromechanical systems by the finite element method using the applied ANSYS package. The investigation were conducted for a thin-walled aluminum shell in the form of half-cylinder.

Sieve element occlusion (SEO) genes encode structural phloem proteins involved in wound sealing of the phloem.

PubMed

Ernst, Antonia M; Jekat, Stephan B; Zielonka, Sascia; Müller, Boje; Neumann, Ulla; Rüping, Boris; Twyman, Richard M; Krzyzanek, Vladislav; Prüfer, Dirk; Noll, Gundula A

2012-07-10

The sieve element occlusion (SEO) gene family originally was delimited to genes encoding structural components of forisomes, which are specialized crystalloid phloem proteins found solely in the Fabaceae. More recently, SEO genes discovered in various non-Fabaceae plants were proposed to encode the common phloem proteins (P-proteins) that plug sieve plates after wounding. We carried out a comprehensive characterization of two tobacco (Nicotiana tabacum) SEO genes (NtSEO). Reporter genes controlled by the NtSEO promoters were expressed specifically in immature sieve elements, and GFP-SEO fusion proteins formed parietal agglomerates in intact sieve elements as well as sieve plate plugs after wounding. NtSEO proteins with and without fluorescent protein tags formed agglomerates similar in structure to native P-protein bodies when transiently coexpressed in Nicotiana benthamiana, and the analysis of these protein complexes by electron microscopy revealed ultrastructural features resembling those of native P-proteins. NtSEO-RNA interference lines were essentially devoid of P-protein structures and lost photoassimilates more rapidly after injury than control plants, thus confirming the role of P-proteins in sieve tube sealing. We therefore provide direct evidence that SEO genes in tobacco encode P-protein subunits that affect translocation. We also found that peptides recently identified in fascicular phloem P-protein plugs from squash (Cucurbita maxima) represent cucurbit members of the SEO family. Our results therefore suggest a common evolutionary origin for P-proteins found in the sieve elements of all dicotyledonous plants and demonstrate the exceptional status of extrafascicular P-proteins in cucurbits.

sp3-hybridized framework structure of group-14 elements discovered by genetic algorithm

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

Nguyen, Manh Cuong; Zhao, Xin; Wang, Cai-Zhuang

2014-05-01

Group-14 elements, including C, Si, Ge, and Sn, can form various stable and metastable structures. Finding new metastable structures of group-14 elements with desirable physical properties for new technological applications has attracted a lot of interest. Using a genetic algorithm, we discovered a new low-energy metastable distorted sp3-hybridized framework structure of the group-14 elements. It has P42/mnm symmetry with 12 atoms per unit cell. The void volume of this structure is as large as 139.7Å3 for Si P42/mnm, and it can be used for gas or metal-atom encapsulation. Band-structure calculations show that P42/mnm structures of Si and Ge are semiconductingmore » with energy band gaps close to the optimal values for optoelectronic or photovoltaic applications. With metal-atom encapsulation, the P42/mnm structure would also be a candidate for rattling-mediated superconducting or used as thermoelectric materials.« less

Identifying Mental Health Elements among Technical University Students Using Fuzzy Delphi Method

NASA Astrophysics Data System (ADS)

Pua, P. K.; Lai, C. S.; Lee, M. F.

2017-08-01

Mental health is a part of our daily life that is often experienced. As a student, mental health issue often encounters a variety of difficult challenges at the higher education institution. A student with good mental health can handle and cope the normal stress of life, capable work productivity, enhance academic performance and able to make contribute to the community. However, rapidly transformation and changing of society have been impacted on students’ mental health, and it will be deteriorated and negatively impact on students if it absence of preventive controlled. This study aimed to identify the element of mental health among the technical university students. A total of 11 experts were selected to analyze the fuzziness consensus of experts. All collected data was analyzed by using the fuzzy Delphi method and the result shows that there are 4 elements of 8 elements that fulfill the requirement consensus of experts, which threshold value is equal and less than 0.2, the percentage of the expert group is more than 75%. The four elements were depression, anxiety, stress, and fear are often experienced by technical university students. In conclusion, precocious actions have to be taken by university and counseling center, parents and non-government organization in order to mitigate the mental health problem faced by students to improve the quality lifestyle students at the university.

Finite element analysis of structural engineering problems using a viscoplastic model incorporating two back stresses

NASA Technical Reports Server (NTRS)

Arya, Vinod K.; Halford, Gary R.

1993-01-01

The feasibility of a viscoplastic model incorporating two back stresses and a drag strength is investigated for performing nonlinear finite element analyses of structural engineering problems. To demonstrate suitability for nonlinear structural analyses, the model is implemented into a finite element program and analyses for several uniaxial and multiaxial problems are performed. Good agreement is shown between the results obtained using the finite element implementation and those obtained experimentally. The advantages of using advanced viscoplastic models for performing nonlinear finite element analyses of structural components are indicated.

Elements of the Chicxulub Impact Structure as Revealed in SRTM and Surface GPS Topographic Data

NASA Technical Reports Server (NTRS)

Kinsland, Gary L.; Sanchez, Gary; Kobrick, Michael; Cardador, Manuel Hurtado

2003-01-01

Pope et al. [1] utilized the elevations from the Petroleos Mexicanos (PEMEX) gravity data files to show that the main component of the surface expression of the Chicxulub Impact Structure is a roughly semi-circular, lowrelief depression about 90 km in diameter. They also identified other topographic features and the elements of the buried impact, which possibly led to the development of these features. These are summarized in Table 1. Kinsland et al. [2] presented a connection between these topographic anomalies, small gravity anomalies and buried structure of the impact. Very recently we have acquired digital topography data from NASA s Shuttle Radar Topography Mission (SRTM). Our subset covers 6 square degrees from 20deg N 91degW to 22deg N 88degW (corner to corner) with a pixel size of about 90m. This area includes all of the identified portion of the crater on land.

Slip as the basic mechanism for formation of deformation relief structural elements

NASA Astrophysics Data System (ADS)

Lychagin, D. V.; Alfyorova, E. A.

2017-07-01

The experimental results of investigation of the nickel single crystal surface morphology after compression deformation are presented. The quasi-periodic character of the deformation profile, common for shear deformation of different types of relief structural elements, is found. It is demonstrated that the morphological manifestation of these structural elements is determined by local shear systems along octahedral planes. The regularities of the deformation structure in these regions defining the material extrusion and intrusion regions and the specific features of disorientation accumulation are established. If reorientation of local regions takes part in the relief element formation, along with octahedral slip, much stronger growth of the surface area is observed. The possibility of application of two-dimensional and three-dimensional surface roughness parameters for description of deformation relief is considered.

Useful DNA polymorphisms are identified by snapback, a midrepetitive element in Tribolium castaneum.

PubMed

Stuart, J J; De Gortari, M J; Hall, P S; Maxwell, M E; Mocelin, G; Brown, S J; Muir, W M

1996-06-01

The red flour bettle, Tribolium castaneum, is both a pest of stored grain products and an important experimental organism. To improve its facility as a genetic model, we are developing DNA fingerprinting methods for this insect. A Tribolium DNA fragment, snapback-1 (SBI), identified among sequences that reassociate before a Cot of 0.03 mol.s/L, was found to produce a banding pattern in restriction endonuclease digested genomic DNA that is characteristic of a midrepetitive element. DNA fingerprints of individual beetles demonstrated that unvarying inherited DNA polymorphism is revealed, and that polymorphism is inherited in a dominant Mendelian fashion. Linkage between bands was minimal. The sequence of SBI was determined, and hybridization experiments indicated that SBI is a fragment of a larger midrepetitive element. Fingerprinting individuals with known inbreeding coefficients indicated that SBI loci have relatively high mutation rates. The possibility that SBI is a fragment of a transposable element is discussed.

Dynamic and thermal response finite element models of multi-body space structural configurations

NASA Technical Reports Server (NTRS)

Edighoffer, Harold H.

1987-01-01

Presented is structural dynamics modeling of two multibody space structural configurations. The first configuration is a generic space station model of a cylindrical habitation module, two solar array panels, radiator panel, and central connecting tube. The second is a 15-m hoop-column antenna. Discussed is the special joint elimination sequence used for these large finite element models, so that eigenvalues could be extracted. The generic space station model aided test configuration design and analysis/test data correlation. The model consisted of six finite element models, one of each substructure and one of all substructures as a system. Static analysis and tests at the substructure level fine-tuned the finite element models. The 15-m hoop-column antenna is a truss column and structural ring interconnected with tension stabilizing cables. To the cables, pretensioned mesh membrane elements were attached to form four parabolic shaped antennae, one per quadrant. Imposing thermal preloads in the cables and mesh elements produced pretension in the finite element model. Thermal preload variation in the 96 control cables was adjusted to maintain antenna shape within the required tolerance and to give pointing accuracy.

Experimental validation of finite element and boundary element methods for predicting structural vibration and radiated noise

NASA Technical Reports Server (NTRS)

Seybert, A. F.; Wu, T. W.; Wu, X. F.

1994-01-01

This research report is presented in three parts. In the first part, acoustical analyses were performed on modes of vibration of the housing of a transmission of a gear test rig developed by NASA. The modes of vibration of the transmission housing were measured using experimental modal analysis. The boundary element method (BEM) was used to calculate the sound pressure and sound intensity on the surface of the housing and the radiation efficiency of each mode. The radiation efficiency of each of the transmission housing modes was then compared to theoretical results for a finite baffled plate. In the second part, analytical and experimental validation of methods to predict structural vibration and radiated noise are presented. A rectangular box excited by a mechanical shaker was used as a vibrating structure. Combined finite element method (FEM) and boundary element method (BEM) models of the apparatus were used to predict the noise level radiated from the box. The FEM was used to predict the vibration, while the BEM was used to predict the sound intensity and total radiated sound power using surface vibration as the input data. Vibration predicted by the FEM model was validated by experimental modal analysis; noise predicted by the BEM was validated by measurements of sound intensity. Three types of results are presented for the total radiated sound power: sound power predicted by the BEM model using vibration data measured on the surface of the box; sound power predicted by the FEM/BEM model; and sound power measured by an acoustic intensity scan. In the third part, the structure used in part two was modified. A rib was attached to the top plate of the structure. The FEM and BEM were then used to predict structural vibration and radiated noise respectively. The predicted vibration and radiated noise were then validated through experimentation.

Integration of Experiments across Diverse Environments Identifies the Genetic Determinants of Variation in Sorghum bicolor Seed Element Composition.

PubMed

Shakoor, Nadia; Ziegler, Greg; Dilkes, Brian P; Brenton, Zachary; Boyles, Richard; Connolly, Erin L; Kresovich, Stephen; Baxter, Ivan

2016-04-01

Seedling establishment and seed nutritional quality require the sequestration of sufficient element nutrients. The identification of genes and alleles that modify element content in the grains of cereals, including sorghum (Sorghum bicolor), is fundamental to developing breeding and selection methods aimed at increasing bioavailable element content and improving crop growth. We have developed a high-throughput work flow for the simultaneous measurement of multiple elements in sorghum seeds. We measured seed element levels in the genotyped Sorghum Association Panel, representing all major cultivated sorghum races from diverse geographic and climatic regions, and mapped alleles contributing to seed element variation across three environments by genome-wide association. We observed significant phenotypic and genetic correlation between several elements across multiple years and diverse environments. The power of combining high-precision measurements with genome-wide association was demonstrated by implementing rank transformation and a multilocus mixed model to map alleles controlling 20 element traits, identifying 255 loci affecting the sorghum seed ionome. Sequence similarity to genes characterized in previous studies identified likely causative genes for the accumulation of zinc, manganese, nickel, calcium, and cadmium in sorghum seeds. In addition to strong candidates for these five elements, we provide a list of candidate loci for several other elements. Our approach enabled the identification of single-nucleotide polymorphisms in strong linkage disequilibrium with causative polymorphisms that can be evaluated in targeted selection strategies for plant breeding and improvement. © 2016 American Society of Plant Biologists. All Rights Reserved.

Structural Responses and Finite Element Modeling of Hakka Tulou Rammed Earth Structures

NASA Astrophysics Data System (ADS)

Sranislawski, Daniel

Hakka Tulous are rammed earth structures that have survived the effects of aging and natural elements upwards of even over a thousand years. These structures have housed the Hakka people of the Fujian Province, China in natural yet modern housing that has provided benefits over newer building materials. The key building material, rammed earth, which is used for the walls of the Hakka Tulou structures, has provided structural stability along with thermal comfort to the respective inhabitants of the Hakka Tulous. Through material testing and analysis this study has examined how the Tulou structures have maintained their structural stability while also providing thermal comfort. Reports of self healing cracks in the rammed earth walls were also analyzed for their validity in this study. The study has found that although the story of the self healing crack cannot be validated, there is reason to believe that with the existence of lime, some type of autogenous healing could occur on a small scale. The study has also found, through the use of nondestructive testing, that both the internal wooden systems (flooring, roof, and column support) and the rammed earth walls, are still structurally sound. Also, rammed earth's high thermal mass along with the use of sufficient shading has allowed for a delay release of heat energy from the walls of the Tulous, thus providing thermal comfort that can be felt during both night and day temperatures. The Hakka Tulou structures have been found to resist destruction from natural disasters such as strong earthquakes even when more modern construction has not. Through finite element modeling, this study has shown that the high volume of rammed earth used in the construction of the Hakka Tulous helps dissipate lateral force energy into much lower stresses for the rammed earth wall. This absorption of lateral force energy allows the rammed earth structures to survive even the strongest of earthquakes experienced in the region. The Hakka

Complete genome sequence of a novel extrachromosomal virus-like element identified in planarian Girardia tigrina

PubMed Central

Rebrikov, Denis V; Bulina, Maria E; Bogdanova, Ekaterina A; Vagner, Loura L; Lukyanov, Sergey A

2002-01-01

Background Freshwater planarians are widely used as models for investigation of pattern formation and studies on genetic variation in populations. Despite extensive information on the biology and genetics of planaria, the occurrence and distribution of viruses in these animals remains an unexplored area of research. Results Using a combination of Suppression Subtractive Hybridization (SSH) and Mirror Orientation Selection (MOS), we compared the genomes of two strains of freshwater planarian, Girardia tigrina. The novel extrachromosomal DNA-containing virus-like element denoted PEVE (Planarian Extrachromosomal Virus-like Element) was identified in one planarian strain. The PEVE genome (about 7.5 kb) consists of two unique regions (Ul and Us) flanked by inverted repeats. Sequence analyses reveal that PEVE comprises two helicase-like sequences in the genome, of which the first is a homolog of a circoviral replication initiator protein (Rep), and the second is similar to the papillomavirus E1 helicase domain. PEVE genome exists in at least two variant forms with different arrangements of single-stranded and double-stranded DNA stretches that correspond to the Us and Ul regions. Using PCR analysis and whole-mount in situ hybridization, we characterized PEVE distribution and expression in the planarian body. Conclusions PEVE is the first viral element identified in free-living flatworms. This element differs from all known viruses and viral elements, and comprises two potential helicases that are homologous to proteins from distant viral phyla. PEVE is unevenly distributed in the worm body, and is detected in specific parenchyma cells. PMID:12065025

A finite element analysis of a 3D auxetic textile structure for composite reinforcement

NASA Astrophysics Data System (ADS)

Ge, Zhaoyang; Hu, Hong; Liu, Yanping

2013-08-01

This paper reports the finite element analysis of an innovative 3D auxetic textile structure consisting of three yarn systems (weft, warp and stitch yarns). Different from conventional 3D textile structures, the proposed structure exhibits an auxetic behaviour under compression and can be used as a reinforcement to manufacture auxetic composites. The geometry of the structure is first described. Then a 3D finite element model is established using ANSYS software and validated by the experimental results. The deformation process of the structure at different compression strains is demonstrated, and the validated finite element model is finally used to simulate the auxetic behaviour of the structure with different structural parameters and yarn properties. The results show that the auxetic behaviour of the proposed structure increases with increasing compression strain, and all the structural parameters and yarn properties have significant effects on the auxetic behaviour of the structure. It is expected that the study could provide a better understanding of 3D auxetic textile structures and could promote their application in auxetic composites.

Prediction of local proximal tibial subchondral bone structural stiffness using subject-specific finite element modeling: Effect of selected density-modulus relationship.

PubMed

Nazemi, S Majid; Amini, Morteza; Kontulainen, Saija A; Milner, Jaques S; Holdsworth, David W; Masri, Bassam A; Wilson, David R; Johnston, James D

2015-08-01

Quantitative computed tomography based subject-specific finite element modeling has potential to clarify the role of subchondral bone alterations in knee osteoarthritis initiation, progression, and pain initiation. Calculation of bone elastic moduli from image data is a basic step when constructing finite element models. However, different relationships between elastic moduli and imaged density (known as density-modulus relationships) have been reported in the literature. The objective of this study was to apply seven different trabecular-specific and two cortical-specific density-modulus relationships from the literature to finite element models of proximal tibia subchondral bone, and identify the relationship(s) that best predicted experimentally measured local subchondral structural stiffness with highest explained variance and least error. Thirteen proximal tibial compartments were imaged via quantitative computed tomography. Imaged bone mineral density was converted to elastic moduli using published density-modulus relationships and mapped to corresponding finite element models. Proximal tibial structural stiffness values were compared to experimentally measured stiffness values from in-situ macro-indentation testing directly on the subchondral bone surface (47 indentation points). Regression lines between experimentally measured and finite element calculated stiffness had R(2) values ranging from 0.56 to 0.77. Normalized root mean squared error varied from 16.6% to 337.6%. Of the 21 evaluated density-modulus relationships in this study, Goulet combined with Snyder and Schneider or Rho appeared most appropriate for finite element modeling of local subchondral bone structural stiffness. Though, further studies are needed to optimize density-modulus relationships and improve finite element estimates of local subchondral bone structural stiffness. Copyright © 2015 Elsevier Ltd. All rights reserved.

Structured representation for core elements of common clinical decision support interventions to facilitate knowledge sharing.

PubMed

Zhou, Li; Hongsermeier, Tonya; Boxwala, Aziz; Lewis, Janet; Kawamoto, Kensaku; Maviglia, Saverio; Gentile, Douglas; Teich, Jonathan M; Rocha, Roberto; Bell, Douglas; Middleton, Blackford

2013-01-01

At present, there are no widely accepted, standard approaches for representing computer-based clinical decision support (CDS) intervention types and their structural components. This study aimed to identify key requirements for the representation of five widely utilized CDS intervention types: alerts and reminders, order sets, infobuttons, documentation templates/forms, and relevant data presentation. An XML schema was proposed for representing these interventions and their core structural elements (e.g., general metadata, applicable clinical scenarios, CDS inputs, CDS outputs, and CDS logic) in a shareable manner. The schema was validated by building CDS artifacts for 22 different interventions, targeted toward guidelines and clinical conditions called for in the 2011 Meaningful Use criteria. Custom style sheets were developed to render the XML files in human-readable form. The CDS knowledge artifacts were shared via a public web portal. Our experience also identifies gaps in existing standards and informs future development of standards for CDS knowledge representation and sharing.

EVA assembly of large space structure element

NASA Technical Reports Server (NTRS)

Bement, L. J.; Bush, H. G.; Heard, W. L., Jr.; Stokes, J. W., Jr.

1981-01-01

The results of a test program to assess the potential of manned extravehicular activity (EVA) assembly of erectable space trusses are described. Seventeen tests were conducted in which six "space-weight" columns were assembled into a regular tetrahedral cell by a team of two "space"-suited test subjects. This cell represents the fundamental "element" of a tetrahedral truss structure. The tests were conducted under simulated zero-gravity conditions. Both manual and simulated remote manipulator system modes were evaluated. Articulation limits of the pressure suit and zero gravity could be accommodated by work stations with foot restraints. The results of this study have confirmed that astronaut EVA assembly of large, erectable space structures is well within man's capabilities.

Adaptive Crack Modeling with Interface Solid Elements for Plain and Fiber Reinforced Concrete Structures.

PubMed

Zhan, Yijian; Meschke, Günther

2017-07-08

The effective analysis of the nonlinear behavior of cement-based engineering structures not only demands physically-reliable models, but also computationally-efficient algorithms. Based on a continuum interface element formulation that is suitable to capture complex cracking phenomena in concrete materials and structures, an adaptive mesh processing technique is proposed for computational simulations of plain and fiber-reinforced concrete structures to progressively disintegrate the initial finite element mesh and to add degenerated solid elements into the interfacial gaps. In comparison with the implementation where the entire mesh is processed prior to the computation, the proposed adaptive cracking model allows simulating the failure behavior of plain and fiber-reinforced concrete structures with remarkably reduced computational expense.

Adaptive Crack Modeling with Interface Solid Elements for Plain and Fiber Reinforced Concrete Structures

PubMed Central

Zhan, Yijian

2017-01-01

The effective analysis of the nonlinear behavior of cement-based engineering structures not only demands physically-reliable models, but also computationally-efficient algorithms. Based on a continuum interface element formulation that is suitable to capture complex cracking phenomena in concrete materials and structures, an adaptive mesh processing technique is proposed for computational simulations of plain and fiber-reinforced concrete structures to progressively disintegrate the initial finite element mesh and to add degenerated solid elements into the interfacial gaps. In comparison with the implementation where the entire mesh is processed prior to the computation, the proposed adaptive cracking model allows simulating the failure behavior of plain and fiber-reinforced concrete structures with remarkably reduced computational expense. PMID:28773130

A new axi-symmetric element for thin walled structures

NASA Astrophysics Data System (ADS)

Cardoso, Rui P. R.; Yoon, Jeong Whan; Dick, Robert E.

2010-03-01

A new axi-symmetric finite element for thin walled structures is presented in this work. It uses the solid-shell element’s concept with only a single element and multiple integration points along the thickness direction. The cross-section of the element is composed of four nodes with two degrees of freedom each. The proposed formulation overcomes many locking pathologies including transverse shear locking, Poisson’s locking and volumetric locking. For transverse shear locking, the formulation uses the selective reduced integration technique, for Poisson’s locking it uses the enhanced assumed strain (EAS) method with only one enhancing variable. The B-bar approach is used to eliminate the isochoric deformations in the hourglass field while the EAS method is used to alleviate the volumetric locking in the constant part of the deformation tensor. Several examples are shown to demonstrate the performance and accuracy of the proposed element with special focus on the numerical simulations for the beverage can industry.

Finite element simulation of adaptive aerospace structures with SMA actuators

NASA Astrophysics Data System (ADS)

Frautschi, Jason; Seelecke, Stefan

2003-07-01

The particular demands of aerospace engineering have spawned many of the developments in the field of adaptive structures. Shape memory alloys are particularly attractive as actuators in these types of structures due to their large strains, high specific work output and potential for structural integration. However, the requisite extensive physical testing has slowed development of potential applications and highlighted the need for a simulation tool for feasibility studies. In this paper we present an implementation of an extended version of the M'ller-Achenbach SMA model into a commercial finite element code suitable for such studies. Interaction between the SMA model and the solution algorithm for the global FE equations is thoroughly investigated with respect to the effect of tolerances and time step size on convergence, computational cost and accuracy. Finally, a simulation of a SMA-actuated flexible trailing edge of an aircraft wing modeled with beam elements is presented.

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.

Model for selecting quality standards for a salad bar through identifying elements of customer satisfaction.

PubMed

Ouellet, D; Norback, J P

1993-11-01

Continuous quality improvement is the new requirement of the Joint Commission on Accreditation of Healthcare Organizations. This means that meeting quality standards will not be enough. Dietitians will need to improve those standards and the way they are selected. Because quality is defined in terms of the customers, all quality improvement projects must start by defining what customers want. Using a salad bar as an example, this article presents and illustrates a technique developed in Japan to identify which elements in a product or service will satisfy or dissatisfy consumers. Using a model and a questionnaire format developed by Kano and coworkers, 273 students were surveyed to classify six quality elements of a salad bar. Four elements showed a dominant "must-be" characteristic: food freshness, labeling of the dressings, no spills in the food, and no spills on the salad bar. The two other elements (food easy to reach and food variety) showed a dominant one-dimensional characteristic. By better understanding consumer perceptions of quality elements, foodservice managers can select quality standards that focus on what really matters to their consumers.

Finite element model updating of riveted joints of simplified model aircraft structure

NASA Astrophysics Data System (ADS)

Yunus, M. A.; Rani, M. N. Abdul; Sani, M. S. M.; Shah, M. A. S. Aziz

2018-04-01

Thin metal sheets are widely used to fabricate a various type of aerospace structures because of its flexibility and easily to form into any type shapes of structure. The riveted joint has turn out to be one of the popular joint types in jointing the aerospace structures because they can be easily be disassembled, maintained and inspected. In this paper, thin metal sheet components are assembled together via riveted joints to form a simplified model of aerospace structure. However, to model the jointed structure that are attached together via the mechanical joints such as riveted joint are very difficult due to local effects. Understandably that the dynamic characteristic of the joined structure can be significantly affected by these joints due to local effects at the mating areas of the riveted joints such as surface contact, clamping force and slips. A few types of element connectors that available in MSC NATRAN/PATRAN have investigated in order to presented as the rivet joints. Thus, the results obtained in term of natural frequencies and mode shapes are then contrasted with experimental counterpart in order to investigate the acceptance level of accuracy between element connectors that are used in modelling the rivet joints of the riveted joints structure. The reconciliation method via finiteelement model updating is used to minimise the discrepancy of the initial finite element model of the riveted joined structure as close as experimental data and their results are discussed.

Nuclear microscopy of sperm cell elemental structure

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

Bench, G.S.; Balhorn, R.; Friz, A.M.

1994-09-28

Theories suggest there is a link between protamine concentrations in individual sperm and male fertility. Previously, biochemical analyses have used pooled samples containing millions of sperm to determine protamine concentrations. These methods have not been able to determine what percentage of morphologically normal sperm are biochemically defective and potentially infertile. Nuclear microscopy has been utilized to measure elemental profiles at the single sperm level. By measuring the amount of phosphorus and sulfur, the total DNA and protamine content in individual sperm from fertile bull and mouse semen have been determined. These values agree with results obtained from other biochemical analyses.more » Nuclear microscopy shows promise for measuring elemental profiles in the chromatin of individual sperm. The technique may be able to resolve theories regarding the importance of protamines to male fertility and identify biochemical defects responsible for certain types of male infertility.« less

Delamination Defect Detection Using Ultrasonic Guided Waves in Advanced Hybrid Structural Elements

NASA Astrophysics Data System (ADS)

Yan, Fei; Qi, Kevin ``Xue''; Rose, Joseph L.; Weiland, Hasso

2010-02-01

Nondestructive testing for multilayered structures is challenging because of increased numbers of layers and plate thicknesses. In this paper, ultrasonic guided waves are applied to detect delamination defects inside a 23-layer Alcoa Advanced Hybrid Structural plate. A semi-analytical finite element (SAFE) method generates dispersion curves and wave structures in order to select appropriate wave structures to detect certain defects. One guided wave mode and frequency is chosen to achieve large in-plane displacements at regions of interest. The interactions of the selected mode with defects are simulated using finite element models. Experiments are conducted and compared with bulk wave measurements. It is shown that guided waves can detect deeply embedded damages inside thick multilayer fiber-metal laminates with suitable mode and frequency selection.

Parallel Finite Element Domain Decomposition for Structural/Acoustic Analysis

NASA Technical Reports Server (NTRS)

Nguyen, Duc T.; Tungkahotara, Siroj; Watson, Willie R.; Rajan, Subramaniam D.

2005-01-01

A domain decomposition (DD) formulation for solving sparse linear systems of equations resulting from finite element analysis is presented. The formulation incorporates mixed direct and iterative equation solving strategics and other novel algorithmic ideas that are optimized to take advantage of sparsity and exploit modern computer architecture, such as memory and parallel computing. The most time consuming part of the formulation is identified and the critical roles of direct sparse and iterative solvers within the framework of the formulation are discussed. Experiments on several computer platforms using several complex test matrices are conducted using software based on the formulation. Small-scale structural examples are used to validate thc steps in the formulation and large-scale (l,000,000+ unknowns) duct acoustic examples are used to evaluate the ORIGIN 2000 processors, and a duster of 6 PCs (running under the Windows environment). Statistics show that the formulation is efficient in both sequential and parallel computing environmental and that the formulation is significantly faster and consumes less memory than that based on one of the best available commercialized parallel sparse solvers.

A conserved RNA structural element within the hepatitis B virus post-transcriptional regulatory element enhance nuclear export of intronless transcripts and repress the splicing mechanism.

PubMed

Visootsat, Akasit; Payungporn, Sunchai; T-Thienprasert, Nattanan P

2015-12-01

Hepatitis B virus (HBV) infection is a primary cause of hepatocellular carcinoma and liver cirrhosis worldwide. To develop novel antiviral drugs, a better understanding of HBV gene expression regulation is vital. One important aspect is to understand how HBV hijacks the cellular machinery to export unspliced RNA from the nucleus. The HBV post-transcriptional regulatory element (HBV PRE) has been proposed to be the HBV RNA nuclear export element. However, the function remains controversial, and the core element is unclear. This study, therefore, aimed to identify functional regulatory elements within the HBV PRE and investigate their functions. Using bioinformatics programs based on sequence conservation and conserved RNA secondary structures, three regulatory elements were predicted, namely PRE 1151-1410, PRE 1520-1620 and PRE 1650-1684. PRE 1151-1410 significantly increased intronless and unspliced luciferase activity in both HepG2 and COS-7 cells. Likewise, PRE 1151-1410 significantly elevated intronless and unspliced HBV surface transcripts in liver cancer cells. Moreover, motif analysis predicted that PRE 1151-1410 contains several regulatory motifs. This study reported the roles of PRE 1151-1410 in intronless transcript nuclear export and the splicing mechanism. Additionally, these results provide knowledge in the field of HBV RNA regulation. Moreover, PRE 1151-1410 may be used to enhance the expression of other mRNAs in intronless reporter plasmids.

Performance assessment of geotechnical structural elements using distributed fiber optic sensing

NASA Astrophysics Data System (ADS)

Monsberger, Christoph; Woschitz, Helmut; Lienhart, Werner; Račanský, Václav; Hayden, Martin

2017-04-01

Geotechnical structural elements are used to underpin heavy structures or to stabilize slopes and embankments. The bearing capacity of these components is usually verified by geotechnical load tests. It is state of the art to measure the resulting deformations with electronic sensors at the surface and therefore, the load distribution along the objects cannot be determined. This paper reports about distributed strain measurements with an optical backscatter reflectometer along geotechnical elements. In addition to the installation of the optical fiber in harsh field conditions, results of investigations of the fiber optic system in the laboratory and the most significant results of the field trials are presented.

Regulatory elements of the floral homeotic gene AGAMOUS identified by phylogenetic footprinting and shadowing.

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

Hong, R. L., Hamaguchi, L., Busch, M. A., and Weigel, D.

2003-06-01

OAK-B135 In Arabidopsis thaliana, cis-regulatory sequences of the floral homeotic gene AGAMOUS (AG) are located in the second intron. This 3 kb intron contains binding sites for two direct activators of AG, LEAFY (LFY) and WUSCHEL (WUS), along with other putative regulatory elements. We have used phylogenetic footprinting and the related technique of phylogenetic shadowing to identify putative cis-regulatory elements in this intron. Among 29 Brassicaceae, several other motifs, but not the LFY and WUS binding sites previously identified, are largely invariant. Using reporter gene analyses, we tested six of these motifs and found that they are all functionally importantmore » for activity of AG regulatory sequences in A. thaliana. Although there is little obvious sequence similarity outside the Brassicaceae, the intron from cucumber AG has at least partial activity in A. thaliana. Our studies underscore the value of the comparative approach as a tool that complements gene-by-gene promoter dissection, but also highlight that sequence-based studies alone are insufficient for a complete identification of cis-regulatory sites.« less

Energy Finite Element Analysis Developments for Vibration Analysis of Composite Aircraft Structures

NASA Technical Reports Server (NTRS)

Vlahopoulos, Nickolas; Schiller, Noah H.

2011-01-01

The Energy Finite Element Analysis (EFEA) has been utilized successfully for modeling complex structural-acoustic systems with isotropic structural material properties. In this paper, a formulation for modeling structures made out of composite materials is presented. An approach based on spectral finite element analysis is utilized first for developing the equivalent material properties for the composite material. These equivalent properties are employed in the EFEA governing differential equations for representing the composite materials and deriving the element level matrices. The power transmission characteristics at connections between members made out of non-isotropic composite material are considered for deriving suitable power transmission coefficients at junctions of interconnected members. These coefficients are utilized for computing the joint matrix that is needed to assemble the global system of EFEA equations. The global system of EFEA equations is solved numerically and the vibration levels within the entire system can be computed. The new EFEA formulation for modeling composite laminate structures is validated through comparison to test data collected from a representative composite aircraft fuselage that is made out of a composite outer shell and composite frames and stiffeners. NASA Langley constructed the composite cylinder and conducted the test measurements utilized in this work.

Dynamic Shape Reconstruction of Three-Dimensional Frame Structures Using the Inverse Finite Element Method

NASA Technical Reports Server (NTRS)

Gherlone, Marco; Cerracchio, Priscilla; Mattone, Massimiliano; Di Sciuva, Marco; Tessler, Alexander

2011-01-01

A robust and efficient computational method for reconstructing the three-dimensional displacement field of truss, beam, and frame structures, using measured surface-strain data, is presented. Known as shape sensing , this inverse problem has important implications for real-time actuation and control of smart structures, and for monitoring of structural integrity. The present formulation, based on the inverse Finite Element Method (iFEM), uses a least-squares variational principle involving strain measures of Timoshenko theory for stretching, torsion, bending, and transverse shear. Two inverse-frame finite elements are derived using interdependent interpolations whose interior degrees-of-freedom are condensed out at the element level. In addition, relationships between the order of kinematic-element interpolations and the number of required strain gauges are established. As an example problem, a thin-walled, circular cross-section cantilevered beam subjected to harmonic excitations in the presence of structural damping is modeled using iFEM; where, to simulate strain-gauge values and to provide reference displacements, a high-fidelity MSC/NASTRAN shell finite element model is used. Examples of low and high-frequency dynamic motion are analyzed and the solution accuracy examined with respect to various levels of discretization and the number of strain gauges.

Nonlinear dynamics of solitary and optically injected two-element laser arrays with four different waveguide structures: a numerical study.

PubMed

Li, Nianqiang; Susanto, H; Cemlyn, B R; Henning, I D; Adams, M J

2018-02-19

We study the nonlinear dynamics of solitary and optically injected two-element laser arrays with a range of waveguide structures. The analysis is performed with a detailed direct numerical simulation, where high-resolution dynamic maps are generated to identify regions of dynamic instability in the parameter space of interest. Our combined one- and two-parameter bifurcation analysis uncovers globally diverse dynamical regimes (steady-state, oscillation, and chaos) in the solitary laser arrays, which are greatly influenced by static design waveguiding structures, the amplitude-phase coupling factor of the electric field, i.e. the linewidth-enhancement factor, as well as the control parameter, e.g. the pump rate. When external optical injection is introduced to one element of the arrays, we show that the whole system can be either injection-locked simultaneously or display rich, different dynamics outside the locking region. The effect of optical injection is to significantly modify the nature and the regions of nonlinear dynamics from those found in the solitary case. We also show similarities and differences (asymmetry) between the oscillation amplitude of the two elements of the array in specific well-defined regions, which hold for all the waveguiding structures considered. Our findings pave the way to a better understanding of dynamic instability in large arrays of lasers.

PLANS; a finite element program for nonlinear analysis of structures. Volume 2: User's manual

NASA Technical Reports Server (NTRS)

Pifko, A.; Armen, H., Jr.; Levy, A.; Levine, H.

1977-01-01

The PLANS system, rather than being one comprehensive computer program, is a collection of finite element programs used for the nonlinear analysis of structures. This collection of programs evolved and is based on the organizational philosophy in which classes of analyses are treated individually based on the physical problem class to be analyzed. Each of the independent finite element computer programs of PLANS, with an associated element library, can be individually loaded and used to solve the problem class of interest. A number of programs have been developed for material nonlinear behavior alone and for combined geometric and material nonlinear behavior. The usage, capabilities, and element libraries of the current programs include: (1) plastic analysis of built-up structures where bending and membrane effects are significant, (2) three dimensional elastic-plastic analysis, (3) plastic analysis of bodies of revolution, and (4) material and geometric nonlinear analysis of built-up structures.

Osmium-Isotope and Platinum-Group-Element Systematics of Impact-Melt Rocks, Chesapeake Bay Impact Structure, Virginia, USA

NASA Technical Reports Server (NTRS)

Lee, Seung Ryeol; Wright Horton, J., Jr.; Walker, Richard J.

2005-01-01

Osmium (Os) isotopes and platinum-group elements (PGEs) are useful for geochemically identifying a meteoritic component within impact structures, because meteorites are typically characterized by low (187)Os/(188)Os ratios and high PGE concentrations. In contrast, most types of crustal target rocks have high radiogenic Os and very low PGE concentrations. We have examined Os isotope and PGE systematics of impact-melt rocks and pre-impact target rocks from a 2004 test hole in the late Eocene Chesapeake Bay impact structure and from nearby coreholes. Our goal is to determine the proportion of the projectile component in the melt rock Additional information is included in the original extended abstract.

On the way to unveiling the atomic structure of superheavy elements

NASA Astrophysics Data System (ADS)

Laatiaoui, Mustapha

2016-12-01

Optical spectroscopy of the transfermium elements (atomic number Z > 100) is nowadays one of the most fascinating and simultaneously challenging tasks in atomic physics. On the one hand, key atomic and even nuclear ground-state properties may be obtained by studying the spectral lines of these heaviest elements. On the other hand, these elements have to be produced "online" by heavy-ion induced fusion-evaporation reactions yielding rates on the order of a few atoms per second at most, which renders their optical spectroscopy extremely difficult. Only recently, a first foray of laser spectroscopy into this heaviest element region was reported. Several atomic transitions in the element nobelium (Z = 102) were observed and characterized, using an ultra-sensitive and highly efficient resonance ionization technique. The findings confirm the predictions and additionally provide a benchmark for theoretical modelling. The work represents an important stepping stone towards experimental studies of the atomic structure of superheavy elements.

Applications of a global nuclear-structure model to studies of the heaviest elements

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

Moeller, P.; Nix, J.R.

1993-10-01

We present some new results on heavy-element nuclear-structure properties calculated on the basis of the finite-range droplet model and folded-Yukawa single-particle potential. Specifically, we discuss calculations of nuclear ground-state masses and microscopic corrections, {alpha}-decay properties, {beta}-decay properties, fission potential-energy surfaces, and spontaneous-fission half-lives. These results, obtained in a global nuclear-structure approach, are particularly reliable for describing the stability properties of the heaviest elements.

Characterization of elemental and structural composition of corrosion scales and deposits formed in drinking water distribution systems.

PubMed

Peng, Ching-Yu; Korshin, Gregory V; Valentine, Richard L; Hill, Andrew S; Friedman, Melinda J; Reiber, Steve H

2010-08-01

Corrosion scales and deposits formed within drinking water distribution systems (DWDSs) have the potential to retain inorganic contaminants. The objective of this study was to characterize the elemental and structural composition of extracted pipe solids and hydraulically-mobile deposits originating from representative DWDSs. Goethite (alpha-FeOOH), magnetite (Fe(3)O(4)) and siderite (FeCO(3)) were the primary crystalline phases identified in most of the selected samples. Among the major constituent elements of the deposits, iron was most prevalent followed, in the order of decreasing prevalence, by sulfur, organic carbon, calcium, inorganic carbon, phosphorus, manganese, magnesium, aluminum and zinc. The cumulative occurrence profiles of iron, sulfur, calcium and phosphorus for pipe specimens and flushed solids were similar. Comparison of relative occurrences of these elements indicates that hydraulic disturbances may have relatively less impact on the release of manganese, aluminum and zinc, but more impact on the release of organic carbon, inorganic carbon, and magnesium. (c) 2010 Elsevier Ltd. All rights reserved.

Storage Area (1942 section), looking east, showing concrete structural elements ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

Storage Area (1942 section), looking east, showing concrete structural elements and wall opening to vaults - Fort McNair, Film Store House, Fort Lesley J. McNair, P Street between Third & Fourth Streets, Southwest, Washington, District of Columbia, DC

Finite element analysis of a deployable space structure

NASA Technical Reports Server (NTRS)

Hutton, D. V.

1982-01-01

To assess the dynamic characteristics of a deployable space truss, a finite element model of the Scientific Applications Space Platform (SASP) truss has been formulated. The model incorporates all additional degrees of freedom associated with the pin-jointed members. Comparison of results with SPAR models of the truss show that the joints of the deployable truss significantly affect the vibrational modes of the structure only if the truss is relatively short.

Symmetric tridiagonal structure preserving finite element model updating problem for the quadratic model

NASA Astrophysics Data System (ADS)

Rakshit, Suman; Khare, Swanand R.; Datta, Biswa Nath

2018-07-01

One of the most important yet difficult aspect of the Finite Element Model Updating Problem is to preserve the finite element inherited structures in the updated model. Finite element matrices are in general symmetric, positive definite (or semi-definite) and banded (tridiagonal, diagonal, penta-diagonal, etc.). Though a large number of papers have been published in recent years on various aspects of solutions of this problem, papers dealing with structure preservation almost do not exist. A novel optimization based approach that preserves the symmetric tridiagonal structures of the stiffness and damping matrices is proposed in this paper. An analytical expression for the global minimum solution of the associated optimization problem along with the results of numerical experiments obtained by both the analytical expressions and by an appropriate numerical optimization algorithm are presented. The results of numerical experiments support the validity of the proposed method.

