Voroprot: an interactive tool for the analysis and visualization of complex geometric features of protein structure.

PubMed

Olechnovic, Kliment; Margelevicius, Mindaugas; Venclovas, Ceslovas

2011-03-01

We present Voroprot, an interactive cross-platform software tool that provides a unique set of capabilities for exploring geometric features of protein structure. Voroprot allows the construction and visualization of the Apollonius diagram (also known as the additively weighted Voronoi diagram), the Apollonius graph, protein alpha shapes, interatomic contact surfaces, solvent accessible surfaces, pockets and cavities inside protein structure. Voroprot is available for Windows, Linux and Mac OS X operating systems and can be downloaded from http://www.ibt.lt/bioinformatics/voroprot/.

How Structure Defines Affinity in Protein-Protein Interactions

PubMed Central

Erijman, Ariel; Rosenthal, Eran; Shifman, Julia M.

2014-01-01

Protein-protein interactions (PPI) in nature are conveyed by a multitude of binding modes involving various surfaces, secondary structure elements and intermolecular interactions. This diversity results in PPI binding affinities that span more than nine orders of magnitude. Several early studies attempted to correlate PPI binding affinities to various structure-derived features with limited success. The growing number of high-resolution structures, the appearance of more precise methods for measuring binding affinities and the development of new computational algorithms enable more thorough investigations in this direction. Here, we use a large dataset of PPI structures with the documented binding affinities to calculate a number of structure-based features that could potentially define binding energetics. We explore how well each calculated biophysical feature alone correlates with binding affinity and determine the features that could be used to distinguish between high-, medium- and low- affinity PPIs. Furthermore, we test how various combinations of features could be applied to predict binding affinity and observe a slow improvement in correlation as more features are incorporated into the equation. In addition, we observe a considerable improvement in predictions if we exclude from our analysis low-resolution and NMR structures, revealing the importance of capturing exact intermolecular interactions in our calculations. Our analysis should facilitate prediction of new interactions on the genome scale, better characterization of signaling networks and design of novel binding partners for various target proteins. PMID:25329579

The Gemini NICI Planet-Finding Campaign: asymmetries in the HD 141569 disc

NASA Astrophysics Data System (ADS)

Biller, Beth A.; Liu, Michael C.; Rice, Ken; Wahhaj, Zahed; Nielsen, Eric; Hayward, Thomas; Kuchner, Marc J.; Close, Laird M.; Chun, Mark; Ftaclas, Christ; Toomey, Douglas W.

2015-07-01

We report here the highest resolution near-IR imaging to date of the HD 141569A disc taken as part of the NICI (near infrared coronagraphic imager) Science Campaign. We recover four main features in the NICI images of the HD 141569 disc discovered in previous Hubble Space Telescope (HST) imaging: (1) an inner ring/spiral feature. Once deprojected, this feature does not appear circular. (2) An outer ring which is considerably brighter on the western side compared to the eastern side, but looks fairly circular in the deprojected image. (3) An additional arc-like feature between the inner and outer ring only evident on the east side. In the deprojected image, this feature appears to complete the circle of the west side inner ring and (4) an evacuated cavity from 175 au inwards. Compared to the previous HST imaging with relatively large coronagraphic inner working angles (IWA), the NICI coronagraph allows imaging down to an IWA of 0.3 arcsec. Thus, the inner edge of the inner ring/spiral feature is well resolved and we do not find any additional disc structures within 175 au. We note some additional asymmetries in this system. Specifically, while the outer ring structure looks circular in this deprojection, the inner bright ring looks rather elliptical. This suggests that a single deprojection angle is not appropriate for this system and that there may be an offset in inclination between the two ring/spiral features. We find an offset of 4 ± 2 au between the inner ring and the star centre, potentially pointing to unseen inner companions.

Automated identification of protein-ligand interaction features using Inductive Logic Programming: a hexose binding case study

PubMed Central

2012-01-01

Background There is a need for automated methods to learn general features of the interactions of a ligand class with its diverse set of protein receptors. An appropriate machine learning approach is Inductive Logic Programming (ILP), which automatically generates comprehensible rules in addition to prediction. The development of ILP systems which can learn rules of the complexity required for studies on protein structure remains a challenge. In this work we use a new ILP system, ProGolem, and demonstrate its performance on learning features of hexose-protein interactions. Results The rules induced by ProGolem detect interactions mediated by aromatics and by planar-polar residues, in addition to less common features such as the aromatic sandwich. The rules also reveal a previously unreported dependency for residues cys and leu. They also specify interactions involving aromatic and hydrogen bonding residues. This paper shows that Inductive Logic Programming implemented in ProGolem can derive rules giving structural features of protein/ligand interactions. Several of these rules are consistent with descriptions in the literature. Conclusions In addition to confirming literature results, ProGolem’s model has a 10-fold cross-validated predictive accuracy that is superior, at the 95% confidence level, to another ILP system previously used to study protein/hexose interactions and is comparable with state-of-the-art statistical learners. PMID:22783946

regSNPs-splicing: a tool for prioritizing synonymous single-nucleotide substitution.

PubMed

Zhang, Xinjun; Li, Meng; Lin, Hai; Rao, Xi; Feng, Weixing; Yang, Yuedong; Mort, Matthew; Cooper, David N; Wang, Yue; Wang, Yadong; Wells, Clark; Zhou, Yaoqi; Liu, Yunlong

2017-09-01

While synonymous single-nucleotide variants (sSNVs) have largely been unstudied, since they do not alter protein sequence, mounting evidence suggests that they may affect RNA conformation, splicing, and the stability of nascent-mRNAs to promote various diseases. Accurately prioritizing deleterious sSNVs from a pool of neutral ones can significantly improve our ability of selecting functional genetic variants identified from various genome-sequencing projects, and, therefore, advance our understanding of disease etiology. In this study, we develop a computational algorithm to prioritize sSNVs based on their impact on mRNA splicing and protein function. In addition to genomic features that potentially affect splicing regulation, our proposed algorithm also includes dozens structural features that characterize the functions of alternatively spliced exons on protein function. Our systematical evaluation on thousands of sSNVs suggests that several structural features, including intrinsic disorder protein scores, solvent accessible surface areas, protein secondary structures, and known and predicted protein family domains, show significant differences between disease-causing and neutral sSNVs. Our result suggests that the protein structure features offer an added dimension of information while distinguishing disease-causing and neutral synonymous variants. The inclusion of structural features increases the predictive accuracy for functional sSNV prioritization.

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

Baghram, Shant; Abolhasani, Ali Akbar; Firouzjahi, Hassan

We study the predictions of anomalous inflationary models on the abundance of structures in large scale structure observations. The anomalous features encoded in primordial curvature perturbation power spectrum are (a): localized feature in momentum space, (b): hemispherical asymmetry and (c): statistical anisotropies. We present a model-independent expression relating the number density of structures to the changes in the matter density variance. Models with localized feature can alleviate the tension between observations and numerical simulations of cold dark matter structures on galactic scales as a possible solution to the missing satellite problem. In models with hemispherical asymmetry we show that themore » abundance of structures becomes asymmetric depending on the direction of observation to sky. In addition, we study the effects of scale-dependent dipole amplitude on the abundance of structures. Using the quasars data and adopting the power-law scaling k{sup n{sub A}-1} for the amplitude of dipole we find the upper bound n{sub A} < 0.6 for the spectral index of the dipole asymmetry. In all cases there is a critical mass scale M{sub c} in which for M M{sub c}) the enhancement in variance induced from anomalous feature decreases (increases) the abundance of dark matter structures in Universe.« less

Structural anomalies in undoped Gallium Arsenide observed in high resolution diffraction imaging with monochromatic synchrotron radiation

NASA Technical Reports Server (NTRS)

Steiner, B.; Kuriyama, M.; Dobbyn, R. C.; Laor, U.; Larson, D.; Brown, M.

1988-01-01

Novel, streak-like disruption features restricted to the plane of diffraction have recently been observed in images obtained by synchrotron radiation diffraction from undoped, semi-insulating gallium arsenide crystals. These features were identified as ensembles of very thin platelets or interfaces lying in (110) planes, and a structural model consisting of antiphase domain boundaries was proposed. We report here the other principal features observed in high resolution monochromatic synchrotron radiation diffraction images: (quasi) cellular structure; linear, very low-angle subgrain boundaries in (110) directions, and surface stripes in a (110) direction. In addition, we report systematic differences in the acceptance angle for images involving various diffraction vectors. When these observations are considered together, a unifying picture emerges. The presence of ensembles of thin (110) antiphase platelet regions or boundaries is generally consistent not only with the streak-like diffraction features but with the other features reported here as well. For the formation of such regions we propose two mechanisms, operating in parallel, that appear to be consistent with the various defect features observed by a variety of techniques.

Structural anomalies in undoped gallium arsenide observed in high-resolution diffraction imaging with monochromatic synchrotron radiation

NASA Technical Reports Server (NTRS)

Steiner, B.; Kuriyama, M.; Dobbyn, R. C.; Laor, U.; Larson, D.

1989-01-01

Novel, streak-like disruption features restricted to the plane of diffraction have recently been observed in images obtained by synchrotron radiation diffraction from undoped, semi-insulating gallium arsenide crystals. These features were identified as ensembles of very thin platelets or interfaces lying in (110) planes, and a structural model consisting of antiphase domain boundaries was proposed. We report here the other principal features observed in high resolution monochromatic synchrotron radiation diffraction images: (quasi) cellular structure; linear, very low-angle subgrain boundaries in (110) directions, and surface stripes in a (110) direction. In addition, we report systematic differences in the acceptance angle for images involving various diffraction vectors. When these observations are considered together, a unifying picture emerges. The presence of ensembles of thin (110) antiphase platelet regions or boundaries is generally consistent not only with the streak-like diffraction features but with the other features reported here as well. For the formation of such regions we propose two mechanisms, operating in parallel, that appear to be consistent with the various defect features observed by a variety of techniques.

Robust Learning of High-dimensional Biological Networks with Bayesian Networks

NASA Astrophysics Data System (ADS)

Nägele, Andreas; Dejori, Mathäus; Stetter, Martin

Structure learning of Bayesian networks applied to gene expression data has become a potentially useful method to estimate interactions between genes. However, the NP-hardness of Bayesian network structure learning renders the reconstruction of the full genetic network with thousands of genes unfeasible. Consequently, the maximal network size is usually restricted dramatically to a small set of genes (corresponding with variables in the Bayesian network). Although this feature reduction step makes structure learning computationally tractable, on the downside, the learned structure might be adversely affected due to the introduction of missing genes. Additionally, gene expression data are usually very sparse with respect to the number of samples, i.e., the number of genes is much greater than the number of different observations. Given these problems, learning robust network features from microarray data is a challenging task. This chapter presents several approaches tackling the robustness issue in order to obtain a more reliable estimation of learned network features.

Guided wave crack detection and size estimation in stiffened structures

NASA Astrophysics Data System (ADS)

Bhuiyan, Md Yeasin; Faisal Haider, Mohammad; Poddar, Banibrata; Giurgiutiu, Victor

2018-03-01

Structural health monitoring (SHM) and nondestructive evaluation (NDE) deals with the nondestructive inspection of defects, corrosion, leaks in engineering structures by using ultrasonic guided waves. In the past, simplistic structures were often considered for analyzing the guided wave interaction with the defects. In this study, we focused on more realistic and relatively complicated structure for detecting any defect by using a non-contact sensing approach. A plate with a stiffener was considered for analyzing the guided wave interactions. Piezoelectric wafer active transducers were used to produce excitation in the structures. The excitation generated the multimodal guided waves (aka Lamb waves) that propagate in the plate with stiffener. The presence of stiffener in the plate generated scattered waves. The direct wave and the additional scattered waves from the stiffener were experimentally recorded and studied. These waves were considered as a pristine case in this research. A fine horizontal semi-circular crack was manufactured by using electric discharge machining in the same stiffener. The presence of crack in the stiffener produces additional scattered waves as well as trapped waves. These scattered waves and trapped wave modes from the cracked stiffener were experimentally measured by using a scanning laser Doppler vibrometer (SLDV). These waves were analyzed and compared with that from the pristine case. The analyses suggested that both size and shape of the horizontal crack may be predicted from the pattern of the scattered waves. Different features (reflection, transmission, and mode-conversion) of the scattered wave signals are analyzed. We found direct transmission feature for incident A0 wave mode and modeconversion feature for incident S0 mode are most suitable for detecting the crack in the stiffener. The reflection feature may give a better idea of sizing the crack.

Semantic data association for planar features in outdoor 6D-SLAM using lidar

NASA Astrophysics Data System (ADS)

Ulas, C.; Temeltas, H.

2013-05-01

Simultaneous Localization and Mapping (SLAM) is a fundamental problem of the autonomous systems in GPS (Global Navigation System) denied environments. The traditional probabilistic SLAM methods uses point features as landmarks and hold all the feature positions in their state vector in addition to the robot pose. The bottleneck of the point-feature based SLAM methods is the data association problem, which are mostly based on a statistical measure. The data association performance is very critical for a robust SLAM method since all the filtering strategies are applied after a known correspondence. For point-features, two different but very close landmarks in the same scene might be confused while giving the correspondence decision when their positions and error covariance matrix are solely taking into account. Instead of using the point features, planar features can be considered as an alternative landmark model in the SLAM problem to be able to provide a more consistent data association. Planes contain rich information for the solution of the data association problem and can be distinguished easily with respect to point features. In addition, planar maps are very compact since an environment has only very limited number of planar structures. The planar features does not have to be large structures like building wall or roofs; the small plane segments can also be used as landmarks like billboards, traffic posts and some part of the bridges in urban areas. In this paper, a probabilistic plane-feature extraction method from 3DLiDAR data and the data association based on the extracted semantic information of the planar features is introduced. The experimental results show that the semantic data association provides very satisfactory result in outdoor 6D-SLAM.

Features and Historical Aspects of the Philippines Educational System

ERIC Educational Resources Information Center

Musa, Sajid; Ziatdinov, Rushan

2012-01-01

This article deals with the features of the Philippine educational system. Additionally, brief and concise information will be given on how the educational system came into existence, the organization and the structure of the system itself. This paper also tackles the obstacles and problems observed in the past and up to the present, and gives…

Structures composing protein domains.

PubMed

Kubrycht, Jaroslav; Sigler, Karel; Souček, Pavel; Hudeček, Jiří

2013-08-01

This review summarizes available data concerning intradomain structures (IS) such as functionally important amino acid residues, short linear motifs, conserved or disordered regions, peptide repeats, broadly occurring secondary structures or folds, etc. IS form structural features (units or elements) necessary for interactions with proteins or non-peptidic ligands, enzyme reactions and some structural properties of proteins. These features have often been related to a single structural level (e.g. primary structure) mostly requiring certain structural context of other levels (e.g. secondary structures or supersecondary folds) as follows also from some examples reported or demonstrated here. In addition, we deal with some functionally important dynamic properties of IS (e.g. flexibility and different forms of accessibility), and more special dynamic changes of IS during enzyme reactions and allosteric regulation. Selected notes concern also some experimental methods, still more necessary tools of bioinformatic processing and clinically interesting relationships. Copyright © 2013 Elsevier Masson SAS. All rights reserved.

Changes in quantitative 3D shape features of the optic nerve head associated with age

NASA Astrophysics Data System (ADS)

Christopher, Mark; Tang, Li; Fingert, John H.; Scheetz, Todd E.; Abramoff, Michael D.

2013-02-01

Optic nerve head (ONH) structure is an important biological feature of the eye used by clinicians to diagnose and monitor progression of diseases such as glaucoma. ONH structure is commonly examined using stereo fundus imaging or optical coherence tomography. Stereo fundus imaging provides stereo views of the ONH that retain 3D information useful for characterizing structure. In order to quantify 3D ONH structure, we applied a stereo correspondence algorithm to a set of stereo fundus images. Using these quantitative 3D ONH structure measurements, eigen structures were derived using principal component analysis from stereo images of 565 subjects from the Ocular Hypertension Treatment Study (OHTS). To evaluate the usefulness of the eigen structures, we explored associations with the demographic variables age, gender, and race. Using regression analysis, the eigen structures were found to have significant (p < 0.05) associations with both age and race after Bonferroni correction. In addition, classifiers were constructed to predict the demographic variables based solely on the eigen structures. These classifiers achieved an area under receiver operating characteristic curve of 0.62 in predicting a binary age variable, 0.52 in predicting gender, and 0.67 in predicting race. The use of objective, quantitative features or eigen structures can reveal hidden relationships between ONH structure and demographics. The use of these features could similarly allow specific aspects of ONH structure to be isolated and associated with the diagnosis of glaucoma, disease progression and outcomes, and genetic factors.

Effects of lung disease on the three-dimensional structure and air flow pattern in the human airway tree

NASA Astrophysics Data System (ADS)

van de Moortele, Tristan; Nemes, Andras; Wendt, Christine; Coletti, Filippo

2016-11-01

The morphological features of the airway tree directly affect the air flow features during breathing, which determines the gas exchange and inhaled particle transport. Lung disease, Chronic Obstructive Pulmonary Disease (COPD) in this study, affects the structural features of the lungs, which in turn negatively affects the air flow through the airways. Here bronchial tree air volume geometries are segmented from Computed Tomography (CT) scans of healthy and diseased subjects. Geometrical analysis of the airway centerlines and corresponding cross-sectional areas provide insight into the specific effects of COPD on the airway structure. These geometries are also used to 3D print anatomically accurate, patient specific flow models. Three-component, three-dimensional velocity fields within these models are acquired using Magnetic Resonance Imaging (MRI). The three-dimensional flow fields provide insight into the change in flow patterns and features. Additionally, particle trajectories are determined using the velocity fields, to identify the fate of therapeutic and harmful inhaled aerosols. Correlation between disease-specific and patient-specific anatomical features with dysfunctional airflow patterns can be achieved by combining geometrical and flow analysis.

17 CFR 229.1113 - (Item 1113) Structure of the transaction.

Code of Federal Regulations, 2010 CFR

2010-04-01

... other structural features designed to enhance credit, facilitate the timely payment of monies due on the... and invested. Also describe the length of time cash will be held pending distributions to security... connection with these securitizations. (e) Master trusts. If one or more additional series or classes have...

Supportability of a High-Yield-Stress Slurry in a New Stereolithography-Based Ceramic Fabrication Process

NASA Astrophysics Data System (ADS)

He, Li; Song, Xuan

2018-03-01

In recent years, ceramic fabrication using stereolithography (SLA) has gained in popularity because of its high accuracy and density that can be achieved in the final part of production. One of the key challenges in ceramic SLA is that support structures are required for building overhanging features, whereas removing these support structures without damaging the components is difficult. In this research, a suspension-enclosing projection-stereolithography process is developed to overcome this challenge. This process uses a high-yield-stress ceramic slurry as the feedstock material and exploits the elastic force of the material to support overhanging features without the need for building additional support structures. Ceramic slurries with different solid loadings are studied to identify the rheological properties most suitable for supporting overhanging features. An analytical model of a double doctor-blade module is established to obtain uniform and thin recoating layers from a high-yield-stress slurry. Several test cases highlight the feasibility of using a high-yield-stress slurry to support overhanging features in SLA.

Supplementary Microstructural Features Induced During Laser Surface Melting of Thermally Sprayed Inconel 625 Coatings

NASA Astrophysics Data System (ADS)

Ahmed, Nauman; Voisey, K. T.; McCartney, D. G.

2014-02-01

Laser surface melting of thermally sprayed coatings has the potential to enhance their corrosion properties by incorporating favorable microstructural changes. Besides homogenizing the as-sprayed structure, laser melting may induce certain microstructural modifications (i.e., supplementary features) in addition to those that directly improve the corrosion performance. Such features, being a direct result of the laser treatment process, are described in this paper which is part of a broader study in which high velocity oxy-fuel sprayed Inconel 625 coatings on mild-steel substrates were treated with a diode laser and the modified microstructure characterized using optical and scanning electron microscopy and x-ray diffraction. The laser treated coating features several different zones, including a region with a microstructure in which there is a continuous columnar dendritic structure through a network of retained oxide stringers.

Dermoscopy of accessory nipples in authors’ own study

PubMed Central

Szymszal, Jan; Silny, Wojciech

2014-01-01

Introduction The accessory nipple (AN) is characterised by its network-like structures, which may suggest the diagnosis of a melanocytic lesion. The knowledge about additional dermoscopic features of AN may greatly minimise the risk of unnecessary surgical excisions. Aim To analyse and present different clinical and dermoscopic forms, in which the AN may appear. Material and methods Ninety AN with dermoscopic features were evaluated in the study, detected in 14 patients between the years 2008 and 2014. Results The most common dermoscopic features of the AN were central, scar-like areas (15/19) and peripheral network-like structures (12/19). A number of cleft-like appearances (8/19) and central network-like structures (7/19) had also been observed. Moreover, among the dermoscopic features, white cobblestone-like structures (7/19), a central round dimpling with a plug (6/19) and fisheye-like structures resembling comedo-like openings (9/19) have all also been noted. There is a statistical significance in the occurrence of white cobblestone-like structures with central network-like structures (Fisher's exact test p = 0.0449). The presence of peripheral network-like structures with the occurrence of central scar-like areas was statistically highly significant (p = 0.0091). The central round dimpling was never observed alongside any central network-like structures in any of the lesions (p = 0.0436). Conclusions Accessory nipples are most commonly characterised by the occurrence of a peripheral network-like structure accompanied by the presence of a scar-like area. PMID:25097482

Structural health monitoring of plates with surface features using guided ultrasonic waves

NASA Astrophysics Data System (ADS)

Fromme, P.

2009-03-01

Distributed array systems for guided ultrasonic waves offer an efficient way for the long-term monitoring of the structural integrity of large plate-like structures. The measurement concept involving baseline subtraction has been demonstrated under laboratory conditions. For the application to real technical structures it needs to be shown that the methodology works equally well in the presence of structural and surface features. Problems employing this structural health monitoring concept can occur due to the presence of additional changes in the signal reflected at undamaged parts of the structure. The influence of the signal processing parameters and transducer placement on the damage detection and localization accuracy is discussed. The use of permanently attached, distributed sensors for the A0 Lamb wave mode has been investigated. Results are presented using experimental data obtained from laboratory measurements and Finite Element simulated signals for a large steel plate with a welded stiffener.

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

Critical Song Features for Auditory Pattern Recognition in Crickets

PubMed Central

Meckenhäuser, Gundula; Hennig, R. Matthias; Nawrot, Martin P.

2013-01-01

Many different invertebrate and vertebrate species use acoustic communication for pair formation. In the cricket Gryllus bimaculatus, females recognize their species-specific calling song and localize singing males by positive phonotaxis. The song pattern of males has a clear structure consisting of brief and regular pulses that are grouped into repetitive chirps. Information is thus present on a short and a long time scale. Here, we ask which structural features of the song critically determine the phonotactic performance. To this end we employed artificial neural networks to analyze a large body of behavioral data that measured females’ phonotactic behavior under systematic variation of artificially generated song patterns. In a first step we used four non-redundant descriptive temporal features to predict the female response. The model prediction showed a high correlation with the experimental results. We used this behavioral model to explore the integration of the two different time scales. Our result suggested that only an attractive pulse structure in combination with an attractive chirp structure reliably induced phonotactic behavior to signals. In a further step we investigated all feature sets, each one consisting of a different combination of eight proposed temporal features. We identified feature sets of size two, three, and four that achieve highest prediction power by using the pulse period from the short time scale plus additional information from the long time scale. PMID:23437054

Feature engineering for MEDLINE citation categorization with MeSH.

PubMed

Jimeno Yepes, Antonio Jose; Plaza, Laura; Carrillo-de-Albornoz, Jorge; Mork, James G; Aronson, Alan R

2015-04-08

Research in biomedical text categorization has mostly used the bag-of-words representation. Other more sophisticated representations of text based on syntactic, semantic and argumentative properties have been less studied. In this paper, we evaluate the impact of different text representations of biomedical texts as features for reproducing the MeSH annotations of some of the most frequent MeSH headings. In addition to unigrams and bigrams, these features include noun phrases, citation meta-data, citation structure, and semantic annotation of the citations. Traditional features like unigrams and bigrams exhibit strong performance compared to other feature sets. Little or no improvement is obtained when using meta-data or citation structure. Noun phrases are too sparse and thus have lower performance compared to more traditional features. Conceptual annotation of the texts by MetaMap shows similar performance compared to unigrams, but adding concepts from the UMLS taxonomy does not improve the performance of using only mapped concepts. The combination of all the features performs largely better than any individual feature set considered. In addition, this combination improves the performance of a state-of-the-art MeSH indexer. Concerning the machine learning algorithms, we find that those that are more resilient to class imbalance largely obtain better performance. We conclude that even though traditional features such as unigrams and bigrams have strong performance compared to other features, it is possible to combine them to effectively improve the performance of the bag-of-words representation. We have also found that the combination of the learning algorithm and feature sets has an influence in the overall performance of the system. Moreover, using learning algorithms resilient to class imbalance largely improves performance. However, when using a large set of features, consideration needs to be taken with algorithms due to the risk of over-fitting. Specific combinations of learning algorithms and features for individual MeSH headings could further increase the performance of an indexing system.

Impact of the rate of the additive process of forming a heavy structure deforming in creep on the development of its technological stresses

NASA Astrophysics Data System (ADS)

Parshin, Dmitry A.

2018-05-01

The additive process of forming a semicircular arched structure by means of layer-by-layer addition of material to its inner surface is simulated. The impact of this process running mode on the development of the technological stresses fields in the structure being formed under the action of gravity under properties of the material creep and aging is examined. In the framework of the linear mechanics of accreted solids a mathematical model of the process under study is offered and numerical experiments are conducted. It is shown that the stress-strain state of the additively formed heavy objects decisively depends on their formation mode. Various practically important trends and features of this dependence are studied.

Diamond field emitter array cathodes and possibilities for employing additive manufacturing for dielectric laser accelerating structures

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

Simakov, Evgenya Ivanovna; Andrews, Heather Lynn; Herman, Matthew Joseph

2016-09-20

These are slides for a presentation at Stanford University. The outline is as follows: Motivation: customers for compact accelerators, LANL's technologies for laser acceleration, DFEA cathodes, and additive manufacturing of micron-size structures. Among the stated conclusions are the following: preliminary study identified DFEA cathodes as promising sources for DLAs--high beam current and small emittance; additive manufacturing with Nanoscribe Professional GT can produce structures with the right scale features for a DLA operating at micron wavelengths (fabrication tolerances need to be studied, DLAs require new materials). Future plans include DLA experiment with a beam produced by the DFEA cathode with fieldmore » emission, demonstration of photoemission from DFEAs, and new structures to print and test.« less

A combined experimental and in silico characterization to highlight additional structural features and properties of a potentially new drug

NASA Astrophysics Data System (ADS)

Bastos, Isadora T. S.; Costa, Fanny N.; Silva, Tiago F.; Barreiro, Eliezer J.; Lima, Lídia M.; Braz, Delson; Lombardo, Giuseppe M.; Punzo, Francesco; Ferreira, Fabio F.; Barroso, Regina C.

2017-10-01

LASSBio-1755 is a new cycloalkyl-N-acylhydrazone parent compound designed for the development of derivatives with antinociceptive and anti-inflammatory activities. Although single crystal X-ray diffraction has been considered as the golden standard in structure determination, we successfully used X-ray powder diffraction data in the structural determination of new synthesized compounds, in order to overcome the bottle-neck due to the difficulties experienced in harvesting good quality single crystals of the compounds. We therefore unequivocally assigned the relative configuration (E) to the imine double bond and a s-cis conformation of the amide function of the N-acylhydrazone compound. These features are confirmed by a computational analysis performed on the basis of molecular dynamics calculations, which are extended not only to the structural characteristics but also to the analysis of the anisotropic atomic displacement parameters, a further information - missed in a typical powder diffraction analysis. The so inferred data were used to perform additional cycles of refinement and eventually generate a new cif file with additional physical information. Furthermore, crystal morphology prediction was performed, which is in agreement with the experimental images acquired by scanning electron microscopy, thus providing useful information on possible alternative paths for better crystallization strategies.

Highly Shocked Low Density Sedimentary Rocks from the Haughton Impact Structure, Devon Island, Nunavut, Canada

NASA Technical Reports Server (NTRS)

Osinski, G. R.; Spray, J. G.

2001-01-01

We present the preliminary results of a detailed investigation of the shock effects in highly shocked, low density sedimentary rocks from the Haughton impact structure. We suggest that some textural features can be explained by carbonate-silicate immiscibility. Additional information is contained in the original extended abstract.

Incidental and Context-Responsive Activation of Structure- and Function-Based Action Features during Object Identification

ERIC Educational Resources Information Center

Lee, Chia-lin; Middleton, Erica; Mirman, Daniel; Kalenine, Solene; Buxbaum, Laurel J.

2013-01-01

Previous studies suggest that action representations are activated during object processing, even when task-irrelevant. In addition, there is evidence that lexical-semantic context may affect such activation during object processing. Finally, prior work from our laboratory and others indicates that function-based ("use") and structure-based…

Toxicological features of maleilated polyflavonoids from Pinus radiata (D. Don.) as potential functional additives for biomaterials design.

PubMed

García, Danny E; Medina, Paulina A; Zúñiga, Valentina I

2017-11-01

Polyflavonoids from Pinus radiata (D. Don.) are an abundant natural oligomers highly desirable as renewable chemicals. However, structural modification of polyflavonoids is a viable strategy in order to use such polyphenols as macrobuilding-blocks for biomaterial design. Polyflavonoids were esterified with three five-member cyclic anhydrides (maleic, itaconic, and citraconic) at 20 °C during 24 h in order to diversify physicochemical-, and biological-properties for agricultural, and food-packaging applications. In addition, the influence of the chemical modification, as well as the chemical structure of the grafting on toxicological features was evaluated. Structural features of derivatives were analyzed by spectroscopy (FT-IR and 1 H-NMR), and the degree of substitution was calculated. Toxicological profile was assessed by using three target species in a wide range of concentration (0.01-100 mgL - 1 ). Effect of polyflavonoids on the growth rate (Selenastrum capricornutum), mortality (Daphnia magna), and germination and radicle length (Lactuca sativa) was determined. Chemical modification affects the toxicological profile on the derivatives in a high extent. Results described remarkable differences in function of the target specie. The bioassays indicate differences of the polyflavonoids toxicological profile associated to the chemical structure of the grafting. Results allowed conclude that polyflavonoids from pine bark show slight toxic properties. Copyright © 2017 Elsevier Ltd. All rights reserved.

Detection of communities with Naming Game-based methods

PubMed Central

Ribeiro, Carlos Henrique Costa

2017-01-01

Complex networks are often organized in groups or communities of agents that share the same features and/or functions, and this structural organization is built naturally with the formation of the system. In social networks, we argue that the dynamic of linguistic interactions of agreement among people can be a crucial factor in generating this community structure, given that sharing opinions with another person bounds them together, and disagreeing constantly would probably weaken the relationship. We present here a computational model of opinion exchange that uncovers the community structure of a network. Our aim is not to present a new community detection method proper, but to show how a model of social communication dynamics can reveal the (simple and overlapping) community structure in an emergent way. Our model is based on a standard Naming Game, but takes into consideration three social features: trust, uncertainty and opinion preference, that are built over time as agents communicate among themselves. We show that the separate addition of each social feature in the Naming Game results in gradual improvements with respect to community detection. In addition, the resulting uncertainty and trust values classify nodes and edges according to role and position in the network. Also, our model has shown a degree of accuracy both for non-overlapping and overlapping communities that are comparable with most algorithms specifically designed for topological community detection. PMID:28797097

Properties of nanostructures obtained by anodization of aluminum in phosphoric acid at moderate potentials

NASA Astrophysics Data System (ADS)

Zaraska, L.; Sulka, G. D.; Jaskuła, M.

2009-01-01

The influence of the process duration, anodizing potential and methanol addition on the structural features of porous anodic alumina formed in a 0.3 M H3PO4 solutions by twostep self-organized anodizing was investigated for potentials ranging from 100 to 170 V. The structural features of porous structures including pore diameter and interpore distance were evaluated from FE-SEM top-view images for samples anodized in the presence and absence of methanol. For the highest studied anodizing time and methanol volume fraction, an excellent agreement between experimental values of the interpore distance and theoretical predictions was observed. The pore arrangement regularity was analyzed for various electrolyte compositions and anodizing potentials. It was found that the regularity ratio of porous alumina increases linearly with increasing anodizing potential and time. The addition of methanol improves the quality of nanostructures and especially better uniformity of pore sizes is observed in the presence of the highest studied methanol content.

Road map to adaptive optimal control. [jet engine control

NASA Technical Reports Server (NTRS)

Boyer, R.

1980-01-01

A building block control structure leading toward adaptive, optimal control for jet engines is developed. This approach simplifies the addition of new features and allows for easier checkout of the control by providing a baseline system for comparison. Also, it is possible to eliminate certain features that do not have payoff by being selective in the addition of new building blocks to be added to the baseline system. The minimum risk approach specifically addresses the need for active identification of the plant to be controlled in real time and real time optimization of the control for the identified plant.

SPAR improved structural-fluid dynamic analysis capability

NASA Technical Reports Server (NTRS)

Pearson, M. L.

1985-01-01

The results of a study whose objective was to improve the operation of the SPAR computer code by improving efficiency, user features, and documentation is presented. Additional capability was added to the SPAR arithmetic utility system, including trigonometric functions, numerical integration, interpolation, and matrix combinations. Improvements were made in the EIG processor. A processor was created to compute and store principal stresses in table-format data sets. An additional capability was developed and incorporated into the plot processor which permits plotting directly from table-format data sets. Documentation of all these features is provided in the form of updates to the SPAR users manual.

Chlorophyll Catabolites in Senescent Leaves of the Plum Tree (Prunus domestica).

PubMed

Erhart, Theresia; Mittelberger, Cecilia; Vergeiner, Clemens; Scherzer, Gerhard; Holzner, Barbara; Robatscher, Peter; Oberhuber, Michael; Kräutler, Bernhard

2016-11-01

In cold extracts of senescent leaves of the plum tree (Prunus domestica ssp. domestica), six colorless non-fluorescent chlorophyll catabolites (NCCs) were characterized, named Pd-NCCs. In addition, several minor NCC fractions were tentatively classified. The structure of the most polar one of the NCCs, named Pd-NCC-32, featured an unprecedented twofold glycosidation pattern. Three of the NCCs are also functionalized at their 3 2 -position by a glucopyranosyl group. In addition, two of these glycosidated NCCs carry a dihydroxyethyl group at their 18-position. In the polar Pd-NCC-32, the latter group is further glycosidated at the terminal 18 2 -position. Four other major Pd-NCCs and one minor Pd-NCC were identified with five NCCs from higher plants known to belong to the 'epi'-series. In addition, tentative structures were derived for two minor fractions, classified as yellow chlorophyll catabolites, which represented (formal) oxidation products of two of the observed Pd-NCCs. The chlorophyll catabolites in leaves of plum feature the same basic structural pattern as those found in leaves of apple and pear trees. © 2016 The Authors. Chemistry & Biodiversity Published by Wiley-VHCA AG, Zurich, Switzerland.

Computer ranking of the sequence of appearance of 73 features of the brain and related structures in staged human embryos during the sixth week of development.

PubMed

O'Rahilly, R; Müller, F; Hutchins, G M; Moore, G W

1987-09-01

The sequence of events in the development of the brain in human embryos, already published for stages 8-15, is here continued for stages 16 and 17. With the aid of a computerized bubble-sort algorithm, 71 individual embryos were ranked in ascending order of the features present. Whereas these numbered 100 in the previous study, the increasing structural complexity gave 27 new features in the two stages now under investigation. The chief characteristics of stage 16 (approximately 37 postovulatory days) are protruding basal nuclei, the caudal olfactory elevation (olfactory tubercle), the tectobulbar tracts, and ascending fibers to the cerebellum. The main features of stage 17 (approximately 41 postovulatory days) are the cortical nucleus of the amygdaloid body, an intermediate layer in the tectum mesencephali, the posterior commissure, and the habenulo-interpeduncular tract. In addition, a typical feature at stage 17 is the crescentic shape of the lens cavity.

Structural and lithologic study of northern coast ranges and Sacramento Valley, California

NASA Technical Reports Server (NTRS)

Rich, E. I. (Principal Investigator)

1973-01-01

The author has identified the following significant results. The pattern of linear systems within the project area has been extended into the western foothill belt of the Sierra Nevada. The chief pattern of linear features in the western Sierran foothill belt trends about N. 10 - 15 deg W., but in the vicinity of the Feather River the trend of the features abruptly changes to about N. 50-60 deg W and appears to be contiguous across the Sacramento Valley with a similar system of linear features in the Coast Ranges. The linear features in the Modoc Plateau and Klamath Mt. areas appear unrelated to the systems detected in the Coast Ranges of Sierran foothill belt. Although the change in trend of the Sierran structural features has been previously suggested and the interrelationship of the Klamath Mt. region with the northern Sierra Nevadas has been postulated, the data obtained from the ERTS-1 imagery strengthens these notions and provides for the first time evidence of a direct connection of the structural trends within the alluviated part of the Sacramento Valley. In addition rocks of Pleistocene and Holocene age are offset by some of the linear features seen on ERTS-1 imagery and hence may record the latest episode of geologic deformation in north-central California.

Discrimination Enhancement with Transient Feature Analysis of a Graphene Chemical Sensor.

PubMed

Nallon, Eric C; Schnee, Vincent P; Bright, Collin J; Polcha, Michael P; Li, Qiliang

2016-01-19

A graphene chemical sensor is subjected to a set of structurally and chemically similar hydrocarbon compounds consisting of toluene, o-xylene, p-xylene, and mesitylene. The fractional change in resistance of the sensor upon exposure to these compounds exhibits a similar response magnitude among compounds, whereas large variation is observed within repetitions for each compound, causing a response overlap. Therefore, traditional features depending on maximum response change will cause confusion during further discrimination and classification analysis. More robust features that are less sensitive to concentration, sampling, and drift variability would provide higher quality information. In this work, we have explored the advantage of using transient-based exponential fitting coefficients to enhance the discrimination of similar compounds. The advantages of such feature analysis to discriminate each compound is evaluated using principle component analysis (PCA). In addition, machine learning-based classification algorithms were used to compare the prediction accuracies when using fitting coefficients as features. The additional features greatly enhanced the discrimination between compounds while performing PCA and also improved the prediction accuracy by 34% when using linear discrimination analysis.

Predication of different stages of Alzheimer's disease using neighborhood component analysis and ensemble decision tree.

PubMed

Jin, Mingwu; Deng, Weishu

2018-05-15

There is a spectrum of the progression from healthy control (HC) to mild cognitive impairment (MCI) without conversion to Alzheimer's disease (AD), to MCI with conversion to AD (cMCI), and to AD. This study aims to predict the different disease stages using brain structural information provided by magnetic resonance imaging (MRI) data. The neighborhood component analysis (NCA) is applied to select most powerful features for prediction. The ensemble decision tree classifier is built to predict which group the subject belongs to. The best features and model parameters are determined by cross validation of the training data. Our results show that 16 out of a total of 429 features were selected by NCA using 240 training subjects, including MMSE score and structural measures in memory-related regions. The boosting tree model with NCA features can achieve prediction accuracy of 56.25% on 160 test subjects. Principal component analysis (PCA) and sequential feature selection (SFS) are used for feature selection, while support vector machine (SVM) is used for classification. The boosting tree model with NCA features outperforms all other combinations of feature selection and classification methods. The results suggest that NCA be a better feature selection strategy than PCA and SFS for the data used in this study. Ensemble tree classifier with boosting is more powerful than SVM to predict the subject group. However, more advanced feature selection and classification methods or additional measures besides structural MRI may be needed to improve the prediction performance. Copyright © 2018 Elsevier B.V. All rights reserved.

Investigation of Time Series Representations and Similarity Measures for Structural Damage Pattern Recognition

PubMed Central

Swartz, R. Andrew

2013-01-01

This paper investigates the time series representation methods and similarity measures for sensor data feature extraction and structural damage pattern recognition. Both model-based time series representation and dimensionality reduction methods are studied to compare the effectiveness of feature extraction for damage pattern recognition. The evaluation of feature extraction methods is performed by examining the separation of feature vectors among different damage patterns and the pattern recognition success rate. In addition, the impact of similarity measures on the pattern recognition success rate and the metrics for damage localization are also investigated. The test data used in this study are from the System Identification to Monitor Civil Engineering Structures (SIMCES) Z24 Bridge damage detection tests, a rigorous instrumentation campaign that recorded the dynamic performance of a concrete box-girder bridge under progressively increasing damage scenarios. A number of progressive damage test case datasets and damage test data with different damage modalities are used. The simulation results show that both time series representation methods and similarity measures have significant impact on the pattern recognition success rate. PMID:24191136

Mineralogy, Three Dimensional Structure, and Oxygen Isotope Ratios of Four Crystalline Particles from Comet 81P/Wild 2

NASA Technical Reports Server (NTRS)

Nakamura, T.; Noguchi, T.; Tsuchiyama, A.; Ushikubo, T.; Kita, N. T.; Valley, J. W.; Zolensky, M. E.; Kakazu, Y.; Sakamoto, K.; Mashio, E.;

Noise-gating to Clean Astrophysical Image Data

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

DeForest, C. E.

I present a family of algorithms to reduce noise in astrophysical images and image sequences, preserving more information from the original data than is retained by conventional techniques. The family uses locally adaptive filters (“noise gates”) in the Fourier domain to separate coherent image structure from background noise based on the statistics of local neighborhoods in the image. Processing of solar data limited by simple shot noise or by additive noise reveals image structure not easily visible in the originals, preserves photometry of observable features, and reduces shot noise by a factor of 10 or more with little to nomore » apparent loss of resolution. This reveals faint features that were either not directly discernible or not sufficiently strongly detected for quantitative analysis. The method works best on image sequences containing related subjects, for example movies of solar evolution, but is also applicable to single images provided that there are enough pixels. The adaptive filter uses the statistical properties of noise and of local neighborhoods in the data to discriminate between coherent features and incoherent noise without reference to the specific shape or evolution of those features. The technique can potentially be modified in a straightforward way to exploit additional a priori knowledge about the functional form of the noise.« less

Noise-gating to Clean Astrophysical Image Data

NASA Astrophysics Data System (ADS)

DeForest, C. E.

2017-04-01

I present a family of algorithms to reduce noise in astrophysical images and image sequences, preserving more information from the original data than is retained by conventional techniques. The family uses locally adaptive filters (“noise gates”) in the Fourier domain to separate coherent image structure from background noise based on the statistics of local neighborhoods in the image. Processing of solar data limited by simple shot noise or by additive noise reveals image structure not easily visible in the originals, preserves photometry of observable features, and reduces shot noise by a factor of 10 or more with little to no apparent loss of resolution. This reveals faint features that were either not directly discernible or not sufficiently strongly detected for quantitative analysis. The method works best on image sequences containing related subjects, for example movies of solar evolution, but is also applicable to single images provided that there are enough pixels. The adaptive filter uses the statistical properties of noise and of local neighborhoods in the data to discriminate between coherent features and incoherent noise without reference to the specific shape or evolution of those features. The technique can potentially be modified in a straightforward way to exploit additional a priori knowledge about the functional form of the noise.

Structure Formation of Ultrathin PEO Films at Solid Interfaces—Complex Pattern Formation by Dewetting and Crystallization

PubMed Central

Braun, Hans-Georg; Meyer, Evelyn

2013-01-01

The direct contact of ultrathin polymer films with a solid substrate may result in thin film rupture caused by dewetting. With crystallisable polymers such as polyethyleneoxide (PEO), molecular self-assembly into partial ordered lamella structures is studied as an additional source of pattern formation. Morphological features in ultrathin PEO films (thickness < 10 nm) result from an interplay between dewetting patterns and diffusion limited growth pattern of ordered lamella growing within the dewetting areas. Besides structure formation of hydrophilic PEO molecules, n-alkylterminated (hydrophobic) PEO oligomers are investigated with respect to self-organization in ultrathin films. Morphological features characteristic for pure PEO are not changed by the presence of the n-alkylgroups. PMID:23385233

F Ring Bright Core Clumps

NASA Image and Video Library

2010-07-20

Bright clumps of ring material and a fan-like structure appear near the core of Saturn tenuous F ring in this mosaic of images from NASA Cassini spacecraft. Such features suggest the existence of additional objects in the F ring.

Role of Side-Chain Molecular Features in Tuning Lower Critical Solution Temperatures (LCSTs) of Oligoethylene Glycol Modified Polypeptides.

PubMed

Gharakhanian, Eric G; Deming, Timothy J

2016-07-07

A series of thermoresponsive polypeptides has been synthesized using a methodology that allowed facile adjustment of side-chain functional groups. The lower critical solution temperature (LCST) properties of these polymers in water were then evaluated relative to systematic molecular modifications in their side-chains. It was found that in addition to the number of ethylene glycol repeats in the side-chains, terminal and linker groups also have substantial and predictable effects on cloud point temperatures (Tcp). In particular, we found that the structure of these polypeptides allowed for inclusion of polar hydroxyl groups, which significantly increased their hydrophilicity and decreased the need to use long oligoethylene glycol repeats to obtain LCSTs. The thioether linkages in these polypeptides were found to provide an additional structural feature for reversible switching of both polypeptide conformation and thermoresponsive properties.

METAShield: Hot Metallic Aeroshell Concept for RLV/SOV

NASA Technical Reports Server (NTRS)

Scotti, Stephen J.; Poteet, Carl C.; Daryabeigi, Kamran; Nowak, Robert J.; Hsu, Su-Yuen; Schmidt, Irvin H.; Ku, Shih-Huei P.

2003-01-01

An innovative fuselage design approach that combines many desirable operational features with a simple and efficient structural approach is being developed by NASA. The approach, named METAShield for MEtallic TransAtmospheric Shield, utilizes lightly loaded, hot aeroshell structures surrounding integral propellant tanks that carry the primary structural loads. The aeroshells are designed to withstand the local pressure loads, transmitting them to the tanks with minimal restraint of thermal growth. No additional thermal protection system protects the METAShield, and a fibrous or multilayer insulation blanket, located in the space between the aeroshell and the tanks, serves as both high temperature and cryogenic insulation for the tanks. The concept is described in detail, and the performance and operational features are highlighted. Initial design results and analyses of the structural, thermal, and thermal-structural performance are described. Computational results evaluating resistance to hypervelocity impact damage, as well as some supporting aerothermal wind tunnel results. are also presented. Future development needs are summarized.

Flow Structures within a Helicopter Rotor Hub Wake

NASA Astrophysics Data System (ADS)

Elbing, Brian; Reich, David; Schmitz, Sven

2015-11-01

A scaled model of a notional helicopter rotor hub was tested in the 48'' Garfield Thomas Water Tunnel at the Applied Research Laboratory Penn State. The measurement suite included total hub drag and wake velocity measurements (LDV, PIV, stereo-PIV) at three downstream locations. The main objective was to understand the spatiotemporal evolution of the unsteady wake between the rotor hub and the nominal location of the empennage (tail). Initial analysis of the data revealed prominent two- and four-per-revolution fluid structures linked to geometric hub features persisting into the wake far-field. In addition, a six-per-revolution fluid structure was observed in the far-field, which is unexpected due to the lack of any hub feature with the corresponding symmetry. This suggests a nonlinear interaction is occurring within the wake to generate these structures. This presentation will provide an overview of the experimental data and analysis with particular emphasis on these six-per-revolution structures.

Advances in the REDCAT software package

PubMed Central

2013-01-01

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

Carbonate Biogenic Structures in Storrs Lake, Bahamas

NASA Technical Reports Server (NTRS)

Byrne, Monica; Morris, Penny A.; Wentworth, Susan J.; Brigmon, Robin L.; McKay, David S.

2001-01-01

Storr's Lake, an inland hypersaline lake on San Salvador Island, Bahamas, contains calcium carbonate-rich lithified mats of filamentous microorganisms, diatoms, associated photosynthetic and chemotrophic bacteria, and trapped sediment. In addition, 16S rRNA analysis indicates the presence of five sulfur-reducing genera of bacteria. These microbes are potential modern-day analogs to some ancient stromatolitic structures. The goals of this study are to identify unique compositional and biogenic features, possibly correlating some of these with some of the sulfate-reducing bacteria. Additional information is contained in the original extended abstract.

Realistic Free-Spins Features Increase Preference for Slot Machines.

PubMed

Taylor, Lorance F; Macaskill, Anne C; Hunt, Maree J

2017-06-01

Despite increasing research into how the structural characteristics of slot machines influence gambling behaviour there have been no experimental investigations into the effect of free-spins bonus features-a structural characteristic that is commonly central to the design of slot machines. This series of three experiments investigated the free-spins feature using slot machine simulations to determine whether participants allocate more wagers to a machine with free spins, and, which components of free-spins features drive this preference. In each experiment, participants were exposed to two computer-simulated slot machines-one with a free-spins feature or similar bonus feature and one without. Participants then completed a testing phase where they could freely switch between the two machines. In Experiment 1, participants did not prefer the machine with a simple free-spins feature. In Experiment 2 the free-spins feature incorporated additional elements such as sounds, animations, and an increased win frequency; participants preferred to gamble on this machine. The Experiment 3 "bonus feature" machine resembled the free spins machine in Experiment 2 except spins were not free; participants showed a clear preference for this machine also. These findings indicate that (1) free-spins features have a major influence over machine choice and (2) the "freeness" of the free-spins bonus features is not an important driver of preference, contrary to self-report and interview research with gamblers.

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

PubMed

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

2002-01-01

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

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

PubMed Central

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

2002-01-01

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

Fifteenth NASTRAN (R) Users' Colloquium

NASA Technical Reports Server (NTRS)

1987-01-01

Numerous applications of the NASA Structural Analysis (NASTRAN) computer program, a general purpose finite element code, are discussed. Additional features that can be added to NASTRAN, interactive plotting of NASTRAN data on microcomputers, mass modeling for bars, the design of wind tunnel models, the analysis of ship structures subjected to underwater explosions, and buckling analysis of radio antennas are among the topics discussed.

GALT protein database: querying structural and functional features of GALT enzyme.

PubMed

d'Acierno, Antonio; Facchiano, Angelo; Marabotti, Anna

2014-09-01

Knowledge of the impact of variations on protein structure can enhance the comprehension of the mechanisms of genetic diseases related to that protein. Here, we present a new version of GALT Protein Database, a Web-accessible data repository for the storage and interrogation of structural effects of variations of the enzyme galactose-1-phosphate uridylyltransferase (GALT), the impairment of which leads to classic Galactosemia, a rare genetic disease. This new version of this database now contains the models of 201 missense variants of GALT enzyme, including heterozygous variants, and it allows users not only to retrieve information about the missense variations affecting this protein, but also to investigate their impact on substrate binding, intersubunit interactions, stability, and other structural features. In addition, it allows the interactive visualization of the models of variants collected into the database. We have developed additional tools to improve the use of the database by nonspecialized users. This Web-accessible database (http://bioinformatica.isa.cnr.it/GALT/GALT2.0) represents a model of tools potentially suitable for application to other proteins that are involved in human pathologies and that are subjected to genetic variations. © 2014 WILEY PERIODICALS, INC.

Mining the key predictors for event outbreaks in social networks

NASA Astrophysics Data System (ADS)

Yi, Chengqi; Bao, Yuanyuan; Xue, Yibo

2016-04-01

It will be beneficial to devise a method to predict a so-called event outbreak. Existing works mainly focus on exploring effective methods for improving the accuracy of predictions, while ignoring the underlying causes: What makes event go viral? What factors that significantly influence the prediction of an event outbreak in social networks? In this paper, we proposed a novel definition for an event outbreak, taking into account the structural changes to a network during the propagation of content. In addition, we investigated features that were sensitive to predicting an event outbreak. In order to investigate the universality of these features at different stages of an event, we split the entire lifecycle of an event into 20 equal segments according to the proportion of the propagation time. We extracted 44 features, including features related to content, users, structure, and time, from each segment of the event. Based on these features, we proposed a prediction method using supervised classification algorithms to predict event outbreaks. Experimental results indicate that, as time goes by, our method is highly accurate, with a precision rate ranging from 79% to 97% and a recall rate ranging from 74% to 97%. In addition, after applying a feature-selection algorithm, the top five selected features can considerably improve the accuracy of the prediction. Data-driven experimental results show that the entropy of the eigenvector centrality, the entropy of the PageRank, the standard deviation of the betweenness centrality, the proportion of re-shares without content, and the average path length are the key predictors for an event outbreak. Our findings are especially useful for further exploring the intrinsic characteristics of outbreak prediction.

Imaging the Buried Chicxulub Crater with Gravity Gradients and Cenotes

NASA Astrophysics Data System (ADS)

Hildebrand, A. R.; Pilkington, M.; Halpenny, J. F.; Ortiz-Aleman, C.; Chavez, R. E.; Urrutia-Fucugauchi, J.; Connors, M.; Graniel-Castro, E.; Camara-Zi, A.; Vasquez, J.

1995-09-01

Differing interpretations of the Bouguer gravity anomaly over the Chicxulub crater, Yucatan Peninsula, Mexico, have yielded diameter estimates of 170 to 320 km. Knowing the crater's size is necessary to quantify the lethal perturbations to the Cretaceous environment associated with its formation. The crater's size (and internal structure) is revealed by the horizontal gradient of the Bouguer gravity anomaly over the structure, and by mapping the karst features of the Yucatan region. To improve our resolution of the crater's gravity signature we collected additional gravity measurements primarily along radial profiles, but also to fill in previously unsurveyed areas. Horizontal gradient analysis of Bouguer gravity data objectively highlights the lateral density contrasts of the impact lithologies and suppresses regional anomalies which may obscure the gravity signature of the Chicxulub crater lithologies. This gradient technique yields a striking circular structure with at least 6 concentric gradient features between 25 and 85 km radius. These features are most distinct in the southwest probably because of denser sampling of the gravity field. Our detailed profiles detected an additional feature and steeper gradients (up to 5 mGal/km) than the original survey. We interpret the outer four gradient maxima to represent concentric faults in the crater's zone of slumping as is also revealed by seismic reflection data. The inner two probably represent the margin of the central uplift and the peak ring and or collapsed transient cavity. Radial gradients in the SW quadrant over the inferred ~40 km-diameter central uplift (4) may represent structural "puckering" as revealed at eroded terrestrial craters. Gradient features related to regional gravity highs and lows are visible outside the crater, but no concentric gradient features are apparent at distances > 90 km radius. The marginal gradient features may be modelled by slump faults as observed in large complex craters on the other terrestrial planets. A modeled fault of 1.5 km displacement (slightly slumped block exterior and impact breccia interior) reproduces the steepest gradient feature. This model is incompatible with models that place these gradient features inside the collapsed transient cavity. Locations of the karst features of the northern Yucatan region were digitized from 1:50,000 topographic maps, which show most but not all the water-filled sinkholes (locally known as cenotes). A prominent ring of cenotes is visible over the crater that is spatially correlated to the outer steep gravity gradient feature. The mapped cenotes constitute an unbiased sampling of the region's karst surface features of >50 m diameter. The gradient maximum and the cenote ring both meander with amplitudes of up to 2 km. The wiggles in the gradient feature and the cenote distribution probably correspond to the "scalloping" observed at the headwall of terraces in large complex craters. A second partial cenote ring exterior to the southwest side of the main ring corresponds to a less-prominent gravity gradient feature. No concentric structure is observable in the distribution of karst features at radii >90 km. The cenote ring is bounded by the outer peripheral steep gradient feature and must be related to it; the slump faults must have been reactivated sufficiently to create fracturing in the overlying and much younger sediment. Long term subsidence, as found at other terrestrial craters is a possible mechanism for the reactivation. Such long term subsidence may be caused by differential compaction or thermal relaxation. Elevations acquired during gravity surveys show that the cenote ring also corresponds to a topographic low along some of its length that probably reflects preferential erosion.

Bio-inspired self-healing structural color hydrogel

PubMed Central

Fu, Fanfan; Chen, Zhuoyue; Zhao, Ze; Wang, Huan; Shang, Luoran; Gu, Zhongze

2017-01-01

Biologically inspired self-healing structural color hydrogels were developed by adding a glucose oxidase (GOX)- and catalase (CAT)-filled glutaraldehyde cross-linked BSA hydrogel into methacrylated gelatin (GelMA) inverse opal scaffolds. The composite hydrogel materials with the polymerized GelMA scaffold could maintain the stability of an inverse opal structure and its resultant structural colors, whereas the protein hydrogel filler could impart self-healing capability through the reversible covalent attachment of glutaraldehyde to lysine residues of BSA and enzyme additives. A series of unprecedented structural color materials could be created by assembling and healing the elements of the composite hydrogel. In addition, as both the GelMA and the protein hydrogels were derived from organisms, the composite materials presented high biocompatibility and plasticity. These features of self-healing structural color hydrogels make them excellent functional materials for different applications. PMID:28533368

Quantifying site-specific physical heterogeneity within an estuarine seascape

USGS Publications Warehouse

Kennedy, Cristina G.; Mather, Martha E.; Smith, Joseph M.