Conserved Structural Elements in the V3 Crown of HIV-1 gp120

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

Jiang, X.; Burke, V; Totrov, M

2010-01-01

Binding of the third variable region (V3) of the HIV-1 envelope glycoprotein gp120 to the cell-surface coreceptors CCR5 or CXCR4 during viral entry suggests that there are conserved structural elements in this sequence-variable region. These conserved elements could serve as epitopes to be targeted by a vaccine against HIV-1. Here we perform a systematic structural analysis of representative human anti-V3 monoclonal antibodies in complex with V3 peptides, revealing that the crown of V3 has four conserved structural elements: an arch, a band, a hydrophobic core and the peptide backbone. These are either unaffected by or are subject to minimal sequencemore » variation. As these regions are targeted by cross-clade neutralizing human antibodies, they provide a blueprint for the design of vaccine immunogens that could elicit broadly cross-reactive protective antibodies.« less

ESPERR: learning strong and weak signals in genomic sequence alignments to identify functional elements.

PubMed

Taylor, James; Tyekucheva, Svitlana; King, David C; Hardison, Ross C; Miller, Webb; Chiaromonte, Francesca

2006-12-01

Genomic sequence signals - such as base composition, presence of particular motifs, or evolutionary constraint - have been used effectively to identify functional elements. However, approaches based only on specific signals known to correlate with function can be quite limiting. When training data are available, application of computational learning algorithms to multispecies alignments has the potential to capture broader and more informative sequence and evolutionary patterns that better characterize a class of elements. However, effective exploitation of patterns in multispecies alignments is impeded by the vast number of possible alignment columns and by a limited understanding of which particular strings of columns may characterize a given class. We have developed a computational method, called ESPERR (evolutionary and sequence pattern extraction through reduced representations), which uses training examples to learn encodings of multispecies alignments into reduced forms tailored for the prediction of chosen classes of functional elements. ESPERR produces a greatly improved Regulatory Potential score, which can discriminate regulatory regions from neutral sites with excellent accuracy ( approximately 94%). This score captures strong signals (GC content and conservation), as well as subtler signals (with small contributions from many different alignment patterns) that characterize the regulatory elements in our training set. ESPERR is also effective for predicting other classes of functional elements, as we show for DNaseI hypersensitive sites and highly conserved regions with developmental enhancer activity. Our software, training data, and genome-wide predictions are available from our Web site (http://www.bx.psu.edu/projects/esperr).

Structural evaluation of the John A. Roebling Suspension Bridge : element level analysis.

DOT National Transportation Integrated Search

2008-07-01

The primary objective of the structural evaluation of the John A. Roebling Bridge is to determine the maximum allowable gross vehicle weight (GVW) that can be carried by the bridge deck structural elements such as the open steel grid deck, channels, ...

Three novel approaches to structural identifiability analysis in mixed-effects models.

PubMed

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

2016-05-06

Structural identifiability is a concept that considers whether the structure of a model together with a set of input-output relations uniquely determines the model parameters. In the mathematical modelling of biological systems, structural identifiability is an important concept since biological interpretations are typically made from the parameter estimates. For a system defined by ordinary differential equations, several methods have been developed to analyse whether the model is structurally identifiable or otherwise. Another well-used modelling framework, which is particularly useful when the experimental data are sparsely sampled and the population variance is of interest, is mixed-effects modelling. However, established identifiability analysis techniques for ordinary differential equations are not directly applicable to such models. In this paper, we present and apply three different methods that can be used to study structural identifiability in mixed-effects models. The first method, called the repeated measurement approach, is based on applying a set of previously established statistical theorems. The second method, called the augmented system approach, is based on augmenting the mixed-effects model to an extended state-space form. The third method, called the Laplace transform mixed-effects extension, is based on considering the moment invariants of the systems transfer function as functions of random variables. To illustrate, compare and contrast the application of the three methods, they are applied to a set of mixed-effects models. Three structural identifiability analysis methods applicable to mixed-effects models have been presented in this paper. As method development of structural identifiability techniques for mixed-effects models has been given very little attention, despite mixed-effects models being widely used, the methods presented in this paper provides a way of handling structural identifiability in mixed-effects models previously not

A Six-Node Curved Triangular Element and a Four-Node Quadrilateral Element for Analysis of Laminated Composite Aerospace Structures

NASA Technical Reports Server (NTRS)

Martin, C. Wayne; Breiner, David M.; Gupta, Kajal K. (Technical Monitor)

2004-01-01

Mathematical development and some computed results are presented for Mindlin plate and shell elements, suitable for analysis of laminated composite and sandwich structures. These elements use the conventional 3 (plate) or 5 (shell) nodal degrees of freedom, have no communicable mechanisms, have no spurious shear energy (no shear locking), have no spurious membrane energy (no membrane locking) and do not require arbitrary reduction of out-of-plane shear moduli or under-integration. Artificial out-of-plane rotational stiffnesses are added at the element level to avoid convergence problems or singularity due to flat spots in shells. This report discusses a 6-node curved triangular element and a 4-node quadrilateral element. Findings show that in regular rectangular meshes, the Martin-Breiner 6-node triangular curved shell (MB6) is approximately equivalent to the conventional 8-node quadrilateral with integration. The 4-node quadrilateral (MB4) has very good accuracy for a 4-node element, and may be preferred in vibration analysis because of narrower bandwidth. The mathematical developments used in these elements, those discussed in the seven appendices, have been applied to elements with 3, 4, 6, and 10 nodes and can be applied to other nodal configurations.

State Children's Cabinets and Councils--Elements of Success Issue 1: Structural Options

ERIC Educational Resources Information Center

Gaines, Elizabeth; Faigley, Ian; Pittman, Karen

2008-01-01

Elements of Success 1: Structural Options outlines the range of current children's cabinet and council structures in place and offers tips and warnings for getting the most effective structure in place. This issue brief builds heavily on interviews conducted by the Forum and on the detailed documentation work done by Susan Robison for the National…

Elemental composition and structural characteristics of as-received TriTaniumTM orthodontic archwire

NASA Astrophysics Data System (ADS)

Ilievska, I.; Petrov, V.; Mihailov, V.; Karatodorov, S.; Andreeva, L.; Zaleski, A.; Mikli, V.; Gueorgieva, M.; Petrova, V.; Stoyanova-Ivanova, A.

2018-03-01

Orthodontic archwires are among the most important devices of fixed orthodontic therapy. Many types of archwires are made available on the market by various manufacturers with different elemental composition and structural characteristics. Knowing this information is important when choosing a suitable archwire for a particular stage of orthodontic treatment. The aim of our study is to characterize a new type orthodontic archwires (TriTaniumTM, American Orthodontics) before their placement in the oral cavity. To achieve the aim, we used modern methods for determining their elemental composition and structural characteristics: laser-induced plasma spectroscopy (LIBS), X-ray diffraction analysis (XRD), scanning electronic microscopy (SEM), energy dispersive X-ray spectroscopy (EDX) and differential scanning calorimetry (DSC). The results obtained from the qualitative elemental analysis by LIBS and the quantitative elemental analysis by EDX showed that Ni and Ti are the main elements in the archwire studied. The room-temperature XRD patterns showed peaks typical for a Ni-Ti alloy with an austenite-type structure. Monitoring the phase transitions by means of DSC measurements in the temperature range from –50 °C to +50 °C, we showed that in TriTaniumTM archwires, besides the austenite to martensite transition, there exists a rhombohedral intermediate phase (R phase). This study will be useful in assisting orthodontists in applying appropriate nickel-titanium orthodontic archwires in the clinical practice.

Causality Analysis: Identifying the Leading Element in a Coupled Dynamical System

PubMed Central

BozorgMagham, Amir E.; Motesharrei, Safa; Penny, Stephen G.; Kalnay, Eugenia

2015-01-01

Physical systems with time-varying internal couplings are abundant in nature. While the full governing equations of these systems are typically unknown due to insufficient understanding of their internal mechanisms, there is often interest in determining the leading element. Here, the leading element is defined as the sub-system with the largest coupling coefficient averaged over a selected time span. Previously, the Convergent Cross Mapping (CCM) method has been employed to determine causality and dominant component in weakly coupled systems with constant coupling coefficients. In this study, CCM is applied to a pair of coupled Lorenz systems with time-varying coupling coefficients, exhibiting switching between dominant sub-systems in different periods. Four sets of numerical experiments are carried out. The first three cases consist of different coupling coefficient schemes: I) Periodic–constant, II) Normal, and III) Mixed Normal/Non-normal. In case IV, numerical experiment of cases II and III are repeated with imposed temporal uncertainties as well as additive normal noise. Our results show that, through detecting directional interactions, CCM identifies the leading sub-system in all cases except when the average coupling coefficients are approximately equal, i.e., when the dominant sub-system is not well defined. PMID:26125157

Network structure and concentration fluctuations in a series of elemental, binary, and tertiary liquids and glasses.

PubMed

Soper, Alan K

2010-10-13

Liquids and glasses continue to produce a lively debate about the nature of the disordered structure in these materials, and whether it is driven by longer range concentration or density fluctuations. One factor often lacking in these studies is an overview of a wide range of structures from which common features of and differences between materials can be identified. Here I examine the structure of a wide range of chain and network, elemental, binary and tertiary liquids and glasses, using available x-ray and neutron diffraction data and combining them with empirical potential structure refinement. Calculation of the Bhatia-Thornton number-number and concentration-concentration structure factors and distribution functions highlights common structural motifs that run through many of the series. It is found that the greatest structural overlap occurs where the nearest-neighbour and second-neighbour coordination numbers are similar for different materials. As these coordination numbers increase, so the structures undergo a sequence of characteristic changes involving increasingly bent bond angle distributions and increased packing fractions. In these regards liquid and amorphous phosphorus appear to be in a structural class of their own, combining both chain-like and network-like characteristics.

A systematic evaluation of expression of HERV-W elements; influence of genomic context, viral structure and orientation

PubMed Central

2011-01-01

Background One member of the W family of human endogenous retroviruses (HERV) appears to have been functionally adopted by the human host. Nevertheless, a highly diversified and regulated transcription from a range of HERV-W elements has been observed in human tissues and cells. Aberrant expression of members of this family has also been associated with human disease such as multiple sclerosis (MS) and schizophrenia. It is not known whether this broad expression of HERV-W elements represents transcriptional leakage or specific transcription initiated from the retroviral promoter in the long terminal repeat (LTR) region. Therefore, potential influences of genomic context, structure and orientation on the expression levels of individual HERV-W elements in normal human tissues were systematically investigated. Results Whereas intronic HERV-W elements with a pseudogene structure exhibited a strong anti-sense orientation bias, intronic elements with a proviral structure and solo LTRs did not. Although a highly variable expression across tissues and elements was observed, systematic effects of context, structure and orientation were also observed. Elements located in intronic regions appeared to be expressed at higher levels than elements located in intergenic regions. Intronic elements with proviral structures were expressed at higher levels than those elements bearing hallmarks of processed pseudogenes or solo LTRs. Relative to their corresponding genes, intronic elements integrated on the sense strand appeared to be transcribed at higher levels than those integrated on the anti-sense strand. Moreover, the expression of proviral elements appeared to be independent from that of their corresponding genes. Conclusions Intronic HERV-W provirus integrations on the sense strand appear to have elicited a weaker negative selection than pseudogene integrations of transcripts from such elements. Our current findings suggest that the previously observed diversified and tissue

Finite Macro-Element Mesh Deformation in a Structured Multi-Block Navier-Stokes Code

NASA Technical Reports Server (NTRS)

Bartels, Robert E.

2005-01-01

A mesh deformation scheme is developed for a structured multi-block Navier-Stokes code consisting of two steps. The first step is a finite element solution of either user defined or automatically generated macro-elements. Macro-elements are hexagonal finite elements created from a subset of points from the full mesh. When assembled, the finite element system spans the complete flow domain. Macro-element moduli vary according to the distance to the nearest surface, resulting in extremely stiff elements near a moving surface and very pliable elements away from boundaries. Solution of the finite element system for the imposed boundary deflections generally produces smoothly varying nodal deflections. The manner in which distance to the nearest surface has been found to critically influence the quality of the element deformation. The second step is a transfinite interpolation which distributes the macro-element nodal deflections to the remaining fluid mesh points. The scheme is demonstrated for several two-dimensional applications.

A multi-element screening method to identify metal targets for blood biomonitoring in green sea turtles (Chelonia mydas).

PubMed

Villa, C A; Finlayson, S; Limpus, C; Gaus, C

2015-04-15

Biomonitoring of blood is commonly used to identify and quantify occupational or environmental exposure to chemical contaminants. Increasingly, this technique has been applied to wildlife contaminant monitoring, including for green turtles, allowing for the non-lethal evaluation of chemical exposure in their nearshore environment. The sources, composition, bioavailability and toxicity of metals in the marine environment are, however, often unknown and influenced by numerous biotic and abiotic factors. These factors can vary considerably across time and space making the selection of the most informative elements for biomonitoring challenging. This study aimed to validate an ICP-MS multi-element screening method for green turtle blood in order to identify and facilitate prioritisation of target metals for subsequent fully quantitative analysis. Multi-element screening provided semiquantitative results for 70 elements, 28 of which were also determined through fully quantitative analysis. Of the 28 comparable elements, 23 of the semiquantitative results had an accuracy between 67% and 112% relative to the fully quantified values. In lieu of any available turtle certified reference materials (CRMs), we evaluated the use of human blood CRMs as a matrix surrogate for quality control, and compared two commonly used sample preparation methods for matrix related effects. The results demonstrate that human blood provides an appropriate matrix for use as a quality control material in the fully quantitative analysis of metals in turtle blood. An example for the application of this screening method is provided by comparing screening results from blood of green turtles foraging in an urban and rural region in Queensland, Australia. Potential targets for future metal biomonitoring in these regions were identified by this approach. Copyright © 2014 Elsevier B.V. All rights reserved.

Creating a Test-Validated Finite-Element Model of the X-56A Aircraft Structure

NASA Technical Reports Server (NTRS)

Pak, Chan-Gi; Truong, Samson

2014-01-01

Small modeling errors in a finite-element model will eventually induce errors in the structural flexibility and mass, thus propagating into unpredictable errors in the unsteady aerodynamics and the control law design. One of the primary objectives of the X-56A Multi-Utility Technology Testbed aircraft is the flight demonstration of active flutter suppression and, therefore, in this study, the identification of the primary and secondary modes for the structural model tuning based on the flutter analysis of the X-56A aircraft. The ground-vibration test-validated structural dynamic finite-element model of the X-56A aircraft is created in this study. The structural dynamic finite-element model of the X-56A aircraft is improved using a model-tuning tool. In this study, two different weight configurations of the X-56A aircraft have been improved in a single optimization run. Frequency and the cross-orthogonality (mode shape) matrix were the primary focus for improvement, whereas other properties such as c.g. location, total weight, and off-diagonal terms of the mass orthogonality matrix were used as constraints. The end result was an improved structural dynamic finite-element model configuration for the X-56A aircraft. Improved frequencies and mode shapes in this study increased average flutter speeds of the X-56A aircraft by 7.6% compared to the baseline model.

Usage of digital image correlation in assessment of behavior of block element pavement structure

NASA Astrophysics Data System (ADS)

Grygierek, M.; Grzesik, B.; Rokitowski, P.; Rusin, T.

2018-05-01

In diagnostics of existing road pavement structures deflection measurements have fundamental meaning, because of ability to assess present stiffness (bearing capacity) of whole layered construction. During test loading the reaction of pavement structure to applied load is measured in central point or in a few points located along a straight on a 1.5 ÷ 1.8 m distance (i.e. Falling Weight Deflectometer) in similar spacing equal to 20 ÷ 30 cm. Typical measuring techniques are productive and precise enough for most common pavement structures such as flexible, semi-rigid and rigid. It should be noted that in experimental research as well as in pavements in complex stress state, measurement techniques allowing observation of pavement deformation in 3D would have been very helpful. A great example of that type of pavements is a block element pavement structure consisting of i.e. paving blocks or stone slabs. Due to high stiffness and confined ability of cooperation of surrounding block elements, in that type of pavements fatigue life is strongly connected with displacement distribution. Unfortunately, typical deflection measurement methods forefend displacement observations and rotation of single block elements like paving blocks or slabs. Another difficult problem is to carry out unmistakable analysis of cooperation between neighboring elements. For more precise observations of displacements state of block element pavements under a wheel load a Digital Image Correlation (DIC) was used. Application of this method for assessment of behavior of stone slabs pavement under a traffic load enabled the monitoring of deformations distribution and encouraged to formulate conclusions about the initiation mechanism and development of damages in this type of pavement structures. Results shown in this article were obtained in field tests executed on an exploited pavement structure with a surface course made of granite slabs with dimensions 0.5x1.0x0.14 m.

A Curved, Elastostatic Boundary Element for Plane Anisotropic Structures

NASA Technical Reports Server (NTRS)

Smeltzer, Stanley S.; Klang, Eric C.

2001-01-01

The plane-stress equations of linear elasticity are used in conjunction with those of the boundary element method to develop a novel curved, quadratic boundary element applicable to structures composed of anisotropic materials in a state of plane stress or plane strain. The curved boundary element is developed to solve two-dimensional, elastostatic problems of arbitrary shape, connectivity, and material type. As a result of the anisotropy, complex variables are employed in the fundamental solution derivations for a concentrated unit-magnitude force in an infinite elastic anisotropic medium. Once known, the fundamental solutions are evaluated numerically by using the known displacement and traction boundary values in an integral formulation with Gaussian quadrature. All the integral equations of the boundary element method are evaluated using one of two methods: either regular Gaussian quadrature or a combination of regular and logarithmic Gaussian quadrature. The regular Gaussian quadrature is used to evaluate most of the integrals along the boundary, and the combined scheme is employed for integrals that are singular. Individual element contributions are assembled into the global matrices of the standard boundary element method, manipulated to form a system of linear equations, and the resulting system is solved. The interior displacements and stresses are found through a separate set of auxiliary equations that are derived using an Airy-type stress function in terms of complex variables. The capabilities and accuracy of this method are demonstrated for a laminated-composite plate with a central, elliptical cutout that is subjected to uniform tension along one of the straight edges of the plate. Comparison of the boundary element results for this problem with corresponding results from an analytical model show a difference of less than 1%.

Finite Element Analysis of an Energy Absorbing Sub-floor Structure

NASA Technical Reports Server (NTRS)

Moore, Scott C.

1995-01-01

As part of the Advanced General Aviation Transportation Experiments program, the National Aeronautics and Space Administration's Langley Research Center is conducting tests to design energy absorbing structures to improve occupant survivability in aircraft crashes. An effort is currently underway to design an Energy Absorbing (EA) sub-floor structure which will reduce occupant loads in an aircraft crash. However, a recent drop test of a fuselage specimen with a proposed EA sub-floor structure demonstrated that the effects of sectioning the fuselage on both the fuselage section's stiffness and the performance of the EA structure were not fully understood. Therefore, attempts are underway to model the proposed sub-floor structure on computers using the DYCAST finite element code to provide a better understanding of the structure's behavior in testing, and in an actual crash.

Finite Element Based HWB Centerbody Structural Optimization and Weight Prediction

NASA Technical Reports Server (NTRS)

Gern, Frank H.

2012-01-01

This paper describes a scalable structural model suitable for Hybrid Wing Body (HWB) centerbody analysis and optimization. The geometry of the centerbody and primary wing structure is based on a Vehicle Sketch Pad (VSP) surface model of the aircraft and a FLOPS compatible parameterization of the centerbody. Structural analysis, optimization, and weight calculation are based on a Nastran finite element model of the primary HWB structural components, featuring centerbody, mid section, and outboard wing. Different centerbody designs like single bay or multi-bay options are analyzed and weight calculations are compared to current FLOPS results. For proper structural sizing and weight estimation, internal pressure and maneuver flight loads are applied. Results are presented for aerodynamic loads, deformations, and centerbody weight.

Response of basic structural elements and B-52 structural components to simulated nuclear overpressure. Volume II-program data (basic structural elements). Final report, 1 June 1977-30 September 1979

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

Syring, R.P.; Grubb, R.L.

1979-09-30

This document reports on the following: (1) experimental determination of the response of 16 basic structural elements and 7 B-52 components to simulated nuclear overpressure environments (utilizing Sandia Corporation's Thunderpipe Shock Tube), (2) analysis of these test specimens utilizing the NOVA-2 computer program, and (3) correlation of test and analysis results.

Finite element structural model of a large, thin, completely free, flat plate. [for large space structures

NASA Technical Reports Server (NTRS)

Joshi, S. M.; Groom, N. J.

1980-01-01

A finite element structural model of a 30.48 m x 30.48 m x 2.54 mm completely free aluminum plate is described and modal frequencies and mode shape data for the first 44 modes are presented. An explanation of the procedure for using the data is also presented. The model should prove useful for the investigation of controller design approaches for large flexible space structures.

Assumed--stress hybrid elements with drilling degrees of freedom for nonlinear analysis of composite structures

NASA Technical Reports Server (NTRS)

Knight, Norman F., Jr. (Principal Investigator)

1996-01-01

The goal of this research project is to develop assumed-stress hybrid elements with rotational degrees of freedom for analyzing composite structures. During the first year of the three-year activity, the effort was directed to further assess the AQ4 shell element and its extensions to buckling and free vibration problems. In addition, the development of a compatible 2-node beam element was to be accomplished. The extensions and new developments were implemented in the Computational Structural Mechanics Testbed COMET. An assessment was performed to verify the implementation and to assess the performance of these elements in terms of accuracy. During the second and third years, extensions to geometrically nonlinear problems were developed and tested. This effort involved working with the nonlinear solution strategy as well as the nonlinear formulation for the elements. This research has resulted in the development and implementation of two additional element processors (ES22 for the beam element and ES24 for the shell elements) in COMET. The software was developed using a SUN workstation and has been ported to the NASA Langley Convex named blackbird. Both element processors are now part of the baseline version of COMET.

Local structures around the substituted elements in mixed layered oxides

PubMed Central

Akama, Shota; Kobayashi, Wataru; Amaha, Kaoru; Niwa, Hideharu; Nitani, Hiroaki; Moritomo, Yutaka

2017-01-01

The chemical substitution of a transition metal (M) is an effective method to improve the functionality of a material, such as its electrochemical, magnetic, and dielectric properties. The substitution, however, causes local lattice distortion because the difference in the ionic radius (r) modifies the local interatomic distances. Here, we systematically investigated the local structures in the pure (x = 0.0) and mixed (x = 0.05 or 0.1) layered oxides, Na(M1−xM′x)O2 (M and M′ are the majority and minority transition metals, respectively), by means of extended X-ray absorption fine structure (EXAFS) analysis. We found that the local interatomic distance (dM-O) around the minority element approaches that around the majority element to reduces the local lattice distortion. We further found that the valence of the minority Mn changes so that its ionic radius approaches that of the majority M. PMID:28252008

Palinspastic reconstruction of structure maps: an automated finite element approach with heterogeneous strain

NASA Astrophysics Data System (ADS)

Dunbar, John A.; Cook, Richard W.

2003-07-01

Existing methods for the palinspastic reconstruction of structure maps do not adequately account for heterogeneous rock strain and hence cannot accurately treat features such as fault terminations and non-cylindrical folds. We propose a new finite element formulation of the map reconstruction problem that treats such features explicitly. In this approach, a model of the map surface, with internal openings that honor the topology of the fault-gap network, is constructed of triangular finite elements. Both model building and reconstruction algorithms are guided by rules relating fault-gap topology to the kinematics of fault motion and are fully automated. We represent the total strain as the sum of a prescribed component of locally homogeneous simple shear and a minimum amount of heterogeneous residual strain. The region within which a particular orientation of simple shear is treated as homogenous can be as small as an individual element or as large as the entire map. For residual strain calculations, we treat the map surface as a hyperelastic membrane. A globally optimum reconstruction is found that unfolds the map while faithfully honoring assigned strain mechanisms, closes fault gaps without overlap or gap and imparts the least possible residual strain in the restored surface. The amount and distribution of the residual strain serves as a diagnostic tool for identifying mapping errors. The method can be used to reconstruct maps offset by any number of faults that terminate, branch and offset each other in arbitrarily complex ways.

TAP 2: A finite element program for thermal analysis of convectively cooled structures

NASA Technical Reports Server (NTRS)

Thornton, E. A.

1980-01-01

A finite element computer program (TAP 2) for steady-state and transient thermal analyses of convectively cooled structures is presented. The program has a finite element library of six elements: two conduction/convection elements to model heat transfer in a solid, two convection elements to model heat transfer in a fluid, and two integrated conduction/convection elements to represent combined heat transfer in tubular and plate/fin fluid passages. Nonlinear thermal analysis due to temperature-dependent thermal parameters is performed using the Newton-Raphson iteration method. Transient analyses are performed using an implicit Crank-Nicolson time integration scheme with consistent or lumped capacitance matrices as an option. Program output includes nodal temperatures and element heat fluxes. Pressure drops in fluid passages may be computed as an option. User instructions and sample problems are presented in appendixes.

Allele frequencies of variants in ultra conserved elements identify selective pressure on transcription factor binding.

PubMed

Silla, Toomas; Kepp, Katrin; Tai, E Shyong; Goh, Liang; Davila, Sonia; Catela Ivkovic, Tina; Calin, George A; Voorhoeve, P Mathijs

2014-01-01

Ultra-conserved genes or elements (UCGs/UCEs) in the human genome are extreme examples of conservation. We characterized natural variations in 2884 UCEs and UCGs in two distinct populations; Singaporean Chinese (n = 280) and Italian (n = 501) by using a pooled sample, targeted capture, sequencing approach. We identify, with high confidence, in these regions the abundance of rare SNVs (MAF<0.5%) of which 75% is not present in dbSNP137. UCEs association studies for complex human traits can use this information to model expected background variation and thus necessary power for association studies. By combining our data with 1000 Genome Project data, we show in three independent datasets that prevalent UCE variants (MAF>5%) are more often found in relatively less-conserved nucleotides within UCEs, compared to rare variants. Moreover, prevalent variants are less likely to overlap transcription factor binding site. Using SNPfold we found no significant influence of RNA secondary structure on UCE conservation. All together, these results suggest UCEs are not under selective pressure as a stretch of DNA but are under differential evolutionary pressure on the single nucleotide level.

Validation of finite element and boundary element methods for predicting structural vibration and radiated noise

NASA Technical Reports Server (NTRS)

Seybert, A. F.; Wu, X. F.; Oswald, Fred B.

1992-01-01

Analytical and experimental validation of methods to predict structural vibration and radiated noise are presented. A rectangular box excited by a mechanical shaker was used as a vibrating structure. Combined finite element method (FEM) and boundary element method (BEM) models of the apparatus were used to predict the noise radiated from the box. The FEM was used to predict the vibration, and the surface vibration was used as input to the BEM to predict the sound intensity and sound power. Vibration predicted by the FEM model was validated by experimental modal analysis. Noise predicted by the BEM was validated by sound intensity measurements. Three types of results are presented for the total radiated sound power: (1) sound power predicted by the BEM modeling using vibration data measured on the surface of the box; (2) sound power predicted by the FEM/BEM model; and (3) sound power measured by a sound intensity scan. The sound power predicted from the BEM model using measured vibration data yields an excellent prediction of radiated noise. The sound power predicted by the combined FEM/BEM model also gives a good prediction of radiated noise except for a shift of the natural frequencies that are due to limitations in the FEM model.

Evaluation of the Clinical LOINC (Logical Observation Identifiers, Names, and Codes) Semantic Structure as a Terminology Model for Standardized Assessment Measures

PubMed Central

Bakken, Suzanne; Cimino, James J.; Haskell, Robert; Kukafka, Rita; Matsumoto, Cindi; Chan, Garrett K.; Huff, Stanley M.

2000-01-01

Objective: The purpose of this study was to test the adequacy of the Clinical LOINC (Logical Observation Identifiers, Names, and Codes) semantic structure as a terminology model for standardized assessment measures. Methods: After extension of the definitions, 1,096 items from 35 standardized assessment instruments were dissected into the elements of the Clinical LOINC semantic structure. An additional coder dissected at least one randomly selected item from each instrument. When multiple scale types occurred in a single instrument, a second coder dissected one randomly selected item representative of each scale type. Results: The results support the adequacy of the Clinical LOINC semantic structure as a terminology model for standardized assessments. Using the revised definitions, the coders were able to dissect into the elements of Clinical LOINC all the standardized assessment items in the sample instruments. Percentage agreement for each element was as follows: component, 100 percent; property, 87.8 percent; timing, 82.9 percent; system/sample, 100 percent; scale, 92.6 percent; and method, 97.6 percent. Discussion: This evaluation was an initial step toward the representation of standardized assessment items in a manner that facilitates data sharing and re-use. Further clarification of the definitions, especially those related to time and property, is required to improve inter-rater reliability and to harmonize the representations with similar items already in LOINC. PMID:11062226

Energy flux and characteristic energy of an elemental auroral structure

NASA Technical Reports Server (NTRS)

Lanchester, B. S.; Palmer, J. R.; Rees, M. H.; Lummerzheim, D.; Kaila, K.; Turunen, T.

1994-01-01

Electron density profiles acquired with the EISCAT radar at 0.2 s time resolution, together with TV images and photometric intensities, were used to study the characteristics of thin (less than 1 km) auroral arc structures that drifted through the field of view of the instruments. It is demonstrated that both high time and space resolution are essential for deriving the input parameters of the electron flux responsible for the elemental auroral structures. One such structure required a 400 mW/sq m (erg/sq cm s) downward energy flux carried by an 8 keV monochromatic electron flux equivalent to a current density of 50 micro Angstrom/sq m.

Structural and functional analysis of mouse Msx1 gene promoter: sequence conservation with human MSX1 promoter points at potential regulatory elements.

PubMed

Gonzalez, S M; Ferland, L H; Robert, B; Abdelhay, E

1998-06-01

Vertebrate Msx genes are related to one of the most divergent homeobox genes of Drosophila, the muscle segment homeobox (msh) gene, and are expressed in a well-defined pattern at sites of tissue interactions. This pattern of expression is conserved in vertebrates as diverse as quail, zebrafish, and mouse in a range of sites including neural crest, appendages, and craniofacial structures. In the present work, we performed structural and functional analyses in order to identify potential cis-acting elements that may be regulating Msx1 gene expression. To this end, a 4.9-kb segment of the 5'-flanking region was sequenced and analyzed for transcription-factor binding sites. Four regions showing a high concentration of these sites were identified. Transfection assays with fragments of regulatory sequences driving the expression of the bacterial lacZ reporter gene showed that a region of 4 kb upstream of the transcription start site contains positive and negative elements responsible for controlling gene expression. Interestingly, a fragment of 130 bp seems to contain the minimal elements necessary for gene expression, as its removal completely abolishes gene expression in cultured cells. These results are reinforced by comparison of this region with the human Msx1 gene promoter, which shows extensive conservation, including many consensus binding sites, suggesting a regulatory role for them.

Finite element modelling of crash response of composite aerospace sub-floor structures

NASA Astrophysics Data System (ADS)

McCarthy, M. A.; Harte, C. G.; Wiggenraad, J. F. M.; Michielsen, A. L. P. J.; Kohlgrüber, D.; Kamoulakos, A.

Composite energy-absorbing structures for use in aircraft are being studied within a European Commission research programme (CRASURV - Design for Crash Survivability). One of the aims of the project is to evaluate the current capabilities of crashworthiness simulation codes for composites modelling. This paper focuses on the computational analysis using explicit finite element analysis, of a number of quasi-static and dynamic tests carried out within the programme. It describes the design of the structures, the analysis techniques used, and the results of the analyses in comparison to the experimental test results. It has been found that current multi-ply shell models are capable of modelling the main energy-absorbing processes at work in such structures. However some deficiencies exist, particularly in modelling fabric composites. Developments within the finite element code are taking place as a result of this work which will enable better representation of composite fabrics.

Electrical connection structure for a superconductor element

DOEpatents

Lallouet, Nicolas; Maguire, James

2010-05-04

The invention relates to an electrical connection structure for a superconductor element cooled by a cryogenic fluid and connected to an electrical bushing, which bushing passes successively through an enclosure at an intermediate temperature between ambient temperature and the temperature of the cryogenic fluid, and an enclosure at ambient temperature, said bushing projecting outside the ambient temperature enclosure. According to the invention, said intermediate enclosure is filled at least in part with a solid material of low thermal conductivity, such as a polyurethane foam or a cellular glass foam. The invention is applicable to connecting a superconductor cable at cryogenic temperature to a device for equipment at ambient temperature.

Simplified and refined finite element approaches for determining stresses and internal forces in geometrically nonlinear structural analysis

NASA Technical Reports Server (NTRS)

Robinson, J. C.

1979-01-01

Two methods for determining stresses and internal forces in geometrically nonlinear structural analysis are presented. The simplified approach uses the mid-deformed structural position to evaluate strains when rigid body rotation is present. The important feature of this approach is that it can easily be used with a general-purpose finite-element computer program. The refined approach uses element intrinsic or corotational coordinates and a geometric transformation to determine element strains from joint displacements. Results are presented which demonstrate the capabilities of these potentially useful approaches for geometrically nonlinear structural analysis.

Structural Health Monitoring Using High-Density Fiber Optic Strain Sensor and Inverse Finite Element Methods

NASA Technical Reports Server (NTRS)

Vazquez, Sixto L.; Tessler, Alexander; Quach, Cuong C.; Cooper, Eric G.; Parks, Jeffrey; Spangler, Jan L.

2005-01-01

In an effort to mitigate accidents due to system and component failure, NASA s Aviation Safety has partnered with industry, academia, and other governmental organizations to develop real-time, on-board monitoring capabilities and system performance models for early detection of airframe structure degradation. NASA Langley is investigating a structural health monitoring capability that uses a distributed fiber optic strain system and an inverse finite element method for measuring and modeling structural deformations. This report describes the constituent systems that enable this structural monitoring function and discusses results from laboratory tests using the fiber strain sensor system and the inverse finite element method to demonstrate structural deformation estimation on an instrumented test article

Shape and Stress Sensing of Multilayered Composite and Sandwich Structures Using an Inverse Finite Element Method

NASA Technical Reports Server (NTRS)

Cerracchio, Priscilla; Gherlone, Marco; Di Sciuva, Marco; Tessler, Alexander

2013-01-01

The marked increase in the use of composite and sandwich material systems in aerospace, civil, and marine structures leads to the need for integrated Structural Health Management systems. A key capability to enable such systems is the real-time reconstruction of structural deformations, stresses, and failure criteria that are inferred from in-situ, discrete-location strain measurements. This technology is commonly referred to as shape- and stress-sensing. Presented herein is a computationally efficient shape- and stress-sensing methodology that is ideally suited for applications to laminated composite and sandwich structures. The new approach employs the inverse Finite Element Method (iFEM) as a general framework and the Refined Zigzag Theory (RZT) as the underlying plate theory. A three-node inverse plate finite element is formulated. The element formulation enables robust and efficient modeling of plate structures instrumented with strain sensors that have arbitrary positions. The methodology leads to a set of linear algebraic equations that are solved efficiently for the unknown nodal displacements. These displacements are then used at the finite element level to compute full-field strains, stresses, and failure criteria that are in turn used to assess structural integrity. Numerical results for multilayered, highly heterogeneous laminates demonstrate the unique capability of this new formulation for shape- and stress-sensing.

Structural identifiability of cyclic graphical models of biological networks with latent variables.

PubMed

Wang, Yulin; Lu, Na; Miao, Hongyu

2016-06-13

Graphical models have long been used to describe biological networks for a variety of important tasks such as the determination of key biological parameters, and the structure of graphical model ultimately determines whether such unknown parameters can be unambiguously obtained from experimental observations (i.e., the identifiability problem). Limited by resources or technical capacities, complex biological networks are usually partially observed in experiment, which thus introduces latent variables into the corresponding graphical models. A number of previous studies have tackled the parameter identifiability problem for graphical models such as linear structural equation models (SEMs) with or without latent variables. However, the limited resolution and efficiency of existing approaches necessarily calls for further development of novel structural identifiability analysis algorithms. An efficient structural identifiability analysis algorithm is developed in this study for a broad range of network structures. The proposed method adopts the Wright's path coefficient method to generate identifiability equations in forms of symbolic polynomials, and then converts these symbolic equations to binary matrices (called identifiability matrix). Several matrix operations are introduced for identifiability matrix reduction with system equivalency maintained. Based on the reduced identifiability matrices, the structural identifiability of each parameter is determined. A number of benchmark models are used to verify the validity of the proposed approach. Finally, the network module for influenza A virus replication is employed as a real example to illustrate the application of the proposed approach in practice. The proposed approach can deal with cyclic networks with latent variables. The key advantage is that it intentionally avoids symbolic computation and is thus highly efficient. Also, this method is capable of determining the identifiability of each single parameter and

Secbase: database module to retrieve secondary structure elements with ligand binding motifs.

PubMed

Koch, Oliver; Cole, Jason; Block, Peter; Klebe, Gerhard

2009-10-01

Secbase is presented as a novel extension module of Relibase. It integrates the information about secondary structure elements into the retrieval facilities of Relibase. The data are accessible via the extended Relibase user interface, and integrated retrieval queries can be addressed using an extended version of Reliscript. The primary information about alpha-helices and beta-sheets is used as provided by the PDB. Furthermore, a uniform classification of all turn families, based on recent clustering methods, and a new helix assignment that is based on this turn classification has been included. Algorithms to analyze the geometric features of helices and beta-strands were also implemented. To demonstrate the performance of the Secbase implementation, some application examples are given. They provide new insights into the involvement of secondary structure elements in ligand binding. A survey of water molecules detected next to the N-terminus of helices is analyzed to show their involvement in ligand binding. Additionally, the parallel oriented NH groups at the alpha-helix N-termini provide special binding motifs to bind particular ligand functional groups with two adjacent oxygen atoms, e.g., as found in negatively charged carboxylate or phosphate groups, respectively. The present study also shows that the specific structure of the first turn of alpha-helices provides a suitable explanation for stabilizing charged structures. The magnitude of the overall helix macrodipole seems to have no or only a minor influence on binding. Furthermore, an overview of the involvement of secondary structure elements with the recognition of some important endogenous ligands such as cofactors shows some distinct preference for particular binding motifs and amino acids.

Creating a Test Validated Structural Dynamic Finite Element Model of the X-56A Aircraft

NASA Technical Reports Server (NTRS)

Pak, Chan-Gi; Truong, Samson

2014-01-01

Small modeling errors in the finite element model will eventually induce errors in the structural flexibility and mass, thus propagating into unpredictable errors in the unsteady aerodynamics and the control law design. One of the primary objectives of the Multi Utility Technology Test-bed, X-56A aircraft, is the flight demonstration of active flutter suppression, and therefore in this study, the identification of the primary and secondary modes for the structural model tuning based on the flutter analysis of the X-56A aircraft. The ground vibration test-validated structural dynamic finite element model of the X-56A aircraft is created in this study. The structural dynamic finite element model of the X-56A aircraft is improved using a model tuning tool. In this study, two different weight configurations of the X-56A aircraft have been improved in a single optimization run. Frequency and the cross-orthogonality (mode shape) matrix were the primary focus for improvement, while other properties such as center of gravity location, total weight, and offdiagonal terms of the mass orthogonality matrix were used as constraints. The end result was a more improved and desirable structural dynamic finite element model configuration for the X-56A aircraft. Improved frequencies and mode shapes in this study increased average flutter speeds of the X-56A aircraft by 7.6% compared to the baseline model.

STARS: An integrated general-purpose finite element structural, aeroelastic, and aeroservoelastic analysis computer program

NASA Technical Reports Server (NTRS)

Gupta, Kajal K.

1991-01-01

The details of an integrated general-purpose finite element structural analysis computer program which is also capable of solving complex multidisciplinary problems is presented. Thus, the SOLIDS module of the program possesses an extensive finite element library suitable for modeling most practical problems and is capable of solving statics, vibration, buckling, and dynamic response problems of complex structures, including spinning ones. The aerodynamic module, AERO, enables computation of unsteady aerodynamic forces for both subsonic and supersonic flow for subsequent flutter and divergence analysis of the structure. The associated aeroservoelastic analysis module, ASE, effects aero-structural-control stability analysis yielding frequency responses as well as damping characteristics of the structure. The program is written in standard FORTRAN to run on a wide variety of computers. Extensive graphics, preprocessing, and postprocessing routines are also available pertaining to a number of terminals.

Guided wave propagation and spectral element method for debonding damage assessment in RC structures

NASA Astrophysics Data System (ADS)

Wang, Ying; Zhu, Xinqun; Hao, Hong; Ou, Jinping

2009-07-01

A concrete-steel interface spectral element is developed to study the guided wave propagation along the steel rebar in the concrete. Scalar damage parameters characterizing changes in the interface (debonding damage) are incorporated into the formulation of the spectral finite element that is used for damage detection of reinforced concrete structures. Experimental tests are carried out on a reinforced concrete beam with embedded piezoelectric elements to verify the performance of the proposed model and algorithm. Parametric studies are performed to evaluate the effect of different damage scenarios on wave propagation in the reinforced concrete structures. Numerical simulations and experimental results show that the method is effective to model wave propagation along the steel rebar in concrete and promising to detect damage in the concrete-steel interface.

Modeling bistable behaviors in morphing structures through finite element simulations.

PubMed

Guo, Qiaohang; Zheng, Huang; Chen, Wenzhe; Chen, Zi

2014-01-01

Bistable structures, exemplified by the Venus flytrap and slap bracelets, can transit between different configurations upon certain external stimulation. Here we study, through three-dimensional finite element simulations, the bistable behaviors in elastic plates in the absence of terminate loads, but with pre-strains in one (or both) of the two composite layers. Both the scenarios with and without a given geometric mis-orientation angle are investigated, the results of which are consistent with recent theoretical and experimental studies. This work can open ample venues for programmable designs of plant/shell structures with large deformations, with applications in designing bio-inspired robotics for biomedical research and morphing/deployable structures in aerospace engineering.

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.

Structural Element Testing in Support of the Design of the NASA Composite Crew Module

NASA Technical Reports Server (NTRS)

Kellas, Sotiris; Jackson, Wade C.; Thesken, John C.; Schleicher, Eric; Wagner, Perry; Kirsch, Michael T.