2017-01-01

Quantifying physical heterogeneity is essential for meaningful ecological research and effective resource management. Spatial patterns of multiple, co-occurring physical features are rarely quantified across a seascape because of methodological challenges. Here, we identified approaches that measured total site-specific heterogeneity, an often overlooked aspect of estuarine ecosystems. Specifically, we examined 23 metrics that quantified four types of common physical features: (1) river and creek confluences, (2) bathymetric variation including underwater drop-offs, (3) land features such as islands/sandbars, and (4) major underwater channel networks. Our research at 40 sites throughout Plum Island Estuary (PIE) provided solutions to two problems. The first problem was that individual metrics that measured heterogeneity of a single physical feature showed different regional patterns. We solved this first problem by combining multiple metrics for a single feature using a within-physical feature cluster analysis. With this approach, we identified sites with four different types of confluences and three different types of underwater drop-offs. The second problem was that when multiple physical features co-occurred, new patterns of total site-specific heterogeneity were created across the seascape. This pattern of total heterogeneity has potential ecological relevance to structure-oriented predators. To address this second problem, we identified sites with similar types of total physical heterogeneity using an across-physical feature cluster analysis. Then, we calculated an additive heterogeneity index, which integrated all physical features at a site. Finally, we tested if site-specific additive heterogeneity index values differed for across-physical feature clusters. In PIE, the sites with the highest additive heterogeneity index values were clustered together and corresponded to sites where a fish predator, adult striped bass (Morone saxatilis), aggregated in a related acoustic tracking study. In summary, we have shown general approaches to quantifying site-specific heterogeneity.

Wireless AE Event and Environmental Monitoring for Wind Turbine Blades at Low Sampling Rates

NASA Astrophysics Data System (ADS)

Bouzid, Omar M.; Tian, Gui Y.; Cumanan, K.; Neasham, J.

Integration of acoustic wireless technology in structural health monitoring (SHM) applications introduces new challenges due to requirements of high sampling rates, additional communication bandwidth, memory space, and power resources. In order to circumvent these challenges, this chapter proposes a novel solution through building a wireless SHM technique in conjunction with acoustic emission (AE) with field deployment on the structure of a wind turbine. This solution requires a low sampling rate which is lower than the Nyquist rate. In addition, features extracted from aliased AE signals instead of reconstructing the original signals on-board the wireless nodes are exploited to monitor AE events, such as wind, rain, strong hail, and bird strike in different environmental conditions in conjunction with artificial AE sources. Time feature extraction algorithm, in addition to the principal component analysis (PCA) method, is used to extract and classify the relevant information, which in turn is used to classify or recognise a testing condition that is represented by the response signals. This proposed novel technique yields a significant data reduction during the monitoring process of wind turbine blades.

A local structure model for network analysis

DOE PAGES

Casleton, Emily; Nordman, Daniel; Kaiser, Mark

2017-04-01

The statistical analysis of networks is a popular research topic with ever widening applications. Exponential random graph models (ERGMs), which specify a model through interpretable, global network features, are common for this purpose. In this study we introduce a new class of models for network analysis, called local structure graph models (LSGMs). In contrast to an ERGM, a LSGM specifies a network model through local features and allows for an interpretable and controllable local dependence structure. In particular, LSGMs are formulated by a set of full conditional distributions for each network edge, e.g., the probability of edge presence/absence, depending onmore » neighborhoods of other edges. Additional model features are introduced to aid in specification and to help alleviate a common issue (occurring also with ERGMs) of model degeneracy. Finally, the proposed models are demonstrated on a network of tornadoes in Arkansas where a LSGM is shown to perform significantly better than a model without local dependence.« less

A local structure model for network analysis

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

Casleton, Emily; Nordman, Daniel; Kaiser, Mark

The statistical analysis of networks is a popular research topic with ever widening applications. Exponential random graph models (ERGMs), which specify a model through interpretable, global network features, are common for this purpose. In this study we introduce a new class of models for network analysis, called local structure graph models (LSGMs). In contrast to an ERGM, a LSGM specifies a network model through local features and allows for an interpretable and controllable local dependence structure. In particular, LSGMs are formulated by a set of full conditional distributions for each network edge, e.g., the probability of edge presence/absence, depending onmore » neighborhoods of other edges. Additional model features are introduced to aid in specification and to help alleviate a common issue (occurring also with ERGMs) of model degeneracy. Finally, the proposed models are demonstrated on a network of tornadoes in Arkansas where a LSGM is shown to perform significantly better than a model without local dependence.« less

Discovery of microscopic evidence for shock metamorphism at the Serpent Mound structure, south-central Ohio: Confirmation of an origin by impact

USGS Publications Warehouse

Carlton, R.W.; Koeberl, C.; Baranoski, M.T.; SchuMacHer, G.A.

1998-01-01

The origin of the Serpent Mound structure in south-central Ohio has been disputed for many years. Clearly, more evidence was needed to resolve the confusion concerning the origin of the Serpent Mound feature either by endogenic processes or by hypervelocity impact. A petrographic study of 21 samples taken from a core 903 m long drilled in the central uplift of the structure provides evidence of shock metamorphism in the form of multiple sets of planar deformation features in quartz grains, as well as the presence of clasts of altered impact-melt rock. Crystallographic orientations of the planar deformation features show maxima at the shock-characteristic planes of {101??3} and {101??2} and additional maxima at {101??1}, {213??1}, and {516??1}. Geochemical analyses of impact breccias show minor enrichments in the abundances of the siderophile elements Cr, Co, Ni, and Ir, indicating the presence of a minor meteoritic component.

Novel drift structures for silicon and compound semiconductor X-ray and gamma-ray detectors

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

Patt, B.E.; Iwanczyk, J.S.

Recently developed silicon- and compound-semiconductor-based drift detector structures have produced excellent performance for charged particles, X-rays, and gamma rays and for low-signal visible light detection. The silicon drift detector (SDD) structures that the authors discuss relate to direct X-ray detectors and scintillation photon detectors coupled with scintillators for gamma rays. Recent designs include several novel features that ensure very low dark current and hence low noise. In addition, application of thin window technology ensures a very high quantum efficiency entrance window on the drift photodetector. The main features of the silicon drift structures for X rays and light detection aremore » very small anode capacitance independent of the overall detector size, low noise, and high throughput. To take advantage of the small detector capacitance, the first stage of the electronics needs to be integrated into the detector anode. In the gamma-ray application, factors other than electronic noise dominate, and there is no need to integrate the electronics into the anode. Thus, a different drift structure is needed in conjunction with a high-Z material. The main features in this case are large active detector volume and electron-only induced signal.« less

Ligand-based and structure-based approaches in identifying ideal pharmacophore against c-Jun N-terminal kinase-3.

PubMed

Kumar, B V S Suneel; Kotla, Rohith; Buddiga, Revanth; Roy, Jyoti; Singh, Sardar Shamshair; Gundla, Rambabu; Ravikumar, Muttineni; Sarma, Jagarlapudi A R P

2011-01-01

Structure and ligand based pharmacophore modeling and docking studies carried out using diversified set of c-Jun N-terminal kinase-3 (JNK3) inhibitors are presented in this paper. Ligand based pharmacophore model (LBPM) was developed for 106 inhibitors of JNK3 using a training set of 21 compounds to reveal structural and chemical features necessary for these molecules to inhibit JNK3. Hypo1 consisted of two hydrogen bond acceptors (HBA), one hydrogen bond donor (HBD), and a hydrophobic (HY) feature with a correlation coefficient (r²) of 0.950. This pharmacophore model was validated using test set containing 85 inhibitors and had a good r² of 0.846. All the molecules were docked using Glide software and interestingly, all the docked conformations showed hydrogen bond interactions with important hinge region amino acids (Gln155 and Met149)and these interactions were compared with Hypo1 features. The results of ligand based pharmacophore model (LBPM)and docking studies are validated each other. The structure based pharmacophore model (SBPM) studies have identified additional features, two hydrogen bond donors and one hydrogen bond acceptor. The combination of these methodologies is useful in designing ideal pharmacophore which provides a powerful tool for the discovery of novel and selective JNK3 inhibitors.

Multiclass Classification for the Differential Diagnosis on the ADHD Subtypes Using Recursive Feature Elimination and Hierarchical Extreme Learning Machine: Structural MRI Study

PubMed Central

Qureshi, Muhammad Naveed Iqbal; Min, Beomjun; Jo, Hang Joon; Lee, Boreom

2016-01-01

The classification of neuroimaging data for the diagnosis of certain brain diseases is one of the main research goals of the neuroscience and clinical communities. In this study, we performed multiclass classification using a hierarchical extreme learning machine (H-ELM) classifier. We compared the performance of this classifier with that of a support vector machine (SVM) and basic extreme learning machine (ELM) for cortical MRI data from attention deficit/hyperactivity disorder (ADHD) patients. We used 159 structural MRI images of children from the publicly available ADHD-200 MRI dataset. The data consisted of three types, namely, typically developing (TDC), ADHD-inattentive (ADHD-I), and ADHD-combined (ADHD-C). We carried out feature selection by using standard SVM-based recursive feature elimination (RFE-SVM) that enabled us to achieve good classification accuracy (60.78%). In this study, we found the RFE-SVM feature selection approach in combination with H-ELM to effectively enable the acquisition of high multiclass classification accuracy rates for structural neuroimaging data. In addition, we found that the most important features for classification were the surface area of the superior frontal lobe, and the cortical thickness, volume, and mean surface area of the whole cortex. PMID:27500640

Multiclass Classification for the Differential Diagnosis on the ADHD Subtypes Using Recursive Feature Elimination and Hierarchical Extreme Learning Machine: Structural MRI Study.

PubMed

Qureshi, Muhammad Naveed Iqbal; Min, Beomjun; Jo, Hang Joon; Lee, Boreom

2016-01-01

The classification of neuroimaging data for the diagnosis of certain brain diseases is one of the main research goals of the neuroscience and clinical communities. In this study, we performed multiclass classification using a hierarchical extreme learning machine (H-ELM) classifier. We compared the performance of this classifier with that of a support vector machine (SVM) and basic extreme learning machine (ELM) for cortical MRI data from attention deficit/hyperactivity disorder (ADHD) patients. We used 159 structural MRI images of children from the publicly available ADHD-200 MRI dataset. The data consisted of three types, namely, typically developing (TDC), ADHD-inattentive (ADHD-I), and ADHD-combined (ADHD-C). We carried out feature selection by using standard SVM-based recursive feature elimination (RFE-SVM) that enabled us to achieve good classification accuracy (60.78%). In this study, we found the RFE-SVM feature selection approach in combination with H-ELM to effectively enable the acquisition of high multiclass classification accuracy rates for structural neuroimaging data. In addition, we found that the most important features for classification were the surface area of the superior frontal lobe, and the cortical thickness, volume, and mean surface area of the whole cortex.

Saturn's dynamic D ring

USGS Publications Warehouse

Hedman, M.M.; Burns, J.A.; Showalter, M.R.; Porco, C.C.; Nicholson, P.D.; Bosh, A.S.; Tiscareno, M.S.; Brown, R.H.; Buratti, B.J.; Baines, K.H.; Clark, R.

2007-01-01

The Cassini spacecraft has provided the first clear images of the D ring since the Voyager missions. These observations show that the structure of the D ring has undergone significant changes over the last 25 years. The brightest of the three ringlets seen in the Voyager images (named D72), has transformed from a narrow, <40-km wide ringlet to a much broader and more diffuse 250-km wide feature. In addition, its center of light has shifted inwards by over 200 km relative to other features in the D ring. Cassini also finds that the locations of other narrow features in the D ring and the structure of the diffuse material in the D ring differ from those measured by Voyager. Furthermore, Cassini has detected additional ringlets and structures in the D ring that were not observed by Voyager. These include a sheet of material just interior to the inner edge of the C ring that is only observable at phase angles below about 60??. New photometric and spectroscopic data from the ISS (Imaging Science Subsystem) and VIMS (Visual and Infrared Mapping Spectrometer) instruments onboard Cassini show the D ring contains a variety of different particle populations with typical particle sizes ranging from 1 to 100 microns. High-resolution images reveal fine-scale structures in the D ring that appear to be variable in time and/or longitude. Particularly interesting is a remarkably regular, periodic structure with a wavelength of ??? 30 ?? km extending between orbital radii of 73,200 and 74,000 km. A similar structure was previously observed in 1995 during the occultation of the star GSC5249-01240, at which time it had a wavelength of ??? 60 ?? km. We interpret this structure as a periodic vertical corrugation in the D ring produced by differential nodal regression of an initially inclined ring. We speculate that this structure may have formed in response to an impact with a comet or meteoroid in early 1984. ?? 2006 Elsevier Inc. All rights reserved.

Power and temperature dependent photoluminescence investigation of the linear polarization at normal and inverted interface transitions in InP/InAlAs and InGaAsP/InAlAs QW structures

NASA Astrophysics Data System (ADS)

Esmaielpour, Hamidreza; Whiteside, Vincent R.; Hirst, Louise C.; Forbes, David V.; Walters, Robert J.; Sellers, Ian R.

We present an investigation of the interface effects for InGaAsP/InAlAs QW and InP/InAlAs QW structures capped with an InP layer. Continuous wave photoluminescence (PL) spectroscopy of these samples at 4 K shows features associated with the interfaces of an InAlAs layer grown on an InP layer (normal interface) and an InP layer grown on an InAlAs material (inverted interface). Power dependent PL of the InGaAsP QW indicates that there are two features related to the inverted interface, whereby the linear polarization of one increases and for the other decreases. In addition, a temperature dependent study of this sample shows that as the temperature increases: the linear polarization for both features decreases; at room temperature, there is negligible polarization effect. A power dependent PL study of the InP QW structure shows both normal and inverted interface transitions have opposing trends in linear polarization. Notably, the temperature dependent PL investigation displays a reduction of polarization degree for the inverted interface: as expected; while an increase of polarization for the normal interface was observed. In addition, power and temperature dependence of peak energy of the interface transitions for both samples will be presented.

Imposed, ordered dust structures and other plasma features in a strongly magnetized plasma

NASA Astrophysics Data System (ADS)

Thomas, Edward; Leblanc, Spencer; Lynch, Brian; Konopka, Uwe; Merlino, Robert; Rosenberg, Marlene

2015-11-01

The Magnetized Dusty Plasma Experiment (MDPX) device has been in operation for just over one year. In that time, the MDPX device has been operating using a uniform magnetic field configuration up to 3.0 Tesla and has successfully produced plasmas and dusty plasmas at high magnetic fields. In these experimental studies, we have made observations of a new type of imposed, ordered structure in a dusty plasma at magnetic fields above 1 T. These dusty plasma structures are shown to scale inversely with neutral pressure and are shown to reflect the spatial structure of a wire mesh placed in the plasma. Additionally, recent measurements have been made that give insights into the effective potential that establishes the ordered structures in the plasma. In this presentation, we report on details of the imposed, ordered dusty plasma structure as well as filamentary features that also appear in the plasma and modify the confinement of the dusty plasma. This work is supported with funding from the NSF and Department of Energy.

Continuous and embedded solutions for SHM of concrete structures using changing electrical potential in self-sensing cement-based composites

NASA Astrophysics Data System (ADS)

Downey, Austin; Garcia-Macias, Enrique; D'Alessandro, Antonella; Laflamme, Simon; Castro-Triguero, Rafael; Ubertini, Filippo

2017-04-01

Interest in the concept of self-sensing structural materials has grown in recent years due to its potential to enable continuous low-cost monitoring of next-generation smart-structures. The development of cement-based smart sensors appears particularly well suited for monitoring applications due to their numerous possible field applications, their ease of use and long-term stability. Additionally, cement-based sensors offer a unique opportunity for structural health monitoring of civil structures because of their compatibility with new or existing infrastructure. Particularly, the addition of conductive carbon nanofillers into a cementitious matrix provides a self-sensing structural material with piezoresistive characteristics sensitive to deformations. The strain-sensing ability is achieved by correlating the external loads with the variation of specific electrical parameters, such as the electrical resistance or impedance. Selection of the correct electrical parameter for measurement to correlate with features of interest is required for the condition assessment task. In this paper, we investigate the potential of using altering electrical potential in cement-based materials doped with carbon nanotubes to measure strain and detect damage in concrete structures. Experimental validation is conducted on small-scale specimens including a steel-reinforced beam of conductive cement paste. Comparisons are made with constant electrical potential and current methods commonly found in the literature. Experimental results demonstrate the ability of the changing electrical potential at detecting features important for assessing the condition of a structure.

The calcium binding properties and structure prediction of the Hax-1 protein.

PubMed

Balcerak, Anna; Rowinski, Sebastian; Szafron, Lukasz M; Grzybowska, Ewa A

2017-01-01

Hax-1 is a protein involved in regulation of different cellular processes, but its properties and exact mechanisms of action remain unknown. In this work, using purified, recombinant Hax-1 and by applying an in vitro autoradiography assay we have shown that this protein binds Ca 2+ . Additionally, we performed structure prediction analysis which shows that Hax-1 displays definitive structural features, such as two α-helices, short β-strands and four disordered segments.

Recent enhancements to the GRIDGEN structured grid generation system

NASA Technical Reports Server (NTRS)

Steinbrenner, John P.; Chawner, John R.

1992-01-01

Significant enhancements are being implemented into the GRIDGEN3D, multiple block, structured grid generation software. Automatic, point-to-point, interblock connectivity will be possible through the addition of the domain entity to GRIDBLOCK's block construction process. Also, the unification of GRIDGEN2D and GRIDBLOCK has begun with the addition of edge grid point distribution capability to GRIDBLOCK. The geometric accuracy of surface grids and the ease with which databases may be obtained is being improved by adding support for standard computer-aided design formats (e.g., PATRAN Neutral and IGES files). Finally, volume grid quality was improved through addition of new SOR algorithm features and the new hybrid control function type to GRIDGEN3D.

The crystal structure of NADPH:ferredoxin reductase from Azotobacter vinelandii.

PubMed Central

Sridhar Prasad, G.; Kresge, N.; Muhlberg, A. B.; Shaw, A.; Jung, Y. S.; Burgess, B. K.; Stout, C. D.

1998-01-01

NADPH:ferredoxin reductase (AvFPR) is involved in the response to oxidative stress in Azotobacter vinelandii. The crystal structure of AvFPR has been determined at 2.0 A resolution. The polypeptide fold is homologous with six other oxidoreductases whose structures have been solved including Escherichia coli flavodoxin reductase (EcFldR) and spinach, and Anabaena ferredoxin:NADP+ reductases (FNR). AvFPR is overall most homologous to EcFldR. The structure is comprised of a N-terminal six-stranded antiparallel beta-barrel domain, which binds FAD, and a C-terminal five-stranded parallel beta-sheet domain, which binds NADPH/NADP+ and has a classical nucleotide binding fold. The two domains associate to form a deep cleft where the NADPH and FAD binding sites are juxtaposed. The structure displays sequence conserved motifs in the region surrounding the two dinucleotide binding sites, which are characteristic of the homologous enzymes. The folded over conformation of FAD in AvFPR is similar to that in EcFldR due to stacking of Phe255 on the adenine ring of FAD, but it differs from that in the FNR enzymes, which lack a homologous aromatic residue. The structure of AvFPR displays three unique features in the environment of the bound FAD. Two features may affect the rate of reduction of FAD: the absence of an aromatic residue stacked on the isoalloxazine ring in the NADPH binding site; and the interaction of a carbonyl group with N10 of the flavin. Both of these features are due to the substitution of a conserved C-terminal tyrosine residue with alanine (Ala254) in AvFPR. An additional unique feature may affect the interaction of AvFPR with its redox partner ferredoxin I (FdI). This is the extension of the C-terminus by three residues relative to EcFldR and by four residues relative to FNR. The C-terminal residue, Lys258, interacts with the AMP phosphate of FAD. Consequently, both phosphate groups are paired with a basic group due to the simultaneous interaction of the FMN phosphate with Arg51 in a conserved FAD binding motif. The fourth feature, common to homologous oxidoreductases, is a concentration of 10 basic residues on the face of the protein surrounding the active site, in addition to Arg51 and Lys258. PMID:9865948

Perspectives for Practice: A New JOSPT Feature to Facilitate Translation of Research Into Practice.

PubMed

Abbott, J Haxby

2016-03-01

In this month's issue, we introduce a new feature, Perspectives for Practice, which aims to interpret new research in the context of established best practice. This 2-page feature is designed to offer clinicians insight into the state of the art: what was known before, what research was done before, what new evidence the present study found, and how we should interpret this new evidence in light of what was known before. The second page of the Perspectives for Practice will provide additional material useful for teaching and discussion. The structure and content of these features will undergo continued development in response to reader feedback, which we welcome.

DNAproDB: an interactive tool for structural analysis of DNA–protein complexes

PubMed Central

Sagendorf, Jared M.

2017-01-01

Abstract Many biological processes are mediated by complex interactions between DNA and proteins. Transcription factors, various polymerases, nucleases and histones recognize and bind DNA with different levels of binding specificity. To understand the physical mechanisms that allow proteins to recognize DNA and achieve their biological functions, it is important to analyze structures of DNA–protein complexes in detail. DNAproDB is a web-based interactive tool designed to help researchers study these complexes. DNAproDB provides an automated structure-processing pipeline that extracts structural features from DNA–protein complexes. The extracted features are organized in structured data files, which are easily parsed with any programming language or viewed in a browser. We processed a large number of DNA–protein complexes retrieved from the Protein Data Bank and created the DNAproDB database to store this data. Users can search the database by combining features of the DNA, protein or DNA–protein interactions at the interface. Additionally, users can upload their own structures for processing privately and securely. DNAproDB provides several interactive and customizable tools for creating visualizations of the DNA–protein interface at different levels of abstraction that can be exported as high quality figures. All functionality is documented and freely accessible at http://dnaprodb.usc.edu. PMID:28431131

Multi-Contrast Multi-Atlas Parcellation of Diffusion Tensor Imaging of the Human Brain

PubMed Central

Tang, Xiaoying; Yoshida, Shoko; Hsu, John; Huisman, Thierry A. G. M.; Faria, Andreia V.; Oishi, Kenichi; Kutten, Kwame; Poretti, Andrea; Li, Yue; Miller, Michael I.; Mori, Susumu

2014-01-01

In this paper, we propose a novel method for parcellating the human brain into 193 anatomical structures based on diffusion tensor images (DTIs). This was accomplished in the setting of multi-contrast diffeomorphic likelihood fusion using multiple DTI atlases. DTI images are modeled as high dimensional fields, with each voxel exhibiting a vector valued feature comprising of mean diffusivity (MD), fractional anisotropy (FA), and fiber angle. For each structure, the probability distribution of each element in the feature vector is modeled as a mixture of Gaussians, the parameters of which are estimated from the labeled atlases. The structure-specific feature vector is then used to parcellate the test image. For each atlas, a likelihood is iteratively computed based on the structure-specific vector feature. The likelihoods from multiple atlases are then fused. The updating and fusing of the likelihoods is achieved based on the expectation-maximization (EM) algorithm for maximum a posteriori (MAP) estimation problems. We first demonstrate the performance of the algorithm by examining the parcellation accuracy of 18 structures from 25 subjects with a varying degree of structural abnormality. Dice values ranging 0.8–0.9 were obtained. In addition, strong correlation was found between the volume size of the automated and the manual parcellation. Then, we present scan-rescan reproducibility based on another dataset of 16 DTI images – an average of 3.73%, 1.91%, and 1.79% for volume, mean FA, and mean MD respectively. Finally, the range of anatomical variability in the normal population was quantified for each structure. PMID:24809486

ASTROS: A multidisciplinary automated structural design tool

NASA Technical Reports Server (NTRS)

Neill, D. J.

1989-01-01

ASTROS (Automated Structural Optimization System) is a finite-element-based multidisciplinary structural optimization procedure developed under Air Force sponsorship to perform automated preliminary structural design. The design task is the determination of the structural sizes that provide an optimal structure while satisfying numerous constraints from many disciplines. In addition to its automated design features, ASTROS provides a general transient and frequency response capability, as well as a special feature to perform a transient analysis of a vehicle subjected to a nuclear blast. The motivation for the development of a single multidisciplinary design tool is that such a tool can provide improved structural designs in less time than is currently needed. The role of such a tool is even more apparent as modern materials come into widespread use. Balancing conflicting requirements for the structure's strength and stiffness while exploiting the benefits of material anisotropy is perhaps an impossible task without assistance from an automated design tool. Finally, the use of a single tool can bring the design task into better focus among design team members, thereby improving their insight into the overall task.

Diabetic Rethinopathy Screening by Bright Lesions Extraction from Fundus Images

NASA Astrophysics Data System (ADS)

Hanđsková, Veronika; Pavlovičova, Jarmila; Oravec, Miloš; Blaško, Radoslav

2013-09-01

Retinal images are nowadays widely used to diagnose many diseases, for example diabetic retinopathy. In our work, we propose the algorithm for the screening application, which identifies the patients with such severe diabetic complication as diabetic retinopathy is, in early phase. In the application we use the patient's fundus photography without any additional examination by an ophtalmologist. After this screening identification, other examination methods should be considered and the patient's follow-up by a doctor is necessary. Our application is composed of three principal modules including fundus image preprocessing, feature extraction and feature classification. Image preprocessing module has the role of luminance normalization, contrast enhancement and optical disk masking. Feature extraction module includes two stages: bright lesions candidates localization and candidates feature extraction. We selected 16 statistical and structural features. For feature classification, we use multilayer perceptron (MLP) with one hidden layer. We classify images into two classes. Feature classification efficiency is about 93 percent.

A Novel Physical Technique for E. Coli Removal from Stormwater

EPA Science Inventory

In addition to heavy metals and polymeric aromatic hydrocarbons(PAHs), pathogens such as E.Coli contribute to the overall pollutant load in urban stormwater runoff. A number of constructed landscape features, collectively known as structural best management practices (BMPs) are e...

Structural features facilitating tumor cell targeting and internalization by bleomycin and its disaccharide.

PubMed

Yu, Zhiqiang; Paul, Rakesh; Bhattacharya, Chandrabali; Bozeman, Trevor C; Rishel, Michael J; Hecht, Sidney M

2015-05-19

We have shown previously that the bleomycin (BLM) carbohydrate moiety can recapitulate the tumor cell targeting effects of the entire BLM molecule, that BLM itself is modular in nature consisting of a DNA-cleaving aglycone which is delivered selectively to the interior of tumor cells by its carbohydrate moiety, and that there are disaccharides structurally related to the BLM disaccharide which are more efficient than the natural disaccharide at tumor cell targeting/uptake. Because BLM sugars can deliver molecular cargoes selectively to tumor cells, and thus potentially form the basis for a novel antitumor strategy, it seemed important to consider additional structural features capable of affecting the efficiency of tumor cell recognition and delivery. These included the effects of sugar polyvalency and net charge (at physiological pH) on tumor cell recognition, internalization, and trafficking. Since these parameters have been shown to affect cell surface recognition, internalization, and distribution in other contexts, this study has sought to define the effects of these structural features on tumor cell recognition by bleomycin and its disaccharide. We demonstrate that both can have a significant effect on tumor cell binding/internalization, and present data which suggests that the metal ions normally bound by bleomycin following clinical administration may significantly contribute to the efficiency of tumor cell uptake, in addition to their characterized function in DNA cleavage. A BLM disaccharide-Cy5** conjugate incorporating the positively charged dipeptide d-Lys-d-Lys was found to associate with both the mitochondria and the nuclear envelope of DU145 cells, suggesting possible cellular targets for BLM disaccharide-cytotoxin conjugates.

Structural Pituitary Abnormalities Associated With CHARGE Syndrome

PubMed Central

Gregory, Louise C.; Gevers, Evelien F.; Baker, Joanne; Kasia, Tessa; Chong, Kling; Josifova, Dragana J.; Caimari, Maria; Bilan, Frederic; McCabe, Mark J.

2013-01-01

Introduction: CHARGE syndrome is a multisystem disorder that, in addition to Kallmann syndrome/isolated hypogonadotrophic hypogonadism, has been associated with anterior pituitary hypoplasia (APH). However, structural abnormalities such as an ectopic posterior pituitary (EPP) have not yet been described in such patients. Objective: The aims of the study were: 1) to describe the association between CHARGE syndrome and a structurally abnormal pituitary gland; and 2) to investigate whether CHD7 variants, which are identified in 65% of CHARGE patients, are common in septo-optic dysplasia /hypopituitarism. Methods: We describe 2 patients with features of CHARGE and EPP. CHD7 was sequenced in these and other patients with septo-optic dysplasia/hypopituitarism. Results: EPP, APH, and GH, TSH, and probable LH/FSH deficiency were present in 1 patient, and EPP and APH with GH, TSH, LH/FSH, and ACTH deficiency were present in another patient, both of whom had features of CHARGE syndrome. Both had variations in CHD7 that were novel and undetected in control cohorts or in the international database of CHARGE patients, but were also present in their unaffected mothers. No CHD7 variants were detected in the patients with septo-optic dysplasia/hypopituitarism without additional CHARGE features. Conclusion: We report a novel association between CHARGE syndrome and structural abnormalities of the pituitary gland in 2 patients with variations in CHD7 that are of unknown significance. However, CHD7 mutations are an uncommon cause of septo-optic dysplasia or hypopituitarism. Our data suggest the need for evaluation of pituitary function/anatomy in patients with CHARGE syndrome. PMID:23526466

Structural Features Facilitating Tumor Cell Targeting and Internalization by Bleomycin and Its Disaccharide

PubMed Central

2016-01-01

We have shown previously that the bleomycin (BLM) carbohydrate moiety can recapitulate the tumor cell targeting effects of the entire BLM molecule, that BLM itself is modular in nature consisting of a DNA-cleaving aglycone which is delivered selectively to the interior of tumor cells by its carbohydrate moiety, and that there are disaccharides structurally related to the BLM disaccharide which are more efficient than the natural disaccharide at tumor cell targeting/uptake. Because BLM sugars can deliver molecular cargoes selectively to tumor cells, and thus potentially form the basis for a novel antitumor strategy, it seemed important to consider additional structural features capable of affecting the efficiency of tumor cell recognition and delivery. These included the effects of sugar polyvalency and net charge (at physiological pH) on tumor cell recognition, internalization, and trafficking. Since these parameters have been shown to affect cell surface recognition, internalization, and distribution in other contexts, this study has sought to define the effects of these structural features on tumor cell recognition by bleomycin and its disaccharide. We demonstrate that both can have a significant effect on tumor cell binding/internalization, and present data which suggests that the metal ions normally bound by bleomycin following clinical administration may significantly contribute to the efficiency of tumor cell uptake, in addition to their characterized function in DNA cleavage. A BLM disaccharide-Cy5** conjugate incorporating the positively charged dipeptide d-Lys-d-Lys was found to associate with both the mitochondria and the nuclear envelope of DU145 cells, suggesting possible cellular targets for BLM disaccharide–cytotoxin conjugates. PMID:25905565

Investigations of High Pressure Acoustic Waves in Resonators with Seal-Like Features

NASA Technical Reports Server (NTRS)

Daniels, Christopher C.; Steinetz, Bruce M.; Finkbeiner, Joshua R.; Li, Xiao-Fan; Raman, Ganesh

2004-01-01

1) Standing waves with maximum pressures of 188 kPa have been produced in resonators containing ambient pressure air; 2) Addition of structures inside the resonator shifts the fundamental frequency and decreases the amplitude of the generated pressure waves; 3) Addition of holes to the resonator does reduce the magnitude of the acoustic waves produced, but their addition does not prohibit the generation of large magnitude non-linear standing waves; 4) The feasibility of reducing leakage using non-linear acoustics has been confirmed.

Advanced applications of scatterometry based optical metrology

NASA Astrophysics Data System (ADS)

Dixit, Dhairya; Keller, Nick; Kagalwala, Taher; Recchia, Fiona; Lifshitz, Yevgeny; Elia, Alexander; Todi, Vinit; Fronheiser, Jody; Vaid, Alok

2017-03-01

The semiconductor industry continues to drive patterning solutions that enable devices with higher memory storage capacity, faster computing performance, and lower cost per transistor. These developments in the field of semiconductor manufacturing along with the overall minimization of the size of transistors require continuous development of metrology tools used for characterization of these complex 3D device architectures. Optical scatterometry or optical critical dimension (OCD) is one of the most prevalent inline metrology techniques in semiconductor manufacturing because it is a quick, precise and non-destructive metrology technique. However, at present OCD is predominantly used to measure the feature dimensions such as line-width, height, side-wall angle, etc. of the patterned nano structures. Use of optical scatterometry for characterizing defects such as pitch-walking, overlay, line edge roughness, etc. is fairly limited. Inspection of process induced abnormalities is a fundamental part of process yield improvement. It provides process engineers with important information about process errors, and consequently helps optimize materials and process parameters. Scatterometry is an averaging technique and extending it to measure the position of local process induced defectivity and feature-to-feature variation is extremely challenging. This report is an overview of applications and benefits of using optical scatterometry for characterizing defects such as pitch-walking, overlay and fin bending for advanced technology nodes beyond 7nm. Currently, the optical scatterometry is based on conventional spectroscopic ellipsometry and spectroscopic reflectometry measurements, but generalized ellipsometry or Mueller matrix spectroscopic ellipsometry data provides important, additional information about complex structures that exhibit anisotropy and depolarization effects. In addition the symmetry-antisymmetry properties associated with Mueller matrix (MM) elements provide an excellent means of measuring asymmetry present in the structure. The useful additional information as well as symmetry-antisymmetry properties of MM elements is used to characterize fin bending, overlay defects and design improvements in the OCD test structures are used to boost OCDs' sensitivity to pitch-walking. In addition, the validity of the OCD based results is established by comparing the results to the top down critical dimensionscanning electron microscope (CD-SEM) and cross-sectional transmission electron microscope (TEM) images.

Spectroscopy and atomic force microscopy of biomass.

PubMed

Tetard, L; Passian, A; Farahi, R H; Kalluri, U C; Davison, B H; Thundat, T

2010-05-01

Scanning probe microscopy has emerged as a powerful approach to a broader understanding of the molecular architecture of cell walls, which may shed light on the challenge of efficient cellulosic ethanol production. We have obtained preliminary images of both Populus and switchgrass samples using atomic force microscopy (AFM). The results show distinctive features that are shared by switchgrass and Populus. These features may be attributable to the lignocellulosic cell wall composition, as the collected images exhibit the characteristic macromolecular globule structures attributable to the lignocellulosic systems. Using both AFM and a single case of mode synthesizing atomic force microscopy (MSAFM) to characterize Populus, we obtained images that clearly show the cell wall structure. The results are of importance in providing a better understanding of the characteristic features of both mature cells as well as developing plant cells. In addition, we present spectroscopic investigation of the same samples.

Iterative feature refinement for accurate undersampled MR image reconstruction

NASA Astrophysics Data System (ADS)

Wang, Shanshan; Liu, Jianbo; Liu, Qiegen; Ying, Leslie; Liu, Xin; Zheng, Hairong; Liang, Dong

2016-05-01

Accelerating MR scan is of great significance for clinical, research and advanced applications, and one main effort to achieve this is the utilization of compressed sensing (CS) theory. Nevertheless, the existing CSMRI approaches still have limitations such as fine structure loss or high computational complexity. This paper proposes a novel iterative feature refinement (IFR) module for accurate MR image reconstruction from undersampled K-space data. Integrating IFR with CSMRI which is equipped with fixed transforms, we develop an IFR-CS method to restore meaningful structures and details that are originally discarded without introducing too much additional complexity. Specifically, the proposed IFR-CS is realized with three iterative steps, namely sparsity-promoting denoising, feature refinement and Tikhonov regularization. Experimental results on both simulated and in vivo MR datasets have shown that the proposed module has a strong capability to capture image details, and that IFR-CS is comparable and even superior to other state-of-the-art reconstruction approaches.

Electron Beam Freeform Fabrication of Titanium Alloy Gradient Structures

NASA Technical Reports Server (NTRS)

Brice, Craig A.; Newman, John A.; Bird, Richard Keith; Shenoy, Ravi N.; Baughman, James M.; Gupta, Vipul K.

2014-01-01

Historically, the structural optimization of aerospace components has been done through geometric methods. A monolithic material is chosen based on the best compromise between the competing design limiting criteria. Then the structure is geometrically optimized to give the best overall performance using the single material chosen. Functionally graded materials offer the potential to further improve structural efficiency by allowing the material composition and/or microstructural features to spatially vary within a single structure. Thus, local properties could be tailored to the local design limiting criteria. Additive manufacturing techniques enable the fabrication of such graded materials and structures. This paper presents the results of a graded material study using two titanium alloys processed using electron beam freeform fabrication, an additive manufacturing process. The results show that the two alloys uniformly mix at various ratios and the resultant static tensile properties of the mixed alloys behave according to rule-of-mixtures. Additionally, the crack growth behavior across an abrupt change from one alloy to the other shows no discontinuity and the crack smoothly transitions from one crack growth regime into another.

Inorganic bromine in organic molecular crystals: Database survey and four case studies

NASA Astrophysics Data System (ADS)

Nemec, Vinko; Lisac, Katarina; Stilinović, Vladimir; Cinčić, Dominik

2017-01-01

We present a Cambridge Structural Database and experimental study of multicomponent molecular crystals containing bromine. The CSD study covers supramolecular behaviour of bromide and tribromide anions as well as halogen bonded dibromine molecules in crystal structures of organic salts and cocrystals, and a study of the geometries and complexities in polybromide anion systems. In addition, we present four case studies of organic structures with bromide, tribromide and polybromide anions as well as the neutral dibromine molecule. These include the first observed crystal with diprotonated phenazine, a double salt of phenazinium bromide and tribromide, a cocrystal of 4-methoxypyridine with the neutral dibromine molecule as a halogen bond donor, as well as bis(4-methoxypyridine)bromonium polybromide. Structural features of the four case studies are in the most part consistent with the statistically prevalent behaviour indicated by the CSD study for given bromine species, although they do exhibit some unorthodox structural features and in that indicate possible supramolecular causes for aberrations from the statistically most abundant (and presumably most favourable) geometries.

Indel PDB: a database of structural insertions and deletions derived from sequence alignments of closely related proteins.

PubMed

Hsing, Michael; Cherkasov, Artem

2008-06-25

Insertions and deletions (indels) represent a common type of sequence variations, which are less studied and pose many important biological questions. Recent research has shown that the presence of sizable indels in protein sequences may be indicative of protein essentiality and their role in protein interaction networks. Examples of utilization of indels for structure-based drug design have also been recently demonstrated. Nonetheless many structural and functional characteristics of indels remain less researched or unknown. We have created a web-based resource, Indel PDB, representing a structural database of insertions/deletions identified from the sequence alignments of highly similar proteins found in the Protein Data Bank (PDB). Indel PDB utilized large amounts of available structural information to characterize 1-, 2- and 3-dimensional features of indel sites. Indel PDB contains 117,266 non-redundant indel sites extracted from 11,294 indel-containing proteins. Unlike loop databases, Indel PDB features more indel sequences with secondary structures including alpha-helices and beta-sheets in addition to loops. The insertion fragments have been characterized by their sequences, lengths, locations, secondary structure composition, solvent accessibility, protein domain association and three dimensional structures. By utilizing the data available in Indel PDB, we have studied and presented here several sequence and structural features of indels. We anticipate that Indel PDB will not only enable future functional studies of indels, but will also assist protein modeling efforts and identification of indel-directed drug binding sites.

Advances in the floral structural characterization of the major subclades of Malpighiales, one of the largest orders of flowering plants

PubMed Central

Endress, Peter K.; Davis, Charles C.; Matthews, Merran L.

2013-01-01

Background and Aims Malpighiales are one of the largest angiosperm orders and have undergone radical systematic restructuring based on molecular phylogenetic studies. The clade has been recalcitrant to molecular phylogenetic reconstruction, but has become much more resolved at the suprafamilial level. It now contains so many newly identified clades that there is an urgent need for comparative studies to understand their structure, biology and evolution. This is especially true because the order contains a disproportionally large diversity of rain forest species and includes numerous agriculturally important plants. This study is a first broad systematic step in this endeavour. It focuses on a comparative structural overview of the flowers across all recently identified suprafamilial clades of Malpighiales, and points towards areas that desperately need attention. Methods The phylogenetic comparative analysis of floral structure for the order is based on our previously published studies on four suprafamilial clades of Malpighiales, including also four related rosid orders (Celastrales, Crossosomatales, Cucurbitales, Oxalidales). In addition, the results are compiled from a survey of over 3000 publications on macrosystematics, floral structure and embryology across all orders of the core eudicots. Key Results Most new suprafamilial clades within Malpighiales are well supported by floral structural features. Inner morphological structures of the gynoecium (i.e. stigmatic lobes, inner shape of the locules, placentation, presence of obturators) and ovules (i.e. structure of the nucellus, thickness of the integuments, presence of vascular bundles in the integuments, presence of an endothelium in the inner integument) appear to be especially suitable for characterizing suprafamilial clades within Malpighiales. Conclusions Although the current phylogenetic reconstruction of Malpighiales is much improved compared with earlier versions, it is incomplete, and further focused phylogenetic and morphological studies are needed. Once all major subclades of Malpighiales are elucidated, more in-depth studies on promising structural features can be conducted. In addition, once the phylogenetic tree of Malpighiales, including closely related orders, is more fully resolved, character optimization studies will be possible to reconstruct evolution of structural and biological features within the order. PMID:23486341

Capturing the Complexity of Additively Manufactured Microstructures

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

Livescu, Veronica; Bronkhorst, Curt Allan; Vander Wiel, Scott Alan

2016-05-12

The underlying mechanisms and kinetics controlling damage nucleation and growth as a function of material microstructure and loading paths are discussed. These experiments indicate that structural features such as grain boundaries, grain size distribution, grain morphology crystallographic texture are all factors that influence mechanical behavior.

Fluid Mechanical Properties of Silkworm Fibroin Solutions

NASA Astrophysics Data System (ADS)

Matsumoto, Akira

2005-11-01

The aqueous solution behavior of silk fibroin is of interest due to the assembly and processing of this protein related to the spinning of protein fibers that exhibit remarkable mechanical properties. To gain insight into the origins of this functional feature, it is desired to determine how the protein behaves under a range of solution conditions. Pure fibroin at different concentrations in water was studied for surface tension, as a measure of surfactancy. In addition, shear induced changes on these solutions in terms of structure and morphology was also determined. Fibroin solutions exhibited shear rate-sensitive viscosity changes and precipitated at a critical shear rate where a dramatic increase of 75-150% of the initial value was observed along with a decrease in viscosity. In surface tension measurements, critical micelle concentrations were in the range of 3-4% w/v. The influence of additional factors, such as sericin protein, divalent and monovalent cations, and pH on the solution behavior in relation to structural and morphological features will also be described.

Effect of growth pressure on the synthesis of vertically aligned carbon nanotubes and their growth termination.

PubMed

Park, Sangeun; Song, Wooseok; Kim, Yooseok; Song, Inkyung; Kim, Sung Hwan; Lee, Su Il; Jang, Sung Won; Parkl, Chong-Yun

2014-07-01

When vertically aligned carbon nanotubes (VACNTs) are synthesized by thermal chemical vapor deposition (TCVD), their structural features such as height and density can be determined by TCVD growth conditions. In this study we investigated the effect of growth pressure on the structural features of VACNTs. Changes in growth pressure significantly affected the height, density, and crystalinity of synthesized VACNTs. In addition, we suggest that the growth termination of VACNTs could be due to the lack of carbon feedstock supply to the center of the VACNT film induced by the pressure-dependent adsorption of amorphous carbon at the edge of the VACNT film. In addition, the field emission characteristics of the VACNT film were carried out. The turn-on voltage of the VACNT film was 1.62 V/microm and the field enhancement factor (beta) was 2478. These results provide useful information for practical applications of VACNTs, such as field emission display and X-ray source.

NCBI GEO: archive for high-throughput functional genomic data.

PubMed

Barrett, Tanya; Troup, Dennis B; Wilhite, Stephen E; Ledoux, Pierre; Rudnev, Dmitry; Evangelista, Carlos; Kim, Irene F; Soboleva, Alexandra; Tomashevsky, Maxim; Marshall, Kimberly A; Phillippy, Katherine H; Sherman, Patti M; Muertter, Rolf N; Edgar, Ron

2009-01-01

The Gene Expression Omnibus (GEO) at the National Center for Biotechnology Information (NCBI) is the largest public repository for high-throughput gene expression data. Additionally, GEO hosts other categories of high-throughput functional genomic data, including those that examine genome copy number variations, chromatin structure, methylation status and transcription factor binding. These data are generated by the research community using high-throughput technologies like microarrays and, more recently, next-generation sequencing. The database has a flexible infrastructure that can capture fully annotated raw and processed data, enabling compliance with major community-derived scientific reporting standards such as 'Minimum Information About a Microarray Experiment' (MIAME). In addition to serving as a centralized data storage hub, GEO offers many tools and features that allow users to effectively explore, analyze and download expression data from both gene-centric and experiment-centric perspectives. This article summarizes the GEO repository structure, content and operating procedures, as well as recently introduced data mining features. GEO is freely accessible at http://www.ncbi.nlm.nih.gov/geo/.

System design of a 1 MW north-facing, solid particle receiver

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

Christian, J.; Ho, C.

Falling solid particle receivers (SPR) utilize small particles as a heat collecting medium within a cavity receiver structure. The components required to operate an SPR include the receiver (to heat the particles), bottom hopper (to catch the falling particles), particle lift elevator (to lift particles back to the top of the receiver), top hopper (to store particles before being dropped through the receiver), and ducting. In addition to the required components, there are additional features needed for an experimental system. These features include: a support structure to house all components, calibration panel to measure incident radiation, cooling loops, and sensorsmore » (flux gages, thermocouples, pressure gages). Each of these components had to be designed to withstand temperatures ranging from ambient to 700 °C. Thermal stresses from thermal expansion become a key factor in these types of high temperature systems. The SPR will be housing ~3000 kg of solid particles. The final system will be tested at the National Solar Thermal Test Facility in Albuquerque, NM.« less

System design of a 1 MW north-facing, solid particle receiver

DOE PAGES

Christian, J.; Ho, C.

2015-05-01

Falling solid particle receivers (SPR) utilize small particles as a heat collecting medium within a cavity receiver structure. The components required to operate an SPR include the receiver (to heat the particles), bottom hopper (to catch the falling particles), particle lift elevator (to lift particles back to the top of the receiver), top hopper (to store particles before being dropped through the receiver), and ducting. In addition to the required components, there are additional features needed for an experimental system. These features include: a support structure to house all components, calibration panel to measure incident radiation, cooling loops, and sensorsmore » (flux gages, thermocouples, pressure gages). Each of these components had to be designed to withstand temperatures ranging from ambient to 700 °C. Thermal stresses from thermal expansion become a key factor in these types of high temperature systems. The SPR will be housing ~3000 kg of solid particles. The final system will be tested at the National Solar Thermal Test Facility in Albuquerque, NM.« less

Nonlocal sparse model with adaptive structural clustering for feature extraction of aero-engine bearings

NASA Astrophysics Data System (ADS)

Zhang, Han; Chen, Xuefeng; Du, Zhaohui; Li, Xiang; Yan, Ruqiang

2016-04-01

Fault information of aero-engine bearings presents two particular phenomena, i.e., waveform distortion and impulsive feature frequency band dispersion, which leads to a challenging problem for current techniques of bearing fault diagnosis. Moreover, although many progresses of sparse representation theory have been made in feature extraction of fault information, the theory also confronts inevitable performance degradation due to the fact that relatively weak fault information has not sufficiently prominent and sparse representations. Therefore, a novel nonlocal sparse model (coined NLSM) and its algorithm framework has been proposed in this paper, which goes beyond simple sparsity by introducing more intrinsic structures of feature information. This work adequately exploits the underlying prior information that feature information exhibits nonlocal self-similarity through clustering similar signal fragments and stacking them together into groups. Within this framework, the prior information is transformed into a regularization term and a sparse optimization problem, which could be solved through block coordinate descent method (BCD), is formulated. Additionally, the adaptive structural clustering sparse dictionary learning technique, which utilizes k-Nearest-Neighbor (kNN) clustering and principal component analysis (PCA) learning, is adopted to further enable sufficient sparsity of feature information. Moreover, the selection rule of regularization parameter and computational complexity are described in detail. The performance of the proposed framework is evaluated through numerical experiment and its superiority with respect to the state-of-the-art method in the field is demonstrated through the vibration signals of experimental rig of aircraft engine bearings.

Modulus and yield stress of drawn LDPE

NASA Astrophysics Data System (ADS)

Thavarungkul, Nandh

Modulus and yield stress were investigated in drawn low density polyethylene (LDPE) film. Uniaxially drawn polymeric films usually show high values of modulus and yield stress, however, studies have normally only been conducted to identify the structural features that determine modulus. In this study small-angle x-ray scattering (SAXS), thermal shrinkage, birefringence, differential scanning calorimetry (DSC), and dynamic mechanical thermal analysis (DMTA) were used to examine, directly and indirectly, the structural features that determine both modulus and yield stress, which are often closely related in undrawn materials. Shish-kebab structures are proposed to account for the mechanical properties in drawn LDPE. The validity of this molecular/morphological model was tested using relationships between static mechanical data and structural and physical parameters. In addition, dynamic mechanical results are also in line with static data in supporting the model. In the machine direction (MD), "shish" and taut tie molecules (TTM) anchored in the crystalline phase account for E; whereas crystal lamellae with contributions from "shish" and TTM determine yield stress. In the transverse direction (TD), the crystalline phase plays an important roll in both modulus and yield stress. Modulus is determined by crystal lamellae functioning as platelet reinforcing elements in the amorphous matrix with an additional contributions from TTM and yield stress is determined by the crystal lamellae's resistance to deformation.

Use of the temporal median and trimmed mean mitigates effects of respiratory motion in multiple-acquisition abdominal diffusion imaging

NASA Astrophysics Data System (ADS)

Jerome, N. P.; Orton, M. R.; d'Arcy, J. A.; Feiweier, T.; Tunariu, N.; Koh, D.-M.; Leach, M. O.; Collins, D. J.

2015-01-01

Respiratory motion commonly confounds abdominal diffusion-weighted magnetic resonance imaging, where averaging of successive samples at different parts of the respiratory cycle, performed in the scanner, manifests the motion as blurring of tissue boundaries and structural features and can introduce bias into calculated diffusion metrics. Storing multiple averages separately allows processing using metrics other than the mean; in this prospective volunteer study, median and trimmed mean values of signal intensity for each voxel over repeated averages and diffusion-weighting directions are shown to give images with sharper tissue boundaries and structural features for moving tissues, while not compromising non-moving structures. Expert visual scoring of derived diffusion maps is significantly higher for the median than for the mean, with modest improvement from the trimmed mean. Diffusion metrics derived from mono- and bi-exponential diffusion models are comparable for non-moving structures, demonstrating a lack of introduced bias from using the median. The use of the median is a simple and computationally inexpensive alternative to complex and expensive registration algorithms, requiring only additional data storage (and no additional scanning time) while returning visually superior images that will facilitate the appropriate placement of regions-of-interest when analysing abdominal diffusion-weighted magnetic resonance images, for assessment of disease characteristics and treatment response.

Use of the temporal median and trimmed mean mitigates effects of respiratory motion in multiple-acquisition abdominal diffusion imaging.

PubMed

Jerome, N P; Orton, M R; d'Arcy, J A; Feiweier, T; Tunariu, N; Koh, D-M; Leach, M O; Collins, D J

2015-01-21

Respiratory motion commonly confounds abdominal diffusion-weighted magnetic resonance imaging, where averaging of successive samples at different parts of the respiratory cycle, performed in the scanner, manifests the motion as blurring of tissue boundaries and structural features and can introduce bias into calculated diffusion metrics. Storing multiple averages separately allows processing using metrics other than the mean; in this prospective volunteer study, median and trimmed mean values of signal intensity for each voxel over repeated averages and diffusion-weighting directions are shown to give images with sharper tissue boundaries and structural features for moving tissues, while not compromising non-moving structures. Expert visual scoring of derived diffusion maps is significantly higher for the median than for the mean, with modest improvement from the trimmed mean. Diffusion metrics derived from mono- and bi-exponential diffusion models are comparable for non-moving structures, demonstrating a lack of introduced bias from using the median. The use of the median is a simple and computationally inexpensive alternative to complex and expensive registration algorithms, requiring only additional data storage (and no additional scanning time) while returning visually superior images that will facilitate the appropriate placement of regions-of-interest when analysing abdominal diffusion-weighted magnetic resonance images, for assessment of disease characteristics and treatment response.

Investigations on the Mechanical Properties of Conducting Polymer Coating-Substrate Structures and Their Influencing Factors

PubMed Central

Wang, Xi-Shu; Tang, Hua-Ping; Li, Xu-Dong; Hua, Xin

2009-01-01

This review covers recent advances and work on the microstructure features, mechanical properties and cracking processes of conducting polymer film/coating- substrate structures under different testing conditions. An attempt is made to characterize and quantify the relationships between mechanical properties and microstructure features. In addition, the film cracking mechanism on the micro scale and some influencing factors that play a significant role in the service of the film-substrate structure are presented. These investigations cover the conducting polymer film/coating nucleation process, microstructure-fracture characterization, translation of brittle-ductile fractures, and cracking processes near the largest inherent macromolecule defects under thermal-mechanical loadings, and were carried out using in situ scanning electron microscopy (SEM) observations, as a novel method for evaluation of interface strength and critical failure stress. PMID:20054470

Transition-metal-substituted indium thiospinels as novel intermediate-band materials: prediction and understanding of their electronic properties.

PubMed

Palacios, P; Aguilera, I; Sánchez, K; Conesa, J C; Wahnón, P

2008-07-25

Results of density-functional calculations for indium thiospinel semiconductors substituted at octahedral sites with isolated transition metals (M=Ti,V) show an isolated partially filled narrow band containing three t2g-type states per M atom inside the usual semiconductor band gap. Thanks to this electronic structure feature, these materials will allow the absorption of photons with energy below the band gap, in addition to the normal light absorption of a semiconductor. To our knowledge, we demonstrate for the first time the formation of an isolated intermediate electronic band structure through M substitution at octahedral sites in a semiconductor, leading to an enhancement of the absorption coefficient in both infrared and visible ranges of the solar spectrum. This electronic structure feature could be applied for developing a new third-generation photovoltaic cell.

Mosaic tetraploidy in a liveborn infant with features of the DiGeorge anomaly.

PubMed

Wullich, B; Henn, W; Groterath, E; Ermis, A; Fuchs, S; Zankl, M

1991-11-01

We report on a liveborn male infant with mosaic tetraploidy who presented with multiple congenital anomalies including features of the DiGeorge anomaly (type I truncus arteriosus with other cardiovascular malformations, thymic hypoplasia, hypocalcemia). No structural chromosome aberrations, namely of chromosome 22, were detected. These findings contribute to the variability of symptoms of the polyploid phenotype. Additionally, the cytogenetic studies in our case emphasize the necessity of investigating fibroblasts in order to evaluate the relevant proportion of aberrant cells in mosaicism.

Earth observation taken by the Expedition 28 crew

NASA Image and Video Library

2011-09-08

ISS028-E-044433 (8 Sept. 2011) --- Bigach Impact Crater in Kazakhstan is featured in this image photographed by an Expedition 28 crew member on the International Space Station. Some meteor impact craters, like Barringer Crater in Arizona, are easily recognizable on the landscape due to well-preserved form and features. Other impact structures, such as Bigach Impact Crater in northeastern Kazakhstan are harder to recognize due to their age, modification by subsequent geologic processes, or even human alteration of the landscape. According to scientists, at approximately 5 million years old, Bigach is a relatively young geologic feature; however active tectonic processes in the region have caused movement of parts of the structure along faults, leading to a somewhat angular appearance (center). The roughly circular rim of the eight kilometers in diameter structure is still discernable around the relatively flat interior in this photograph. In addition to modification by faulting and erosion, the interior of the impact structure has also been used for agricultural activities, as indicated by the presence of tan regular graded fields. Other rectangular agricultural fields are visible to the northeast and east. The closest settlement, Novopavlovka, is barely visible near the top of the image.

Morphometry Based on Effective and Accurate Correspondences of Localized Patterns (MEACOLP)

PubMed Central

Wang, Hu; Ren, Yanshuang; Bai, Lijun; Zhang, Wensheng; Tian, Jie

2012-01-01

Local features in volumetric images have been used to identify correspondences of localized anatomical structures for brain morphometry. However, the correspondences are often sparse thus ineffective in reflecting the underlying structures, making it unreliable to evaluate specific morphological differences. This paper presents a morphometry method (MEACOLP) based on correspondences with improved effectiveness and accuracy. A novel two-level scale-invariant feature transform is used to enhance the detection repeatability of local features and to recall the correspondences that might be missed in previous studies. Template patterns whose correspondences could be commonly identified in each group are constructed to serve as the basis for morphometric analysis. A matching algorithm is developed to reduce the identification errors by comparing neighboring local features and rejecting unreliable matches. The two-sample t-test is finally adopted to analyze specific properties of the template patterns. Experiments are performed on the public OASIS database to clinically analyze brain images of Alzheimer's disease (AD) and normal controls (NC). MEACOLP automatically identifies known morphological differences between AD and NC brains, and characterizes the differences well as the scaling and translation of underlying structures. Most of the significant differences are identified in only a single hemisphere, indicating that AD-related structures are characterized by strong anatomical asymmetry. In addition, classification trials to differentiate AD subjects from NC confirm that the morphological differences are reliably related to the groups of interest. PMID:22540000

Application of PALSAR-2 Remote Sensing Data for Landslide Hazard Mapping in Kelantan River Basin, Peninsular Malaysia

NASA Astrophysics Data System (ADS)

Beiranvand Pour, Amin; Hashim, Mazlan

2016-06-01

Yearly, several landslides ensued during heavy monsoons rainfall in Kelantan river basin, peninsular Malaysia, which are obviously connected to geological structures and topographical features of the region. In this study, the recently launched Phased Array type L-band Synthetic Aperture Radar-2 (PALSAR-2) onboard the Advanced Land Observing Satellite-2 (ALOS-2), remote sensing data were used to map geological structural and topographical features in the Kelantan river basin for identification of high potential risk and susceptible zones for landslides. Adaptive Local Sigma filter was selected and applied to accomplish speckle reduction and preserving both edges and features in PALSAR-2 fine mode observation images. Different polarization images were integrated to enhance geological structures. Additionally, directional filters were applied to the PALSAR-2 Local Sigma resultant image for edge enhancement and detailed identification of linear features. Several faults, drainage patterns and lithological contact layers were identified at regional scale. In order to assess the results, fieldwork and GPS survey were conducted in the landslide affected zones in the Kelantan river basin. Results demonstrate the most of the landslides were associated with N-S, NNW-SSE and NE-SW trending faults, angulated drainage pattern and metamorphic and Quaternary units. Consequently, structural and topographical geology maps were produced for Kelantan river basin using PALSAR-2 data, which could be broadly applicable for landslide hazard mapping.