2012-01-01

In January 2007, the NASA Administrator and Associate Administrator for the Exploration Systems Mission Directorate chartered the NASA Engineering and Safety Center (NESC) to design, build, and test a full-scale Composite Crew Module (CCM). For the design and manufacturing of the CCM, the team adopted the building block approach where design and manufacturing risks were mitigated through manufacturing trials and structural testing at various levels of complexity. Following NASA's Structural Design Verification Requirements, a further objective was the verification of design analysis methods and the provision of design data for critical structural features. Test articles increasing in complexity from basic material characterization coupons through structural feature elements and large structural components, to full-scale structures were evaluated. This paper discusses only four elements tests three of which include joints and one that includes a tapering honeycomb core detail. For each test series included are specimen details, instrumentation, test results, a brief analysis description, test analysis correlation and conclusions.

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.

Response of basic structural elements and B-52 structural components to simulated nuclear overpressure. Volume I-program description and results (basic structural elements). Final report, 1 June 1977-30 September 1979

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

Syring, R.P.; Grubb, R.L.

1979-09-30

This document reports on the following: (1) experimental determination of the response of 16 basic structural elements and 7 B-52 components to simulated nuclear overpressure environments (utilizing Sandia Corporation's Thunderpipe Shock Tube), (2) analysis of these test specimens utilizing the NOVA-2 computer program, and (3) correlation of test and analysis results.

Optimizing finite element predictions of local subchondral bone structural stiffness using neural network-derived density-modulus relationships for proximal tibial subchondral cortical and trabecular bone.

PubMed

Nazemi, S Majid; Amini, Morteza; Kontulainen, Saija A; Milner, Jaques S; Holdsworth, David W; Masri, Bassam A; Wilson, David R; Johnston, James D

2017-01-01

Quantitative computed tomography based subject-specific finite element modeling has potential to clarify the role of subchondral bone alterations in knee osteoarthritis initiation, progression, and pain. However, it is unclear what density-modulus equation(s) should be applied with subchondral cortical and subchondral trabecular bone when constructing finite element models of the tibia. Using a novel approach applying neural networks, optimization, and back-calculation against in situ experimental testing results, the objective of this study was to identify subchondral-specific equations that optimized finite element predictions of local structural stiffness at the proximal tibial subchondral surface. Thirteen proximal tibial compartments were imaged via quantitative computed tomography. Imaged bone mineral density was converted to elastic moduli using multiple density-modulus equations (93 total variations) then mapped to corresponding finite element models. For each variation, root mean squared error was calculated between finite element prediction and in situ measured stiffness at 47 indentation sites. Resulting errors were used to train an artificial neural network, which provided an unlimited number of model variations, with corresponding error, for predicting stiffness at the subchondral bone surface. Nelder-Mead optimization was used to identify optimum density-modulus equations for predicting stiffness. Finite element modeling predicted 81% of experimental stiffness variance (with 10.5% error) using optimized equations for subchondral cortical and trabecular bone differentiated with a 0.5g/cm 3 density. In comparison with published density-modulus relationships, optimized equations offered improved predictions of local subchondral structural stiffness. Further research is needed with anisotropy inclusion, a smaller voxel size and de-blurring algorithms to improve predictions. Copyright © 2016 Elsevier Ltd. All rights reserved.

Incorporation mechanisms of actinide elements into the structures of U 6+ phases formed during the oxidation of spent nuclear fuel

NASA Astrophysics Data System (ADS)

Burns, Peter C.; Ewing, Rodney C.; Miller, Mark L.

1997-05-01

Uranyl oxide hydrate and uranyl silicate phases will form due to the corrosion and alteration of spent nuclear fuel under oxidizing conditions in silica-bearing solution. The actinide elements in the spent fuel may be incorporated into the structures of these secondary U6+ phases during the long-term corrosion of the UO 2 in spent fuel. The incorporation of actinide elements into the crystal structures of the alteration products may decrease actinide mobility. The crystal chemistry of the various oxidation states of the actinide elements of environmental concern is examined to identify possible incorporation mechanisms. The substitutions Pu 6+U 6+ and (Pu 5+, Np 5+)U 6+ should readily occur in many U 6+ structures, although structural modification may be required to satisfy local bond-valence requirements. Crystal-chemical characteristics of the U 6+ phases indicate that An 4+ (An: actinide)U 6+ substitution is likely to occur in the sheets of uranyl polyhedra that occur in the structures of the minerals schoepite, [(UO 2) 8O 2(OH) 12](H 2O) 12, ianthinite, [U 24+ (UO 2) 4O 6(OH) 4(H 2O) 4](H 2O) 5, becquerelite, Ca[(UO 2) 3O 2(OH) 3] 2(H 2O) 8, compreignacite, K 2[(UO 2) 3O 2(OH) 3] 2(H 2O) 8, α-uranophane, Ca[(UO 2)(SiO 3OH)] 2(H 2O) 5, and boltwoodite, K(H 2O)[(UO 2)(SiO 4)], all of which are likely to form due to the oxidation and alteration of the UO 2 in spent fuel. The incorporation of An 3+ into the sheets of the structures of α-uranophane and boltwoodite, as well as interlayer sites of various uranyl phases, may occur.

Spectrally formulated user-defined element in conventional finite element environment for wave motion analysis in 2-D composite structures

NASA Astrophysics Data System (ADS)

Khalili, Ashkan; Jha, Ratneshwar; Samaratunga, Dulip

2016-11-01

Wave propagation analysis in 2-D composite structures is performed efficiently and accurately through the formulation of a User-Defined Element (UEL) based on the wavelet spectral finite element (WSFE) method. The WSFE method is based on the first-order shear deformation theory which yields accurate results for wave motion at high frequencies. The 2-D WSFE model is highly efficient computationally and provides a direct relationship between system input and output in the frequency domain. The UEL is formulated and implemented in Abaqus (commercial finite element software) for wave propagation analysis in 2-D composite structures with complexities. Frequency domain formulation of WSFE leads to complex valued parameters, which are decoupled into real and imaginary parts and presented to Abaqus as real values. The final solution is obtained by forming a complex value using the real number solutions given by Abaqus. Five numerical examples are presented in this article, namely undamaged plate, impacted plate, plate with ply drop, folded plate and plate with stiffener. Wave motions predicted by the developed UEL correlate very well with Abaqus simulations. The results also show that the UEL largely retains computational efficiency of the WSFE method and extends its ability to model complex features.

Epigenomic Elements Analyses for Promoters Identify ESRRG as a New Susceptibility Gene for Obesity-related Traits

PubMed Central

Dong, Shan-Shan; Guo, Yan; Zhu, Dong-Li; Chen, Xiao-Feng; Wu, Xiao-Ming; Shen, Hui; Chen, Xiang-Ding; Tan, Li-Jun; Tian, Qing; Deng, Hong-Wen; Yang, Tie-Lin

2016-01-01

OBJECTIVES With ENCODE epigenomic data and results from published genome-wide association studies (GWASs), we aimed to find regulatory signatures of obesity genes and discover novel susceptibility genes. METHODS Obesity genes were obtained from public GWASs databases and their promoters were annotated based on the regulatory elements information. Significantly enriched or depleted epigenomic elements in the promoters of obesity genes were evaluated and all human genes were then prioritized according to the existence of the selected elements to predict new candidate genes. Top ranked genes were subsequently applied to validate their associations with obesity-related traits in three independent in-house GWASs samples. RESULTS We identified RAD21 and EZH2 as over-represented, STAT2 and IRF3 as depleted transcription factors. Histone modification of H3K9me3 and chromatin state segmentation of “poised promoter” and “repressed” were overrepresented. All genes were prioritized and we selected the top five genes for validation at population level. Combined results from the three GWASs samples, rs7522101 in ESRRG remained significantly associated with BMI after multiple testing corrections (P = 7.25 × 10−5). It was also associated with β-cell function (P = 1.99 × 10−3) and fasting glucose level (P < 0.05) in the meta-analyses of glucose and insulin-related traits consortium (MAGIC) dataset. CONCLUSIONS In summary, we identified epigenomic characteristics for obesity genes and suggested ESRRG as a novel obesity susceptibility gene. PMID:27113491

Finite element analysis and genetic algorithm optimization design for the actuator placement on a large adaptive structure

NASA Astrophysics Data System (ADS)

Sheng, Lizeng

The dissertation focuses on one of the major research needs in the area of adaptive/intelligent/smart structures, the development and application of finite element analysis and genetic algorithms for optimal design of large-scale adaptive structures. We first review some basic concepts in finite element method and genetic algorithms, along with the research on smart structures. Then we propose a solution methodology for solving a critical problem in the design of a next generation of large-scale adaptive structures---optimal placements of a large number of actuators to control thermal deformations. After briefly reviewing the three most frequently used general approaches to derive a finite element formulation, the dissertation presents techniques associated with general shell finite element analysis using flat triangular laminated composite elements. The element used here has three nodes and eighteen degrees of freedom and is obtained by combining a triangular membrane element and a triangular plate bending element. The element includes the coupling effect between membrane deformation and bending deformation. The membrane element is derived from the linear strain triangular element using Cook's transformation. The discrete Kirchhoff triangular (DKT) element is used as the plate bending element. For completeness, a complete derivation of the DKT is presented. Geometrically nonlinear finite element formulation is derived for the analysis of adaptive structures under the combined thermal and electrical loads. Next, we solve the optimization problems of placing a large number of piezoelectric actuators to control thermal distortions in a large mirror in the presence of four different thermal loads. We then extend this to a multi-objective optimization problem of determining only one set of piezoelectric actuator locations that can be used to control the deformation in the same mirror under the action of any one of the four thermal loads. A series of genetic algorithms

Torque sensor having a spoked sensor element support structure

NASA Technical Reports Server (NTRS)

Lurie, Boris J. (Inventor); Schier, J. Alan (Inventor)

1990-01-01

Piezoelectric sensor devices are attached across pairs of circularly arranged spokes arrayed on the periphery of an annular ring. The sensor devices each include a preloaded steel ball mounting arrangement for mounting a piezoelectric sensor element. A first circular interface plate on one side of the sensor structure attaches to alternate one of the spokes, and a circular interface plate on the opposite side of the same diameter as the first interface plate attaches to the remaining spokes.

Aircraft wing structural design optimization based on automated finite element modelling and ground structure approach

NASA Astrophysics Data System (ADS)

Yang, Weizhu; Yue, Zhufeng; Li, Lei; Wang, Peiyan

2016-01-01

An optimization procedure combining an automated finite element modelling (AFEM) technique with a ground structure approach (GSA) is proposed for structural layout and sizing design of aircraft wings. The AFEM technique, based on CATIA VBA scripting and PCL programming, is used to generate models automatically considering the arrangement of inner systems. GSA is used for local structural topology optimization. The design procedure is applied to a high-aspect-ratio wing. The arrangement of the integral fuel tank, landing gear and control surfaces is considered. For the landing gear region, a non-conventional initial structural layout is adopted. The positions of components, the number of ribs and local topology in the wing box and landing gear region are optimized to obtain a minimum structural weight. Constraints include tank volume, strength, buckling and aeroelastic parameters. The results show that the combined approach leads to a greater weight saving, i.e. 26.5%, compared with three additional optimizations based on individual design approaches.

An Innovative Structural Mode Selection Methodology: Application for the X-33 Launch Vehicle Finite Element Model

NASA Technical Reports Server (NTRS)

Hidalgo, Homero, Jr.

2000-01-01

An innovative methodology for determining structural target mode selection and mode selection based on a specific criterion is presented. An effective approach to single out modes which interact with specific locations on a structure has been developed for the X-33 Launch Vehicle Finite Element Model (FEM). We presented Root-Sum-Square (RSS) displacement method computes resultant modal displacement for each mode at selected degrees of freedom (DOF) and sorts to locate modes with highest values. This method was used to determine modes, which most influenced specific locations/points on the X-33 flight vehicle such as avionics control components, aero-surface control actuators, propellant valve and engine points for use in flight control stability analysis and for flight POGO stability analysis. Additionally, the modal RSS method allows for primary or global target vehicle modes to also be identified in an accurate and efficient manner.

Cross-sectional mapping for refined beam elements with applications to shell-like structures

NASA Astrophysics Data System (ADS)

Pagani, A.; de Miguel, A. G.; Carrera, E.

2017-06-01

This paper discusses the use of higher-order mapping functions for enhancing the physical representation of refined beam theories. Based on the Carrera unified formulation (CUF), advanced one-dimensional models are formulated by expressing the displacement field as a generic expansion of the generalized unknowns. According to CUF, a novel physically/geometrically consistent model is devised by employing Legendre-like polynomial sets to approximate the generalized unknowns at the cross-sectional level, whereas a local mapping technique based on the blending functions method is used to describe the exact physical boundaries of the cross-section domain. Classical and innovative finite element methods, including hierarchical p-elements and locking-free integration schemes, are utilized to solve the governing equations of the unified beam theory. Several numerical applications accounting for small displacements/rotations and strains are discussed, including beam structures with cross-sectional curved edges, cylindrical shells, and thin-walled aeronautical wing structures with reinforcements. The results from the proposed methodology are widely assessed by comparisons with solutions from the literature and commercial finite element software tools. The attention is focussed on the high computational efficiency and the marked capabilities of the present beam model, which can deal with a broad spectrum of structural problems with unveiled accuracy in terms of geometrical representation of the domain boundaries.

Power flows and Mechanical Intensities in structural finite element analysis

NASA Technical Reports Server (NTRS)

Hambric, Stephen A.

1989-01-01

The identification of power flow paths in dynamically loaded structures is an important, but currently unavailable, capability for the finite element analyst. For this reason, methods for calculating power flows and mechanical intensities in finite element models are developed here. Formulations for calculating input and output powers, power flows, mechanical intensities, and power dissipations for beam, plate, and solid element types are derived. NASTRAN is used to calculate the required velocity, force, and stress results of an analysis, which a post-processor then uses to calculate power flow quantities. The SDRC I-deas Supertab module is used to view the final results. Test models include a simple truss and a beam-stiffened cantilever plate. Both test cases showed reasonable power flow fields over low to medium frequencies, with accurate power balances. Future work will include testing with more complex models, developing an interactive graphics program to view easily and efficiently the analysis results, applying shape optimization methods to the problem with power flow variables as design constraints, and adding the power flow capability to NASTRAN.

Exact finite element method analysis of viscoelastic tapered structures to transient loads

NASA Technical Reports Server (NTRS)

Spyrakos, Constantine Chris

1987-01-01

A general method is presented for determining the dynamic torsional/axial response of linear structures composed of either tapered bars or shafts to transient excitations. The method consists of formulating and solving the dynamic problem in the Laplace transform domain by the finite element method and obtaining the response by a numerical inversion of the transformed solution. The derivation of the torsional and axial stiffness matrices is based on the exact solution of the transformed governing equation of motion, and it consequently leads to the exact solution of the problem. The solution permits treatment of the most practical cases of linear tapered bars and shafts, and employs modeling of structures with only one element per member which reduces the number of degrees of freedom involved. The effects of external viscous or internal viscoelastic damping are also taken into account.

Structural Analysis of Technical-Tactical Elements in Table Tennis and their Role in Different Playing Zones

PubMed Central

Munivrana, Goran; Petrinović, Lidija Zekan; Kondrič, Miran

2015-01-01

For the purpose of determining the overall structure of technical-tactical elements in table tennis and evaluating their role in different playing zones around the table, a new measuring instrument (a questionnaire) was formulated that took advantage of the expert knowledge of top, world class table tennis coaches. The results of the hierarchical taxonomic (cluster) analysis showed that the overall structure of the technical-tactical elements forming the table tennis technique could be divided into three basic groups; a group of technical-tactical elements (A) used in the phase of preparing one’s own and disabling the opponent’s attack; a group of technical-tactical elements (B) used in the phase of attack and counterattack; and a group of technical-tactical elements (C) used in the phase of defense. The differences among the obtained groups of table tennis elements were determined by applying the Kruskal-Wallis test, while relations between the groups and their role in different playing zones around the table were analyzed by comparing the average values of the experts’ scores. PMID:26557204

Structural Analysis of Technical-Tactical Elements in Table Tennis and their Role in Different Playing Zones.

PubMed

Munivrana, Goran; Petrinović, Lidija Zekan; Kondrič, Miran

2015-09-29

For the purpose of determining the overall structure of technical-tactical elements in table tennis and evaluating their role in different playing zones around the table, a new measuring instrument (a questionnaire) was formulated that took advantage of the expert knowledge of top, world class table tennis coaches. The results of the hierarchical taxonomic (cluster) analysis showed that the overall structure of the technical-tactical elements forming the table tennis technique could be divided into three basic groups; a group of technical-tactical elements (A) used in the phase of preparing one's own and disabling the opponent's attack; a group of technical-tactical elements (B) used in the phase of attack and counterattack; and a group of technical-tactical elements (C) used in the phase of defense. The differences among the obtained groups of table tennis elements were determined by applying the Kruskal-Wallis test, while relations between the groups and their role in different playing zones around the table were analyzed by comparing the average values of the experts' scores.

Epigenomic elements analyses for promoters identify ESRRG as a new susceptibility gene for obesity-related traits.

PubMed

Dong, S-S; Guo, Y; Zhu, D-L; Chen, X-F; Wu, X-M; Shen, H; Chen, X-D; Tan, L-J; Tian, Q; Deng, H-W; Yang, T-L

2016-07-01

With ENCODE epigenomic data and results from published genome-wide association studies (GWASs), we aimed to find regulatory signatures of obesity genes and discover novel susceptibility genes. Obesity genes were obtained from public GWAS databases and their promoters were annotated based on the regulatory element information. Significantly enriched or depleted epigenomic elements in the promoters of obesity genes were evaluated and all human genes were then prioritized according to the existence of the selected elements to predict new candidate genes. Top-ranked genes were subsequently applied to validate their associations with obesity-related traits in three independent in-house GWAS samples. We identified RAD21 and EZH2 as over-represented, and STAT2 (signal transducer and activator of transcription 2) and IRF3 (interferon regulatory transcription factor 3) as depleted transcription factors. Histone modification of H3K9me3 and chromatin state segmentation of 'poised promoter' and 'repressed' were over-represented. All genes were prioritized and we selected the top five genes for validation at the population level. Combining results from the three GWAS samples, rs7522101 in ESRRG (estrogen-related receptor-γ) remained significantly associated with body mass index after multiple testing corrections (P=7.25 × 10(-5)). It was also associated with β-cell function (P=1.99 × 10(-3)) and fasting glucose level (P<0.05) in the meta-analyses of glucose and insulin-related traits consortium (MAGIC) data set.Cnoclusions:In summary, we identified epigenomic characteristics for obesity genes and suggested ESRRG as a novel obesity-susceptibility gene.

Phylogenetic Conflict in Bears Identified by Automated Discovery of Transposable Element Insertions in Low-Coverage Genomes

PubMed Central

Gallus, Susanne; Janke, Axel

2017-01-01

Abstract Phylogenetic reconstruction from transposable elements (TEs) offers an additional perspective to study evolutionary processes. However, detecting phylogenetically informative TE insertions requires tedious experimental work, limiting the power of phylogenetic inference. Here, we analyzed the genomes of seven bear species using high-throughput sequencing data to detect thousands of TE insertions. The newly developed pipeline for TE detection called TeddyPi (TE detection and discovery for Phylogenetic Inference) identified 150,513 high-quality TE insertions in the genomes of ursine and tremarctine bears. By integrating different TE insertion callers and using a stringent filtering approach, the TeddyPi pipeline produced highly reliable TE insertion calls, which were confirmed by extensive in vitro validation experiments. Analysis of single nucleotide substitutions in the flanking regions of the TEs shows that these substitutions correlate with the phylogenetic signal from the TE insertions. Our phylogenomic analyses show that TEs are a major driver of genomic variation in bears and enabled phylogenetic reconstruction of a well-resolved species tree, despite strong signals for incomplete lineage sorting and introgression. The analyses show that the Asiatic black, sun, and sloth bear form a monophyletic clade, in which phylogenetic incongruence originates from incomplete lineage sorting. TeddyPi is open source and can be adapted to various TE and structural variation callers. The pipeline makes it possible to confidently extract thousands of TE insertions even from low-coverage genomes (∼10×) of nonmodel organisms. This opens new possibilities for biologists to study phylogenies and evolutionary processes as well as rates and patterns of (retro-)transposition and structural variation. PMID:28985298

GenSSI 2.0: multi-experiment structural identifiability analysis of SBML models.

PubMed

Ligon, Thomas S; Fröhlich, Fabian; Chis, Oana T; Banga, Julio R; Balsa-Canto, Eva; Hasenauer, Jan

2018-04-15

Mathematical modeling using ordinary differential equations is used in systems biology to improve the understanding of dynamic biological processes. The parameters of ordinary differential equation models are usually estimated from experimental data. To analyze a priori the uniqueness of the solution of the estimation problem, structural identifiability analysis methods have been developed. We introduce GenSSI 2.0, an advancement of the software toolbox GenSSI (Generating Series for testing Structural Identifiability). GenSSI 2.0 is the first toolbox for structural identifiability analysis to implement Systems Biology Markup Language import, state/parameter transformations and multi-experiment structural identifiability analysis. In addition, GenSSI 2.0 supports a range of MATLAB versions and is computationally more efficient than its previous version, enabling the analysis of more complex models. GenSSI 2.0 is an open-source MATLAB toolbox and available at https://github.com/genssi-developer/GenSSI. thomas.ligon@physik.uni-muenchen.de or jan.hasenauer@helmholtz-muenchen.de. Supplementary data are available at Bioinformatics online.

Creating a Test Validated Structural Dynamic Finite Element Model of the Multi-Utility Technology Test Bed Aircraft

NASA Technical Reports Server (NTRS)

Pak, Chan-Gi; Truong, Samson S.

2014-01-01

Small modeling errors in the finite element model will eventually induce errors in the structural flexibility and mass, thus propagating into unpredictable errors in the unsteady aerodynamics and the control law design. One of the primary objectives of Multi Utility Technology Test Bed, X-56A, aircraft is the flight demonstration of active flutter suppression, and therefore in this study, the identification of the primary and secondary modes for the structural model tuning based on the flutter analysis of X-56A. The ground vibration test validated structural dynamic finite element model of the X-56A is created in this study. The structural dynamic finite element model of the X-56A is improved using a model tuning tool. In this study, two different weight configurations of the X-56A have been improved in a single optimization run.

Curvilinear steel elements in load-bearing structures of high-rise building spatial frames

NASA Astrophysics Data System (ADS)

Ibragimov, Alexander; Danilov, Alexander

2018-03-01

The application of curvilinear elements in load-bearing metal structures of high-rise buildings supposes ensuring of their bearing capacity and serviceability. There may exist a great variety of shapes and orientations of such structural elements. In particular, it may be various flat curves of an open or closed oval profile such as circular or parabolic arch or ellipse. The considered approach implies creating vast internal volumes without loss in the load-bearing capacity of the frame. The basic concept makes possible a wide variety of layout and design solutions. The presence of free internal spaces of large volume in "skyscraper" type buildings contributes to resolving a great number of problems, including those of communicative nature. The calculation results confirm the basic assumptions.

Solution NMR structure of hypothetical protein CV_2116 encoded by a viral prophage element in Chromobacterium violaceum.

PubMed

Yang, Yunhuang; Ramelot, Theresa A; Cort, John R; Garcia, Maite; Yee, Adelinda; Arrowsmith, Cheryl H; Kennedy, Michael A

2012-01-01

CV_2116 is a small hypothetical protein of 82 amino acids from the Gram-negative coccobacillus Chromobacterium violaceum. A PSI-BLAST search using the CV_2116 sequence as a query identified only one hit (E = 2e(-07)) corresponding to a hypothetical protein OR16_04617 from Cupriavidus basilensis OR16, which failed to provide insight into the function of CV_2116. The CV_2116 gene was cloned into the p15TvLic expression plasmid, transformed into E. coli, and (13)C- and (15)N-labeled NMR samples of CV_2116 were overexpressed in E. coli and purified for structure determination using NMR spectroscopy. The resulting high-quality solution NMR structure of CV_2116 revealed a novel α + β fold containing two anti-parallel β-sheets in the N-terminal two-thirds of the protein and one α-helix in the C-terminal third of the protein. CV_2116 does not belong to any known protein sequence family and a Dali search indicated that no similar structures exist in the protein data bank. Although no function of CV_2116 could be derived from either sequence or structural similarity searches, the neighboring genes of CV_2116 encode various proteins annotated as similar to bacteriophage tail assembly proteins. Interestingly, C. violaceum exhibits an extensive network of bacteriophage tail-like structures that likely result from lateral gene transfer by incorporation of viral DNA into its genome (prophages) due to bacteriophage infection. Indeed, C. violaceum has been shown to contain four prophage elements and CV_2116 resides in the fourth of these elements. Analysis of the putative operon in which CV_2116 resides indicates that CV_2116 might be a component of the bacteriophage tail-like assembly that occurs in C. violaceum.

Nucleosome core particles containing a poly(dA.dT) sequence element exhibit a locally distorted DNA structure.

PubMed

Bao, Yunhe; White, Cindy L; Luger, Karolin

2006-08-25

Poly(dA.dT) DNA sequence elements are thought to promote transcription by either excluding nucleosomes or by altering their structural or dynamic properties. Here, the stability and structure of a defined nucleosome core particle containing a 16 base-pair poly(dA.dT) element (A16 NCP) was investigated. The A16 NCP requires a significantly higher temperature for histone octamer sliding in vitro compared to comparable nucleosomes that do not contain a poly(dA.dT) element. Fluorescence resonance energy transfer showed that the interactions between the nucleosomal DNA ends and the histone octamer were destabilized in A16 NCP. The crystal structure of A16 NCP was determined to a resolution of 3.2 A. The overall structure was maintained except for local deviations in DNA conformation. These results are consistent with previous in vivo and in vitro observations that poly(dA.dT) elements cause only modest changes in DNA accessibility and modest increases in steady-state transcription levels.

Static aeroelastic analysis of wings using Euler/Navier-Stokes equations coupled with improved wing-box finite element structures

NASA Technical Reports Server (NTRS)

Guruswamy, Guru P.; MacMurdy, Dale E.; Kapania, Rakesh K.

1994-01-01

Strong interactions between flow about an aircraft wing and the wing structure can result in aeroelastic phenomena which significantly impact aircraft performance. Time-accurate methods for solving the unsteady Navier-Stokes equations have matured to the point where reliable results can be obtained with reasonable computational costs for complex non-linear flows with shock waves, vortices and separations. The ability to combine such a flow solver with a general finite element structural model is key to an aeroelastic analysis in these flows. Earlier work involved time-accurate integration of modal structural models based on plate elements. A finite element model was developed to handle three-dimensional wing boxes, and incorporated into the flow solver without the need for modal analysis. Static condensation is performed on the structural model to reduce the structural degrees of freedom for the aeroelastic analysis. Direct incorporation of the finite element wing-box structural model with the flow solver requires finding adequate methods for transferring aerodynamic pressures to the structural grid and returning deflections to the aerodynamic grid. Several schemes were explored for handling the grid-to-grid transfer of information. The complex, built-up nature of the wing-box complicated this transfer. Aeroelastic calculations for a sample wing in transonic flow comparing various simple transfer schemes are presented and discussed.

Challenges in Integrating Nondestructive Evaluation and Finite Element Methods for Realistic Structural Analysis

NASA Technical Reports Server (NTRS)

Abdul-Aziz, Ali; Baaklini, George Y.; Zagidulin, Dmitri; Rauser, Richard W.

2000-01-01

Capabilities and expertise related to the development of links between nondestructive evaluation (NDE) and finite element analysis (FEA) at Glenn Research Center (GRC) are demonstrated. Current tools to analyze data produced by computed tomography (CT) scans are exercised to help assess the damage state in high temperature structural composite materials. A utility translator was written to convert velocity (an image processing software) STL data file to a suitable CAD-FEA type file. Finite element analyses are carried out with MARC, a commercial nonlinear finite element code, and the analytical results are discussed. Modeling was established by building MSC/Patran (a pre and post processing finite element package) generated model and comparing it to a model generated by Velocity in conjunction with MSC/Patran Graphics. Modeling issues and results are discussed in this paper. The entire process that outlines the tie between the data extracted via NDE and the finite element modeling and analysis is fully described.

Effects of thirty elements on bone metabolism.

PubMed

Dermience, Michael; Lognay, Georges; Mathieu, Françoise; Goyens, Philippe

2015-10-01

The human skeleton, made of 206 bones, plays vital roles including supporting the body, protecting organs, enabling movement, and storing minerals. Bones are made of organic structures, intimately connected with an inorganic matrix produced by bone cells. Many elements are ubiquitous in our environment, and many impact bone metabolism. Most elements have antagonistic actions depending on concentration. Indeed, some elements are essential, others are deleterious, and many can be both. Several pathways mediate effects of element deficiencies or excesses on bone metabolism. This paper aims to identify all elements that impact bone health and explore the mechanisms by which they act. To date, this is the first time that the effects of thirty minerals on bone metabolism have been summarized. Copyright © 2015 Elsevier GmbH. All rights reserved.

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

Military handbook: Metallic materials and elements for aerospace vehicle structures, volume 1

NASA Astrophysics Data System (ADS)

1994-11-01

Since many aerospace companies manufacture both commercial and military products, the standardization of metallic materials design data, which are acceptable to government procuring or certification agencies, is very beneficial to those manufacturers as well as governmental agencies. Although the design requirements for military and commercial products may differ greatly, the required design values for the strength of materials and elements and other needed material characteristics are often identical. Therefore this publication is to provide standardized design values and related design information for metallic materials and structural elements used in aerospace structures. The data contained herein or from approved items in the minutes of MIL-RDBK-5 coordination meetings are acceptable to the Air Force, the Navy, the Army, and the Federal Aviation Administration. Approval by the procuring or certificating agency must be obtained for the use of design values for products not contained herein.

Application of the multi-scale finite element method to wave propagation problems in damaged structures

NASA Astrophysics Data System (ADS)

Casadei, F.; Ruzzene, M.

2011-04-01

This work illustrates the possibility to extend the field of application of the Multi-Scale Finite Element Method (MsFEM) to structural mechanics problems that involve localized geometrical discontinuities like cracks or notches. The main idea is to construct finite elements with an arbitrary number of edge nodes that describe the actual geometry of the damage with shape functions that are defined as local solutions of the differential operator of the specific problem according to the MsFEM approach. The small scale information are then brought to the large scale model through the coupling of the global system matrices that are assembled using classical finite element procedures. The efficiency of the method is demonstrated through selected numerical examples that constitute classical problems of great interest to the structural health monitoring community.

Neurotoxic Doses of Chronic Methamphetamine Trigger Retrotransposition of the Identifier Element in Rat Dorsal Dentate Gyrus

PubMed Central

Moszczynska, Anna; Burghardt, Kyle J.; Yu, Dongyue

2017-01-01

Short interspersed elements (SINEs) are typically silenced by DNA hypermethylation in somatic cells, but can retrotranspose in proliferating cells during adult neurogenesis. Hypomethylation caused by disease pathology or genotoxic stress leads to genomic instability of SINEs. The goal of the present investigation was to determine whether neurotoxic doses of binge or chronic methamphetamine (METH) trigger retrotransposition of the identifier (ID) element, a member of the rat SINE family, in the dentate gyrus genomic DNA. Adult male Sprague-Dawley rats were treated with saline or high doses of binge or chronic METH and sacrificed at three different time points thereafter. DNA methylation analysis, immunohistochemistry and next-generation sequencing (NGS) were performed on the dorsal dentate gyrus samples. Binge METH triggered hypomethylation, while chronic METH triggered hypermethylation of the CpG-2 site. Both METH regimens were associated with increased intensities in poly(A)-binding protein 1 (PABP1, a SINE regulatory protein)-like immunohistochemical staining in the dentate gyrus. The amplification of several ID element sequences was significantly higher in the chronic METH group than in the control group a week after METH, and they mapped to genes coding for proteins regulating cell growth and proliferation, transcription, protein function as well as for a variety of transporters. The results suggest that chronic METH induces ID element retrotransposition in the dorsal dentate gyrus and may affect hippocampal neurogenesis. PMID:28272323

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 3

Terminological aspects of data elements

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

Strehlow, R.A.; Kenworthey, W.H. Jr.; Schuldt, R.E.

1991-01-01

The creation and display of data comprise a process that involves a sequence of steps requiring both semantic and systems analysis. An essential early step in this process is the choice, definition, and naming of data element concepts and is followed by the specification of other needed data element concept attributes. The attributes and the values of data element concept remain associated with them from their birth as a concept to a generic data element that serves as a template for final application. Terminology is, therefore, centrally important to the entire data creation process. Smooth mapping from natural language tomore » a database is a critical aspect of database, and consequently, it requires terminology standardization from the outset of database work. In this paper the semantic aspects of data elements are analyzed and discussed. Seven kinds of data element concept information are considered and those that require terminological development and standardization are identified. The four terminological components of a data element are the hierarchical type of a concept, functional dependencies, schematas showing conceptual structures, and definition statements. These constitute the conventional role of terminology in database design. 12 refs., 8 figs., 1 tab.« less

Influence of Finite Element Size in Residual Strength Prediction of Composite Structures

NASA Technical Reports Server (NTRS)

Satyanarayana, Arunkumar; Bogert, Philip B.; Karayev, Kazbek Z.; Nordman, Paul S.; Razi, Hamid

2012-01-01

The sensitivity of failure load to the element size used in a progressive failure analysis (PFA) of carbon composite center notched laminates is evaluated. The sensitivity study employs a PFA methodology previously developed by the authors consisting of Hashin-Rotem intra-laminar fiber and matrix failure criteria and a complete stress degradation scheme for damage simulation. The approach is implemented with a user defined subroutine in the ABAQUS/Explicit finite element package. The effect of element size near the notch tips on residual strength predictions was assessed for a brittle failure mode with a parametric study that included three laminates of varying material system, thickness and stacking sequence. The study resulted in the selection of an element size of 0.09 in. X 0.09 in., which was later used for predicting crack paths and failure loads in sandwich panels and monolithic laminated panels. Comparison of predicted crack paths and failure loads for these panels agreed well with experimental observations. Additionally, the element size vs. normalized failure load relationship, determined in the parametric study, was used to evaluate strength-scaling factors for three different element sizes. The failure loads predicted with all three element sizes provided converged failure loads with respect to that corresponding with the 0.09 in. X 0.09 in. element size. Though preliminary in nature, the strength-scaling concept has the potential to greatly reduce the computational time required for PFA and can enable the analysis of large scale structural components where failure is dominated by fiber failure in tension.

Consistent linearization of the element-independent corotational formulation for the structural analysis of general shells

NASA Technical Reports Server (NTRS)

Rankin, C. C.

1988-01-01

A consistent linearization is provided for the element-dependent corotational formulation, providing the proper first and second variation of the strain energy. As a result, the warping problem that has plagued flat elements has been overcome, with beneficial effects carried over to linear solutions. True Newton quadratic convergence has been restored to the Structural Analysis of General Shells (STAGS) code for conservative loading using the full corotational implementation. Some implications for general finite element analysis are discussed, including what effect the automatic frame invariance provided by this work might have on the development of new, improved elements.

A finite element-boundary integral method for scattering and radiation by two- and three-dimensional structures

NASA Technical Reports Server (NTRS)

Jin, Jian-Ming; Volakis, John L.; Collins, Jeffery D.

1991-01-01

A review of a hybrid finite element-boundary integral formulation for scattering and radiation by two- and three-composite structures is presented. In contrast to other hybrid techniques involving the finite element method, the proposed one is in principle exac, and can be implemented using a low O(N) storage. This is of particular importance for large scale applications and is a characteristic of the boundary chosen to terminate the finite-element mesh, usually as close to the structure as possible. A certain class of these boundaries lead to convolutional boundary integrals which can be evaluated via the fast Fourier transform (FFT) without a need to generate a matrix; thus, retaining the O(N) storage requirement.

A Finite Element Procedure for Calculating Fluid-Structure Interaction Using MSC/NASTRAN

NASA Technical Reports Server (NTRS)

Chargin, Mladen; Gartmeier, Otto

1990-01-01

This report is intended to serve two purposes. The first is to present a survey of the theoretical background of the dynamic interaction between a non-viscid, compressible fluid and an elastic structure is presented. Section one presents a short survey of the application of the finite element method (FEM) to the area of fluid-structure-interaction (FSI). Section two describes the mathematical foundation of the structure and fluid with special emphasis on the fluid. The main steps in establishing the finite element (FE) equations for the fluid structure coupling are discussed in section three. The second purpose is to demonstrate the application of MSC/NASTRAN to the solution of FSI problems. Some specific topics, such as fluid structure analogy, acoustic absorption, and acoustic contribution analysis are described in section four. Section five deals with the organization of the acoustic procedure flowchart. Section six includes the most important information that a user needs for applying the acoustic procedure to practical FSI problems. Beginning with some rules concerning the FE modeling of the coupled system, the NASTRAN USER DECKs for the different steps are described. The goal of section seven is to demonstrate the use of the acoustic procedure with some examples. This demonstration includes an analytic verification of selected FE results. The analytical description considers only some aspects of FSI and is not intended to be mathematically complete. Finally, section 8 presents an application of the acoustic procedure to vehicle interior acoustic analysis with selected results.

Integrating genome-wide association study summaries and element-gene interaction datasets identified multiple associations between elements and complex diseases.

PubMed

He, Awen; Wang, Wenyu; Prakash, N Tejo; Tinkov, Alexey A; Skalny, Anatoly V; Wen, Yan; Hao, Jingcan; Guo, Xiong; Zhang, Feng

2018-03-01

Chemical elements are closely related to human health. Extensive genomic profile data of complex diseases offer us a good opportunity to systemically investigate the relationships between elements and complex diseases/traits. In this study, we applied gene set enrichment analysis (GSEA) approach to detect the associations between elements and complex diseases/traits though integrating element-gene interaction datasets and genome-wide association study (GWAS) data of complex diseases/traits. To illustrate the performance of GSEA, the element-gene interaction datasets of 24 elements were extracted from the comparative toxicogenomics database (CTD). GWAS summary datasets of 24 complex diseases or traits were downloaded from the dbGaP or GEFOS websites. We observed significant associations between 7 elements and 13 complex diseases or traits (all false discovery rate (FDR) < 0.05), including reported relationships such as aluminum vs. Alzheimer's disease (FDR = 0.042), calcium vs. bone mineral density (FDR = 0.031), magnesium vs. systemic lupus erythematosus (FDR = 0.012) as well as novel associations, such as nickel vs. hypertriglyceridemia (FDR = 0.002) and bipolar disorder (FDR = 0.027). Our study results are consistent with previous biological studies, supporting the good performance of GSEA. Our analyzing results based on GSEA framework provide novel clues for discovering causal relationships between elements and complex diseases. © 2017 WILEY PERIODICALS, INC.

NanoSIMS Reveals New Structural and Elemental Signatures of Early Life

NASA Technical Reports Server (NTRS)

Oehler, Dorothy Z.; Mostefaoui, Smail; Meibom, Anders; Selo, Madeleine; Robert, Francois; McKay, David S.

2006-01-01

The young technology of NanoSIMS is unlocking new information from organic matter in ancient sediments. We have used this technique to characterize sub-micron scale element composition of Proterozoic organics that are clearly biogenic as a guide for interpreting problematic structures in terrestrial or extraterrestrial samples. We used the NanoSIMS 50 of the National Museum of Natural History in Paris to map carbon, nitrogen (as CN), and sulfur in organic structures from the approximately 0.8 Ga Bitter Springs Formation. We analyzed spheroidal and filamentous microfossils as well as organic laminae that appeared amorphous by optical and scanning electron microscopy. In clear-cut microfossils, a coincidence between optical images and NanoSIMS element maps suggests a biological origin for the mapped carbon, sulfur, and nitrogen; this conclusion is supported by high resolution NanoSIMS maps showing identical spatial distributions of C, CN and S. High resolution images also demonstrate distinctive nano structure of the filaments and spheroids. In the amorphous laminae, NanoSIMS reveals morphologies reminiscent of compressed microfossils. Distinct CN/C ratios of the spheroids, filaments, and laminae may reflect their biological precursors (cell walls, cyanobacterial sheaths, and microbial communities/biofilms, respectively). Similar amorphous laminae comprise a preponderance of the organic matter in many Precambrian deposits. Thus it is possible that NanoSIMS will provide fresh insight into a large body of previously uninterpretable material. Additionally, NanoSIMS analysis may establish new biosignatures that will be helpful for assessing the origin and biogenicity of controversial Archean structures and any organic materials that may occur in Martian or other extraterrestrial samples.

Implementation of structural response sensitivity calculations in a large-scale finite-element analysis system

NASA Technical Reports Server (NTRS)

Giles, G. L.; Rogers, J. L., Jr.

1982-01-01

The methodology used to implement structural sensitivity calculations into a major, general-purpose finite-element analysis system (SPAR) is described. This implementation includes a generalized method for specifying element cross-sectional dimensions as design variables that can be used in analytically calculating derivatives of output quantities from static stress, vibration, and buckling analyses for both membrane and bending elements. Limited sample results for static displacements and stresses are presented to indicate the advantages of analytically calculating response derivatives compared to finite difference methods. Continuing developments to implement these procedures into an enhanced version of SPAR are also discussed.

Improved accuracy for finite element structural analysis via an integrated force method

NASA Technical Reports Server (NTRS)

Patnaik, S. N.; Hopkins, D. A.; Aiello, R. A.; Berke, L.

1992-01-01

A comparative study was carried out to determine the accuracy of finite element analyses based on the stiffness method, a mixed method, and the new integrated force and dual integrated force methods. The numerical results were obtained with the following software: MSC/NASTRAN and ASKA for the stiffness method; an MHOST implementation method for the mixed method; and GIFT for the integrated force methods. The results indicate that on an overall basis, the stiffness and mixed methods present some limitations. The stiffness method generally requires a large number of elements in the model to achieve acceptable accuracy. The MHOST method tends to achieve a higher degree of accuracy for course models than does the stiffness method implemented by MSC/NASTRAN and ASKA. The two integrated force methods, which bestow simultaneous emphasis on stress equilibrium and strain compatibility, yield accurate solutions with fewer elements in a model. The full potential of these new integrated force methods remains largely unexploited, and they hold the promise of spawning new finite element structural analysis tools.