Meteoroid and debris special investigation group data acquisition procedures

NASA Technical Reports Server (NTRS)

See, Thomas H.; Allbrooks, Martha K.; Atkinson, Dale R.; Sapp, Clyde A.; Simon, Charles G.; Zolensky, Mike E.

1992-01-01

The entire LDEF spacecraft was examined by M&D SIG for impact (i.e., craters greater than or = 0.5 mm and penetrations greater than or = 0.3 mm in diameter) and related features (e.g., debris, secondaries). During the various detailed surveys conducted at NASA Kennedy, approx. 5,000 impact related features were photodocumented, and their locations measured and recorded; an additional approx. 30,000 smaller features were counted. The equipment and techniques used by the M&D SIG permitted the determination and recording of the locations and diameters of the 5,000 imaged features. A variety of experimental and LDEF structural hardware was acquired by the M&D SIG and is presently being examined and curated at NASA Johnson.

Building the Peanut: Simulations and Observations of Peanut-shaped Structures and Ansae in Face-on Disk Galaxies

NASA Astrophysics Data System (ADS)

Saha, Kanak; Graham, Alister W.; Rodríguez-Herranz, Isabel

2018-01-01

Peanut/x-shaped features observed in a significant fraction of disk galaxies are thought to have formed from vertically buckled bars. Despite being three-dimensional structures, they are preferentially detected in near edge-on projection. Only a few galaxies are found to have displayed such structures when their disks are relatively face-on—suggesting that either they are generally weak in face-on projection or many may be hidden by the light of their galaxy’s face-on disk. Here, we report on three (collisionless) simulated galaxies displaying peanut-shaped structures when their disks are seen both face-on and edge-on—resembling a three-dimensional peanut or dumbbell. Furthermore, these structures are accompanied by ansae and an outer ring at the end of the bar—as seen in real galaxies such as IC 5240. The same set of quantitative parameters used to measure peanut structures in real galaxies has been determined for the simulated galaxies, and a broad agreement is found. In addition, the peanut length grows in tandem with the bar, and is a maximum at half the length of the bar. Beyond the cutoff of these peanut structures, toward the end of the bar, we discover a new positive/negative feature in the B 6 radial profile associated with the isophotes of the ansae/ring. Our simulated, self-gravitating, three-dimensional peanut structures display cylindrical rotation even in the near-face-on disk projection. In addition, we report on a kinematic pinch in the velocity map along the bar minor axis, matching that seen in the surface density map.

Structural and physicochemical characterization of thermoplastic corn starch films containing microalgae.

PubMed

Fabra, María José; Martínez-Sanz, Marta; Gómez-Mascaraque, L G; Gavara, Rafael; López-Rubio, Amparo

2018-04-15

This work provides an in-depth analysis on how the addition of different microalgae species (Nannochloropsis, Spirulina and Scenedesmus) affected the structural and physicochemical properties of thermoplastic corn starch biocomposites. Structural characterization was conducted by combined SAXS/WAXS experiments and it was correlated with mechanical and barrier properties of the biocomposites. A water vapour permeability drop of ca. 54% was observed upon addition of the different microalgae species. The oxygen permeability and the mechanical properties of biocomposites containing Spirulina or Scenedesmus were not improved since the presence of microalgae hindered the re-arrangement and packing of the lamellar structure of starch polymeric chains, according to the SAXS results. Nannochloropsis caused a great reduction of the matrix rigidity and, the oxygen permeability was also improved. Therefore, all of these features make the Nannochloropsis biocomposites an alternative to generate biodegradable food packaging materials with the additional advantage that they can be easily scaled-up. Copyright © 2018 Elsevier Ltd. All rights reserved.

Effects of moiré lattice structure on electronic properties of graphene

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

Huang, Lunan; Wu, Yun; Hershberger, M. T.

Here, we study structural and electronic properties of graphene grown on silicone carbide (SiC) substrate using a scanning tunneling microscope, spot-profile-analysis low-energy electron diffraction, and angle-resolved photoemission spectroscopy. We find several new replicas of Dirac cones in the Brillouin zone. Their locations can be understood in terms of a combination of basis vectors linked to SiC 6 × 6 and graphene 6√3×6√3 reconstruction. Therefore, these new features originate from the moiré caused by the lattice mismatch between SiC and graphene. More specifically, Dirac cone replicas are caused by underlying weak modulation of the ionic potential by the substrate that ismore » then experienced by the electrons in the graphene. We also demonstrate that this effect is equally strong in single- and trilayer graphene; therefore, the additional Dirac cones are intrinsic features rather than the result of photoelectron diffraction. These new features in the electronic structure are very important for the interpretation of recent transport measurements and can assist in tuning the properties of graphene for practical applications.« less

Effects of moiré lattice structure on electronic properties of graphene

NASA Astrophysics Data System (ADS)

Huang, Lunan; Wu, Yun; Hershberger, M. T.; Mou, Daixiang; Schrunk, Benjamin; Tringides, Michael C.; Hupalo, Myron; Kaminski, Adam

2017-07-01

We study structural and electronic properties of graphene grown on silicone carbide (SiC) substrate using a scanning tunneling microscope, spot-profile-analysis low-energy electron diffraction, and angle-resolved photoemission spectroscopy. We find several new replicas of Dirac cones in the Brillouin zone. Their locations can be understood in terms of a combination of basis vectors linked to SiC 6 × 6 and graphene 6 √{3 }×6 √{3 } reconstruction. Therefore, these new features originate from the moiré caused by the lattice mismatch between SiC and graphene. More specifically, Dirac cone replicas are caused by underlying weak modulation of the ionic potential by the substrate that is then experienced by the electrons in the graphene. We also demonstrate that this effect is equally strong in single- and trilayer graphene; therefore, the additional Dirac cones are intrinsic features rather than the result of photoelectron diffraction. These new features in the electronic structure are very important for the interpretation of recent transport measurements and can assist in tuning the properties of graphene for practical applications.

Effects of moiré lattice structure on electronic properties of graphene

DOE PAGES

Huang, Lunan; Wu, Yun; Hershberger, M. T.; ...

2017-07-10

Here, we study structural and electronic properties of graphene grown on silicone carbide (SiC) substrate using a scanning tunneling microscope, spot-profile-analysis low-energy electron diffraction, and angle-resolved photoemission spectroscopy. We find several new replicas of Dirac cones in the Brillouin zone. Their locations can be understood in terms of a combination of basis vectors linked to SiC 6 × 6 and graphene 6√3×6√3 reconstruction. Therefore, these new features originate from the moiré caused by the lattice mismatch between SiC and graphene. More specifically, Dirac cone replicas are caused by underlying weak modulation of the ionic potential by the substrate that ismore » then experienced by the electrons in the graphene. We also demonstrate that this effect is equally strong in single- and trilayer graphene; therefore, the additional Dirac cones are intrinsic features rather than the result of photoelectron diffraction. These new features in the electronic structure are very important for the interpretation of recent transport measurements and can assist in tuning the properties of graphene for practical applications.« less

Real-space processing of helical filaments in SPARX

PubMed Central

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

2012-01-01

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

GFP-like proteins as ubiquitous metazoan superfamily: evolution of functional features and structural complexity.

PubMed

Shagin, Dmitry A; Barsova, Ekaterina V; Yanushevich, Yurii G; Fradkov, Arkady F; Lukyanov, Konstantin A; Labas, Yulii A; Semenova, Tatiana N; Ugalde, Juan A; Meyers, Ann; Nunez, Jose M; Widder, Edith A; Lukyanov, Sergey A; Matz, Mikhail V

2004-05-01

Homologs of the green fluorescent protein (GFP), including the recently described GFP-like domains of certain extracellular matrix proteins in Bilaterian organisms, are remarkably similar at the protein structure level, yet they often perform totally unrelated functions, thereby warranting recognition as a superfamily. Here we describe diverse GFP-like proteins from previously undersampled and completely new sources, including hydromedusae and planktonic Copepoda. In hydromedusae, yellow and nonfluorescent purple proteins were found in addition to greens. Notably, the new yellow protein seems to follow exactly the same structural solution to achieving the yellow color of fluorescence as YFP, an engineered yellow-emitting mutant variant of GFP. The addition of these new sequences made it possible to resolve deep-level phylogenetic relationships within the superfamily. Fluorescence (most likely green) must have already existed in the common ancestor of Cnidaria and Bilateria, and therefore GFP-like proteins may be responsible for fluorescence and/or coloration in virtually any animal. At least 15 color diversification events can be inferred following the maximum parsimony principle in Cnidaria. Origination of red fluorescence and nonfluorescent purple-blue colors on several independent occasions provides a remarkable example of convergent evolution of complex features at the molecular level.

Characterization of Novel Plasmonic, Photonic, and Semiconductor Microstructures

NASA Astrophysics Data System (ADS)

Sears, Jasmine Soria

The fields of telecommunications and optoelectronics are under constant pressure to shrink devices and reduce power consumption. Micro-scale photonic and plasmonic structures can trap light and enhance the brightness of active emitters; thus, these types of structures are promising avenues to accomplishing the goals of miniaturization and efficiency. A deeper understanding of specific structures is important in order to gauge their suitability for specific applications. In this dissertation, two types of microstructures are explored: one-dimensional silicon photonic crystals and self-assembled indium islands. This dissertation will provide novel characterization of these structures and a description of how to utilize or compensate for the observed features. A photonic crystal can act as a tiny resonator for certain wavelengths, making it a promising structure for applications that require extremely small lasers. However, because of silicon’s indirect bandgap, a silicon photonic crystal cavity would require the addition of an active emitter to function as a light source. Attempts to incorporate erbium into these cavities, and the observation of an unusual coupling phenomenon, will be discussed. Self-assembled indium islands are plasmonic structures that can be grown via molecular beam epitaxy. In theory, these islands should be pure indium nanoantennas on top of a smooth gallium arsenide substrate. In practice, the component materials are less segregated than predicted, giving rise to unexpected hollow dome shapes and a sub-surface indium layer. Although these features were not an intended result of indium island growth, they provide information regarding the island formation process and potentially contribute additional applications.

An ensemble-of-classifiers based approach for early diagnosis of Alzheimer's disease: classification using structural features of brain images.

PubMed

Farhan, Saima; Fahiem, Muhammad Abuzar; Tauseef, Huma

2014-01-01

Structural brain imaging is playing a vital role in identification of changes that occur in brain associated with Alzheimer's disease. This paper proposes an automated image processing based approach for the identification of AD from MRI of the brain. The proposed approach is novel in a sense that it has higher specificity/accuracy values despite the use of smaller feature set as compared to existing approaches. Moreover, the proposed approach is capable of identifying AD patients in early stages. The dataset selected consists of 85 age and gender matched individuals from OASIS database. The features selected are volume of GM, WM, and CSF and size of hippocampus. Three different classification models (SVM, MLP, and J48) are used for identification of patients and controls. In addition, an ensemble of classifiers, based on majority voting, is adopted to overcome the error caused by an independent base classifier. Ten-fold cross validation strategy is applied for the evaluation of our scheme. Moreover, to evaluate the performance of proposed approach, individual features and combination of features are fed to individual classifiers and ensemble based classifier. Using size of left hippocampus as feature, the accuracy achieved with ensemble of classifiers is 93.75%, with 100% specificity and 87.5% sensitivity.

BSIFT: toward data-independent codebook for large scale image search.

PubMed

Zhou, Wengang; Li, Houqiang; Hong, Richang; Lu, Yijuan; Tian, Qi

2015-03-01

Bag-of-Words (BoWs) model based on Scale Invariant Feature Transform (SIFT) has been widely used in large-scale image retrieval applications. Feature quantization by vector quantization plays a crucial role in BoW model, which generates visual words from the high- dimensional SIFT features, so as to adapt to the inverted file structure for the scalable retrieval. Traditional feature quantization approaches suffer several issues, such as necessity of visual codebook training, limited reliability, and update inefficiency. To avoid the above problems, in this paper, a novel feature quantization scheme is proposed to efficiently quantize each SIFT descriptor to a descriptive and discriminative bit-vector, which is called binary SIFT (BSIFT). Our quantizer is independent of image collections. In addition, by taking the first 32 bits out from BSIFT as code word, the generated BSIFT naturally lends itself to adapt to the classic inverted file structure for image indexing. Moreover, the quantization error is reduced by feature filtering, code word expansion, and query sensitive mask shielding. Without any explicit codebook for quantization, our approach can be readily applied in image search in some resource-limited scenarios. We evaluate the proposed algorithm for large scale image search on two public image data sets. Experimental results demonstrate the index efficiency and retrieval accuracy of our approach.

Enzymatic Inverse Opal Hydrogel Particles for Biocatalyst.

PubMed

Wang, Huan; Gu, Hongcheng; Chen, Zhuoyue; Shang, Luoran; Zhao, Ze; Gu, Zhongze; Zhao, Yuanjin

2017-04-19

Enzymatic carriers have a demonstrated value for chemical reactions and industrial applications. Here, we present a novel kind of inverse opal hydrogel particles as the enzymatic carriers. The particles were negatively replicated from spherical colloidal crystal templates by using magnetic nanoparticles tagged acrylamide hydrogel. Thus, they were endowed with the features of monodispersity, small volume, complete penetrating structure, and controllable motion, which are all beneficial for improving the efficiency of biocatalysis. In addition, due to the ordered porous nanostructure, the inverse opal hydrogel particles were imparted with unique photonic band gaps (PBGs) and vivid structural colors for encoding varieties of immobilized enzymes and for constructing a multienzymes biocatalysis system. These features of the inverse opal hydrogel particles indicate that they are ideal enzymatic carriers for biocatalysis.

Effect of microstructure on the elasto-viscoplastic deformation of dual phase titanium structures

NASA Astrophysics Data System (ADS)

Ozturk, Tugce; Rollett, Anthony D.

2018-02-01

The present study is devoted to the creation of a process-structure-property database for dual phase titanium alloys, through a synthetic microstructure generation method and a mesh-free fast Fourier transform based micromechanical model that operates on a discretized image of the microstructure. A sensitivity analysis is performed as a precursor to determine the statistically representative volume element size for creating 3D synthetic microstructures based on additively manufactured Ti-6Al-4V characteristics, which are further modified to expand the database for features of interest, e.g., lath thickness. Sets of titanium hardening parameters are extracted from literature, and The relative effect of the chosen microstructural features is quantified through comparisons of average and local field distributions.

Reinforcement learning algorithms for robotic navigation in dynamic environments.

PubMed

Yen, Gary G; Hickey, Travis W

2004-04-01

The purpose of this study was to examine improvements to reinforcement learning (RL) algorithms in order to successfully interact within dynamic environments. The scope of the research was that of RL algorithms as applied to robotic navigation. Proposed improvements include: addition of a forgetting mechanism, use of feature based state inputs, and hierarchical structuring of an RL agent. Simulations were performed to evaluate the individual merits and flaws of each proposal, to compare proposed methods to prior established methods, and to compare proposed methods to theoretically optimal solutions. Incorporation of a forgetting mechanism did considerably improve the learning times of RL agents in a dynamic environment. However, direct implementation of a feature-based RL agent did not result in any performance enhancements, as pure feature-based navigation results in a lack of positional awareness, and the inability of the agent to determine the location of the goal state. Inclusion of a hierarchical structure in an RL agent resulted in significantly improved performance, specifically when one layer of the hierarchy included a feature-based agent for obstacle avoidance, and a standard RL agent for global navigation. In summary, the inclusion of a forgetting mechanism, and the use of a hierarchically structured RL agent offer substantially increased performance when compared to traditional RL agents navigating in a dynamic environment.

Acceleration Testing: A Better, Faster, Cheaper Alternative for Strength Qualification Testing

NASA Technical Reports Server (NTRS)

Mattiello, Carmine F.

1997-01-01

This paper addresses the advantages of utilizing a centrifuge test over the conventional static load test methods to structurally qualify aerospace structures. Three recent test cases are reviewed and used as examples to highlight these benefits. In addition, the overall capability of Goddard's High Capacity Centrifuge (HCC) is outlined along with some unique features that were designed specifically to reduce costs, test turn around time, and increase test item safety.

Recognizing and dating prehistoric liquefaction features: Lessons learned in the New Madrid seismic zone, central United States

USGS Publications Warehouse

Tuttle, M.P.; Schweig, E.S.

1996-01-01

The New Madrid seismic zone (NMSZ), which experienced severe liquefaction during the great New Madrid, Missouri, earthquakes of 1811 and 1812 as well as during several prehistoric earthquakes, is a superb laboratory for the study of world-class, arthquake-induced liquefaction features and their use in paleoseismology. In seismically active regions like the NMSZ, frequent large earthquakes can produce a complex record of liquefaction events that is difficult to interpret. Lessons learned studying liquefaction features in the NMSZ may help to unravel the paleoseismic record in other seismically active regions. Soil characteristics of liquefaction features, as well as their structural and sratigraphic relations to Native American occupation horizons and other cultural features, an help to distinguish prehistoric liquefaction features from historic features. In addition, analyses of artifact assemblages and botanical content of cultural horizons can help to narrow the age ranges of liquefaction features. Future research should focus on methods for defining source areas and estimating magnitudes of prehistoric earthquakes from liquefaction features. Also, new methods for dating liquefaction features are needed.

Distributed cable sensors with memory feature for post-disaster damage assessment

NASA Astrophysics Data System (ADS)

Chen, Genda; McDaniel, Ryan D.; Pommerenke, David J.; Sun, Shishuang

2005-05-01

A new design of distributed crack sensors is presented for the condition assessment of reinforced concrete (RC) structures during and immediately after an earthquake event. This study is mainly focused on the performance of cable sensors under dynamic loading, particularly their ability to memorize the crack history of an RC member. This unique memory feature enables the post-earthquake condition assessment of structural members such as RC columns, in which the earthquake-induced cracks are closed immediately after an earthquake event due to gravity loads and they are visually undetectable. Factors affecting the onset of the memory feature were investigated experimentally with small-scale RC beams under cyclic loading. Test results indicated that both crack width and the number of loading cycles were instrumental in the onset of the memory feature of cable sensors. Practical issues related to dynamic acquisition with the sensors were discussed. The sensors were proven to be fatigue resistant from the shake table tests of RC columns. They continued to show useful signal after the columns can no longer support additional loads.

Nigel: A Systemic Grammar for Text Generation.

ERIC Educational Resources Information Center

Mann, William C.; Matthiessen, Christian M. I. M.

This three-paper report describes Nigel, a large, programmed grammar of English which has been created in the framework of systemic linguistics begun by Halliday, and which, in addition to specifying functions and structures of English, has a novel semantic stratum which specifies the situations for use of each grammatical feature. The…

Fabrication of two-dimensional visible wavelength nanoscale plasmonic structures using hydrogen silsesquioxane based resist

NASA Astrophysics Data System (ADS)

Smith, Kyle Z.; Gadde, Akshitha; Kadiyala, Anand; Dawson, Jeremy M.

2016-03-01

In recent years, the global market for biosensors has continued to increase in combination with their expanding use in areas such as biodefense/detection, home diagnostics, biometric identification, etc. A constant necessity for inexpensive, portable bio-sensing methods, while still remaining simple to understand and operate, is the motivation behind novel concepts and designs. Labeled visible spectrum bio-sensing systems provide instant feedback that is both simple and easy to work with, but are limited by the light intensity thresholds required by the imaging systems. In comparison, label-free bio-sensing systems and other detection modalities like electrochemical, frequency resonance, thermal change, etc., can require additional technical processing steps to convey the final result, increasing the system's complexity and possibly the time required for analysis. Further decrease in the detection limit can be achieved through the addition of plasmonic structures into labeled bio-sensing systems. Nano-structures that operate in the visible spectrum have feature sizes typically in the order of the operating wavelength, calling for high aspect ratio nanoscale fabrication capabilities. In order to achieve these dimensions, electron beam lithography (EBL) is used due to its accurate feature production. Hydrogen silsesquioxane (HSQ) based electron beam resist is chosen for one of its benefits, which is after exposure to oxygen plasma, the patterned resist cures into silicon dioxide (SiO2). These cured features in conjunction with nanoscale gold particles help in producing a high electric field through dipole generation. In this work, a detailed process flow of the fabrication of square lattice of plasmonic structures comprising of gold coated silicon dioxide pillars designed to operate at 560 nm wavelength and produce an intensity increase of roughly 100 percent will be presented.

Multi-channel MRI segmentation of eye structures and tumors using patient-specific features

PubMed Central

Ciller, Carlos; De Zanet, Sandro; Kamnitsas, Konstantinos; Maeder, Philippe; Glocker, Ben; Munier, Francis L.; Rueckert, Daniel; Thiran, Jean-Philippe

2017-01-01

Retinoblastoma and uveal melanoma are fast spreading eye tumors usually diagnosed by using 2D Fundus Image Photography (Fundus) and 2D Ultrasound (US). Diagnosis and treatment planning of such diseases often require additional complementary imaging to confirm the tumor extend via 3D Magnetic Resonance Imaging (MRI). In this context, having automatic segmentations to estimate the size and the distribution of the pathological tissue would be advantageous towards tumor characterization. Until now, the alternative has been the manual delineation of eye structures, a rather time consuming and error-prone task, to be conducted in multiple MRI sequences simultaneously. This situation, and the lack of tools for accurate eye MRI analysis, reduces the interest in MRI beyond the qualitative evaluation of the optic nerve invasion and the confirmation of recurrent malignancies below calcified tumors. In this manuscript, we propose a new framework for the automatic segmentation of eye structures and ocular tumors in multi-sequence MRI. Our key contribution is the introduction of a pathological eye model from which Eye Patient-Specific Features (EPSF) can be computed. These features combine intensity and shape information of pathological tissue while embedded in healthy structures of the eye. We assess our work on a dataset of pathological patient eyes by computing the Dice Similarity Coefficient (DSC) of the sclera, the cornea, the vitreous humor, the lens and the tumor. In addition, we quantitatively show the superior performance of our pathological eye model as compared to the segmentation obtained by using a healthy model (over 4% DSC) and demonstrate the relevance of our EPSF, which improve the final segmentation regardless of the classifier employed. PMID:28350816

A spectral-structural bag-of-features scene classifier for very high spatial resolution remote sensing imagery

NASA Astrophysics Data System (ADS)

Zhao, Bei; Zhong, Yanfei; Zhang, Liangpei

2016-06-01

Land-use classification of very high spatial resolution remote sensing (VHSR) imagery is one of the most challenging tasks in the field of remote sensing image processing. However, the land-use classification is hard to be addressed by the land-cover classification techniques, due to the complexity of the land-use scenes. Scene classification is considered to be one of the expected ways to address the land-use classification issue. The commonly used scene classification methods of VHSR imagery are all derived from the computer vision community that mainly deal with terrestrial image recognition. Differing from terrestrial images, VHSR images are taken by looking down with airborne and spaceborne sensors, which leads to the distinct light conditions and spatial configuration of land cover in VHSR imagery. Considering the distinct characteristics, two questions should be answered: (1) Which type or combination of information is suitable for the VHSR imagery scene classification? (2) Which scene classification algorithm is best for VHSR imagery? In this paper, an efficient spectral-structural bag-of-features scene classifier (SSBFC) is proposed to combine the spectral and structural information of VHSR imagery. SSBFC utilizes the first- and second-order statistics (the mean and standard deviation values, MeanStd) as the statistical spectral descriptor for the spectral information of the VHSR imagery, and uses dense scale-invariant feature transform (SIFT) as the structural feature descriptor. From the experimental results, the spectral information works better than the structural information, while the combination of the spectral and structural information is better than any single type of information. Taking the characteristic of the spatial configuration into consideration, SSBFC uses the whole image scene as the scope of the pooling operator, instead of the scope generated by a spatial pyramid (SP) commonly used in terrestrial image classification. The experimental results show that the whole image as the scope of the pooling operator performs better than the scope generated by SP. In addition, SSBFC codes and pools the spectral and structural features separately to avoid mutual interruption between the spectral and structural features. The coding vectors of spectral and structural features are then concatenated into a final coding vector. Finally, SSBFC classifies the final coding vector by support vector machine (SVM) with a histogram intersection kernel (HIK). Compared with the latest scene classification methods, the experimental results with three VHSR datasets demonstrate that the proposed SSBFC performs better than the other classification methods for VHSR image scenes.

Solid State Chemistry of Clathrate Phases: Crystal Structure, Chemical Bonding and Preparation Routes

NASA Astrophysics Data System (ADS)

Baitinger, Michael; Böhme, Bodo; Ormeci, Alim; Grin, Yuri

Clathrates represent a family of inorganic materials called cage compounds. The key feature of their crystal structures is a three-dimensional (host) framework bearing large cavities (cages) with 20-28 vertices. These polyhedral cages bear—as a rule—guest species. Depending on the formal charge of the framework, clathrates are grouped in anionic, cationic and neutral. While the bonding in the framework is of (polar) covalent nature, the guest-host interaction can be ionic, covalent or even van-der Waals, depending on the chemical composition of the clathrates. The chemical composition and structural features of the cationic clathrates can be described by the enhanced Zintl concept, whereas the composition of the anionic clathrates deviates often from the Zintl counts, indicating additional atomic interactions in comparison with the ionic-covalent Zintl model. These interactions can be visualized and studied by applying modern quantum chemical approaches such as electron localizability.

13C NMR spectroscopy of the insoluble carbon of carbonaceous chondrites

NASA Technical Reports Server (NTRS)

Cronin, J. R.; Pizzarello, S.; Frye, J. S.

1987-01-01

13C NMR spectra have been obtained of the insoluble carbon residues resulting from HF-digestion of three carbonaceous chondrites, Orgueil (C1), Murchison (CM2), and Allende (CV3). Spectra obtained using the cross polarization magic-angle spinning technique show two major features attributable respectively to carbon in aliphatic/olefinic structures. The spectrum obtained from the Allende sample was weak, presumably as a consequence of its low hydrogen content. Single pulse excitation spectra, which do not depend on 1H-13C polarization transfer for signal enhancement were also obtained. These spectra, which may be more representative of the total carbon in the meteorite samples, indicate a greater content of carbon in aromatic/olefinic structures. These results suggest that extensive polycyclic aromatic sheets are important structural features of the insoluble carbon of all three meteorites. The Orgueil and Murchison materials contain additional hydrogenated aromatic/olefinic and aliphatic groups.

In silico methods for co-transcriptional RNA secondary structure prediction and for investigating alternative RNA structure expression.

PubMed

Meyer, Irmtraud M

2017-05-01

RNA transcripts are the primary products of active genes in any living organism, including many viruses. Their cellular destiny not only depends on primary sequence signals, but can also be determined by RNA structure. Recent experimental evidence shows that many transcripts can be assigned more than a single functional RNA structure throughout their cellular life and that structure formation happens co-transcriptionally, i.e. as the transcript is synthesised in the cell. Moreover, functional RNA structures are not limited to non-coding transcripts, but can also feature in coding transcripts. The picture that now emerges is that RNA structures constitute an additional layer of information that can be encoded in any RNA transcript (and on top of other layers of information such as protein-context) in order to exert a wide range of functional roles. Moreover, different encoded RNA structures can be expressed at different stages of a transcript's life in order to alter the transcript's behaviour depending on its actual cellular context. Similar to the concept of alternative splicing for protein-coding genes, where a single transcript can yield different proteins depending on cellular context, it is thus appropriate to propose the notion of alternative RNA structure expression for any given transcript. This review introduces several computational strategies that my group developed to detect different aspects of RNA structure expression in vivo. Two aspects are of particular interest to us: (1) RNA secondary structure features that emerge during co-transcriptional folding and (2) functional RNA structure features that are expressed at different times of a transcript's life and potentially mutually exclusive. Copyright © 2017. Published by Elsevier Inc.

Anodization: a promising nano-modification technique of titanium implants for orthopedic applications.

PubMed

Yao, Chang; Webster, Thomas J

2006-01-01

Anodization is a well-established surface modification technique that produces protective oxide layers on valve metals such as titanium. Many studies have used anodization to produce micro-porous titanium oxide films on implant surfaces for orthopedic applications. An additional hydrothermal treatment has also been used in conjunction with anodization to deposit hydroxyapatite on titanium surfaces; this is in contrast to using traditional plasma spray deposition techniques. Recently, the ability to create nanometer surface structures (e.g., nano-tubular) via anodization of titanium implants in fluorine solutions have intrigued investigators to fabricate nano-scale surface features that mimic the natural bone environment. This paper will present an overview of anodization techniques used to produce micro-porous titanium oxide structures and nano-tubular oxide structures, subsequent properties of these anodized titanium surfaces, and ultimately their in vitro as well as in vivo biological responses pertinent for orthopedic applications. Lastly, this review will emphasize why anodized titanium structures that have nanometer surface features enhance bone forming cell functions.

Special features of changes in the structure and mechanical properties of oxygen-free pure and yttrium-alloyed copper after vacuum induction remelting

NASA Astrophysics Data System (ADS)

Kamyshanchenko, N. V.; Galtsev, A. V.; Durykhin, M. I.; Neklyudov, I. M.; Borts, B. V.; Shevchenko, S. V.

2011-03-01

Properties of oxygen-free copper with a microadditive of yttrium and without it are studied after vacuum induction remelting. The ingots are subjected to intense hot pressing and subsequent rolling to various degrees of reduction. The effects of the annealing temperature on the structure and of the anisotropy of the structure on the strength properties of the copper are determined. The properties of copper with an additive of yttrium and without it are compared.

Case study of 3D fingerprints applications

PubMed Central

Liu, Feng; Liang, Jinrong; Shen, Linlin; Yang, Meng; Zhang, David; Lai, Zhihui

2017-01-01

Human fingers are 3D objects. More information will be provided if three dimensional (3D) fingerprints are available compared with two dimensional (2D) fingerprints. Thus, this paper firstly collected 3D finger point cloud data by Structured-light Illumination method. Additional features from 3D fingerprint images are then studied and extracted. The applications of these features are finally discussed. A series of experiments are conducted to demonstrate the helpfulness of 3D information to fingerprint recognition. Results show that a quick alignment can be easily implemented under the guidance of 3D finger shape feature even though this feature does not work for fingerprint recognition directly. The newly defined distinctive 3D shape ridge feature can be used for personal authentication with Equal Error Rate (EER) of ~8.3%. Also, it is helpful to remove false core point. Furthermore, a promising of EER ~1.3% is realized by combining this feature with 2D features for fingerprint recognition which indicates the prospect of 3D fingerprint recognition. PMID:28399141

Case study of 3D fingerprints applications.

PubMed

Liu, Feng; Liang, Jinrong; Shen, Linlin; Yang, Meng; Zhang, David; Lai, Zhihui

2017-01-01

Human fingers are 3D objects. More information will be provided if three dimensional (3D) fingerprints are available compared with two dimensional (2D) fingerprints. Thus, this paper firstly collected 3D finger point cloud data by Structured-light Illumination method. Additional features from 3D fingerprint images are then studied and extracted. The applications of these features are finally discussed. A series of experiments are conducted to demonstrate the helpfulness of 3D information to fingerprint recognition. Results show that a quick alignment can be easily implemented under the guidance of 3D finger shape feature even though this feature does not work for fingerprint recognition directly. The newly defined distinctive 3D shape ridge feature can be used for personal authentication with Equal Error Rate (EER) of ~8.3%. Also, it is helpful to remove false core point. Furthermore, a promising of EER ~1.3% is realized by combining this feature with 2D features for fingerprint recognition which indicates the prospect of 3D fingerprint recognition.

An examination of the relationship between childhood emotional abuse and borderline personality disorder features: the role of difficulties with emotion regulation.

PubMed

Kuo, Janice R; Khoury, Jennifer E; Metcalfe, Rebecca; Fitzpatrick, Skye; Goodwill, Alasdair

2015-01-01

Childhood abuse has been consistently linked with borderline personality disorder (BPD) and recent studies suggest that some forms of childhood abuse might be uniquely related to both BPD and BPD features. In addition, difficulties with emotion regulation have been found to be associated with childhood abuse, BPD, as well as BPD features. The present study examined (1) whether frequency of childhood emotional abuse is uniquely associated with BPD feature severity when controlling for other forms of childhood abuse and (2) whether difficulties with emotion regulation accounts for the relationship between childhood emotional abuse and BPD feature severity. A sample of undergraduates (n=243) completed the Childhood Trauma Questionnaire - Short Form, Difficulties in Emotion Regulation Scale, and Borderline Symptom List-23. Multiple regression analyses and Structural Equation Modeling were conducted. Results indicated that frequency of childhood emotional abuse (and not sexual or physical abuse) was uniquely associated with BPD feature severity. In addition, while there was no direct path between childhood emotional abuse, childhood physical abuse, or childhood sexual abuse and BPD features, there was an indirect relationship between childhood emotional abuse and BPD features through difficulties with emotion regulation. These findings suggest that, of the different forms of childhood abuse, emotional abuse specifically, may have a developmental role in BPD pathology. Prevention and treatment of BPD pathology might benefit from the provision of emotion regulation strategies. Copyright © 2014 Elsevier Ltd. All rights reserved.

A method of plane geometry primitive presentation

NASA Astrophysics Data System (ADS)

Jiao, Anbo; Luo, Haibo; Chang, Zheng; Hui, Bin

2014-11-01

Point feature and line feature are basic elements in object feature sets, and they play an important role in object matching and recognition. On one hand, point feature is sensitive to noise; on the other hand, there are usually a huge number of point features in an image, which makes it complex for matching. Line feature includes straight line segment and curve. One difficulty in straight line segment matching is the uncertainty of endpoint location, the other is straight line segment fracture problem or short straight line segments joined to form long straight line segment. While for the curve, in addition to the above problems, there is another difficulty in how to quantitatively describe the shape difference between curves. Due to the problems of point feature and line feature, the robustness and accuracy of target description will be affected; in this case, a method of plane geometry primitive presentation is proposed to describe the significant structure of an object. Firstly, two types of primitives are constructed, they are intersecting line primitive and blob primitive. Secondly, a line segment detector (LSD) is applied to detect line segment, and then intersecting line primitive is extracted. Finally, robustness and accuracy of the plane geometry primitive presentation method is studied. This method has a good ability to obtain structural information of the object, even if there is rotation or scale change of the object in the image. Experimental results verify the robustness and accuracy of this method.

Aryl-Aryl Interactions in Designed Peptide Folds: Spectroscopic Characteristics and Placement Issues for Optimal Structure Stabilization

PubMed Central

Anderson, Jordan M.; Kier, Brandon; Jurban, Brice; Byrne, Aimee; Shu, Irene; Eidenschink, Lisa A.; Shcherbakov, Alexander A.; Hudson, Mike; Fesinmeyer, R. M.; Andersen, Niels H.

2017-01-01

We have extended our studies of Trp/Trp to other Aryl/Aryl through-space interactions that stabilize hairpins and other small polypeptide folds. Herein we detail the NMR and CD spectroscopic features of these types of interactions. NMR data remains the best diagnostic for characterizing the common T-shape orientation. Designated as an edge-to-face (EtF or FtE) interaction, large ring current shifts are produced at the edge aryl ring hydrogens and, in most cases, large exciton couplets appear in the far UV circular dichroic (CD) spectrum. The preference for the face aryl in FtE clusters is W≫Y≥F (there are some exceptions in the Y/F order); this sequence corresponds to the order of fold stability enhancement and always predicts the amplitude of the lower energy feature of the exciton couplet in the CD spectrum. The CD spectra for FtE W/W, W/Y, Y/W, and Y/Y pairs all include an intense feature at 225–232 nm. An additional couplet feature seen for W/Y, W/F, Y/Y and F/Y clusters, is a negative feature at 197–200 nm. Tyr/Tyr (as well as F/Y and F/F) interactions produce much smaller exciton couplet amplitudes. The Trp-cage fold was employed to search for the CD effects of other Trp/Trp and Trp/Tyr cluster geometries: several were identified. In this account, we provide additional examples of the application of cross-strand aryl/aryl clusters for the design of stable β-sheet models and a scale of fold stability increments associated with all possible FtE Ar/Ar clusters in several structural contexts. PMID:26850220

Estimating standard errors in feature network models.

PubMed

Frank, Laurence E; Heiser, Willem J

2007-05-01

Feature network models are graphical structures that represent proximity data in a discrete space while using the same formalism that is the basis of least squares methods employed in multidimensional scaling. Existing methods to derive a network model from empirical data only give the best-fitting network and yield no standard errors for the parameter estimates. The additivity properties of networks make it possible to consider the model as a univariate (multiple) linear regression problem with positivity restrictions on the parameters. In the present study, both theoretical and empirical standard errors are obtained for the constrained regression parameters of a network model with known features. The performance of both types of standard error is evaluated using Monte Carlo techniques.

Features of optical surfaces of multifocal diffractive-refractive eye lenses

NASA Astrophysics Data System (ADS)

Lenkova, G. A.

2017-09-01

This paper considers shape features of the surface structures of multifocal intraocular lenses (IOLs), which, unlike bifocal IOLs, generate additional foci or extends the depth of focus, which not only corrects near and far vision but also provides good vision at intermediate distances. Expansion of the field of clear vision is achieved due to the effects of diffraction, interference, and refraction (change in the radius of curvature of the lens surface). The optical characteristics of the most famous multifocal IOLs (trifocal and quadrafocal lenses and lenses with extended focal area) are given.

Morphological characters of the thickbody skate Amblyraja frerichsi (Krefft 1968) (Rajiformes: Rajidae), with notes on its biology.

PubMed

Bustamante, Carlos; Lamilla, Julio; Concha, Francisco; Ebert, David A; Bennett, Michael B

2012-01-01

Detailed descriptions of morphological features, morphometrics, neurocranium anatomy, clasper structure and egg case descriptions are provided for the thickbody skate Amblyraja frerichsi; a rare, deep-water species from Chile, Argentina and Falkland Islands. The species diagnosis is complemented from new observations and aspects such as colour, size and distribution are described. Geographic and bathymetric distributional ranges are discussed as relevant features of this taxońs biology. Additionally, the conservation status is assessed including bycatch records from Chilean fisheries.

Morphological Characters of the Thickbody Skate Amblyraja frerichsi (Krefft 1968) (Rajiformes: Rajidae), with Notes on Its Biology

PubMed Central

Bustamante, Carlos; Lamilla, Julio; Concha, Francisco; Ebert, David A.; Bennett, Michael B.

2012-01-01

Detailed descriptions of morphological features, morphometrics, neurocranium anatomy, clasper structure and egg case descriptions are provided for the thickbody skate Amblyraja frerichsi; a rare, deep-water species from Chile, Argentina and Falkland Islands. The species diagnosis is complemented from new observations and aspects such as colour, size and distribution are described. Geographic and bathymetric distributional ranges are discussed as relevant features of this taxońs biology. Additionally, the conservation status is assessed including bycatch records from Chilean fisheries. PMID:22768186

Weighted Feature Significance: A Simple, Interpretable Model of Compound Toxicity Based on the Statistical Enrichment of Structural Features

PubMed Central

Huang, Ruili; Southall, Noel; Xia, Menghang; Cho, Ming-Hsuang; Jadhav, Ajit; Nguyen, Dac-Trung; Inglese, James; Tice, Raymond R.; Austin, Christopher P.

2009-01-01

In support of the U.S. Tox21 program, we have developed a simple and chemically intuitive model we call weighted feature significance (WFS) to predict the toxicological activity of compounds, based on the statistical enrichment of structural features in toxic compounds. We trained and tested the model on the following: (1) data from quantitative high–throughput screening cytotoxicity and caspase activation assays conducted at the National Institutes of Health Chemical Genomics Center, (2) data from Salmonella typhimurium reverse mutagenicity assays conducted by the U.S. National Toxicology Program, and (3) hepatotoxicity data published in the Registry of Toxic Effects of Chemical Substances. Enrichments of structural features in toxic compounds are evaluated for their statistical significance and compiled into a simple additive model of toxicity and then used to score new compounds for potential toxicity. The predictive power of the model for cytotoxicity was validated using an independent set of compounds from the U.S. Environmental Protection Agency tested also at the National Institutes of Health Chemical Genomics Center. We compared the performance of our WFS approach with classical classification methods such as Naive Bayesian clustering and support vector machines. In most test cases, WFS showed similar or slightly better predictive power, especially in the prediction of hepatotoxic compounds, where WFS appeared to have the best performance among the three methods. The new algorithm has the important advantages of simplicity, power, interpretability, and ease of implementation. PMID:19805409

Human Chromosome 7: DNA Sequence and Biology

PubMed Central

Scherer, Stephen W.; Cheung, Joseph; MacDonald, Jeffrey R.; Osborne, Lucy R.; Nakabayashi, Kazuhiko; Herbrick, Jo-Anne; Carson, Andrew R.; Parker-Katiraee, Layla; Skaug, Jennifer; Khaja, Razi; Zhang, Junjun; Hudek, Alexander K.; Li, Martin; Haddad, May; Duggan, Gavin E.; Fernandez, Bridget A.; Kanematsu, Emiko; Gentles, Simone; Christopoulos, Constantine C.; Choufani, Sanaa; Kwasnicka, Dorota; Zheng, Xiangqun H.; Lai, Zhongwu; Nusskern, Deborah; Zhang, Qing; Gu, Zhiping; Lu, Fu; Zeesman, Susan; Nowaczyk, Malgorzata J.; Teshima, Ikuko; Chitayat, David; Shuman, Cheryl; Weksberg, Rosanna; Zackai, Elaine H.; Grebe, Theresa A.; Cox, Sarah R.; Kirkpatrick, Susan J.; Rahman, Nazneen; Friedman, Jan M.; Heng, Henry H. Q.; Pelicci, Pier Giuseppe; Lo-Coco, Francesco; Belloni, Elena; Shaffer, Lisa G.; Pober, Barbara; Morton, Cynthia C.; Gusella, James F.; Bruns, Gail A. P.; Korf, Bruce R.; Quade, Bradley J.; Ligon, Azra H.; Ferguson, Heather; Higgins, Anne W.; Leach, Natalia T.; Herrick, Steven R.; Lemyre, Emmanuelle; Farra, Chantal G.; Kim, Hyung-Goo; Summers, Anne M.; Gripp, Karen W.; Roberts, Wendy; Szatmari, Peter; Winsor, Elizabeth J. T.; Grzeschik, Karl-Heinz; Teebi, Ahmed; Minassian, Berge A.; Kere, Juha; Armengol, Lluis; Pujana, Miguel Angel; Estivill, Xavier; Wilson, Michael D.; Koop, Ben F.; Tosi, Sabrina; Moore, Gudrun E.; Boright, Andrew P.; Zlotorynski, Eitan; Kerem, Batsheva; Kroisel, Peter M.; Petek, Erwin; Oscier, David G.; Mould, Sarah J.; Döhner, Hartmut; Döhner, Konstanze; Rommens, Johanna M.; Vincent, John B.; Venter, J. Craig; Li, Peter W.; Mural, Richard J.; Adams, Mark D.; Tsui, Lap-Chee

2010-01-01

DNA sequence and annotation of the entire human chromosome 7, encompassing nearly 158 million nucleotides of DNA and 1917 gene structures, are presented. To generate a higher order description, additional structural features such as imprinted genes, fragile sites, and segmental duplications were integrated at the level of the DNA sequence with medical genetic data, including 440 chromosome rearrangement breakpoints associated with disease. This approach enabled the discovery of candidate genes for developmental diseases including autism. PMID:12690205

Identification of DNA-Binding Proteins Using Mixed Feature Representation Methods.

PubMed

Qu, Kaiyang; Han, Ke; Wu, Song; Wang, Guohua; Wei, Leyi

2017-09-22

DNA-binding proteins play vital roles in cellular processes, such as DNA packaging, replication, transcription, regulation, and other DNA-associated activities. The current main prediction method is based on machine learning, and its accuracy mainly depends on the features extraction method. Therefore, using an efficient feature representation method is important to enhance the classification accuracy. However, existing feature representation methods cannot efficiently distinguish DNA-binding proteins from non-DNA-binding proteins. In this paper, a multi-feature representation method, which combines three feature representation methods, namely, K-Skip-N-Grams, Information theory, and Sequential and structural features (SSF), is used to represent the protein sequences and improve feature representation ability. In addition, the classifier is a support vector machine. The mixed-feature representation method is evaluated using 10-fold cross-validation and a test set. Feature vectors, which are obtained from a combination of three feature extractions, show the best performance in 10-fold cross-validation both under non-dimensional reduction and dimensional reduction by max-relevance-max-distance. Moreover, the reduced mixed feature method performs better than the non-reduced mixed feature technique. The feature vectors, which are a combination of SSF and K-Skip-N-Grams, show the best performance in the test set. Among these methods, mixed features exhibit superiority over the single features.

New Nomenclatures for Heat Treatments of Additively Manufactured Titanium Alloys

NASA Astrophysics Data System (ADS)

Baker, Andrew H.; Collins, Peter C.; Williams, James C.

2017-07-01

The heat-treatment designations and microstructure nomenclatures for many structural metallic alloys were established for traditional metals processing, such as casting, hot rolling or forging. These terms do not necessarily apply for additively manufactured (i.e., three-dimensionally printed or "3D printed") metallic structures. The heat-treatment terminology for titanium alloys generally implies the heat-treatment temperatures and their sequence relative to a thermomechanical processing step (e.g., forging, rolling). These designations include: β-processing, α + β-processing, β-annealing, duplex annealing and mill annealing. Owing to the absence of a thermomechanical processing step, these traditional designations can pose a problem when titanium alloys are first produced via additive manufacturing, and then heat-treated. This communication proposes new nomenclatures for heat treatments of additively manufactured titanium alloys, and uses the distinct microstructural features to provide a correlation between traditional nomenclature and the proposed nomenclature.

Additive manufacturing of biologically-inspired materials.

PubMed

Studart, André R

2016-01-21

Additive manufacturing (AM) technologies offer an attractive pathway towards the fabrication of functional materials featuring complex heterogeneous architectures inspired by biological systems. In this paper, recent research on the use of AM approaches to program the local chemical composition, structure and properties of biologically-inspired materials is reviewed. A variety of structural motifs found in biological composites have been successfully emulated in synthetic systems using inkjet-based, direct-writing, stereolithography and slip casting technologies. The replication in synthetic systems of design principles underlying such structural motifs has enabled the fabrication of lightweight cellular materials, strong and tough composites, soft robots and autonomously shaping structures with unprecedented properties and functionalities. Pushing the current limits of AM technologies in future research should bring us closer to the manufacturing capabilities of living organisms, opening the way for the digital fabrication of advanced materials with superior performance, lower environmental impact and new functionalities.

Selective Photophysical Modification on Light-Emitting Polymer Films for Micro- and Nano-Patterning

PubMed Central

Zhang, Xinping; Liu, Feifei; Li, Hongwei

2016-01-01

Laser-induced cross-linking in polymeric semiconductors was utilized to achieve micro- and nano-structuring in thin films. Single- and two-photon cross-linking processes led to the reduction in both the refractive index and thickness of the polymer films. The resultant photonic structures combine the features of both relief- and phase-gratings. Selective cross-linking in polymer blend films based on different optical response of different molecular phases enabled “solidification” of the phase-separation scheme, providing a stable template for further photonic structuring. Dielectric and metallic structures are demonstrated for the fabrication methods using cross-linking in polymer films. Selective cross-linking enables direct patterning into polymer films without introducing additional fabrication procedures or additional materials. The diffraction processes of the emission of the patterned polymeric semiconductors may provide enhanced output coupling for light-emitting diodes or distributed feedback for lasers. PMID:28773248

Strong nonadditivity as a key structure-activity relationship feature: distinguishing structural changes from assay artifacts.

PubMed

Kramer, Christian; Fuchs, Julian E; Liedl, Klaus R

2015-03-23

Nonadditivity in protein-ligand affinity data represents highly instructive structure-activity relationship (SAR) features that indicate structural changes and have the potential to guide rational drug design. At the same time, nonadditivity is a challenge for both basic SAR analysis as well as many ligand-based data analysis techniques such as Free-Wilson Analysis and Matched Molecular Pair analysis, since linear substituent contribution models inherently assume additivity and thus do not work in such cases. While structural causes for nonadditivity have been analyzed anecdotally, no systematic approaches to interpret and use nonadditivity prospectively have been developed yet. In this contribution, we lay the statistical framework for systematic analysis of nonadditivity in a SAR series. First, we develop a general metric to quantify nonadditivity. Then, we demonstrate the non-negligible impact of experimental uncertainty that creates apparent nonadditivity, and we introduce techniques to handle experimental uncertainty. Finally, we analyze public SAR data sets for strong nonadditivity and use recourse to the original publications and available X-ray structures to find structural explanations for the nonadditivity observed. We find that all cases of strong nonadditivity (ΔΔpKi and ΔΔpIC50 > 2.0 log units) with sufficient structural information to generate reasonable hypothesis involve changes in binding mode. With the appropriate statistical basis, nonadditivity analysis offers a variety of new attempts for various areas in computer-aided drug design, including the validation of scoring functions and free energy perturbation approaches, binding pocket classification, and novel features in SAR analysis tools.

Digital surfaces and thicknesses of selected hydrogeologic units of the Floridan aquifer system in Florida and parts of Georgia, Alabama, and South Carolina

USGS Publications Warehouse

Williams, Lester J.; Dixon, Joann F.

2015-01-01

Digital surfaces and thicknesses of selected hydrogeologic units of the Floridan aquifer system were developed to define an updated hydrogeologic framework as part of the U.S. Geological Survey Groundwater Resources Program. The dataset contains structural surfaces depicting the top and base of the aquifer system, its major and minor hydrogeologic units and zones, geophysical marker horizons, and the altitude of the 10,000-milligram-per-liter total dissolved solids boundary that defines the approximate fresh and saline parts of the aquifer system. The thicknesses of selected major and minor units or zones were determined by interpolating points of known thickness or from raster surface subtraction of the structural surfaces. Additional data contained include clipping polygons; regional polygon features that represent geologic or hydrogeologic aspects of the aquifers and the minor units or zones; data points used in the interpolation; and polygon and line features that represent faults, boundaries, and other features in the aquifer system.

Citation Sentiment Analysis in Clinical Trial Papers

PubMed Central

Xu, Jun; Zhang, Yaoyun; Wu, Yonghui; Wang, Jingqi; Dong, Xiao; Xu, Hua

2015-01-01

In scientific writing, positive credits and negative criticisms can often be seen in the text mentioning the cited papers, providing useful information about whether a study can be reproduced or not. In this study, we focus on citation sentiment analysis, which aims to determine the sentiment polarity that the citation context carries towards the cited paper. A citation sentiment corpus was annotated first on clinical trial papers. The effectiveness of n-gram and sentiment lexicon features, and problem-specified structure features for citation sentiment analysis were then examined using the annotated corpus. The combined features from the word n-grams, the sentiment lexicons and the structure information achieved the highest Micro F-score of 0.860 and Macro-F score of 0.719, indicating that it is feasible to use machine learning methods for citation sentiment analysis in biomedical publications. A comprehensive comparison between citation sentiment analysis of clinical trial papers and other general domains were conducted, which additionally highlights the unique challenges within this domain. PMID:26958274

Blurred Palmprint Recognition Based on Stable-Feature Extraction Using a Vese–Osher Decomposition Model

PubMed Central

Hong, Danfeng; Su, Jian; Hong, Qinggen; Pan, Zhenkuan; Wang, Guodong

2014-01-01

As palmprints are captured using non-contact devices, image blur is inevitably generated because of the defocused status. This degrades the recognition performance of the system. To solve this problem, we propose a stable-feature extraction method based on a Vese–Osher (VO) decomposition model to recognize blurred palmprints effectively. A Gaussian defocus degradation model is first established to simulate image blur. With different degrees of blurring, stable features are found to exist in the image which can be investigated by analyzing the blur theoretically. Then, a VO decomposition model is used to obtain structure and texture layers of the blurred palmprint images. The structure layer is stable for different degrees of blurring (this is a theoretical conclusion that needs to be further proved via experiment). Next, an algorithm based on weighted robustness histogram of oriented gradients (WRHOG) is designed to extract the stable features from the structure layer of the blurred palmprint image. Finally, a normalized correlation coefficient is introduced to measure the similarity in the palmprint features. We also designed and performed a series of experiments to show the benefits of the proposed method. The experimental results are used to demonstrate the theoretical conclusion that the structure layer is stable for different blurring scales. The WRHOG method also proves to be an advanced and robust method of distinguishing blurred palmprints. The recognition results obtained using the proposed method and data from two palmprint databases (PolyU and Blurred–PolyU) are stable and superior in comparison to previous high-performance methods (the equal error rate is only 0.132%). In addition, the authentication time is less than 1.3 s, which is fast enough to meet real-time demands. Therefore, the proposed method is a feasible way of implementing blurred palmprint recognition. PMID:24992328

Blurred palmprint recognition based on stable-feature extraction using a Vese-Osher decomposition model.

PubMed

Hong, Danfeng; Su, Jian; Hong, Qinggen; Pan, Zhenkuan; Wang, Guodong

2014-01-01

As palmprints are captured using non-contact devices, image blur is inevitably generated because of the defocused status. This degrades the recognition performance of the system. To solve this problem, we propose a stable-feature extraction method based on a Vese-Osher (VO) decomposition model to recognize blurred palmprints effectively. A Gaussian defocus degradation model is first established to simulate image blur. With different degrees of blurring, stable features are found to exist in the image which can be investigated by analyzing the blur theoretically. Then, a VO decomposition model is used to obtain structure and texture layers of the blurred palmprint images. The structure layer is stable for different degrees of blurring (this is a theoretical conclusion that needs to be further proved via experiment). Next, an algorithm based on weighted robustness histogram of oriented gradients (WRHOG) is designed to extract the stable features from the structure layer of the blurred palmprint image. Finally, a normalized correlation coefficient is introduced to measure the similarity in the palmprint features. We also designed and performed a series of experiments to show the benefits of the proposed method. The experimental results are used to demonstrate the theoretical conclusion that the structure layer is stable for different blurring scales. The WRHOG method also proves to be an advanced and robust method of distinguishing blurred palmprints. The recognition results obtained using the proposed method and data from two palmprint databases (PolyU and Blurred-PolyU) are stable and superior in comparison to previous high-performance methods (the equal error rate is only 0.132%). In addition, the authentication time is less than 1.3 s, which is fast enough to meet real-time demands. Therefore, the proposed method is a feasible way of implementing blurred palmprint recognition.

Benchmarking Alumni Relations in Community Colleges: Findings from a 2015 CASE Survey. CASE White Paper

ERIC Educational Resources Information Center

Paradise, Andrew

2016-01-01

Building on the inaugural survey conducted three years prior, the 2015 CASE Community College Alumni Relations survey collected additional insightful data on staffing, structure, communications, engagement, and fundraising. This white paper features key data on alumni relations programs at community colleges across the United States. The paper…

Cartilage Tissue Engineering with Silk Fibroin Scaffolds Fabricated by Indirect Additive Manufacturing Technology.

PubMed

Chen, Chih-Hao; Liu, Jolene Mei-Jun; Chua, Chee-Kai; Chou, Siaw-Meng; Shyu, Victor Bong-Hang; Chen, Jyh-Ping

2014-03-13

Advanced tissue engineering (TE) technology based on additive manufacturing (AM) can fabricate scaffolds with a three-dimensional (3D) environment suitable for cartilage regeneration. Specifically, AM technology may allow the incorporation of complex architectural features. The present study involves the fabrication of 3D TE scaffolds by an indirect AM approach using silk fibroin (SF). From scanning electron microscopic observations, the presence of micro-pores and interconnected channels within the scaffold could be verified, resulting in a TE scaffold with both micro- and macro-structural features. The intrinsic properties, such as the chemical structure and thermal characteristics of SF, were preserved after the indirect AM manufacturing process. In vitro cell culture within the SF scaffold using porcine articular chondrocytes showed a steady increase in cell numbers up to Day 14. The specific production (per cell basis) of the cartilage-specific extracellular matrix component (collagen Type II) was enhanced with culture time up to 12 weeks, indicating the re-differentiation of chondrocytes within the scaffold. Subcutaneous implantation of the scaffold-chondrocyte constructs in nude mice also confirmed the formation of ectopic cartilage by histological examination and immunostaining.

The Function of Embryonic Stem Cell-expressed RAS (E-RAS), a Unique RAS Family Member, Correlates with Its Additional Motifs and Its Structural Properties.

PubMed

Nakhaei-Rad, Saeideh; Nakhaeizadeh, Hossein; Kordes, Claus; Cirstea, Ion C; Schmick, Malte; Dvorsky, Radovan; Bastiaens, Philippe I H; Häussinger, Dieter; Ahmadian, Mohammad Reza

2015-06-19

E-RAS is a member of the RAS family specifically expressed in embryonic stem cells, gastric tumors, and hepatic stellate cells. Unlike classical RAS isoforms (H-, N-, and K-RAS4B), E-RAS has, in addition to striking and remarkable sequence deviations, an extended 38-amino acid-long unique N-terminal region with still unknown functions. We investigated the molecular mechanism of E-RAS regulation and function with respect to its sequence and structural features. We found that N-terminal extension of E-RAS is important for E-RAS signaling activity. E-RAS protein most remarkably revealed a different mode of effector interaction as compared with H-RAS, which correlates with deviations in the effector-binding site of E-RAS. Of all these residues, tryptophan 79 (arginine 41 in H-RAS), in the interswitch region, modulates the effector selectivity of RAS proteins from H-RAS to E-RAS features. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Advances toward multifunctional cholinesterase and β-amyloid aggregation inhibitors.

PubMed

Panek, Dawid; Wichur, Tomasz; Godyń, Justyna; Pasieka, Anna; Malawska, Barbara

2017-10-01

The emergence of a multitarget design approach in the development of new potential anti-Alzheimer's disease agents has resulted in the discovery of many multifunctional compounds focusing on various targets. Among them the largest group comprises inhibitors of both cholinesterases, with additional anti-β-amyloid aggregation activity. This review describes recent advances in this research area and presents the most interesting compounds reported over a 2-year span (2015-2016). The majority of hybrids possess heterodimeric structures obtained by linking structurally active fragments interacting with different targets. Multipotent cholinesterase inhibitors with β-amyloid antiaggregating activity may additionally possess antioxidative, neuroprotective or metal-chelating properties or less common features such as anti-β-secretase or τ-antiaggregation activity.

Edge modulation of electronics and transport properties of cliff-edge phosphorene nanoribbons

NASA Astrophysics Data System (ADS)

Guo, Caixia; Wang, Tianxing; Xia, Congxin; Liu, Yufang

2017-12-01

Based on the first-principles calculations, we study the electronic structures and transport properties of cliff-like edge phosphorene nanoribbons (CPNRs), considering different types of edge passivation. The band structures of bare CPNRs possess the metallic features; while hydrogen (H), fluorine (F), chlorine (Cl) and oxygen (O) atoms-passivated CPNRs are semiconductor materials, and the band gap values monotonically decrease when the ribbon width increases. Moreover, the H and F-passivated CPNRs exhibit the direct band gap characteristics, while the Cl and O-passivated cases show the features of indirect band gap. In addition, the edge passivated CPNRs are more energetically stable than bare edge case. Meanwhile, our results also show that the transport properties of the CPNRs can be obviously influenced by the different edge passivation.

Broad Learning System: An Effective and Efficient Incremental Learning System Without the Need for Deep Architecture.

PubMed

Chen, C L Philip; Liu, Zhulin

2018-01-01

Broad Learning System (BLS) that aims to offer an alternative way of learning in deep structure is proposed in this paper. Deep structure and learning suffer from a time-consuming training process because of a large number of connecting parameters in filters and layers. Moreover, it encounters a complete retraining process if the structure is not sufficient to model the system. The BLS is established in the form of a flat network, where the original inputs are transferred and placed as "mapped features" in feature nodes and the structure is expanded in wide sense in the "enhancement nodes." The incremental learning algorithms are developed for fast remodeling in broad expansion without a retraining process if the network deems to be expanded. Two incremental learning algorithms are given for both the increment of the feature nodes (or filters in deep structure) and the increment of the enhancement nodes. The designed model and algorithms are very versatile for selecting a model rapidly. In addition, another incremental learning is developed for a system that has been modeled encounters a new incoming input. Specifically, the system can be remodeled in an incremental way without the entire retraining from the beginning. Satisfactory result for model reduction using singular value decomposition is conducted to simplify the final structure. Compared with existing deep neural networks, experimental results on the Modified National Institute of Standards and Technology database and NYU NORB object recognition dataset benchmark data demonstrate the effectiveness of the proposed BLS.

Method for forming suspended micromechanical structures

DOEpatents

Fleming, James G.

2000-01-01

A micromachining method is disclosed for forming a suspended micromechanical structure from {111} crystalline silicon. The micromachining method is based on the use of anisotropic dry etching to define lateral features of the structure which are etched down into a {111}-silicon substrate to a first etch depth, thereby forming sidewalls of the structure. The sidewalls are then coated with a protection layer, and the substrate is dry etched to a second etch depth to define a spacing of the structure from the substrate. A selective anisotropic wet etchant (e.g. KOH, EDP, TMAH, NaOH or CsOH) is used to laterally undercut the structure between the first and second etch depths, thereby forming a substantially planar lower surface of the structure along a {111} crystal plane that is parallel to an upper surface of the structure. The lateral extent of undercutting by the wet etchant is controlled and effectively terminated by either timing the etching, by the location of angled {111}-silicon planes or by the locations of preformed etch-stops. This present method allows the formation of suspended micromechanical structures having large vertical dimensions and large masses while allowing for detailed lateral features which can be provided by dry etch definition. Additionally, the method of the present invention is compatible with the formation of electronic circuitry on the substrate.

Local Feature Selection for Data Classification.

PubMed

Armanfard, Narges; Reilly, James P; Komeili, Majid

2016-06-01

Typical feature selection methods choose an optimal global feature subset that is applied over all regions of the sample space. In contrast, in this paper we propose a novel localized feature selection (LFS) approach whereby each region of the sample space is associated with its own distinct optimized feature set, which may vary both in membership and size across the sample space. This allows the feature set to optimally adapt to local variations in the sample space. An associated method for measuring the similarities of a query datum to each of the respective classes is also proposed. The proposed method makes no assumptions about the underlying structure of the samples; hence the method is insensitive to the distribution of the data over the sample space. The method is efficiently formulated as a linear programming optimization problem. Furthermore, we demonstrate the method is robust against the over-fitting problem. Experimental results on eleven synthetic and real-world data sets demonstrate the viability of the formulation and the effectiveness of the proposed algorithm. In addition we show several examples where localized feature selection produces better results than a global feature selection method.

Self-Assembling Block Copolymer Resist Mixtures towards Lithographic Resists for Sub-10 nm Features

NASA Astrophysics Data System (ADS)

Chandler, Curran; Daga, Vikram; Watkins, James

2009-03-01

Significant improvements in 193 nm photolithography have enabled the extension of device feature sizes beyond the 45 nm and 32 nm nodes, yet uncertainty lies beyond 22 nm features as no single replacement has emerged. Here we show that low molecular weight, nonionic block copolymer surfactant blends are capable of self-assembling into highly ordered domains with feature sizes on the order of 5 nm. These surfactants, most of which lack the required χN for microphase separation on their own, exhibit strong segregation and long-range order upon addition of a component capable of multi-point hydrogen bonding that is specific for one of the blocks in the copolymer. This has been demonstrated by our SAXS data for several Pluronic (PEO-b-PPO-b-PEO) and Brij (PEO-b-[CH2]nCH3) surfactants of various molecular weights and PEO volume fractions. Furthermore, we employ these highly-ordered systems as thin film, nanolithographic etch masks for the transfer of sub-10 nm patterns into silicon-based substrates. Small molecule, hydrogen bonding additives containing aromatic or silsesquioxane structure are also used to tune etch contrast between the blocks which is important for reducing line edge roughness (LER) of such small features.

Feature based Weld-Deposition for Additive Manufacturing of Complex Shapes

NASA Astrophysics Data System (ADS)

Panchagnula, Jayaprakash Sharma; Simhambhatla, Suryakumar

2018-06-01

Fabricating functional metal parts using Additive Manufacturing (AM) is a leading trend. However, realizing overhanging features has been a challenge due to the lack of support mechanism for metals. Powder-bed fusion techniques like, Selective Laser Sintering (SLS) employ easily-breakable-scaffolds made of the same material to realize the overhangs. However, the same approach is not extendible to deposition processes like laser or arc based direct energy deposition processes. Although it is possible to realize small overhangs by exploiting the inherent overhanging capability of the process or by blinding some small features like holes, the same cannot be extended for more complex geometries. The current work presents a novel approach for realizing complex overhanging features without the need of support structures. This is possible by using higher order kinematics and suitably aligning the overhang with the deposition direction. Feature based non-uniform slicing and non-uniform area-filling are some vital concepts required in realizing the same and are briefly discussed here. This method can be used to fabricate and/or repair fully dense and functional components for various engineering applications. Although this approach has been implemented for weld-deposition based system, the same can be extended to any other direct energy deposition processes also.

Deterministic object tracking using Gaussian ringlet and directional edge features

NASA Astrophysics Data System (ADS)

Krieger, Evan W.; Sidike, Paheding; Aspiras, Theus; Asari, Vijayan K.

2017-10-01

Challenges currently existing for intensity-based histogram feature tracking methods in wide area motion imagery (WAMI) data include object structural information distortions, background variations, and object scale change. These issues are caused by different pavement or ground types and from changing the sensor or altitude. All of these challenges need to be overcome in order to have a robust object tracker, while attaining a computation time appropriate for real-time processing. To achieve this, we present a novel method, Directional Ringlet Intensity Feature Transform (DRIFT), which employs Kirsch kernel filtering for edge features and a ringlet feature mapping for rotational invariance. The method also includes an automatic scale change component to obtain accurate object boundaries and improvements for lowering computation times. We evaluated the DRIFT algorithm on two challenging WAMI datasets, namely Columbus Large Image Format (CLIF) and Large Area Image Recorder (LAIR), to evaluate its robustness and efficiency. Additional evaluations on general tracking video sequences are performed using the Visual Tracker Benchmark and Visual Object Tracking 2014 databases to demonstrate the algorithms ability with additional challenges in long complex sequences including scale change. Experimental results show that the proposed approach yields competitive results compared to state-of-the-art object tracking methods on the testing datasets.

Sequential structural damage diagnosis algorithm using a change point detection method

NASA Astrophysics Data System (ADS)

Noh, H.; Rajagopal, R.; Kiremidjian, A. S.

2013-11-01

This paper introduces a damage diagnosis algorithm for civil structures that uses a sequential change point detection method. The general change point detection method uses the known pre- and post-damage feature distributions to perform a sequential hypothesis test. In practice, however, the post-damage distribution is unlikely to be known a priori, unless we are looking for a known specific type of damage. Therefore, we introduce an additional algorithm that estimates and updates this distribution as data are collected using the maximum likelihood and the Bayesian methods. We also applied an approximate method to reduce the computation load and memory requirement associated with the estimation. The algorithm is validated using a set of experimental data collected from a four-story steel special moment-resisting frame and multiple sets of simulated data. Various features of different dimensions have been explored, and the algorithm was able to identify damage, particularly when it uses multidimensional damage sensitive features and lower false alarm rates, with a known post-damage feature distribution. For unknown feature distribution cases, the post-damage distribution was consistently estimated and the detection delays were only a few time steps longer than the delays from the general method that assumes we know the post-damage feature distribution. We confirmed that the Bayesian method is particularly efficient in declaring damage with minimal memory requirement, but the maximum likelihood method provides an insightful heuristic approach.

Chemometric analysis of correlations between electronic absorption characteristics and structural and/or physicochemical parameters for ampholytic substances of biological and pharmaceutical relevance.

PubMed

Judycka-Proma, U; Bober, L; Gajewicz, A; Puzyn, T; Błażejowski, J

2015-03-05

Forty ampholytic compounds of biological and pharmaceutical relevance were subjected to chemometric analysis based on unsupervised and supervised learning algorithms. This enabled relations to be found between empirical spectral characteristics derived from electronic absorption data and structural and physicochemical parameters predicted by quantum chemistry methods or phenomenological relationships based on additivity rules. It was found that the energies of long wavelength absorption bands are correlated through multiparametric linear relationships with parameters reflecting the bulkiness features of the absorbing molecules as well as their nucleophilicity and electrophilicity. These dependences enable the quantitative analysis of spectral features of the compounds, as well as a comparison of their similarities and certain pharmaceutical and biological features. Three QSPR models to predict the energies of long-wavelength absorption in buffers with pH=2.5 and pH=7.0, as well as in methanol, were developed and validated in this study. These models can be further used to predict the long-wavelength absorption energies of untested substances (if they are structurally similar to the training compounds). Copyright © 2014 Elsevier B.V. All rights reserved.

BioSAVE: display of scored annotation within a sequence context.

PubMed

Pollock, Richard F; Adryan, Boris

2008-03-20

Visualization of sequence annotation is a common feature in many bioinformatics tools. For many applications it is desirable to restrict the display of such annotation according to a score cutoff, as biological interpretation can be difficult in the presence of the entire data. Unfortunately, many visualisation solutions are somewhat static in the way they handle such score cutoffs. We present BioSAVE, a sequence annotation viewer with on-the-fly selection of visualisation thresholds for each feature. BioSAVE is a versatile OS X program for visual display of scored features (annotation) within a sequence context. The program reads sequence and additional supplementary annotation data (e.g., position weight matrix matches, conservation scores, structural domains) from a variety of commonly used file formats and displays them graphically. Onscreen controls then allow for live customisation of these graphics, including on-the-fly selection of visualisation thresholds for each feature. Possible applications of the program include display of transcription factor binding sites in a genomic context or the visualisation of structural domain assignments in protein sequences and many more. The dynamic visualisation of these annotations is useful, e.g., for the determination of cutoff values of predicted features to match experimental data. Program, source code and exemplary files are freely available at the BioSAVE homepage.

BioSAVE: Display of scored annotation within a sequence context

PubMed Central

Pollock, Richard F; Adryan, Boris

2008-01-01

Background Visualization of sequence annotation is a common feature in many bioinformatics tools. For many applications it is desirable to restrict the display of such annotation according to a score cutoff, as biological interpretation can be difficult in the presence of the entire data. Unfortunately, many visualisation solutions are somewhat static in the way they handle such score cutoffs. Results We present BioSAVE, a sequence annotation viewer with on-the-fly selection of visualisation thresholds for each feature. BioSAVE is a versatile OS X program for visual display of scored features (annotation) within a sequence context. The program reads sequence and additional supplementary annotation data (e.g., position weight matrix matches, conservation scores, structural domains) from a variety of commonly used file formats and displays them graphically. Onscreen controls then allow for live customisation of these graphics, including on-the-fly selection of visualisation thresholds for each feature. Conclusion Possible applications of the program include display of transcription factor binding sites in a genomic context or the visualisation of structural domain assignments in protein sequences and many more. The dynamic visualisation of these annotations is useful, e.g., for the determination of cutoff values of predicted features to match experimental data. Program, source code and exemplary files are freely available at the BioSAVE homepage. PMID:18366701

Additive Mixing and Conformal Coating of Noniridescent Structural Colors with Robust Mechanical Properties Fabricated by Atomization Deposition.

PubMed

Li, Qingsong; Zhang, Yafeng; Shi, Lei; Qiu, Huihui; Zhang, Suming; Qi, Ning; Hu, Jianchen; Yuan, Wei; Zhang, Xiaohua; Zhang, Ke-Qin

2018-04-24

Artificial structural colors based on short-range-ordered amorphous photonic structures (APSs) have attracted great scientific and industrial interest in recent years. However, the previously reported methods of self-assembling colloidal nanoparticles lack fine control of the APS coating and fixation on substrates and poorly realize three-dimensional (3D) conformal coatings for objects with irregular or highly curved surfaces. In this paper, atomization deposition of silica colloidal nanoparticles with poly(vinyl alcohol) as the additive is proposed to solve the above problems. By finely controlling the thicknesses of APS coatings, additive mixing of noniridescent structural colors is easily realized. Based on the intrinsic omnidirectional feature of atomization, a one-step 3D homogeneous conformal coating is also readily realized on various irregular or highly curved surfaces, including papers, resins, metal plates, ceramics, and flexible silk fabrics. The vivid coatings on silk fabrics by atomization deposition possess robust mechanical properties, which are confirmed by rubbing and laundering tests, showing great potential in developing an environmentally friendly coloring technique in the textile industry.

Reversible Flip-Flops in Quantum-Dot Cellular Automata

NASA Astrophysics Data System (ADS)

Rad, Samaneh Kazemi; Heikalabad, Saeed Rasouli

2017-09-01

Quantum-dot cellular automata is a new technology to design the efficient combinational and sequential circuits at the nano-scale. This technology has many desirable advantages compared to the CMOS technology such as low power consumption, less occupation area and low latency. These features make it suitable for use in flip-flop design. In this paper, with knowing the characteristics of reversible logic, we design new structures for flip-flops. The operations of these structures are evaluated with QCADesigner Version 2.0.3 simulator. In addition, we calculate the power dissipation of these structures by QCAPro tool. The results illustrated that proposed structures are efficient compared to the previous ones.

A Statistical Test of the Relationship between Galactic HI Structure and Small-scale Structure in the Cosmic Microwave Background

NASA Astrophysics Data System (ADS)

Verschuur, Gerrit L.

2014-06-01

The archive of IRIS, PLANCK and WMAP data available at the IRSA website of IPAC allows the apparent associations between galactic neutral hydrogen (HI) features and small-scale structure in WMAP and PLANCK data to be closely examined. In addition, HI new observations made with the Green Bank Telescope are used to perform a statistical test of putative associations. It is concluded that attention should be paid to the possibility that some of the small-scale structure found in WMAP and PLANCK data harbors the signature of a previously unrecognized source of high-frequency continuum emission in the Galaxy.

Molecular engineering of phosphole-based conjugated materials

NASA Astrophysics Data System (ADS)

Ren, Yi

The work in this thesis focuses on the molecular engineering of phosphorus-based conjugated materials. In the first part (Chapters Two and Three), new phosphorus-based conjugated systems were designed and synthesized to study the effect of the heteroelement on the electronic properties of the π-conjugated systems. The second part (Chapters Four and Five) deals with the self-assembly features of specifically designed phosphorus-based conjugated systems. In Chapter Two, electron-poor and electron-rich aromatic substituents were introduced to the dithienophosphole core in order to balance the electron-accepting and electron-donating character of the systems. Furthermore, an intriguing intramolecular charge transfer process could be observed between two dithienophosphole cores in a bridged bisphosphole-system. In Chapter Three, a secondary heteroelement (Si, P, S) was incorporated in the phosphorus-based conjugated systems. Extensive structure-property studies revealed that the secondary heteroelement can effectively manipulate the communication in phosphinine-based systems. The study of a heterotetracene system allowed for selectively applying distinct heteroatom (S/P) chemistries, which offers a powerful tool for the modification of the electronic structure of the system. More importantly, the heteroatom-specific electronic nature (S/P) can be utilized to selectively control different photophysical aspects (energy gap and fluorescence quantum yield). Furthermore, additional molecular engineering of the heterotetracene provided access to well-defined 1D microstructures, which opened the door for designing multi-functional self-assembled phosphorus-based materials. In Chapter Four, the self-organizing phosphole-lipid system is introduced, which combines the features of phospholipids with the electronics of phospholes. Its amphiphilic nature induces intriguing self-assembly features - liquid crystal and soft crystal architectures, both exhibiting well-organized lamellar structure at a wide range of temperatures. Importantly, its dynamic structure endows the phosphole-lipid system with intriguing external stimuli-responsive features allowing for the modification of the emission of the system without further chemical modification. Chapter Five describes how further molecular engineering allowed for access to a series of new highly fluorescent phosphole-lipid organogels. Remarkably, the external-stimuli responsive features of the system can be amplified in a donor-acceptor system accessible through changes in long distance fluorescence resonance energy transfer processes. In addition, the first fluorescent liquid phospholes could also be accessed in the context of the work on the new phosphole-lipid system.

Recognition of emotions using multimodal physiological signals and an ensemble deep learning model.

PubMed

Yin, Zhong; Zhao, Mengyuan; Wang, Yongxiong; Yang, Jingdong; Zhang, Jianhua

2017-03-01

Using deep-learning methodologies to analyze multimodal physiological signals becomes increasingly attractive for recognizing human emotions. However, the conventional deep emotion classifiers may suffer from the drawback of the lack of the expertise for determining model structure and the oversimplification of combining multimodal feature abstractions. In this study, a multiple-fusion-layer based ensemble classifier of stacked autoencoder (MESAE) is proposed for recognizing emotions, in which the deep structure is identified based on a physiological-data-driven approach. Each SAE consists of three hidden layers to filter the unwanted noise in the physiological features and derives the stable feature representations. An additional deep model is used to achieve the SAE ensembles. The physiological features are split into several subsets according to different feature extraction approaches with each subset separately encoded by a SAE. The derived SAE abstractions are combined according to the physiological modality to create six sets of encodings, which are then fed to a three-layer, adjacent-graph-based network for feature fusion. The fused features are used to recognize binary arousal or valence states. DEAP multimodal database was employed to validate the performance of the MESAE. By comparing with the best existing emotion classifier, the mean of classification rate and F-score improves by 5.26%. The superiority of the MESAE against the state-of-the-art shallow and deep emotion classifiers has been demonstrated under different sizes of the available physiological instances. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Improving link prediction in complex networks by adaptively exploiting multiple structural features of networks

NASA Astrophysics Data System (ADS)

Ma, Chuang; Bao, Zhong-Kui; Zhang, Hai-Feng

2017-10-01

So far, many network-structure-based link prediction methods have been proposed. However, these methods only highlight one or two structural features of networks, and then use the methods to predict missing links in different networks. The performances of these existing methods are not always satisfied in all cases since each network has its unique underlying structural features. In this paper, by analyzing different real networks, we find that the structural features of different networks are remarkably different. In particular, even in the same network, their inner structural features are utterly different. Therefore, more structural features should be considered. However, owing to the remarkably different structural features, the contributions of different features are hard to be given in advance. Inspired by these facts, an adaptive fusion model regarding link prediction is proposed to incorporate multiple structural features. In the model, a logistic function combing multiple structural features is defined, then the weight of each feature in the logistic function is adaptively determined by exploiting the known structure information. Last, we use the "learnt" logistic function to predict the connection probabilities of missing links. According to our experimental results, we find that the performance of our adaptive fusion model is better than many similarity indices.

Effects of star-shape poly(alkyl methacrylate) arm uniformity on lubricant properties

DOE PAGES

Robinson, Joshua W.; Qu, Jun; Erck, Robert; ...

2016-03-29

Star-shaped poly(alkyl methacrylate)s (PAMAs) were prepared and blended into an additive-free engine oil to assess the structure property relationship between macromolecular structure and lubricant performance. These additives were designed with a comparable number of repeating units per arm and the number of arms was varied between 3 and 6. Well-defined star-shaped PAMAs were synthesized by atom transfer radical polymerization (ATRP) via a core-first strategy from multi-functional headgroups. Observations of the polymer-oil blends suggest that stars with less than four arms are favorable as a viscosity index improver (VII), and molecular weight dominates viscosity-related effects over other structural features. Star-shaped PAMAs,more » as oil additives, effectively reduce the friction coefficient in both mixed and boundary lubrication regime. Several analogs outperformed commercial VIIs in both viscosity and friction performance. Furthermore, increased wear rates were observed for these star-shaped PAMAs in the boundary lubrication regime suggesting pressure-sensitive conformations may exist.« less

A Corner-Point-Grid-Based Voxelization Method for Complex Geological Structure Model with Folds

NASA Astrophysics Data System (ADS)

Chen, Qiyu; Mariethoz, Gregoire; Liu, Gang

2017-04-01

3D voxelization is the foundation of geological property modeling, and is also an effective approach to realize the 3D visualization of the heterogeneous attributes in geological structures. The corner-point grid is a representative data model among all voxel models, and is a structured grid type that is widely applied at present. When carrying out subdivision for complex geological structure model with folds, we should fully consider its structural morphology and bedding features to make the generated voxels keep its original morphology. And on the basis of which, they can depict the detailed bedding features and the spatial heterogeneity of the internal attributes. In order to solve the shortage of the existing technologies, this work puts forward a corner-point-grid-based voxelization method for complex geological structure model with folds. We have realized the fast conversion from the 3D geological structure model to the fine voxel model according to the rule of isocline in Ramsay's fold classification. In addition, the voxel model conforms to the spatial features of folds, pinch-out and other complex geological structures, and the voxels of the laminas inside a fold accords with the result of geological sedimentation and tectonic movement. This will provide a carrier and model foundation for the subsequent attribute assignment as well as the quantitative analysis and evaluation based on the spatial voxels. Ultimately, we use examples and the contrastive analysis between the examples and the Ramsay's description of isoclines to discuss the effectiveness and advantages of the method proposed in this work when dealing with the voxelization of 3D geologic structural model with folds based on corner-point grids.

PRSEUS Pressure Cube Test Data and Response

NASA Technical Reports Server (NTRS)

Lovejoy, Andrew E.

2013-01-01

NASA s Environmentally Responsible Aviation (ERA) Program is examining the hybrid wing body (HWB) aircraft, among others, in an effort to increase the fuel efficiency of commercial aircraft. The HWB design combines features of a flying wing with features of conventional transport aircraft, and has the advantage of simultaneously increasing both fuel efficiency and payload. Recent years have seen an increased focus on the structural performance of the HWB. The key structural challenge of a HWB airframe is the ability to create a cost and weight efficient, non-circular, pressurized shell. Conventional round fuselage sections react cabin pressure by hoop tension. However, the structural configuration of the HWB subjects the majority of the structural panels to bi-axial, in-plane loads in addition to the internal cabin pressure, which requires more thorough examination and analysis than conventional transport aircraft components having traditional and less complex load paths. To address this issue, while keeping structural weights low, extensive use of advanced composite materials is made. This report presents the test data and preliminary conclusions for a pressurized cube test article that utilizes Boeing's Pultruded Rod Stitched Efficient Unitized Structure (PRSEUS), and which is part of the building block approach used for HWB development.

Method of fan sound mode structure determination computer program user's manual: Modal calculation program

NASA Technical Reports Server (NTRS)

Pickett, G. F.; Wells, R. A.; Love, R. A.

1977-01-01

A computer user's manual describing the operation and the essential features of the Modal Calculation Program is presented. The modal Calculation Program calculates the amplitude and phase of modal structures by means of acoustic pressure measurements obtained from microphones placed at selected locations within the fan inlet duct. In addition, the Modal Calculation Program also calculates the first-order errors in the modal coefficients that are due to tolerances in microphone location coordinates and inaccuracies in the acoustic pressure measurements.

Time stamping of single optical photons with 10 ns resolution

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

Chakaberia, Irakli; Cotlet, Mircea; Fisher-Levine, Merlin

High spatial and temporal resolution are key features for many modern applications, e.g. mass spectrometry, probing the structure of materials via neutron scattering, studying molecular structure, etc. Fast imaging also provides the capability of coincidence detection, and the further addition of sensitivity to single optical photons with the capability of timestamping them further broadens the field of potential applications. Here, photon counting is already widely used in X-ray imaging, where the high energy of the photons makes their detection easier.

Time stamping of single optical photons with 10 ns resolution

DOE PAGES

Chakaberia, Irakli; Cotlet, Mircea; Fisher-Levine, Merlin; ...

2017-05-08

High spatial and temporal resolution are key features for many modern applications, e.g. mass spectrometry, probing the structure of materials via neutron scattering, studying molecular structure, etc. Fast imaging also provides the capability of coincidence detection, and the further addition of sensitivity to single optical photons with the capability of timestamping them further broadens the field of potential applications. Here, photon counting is already widely used in X-ray imaging, where the high energy of the photons makes their detection easier.

Nonlinear mechanics of non-rigid origami: an efficient computational approach

NASA Astrophysics Data System (ADS)

Liu, K.; Paulino, G. H.

2017-10-01

Origami-inspired designs possess attractive applications to science and engineering (e.g. deployable, self-assembling, adaptable systems). The special geometric arrangement of panels and creases gives rise to unique mechanical properties of origami, such as reconfigurability, making origami designs well suited for tunable structures. Although often being ignored, origami structures exhibit additional soft modes beyond rigid folding due to the flexibility of thin sheets that further influence their behaviour. Actual behaviour of origami structures usually involves significant geometric nonlinearity, which amplifies the influence of additional soft modes. To investigate the nonlinear mechanics of origami structures with deformable panels, we present a structural engineering approach for simulating the nonlinear response of non-rigid origami structures. In this paper, we propose a fully nonlinear, displacement-based implicit formulation for performing static/quasi-static analyses of non-rigid origami structures based on `bar-and-hinge' models. The formulation itself leads to an efficient and robust numerical implementation. Agreement between real models and numerical simulations demonstrates the ability of the proposed approach to capture key features of origami behaviour.

Nonlinear mechanics of non-rigid origami: an efficient computational approach.

PubMed

Liu, K; Paulino, G H

2017-10-01

Origami-inspired designs possess attractive applications to science and engineering (e.g. deployable, self-assembling, adaptable systems). The special geometric arrangement of panels and creases gives rise to unique mechanical properties of origami, such as reconfigurability, making origami designs well suited for tunable structures. Although often being ignored, origami structures exhibit additional soft modes beyond rigid folding due to the flexibility of thin sheets that further influence their behaviour. Actual behaviour of origami structures usually involves significant geometric nonlinearity, which amplifies the influence of additional soft modes. To investigate the nonlinear mechanics of origami structures with deformable panels, we present a structural engineering approach for simulating the nonlinear response of non-rigid origami structures. In this paper, we propose a fully nonlinear, displacement-based implicit formulation for performing static/quasi-static analyses of non-rigid origami structures based on 'bar-and-hinge' models. The formulation itself leads to an efficient and robust numerical implementation. Agreement between real models and numerical simulations demonstrates the ability of the proposed approach to capture key features of origami behaviour.

Magnetization transfer and adiabatic R 1ρ MRI in the brainstem of Parkinson's disease.

PubMed

Tuite, Paul J; Mangia, Silvia; Tyan, Andrew E; Lee, Michael K; Garwood, Michael; Michaeli, Shalom

2012-06-01

In addition to classic midbrain pathology, Parkinson's disease (PD) is accompanied by changes in pontine and medullary brainstem structures. These additional abnormalities may underlie non-motor features as well as play a role in motor disability. Using novel magnetic resonance imaging (MRI) methods based on rotating frame adiabatic R(1ρ) (i.e., measurements of longitudinal relaxation during adiabatic full passage pulses) and modified magnetization transfer (MT) MRI mapping, we sought to identify brainstem alterations in nine individuals with mild-moderate PD (off medication) and ten age-matched controls at 4 T. We discovered significant differences in MRI parameters between midbrain and medullary brainstem structures in control subjects as compared to PD patients. These findings support the presence of underlying functional/structural brainstem changes in mild-moderate PD. Copyright © 2012 Elsevier Ltd. All rights reserved.

Method of making organic light emitting devices

DOEpatents

Shiang, Joseph John [Niskayuna, NY; Janora, Kevin Henry [Schenectady, NY; Parthasarathy, Gautam [Saratoga Springs, NY; Cella, James Anthony [Clifton Park, NY; Chichak, Kelly Scott [Clifton Park, NY

2011-03-22

The present invention provides a method for the preparation of organic light-emitting devices comprising a bilayer structure made by forming a first film layer comprising an electroactive material and an INP precursor material, and exposing the first film layer to a radiation source under an inert atmosphere to generate an interpenetrating network polymer composition comprising the electroactive material. At least one additional layer is disposed on the reacted first film layer to complete the bilayer structure. The bilayer structure is comprised within an organic light-emitting device comprising standard features such as electrodes and optionally one or more additional layers serving as a bipolar emission layer, a hole injection layer, an electron injection layer, an electron transport layer, a hole transport layer, exciton-hole transporting layer, exciton-electron transporting layer, a hole transporting emission layer, or an electron transporting emission layer.

Quantification of Lignin and Its Structural Features in Plant Biomass Using 13C Lignin as Internal Standard for Pyrolysis-GC-SIM-MS.

PubMed

van Erven, Gijs; de Visser, Ries; Merkx, Donny W H; Strolenberg, Willem; de Gijsel, Peter; Gruppen, Harry; Kabel, Mirjam A

2017-10-17

Understanding the mechanisms underlying plant biomass recalcitrance at the molecular level can only be achieved by accurate analyses of both the content and structural features of the molecules involved. Current quantification of lignin is, however, majorly based on unspecific gravimetric analysis after sulfuric acid hydrolysis. Hence, our research aimed at specific lignin quantification with concurrent characterization of its structural features. Hereto, for the first time, a polymeric 13 C lignin was used as internal standard (IS) for lignin quantification via analytical pyrolysis coupled to gas chromatography with mass-spectrometric detection in selected ion monitoring mode (py-GC-SIM-MS). In addition, relative response factors (RRFs) for the various pyrolysis products obtained were determined and applied. First, 12 C and 13 C lignin were isolated from nonlabeled and uniformly 13 C labeled wheat straw, respectively, and characterized by heteronuclear single quantum coherence (HSQC), nuclear magnetic resonance (NMR), and py-GC/MS. The two lignin isolates were found to have identical structures. Second, 13 C-IS based lignin quantification by py-GC-SIM-MS was validated in reconstituted biomass model systems with known contents of the 12 C lignin analogue and was shown to be extremely accurate (>99.9%, R 2 > 0.999) and precise (RSD < 1.5%). Third, 13 C-IS based lignin quantification was applied to four common poaceous biomass sources (wheat straw, barley straw, corn stover, and sugar cane bagasse), and lignin contents were in good agreement with the total gravimetrically determined lignin contents. Our robust method proves to be a promising alternative for the high-throughput quantification of lignin in milled biomass samples directly and simultaneously provides a direct insight into the structural features of lignin.

Quantification of Lignin and Its Structural Features in Plant Biomass Using 13C Lignin as Internal Standard for Pyrolysis-GC-SIM-MS

PubMed Central

2017-01-01

Understanding the mechanisms underlying plant biomass recalcitrance at the molecular level can only be achieved by accurate analyses of both the content and structural features of the molecules involved. Current quantification of lignin is, however, majorly based on unspecific gravimetric analysis after sulfuric acid hydrolysis. Hence, our research aimed at specific lignin quantification with concurrent characterization of its structural features. Hereto, for the first time, a polymeric 13C lignin was used as internal standard (IS) for lignin quantification via analytical pyrolysis coupled to gas chromatography with mass-spectrometric detection in selected ion monitoring mode (py-GC-SIM-MS). In addition, relative response factors (RRFs) for the various pyrolysis products obtained were determined and applied. First, 12C and 13C lignin were isolated from nonlabeled and uniformly 13C labeled wheat straw, respectively, and characterized by heteronuclear single quantum coherence (HSQC), nuclear magnetic resonance (NMR), and py-GC/MS. The two lignin isolates were found to have identical structures. Second, 13C-IS based lignin quantification by py-GC-SIM-MS was validated in reconstituted biomass model systems with known contents of the 12C lignin analogue and was shown to be extremely accurate (>99.9%, R2 > 0.999) and precise (RSD < 1.5%). Third, 13C-IS based lignin quantification was applied to four common poaceous biomass sources (wheat straw, barley straw, corn stover, and sugar cane bagasse), and lignin contents were in good agreement with the total gravimetrically determined lignin contents. Our robust method proves to be a promising alternative for the high-throughput quantification of lignin in milled biomass samples directly and simultaneously provides a direct insight into the structural features of lignin. PMID:28926698

Structural health monitoring for ship structures

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

Farrar, Charles; Park, Gyuhae; Angel, Marian

2009-01-01

Currently the Office of Naval Research is supporting the development of structural health monitoring (SHM) technology for U.S. Navy ship structures. This application is particularly challenging because of the physical size of these structures, the widely varying and often extreme operational and environmental conditions associated with these ships missions, lack of data from known damage conditions, limited sensing that was not designed specifically for SHM, and the management of the vast amounts of data that can be collected during a mission. This paper will first define a statistical pattern recognition paradigm for SHM by describing the four steps of (1)more » Operational Evaluation, (2) Data Acquisition, (3) Feature Extraction, and (4) Statistical Classification of Features as they apply to ship structures. Note that inherent in the last three steps of this process are additional tasks of data cleansing, compression, normalization and fusion. The presentation will discuss ship structure SHM challenges in the context of applying various SHM approaches to sea trials data measured on an aluminum multi-hull high-speed ship, the HSV-2 Swift. To conclude, the paper will discuss several outstanding issues that need to be addressed before SHM can make the transition from a research topic to actual field applications on ship structures and suggest approaches for addressing these issues.« less

A structural and theoretical study of the alkylammonium nitrates forefather: Liquid methylammonium nitrate

NASA Astrophysics Data System (ADS)

Gontrani, Lorenzo; Caminiti, Ruggero; Salma, Umme; Campetella, Marco

2017-09-01

We present here a structural and vibrational analysis of melted methylammonium nitrate, the simplest compound of the family of alkylammonium nitrates. The static and dynamical features calculated were endorsed by comparing the experimental X-ray data with the theoretical ones. A reliable description cannot be obtained with classical molecular dynamics owing to polarization effects. Contrariwise, the structure factor and the vibrational frequencies obtained from ab initio molecular dynamics trajectories are in very good agreement with the experiment. A careful analysis has provided additional information on the complex hydrogen bonding network that exists in this liquid.

MCORES: a system for noun phrase coreference resolution for clinical records.

PubMed

Bodnari, Andreea; Szolovits, Peter; Uzuner, Özlem

2012-01-01

Narratives of electronic medical records contain information that can be useful for clinical practice and multi-purpose research. This information needs to be put into a structured form before it can be used by automated systems. Coreference resolution is a step in the transformation of narratives into a structured form. This study presents a medical coreference resolution system (MCORES) for noun phrases in four frequently used clinical semantic categories: persons, problems, treatments, and tests. MCORES treats coreference resolution as a binary classification task. Given a pair of concepts from a semantic category, it determines coreferent pairs and clusters them into chains. MCORES uses an enhanced set of lexical, syntactic, and semantic features. Some MCORES features measure the distance between various representations of the concepts in a pair and can be asymmetric. MCORES was compared with an in-house baseline that uses only single-perspective 'token overlap' and 'number agreement' features. MCORES was shown to outperform the baseline; its enhanced features contribute significantly to performance. In addition to the baseline, MCORES was compared against two available third-party, open-domain systems, RECONCILE(ACL09) and the Beautiful Anaphora Resolution Toolkit (BART). MCORES was shown to outperform both of these systems on clinical records.

Extensions of algebraic image operators: An approach to model-based vision

NASA Technical Reports Server (NTRS)

Lerner, Bao-Ting; Morelli, Michael V.

1990-01-01

Researchers extend their previous research on a highly structured and compact algebraic representation of grey-level images which can be viewed as fuzzy sets. Addition and multiplication are defined for the set of all grey-level images, which can then be described as polynomials of two variables. Utilizing this new algebraic structure, researchers devised an innovative, efficient edge detection scheme. An accurate method for deriving gradient component information from this edge detector is presented. Based upon this new edge detection system researchers developed a robust method for linear feature extraction by combining the techniques of a Hough transform and a line follower. The major advantage of this feature extractor is its general, object-independent nature. Target attributes, such as line segment lengths, intersections, angles of intersection, and endpoints are derived by the feature extraction algorithm and employed during model matching. The algebraic operators are global operations which are easily reconfigured to operate on any size or shape region. This provides a natural platform from which to pursue dynamic scene analysis. A method for optimizing the linear feature extractor which capitalizes on the spatially reconfiguration nature of the edge detector/gradient component operator is discussed.

Effects of anodizing parameters and heat treatment on nanotopographical features, bioactivity, and cell culture response of additively manufactured porous titanium.

PubMed

Amin Yavari, S; Chai, Y C; Böttger, A J; Wauthle, R; Schrooten, J; Weinans, H; Zadpoor, A A

2015-06-01

Anodizing could be used for bio-functionalization of the surfaces of titanium alloys. In this study, we use anodizing for creating nanotubes on the surface of porous titanium alloy bone substitutes manufactured using selective laser melting. Different sets of anodizing parameters (voltage: 10 or 20V anodizing time: 30min to 3h) are used for anodizing porous titanium structures that were later heat treated at 500°C. The nanotopographical features are examined using electron microscopy while the bioactivity of anodized surfaces is measured using immersion tests in the simulated body fluid (SBF). Moreover, the effects of anodizing and heat treatment on the performance of one representative anodized porous titanium structures are evaluated using in vitro cell culture assays using human periosteum-derived cells (hPDCs). It has been shown that while anodizing with different anodizing parameters results in very different nanotopographical features, i.e. nanotubes in the range of 20 to 55nm, anodized surfaces have limited apatite-forming ability regardless of the applied anodizing parameters. The results of in vitro cell culture show that both anodizing, and thus generation of regular nanotopographical feature, and heat treatment improve the cell culture response of porous titanium. In particular, cell proliferation measured using metabolic activity and DNA content was improved for anodized and heat treated as well as for anodized but not heat-treated specimens. Heat treatment additionally improved the cell attachment of porous titanium surfaces and upregulated expression of osteogenic markers. Anodized but not heat-treated specimens showed some limited signs of upregulated expression of osteogenic markers. In conclusion, while varying the anodizing parameters creates different nanotube structure, it does not improve apatite-forming ability of porous titanium. However, both anodizing and heat treatment at 500°C improve the cell culture response of porous titanium. Copyright © 2015 Elsevier B.V. All rights reserved.

A Target-Less Vision-Based Displacement Sensor Based on Image Convex Hull Optimization for Measuring the Dynamic Response of Building Structures.

PubMed

Choi, Insub; Kim, JunHee; Kim, Donghyun

2016-12-08

Existing vision-based displacement sensors (VDSs) extract displacement data through changes in the movement of a target that is identified within the image using natural or artificial structure markers. A target-less vision-based displacement sensor (hereafter called "TVDS") is proposed. It can extract displacement data without targets, which then serve as feature points in the image of the structure. The TVDS can extract and track the feature points without the target in the image through image convex hull optimization, which is done to adjust the threshold values and to optimize them so that they can have the same convex hull in every image frame and so that the center of the convex hull is the feature point. In addition, the pixel coordinates of the feature point can be converted to physical coordinates through a scaling factor map calculated based on the distance, angle, and focal length between the camera and target. The accuracy of the proposed scaling factor map was verified through an experiment in which the diameter of a circular marker was estimated. A white-noise excitation test was conducted, and the reliability of the displacement data obtained from the TVDS was analyzed by comparing the displacement data of the structure measured with a laser displacement sensor (LDS). The dynamic characteristics of the structure, such as the mode shape and natural frequency, were extracted using the obtained displacement data, and were compared with the numerical analysis results. TVDS yielded highly reliable displacement data and highly accurate dynamic characteristics, such as the natural frequency and mode shape of the structure. As the proposed TVDS can easily extract the displacement data even without artificial or natural markers, it has the advantage of extracting displacement data from any portion of the structure in the image.

Application of PALSAR-2 remote sensing data for structural geology and topographic mapping in Kelantan river basin, Malaysia

NASA Astrophysics Data System (ADS)

Beiranvand Pour, Amin; Hashim, Mazlan

2016-06-01

Natural hazards of geological origin are one of major problem during heavy monsoons rainfall in Kelantan state, peninsular Malaysia. Several landslides occur in this region are obviously connected to geological and topographical features, every year. Satellite synthetic aperture radar (SAR) data are particularly applicable for detection of geological structural and topographical features in tropical conditions. In this study, Phased Array type L-band Synthetic Aperture Radar (PALSAR-2), remote sensing data were used to identify high potential risk and susceptible zones for landslide in the Kelantan river basin. Adaptive Local Sigma filter was selected and applied to accomplish speckle reduction and preserving both edges and features in PALSAR-2 fine mode observation images. Different polarization images were integrated to enhance geological structures. Additionally, directional filters were applied to the PALSAR-2 Local Sigma resultant image for edge enhancement and detailed identification of linear features. Several faults, drainage patterns and lithological contact layers were identified at regional scale. In order to assess the results, fieldwork and GPS survey were conducted in the landslide affected zones in the Kelantan river basin. Results demonstrate the most of the landslides were associated with N-S, NNW-SSE and NE-SW trending faults, angulate drainage pattern and metamorphic and Quaternary units. Consequently, geologic structural map were produced for Kelantan river basin using recent PALSAR-2 data, which could be broadly applicable for landslide hazard assessment and delineation of high potential risk and susceptible areas. Landslide mitigation programmes could be conducted in the landslide recurrence regions for reducing catastrophes leading to economic losses and death.

SMOQ: a tool for predicting the absolute residue-specific quality of a single protein model with support vector machines

PubMed Central

2014-01-01

Background It is important to predict the quality of a protein structural model before its native structure is known. The method that can predict the absolute local quality of individual residues in a single protein model is rare, yet particularly needed for using, ranking and refining protein models. Results We developed a machine learning tool (SMOQ) that can predict the distance deviation of each residue in a single protein model. SMOQ uses support vector machines (SVM) with protein sequence and structural features (i.e. basic feature set), including amino acid sequence, secondary structures, solvent accessibilities, and residue-residue contacts to make predictions. We also trained a SVM model with two new additional features (profiles and SOV scores) on 20 CASP8 targets and found that including them can only improve the performance when real deviations between native and model are higher than 5Å. The SMOQ tool finally released uses the basic feature set trained on 85 CASP8 targets. Moreover, SMOQ implemented a way to convert predicted local quality scores into a global quality score. SMOQ was tested on the 84 CASP9 single-domain targets. The average difference between the residue-specific distance deviation predicted by our method and the actual distance deviation on the test data is 2.637Å. The global quality prediction accuracy of the tool is comparable to other good tools on the same benchmark. Conclusion SMOQ is a useful tool for protein single model quality assessment. Its source code and executable are available at: http://sysbio.rnet.missouri.edu/multicom_toolbox/. PMID:24776231

SMOQ: a tool for predicting the absolute residue-specific quality of a single protein model with support vector machines.

PubMed

Cao, Renzhi; Wang, Zheng; Wang, Yiheng; Cheng, Jianlin

2014-04-28

It is important to predict the quality of a protein structural model before its native structure is known. The method that can predict the absolute local quality of individual residues in a single protein model is rare, yet particularly needed for using, ranking and refining protein models. We developed a machine learning tool (SMOQ) that can predict the distance deviation of each residue in a single protein model. SMOQ uses support vector machines (SVM) with protein sequence and structural features (i.e. basic feature set), including amino acid sequence, secondary structures, solvent accessibilities, and residue-residue contacts to make predictions. We also trained a SVM model with two new additional features (profiles and SOV scores) on 20 CASP8 targets and found that including them can only improve the performance when real deviations between native and model are higher than 5Å. The SMOQ tool finally released uses the basic feature set trained on 85 CASP8 targets. Moreover, SMOQ implemented a way to convert predicted local quality scores into a global quality score. SMOQ was tested on the 84 CASP9 single-domain targets. The average difference between the residue-specific distance deviation predicted by our method and the actual distance deviation on the test data is 2.637Å. The global quality prediction accuracy of the tool is comparable to other good tools on the same benchmark. SMOQ is a useful tool for protein single model quality assessment. Its source code and executable are available at: http://sysbio.rnet.missouri.edu/multicom_toolbox/.

Inkjet Printing of Functional and Structural Materials: Fluid Property Requirements, Feature Stability, and Resolution

NASA Astrophysics Data System (ADS)

Derby, Brian

2010-08-01

Inkjet printing is viewed as a versatile manufacturing tool for applications in materials fabrication in addition to its traditional role in graphics output and marking. The unifying feature in all these applications is the dispensing and precise positioning of very small volumes of fluid (1-100 picoliters) on a substrate before transformation to a solid. The application of inkjet printing to the fabrication of structures for structural or functional materials applications requires an understanding as to how the physical processes that operate during inkjet printing interact with the properties of the fluid precursors used. Here we review the current state of understanding of the mechanisms of drop formation and how this defines the fluid properties that are required for a given liquid to be printable. The interactions between individual drops and the substrate as well as between adjacent drops are important in defining the resolution and accuracy of printed objects. Pattern resolution is limited by the extent to which a liquid drop spreads on a substrate and how spreading changes with the overlap of adjacent drops to form continuous features. There are clearly defined upper and lower bounds to the width of a printed continuous line, which can be defined in terms of materials and process variables. Finer-resolution features can be achieved through appropriate patterning and structuring of the substrate prior to printing, which is essential if polymeric semiconducting devices are to be fabricated. Low advancing and receding contact angles promote printed line stability but are also more prone to solute segregation or “coffee staining” on drying.

New capacities and modifications for NASTRAN level 17.5 at DTNSRDC

NASA Technical Reports Server (NTRS)

Hurwitz, M. M.

1980-01-01

Since 1970 DTNSRDC has been modifying NASTRAN to suite various Navy requirements. These modifications include capabilities as well as user conveniences and error corrections. The new features added to NASTRAN Level 17.5 are described. The subject areas of the additions include magnetostatics, piezoelectricity, fluid structure interactions, isoparametric finite elements, and shock design for shipboard equipment.

Mineral deposits in western Saudi Arabia; a preliminary report

USGS Publications Warehouse

Roberts, Ralph Jackson; Greenwood, William R.; Worl, Ronald G.; Dodge, F.C.W.; Kiilsgaard, Thor H.

1975-01-01

In order to effectively carry on a search for new mineral deposits, the belts should be mapped in detail, with emphasis on the delineation of stratigraphic and structural features that control metallization. In addition, geochemical and geophysical studies should be made of promising areas to outline exploration targets. These targets could then be systematically explored.

Quality of Child Care Using the Environment Rating Scales: A Meta-Analysis of International Studies

ERIC Educational Resources Information Center

Vermeer, Harriet J.; van IJzendoorn, Marinus H.; Cárcamo, Rodrigo A.; Harrison, Linda J.

2016-01-01

The current study provides a systematic examination of child care quality around the globe, using the Environment Rating Scales (ERS). Additional goals of this study are to examine associations between ERS process quality and structural features (group size, caregiver-child ratio) that underpin quality and between ERS and more proximal aspects of…

The newly expanded KSC Visitors Complex features a new ticket plaza, information center, exhibits an

NASA Technical Reports Server (NTRS)

1999-01-01

The $13 million expansion to KSC's Visitor Complex includes a new International Space Station-themed ticket plaza, featuring a structure of overhanging solar panels and astronauts performing assembly tasks. Other additions are a new information center, a walk-through Robot Scouts exhibit, a wildlife exhibit, and the film Quest for Life in a new 300-seat theater. The KSC Visitor Complex was inaugurated three decades ago and is now one of the top five tourist attractions in Florida. It is located on S.R. 407, east of I-95, within the Merritt Island National Wildlife Refuge.

The newly expanded KSC Visitors Complex features a new ticket plaza, information center, exhibits an

NASA Technical Reports Server (NTRS)

1999-01-01

At the grand opening of the newly expanded KSC Visitor Complex, Center Director Roy Bridges addresses guests and the media. The $13 million addition to the Visitor Complex includes an International Space Station-themed ticket plaza, featuring a structure of overhanging solar panels and astronauts performing assembly tasks, a new information center, films, and exhibits. The KSC Visitor Complex was inaugurated three decades ago and is now one of the top five tourist attractions in Florida. It is located on S.R. 407, east of I-95, within the Merritt Island National Wildlife Refuge.

The newly expanded KSC Visitors Complex features a new ticket plaza, information center, exhibits an

NASA Technical Reports Server (NTRS)

1999-01-01

The $13 million expansion to KSC's Visitor Complex includes a new International Space Station-themed ticket plaza, featuring a structure of overhanging solar panels and astronauts performing assembly tasks. Other additions are the new information center, a walk-through Robot Scouts exhibit, a wildlife exhibit, and the film Quest for Life in a new 300-seat theater. The KSC Visitor Complex was inaugurated three decades ago and is now one of the top five tourist attractions in Florida. It is located on S.R. 407, east of I-95, within the Merritt Island National Wildlife Refuge.

Sensory Hair Cells: An Introduction to Structure and Physiology.

PubMed

McPherson, Duane R

2018-06-18

Sensory hair cells are specialized secondary sensory cells that mediate our senses of hearing, balance, linear acceleration, and angular acceleration (head rotation). In addition, hair cells in fish and amphibians mediate sensitivity to water movement through the lateral line system, and closely related electroreceptive cells mediate sensitivity to low-voltage electric fields in the aquatic environment of many fish species and several species of amphibian.Sensory hair cells share many structural and functional features across all vertebrate groups, while at the same time they are specialized for employment in a wide variety of sensory tasks. The complexity of hair cell structure is large, and the diversity of hair cell applications in sensory systems exceeds that seen for most, if not all, sensory cell types. The intent of this review is to summarize the more significant structural features and some of the more interesting and important physiological mechanisms that have been elucidated thus far. Outside vertebrates, hair cells are only known to exist in the coronal organ of tunicates. Electrical resonance, electromotility, and their exquisite mechanical sensitivity all contribute to the attractiveness of hair cells as a research subject.

Characterization and Comparison of the Structural Features, Immune-Modulatory and Anti-Avian Influenza Virus Activities Conferred by Three Algal Sulfated Polysaccharides

PubMed Central

Song, Lin; Chen, Xiaolin; Liu, Xiaodong; Zhang, Fubo; Hu, Linfeng; Yue, Yang; Li, Kecheng; Li, Pengcheng

2015-01-01

Three marine macroalgae, i.e., Grateloupia filicina, Ulva pertusa and Sargassum qingdaoense, were selected as the deputies of Rhodophyta, Chlorophyta and Ochrophyta for comparative analysis of the molecular structures and biological activities of sulfated polysaccharides (SP). The ratio of water-soluble polysaccharides, the monosaccharide composition and the sulfated contents of three extracted SPs were determined, and their structures were characterized by Fourier transformation infrared spectroscopy. In addition, biological activity analysis showed that all three SPs had immune-modulatory activity both in vitro and in vivo, and SPs from S. qingdaoense had the best effect. Further bioassays showed that three SPs could not only enhance the immunity level stimulated by inactivated avian influenza virus (AIV) in vivo but also significantly inhibited the activity of activated AIV (H9N2 subtype) in vitro. G. filicina SP exhibited the strongest anti-AIV activity. These results revealed the variations in structural features and bioactivities among three SPs and indicated the potential adjuvants for immune-enhancement and anti-AIV. PMID:26729137

Optimum design for effective water transport through a double-layered porous hydrogel inspired by plant leaves

NASA Astrophysics Data System (ADS)

Kim, Hyejeong; Kim, Hyeonjeong; Huh, Hyungkyu; Hwang, Hyung Ju; Lee, Sang Joon

2014-11-01

Plant leaves are generally known to have optimized morphological structure in response to environmental changes for efficient water usage. However, the advantageous features of plant leaves are not fully utilized in engineering fields yet, since the optimum design in internal structure of plant leaves is unclear. In this study, the tissue organization of the hydraulic pathways inside plant leaves was investigated. Water transport through double-layered porous hydrogel models analogous to mesophyll cells was experimentally observed. In addition, computational experiment and theoretical analysis were applied to the model systems to find the optimal design for efficient water transport. As a result, the models with lower porosity or with pores distributed widely in the structure exhibit efficient mass transport. Our theoretical prediction supports that structural features of plant leaves guarantee sufficient water supply as survival strategy. This study may provide a new framework for investigating the biophysical principles governing the morphological optimization of plant leaves and for designing microfluidic devices to enhance mass transport ability. This study was supported by the National Research Foundation of Korea and funded by the Korean government.

Linking structural features from mitochondrial and bacterial F-type ATP synthases to their distinct mechanisms of ATPase inhibition.

PubMed

Krah, Alexander

2015-10-01

ATP synthases are molecular motors, which synthesize ATP, the ubiquitous energy source in all living cells. They use an electrochemical gradient to drive a rotation in the membrane embedded Fo domain, namely the c-ring, causing a conformational change in the soluble F1 domain which leads to the catalytic event. In the opposite fashion, they can also hydrolyse ATP to maintain the ion gradient across the membrane. To prevent wasteful ATP hydrolysis, bacteria and mammals have developed peculiar mechanistic features in addition to a common one, namely MgADP inhibition. Here I discuss the distinct ATPase inhibition mechanism in mitochondrial (IF1) and bacterial (subunits ε and ζ) F-type ATP synthases, based on available structural, biophysical and biochemical data. Copyright © 2015 Elsevier Ltd. All rights reserved.

Event-related potentials to structural familiar face incongruity processing.

PubMed

Jemel, B; George, N; Olivares, E; Fiori, N; Renault, B

1999-07-01

Thirty scalp sites were used to investigate the specific topography of the event-related potentials (ERPs) related to face associative priming when masked eyes of familiar faces were completed with either the proper features or incongruent ones. The enhanced negativity of N210 and N350, due to structural incongruity of faces, have a "category specific" inferotemporal localization on the scalp. Additional analyses support the existence of multiple ERP features within the temporal interval typically associated with N400 (N350 and N380), involving occipitotemporal and centroparietal areas. Seven reliable dipole locations have been evidenced using the brain electrical source analysis algorithm. Some of these localizations (fusiform, parahippocampal) are already known to be involved in face recognition, the other ones being related to general cognitive processes related to the task's demand. Because of their specific topography, the observed effects suggest that the face structural congruency process might involve early specialized neocortical areas in parallel with cortical memory circuits in the integration of perceptual and cognitive face processing.

A framework for solving ill-structured community problems

NASA Astrophysics Data System (ADS)

Keller, William Cotesworth

A multifaceted protocol for solving ill-structured community problems has been developed. It embodies the lessons learned from the past by refining and extending features of previous models from the systems thinkers, and the fields of behavioral decision making and creative problem solving. The protocol also embraces additional features needed to address the unique aspects of community decision situations. The essential elements of the protocol are participants from the community, a problem-solving process, a systems picture, a facilitator, a modified Delphi method of communications, and technical expertise. This interdisciplinary framework has been tested by a quasi experiment with a real world community problem (the high cost of electrical power on Long Island, NY). Results indicate the protocol can enable members of the community to understand a complicated, ill-structured problem and guide them to action to solve the issue. However, the framework takes time (over one year in the test case) and will be inappropriate for crises where quick action is needed.

Cyclohexane Rings Reduce Membrane Permeability to Small Ions in Archaea-Inspired Tetraether Lipids.