Identifying DNA-binding proteins using structural motifs and the electrostatic potential

PubMed Central

Shanahan, Hugh P.; Garcia, Mario A.; Jones, Susan; Thornton, Janet M.

2004-01-01

Robust methods to detect DNA-binding proteins from structures of unknown function are important for structural biology. This paper describes a method for identifying such proteins that (i) have a solvent accessible structural motif necessary for DNA-binding and (ii) a positive electrostatic potential in the region of the binding region. We focus on three structural motifs: helix–turn-helix (HTH), helix–hairpin–helix (HhH) and helix–loop–helix (HLH). We find that the combination of these variables detect 78% of proteins with an HTH motif, which is a substantial improvement over previous work based purely on structural templates and is comparable to more complex methods of identifying DNA-binding proteins. Similar true positive fractions are achieved for the HhH and HLH motifs. We see evidence of wide evolutionary diversity for DNA-binding proteins with an HTH motif, and much smaller diversity for those with an HhH or HLH motif. PMID:15356290

Coupled Finite Volume and Finite Element Method Analysis of a Complex Large-Span Roof Structure

NASA Astrophysics Data System (ADS)

Szafran, J.; Juszczyk, K.; Kamiński, M.

2017-12-01

The main goal of this paper is to present coupled Computational Fluid Dynamics and structural analysis for the precise determination of wind impact on internal forces and deformations of structural elements of a longspan roof structure. The Finite Volume Method (FVM) serves for a solution of the fluid flow problem to model the air flow around the structure, whose results are applied in turn as the boundary tractions in the Finite Element Method problem structural solution for the linear elastostatics with small deformations. The first part is carried out with the use of ANSYS 15.0 computer system, whereas the FEM system Robot supports stress analysis in particular roof members. A comparison of the wind pressure distribution throughout the roof surface shows some differences with respect to that available in the engineering designing codes like Eurocode, which deserves separate further numerical studies. Coupling of these two separate numerical techniques appears to be promising in view of future computational models of stochastic nature in large scale structural systems due to the stochastic perturbation method.

Phylogenetic Conflict in Bears Identified by Automated Discovery of Transposable Element Insertions in Low-Coverage Genomes.

PubMed

Lammers, Fritjof; Gallus, Susanne; Janke, Axel; Nilsson, Maria A

2017-10-01

Phylogenetic reconstruction from transposable elements (TEs) offers an additional perspective to study evolutionary processes. However, detecting phylogenetically informative TE insertions requires tedious experimental work, limiting the power of phylogenetic inference. Here, we analyzed the genomes of seven bear species using high-throughput sequencing data to detect thousands of TE insertions. The newly developed pipeline for TE detection called TeddyPi (TE detection and discovery for Phylogenetic Inference) identified 150,513 high-quality TE insertions in the genomes of ursine and tremarctine bears. By integrating different TE insertion callers and using a stringent filtering approach, the TeddyPi pipeline produced highly reliable TE insertion calls, which were confirmed by extensive in vitro validation experiments. Analysis of single nucleotide substitutions in the flanking regions of the TEs shows that these substitutions correlate with the phylogenetic signal from the TE insertions. Our phylogenomic analyses show that TEs are a major driver of genomic variation in bears and enabled phylogenetic reconstruction of a well-resolved species tree, despite strong signals for incomplete lineage sorting and introgression. The analyses show that the Asiatic black, sun, and sloth bear form a monophyletic clade, in which phylogenetic incongruence originates from incomplete lineage sorting. TeddyPi is open source and can be adapted to various TE and structural variation callers. The pipeline makes it possible to confidently extract thousands of TE insertions even from low-coverage genomes (∼10×) of nonmodel organisms. This opens new possibilities for biologists to study phylogenies and evolutionary processes as well as rates and patterns of (retro-)transposition and structural variation. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

New group-V elemental bilayers: A tunable structure model with four-, six-, and eight-atom rings

NASA Astrophysics Data System (ADS)

Kong, Xiangru; Li, Linyang; Leenaerts, Ortwin; Liu, Xiong-Jun; Peeters, François M.

2017-07-01

Two-dimensional group-V elemental materials have attracted widespread attention due to their nonzero band gap while displaying high electron mobility. Using first-principles calculations, we propose a series of new elemental bilayers with group-V elements (Bi, Sb, As). Our study reveals the dynamical stability of four-, six-, and eight-atom ring structures, demonstrating their possible coexistence in such bilayer systems. The proposed structures for Sb and As are large-gap semiconductors that are potentially interesting for applications in future nanodevices. The Bi structures have nontrivial topological properties with a direct nontrivial band gap. The nontrivial gap is shown to arise from a band inversion at the Brillouin zone center due to the strong intrinsic spin-orbit coupling in Bi atoms. Moreover, we demonstrate the possibility of tuning the properties of these materials by enhancing the ratio of six-atom rings to four- and eight-atom rings, which results in wider nontrivial band gaps and lower formation energies.

Compliance control with embedded neural elements

NASA Technical Reports Server (NTRS)

Venkataraman, S. T.; Gulati, S.

1992-01-01

The authors discuss a control approach that embeds the neural elements within a model-based compliant control architecture for robotic tasks that involve contact with unstructured environments. Compliance control experiments have been performed on actual robotics hardware to demonstrate the performance of contact control schemes with neural elements. System parameters were identified under the assumption that environment dynamics have a fixed nonlinear structure. A robotics research arm, placed in contact with a single degree-of-freedom electromechanical environment dynamics emulator, was commanded to move through a desired trajectory. The command was implemented by using a compliant control strategy.

Probabilistic Finite Element Analysis & Design Optimization for Structural Designs

NASA Astrophysics Data System (ADS)

Deivanayagam, Arumugam

This study focuses on implementing probabilistic nature of material properties (Kevlar® 49) to the existing deterministic finite element analysis (FEA) of fabric based engine containment system through Monte Carlo simulations (MCS) and implementation of probabilistic analysis in engineering designs through Reliability Based Design Optimization (RBDO). First, the emphasis is on experimental data analysis focusing on probabilistic distribution models which characterize the randomness associated with the experimental data. The material properties of Kevlar® 49 are modeled using experimental data analysis and implemented along with an existing spiral modeling scheme (SMS) and user defined constitutive model (UMAT) for fabric based engine containment simulations in LS-DYNA. MCS of the model are performed to observe the failure pattern and exit velocities of the models. Then the solutions are compared with NASA experimental tests and deterministic results. MCS with probabilistic material data give a good prospective on results rather than a single deterministic simulation results. The next part of research is to implement the probabilistic material properties in engineering designs. The main aim of structural design is to obtain optimal solutions. In any case, in a deterministic optimization problem even though the structures are cost effective, it becomes highly unreliable if the uncertainty that may be associated with the system (material properties, loading etc.) is not represented or considered in the solution process. Reliable and optimal solution can be obtained by performing reliability optimization along with the deterministic optimization, which is RBDO. In RBDO problem formulation, in addition to structural performance constraints, reliability constraints are also considered. This part of research starts with introduction to reliability analysis such as first order reliability analysis, second order reliability analysis followed by simulation technique that

The central element of the synaptonemal complex in mice is organized as a bilayered junction structure.

PubMed

Hernández-Hernández, Abrahan; Masich, Sergej; Fukuda, Tomoyuki; Kouznetsova, Anna; Sandin, Sara; Daneholt, Bertil; Höög, Christer

2016-06-01

The synaptonemal complex transiently stabilizes pairing interactions between homologous chromosomes during meiosis. Assembly of the synaptonemal complex is mediated through integration of opposing transverse filaments into a central element, a process that is poorly understood. We have, here, analyzed the localization of the transverse filament protein SYCP1 and the central element proteins SYCE1, SYCE2 and SYCE3 within the central region of the synaptonemal complex in mouse spermatocytes using immunoelectron microscopy. Distribution of immuno-gold particles in a lateral view of the synaptonemal complex, supported by protein interaction data, suggest that the N-terminal region of SYCP1 and SYCE3 form a joint bilayered central structure, and that SYCE1 and SYCE2 localize in between the two layers. We find that disruption of SYCE2 and TEX12 (a fourth central element protein) localization to the central element abolishes central alignment of the N-terminal region of SYCP1. Thus, our results show that all four central element proteins, in an interdependent manner, contribute to stabilization of opposing N-terminal regions of SYCP1, forming a bilayered transverse-filament-central-element junction structure that promotes synaptonemal complex formation and synapsis. © 2016. Published by The Company of Biologists Ltd.

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

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.

Identify High-Quality Protein Structural Models by Enhanced K-Means.

PubMed

Wu, Hongjie; Li, Haiou; Jiang, Min; Chen, Cheng; Lv, Qiang; Wu, Chuang

2017-01-01

Background. One critical issue in protein three-dimensional structure prediction using either ab initio or comparative modeling involves identification of high-quality protein structural models from generated decoys. Currently, clustering algorithms are widely used to identify near-native models; however, their performance is dependent upon different conformational decoys, and, for some algorithms, the accuracy declines when the decoy population increases. Results. Here, we proposed two enhanced K -means clustering algorithms capable of robustly identifying high-quality protein structural models. The first one employs the clustering algorithm SPICKER to determine the initial centroids for basic K -means clustering ( SK -means), whereas the other employs squared distance to optimize the initial centroids ( K -means++). Our results showed that SK -means and K -means++ were more robust as compared with SPICKER alone, detecting 33 (59%) and 42 (75%) of 56 targets, respectively, with template modeling scores better than or equal to those of SPICKER. Conclusions. We observed that the classic K -means algorithm showed a similar performance to that of SPICKER, which is a widely used algorithm for protein-structure identification. Both SK -means and K -means++ demonstrated substantial improvements relative to results from SPICKER and classical K -means.

Identify High-Quality Protein Structural Models by Enhanced K-Means

PubMed Central

Li, Haiou; Chen, Cheng; Lv, Qiang; Wu, Chuang

2017-01-01

Background. One critical issue in protein three-dimensional structure prediction using either ab initio or comparative modeling involves identification of high-quality protein structural models from generated decoys. Currently, clustering algorithms are widely used to identify near-native models; however, their performance is dependent upon different conformational decoys, and, for some algorithms, the accuracy declines when the decoy population increases. Results. Here, we proposed two enhanced K-means clustering algorithms capable of robustly identifying high-quality protein structural models. The first one employs the clustering algorithm SPICKER to determine the initial centroids for basic K-means clustering (SK-means), whereas the other employs squared distance to optimize the initial centroids (K-means++). Our results showed that SK-means and K-means++ were more robust as compared with SPICKER alone, detecting 33 (59%) and 42 (75%) of 56 targets, respectively, with template modeling scores better than or equal to those of SPICKER. Conclusions. We observed that the classic K-means algorithm showed a similar performance to that of SPICKER, which is a widely used algorithm for protein-structure identification. Both SK-means and K-means++ demonstrated substantial improvements relative to results from SPICKER and classical K-means. PMID:28421198

Nonlinear finite element modeling of vibration control of plane rod-type structural members with integrated piezoelectric patches

NASA Astrophysics Data System (ADS)

Chróścielewski, Jacek; Schmidt, Rüdiger; Eremeyev, Victor A.

2018-05-01

This paper addresses modeling and finite element analysis of the transient large-amplitude vibration response of thin rod-type structures (e.g., plane curved beams, arches, ring shells) and its control by integrated piezoelectric layers. A geometrically nonlinear finite beam element for the analysis of piezolaminated structures is developed that is based on the Bernoulli hypothesis and the assumptions of small strains and finite rotations of the normal. The finite element model can be applied to static, stability, and transient analysis of smart structures consisting of a master structure and integrated piezoelectric actuator layers or patches attached to the upper and lower surfaces. Two problems are studied extensively: (i) FE analyses of a clamped semicircular ring shell that has been used as a benchmark problem for linear vibration control in several recent papers are critically reviewed and extended to account for the effects of structural nonlinearity and (ii) a smart circular arch subjected to a hydrostatic pressure load is investigated statically and dynamically in order to study the shift of bifurcation and limit points, eigenfrequencies, and eigenvectors, as well as vibration control for loading conditions which may lead to dynamic loss of stability.

Vertical velocity structure and geometry of clear air convective elements

NASA Technical Reports Server (NTRS)

Rowland, J. R.; Arnold, A.

1975-01-01

The paper discusses observations of individual convective elements with a high-power narrow-beam scanning radar, an FM-CW radar, and an acoustic sounder, including the determination of the vertical air velocity patterns of convective structures with the FM-CW radar and acoustic sounder. Data are presented which link the observed velocity structure and geometrical patterns to previously proposed models of boundary layer convection. It is shown that the high-power radar provides a clear three-dimensional picture of convective cells and fields over a large area with a resolution of 150 m, where the convective cells are roughly spherical. Analysis of time-height records of the FM-CW radar and acoustic sounder confirms the downdraft-entrainment mechanism of the convective cell. The Doppler return of the acoustic sounder and the insect-trail slopes on FM-CW radar records are independent but redundant methods for obtaining the vertical velocity patterns of convective structures.

Improved finite-element methods for rotorcraft structures

NASA Technical Reports Server (NTRS)

Hinnant, Howard E.

1991-01-01

An overview of the research directed at improving finite-element methods for rotorcraft airframes is presented. The development of a modification to the finite element method which eliminates interelement discontinuities is covered. The following subject areas are discussed: geometric entities, interelement continuity, dependent rotational degrees of freedom, and adaptive numerical integration. This new methodology is being implemented as an anisotropic, curvilinear, p-version, beam, shell, and brick finite element program.

Probing Xist RNA Structure in Cells Using Targeted Structure-Seq

PubMed Central

Rutenberg-Schoenberg, Michael; Simon, Matthew D.

2015-01-01

The long non-coding RNA (lncRNA) Xist is a master regulator of X-chromosome inactivation in mammalian cells. Models for how Xist and other lncRNAs function depend on thermodynamically stable secondary and higher-order structures that RNAs can form in the context of a cell. Probing accessible RNA bases can provide data to build models of RNA conformation that provide insight into RNA function, molecular evolution, and modularity. To study the structure of Xist in cells, we built upon recent advances in RNA secondary structure mapping and modeling to develop Targeted Structure-Seq, which combines chemical probing of RNA structure in cells with target-specific massively parallel sequencing. By enriching for signals from the RNA of interest, Targeted Structure-Seq achieves high coverage of the target RNA with relatively few sequencing reads, thus providing a targeted and scalable approach to analyze RNA conformation in cells. We use this approach to probe the full-length Xist lncRNA to develop new models for functional elements within Xist, including the repeat A element in the 5’-end of Xist. This analysis also identified new structural elements in Xist that are evolutionarily conserved, including a new element proximal to the C repeats that is important for Xist function. PMID:26646615

Structure and transcriptional impact of divergent repetitive elements inserted within Phanerochaete chrysosporium strain RP-78 genes

Treesearch

Luis F. Larrondo; Paulo Canessa; Rafael Vicuna; Philip Stewart; Amber Vanden Wymelenberg; Dan Cullen

2007-01-01

We describe the structure, organization, and transcriptional impact of repetitive elements within the lignin-degrading basidiomycete, Phanerochaete chrysosporium. Searches of the P. chrysosporium genome revealed five copies of pce1, a 1,750-nt non-autonomous, class II element. Alleles encoding a putative glucosyltransferase and a cytochrome P450 harbor pce insertions...

Read count-based method for high-throughput allelic genotyping of transposable elements and structural variants.

PubMed

Kuhn, Alexandre; Ong, Yao Min; Quake, Stephen R; Burkholder, William F

2015-07-08

Like other structural variants, transposable element insertions can be highly polymorphic across individuals. Their functional impact, however, remains poorly understood. Current genome-wide approaches for genotyping insertion-site polymorphisms based on targeted or whole-genome sequencing remain very expensive and can lack accuracy, hence new large-scale genotyping methods are needed. We describe a high-throughput method for genotyping transposable element insertions and other types of structural variants that can be assayed by breakpoint PCR. The method relies on next-generation sequencing of multiplex, site-specific PCR amplification products and read count-based genotype calls. We show that this method is flexible, efficient (it does not require rounds of optimization), cost-effective and highly accurate. This method can benefit a wide range of applications from the routine genotyping of animal and plant populations to the functional study of structural variants in humans.

Variant-aware saturating mutagenesis using multiple Cas9 nucleases identifies regulatory elements at trait-associated loci.

PubMed

Canver, Matthew C; Lessard, Samuel; Pinello, Luca; Wu, Yuxuan; Ilboudo, Yann; Stern, Emily N; Needleman, Austen J; Galactéros, Frédéric; Brugnara, Carlo; Kutlar, Abdullah; McKenzie, Colin; Reid, Marvin; Chen, Diane D; Das, Partha Pratim; A Cole, Mitchel; Zeng, Jing; Kurita, Ryo; Nakamura, Yukio; Yuan, Guo-Cheng; Lettre, Guillaume; Bauer, Daniel E; Orkin, Stuart H

2017-04-01

Cas9-mediated, high-throughput, saturating in situ mutagenesis permits fine-mapping of function across genomic segments. Disease- and trait-associated variants identified in genome-wide association studies largely cluster at regulatory loci. Here we demonstrate the use of multiple designer nucleases and variant-aware library design to interrogate trait-associated regulatory DNA at high resolution. We developed a computational tool for the creation of saturating-mutagenesis libraries with single or multiple nucleases with incorporation of variants. We applied this methodology to the HBS1L-MYB intergenic region, which is associated with red-blood-cell traits, including fetal hemoglobin levels. This approach identified putative regulatory elements that control MYB expression. Analysis of genomic copy number highlighted potential false-positive regions, thus emphasizing the importance of off-target analysis in the design of saturating-mutagenesis experiments. Together, these data establish a widely applicable high-throughput and high-resolution methodology to identify minimal functional sequences within large disease- and trait-associated regions.

Identifying Structural Flow Defects in Disordered Solids Using Machine-Learning Methods

NASA Astrophysics Data System (ADS)

Cubuk, E. D.; Schoenholz, S. S.; Rieser, J. M.; Malone, B. D.; Rottler, J.; Durian, D. J.; Kaxiras, E.; Liu, A. J.

2015-03-01

We use machine-learning methods on local structure to identify flow defects—or particles susceptible to rearrangement—in jammed and glassy systems. We apply this method successfully to two very different systems: a two-dimensional experimental realization of a granular pillar under compression and a Lennard-Jones glass in both two and three dimensions above and below its glass transition temperature. We also identify characteristics of flow defects that differentiate them from the rest of the sample. Our results show it is possible to discern subtle structural features responsible for heterogeneous dynamics observed across a broad range of disordered materials.

Designing synthetic RNAs to determine the relevance of structural motifs in picornavirus IRES elements

NASA Astrophysics Data System (ADS)

Fernandez-Chamorro, Javier; Lozano, Gloria; Garcia-Martin, Juan Antonio; Ramajo, Jorge; Dotu, Ivan; Clote, Peter; Martinez-Salas, Encarnacion

2016-04-01

The function of Internal Ribosome Entry Site (IRES) elements is intimately linked to their RNA structure. Viral IRES elements are organized in modular domains consisting of one or more stem-loops that harbor conserved RNA motifs critical for internal initiation of translation. A conserved motif is the pyrimidine-tract located upstream of the functional initiation codon in type I and II picornavirus IRES. By computationally designing synthetic RNAs to fold into a structure that sequesters the polypyrimidine tract in a hairpin, we establish a correlation between predicted inaccessibility of the pyrimidine tract and IRES activity, as determined in both in vitro and in vivo systems. Our data supports the hypothesis that structural sequestration of the pyrimidine-tract within a stable hairpin inactivates IRES activity, since the stronger the stability of the hairpin the higher the inhibition of protein synthesis. Destabilization of the stem-loop immediately upstream of the pyrimidine-tract also decreases IRES activity. Our work introduces a hybrid computational/experimental method to determine the importance of structural motifs for biological function. Specifically, we show the feasibility of using the software RNAiFold to design synthetic RNAs with particular sequence and structural motifs that permit subsequent experimental determination of the importance of such motifs for biological function.

Elemental concentration analysis in brain structures from young, adult and old Wistar rats by total reflection X-ray fluorescence with synchrotron radiation

NASA Astrophysics Data System (ADS)

Serpa, R. F. B.; de Jesus, E. F. O.; Anjos, M. J.; do Carmo, M. G. T.; Moreira, S.; Rocha, M. S.; Martinez, A. M. B.; Lopes, R. T.

2006-11-01

The knowledge of the spatial distribution and the local concentration of trace elements in tissues are of great importance since trace elements are involved in a number of metabolic and physiological processes in the human body, and their deficiency and excess may lead to different metabolic disorders. In this way, the main goal of this work is to compare the elemental concentration in different brain structures, namely temporal cortex, entorhinal cortex, visual cortex and hippocampus, from Wistar female rats ( n = 15) with different ages: 2, 8 and 48 weeks. The measurements were performed at the Synchrotron Light Brazilian Laboratory, Campinas, São Paulo, Brazil. In the entorhinal cortex, the following elements decreased with age: Zn, S, Cl, K, Ca and Br. In the temporal cortex, Ca, Fe and Br levels increased with aging and on the other hand, P, S, Cl, K and Rb levels decreased with aging. In the visual cortex almost all the elements decreased with aging: Cl, Ca, Fe, Ni and Zn. In the hippocampus, in turn, most of the elements identified, increased with aging: Al, P, S, K, Fe, Cu, Zn and Rb. The increase of Fe with aging in the hippocampus is an important fact that will be studied, since it is involved in oxidative stress. It is believed that oxidative stress is the one of the main causes responsible for neuronal death in Parkinson's disease.

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.

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…

Probalistic Finite Elements (PFEM) structural dynamics and fracture mechanics

NASA Technical Reports Server (NTRS)

Liu, Wing-Kam; Belytschko, Ted; Mani, A.; Besterfield, G.

1989-01-01

The purpose of this work is to develop computationally efficient methodologies for assessing the effects of randomness in loads, material properties, and other aspects of a problem by a finite element analysis. The resulting group of methods is called probabilistic finite elements (PFEM). The overall objective of this work is to develop methodologies whereby the lifetime of a component can be predicted, accounting for the variability in the material and geometry of the component, the loads, and other aspects of the environment; and the range of response expected in a particular scenario can be presented to the analyst in addition to the response itself. Emphasis has been placed on methods which are not statistical in character; that is, they do not involve Monte Carlo simulations. The reason for this choice of direction is that Monte Carlo simulations of complex nonlinear response require a tremendous amount of computation. The focus of efforts so far has been on nonlinear structural dynamics. However, in the continuation of this project, emphasis will be shifted to probabilistic fracture mechanics so that the effect of randomness in crack geometry and material properties can be studied interactively with the effect of random load and environment.

Structural and practical identifiability analysis of S-system.

PubMed

Zhan, Choujun; Li, Benjamin Yee Shing; Yeung, Lam Fat

2015-12-01

In the field of systems biology, biological reaction networks are usually modelled by ordinary differential equations. A sub-class, the S-systems representation, is a widely used form of modelling. Existing S-systems identification techniques assume that the system itself is always structurally identifiable. However, due to practical limitations, biological reaction networks are often only partially measured. In addition, the captured data only covers a limited trajectory, therefore data can only be considered as a local snapshot of the system responses with respect to the complete set of state trajectories over the entire state space. Hence the estimated model can only reflect partial system dynamics and may not be unique. To improve the identification quality, the structural and practical identifiablility of S-system are studied. The S-system is shown to be identifiable under a set of assumptions. Then, an application on yeast fermentation pathway was conducted. Two case studies were chosen; where the first case is based on a larger state trajectories and the second case is based on a smaller one. By expanding the dataset which span a relatively larger state space, the uncertainty of the estimated system can be reduced. The results indicated that initial concentration is related to the practical identifiablity.

Regulatory element-based prediction identifies new susceptibility regulatory variants for osteoporosis.

PubMed

Yao, Shi; Guo, Yan; Dong, Shan-Shan; Hao, Ruo-Han; Chen, Xiao-Feng; Chen, Yi-Xiao; Chen, Jia-Bin; Tian, Qing; Deng, Hong-Wen; Yang, Tie-Lin

2017-08-01

Despite genome-wide association studies (GWASs) have identified many susceptibility genes for osteoporosis, it still leaves a large part of missing heritability to be discovered. Integrating regulatory information and GWASs could offer new insights into the biological link between the susceptibility SNPs and osteoporosis. We generated five machine learning classifiers with osteoporosis-associated variants and regulatory features data. We gained the optimal classifier and predicted genome-wide SNPs to discover susceptibility regulatory variants. We further utilized Genetic Factors for Osteoporosis Consortium (GEFOS) and three in-house GWASs samples to validate the associations for predicted positive SNPs. The random forest classifier performed best among all machine learning methods with the F1 score of 0.8871. Using the optimized model, we predicted 37,584 candidate SNPs for osteoporosis. According to the meta-analysis results, a list of regulatory variants was significantly associated with osteoporosis after multiple testing corrections and contributed to the expression of known osteoporosis-associated protein-coding genes. In summary, combining GWASs and regulatory elements through machine learning could provide additional information for understanding the mechanism of osteoporosis. The regulatory variants we predicted will provide novel targets for etiology research and treatment of osteoporosis.

Wakefield Simulation of CLIC PETS Structure Using Parallel 3D Finite Element Time-Domain Solver T3P

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

Candel, A.; Kabel, A.; Lee, L.

In recent years, SLAC's Advanced Computations Department (ACD) has developed the parallel 3D Finite Element electromagnetic time-domain code T3P. Higher-order Finite Element methods on conformal unstructured meshes and massively parallel processing allow unprecedented simulation accuracy for wakefield computations and simulations of transient effects in realistic accelerator structures. Applications include simulation of wakefield damping in the Compact Linear Collider (CLIC) power extraction and transfer structure (PETS).

Co-simulation coupling spectral/finite elements for 3D soil/structure interaction problems

NASA Astrophysics Data System (ADS)

Zuchowski, Loïc; Brun, Michael; De Martin, Florent

2018-05-01

The coupling between an implicit finite elements (FE) code and an explicit spectral elements (SE) code has been explored for solving the elastic wave propagation in the case of soil/structure interaction problem. The coupling approach is based on domain decomposition methods in transient dynamics. The spatial coupling at the interface is managed by a standard coupling mortar approach, whereas the time integration is dealt with an hybrid asynchronous time integrator. An external coupling software, handling the interface problem, has been set up in order to couple the FE software Code_Aster with the SE software EFISPEC3D.

The forced vibration of one-dimensional multi-coupled periodic structures: An application to finite element analysis

NASA Astrophysics Data System (ADS)

Mead, Denys J.

2009-01-01

A general theory for the forced vibration of multi-coupled one-dimensional periodic structures is presented as a sequel to a much earlier general theory for free vibration. Starting from the dynamic stiffness matrix of a single multi-coupled periodic element, it derives matrix equations for the magnitudes of the characteristic free waves excited in the whole structure by prescribed harmonic forces and/or displacements acting at a single periodic junction. The semi-infinite periodic system excited at its end is first analysed to provide the basis for analysing doubly infinite and finite periodic systems. In each case, total responses are found by considering just one periodic element. An already-known method of reducing the size of the computational problem is reexamined, expanded and extended in detail, involving reduction of the dynamic stiffness matrix of the periodic element through a wave-coordinate transformation. Use of the theory is illustrated in a combined periodic structure+finite element analysis of the forced harmonic in-plane motion of a uniform flat plate. Excellent agreement between the computed low-frequency responses and those predicted by simple engineering theories validates the detailed formulations of the paper. The primary purpose of the paper is not towards a specific application but to present a systematic and coherent forced vibration theory, carefully linked with the existing free-wave theory.

Identifying Causal Elements in the Thematic-Fantasy Play Paradigm.

ERIC Educational Resources Information Center

Pellegrini, Anthony D.

The intent of this study was to examine the effectiveness of elements of the thematic-fantasy play training paradigm in facilitating children's immediate and maintained story comprehension. Thematic-fantasy play was defined as play in which children enact themes and events not related to their everyday experience, as when they act out a fairy…

Finite element analysis of steady and transiently moving/rolling nonlinear viscoelastic structure. II - Shell and three-dimensional simulations

NASA Technical Reports Server (NTRS)

Kennedy, Ronald; Padovan, Joe

1987-01-01

In a three-part series of papers, a generalized finite element solution strategy is developed to handle traveling load problems in rolling, moving and rotating structure. The main thrust of this section consists of the development of three-dimensional and shell type moving elements. In conjunction with this work, a compatible three-dimensional contact strategy is also developed. Based on these modeling capabilities, extensive analytical and experimental benchmarking is presented. Such testing includes traveling loads in rotating structure as well as low- and high-speed rolling contact involving standing wave-type response behavior. These point to the excellent modeling capabilities of moving element strategies.

Improved accuracy for finite element structural analysis via a new integrated force method

NASA Technical Reports Server (NTRS)

Patnaik, Surya N.; Hopkins, Dale A.; Aiello, Robert A.; Berke, Laszlo

1992-01-01

A comparative study was carried out to determine the accuracy of finite element analyses based on the stiffness method, a mixed method, and the new integrated force and dual integrated force methods. The numerical results were obtained with the following software: MSC/NASTRAN and ASKA for the stiffness method; an MHOST implementation method for the mixed method; and GIFT for the integrated force methods. The results indicate that on an overall basis, the stiffness and mixed methods present some limitations. The stiffness method generally requires a large number of elements in the model to achieve acceptable accuracy. The MHOST method tends to achieve a higher degree of accuracy for course models than does the stiffness method implemented by MSC/NASTRAN and ASKA. The two integrated force methods, which bestow simultaneous emphasis on stress equilibrium and strain compatibility, yield accurate solutions with fewer elements in a model. The full potential of these new integrated force methods remains largely unexploited, and they hold the promise of spawning new finite element structural analysis tools.

Secondary structure model of the RNA recognized by the reverse transcriptase from the R2 retrotransposable element.

PubMed Central

Mathews, D H; Banerjee, A R; Luan, D D; Eickbush, T H; Turner, D H

1997-01-01

RNA transcripts corresponding to the 250-nt 3' untranslated region of the R2 non-LTR retrotransposable element are recognized by the R2 reverse transcriptase and are sufficient to serve as templates in the target DNA-primed reverse transcription (TPRT) reaction. The R2 protein encoded by the Bombyx mori R2 can recognize this region from both the B. mori and Drosophila melanogaster R2 elements even though these regions show little nucleotide sequence identity. A model for the RNA secondary structure of the 3' untranslated region of the D. melanogaster R2 retrotransposon was developed by sequence comparison of 10 species aided by free energy minimization. Chemical modification experiments are consistent with this prediction. A secondary structure model for the 3' untranslated region of R2 RNA from the R2 element from B. mori was obtained by a combination of chemical modification data and free energy minimization. These two secondary structure models, found independently, share several common sites. This study shows the utility of combining free energy minimization, sequence comparison, and chemical modification to model an RNA secondary structure. PMID:8990394

Structural characterization and regulatory element analysis of the heart isoform of cytochrome c oxidase VIa

NASA Technical Reports Server (NTRS)

Wan, B.; Moreadith, R. W.; Blomqvist, C. G. (Principal Investigator)

1995-01-01

In order to investigate the mechanism(s) governing the striated muscle-specific expression of cytochrome c oxidase VIaH we have characterized the murine gene and analyzed its transcriptional regulatory elements in skeletal myogenic cell lines. The gene is single copy, spans 689 base pairs (bp), and is comprised of three exons. The 5'-ends of transcripts from the gene are heterogeneous, but the most abundant transcript includes a 5'-untranslated region of 30 nucleotides. When fused to the luciferase reporter gene, the 3.5-kilobase 5'-flanking region of the gene directed the expression of the heterologous protein selectively in differentiated Sol8 cells and transgenic mice, recapitulating the pattern of expression of the endogenous gene. Deletion analysis identified a 300-bp fragment sufficient to direct the myotube-specific expression of luciferase in Sol8 cells. The region lacks an apparent TATA element, and sequence motifs predicted to bind NRF-1, NRF-2, ox-box, or PPAR factors known to regulate other nuclear genes encoding mitochondrial proteins are not evident. Mutational analysis, however, identified two cis-elements necessary for the high level expression of the reporter protein: a MEF2 consensus element at -90 to -81 bp and an E-box element at -147 to -142 bp. Additional E-box motifs at closely located positions were mutated without loss of transcriptional activity. The dependence of transcriptional activation of cytochrome c oxidase VIaH on cis-elements similar to those found in contractile protein genes suggests that the striated muscle-specific expression is coregulated by mechanisms that control the lineage-specific expression of several contractile and cytosolic proteins.

PLANS: A finite element program for nonlinear analysis of structures. Volume 1: Theoretical manual

NASA Technical Reports Server (NTRS)

Pifko, A.; Levine, H. S.; Armen, H., Jr.

1975-01-01

The PLANS system is described which is a finite element program for nonlinear analysis. The system represents a collection of special purpose computer programs each associated with a distinct physical problem class. Modules of PLANS specifically referenced and described in detail include: (1) REVBY, for the plastic analysis of bodies of revolution; (2) OUT-OF-PLANE, for the plastic analysis of 3-D built-up structures where membrane effects are predominant; (3) BEND, for the plastic analysis of built-up structures where bending and membrane effects are significant; (4) HEX, for the 3-D elastic-plastic analysis of general solids; and (5) OUT-OF-PLANE-MG, for material and geometrically nonlinear analysis of built-up structures. The SATELLITE program for data debugging and plotting of input geometries is also described. The theoretical foundations upon which the analysis is based are presented. Discussed are the form of the governing equations, the methods of solution, plasticity theories available, a general system description and flow of the programs, and the elements available for use.

Element-selective investigation of domain structure in CoPd and FePd alloys using small-angle soft X-ray scattering

NASA Astrophysics Data System (ADS)

Weier, C.; Adam, R.; Frömter, R.; Bach, J.; Winkler, G.; Kobs, A.; Oepen, H. P.; Grychtol, P.; Kapteyn, H. C.; Murnane, M. M.; Schneider, C. M.

2014-03-01

Recent optical pump-probe experiments on magnetic multilayers and alloys identified perpendicular spin superdiffusion as one of possible mechanisms responsible for femtosecond magnetization dynamics. On the other hand, no strong evidence for the ultrafast lateral spin transport has been reported, so far. To address this question, we studied magnetic domain structure of CoPd and FePd thin films using small-angle scattering of soft X-rays. By tuning the synchrotron-generated X-rays to the absorption edges of Fe or Co we recorded Fourier images of the magnetic domain structure corresponding to a chosen element. Applying in - situ magnetic fields resulted in pronounced rearrangement of domain structure that was clearly observed in scattering images. Our analysis of both the stand-alone, as well as magnetically coupled CoPd/FePd layers provides insight into the formation of domains under small magnetic field perturbations and pave the way to better understanding of transient changes expected in magneto-dynamic measurements.

New functionalities in abundant element oxides: ubiquitous element strategy

PubMed Central

Hosono, Hideo; Hayashi, Katsuro; Kamiya, Toshio; Atou, Toshiyuki; Susaki, Tomofumi

2011-01-01

While most ceramics are composed of ubiquitous elements (the ten most abundant elements within the Earth's crust), many advanced materials are based on rare elements. A ‘rare-element crisis’ is approaching owing to the imbalance between the limited supply of rare elements and the increasing demand. Therefore, we propose a ‘ubiquitous element strategy’ for materials research, which aims to apply abundant elements in a variety of innovative applications. Creation of innovative oxide materials and devices based on conventional ceramics is one specific challenge. This review describes the concept of ubiquitous element strategy and gives some highlights of our recent research on the synthesis of electronic, thermionic and structural materials using ubiquitous elements. PMID:27877391

A finite element-boundary integral method for scattering and radiation by two- and three-dimensional structures

NASA Technical Reports Server (NTRS)

Jin, Jian-Ming; Volakis, John L.; Collins, Jeffery D.

1991-01-01

A review of a hybrid finite element-boundary integral formulation for scattering and radiation by two- and three-dimensional composite structures is presented. In contrast to other hybrid techniques involving the finite element method, the proposed one is in principle exact and can be implemented using a low O(N) storage. This is of particular importance for large scale applications and is a characteristic of the boundary chosen to terminate the finite element mesh, usually as close to the structure as possible. A certain class of these boundaries lead to convolutional boundary integrals which can be evaluated via the fast Fourier transform (FFT) without a need to generate a matrix; thus, retaining the O(N) storage requirement. The paper begins with a general description of the method. A number of two- and three-dimensional applications are then given, including numerical computations which demonstrate the method's accuracy, efficiency, and capability.

Prosodic Structure as a Parallel to Musical Structure

PubMed Central

Heffner, Christopher C.; Slevc, L. Robert

2015-01-01

What structural properties do language and music share? Although early speculation identified a wide variety of possibilities, the literature has largely focused on the parallels between musical structure and syntactic structure. Here, we argue that parallels between musical structure and prosodic structure deserve more attention. We review the evidence for a link between musical and prosodic structure and find it to be strong. In fact, certain elements of prosodic structure may provide a parsimonious comparison with musical structure without sacrificing empirical findings related to the parallels between language and music. We then develop several predictions related to such a hypothesis. PMID:26733930

High-resolution structural and elemental analyses of calcium storage structures synthesized by the noble crayfish Astacus astacus.

PubMed

Luquet, Gilles; Salomé, Murielle; Ziegler, Andreas; Paris, Céline; Percot, Aline; Dauphin, Yannicke

2016-11-01

During premolt, crayfish develop deposits of calcium ions, called gastroliths, in their stomach wall. The stored calcium is used for the calcification of parts of the skeleton regularly renewed for allowing growth. Structural and molecular analyses of gastroliths have been primarily performed on three crayfish species, Orconectes virilis, Procambarus clarkii, and more recently, Cherax quadricarinatus. We have performed high-resolution analyses of gastroliths from the native noble crayfish, Astacus astacus, focusing on the microstructure, the mineralogical and elemental composition and distribution in a comparative perspective. Field emission scanning electron microscopy (FESEM) and atomic force microscopy (AFM) observations showed a classical layered microstructure composed of 200-nm diameter granules aligned along fibers. These granules are themselves composed of agglomerated nanogranules of 50nm-mean diameters. Denser regions of bigger fused granules are also present. Micro-Raman spectroscopy show that if A. astacus gastroliths, similarly to the other analyzed gastroliths, are mainly composed of amorphous calcium carbonate (ACC), they are also rich in amorphous calcium phosphate (ACP). The presence of a carotenoid pigment is also observed in A. astacus gastrolith contrary to C. quadricarinatus. Energy-dispersive X-ray spectroscopy (EDX) analyses demonstrate the presence of minor elements such as Mg, Sr, Si and P. The distribution of this last element is particularly heterogeneous. X-ray absorption near edge structure spectroscopy (XANES) reveals an alternation of layers more or less rich in phosphorus evidenced in the mineral phase as well as in the organic matrix in different molecular forms. Putative functions of the different P-comprising molecules are discussed. Copyright © 2016 Elsevier Inc. All rights reserved.

Genome-Wide Profiling of p63 DNA–Binding Sites Identifies an Element that Regulates Gene Expression during Limb Development in the 7q21 SHFM1 Locus

PubMed Central

Oti, Martin; Dutilh, Bas E.; Alonso, M. Eva; de la Calle-Mustienes, Elisa; Smeenk, Leonie; Rinne, Tuula; Parsaulian, Lilian; Bolat, Emine; Jurgelenaite, Rasa; Huynen, Martijn A.; Hoischen, Alexander; Veltman, Joris A.; Brunner, Han G.; Roscioli, Tony; Oates, Emily; Wilson, Meredith; Manzanares, Miguel; Gómez-Skarmeta, José Luis; Stunnenberg, Hendrik G.; Lohrum, Marion; van Bokhoven, Hans; Zhou, Huiqing

2010-01-01

Heterozygous mutations in p63 are associated with split hand/foot malformations (SHFM), orofacial clefting, and ectodermal abnormalities. Elucidation of the p63 gene network that includes target genes and regulatory elements may reveal new genes for other malformation disorders. We performed genome-wide DNA–binding profiling by chromatin immunoprecipitation (ChIP), followed by deep sequencing (ChIP–seq) in primary human keratinocytes, and identified potential target genes and regulatory elements controlled by p63. We show that p63 binds to an enhancer element in the SHFM1 locus on chromosome 7q and that this element controls expression of DLX6 and possibly DLX5, both of which are important for limb development. A unique micro-deletion including this enhancer element, but not the DLX5/DLX6 genes, was identified in a patient with SHFM. Our study strongly indicates disruption of a non-coding cis-regulatory element located more than 250 kb from the DLX5/DLX6 genes as a novel disease mechanism in SHFM1. These data provide a proof-of-concept that the catalogue of p63 binding sites identified in this study may be of relevance to the studies of SHFM and other congenital malformations that resemble the p63-associated phenotypes. PMID:20808887

Moral deliberation and nursing ethics cases: elements of a methodological proposal.

PubMed

Schneider, Dulcinéia Ghizoni; Ramos, Flávia Regina Souza

2012-11-01

A qualitative study with an exploratory, descriptive and documentary design that was conducted with the objective of identifying the elements to constitute a method for the analysis of accusations of and proceedings for professional ethics infringements. The method is based on underlying elements identified inductively during analysis of professional ethics hearings judged by and filed in the archives of the Regional Nursing Board of Santa Catarina, Brazil, between 1999 and 2007. The strategies developed were based on the results of an analysis of the findings of fact (occurrences/infractions, causes and outcomes) contained in the records of 128 professional ethics hearings and on the structural elements (statements, rules and practices) identified in five example professional ethics cases. The strategies suggested for evaluating accusations of ethics infringements and the procedures involved in deliberating on ethics hearings constitute a generic proposal that will require adaptation to the context of specific professional ethics accusations.

[Effects of rare earth elements on soil fauna community structure and their ecotoxicity to Holotrichia parallela].

PubMed

Li, Guiting; Jiang, Junqi; Chen, Jie; Zou, Yunding; Zhang, Xincai

2006-01-01

By the method of OECD filter paper contact, this paper studied the effects of applied rare earth elements on soil fauna community structure and their ecological toxicity to Holotrichia parallela in bean field. The results showed that there were no significant differences between the treatments and the control in soil fauna species, quantity of main species, and diversity index. Urgent and chronic toxic test showed that the differences between the treatments and the control were not significant. It was suggested that within the range of test dosages, rare earth elements had little ecological toxicity to Holotrichia parallela, and did not change the soil fauna community structure.

Identifying Structure-Property Relationships Through DREAM.3D Representative Volume Elements and DAMASK Crystal Plasticity Simulations: An Integrated Computational Materials Engineering Approach

NASA Astrophysics Data System (ADS)

Diehl, Martin; Groeber, Michael; Haase, Christian; Molodov, Dmitri A.; Roters, Franz; Raabe, Dierk

2017-05-01

Predicting, understanding, and controlling the mechanical behavior is the most important task when designing structural materials. Modern alloy systems—in which multiple deformation mechanisms, phases, and defects are introduced to overcome the inverse strength-ductility relationship—give raise to multiple possibilities for modifying the deformation behavior, rendering traditional, exclusively experimentally-based alloy development workflows inappropriate. For fast and efficient alloy design, it is therefore desirable to predict the mechanical performance of candidate alloys by simulation studies to replace time- and resource-consuming mechanical tests. Simulation tools suitable for this task need to correctly predict the mechanical behavior in dependence of alloy composition, microstructure, texture, phase fractions, and processing history. Here, an integrated computational materials engineering approach based on the open source software packages DREAM.3D and DAMASK (Düsseldorf Advanced Materials Simulation Kit) that enables such virtual material development is presented. More specific, our approach consists of the following three steps: (1) acquire statistical quantities that describe a microstructure, (2) build a representative volume element based on these quantities employing DREAM.3D, and (3) evaluate the representative volume using a predictive crystal plasticity material model provided by DAMASK. Exemplarily, these steps are here conducted for a high-manganese steel.

Identifying calcium sources at an acid deposition-impacted spruce forest: a strontium isotope, alkaline earth element multi-tracer approach

Treesearch

Thomas D. Bullen; Scott W. Bailey

2005-01-01

Depletion of calcium from forest soils has important implications for forest productivity and health. Ca is available to fine feeder roots from a number of soil organic and mineral sources. but identifying the primary source or changes of sources in response to environmental change is problematic. We used strontium isotope and alkaline earth element concentration...

Finite element analysis of steady and transiently moving/rolling nonlinear viscoelastic structure. I - Theory

NASA Technical Reports Server (NTRS)

Padovan, Joe

1987-01-01

In a three-part series of papers, a generalized finite element analysis scheme is developed to handle the steady and transient response of moving/rolling nonlinear viscoelastic structure. This paper considers the development of the moving/rolling element strategy, including the effects of large deformation kinematics and viscoelasticity modeled by fractional integrodifferential operators. To improve the solution strategy, a special hierarchical constraint procedure is developed for the case of steady rolling/translating, as well as a transient scheme involving the use of a Grunwaldian representation of the fractional operator.

Acoustic coupled fluid-structure interactions using a unified fast multipole boundary element method.

PubMed

Wilkes, Daniel R; Duncan, Alec J

2015-04-01

This paper presents a numerical model for the acoustic coupled fluid-structure interaction (FSI) of a submerged finite elastic body using the fast multipole boundary element method (FMBEM). The Helmholtz and elastodynamic boundary integral equations (BIEs) are, respectively, employed to model the exterior fluid and interior solid domains, and the pressure and displacement unknowns are coupled between conforming meshes at the shared boundary interface to achieve the acoustic FSI. The low frequency FMBEM is applied to both BIEs to reduce the algorithmic complexity of the iterative solution from O(N(2)) to O(N(1.5)) operations per matrix-vector product for N boundary unknowns. Numerical examples are presented to demonstrate the algorithmic and memory complexity of the method, which are shown to be in good agreement with the theoretical estimates, while the solution accuracy is comparable to that achieved by a conventional finite element-boundary element FSI model.

Layerwise Mechanics and Finite Elements for Smart Composite Structures with Piezoelectric Actuators and Sensors

NASA Technical Reports Server (NTRS)

Saravanos, Dimitris A.; Heyliger, Paul R.; Hopkins, Dale A.

1996-01-01

Recent developments on layerwise mechanics for the analysis of composite laminates and structures with piezoelectric actuators and sensors are reviewed. The mechanics implement layerwise representations of displacements and electric potential, and can model both the global and local electromechanical response of smart composite structures. The corresponding finite-element implementations for the static and dynamic analysis of smart piezoelectric composite structures are also summarized. Select application illustrate the accuracy, robustness and capability of the developed mechanics to capture the global and local dynamic response of thin and/or thick laminated piezoelectric plates.

Structural Anomalies Detected in Ceramic Matrix Composites Using Combined Nondestructive Evaluation and Finite Element Analysis (NDE and FEA)

NASA Technical Reports Server (NTRS)

Abdul-Aziz, Ali; Baaklini, George Y.; Bhatt, Ramakrishna T.

2003-01-01

Most reverse engineering approaches involve imaging or digitizing an object and then creating a computerized reconstruction that can be integrated, in three dimensions, into a particular design environment. The rapid prototyping technique builds high-quality physical prototypes directly from computer-aided design files. This fundamental technique for interpreting and interacting with large data sets is being used here via Velocity2 (an integrated image-processing software, ref. 1) using computed tomography (CT) data to produce a prototype three-dimensional test specimen model for analyses. A study at the NASA Glenn Research Center proposes to use these capabilities to conduct a combined nondestructive evaluation (NDE) and finite element analysis (FEA) to screen pretest and posttest structural anomalies in structural components. A tensile specimen made of silicon nitrite (Si3N4) ceramic matrix composite was considered to evaluate structural durability and deformity. Ceramic matrix composites are being sought as candidate materials to replace nickel-base superalloys for turbine engine applications. They have the unique characteristics of being able to withstand higher operating temperatures and harsh combustion environments. In addition, their low densities relative to metals help reduce component mass (ref. 2). Detailed three-dimensional volume rendering of the tensile test specimen was successfully carried out with Velocity2 (ref. 1) using two-dimensional images that were generated via computed tomography. Subsequent, three-dimensional finite element analyses were performed, and the results obtained were compared with those predicted by NDE-based calculations and experimental tests. It was shown that Velocity2 software can be used to render a three-dimensional object from a series of CT scan images with a minimum level of complexity. The analytical results (ref. 3) show that the high-stress regions correlated well with the damage sites identified by the CT scans

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

Development of an Anatomically Accurate Finite Element Human Ocular Globe Model for Blast-Related Fluid-Structure Interaction Studies

DTIC Science & Technology

2017-02-01

ARL-TR-7945 ● FEB 2017 US Army Research Laboratory Development of an Anatomically Accurate Finite Element Human Ocular Globe...ARL-TR-7945 ● FEB 2017 US Army Research Laboratory Development of an Anatomically Accurate Finite Element Human Ocular Globe Model... Finite Element Human Ocular Globe Model for Blast-Related Fluid-Structure Interaction Studies 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM

Developmentally arrested structures preceding cerebellar tumors in von Hippel–Lindau disease

PubMed Central

Shively, Sharon B; Falke, Eric A; Li, Jie; Tran, Maxine G B; Thompson, Eli R; Maxwell, Patrick H; Roessler, Erich; Oldfield, Edward H; Lonser, Russell R; Vortmeyer, Alexander O

2011-01-01

There is increasing evidence that suggests that knockout of tumor-suppressor gene function causes developmental arrest and protraction of cellular differentiation. In the peripheral nervous system of patients with the tumor-suppressor gene disorder, von Hippel–Lindau disease, we have demonstrated developmentally arrested structural elements composed of hemangioblast progenitor cells. Some developmentally arrested structural elements progress to a frank tumor, hemangioblastoma. However, in von Hippel–Lindau disease, hemangioblastomas are frequently observed in the cerebellum, suggesting an origin in the central nervous system. We performed a structural and topographic analysis of cerebellar tissues obtained from von Hippel–Lindau disease patients to identify and characterize developmentally arrested structural elements in the central nervous system. We examined the entire cerebella of five tumor-free von Hippel–Lindau disease patients and of three non-von Hippel–Lindau disease controls. In all, 9 cerebellar developmentally arrested structural elements were detected and topographically mapped in 385 blocks of von Hippel–Lindau disease cerebella. No developmentally arrested structural elements were seen in 214 blocks from control cerebella. Developmentally arrested structural elements are composed of poorly differentiated cells that express hypoxia-inducible factor (HIF)2α, but not HIF1α or brachyury, and preferentially involve the molecular layer of the dorsum cerebelli. For the first time, we identify and characterize developmentally arrested structural elements in the central nervous system of von Hippel–Lindau patients. We provide evidence that developmentally arrested structural elements in the cerebellum are composed of developmentally arrested hemangioblast progenitor cells in the molecular layer of the dorsum cerebelli. PMID:21499240

Perspectives Of Employment Of Pultruded FRP Structural Elements In Seismic Engineering Field

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

Russo, Salvatore; Silvestri, Mirko

2008-07-08

Today the employment of FRP material in structural engineering is in common use, with excellent results in term of applications especially as reinforcement of existing structures. This success is related to the very reduced weight of FRP material, to its performance in term of strength and durability and thanks to the easy use in technical application. There is a modern way to use this material disguised as structural pultruded element (with weight equal to 1600-1800 kg/m{sup 3}) in new constructions, local reinforcements and in other seismic applications. Actually the international technical and scientific literature in form of draft, recommendations andmore » researches on this topic is very rich also taking into account Italian contribution. Some interesting applications of all FRP structures in seismic engineering field are showed in this research in real terms and in form of capability.« less

Multigrid finite element method in stress analysis of three-dimensional elastic bodies of heterogeneous structure

NASA Astrophysics Data System (ADS)

Matveev, A. D.

2016-11-01

To calculate the three-dimensional elastic body of heterogeneous structure under static loading, a method of multigrid finite element is provided, when implemented on the basis of algorithms of finite element method (FEM), using homogeneous and composite threedimensional multigrid finite elements (MFE). Peculiarities and differences of MFE from the currently available finite elements (FE) are to develop composite MFE (without increasing their dimensions), arbitrarily small basic partition of composite solids consisting of single-grid homogeneous FE of the first order can be used, i.e. in fact, to use micro approach in finite element form. These small partitions allow one to take into account in MFE, i.e. in the basic discrete models of composite solids, complex heterogeneous and microscopically inhomogeneous structure, shape, the complex nature of the loading and fixation and describe arbitrarily closely the stress and stain state by the equations of three-dimensional elastic theory without any additional simplifying hypotheses. When building the m grid FE, m of nested grids is used. The fine grid is generated by a basic partition of MFE, the other m —1 large grids are applied to reduce MFE dimensionality, when m is increased, MFE dimensionality becomes smaller. The procedures of developing MFE of rectangular parallelepiped, irregular shape, plate and beam types are given. MFE generate the small dimensional discrete models and numerical solutions with a high accuracy. An example of calculating the laminated plate, using three-dimensional 3-grid FE and the reference discrete model is given, with that having 2.2 milliards of FEM nodal unknowns.

Estimating and Identifying Unspecified Correlation Structure for Longitudinal Data

PubMed Central

Hu, Jianhua; Wang, Peng; Qu, Annie

2014-01-01

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

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.

Use of structured decision making to identify monitoring variables and management priorities for salt marsh ecosystems

USGS Publications Warehouse

Neckles, Hilary A.; Lyons, James E.; Guntenspergen, Glenn R.; Shriver, W. Gregory; Adamowicz, Susan C.

2015-01-01

Most salt marshes in the USA have been degraded by human activities, and coastal managers are faced with complex choices among possible actions to restore or enhance ecosystem integrity. We applied structured decision making (SDM) to guide selection of monitoring variables and management priorities for salt marshes within the National Wildlife Refuge System in the northeastern USA. In general, SDM is a systematic process for decomposing a decision into its essential elements. We first engaged stakeholders in clarifying regional salt marsh decision problems, defining objectives and attributes to evaluate whether objectives are achieved, and developing a pool of alternative management actions for achieving objectives. Through this process, we identified salt marsh attributes that were applicable to monitoring National Wildlife Refuges on a regional scale and that targeted management needs. We then analyzed management decisions within three salt marsh units at Prime Hook National Wildlife Refuge, coastal Delaware, as a case example of prioritizing management alternatives. Values for salt marsh attributes were estimated from 2 years of baseline monitoring data and expert opinion. We used linear value modeling to aggregate multiple attributes into a single performance score for each alternative, constrained optimization to identify alternatives that maximized total management benefits subject to refuge-wide cost constraints, and used graphical analysis to identify the optimal set of alternatives for the refuge. SDM offers an efficient, transparent approach for integrating monitoring into management practice and improving the quality of management decisions.

Structure-preserving spectral element method in attenuating seismic wave modeling

NASA Astrophysics Data System (ADS)

Cai, Wenjun; Zhang, Huai

2016-04-01

This work describes the extension of the conformal symplectic method to solve the damped acoustic wave equation and the elastic wave equations in the framework of the spectral element method. The conformal symplectic method is a variation of conventional symplectic methods to treat non-conservative time evolution problems which has superior behaviors in long-time stability and dissipation preservation. To construct the conformal symplectic method, we first reformulate the damped acoustic wave equation and the elastic wave equations in their equivalent conformal multi-symplectic structures, which naturally reveal the intrinsic properties of the original systems, especially, the dissipation laws. We thereafter separate each structures into a conservative Hamiltonian system and a purely dissipative ordinary differential equation system. Based on the splitting methodology, we solve the two subsystems respectively. The dissipative one is cheaply solved by its analytic solution. While for the conservative system, we combine a fourth-order symplectic Nyström method in time and the spectral element method in space to cover the circumstances in realistic geological structures involving complex free-surface topography. The Strang composition method is adopted thereby to concatenate the corresponding two parts of solutions and generate the completed numerical scheme, which is conformal symplectic and can therefore guarantee the numerical stability and dissipation preservation after a large time modeling. Additionally, a relative larger Courant number than that of the traditional Newmark scheme is found in the numerical experiments in conjunction with a spatial sampling of approximately 5 points per wavelength. A benchmark test for the damped acoustic wave equation validates the effectiveness of our proposed method in precisely capturing dissipation rate. The classical Lamb problem is used to demonstrate the ability of modeling Rayleigh-wave propagation. More comprehensive

Structural identifiability analyses of candidate models for in vitro Pitavastatin hepatic uptake.

PubMed

Grandjean, Thomas R B; Chappell, Michael J; Yates, James W T; Evans, Neil D

2014-05-01

In this paper a review of the application of four different techniques (a version of the similarity transformation approach for autonomous uncontrolled systems, a non-differential input/output observable normal form approach, the characteristic set differential algebra and a recent algebraic input/output relationship approach) to determine the structural identifiability of certain in vitro nonlinear pharmacokinetic models is provided. The Organic Anion Transporting Polypeptide (OATP) substrate, Pitavastatin, is used as a probe on freshly isolated animal and human hepatocytes. Candidate pharmacokinetic non-linear compartmental models have been derived to characterise the uptake process of Pitavastatin. As a prerequisite to parameter estimation, structural identifiability analyses are performed to establish that all unknown parameters can be identified from the experimental observations available. Copyright © 2013. Published by Elsevier Ireland Ltd.

Controlling the intermediate structure of an ionic liquid for f-block element separations

DOE PAGES

Abney, Carter W.; Do, Changwoo; Luo, Huimin; ...

2017-04-19

Recent research has revealed molecular structure beyond the inner coordination sphere is essential in defining the performance of separations processes, but nevertheless remains largely unexplored. Here we apply small angle neutron scattering (SANS) and x-ray absorption fine structure (XAFS) spectroscopy to investigate the structure of an ionic liquid system studied for f-block element separations. SANS data reveal dramatic changes in the ionic liquid microstructure (~150 Å) which we demonstrate can be controlled by judicious selection of counter ion. Mesoscale structural features (> 500 Å) are also observed as a function of metal concentration. XAFS analysis supports formation of extended aggregatemore » structures, similar to those observed in traditional solvent extraction processes, and suggest additional parallels may be drawn from further study. As a result, achieving precise tunability over the intermediate features is an important development in controlling mesoscale structure and realizing advanced new forms of soft matter.« less

Optimum structural design with plate bending elements - A survey

NASA Technical Reports Server (NTRS)

Haftka, R. T.; Prasad, B.

1981-01-01

A survey is presented of recently published papers in the field of optimum structural design of plates, largely with respect to the minimum-weight design of plates subject to such constraints as fundamental frequency maximization. It is shown that, due to the availability of powerful computers, the trend in optimum plate design is away from methods tailored to specific geometry and loads and toward methods that can be easily programmed for any kind of plate, such as finite element methods. A corresponding shift is seen in optimization from variational techniques to numerical optimization algorithms. Among the topics covered are fully stressed design and optimality criteria, mathematical programming, smooth and ribbed designs, design against plastic collapse, buckling constraints, and vibration constraints.

A non-contacting approach for full field dynamic strain monitoring of rotating structures using the photogrammetry, finite element, and modal expansion techniques

NASA Astrophysics Data System (ADS)

Baqersad, Javad

Health monitoring of rotating structures such as wind turbines and helicopter rotors is generally performed using conventional sensors that provide a limited set of data at discrete locations near or on the hub. These sensors usually provide no data on the blades or interior locations where failures may occur. Within this work, an unique expansion algorithm was extended and combined with finite element (FE) modeling and an optical measurement technique to identify the dynamic strain in rotating structures. The merit of the approach is shown by using the approach to predict the dynamic strain on a small non-rotating and rotating wind turbine. A three-bladed wind turbine having 2.3-meter long blades was placed in a semi-built-in boundary condition using a hub, a machining chuck, and a steel block. A finite element model of the three wind turbine blades assembled to the hub was created and used to extract resonant frequencies and mode shapes. The FE model was validated and updated using experimental modal tests. For the non-rotating optical test, the turbine was excited using a sinusoidal excitation, a pluck test, arbitrary impacts on three blades, and random force excitations with a mechanical shaker. The response of the structure to the excitations was measured using three-dimensional point tracking. A pair of high-speed cameras was used to measure the displacement of optical targets on the structure when the blades were vibrating. The measured displacements at discrete locations were expanded and applied to the finite element model of the structure to extract the full-field dynamic strain. The results of the work show an excellent correlation between the strain predicted using the proposed approach and the strain measured with strain-gages for all of the three loading conditions. Similar to the non-rotating case, optical measurements were also preformed on a rotating wind turbine. The point tracking technique measured both rigid body displacement and flexible

Studies of finite element analysis of composite material structures

NASA Technical Reports Server (NTRS)

Douglas, D. O.; Holzmacher, D. E.; Lane, Z. C.; Thornton, E. A.

1975-01-01

Research in the area of finite element analysis is summarized. Topics discussed include finite element analysis of a picture frame shear test, BANSAP (a bandwidth reduction program for SAP IV), FEMESH (a finite element mesh generation program based on isoparametric zones), and finite element analysis of a composite bolted joint specimens.

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.

Ice cream structural elements that affect melting rate and hardness.

PubMed

Muse, M R; Hartel, R W

2004-01-01

Statistical models were developed to reveal which structural elements of ice cream affect melting rate and hardness. Ice creams were frozen in a batch freezer with three types of sweetener, three levels of the emulsifier polysorbate 80, and two different draw temperatures to produce ice creams with a range of microstructures. Ice cream mixes were analyzed for viscosity, and finished ice creams were analyzed for air cell and ice crystal size, overrun, and fat destabilization. The ice phase volume of each ice cream were calculated based on the freezing point of the mix. Melting rate and hardness of each hardened ice cream was measured and correlated with the structural attributes by using analysis of variance and multiple linear regression. Fat destabilization, ice crystal size, and the consistency coefficient of the mix were found to affect the melting rate of ice cream, whereas hardness was influenced by ice phase volume, ice crystal size, overrun, fat destabilization, and the rheological properties of the mix.

Parallel processing in finite element structural analysis

NASA Technical Reports Server (NTRS)

Noor, Ahmed K.

1987-01-01

A brief review is made of the fundamental concepts and basic issues of parallel processing. Discussion focuses on parallel numerical algorithms, performance evaluation of machines and algorithms, and parallelism in finite element computations. A computational strategy is proposed for maximizing the degree of parallelism at different levels of the finite element analysis process including: 1) formulation level (through the use of mixed finite element models); 2) analysis level (through additive decomposition of the different arrays in the governing equations into the contributions to a symmetrized response plus correction terms); 3) numerical algorithm level (through the use of operator splitting techniques and application of iterative processes); and 4) implementation level (through the effective combination of vectorization, multitasking and microtasking, whenever available).

Efficient finite element modelling for the investigation of the dynamic behaviour of a structure with bolted joints

NASA Astrophysics Data System (ADS)

Omar, R.; Rani, M. N. Abdul; Yunus, M. A.; Mirza, W. I. I. Wan Iskandar; Zin, M. S. Mohd

2018-04-01

A simple structure with bolted joints consists of the structural components, bolts and nuts. There are several methods to model the structures with bolted joints, however there is no reliable, efficient and economic modelling methods that can accurately predict its dynamics behaviour. Explained in this paper is an investigation that was conducted to obtain an appropriate modelling method for bolted joints. This was carried out by evaluating four different finite element (FE) models of the assembled plates and bolts namely the solid plates-bolts model, plates without bolt model, hybrid plates-bolts model and simplified plates-bolts model. FE modal analysis was conducted for all four initial FE models of the bolted joints. Results of the FE modal analysis were compared with the experimental modal analysis (EMA) results. EMA was performed to extract the natural frequencies and mode shapes of the test physical structure with bolted joints. Evaluation was made by comparing the number of nodes, number of elements, elapsed computer processing unit (CPU) time, and the total percentage of errors of each initial FE model when compared with EMA result. The evaluation showed that the simplified plates-bolts model could most accurately predict the dynamic behaviour of the structure with bolted joints. This study proved that the reliable, efficient and economic modelling of bolted joints, mainly the representation of the bolting, has played a crucial element in ensuring the accuracy of the dynamic behaviour prediction.

The structure of distractor-response bindings: Conditions for configural and elemental integration.

PubMed

Moeller, Birte; Frings, Christian; Pfister, Roland

2016-04-01

Human action control is influenced by bindings between perceived stimuli and responses carried out in their presence. Notably, responses given to a target stimulus can also be integrated with additional response-irrelevant distractor stimuli that accompany the target (distractor-response binding). Subsequently reencountering such a distractor then retrieves the associated response. Although a large body of evidence supports the existence of this effect, the specific structure of distractor-response bindings is still unclear. Here, we test the predictions derived from 2 possible assumptions about the structure of bindings between distractors and responses. According to a configural approach, the entire distractor object is integrated with a response, and only upon repetition of the entire distractor object the associated response would be retrieved. According to an elemental approach, one would predict integration of individual distractor features with the response and retrieval due to the repetition of an individual distractor feature. Four experiments indicate that both, configural and elemental bindings exist and specify boundary conditions for each type of binding. These findings provide detailed insights into the architecture of bindings between response-irrelevant stimuli and actions and thus allow for specifying how distractor stimuli influence human behavior. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

The sieve element occlusion gene family in dicotyledonous plants

PubMed Central

Jekat, Stephan B; Nordzieke, Steffen; Reineke, Anna R; Müller, Boje; Bornberg-Bauer, Erich; Noll, Gundula A

2011-01-01

Sieve element occlusion (SEO) genes encoding forisome subunits have been identified in Medicago truncatula and other legumes. Forisomes are structural phloem proteins uniquely found in Fabaceae sieve elements. They undergo a reversible conformational change after wounding, from a condensed to a dispersed state, thereby blocking sieve tube translocation and preventing the loss of photoassimilates. Recently, we identified SEO genes in several non-Fabaceae plants (lacking forisomes) and concluded that they most probably encode conventional non-forisome P-proteins. Molecular and phylogenetic analysis of the SEO gene family has identified domains that are characteristic for SEO proteins. Here, we extended our phylogenetic analysis by including additional SEO genes from several diverse species based on recently published genomic data. Our results strengthen the original assumption that SEO genes seem to be widespread in dicotyledonous angiosperms, and further underline the divergent evolution of SEO genes within the Fabaceae. PMID:21422825

The sieve element occlusion gene family in dicotyledonous plants.

PubMed

Ernst, Antonia M; Rüping, Boris; Jekat, Stephan B; Nordzieke, Steffen; Reineke, Anna R; Müller, Boje; Bornberg-Bauer, Erich; Prüfer, Dirk; Noll, Gundula A

2011-01-01

Sieve element occlusion (SEO) genes encoding forisome subunits have been identified in Medicago truncatula and other legumes. Forisomes are structural phloem proteins uniquely found in Fabaceae sieve elements. They undergo a reversible conformational change after wounding, from a condensed to a dispersed state, thereby blocking sieve tube translocation and preventing the loss of photoassimilates. Recently, we identified SEO genes in several non-Fabaceae plants (lacking forisomes) and concluded that they most probably encode conventional non-forisome P-proteins. Molecular and phylogenetic analysis of the SEO gene family has identified domains that are characteristic for SEO proteins. Here, we extended our phylogenetic analysis by including additional SEO genes from several diverse species based on recently published genomic data. Our results strengthen the original assumption that SEO genes seem to be widespread in dicotyledonous angiosperms, and further underline the divergent evolution of SEO genes within the Fabaceae.

The influence of doping element on structural and luminescent characteristics of ZnS thin films

NASA Astrophysics Data System (ADS)

Kryshtab, T.; Khomchenko, V. S.; Andraca-Adame, J. A.; Rodionov, V. E.; Khachatryan, V. B.; Tzyrkunov, Yu. A.

2006-10-01

For the fabrication of green and blue emitting ZnS structures the elements of I, III, and VII groups (Cu, Al, Ga, Cl) are used as dopants. The influence of type of impurity, doping technique, and type of substrate on crystalline structure and surface morphology together with luminescent properties was investigated. The doping of thin films was realized during the growth process and/or post-deposition thermal treatment. ZnS thin films were deposited by physical (EBE) and chemical (MOCVD) methods onto glass or ceramic (BaTiO 3) substrates. Closed spaced evaporation and thermodiffusion methods were used for the post-deposition doping of ZnS films. X-ray diffraction (XRD) techniques, atomic force microscopy (AFM), and measurements of photoluminescent (PL) spectra were used for the investigations. It was shown that the doping by the elements of I (Cu) and III (Al, Ga) groups does not change the crystal structure during the thermal treatment up to 1000 ∘C, whereas simultaneous use of the elements of I (Cu) and VII (Cl) groups leads to decrease of the phase transition temperature to 800 ∘C. The presence of impurities in the growth process leads to a grain size increase. At post-deposition treatment Ga and Cl act as activators of recrystallization process. The transition of ZnS sphalerite lattice to wurtzite one leads to the displacement of the blue emission band position towards the short-wavelength range by 10 nm.

Second order nonlinear equations of motion for spinning highly flexible line-elements. [for spacecraft solar sail

NASA Technical Reports Server (NTRS)

Salama, M.; Trubert, M.

1979-01-01

A formulation is given for the second order nonlinear equations of motion for spinning line-elements having little or no intrinsic structural stiffness. Such elements have been employed in recent studies of structural concepts for future large space structures such as the Heliogyro solar sailer. The derivation is based on Hamilton's variational principle and includes the effect of initial geometric imperfections (axial, curvature, and twist) on the line-element dynamics. For comparison with previous work, the nonlinear equations are reduced to a linearized form frequently found in the literature. The comparison has revealed several new spin-stiffening terms that have not been previously identified and/or retained. They combine geometric imperfections, rotary inertia, Coriolis, and gyroscopic terms.

Multiple genome alignment for identifying the core structure among moderately related microbial genomes.

PubMed

Uchiyama, Ikuo

2008-10-31

Identifying the set of intrinsically conserved genes, or the genomic core, among related genomes is crucial for understanding prokaryotic genomes where horizontal gene transfers are common. Although core genome identification appears to be obvious among very closely related genomes, it becomes more difficult when more distantly related genomes are compared. Here, we consider the core structure as a set of sufficiently long segments in which gene orders are conserved so that they are likely to have been inherited mainly through vertical transfer, and developed a method for identifying the core structure by finding the order of pre-identified orthologous groups (OGs) that maximally retains the conserved gene orders. The method was applied to genome comparisons of two well-characterized families, Bacillaceae and Enterobacteriaceae, and identified their core structures comprising 1438 and 2125 OGs, respectively. The core sets contained most of the essential genes and their related genes, which were primarily included in the intersection of the two core sets comprising around 700 OGs. The definition of the genomic core based on gene order conservation was demonstrated to be more robust than the simpler approach based only on gene conservation. We also investigated the core structures in terms of G+C content homogeneity and phylogenetic congruence, and found that the core genes primarily exhibited the expected characteristic, i.e., being indigenous and sharing the same history, more than the non-core genes. The results demonstrate that our strategy of genome alignment based on gene order conservation can provide an effective approach to identify the genomic core among moderately related microbial genomes.

Identifying three-dimensional structures of autophosphorylation complexes in crystals of protein kinases

PubMed Central

Xu, Qifang; Malecka, Kimberly L.; Fink, Lauren; Jordan, E. Joseph; Duffy, Erin; Kolander, Samuel; Peterson, Jeffrey; Dunbrack, Roland L.

2016-01-01

Protein kinase autophosphorylation is a common regulatory mechanism in cell signaling pathways. Crystal structures of several homomeric protein kinase complexes have a serine, threonine, or tyrosine autophosphorylation site of one kinase monomer located in the active site of another monomer, a structural complex that we call an “autophosphorylation complex.” We developed and applied a structural bioinformatics method to identify all such autophosphorylation kinase complexes in X-ray crystallographic structures in the Protein Data Bank (PDB). We identified 15 autophosphorylation complexes in the PDB, of which 5 complexes had not previously been described in the publications describing the crystal structures. These 5 consist of tyrosine residues in the N-terminal juxtamembrane regions of colony stimulating factor 1 receptor (CSF1R, Tyr561) and EPH receptor A2 (EPHA2, Tyr594), tyrosine residues in the activation loops of the SRC kinase family member LCK (Tyr394) and insulin-like growth factor 1 receptor (IGF1R, Tyr1166), and a serine in a nuclear localization signal region of CDC-like kinase 2 (CLK2, Ser142). Mutations in the complex interface may alter autophosphorylation activity and contribute to disease; therefore we mutated residues in the autophosphorylation complex interface of LCK and found that two mutations impaired autophosphorylation (T445V and N446A) and mutation of Pro447 to Ala, Gly, or Leu increased autophosphorylation. The identified autophosphorylation sites are conserved in many kinases, suggesting that, by homology, these complexes may provide insight into autophosphorylation complex interfaces of kinases that are relevant drug targets. PMID:26628682

Identifying Elements Critical for Functional and Sustainable Professional Learning Communities

ERIC Educational Resources Information Center

Richmond, Gail; Manokore, Viola

2011-01-01

In this paper, we examined data collected as part of a 5-year project designed to foster reform-based urban science teaching through teachers' communities of inquiry. Drawing upon a distributed leadership framework, we analyzed teacher "talk" during professional learning community (PLC) meetings. This analysis yielded five elements:…

Powder diffraction and crystal structure prediction identify four new coumarin polymorphs

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

Shtukenberg, Alexander G.; Zhu, Qiang; Carter, Damien J.

Coumarin, a simple, commodity chemical isolated from beans in 1820, has, to date, only yielded one solid state structure. Here, we report a rich polymorphism of coumarin grown from the melt. Four new metastable forms were identified and their crystal structures were solved using a combination of computational crystal structure prediction algorithms and X-ray powder diffraction. With five crystal structures, coumarin has become one of the few rigid molecules showing extensive polymorphism at ambient conditions. We demonstrate the crucial role of advanced electronic structure calculations including many-body dispersion effects for accurate ranking of the stability of coumarin polymorphs and themore » need to account for anharmonic vibrational contributions to their free energy. As such, coumarin is a model system for studying weak intermolecular interactions, crystallization mechanisms, and kinetic effects.« less

Powder diffraction and crystal structure prediction identify four new coumarin polymorphs

DOE PAGES

Shtukenberg, Alexander G.; Zhu, Qiang; Carter, Damien J.; ...

2017-05-15

Coumarin, a simple, commodity chemical isolated from beans in 1820, has, to date, only yielded one solid state structure. Here, we report a rich polymorphism of coumarin grown from the melt. Four new metastable forms were identified and their crystal structures were solved using a combination of computational crystal structure prediction algorithms and X-ray powder diffraction. With five crystal structures, coumarin has become one of the few rigid molecules showing extensive polymorphism at ambient conditions. We demonstrate the crucial role of advanced electronic structure calculations including many-body dispersion effects for accurate ranking of the stability of coumarin polymorphs and themore » need to account for anharmonic vibrational contributions to their free energy. As such, coumarin is a model system for studying weak intermolecular interactions, crystallization mechanisms, and kinetic effects.« less

Development of Finite Elements for Two-Dimensional Structural Analysis Using the Integrated Force Method

NASA Technical Reports Server (NTRS)

Kaljevic, Igor; Patnaik, Surya N.; Hopkins, Dale A.

1996-01-01

The Integrated Force Method has been developed in recent years for the analysis of structural mechanics problems. This method treats all independent internal forces as unknown variables that can be calculated by simultaneously imposing equations of equilibrium and compatibility conditions. In this paper a finite element library for analyzing two-dimensional problems by the Integrated Force Method is presented. Triangular- and quadrilateral-shaped elements capable of modeling arbitrary domain configurations are presented. The element equilibrium and flexibility matrices are derived by discretizing the expressions for potential and complementary energies, respectively. The displacement and stress fields within the finite elements are independently approximated. The displacement field is interpolated as it is in the standard displacement method, and the stress field is approximated by using complete polynomials of the correct order. A procedure that uses the definitions of stress components in terms of an Airy stress function is developed to derive the stress interpolation polynomials. Such derived stress fields identically satisfy the equations of equilibrium. Moreover, the resulting element matrices are insensitive to the orientation of local coordinate systems. A method is devised to calculate the number of rigid body modes, and the present elements are shown to be free of spurious zero-energy modes. A number of example problems are solved by using the present library, and the results are compared with corresponding analytical solutions and with results from the standard displacement finite element method. The Integrated Force Method not only gives results that agree well with analytical and displacement method results but also outperforms the displacement method in stress calculations.

Toward a Broader Concept of Value: Identifying and Defining Elements for an Expanded Cost-Effectiveness Analysis.

PubMed

Garrison, Louis P; Kamal-Bahl, Sachin; Towse, Adrian

2017-02-01

This commentary identifies and defines potentially useful expansions to traditional cost-effectiveness analysis as often used in health technology assessment. Since the seminal 1977 article by Weinstein and Stason, the recommended approach has been the use of the incremental cost-effectiveness ratio based on the metric of the cost per quality-adjusted life-year gained, allowing comparisons across different technologies. An expanded framework, incorporating a wider range of the elements of value, is proposed. In addition to the core value drivers of health gain and other health system cost savings (if any), we propose adding other less recognized elements related to the value of knowing and informational externalities. We describe each of five factors related to the value of knowing: 1) a reduction in uncertainty, reflecting the benefit of a companion diagnostic increasing the certainty of a patient׳s response to a medicine; 2) insurance value related to greater peace of mind due to protection against catastrophic health and financial loss; 3) the value of hope for a "cure," leading individuals to become risk seekers in some circumstances; 4) real option value due to life extension opening possibilities for individuals to benefit from future innovation; and 5) spillovers or externalities arising from benefits of scientific advances that cannot be entirely appropriated by those making the advances. Further thought and research are needed on how best to measure and integrate these elements into an incremental value framework and on coverage and pricing decisions. Copyright © 2017 International Society for Pharmacoeconomics and Outcomes Research (ISPOR). Published by Elsevier Inc. All rights reserved.

Elements of the Chicxulub Impact Structure as revealed in SRTM and surface GPS topographic data

NASA Astrophysics Data System (ADS)

Kobrick, M.; Kinsland, G. L.; Sanchez, G.; Cardador, M. H.

2003-04-01

Pope et al have utilized elevations from the Petroleos Mexicanos (PEMEX) gravity data files to show that the main component of the surface expression of the Chicxu-lub Impact Structure is a roughly semi-circular, low-relief depression about 90 km in diameter. They also identified other topographic features and the elements of the buried impact which possibly led to the development of these features. Kinsland et al presented a connection between these topographic anomalies, small gravity anomalies and buried structure of the impact. Shaded relief images from recently acquired SRTM elevation data clearly show the circular depression of the crater and the moat/cenote ring. In addition we can readily identify Inner trough 1, Inner trough 2 and Outer trough as defined by Pope et al. The agreement between the topographic maps of Pope et al, Kinsland et al and SRTM data are remarkable considering that the distribution and types of data in the sets are so different. We also have ground topographic data collected with a special "autonomous differ-ential GPS" system during summer 2002. Profiles from these data generally agree with both the gravity data based topographic maps and profiles extracted from the SRTM data. Preliminary analyses of our new data, SRTM and GPS, have uncovered features not previously recognized: 1) as shown by the GPS data the moat/cenote ring consists of two distinct depressions separated by about 10 km...perhaps separate ring faults, 2) in the SRTM data over the southern part of the crater and on southward for perhaps 20 km beyond the moat/ cenote ring there exists a pattern, as yet unexplained, of roughly concentric topographic features whose center lies at about 21deg 40min N and 89deg 25min W, about 50km NNE of the moat/cenote ring center. The corroboration and better definition of the previously recognized topographic features yielded by the two new forms of data strengthens the cases for these fea-tures and for their relevance to the underlying

The domain structure and distribution of Alu elements in long noncoding RNAs and mRNAs

PubMed Central

Kim, Eugene Z.; Wespiser, Adam R.; Caffrey, Daniel R.

2016-01-01

Approximately 75% of the human genome is transcribed and many of these spliced transcripts contain primate-specific Alu elements, the most abundant mobile element in the human genome. The majority of exonized Alu elements are located in long noncoding RNAs (lncRNAs) and the untranslated regions of mRNA, with some performing molecular functions. To further assess the potential for Alu elements to be repurposed as functional RNA domains, we investigated the distribution and evolution of Alu elements in spliced transcripts. Our analysis revealed that Alu elements are underrepresented in mRNAs and lncRNAs, suggesting that most exonized Alu elements arising in the population are rare or deleterious to RNA function. When mRNAs and lncRNAs retain exonized Alu elements, they have a clear preference for Alu dimers, left monomers, and right monomers. mRNAs often acquire Alu elements when their genes are duplicated within Alu-rich regions. In lncRNAs, reverse-oriented Alu elements are significantly enriched and are not restricted to the 3′ and 5′ ends. Both lncRNAs and mRNAs primarily contain the Alu J and S subfamilies that were amplified relatively early in primate evolution. Alu J subfamilies are typically overrepresented in lncRNAs, whereas the Alu S dimer is overrepresented in mRNAs. The sequences of Alu dimers tend to be constrained in both lncRNAs and mRNAs, whereas the left and right monomers are constrained within particular Alu subfamilies and classes of RNA. Collectively, these findings suggest that Alu-containing RNAs are capable of forming stable structures and that some of these Alu domains might have novel biological functions. PMID:26654912

Shape Effect of Electrochemical Chloride Extraction in Structural Reinforced Concrete Elements Using a New Cement-Based Anodic System

PubMed Central

Carmona, Jesús; Climent, Miguel-Ángel; Antón, Carlos; de Vera, Guillem; Garcés, Pedro

2015-01-01

This article shows the research carried out by the authors focused on how the shape of structural reinforced concrete elements treated with electrochemical chloride extraction can affect the efficiency of this process. Assuming the current use of different anode systems, the present study considers the comparison of results between conventional anodes based on Ti-RuO2 wire mesh and a cement-based anodic system such as a paste of graphite-cement. Reinforced concrete elements of a meter length were molded to serve as laboratory specimens, to closely represent authentic structural supports, with circular and rectangular sections. Results confirm almost equal performances for both types of anode systems when electrochemical chloride extraction is applied to isotropic structural elements. In the case of anisotropic ones, such as rectangular sections with no uniformly distributed rebar, differences in electrical flow density were detected during the treatment. Those differences were more extreme for Ti-RuO2 mesh anode system. This particular shape effect is evidenced by obtaining the efficiencies of electrochemical chloride extraction in different points of specimens.

A New Axi-Symmetric Element for Thin Walled Structures

NASA Astrophysics Data System (ADS)

Cardoso, Rui P. R.; Yoon, Jeong Whan; Dick, Robert E.

2010-06-01

A new axi-symmetric finite element for sheet metal forming applications is presented in this work. It uses the solid-shell element's concept with only a single element layer and multiple integration points along the thickness direction. The cross section of the element is composed of four nodes with two degrees of freedom each. The proposed formulation overcomes major locking pathologies including transverse shear locking, Poisson's locking and volumetric locking. Some examples are shown to demonstrate the performance and accuracy of the proposed element with special focus on the numerical simulations for the beverage can industry.

A novel approach in formulation of special transition elements: Mesh interface elements

NASA Technical Reports Server (NTRS)

Sarigul, Nesrin

1991-01-01

The objective of this research program is in the development of more accurate and efficient methods for solution of singular problems encountered in various branches of mechanics. The research program can be categorized under three levels. The first two levels involve the formulation of a new class of elements called 'mesh interface elements' (MIE) to connect meshes of traditional elements either in three dimensions or in three and two dimensions. The finite element formulations are based on boolean sum and blending operators. MEI are being formulated and tested in this research to account for the steep gradients encountered in aircraft and space structure applications. At present, the heat transfer and structural analysis problems are being formulated from uncoupled theory point of view. The status report: (1) summarizes formulation for heat transfer and structural analysis; (2) explains formulation of MEI; (3) examines computational efficiency; and (4) shows verification examples.

The effect of tissue structure and soil chemistry on trace element uptake in fossils

NASA Astrophysics Data System (ADS)

Hinz, Emily A.; Kohn, Matthew J.