PubMed

Koyanagi, Takaoki; Leriche, Geoffray; Onofrei, David; Holland, Gregory P; Mayer, Michael; Yang, Jerry

2016-01-26

Extremophile archaeal organisms overcome problems of membrane permeability by producing lipids with structural elements that putatively improve membrane integrity compared to lipids from other life forms. Herein, we describe a series of lipids that mimic some key structural features of archaeal lipids, such as: 1) single tethering of lipid tails to create fully transmembrane tetraether lipids and 2) the incorporation of small rings into these tethered segments. We found that membranes formed from pure tetraether lipids leaked small ions at a rate that was about two orders of magnitude slower than common bilayer-forming lipids. Incorporation of cyclopentane rings into the tetraether lipids did not affect membrane leakage, whereas a cyclohexane ring reduced leakage by an additional 40 %. These results show that mimicking certain structural features of natural archaeal lipids results in improved membrane integrity, which may help overcome limitations of many current lipid-based technologies. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The Power of Materials Science Tools for Gaining Insights into Organic Semiconductors

NASA Astrophysics Data System (ADS)

Treat, Neil D.; Westacott, Paul; Stingelin, Natalie

2015-07-01

The structure of organic semiconductors can be complex because features from the molecular level (such as molecular conformation) to the micrometer scale (such as the volume fraction and composition of phases, phase distribution, and domain size) contribute to the definition of the optoelectronic landscape of the final architectures and, hence, to device performance. As a consequence, a detailed understanding of how to manipulate molecular ordering, e.g., through knowledge of relevant phase transitions, of the solidification process, of relevant solidification mechanisms, and of kinetic factors, is required to induce the desired optoelectronic response. In this review, we discuss relevant structural features of single-component and multicomponent systems; provide a case study of the multifaceted structure that polymer:fullerene systems can adopt; and highlight relevant solidification mechanisms such as nucleation and growth, liquid-liquid phase separation, and spinodal decomposition. In addition, cocrystal formation, solid solutions, and eutectic systems are treated and their relevance within the optoelectronic area emphasized.

Assessment of groundwater potentiality using geophysical techniques in Wadi Allaqi basin, Eastern Desert, Egypt - Case study

NASA Astrophysics Data System (ADS)

Helaly, Ahmad Sobhy

2017-12-01

Electrical resistivity surveying has been carried out for the determination of the thickness and resistivity of layered media in Wadi Allaqi, Eastern Desert, Egypt. That is widely used geophysical tool for the purpose of assessing the groundwater potential and siting the best locations for boreholes in the unconfined Nubian Sandstone aquifers within the study area. This has been done using thirteen 1D Vertical Electrical Sounding (VES) surveys. 1D-VES surveys provide only layered model structures for the subsurface and do not provide comprehensive information for interpreting the structure and extent of subsurface hydro-geological features. The integration of two-dimensional (2D) geophysical techniques for groundwater prospecting has been done to provide a more detailed identification for the subsurface hydro-geological features from which potential sites for successful borehole locations are recognized. In addition, five magnetic profiles were measured for basement depth determination, expected geological structures and thickness of sedimentary succession that could include some basins suitable for groundwater accumulation as groundwater aquifers.

Helium induced fine structure in the electronic spectra of anthracene derivatives doped into superfluid helium nanodroplets

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

Pentlehner, D.; Slenczka, A., E-mail: alkwin.slenczka@chemie.uni-regensburg.de

2015-01-07

Electronic spectra of organic molecules doped into superfluid helium nanodroplets show characteristic features induced by the helium environment. Besides a solvent induced shift of the electronic transition frequency, in many cases, a spectral fine structure can be resolved for electronic and vibronic transitions which goes beyond the expected feature of a zero phonon line accompanied by a phonon wing as known from matrix isolation spectroscopy. The spectral shape of the zero phonon line and the helium induced phonon wing depends strongly on the dopant species. Phonon wings, for example, are reported ranging from single or multiple sharp transitions to broadmore » (Δν > 100 cm{sup −1}) diffuse signals. Despite the large number of example spectra in the literature, a quantitative understanding of the helium induced fine structure of the zero phonon line and the phonon wing is missing. Our approach is a systematic investigation of related molecular compounds, which may help to shed light on this key feature of microsolvation in superfluid helium droplets. This paper is part of a comparative study of the helium induced fine structure observed in electronic spectra of anthracene derivatives with particular emphasis on a spectrally sharp multiplet splitting at the electronic origin. In addition to previously discussed species, 9-cyanoanthracene and 9-chloroanthracene will be presented in this study for the first time.« less

Bioinspired Cellular Structures: Additive Manufacturing and Mechanical Properties

NASA Astrophysics Data System (ADS)

Stampfl, J.; Pettermann, H. E.; Liska, R.

Biological materials (e.g., wood, trabecular bone, marine skeletons) rely heavily on the use of cellular architecture, which provides several advantages. (1) The resulting structures can bear the variety of "real life" load spectra using a minimum of a given bulk material, featuring engineering lightweight design principles. (2) The inside of the structures is accessible to body fluids which deliver the required nutrients. (3) Furthermore, cellular architectures can grow organically by adding or removing individual struts or by changing the shape of the constituting elements. All these facts make the use of cellular architectures a reasonable choice for nature. Using additive manufacturing technologies (AMT), it is now possible to fabricate such structures for applications in engineering and biomedicine. In this chapter, we present methods that allow the 3D computational analysis of the mechanical properties of cellular structures with open porosity. Various different cellular architectures including disorder are studied. In order to quantify the influence of architecture, the apparent density is always kept constant. Furthermore, it is shown that how new advanced photopolymers can be used to tailor the mechanical and functional properties of the fabricated structures.

Feature and Statistical Model Development in Structural Health Monitoring

NASA Astrophysics Data System (ADS)

Kim, Inho

All structures suffer wear and tear because of impact, excessive load, fatigue, corrosion, etc. in addition to inherent defects during their manufacturing processes and their exposure to various environmental effects. These structural degradations are often imperceptible, but they can severely affect the structural performance of a component, thereby severely decreasing its service life. Although previous studies of Structural Health Monitoring (SHM) have revealed extensive prior knowledge on the parts of SHM processes, such as the operational evaluation, data processing, and feature extraction, few studies have been conducted from a systematical perspective, the statistical model development. The first part of this dissertation, the characteristics of inverse scattering problems, such as ill-posedness and nonlinearity, reviews ultrasonic guided wave-based structural health monitoring problems. The distinctive features and the selection of the domain analysis are investigated by analytically searching the conditions of the uniqueness solutions for ill-posedness and are validated experimentally. Based on the distinctive features, a novel wave packet tracing (WPT) method for damage localization and size quantification is presented. This method involves creating time-space representations of the guided Lamb waves (GLWs), collected at a series of locations, with a spatially dense distribution along paths at pre-selected angles with respect to the direction, normal to the direction of wave propagation. The fringe patterns due to wave dispersion, which depends on the phase velocity, are selected as the primary features that carry information, regarding the wave propagation and scattering. The following part of this dissertation presents a novel damage-localization framework, using a fully automated process. In order to construct the statistical model for autonomous damage localization deep-learning techniques, such as restricted Boltzmann machine and deep belief network, are trained and utilized to interpret nonlinear far-field wave patterns. Next, a novel bridge scour estimation approach that comprises advantages of both empirical and data-driven models is developed. Two field datasets from the literature are used, and a Support Vector Machine (SVM), a machine-learning algorithm, is used to fuse the field data samples and classify the data with physical phenomena. The Fast Non-dominated Sorting Genetic Algorithm (NSGA-II) is evaluated on the model performance objective functions to search for Pareto optimal fronts.

3D Printing Polymers with Supramolecular Functionality for Biological Applications.

PubMed

Pekkanen, Allison M; Mondschein, Ryan J; Williams, Christopher B; Long, Timothy E

2017-09-11

Supramolecular chemistry continues to experience widespread growth, as fine-tuned chemical structures lead to well-defined bulk materials. Previous literature described the roles of hydrogen bonding, ionic aggregation, guest/host interactions, and π-π stacking to tune mechanical, viscoelastic, and processing performance. The versatility of reversible interactions enables the more facile manufacturing of molded parts with tailored hierarchical structures such as tissue engineered scaffolds for biological applications. Recently, supramolecular polymers and additive manufacturing processes merged to provide parts with control of the molecular, macromolecular, and feature length scales. Additive manufacturing, or 3D printing, generates customizable constructs desirable for many applications, and the introduction of supramolecular interactions will potentially increase production speed, offer a tunable surface structure for controlling cell/scaffold interactions, and impart desired mechanical properties through reinforcing interlayer adhesion and introducing gradients or self-assembled structures. This review details the synthesis and characterization of supramolecular polymers suitable for additive manufacture and biomedical applications as well as the use of supramolecular polymers in additive manufacturing for drug delivery and complex tissue scaffold formation. The effect of supramolecular assembly and its dynamic behavior offers potential for controlling the anisotropy of the printed objects with exquisite geometrical control. The potential for supramolecular polymers to generate well-defined parts, hierarchical structures, and scaffolds with gradient properties/tuned surfaces provides an avenue for developing next-generation biomedical devices and tissue scaffolds.

Influence of Cu, Au and Ag on structural and surface properties of bioactive coatings based on titanium.

PubMed

Wojcieszak, D; Mazur, M; Kalisz, M; Grobelny, M

2017-02-01

In this work influence of copper, silver and gold additives on structural and surface properties of biologically active thin films based on titanium have been described. Coatings were prepared by magnetron sputtering method. During each process metallic discs (targets) - Ti and the additive (Cu, Ag or Au) were co-sputtered in argon atmosphere. Structural investigation of as-deposited coatings was performed with the aid of XRD and SEM/EDS method. It was found that all prepared thin films were homogenous. Addition of Cu, Ag and Au resulted in nanocrystalline structure. Moreover, influence of these additives on hardness and antibacterial activity of titanium coatings was also studied. Ti-Cu, Ti-Ag and Ti-Au films had lower hardness as-compared to Ti. According to AAS results the difference of their activity was related to the ion migration process. It was found that Ti-Ag and Ti-Au coatings had biocidal effect related to direct contact of their surface with microorganisms. In the case of Ti-Cu antimicrobial activity had direct and indirect nature due to efficient ion migration process from the film surface to the surrounding environment. Functional features of coatings such as wettability and corrosion resistance were also examined and included in the comprehensive analysis. Copyright © 2016 Elsevier B.V. All rights reserved.

Structure-sensitive film materials based on polyvinyl alcohol compositions with polyacids

NASA Astrophysics Data System (ADS)

Lazareva, Tatjana G.; Iljushenko, Irina A.

1995-05-01

The influence of polyacidic additives (silicotungstic acid -- STA, carboxymethylcellulose -- Na-CMC, polymethacrylic acid -- PMA, polyacrylic acid -- PAA) on the molecular mobility of film composition based on polyvinyl alcohol (PVA) in the temperature range 20 - 200 degree(s)C has been evaluated. It has been concluded that interpolymer complexes are formed due to hydrogen bonding of the PVA and polyacidic additive molecules, which results in the change of the PVA stereoregularity. The formation of the complexes depends on the type and concentration of the polyacidic additive, the process of (alpha) -relaxation and, in a certain concentration range of the additive, increases the molecular mobility of the kinetic segments surrounding the complex. The influence of short-term UV-irradiation on the structure and properties of such materials has been investigated. A possibility of the reversible change of molecular mobility and stereoregularity of the examined compositions as a result of short-term UV-irradiation has been established. Introduction of polyacids into the PVA structure gives rise to the electrosensitivity, i.e., the ability to change structure under the action of an electric field. In this case the distinguishing feature is the relation between the molecular mobility and electrosensitivity in the range of parameters where the (alpha) - relaxation occurs.

CCProf: exploring conformational change profile of proteins

PubMed Central

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

2016-01-01

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

Protein single-model quality assessment by feature-based probability density functions.

PubMed

Cao, Renzhi; Cheng, Jianlin

2016-04-04

Protein quality assessment (QA) has played an important role in protein structure prediction. We developed a novel single-model quality assessment method-Qprob. Qprob calculates the absolute error for each protein feature value against the true quality scores (i.e. GDT-TS scores) of protein structural models, and uses them to estimate its probability density distribution for quality assessment. Qprob has been blindly tested on the 11th Critical Assessment of Techniques for Protein Structure Prediction (CASP11) as MULTICOM-NOVEL server. The official CASP result shows that Qprob ranks as one of the top single-model QA methods. In addition, Qprob makes contributions to our protein tertiary structure predictor MULTICOM, which is officially ranked 3rd out of 143 predictors. The good performance shows that Qprob is good at assessing the quality of models of hard targets. These results demonstrate that this new probability density distribution based method is effective for protein single-model quality assessment and is useful for protein structure prediction. The webserver of Qprob is available at: http://calla.rnet.missouri.edu/qprob/. The software is now freely available in the web server of Qprob.

Deep learning of support vector machines with class probability output networks.

PubMed

Kim, Sangwook; Yu, Zhibin; Kil, Rhee Man; Lee, Minho

2015-04-01

Deep learning methods endeavor to learn features automatically at multiple levels and allow systems to learn complex functions mapping from the input space to the output space for the given data. The ability to learn powerful features automatically is increasingly important as the volume of data and range of applications of machine learning methods continues to grow. This paper proposes a new deep architecture that uses support vector machines (SVMs) with class probability output networks (CPONs) to provide better generalization power for pattern classification problems. As a result, deep features are extracted without additional feature engineering steps, using multiple layers of the SVM classifiers with CPONs. The proposed structure closely approaches the ideal Bayes classifier as the number of layers increases. Using a simulation of classification problems, the effectiveness of the proposed method is demonstrated. Copyright © 2014 Elsevier Ltd. All rights reserved.

Pathogenic features and characteristics of food borne pathogens biofilm: Biomass, viability and matrix.

PubMed

Lin, Shiqi; Yang, Ling; Chen, Gu; Li, Bing; Chen, Dingqiang; Li, Lin; Xu, Zhenbo

2017-10-01

Biofilm is a ubiquitous growth pattern of bacterial species survival but is notorious for its threat on public health and food contamination. Extensive studies of the biofilm structure, formation, quantification, quorum sensing system and underlying control strategies have been reported during the past decades. Insightful elucidation of the pathogenic features and characteristic of bacterial biofilm can facilitate in devising appropriate control strategies for biofilm eradication. Therefore, this review mainly summarized the pathogenic features of biofilms from food borne microorganisms, including the biomass (which could be quantified using crystal violet and fluorogenic dye Syto9 assays), viability (which could be determined by tetrazolium salts, fluorescein diacetate, resazurin staining and alamar blue assays) and matrix (which are commonly detected by dimethyl methylene blue and wheat germ agglutinin assays). In addition, three features were further compared with its particular benefits in specific application. Copyright © 2017 Elsevier Ltd. All rights reserved.

Spectral-spatial classification of hyperspectral image using three-dimensional convolution network

NASA Astrophysics Data System (ADS)

Liu, Bing; Yu, Xuchu; Zhang, Pengqiang; Tan, Xiong; Wang, Ruirui; Zhi, Lu

2018-01-01

Recently, hyperspectral image (HSI) classification has become a focus of research. However, the complex structure of an HSI makes feature extraction difficult to achieve. Most current methods build classifiers based on complex handcrafted features computed from the raw inputs. The design of an improved 3-D convolutional neural network (3D-CNN) model for HSI classification is described. This model extracts features from both the spectral and spatial dimensions through the application of 3-D convolutions, thereby capturing the important discrimination information encoded in multiple adjacent bands. The designed model views the HSI cube data altogether without relying on any pre- or postprocessing. In addition, the model is trained in an end-to-end fashion without any handcrafted features. The designed model was applied to three widely used HSI datasets. The experimental results demonstrate that the 3D-CNN-based method outperforms conventional methods even with limited labeled training samples.

Nakhla: a Martian Meteorite with Indigenous Organic Carbonaceous Features

NASA Technical Reports Server (NTRS)

McKay, D. S.; Gibson, E. K.; Thomas-Keprta, K. L.; Clemett, S. J.; Le, L.; Rahman, Z.; Wentworth, S. J.

2011-01-01

The Nakhla meteorite possesses discrete, well defined, structurally coherent morphologies of carbonaceous phases present within iddingsite alteration zones. Based upon both isotopic measurements and analysis of organic phases the presence of pre-terrestrial organics is now recognized. Within the microcrystalline layers of Nakhla s iddingsite, discrete clusters of salt crystals are present. These salts are predominantly halite (NaCl) with minor MgCl2 crystals. Some CaSO4, likely gypsum, appears to be partially intergrown with some of the halite. EDX mapping shows discrete C-rich features are interspersed among these crystals. A hollow semi-spherical bowl structure ( 3 m ) has been identified and analyzed after using a focused ion beam (FIB) to cut a transverse TEM thin section of the feature and the underlying iddingsite. TEM/EDX analysis reveals that the feature is primarily carbonaceous containing C with lesser amounts of Si, S, Ca, Cl, F, Na, and minor Mn and Fe; additionally a small peak consistent with N, which has been previously seen in Nakhla carbonaceous matter, is also present. Selected area electron diffraction (SAED) shows that this C-rich material is amorphous (lacking any long-range crystallographic order) and is not graphite or carbonate. Micro-Raman spectra acquired from the same surface from which the FIB section was extracted demonstrate a typical kerogen-like D and G band structure with a weak absorption peak at 1350 and a stronger peak at 1600/cm. The C-rich feature is intimately associated with both the surrounding halite and underlying iddingsite matrix. Both iddingsite and salts are interpreted as having formed as evaporate assemblages from progressive evaporation of water bodies on Mars. This assemblage, sans the carbonaceous moieties, closely resembles iddingsite alteration features previously described which were interpreted as indigenous Martian assemblages. These distinctive macromolecular carbonaceous structures in Nakhla may represent one of the sources of the high molecular weight organic material previously identified in Nakhla. While we do not speculate on the origin of these unique carbonaceous structures, we note that the significance of such observations is that it may allow us to construct a C-cycle for Mars based on the C chemistry of the Martian meteorites with obvious implications for astrobiology and the prebiotic evolution of Mars. In any case, our observations strongly suggest that organic C exists as micrometersize, discrete structures on Mars.

A novel structural tree for wrap-proteins, a subclass of (α+β)-proteins.

PubMed

Boshkova, Eugenia A; Gordeev, Alexey B; Efimov, Alexander V

2014-01-01

In this paper, a novel structural subclass of (α+β)-proteins is presented. A characteristic feature of these proteins and domains is that they consist of strongly twisted and coiled β-sheets wrapped around one or two α-helices, so they are referred to here as wrap-proteins. It is shown that overall folds of the wrap-proteins can be obtained by stepwise addition of α-helices and/or β-strands to the strongly twisted and coiled β-hairpin taken as the starting structure in modeling. As a result of modeling, a structural tree for the wrap-proteins was constructed that includes 201 folds of which 49 occur in known nonhomologous proteins.

Structural properties of prokaryotic promoter regions correlate with functional features.

PubMed

Meysman, Pieter; Collado-Vides, Julio; Morett, Enrique; Viola, Roberto; Engelen, Kristof; Laukens, Kris

2014-01-01

The structural properties of the DNA molecule are known to play a critical role in transcription. In this paper, the structural profiles of promoter regions were studied within the context of their diversity and their function for eleven prokaryotic species; Escherichia coli, Klebsiella pneumoniae, Salmonella Typhimurium, Pseudomonas auroginosa, Geobacter sulfurreducens Helicobacter pylori, Chlamydophila pneumoniae, Synechocystis sp., Synechoccocus elongates, Bacillus anthracis, and the archaea Sulfolobus solfataricus. The main anchor point for these promoter regions were transcription start sites identified through high-throughput experiments or collected within large curated databases. Prokaryotic promoter regions were found to be less stable and less flexible than the genomic mean across all studied species. However, direct comparison between species revealed differences in their structural profiles that can not solely be explained by the difference in genomic GC content. In addition, comparison with functional data revealed that there are patterns in the promoter structural profiles that can be linked to specific functional loci, such as sigma factor regulation or transcription factor binding. Interestingly, a novel structural element clearly visible near the transcription start site was found in genes associated with essential cellular functions and growth in several species. Our analyses reveals the great diversity in promoter structural profiles both between and within prokaryotic species. We observed relationships between structural diversity and functional features that are interesting prospects for further research to yet uncharacterized functional loci defined by DNA structural properties.

Atom-Economical Dimerization Strategy by the Rhodium-Catalyzed Addition of Carboxylic Acids to Allenes: Protecting-Group-Free Synthesis of Clavosolide A and Late-Stage Modification.

PubMed

Haydl, Alexander M; Breit, Bernhard

2015-12-14

Natural products of polyketide origin with a high level of symmetry, in particular C2 -symmetric diolides as a special macrolactone-based product class, often possess a broad spectrum of biological activity. An efficient route to this important structural motif was developed as part of a concise and highly convergent synthesis of clavosolide A. This strategy features an atom-economic "head-to-tail" dimerization by the stereoselective rhodium-catalyzed addition of carboxylic acids to terminal allenes with the simultaneous construction of two new stereocenters. The excellent efficiency and selectivity with which the C2 -symmetric core structures were obtained are remarkable considering the outcome under classical dimerization conditions. Furthermore, this approach facilitates late-stage modification and provides ready access to potential new lead structures. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Evaluation of feature selection algorithms for classification in temporal lobe epilepsy based on MR images

NASA Astrophysics Data System (ADS)

Lai, Chunren; Guo, Shengwen; Cheng, Lina; Wang, Wensheng; Wu, Kai

2017-02-01

It's very important to differentiate the temporal lobe epilepsy (TLE) patients from healthy people and localize the abnormal brain regions of the TLE patients. The cortical features and changes can reveal the unique anatomical patterns of brain regions from the structural MR images. In this study, structural MR images from 28 normal controls (NC), 18 left TLE (LTLE), and 21 right TLE (RTLE) were acquired, and four types of cortical feature, namely cortical thickness (CTh), cortical surface area (CSA), gray matter volume (GMV), and mean curvature (MCu), were explored for discriminative analysis. Three feature selection methods, the independent sample t-test filtering, the sparse-constrained dimensionality reduction model (SCDRM), and the support vector machine-recursive feature elimination (SVM-RFE), were investigated to extract dominant regions with significant differences among the compared groups for classification using the SVM classifier. The results showed that the SVM-REF achieved the highest performance (most classifications with more than 92% accuracy), followed by the SCDRM, and the t-test. Especially, the surface area and gray volume matter exhibited prominent discriminative ability, and the performance of the SVM was improved significantly when the four cortical features were combined. Additionally, the dominant regions with higher classification weights were mainly located in temporal and frontal lobe, including the inferior temporal, entorhinal cortex, fusiform, parahippocampal cortex, middle frontal and frontal pole. It was demonstrated that the cortical features provided effective information to determine the abnormal anatomical pattern and the proposed method has the potential to improve the clinical diagnosis of the TLE.

Hand Motion Classification Using a Multi-Channel Surface Electromyography Sensor

PubMed Central

Tang, Xueyan; Liu, Yunhui; Lv, Congyi; Sun, Dong

2012-01-01

The human hand has multiple degrees of freedom (DOF) for achieving high-dexterity motions. Identifying and replicating human hand motions are necessary to perform precise and delicate operations in many applications, such as haptic applications. Surface electromyography (sEMG) sensors are a low-cost method for identifying hand motions, in addition to the conventional methods that use data gloves and vision detection. The identification of multiple hand motions is challenging because the error rate typically increases significantly with the addition of more hand motions. Thus, the current study proposes two new methods for feature extraction to solve the problem above. The first method is the extraction of the energy ratio features in the time-domain, which are robust and invariant to motion forces and speeds for the same gesture. The second method is the extraction of the concordance correlation features that describe the relationship between every two channels of the multi-channel sEMG sensor system. The concordance correlation features of a multi-channel sEMG sensor system were shown to provide a vast amount of useful information for identification. Furthermore, a new cascaded-structure classifier is also proposed, in which 11 types of hand gestures can be identified accurately using the newly defined features. Experimental results show that the success rate for the identification of the 11 gestures is significantly high. PMID:22438703

Real-space post-processing correction of thermal drift and piezoelectric actuator nonlinearities in scanning tunneling microscope images.

PubMed

Yothers, Mitchell P; Browder, Aaron E; Bumm, Lloyd A

2017-01-01

We have developed a real-space method to correct distortion due to thermal drift and piezoelectric actuator nonlinearities on scanning tunneling microscope images using Matlab. The method uses the known structures typically present in high-resolution atomic and molecularly resolved images as an internal standard. Each image feature (atom or molecule) is first identified in the image. The locations of each feature's nearest neighbors are used to measure the local distortion at that location. The local distortion map across the image is simultaneously fit to our distortion model, which includes thermal drift in addition to piezoelectric actuator hysteresis and creep. The image coordinates of the features and image pixels are corrected using an inverse transform from the distortion model. We call this technique the thermal-drift, hysteresis, and creep transform. Performing the correction in real space allows defects, domain boundaries, and step edges to be excluded with a spatial mask. Additional real-space image analyses are now possible with these corrected images. Using graphite(0001) as a model system, we show lattice fitting to the corrected image, averaged unit cell images, and symmetry-averaged unit cell images. Statistical analysis of the distribution of the image features around their best-fit lattice sites measures the aggregate noise in the image, which can be expressed as feature confidence ellipsoids.

Real-space post-processing correction of thermal drift and piezoelectric actuator nonlinearities in scanning tunneling microscope images

NASA Astrophysics Data System (ADS)

Yothers, Mitchell P.; Browder, Aaron E.; Bumm, Lloyd A.

2017-01-01

We have developed a real-space method to correct distortion due to thermal drift and piezoelectric actuator nonlinearities on scanning tunneling microscope images using Matlab. The method uses the known structures typically present in high-resolution atomic and molecularly resolved images as an internal standard. Each image feature (atom or molecule) is first identified in the image. The locations of each feature's nearest neighbors are used to measure the local distortion at that location. The local distortion map across the image is simultaneously fit to our distortion model, which includes thermal drift in addition to piezoelectric actuator hysteresis and creep. The image coordinates of the features and image pixels are corrected using an inverse transform from the distortion model. We call this technique the thermal-drift, hysteresis, and creep transform. Performing the correction in real space allows defects, domain boundaries, and step edges to be excluded with a spatial mask. Additional real-space image analyses are now possible with these corrected images. Using graphite(0001) as a model system, we show lattice fitting to the corrected image, averaged unit cell images, and symmetry-averaged unit cell images. Statistical analysis of the distribution of the image features around their best-fit lattice sites measures the aggregate noise in the image, which can be expressed as feature confidence ellipsoids.

Hand motion classification using a multi-channel surface electromyography sensor.

PubMed

Tang, Xueyan; Liu, Yunhui; Lv, Congyi; Sun, Dong

2012-01-01

The human hand has multiple degrees of freedom (DOF) for achieving high-dexterity motions. Identifying and replicating human hand motions are necessary to perform precise and delicate operations in many applications, such as haptic applications. Surface electromyography (sEMG) sensors are a low-cost method for identifying hand motions, in addition to the conventional methods that use data gloves and vision detection. The identification of multiple hand motions is challenging because the error rate typically increases significantly with the addition of more hand motions. Thus, the current study proposes two new methods for feature extraction to solve the problem above. The first method is the extraction of the energy ratio features in the time-domain, which are robust and invariant to motion forces and speeds for the same gesture. The second method is the extraction of the concordance correlation features that describe the relationship between every two channels of the multi-channel sEMG sensor system. The concordance correlation features of a multi-channel sEMG sensor system were shown to provide a vast amount of useful information for identification. Furthermore, a new cascaded-structure classifier is also proposed, in which 11 types of hand gestures can be identified accurately using the newly defined features. Experimental results show that the success rate for the identification of the 11 gestures is significantly high.

A particle swarm optimized kernel-based clustering method for crop mapping from multi-temporal polarimetric L-band SAR observations

NASA Astrophysics Data System (ADS)

Tamiminia, Haifa; Homayouni, Saeid; McNairn, Heather; Safari, Abdoreza

2017-06-01

Polarimetric Synthetic Aperture Radar (PolSAR) data, thanks to their specific characteristics such as high resolution, weather and daylight independence, have become a valuable source of information for environment monitoring and management. The discrimination capability of observations acquired by these sensors can be used for land cover classification and mapping. The aim of this paper is to propose an optimized kernel-based C-means clustering algorithm for agriculture crop mapping from multi-temporal PolSAR data. Firstly, several polarimetric features are extracted from preprocessed data. These features are linear polarization intensities, and several statistical and physical based decompositions such as Cloude-Pottier, Freeman-Durden and Yamaguchi techniques. Then, the kernelized version of hard and fuzzy C-means clustering algorithms are applied to these polarimetric features in order to identify crop types. The kernel function, unlike the conventional partitioning clustering algorithms, simplifies the non-spherical and non-linearly patterns of data structure, to be clustered easily. In addition, in order to enhance the results, Particle Swarm Optimization (PSO) algorithm is used to tune the kernel parameters, cluster centers and to optimize features selection. The efficiency of this method was evaluated by using multi-temporal UAVSAR L-band images acquired over an agricultural area near Winnipeg, Manitoba, Canada, during June and July in 2012. The results demonstrate more accurate crop maps using the proposed method when compared to the classical approaches, (e.g. 12% improvement in general). In addition, when the optimization technique is used, greater improvement is observed in crop classification, e.g. 5% in overall. Furthermore, a strong relationship between Freeman-Durden volume scattering component, which is related to canopy structure, and phenological growth stages is observed.

Hair Follicle Nevus With Features of Comedo Nevus: An Expanding Spectrum.

PubMed

Nagarajan, Priyadharsini; Bartholomew, Timothy S; Allen, Carl M; Peters, Sara B

2016-06-01

Hair follicle nevus (HFN) is a rare hamartomatous lesion of the folliculosebaceous unit, with or without admixed fibroadipose or muscular tissue. It typically has a congenital presentation in the preauricular area of infants and is frequently confused with an accessory tragus. Acquired tumors with similar histopathologic features have been described infrequently during adolescence and adult life. We report yet another unique presentation of this unusual lesion in a 4-year-old girl who had a long-standing tumor of the nasal columella that started growing rapidly after trauma. Histopathologic examination revealed increased numbers of hair follicles, some of which were associated with diminutive sebaceous glands, with no associated central cystic structure. In addition, the infundibula of the follicles were dilated and filled with keratinous debris. Although these hamartomas are common in the head and neck region, to our knowledge, this is the first report of a HFN at this anatomic location. In addition, this tumor has an overall architecture of a HFN but is accompanied by features of a comedo nevus. We also present a review of the literature and summarize the current diagnostic criteria for HFN.

Saqqar: A 34 km diameter impact structure in Saudi Arabia

NASA Astrophysics Data System (ADS)

Kenkmann, Thomas; Afifi, Abdulkader M.; Stewart, Simon A.; Poelchau, Michael H.; Cook, Douglas J.; Neville, Allen S.

2015-11-01

Here we present the first proof of an impact origin for the Saqqar circular structure in northwestern Saudi Arabia (Neville et al. ), with an apparent diameter of 34 km, centered at 29°35'N, 38°42'E. The structure is formed in Cambrian-Devonian siliciclastics and is unconformably overlain by undeformed Cretaceous and Paleogene sediments. The age of impact is not well constrained and lies somewhere between 410 and 70 Ma. The subsurface structure is constrained by 2-D reflection seismic profiles and six drilled wells. First-order structural features are a central uplift that rises approximately 2 km above regional datums, surrounded by a ring syncline. The crater rim is defined by circumferential normal faults. The central uplift and ring syncline correspond to a Bouguer gravity high and an annular ring-like low, respectively. The wells were drilled within the central uplift, the deepest among them exceed 2 km depth. Sandstone core samples from these wells show abundant indicators of a shock metamorphic overprint. Planar deformation features (PDFs) were measured with orientations along (0001), {101¯3}, and less frequently along {101¯1} and {101¯4}. Planar fractures (PFs) predominantly occur along (0001) and {101¯1}, and are locally associated with feather features (FFs). In addition, some shocked feldspar grains and strongly deformed mica flakes were found. The recorded shock pressure ranges between 5 and 15 GPa. The preserved level of shock and the absence of an allochthonous crater fill suggest that Saqqar was eroded by 1-2 km between the Devonian and Maastrichtian. The documentation of unequivocal shock features proves the formation of the Saqqar structure by a hypervelocity impact event.

Modeling process-structure-property relationships for additive manufacturing

NASA Astrophysics Data System (ADS)

Yan, Wentao; Lin, Stephen; Kafka, Orion L.; Yu, Cheng; Liu, Zeliang; Lian, Yanping; Wolff, Sarah; Cao, Jian; Wagner, Gregory J.; Liu, Wing Kam

2018-02-01

This paper presents our latest work on comprehensive modeling of process-structure-property relationships for additive manufacturing (AM) materials, including using data-mining techniques to close the cycle of design-predict-optimize. To illustrate the processstructure relationship, the multi-scale multi-physics process modeling starts from the micro-scale to establish a mechanistic heat source model, to the meso-scale models of individual powder particle evolution, and finally to the macro-scale model to simulate the fabrication process of a complex product. To link structure and properties, a highefficiency mechanistic model, self-consistent clustering analyses, is developed to capture a variety of material response. The model incorporates factors such as voids, phase composition, inclusions, and grain structures, which are the differentiating features of AM metals. Furthermore, we propose data-mining as an effective solution for novel rapid design and optimization, which is motivated by the numerous influencing factors in the AM process. We believe this paper will provide a roadmap to advance AM fundamental understanding and guide the monitoring and advanced diagnostics of AM processing.

Electron petrography of silica polymorphs associated with pseudotachylite, Vredefort structure, South Africa

NASA Technical Reports Server (NTRS)

White, J. C.

1992-01-01

High-pressure silica polymorphs (coesite and stishovite) were described from the Vredefort structure in association with pseudotachylite veinlets. In addition to the fundamental significance of the polymorphs to genetic interpretations of the structure, it was additionally argued that the type of pseudotachylite with which they occur forms during the compressional phase of the shock process, while the larger, classic pseudotachylite occurrences are barren of polymorphs and formed during passage of the rarefaction wave. This identification of temporal relationships among transient shock features at a regional scale is similar to observations from the Manicouagan structure, Quebec, where texturally distinct diaplectic plagioclase glasses formed during both compressional and decompressional phases of the shock process. The clarification of such relationships impinges directly on interpretations of natural shock processes and the identification of high probability targets for polymorph searches. Detailed analytical scanning (SEM) and transmission electron microscopy (TEM) were utilized to further establish the nature of both the pseudotachylite and the silica polymorph occurrences in the Vredefort rocks. The results of this investigation are discussed.

Self-assembled nanoparticle arrays as nanomasks for pattern transfer

NASA Astrophysics Data System (ADS)

Sachan, M.; Bonnoit, C.; Hogg, C.; Evarts, E.; Bain, J. A.; Majetich, S. A.; Park, J.-H.; Zhu, J.-G.

2008-07-01

Argon ion milling was used to transfer the pattern of sparse 12 nm iron oxide nanoparticles into underlying thin films of Pt and magnetic tunnel junction stacks and quantify their etching rates and morphological evolution. Under typical milling conditions, Pt milled at 10 nm min-1, while the isolated particles of iron oxide used for the mask milled at 5 nm min-1. Dilute dispersions of nanoparticles were used to produce the sparse nanomasks, and high resolution scanning electron microscopy (SEM) and atomic force microscopy were used to monitor the evolution of etched structures as a function of milling time. SEM measurements indicate an apparent 20% increase in feature diameter before the features began to diminish under additional milling, suggesting redeposition as a limiting feature in the milling of dense arrays. Simulations of the milling process in nanoparticle arrays that include redeposition are consistent with this observation. These simulations predict that an edge-to-edge spacing of 3 nm in a dense array is feasible, but that redeposition reduces the final structure aspect ratio from that of the masking array by as much as a factor of two.

Recent crustal movements and seismicity in the western coastal region of peninsular India

NASA Astrophysics Data System (ADS)

Kailasam, L. N.

1983-09-01

Recent crustal movements, tectonics and seismicity of the western coastal region of peninsular India have been studied in detail in the very recent past. Prominent geomorphic features and large-scale manifestation of Holocene deformation and crustal movements have been noticed and studied over this coastal region from the Gulf of Cambay to the southernmost parts of Kerala, evidence for which is afforded in the form of Recent and sub-Recent raised beaches, sandbars, raised old terraces, pebble beds, etc. The sedimentary formations in this narrow coastal belt include Neogene and Quaternary sediments. The Bouguer gravity map of the western coastal tract shows some prominent gravity features extending into the offshore regions, suggestive of some significant tectonic and structural features. The seismic data in the offshore regions bring out some prominent roughly northwest-southeast as well as east-west faults and shears, in addition to prominent structural "highs" off the Bombay and Ratnagiri coast which have proved oil. The seismicity in this coastal tract as well as the faulted western margin of the western continental shelf in the Arabian Sea is generally of magnitude 3-6.

Plasticity-Driven Self-Organization under Topological Constraints Accounts for Non-random Features of Cortical Synaptic Wiring

PubMed Central

Miner, Daniel; Triesch, Jochen

2016-01-01

Understanding the structure and dynamics of cortical connectivity is vital to understanding cortical function. Experimental data strongly suggest that local recurrent connectivity in the cortex is significantly non-random, exhibiting, for example, above-chance bidirectionality and an overrepresentation of certain triangular motifs. Additional evidence suggests a significant distance dependency to connectivity over a local scale of a few hundred microns, and particular patterns of synaptic turnover dynamics, including a heavy-tailed distribution of synaptic efficacies, a power law distribution of synaptic lifetimes, and a tendency for stronger synapses to be more stable over time. Understanding how many of these non-random features simultaneously arise would provide valuable insights into the development and function of the cortex. While previous work has modeled some of the individual features of local cortical wiring, there is no model that begins to comprehensively account for all of them. We present a spiking network model of a rodent Layer 5 cortical slice which, via the interactions of a few simple biologically motivated intrinsic, synaptic, and structural plasticity mechanisms, qualitatively reproduces these non-random effects when combined with simple topological constraints. Our model suggests that mechanisms of self-organization arising from a small number of plasticity rules provide a parsimonious explanation for numerous experimentally observed non-random features of recurrent cortical wiring. Interestingly, similar mechanisms have been shown to endow recurrent networks with powerful learning abilities, suggesting that these mechanism are central to understanding both structure and function of cortical synaptic wiring. PMID:26866369

Gas hydrate and spatial venting variations in the continental margin offshore Southwestern Taiwan

NASA Astrophysics Data System (ADS)

Lin, S.; Lim, Y.; Hsieh, W.; Yang, T.; Wang, Y.

2006-12-01

Strong BSR, high methane contents and rapid sulfate reduction were found in the continental margin sediments offshore southwestern Taiwan. In order to identify the venting phenomena and its relationship with gas hydrate, this research investigate sea floor vent features using WHOI?|s Towcam system as well as piston core in the study region. A total of 10 dives were conducted on board the r/v OR-1. Pore water sulfate, dissolved sulfide, methane, chloride, del O18 ratio, sediment organic carbon, carbonate content and carbonate del C13 ratio, pyrite-S were measured Large spatial variations were found based on pictures obtained from Towcam system and piston cores. Active venting features include bacteria mat, live dense bivalve patches, gas plume, temperature and salinity fluctuations, rapid sulfate reduction and high concentrations of methane in sediments. In addition, vent chimney, pockmark and large authigenic carbonate buildup were also observed in the active venting area. In contrast, in some areas without active venting features, scatter dead chimney, semi- buried carbonate structures, and dead bivalves were found. Total sulfate depletion was found at depth as shallow as 1 meter below sediment water interface in area near active vent whereas almost no sulfate depletion was observed in areas without any vent feature. Stages of carbonate build up existed, with initial phase dominated by small tube, chimney, and later with massive carbonate structures protruding the sea floor. The appearances of massive carbonate buildup structures seemed to indicate the end stage of gas hydrate venting phenomena.

Effective Moment Feature Vectors for Protein Domain Structures

PubMed Central

Shi, Jian-Yu; Yiu, Siu-Ming; Zhang, Yan-Ning; Chin, Francis Yuk-Lun

2013-01-01

Imaging processing techniques have been shown to be useful in studying protein domain structures. The idea is to represent the pairwise distances of any two residues of the structure in a 2D distance matrix (DM). Features and/or submatrices are extracted from this DM to represent a domain. Existing approaches, however, may involve a large number of features (100–400) or complicated mathematical operations. Finding fewer but more effective features is always desirable. In this paper, based on some key observations on DMs, we are able to decompose a DM image into four basic binary images, each representing the structural characteristics of a fundamental secondary structure element (SSE) or a motif in the domain. Using the concept of moments in image processing, we further derive 45 structural features based on the four binary images. Together with 4 features extracted from the basic images, we represent the structure of a domain using 49 features. We show that our feature vectors can represent domain structures effectively in terms of the following. (1) We show a higher accuracy for domain classification. (2) We show a clear and consistent distribution of domains using our proposed structural vector space. (3) We are able to cluster the domains according to our moment features and demonstrate a relationship between structural variation and functional diversity. PMID:24391828

Asymmetric Michael Addition Mediated by Chiral Ionic Liquids.

PubMed

Suzuki, Yumiko

2018-06-01

Chiral ionic liquids with a focus on their applications in asymmetric Michael additions and related reactions were reviewed. The examples were classified on the basis of the mode of asymmetric induction (e.g., external induction/non-covalent interaction or internal induction/covalent bond formation), the roles in reactions (as a solvent or catalyst), and their structural features (e.g., imidazolium-based chiral cations, other chiral oniums; proline derivatives). Most of the reactions with high chiral induction are Michael addition of ketones or aldehydes to chalcones or nitrostyrenes where proline-derived chiral ionic liquids catalyze the reaction through enamine/ iminium formation. Many reports demonstrate the recyclability of ionic liquid-tagged pyrrolidines.

Determining Synthetic Routes to Consumer Product Ingredients through the Use of Electronic Resources

ERIC Educational Resources Information Center

Love, Brian E.; Bennett, Lisa J.

2016-01-01

An activity is described in which students in the first semester of a two semester organic chemistry laboratory class are introduced to the use of SciFinder. Students are required to determine the structures of three compounds as well as additional information regarding the synthesis of one of them using some of the features available in SciFinder.

SIGMA Release v1.2 - Capabilities, Enhancements and Fixes

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

Mahadevan, Vijay; Grindeanu, Iulian R.; Ray, Navamita

In this report, we present details on SIGMA toolkit along with its component structure, capabilities, and feature additions in FY15, release cycles, and continuous integration process. These software processes along with updated documentation are imperative to successfully integrate and utilize in several applications including the SHARP coupled analysis toolkit for reactor core systems funded under the NEAMS DOE-NE program.

A petrographic and geochemical investigation into the Gatun structure, a possible Tertiary impact structure near Gamboa, Republic de Panama

NASA Astrophysics Data System (ADS)

Tornabene, L. L.; Ryan, J. G.; Stewart, R. H.

2001-05-01

The Gatun Structure, (Latitude N 09 deg 05' 58.1", Longitude W 79 deg 47' 21.8", situated in the triple-canopy rainforest 10 km to the WSW of the Gamboa and about 2 km south of the Isle of Barbacoas, Republic de Panama), is a partially inundated, quasi-concentric surface feature 2.2km in diameter, which appears in aerial photographs and in radar imagery as an arcuate chain of islands with a raised central feature. Although deeply eroded, the structure possesses traits consistent with complex crater morphology: an elevated circular central uplift feature approximately 500-600 m in diameter and 50m high, and arcuate boundary ridges (a possible rim structure) ranging from 50-100 meters high. Within the central peak, highly altered and fractured siltstone of the Gatuncillo formation (Eocene) are uplifted and exposed through surrounding calcareous units of the Caimito formation (Oligocene), the major target rocks in the structure. The structure is crosscut by numerous dikes of unshocked basalt and basaltic andesite related to volcanism along the Panamanian segment of the Central American arc to the south. Analysis of mineral assemblages of units within the structure, and mineral compositions were measured via SEM-EDS and electron microprobe, using the JEOL SEM-Probe facility at the Center for the Study of Materials in Extreme Conditions (CeSMEC) at Florida International University. Bulk chemical and trace element analysis of whole rock samples were conducted via DC Plasma spectrometry at USF. Occurring concentrically within the structure, are limestones with anomalous spherical glass inclusions, both black and white hypocrystalline glasses (melt rocks?), lithic breccias, and melt-bearing breccias, some of which contain flow banding and evidence of selective melting. Three types of spherules (glass, fluid-drop and lithic), a pyroxene-quartz "necklace" disequilibrium structure and possibly shocked amphibole are all petrographic indicators of a possible impact event. In addition, the presence of maskelynite has been based on petrography, SEM-EDS and by RAMAN spectroscopy. RAMAN results indicated that many plagioclase grains in a blue-green clast bering breccia (suevite?) were highly disordered and amorphous. Considering the distance of the Gatun structure from the explosive volcanism of Panamanian arc (approximately 30 km away), and the presence of spherules, maskelynite and other disequilibrium shock features, an impact origin is our preferred interpretation for the Gatun structure.

Analysis of nanopore arrangement and structural features of anodic alumina layers formed by two-step anodizing in oxalic acid using the dedicated executable software

NASA Astrophysics Data System (ADS)

Zaraska, Leszek; Stępniowski, Wojciech J.; Sulka, Grzegorz D.; Ciepiela, Eryk; Jaskuła, Marian

2014-02-01

Anodic porous alumina layers were fabricated by a two-step self-organized anodization in 0.3 M oxalic acid under various anodizing potentials ranging from 30 to 60 V at two different temperatures (10 and 17 ∘C). The effect of anodizing conditions on structural features and pore arrangement of AAO was investigated in detail by using the dedicated executable publication combined with ImageJ software. With increasing anodizing potential, a linear increase of the average pore diameter, interpore distance, wall thickness and barrier layer thickness, as well as a decrease of the pore density, were observed. In addition, the higher pore diameter and porosity values were obtained for samples anodized at the elevated temperature, independently of the anodizing potential. A degree of pore order was investigated on the basis of Delaunay triangulations (defect maps) and calculation of pair distribution or angle distribution functions (PDF or ADF), respectively. All methods confirmed that in order to obtain nanoporous alumina with the best, hexagonal pore arrangement, the potential of 40 V should be applied during anodization. It was confirmed that the dedicated executable publication can be used to a fast and complex analysis of nanopore arrangement and structural features of nanoporous oxide layers.

Transverse magnetic field impact on waveguide modes of photonic crystals.

PubMed

Sylgacheva, Daria; Khokhlov, Nikolai; Kalish, Andrey; Dagesyan, Sarkis; Prokopov, Anatoly; Shaposhnikov, Alexandr; Berzhansky, Vladimir; Nur-E-Alam, Mohammad; Vasiliev, Mikhail; Alameh, Kamal; Belotelov, Vladimir

2016-08-15

This Letter presents a theoretical and experimental study of waveguide modes of one-dimensional magneto-photonic crystals magnetized in the in-plane direction. It is shown that the propagation constants of the TM waveguide modes are sensitive to the transverse magnetization and the spectrum of the transverse magneto-optical Kerr effect has resonant features at mode excitation frequencies. Two types of structures are considered: a non-magnetic photonic crystal with an additional magnetic layer on top and a magneto-photonic crystal with a magnetic layer within each period. We found that the magneto-optical non-reciprocity effect is greater in the first case: it has a magnitude of δ∼10^-4, while the second structure type demonstrates δ∼10^-5 only, due to the higher asymmetry of the claddings of the magnetic layer. Experimental observations show resonant features in the optical and magneto-optical Kerr effect spectra. The measured dispersion properties are in good agreement with the theoretical predictions. An amplitude of light intensity modulation of up to 2.5% was observed for waveguide mode excitation within the magnetic top layer of the non-magnetic photonic crystal structure. The presented theoretical approach may be utilized for the design of magneto-optical sensors and modulators requiring pre-determined spectral features.

Aggregation of p-Sulfonatocalixarene-Based Amphiphiles and Supra-Amphiphiles

PubMed Central

Basilio, Nuno; Francisco, Vitor; Garcia-Rio, Luis

2013-01-01

p-Sulfonatocalixarenes are a special class of water soluble macrocyclic molecules made of 4-hydroxybenzenesulfonate units linked by methylene bridges. One of the main features of these compounds relies on their ability to form inclusion complexes with cationic and neutral species. This feature, together with their water solubility and apparent biological compatibility, had enabled them to emerge as one the most important host receptors in supramolecular chemistry. Attachment of hydrophobic alkyl chains to these compounds leads to the formation of macrocyclic host molecules with amphiphilic properties. Like other oligomeric surfactants, these compounds present improved performance with respect to their monomeric counterparts. In addition, they hold their recognition abilities and present several structural features that depend on the size of the macrocycle and on the length of the alkyl chain, such as preorganization, flexibility and adopted conformations, which make these molecules very interesting to study structure-aggregation relationships. Moreover, the recognition abilities of p-sulfonatocalixarenes enable them to be applied in the design of amphiphiles constructed from non-covalent, rather than covalent, bonds (supramolecular amphiphiles). In this review, we summarize the developments made on the design and synthesis of p-sulfonatocalixarenes-based surfactants, the characterization of their self-assembly properties and on how their structure affects these properties. PMID:23380960

Cartilage Tissue Engineering with Silk Fibroin Scaffolds Fabricated by Indirect Additive Manufacturing Technology

PubMed Central

Chen, Chih-Hao; Liu, Jolene Mei-Jun; Chua, Chee-Kai; Chou, Siaw-Meng; Shyu, Victor Bong-Hang; Chen, Jyh-Ping

2014-01-01

Advanced tissue engineering (TE) technology based on additive manufacturing (AM) can fabricate scaffolds with a three-dimensional (3D) environment suitable for cartilage regeneration. Specifically, AM technology may allow the incorporation of complex architectural features. The present study involves the fabrication of 3D TE scaffolds by an indirect AM approach using silk fibroin (SF). From scanning electron microscopic observations, the presence of micro-pores and interconnected channels within the scaffold could be verified, resulting in a TE scaffold with both micro- and macro-structural features. The intrinsic properties, such as the chemical structure and thermal characteristics of SF, were preserved after the indirect AM manufacturing process. In vitro cell culture within the SF scaffold using porcine articular chondrocytes showed a steady increase in cell numbers up to Day 14. The specific production (per cell basis) of the cartilage-specific extracellular matrix component (collagen Type II) was enhanced with culture time up to 12 weeks, indicating the re-differentiation of chondrocytes within the scaffold. Subcutaneous implantation of the scaffold-chondrocyte constructs in nude mice also confirmed the formation of ectopic cartilage by histological examination and immunostaining. PMID:28788558

Crystal structure of a lipoxygenase from Cyanothece sp. may reveal novel features for substrate acquisition[S

PubMed Central

Newie, Julia; Andreou, Alexandra; Neumann, Piotr; Einsle, Oliver; Feussner, Ivo; Ficner, Ralf

2016-01-01

In eukaryotes, oxidized PUFAs, so-called oxylipins, are vital signaling molecules. The first step in their biosynthesis may be catalyzed by a lipoxygenase (LOX), which forms hydroperoxides by introducing dioxygen into PUFAs. Here we characterized CspLOX1, a phylogenetically distant LOX family member from Cyanothece sp. PCC 8801 and determined its crystal structure. In addition to the classical two domains found in plant, animal, and coral LOXs, we identified an N-terminal helical extension, reminiscent of the long α-helical insertion in Pseudomonas aeruginosa LOX. In liposome flotation studies, this helical extension, rather than the β-barrel domain, was crucial for a membrane binding function. Additionally, CspLOX1 could oxygenate 1,2-diarachidonyl-sn-glycero-3-phosphocholine, suggesting that the enzyme may act directly on membranes and that fatty acids bind to the active site in a tail-first orientation. This binding mode is further supported by the fact that CspLOX1 catalyzed oxygenation at the n-10 position of both linoleic and arachidonic acid, resulting in 9R- and 11R-hydroperoxides, respectively. Together these results reveal unifying structural features of LOXs and their function. While the core of the active site is important for lipoxygenation and thus highly conserved, peripheral domains functioning in membrane and substrate binding are more variable. PMID:26667668

Three Types of Flower Structures in a Divergent-Wrench Fault Zone

NASA Astrophysics Data System (ADS)

Huang, Lei; Liu, Chi-yang

2017-12-01

Flower structures are typical features of wrench fault zones. In conventional studies, two distinct kinds of flower structures have been identified based on differences in their internal structural architecture: (1) negative flower structures characterized by synforms and normal separations and (2) positive flower structures characterized by antiforms and reverse separations. In addition to negative and positive flower structures, in this study, a third kind of flower structure was identified in a divergent-wrench fault zone, a hybrid characterized by both antiforms and normal separations. Negative flower structures widely occur in divergent-wrench fault zones, and their presence indicates the combined effects of extensional and strike-slip motion. In contrast, positive and hybrid flower structures occur only in fault restraining bends and step overs. A hybrid flower structure can be considered as product of a kind of structural deformation typical of divergent-wrench zones; it is the result of the combined effects of extensional, compressional, and strike-slip strains under a locally appropriate compressional environment. The strain situation in it represents the transition stage that in between positive and negative flower structures. Kinematic and dynamic characteristics of the hybrid flower structures indicate the salient features of structural deformation in restraining bends and step overs along divergent-wrench faults, including the coexistence of three kinds of strains (i.e., compression, extension, and strike-slip) and synchronous presence of compressional (i.e., typical fault-bend fold) and extensional (normal faults) deformation in the same place. Hybrid flower structures are also favorable for the accumulation of hydrocarbons because of their special structural configuration in divergent-wrench fault zones.

Observational Tests of the Mars Ocean Hypothesis: Selected MOC and MOLA Results

NASA Technical Reports Server (NTRS)

Parker, T. J.; Banerdt, W. B.

1999-01-01

We have begun a detailed analysis of the evidence for and topography of features identified as potential shorelines that have been im-aged by the Mars Orbiter Camera (MOC) during the Aerobraking Hiatus and Science Phasing Orbit periods of the Mars Global Surveyor (MGS) mission. MOC images, comparable in resolution to high-altitude terrestrial aerial photographs, are particularly well suited to address the morphological expressions of these features at scales comparable to known shore morphologies on Earth. Particularly useful are examples of detailed relationships between potential shore features, such as erosional (and depositional) terraces have been cut into "familiar" pre-existing structures and topography in a fashion that points to a shoreline interpretation as the most likely mechanism for their formation. Additional information is contained in the original extended abstract.

Giant axonal neuropathy-like disease in an Alexandrine parrot (Psittacula eupatria).

PubMed

Stent, Andrew; Gosbell, Matthew; Tatarczuch, Liliana; Summers, Brian A

2015-09-01

A chronic progressive neurological condition in an Alexandrine parrot (Psittacula eupatria) was manifest as intention tremors, incoordination, and seizure activity. Histology revealed large eosinophilic bodies throughout the central nervous system, and electron microscopy demonstrated that these bodies were greatly expanded axons distended by short filamentous structures that aggregated to form long strands. The presence of periodic acid-Schiff-positive material within the neuronal bodies of Purkinje cells and ganglionic neurons is another distinctive feature of this disease. The histological features of this case display some features consistent with giant axonal neuropathy as reported in humans and dogs. Based on investigation of the lineage in this case, an underlying inherited defect is suspected, but some additional factor appears to have altered the specific disease presentation in this bird. © 2015 The Author(s).

Novel Drift Structures for Silicon and Compound Semiconductor X-Ray and Gamma-Ray Detectors

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

Bradley E. Patt; Jan S. Iwanczyk

Recently developed silicon- and compound-semiconductor-based drift detector structures have produced excellent performance for charged particles, X rays, and gamma rays and for low-signal visible light detection. The silicon drift detector (SDD) structures that we discuss relate to direct X-ray detectors and scintillation photon detectors coupled with scintillators for gamma rays. Recent designs include several novel features that ensure very low dark current (both bulk silicon dark current and surface dark current) and hence low noise. In addition, application of thin window technology ensures a very high quantum efficiency entrance window on the drift photodetector.

Evaluating Measurement of Dynamic Constructs: Defining a Measurement Model of Derivatives

PubMed Central

Estabrook, Ryne

2015-01-01

While measurement evaluation has been embraced as an important step in psychological research, evaluating measurement structures with longitudinal data is fraught with limitations. This paper defines and tests a measurement model of derivatives (MMOD), which is designed to assess the measurement structure of latent constructs both for analyses of between-person differences and for the analysis of change. Simulation results indicate that MMOD outperforms existing models for multivariate analysis and provides equivalent fit to data generation models. Additional simulations show MMOD capable of detecting differences in between-person and within-person factor structures. Model features, applications and future directions are discussed. PMID:24364383

Features of Wear-Resistant Cast Iron Coating Formation During Plasma-Powder Surfacing

NASA Astrophysics Data System (ADS)

Vdovin, K. N.; Emelyushin, A. N.; Nefed'ev, S. P.

2017-09-01

The structure of coatings deposited on steel 45 by plasma-powder surfacing of white wear-resistant cast iron is studied. The effects of surfacing regime and additional production effects on the welding bath during surfacing produced by current modulation, accelerated cooling of the deposited beads by blowing with air, and accelerated cooling of the substrate with running water on the structure, are determined. A new composition is suggested for powder material for depositing wear-resistant and corrosion-resistant coatings on a carbon steel by the plasma-powder process.

Development of immobilized ligands for actinide separations. Final report, June 1991--May 1994

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

Paine, R.T.

1994-06-01

Primary goals during this grant period were to (1) synthesize new bifunctional chelating ligands, (2) characterize the structural features of the Ln and An coordination complexes formed by these ligands, (3) use structural data to iteratively design new classes of multifunctional ligands, and (4) explore additional routes for attachment of key ligands to solid supports that could be useful for chromatographic separations. Some highlights of recently published work as well as a summary of submitted, unpublished and/or still in progress research are outlined.

Development of near β titanium alloy with high strength and superplastic properties

NASA Astrophysics Data System (ADS)

Naydenkin, E. V.; Ratochka, I. V.; Mishin, I. P.; Lykova, O. N.

2017-12-01

Ultrafine-grained (UFG) structure with an average element size of about 0.25 µm was obtained in a near β titanium alloy under severe plastic deformation by abc pressing. It is shown that the formation of such structure greatly increases the ultimate strength of the alloy compared to its coarse-grained state (up to 1610 MPa). In addition, the UFG alloy features improved superplastic characteristics under tension at temperatures of 973-1073 K: its elongation to failure exceeds 1300% and the flow stress decreases to several MPa.

Spiral Galaxy Lensing: A Model with Twist

NASA Astrophysics Data System (ADS)

Bell, Steven R.; Ernst, Brett; Fancher, Sean; Keeton, Charles R.; Komanduru, Abi; Lundberg, Erik

2014-12-01

We propose a single galaxy gravitational lensing model with a mass density that has a spiral structure. Namely, we extend the arcsine gravitational lens (a truncated singular isothermal elliptical model), adding an additional parameter that controls the amount of spiraling in the structure of the mass density. An important feature of our model is that, even though the mass density is sophisticated, we succeed in integrating the deflection term in closed form using a Gauss hypergeometric function. When the spiraling parameter is set to zero, this reduces to the arcsine lens.

Pultruded Rod/Overwrap Testing for Various Stitched Stringer Configurations

NASA Technical Reports Server (NTRS)

Leone, Frank A., Jr.

2016-01-01

The unidirectional carbon pultruded rod running through the tops of the stringers is a key design feature of the Pultruded Rod Efficient Unitized Structure (PRSEUS) concept as applied to aircraft fuselage structure. Reported herein are the test methods and results from a test campaign in which the strength of the rod/overwrap interface of various PRSEUS stringer configurations were characterized. The different stringer configurations included different materials and stacking sequences for the stringer overwrap and whether or not an additional layer of adhesive was included between the rod and the overwrap.

Structural Associations of Symptomatic Knee Osteoarthritis

PubMed Central

Stoppiello, Laura A; Mapp, Paul I; Wilson, Deborah; Hill, Roger; Scammell, Brigitte E; Walsh, David A

2014-01-01

Objective Structural changes of osteoarthritis (OA) may occur in the absence of pain. In this study, we aimed to identify histopathologic features that are associated with symptomatic knee OA. Methods Medial tibial plateaus and synovium samples were obtained at the time of total knee replacement (TKR) surgery for OA (advanced OA group) or were obtained postmortem from subjects who had not sought medical attention for knee pain during the last year of life (non-OA control group). To identify features of OA, we compared the patients with advanced OA with the age-matched non-OA controls (n = 26 per group). To identify OA features associated with symptoms, we compared two additional groups of subjects who were matched for severity of chondropathy (n = 29 per group): patients undergoing TKR for symptomatic OA (symptomatic chondropathy group) and postmortem subjects with similar severity of chondropathy who were asymptomatic during the last year of life (asymptomatic chondropathy group). The histologic features of the samples were graded, and immunoreactivities for macrophages (CD68) and nerve growth factor (NGF) in the synovium were quantified. The cellular localization of synovial NGF was determined by double immunofluorescence analysis. Results Advanced OA cases displayed more severe changes in the synovium (synovitis, increased synovial NGF, and CD68-immunoreactive macrophages) and cartilage (loss of cartilage surface integrity, loss of proteoglycan, tidemark breaching, and alterations in chondrocyte morphology) than did the non-OA controls. Synovial NGF was localized predominantly to fibroblasts and to some macrophages. The symptomatic chondropathy group displayed greater levels of synovitis, synovial NGF, and loss of cartilage integrity, in addition to alterations in chondrocyte morphology, than did the asymptomatic chondropathy group (P < 0.05 for each comparison). Conclusion Synovitis, increased synovial NGF, alterations in chondrocyte morphology, and loss of cartilage integrity are features of knee OA that may be associated with symptoms. PMID:25049144

An integrated simulator of structure and anisotropic flow in gas diffusion layers with hydrophobic additives

NASA Astrophysics Data System (ADS)

Burganos, Vasilis N.; Skouras, Eugene D.; Kalarakis, Alexandros N.

2017-10-01

The lattice-Boltzmann (LB) method is used in this work to reproduce the controlled addition of binder and hydrophobicity-promoting agents, like polytetrafluoroethylene (PTFE), into gas diffusion layers (GDLs) and to predict flow permeabilities in the through- and in-plane directions. The present simulator manages to reproduce spreading of binder and hydrophobic additives, sequentially, into the neat fibrous layer using a two-phase flow model. Gas flow simulation is achieved by the same code, sidestepping the need for a post-processing flow code and avoiding the usual input/output and data interface problems that arise in other techniques. Compression effects on flow anisotropy of the impregnated GDL are also studied. The permeability predictions for different compression levels and for different binder or PTFE loadings are found to compare well with experimental data for commercial GDL products and with computational fluid dynamics (CFD) predictions. Alternatively, the PTFE-impregnated structure is reproduced from Scanning Electron Microscopy (SEM) images using an independent, purely geometrical approach. A comparison of the two approaches is made regarding their adequacy to reproduce correctly the main structural features of the GDL and to predict anisotropic flow permeabilities at different volume fractions of binder and hydrophobic additives.

GRAMPS: a graphics language interpreter for real-time, interactive, three-dimensional picture editing and animation

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

O'Donnell, T.J.; Olson, A.J.

1981-08-01

GRAMPS, a graphics language interpreter has been developed in FORTRAN 77 to be used in conjunction with an interactive vector display list processor (Evans and Sutherland Multi-Picture-System). Several of the features of the language make it very useful and convenient for real-time scene construction, manipulation and animation. The GRAMPS language syntax allows natural interaction with scene elements as well as easy, interactive assignment of graphics input devices. GRAMPS facilitates the creation, manipulation and copying of complex nested picture structures. The language has a powerful macro feature that enables new graphics commands to be developed and incorporated interactively. Animation may bemore » achieved in GRAMPS by two different, yet mutually compatible means. Picture structures may contain framed data, which consist of a sequence of fixed objects. These structures may be displayed sequentially to give a traditional frame animation effect. In addition, transformation information on picture structures may be saved at any time in the form of new macro commands that will transform these structures from one saved state to another in a specified number of steps, yielding an interpolated transformation animation effect. An overview of the GRAMPS command structure is given and several examples of application of the language to molecular modeling and animation are presented.« less

Structural features, kinetics and SAR study of radical scavenging and antioxidant activities of phenolic and anilinic compounds

PubMed Central

2013-01-01

Background Phenolic compounds are widely distributed in plant kingdom and constitute one of the most important classes of natural and synthetic antioxidants. In the present study fifty one natural and synthetic structurally variant phenolic, enolic and anilinic compounds were examined as antioxidants and radical scavengers against DPPH, hydroxyl and peroxyl radicals. The structural diversity of the used phenolic compounds includes monophenols with substituents frequently present in natural phenols e.g. alkyl, alkoxy, ester and carboxyl groups, besides many other electron donating and withdrawing groups, in addition to polyphenols with 1–3 hydroxyl groups and aminophenols. Some common groups e.g. alkyl, carboxyl, amino and second OH groups were incorporated in ortho, meta and para positions. Results SAR study indicates that the most important structural feature of phenolic compounds required to possess good antiradical and antioxidant activities is the presence of a second hydroxyl or an amino group in o- or p-position because of their strong electron donating effect in these positions and the formation of a stable quinone-like products upon two hydrogen-atom transfer process; otherwise, the presence of a number of alkoxy (in o or p-position) and /or alkyl groups (in o, m or p-position) should be present to stabilize the resulted phenoxyl radical and reach good activity. Anilines showed also similar structural feature requirements as phenols to achieve good activities, except o-diamines which gave low activity because of the high energy of the resulted 1,2-dimine product upon the 2H-transfer process. Enols with ene-1,2-diol structure undergo the same process and give good activity. Good correlations were obtained between DPPH inhibition and inhibition of both OH and peroxyl radicals. In addition, good correlations were obtained between DPPH inhibition and antioxidant activities in sunflower oil and liver homogenate systems. Conclusions In conclusion, the structures of good anti radical and antioxidant phenols and anilines are defined. The obtained good correlations imply that measuring anti DPPH activity can be used as a simple predictive test for the anti hydroxyl and peroxyl radical, and antioxidant activities. Kinetic measurements showed that strong antioxidants with high activity have also high reaction rates indicating that factors stabilizing the phenoxyl radicals lower also the activation energy of the hydrogen transfer process. PMID:23497653

Neural network analysis for geological interpretation of tomographic images beneath the Japan Islands

NASA Astrophysics Data System (ADS)

Kuwatani, T.; Toriumi, M.

2009-12-01

Recent advances in methodologies of geophysical observations, such as seismic tomography, seismic reflection method and geomagnetic method, provide us a large amount and a wide variety of data for physical properties of a crust and upper mantle (e.g. Matsubara et al. (2008)). However, it has still been difficult to specify a rock type and its physical conditions, mainly because (1) available data usually have a lot of error and uncertainty, and (2) physical properties of rocks are greatly affected by fluid and microstructures. The objective interpretation and quantitative evaluation for lithology and fluid-related structure require the statistical analyses of integrated geophysical and geological data. Self-Organizing Maps (SOMs) are unsupervised artificial neural networks that map the input space into clusters in a topological form whose organization is related to trends in the input data (Kohonen 2001). SOMs are powerful neural network techniques to classify and interpret multiattribute data sets. Results of SOM classifications can be represented as 2D images, called feature maps which illustrate the complexity and interrelationships among input data sets. Recently, some works have used SOM in order to interpret multidimensional, non-linear, and highly noised geophysical data for purposes of geological prediction (e.g. Klose 2006; Tselentis et al. 2007; Bauer et al. 2008). This paper describes the application of SOM to the 3D velocity structure beneath the whole Japan islands (e.g. Matsubara et al. 2008). From the obtained feature maps, we can specify the lithology and qualitatively evaluate the effect of fluid-related structures. Moreover, re-projection of feature maps onto the 3D velocity structures resulted in detailed images of the structures within the plates. The Pacific plate and the Philippine Sea plate subducting beneath the Eurasian plate can be imaged more clearly than the original P- and S-wave velocity structures. In order to understand more precise prediction of lithology and its structure, we will use the additional input data sets, such as tomographic images of random velocity fluctuation (Takahashi et al. 2009) and b-value mapping data. Additionally, different kinds of data sets, including the experimental and petrological results (e.g. Christensen 1991; Hacker et al. 2003) can be applied to our analyses.

CTAB-Aided Synthesis of Stacked V2O5 Nanosheets: Morphology, Electrochemical Features and Asymmetric Device Performance

NASA Astrophysics Data System (ADS)

Saravanakumar, B.; Maruthamuthu, S.; Umadevi, V.; Saravanan, V.

To accomplish superior performance in supercapacitors, a fresh class of electrode materials with advantageous structures is essential. Owing to its rich electrochemical activity, vanadium oxides are considered to be an attractive electrode material for energy storing devices. In this work, vanadium pentoxide (V2O5) nanostructures were prepared using surfactant (CTAB)-assisted hydrothermal route. Stacked V2O5 sheets enable additional channels for electrolyte ion intercalation. These stacked V2O5 nanosheets show highest specific capacitance of 466Fg-1 at 0.5Ag-1. In addition, it exhibits good rate capacity, lower value of charge transfer resistance and good stability when used as an electrode material for supercapacitors. Further, an asymmetric supercapacitor device was assembled utilizing the stacked V2O5 sheets and activated carbon as electrodes. The electrochemical features of the device are also discussed.

Application of alkyne-TCNQ addition reaction to polymerization.

PubMed

Washino, Yusuke; Michinobu, Tsuyoshi

2011-04-19

The polymerization using a high-yielding addition reaction between electron-rich alkynes and 7,7,8,8-tetracyanoquinodimethane (TCNQ) derivatives is described. The bifunctional monomer containing two TCNQ moieties and the counter comonomer bearing two dialkylaniline (DAA)-substituted alkynes are reacted in 1,2-dichloroethane under mild heating conditions. At the high monomer concentrations, high molecular weight linear polymers are obtained, while the reaction at the low monomer concentrations produces a significant amount of the cyclic compounds. A clear relationship between the monomer concentration and the cyclic compound amount is demonstrated. The obtained polymers feature a sufficient thermal stability with the decomposition temperature exceeding 300  °C as well as strong charge-transfer (CT) bands and redox activities ascribed to the produced donor-acceptor moieties. These features are also used to optimize the polymerization conditions and to estimate the chemical structures. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The structure of people's hair.

PubMed

Yang, Fei-Chi; Zhang, Yuchen; Rheinstädter, Maikel C

2014-01-01

Hair is a filamentous biomaterial consisting mainly of proteins in particular keratin. The structure of human hair is well known: the medulla is a loosely packed, disordered region near the centre of the hair surrounded by the cortex, which contains the major part of the fibre mass, mainly consisting of keratin proteins and structural lipids. The cortex is surrounded by the cuticle, a layer of dead, overlapping cells forming a protective layer around the hair. The corresponding structures have been studied extensively using a variety of different techniques, such as light, electron and atomic force microscopes, and also X-ray diffraction. We were interested in the question how much the molecular hair structure differs from person to person, between male and female hair, hair of different appearances such as colour and waviness. We included hair from parent and child, identical and fraternal twins in the study to see if genetically similar hair would show similar structural features. The molecular structure of the hair samples was studied using high-resolution X-ray diffraction, which covers length scales from molecules up to the organization of secondary structures. Signals due to the coiled-coil phase of α-helical keratin proteins, intermediate keratin filaments in the cortex and from the lipid layers in the cell membrane complex were observed in the specimen of all individuals, with very small deviations. Despite the relatively small number of individuals (12) included in this study, some conclusions can be drawn. While the general features were observed in all individuals and the corresponding molecular structures were almost identical, additional signals were observed in some specimen and assigned to different types of lipids in the cell membrane complex. Genetics seem to play a role in this composition as identical patterns were observed in hair from father and daughter and identical twins, however, not for fraternal twins. Identification and characterization of these features is an important step towards the detection of abnormalities in the molecular structure of hair as a potential diagnostic tool for certain diseases.

Structural features based genome-wide characterization and prediction of nucleosome organization

PubMed Central

2012-01-01

Background Nucleosome distribution along chromatin dictates genomic DNA accessibility and thus profoundly influences gene expression. However, the underlying mechanism of nucleosome formation remains elusive. Here, taking a structural perspective, we systematically explored nucleosome formation potential of genomic sequences and the effect on chromatin organization and gene expression in S. cerevisiae. Results We analyzed twelve structural features related to flexibility, curvature and energy of DNA sequences. The results showed that some structural features such as DNA denaturation, DNA-bending stiffness, Stacking energy, Z-DNA, Propeller twist and free energy, were highly correlated with in vitro and in vivo nucleosome occupancy. Specifically, they can be classified into two classes, one positively and the other negatively correlated with nucleosome occupancy. These two kinds of structural features facilitated nucleosome binding in centromere regions and repressed nucleosome formation in the promoter regions of protein-coding genes to mediate transcriptional regulation. Based on these analyses, we integrated all twelve structural features in a model to predict more accurately nucleosome occupancy in vivo than the existing methods that mainly depend on sequence compositional features. Furthermore, we developed a novel approach, named DLaNe, that located nucleosomes by detecting peaks of structural profiles, and built a meta predictor to integrate information from different structural features. As a comparison, we also constructed a hidden Markov model (HMM) to locate nucleosomes based on the profiles of these structural features. The result showed that the meta DLaNe and HMM-based method performed better than the existing methods, demonstrating the power of these structural features in predicting nucleosome positions. Conclusions Our analysis revealed that DNA structures significantly contribute to nucleosome organization and influence chromatin structure and gene expression regulation. The results indicated that our proposed methods are effective in predicting nucleosome occupancy and positions and that these structural features are highly predictive of nucleosome organization. The implementation of our DLaNe method based on structural features is available online. PMID:22449207

A feature refinement approach for statistical interior CT reconstruction

NASA Astrophysics Data System (ADS)

Hu, Zhanli; Zhang, Yunwan; Liu, Jianbo; Ma, Jianhua; Zheng, Hairong; Liang, Dong

2016-07-01

Interior tomography is clinically desired to reduce the radiation dose rendered to patients. In this work, a new statistical interior tomography approach for computed tomography is proposed. The developed design focuses on taking into account the statistical nature of local projection data and recovering fine structures which are lost in the conventional total-variation (TV)—minimization reconstruction. The proposed method falls within the compressed sensing framework of TV minimization, which only assumes that the interior ROI is piecewise constant or polynomial and does not need any additional prior knowledge. To integrate the statistical distribution property of projection data, the objective function is built under the criteria of penalized weighed least-square (PWLS-TV). In the implementation of the proposed method, the interior projection extrapolation based FBP reconstruction is first used as the initial guess to mitigate truncation artifacts and also provide an extended field-of-view. Moreover, an interior feature refinement step, as an important processing operation is performed after each iteration of PWLS-TV to recover the desired structure information which is lost during the TV minimization. Here, a feature descriptor is specifically designed and employed to distinguish structure from noise and noise-like artifacts. A modified steepest descent algorithm is adopted to minimize the associated objective function. The proposed method is applied to both digital phantom and in vivo Micro-CT datasets, and compared to FBP, ART-TV and PWLS-TV. The reconstruction results demonstrate that the proposed method performs better than other conventional methods in suppressing noise, reducing truncated and streak artifacts, and preserving features. The proposed approach demonstrates its potential usefulness for feature preservation of interior tomography under truncated projection measurements.

A feature refinement approach for statistical interior CT reconstruction.

PubMed

Hu, Zhanli; Zhang, Yunwan; Liu, Jianbo; Ma, Jianhua; Zheng, Hairong; Liang, Dong

2016-07-21

Interior tomography is clinically desired to reduce the radiation dose rendered to patients. In this work, a new statistical interior tomography approach for computed tomography is proposed. The developed design focuses on taking into account the statistical nature of local projection data and recovering fine structures which are lost in the conventional total-variation (TV)-minimization reconstruction. The proposed method falls within the compressed sensing framework of TV minimization, which only assumes that the interior ROI is piecewise constant or polynomial and does not need any additional prior knowledge. To integrate the statistical distribution property of projection data, the objective function is built under the criteria of penalized weighed least-square (PWLS-TV). In the implementation of the proposed method, the interior projection extrapolation based FBP reconstruction is first used as the initial guess to mitigate truncation artifacts and also provide an extended field-of-view. Moreover, an interior feature refinement step, as an important processing operation is performed after each iteration of PWLS-TV to recover the desired structure information which is lost during the TV minimization. Here, a feature descriptor is specifically designed and employed to distinguish structure from noise and noise-like artifacts. A modified steepest descent algorithm is adopted to minimize the associated objective function. The proposed method is applied to both digital phantom and in vivo Micro-CT datasets, and compared to FBP, ART-TV and PWLS-TV. The reconstruction results demonstrate that the proposed method performs better than other conventional methods in suppressing noise, reducing truncated and streak artifacts, and preserving features. The proposed approach demonstrates its potential usefulness for feature preservation of interior tomography under truncated projection measurements.

Graph wavelet alignment kernels for drug virtual screening.

PubMed

Smalter, Aaron; Huan, Jun; Lushington, Gerald

2009-06-01

In this paper, we introduce a novel statistical modeling technique for target property prediction, with applications to virtual screening and drug design. In our method, we use graphs to model chemical structures and apply a wavelet analysis of graphs to summarize features capturing graph local topology. We design a novel graph kernel function to utilize the topology features to build predictive models for chemicals via Support Vector Machine classifier. We call the new graph kernel a graph wavelet-alignment kernel. We have evaluated the efficacy of the wavelet-alignment kernel using a set of chemical structure-activity prediction benchmarks. Our results indicate that the use of the kernel function yields performance profiles comparable to, and sometimes exceeding that of the existing state-of-the-art chemical classification approaches. In addition, our results also show that the use of wavelet functions significantly decreases the computational costs for graph kernel computation with more than ten fold speedup.

Aging in complex interdependency networks.

PubMed

Vural, Dervis C; Morrison, Greg; Mahadevan, L

2014-02-01

Although species longevity is subject to a diverse range of evolutionary forces, the mortality curves of a wide variety of organisms are rather similar. Here we argue that qualitative and quantitative features of aging can be reproduced by a simple model based on the interdependence of fault-prone agents on one other. In addition to fitting our theory to the empiric mortality curves of six very different organisms, we establish the dependence of lifetime and aging rate on initial conditions, damage and repair rate, and system size. We compare the size distributions of disease and death and see that they have qualitatively different properties. We show that aging patterns are independent of the details of interdependence network structure, which suggests that aging is a many-body effect, and that the qualitative and quantitative features of aging are not sensitively dependent on the details of dependency structure or its formation.

Design and evaluation of a modular lower limb exoskeleton for rehabilitation.

PubMed

Dos Santos, Wilian M; Nogueira, Samuel L; de Oliveira, Gustavo C; Pena, Guido G; Siqueira, Adriano A G

2017-07-01

This paper deals with the evaluation of an exoskeleton designed for assisting individuals to rehabilitate compromised lower limb movements resulting from stroke or incomplete spinal cord injury. The exoskeleton is composed of lightweight tubular structures and six free joints that provide a modular feature to the system. This feature allows the exoskeleton to be adapted to assist the movement of one or more patient joints. The actuation of the exoskeleton is also modular, and can be performed passively, by means of springs and dampers, or actively through actuators. In addition, its telescopic tubular links, developed to adjust the size of the links in order to align the joints of the exoskeleton with patient joints, allows the exoskeleton to be adjustable to fit different patients. Experiments considering the interaction between a healthy subject and the exoskeleton are performed to evaluate the influence of the exoskeleton structure on kinematic and muscular activity profiles during walking.

Analysis of Surface and Bulk Behavior in Ni-Pd Alloys

NASA Technical Reports Server (NTRS)

Bozzolo, Guillermo; Noebe, Rondald D.

2003-01-01

The most salient features of the surface structure and bulk behavior of Ni-Pd alloys have been studied using the BFS method for alloys. Large-scale atomistic simulations were performed to investigate surface segregation profiles as a function of temperature, crystal face, and composition. Pd enrichment of the first layer was observed in (111) and (100) surfaces, and enrichment of the top two layers occurred for (110) surfaces. In all cases, the segregation profile shows alternate planes enriched and depleted in Pd. In addition, the phase structure of bulk Ni-Pd alloys as a function of temperature and composition was studied. A weak ordering tendency was observed at low temperatures, which helps explain the compositional oscillations in the segregation profiles. Finally, based on atom-by-atom static energy calculations, a comprehensive explanation for the observed surface and bulk features will be presented in terms of competing chemical and strain energy effects.

The widetilde{A}←widetilde{X} ABSORPTION SPECTRUM OF 2-NITROOXYBUTYL PEROXY RADICAL

NASA Astrophysics Data System (ADS)

Eddingsaas, Nathan; Takematsu, Kana; Okumura, Mitchio

2009-06-01

The nitrate radical is an important atmospheric oxidant in the nighttime sky. Nitrate radicals react by addition to alkenes, and in the presence of oxygen form nitrooxyalkyl peroxy radicals. The peroxy radical formed from the reaction of 2-butene, nitrate radical, and oxygen was detected by cavity ringdown spectroscopy (CRDS) via its widetilde{A}←widetilde{X} electronic absorption spectrum. The widetilde{A}←widetilde{X} electronic transition is a bound-bound transition with enough structure to distinguish between different peroxy radicals as well as different conformers of the same peroxy radical. Two conformers of the nitrooxybutyl peroxy radical have been observed; the absorption features are red shifted from the same absorption features of sec-butyl peroxy radical. Calculations on the structure of nitrooxyalkyl peroxy radicals and general trends of the position of the widetilde{A}←widetilde{X} absorption transitions have also been performed and compared to those of unsubstituted peroxy radicals.

An investigation of chaotic Kolmogorov flows

NASA Technical Reports Server (NTRS)

Platt, N.; Sirovich, L.; Fitzmaurice, N.

1990-01-01

A two dimensional flow governed by the incompressible Navier-Stokes equations with a steady spatially periodic forcing (known as the Kolmogorov flow) is numerically simulated. The behavior of the flow and its transition states as the Reynolds number (Re) varies is investigated in detail, as well as a number of the flow features. A sequence of bifurcations is shown to take place in the flow as Re varied. Two main regimes of the flow were observed: small and large scale structure regimes corresponding to different ranges of Re. Each of the regimes includes a number of quasiperiodic, chaotic, and relaminarization windows. In addition, each range contains a chaotic window with non-ergodic chaotic attractors. Spatially disordered, but temporally steady states were discovered in large scale structure regime. Features of the diverse cases are displayed in terms of the temporal power spectrum, Poincare sections and, where possible, Lyapunov exponents and Kaplan-Yorke dimension.

ARC-1980-A80-7034

NASA Image and Video Library

1980-11-12

Range : 660,000 kilometers (400,000 miles) Time : 5:05 am PST This Voyager 1 picture of Mimas shows a large impact structure at 110 degrees W Long., located on that face of the moon which leads Mimas in its orbit. The feature, about 130 kilometers in diameter (80 miles), is more than 1/4 the diameter of the entire moon. This is a particularly interesting feature in view of its large diameter compared with the size of the satellite, and may have the largest crater diameter/satillite diameter ratio in the solar system. The crater has a raised rim and central peak, typical of large impact structures on terrestrial planets. Additional smaller craters, 15-45 kilometers in diameter, can be seen scattered across the surface, particularly alon the terminator. Mimas is one of the smaller Saturnian satellites with a low density implying its chief component is ice.

Development of purely structure-based pharmacophores for the topoisomerase I-DNA-ligand binding pocket

NASA Astrophysics Data System (ADS)

Drwal, Malgorzata N.; Agama, Keli; Pommier, Yves; Griffith, Renate

2013-12-01

Purely structure-based pharmacophores (SBPs) are an alternative method to ligand-based approaches and have the advantage of describing the entire interaction capability of a binding pocket. Here, we present the development of SBPs for topoisomerase I, an anticancer target with an unusual ligand binding pocket consisting of protein and DNA atoms. Different approaches to cluster and select pharmacophore features are investigated, including hierarchical clustering and energy calculations. In addition, the performance of SBPs is evaluated retrospectively and compared to the performance of ligand- and complex-based pharmacophores. SBPs emerge as a valid method in virtual screening and a complementary approach to ligand-focussed methods. The study further reveals that the choice of pharmacophore feature clustering and selection methods has a large impact on the virtual screening hit lists. A prospective application of the SBPs in virtual screening reveals that they can be used successfully to identify novel topoisomerase inhibitors.

Depth-time interpolation of feature trends extracted from mobile microelectrode data with kernel functions.

PubMed

Wong, Stephen; Hargreaves, Eric L; Baltuch, Gordon H; Jaggi, Jurg L; Danish, Shabbar F

2012-01-01

Microelectrode recording (MER) is necessary for precision localization of target structures such as the subthalamic nucleus during deep brain stimulation (DBS) surgery. Attempts to automate this process have produced quantitative temporal trends (feature activity vs. time) extracted from mobile MER data. Our goal was to evaluate computational methods of generating spatial profiles (feature activity vs. depth) from temporal trends that would decouple automated MER localization from the clinical procedure and enhance functional localization in DBS surgery. We evaluated two methods of interpolation (standard vs. kernel) that generated spatial profiles from temporal trends. We compared interpolated spatial profiles to true spatial profiles that were calculated with depth windows, using correlation coefficient analysis. Excellent approximation of true spatial profiles is achieved by interpolation. Kernel-interpolated spatial profiles produced superior correlation coefficient values at optimal kernel widths (r = 0.932-0.940) compared to standard interpolation (r = 0.891). The choice of kernel function and kernel width resulted in trade-offs in smoothing and resolution. Interpolation of feature activity to create spatial profiles from temporal trends is accurate and can standardize and facilitate MER functional localization of subcortical structures. The methods are computationally efficient, enhancing localization without imposing additional constraints on the MER clinical procedure during DBS surgery. Copyright © 2012 S. Karger AG, Basel.

Statistical molecular design of balanced compound libraries for QSAR modeling.

PubMed

Linusson, A; Elofsson, M; Andersson, I E; Dahlgren, M K

2010-01-01

A fundamental step in preclinical drug development is the computation of quantitative structure-activity relationship (QSAR) models, i.e. models that link chemical features of compounds with activities towards a target macromolecule associated with the initiation or progression of a disease. QSAR models are computed by combining information on the physicochemical and structural features of a library of congeneric compounds, typically assembled from two or more building blocks, and biological data from one or more in vitro assays. Since the models provide information on features affecting the compounds' biological activity they can be used as guides for further optimization. However, in order for a QSAR model to be relevant to the targeted disease, and drug development in general, the compound library used must contain molecules with balanced variation of the features spanning the chemical space believed to be important for interaction with the biological target. In addition, the assays used must be robust and deliver high quality data that are directly related to the function of the biological target and the associated disease state. In this review, we discuss and exemplify the concept of statistical molecular design (SMD) in the selection of building blocks and final synthetic targets (i.e. compounds to synthesize) to generate information-rich, balanced libraries for biological testing and computation of QSAR models.

Simulation of metal additive manufacturing microstructures using kinetic Monte Carlo

DOE PAGES

Rodgers, Theron M.; Madison, Jonathan D.; Tikare, Veena

2017-04-19

Additive manufacturing (AM) is of tremendous interest given its ability to realize complex, non-traditional geometries in engineered structural materials. But, microstructures generated from AM processes can be equally, if not more, complex than their conventionally processed counterparts. While some microstructural features observed in AM may also occur in more traditional solidification processes, the introduction of spatially and temporally mobile heat sources can result in significant microstructural heterogeneity. While grain size and shape in metal AM structures are understood to be highly dependent on both local and global temperature profiles, the exact form of this relation is not well understood. Wemore » implement an idealized molten zone and temperature-dependent grain boundary mobility in a kinetic Monte Carlo model to predict three-dimensional grain structure in additively manufactured metals. In order to demonstrate the flexibility of the model, synthetic microstructures are generated under conditions mimicking relatively diverse experimental results present in the literature. Simulated microstructures are then qualitatively and quantitatively compared to their experimental complements and are shown to be in good agreement.« less

Phase transformations in the reaction cell of TiNi-based sintered systems

NASA Astrophysics Data System (ADS)

Artyukhova, Nadezhda; Anikeev, Sergey; Yasenchuk, Yuriy; Chekalkin, Timofey; Gunther, Victor; Kaftaranova, Maria; Kang, Ji-Hoon; Kim, Ji-Soon

2018-05-01

The present work addresses the structural-phase state changes of porous TiNi-based compounds fabricated by reaction sintering (RS) of Ti and Ni powders with Co, Mo, and no additives introduced. The study also emphasizes the features of a reaction cell (RC) during the transition from the solid- to liquid-phase sintering. Mechanisms of phase transformations occurring in the solid phase, involving the low-melting Ti2Ni phase within the RC, have been highlighted. Also, the intermediate Ti2Ni phase had a crucial role to provide both the required RS behavior and modified phase composition of RS samples, and besides, it is found to be responsible for the near-equiatomic TiNi saturation of the melt. Both cobalt and molybdenum additives are shown to cause additional structuring of the transition zone (TZ) at the Ti2Ni‑TiNi interface and broadening of this zone. The impact of Co and Mo on the Ti2Ni phase is evident through fissuring of this phase layer, which is referred to solidified stresses increased in the layer due to post-alloying defects in the structure.

Feature-to-Feature Inference Under Conditions of Cue Restriction and Dimensional Correlation.

PubMed

Lancaster, Matthew E; Homa, Donald

2017-01-01

The present study explored feature-to-feature and label-to-feature inference in a category task for different category structures. In the correlated condition, each of the 4 dimensions comprising the category was positively correlated to each other and to the category label. In the uncorrelated condition, no correlation existed between the 4 dimensions comprising the category, although the dimension to category label correlation matched that of the correlated condition. After learning, participants made inference judgments of a missing feature, given 1, 2, or 3 feature cues; on half the trials, the category label was also included as a cue. The results showed superior inference of features following training on the correlated structure, with accurate inference when only a single feature was presented. In contrast, a single-feature cue resulted in chance levels of inference for the uncorrelated structure. Feature inference systematically improved with number of cues after training on the correlated structure. Surprisingly, a similar outcome was obtained for the uncorrelated structure, an outcome that must have reflected mediation via the category label. A descriptive model is briefly introduced to explain the results, with a suggestion that this paradigm might be profitably extended to hierarchical structures where the levels of feature-to-feature inference might vary with the depth of the hierarchy.

Novel chromatin texture features for the classification of pap smears

NASA Astrophysics Data System (ADS)

Bejnordi, Babak E.; Moshavegh, Ramin; Sujathan, K.; Malm, Patrik; Bengtsson, Ewert; Mehnert, Andrew

2013-03-01

This paper presents a set of novel structural texture features for quantifying nuclear chromatin patterns in cells on a conventional Pap smear. The features are derived from an initial segmentation of the chromatin into bloblike texture primitives. The results of a comprehensive feature selection experiment, including the set of proposed structural texture features and a range of different cytology features drawn from the literature, show that two of the four top ranking features are structural texture features. They also show that a combination of structural and conventional features yields a classification performance of 0.954±0.019 (AUC±SE) for the discrimination of normal (NILM) and abnormal (LSIL and HSIL) slides. The results of a second classification experiment, using only normal-appearing cells from both normal and abnormal slides, demonstrates that a single structural texture feature measuring chromatin margination yields a classification performance of 0.815±0.019. Overall the results demonstrate the efficacy of the proposed structural approach and that it is possible to detect malignancy associated changes (MACs) in Papanicoloau stain.

Ballistic missile precession frequency extraction by spectrogram's texture

NASA Astrophysics Data System (ADS)

Wu, Longlong; Xu, Shiyou; Li, Gang; Chen, Zengping

2013-10-01

In order to extract precession frequency, an crucial parameter in ballistic target recognition, which reflected the kinematical characteristics as well as structural and mass distribution features, we developed a dynamic RCS signal model for a conical ballistic missile warhead, with a log-norm multiplicative noise, substituting the familiar additive noise, derived formulas of micro-Doppler induced by precession motion, and analyzed time-varying micro-Doppler features utilizing time-frequency transforms, extracted precession frequency by measuring the spectrogram's texture, verified them by computer simulation studies. Simulation demonstrates the excellent performance of the method proposed in extracting the precession frequency, especially in the case of low SNR.

Somatoparaphrenia: evolving theories and concepts.

PubMed

Feinberg, Todd E; Venneri, Annalena

2014-12-01

Somatoparaphrenia, a syndrome that involves at a minimum unawareness of ownership of a body part, in addition involves productive features including delusional misidentification and confabulation. In this review we describe some of the clinical and neuroanatomical features of somatoparaphrenia highlighting its delusional and confabulatory aspects. Possible theoretical frameworks are reviewed taking into account cognitive, psychodynamic, and philosophical views. We suggest that future studies should approach this syndrome through investigations of structural and functional connectivity and focus on the possible interplay between alterations in major functional networks of the brain, such as the default mode and salience networks, but also take into account motivational variables. Copyright © 2014 Elsevier Ltd. All rights reserved.

Identification Of Minangkabau Landscape Characters

NASA Astrophysics Data System (ADS)

Asrina, M.; Gunawan, A.; Aris, Munandar

2017-10-01

Minangkabau is one of cultures in indonesia which occupies landscape intact. Landscape of Minangkabau have a very close relationship with the culture of the people. Uniqueness of Minangkabau culture and landscape forming an inseparable characterunity. The landscape is necessarily identified to know the inherent landscape characters. The objective of this study was to identify the character of the Minangkabau landscape characterizes its uniqueness. The study was conducted by using descriptive method comprised literature review and field observasion. Observed the landscape characters comprised two main features, they were major and minor features. Indetification of the features was conducted in two original areas (darek) of the Minangkabau traditional society. The research results showed that major features or natural features of the landscape were predominantly landform, landcover, and hidrology. All luhak (districts) of Minangkabau showed similar main features such as hill, canyon, lake, valley, and forest. The existence of natural features such as hills, canyon and valleys characterizes the nature of minangkabau landscape. Minor features formed by Minangkabau cultural society were agricultural land and settlement. Rumah gadang (big house) is one of famous minor features characterizes the Minangkabau culture. In addition, several historical artefacts of building and others structure may strengthen uniqueness of the Minangkabau landscape character, such as The royal palace, inscription, and tunnels.

Surface and deep structures in graphics comprehension.

PubMed

Schnotz, Wolfgang; Baadte, Christiane

2015-05-01

Comprehension of graphics can be considered as a process of schema-mediated structure mapping from external graphics on internal mental models. Two experiments were conducted to test the hypothesis that graphics possess a perceptible surface structure as well as a semantic deep structure both of which affect mental model construction. The same content was presented to different groups of learners by graphics from different perspectives with different surface structures but the same deep structure. Deep structures were complementary: major features of the learning content in one experiment became minor features in the other experiment, and vice versa. Text was held constant. Participants were asked to read, understand, and memorize the learning material. Furthermore, they were either instructed to process the material from the perspective supported by the graphic or from an alternative perspective, or they received no further instruction. After learning, they were asked to recall the learning content from different perspectives by completing graphs of different formats as accurately as possible. Learners' recall was more accurate if the format of recall was the same as the learning format which indicates surface structure influences. However, participants also showed more accurate recall when they remembered the content from a perspective emphasizing the deep structure, regardless of the graphics format presented before. This included better recall of what they had not seen than of what they really had seen before. That is, deep structure effects overrode surface effects. Depending on context conditions, stimulation of additional cognitive processing by instruction had partially positive and partially negative effects.

Multigap superconductivity and strong electron-boson coupling in Fe-based superconductors: a point-contact Andreev-reflection study of Ba(Fe(1-x)Co(x))2As2 single crystals.

PubMed

Tortello, M; Daghero, D; Ummarino, G A; Stepanov, V A; Jiang, J; Weiss, J D; Hellstrom, E E; Gonnelli, R S

2010-12-03

Directional point-contact Andreev-reflection measurements in Ba(Fe(1-x)Co(x))2As2 single crystals (T(c) = 24.5 K) indicate the presence of two superconducting gaps with no line nodes on the Fermi surface. The point-contact Andreev-reflection spectra also feature additional structures related to the electron-boson interaction, from which the characteristic boson energy Ω(b)(T) is obtained, very similar to the spin-resonance energy observed in neutron scattering experiments. Both the gaps and the additional structures can be reproduced within a three-band s ± Eliashberg model by using an electron-boson spectral function peaked at Ω(0) = 12 meV ≃ Ω(b)(0).

Incidental and context-responsive activation of structure- and function-based action features during object identification

PubMed Central

Lee, Chia-lin; Middleton, Erica; Mirman, Daniel; Kalénine, Solène; Buxbaum, Laurel J.

2012-01-01

Previous studies suggest that action representations are activated during object processing, even when task-irrelevant. In addition, there is evidence that lexical-semantic context may affect such activation during object processing. Finally, prior work from our laboratory and others indicates that function-based (“use”) and structure-based (“move”) action subtypes may differ in their activation characteristics. Most studies assessing such effects, however, have required manual object-relevant motor responses, thereby plausibly influencing the activation of action representations. The present work utilizes eyetracking and a Visual World Paradigm task without object-relevant actions to assess the time course of activation of action representations, as well as their responsiveness to lexical-semantic context. In two experiments, participants heard a target word and selected its referent from an array of four objects. Gaze fixations on non-target objects signal activation of features shared between targets and non-targets. The experiments assessed activation of structure-based (Experiment 1) or function-based (Experiment 2) distractors, using neutral sentences (“S/he saw the …”) or sentences with a relevant action verb (Experiment 1: “S/he picked up the……”; Experiment 2: “S/he used the….”). We observed task-irrelevant activations of action information in both experiments. In neutral contexts, structure-based activation was relatively faster-rising but more transient than function-based activation. Additionally, action verb contexts reliably modified patterns of activation in both Experiments. These data provide fine-grained information about the dynamics of activation of function-based and structure-based actions in neutral and action-relevant contexts, in support of the “Two Action System” model of object and action processing (e.g., Buxbaum & Kalénine, 2010). PMID:22390294

Copper Selenidophosphates Cu4P2Se6, Cu4P3Se4, Cu4P4Se3, and CuP2Se, Featuring Zero-, One-, and Two-Dimensional Anions.

PubMed

Kuhn, Alexander; Schoop, Leslie M; Eger, Roland; Moudrakovski, Igor; Schwarzmüller, Stefan; Duppel, Viola; Kremer, Reinhard K; Oeckler, Oliver; Lotsch, Bettina V

2016-08-15

Five new compounds in the Cu/P/Se phase diagram have been synthesized, and their crystal structures have been determined. The crystal structures of these compounds comprise four previously unreported zero-, one-, and two-dimensional selenidophosphate anions containing low-valent phosphorus. In addition to two new modifications of Cu4P2Se6 featuring the well-known hexaselenidohypodiphosphate(IV) ion, there are three copper selenidophosphates with low-valent P: Cu4P3Se4 contains two different new anions, (i) a monomeric (zero-dimensional) selenidophosphate anion [P2Se4](4-) and (ii) a one-dimensional selenidophosphate anion [Formula: see text], which is related to the well-known gray-Se-like [Formula: see text] Zintl anion. Cu4P4Se3 contains one-dimensional [Formula: see text] polyanions, whereas CuP2Se contains the 2D selenidophosphate [Formula: see text] polyanion. It consists of charge-neutral CuP2Se layers separated by a van der Waals gap which is very rare for a Zintl-type phase. Hence, besides black P, CuP2Se constitutes a new possible source of 2D oxidized phosphorus containing layers for intercalation or exfoliation experiments. Additionally, the electronic structures and some fundamental physical properties of the new compounds are reported. All compounds are semiconducting with indirect band gaps of the orders of around 1 eV. The phases reported here add to the structural diversity of chalcogenido phosphates. The structural variety of this family of compounds may translate into a variety of tunable physical properties.

Imperfectly geometric shapes of nanograting structures as solar absorbers with superior performance for solar cells.

PubMed

Nguyen-Huu, Nghia; Cada, Michael; Pištora, Jaromír

2014-03-10

The expectation of perfectly geometric shapes of subwavelength grating (SWG) structures such as smoothness of sidewalls and sharp corners and nonexistence of grating defects is not realistic due to micro/nanofabrication processes. This work numerically investigates optical properties of an optimal solar absorber comprising a single-layered silicon (Si) SWG deposited on a finite Si substrate, with a careful consideration given to effects of various types of its imperfect geometry. The absorptance spectra of the solar absorber with different geometric shapes, namely, the grating with attached nanometer-sized features at the top and bottom of sidewalls and periodic defects within four and ten grating periods are investigated comprehensively. It is found that the grating with attached features at the bottom absorbs more energy than both the one at the top and the perfect grating. In addition, it is shown that the grating with defects in each fourth period exhibits the highest average absorptance (91%) compared with that of the grating having defects in each tenth period (89%), the grating with attached features (89%), and the perfect one (86%). Moreover, the results indicate that the absorptance spectrum of the imperfect structures is insensitive to angles of incidence. Furthermore, the absorptance enhancement is clearly demonstrated by computing magnetic field, energy density, and Poynting vector distributions. The results presented in this study prove that imperfect geometries of the nanograting structure display a higher absorptance than the perfect one, and provide such a practical guideline for nanofabrication capabilities necessary to be considered by structure designers.

Synthesis and characterization of high-surface-area millimeter-sized silica beads with hierarchical multi-modal pore structure by the addition of agar

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

Han, Yosep; Choi, Junhyun; Tong, Meiping, E-mail: tongmeiping@iee.pku.edu.cn

2014-04-01

Millimeter-sized spherical silica foams (SSFs) with hierarchical multi-modal pore structure featuring high specific surface area and ordered mesoporous frameworks were successfully prepared using aqueous agar addition, foaming and drop-in-oil processes. The pore-related properties of the prepared spherical silica (SSs) and SSFs were systematically characterized by field emission-scanning electron microscopy (FE-SEM), transmission electron microscopy (TEM), small-angle X-ray diffraction (SAXRD), Hg intrusion porosimetry, and N{sub 2} adsorption–desorption isotherm measurements. Improvements in the BET surface area and total pore volume were observed at 504 m{sup 2} g{sup −1} and 5.45 cm{sup 3} g{sup −1}, respectively, after an agar addition and foaming process. Despitemore » the increase in the BET surface area, the mesopore wall thickness and the pore size of the mesopores generated from the block copolymer with agar addition were unchanged based on the SAXRD, TEM, and BJH methods. The SSFs prepared in the present study were confirmed to have improved BET surface area and micropore volume through the agar loading, and to exhibit interconnected 3-dimensional network macropore structure leading to the enhancement of total porosity and BET surface area via the foaming process. - Highlights: • Millimeter-sized spherical silica foams (SSFs) are successfully prepared. • SSFs exhibit high BET surface area and ordered hierarchical pore structure. • Agar addition improves BET surface area and micropore volume of SSFs. • Foaming process generates interconnected 3-D network macropore structure of SSFs.« less

The influence of anisotropy on the core structure of Shockley partial dislocations within FCC materials

NASA Astrophysics Data System (ADS)

Szajewski, B. A.; Hunter, A.; Luscher, D. J.; Beyerlein, I. J.

2018-01-01

Both theoretical and numerical models of dislocations often necessitate the assumption of elastic isotropy to retain analytical tractability in addition to reducing computational load. As dislocation based models evolve towards physically realistic material descriptions, the assumption of elastic isotropy becomes increasingly worthy of examination. We present an analytical dislocation model for calculating the full dissociated core structure of dislocations within anisotropic face centered cubic (FCC) crystals as a function of the degree of material elastic anisotropy, two misfit energy densities on the γ-surface ({γ }{{isf}}, {γ }{{usf}}) and the remaining elastic constants. Our solution is independent of any additional features of the γ-surface. Towards this pursuit, we first demonstrate that the dependence of the anisotropic elasticity tensor on the orientation of the dislocation line within the FCC crystalline lattice is small and may be reasonably neglected for typical materials. With this approximation, explicit analytic solutions for the anisotropic elasticity tensor {B} for both nominally edge and screw dislocations within an FCC crystalline lattice are devised, and employed towards defining a set of effective isotropic elastic constants which reproduce fully anisotropic results, however do not retain the bulk modulus. Conversely, Hill averaged elastic constants which both retain the bulk modulus and reasonably approximate the dislocation core structure are employed within subsequent numerical calculations. We examine a wide range of materials within this study, and the features of each partial dislocation core are sufficiently localized that application of discrete linear elasticity accurately describes the separation of each partial dislocation core. In addition, the local features (the partial dislocation core distribution) are well described by a Peierls-Nabarro dislocation model. We develop a model for the displacement profile which depends upon two disparate dislocation length scales which describe the core structure; (i) the equilibrium stacking fault width between two Shockley partial dislocations, R eq and (ii) the maximum slip gradient, χ, of each Shockley partial dislocation. We demonstrate excellent agreement between our own analytic predictions, numerical calculations, and R eq computed directly by both ab-initio and molecular statics methods found elsewhere within the literature. The results suggest that understanding of various plastic mechanisms, e.g., cross-slip and nucleation may be augmented with the inclusion of elastic anisotropy.

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 collapsed crater structure.

Applying the LANL Statistical Pattern Recognition Paradigm for Structural Health Monitoring to Data from a Surface-Effect Fast Patrol Boat

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

Hoon Sohn; Charles Farrar; Norman Hunter

2001-01-01

This report summarizes the analysis of fiber-optic strain gauge data obtained from a surface-effect fast patrol boat being studied by the staff at the Norwegian Defense Research Establishment (NDRE) in Norway and the Naval Research Laboratory (NRL) in Washington D.C. Data from two different structural conditions were provided to the staff at Los Alamos National Laboratory. The problem was then approached from a statistical pattern recognition paradigm. This paradigm can be described as a four-part process: (1) operational evaluation, (2) data acquisition & cleansing, (3) feature extraction and data reduction, and (4) statistical model development for feature discrimination. Given thatmore » the first two portions of this paradigm were mostly completed by the NDRE and NRL staff, this study focused on data normalization, feature extraction, and statistical modeling for feature discrimination. The feature extraction process began by looking at relatively simple statistics of the signals and progressed to using the residual errors from auto-regressive (AR) models fit to the measured data as the damage-sensitive features. Data normalization proved to be the most challenging portion of this investigation. A novel approach to data normalization, where the residual errors in the AR model are considered to be an unmeasured input and an auto-regressive model with exogenous inputs (ARX) is then fit to portions of the data exhibiting similar waveforms, was successfully applied to this problem. With this normalization procedure, a clear distinction between the two different structural conditions was obtained. A false-positive study was also run, and the procedure developed herein did not yield any false-positive indications of damage. Finally, the results must be qualified by the fact that this procedure has only been applied to very limited data samples. A more complete analysis of additional data taken under various operational and environmental conditions as well as other structural conditions is necessary before one can definitively state that the procedure is robust enough to be used in practice.« less

Sequential projection pursuit for optimised vibration-based damage detection in an experimental wind turbine blade

NASA Astrophysics Data System (ADS)

Hoell, Simon; Omenzetter, Piotr

2018-02-01

To advance the concept of smart structures in large systems, such as wind turbines (WTs), it is desirable to be able to detect structural damage early while using minimal instrumentation. Data-driven vibration-based damage detection methods can be competitive in that respect because global vibrational responses encompass the entire structure. Multivariate damage sensitive features (DSFs) extracted from acceleration responses enable to detect changes in a structure via statistical methods. However, even though such DSFs contain information about the structural state, they may not be optimised for the damage detection task. This paper addresses the shortcoming by exploring a DSF projection technique specialised for statistical structural damage detection. High dimensional initial DSFs are projected onto a low-dimensional space for improved damage detection performance and simultaneous computational burden reduction. The technique is based on sequential projection pursuit where the projection vectors are optimised one by one using an advanced evolutionary strategy. The approach is applied to laboratory experiments with a small-scale WT blade under wind-like excitations. Autocorrelation function coefficients calculated from acceleration signals are employed as DSFs. The optimal numbers of projection vectors are identified with the help of a fast forward selection procedure. To benchmark the proposed method, selections of original DSFs as well as principal component analysis scores from these features are additionally investigated. The optimised DSFs are tested for damage detection on previously unseen data from the healthy state and a wide range of damage scenarios. It is demonstrated that using selected subsets of the initial and transformed DSFs improves damage detectability compared to the full set of features. Furthermore, superior results can be achieved by projecting autocorrelation coefficients onto just a single optimised projection vector.

Neighborhood alcohol outlet density and rates of child abuse and neglect: moderating effects of access to substance abuse services.

PubMed

Morton, Cory M; Simmel, Cassandra; Peterson, N Andrew

2014-05-01

This study investigates the relationship between concentrations of on- and off-premises alcohol outlets and rates of child abuse and neglect. Additionally, the study seeks to locate protective features of a neighborhood's built environment by investigating the potentially moderating role that access to substance abuse treatment and prevention services plays in the relationship between alcohol outlet density and child maltreatment. Using a cross-sectional design, this ecological study utilized data from 163 census tracts in Bergen County, New Jersey, on reports of child abuse and neglect, alcohol outlets, substance abuse treatment and prevention facilities, and the United States Census to investigate the linkages between socioeconomic structure, alcohol availability, and access to substance abuse service facilities on rates of child abuse and neglect. Findings indicate areas with a greater concentration of on-premises alcohol outlets (i.e., bars) had higher rates of child neglect, and those with easier access to substance abuse services had lower rates of neglect, controlling for neighborhood demographic and socioeconomic structure. Additionally, the relationship between on-premises alcohol outlet density and rates of child neglect was moderated by the presence of substance abuse service facilities. A greater concentration of off-premises outlets (i.e., liquor stores) was associated with lower rates of physical abuse. Findings suggest that the built environment and socioeconomic structure of neighborhoods have important consequences for child well-being. The implications for future research on the structural features of neighborhoods that are associated with child well-being are discussed. Copyright © 2014 Elsevier Ltd. All rights reserved.

Neighborhood Alcohol Outlet Density and Rates of Child Abuse and Neglect: Moderating Effects of Access to Substance Abuse Services

PubMed Central

Morton, Cory M.; Simmel, Cassandra; Peterson, N. Andrew

2014-01-01

This study investigates the relationship between concentrations of on- and off-premises alcohol outlets and rates of child abuse and neglect. Additionally, the study seeks to locate protective features of a neighborhood's built environment by investigating the potentially moderating role that access to substance abuse treatment and prevention services plays in the relationship between alcohol outlet density and child maltreatment. Using a cross-sectional design, this ecological study utilized data from 163 census tracts in Bergen County, New Jersey, on reports of child abuse and neglect, alcohol outlets, substance abuse treatment and prevention facilities, and the United States Census to investigate the linkages between socioeconomic structure, alcohol availability, and access to substance abuse service facilities on rates of child abuse and neglect. Findings indicate areas with a greater concentration of on-premises alcohol outlets (i.e., bars) had higher rates of child neglect, and those with easier access to substance abuse services had lower rates of neglect, controlling for neighborhood demographic and socioeconomic structure. Additionally, the relationship between on-premises alcohol outlet density and rates of child neglect was moderated by the presence of substance abuse service facilities. A greater concentration of off-premises outlets (i.e., liquor stores) was associated with lower rates of physical abuse. Findings suggest that the built environment and socioeconomic structure of neighborhoods have important consequences for child well-being. The implications for future research on the structural features of neighborhoods that are associated with child well-being are discussed. PMID:24529493

3D WHOLE-PROMINENCE FINE STRUCTURE MODELING. II. PROMINENCE EVOLUTION

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

Gunár, Stanislav; Mackay, Duncan H.

2015-10-20

We use the new three-dimensional (3D) whole-prominence fine structure model to study the evolution of prominences and their fine structures in response to changes in the underlying photospheric magnetic flux distribution. The applied model combines a detailed 3D prominence magnetic field configuration with a realistic description of the prominence plasma distributed along multiple fine structures. In addition, we utilize an approximate Hα visualization technique to study the evolution of the visible cool prominence plasma both in emission (prominence) and absorption (filament). We show that the initial magnetic field configuration of the modeled prominence is significantly disturbed by the changing positionmore » of a single polarity of a magnetic bipole as the bipole is advected toward the main body of the filament. This leads to the creation of a barb, which becomes the dominant feature visible in the synthetic Hα images of both the prominence and filament views. The evolution of the bipole also creates conditions that lead to the disappearance and reappearance of large portions of the main body. We also show that an arch-like region containing a dark void (a bubble) can be naturally produced in the synthetic prominence Hα images. While not visible in terms of the magnetic field lines, it is due to a lack of Hα emission from low-pressure, low-density plasma located in shallow magnetic dips lying along the lines of sight intersecting the dark void. In addition, a quasi-vertical small-scale feature consisting of short and deep dips, piled one above the other, is produced.« less

Structural studies of G protein-coupled receptors.

PubMed

Lu, Mengjie; Wu, Beili

2016-11-01

G protein-coupled receptors (GPCRs) comprise the largest membrane protein family. These receptors sense a variety of signaling molecules, activate multiple intracellular signal pathways, and act as the targets of over 40% of marketed drugs. Recent progress on GPCR structural studies provides invaluable insights into the structure-function relationship of the GPCR superfamily, deepening our understanding about the molecular mechanisms of GPCR signal transduction. Here, we review recent breakthroughs on GPCR structure determination and the structural features of GPCRs, and take the structures of chemokine receptor CCR5 and purinergic receptors P2Y 1 R and P2Y 12 R as examples to discuss the importance of GPCR structures on functional studies and drug discovery. In addition, we discuss the prospect of GPCR structure-based drug discovery. © 2016 IUBMB Life, 68(11):894-903, 2016. © 2016 International Union of Biochemistry and Molecular Biology.

PDB file parser and structure class implemented in Python.

PubMed

Hamelryck, Thomas; Manderick, Bernard

2003-11-22

The biopython project provides a set of bioinformatics tools implemented in Python. Recently, biopython was extended with a set of modules that deal with macromolecular structure. Biopython now contains a parser for PDB files that makes the atomic information available in an easy-to-use but powerful data structure. The parser and data structure deal with features that are often left out or handled inadequately by other packages, e.g. atom and residue disorder (if point mutants are present in the crystal), anisotropic B factors, multiple models and insertion codes. In addition, the parser performs some sanity checking to detect obvious errors. The Biopython distribution (including source code and documentation) is freely available (under the Biopython license) from http://www.biopython.org

Three-dimensionally networked graphene hydroxide with giant pores and its application in supercapacitors

PubMed Central

Lee, Dongwook; Seo, Jiwon

2014-01-01

The three-dimensionally networked and layered structure of graphene hydroxide (GH) was investigated. After lengthy immersion in a NaOH solution, most of the epoxy groups in the graphene oxide were destroyed, and more hydroxyl groups were generated, transforming the graphene oxide into graphene hydroxide. Additionally, benzoic acid groups were formed, and the ether groups link the neighboring layers, creating a near-3D structure in the GH. To utilize these unique structural features, electrodes with large pores for use in supercapacitors were fabricated using thermal reduction in vacuum. The reduced GH maintained its layered structure and developed a lot of large of pores between/inside the layers. The GH electrodes exhibited high gravimetric as well as high volumetric capacitance. PMID:25492227

Three-dimensionally networked graphene hydroxide with giant pores and its application in supercapacitors

NASA Astrophysics Data System (ADS)

Lee, Dongwook; Seo, Jiwon

2014-12-01

The three-dimensionally networked and layered structure of graphene hydroxide (GH) was investigated. After lengthy immersion in a NaOH solution, most of the epoxy groups in the graphene oxide were destroyed, and more hydroxyl groups were generated, transforming the graphene oxide into graphene hydroxide. Additionally, benzoic acid groups were formed, and the ether groups link the neighboring layers, creating a near-3D structure in the GH. To utilize these unique structural features, electrodes with large pores for use in supercapacitors were fabricated using thermal reduction in vacuum. The reduced GH maintained its layered structure and developed a lot of large of pores between/inside the layers. The GH electrodes exhibited high gravimetric as well as high volumetric capacitance.