2010-06-01

Trace element profiles for common divalent cations (Sr, Zn, Ba), rare-earth elements (REE), Y, U, and Th were measured in fossil bones and teeth from the c. 25 ka Merrell locality, Montana, USA, by using laser-ablation ICP-MS. Multiple traverses in teeth were transformed into 2-D trace element maps for visualizing structural influences on trace element uptake. Trace element compositions of different soils from the fossil site were also analyzed by solution ICP-MS, employing progressive leaches that included distilled H 2O, 0.1 M acetic acid, and microwave digestion in concentrated HCl-HNO 3. In teeth, trace element uptake in enamel is 2-4 orders of magnitude slower than in dentine, forming an effective trace element barrier. Uptake in dentine parallel to the dentine-enamel interface is enhanced by at least 2 orders of magnitude compared to transverse, causing trace element "plumes" down the tooth core. In bone, U, Ba and Sr are nearly homogeneous, implying diffusivities ˜5 orders of magnitude faster than in enamel and virtually complete equilibration with host soils. In contrast all REE show strong depletions inward, with stepwise linear segments in log-normal or inverse complementary error function plots; these data require a multi-medium diffusion model, with about 2 orders of magnitude difference in slowest vs. fastest diffusivities. Differences in REE diffusivities in bone (slow) vs. dentine (fast) reflect different partition coefficients ( Kd's). Although acid leaches and bulk digestion of soils yield comparable fossil-soil Kd's among different elements, natural solutions are expected to be neutral to slightly basic. Distilled H 2O leachates instead reveal radically different Kd's in bone for REE than for U-Sr-Ba, suggest orders of magnitude lower effective diffusivities for REE, and readily explain steep vs. flat profiles for REE vs. U-Sr-Ba, respectively. Differences among REE Kd's and diffusivities may explain inward changes in Ce anomalies. Acid washes

New markers to identify the provenance of lapis lazuli: trace elements in pyrite by means of micro-PIXE

NASA Astrophysics Data System (ADS)

Re, A.; Angelici, D.; Lo Giudice, A.; Maupas, E.; Giuntini, L.; Calusi, S.; Gelli, N.; Massi, M.; Borghi, A.; Gallo, L. M.; Pratesi, G.; Mandò, P. A.

2013-04-01

Lapis lazuli has been used for glyptics and carving since the fifth millennium BC to produce jewels, amulets, seals, inlays, etc; the identification of the origin of the stone used for carving artworks may be valuable for reconstructing old trade routes. Since ancient lapis lazuli art objects are precious, only non-destructive techniques can be used to identify their provenance, and ion beam analysis (IBA) techniques allow us to characterise this stone in a fully non-invasive way. In addition, by using an ion microprobe, we have been able to focus the analysis on single crystals, as their typical dimensions may range from a few microns to hundreds of microns. Provenance markers, identified in previous IBA studies and already presented elsewhere, were based on the presence/absence of mineral phases, on the presence/quantity of trace elements inside a phase and on characteristic features of the luminescence spectra. In this work, a systematic study on pyrite crystals, a common accessory mineral in lapis lazuli, was carried out, following a multi-technique approach: optical microscopy and SEM-EDX to select crystals for successive trace element micro-PIXE measurements at two Italian facilities, the INFN Laboratori Nazionali di Legnaro and the INFN LABEC laboratory in Firenze. The results of this work allowed us to obtain new markers for lapis lazuli provenance identification.

Novel Structure of Enterococcus faecium-Originated ermB-Positive Tn1546-Like Element in Staphylococcus aureus.

PubMed

Wan, Tsai-Wen; Hung, Wei-Chun; Tsai, Jui-Chang; Lin, Yu-Tzu; Lee, Hao; Hsueh, Po-Ren; Lee, Tai-Fen; Teng, Lee-Jene

2016-10-01

We determined the resistance determinants in 274 erythromycin-resistant methicillin-susceptible Staphylococcus aureus (MSSA) isolates during a 13-year period, 2000 to 2012. The resistance phenotypes, inducible macrolide-lincosamide-streptogramin (iMLS), constitutive MLS (cMLS), and macrolide-streptogramin (MS) resistance phenotypes, were examined by a double-disk diffusion D test. The ermB gene was more frequent (35%; 97/274) than ermC (27%; 75/274) or ermA (21%; 58/274). All 97 ermB-positive isolates harbored Tn551 and IS1216V The majority (89/97) of ermB-positive isolates displayed the cMLS phenotype and carried mobile element structure (MES)-like structures, which has been previously reported in sequence type 59 (ST59) methicillin-resistant S. aureus (MRSA). The remaining 8 ermB-carrying isolates, belonging to ST7 (n = 4), ST5 (n = 3), and ST59 (n = 1), were sasK intact and did not carry MES-like structures. Unlike a MES-like structure that was located on the chromosome, the ermB elements on sasK-intact isolates were located on plasmids by S1 nuclease pulsed-field gel electrophoresis (PFGE) analysis and conjugation tests. Sequence data for the ermB-containing region (14,566 bp) from ST59 NTUH_3874 revealed that the best match was a Tn1546-like element in plasmid pMCCL2 DNA (GenBank accession number AP009486) of Macrococcus caseolyticus Tn1546 is recognized as an enterococcal transposon and was known from the vancomycin resistance gene cluster in vancomycin-resistant Enterococcus (VRE). So far, acquisitions of Tn1546 in S. aureus have occurred in clonal complex 5 (CC5) MRSA, but not in MSSA. This is the first report that MSSA harbors an Enterococcus faecium-originated ermB-positive Tn1546-like element located on a plasmid. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Building Finite Element Models to Investigate Zebrafish Jaw Biomechanics.

PubMed

Brunt, Lucy H; Roddy, Karen A; Rayfield, Emily J; Hammond, Chrissy L

2016-12-03

Skeletal morphogenesis occurs through tightly regulated cell behaviors during development; many cell types alter their behavior in response to mechanical strain. Skeletal joints are subjected to dynamic mechanical loading. Finite element analysis (FEA) is a computational method, frequently used in engineering that can predict how a material or structure will respond to mechanical input. By dividing a whole system (in this case the zebrafish jaw skeleton) into a mesh of smaller 'finite elements', FEA can be used to calculate the mechanical response of the structure to external loads. The results can be visualized in many ways including as a 'heat map' showing the position of maximum and minimum principal strains (a positive principal strain indicates tension while a negative indicates compression. The maximum and minimum refer the largest and smallest strain). These can be used to identify which regions of the jaw and therefore which cells are likely to be under particularly high tensional or compressional loads during jaw movement and can therefore be used to identify relationships between mechanical strain and cell behavior. This protocol describes the steps to generate Finite Element models from confocal image data on the musculoskeletal system, using the zebrafish lower jaw as a practical example. The protocol leads the reader through a series of steps: 1) staining of the musculoskeletal components, 2) imaging the musculoskeletal components, 3) building a 3 dimensional (3D) surface, 4) generating a mesh of Finite Elements, 5) solving the FEA and finally 6) validating the results by comparison to real displacements seen in movements of the fish jaw.

Magnetic alginate microfibers as scaffolding elements for the fabrication of microvascular-like structures.

PubMed

Sun, Tao; Shi, Qing; Huang, Qiang; Wang, Huaping; Xiong, Xiaolu; Hu, Chengzhi; Fukuda, Toshio

2018-01-15

Traditional cell-encapsulating scaffolds may elicit adverse host responses and inhomogeneity in cellular distribution. Thus, fabrication techniques for cellular self-assembly with micro-scaffold incorporation have been used recently to generate toroidal cellular modules for the bottom-up construction of vascular-like structures. The micro-scaffolds show advantage in promoting tissue formation. However, owing to the lack of annular cell micro-scaffolds, it remains a challenge to engineer micro-scale toroidal cellular modules (micro-TCMs) to fabricate microvascular-like structures. Here, magnetic alginate microfibers (MAMs) are used as scaffolding elements, where a winding strategy enables them to be formed into micro-rings as annular cell micro-scaffolds. These micro-rings were investigated for NIH/3T3 fibroblast growth as a function of surface chemistry and MAM size. Afterwards, micro-TCMs were successfully fabricated with the formation of NIH/3T3 fibroblasts and extracellular matrix layers on the three-dimensional micro-ring surfaces. Simple non-contact magnetic assembly was used to stack the micro-TCMs along a micro-pillar, after which cell fusion rapidly connected the assembled micro-TCMs into a microvascular-like structure. Endothelial cells or drugs encapsulated in the MAMs could be included in the microvascular-like structures as in vitro cellular models for vascular tissue engineering, or as miniaturization platforms for pharmaceutical drug testing in the future. Magnetic alginate microfibers functioned as scaffolding elements for guiding cell growth in micro-scale toroidal cellular modules (micro-TCMs) and provided a magnetic functionality to the micro-TCMs for non-contact 3D assembly in external magnetic fields. By using the liquid/air interface, the non-contact spatial manipulation of the micro-TCMs in the liquid environment was performed with a cost-effective motorized electromagnetic needle. A new biofabrication paradigm of construct of microvascular

Structure, diversity, and mobility of the Salmonella pathogenicity island 7 family of integrative and conjugative elements within Enterobacteriaceae.

PubMed

Seth-Smith, Helena M B; Fookes, Maria C; Okoro, Chinyere K; Baker, Stephen; Harris, Simon R; Scott, Paul; Pickard, Derek; Quail, Michael A; Churcher, Carol; Sanders, Mandy; Harmse, Johan; Dougan, Gordon; Parkhill, Julian; Thomson, Nicholas R

2012-03-01

Integrative and conjugative elements (ICEs) are self-mobile genetic elements found in the genomes of some bacteria. These elements may confer a fitness advantage upon their host bacteria through the cargo genes that they carry. Salmonella pathogenicity island 7 (SPI-7), found within some pathogenic strains of Salmonella enterica, possesses features indicative of an ICE and carries genes implicated in virulence. We aimed to identify and fully analyze ICEs related to SPI-7 within the genus Salmonella and other Enterobacteriaceae. We report the sequence of two novel SPI-7-like elements, found within strains of Salmonella bongori, which share 97% nucleotide identity over conserved regions with SPI-7 and with each other. Although SPI-7 within Salmonella enterica serovar Typhi appears to be fixed within the chromosome, we present evidence that these novel elements are capable of excision and self-mobility. Phylogenetic analyses show that these Salmonella mobile elements share an ancestor which existed approximately 3.6 to 15.8 million years ago. Additionally, we identified more distantly related ICEs, with distinct cargo regions, within other strains of Salmonella as well as within Citrobacter, Erwinia, Escherichia, Photorhabdus, and Yersinia species. In total, we report on a collection of 17 SPI-7 related ICEs within enterobacterial species, of which six are novel. Using comparative and mutational studies, we have defined a core of 27 genes essential for conjugation. We present a growing family of SPI-7-related ICEs whose mobility, abundance, and cargo variability indicate that these elements may have had a large impact on the evolution of the Enterobacteriaceae.

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.

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 large scale structures at 1 AU using fluctuations and wavelets

NASA Astrophysics Data System (ADS)

Niembro, T.; Lara, A.

2016-12-01

The solar wind (SW) is inhomogeneous and it is dominated for two types of flows: one quasi-stationary and one related to large scale transients (such as coronal mass ejections and co-rotating interaction regions). The SW inhomogeneities can be study as fluctuations characterized by a wide range of length and time scales. We are interested in the study of the characteristic fluctuations caused by large scale transient events. To do so, we define the vector space F with the normalized moving monthly/annual deviations as the orthogonal basis. Then, we compute the norm in this space of the solar wind parameters (velocity, magnetic field, density and temperature) fluctuations using WIND data from August 1992 to August 2015. This norm gives important information about the presence of a large structure disturbance in the solar wind and by applying a wavelet transform to this norm, we are able to determine, without subjectivity, the duration of the compression regions of these large transient structures and, even more, to identify if the structure corresponds to a single or complex (or merged) event. With this method we have automatically detected most of the events identified and published by other authors.

A Dual Super-Element Domain Decomposition Approach for Parallel Nonlinear Finite Element Analysis

NASA Astrophysics Data System (ADS)

Jokhio, G. A.; Izzuddin, B. A.

2015-05-01

This article presents a new domain decomposition method for nonlinear finite element analysis introducing the concept of dual partition super-elements. The method extends ideas from the displacement frame method and is ideally suited for parallel nonlinear static/dynamic analysis of structural systems. In the new method, domain decomposition is realized by replacing one or more subdomains in a "parent system," each with a placeholder super-element, where the subdomains are processed separately as "child partitions," each wrapped by a dual super-element along the partition boundary. The analysis of the overall system, including the satisfaction of equilibrium and compatibility at all partition boundaries, is realized through direct communication between all pairs of placeholder and dual super-elements. The proposed method has particular advantages for matrix solution methods based on the frontal scheme, and can be readily implemented for existing finite element analysis programs to achieve parallelization on distributed memory systems with minimal intervention, thus overcoming memory bottlenecks typically faced in the analysis of large-scale problems. Several examples are presented in this article which demonstrate the computational benefits of the proposed parallel domain decomposition approach and its applicability to the nonlinear structural analysis of realistic structural systems.

Gα12 structural determinants of Hsp90 interaction are necessary for serum response element-mediated transcriptional activation.

PubMed

Montgomery, Ellyn R; Temple, Brenda R S; Peters, Kimberly A; Tolbert, Caitlin E; Booker, Brandon K; Martin, Joseph W; Hamilton, Tyler P; Tagliatela, Alicia C; Smolski, William C; Rogers, Stephen L; Jones, Alan M; Meigs, Thomas E

2014-04-01

The G12/13 class of heterotrimeric G proteins, comprising the α-subunits Gα12 and Gα13, regulates multiple aspects of cellular behavior, including proliferation and cytoskeletal rearrangements. Although guanine nucleotide exchange factors for the monomeric G protein Rho (RhoGEFs) are well characterized as effectors of this G protein class, a variety of other downstream targets has been reported. To identify Gα12 determinants that mediate specific protein interactions, we used a structural and evolutionary comparison between the G12/13, Gs, Gi, and Gq classes to identify "class-distinctive" residues in Gα12 and Gα13. Mutation of these residues in Gα12 to their deduced ancestral forms revealed a subset necessary for activation of serum response element (SRE)-mediated transcription, a G12/13-stimulated pathway implicated in cell proliferative signaling. Unexpectedly, this subset of Gα12 mutants showed impaired binding to heat-shock protein 90 (Hsp90) while retaining binding to RhoGEFs. Corresponding mutants of Gα13 exhibited robust SRE activation, suggesting a Gα12-specific mechanism, and inhibition of Hsp90 by geldanamycin or small interfering RNA-mediated lowering of Hsp90 levels resulted in greater downregulation of Gα12 than Gα13 signaling in SRE activation experiments. Furthermore, the Drosophila G12/13 homolog Concertina was unable to signal to SRE in mammalian cells, and Gα12:Concertina chimeras revealed Gα12-specific determinants of SRE activation within the switch regions and a C-terminal region. These findings identify Gα12 determinants of SRE activation, implicate Gα12:Hsp90 interaction in this signaling mechanism, and illuminate structural features that arose during evolution of Gα12 and Gα13 to allow bifurcated mechanisms of signaling to a common cell proliferative pathway.

An automatic granular structure generation and finite element analysis of heterogeneous semi-solid materials

NASA Astrophysics Data System (ADS)

Sharifi, Hamid; Larouche, Daniel

2015-09-01

The quality of cast metal products depends on the capacity of the semi-solid metal to sustain the stresses generated during the casting. Predicting the evolution of these stresses with accuracy in the solidification interval should be highly helpful to avoid the formation of defects like hot tearing. This task is however very difficult because of the heterogeneous nature of the material. In this paper, we propose to evaluate the mechanical behaviour of a metal during solidification using a mesh generation technique of the heterogeneous semi-solid material for a finite element analysis at the microscopic level. This task is done on a two-dimensional (2D) domain in which the granular structure of the solid phase is generated surrounded by an intergranular and interdendritc liquid phase. Some basic solid grains are first constructed and projected in the 2D domain with random orientations and scale factors. Depending on their orientation, the basic grains are combined to produce larger grains or separated by a liquid film. Different basic grain shapes can produce different granular structures of the mushy zone. As a result, using this automatic grain generation procedure, we can investigate the effect of grain shapes and sizes on the thermo-mechanical behaviour of the semi-solid material. The granular models are automatically converted to the finite element meshes. The solid grains and the liquid phase are meshed properly using quadrilateral elements. This method has been used to simulate the microstructure of a binary aluminium-copper alloy (Al-5.8 wt% Cu) when the fraction solid is 0.92. Using the finite element method and the Mie-Grüneisen equation of state for the liquid phase, the transient mechanical behaviour of the mushy zone under tensile loading has been investigated. The stress distribution and the bridges, which are formed during the tensile loading, have been detected.

Identifying local structural states in atomic imaging by computer vision

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

Laanait, Nouamane; Ziatdinov, Maxim; He, Qian

The availability of atomically resolved imaging modalities enables an unprecedented view into the local structural states of materials, which manifest themselves by deviations from the fundamental assumptions of periodicity and symmetry. Consequently, approaches that aim to extract these local structural states from atomic imaging data with minimal assumptions regarding the average crystallographic configuration of a material are indispensable to advances in structural and chemical investigations of materials. Here, we present an approach to identify and classify local structural states that is rooted in computer vision. This approach introduces a definition of a structural state that is composed of both localmore » and non-local information extracted from atomically resolved images, and is wholly untethered from the familiar concepts of symmetry and periodicity. Instead, this approach relies on computer vision techniques such as feature detection, and concepts such as scale-invariance. We present the fundamental aspects of local structural state extraction and classification by application to simulated scanning transmission electron microscopy images, and analyze the robustness of this approach in the presence of common instrumental factors such as noise, limited spatial resolution, and weak contrast. Finally, we apply this computer vision-based approach for the unsupervised detection and classification of local structural states in an experimental electron micrograph of a complex oxides interface, and a scanning tunneling micrograph of a defect engineered multilayer graphene surface.« less

Identifying local structural states in atomic imaging by computer vision

DOE PAGES

Laanait, Nouamane; Ziatdinov, Maxim; He, Qian; ...

2016-11-02

The availability of atomically resolved imaging modalities enables an unprecedented view into the local structural states of materials, which manifest themselves by deviations from the fundamental assumptions of periodicity and symmetry. Consequently, approaches that aim to extract these local structural states from atomic imaging data with minimal assumptions regarding the average crystallographic configuration of a material are indispensable to advances in structural and chemical investigations of materials. Here, we present an approach to identify and classify local structural states that is rooted in computer vision. This approach introduces a definition of a structural state that is composed of both localmore » and non-local information extracted from atomically resolved images, and is wholly untethered from the familiar concepts of symmetry and periodicity. Instead, this approach relies on computer vision techniques such as feature detection, and concepts such as scale-invariance. We present the fundamental aspects of local structural state extraction and classification by application to simulated scanning transmission electron microscopy images, and analyze the robustness of this approach in the presence of common instrumental factors such as noise, limited spatial resolution, and weak contrast. Finally, we apply this computer vision-based approach for the unsupervised detection and classification of local structural states in an experimental electron micrograph of a complex oxides interface, and a scanning tunneling micrograph of a defect engineered multilayer graphene surface.« less

Finite element analysis of CFRP reinforced silo structure design method

NASA Astrophysics Data System (ADS)

Yuan, Long; Xu, Xinsheng

2017-11-01

Because of poor construction, there is a serious problem of concrete quality in the silo project, which seriously affects the safe use of the structure. Concrete quality problems are mainly seen in three aspects: concrete strength cannot meet the design requirements, concrete cracking phenomenon is serious, and the unreasonable concrete vibration leads to a lot of honeycombs and surface voids. Silos are usually reinforced by carbon fiber cloth in order to ensure the safe use of silos. By the example of an alumina silo in a fly ash plant in Binzhou, Shandong Province, the alumina silo project was tested and examined on site. According to filed test results, the actual concrete strength was determined, and the damage causes of the silo was analysed. Then, a finite element analysis model of this silo was established, the CFRP cloth reinforcement method was adopted to strengthen the silo, and other technology like additional reinforcement, rebar planting, carbon fiber bonding technology was also expounded. The research of this paper is of great significance to the design and construction of silo structure.

Identifying Novel Molecular Structures for Advanced Melanoma by Ligand-Based Virtual Screening

PubMed Central

Wang, Zhao; Lu, Yan; Seibel, William; Miller, Duane D.; Li, Wei

2009-01-01

We recently discovered a new class of thiazole analogs that are highly potent against melanoma cells. To expand the structure-activity relationship study and to explore potential new molecular scaffolds, we performed extensive ligand-based virtual screening against a compound library containing 342,910 small molecules. Two different approaches of virtual screening were carried out using the structure of our lead molecule: 1) connectivity-based search using Scitegic Pipeline Pilot from Accelerys and 2) molecular shape similarity search using Schrodinger software. Using a testing compound library, both approaches can rank similar compounds very high and rank dissimilar compounds very low, thus validating our screening methods. Structures identified from these searches were analyzed, and selected compounds were tested in vitro to assess their activity against melanoma cancer cell lines. Several molecules showed good anticancer activity. While none of the identified compounds showed better activity than our lead compound, they provided important insight into structural modifications for our lead compound and also provided novel platforms on which we can optimize new classes of anticancer compounds. One of the newly synthesized analogs based on this virtual screening has improved potency and selectivity against melanoma. PMID:19445498

A modified Finite Element-Transfer Matrix for control design of space structures

NASA Technical Reports Server (NTRS)

Tan, T.-M.; Yousuff, A.; Bahar, L. Y.; Konstandinidis, M.

1990-01-01

The Finite Element-Transfer Matrix (FETM) method was developed for reducing the computational efforts involved in structural analysis. While being widely used by structural analysts, this method does, however, have certain limitations, particularly when used for the control design of large flexible structures. In this paper, a new formulation based on the FETM method is presented. The new method effectively overcomes the limitations in the original FETM method, and also allows an easy construction of reduced models that are tailored for the control design. Other advantages of this new method include the ability to extract open loop frequencies and mode shapes with less computation, and simplification of the design procedures for output feedback, constrained compensation, and decentralized control. The development of this new method and the procedures for generating reduced models using this method are described in detail and the role of the reduced models in control design is discussed through an illustrative example.

Polymorphism in Elemental Silicon: Probabilistic Interpretation of the Realizability of Metastable Structures

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

Stevanovic, Vladan; Jones, Eric

With few systems of technological interest having been studied as extensively as elemental silicon, there currently exists a wide disparity between the number of predicted low-energy silicon polymorphs and those that have been experimentally realized as metastable at ambient conditions. We put forward an explanation for this disparity wherein the likelihood of formation of a given polymorph under near-equilibrium conditions can be estimated on the basis of mean-field isothermal-isobaric (N,p,T) ensemble statistics. The probability that a polymorph will be experimentally realized is shown to depend upon both the hypervolume of that structure's potential energy basin of attraction and a Boltzmannmore » factor weight containing the polymorph's potential enthalpy per particle. Both attributes are calculated using density functional theory relaxations of randomly generated initial structures. We find that the metastable polymorphism displayed by silicon can be accounted for using this framework to the exclusion of a very large number of other low-energy structures.« less

Identifying mRNA sequence elements for target recognition by human Argonaute proteins

PubMed Central

Li, Jingjing; Kim, TaeHyung; Nutiu, Razvan; Ray, Debashish; Hughes, Timothy R.; Zhang, Zhaolei

2014-01-01

It is commonly known that mammalian microRNAs (miRNAs) guide the RNA-induced silencing complex (RISC) to target mRNAs through the seed-pairing rule. However, recent experiments that coimmunoprecipitate the Argonaute proteins (AGOs), the central catalytic component of RISC, have consistently revealed extensive AGO-associated mRNAs that lack seed complementarity with miRNAs. We herein test the hypothesis that AGO has its own binding preference within target mRNAs, independent of guide miRNAs. By systematically analyzing the data from in vivo cross-linking experiments with human AGOs, we have identified a structurally accessible and evolutionarily conserved region (∼10 nucleotides in length) that alone can accurately predict AGO–mRNA associations, independent of the presence of miRNA binding sites. Within this region, we further identified an enriched motif that was replicable on independent AGO-immunoprecipitation data sets. We used RNAcompete to enumerate the RNA-binding preference of human AGO2 to all possible 7-mer RNA sequences and validated the AGO motif in vitro. These findings reveal a novel function of AGOs as sequence-specific RNA-binding proteins, which may aid miRNAs in recognizing their targets with high specificity. PMID:24663241

Translating the Elements of Health Governance for Integrated Care from Theory to Practice: A Case Study Approach.

PubMed

Nicholson, Caroline; Hepworth, Julie; Burridge, Letitia; Marley, John; Jackson, Claire

2018-01-31

Against a paucity of evidence, a model describing elements of health governance best suited to achieving integrated care internationally was developed. The aim of this study was to explore how health meso-level organisations used, or planned to use, the governance elements. A case study design was used to offer two contrasting contexts of health governance. Semi-structured interviews were conducted with participants who held senior governance roles. Data were thematically analysed to identify if the elements of health governance were being used, or intended to be in the future. While all participants agreed that the ten elements were essential to developing future integrated care, most were not used. Three major themes were identified: (1) organisational versus system focus, (2) leadership and culture, and, (3) community (dis)engagement. Several barriers and enablers to the use of the elements were identified and would require addressing in order to make evidence-based changes. Despite a clear international policy direction in support of integrated care this study identified a number of significant barriers to its implementation. The study reconfirmed that a focus on all ten elements of health governance is essential to achieve integrated care.

Translating the Elements of Health Governance for Integrated Care from Theory to Practice: A Case Study Approach

PubMed Central

Hepworth, Julie; Burridge, Letitia; Marley, John; Jackson, Claire

2018-01-01

Introduction: Against a paucity of evidence, a model describing elements of health governance best suited to achieving integrated care internationally was developed. The aim of this study was to explore how health meso-level organisations used, or planned to use, the governance elements. Methods: A case study design was used to offer two contrasting contexts of health governance. Semi-structured interviews were conducted with participants who held senior governance roles. Data were thematically analysed to identify if the elements of health governance were being used, or intended to be in the future. Results: While all participants agreed that the ten elements were essential to developing future integrated care, most were not used. Three major themes were identified: (1) organisational versus system focus, (2) leadership and culture, and, (3) community (dis)engagement. Discussion: Several barriers and enablers to the use of the elements were identified and would require addressing in order to make evidence-based changes. Conclusion: Despite a clear international policy direction in support of integrated care this study identified a number of significant barriers to its implementation. The study reconfirmed that a focus on all ten elements of health governance is essential to achieve integrated care. PMID:29588645

Space platform expendables resupply concept definition study. Volume 3: Work breakdown structure and work breakdown structure dictionary

NASA Technical Reports Server (NTRS)

1984-01-01

The work breakdown structure (WBS) for the Space Platform Expendables Resupply Concept Definition Study is described. The WBS consists of a list of WBS elements, a dictionary of element definitions, and an element logic diagram. The list and logic diagram identify the interrelationships of the elements. The dictionary defines the types of work that may be represented by or be classified under each specific element. The Space Platform Expendable Resupply WBS was selected mainly to support the program planning, scheduling, and costing performed in the programmatics task (task 3). The WBS is neither a statement-of-work nor a work authorization document. Rather, it is a framework around which to define requirements, plan effort, assign responsibilities, allocate and control resources, and report progress, expenditures, technical performance, and schedule performance. The WBS element definitions are independent of make-or-buy decisions, organizational structure, and activity locations unless exceptions are specifically stated.

Finite element analysis of steady and transiently moving/rolling nonlinear viscoelastic structure. III - Impact/contact simulations

NASA Technical Reports Server (NTRS)

Nakajima, Yukio; Padovan, Joe

1987-01-01

In a three-part series of papers, a generalized finite element methodology is formulated to handle traveling load problems involving large deformation fields in structure composed of viscoelastic media. The main thrust of this paper is to develop an overall finite element methodology and associated solution algorithms to handle the transient aspects of moving problems involving contact impact type loading fields. Based on the methodology and algorithms formulated, several numerical experiments are considered. These include the rolling/sliding impact of tires with road obstructions.

Structural and elemental changes in glioblastoma cells in situ: complementary imaging with high resolution visible light- and X-ray microscopy

DOE PAGES

Ducic, Tanja; Paunesku, Tatjana; Chen, Si; ...

2016-12-09

The glioblastoma (GBM) is characterized by a short median survival and an almost 100% tumor related mortality. GBM cells exhibit highly invasive behavior whose mechanisms are not yet fully understood. The present study explores application of X-ray and visible light microscopy to display the elemental and structural images of cells from 3 patient derived GMB samples and an established GMB cell line. Slight differences in elemental concentrations, in actin cytoskeleton organization and cell morphology were noted between all cells types by X-ray fluorescence and full field soft X-ray microscopy, as well as the Structured Illumination Super-resolution Microscope (SIM). Different samplemore » preparation approaches were used to match each imaging technique. While preparation for SIM included cell fixation and staining, intact frozen hydrated cells were used for the trace element imaging by hard X-ray fluorescence and exploration of the structural features by soft X-ray absorption tomography. In conclusion, each technique documented differences between samples with regard to morphology and elemental composition and underscored the importance of use of multiple patient derived samples for detailed GBM study.« less

Structural and elemental changes in glioblastoma cells in situ: complementary imaging with high resolution visible light- and X-ray microscopy

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

Ducic, Tanja; Paunesku, Tatjana; Chen, Si

The glioblastoma (GBM) is characterized by a short median survival and an almost 100% tumor related mortality. GBM cells exhibit highly invasive behavior whose mechanisms are not yet fully understood. The present study explores application of X-ray and visible light microscopy to display the elemental and structural images of cells from 3 patient derived GMB samples and an established GMB cell line. Slight differences in elemental concentrations, in actin cytoskeleton organization and cell morphology were noted between all cells types by X-ray fluorescence and full field soft X-ray microscopy, as well as the Structured Illumination Super-resolution Microscope (SIM). Different samplemore » preparation approaches were used to match each imaging technique. While preparation for SIM included cell fixation and staining, intact frozen hydrated cells were used for the trace element imaging by hard X-ray fluorescence and exploration of the structural features by soft X-ray absorption tomography. In conclusion, each technique documented differences between samples with regard to morphology and elemental composition and underscored the importance of use of multiple patient derived samples for detailed GBM study.« less

Correlation of finite-element structural dynamic analysis with measured free vibration characteristics for a full-scale helicopter fuselage

NASA Technical Reports Server (NTRS)

Kenigsberg, I. J.; Dean, M. W.; Malatino, R.

1974-01-01

The correlation achieved with each program provides the material for a discussion of modeling techniques developed for general application to finite-element dynamic analyses of helicopter airframes. Included are the selection of static and dynamic degrees of freedom, cockpit structural modeling, and the extent of flexible-frame modeling in the transmission support region and in the vicinity of large cut-outs. The sensitivity of predicted results to these modeling assumptions are discussed. Both the Sikorsky Finite-Element Airframe Vibration analysis Program (FRAN/Vibration Analysis) and the NASA Structural Analysis Program (NASTRAN) have been correlated with data taken in full-scale vibration tests of a modified CH-53A helicopter.

Investigation of deformation of elements of three-dimensional reinforced concrete structures located in the soil, interacting with each other through rubber gaskets

NASA Astrophysics Data System (ADS)

Berezhnoi, D. V.; Balafendieva, I. S.; Sachenkov, A. A.; Sekaeva, L. R.

2017-06-01

In work the technique of calculation of elements of three-dimensional reinforced concrete substructures located in a soil, interacting with each other through rubber linings is realized. To describe the interaction of deformable structures with the ground, special “semi-infinite” finite elements are used. A technique has been implemented that allows one to describe the contact interaction of three-dimensional structures by means of a special contact finite element with specific properties. The obtained numerical results are compared with the experimental data, their good agreement is noted.

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.

Construction of a three-dimensional finite element model of maxillary first molar and it's supporting structures

PubMed Central

Begum, M. Sameena; Dinesh, M. R.; Tan, Kenneth F. H.; Jairaj, Vani; Md Khalid, K.; Singh, Varun Pratap

2015-01-01

The finite element method (FEM) is a powerful computational tool for solving stress-strain problems; its ability to handle material inhomogeneity and complex shapes makes the FEM, the most suitable method for the analysis of internal stress levels in the tooth, periodontium, and alveolar bone. This article intends to explain the steps involved in the generation of a three-dimensional finite element model of tooth, periodontal ligament (PDL) and alveolar bone, as the procedure of modeling is most important because the result is based on the nature of the modeling systems. Finite element analysis offers a means of determining strain-stress levels in the tooth, ligament, and bone structures for a broad range of orthodontic loading scenarios without producing tissue damage. PMID:26538895

Blood lead: Its effect on trace element levels and iron structure in hemoglobin

NASA Astrophysics Data System (ADS)

Jin, C.; Li, Y.; Li, Y. L.; Zou, Y.; Zhang, G. L.; Normura, M.; Zhu, G. Y.

2008-08-01

Lead is a ubiquitous environmental pollutant that induce a broad range of physiological and biochemical dysfunctions. The purpose of this study was to investigate its effects on trace elements and the iron structure in hemoglobin. Blood samples were collected from rats that had been exposed to lead. The concentration of trace elements in whole blood and blood plasma was determined by ICP-MS and the results indicate that lead exists mainly in the red blood cells and only about 1-3% in the blood plasma. Following lead exposure, the concentrations of zinc and iron in blood decrease, as does the hemoglobin level. This indicates that the heme biosynthetic pathway is inhibited by lead toxicity and that lead poisoning-associated anemia occurs. The selenium concentration also decreases after lead exposure, which may lead to an increased rate of free radical production. The effect of lead in the blood on iron structure in hemoglobin was determined by EXAFS. After lead exposure, the Fe-O bond length increases by about 0.07 Å and the Fe-Np bond length slightly increases, but the Fe-N ɛ bond length remains unchanged. This indicates that the blood content of Hb increases, but that the content of HbO 2 decreases.

Future Launch Vehicle Structures - Expendable and Reusable Elements

NASA Astrophysics Data System (ADS)

Obersteiner, M. H.; Borriello, G.

2002-01-01

Further evolution of existing expendable launch vehicles will be an obvious element influencing the future of space transportation. Besides this reusability might be the change with highest potential for essential improvement. The expected cost reduction and finally contributing to this, the improvement of reliability including safe mission abort capability are driving this idea. Although there are ideas of semi-reusable launch vehicles, typically two stages vehicles - reusable first stage or booster(s) and expendable second or upper stage - it should be kept in mind that the benefit of reusability will only overwhelm if there is a big enough share influencing the cost calculation. Today there is the understanding that additional technology preparation and verification will be necessary to master reusability and get enough benefits compared with existing launch vehicles. This understanding is based on several technology and system concepts preparation and verification programmes mainly done in the US but partially also in Europe and Japan. The major areas of necessary further activities are: - System concepts including business plan considerations - Sub-system or component technologies refinement - System design and operation know-how and capabilities - Verification and demonstration oriented towards future mission mastering: One of the most important aspects for the creation of those coming programmes and activities will be the iterative process of requirements definition derived from concepts analyses including economical considerations and the results achieved and verified within technology and verification programmes. It is the intention of this paper to provide major trends for those requirements focused on future launch vehicles structures. This will include the aspects of requirements only valid for reusable launch vehicles and those common for expendable, semi-reusable and reusable launch vehicles. Structures and materials is and will be one of the

Nonlinear analysis of structures. [within framework of finite element method

NASA Technical Reports Server (NTRS)

Armen, H., Jr.; Levine, H.; Pifko, A.; Levy, A.

1974-01-01

The development of nonlinear analysis techniques within the framework of the finite-element method is reported. Although the emphasis is concerned with those nonlinearities associated with material behavior, a general treatment of geometric nonlinearity, alone or in combination with plasticity is included, and applications presented for a class of problems categorized as axisymmetric shells of revolution. The scope of the nonlinear analysis capabilities includes: (1) a membrane stress analysis, (2) bending and membrane stress analysis, (3) analysis of thick and thin axisymmetric bodies of revolution, (4) a general three dimensional analysis, and (5) analysis of laminated composites. Applications of the methods are made to a number of sample structures. Correlation with available analytic or experimental data range from good to excellent.

Development of an integrated BEM approach for hot fluid structure interaction: BEST-FSI: Boundary Element Solution Technique for Fluid Structure Interaction

NASA Technical Reports Server (NTRS)

Dargush, G. F.; Banerjee, P. K.; Shi, Y.

1992-01-01

As part of the continuing effort at NASA LeRC to improve both the durability and reliability of hot section Earth-to-orbit engine components, significant enhancements must be made in existing finite element and finite difference methods, and advanced techniques, such as the boundary element method (BEM), must be explored. The BEM was chosen as the basic analysis tool because the critical variables (temperature, flux, displacement, and traction) can be very precisely determined with a boundary-based discretization scheme. Additionally, model preparation is considerably simplified compared to the more familiar domain-based methods. Furthermore, the hyperbolic character of high speed flow is captured through the use of an analytical fundamental solution, eliminating the dependence of the solution on the discretization pattern. The price that must be paid in order to realize these advantages is that any BEM formulation requires a considerable amount of analytical work, which is typically absent in the other numerical methods. All of the research accomplishments of a multi-year program aimed toward the development of a boundary element formulation for the study of hot fluid-structure interaction in Earth-to-orbit engine hot section components are detailed. Most of the effort was directed toward the examination of fluid flow, since BEM's for fluids are at a much less developed state. However, significant strides were made, not only in the analysis of thermoviscous fluids, but also in the solution of the fluid-structure interaction problem.

The Application of Finite Element Solution Techniques in Structural Analysis on a Microcomputer.

DTIC Science & Technology

1981-12-01

my wife for her support of this research project and the amount of time she spent helping me in preparation. Thanks go to the personnel at Computer...questions which had to be answered concerning the microcomputer in relation to a sequentially programmed finite element program. The first was how big...central site, then usefullness of the microcomputer is limited. The first series of problems consisted of a simple truss structure, which was expanded

Probabilistic boundary element method

NASA Technical Reports Server (NTRS)

Cruse, T. A.; Raveendra, S. T.

1989-01-01

The purpose of the Probabilistic Structural Analysis Method (PSAM) project is to develop structural analysis capabilities for the design analysis of advanced space propulsion system hardware. The boundary element method (BEM) is used as the basis of the Probabilistic Advanced Analysis Methods (PADAM) which is discussed. The probabilistic BEM code (PBEM) is used to obtain the structural response and sensitivity results to a set of random variables. As such, PBEM performs analogous to other structural analysis codes such as finite elements in the PSAM system. For linear problems, unlike the finite element method (FEM), the BEM governing equations are written at the boundary of the body only, thus, the method eliminates the need to model the volume of the body. However, for general body force problems, a direct condensation of the governing equations to the boundary of the body is not possible and therefore volume modeling is generally required.

Updating finite element dynamic models using an element-by-element sensitivity methodology

NASA Technical Reports Server (NTRS)

Farhat, Charbel; Hemez, Francois M.

1993-01-01

A sensitivity-based methodology for improving the finite element model of a given structure using test modal data and a few sensors is presented. The proposed method searches for both the location and sources of the mass and stiffness errors and does not interfere with the theory behind the finite element model while correcting these errors. The updating algorithm is derived from the unconstrained minimization of the squared L sub 2 norms of the modal dynamic residuals via an iterative two-step staggered procedure. At each iteration, the measured mode shapes are first expanded assuming that the model is error free, then the model parameters are corrected assuming that the expanded mode shapes are exact. The numerical algorithm is implemented in an element-by-element fashion and is capable of 'zooming' on the detected error locations. Several simulation examples which demonstate the potential of the proposed methodology are discussed.

Structured populations of Sulfolobus acidocaldarius with susceptibility to mobile genetic elements

USGS Publications Warehouse

Anderson, Rika E.; Kouris, Angela; Seward, Christopher H.; Campbell, Kate M.; Whitaker, Rachel J.

2017-01-01

The impact of a structured environment on genome evolution can be determined through comparative population genomics of species that live in the same habitat. Recent work comparing three genome sequences of Sulfolobus acidocaldarius suggested that highly structured, extreme, hot spring environments do not limit dispersal of this thermoacidophile, in contrast to other co-occurring Sulfolobus species. Instead, a high level of conservation among these three S. acidocaldarius genomes was hypothesized to result from rapid, global-scale dispersal promoted by low susceptibility to viruses that sets S. acidocaldarius apart from its sister Sulfolobus species. To test this hypothesis, we conducted a comparative analysis of 47 genomes of S. acidocaldarius from spatial and temporal sampling of two hot springs in Yellowstone National Park. While we confirm the low diversity in the core genome, we observe differentiation among S. acidocaldarius populations, likely resulting from low migration among hot spring “islands” in Yellowstone National Park. Patterns of genomic variation indicate that differing geological contexts result in the elimination or preservation of diversity among differentiated populations. We observe multiple deletions associated with a large genomic island rich in glycosyltransferases, differential integrations of the Sulfolobus turreted icosahedral virus, as well as two different plasmid elements. These data demonstrate that neither rapid dispersal nor lack of mobile genetic elements result in low diversity in the S. acidocaldariusgenomes. We suggest instead that significant differences in the recent evolutionary history, or the intrinsic evolutionary rates, of sister Sulfolobusspecies result in the relatively low diversity of the S. acidocaldarius genome.

Scanning Probe Microscopy for Identifying the Component Materials of a Nanostripe Structure

NASA Astrophysics Data System (ADS)

Mizuno, Akira; Ando, Yasuhisa

2010-08-01

The authors prepared a nanostripe structure in which two types of metal are arranged alternately, and successfully identified the component materials using scanning probe microscopy (SPM) to measure the lateral force distribution image. The nanostripe structure was prepared using a new method developed by the authors and joint development members. The lateral force distribution image was measured in both friction force microscopy (FFM) and lateral modulation friction force microscopy (LM-FFM) modes. In FFM mode, the effect of slope angle appeared in the lateral force distribution image; therefore, no difference in the type of material was observed. On the other hand, in LM-FFM mode, the effect of surface curvature was observed in the lateral force distribution image. A higher friction force on chromium than on gold was identified, enabling material identification.