Three-dimensionally networked graphene hydroxide with giant pores and its application in supercapacitors.

PubMed

Lee, Dongwook; Seo, Jiwon

2014-12-10

The three-dimensionally networked and layered structure of graphene hydroxide (GH) was investigated. After lengthy immersion in a NaOH solution, most of the epoxy groups in the graphene oxide were destroyed, and more hydroxyl groups were generated, transforming the graphene oxide into graphene hydroxide. Additionally, benzoic acid groups were formed, and the ether groups link the neighboring layers, creating a near-3D structure in the GH. To utilize these unique structural features, electrodes with large pores for use in supercapacitors were fabricated using thermal reduction in vacuum. The reduced GH maintained its layered structure and developed a lot of large of pores between/inside the layers. The GH electrodes exhibited high gravimetric as well as high volumetric capacitance.

New software for statistical analysis of Cambridge Structural Database data

PubMed Central

Sykes, Richard A.; McCabe, Patrick; Allen, Frank H.; Battle, Gary M.; Bruno, Ian J.; Wood, Peter A.

2011-01-01

A collection of new software tools is presented for the analysis of geometrical, chemical and crystallographic data from the Cambridge Structural Database (CSD). This software supersedes the program Vista. The new functionality is integrated into the program Mercury in order to provide statistical, charting and plotting options alongside three-dimensional structural visualization and analysis. The integration also permits immediate access to other information about specific CSD entries through the Mercury framework, a common requirement in CSD data analyses. In addition, the new software includes a range of more advanced features focused towards structural analysis such as principal components analysis, cone-angle correction in hydrogen-bond analyses and the ability to deal with topological symmetry that may be exhibited in molecular search fragments. PMID:22477784

Data mining the PDB for glyco-related data.

PubMed

Lütteke, Thomas; von der Lieth, Claus W

2009-01-01

The 3D structural data of glycoprotein or protein-carbohydrate complexes that are found in the Protein Data Bank (PDB) are an interesting data source for glycobiologists. Unfortunately, carbohydrate components are difficult to find with the means provided by the PDB. The GLYCOSCIENCES.de internet portal offers a variety of tools and databases to locate and analyze these structures. This chapter describes how to find PDB entries that feature a specific carbohydrate structure and how to locate carbohydrate residues in a 3D structure file and to check their consistency. In addition to this, methods to statistically analyze torsion angles and the abundance of amino acids both in the neighborhood of glycosylation sites and in the spatial vicinity of non-covalently bound carbohydrate chains are summarized.

Analytical study of sandwich structures using Euler-Bernoulli beam equation

NASA Astrophysics Data System (ADS)

Xue, Hui; Khawaja, H.

2017-01-01

This paper presents an analytical study of sandwich structures. In this study, the Euler-Bernoulli beam equation is solved analytically for a four-point bending problem. Appropriate initial and boundary conditions are specified to enclose the problem. In addition, the balance coefficient is calculated and the Rule of Mixtures is applied. The focus of this study is to determine the effective material properties and geometric features such as the moment of inertia of a sandwich beam. The effective parameters help in the development of a generic analytical correlation for complex sandwich structures from the perspective of four-point bending calculations. The main outcomes of these analytical calculations are the lateral displacements and longitudinal stresses for each particular material in the sandwich structure.

Pore- and micro-structural characterization of a novel structural binder based on iron carbonation

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

Das, Sumanta, E-mail: Sumanta.Das@asu.edu; Stone, David, E-mail: dajstone@gmail.com; Convey, Diana, E-mail: Diana.Convey@asu.edu

2014-12-15

The pore- and micro-structural features of a novel binding material based on the carbonation of waste metallic iron powder are reported in this paper. The binder contains metallic iron powder as the major ingredient, followed by additives containing silica and alumina to facilitate favorable reaction product formation. Compressive strengths sufficient for a majority of concrete applications are attained. The material pore structure is investigated primarily through mercury intrusion porosimetry whereas electron microscopy is used for microstructural characterization. Reduction in the overall porosity and the average pore size with an increase in carbonation duration from 1 day to 4 days ismore » noticed. The pore structure features are used in predictive models for gas and moisture transport (water vapor diffusivity and moisture permeability) through the porous medium which dictates its long-term durability when used in structural applications. Comparisons of the pore structure with those of a Portland cement paste are also provided. The morphology of the reaction products in the iron-based binder, and the distribution of constituent elements in the microstructure are also reported. - Highlights: • Carbonation of iron produces a dense microstructure. • Pore volume in iron carbonate lower, critical size higher than those in OPC pastes • Reaction product contains iron, carbon, silicon, aluminum and calcium. • Power-law for porosity-moisture permeability relationship was established.« less

Biomacromolecular quantitative structure-activity relationship (BioQSAR): a proof-of-concept study on the modeling, prediction and interpretation of protein-protein binding affinity.

PubMed

Zhou, Peng; Wang, Congcong; Tian, Feifei; Ren, Yanrong; Yang, Chao; Huang, Jian

2013-01-01

Quantitative structure-activity relationship (QSAR), a regression modeling methodology that establishes statistical correlation between structure feature and apparent behavior for a series of congeneric molecules quantitatively, has been widely used to evaluate the activity, toxicity and property of various small-molecule compounds such as drugs, toxicants and surfactants. However, it is surprising to see that such useful technique has only very limited applications to biomacromolecules, albeit the solved 3D atom-resolution structures of proteins, nucleic acids and their complexes have accumulated rapidly in past decades. Here, we present a proof-of-concept paradigm for the modeling, prediction and interpretation of the binding affinity of 144 sequence-nonredundant, structure-available and affinity-known protein complexes (Kastritis et al. Protein Sci 20:482-491, 2011) using a biomacromolecular QSAR (BioQSAR) scheme. We demonstrate that the modeling performance and predictive power of BioQSAR are comparable to or even better than that of traditional knowledge-based strategies, mechanism-type methods and empirical scoring algorithms, while BioQSAR possesses certain additional features compared to the traditional methods, such as adaptability, interpretability, deep-validation and high-efficiency. The BioQSAR scheme could be readily modified to infer the biological behavior and functions of other biomacromolecules, if their X-ray crystal structures, NMR conformation assemblies or computationally modeled structures are available.

Structures, molecular orbitals and UV-vis spectra investigations on methyl 1-benzyl-1H-1,2,3-triazole-4-carboxylate: a computational study.

PubMed

Wang, Tsang-Hsiu; Chu, Hsing-Yu; Wang, I-Teng

2014-10-15

The methyl 1-benzyl-1H-1,2,3-triazole-4-carboxylate (C11H11N3O2) has been studied by theoretically methods. The structure of this compound is optimized by density functional theory (DFT), the second-order Møller-Plesset perturbation theory (MP2) and G3 theory (G3(MP2)) levels. Our calculation results are in very good agreement with experimental values. Compared to a perfect pentagonal structure, the geometrical structures of C11H11N3O2 show a little distortion of 1,2,3-triazole ring due to the highly electronegativity of substitution groups. In addition, dipole moment and frontier molecular orbitals (FMOs) of the C11H11N3O2 are calculated as well. Because of solvent effect, the HOMO-LUMO energy gap in methanol is predicted to be smaller than in gas phase by 0.367eV. The simulated UV-vis spectra are investigated by time-dependent density functional theory (TD-DFT), and two obviously absorption features have been predicted. These two absorption features are located between 170nm and 210nm, which is in ultraviolet C range. Moreover, the UV absorption features in methanol are predicted to be more intense than in gas phase; besides, the red shift is predicted in methanol as well. Copyright © 2014 Elsevier B.V. All rights reserved.

Interactive Raster Data Structure Study.

DTIC Science & Technology

1983-01-01

update. In a cartographic editing environment the data to be used . is very temporal and dynamic in nature , Changes in the data being addressed should...draft them. This allowed for the natural conceptualization of digital data as features. This trait has been observed as a result of functions being...performing * cartographic manipulations. In the compilation and revision environment P where data is temporal in nature , additional processing leads to

Asymmetric hindwing foldings in rove beetles.

PubMed

Saito, Kazuya; Yamamoto, Shuhei; Maruyama, Munetoshi; Okabe, Yoji

2014-11-18

Foldable wings of insects are the ultimate deployable structures and have attracted the interest of aerospace engineering scientists as well as entomologists. Rove beetles are known to fold their wings in the most sophisticated ways that have right-left asymmetric patterns. However, the specific folding process and the reason for this asymmetry remain unclear. This study reveals how these asymmetric patterns emerge as a result of the folding process of rove beetles. A high-speed camera was used to reveal the details of the wing-folding movement. The results show that these characteristic asymmetrical patterns emerge as a result of simultaneous folding of overlapped wings. The revealed folding mechanisms can achieve not only highly compact wing storage but also immediate deployment. In addition, the right and left crease patterns are interchangeable, and thus each wing internalizes two crease patterns and can be folded in two different ways. This two-way folding gives freedom of choice for the folding direction to a rove beetle. The use of asymmetric patterns and the capability of two-way folding are unique features not found in artificial structures. These features have great potential to extend the design possibilities for all deployable structures, from space structures to articles of daily use.

Automated diagnosis of Alzheimer's disease with multi-atlas based whole brain segmentations

NASA Astrophysics Data System (ADS)

Luo, Yuan; Tang, Xiaoying

2017-03-01

Voxel-based analysis is widely used in quantitative analysis of structural brain magnetic resonance imaging (MRI) and automated disease detection, such as Alzheimer's disease (AD). However, noise at the voxel level may cause low sensitivity to AD-induced structural abnormalities. This can be addressed with the use of a whole brain structural segmentation approach which greatly reduces the dimension of features (the number of voxels). In this paper, we propose an automatic AD diagnosis system that combines such whole brain segmen- tations with advanced machine learning methods. We used a multi-atlas segmentation technique to parcellate T1-weighted images into 54 distinct brain regions and extract their structural volumes to serve as the features for principal-component-analysis-based dimension reduction and support-vector-machine-based classification. The relationship between the number of retained principal components (PCs) and the diagnosis accuracy was systematically evaluated, in a leave-one-out fashion, based on 28 AD subjects and 23 age-matched healthy subjects. Our approach yielded pretty good classification results with 96.08% overall accuracy being achieved using the three foremost PCs. In addition, our approach yielded 96.43% specificity, 100% sensitivity, and 0.9891 area under the receiver operating characteristic curve.

Splicing-Related Features of Introns Serve to Propel Evolution

PubMed Central

Luo, Yuping; Li, Chun; Gong, Xi; Wang, Yanlu; Zhang, Kunshan; Cui, Yaru; Sun, Yi Eve; Li, Siguang

2013-01-01

The role of spliceosomal intronic structures played in evolution has only begun to be elucidated. Comparative genomic analyses of fungal snoRNA sequences, which are often contained within introns and/or exons, revealed that about one-third of snoRNA-associated introns in three major snoRNA gene clusters manifested polymorphisms, likely resulting from intron loss and gain events during fungi evolution. Genomic deletions can clearly be observed as one mechanism underlying intron and exon loss, as well as generation of complex introns where several introns lie in juxtaposition without intercalating exons. Strikingly, by tracking conserved snoRNAs in introns, we found that some introns had moved from one position to another by excision from donor sites and insertion into target sties elsewhere in the genome without needing transposon structures. This study revealed the origin of many newly gained introns. Moreover, our analyses suggested that intron-containing sequences were more prone to sustainable structural changes than DNA sequences without introns due to intron's ability to jump within the genome via unknown mechanisms. We propose that splicing-related structural features of introns serve as an additional motor to propel evolution. PMID:23516505

Generation of the first structure-based pharmacophore model containing a selective "zinc binding group" feature to identify potential glyoxalase-1 inhibitors.

PubMed

Al-Balas, Qosay; Hassan, Mohammad; Al-Oudat, Buthina; Alzoubi, Hassan; Mhaidat, Nizar; Almaaytah, Ammar

2012-11-22

Within this study, a unique 3D structure-based pharmacophore model of the enzyme glyoxalase-1 (Glo-1) has been revealed. Glo-1 is considered a zinc metalloenzyme in which the inhibitor binding with zinc atom at the active site is crucial. To our knowledge, this is the first pharmacophore model that has a selective feature for a "zinc binding group" which has been customized within the structure-based pharmacophore model of Glo-1 to extract ligands that possess functional groups able to bind zinc atom solely from database screening. In addition, an extensive 2D similarity search using three diverse similarity techniques (Tanimoto, Dice, Cosine) has been performed over the commercially available "Zinc Clean Drug-Like Database" that contains around 10 million compounds to help find suitable inhibitors for this enzyme based on known inhibitors from the literature. The resultant hits were mapped over the structure based pharmacophore and the successful hits were further docked using three docking programs with different pose fitting and scoring techniques (GOLD, LibDock, CDOCKER). Nine candidates were suggested to be novel Glo-1 inhibitors containing the "zinc binding group" with the highest consensus scoring from docking.

Assessing future vent opening locations at the Somma-Vesuvio volcanic complex: 1. A new information geodatabase with uncertainty characterizations

NASA Astrophysics Data System (ADS)

Tadini, A.; Bisson, M.; Neri, A.; Cioni, R.; Bevilacqua, A.; Aspinall, W. P.

2017-06-01

This study presents new and revised data sets about the spatial distribution of past volcanic vents, eruptive fissures, and regional/local structures of the Somma-Vesuvio volcanic system (Italy). The innovative features of the study are the identification and quantification of important sources of uncertainty affecting interpretations of the data sets. In this regard, the spatial uncertainty of each feature is modeled by an uncertainty area, i.e., a geometric element typically represented by a polygon drawn around points or lines. The new data sets have been assembled as an updatable geodatabase that integrates and complements existing databases for Somma-Vesuvio. The data are organized into 4 data sets and stored as 11 feature classes (points and lines for feature locations and polygons for the associated uncertainty areas), totaling more than 1700 elements. More specifically, volcanic vent and eruptive fissure elements are subdivided into feature classes according to their associated eruptive styles: (i) Plinian and sub-Plinian eruptions (i.e., large- or medium-scale explosive activity); (ii) violent Strombolian and continuous ash emission eruptions (i.e., small-scale explosive activity); and (iii) effusive eruptions (including eruptions from both parasitic vents and eruptive fissures). Regional and local structures (i.e., deep faults) are represented as linear feature classes. To support interpretation of the eruption data, additional data sets are provided for Somma-Vesuvio geological units and caldera morphological features. In the companion paper, the data presented here, and the associated uncertainties, are used to develop a first vent opening probability map for the Somma-Vesuvio caldera, with specific attention focused on large or medium explosive events.

On type B cyclogenesis in a quasi-geostrophic model

NASA Astrophysics Data System (ADS)

Grotjahn, Richard

2005-01-01

A quasi-geostrophic (QG) model is used to approximate some aspects of 'type B' cyclogenesis as described in an observational paper that appeared several decades earlier in this journal. Though often cited, that earlier work has some ambiguity that has propagated into subsequent analyses. The novel aspects examined here include allowing advective nonlinearity to distort and amplify structures that are quasi-coherent and nearly stable in a linear form of the model; also, separate upper and lower structures are localized in space. Cases are studied separately where the upper trough tracks across different low-level features: an enhanced baroclinic zone (stronger horizontal temperature gradient) or a region of augmented temperature. Growth by superposition of lower and upper features is excluded by experimental design. The dynamics are evaluated with the vertical motion equation, the QG vorticity equation, the QG perturbation energy equation, and 'potential-vorticity thinking'. Results are compared against 'control' cases having no additional low-level features. Nonlinearity is examined relative to a corresponding linear calculation and is generally positive. The results are perhaps richer than the seminal article might imply, because growth is enhanced not only when properties of the lower feature reinforce growth but also when the lower feature opposes decay of the upper feature. For example, growth is enhanced where low-level warm advection introduces rising warm air to oppose the rising cold air ahead of the upper trough. Such growth is magnified when adjacent warm and cold anomalies have a strong baroclinic zone between them. The enhanced growth triggers an upstream tilt in the solution whose properties further accelerate the growth.

Concept-based query language approach to enterprise information systems

NASA Astrophysics Data System (ADS)

Niemi, Timo; Junkkari, Marko; Järvelin, Kalervo

2014-01-01

In enterprise information systems (EISs) it is necessary to model, integrate and compute very diverse data. In advanced EISs the stored data often are based both on structured (e.g. relational) and semi-structured (e.g. XML) data models. In addition, the ad hoc information needs of end-users may require the manipulation of data-oriented (structural), behavioural and deductive aspects of data. Contemporary languages capable of treating this kind of diversity suit only persons with good programming skills. In this paper we present a concept-oriented query language approach to manipulate this diversity so that the programming skill requirements are considerably reduced. In our query language, the features which need technical knowledge are hidden in application-specific concepts and structures. Therefore, users need not be aware of the underlying technology. Application-specific concepts and structures are represented by the modelling primitives of the extended RDOOM (relational deductive object-oriented modelling) which contains primitives for all crucial real world relationships (is-a relationship, part-of relationship, association), XML documents and views. Our query language also supports intensional and extensional-intensional queries, in addition to conventional extensional queries. In its query formulation, the end-user combines available application-specific concepts and structures through shared variables.

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

Levakhina, Y. M.; Mueller, J.; Buzug, T. M.

Purpose: This paper introduces a nonlinear weighting scheme into the backprojection operation within the simultaneous algebraic reconstruction technique (SART). It is designed for tomosynthesis imaging of objects with high-attenuation features in order to reduce limited angle artifacts. Methods: The algorithm estimates which projections potentially produce artifacts in a voxel. The contribution of those projections into the updating term is reduced. In order to identify those projections automatically, a four-dimensional backprojected space representation is used. Weighting coefficients are calculated based on a dissimilarity measure, evaluated in this space. For each combination of an angular view direction and a voxel position anmore » individual weighting coefficient for the updating term is calculated. Results: The feasibility of the proposed approach is shown based on reconstructions of the following real three-dimensional tomosynthesis datasets: a mammography quality phantom, an apple with metal needles, a dried finger bone in water, and a human hand. Datasets have been acquired with a Siemens Mammomat Inspiration tomosynthesis device and reconstructed using SART with and without suggested weighting. Out-of-focus artifacts are described using line profiles and measured using standard deviation (STD) in the plane and below the plane which contains artifact-causing features. Artifacts distribution in axial direction is measured using an artifact spread function (ASF). The volumes reconstructed with the weighting scheme demonstrate the reduction of out-of-focus artifacts, lower STD (meaning reduction of artifacts), and narrower ASF compared to nonweighted SART reconstruction. It is achieved successfully for different kinds of structures: point-like structures such as phantom features, long structures such as metal needles, and fine structures such as trabecular bone structures. Conclusions: Results indicate the feasibility of the proposed algorithm to reduce typical tomosynthesis artifacts produced by high-attenuation features. The proposed algorithm assigns weighting coefficients automatically and no segmentation or tissue-classification steps are required. The algorithm can be included into various iterative reconstruction algorithms with an additive updating strategy. It can also be extended to computed tomography case with the complete set of angular data.« less

Three-dimensional radar imaging of structures and craters in the Martian polar caps.

PubMed

Putzig, Nathaniel E; Smith, Isaac B; Perry, Matthew R; Foss, Frederick J; Campbell, Bruce A; Phillips, Roger J; Seu, Roberto

2018-07-01

Over the last decade, observations acquired by the Shallow Radar (SHARAD) sounder on individual passes of the Mars Reconnaissance Orbiter have revealed the internal structure of the Martian polar caps and provided new insights into the formation of the icy layers within and their relationship to climate. However, a complete picture of the cap interiors has been hampered by interfering reflections from off-nadir surface features and signal losses associated with sloping structures and scattering. Foss et al. (2017) addressed these limitations by assembling three-dimensional data volumes of SHARAD observations from thousands of orbital passes over each polar region and applying geometric corrections simultaneously. The radar volumes provide unprecedented views of subsurface features, readily imaging structures previously inferred from time-intensive manual analysis of single-orbit data (e.g., trough-bounding surfaces, a buried chasma, and a basal unit in the north, massive carbon-dioxide ice deposits and discontinuous layered sequences in the south). Our new mapping of the carbon-dioxide deposits yields a volume of 16,500 km 3 , 11% larger than the prior estimate. In addition, the radar volumes newly reveal other structures, including what appear to be buried impact craters with no surface expression. Our first assessment of 21 apparent craters at the base of the north polar layered deposits suggests a Hesperian age for the substrate, consistent with that of the surrounding plains as determined from statistics of surface cratering rates. Planned mapping of similar features throughout both polar volumes may provide new constraints on the age of the icy layered deposits. The radar volumes also provide new topographic data between the highest latitudes observed by the Mars Orbiter Laser Altimeter and those observed by SHARAD. In general, mapping of features in these radar volumes is placing new constraints on the nature and evolution of the polar deposits and associated climate changes.

Three-dimensional radar imaging of structures and craters in the Martian polar caps

NASA Astrophysics Data System (ADS)

Putzig, Nathaniel E.; Smith, Isaac B.; Perry, Matthew R.; Foss, Frederick J.; Campbell, Bruce A.; Phillips, Roger J.; Seu, Roberto

2018-07-01

Over the last decade, observations acquired by the Shallow Radar (SHARAD) sounder on individual passes of the Mars Reconnaissance Orbiter have revealed the internal structure of the Martian polar caps and provided new insights into the formation of the icy layers within and their relationship to climate. However, a complete picture of the cap interiors has been hampered by interfering reflections from off-nadir surface features and signal losses associated with sloping structures and scattering. Foss et al. (The Leading Edge 36, 43-57, 2017, https://doi.org/10.1190/tle36010043.1) addressed these limitations by assembling three-dimensional data volumes of SHARAD observations from thousands of orbital passes over each polar region and applying geometric corrections simultaneously. The radar volumes provide unprecedented views of subsurface features, readily imaging structures previously inferred from time-intensive manual analysis of single-orbit data (e.g., trough-bounding surfaces, a buried chasma, and a basal unit in the north, massive carbon-dioxide ice deposits and discontinuous layered sequences in the south). Our new mapping of the carbon-dioxide deposits yields a volume of 16,500 km3, 11% larger than the prior estimate. In addition, the radar volumes newly reveal other structures, including what appear to be buried impact craters with no surface expression. Our first assessment of 21 apparent craters at the base of the north polar layered deposits suggests a Hesperian age for the substrate, consistent with that of the surrounding plains as determined from statistics of surface cratering rates. Planned mapping of similar features throughout both polar volumes may provide new constraints on the age of the icy layered deposits. The radar volumes also provide new topographic data between the highest latitudes observed by the Mars Orbiter Laser Altimeter and those observed by SHARAD. In general, mapping of features in these radar volumes is placing new constraints on the nature and evolution of the polar deposits and associated climate changes.

Cross Flow Parameter Calculation for Aerodynamic Analysis

NASA Technical Reports Server (NTRS)

Norman, David, Jr. (Inventor)

2014-01-01

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

A graph lattice approach to maintaining and learning dense collections of subgraphs as image features.

PubMed

Saund, Eric

2013-10-01

Effective object and scene classification and indexing depend on extraction of informative image features. This paper shows how large families of complex image features in the form of subgraphs can be built out of simpler ones through construction of a graph lattice—a hierarchy of related subgraphs linked in a lattice. Robustness is achieved by matching many overlapping and redundant subgraphs, which allows the use of inexpensive exact graph matching, instead of relying on expensive error-tolerant graph matching to a minimal set of ideal model graphs. Efficiency in exact matching is gained by exploitation of the graph lattice data structure. Additionally, the graph lattice enables methods for adaptively growing a feature space of subgraphs tailored to observed data. We develop the approach in the domain of rectilinear line art, specifically for the practical problem of document forms recognition. We are especially interested in methods that require only one or very few labeled training examples per category. We demonstrate two approaches to using the subgraph features for this purpose. Using a bag-of-words feature vector we achieve essentially single-instance learning on a benchmark forms database, following an unsupervised clustering stage. Further performance gains are achieved on a more difficult dataset using a feature voting method and feature selection procedure.

Nonequilibrium Conditions Explain Spatial Variability in Genetic Structuring of Little Penguin (Eudyptula minor)

PubMed Central

Peucker, Amanda J.; Valautham, Sureen K.; Styan, Craig A.; Dann, Peter

2015-01-01

Factors responsible for spatial structuring of population genetic variation are varied, and in many instances there may be no obvious explanations for genetic structuring observed, or those invoked may reflect spurious correlations. A study of little penguins (Eudyptula minor) in southeast Australia documented low spatial structuring of genetic variation with the exception of colonies at the western limit of sampling, and this distinction was attributed to an intervening oceanographic feature (Bonney Upwelling), differences in breeding phenology, or sea level change. Here, we conducted sampling across the entire Australian range, employing additional markers (12 microsatellites and mitochondrial DNA, 697 individuals, 17 colonies). The zone of elevated genetic structuring previously observed actually represents the eastern half of a genetic cline, within which structuring exists over much shorter spatial scales than elsewhere. Colonies separated by as little as 27 km in the zone are genetically distinguishable, while outside the zone, homogeneity cannot be rejected at scales of up to 1400 km. Given a lack of additional physical or environmental barriers to gene flow, the zone of elevated genetic structuring may reflect secondary contact of lineages (with or without selection against interbreeding), or recent colonization and expansion from this region. This study highlights the importance of sampling scale to reveal the cause of genetic structuring. PMID:25833231

Detecting double compressed MPEG videos with the same quantization matrix and synchronized group of pictures structure

NASA Astrophysics Data System (ADS)

Aghamaleki, Javad Abbasi; Behrad, Alireza

2018-01-01

Double compression detection is a crucial stage in digital image and video forensics. However, the detection of double compressed videos is challenging when the video forger uses the same quantization matrix and synchronized group of pictures (GOP) structure during the recompression history to conceal tampering effects. A passive approach is proposed for detecting double compressed MPEG videos with the same quantization matrix and synchronized GOP structure. To devise the proposed algorithm, the effects of recompression on P frames are mathematically studied. Then, based on the obtained guidelines, a feature vector is proposed to detect double compressed frames on the GOP level. Subsequently, sparse representations of the feature vectors are used for dimensionality reduction and enrich the traces of recompression. Finally, a support vector machine classifier is employed to detect and localize double compression in temporal domain. The experimental results show that the proposed algorithm achieves the accuracy of more than 95%. In addition, the comparisons of the results of the proposed method with those of other methods reveal the efficiency of the proposed algorithm.

Occurrence and structure of epipharyngeal pouches in bears (Ursidae)

PubMed Central

WEISSENGRUBER, G. E.; FORSTENPOINTNER, G.; KÜBBER-HEISS, A.; RIEDELBERGER, K.; SCHWAMMER, H.; GANZBERGER, K.

2001-01-01

The infrequent mention of epipharyngeal pouches occurring in some species of bears indicates the scarcity of morphological and functional knowledge about these structures. In order to provide precise morphological data on the structure of these remarkable formations and to verify their taxonomic utility, the pharyngeal regions of 1 spectacled bear and 3 brown bears were examined. All these individuals possessed epipharyngeal pouches, which are tubular, blind-ending outpouchings of the caudodorsal pharyngeal wall equipped with respiratory epithelium and a thick layer of elastic fibres. While the spectacled bear and Ursus arctos syriacus possessed a single pouch on the caudodorsal wall of the nasopharynx, in Ursus arctos and Ursus arctos beringianus 2 unequally sized pouches were present. Two additional sacs of smaller size, representing outpouchings of the lateral pharyngeal wall, occurred in the spectacled bear. These findings prove epipharyngeal pouches to be constant and unique morphological features of the family Ursidae, the anatomical features suggesting involvement in the respiratory system most probably in important aspects of ursid phonation. This is the first description of epipharyngeal pouches in the spectacled bear. PMID:11322723

Optimal design of high damping force engine mount featuring MR valve structure with both annular and radial flow paths

NASA Astrophysics Data System (ADS)

Nguyen, Q. H.; Choi, S. B.; Lee, Y. S.; Han, M. S.

2013-11-01

This paper focuses on the optimal design of a compact and high damping force engine mount featuring magnetorheological fluid (MRF). In the mount, a MR valve structure with both annular and radial flows is employed to generate a high damping force. First, the configuration and working principle of the proposed MR mount is introduced. The MRF flows in the mount are then analyzed and the governing equations of the MR mount are derived based on the Bingham plastic behavior of the MRF. An optimal design of the MR mount is then performed to find the optimal structure of the MR valve to generate a maximum damping force with certain design constraints. In addition, the gap size of MRF ducts is empirically chosen considering the ‘lockup’ problem of the mount at high frequency. Performance of the optimized MR mount is then evaluated based on finite element analysis and discussions on performance results of the optimized MR mount are given. The effectiveness of the proposed MR engine mount is demonstrated via computer simulation by presenting damping force and power consumption.

[Morphometric features of the structure of the central nucleus of the amygdala in men and women].

PubMed

Antyukhov, A D

2015-01-01

To identify the interhemispheric asymmetry in the structure of the central nucleus of the amygdala in men and women. Morphometric features of the structure of neurons of the central nucleus amygdala complex were studied in histological sections of the brain of 6 men and 6 women (24 hemispheres), aged 19 to 55 years, with no lifetime diagnosis of mental or neurological disease. The value of the profile fields of neurons of the central nucleus amygdala complex in the left and right hemispheres of the brain were investigated. In women, the average value of neurons in the left hemisphere was somewhat greater than in the right hemisphere, while in men this value was greater in the right hemisphere. The interhemispheric morphometric differences were not significant regardless of gender. In addition, the quantity of relevant fields of neurons in the central nucleus of the amygdala in women was significantly larger than that of men in both hemispheres. The authors attempted to associate the results obtained in the study with emotional perception in men and women.

Decoupling Activation of Heme Biosynthesis from Anaerobic Toxicity in a Molecule Active in Staphylococcus aureus.

PubMed

Dutter, Brendan F; Mike, Laura A; Reid, Paul R; Chong, Katherine M; Ramos-Hunter, Susan J; Skaar, Eric P; Sulikowski, Gary A

2016-05-20

Small molecules active in the pathogenic bacterium Staphylococcus aureus are valuable tools for the study of its basic biology and pathogenesis, and many molecules may provide leads for novel therapeutics. We have previously reported a small molecule, 1, which activates endogenous heme biosynthesis in S. aureus, leading to an accumulation of intracellular heme. In addition to this novel activity, 1 also exhibits toxicity towards S. aureus growing under fermentative conditions. To determine if these activities are linked and establish what features of the molecule are required for activity, we synthesized a library of analogs around the structure of 1 and screened them for activation of heme biosynthesis and anaerobic toxicity to investigate structure-activity relationships. The results of this analysis suggest that these activities are not linked. Furthermore, we have identified the structural features that promote each activity and have established two classes of molecules: activators of heme biosynthesis and inhibitors of anaerobic growth. These molecules will serve as useful probes for their respective activities without concern for the off target effects of the parent compound.

Structural study and conformational behavior of the two different lipopolysaccharide O-antigens produced by the cystic fibrosis pathogen Burkholderia multivorans.

PubMed

Ieranò, Teresa; Silipo, Alba; Cescutti, Paola; Leone, Maria Rosaria; Rizzo, Roberto; Lanzetta, Rosa; Parrilli, Michelangelo; Molinaro, Antonio

2009-07-20

Lipopolysaccharides (LPSs) are virulence factors expressed by gram-negative bacteria; they are among those mainly responsible for bacterial virulence. In this work we define the primary structure and the conformational features of the O-chain from the LPS produced by the highly virulent clinical isolate Burkholderia multivorans strain C1576, an opportunistic human pathogen isolated in a cystic fibrosis center and causative of an outbreak with lethal outcome. We demonstrate that the LPS from this clinical isolate consists of two O-polysaccharide chains present in different amounts and made up of repeating units, both containing deoxy sugar. Additionally, conformational studies have been performed to establish and compare the spatial arrangements of the two polysaccharides and differences in their shape have been highlighted. The comprehension of the structural and conformational features of the two repeating units may help to explain their biological significance, the molecular shape of the bacterial external surface, and the comprehension at the molecular level of the recognition mechanisms of the antibodies.

Plasmonic nanostructures through DNA-assisted lithography

PubMed Central

Shen, Boxuan; Linko, Veikko; Tapio, Kosti; Pikker, Siim; Lemma, Tibebe; Gopinath, Ashwin; Gothelf, Kurt V.; Kostiainen, Mauri A.; Toppari, J. Jussi

2018-01-01

Programmable self-assembly of nucleic acids enables the fabrication of custom, precise objects with nanoscale dimensions. These structures can be further harnessed as templates to build novel materials such as metallic nanostructures, which are widely used and explored because of their unique optical properties and their potency to serve as components of novel metamaterials. However, approaches to transfer the spatial information of DNA constructions to metal nanostructures remain a challenge. We report a DNA-assisted lithography (DALI) method that combines the structural versatility of DNA origami with conventional lithography techniques to create discrete, well-defined, and entirely metallic nanostructures with designed plasmonic properties. DALI is a parallel, high-throughput fabrication method compatible with transparent substrates, thus providing an additional advantage for optical measurements, and yields structures with a feature size of ~10 nm. We demonstrate its feasibility by producing metal nanostructures with a chiral plasmonic response and bowtie-shaped nanoantennas for surface-enhanced Raman spectroscopy. We envisage that DALI can be generalized to large substrates, which would subsequently enable scale-up production of diverse metallic nanostructures with tailored plasmonic features. PMID:29423446

In vitro developmental model of the gastrointestinal tract from mouse embryonic stem cells.

PubMed

Torihashi, Shigeko; Kuwahara, Masaki; Kurahashi, Masaaki

2007-10-01

Mouse embryonic stem (ES) cells are pluripotent and retain their potential to form cells, tissues and organs originated from three embryonic germ layers. Recently, we developed in vitro organ--gut-like structures--from mouse ES cells. They had basically similar morphological features to a mouse gastrointestinal tract in vivo composed of three distinct layers (i.e., epithelium, connective tissue and musculature). Gut-like structures showed spontaneous contractions derived from pacemaker cells (interstitial cells of Cajal) in the musculature. We also examined their formation process and expression pattern of transcription factors crucial for gut organogenesis such as Id2, Sox17, HNF3beta/Foxa2 and GATA4. We found that they mimic the development of embryonic gut in vivo and showed a similar expression pattern of common transcription factors. They also maintain their developmental potential after transplantation to a renal capsule. Therefore, gut-like structures are suitable for in vitro models of gastrointestinal tracts and their development. In addition, we pointed out several unique features different from gut in vivo that provide useful and advantageous tools to investigate the developmental mechanism of the gastrointestinal tract.

Candida albicans Agglutinin-Like Sequence (Als) Family Vignettes: A Review of Als Protein Structure and Function

PubMed Central

Hoyer, Lois L.; Cota, Ernesto

2016-01-01

Approximately two decades have passed since the description of the first gene in the Candida albicans ALS (agglutinin-like sequence) family. Since that time, much has been learned about the composition of the family and the function of its encoded cell-surface glycoproteins. Solution of the structure of the Als adhesive domain provides the opportunity to evaluate the molecular basis for protein function. This review article is formatted as a series of fundamental questions and explores the diversity of the Als proteins, as well as their role in ligand binding, aggregative effects, and attachment to abiotic surfaces. Interaction of Als proteins with each other, their functional equivalence, and the effects of protein abundance on phenotypic conclusions are also examined. Structural features of Als proteins that may facilitate invasive function are considered. Conclusions that are firmly supported by the literature are presented while highlighting areas that require additional investigation to reveal basic features of the Als proteins, their relatedness to each other, and their roles in C. albicans biology. PMID:27014205

Molecular recognition principles and stationary-phase characteristics of topoisomer-selective chemoaffinity materials for chromatographic separation of circular plasmid DNA topoisomers.

PubMed

Mahut, Marek; Lindner, Wolfgang; Lämmerhofer, Michael

2012-01-18

We recently discovered the molecular recognition capability of a quinine carbamate ligand attached to silica as a powerful chemoaffinity material for the chromatographic separation of circular plasmid topoisomers of different linking numbers. In this paper we develop structure-selectivity relationship studies to figure out the essential structural features for topoisomer recognition. By varying different moieties of the original cinchonan-derived selector, it was shown that intercalation by the quinoline moiety of the ligand as assumed initially as the working hypothesis is not an essential feature for topoisomer recognition during chromatography. We found that the key elements for topoisomer selectivity are the presence of a rigid weak anion-exchange site and a H-donor site separated from each other in a defined distance by a 4-atom spacer. Additionally, incorporation of the weak anion-exchange site into a cyclic ring structure provides greater rigidity of the ligand molecule and turned out to be advantageous, if not mandatory, for (close to) baseline separation. © 2011 American Chemical Society

Synthesis, activity and pharmacophore development for isatin-β-thiosemicarbazones with selective activity towards multidrug resistant cellsa

PubMed Central

Hall, Matthew D.; Salam, Noeris K.; Hellawell, Jennifer L.; Fales, Henry M.; Kensler, Caroline B.; Ludwig, Joseph A.; Szakacs, Gergely; Hibbs, David E.; Gottesman, Michael M.

2009-01-01

We have recently identified a new class of compounds that selectively kill cells that express P-glycoprotein (P-gp, MDR1), the ATPase efflux pump that confers multidrug resistance on cancer cells. Several isatin-β-thiosemicarbazones from our initial study have been validated, and a range of analogs synthesized and tested. A number demonstrated improved MDR1-selective activity over the lead, NSC73306 (1). Pharmacophores for cytotoxicity and MDR1-selectivity were generated to delineate the structural features required for activity. The MDR1-selective pharmacophore highlights the importance of aromatic/hydrophobic features at the N4 position of the thiosemicarbazone, and the reliance on the isatin moiety as key bioisosteric contributors. Additionally, a quantitative structure-activity relationship (QSAR) model that yielded a cross-validated correlation coefficient of 0.85 effectively predicts the cytotoxicty of untested thiosemicarbazones. Together, the models serve as effective approaches for predicting structures with MDR1-selective activity, and aid in directing the search for the mechanism of action of 1. PMID:19397322

Color is processed less efficiently than orientation in change detection but more efficiently in visual search.

PubMed

Huang, Liqiang

2015-05-01

Basic visual features (e.g., color, orientation) are assumed to be processed in the same general way across different visual tasks. Here, a significant deviation from this assumption was predicted on the basis of the analysis of stimulus spatial structure, as characterized by the Boolean-map notion. If a task requires memorizing the orientations of a set of bars, then the map consisting of those bars can be readily used to hold the overall structure in memory and will thus be especially useful. If the task requires visual search for a target, then the map, which contains only an overall structure, will be of little use. Supporting these predictions, the present study demonstrated that in comparison to stimulus colors, bar orientations were processed more efficiently in change-detection tasks but less efficiently in visual search tasks (Cohen's d = 4.24). In addition to offering support for the role of the Boolean map in conscious access, the present work also throws doubts on the generality of processing visual features. © The Author(s) 2015.

Structural features of soluble cereal arabinoxylan fibers associated with a slow rate of in vitro fermentation by human fecal microbiota.

PubMed

Rumpagaporn, Pinthip; Reuhs, Brad L; Kaur, Amandeep; Patterson, John A; Keshavarzian, Ali; Hamaker, Bruce R

2015-10-05

Most soluble dietary fibers ferment rapidly in the proximal colon, potentially causing discomfort and poor tolerability. Alkali-extracted arabinoxylan isolates from corn, wheat, rice and sorghum brans were prepared, through hydrolysis (except sorghum) and ethanol fractionation, to have a broad range of initial fermentation rates, and their linkage patterns were determined to understand structural aspects related to slow fermentation rate. They were all highly branched polymers with degree of substitution greater than 64%. There was no relationship of molecular mass, arabinose:xylose ratio, or degree of substitution to fermentation rate patterns. Slow fermenting wheat and corn arabinoxylans had much higher amount of terminal xylose in branches than fast fermenting rice and sorghum arabinoxylans. The slowest fermenting wheat arabinoxylan additionally contained a complex trisaccharide side chain with two arabinoses linked at the O-2 and O-3 positions of an arabinose that is O-2 linked to the xylan backbone. Structural features were proposed for tolerable slowly fermentable arabinoxylan with possible beneficial fermentation function into the distal colon. Copyright © 2015 Elsevier Ltd. All rights reserved.

Asymmetric Michael Addition Mediated by Chiral Ionic Liquids

PubMed Central

Suzuki, Yumiko

2018-01-01

Chiral ionic liquids with a focus on their applications in asymmetric Michael additions and related reactions were reviewed. The examples were classified on the basis of the mode of asymmetric induction (e.g., external induction/non-covalent interaction or internal induction/covalent bond formation), the roles in reactions (as a solvent or catalyst), and their structural features (e.g., imidazolium-based chiral cations, other chiral oniums; proline derivatives). Most of the reactions with high chiral induction are Michael addition of ketones or aldehydes to chalcones or nitrostyrenes where proline-derived chiral ionic liquids catalyze the reaction through enamine/ iminium formation. Many reports demonstrate the recyclability of ionic liquid-tagged pyrrolidines. PMID:29861702

Search for low-latitude atmospheric hydrocarbon variations on Jupiter from Juno-UVS measurements

NASA Astrophysics Data System (ADS)

Hue, V.; Gladstone, R.; Greathouse, T.; Versteeg, M.; Davis, M. W.; Gerard, J. C. M. C.; Grodent, D. C.; Bonfond, B.; Bolton, S. J.; Levin, S.; Connerney, J. E. P.

2016-12-01

The Juno mission offers the opportunity to study Jupiter, from its inner structure, up to its magnetospheric environment. Juno was launched on August 2011 and its Jupiter orbit insertion (JOI) occurred on July 4th 2016. The nominal Juno mission involves 35 science polar-orbits of 14-days period, with perijove and apojove distances located at 0.06 Rj and 45 Rj, respectively. Juno-UVS is a UV spectrograph with a bandpass of 70<λ<205 nm, designed to characterize Jupiter UV emissions. One of the main additions of UVS compared to its predecessors (New Horizons- and Rosetta- Alice, LRO-LAMP) is a 2.54 mm tantalum shielding, to protect it from the harsh radiation environment at Jupiter, and a scan mirror, to allow for targeting specific auroral and atmospheric features at +/- 30° perpendicular to the Juno spin plane. It will provide new constraints on Jupiter's auroral morphology, spectral features, and vertical structure, while providing remote-sensing constraints for the onboard waves and particle instruments. It will also be used to probe upper-atmospheric composition through absorption features found in the UV spectra using reflected solar UV radiation. For example, stratospheric hydrocarbons such as C2H2 and C2H6 are known to absorb significantly in the 150-180 nm regions, and these absorption features can be used to determine their abundances. We will present our search for the spectroscopic features seen in Jupiter's reflected sunlight during the first perijove.

GaN-based light emitting diodes using p-type trench structure for improving internal quantum efficiency

NASA Astrophysics Data System (ADS)

Kim, Garam; Sun, Min-Chul; Kim, Jang Hyun; Park, Euyhwan; Park, Byung-Gook

2017-01-01

In order to improve the internal quantum efficiency of GaN-based LEDs, a LED structure featuring a p-type trench in the multi-quantum well (MQW) is proposed. This structure has effects on spreading holes into the MQW and reducing the quantum-confined stark effect (QCSE). In addition, two simple fabrication methods using electron-beam (e-beam) lithography or selective wet etching for manufacturing the p-type structure are also proposed. From the measurement results of the manufactured GaN-based LEDs, it is confirmed that the proposed structure using e-beam lithography or selective wet etching shows improved light output power compared to the conventional structure because of more uniform hole distribution. It is also confirmed that the proposed structure formed by e-beam lithography has a significant effect on strain relaxation and reduction in the QCSE from the electro-luminescence measurement.

A Method for WD40 Repeat Detection and Secondary Structure Prediction

PubMed Central

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

2013-01-01

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

Moving beyond Watson-Crick models of coarse grained DNA dynamics.

PubMed

Linak, Margaret C; Tourdot, Richard; Dorfman, Kevin D

2011-11-28

DNA produces a wide range of structures in addition to the canonical B-form of double-stranded DNA. Some of these structures are stabilized by Hoogsteen bonds. We developed an experimentally parameterized, coarse-grained model that incorporates such bonds. The model reproduces many of the microscopic features of double-stranded DNA and captures the experimental melting curves for a number of short DNA hairpins, even when the open state forms complicated secondary structures. We demonstrate the utility of the model by simulating the folding of a thrombin aptamer, which contains G-quartets, and strand invasion during triplex formation. Our results highlight the importance of including Hoogsteen bonding in coarse-grained models of DNA.

Intermolecular hydrogen bonded and self-assembled β-pleated sheet structures of β-sulfidocarbonyls

NASA Astrophysics Data System (ADS)

Hussain, Sahid; Das, Gopal; Chaudhuri, Mihir K.

2007-06-01

The three crystal structures of β-sulfidocarbonyls 1, 2 and 3 synthesized from the reaction of acryl amide with cystiene, 1,2-dithiol and 1,3-dithiols, respectively, in water catalyzed by borax, have been determined at 273 K. The characteristic features of the structures are self-assembly through intermolecular hydrogen bonding leading to infinite chains of molecules in one direction, in addition to the stacking of layers of such molecular chains in the perpendicular direction ultimately giving rise to β-pleated sheets of 3D molecular network involving N-H⋯O, C-H⋯O and C-H⋯S bonding in the crystal lattice.

The structural analysis of the mitochondrial SSUrRNA implies a close phylogenetic relationship between mitochondria from plants and from the heterotrophic alga Prototheca wickerhamii.

PubMed

Wolff, G; Kück, U

1990-04-01

The gene for the mitochondrial small subunit rRNA (SSUrRNA) from the heterotrophic alga Prototheca wickerhamii has been isolated from a gene library of extranuclear DNA. Sequence and structural analyses allow the determination of a secondary structure model for this rRNA. In addition, several sequence motifs are present which are typically found in SSUrRNAs of various mitochondrial origins. Unexpectedly, the Prototheca RNA sequence has more features in common with mitochondrial SSUrRNAs from plants than with that from the green alga Chlamydomonas reinhardtii. The phylogenetic relationship between mitochondria from plants and algae is discussed.

Primary acoustic signal structure during free falling drop collision with a water surface

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

Chashechkin, Yu. D., E-mail: chakin@ipmnet.ru; Prokhorov, V. E., E-mail: prohorov@ipmnet.ru

2016-04-15

Consistent optical and acoustic techniques have been used to study the structure of hydrodynamic disturbances and acoustic signals generated as a free falling drop penetrates water. The relationship between the structures of hydrodynamic and acoustic perturbations arising as a result of a falling drop contacting with the water surface and subsequent immersion into water is traced. The primary acoustic signal is characterized, in addition to stably reproduced features (steep leading edge followed by long decay with local pressure maxima), by irregular high-frequency packets, which are studied for the first time. Reproducible experimental data are used to recognize constant and variablemore » components of the primary acoustic signal.« less

Learning about the internal structure of categories through classification and feature inference.

PubMed

Jee, Benjamin D; Wiley, Jennifer

2014-01-01

Previous research on category learning has found that classification tasks produce representations that are skewed toward diagnostic feature dimensions, whereas feature inference tasks lead to richer representations of within-category structure. Yet, prior studies often measure category knowledge through tasks that involve identifying only the typical features of a category. This neglects an important aspect of a category's internal structure: how typical and atypical features are distributed within a category. The present experiments tested the hypothesis that inference learning results in richer knowledge of internal category structure than classification learning. We introduced several new measures to probe learners' representations of within-category structure. Experiment 1 found that participants in the inference condition learned and used a wider range of feature dimensions than classification learners. Classification learners, however, were more sensitive to the presence of atypical features within categories. Experiment 2 provided converging evidence that classification learners were more likely to incorporate atypical features into their representations. Inference learners were less likely to encode atypical category features, even in a "partial inference" condition that focused learners' attention on the feature dimensions relevant to classification. Overall, these results are contrary to the hypothesis that inference learning produces superior knowledge of within-category structure. Although inference learning promoted representations that included a broad range of category-typical features, classification learning promoted greater sensitivity to the distribution of typical and atypical features within categories.

Structural MRI-based detection of Alzheimer's disease using feature ranking and classification error.

PubMed

Beheshti, Iman; Demirel, Hasan; Farokhian, Farnaz; Yang, Chunlan; Matsuda, Hiroshi

2016-12-01

This paper presents an automatic computer-aided diagnosis (CAD) system based on feature ranking for detection of Alzheimer's disease (AD) using structural magnetic resonance imaging (sMRI) data. The proposed CAD system is composed of four systematic stages. First, global and local differences in the gray matter (GM) of AD patients compared to the GM of healthy controls (HCs) are analyzed using a voxel-based morphometry technique. The aim is to identify significant local differences in the volume of GM as volumes of interests (VOIs). Second, the voxel intensity values of the VOIs are extracted as raw features. Third, the raw features are ranked using a seven-feature ranking method, namely, statistical dependency (SD), mutual information (MI), information gain (IG), Pearson's correlation coefficient (PCC), t-test score (TS), Fisher's criterion (FC), and the Gini index (GI). The features with higher scores are more discriminative. To determine the number of top features, the estimated classification error based on training set made up of the AD and HC groups is calculated, with the vector size that minimized this error selected as the top discriminative feature. Fourth, the classification is performed using a support vector machine (SVM). In addition, a data fusion approach among feature ranking methods is introduced to improve the classification performance. The proposed method is evaluated using a data-set from ADNI (130 AD and 130 HC) with 10-fold cross-validation. The classification accuracy of the proposed automatic system for the diagnosis of AD is up to 92.48% using the sMRI data. An automatic CAD system for the classification of AD based on feature-ranking method and classification errors is proposed. In this regard, seven-feature ranking methods (i.e., SD, MI, IG, PCC, TS, FC, and GI) are evaluated. The optimal size of top discriminative features is determined by the classification error estimation in the training phase. The experimental results indicate that the performance of the proposed system is comparative to that of state-of-the-art classification models. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Practical otic anatomy and physiology of the dog and cat.

PubMed

Njaa, Bradley L; Cole, Lynette K; Tabacca, Natalie

2012-11-01

Knowledge of the normal structure and function of the canine and feline ear is critical to be able to diagnose abnormalities that either involve the ear or originate within one or more of the ear compartments. In addition, a veterinarian must be aware of various structures within or associated with the ear so that they are not damaged or destroyed while treating an animal with otic disease. This article provides a brief discussion of the various anatomic features of the ear and normal physiology of portions of the ear. Copyright © 2012 Elsevier Inc. All rights reserved.

Spectral confocal reflection microscopy using a white light source

NASA Astrophysics Data System (ADS)

Booth, M.; Juškaitis, R.; Wilson, T.

2008-08-01

We present a reflection confocal microscope incorporating a white light supercontinuum source and spectral detection. The microscope provides images resolved spatially in three-dimensions, in addition to spectral resolution covering the wavelength range 450-650nm. Images and reflection spectra of artificial and natural specimens are presented, showing features that are not normally revealed in conventional microscopes or confocal microscopes using discrete line lasers. The specimens include thin film structures on semiconductor chips, iridescent structures in Papilio blumei butterfly scales, nacre from abalone shells and opal gemstones. Quantitative size and refractive index measurements of transparent beads are derived from spectral interference bands.

A Cost-Effective Energy-Recovering Sustain Driving Circuit for ac Plasma Display Panels

NASA Astrophysics Data System (ADS)

Lim, Jae Kwang; Tae, Heung-Sik; Choi, Byungcho; Kim, Seok Gi

A new sustain driving circuit, featuring an energy-recovering function with simple structure and minimal component count, is proposed as a cost-effective solution for driving plasma display panels during the sustaining period. Compared with existing solutions, the proposed circuit reduces the number of semiconductor switches and reactive circuit components without compromising the circuit performance and gas-discharging characteristics. In addition, the proposed circuit utilizes the harness wire as an inductive circuit component, thereby further simplifying the circuit structure. The performance of the proposed circuit is confirmed with a 42-inch plasma display panel.

New emission features in the 11-13 micron region and their relationship to polycyclic aromatic hydrocarbons

NASA Technical Reports Server (NTRS)

Witteborn, F. C.; Sandford, S. A.; Bregman, J. D.; Allamandola, L. J.; Cohen, M.; Wooden, D. H.; Graps, A. L.

1989-01-01

Moderate-resolution spectra of NGC 7027, HD 44179, IRAS 2182+5050, and BD +30 deg 3639 are presented, showing that the 11.3-micron feature actually peaks at 11.22 microns. Evidence is found for new emission features near 11.9 and 12.7 microns, supporting an origin from PAHs. Also, the observed asymmetry of the 11.3-micron band is consistent with the anharmonicity expected in the C-H out-of-plane bending mode in PAHs. The analysis of the 11-13-micron emission suggests that the molecular structures of the most intensely emitting free PAHs vary between the high-excitation environment in NGC 7027 and the low-excitation but high-flux environment close to HD 44179. In addition, a series of regularly spaced features between 10 and 11 microns is detected in the spectrum of HD 44179, suggesting that a simple polyatomic hydride is present in the object's gas phase.

Evaluating a variety of text-mined features for automatic protein function prediction with GOstruct.

PubMed

Funk, Christopher S; Kahanda, Indika; Ben-Hur, Asa; Verspoor, Karin M

2015-01-01

Most computational methods that predict protein function do not take advantage of the large amount of information contained in the biomedical literature. In this work we evaluate both ontology term co-mention and bag-of-words features mined from the biomedical literature and analyze their impact in the context of a structured output support vector machine model, GOstruct. We find that even simple literature based features are useful for predicting human protein function (F-max: Molecular Function =0.408, Biological Process =0.461, Cellular Component =0.608). One advantage of using literature features is their ability to offer easy verification of automated predictions. We find through manual inspection of misclassifications that some false positive predictions could be biologically valid predictions based upon support extracted from the literature. Additionally, we present a "medium-throughput" pipeline that was used to annotate a large subset of co-mentions; we suggest that this strategy could help to speed up the rate at which proteins are curated.

Long-lived volcanism within Argyre basin, Mars

NASA Astrophysics Data System (ADS)

Williams, Jean-Pierre; Dohm, James M.; Soare, Richard J.; Flahaut, Jessica; Lopes, Rosaly M. C.; Pathare, Asmin V.; Fairén, Alberto G.; Schulze-Makuch, Dirk; Buczkowski, Debra L.

2017-09-01

The Argyre basin, one of the largest impact structures on Mars with a diameter >1200 km, formed in the Early Noachian ∼3.93 Ga. The basin has collected volatiles and other material through time, and experienced partial infilling with water evident from stratigraphic sequences, crater statistics, topography, and geomorphology. Although volcanism has not been previously associated with the Argyre basin, our study of the northwest portion of the basin floor has revealed landforms suggesting volcanic and tectonic activity occurred including Argyre Mons, a ∼50 km wide volcanic-structure formed ∼3 Ga. Giant polygons with a similar surface age are also identified on terrain adjacent to the base of Argyre Mons, indicating the structure may have formed in a water-rich environment. In addition to Argyre Mons, cones, vents, mounds, dikes, and cavi or hollows, many of which are associated with extensional tectonics, are observed in the region. Multiple features appear to disrupt icy (and largely uncratered) terrain indicating a relatively young, Late Amazonian, formation age for at least some of the volcanic and tectonic features. The discovery of Argyre Mons, along with additional endogenic modification of the basin floor, suggests that the region has experienced episodes of volcanism over a protracted period of time. This has implications for habitability as the basin floor has been a region of elevated heat flow coupled with liquid water, water ice, and accumulation of sediments of diverse provenance with ranging geochemistry, along with magma-water interactions.

Conjoined twin piglets with duplicated cranial and caudal axes.

PubMed

McManus, C A; Partlow, G D; Fisher, K R

1994-06-01

Twins with doubling of the cranial and caudal poles, yet having a single thorax, are rare. One set of diprosopus, dipygus porcine conjoined twins was studied. In addition to the conjoining anomaly, these twins also exhibited ambiguous internal reproductive features. The twins had two snouts, three eyes, a single thorax, and were duplicated from the umbilicus caudally. Radiography indicated a single vertebral column in the cervical region. The vertebral columns were separate caudally from this point. There was a total of six limbs--one pair of forelimbs and two pairs of hindlimbs. Many medial structures failed to develop in these twins. Medial cranial nerves V-XII were absent or displaced although apparently normal laterally. The medial palates were present but shortened, whereas the medial mandibular rami had folded back on themselves rostrally to form a midline mass between the two chins. Each twin had only one lateral kidney and one lateral testis. Medial scrotal sacs were present but devoid of a testis. There was a midline, "uterine"-like structure which crossed between the twins. However, histological analysis of this structure revealed it to be dysplastic testicular tissue. The relationship between the abnormal reproductive features in these twins and the conjoining is unclear. The anatomy of these twins, in addition to the literature reviewed, illustrates the internal anatomical heterogeneity of grossly similar conjoined twins. A review of the literature also suggests that conjoined twinning may be more common in swine than was previously suspected.