STANDARDIZING THE STRUCTURE OF STROKE CLINICAL AND EPIDEMIOLOGIC RESEARCH DATA: THE NINDS STROKE COMMON DATA ELEMENT (CDE) PROJECT

PubMed Central

Saver, Jeffrey L.; Warach, Steven; Janis, Scott; Odenkirchen, Joanne; Becker, Kyra; Benavente, Oscar; Broderick, Joseph; Dromerick, Alexander W.; Duncan, Pamela; Elkind, Mitchell S. V.; Johnston, Karen; Kidwell, Chelsea S.; Meschia, James F.; Schwamm, Lee

2012-01-01

Background and Purpose The National Institute of Neurological Disorders and Stroke initiated development of stroke-specific Common Data Elements (CDEs) as part of a project to develop data standards for funded clinical research in all fields of neuroscience. Standardizing data elements in translational, clinical and population research in cerebrovascular disease could decrease study start-up time, facilitate data sharing, and promote well-informed clinical practice guidelines. Methods A Working Group of diverse experts in cerebrovascular clinical trials, epidemiology, and biostatistics met regularly to develop a set of Stroke CDEs, selecting among, refining, and adding to existing, field-tested data elements from national registries and funded trials and studies. Candidate elements were revised based on comments from leading national and international neurovascular research organizations and the public. Results The first iteration of the NINDS stroke-specific CDEs comprises 980 data elements spanning nine content areas: 1) Biospecimens and Biomarkers; 2) Hospital Course and Acute Therapies; 3) Imaging; 4) Laboratory Tests and Vital Signs; 5) Long Term Therapies; 6) Medical History and Prior Health Status; 7) Outcomes and Endpoints; 8) Stroke Presentation; 9) Stroke Types and Subtypes. A CDE website provides uniform names and structures for each element, a data dictionary, and template case report forms (CRFs) using the CDEs. Conclusion Stroke-specific CDEs are now available as standardized, scientifically-vetted variable structures to facilitate data collection and data sharing in cerebrovascular patient-oriented research. The CDEs are an evolving resource that will be iteratively improved based on investigator use, new technologies, and emerging concepts and research findings. PMID:22308239

SINE_scan: an efficient tool to discover short interspersed nuclear elements (SINEs) in large-scale genomic datasets.

PubMed

Mao, Hongliang; Wang, Hao

2017-03-01

Short Interspersed Nuclear Elements (SINEs) are transposable elements (TEs) that amplify through a copy-and-paste mode via RNA intermediates. The computational identification of new SINEs are challenging because of their weak structural signals and rapid diversification in sequences. Here we report SINE_Scan, a highly efficient program to predict SINE elements in genomic DNA sequences. SINE_Scan integrates hallmark of SINE transposition, copy number and structural signals to identify a SINE element. SINE_Scan outperforms the previously published de novo SINE discovery program. It shows high sensitivity and specificity in 19 plant and animal genome assemblies, of which sizes vary from 120 Mb to 3.5 Gb. It identifies numerous new families and substantially increases the estimation of the abundance of SINEs in these genomes. The code of SINE_Scan is freely available at http://github.com/maohlzj/SINE_Scan , implemented in PERL and supported on Linux. wangh8@fudan.edu.cn. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

SINE_scan: an efficient tool to discover short interspersed nuclear elements (SINEs) in large-scale genomic datasets

PubMed Central

Mao, Hongliang

2017-01-01

Abstract Motivation: Short Interspersed Nuclear Elements (SINEs) are transposable elements (TEs) that amplify through a copy-and-paste mode via RNA intermediates. The computational identification of new SINEs are challenging because of their weak structural signals and rapid diversification in sequences. Results: Here we report SINE_Scan, a highly efficient program to predict SINE elements in genomic DNA sequences. SINE_Scan integrates hallmark of SINE transposition, copy number and structural signals to identify a SINE element. SINE_Scan outperforms the previously published de novo SINE discovery program. It shows high sensitivity and specificity in 19 plant and animal genome assemblies, of which sizes vary from 120 Mb to 3.5 Gb. It identifies numerous new families and substantially increases the estimation of the abundance of SINEs in these genomes. Availability and Implementation: The code of SINE_Scan is freely available at http://github.com/maohlzj/SINE_Scan, implemented in PERL and supported on Linux. Contact: wangh8@fudan.edu.cn Supplementary information: Supplementary data are available at Bioinformatics online. PMID:28062442

A finite element formulation for scattering from electrically large 2-dimensional structures

NASA Technical Reports Server (NTRS)

Ross, Daniel C.; Volakis, John L.

1992-01-01

A finite element formulation is given using the scattered field approach with a fictitious material absorber to truncate the mesh. The formulation includes the use of arbitrary approximation functions so that more accurate results can be achieved without any modification to the software. Additionally, non-polynomial approximation functions can be used, including complex approximation functions. The banded system that results is solved with an efficient sparse/banded iterative scheme and as a consequence, large structures can be analyzed. Results are given for simple cases to verify the formulation and also for large, complex geometries.

Fatigue assessment for selected connections of structural steel bridge components using the finite elements method

NASA Astrophysics Data System (ADS)

Śledziewski, Krzysztof

2018-01-01

Material fatigue it is one of the most frequent causes of steel bridge failures, particularly the bridges already existing. Thus, the procedure of fatigue life assessment is one of the most relevant procedures in a comprehensive assessment of load-carrying capacity and service life of the structure. A reliable assessment of the fatigue life is predominantly decisive for estimation of the remaining service life. Hitherto, calculation methods of welded joints took into account only stresses occurring in cross sections of whole elements and did not take into account stress concentration occurring in the vicinity of the weld, caused by geometrical aspects of the detail. At present, use of the Finite Element Analysis, makes possible looking for more accurate approach to the fatigue design of steel structures. The method of geometrical stresses is just such approach which is based on definition of stresses which take into account geometry of the detail. The study presents fatigue assessment of a representative type of welded joint in welded bridge structures. The testing covered longitudinal attachments. The main analyses were carried out on the basis of FEM and the method of local stresses, so-called "hot-spot" stresses. The obtained values of stresses were compared with the values obtained in accordance with the method of nominal stress.

Finite Element Simulation of Low Velocity Impact Damage on an Aeronautical Carbon Composite Structure

NASA Astrophysics Data System (ADS)

Lemanle Sanga, Roger Pierre; Garnier, Christian; Pantalé, Olivier

2016-12-01

Low velocity barely visible impact damage (BVID) in laminated carbon composite structures has a major importance for aeronautical industries. This contribution leads with the development of finite element models to simulate the initiation and the propagation of internal damage inside a carbon composite structure due by a low velocity impact. Composite plates made from liquid resin infusion process (LRI) have been subjected to low energy impacts (around 25 J) using a drop weight machine. In the experimental procedure, the internal damage is evaluated using an infrared thermographic camera while the indentation depth of the face is measured by optical measurement technique. In a first time we developed a robust model using homogenised shells based on degenerated tri-dimensional brick elements and in a second time we decided to modelize the whole stacking sequence of homogeneous layers and cohesive interlaminar interfaces in order to compare and validate the obtained results. Both layer and interface damage initiation and propagation models based on the Hashin and the Benzeggagh-Kenane criteria have been used for the numerical simulations. Comparison of numerical results and experiments has shown the accuracy of the proposed models.

Finite element modeling of temperature load effects on the vibration of local modes in multi-cable structures

NASA Astrophysics Data System (ADS)

Treyssède, Fabien

2018-01-01

Understanding thermal effects on the vibration of local (cable-dominant) modes in multi-cable structures is a complicated task. The main difficulty lies in the modification by temperature change of cable tensions, which are then undetermined. This paper applies a finite element procedure to investigate the effects of thermal loads on the linear dynamics of prestressed self-weighted multi-cable structures. Provided that boundary conditions are carefully handled, the discretization of cables with nonlinear curved beam elements can properly represent the thermoelastic behavior of cables as well as their linearized dynamics. A three-step procedure that aims to replace applied pretension forces with displacement continuity conditions is used. Despite an increase in the computational cost related to beam rotational degrees of freedom, such an approach has several advantages. Nonlinear beam finite elements are usually available in commercial codes. The overall method follows a thermoelastic geometrically non-linear analysis and hereby includes the main sources of non-linearities in multi-cable structures. The effects of cable bending stiffness, which can be significant, are also naturally accounted for. The accuracy of the numerical approach is assessed thanks to an analytical model for the vibration of a single inclined cable under temperature change. Then, the effects of thermal loads are investigated for two cable bridges, highlighting how natural frequencies can be affected by temperature. Although counterintuitive, a reverse relative change of natural frequency may occur for certain local modes. This phenomenon can be explained by two distinct mechanisms, one related to the physics intrinsic to cables and the other related to the thermal deflection of the superstructure. Numerical results show that cables cannot be isolated from the rest of the structure and the importance of modeling the whole structure for a quantitative analysis of temperature effects on the

Combining the Finite Element Method with Structural Connectome-based Analysis for Modeling Neurotrauma: Connectome Neurotrauma Mechanics

PubMed Central

Kraft, Reuben H.; Mckee, Phillip Justin; Dagro, Amy M.; Grafton, Scott T.

2012-01-01

This article presents the integration of brain injury biomechanics and graph theoretical analysis of neuronal connections, or connectomics, to form a neurocomputational model that captures spatiotemporal characteristics of trauma. We relate localized mechanical brain damage predicted from biofidelic finite element simulations of the human head subjected to impact with degradation in the structural connectome for a single individual. The finite element model incorporates various length scales into the full head simulations by including anisotropic constitutive laws informed by diffusion tensor imaging. Coupling between the finite element analysis and network-based tools is established through experimentally-based cellular injury thresholds for white matter regions. Once edges are degraded, graph theoretical measures are computed on the “damaged” network. For a frontal impact, the simulations predict that the temporal and occipital regions undergo the most axonal strain and strain rate at short times (less than 24 hrs), which leads to cellular death initiation, which results in damage that shows dependence on angle of impact and underlying microstructure of brain tissue. The monotonic cellular death relationships predict a spatiotemporal change of structural damage. Interestingly, at 96 hrs post-impact, computations predict no network nodes were completely disconnected from the network, despite significant damage to network edges. At early times () network measures of global and local efficiency were degraded little; however, as time increased to 96 hrs the network properties were significantly reduced. In the future, this computational framework could help inform functional networks from physics-based structural brain biomechanics to obtain not only a biomechanics-based understanding of injury, but also neurophysiological insight. PMID:22915997

Electro-mechanical analysis of composite and sandwich multilayered structures by shell elements with node-dependent kinematics

NASA Astrophysics Data System (ADS)

Carrera; Valvano; Kulikov

2018-01-01

In this work, a new class of finite elements for the analysis of composite and sandwich shells embedding piezoelectric skins and patches is proposed. The main idea of models coupling is developed by presenting the concept of nodal dependent kinematics where the same finite element can present at each node a different approximation of the main unknowns by setting a node-wise through-the-thickness approximation base. In a global/local approach scenario, the computational costs can be reduced drastically by assuming refined theories only in those zones/nodes of the structural domain where the resulting strain and stress states, and their electro-mechanical coupling present a complex distribution. Several numerical investigations are carried out to validate the accuracy and efficiency of the present shell element. An accurate representation of mechanical stresses and electric displacements in localized zones is possible with reduction of the computational costs if an accurate distribution of the higher-order kinematic capabilities is performed. On the contrary, the accuracy of the solution in terms of mechanical displacements and electric potential values depends on the global approximation over the whole structure. The efficacy of the present node-dependent variable kinematic models, thus, depends on the characteristics of the problem under consideration as well as on the required analysis type.

Elements That Define Recovery: The Experiential Perspective

PubMed Central

Kaskutas, Lee Ann; Borkman, Thomasina J; Laudet, Alexandre; Ritter, Lois A; Witbrodt, Jane; Subbaraman, Meenakshi Sabina; Stunz, Aina; Bond, Jason

2014-01-01

Objective: Although recovery increasingly guides substance use disorder services and policy, definitions of recovery continue to lack specificity, thereby hindering measure development and research. The goal of this study was to move the substance use disorders field beyond broad definitions by empirically identifying the domains and specific elements of recovery as experienced by persons in recovery from diverse pathways. Method: An Internet-based survey was completed by 9,341 individuals (54% female) who self-identified as being in recovery, recovered, in medication-assisted recovery, or as having had a problem with alcohol or drugs (but no longer do). Respondents were recruited via extensive outreach with treatment and recovery organizations, electronic media, and self-help groups. The survey included 47 recovery elements developed through qualitative work followed by an iterative reduction process. Exploratory and confirmatory factor analyses were conducted using split-half samples, followed by sensitivity analyses for key sample groupings. Results: Four recovery domains with 35 recovery elements emerged: abstinence in recovery, essentials of recovery, enriched recovery, and spirituality of recovery. The four-factor structure was robust regardless of length of recovery, 12-step or treatment exposure, and current substance use status. Four uncommon elements did not load on any factor but are presented to indicate the diversity of definitions. Conclusions: Our empirical findings offer specific items that can be used in evaluating recovery-oriented systems of care. Researchers studying recovery should include measures that extend beyond substance use and encompass elements such as those examined here—e.g., self-care, concern for others, personal growth, and developing ways of being that sustain change in substance use. PMID:25343658

Testing the Big Bang: Light elements, neutrinos, dark matter and large-scale structure

NASA Technical Reports Server (NTRS)

Schramm, David N.

1991-01-01

Several experimental and observational tests of the standard cosmological model are examined. In particular, a detailed discussion is presented regarding: (1) nucleosynthesis, the light element abundances, and neutrino counting; (2) the dark matter problems; and (3) the formation of galaxies and large-scale structure. Comments are made on the possible implications of the recent solar neutrino experimental results for cosmology. An appendix briefly discusses the 17 keV thing and the cosmological and astrophysical constraints on it.

Genomic Identification and Analysis of Shared Cis-regulator Elements in a Developmentally Critical homeobox Cluster

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

Chris Amemiya

2003-04-01

The goals of this project were to isolate, characterize, and sequence the Dlx3/Dlx7 bigene cluster from twelve different species of mammals. The Dlx3 and Dlx7 genes are known to encode homeobox transcription factors involved in patterning of structures in the vertebrate jaw as well as vertebrate limbs. Genomic sequences from the respective taxa will subsequently be compared in order to identify conserved non-coding sequences that are potential cis-regulatory elements. Based on the comparisons they will fashion transgenic mouse experiments to functionally test the strength of the potential cis-regulatory elements. A goal of the project is to attempt to identify thosemore » elements that may function in coordinately regulating both Dlx3 and Dlx7 functions.« less

Live imaging of companion cells and sieve elements in Arabidopsis leaves.

PubMed

Cayla, Thibaud; Batailler, Brigitte; Le Hir, Rozenn; Revers, Frédéric; Anstead, James A; Thompson, Gary A; Grandjean, Olivier; Dinant, Sylvie

2015-01-01

The phloem is a complex tissue composed of highly specialized cells with unique subcellular structures and a compact organization that is challenging to study in vivo at cellular resolution. We used confocal scanning laser microscopy and subcellular fluorescent markers in companion cells and sieve elements, for live imaging of the phloem in Arabidopsis leaves. This approach provided a simple framework for identifying phloem cell types unambiguously. It highlighted the compactness of the meshed network of organelles within companion cells. By contrast, within the sieve elements, unknown bodies were observed in association with the PP2-A1:GFP, GFP:RTM1 and RTM2:GFP markers at the cell periphery. The phloem lectin PP2-A1:GFP marker was found in the parietal ground matrix. Its location differed from that of the P-protein filaments, which were visualized with SEOR1:GFP and SEOR2:GFP. PP2-A1:GFP surrounded two types of bodies, one of which was identified as mitochondria. This location suggested that it was embedded within the sieve element clamps, specific structures that may fix the organelles to each another or to the plasma membrane in the sieve tubes. GFP:RTM1 was associated with a class of larger bodies, potentially corresponding to plastids. PP2-A1:GFP was soluble in the cytosol of immature sieve elements. The changes in its subcellular localization during differentiation provide an in vivo blueprint for monitoring this process. The subcellular features obtained with these companion cell and sieve element markers can be used as landmarks for exploring the organization and dynamics of phloem cells in vivo.

Live Imaging of Companion Cells and Sieve Elements in Arabidopsis Leaves

PubMed Central

Cayla, Thibaud; Batailler, Brigitte; Le Hir, Rozenn; Revers, Frédéric; Anstead, James A.; Thompson, Gary A.; Grandjean, Olivier; Dinant, Sylvie

2015-01-01

The phloem is a complex tissue composed of highly specialized cells with unique subcellular structures and a compact organization that is challenging to study in vivo at cellular resolution. We used confocal scanning laser microscopy and subcellular fluorescent markers in companion cells and sieve elements, for live imaging of the phloem in Arabidopsis leaves. This approach provided a simple framework for identifying phloem cell types unambiguously. It highlighted the compactness of the meshed network of organelles within companion cells. By contrast, within the sieve elements, unknown bodies were observed in association with the PP2-A1:GFP, GFP:RTM1 and RTM2:GFP markers at the cell periphery. The phloem lectin PP2-A1:GFP marker was found in the parietal ground matrix. Its location differed from that of the P-protein filaments, which were visualized with SEOR1:GFP and SEOR2:GFP. PP2-A1:GFP surrounded two types of bodies, one of which was identified as mitochondria. This location suggested that it was embedded within the sieve element clamps, specific structures that may fix the organelles to each another or to the plasma membrane in the sieve tubes. GFP:RTM1 was associated with a class of larger bodies, potentially corresponding to plastids. PP2-A1:GFP was soluble in the cytosol of immature sieve elements. The changes in its subcellular localization during differentiation provide an in vivo blueprint for monitoring this process. The subcellular features obtained with these companion cell and sieve element markers can be used as landmarks for exploring the organization and dynamics of phloem cells in vivo. PMID:25714357

Identifying block structure in the Pacific Northwest, USA

USGS Publications Warehouse

Savage, James C.; Wells, Ray E.

2015-01-01

We have identified block structure in the Pacific Northwest (west of 116°W between 38°N and 49°N) by clustering GPS stations so that the same Euler vector approximates the velocity of each station in a cluster. Given the total number k of clusters desired, the clustering procedure finds the best assignment of stations to clusters. Clustering is calculated for k= 2 to 14. In geographic space, cluster boundaries that remain relatively stable as k is increased are tentatively identified as block boundaries. That identification is reinforced if the cluster boundary coincides with a geologic feature. Boundaries identified in northern California and Nevada are the Central Nevada Seismic Belt, the west side of the Northern Walker Lane Belt, and the Bartlett Springs Fault. Three blocks cover all of Oregon and Washington. The principal block boundary there extends west-northwest along the Brothers Fault Zone, then north and northwest along the eastern boundary of Siletzia, the accreted oceanic basement of the forearc. East of this boundary is the Intermountain block, its eastern boundary undefined. A cluster boundary at Cape Blanco subdivides the forearc along the faulted southern margin of Siletzia. South of Cape Blanco the Klamath Mountains-Basin and Range block extends east to the Central Nevada Seismic Belt and south to the Sierra Nevada-Great Valley block. The Siletzia block north of Cape Blanco coincides almost exactly with the accreted Siletz terrane. The cluster boundary in the eastern Olympic Peninsula may mark permanent shortening of Siletzia against the Intermountain block.

Identification of light elements in silicon nitride by aberration-corrected scanning transmission electron microscopy.

PubMed

Idrobo, Juan C; Walkosz, Weronika; Klie, Robert F; Oğüt, Serdar

2012-12-01

In silicon nitride structural ceramics, the overall mechanical and thermal properties are controlled by the atomic and electronic structures at the interface between the ceramic grains and the amorphous intergranular films (IGFs) formed by various sintering additives. In the last ten years the atomic arrangements of heavy elements (rare-earths) at the Si(3)N(4)/IGF interfaces have been resolved. However, the atomic position of light elements, without which it is not possible to obtain a complete description of the interfaces, has been lacking. This review article details the authors' efforts to identify the atomic arrangement of light elements such as nitrogen and oxygen at the Si(3)N(4)/SiO(2) interface and in bulk Si(3)N(4) using aberration-corrected scanning transmission electron microscopy. Published by Elsevier B.V.

A Highly Flexible, Automated System Providing Reliable Sample Preparation in Element- and Structure-Specific Measurements.

PubMed

Vorberg, Ellen; Fleischer, Heidi; Junginger, Steffen; Liu, Hui; Stoll, Norbert; Thurow, Kerstin

2016-10-01

Life science areas require specific sample pretreatment to increase the concentration of the analytes and/or to convert the analytes into an appropriate form for the detection and separation systems. Various workstations are commercially available, allowing for automated biological sample pretreatment. Nevertheless, due to the required temperature, pressure, and volume conditions in typical element and structure-specific measurements, automated platforms are not suitable for analytical processes. Thus, the purpose of the presented investigation was the design, realization, and evaluation of an automated system ensuring high-precision sample preparation for a variety of analytical measurements. The developed system has to enable system adaption and high performance flexibility. Furthermore, the system has to be capable of dealing with the wide range of required vessels simultaneously, allowing for less cost and time-consuming process steps. However, the system's functionality has been confirmed in various validation sequences. Using element-specific measurements, the automated system was up to 25% more precise compared to the manual procedure and as precise as the manual procedure using structure-specific measurements. © 2015 Society for Laboratory Automation and Screening.

Identification of both copy number variation-type and constant-type core elements in a large segmental duplication region of the mouse genome

PubMed Central

2013-01-01

Background Copy number variation (CNV), an important source of diversity in genomic structure, is frequently found in clusters called CNV regions (CNVRs). CNVRs are strongly associated with segmental duplications (SDs), but the composition of these complex repetitive structures remains unclear. Results We conducted self-comparative-plot analysis of all mouse chromosomes using the high-speed and large-scale-homology search algorithm SHEAP. For eight chromosomes, we identified various types of large SD as tartan-checked patterns within the self-comparative plots. A complex arrangement of diagonal split lines in the self-comparative-plots indicated the presence of large homologous repetitive sequences. We focused on one SD on chromosome 13 (SD13M), and developed SHEPHERD, a stepwise ab initio method, to extract longer repetitive elements and to characterize repetitive structures in this region. Analysis using SHEPHERD showed the existence of 60 core elements, which were expected to be the basic units that form SDs within the repetitive structure of SD13M. The demonstration that sequences homologous to the core elements (>70% homology) covered approximately 90% of the SD13M region indicated that our method can characterize the repetitive structure of SD13M effectively. Core elements were composed largely of fragmented repeats of a previously identified type, such as long interspersed nuclear elements (LINEs), together with partial genic regions. Comparative genome hybridization array analysis showed that whereas 42 core elements were components of CNVR that varied among mouse strains, 8 did not vary among strains (constant type), and the status of the others could not be determined. The CNV-type core elements contained significantly larger proportions of long terminal repeat (LTR) types of retrotransposon than the constant-type core elements, which had no CNV. The higher divergence rates observed in the CNV-type core elements than in the constant type indicate that the

DiRE: identifying distant regulatory elements of co-expressed genes

PubMed Central

Gotea, Valer; Ovcharenko, Ivan

2008-01-01

Regulation of gene expression in eukaryotic genomes is established through a complex cooperative activity of proximal promoters and distant regulatory elements (REs) such as enhancers, repressors and silencers. We have developed a web server named DiRE, based on the Enhancer Identification (EI) method, for predicting distant regulatory elements in higher eukaryotic genomes, namely for determining their chromosomal location and functional characteristics. The server uses gene co-expression data, comparative genomics and profiles of transcription factor binding sites (TFBSs) to determine TFBS-association signatures that can be used for discriminating specific regulatory functions. DiRE's unique feature is its ability to detect REs outside of proximal promoter regions, as it takes advantage of the full gene locus to conduct the search. DiRE can predict common REs for any set of input genes for which the user has prior knowledge of co-expression, co-function or other biologically meaningful grouping. The server predicts function-specific REs consisting of clusters of specifically-associated TFBSs and it also scores the association of individual transcription factors (TFs) with the biological function shared by the group of input genes. Its integration with the Array2BIO server allows users to start their analysis with raw microarray expression data. The DiRE web server is freely available at http://dire.dcode.org. PMID:18487623

Location and orientation of panel on the screen as a structural visual element to highlight text displayed

NASA Astrophysics Data System (ADS)

Léger, Laure; Chevalier, Aline

2017-07-01

Searching for information on the internet has become a daily activity. It is considered to be a complex cognitive activity that involves visual attention. Many studies have demonstrated that users' information search are affected both by the spatial configuration of words and the elements displayed on the screen: elements that are used to structure web pages. One of these elements, the web panel, contains information. Web panel is a rectangular area with a colored background that was used to highlighting content presented in this specific rectangular area. Our general hypothesis was that the presence of a panel on a web page would affect the structure of a word display, as a result, information search accuracy. We carried out an experiment in which we manipulated the presence vs. the absence of a panel, as well as its orientation on the screen (vertical vs. horizontal). Twenty participants were asked to answer questions while their eye movements were recorded. Results showed that the presence of a panel resulted in reduced accuracy and shorter response times. Panel orientation affected scanpaths, especially when they were orientated vertically. We discuss these findings and suggest ways in which this research could be developed further in future.

Failure mechanisms in energy-absorbing composite structures

NASA Astrophysics Data System (ADS)

Johnson, Alastair F.; David, Matthew

2010-11-01

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

The interaction between the yeast telomerase RNA and the Est1 protein requires three structural elements.

PubMed

Lubin, Johnathan W; Tucey, Timothy M; Lundblad, Victoria

2012-09-01

In the budding yeast Saccharomyces cerevisiae, the telomerase enzyme is composed of a 1.3-kb TLC1 RNA that forms a complex with Est2 (the catalytic subunit) and two regulatory proteins, Est1 and Est3. Previous work has identified a conserved 5-nt bulge, present in a long helical arm of TLC1, which mediates binding of Est1 to TLC1. However, increased expression of Est1 can bypass the consequences of removal of this RNA bulge, indicating that there are additional binding site(s) for Est1 on TLC1. We report here that a conserved single-stranded internal loop immediately adjacent to the bulge is also required for the Est1-RNA interaction; furthermore, a TLC1 variant that lacks this internal loop but retains the bulge cannot be suppressed by Est1 overexpression, arguing that the internal loop may be a more critical element for Est1 binding. An additional structural feature consisting of a single-stranded region at the base of the helix containing the bulge and internal loop also contributes to recognition of TLC1 by Est1, potentially by providing flexibility to this helical arm. Association of Est1 with each of these TLC1 motifs was assessed using a highly sensitive biochemical assay that simultaneously monitors the relative levels of the Est1 and Est2 proteins in the telomerase complex. The identification of three elements of TLC1 that are required for Est1 association provides a detailed view of this particular protein-RNA interaction.

The relationship between structural stability and electrochemical performance of multi-element doped alpha nickel hydroxide

NASA Astrophysics Data System (ADS)

Miao, Chengcheng; Zhu, Yanjuan; Huang, Liangguo; Zhao, Tengqi

2015-01-01

The multi-element doped alpha nickel hydroxide has been prepared by supersonic co-precipitation method. Three kinds of samples A, B and C are prepared by chemically coprecipitating Ni/Al, Ni/Al/Mn and Ni/Al/Mn/Yb, respectively. Inductively coupled plasma atomic emission spectroscopy (ICP-AES), Particle size distribution (PSD) measurement, X-ray diffraction (XRD), scanning electron microscope (SEM) and Fourier transform infrared spectroscopy (FT-IR) are used to characterize the physical properties of the synthesized α-Ni(OH)2 samples, such as chemical composition, morphology, structural stability of the crystal. The results show that all samples are nano-sized materials and the interlayer spacing becomes larger and the structural stability becomes better with the increase of doped elements and doped ratio. The prepared alpha nickel hydroxide samples are added into micro-sized beta nickel hydroxide to form biphase electrode materials for Ni-MH battery. The electrochemical characterization of the biphase electrodes, including cyclic voltammetry (CV) and charge/discharge test, are also performed. The results demonstrate that the biphase electrode with sample C exhibits better electrochemical reversibility and cyclic stability, higher charge efficient and discharge potential, larger proton diffusion coefficient (5.81 × 10-12 cm2 s-1) and discharge capacity (309.0 mAh g-1). Hence, it indicates that all doped elements can produce the synergic effect and further improve the electrochemical properties of the alpha nickel hydroxide.

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

Nonlinear finite element model updating for damage identification of civil structures using batch Bayesian estimation

NASA Astrophysics Data System (ADS)

Ebrahimian, Hamed; Astroza, Rodrigo; Conte, Joel P.; de Callafon, Raymond A.

2017-02-01

This paper presents a framework for structural health monitoring (SHM) and damage identification of civil structures. This framework integrates advanced mechanics-based nonlinear finite element (FE) modeling and analysis techniques with a batch Bayesian estimation approach to estimate time-invariant model parameters used in the FE model of the structure of interest. The framework uses input excitation and dynamic response of the structure and updates a nonlinear FE model of the structure to minimize the discrepancies between predicted and measured response time histories. The updated FE model can then be interrogated to detect, localize, classify, and quantify the state of damage and predict the remaining useful life of the structure. As opposed to recursive estimation methods, in the batch Bayesian estimation approach, the entire time history of the input excitation and output response of the structure are used as a batch of data to estimate the FE model parameters through a number of iterations. In the case of non-informative prior, the batch Bayesian method leads to an extended maximum likelihood (ML) estimation method to estimate jointly time-invariant model parameters and the measurement noise amplitude. The extended ML estimation problem is solved efficiently using a gradient-based interior-point optimization algorithm. Gradient-based optimization algorithms require the FE response sensitivities with respect to the model parameters to be identified. The FE response sensitivities are computed accurately and efficiently using the direct differentiation method (DDM). The estimation uncertainties are evaluated based on the Cramer-Rao lower bound (CRLB) theorem by computing the exact Fisher Information matrix using the FE response sensitivities with respect to the model parameters. The accuracy of the proposed uncertainty quantification approach is verified using a sampling approach based on the unscented transformation. Two validation studies, based on realistic

Identifying structural styles in Colombia

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

Wilson, W.P.; Van Nieuwenhuise, R.E.; Steuer, M.R.

1996-08-01

Much of our understanding of the Earth is from the study of surface geology and seismic, but many surface structures are responses to deformation which occurred below sedimentary layers. The practice within the petroleum industry is to use top-down processes of analyzing the surface to understand the subsurface, and observed surface structural styles tend to influence seismic interpretations. Yet many conditions which influenced the structural styles seen at the surface are different at depth. Since seismic is a time representation of the Earth, many interpretation pitfalls may exist within areas of complex geology. Also, its reliability decreases with depth andmore » with increasing geologic complexity. Forward modeling and pre-stack depth migration technologies are used to provide true depth images of the seismic data. Even with these advances in seismic imaging technology, the interpreter needs to incorporate additional data into the interpretation. Accurate structural identification requires the interpreter to integrate seismic with surface geology, remote sensing, gravity, magnetic data, geochemistry, fault-plane solutions from earthquakes, and regional tectonic studies. Incorporating these types of data into the interpretation will help us learn how basement is involved in the deformation of overlying sediments. A study of the Eastern Cordillera of Colombia shows the deformation to be dominantly transpressional in style. Euler deconvolution of the areomagnetic data shows a highly fractured basement, steep fault lineaments, en echelon structures, and complex fault patterns, all of which would be typical of wrench-type deformation. Available surface geology, regional studies, earthquake data, and forward modeling support this interpretation.« less

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.

Inverted repeat Alu elements in the human lincRNA-p21 adopt a conserved secondary structure that regulates RNA function

PubMed Central

Chillón, Isabel; Pyle, Anna M.

2016-01-01

LincRNA-p21 is a long intergenic non-coding RNA (lincRNA) involved in the p53-mediated stress response. We sequenced the human lincRNA-p21 (hLincRNA-p21) and found that it has a single exon that includes inverted repeat Alu elements (IRAlus). Sense and antisense Alu elements fold independently of one another into a secondary structure that is conserved in lincRNA-p21 among primates. Moreover, the structures formed by IRAlus are involved in the localization of hLincRNA-p21 in the nucleus, where hLincRNA-p21 colocalizes with paraspeckles. Our results underscore the importance of IRAlus structures for the function of hLincRNA-p21 during the stress response. PMID:27378782

Asynchronous Communication: Investigating the Influences of Relational Elements and Background on the Framing Structure of Emails

ERIC Educational Resources Information Center

AlAfnan, Mohammad Awad

2015-01-01

This study explored the influences of relational elements and the background of communicators on the framing structure of email messages that were exchanged in an educational Institute in Malaysia. The investigation revealed that social distance played a more significant role than power relations as Malaysian respondents are, generally, more…

Exploring innovative techniques for identifying geochemical elements as fingerprints of sediment sources in an agricultural catchment of Argentina affected by soil erosion.

PubMed

Torres Astorga, Romina; de Los Santos Villalobos, Sergio; Velasco, Hugo; Domínguez-Quintero, Olgioly; Pereira Cardoso, Renan; Meigikos Dos Anjos, Roberto; Diawara, Yacouba; Dercon, Gerd; Mabit, Lionel

2018-05-15

Identification of hot spots of land degradation is strongly related with the selection of soil tracers for sediment pathways. This research proposes the complementary and integrated application of two analytical techniques to select the most suitable fingerprint tracers for identifying the main sources of sediments in an agricultural catchment located in Central Argentina with erosive loess soils. Diffuse reflectance Fourier transformed in the mid-infrared range (DRIFT-MIR) spectroscopy and energy-dispersive X-ray fluorescence (EDXRF) were used for a suitable fingerprint selection. For using DRIFT-MIR spectroscopy as fingerprinting technique, calibration through quantitative parameters is needed to link and correlate DRIFT-MIR spectra with soil tracers. EDXRF was used in this context for determining the concentrations of geochemical elements in soil samples. The selected tracers were confirmed using two artificial mixtures composed of known proportions of soil collected in different sites with distinctive soil uses. These fingerprint elements were used as parameters to build a predictive model with the whole set of DRIFT-MIR spectra. Fingerprint elements such as phosphorus, iron, calcium, barium, and titanium were identified for obtaining a suitable reconstruction of the source proportions in the artificial mixtures. Mid-infrared spectra produced successful prediction models (R 2  = 0.91) for Fe content and moderate useful prediction (R 2  = 0.72) for Ti content. For Ca, P, and Ba, the R 2 were 0.44, 0.58, and 0.59 respectively.

Research in Structures and Dynamics, 1984

NASA Technical Reports Server (NTRS)

Hayduk, R. J. (Compiler); Noor, A. K. (Compiler)

1984-01-01

A symposium on advanced and trends in structures and dynamics was held to communicate new insights into physical behavior and to identify trends in the solution procedures for structures and dynamics problems. Pertinent areas of concern were (1) multiprocessors, parallel computation, and database management systems, (2) advances in finite element technology, (3) interactive computing and optimization, (4) mechanics of materials, (5) structural stability, (6) dynamic response of structures, and (7) advanced computer applications.

Crystal Structure Prediction via Deep Learning.

PubMed

Ryan, Kevin; Lengyel, Jeff; Shatruk, Michael

2018-06-06

We demonstrate the application of deep neural networks as a machine-learning tool for the analysis of a large collection of crystallographic data contained in the crystal structure repositories. Using input data in the form of multi-perspective atomic fingerprints, which describe coordination topology around unique crystallographic sites, we show that the neural-network model can be trained to effectively distinguish chemical elements based on the topology of their crystallographic environment. The model also identifies structurally similar atomic sites in the entire dataset of ~50000 crystal structures, essentially uncovering trends that reflect the periodic table of elements. The trained model was used to analyze templates derived from the known binary and ternary crystal structures in order to predict the likelihood to form new compounds that could be generated by placing elements into these structural templates in combinatorial fashion. Statistical analysis of predictive performance of the neural-network model, which was applied to a test set of structures never seen by the model during training, indicates its ability to predict known elemental compositions with a high likelihood of success. In ~30% of cases, the known compositions were found among top-10 most likely candidates proposed by the model. These results suggest that the approach developed in this work can be used to effectively guide the synthetic efforts in the discovery of new materials, especially in the case of systems composed of 3 or more chemical elements.

Large-scale genome-wide analysis identifies genetic variants associated with cardiac structure and function

PubMed Central

Wild, Philipp S.; Felix, Janine F.; Schillert, Arne; Chen, Ming-Huei; Leening, Maarten J.G.; Völker, Uwe; Großmann, Vera; Brody, Jennifer A.; Irvin, Marguerite R.; Shah, Sanjiv J.; Pramana, Setia; Lieb, Wolfgang; Schmidt, Reinhold; Stanton, Alice V.; Malzahn, Dörthe; Lyytikäinen, Leo-Pekka; Tiller, Daniel; Smith, J. Gustav; Di Tullio, Marco R.; Musani, Solomon K.; Morrison, Alanna C.; Pers, Tune H.; Morley, Michael; Kleber, Marcus E.; Aragam, Jayashri; Bis, Joshua C.; Bisping, Egbert; Broeckel, Ulrich; Cheng, Susan; Deckers, Jaap W.; Del Greco M, Fabiola; Edelmann, Frank; Fornage, Myriam; Franke, Lude; Friedrich, Nele; Harris, Tamara B.; Hofer, Edith; Hofman, Albert; Huang, Jie; Hughes, Alun D.; Kähönen, Mika; investigators, KNHI; Kruppa, Jochen; Lackner, Karl J.; Lannfelt, Lars; Laskowski, Rafael; Launer, Lenore J.; Lindgren, Cecilia M.; Loley, Christina; Mayet, Jamil; Medenwald, Daniel; Morris, Andrew P.; Müller, Christian; Müller-Nurasyid, Martina; Nappo, Stefania; Nilsson, Peter M.; Nuding, Sebastian; Nutile, Teresa; Peters, Annette; Pfeufer, Arne; Pietzner, Diana; Pramstaller, Peter P.; Raitakari, Olli T.; Rice, Kenneth M.; Rotter, Jerome I.; Ruohonen, Saku T.; Sacco, Ralph L.; Samdarshi, Tandaw E.; Sharp, Andrew S.P.; Shields, Denis C.; Sorice, Rossella; Sotoodehnia, Nona; Stricker, Bruno H.; Surendran, Praveen; Töglhofer, Anna M.; Uitterlinden, André G.; Völzke, Henry; Ziegler, Andreas; Münzel, Thomas; März, Winfried; Cappola, Thomas P.; Hirschhorn, Joel N.; Mitchell, Gary F.; Smith, Nicholas L.; Fox, Ervin R.; Dueker, Nicole D.; Jaddoe, Vincent W.V.; Melander, Olle; Lehtimäki, Terho; Ciullo, Marina; Hicks, Andrew A.; Lind, Lars; Gudnason, Vilmundur; Pieske, Burkert; Barron, Anthony J.; Zweiker, Robert; Schunkert, Heribert; Ingelsson, Erik; Liu, Kiang; Arnett, Donna K.; Psaty, Bruce M.; Blankenberg, Stefan; Larson, Martin G.; Felix, Stephan B.; Franco, Oscar H.; Zeller, Tanja; Vasan, Ramachandran S.; Dörr, Marcus

2017-01-01

BACKGROUND. Understanding the genetic architecture of cardiac structure and function may help to prevent and treat heart disease. This investigation sought to identify common genetic variations associated with inter-individual variability in cardiac structure and function. METHODS. A GWAS meta-analysis of echocardiographic traits was performed, including 46,533 individuals from 30 studies (EchoGen consortium). The analysis included 16 traits of left ventricular (LV) structure, and systolic and diastolic function. RESULTS. The discovery analysis included 21 cohorts for structural and systolic function traits (n = 32,212) and 17 cohorts for diastolic function traits (n = 21,852). Replication was performed in 5 cohorts (n = 14,321) and 6 cohorts (n = 16,308), respectively. Besides 5 previously reported loci, the combined meta-analysis identified 10 additional genome-wide significant SNPs: rs12541595 near MTSS1 and rs10774625 in ATXN2 for LV end-diastolic internal dimension; rs806322 near KCNRG, rs4765663 in CACNA1C, rs6702619 near PALMD, rs7127129 in TMEM16A, rs11207426 near FGGY, rs17608766 in GOSR2, and rs17696696 in CFDP1 for aortic root diameter; and rs12440869 in IQCH for Doppler transmitral A-wave peak velocity. Findings were in part validated in other cohorts and in GWAS of related disease traits. The genetic loci showed associations with putative signaling pathways, and with gene expression in whole blood, monocytes, and myocardial tissue. CONCLUSION. The additional genetic loci identified in this large meta-analysis of cardiac structure and function provide insights into the underlying genetic architecture of cardiac structure and warrant follow-up in future functional studies. FUNDING. For detailed information per study, see Acknowledgments. PMID:28394258

Identification of structural variation in mouse genomes.

PubMed

Keane, Thomas M; Wong, Kim; Adams, David J; Flint, Jonathan; Reymond, Alexandre; Yalcin, Binnaz

2014-01-01

Structural variation is variation in structure of DNA regions affecting DNA sequence length and/or orientation. It generally includes deletions, insertions, copy-number gains, inversions, and transposable elements. Traditionally, the identification of structural variation in genomes has been challenging. However, with the recent advances in high-throughput DNA sequencing and paired-end mapping (PEM) methods, the ability to identify structural variation and their respective association to human diseases has improved considerably. In this review, we describe our current knowledge of structural variation in the mouse, one of the prime model systems for studying human diseases and mammalian biology. We further present the evolutionary implications of structural variation on transposable elements. We conclude with future directions on the study of structural variation in mouse genomes that will increase our understanding of molecular architecture and functional consequences of structural variation.

Identifying calcium sources at an acid deposition-impacted spruce forest: A strontium isotope, alkaline earth element multi-tracer approach

USGS Publications Warehouse

Bullen, T.D.; Bailey, S.W.

2005-01-01

Depletion of calcium from forest soils has important implications for forest productivity and health. Ca is available to fine feeder roots from a number of soil organic and mineral sources, but identifying the primary source or changes of sources in response to environmental change is problematic. We used strontium isotope and alkaline earth element concentration ratios of trees and soils to discern the record of Ca sources for red spruce at a base-poor, acid deposition-impacted watershed. We measured 87Sr/86Sr and chemical compositions of cross-sectional stemwood cores of red spruce, other spruce tissues and sequential extracts of co-located soil samples. 87Sr/86Sr and Sr/Ba ratios together provide a tracer of alkaline earth element sources that distinguishes the plant-available fraction of the shallow organic soils from those of deeper organic and mineral soils. Ca/Sr ratios proved less diagnostic, due to within-tree processes that fractionate these elements from each other. Over the growth period from 1870 to 1960, 87Sr/86Sr and Sr/Ba ratios of stemwood samples became progressively more variable and on average trended toward values that considered together are characteristic of the uppermost forest floor. In detail the stemwood chemistry revealed an episode of simultaneous enhanced uptake of all alkaline earth elements during the growth period from 1930 to 1960, coincident with reported local and regional increases in atmospheric inputs of inorganic acidity. We attribute the temporal trends in stemwood chemistry to progressive shallowing of the effective depth of alkaline earth element uptake by fine roots over this growth period, due to preferential concentration of fine roots in the upper forest floor coupled with reduced nutrient uptake by roots in the lower organic and upper mineral soils in response to acid-induced aluminum toxicity. Although both increased atmospheric deposition and selective weathering of Ca-rich minerals such as apatite provide possible

The Associative Structure of Memory for Multi-Element Events

PubMed Central

2013-01-01

The hippocampus is thought to be an associative memory “convergence zone,” binding together the multimodal elements of an experienced event into a single engram. This predicts a degree of dependency between the retrieval of the different elements comprising an event. We present data from a series of studies designed to address this prediction. Participants vividly imagined a series of person–location–object events, and memory for these events was assessed across multiple trials of cued retrieval. Consistent with the prediction, a significant level of dependency was found between the retrieval of different elements from the same event. Furthermore, the level of dependency was sensitive both to retrieval task, with higher dependency during cued recall than cued recognition, and to subjective confidence. We propose a simple model, in which events are stored as multiple pairwise associations between individual event elements, and dependency is captured by a common factor that varies across events. This factor may relate to between-events modulation of the strength of encoding, or to a process of within-event “pattern completion” at retrieval. The model predicts the quantitative pattern of dependency in the data when changes in the level of guessing with retrieval task and confidence are taken into account. Thus, we find direct behavioral support for the idea that memory for complex multimodal events depends on the pairwise associations of their constituent elements and that retrieval of the various elements corresponding to the same event reflects a common factor that varies from event to event. PMID:23915127

Electronic structure of trioxide, oxoperoxide, oxosuperoxide, and ozonide clusters of the 3d elements: density functional theory study.

PubMed

Uzunova, Ellie L

2011-03-03

The trioxide clusters with stoichiometry MO3, and the structural isomers with side-on and end-on bonded oxygen atoms, are studied by DFT with the B1LYP functional. For the first half of the 3d elements row (Sc to Cr), pyramidal or distorted pyramidal structures dominate among the trioxide and oxoperoxide ground states, while the remaining elements form planar trioxides, oxoperoxides, oxosuperoxides, and ozonides. Low-lying trioxide clusters are formed by Ti, V, Cr, and Mn, among which the distorted pyramidal VO3 in the (2)A'' state, the pyramidal CrO3 in the (1)A1 state, and the planar MnO3 in the (2)A1' state are global minima. With the exception of the middle-row elements Mn, Fe, and Co, the magnetic moment of the ground-state clusters is formed with a major contribution from unpaired electrons located at the oxygen atoms. The stability of trioxides and oxoperoxides toward release of molecular oxygen is significantly higher for Sc, Ti, and V than for the remaining elements of the row. A trend of increasing the capability to dissociate one oxygen molecule is observed from Cr to Cu, with the exception of OFe(O2) being more reactive than OCo(O2). A gradual increase of reactivity from Ti to Cu is observed for the complete fragmentation reaction M + O + O2.

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.

A Procedure for Modeling Structural Component/Attachment Failure Using Transient Finite Element Analysis

NASA Technical Reports Server (NTRS)

Lovejoy, Andrew E.; Jegley, Dawn C. (Technical Monitor)

2007-01-01

Structures often comprise smaller substructures that are connected to each other or attached to the ground by a set of finite connections. Under static loading one or more of these connections may exceed allowable limits and be deemed to fail. Of particular interest is the structural response when a connection is severed (failed) while the structure is under static load. A transient failure analysis procedure was developed by which it is possible to examine the dynamic effects that result from introducing a discrete failure while a structure is under static load. The failure is introduced by replacing a connection load history by a time-dependent load set that removes the connection load at the time of failure. The subsequent transient response is examined to determine the importance of the dynamic effects by comparing the structural response with the appropriate allowables. Additionally, this procedure utilizes a standard finite element transient analysis that is readily available in most commercial software, permitting the study of dynamic failures without the need to purchase software specifically for this purpose. The procedure is developed and explained, demonstrated on a simple cantilever box example, and finally demonstrated on a real-world example, the American Airlines Flight 587 (AA587) vertical tail plane (VTP).

Precise colocalization of interacting structural and pigmentary elements generates extensive color pattern variation in Phelsuma lizards

PubMed Central

2013-01-01

Background Color traits in animals play crucial roles in thermoregulation, photoprotection, camouflage, and visual communication, and are amenable to objective quantification and modeling. However, the extensive variation in non-melanic pigments and structural colors in squamate reptiles has been largely disregarded. Here, we used an integrated approach to investigate the morphological basis and physical mechanisms generating variation in color traits in tropical day geckos of the genus Phelsuma. Results Combining histology, optics, mass spectrometry, and UV and Raman spectroscopy, we found that the extensive variation in color patterns within and among Phelsuma species is generated by complex interactions between, on the one hand, chromatophores containing yellow/red pteridine pigments and, on the other hand, iridophores producing structural color by constructive interference of light with guanine nanocrystals. More specifically, we show that 1) the hue of the vivid dorsolateral skin is modulated both by variation in geometry of structural, highly ordered narrowband reflectors, and by the presence of yellow pigments, and 2) that the reflectivity of the white belly and of dorsolateral pigmentary red marks, is increased by underlying structural disorganized broadband reflectors. Most importantly, these interactions require precise colocalization of yellow and red chromatophores with different types of iridophores, characterized by ordered and disordered nanocrystals, respectively. We validated these results through numerical simulations combining pigmentary components with a multilayer interferential optical model. Finally, we show that melanophores form dark lateral patterns but do not significantly contribute to variation in blue/green or red coloration, and that changes in the pH or redox state of pigments provide yet another source of color variation in squamates. Conclusions Precisely colocalized interacting pigmentary and structural elements generate extensive

Damage detection of structures identified with deterministic-stochastic models using seismic data.

PubMed

Huang, Ming-Chih; Wang, Yen-Po; Chang, Ming-Lian

2014-01-01

A deterministic-stochastic subspace identification method is adopted and experimentally verified in this study to identify the equivalent single-input-multiple-output system parameters of the discrete-time state equation. The method of damage locating vector (DLV) is then considered for damage detection. A series of shaking table tests using a five-storey steel frame has been conducted. Both single and multiple damage conditions at various locations have been considered. In the system identification analysis, either full or partial observation conditions have been taken into account. It has been shown that the damaged stories can be identified from global responses of the structure to earthquakes if sufficiently observed. In addition to detecting damage(s) with respect to the intact structure, identification of new or extended damages of the as-damaged counterpart has also been studied. This study gives further insights into the scheme in terms of effectiveness, robustness, and limitation for damage localization of frame systems.

High Throughput Analyses of Budding Yeast ARSs Reveal New DNA Elements Capable of Conferring Centromere-Independent Plasmid Propagation

PubMed Central

Hoggard, Timothy; Liachko, Ivan; Burt, Cassaundra; Meikle, Troy; Jiang, Katherine; Craciun, Gheorghe; Dunham, Maitreya J.; Fox, Catherine A.

2016-01-01

The ability of plasmids to propagate in Saccharomyces cerevisiae has been instrumental in defining eukaryotic chromosomal control elements. Stable propagation demands both plasmid replication, which requires a chromosomal replication origin (i.e., an ARS), and plasmid distribution to dividing cells, which requires either a chromosomal centromere for segregation or a plasmid-partitioning element. While our knowledge of yeast ARSs and centromeres is relatively advanced, we know less about chromosomal regions that can function as plasmid partitioning elements. The Rap1 protein-binding site (RAP1) present in transcriptional silencers and telomeres of budding yeast is a known plasmid-partitioning element that functions to anchor a plasmid to the inner nuclear membrane (INM), which in turn facilitates plasmid distribution to daughter cells. This Rap1-dependent INM-anchoring also has an important chromosomal role in higher-order chromosomal structures that enhance transcriptional silencing and telomere stability. Thus, plasmid partitioning can reflect fundamental features of chromosome structure and biology, yet a systematic screen for plasmid partitioning elements has not been reported. Here, we couple deep sequencing with competitive growth experiments of a plasmid library containing thousands of short ARS fragments to identify new plasmid partitioning elements. Competitive growth experiments were performed with libraries that differed only in terms of the presence or absence of a centromere. Comparisons of the behavior of ARS fragments in the two experiments allowed us to identify sequences that were likely to drive plasmid partitioning. In addition to the silencer RAP1 site, we identified 74 new putative plasmid-partitioning motifs predicted to act as binding sites for DNA binding proteins enriched for roles in negative regulation of gene expression and G2/M-phase associated biology. These data expand our knowledge of chromosomal elements that may function in plasmid

Identifying Type Ia Supernova Mechanisms in Dwarf Spheroidal Galaxies through Analysis of Iron-peak Elemental Abundances

NASA Astrophysics Data System (ADS)

Guo, Rachel; Xie, Justin Long; Kirby, Evan N.

2017-01-01

Through the fusion of nucleons to produce elements heavier than hydrogen and helium, stellar nucleosynthesis produces most of the elements in the universe. Such is the case in a supernova explosion, which creates most of the elements on the periodic table—including iron-peak elements, atomic numbers 21 through 30—through nucleosynthesis and ejects them into the interstellar medium. In this study, we determine the best theoretical supernova model appropriate for the stars in the dwarf spheroidal galaxies Sculptor, Fornax, Ursa Minor, and Leo II by calculating the abundances of iron-peak elements in these stars. To determine iron-peak elemental abundances, we compare synthesized spectra with observed spectra from medium-resolution spectroscopy and determine the best-fitting spectrum by way of a chi-squared minimization. Through inspecting the relationship between the iron-peak element abundances and the abundance of iron itself and by comparing them to previously hypothesized supernova model theories, we discover that the near-Chandrasekhar mass “n1” model, as predicted by Seitenzahl et al., most accurately represents the trends and patterns within our data, presenting new insight into Type Ia supernovae mechanisms within the Milky Way and beyond.

Accurate structure prediction of peptide–MHC complexes for identifying highly immunogenic antigens

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

Park, Min-Sun; Park, Sung Yong; Miller, Keith R.

2013-11-01

Designing an optimal HIV-1 vaccine faces the challenge of identifying antigens that induce a broad immune capacity. One factor to control the breadth of T cell responses is the surface morphology of a peptide–MHC complex. Here, we present an in silico protocol for predicting peptide–MHC structure. A robust signature of a conformational transition was identified during all-atom molecular dynamics, which results in a model with high accuracy. A large test set was used in constructing our protocol and we went another step further using a blind test with a wild-type peptide and two highly immunogenic mutants, which predicted substantial conformationalmore » changes in both mutants. The center residues at position five of the analogs were configured to be accessible to solvent, forming a prominent surface, while the residue of the wild-type peptide was to point laterally toward the side of the binding cleft. We then experimentally determined the structures of the blind test set, using high resolution of X-ray crystallography, which verified predicted conformational changes. Our observation strongly supports a positive association of the surface morphology of a peptide–MHC complex to its immunogenicity. Our study offers the prospect of enhancing immunogenicity of vaccines by identifying MHC binding immunogens.« less

Progression in structural, magnetic and electrical properties of La-doped group IV elements

NASA Astrophysics Data System (ADS)

Deepapriya, S.; Annie Vinosha, P.; Rodney, John D.; Jerome Das, S.

2018-04-01

Progression of group IV elements such as zinc ferrite (ZnFe2O4), cobalt ferrite (CoFe2O4) was synthesized by doping lanthanum (La), via adopting a facile co-precipitation method. Doping hefty rare earth ion in spinel structure can amend to the physical properties of the lattice, which can be used in the enhancement of magnetic and electrical properties of the as-synthesized nanomaterial, it is vital to metamorphose and optimize its micro structural and magnetic features. The structural properties of the samples was analysed by powder X-ray diffraction (XRD), Fourier transform infrared (FTIR), Transmission electron microscopy (TEM) and UV-visible spectral analysis (UV-vis) reveals the optical property and optical band gap. The magnetic properties were evaluated using a vibrating sample magnetometer (VSM), the presence of functional group was confirmed by FTIR. XRD analyses elucidates that the synthesized samples zinc and cobalt had a spinel structure. From TEM analyses the morphology and diameter of the particle was observed. The substituted rare earth ions in Zinc ferrite inhibit the grain growth of the materials in an efficient manner compared with that of the Cobalt ferrite.

Probing the Structures of Viral RNA Regulatory Elements with SHAPE and Related Methodologies

PubMed Central

Rausch, Jason W.; Sztuba-Solinska, Joanna; Le Grice, Stuart F. J.

2018-01-01

Viral RNAs were selected by evolution to possess maximum functionality in a minimal sequence. Depending on the classification of the virus and the type of RNA in question, viral RNAs must alternately be replicated, spliced, transcribed, transported from the nucleus into the cytoplasm, translated and/or packaged into nascent virions, and in most cases, provide the sequence and structural determinants to facilitate these processes. One consequence of this compact multifunctionality is that viral RNA structures can be exquisitely complex, often involving intermolecular interactions with RNA or protein, intramolecular interactions between sequence segments separated by several thousands of nucleotides, or specialized motifs such as pseudoknots or kissing loops. The fluidity of viral RNA structure can also present a challenge when attempting to characterize it, as genomic RNAs especially are likely to sample numerous conformations at various stages of the virus life cycle. Here we review advances in chemoenzymatic structure probing that have made it possible to address such challenges with respect to cis-acting elements, full-length viral genomes and long non-coding RNAs that play a major role in regulating viral gene expression. PMID:29375504

Quality assessment of structure and language elements of written responses given by seven Scandinavian drug information centres.

PubMed

Reppe, Linda Amundstuen; Spigset, Olav; Kampmann, Jens Peter; Damkier, Per; Christensen, Hanne Rolighed; Böttiger, Ylva; Schjøtt, Jan

2017-05-01

The aim of this study was to identify structure and language elements affecting the quality of responses from Scandinavian drug information centres (DICs). Six different fictitious drug-related queries were sent to each of seven Scandinavian DICs. The centres were blinded for which queries were part of the study. The responses were assessed qualitatively by six clinical pharmacologists (internal experts) and six general practitioners (GPs, external experts). In addition, linguistic aspects of the responses were evaluated by a plain language expert. The quality of responses was generally judged as satisfactory to good. Presenting specific advice and conclusions were considered to improve the quality of the responses. However, small nuances in language formulations could affect the individual judgments of the experts, e.g. on whether or not advice was given. Some experts preferred the use of primary sources to the use of secondary and tertiary sources. Both internal and external experts criticised the use of abbreviations, professional terminology and study findings that was left unexplained. The plain language expert emphasised the importance of defining and explaining pharmacological terms to ensure that enquirers understand the response as intended. In addition, more use of active voice and less compressed text structure would be desirable. This evaluation of responses to DIC queries may give some indications on how to improve written responses on drug-related queries with respect to language and text structure. Giving specific advice and precise conclusions and avoiding too compressed language and non-standard abbreviations may aid to reach this goal.

The identification of clinically important elements within medical journal abstracts: Patient-Population-Problem, Exposure-Intervention, Comparison, Outcome, Duration and Results (PECODR).

PubMed

Dawes, Martin; Pluye, Pierre; Shea, Laura; Grad, Roland; Greenberg, Arlene; Nie, Jian-Yun

2007-01-01

Information retrieval in primary care is becoming more difficult as the volume of medical information held in electronic databases expands. The lexical structure of this information might permit automatic indexing and improved retrieval. To determine the possibility of identifying the key elements of clinical studies, namely Patient-Population-Problem, Exposure-Intervention, Comparison, Outcome, Duration and Results (PECODR), from abstracts of medical journals. We used a convenience sample of 20 synopses from the journal Evidence-Based Medicine (EBM) and their matching original journal article abstracts obtained from PubMed. Three independent primary care professionals identified PECODR-related extracts of text. Rules were developed to define each PECODR element and the selection process of characters, words, phrases and sentences. From the extracts of text related to PECODR elements, potential lexical patterns that might help identify those elements were proposed and assessed using NVivo software. A total of 835 PECODR-related text extracts containing 41,263 individual text characters were identified from 20 EBM journal synopses. There were 759 extracts in the corresponding PubMed abstracts containing 31,947 characters. PECODR elements were found in nearly all abstracts and synopses with the exception of duration. There was agreement on 86.6% of the extracts from the 20 EBM synopses and 85.0% on the corresponding PubMed abstracts. After consensus this rose to 98.4% and 96.9% respectively. We found potential text patterns in the Comparison, Outcome and Results elements of both EBM synopses and PubMed abstracts. Some phrases and words are used frequently and are specific for these elements in both synopses and abstracts. Results suggest a PECODR-related structure exists in medical abstracts and that there might be lexical patterns specific to these elements. More sophisticated computer-assisted lexical-semantic analysis might refine these results, and pave the way

Cis-acting RNA elements in the Hepatitis C virus RNA genome

PubMed Central

Sagan, Selena M.; Chahal, Jasmin; Sarnow, Peter

2017-01-01

Hepatitis C virus (HCV) infection is a rapidly increasing global health problem with an estimated 170 million people infected worldwide. HCV is a hepatotropic, positive-sense RNA virus of the family Flaviviridae. As a positive-sense RNA virus, the HCV genome itself must serve as a template for translation, replication and packaging. The viral RNA must therefore be a dynamic structure that is able to readily accommodate structural changes to expose different regions of the genome to viral and cellular proteins to carry out the HCV life cycle. The ∼9600 nucleotide viral genome contains a single long open reading frame flanked by 5′ and 3′ non-coding regions that contain cis-acting RNA elements important for viral translation, replication and stability. Additional cis-acting RNA elements have also been identified in the coding sequences as well as in the 3′ end of the negative-strand replicative intermediate. Herein, we provide an overview of the importance of these cis-acting RNA elements in the HCV life cycle. PMID:25576644

Electronic Structure of Actinides under Pressure

NASA Astrophysics Data System (ADS)

Johansson, Borje

2006-03-01

The series of heavy radioactive elements known as the actinides all have similar elemental properties. However, when the volume per atom in the condensed phase is illustrated as a function of atomic number, perhaps the most dramatic anomaly in the periodic table becomes apparent. The atomic volume of americium is almost 50% larger than it is for the preceding element plutonium. For the element after americium, curium, the atomic volume is very close to that of americium. The same holds also for the next elements berkelium and californium. Accordingly from americium and onwards the actinides behave very similar to the corresponding rare-earth elements - a second lanthanide series of metallic elements can be identified. This view is strongly supported by the fact that all these elements adopt the dhcp structure, a structure typical for the lanthanides. The reason for this behavior is found in the behavior of the 5f electrons. For the earlier actinides, up to and including plutonium, the 5f electrons form metallic states and contribute most significantly to the bonding. In Np and Pu they even dominate the bonding, while all of a sudden they become localized in Am, very much like the 4f electrons in the lanthanide series, and contribute no longer to the cohesion. This withdrawal of 5f bonding gives rise to the large volume expansion between plutonium and americium. This difference between the light and heavy actinide suggests that it would be most worthwhile to strongly compress the transplutonium elements, thereby forcing the individual 5f electron wave functions into strong contact with each other (overlap). Recently high pressure experiments have been performed for americium and curium and dramatic crystal structure changes have been observed. These results and other high pressure data will be discussed in relation to the basic electronic structure of these elements.

Proteome-wide Structural Analysis of PTM Hotspots Reveals Regulatory Elements Predicted to Impact Biological Function and Disease.

PubMed

Torres, Matthew P; Dewhurst, Henry; Sundararaman, Niveda

2016-11-01

Post-translational modifications (PTMs) regulate protein behavior through modulation of protein-protein interactions, enzymatic activity, and protein stability essential in the translation of genotype to phenotype in eukaryotes. Currently, less than 4% of all eukaryotic PTMs are reported to have biological function - a statistic that continues to decrease with an increasing rate of PTM detection. Previously, we developed SAPH-ire (Structural Analysis of PTM Hotspots) - a method for the prioritization of PTM function potential that has been used effectively to reveal novel PTM regulatory elements in discrete protein families (Dewhurst et al., 2015). Here, we apply SAPH-ire to the set of eukaryotic protein families containing experimental PTM and 3D structure data - capturing 1,325 protein families with 50,839 unique PTM sites organized into 31,747 modified alignment positions (MAPs), of which 2010 (∼6%) possess known biological function. Here, we show that using an artificial neural network model (SAPH-ire NN) trained to identify MAP hotspots with biological function results in prediction outcomes that far surpass the use of single hotspot features, including nearest neighbor PTM clustering methods. We find the greatest enhancement in prediction for positions with PTM counts of five or less, which represent 98% of all MAPs in the eukaryotic proteome and 90% of all MAPs found to have biological function. Analysis of the top 1092 MAP hotspots revealed 267 of truly unknown function (containing 5443 distinct PTMs). Of these, 165 hotspots could be mapped to human KEGG pathways for normal and/or disease physiology. Many high-ranking hotspots were also found to be disease-associated pathogenic sites of amino acid substitution despite the lack of observable PTM in the human protein family member. Taken together, these experiments demonstrate that the functional relevance of a PTM can be predicted very effectively by neural network models, revealing a large but testable

Proteome-wide Structural Analysis of PTM Hotspots Reveals Regulatory Elements Predicted to Impact Biological Function and Disease*

PubMed Central

Dewhurst, Henry; Sundararaman, Niveda

2016-01-01

Post-translational modifications (PTMs) regulate protein behavior through modulation of protein-protein interactions, enzymatic activity, and protein stability essential in the translation of genotype to phenotype in eukaryotes. Currently, less than 4% of all eukaryotic PTMs are reported to have biological function - a statistic that continues to decrease with an increasing rate of PTM detection. Previously, we developed SAPH-ire (Structural Analysis of PTM Hotspots) - a method for the prioritization of PTM function potential that has been used effectively to reveal novel PTM regulatory elements in discrete protein families (Dewhurst et al., 2015). Here, we apply SAPH-ire to the set of eukaryotic protein families containing experimental PTM and 3D structure data - capturing 1,325 protein families with 50,839 unique PTM sites organized into 31,747 modified alignment positions (MAPs), of which 2010 (∼6%) possess known biological function. Here, we show that using an artificial neural network model (SAPH-ire NN) trained to identify MAP hotspots with biological function results in prediction outcomes that far surpass the use of single hotspot features, including nearest neighbor PTM clustering methods. We find the greatest enhancement in prediction for positions with PTM counts of five or less, which represent 98% of all MAPs in the eukaryotic proteome and 90% of all MAPs found to have biological function. Analysis of the top 1092 MAP hotspots revealed 267 of truly unknown function (containing 5443 distinct PTMs). Of these, 165 hotspots could be mapped to human KEGG pathways for normal and/or disease physiology. Many high-ranking hotspots were also found to be disease-associated pathogenic sites of amino acid substitution despite the lack of observable PTM in the human protein family member. Taken together, these experiments demonstrate that the functional relevance of a PTM can be predicted very effectively by neural network models, revealing a large but testable

Nezha, a novel active miniature inverted-repeat transposable element in cyanobacteria

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

Zhou Fengfeng; Tran Thao; Xu Ying

2008-01-25

Miniature inverted-repeat transposable elements (MITEs) were first identified in plants and exerted extensive proliferations throughout eukaryotic and archaeal genomes. But very few MITEs have been characterized in bacteria. We identified a novel MITE, called Nezha, in cyanobacteria Anabaena variabilis ATCC 29413 and Nostoc sp. PCC 7120. Nezha, like most previously known MITEs in other organisms, is small in size, non-coding, carrying TIR and DR signals, and of potential to form a stable RNA secondary structure, and it tends to insert into A+T-rich regions. Recent transpositions of Nezha were observed in A. variabilis ATCC 29413 and Nostoc sp. PCC 7120, respectively.more » Nezha might have proliferated recently with aid from the transposase encoded by ISNpu3-like elements. A possible horizontal transfer event of Nezha from cyanobacteria to Polaromonas JS666 is also observed.« less

Identifying Breast Cancer Oncogenes

DTIC Science & Technology

2009-10-01

study by Boehm et al. (2007) identified IKBKE as a breast cancer oncogene that cooperates with HMLE -MEKDD to replace the function of myr-AKT in...1-0767 TITLE: Identifying Breast Cancer Oncogenes ~ PRINCIPAL INVESTIGATOR: Yashaswi Shrestha...Identifying Breast Cancer Oncogenes 5a. CONTRACT NUMBER W81XWH-08-1-0767 5b. GRANT NUMBER BC083061 - PreDoc 5c. PROGRAM ELEMENT NUMBER 6

A structure-exploiting numbering algorithm for finite elements on extruded meshes, and its performance evaluation in Firedrake

NASA Astrophysics Data System (ADS)

Bercea, Gheorghe-Teodor; McRae, Andrew T. T.; Ham, David A.; Mitchell, Lawrence; Rathgeber, Florian; Nardi, Luigi; Luporini, Fabio; Kelly, Paul H. J.

2016-10-01

We present a generic algorithm for numbering and then efficiently iterating over the data values attached to an extruded mesh. An extruded mesh is formed by replicating an existing mesh, assumed to be unstructured, to form layers of prismatic cells. Applications of extruded meshes include, but are not limited to, the representation of three-dimensional high aspect ratio domains employed by geophysical finite element simulations. These meshes are structured in the extruded direction. The algorithm presented here exploits this structure to avoid the performance penalty traditionally associated with unstructured meshes. We evaluate the implementation of this algorithm in the Firedrake finite element system on a range of low compute intensity operations which constitute worst cases for data layout performance exploration. The experiments show that having structure along the extruded direction enables the cost of the indirect data accesses to be amortized after 10-20 layers as long as the underlying mesh is well ordered. We characterize the resulting spatial and temporal reuse in a representative set of both continuous-Galerkin and discontinuous-Galerkin discretizations. On meshes with realistic numbers of layers the performance achieved is between 70 and 90 % of a theoretical hardware-specific limit.

Exploration of multi-fold symmetry element-loaded superconducting radio frequency structure for reliable acceleration of low- & medium-beta ion species

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

Huang, Shichun; Geng, Rongli

2015-09-01

Reliable acceleration of low- to medium-beta proton or heavy ion species is needed for future high-current superconducting radio frequency (SRF) accelerators. Due to the high-Q nature of an SRF resonator, it is sensitive to many factors such as electron loading (from either the accelerated beam or from parasitic field emitted electrons), mechanical vibration, and liquid helium bath pressure fluctuation etc. To increase the stability against those factors, a mechanically strong and stable RF structure is desirable. Guided by this consideration, multi-fold symmetry element-loaded SRF structures (MFSEL), cylindrical tanks with multiple (n>=3) rod-shaped radial elements, are being explored. The top goalmore » of its optimization is to improve mechanical stability. A natural consequence of this structure is a lowered ratio of the peak surface electromagnetic field to the acceleration gradient as compared to the traditional spoke cavity. A disadvantage of this new structure is an increased size for a fixed resonant frequency and optimal beta. This paper describes the optimization of the electro-magnetic (EM) design and preliminary mechanical analysis for such structures.« less

Effects of biomotor structures on performance of competitive gymnastics elements in elementary school male sixth-graders.

PubMed

Delas, Suncica; Zagorac, Nebojsa; Katić, Ratko

2008-06-01

In order to identify the biomotor systems that determine performance of competitive gymnastics elements in elementary school male sixth-graders, factor structures of morphological characteristics and basic motor abilities were determined first, followed by relations of the morphological-motor system factors obtained with a set of criterion variables evaluating specific motor skills in competitive gymnastics in 110 male children aged 12 years +/- 3 months. Factor analysis of 17 morphological measures produced three morphological factors: factor of mesoectoendomorphy (general morphological factor) and factor of pronounced endomorphy, i.e. excessive adipose tissue, along with low skeleton longitudinality. Factor analysis of 16 motor variables yielded four motor factors: factor of general motoricity; factor integrating leg flexibility and arm explosiveness; factor juxtaposing body flexibility and repetitive leg strength; and factor predominantly defining leg movement frequency. Three significant canonical correlations, i.e. linear combinations, explained the association between the set of six latent variables of the morphological and basic motor system, and five variables assessing the knowledge in competitive gymnastics. The first canonical linear combination was based on the favorable and predominant impact of the general motor factor (a system integrating leg explosiveness, whole body coordination, relative arm and trunk strength, and arm movement frequency), along with unfavorable effect of morphological factors on the gymnastics elements performance, squat vault and handstand in particular The relation of the second pair of canonical factors pointed to the effects of leg flexibility and arm explosiveness on the cartwheel and backward pullover mount performance, whereas the relation of the third pair of canonical factors showed a favorable impact of the general morphological factor and leg movement frequency regulator on the forward shoulderkip from increase

Effects of biomotor structures on performance of competitive gymnastics elements in elementary school female sixth-graders.

PubMed

Delas, Suncica; Babin, Josip; Katić, Ratko

2007-12-01

In order to identify biomotor systems that determine performance of competitive gymnastics elements in elementary school female sixth-graders, factor structures of morphological characteristics and basic motor abilities were determined first, followed by relations of the morphological-motor system factors obtained with a set of criterion variables evaluating specific motor skills in competitive gymnastics in 126 female children aged 12 years +/- 3 months. Factor analysis of 17 morphological measures yielded three morphological factors: factor of mesoendomorphy and/or adipose body voluminosity; factor of longitudinal body dimensionality; and factor of transverse arm dimensionality. Factor analysis of 16 motor variables produced four motor factors: general motoricity factor (motor system); general speed factor; factor of explosive strength of throwing type (arm explosiveness); and factor of arm and leg flexibility. Three significant canonical correlations, i.e. linear combinations, explained the association between the set of seven latent variables of the morphological and basic motor system, and five variables evaluating the knowledge in competitive gymnastics. The first canonical linear combination was based on a favorable and predominant impact of the general motor factor (a system integrating whole body coordination, leg explosiveness, relative arm strength, arm movement frequency and body flexibility) on performance of gymnastics elements, cartwheel, handstand and backward pullover mount in particular, and to a lesser extent front scale and double leg pirouette for 180 degrees. The relation of the second pair of canonical factors additionally explained the role of transverse dimensionality of arm skeleton, arm flexibility and explosiveness in performing cartwheel and squat vault, whereas the relation of the third pair of canonical factors explained the unfavorable impact of adipose voluminosity on the performance of squat vault and backward pullover mount.

Effects of Contamination and Cleaning on Parachute Structural Textile Elements

NASA Technical Reports Server (NTRS)

Mollmann, Catherine

2017-01-01

Throughout their lifecycle, parachute textiles come into contact with various other substances. This contact may occur during manufacturing and repair, storage and transportation, packing, or actual use. While this interaction does not always result in negative repercussions, it may cause a loss in material strength. This paper examines the strength degradation due to several contaminants as well as the effects of cleaning agents on common parachute materials. Materials tested were: Kevlar cord and webbing, Nylon broadcloth and webbing, and Vectran cord; all of these constitute the major structural elements for CPAS (Capsule Parachute Assembly System), the parachute system for the NASA Orion Crew Module. Contaminants tested were: sewing machine oil, dried stamping ink, dirt, basting glue, Sergene, and rust. Recommendations for cleaning (or not cleaning) these materials with respect to each of the contaminants are given in this paper, as well as recommendations for future tests.

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

PubMed Central

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

2013-01-01

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

BoS: a large and diverse family of short interspersed elements (SINEs) in Brassica oleracea.

PubMed

Zhang, Xiaoyu; Wessler, Susan R

2005-05-01

Short interspersed elements (SINEs) are nonautonomous non-LTR retrotransposons that populate eukaryotic genomes. Numerous SINE families have been identified in animals, whereas only a few have been described in plants. Here we describe a new family of SINEs, named BoS, that is widespread in Brassicaceae and present at approximately 2000 copies in Brassica oleracea. In addition to sharing a modular structure and target site preference with previously described SINEs, BoS elements have several unusual features. First, the head regions of BoS RNAs can adopt a distinct hairpin-like secondary structure. Second, with 15 distinct subfamilies, BoS represents one of the most diverse SINE families described to date. Third, several of the subfamilies have a mosaic structure that has arisen through the exchange of sequences between existing subfamilies, possibly during retrotransposition. Analysis of BoS subfamilies indicate that they were active during various time periods through the evolution of Brassicaceae and that active elements may still reside in some Brassica species. As such, BoS elements may be a valuable tool as phylogenetic makers for resolving outstanding issues in the evolution of species in the Brassicaceae family.

Improving Stiffness-to-weight Ratio of Spot-welded Structures based upon Nonlinear Finite Element Modelling

NASA Astrophysics Data System (ADS)

Zhang, Shengyong

2017-07-01

Spot welding has been widely used for vehicle body construction due to its advantages of high speed and adaptability for automation. An effort to increase the stiffness-to-weight ratio of spot-welded structures is investigated based upon nonlinear finite element analysis. Topology optimization is conducted for reducing weight in the overlapping regions by choosing an appropriate topology. Three spot-welded models (lap, doubt-hat and T-shape) that approximate “typical” vehicle body components are studied for validating and illustrating the proposed method. It is concluded that removing underutilized material from overlapping regions can result in a significant increase in structural stiffness-to-weight ratio.

In situ assessment of structural timber elements of a historic building by infrared thermography and ultrasonic velocity

NASA Astrophysics Data System (ADS)

Kandemir-Yucel, A.; Tavukcuoglu, A.; Caner-Saltik, E. N.

2007-01-01

The infrared thermography (IRT) and the ultrasonic velocity measurements (UVM) promise to be particularly important to assess the state of deterioration and the adequacy of the boundary and microclimatic conditions for timber elements. These non-destructive methods supported by laboratory analyses of timber samples were conducted on a 13th century monument, Aslanhane Mosque in Ankara, Turkey. The combined interpretation of the results was done to assess the condition of structural timber elements in terms of their state of preservation, the dampness problems and the recent incompatible repairs affecting them. Results indicated that moist areas in the structure were associated with roof drainage problems and the repairs undertaken with cement-based mortars and plasters and oil-based paints. Juxtaposition of the IRT and UVM together with laboratory analyses was found to be useful to assess the soundness of timber, enhanced the accuracy and effectiveness of the survey and facilitated to build up the urgent and long-term conservation programs.

Coupled mixed-field laminate theory and finite element for smart piezoelectric composite shell structures

NASA Technical Reports Server (NTRS)

Saravanos, Dimitris A.

1996-01-01

Mechanics for the analysis of laminated composite shells with piezoelectric actuators and sensors are presented. A new mixed-field laminate theory for piezoelectric shells is formulated in curvilinear coordinates which combines single-layer assumptions for the displacements and a layerwise representation for the electric potential. The resultant coupled governing equations for curvilinear piezoelectric laminates are described. Structural mechanics are subsequently developed and an 8-node finite-element is formulated for the static and dynamic analysis of adaptive composite structures of general laminations containing piezoelectric layers. Evaluations of the method and comparisons with reported results are presented for laminated piezoelectric-composite plates, a closed cylindrical shell with a continuous piezoceramic layer and a laminated composite semi-circular cantilever shell with discrete cylindrical piezoelectric actuators and/or sensors.

Hexahedral finite element mesh coarsening using pillowing technique

DOEpatents

Staten, Matthew L [Pittsburgh, PA; Woodbury, Adam C [Provo, UT; Benzley, Steven E [Provo, UT; Shepherd, Jason F [Edgewood, NM

2012-06-05

A techniques for coarsening a hexahedral mesh is described. The technique includes identifying a coarsening region within a hexahedral mesh to be coarsened. A boundary sheet of hexahedral elements is inserted into the hexahedral mesh around the coarsening region. A column of hexahedral elements is identified within the boundary sheet. The column of hexahedral elements is collapsed to create an extraction sheet of hexahedral elements contained within the coarsening region. Then, the extraction sheet of hexahedral elements is extracted to coarsen the hexahedral mesh.

E622, a miniature, virulence-associated mobile element.

PubMed

Stavrinides, John; Kirzinger, Morgan W B; Beasley, Federico C; Guttman, David S

2012-01-01

Miniature inverted terminal repeat elements (MITEs) are nonautonomous mobile elements that have a significant impact on bacterial evolution. Here we characterize E622, a 611-bp virulence-associated MITE from Pseudomonas syringae, which contains no coding region but has almost perfect 168-bp inverted repeats. Using an antibiotic coupling assay, we show that E622 is transposable and can mobilize an antibiotic resistance gene contained between its borders. Its predicted parent element, designated TnE622, has a typical transposon structure with a three-gene operon, consisting of resolvase, integrase, and exeA-like genes, which is bounded by the same terminal inverted repeats as E622. A broader genome level survey of the E622/TnE622 inverted repeats identified homologs in Pseudomonas, Salmonella, Shewanella, Erwinia, Pantoea, and the cyanobacteria Nostoc and Cyanothece, many of which appear to encompass known virulence genes, including genes encoding toxins, enzymes, and type III secreted effectors. Its association with niche-specific genetic determinants, along with its persistence and evolutionary diversification, indicates that this mobile element family has played a prominent role in the evolution of many agriculturally and clinically relevant pathogenic bacteria.

Structural and Practical Identifiability Analysis of Zika Epidemiological Models.

PubMed

Tuncer, Necibe; Marctheva, Maia; LaBarre, Brian; Payoute, Sabrina

2018-06-13

The Zika virus (ZIKV) epidemic has caused an ongoing threat to global health security and spurred new investigations of the virus. Use of epidemiological models for arbovirus diseases can be a powerful tool to assist in prevention and control of the emerging disease. In this article, we introduce six models of ZIKV, beginning with a general vector-borne model and gradually including different transmission routes of ZIKV. These epidemiological models use various combinations of disease transmission (vector and direct) and infectious classes (asymptomatic and pregnant), with addition to loss of immunity being included. The disease-induced death rate is omitted from the models. We test the structural and practical identifiability of the models to find whether unknown model parameters can uniquely be determined. The models were fit to obtain time-series data of cumulative incidences and pregnant infections from the Florida Department of Health Daily Zika Update Reports. The average relative estimation errors (AREs) were computed from the Monte Carlo simulations to further analyze the identifiability of the models. We show that direct transmission rates are not practically identifiable; however, fixed recovery rates improve identifiability overall. We found ARE is low for each model (only slightly higher for those that account for a pregnant class) and help to confirm a reproduction number greater than one at the start of the Florida epidemic. Basic reproduction number, [Formula: see text], is an epidemiologically important threshold value which gives the number of secondary cases generated by one infected individual in a totally susceptible population in duration of infectiousness. Elasticity of the reproduction numbers suggests that the mosquito-to-human ratio, mosquito life span and biting rate have the greatest potential for reducing the reproduction number of Zika, and therefore, corresponding control measures need to be focused on.

Imprinting high-gradient topographical structures onto optical surfaces using magnetorheological finishing: manufacturing corrective optical elements for high-power laser applications.

PubMed

Menapace, Joseph A; Ehrmann, Paul E; Bayramian, Andrew J; Bullington, Amber; Di Nicola, Jean-Michel G; Haefner, Constantin; Jarboe, Jeffrey; Marshall, Christopher; Schaffers, Kathleen I; Smith, Cal

2016-07-01

Corrective optical elements form an important part of high-precision optical systems. We have developed a method to manufacture high-gradient corrective optical elements for high-power laser systems using deterministic magnetorheological finishing (MRF) imprinting technology. Several process factors need to be considered for polishing ultraprecise topographical structures onto optical surfaces using MRF. They include proper selection of MRF removal function and wheel sizes, detailed MRF tool and interferometry alignment, and optimized MRF polishing schedules. Dependable interferometry also is a key factor in high-gradient component manufacture. A wavefront attenuating cell, which enables reliable measurement of gradients beyond what is attainable using conventional interferometry, is discussed. The results of MRF imprinting a 23 μm deep structure containing gradients over 1.6 μm / mm onto a fused-silica window are presented as an example of the technique's capabilities. This high-gradient element serves as a thermal correction plate in the high-repetition-rate advanced petawatt laser system currently being built at Lawrence Livermore National Laboratory.

Analysis of wave motion in one-dimensional structures through fast-Fourier-transform-based wavelet finite element method

NASA Astrophysics Data System (ADS)

Shen, Wei; Li, Dongsheng; Zhang, Shuaifang; Ou, Jinping

2017-07-01

This paper presents a hybrid method that combines the B-spline wavelet on the interval (BSWI) finite element method and spectral analysis based on fast Fourier transform (FFT) to study wave propagation in One-Dimensional (1D) structures. BSWI scaling functions are utilized to approximate the theoretical wave solution in the spatial domain and construct a high-accuracy dynamic stiffness matrix. Dynamic reduction on element level is applied to eliminate the interior degrees of freedom of BSWI elements and substantially reduce the size of the system matrix. The dynamic equations of the system are then transformed and solved in the frequency domain through FFT-based spectral analysis which is especially suitable for parallel computation. A comparative analysis of four different finite element methods is conducted to demonstrate the validity and efficiency of the proposed method when utilized in high-frequency wave problems. Other numerical examples are utilized to simulate the influence of crack and delamination on wave propagation in 1D rods and beams. Finally, the errors caused by FFT and their corresponding solutions are presented.

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

PubMed