Prediction of beta-turns and beta-turn types by a novel bidirectional Elman-type recurrent neural network with multiple output layers (MOLEBRNN).

PubMed

Kirschner, Andreas; Frishman, Dmitrij

2008-10-01

Prediction of beta-turns from amino acid sequences has long been recognized as an important problem in structural bioinformatics due to their frequent occurrence as well as their structural and functional significance. Because various structural features of proteins are intercorrelated, secondary structure information has been often employed as an additional input for machine learning algorithms while predicting beta-turns. Here we present a novel bidirectional Elman-type recurrent neural network with multiple output layers (MOLEBRNN) capable of predicting multiple mutually dependent structural motifs and demonstrate its efficiency in recognizing three aspects of protein structure: beta-turns, beta-turn types, and secondary structure. The advantage of our method compared to other predictors is that it does not require any external input except for sequence profiles because interdependencies between different structural features are taken into account implicitly during the learning process. In a sevenfold cross-validation experiment on a standard test dataset our method exhibits the total prediction accuracy of 77.9% and the Mathew's Correlation Coefficient of 0.45, the highest performance reported so far. It also outperforms other known methods in delineating individual turn types. We demonstrate how simultaneous prediction of multiple targets influences prediction performance on single targets. The MOLEBRNN presented here is a generic method applicable in a variety of research fields where multiple mutually depending target classes need to be predicted. http://webclu.bio.wzw.tum.de/predator-web/.

Modeling the dynamic crush of impact mitigating materials

NASA Astrophysics Data System (ADS)

Logan, R. W.; McMichael, L. D.

1995-05-01

Crushable materials are commonly utilized in the design of structural components to absorb energy and mitigate shock during the dynamic impact of a complex structure, such as an automobile chassis or drum-type shipping container. The development and application of several finite-element material models which have been developed at various times at LLNL for DYNA3D are discussed. Between the models, they are able to account for several of the predominant mechanisms which typically influence the dynamic mechanical behavior of crushable materials. One issue we addressed was that no single existing model would account for the entire gambit of constitutive features which are important for crushable materials. Thus, we describe the implementation and use of an additional material model which attempts to provide a more comprehensive model of the mechanics of crushable material behavior. This model combines features of the pre-existing DYNA models and incorporates some new features as well in an invariant large-strain formulation. In addition to examining the behavior of a unit cell in uniaxial compression, two cases were chosen to evaluate the capabilities and accuracy of the various material models in DYNA. In the first case, a model for foam filled box beams was developed and compared to test data from a four-point bend test. The model was subsequently used to study its effectiveness in energy absorption in an aluminum extrusion, spaceframe, vehicle chassis. The second case examined the response of the AT-400A shipping container and the performance of the overpack material during accident environments selected from 10CFR71 and IAEA regulations.

MULTI-WAVELENGTH POLARIMETRY AND SPECTRAL STUDY OF THE M87 JET DURING 2002–2008

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

Avachat, Sayali S.; Perlman, Eric S.; Adams, Steven C.

We present a multi-wavelength polarimetric and spectral study of the M87 jet obtained at sub-arcsecond resolution between 2002 and 2008. The observations include multi-band archival VLA polarimetry data sets along with Hubble Space Telescope ( HST ) imaging polarimetry. These observations have better angular resolution than previous work by factors of 2–3 and in addition, allow us to explore the time domain. These observations envelop the huge flare in HST-1 located 0.″86 from the nucleus. The increased resolution enables us to view more structure in each knot, showing several resolved sub-components. We also see apparent helical structure in the polarizationmore » vectors in several knots, with polarization vectors turning either clockwise or counterclockwise near the flux maxima in various places as well as showing filamentary undulations. Some of these characteristics are correlated with flux and polarization maxima while others are not. We also examine the total flux and fractional polarization and look for changes in both radio and optical since the observations of Perlman et al. (1999) and test them against various models based on shocks and instabilities in the jet. Our results are broadly consistent with previous spine-sheath models and recollimation shock models; however, they require additional combinations of features to explain the observed complexity, e.g., shearing of magnetic field lines near the jet surface and compression of the toroidal component near shocks. In particular, in many regions we find apparently helical features both in total flux and polarization. We discuss the physical interpretation of these features.« less

Morphology of basal cell carcinoma in high definition optical coherence tomography: en-face and slice imaging mode, and comparison with histology.

PubMed

Maier, T; Braun-Falco, M; Hinz, T; Schmid-Wendtner, M H; Ruzicka, T; Berking, C

2013-01-01

Optical coherence tomography (OCT) allows real-time, in vivo examination of basal cell carcinoma (BCC). A new high definition OCT with high lateral and axial resolution in a horizontal (en-face) and vertical (slice) imaging mode offers additional information in the diagnosis of BCC and may potentially replace invasive diagnostic biopsies. To define the characteristic morphologic features of BCC by using high definition optical coherence tomography (HD-OCT) compared to conventional histology. A total of 22 BCCs were examined preoperatively by HD-OCT in the en-face and slice imaging mode and characteristic features were evaluated in comparison to the histopathological findings. The following features were found in the en-face mode of HD-OCT: lobulated nodules (20/22), peripheral rimming (17/22), epidermal disarray (21/22), dilated vessels (11/22) and variably refractile stroma (19/22). In the slice imaging mode the following characteristics were found: grey/dark oval structures (18/22), peripheral rimming (13/22), destruction of layering (22/22), dilated vessels (7/22) and peritumoural bright stroma (11/22). In the en-face mode the lobulated structure of the BCC was more distinct than in the slice mode compared to histology. HD-OCT with a horizontal and vertical imaging mode offers additional information in the diagnosis of BCC compared to conventional OCT imaging and enhances the feasibility of non-invasive diagnostics of BCC. © 2012 The Authors. Journal of the European Academy of Dermatology and Venereology © 2012 European Academy of Dermatology and Venereology.

Strike-Slip Faulting Processes on Ganymede: Global Morphological Mapping and Structural Interpretation of Grooved and Transitional Terrains

NASA Astrophysics Data System (ADS)

Burkhard, L. M.; Cameron, M. E.; Smith-Konter, B. R.; Seifert, F.; Pappalardo, R. T.; Collins, G. C.

2015-12-01

Ganymede's fractured surface reveals many large-scale, morphologically distinct regions of inferred distributed shear and strike-slip faulting that may be important to the structural development of its surface and in the transition from dark to light (grooved) materials. To better understand the role of strike-slip tectonism in shaping Ganymede's complex icy surface, we perform a detailed mapping of key examples of strike-slip morphologies (i.e., en echelon structures, strike-slip duplexes, laterally offset pre-existing features, and possible strained craters) from Galileo and Voyager images. We focus on complex structures associated with grooved terrain (e.g. Nun Sulcus, Dardanus Sulcus, Tiamat Sulcus, and Arbela Sulcus) and terrains transitional from dark to light terrain (e.g. the boundary between Nippur Sulcus and Marius Regio, including Byblus Sulcus and Philus Sulcus). Detailed structural interpretations suggest strong evidence of strike-slip faulting in some regions (i.e., Nun and Dardanus Sulcus); however, further investigation of additional strike-slip structures is required of less convincing regions (i.e., Byblus Sulcus). Where applicable, these results are synthesized into a global database representing an inferred sense of shear for many of Ganymede's fractures. Moreover, when combined with existing observations of extensional features, these results help to narrow down the range of possible principal stress directions that could have acted at the regional or global scale to produce grooved terrain on Ganymede.

Effects of dynamic text in an AAC app on sight word reading for individuals with autism spectrum disorder.

PubMed

Caron, Jessica; Light, Janice; Holyfield, Christine; McNaughton, David

2018-06-01

The purpose of this study was to investigate the effects of Transition to Literacy (T2L) software features (i.e., dynamic text and speech output upon selection of a graphic symbol) within a grid display in an augmentative and alternative communication (AAC) app, on the sight word reading skills of individuals with autism spectrum disorders (ASD) and complex communication needs. The study implemented a single-subject multiple probe research design across one set of three participants. The same design was utilized with an additional set of two participants. As part of the intervention, the participants were exposed to an AAC app with the T2L features during a highly structured matching task. With only limited exposure to the features, the five participants all demonstrated increased accuracy of identification of 12 targeted sight words. This study provides preliminary evidence that redesigning AAC apps to include the provision of dynamic text combined with speech output, can positively impact the sight-word reading of participants during a structured task. This adaptation in AAC system design could be used to complement literacy instruction and to potentially infuse components of literacy learning into daily communication.

Sex differences in face gender recognition: an event-related potential study.

PubMed

Sun, Yueting; Gao, Xiaochao; Han, Shihui

2010-04-23

Multiple level neurocognitive processes are involved in face processing in humans. The present study examined whether the early face processing such as structural encoding is modulated by task demands that manipulate attention to perceptual or social features of faces and such an effect, if any, is different between men and women. Event-related brain potentials were recorded from male and female adults while they identified a low-level perceptual feature of faces (i.e., face orientation) and a high-level social feature of faces (i.e., gender). We found that task demands that required the processing of face orientations or face gender resulted in modulations of both the early occipital/temporal negativity (N170) and the late central/parietal positivity (P3). The N170 amplitude was smaller in the gender relative to the orientation identification task whereas the P3 amplitude was larger in the gender identification task relative to the orientation identification task. In addition, these effects were much stronger in women than in men. Our findings suggest that attention to social information in faces such as gender modulates both the early encoding of facial structures and late evaluative process of faces to a greater degree in women than in men.

Chinese character recognition based on Gabor feature extraction and CNN

NASA Astrophysics Data System (ADS)

Xiong, Yudian; Lu, Tongwei; Jiang, Yongyuan

2018-03-01

As an important application in the field of text line recognition and office automation, Chinese character recognition has become an important subject of pattern recognition. However, due to the large number of Chinese characters and the complexity of its structure, there is a great difficulty in the Chinese character recognition. In order to solve this problem, this paper proposes a method of printed Chinese character recognition based on Gabor feature extraction and Convolution Neural Network(CNN). The main steps are preprocessing, feature extraction, training classification. First, the gray-scale Chinese character image is binarized and normalized to reduce the redundancy of the image data. Second, each image is convoluted with Gabor filter with different orientations, and the feature map of the eight orientations of Chinese characters is extracted. Third, the feature map through Gabor filters and the original image are convoluted with learning kernels, and the results of the convolution is the input of pooling layer. Finally, the feature vector is used to classify and recognition. In addition, the generalization capacity of the network is improved by Dropout technology. The experimental results show that this method can effectively extract the characteristics of Chinese characters and recognize Chinese characters.

Neuromuscular disease classification system

NASA Astrophysics Data System (ADS)

Sáez, Aurora; Acha, Begoña; Montero-Sánchez, Adoración; Rivas, Eloy; Escudero, Luis M.; Serrano, Carmen

2013-06-01

Diagnosis of neuromuscular diseases is based on subjective visual assessment of biopsies from patients by the pathologist specialist. A system for objective analysis and classification of muscular dystrophies and neurogenic atrophies through muscle biopsy images of fluorescence microscopy is presented. The procedure starts with an accurate segmentation of the muscle fibers using mathematical morphology and a watershed transform. A feature extraction step is carried out in two parts: 24 features that pathologists take into account to diagnose the diseases and 58 structural features that the human eye cannot see, based on the assumption that the biopsy is considered as a graph, where the nodes are represented by each fiber, and two nodes are connected if two fibers are adjacent. A feature selection using sequential forward selection and sequential backward selection methods, a classification using a Fuzzy ARTMAP neural network, and a study of grading the severity are performed on these two sets of features. A database consisting of 91 images was used: 71 images for the training step and 20 as the test. A classification error of 0% was obtained. It is concluded that the addition of features undetectable by the human visual inspection improves the categorization of atrophic patterns.

Disordered amorphous calcium carbonate from direct precipitation

DOE PAGES

Farhadi Khouzani, Masoud; Chevrier, Daniel M.; Güttlein, Patricia; ...

2015-06-01

Amorphous calcium carbonate (ACC) is known to play a prominent role in biomineralization. Different studies on the structure of biogenic ACCs have illustrated that they can have distinct short-range orders. However, the origin of so-called proto-structures in synthetic and additive-free ACCs is not well understood. In the current work, ACC has been synthesised in iso-propanolic media by direct precipitation from ionic precursors, and analysed utilising a range of different techniques. The data suggest that this additive-free type of ACC does not resemble clear proto-structural motifs relating to any crystalline polymorph. This can be explained by the undefined pH value inmore » iso-propanolic media, and the virtually instantaneous precipitation. Altogether, this work suggests that aqueous systems and pathways involving pre-nucleation clusters are required for the generation of clear proto-structural features in ACC. Experiments on the ACC-to-crystalline transformation in solution with and without ethanol highlight that polymorph selection is under kinetic control, while the presence of ethanol can control dissolution re-crystallisation pathways.« less

Evidence of ion intercalation mediated band structure modification and opto-ionic coupling in lithium niobite

NASA Astrophysics Data System (ADS)

Shank, Joshua C.; Tellekamp, M. Brooks; Doolittle, W. Alan

2015-01-01

The theoretically suggested band structure of the novel p-type semiconductor lithium niobite (LiNbO2), the direct coupling of photons to ion motion, and optically induced band structure modifications are investigated by temperature dependent photoluminescence. LiNbO2 has previously been used as a memristor material but is shown here to be useful as a sensor owing to the electrical, optical, and chemical ease of lithium removal and insertion. Despite the high concentration of vacancies present in lithium niobite due to the intentional removal of lithium atoms, strong photoluminescence spectra are observed even at room temperature that experimentally confirm the suggested band structure implying transitions from a flat conduction band to a degenerate valence band. Removal of small amounts of lithium significantly modifies the photoluminescence spectra including additional larger than stoichiometric-band gap features. Sufficient removal of lithium results in the elimination of the photoluminescence response supporting the predicted transition from a direct to indirect band gap semiconductor. In addition, non-thermal coupling between the incident laser and lithium ions is observed and results in modulation of the electrical impedance.

Genetic and Biochemical Map for the Biosynthesis of Occidiofungin, an Antifungal Produced by Burkholderia contaminans Strain MS14 ▿†

PubMed Central

Gu, Ganyu; Smith, Leif; Liu, Aixin; Lu, Shi-En

2011-01-01

A striking feature of Burkholderia contaminans strain MS14 is the production of a glycolipopeptide named occidiofungin. Occidiofungin has a broad range of antifungal activities against plant and animal pathogens. In this study, a complete covalent structure characterization and identification of the whole genomic DNA region for the occidiofungin gene (ocf) cluster are described. Discovery of the presence of 2,4-diaminobutyric acid and 3-chloro-β-hydroxytyrosine and elucidation of the structure of a novel C18 fatty amino acid residue have been achieved. In addition, seven additional putative open reading frames (the genes from ocfI to ocfN [ocfI-N] and ORF16) were identified. Transcription of all the putative genes ocfI-N identified in the region except ORF16 was regulated by both ambR1 and ambR2. Elucidation of the structure and the ocf gene cluster provides insight into the biosynthesis of occidiofungin and promotes future aims at understanding the biosynthetic machinery. This work provides new avenues for optimizing the production and synthesis of structural analogs of occidiofungin. PMID:21742901

Glycosyltransferases A and B: Four Critical Amino Acids Determine Blood Type

NASA Astrophysics Data System (ADS)

Rose, Natisha L.; Palcic, Monica M.; Evans, Stephen V.

2005-12-01

Human A, B, and O blood type is determined by the presence or absence of distinct carbohydrate structures on red blood cells. Type O individuals have α-fucose(1→2)galactose disaccharides [O(H) structures] on their cell surfaces while in type A or B individuals, the O antigen is capped by the addition of an α- N -acetylgalactosamine or α-galactose residue, respectively. The addition of these monosaccharides is catalyzed by glycosyltransferase A (GTA) or glycosyltransferase B (GTB). These are homologous enzymes differing by only 4 amino acids out of 354 that change the specificity from GTA to GTB. In this review the chemistry of the blood group ABO system and the role of GTA, GTB, and the four critical amino acids in determining blood group status are discussed. See JCE Featured Molecules .

Naval Research Reviews. Volume XXXIII. Number 2,

DTIC Science & Technology

1981-01-01

and filler metal addition. ratio weld is a characteristic of a keyhole -produced The most distinctive feature of LB welding , weld . T /h III laser Ii...evolved from these radiation for precision operation, such as hole-drill- efforts include a 3kW CO. laser /workstation system ing, trimming, and welding ...asso- Laser Surface Modifications ciated with thick-section welding of naval structure and surface modification for improved corrosion and The high

Amino-Acid Network Clique Analysis of Protein Mutation Non-Additive Effects: A Case Study of Lysozme.

PubMed

Ming, Dengming; Chen, Rui; Huang, He

2018-05-10

Optimizing amino-acid mutations in enzyme design has been a very challenging task in modern bio-industrial applications. It is well known that many successful designs often hinge on extensive correlations among mutations at different sites within the enzyme, however, the underpinning mechanism for these correlations is far from clear. Here, we present a topology-based model to quantitively characterize non-additive effects between mutations. The method is based on the molecular dynamic simulations and the amino-acid network clique analysis. It examines if the two mutation sites of a double-site mutation fall into to a 3-clique structure, and associates such topological property of mutational site spatial distribution with mutation additivity features. We analyzed 13 dual mutations of T4 phage lysozyme and found that the clique-based model successfully distinguishes highly correlated or non-additive double-site mutations from those additive ones whose component mutations have less correlation. We also applied the model to protein Eglin c whose structural topology is significantly different from that of T4 phage lysozyme, and found that the model can, to some extension, still identify non-additive mutations from additive ones. Our calculations showed that mutation non-additive effects may heavily depend on a structural topology relationship between mutation sites, which can be quantitatively determined using amino-acid network k -cliques. We also showed that double-site mutation correlations can be significantly altered by exerting a third mutation, indicating that more detailed physicochemical interactions should be considered along with the network clique-based model for better understanding of this elusive mutation-correlation principle.

* Fabrication and Characterization of Biphasic Silk Fibroin Scaffolds for Tendon/Ligament-to-Bone Tissue Engineering.

PubMed

Font Tellado, Sònia; Bonani, Walter; Balmayor, Elizabeth R; Foehr, Peter; Motta, Antonella; Migliaresi, Claudio; van Griensven, Martijn

2017-08-01

Tissue engineering is an attractive strategy for tendon/ligament-to-bone interface repair. The structure and extracellular matrix composition of the interface are complex and allow for a gradual mechanical stress transfer between tendons/ligaments and bone. Thus, scaffolds mimicking the structural features of the native interface may be able to better support functional tissue regeneration. In this study, we fabricated biphasic silk fibroin scaffolds designed to mimic the gradient in collagen molecule alignment present at the interface. The scaffolds had two different pore alignments: anisotropic at the tendon/ligament side and isotropic at the bone side. Total porosity ranged from 50% to 80% and the majority of pores (80-90%) were <100-300 μm. Young's modulus varied from 689 to 1322 kPa depending on the type of construct. In addition, human adipose-derived mesenchymal stem cells were cultured on the scaffolds to evaluate the effect of pore morphology on cell proliferation and gene expression. Biphasic scaffolds supported cell attachment and influenced cytoskeleton organization depending on pore alignment. In addition, the gene expression of tendon/ligament, enthesis, and cartilage markers significantly changed depending on pore alignment in each region of the scaffolds. In conclusion, the biphasic scaffolds fabricated in this study show promising features for tendon/ligament-to-bone tissue engineering.

Synthesis, biological evaluation, and 3D QSAR study of 2-methyl-4-oxo-3-oxetanylcarbamic acid esters as N-acylethanolamine acid amidase (NAAA) inhibitors.

PubMed

Ponzano, Stefano; Berteotti, Anna; Petracca, Rita; Vitale, Romina; Mengatto, Luisa; Bandiera, Tiziano; Cavalli, Andrea; Piomelli, Daniele; Bertozzi, Fabio; Bottegoni, Giovanni

2014-12-11

N-(2-Oxo-3-oxetanyl)carbamic acid esters have recently been reported to be noncompetitive inhibitors of the N-acylethanolamine acid amidase (NAAA) potentially useful for the treatment of pain and inflammation. In the present study, we further explored the structure-activity relationships of the carbamic acid ester side chain of 2-methyl-4-oxo-3-oxetanylcarbamic acid ester derivatives. Additional favorable features in the design of potent NAAA inhibitors have been found together with the identification of a single digit nanomolar inhibitor. In addition, we devised a 3D QSAR using the atomic property field method. The model turned out to be able to account for the structural variability and was prospectively validated by designing, synthesizing, and testing novel inhibitors. The fairly good agreement between predictions and experimental potency values points to this 3D QSAR model as the first example of quantitative structure-activity relationships in the field of NAAA inhibitors.

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

Rodgers, Theron M.; Madison, Jonathan D.; Tikare, Veena

Additive manufacturing (AM) is of tremendous interest given its ability to realize complex, non-traditional geometries in engineered structural materials. But, microstructures generated from AM processes can be equally, if not more, complex than their conventionally processed counterparts. While some microstructural features observed in AM may also occur in more traditional solidification processes, the introduction of spatially and temporally mobile heat sources can result in significant microstructural heterogeneity. While grain size and shape in metal AM structures are understood to be highly dependent on both local and global temperature profiles, the exact form of this relation is not well understood. Wemore » implement an idealized molten zone and temperature-dependent grain boundary mobility in a kinetic Monte Carlo model to predict three-dimensional grain structure in additively manufactured metals. In order to demonstrate the flexibility of the model, synthetic microstructures are generated under conditions mimicking relatively diverse experimental results present in the literature. Simulated microstructures are then qualitatively and quantitatively compared to their experimental complements and are shown to be in good agreement.« less

A naturalistic study of railway controllers.

PubMed

Farrington-Darby, T; Wilson, John R; Norris, B J; Clarke, Theresa

There is an increasing prevalence for work to be analysed through naturalistic study, especially using ethnographically derived methods of enquiry and qualitative field research. The relatively unexplored domain of railway control (in comparison to signalling) in the UK is described in terms of features derived from observations and semi-structured interviews. In addition, task diagrams (a technique taken from the Applied Cognitive Task Analysis toolkit) are used to represent controllers' core elements of work, i.e. to manage events or incidents, and to identify the challenging steps in the process. The work features identified, the task diagrams, and the steps identified as challenging form a basis from which future ergonomics studies on railway controllers in the UK will be carried out.

Automatic programming of arc welding robots

NASA Astrophysics Data System (ADS)

Padmanabhan, Srikanth

Automatic programming of arc welding robots requires the geometric description of a part from a solid modeling system, expert weld process knowledge and the kinematic arrangement of the robot and positioner automatically. Current commercial solid models are incapable of storing explicitly product and process definitions of weld features. This work presents a paradigm to develop a computer-aided engineering environment that supports complete weld feature information in a solid model and to create an automatic programming system for robotic arc welding. In the first part, welding features are treated as properties or attributes of an object, features which are portions of the object surface--the topological boundary. The structure for representing the features and attributes is a graph called the Welding Attribute Graph (WAGRAPH). The method associates appropriate weld features to geometric primitives, adds welding attributes, and checks the validity of welding specifications. A systematic structure is provided to incorporate welding attributes and coordinate system information in a CSG tree. The specific implementation of this structure using a hybrid solid modeler (IDEAS) and an object-oriented programming paradigm is described. The second part provides a comprehensive methodology to acquire and represent weld process knowledge required for the proper selection of welding schedules. A methodology of knowledge acquisition using statistical methods is proposed. It is shown that these procedures did little to capture the private knowledge of experts (heuristics), but helped in determining general dependencies, and trends. A need was established for building the knowledge-based system using handbook knowledge and to allow the experts further to build the system. A methodology to check the consistency and validity for such knowledge addition is proposed. A mapping shell designed to transform the design features to application specific weld process schedules is described. A new approach using fixed path modified continuation methods is proposed in the final section to plan continuously the trajectory of weld seams in an integrated welding robot and positioner environment. The joint displacement, velocity, and acceleration histories all along the path as a function of the path parameter for the best possible welding condition are provided for the robot and the positioner to track various paths normally encountered in arc welding.

Optimizing Radiometric Processing and Feature Extraction of Drone Based Hyperspectral Frame Format Imagery for Estimation of Yield Quantity and Quality of a Grass Sward

NASA Astrophysics Data System (ADS)

Näsi, R.; Viljanen, N.; Oliveira, R.; Kaivosoja, J.; Niemeläinen, O.; Hakala, T.; Markelin, L.; Nezami, S.; Suomalainen, J.; Honkavaara, E.

2018-04-01

Light-weight 2D format hyperspectral imagers operable from unmanned aerial vehicles (UAV) have become common in various remote sensing tasks in recent years. Using these technologies, the area of interest is covered by multiple overlapping hypercubes, in other words multiview hyperspectral photogrammetric imagery, and each object point appears in many, even tens of individual hypercubes. The common practice is to calculate hyperspectral orthomosaics utilizing only the most nadir areas of the images. However, the redundancy of the data gives potential for much more versatile and thorough feature extraction. We investigated various options of extracting spectral features in the grass sward quantity evaluation task. In addition to the various sets of spectral features, we used photogrammetry-based ultra-high density point clouds to extract features describing the canopy 3D structure. Machine learning technique based on the Random Forest algorithm was used to estimate the fresh biomass. Results showed high accuracies for all investigated features sets. The estimation results using multiview data provided approximately 10 % better results than the most nadir orthophotos. The utilization of the photogrammetric 3D features improved estimation accuracy by approximately 40 % compared to approaches where only spectral features were applied. The best estimation RMSE of 239 kg/ha (6.0 %) was obtained with multiview anisotropy corrected data set and the 3D features.

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

NASA Technical Reports Server (NTRS)

Lieneweg, Udo

1988-01-01

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

Discriminant analysis of multiple cortical changes in mild cognitive impairment

NASA Astrophysics Data System (ADS)

Wu, Congling; Guo, Shengwen; Lai, Chunren; Wu, Yupeng; Zhao, Di; Jiang, Xingjun

2017-02-01

To reveal the differences in brain structures and morphological changes between the mild cognitive impairment (MCI) and the normal control (NC), analyze and predict the risk of MCI conversion. First, the baseline and 2-year longitudinal follow-up magnetic resonance (MR) images of 73 NC, 46 patients with stable MCI (sMCI) and 40 patients with converted MCI (cMCI) were selected. Second, the FreeSurfer was used to extract the cortical features, including the cortical thickness, surface area, gray matter volume and mean curvature. Third, the support vector machine-recursive feature elimination method (SVM-RFE) were adopted to determine salient features for effective discrimination. Finally, the distribution and importance of essential brain regions were described. The experimental results showed that the cortical thickness and gray matter volume exhibited prominent capability in discrimination, and surface area and mean curvature behaved relatively weak. Furthermore, the combination of different morphological features, especially the baseline combined with the longitudinal changes, can be used to evidently improve the performance of classification. In addition, brain regions with high weights predominately located in the temporal lobe and the frontal lobe, which were relative to emotional control and memory functions. It suggests that there were significant different patterns in the brain structure and changes between the compared group, which could not only be effectively applied for classification, but also be used to evaluate and predict the conversion of the patients with MCI.

Functional MRI registration with tissue-specific patch-based functional correlation tensors.

PubMed

Zhou, Yujia; Zhang, Han; Zhang, Lichi; Cao, Xiaohuan; Yang, Ru; Feng, Qianjin; Yap, Pew-Thian; Shen, Dinggang

2018-06-01

Population studies of brain function with resting-state functional magnetic resonance imaging (rs-fMRI) rely on accurate intersubject registration of functional areas. This is typically achieved through registration using high-resolution structural images with more spatial details and better tissue contrast. However, accumulating evidence has suggested that such strategy cannot align functional regions well because functional areas are not necessarily consistent with anatomical structures. To alleviate this problem, a number of registration algorithms based directly on rs-fMRI data have been developed, most of which utilize functional connectivity (FC) features for registration. However, most of these methods usually extract functional features only from the thin and highly curved cortical grey matter (GM), posing great challenges to accurate estimation of whole-brain deformation fields. In this article, we demonstrate that additional useful functional features can also be extracted from the whole brain, not restricted to the GM, particularly the white-matter (WM), for improving the overall functional registration. Specifically, we quantify local anisotropic correlation patterns of the blood oxygenation level-dependent (BOLD) signals using tissue-specific patch-based functional correlation tensors (ts-PFCTs) in both GM and WM. Functional registration is then performed by integrating the features from different tissues using the multi-channel large deformation diffeomorphic metric mapping (mLDDMM) algorithm. Experimental results show that our method achieves superior functional registration performance, compared with conventional registration methods. © 2018 Wiley Periodicals, Inc.

Optimization of the structural configuration of ICBA/P3HT photovoltaic cells

NASA Astrophysics Data System (ADS)

Nemnes, G. A.; Iftimie, Sorina; Palici, Alexandra; Nicolaev, Adela; Mitran, T. L.; Radu, A.; Antohe, S.

2017-12-01

We investigate a possible route for optimization of organic P3HT:ICBA photovoltaic cells. In order to ensure a more efficient charge separation and collection at the electrodes, two- and three-layer structures are produced, where additional P3HT and ICBA single layers are placed adjacent to the mixed layer. The J-V characteristics are modeled using Monte-Carlo simulations in a flexible computational framework, reproducing the typical morphologies of the active layers. We discuss the implications of the structural modifications, in particular the enhancement of the open circuit voltage. Qualitative features of the theoretical simulations are validated by experiment. The proposed fabrication technique of using solvents with different boiling points for successive deposition of the individual layers may constitute an accessible route for producing optimized solar cell structures.

Design of high strength polymer metal interfaces by laser microstructured surfaces

NASA Astrophysics Data System (ADS)

Steinert, P.; Dittes, A.; Schimmelpfennig, R.; Scharf, I.; Lampke, T.; Schubert, A.

2018-06-01

In the areas of automotive, aeronautics and civil structures, lightweight construction is a current and a future need. Thus, multi material design has rapidly grown in importance, especially hybrid materials based on fiber reinforced plastics and aluminum offer great potential. Therefore, mechanical interlocking is a convenient way of designing the interface. Laser structuring is already used to generate a variety of surface topographies leading to high bond strengths. This paper investigates different laser structures aiming on highest joint strengths for aluminum and glass fiber reinforced polyamide 6 interfaces. Self-organizing pin structures comprised by additional micro/nano features as well as drilled hole structures, both ranging on the micrometer range, are compared to corundum blasting as a standard method for surface conditioning. For the presented surface structures, thermal joining and ultrasonic assisted joining are regarded towards their potential for an optimum joint design.

Deep X-ray Observations of an Ongoing Merger and 400 Myr of AGN Activity in Cygnus A

NASA Astrophysics Data System (ADS)

Wise, Michael W.; De Vries, Martijn; Nulsen, Paul; Snios, Bradford; Birkinshaw, Mark; Worrall, Diana; Duffy, Ryan; Halbesma, Timo; Donnert, Julius; Hardcastle, Martin

2017-08-01

We present a detailed spatial and spectral analysis of the large-scale X-ray emission associated with the merging cluster of galaxies containing the powerful Cygnus A radio galaxy. Using a new 1 Msec exposure from the ongoing Chandra XVP project, we have mapped the large-scale structure, temperature and abundance of the ICM in a 1 Mpc x 1 Mpc region surrounding Cygnus A. This new, deep exposure resolves unprecedented detail in the jets, lobes, and cocoon shock associated with Cygnus A, and provides new insights into the emission mechanisms that produce these features as well as implications for the ongoing activity of the central AGN. On larger scales, these new data reveal complex and dramatic temperature, pressure, entropy and metallicity structure in the ICM surrounding Cygnus A. We confirm the presence of large-scale X-ray emission associated with the two merging cluster components seen previously in lower resolution data. The temperature structure on the scale of the merger exhibits an asymmetric enhancement to the NW consistent with projected hotter gas from the merger shock. Using the derived density and temperature profiles in the two merging sub-cluster components as inputs, we have constructed a grid of hydro-dynamical simulations to constrain the geometry of the merger system. These models imply a pre-merger system with a 1:1 mass ratio at the virial radius with an inclination toward the line of sight of 35-45 deg. In addition to the merger-induced temperature asymmetry, we find evidence for additional surface brightness and temperature features indicative of previous outburst activity in Cygnus A over the past 400 Myr. Based on the location and strength of these features, we derive the energy associated with these previous outbursts and place constraints on the growth of the black hole in Cygnus A over that timescale.

Integration of Point Clouds and Images Acquired from a Low-Cost NIR Camera Sensor for Cultural Heritage Purposes

NASA Astrophysics Data System (ADS)

Kedzierski, M.; Walczykowski, P.; Wojtkowska, M.; Fryskowska, A.

2017-08-01

Terrestrial Laser Scanning is currently one of the most common techniques for modelling and documenting structures of cultural heritage. However, only geometric information on its own, without the addition of imagery data is insufficient when formulating a precise statement about the status of studies structure, for feature extraction or indicating the sites to be restored. Therefore, the Authors propose the integration of spatial data from terrestrial laser scanning with imaging data from low-cost cameras. The use of images from low-cost cameras makes it possible to limit the costs needed to complete such a study, and thus, increasing the possibility of intensifying the frequency of photographing and monitoring of the given structure. As a result, the analysed cultural heritage structures can be monitored more closely and in more detail, meaning that the technical documentation concerning this structure is also more precise. To supplement the laser scanning information, the Authors propose using both images taken both in the near-infrared range and in the visible range. This choice is motivated by the fact that not all important features of historical structures are always visible RGB, but they can be identified in NIR imagery, which, with the additional merging with a three-dimensional point cloud, gives full spatial information about the cultural heritage structure in question. The Authors proposed an algorithm that automates the process of integrating NIR images with a point cloud using parameters, which had been calculated during the transformation of RGB images. A number of conditions affecting the accuracy of the texturing had been studies, in particular, the impact of the geometry of the distribution of adjustment points and their amount on the accuracy of the integration process, the correlation between the intensity value and the error on specific points using images in different ranges of the electromagnetic spectrum and the selection of the optimal method of transforming the acquired imagery. As a result of the research, an innovative solution was achieved, giving high accuracy results and taking into account a number of factors important in the creation of the documentation of historical structures. In addition, thanks to the designed algorithm, the final result can be obtained in a very short time at a high level of automation, in relation to similar types of studies, meaning that it would be possible to obtain a significant data set for further analyses and more detailed monitoring of the state of the historical structures.

Effect of Proximity of Features on the Damage Threshold During Submicron Additive Manufacturing Via Two-Photon Polymerization

DOE PAGES

Saha, Sourabh K.; Divin, Chuck; Cuadra, Jefferson A.; ...

2017-05-12

Two-photon polymerization (TPP) is a laser writing process that enables fabrication of millimeter scale three-dimensional (3D) structures with submicron features. In TPP, writing is achieved via nonlinear two-photon absorption that occurs at high laser intensities. Thus, it is essential to carefully select the incident power to prevent laser damage during polymerization. Currently, the feasible range of laser power is identified by writing small test patterns at varying power levels. Here in this paper, we demonstrate that the results of these tests cannot be generalized, because the damage threshold power depends on the proximity of features and reduces by as muchmore » as 47% for overlapping features. We have identified that this reduction occurs primarily due to an increase in the single-photon absorptivity of the resin after curing. We have captured the damage from proximity effects via X-ray 3D computed tomography (CT) images of a non-homogenous part that has varying feature density. Part damage manifests as internal spherical voids that arise due to boiling of the resist. We have empirically quantified this proximity effect by identifying the damage threshold power at different writing speeds and feature overlap spacings. In addition, we present a first-order analytical model that captures the scaling of this proximity effect. Based on this model and the experiments, we have identified that the proximity effect is more significant at high writing speeds; therefore, it adversely affects the scalability of manufacturing. The scaling laws and the empirical data generated here can be used to select the appropriate TPP writing parameters.« less

Effect of Proximity of Features on the Damage Threshold During Submicron Additive Manufacturing Via Two-Photon Polymerization

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

Saha, Sourabh K.; Divin, Chuck; Cuadra, Jefferson A.

Two-photon polymerization (TPP) is a laser writing process that enables fabrication of millimeter scale three-dimensional (3D) structures with submicron features. In TPP, writing is achieved via nonlinear two-photon absorption that occurs at high laser intensities. Thus, it is essential to carefully select the incident power to prevent laser damage during polymerization. Currently, the feasible range of laser power is identified by writing small test patterns at varying power levels. Here in this paper, we demonstrate that the results of these tests cannot be generalized, because the damage threshold power depends on the proximity of features and reduces by as muchmore » as 47% for overlapping features. We have identified that this reduction occurs primarily due to an increase in the single-photon absorptivity of the resin after curing. We have captured the damage from proximity effects via X-ray 3D computed tomography (CT) images of a non-homogenous part that has varying feature density. Part damage manifests as internal spherical voids that arise due to boiling of the resist. We have empirically quantified this proximity effect by identifying the damage threshold power at different writing speeds and feature overlap spacings. In addition, we present a first-order analytical model that captures the scaling of this proximity effect. Based on this model and the experiments, we have identified that the proximity effect is more significant at high writing speeds; therefore, it adversely affects the scalability of manufacturing. The scaling laws and the empirical data generated here can be used to select the appropriate TPP writing parameters.« less

Eyes Matched to the Prize: The State of Matched Filters in Insect Visual Circuits.

PubMed

Kohn, Jessica R; Heath, Sarah L; Behnia, Rudy

2018-01-01

Confronted with an ever-changing visual landscape, animals must be able to detect relevant stimuli and translate this information into behavioral output. A visual scene contains an abundance of information: to interpret the entirety of it would be uneconomical. To optimally perform this task, neural mechanisms exist to enhance the detection of important features of the sensory environment while simultaneously filtering out irrelevant information. This can be accomplished by using a circuit design that implements specific "matched filters" that are tuned to relevant stimuli. Following this rule, the well-characterized visual systems of insects have evolved to streamline feature extraction on both a structural and functional level. Here, we review examples of specialized visual microcircuits for vital behaviors across insect species, including feature detection, escape, and estimation of self-motion. Additionally, we discuss how these microcircuits are modulated to weigh relevant input with respect to different internal and behavioral states.

The precursors effects on biomimetic hydroxyapatite ceramic powders.

PubMed

Yoruç, Afife Binnaz Hazar; Aydınoğlu, Aysu

2017-06-01

In this study, effects of the starting material on chemical, physical, and biological properties of biomimetic hydroxyapatite ceramic powders (BHA) were investigated. Characterization and chemical analysis of BHA powders were performed by using XRD, FT-IR, and ICP-AES. Microstructural features such as size and morphology of the resulting BHA powders were characterized by using BET, nano particle sizer, pycnometer, and SEM. Additionally, biological properties of the BHA ceramic powders were also investigated by using water-soluble tetrazolium salts test (WST-1). According to the chemical analysis of BHA ceramic powders, chemical structures of ceramics which are prepared under different conditions and by using different starting materials show differences. Ceramic powders which are produced at 80°C are mainly composed of hydroxyapatite, dental hydroxyapatite (contain Na and Mg elements in addition to Ca), and calcium phosphate sulfide. However, these structures are altered at high temperatures such as 900°C depending on the features of starting materials and form various calcium phosphate ceramics and/or their mixtures such as Na-Mg-hydroxyapatite, hydroxyapatite, Mg-Whitlockit, and chloroapatite. In vitro cytotoxicity studies showed that amorphous ceramics produced at 80°C and ceramics containing chloroapatite structure as main or secondary phases were found to be extremely cytotoxic. Furthermore, cell culture studies showed that highly crystalline pure hydroxyapatite structures were extremely cytotoxic due to their high crystallinity values. Consequently, the current study indicates that the selection of starting materials which can be used in the production of calcium phosphate ceramics is very important. It is possible to produce calcium phosphate ceramics which have sufficient biocompatibility at physiological pH values and by using appropriate starting materials. Copyright © 2017 Elsevier B.V. All rights reserved.

Geological remote sensing signatures of terrestrial impact craters

NASA Technical Reports Server (NTRS)

Garvin, J. B.; Schnetzler, C.; Grieve, R. A. F.

1988-01-01

Geological remote sensing techniques can be used to investigate structural, depositional, and shock metamorphic effects associated with hypervelocity impact structures, some of which may be linked to global Earth system catastrophies. Although detailed laboratory and field investigations are necessary to establish conclusive evidence of an impact origin for suspected crater landforms, the synoptic perspective provided by various remote sensing systems can often serve as a pathfinder to key deposits which can then be targetted for intensive field study. In addition, remote sensing imagery can be used as a tool in the search for impact and other catastrophic explosion landforms on the basis of localized disruption and anomaly patterns. In order to reconstruct original dimensions of large, complex impact features in isolated, inaccessible regions, remote sensing imagery can be used to make preliminary estimates in the absence of field geophysical surveys. The experienced gained from two decades of planetary remote sensing of impact craters on the terrestrial planets, as well as the techniques developed for recognizing stages of degradation and initial crater morphology, can now be applied to the problem of discovering and studying eroded impact landforms on Earth. Preliminary results of remote sensing analyses of a set of terrestrial impact features in various states of degradation, geologic settings, and for a broad range of diameters and hence energies of formation are summarized. The intention is to develop a database of remote sensing signatures for catastrophic impact landforms which can then be used in EOS-era global surveys as the basis for locating the possibly hundreds of missing impact structures. In addition, refinement of initial dimensions of extremely recent structures such as Zhamanshin and Bosumtwi is an important objective in order to permit re-evaluation of global Earth system responses associated with these types of events.

The latent structure of alcohol misuse in young adults: Do taxometric results differ as a function of prior criminal history?

PubMed

Walters, Glenn D

2015-12-01

The purpose of this study was to determine whether the latent structure of alcohol misuse is categorical or continuous in male and female adults with and without a history of prior criminal offending. Data from 3452 (1530 male, 1922 female) 27-to-32 year old members of the National Longitudinal Study of Adolescent to Adult Health (Add Health) were subjected to taxometric analysis using three nonredundant taxometric procedures--mean above minus below a cut (MAMBAC), maximum covariance (MAXCOV), and latent mode factor analysis (L-Mode). Analyses produced results consistent with categorical latent structure in males with a previous history of criminal offending but not in males without a previous history of criminal offending or females with or without a history of criminal offending. The findings from the other groups were indeterminate for the most part (i.e., neither categorical nor continuous). The presumptive taxon was validated by testing differences in age of onset and frequency of criminal arrest and drunkenness between the putative taxon and the upper portion of the complement. As predicted, all four validation outcomes were significantly worse in the taxon group. On the basis of these results it is concluded that alcohol misuse in young adults may have features of both categorical and continuous latent structure and that the categorical aspects are more prominent in males with a history of offending behavior. Additional research is required to determine which aspects and features of alcohol misuse are categorical and which aspects and features are continuous. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Robust Classification and Segmentation of Planar and Linear Features for Construction Site Progress Monitoring and Structural Dimension Compliance Control

NASA Astrophysics Data System (ADS)

Maalek, R.; Lichti, D. D.; Ruwanpura, J.

2015-08-01

The application of terrestrial laser scanners (TLSs) on construction sites for automating construction progress monitoring and controlling structural dimension compliance is growing markedly. However, current research in construction management relies on the planned building information model (BIM) to assign the accumulated point clouds to their corresponding structural elements, which may not be reliable in cases where the dimensions of the as-built structure differ from those of the planned model and/or the planned model is not available with sufficient detail. In addition outliers exist in construction site datasets due to data artefacts caused by moving objects, occlusions and dust. In order to overcome the aforementioned limitations, a novel method for robust classification and segmentation of planar and linear features is proposed to reduce the effects of outliers present in the LiDAR data collected from construction sites. First, coplanar and collinear points are classified through a robust principal components analysis procedure. The classified points are then grouped using a robust clustering method. A method is also proposed to robustly extract the points belonging to the flat-slab floors and/or ceilings without performing the aforementioned stages in order to preserve computational efficiency. The applicability of the proposed method is investigated in two scenarios, namely, a laboratory with 30 million points and an actual construction site with over 150 million points. The results obtained by the two experiments validate the suitability of the proposed method for robust segmentation of planar and linear features in contaminated datasets, such as those collected from construction sites.

Chemical, Physical, and Biological Factors Shape Littoral Invertebrate Community Structure in Coal-Mining End-Pit Lakes

NASA Astrophysics Data System (ADS)

Luek, Andreas; Rasmussen, Joseph B.

2017-04-01

Aquatic invertebrates form the base of the consumer food web in lakes. In coal-mining end-pit lakes, invertebrates are exposed to an environment with potentially challenging physical and chemical features. We hypothesized that the physical and chemical features of end-pit lakes reduce critical littoral habitat and thus reduce invertebrate diversity, thereby limiting the potential for these lakes to be naturalized. We used a multivariate approach using principle component analysis and redundancy analysis to study relationships between invertebrate community structure, habitat features, and water quality in five end-pit lakes and five natural lakes in the Rocky Mountain foothills of west-central Alberta, Canada. Results show a significantly different invertebrate community structure was present in end-pit lakes as compared with reference lakes in the same region, which could be accounted for by water hardness, conductivity, slope of the littoral zone, and phosphorus concentrations. Habitat diversity in end-pit lakes was also limited, cover provided by macrophytes was scarce, and basin slopes were significantly steeper in pit lakes. Although water chemistry is currently the strongest influencing factor on the invertebrate community, physical challenges of habitat homogeneity and steep slopes in the littoral zones were identified as major drivers of invertebrate community structure. The addition of floating wetlands to the littoral zone of existing pit lakes can add habitat complexity without the need for large-scale alterations to basing morphology, while impermeable capping of waste-rock and the inclusion of littoral habitat in the planning process of new pit lakes can improve the success of integrating new pit lakes into the landscape.

Trans-Dimensional Bayesian Imaging of 3-D Crustal and Upper Mantle Structure in Northeast Asia

NASA Astrophysics Data System (ADS)

Kim, S.; Tkalcic, H.; Rhie, J.; Chen, Y.

2016-12-01

Imaging 3-D structures using stepwise inversions of ambient noise and receiver function data is now a routine work. Here, we carry out the inversion in the trans-dimensional and hierarchical extension of the Bayesian framework to obtain rigorous estimates of uncertainty and high-resolution images of crustal and upper mantle structures beneath Northeast (NE) Asia. The methods inherently account for data sensitivities by means of using adaptive parameterizations and treating data noise as free parameters. Therefore, parsimonious results from the methods are balanced out between model complexity and data fitting. This allows fully exploiting data information, preventing from over- or under-estimation of the data fit, and increases model resolution. In addition, the reliability of results is more rigorously checked through the use of Bayesian uncertainties. It is shown by various synthetic recovery tests that complex and spatially variable features are well resolved in our resulting images of NE Asia. Rayleigh wave phase and group velocity tomograms (8-70 s), a 3-D shear-wave velocity model from depth inversions of the estimated dispersion maps, and regional 3-D models (NE China, the Korean Peninsula, and the Japanese islands) from joint inversions with receiver function data of dense networks are presented. High-resolution models are characterized by a number of tectonically meaningful features. We focus our interpretation on complex patterns of sub-lithospheric low velocity structures that extend from back-arc regions to continental margins. We interpret the anomalies in conjunction with distal and distributed intraplate volcanoes in NE Asia. Further discussion on other imaged features will be presented.

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

Lin, Jiusheng; van den Bedem, Henry; Brunger, Axel T.

Calmodulin (CaM) is the primary calcium signaling protein in eukaryotes and has been extensively studied using various biophysical techniques. Prior crystal structures have noted the presence of ambiguous electron density in both hydrophobic binding pockets of Ca 2+-CaM, but no assignment of these features has been made. In addition, Ca 2+-CaM samples many conformational substates in the crystal and accurately modeling the full range of this functionally important disorder is challenging. In order to characterize these features in a minimally biased manner, a 1.0 Å resolution single-wavelength anomalous diffraction data set was measured for selenomethionine-substituted Ca 2+-CaM. Density-modified electron-density mapsmore » enabled the accurate assignment of Ca 2+-CaM main-chain and side-chain disorder. These experimental maps also substantiate complex disorder models that were automatically built using low-contour features of model-phased electron density. Furthermore, experimental electron-density maps reveal that 2-methyl-2,4-pentanediol (MPD) is present in the C-terminal domain, mediates a lattice contact between N-terminal domains and may occupy the N-terminal binding pocket. The majority of the crystal structures of target-free Ca 2+-CaM have been derived from crystals grown using MPD as a precipitant, and thus MPD is likely to be bound in functionally critical regions of Ca 2+-CaM in most of these structures. The adventitious binding of MPD helps to explain differences between the Ca 2+-CaM crystal and solution structures and is likely to favor more open conformations of the EF-hands in the crystal.« less

Chemical, Physical, and Biological Factors Shape Littoral Invertebrate Community Structure in Coal-Mining End-Pit Lakes.

PubMed

Luek, Andreas; Rasmussen, Joseph B

2017-04-01

Aquatic invertebrates form the base of the consumer food web in lakes. In coal-mining end-pit lakes, invertebrates are exposed to an environment with potentially challenging physical and chemical features. We hypothesized that the physical and chemical features of end-pit lakes reduce critical littoral habitat and thus reduce invertebrate diversity, thereby limiting the potential for these lakes to be naturalized. We used a multivariate approach using principle component analysis and redundancy analysis to study relationships between invertebrate community structure, habitat features, and water quality in five end-pit lakes and five natural lakes in the Rocky Mountain foothills of west-central Alberta, Canada. Results show a significantly different invertebrate community structure was present in end-pit lakes as compared with reference lakes in the same region, which could be accounted for by water hardness, conductivity, slope of the littoral zone, and phosphorus concentrations. Habitat diversity in end-pit lakes was also limited, cover provided by macrophytes was scarce, and basin slopes were significantly steeper in pit lakes. Although water chemistry is currently the strongest influencing factor on the invertebrate community, physical challenges of habitat homogeneity and steep slopes in the littoral zones were identified as major drivers of invertebrate community structure. The addition of floating wetlands to the littoral zone of existing pit lakes can add habitat complexity without the need for large-scale alterations to basing morphology, while impermeable capping of waste-rock and the inclusion of littoral habitat in the planning process of new pit lakes can improve the success of integrating new pit lakes into the landscape.

DMS-MaPseq for genome-wide or targeted RNA structure probing in vivo.

PubMed

Zubradt, Meghan; Gupta, Paromita; Persad, Sitara; Lambowitz, Alan M; Weissman, Jonathan S; Rouskin, Silvi

2017-01-01

Coupling of structure-specific in vivo chemical modification to next-generation sequencing is transforming RNA secondary structure studies in living cells. The dominant strategy for detecting in vivo chemical modifications uses reverse transcriptase truncation products, which introduce biases and necessitate population-average assessments of RNA structure. Here we present dimethyl sulfate (DMS) mutational profiling with sequencing (DMS-MaPseq), which encodes DMS modifications as mismatches using a thermostable group II intron reverse transcriptase. DMS-MaPseq yields a high signal-to-noise ratio, can report multiple structural features per molecule, and allows both genome-wide studies and focused in vivo investigations of even low-abundance RNAs. We apply DMS-MaPseq for the first analysis of RNA structure within an animal tissue and to identify a functional structure involved in noncanonical translation initiation. Additionally, we use DMS-MaPseq to compare the in vivo structure of pre-mRNAs with their mature isoforms. These applications illustrate DMS-MaPseq's capacity to dramatically expand in vivo analysis of RNA structure.

Random forest classification of large volume structures for visuo-haptic rendering in CT images

NASA Astrophysics Data System (ADS)

Mastmeyer, Andre; Fortmeier, Dirk; Handels, Heinz

2016-03-01

For patient-specific voxel-based visuo-haptic rendering of CT scans of the liver area, the fully automatic segmentation of large volume structures such as skin, soft tissue, lungs and intestine (risk structures) is important. Using a machine learning based approach, several existing segmentations from 10 segmented gold-standard patients are learned by random decision forests individually and collectively. The core of this paper is feature selection and the application of the learned classifiers to a new patient data set. In a leave-some-out cross-validation, the obtained full volume segmentations are compared to the gold-standard segmentations of the untrained patients. The proposed classifiers use a multi-dimensional feature space to estimate the hidden truth, instead of relying on clinical standard threshold and connectivity based methods. The result of our efficient whole-body section classification are multi-label maps with the considered tissues. For visuo-haptic simulation, other small volume structures would have to be segmented additionally. We also take a look into these structures (liver vessels). For an experimental leave-some-out study consisting of 10 patients, the proposed method performs much more efficiently compared to state of the art methods. In two variants of leave-some-out experiments we obtain best mean DICE ratios of 0.79, 0.97, 0.63 and 0.83 for skin, soft tissue, hard bone and risk structures. Liver structures are segmented with DICE 0.93 for the liver, 0.43 for blood vessels and 0.39 for bile vessels.

Structural insight into the binding interactions of modeled structure of Arabidopsis thaliana urease with urea: an in silico study.

PubMed

Yata, Vinod Kumar; Thapa, Arun; Mattaparthi, Venkata Satish Kumar

2015-01-01

Urease (EC 3.5.1.5., urea amidohydrolase) catalyzes the hydrolysis of urea to ammonia and carbon dioxide. Urease is present to a greater abundance in plants and plays significant role related to nitrogen recycling from urea. But little is known about the structure and function of the urease derived from the Arabidopsis thaliana, the model system of choice for research in plant biology. In this study, a three-dimensional structural model of A. thaliana urease was constructed using computer-aided molecular modeling technique. The characteristic structural features of the modeled structure were then studied using atomistic molecular dynamics simulation. It was observed that the modeled structure was stable and regions between residues index (50-80, 500-700) to be significantly flexible. From the docking studies, we detected the possible binding interactions of modeled urease with urea. Ala399, Ile675, Thr398, and Thr679 residues of A. thaliana urease were observed to be significantly involved in binding with the substrate urea. We also compared the docking studies of ureases from other sources such as Canavalia ensiformis, Helicobacter pylori, and Bacillus pasteurii. In addition, we carried out mutation analysis to find the highly mutable amino acid residues of modeled A. thaliana urease. In this particular study, we observed Met485, Tyr510, Ser786, Val426, and Lys765 to be highly mutable amino acids. These results are significant for the mutagenesis analysis. As a whole, this study expounds the salient structural features as well the binding interactions of the modeled structure of A. thaliana urease.

Chinese wine classification system based on micrograph using combination of shape and structure features

NASA Astrophysics Data System (ADS)

Wan, Yi

2011-06-01

Chinese wines can be classification or graded by the micrographs. Micrographs of Chinese wines show floccules, stick and granule of variant shape and size. Different wines have variant microstructure and micrographs, we study the classification of Chinese wines based on the micrographs. Shape and structure of wines' particles in microstructure is the most important feature for recognition and classification of wines. So we introduce a feature extraction method which can describe the structure and region shape of micrograph efficiently. First, the micrographs are enhanced using total variation denoising, and segmented using a modified Otsu's method based on the Rayleigh Distribution. Then features are extracted using proposed method in the paper based on area, perimeter and traditional shape feature. Eight kinds total 26 features are selected. Finally, Chinese wine classification system based on micrograph using combination of shape and structure features and BP neural network have been presented. We compare the recognition results for different choices of features (traditional shape features or proposed features). The experimental results show that the better classification rate have been achieved using the combinational features proposed in this paper.

Structural features that predict real-value fluctuations of globular proteins.

PubMed

Jamroz, Michal; Kolinski, Andrzej; Kihara, Daisuke

2012-05-01

It is crucial to consider dynamics for understanding the biological function of proteins. We used a large number of molecular dynamics (MD) trajectories of nonhomologous proteins as references and examined static structural features of proteins that are most relevant to fluctuations. We examined correlation of individual structural features with fluctuations and further investigated effective combinations of features for predicting the real value of residue fluctuations using the support vector regression (SVR). It was found that some structural features have higher correlation than crystallographic B-factors with fluctuations observed in MD trajectories. Moreover, SVR that uses combinations of static structural features showed accurate prediction of fluctuations with an average Pearson's correlation coefficient of 0.669 and a root mean square error of 1.04 Å. This correlation coefficient is higher than the one observed in predictions by the Gaussian network model (GNM). An advantage of the developed method over the GNMs is that the former predicts the real value of fluctuation. The results help improve our understanding of relationships between protein structure and fluctuation. Furthermore, the developed method provides a convienient practial way to predict fluctuations of proteins using easily computed static structural features of proteins. Copyright © 2012 Wiley Periodicals, Inc.

Structural features that predict real-value fluctuations of globular proteins

PubMed Central

Jamroz, Michal; Kolinski, Andrzej; Kihara, Daisuke

2012-01-01

It is crucial to consider dynamics for understanding the biological function of proteins. We used a large number of molecular dynamics trajectories of non-homologous proteins as references and examined static structural features of proteins that are most relevant to fluctuations. We examined correlation of individual structural features with fluctuations and further investigated effective combinations of features for predicting the real-value of residue fluctuations using the support vector regression. It was found that some structural features have higher correlation than crystallographic B-factors with fluctuations observed in molecular dynamics trajectories. Moreover, support vector regression that uses combinations of static structural features showed accurate prediction of fluctuations with an average Pearson’s correlation coefficient of 0.669 and a root mean square error of 1.04 Å. This correlation coefficient is higher than the one observed for the prediction by the Gaussian network model. An advantage of the developed method over the Gaussian network models is that the former predicts the real-value of fluctuation. The results help improve our understanding of relationships between protein structure and fluctuation. Furthermore, the developed method provides a convienient practial way to predict fluctuations of proteins using easily computed static structural features of proteins. PMID:22328193

Comparison of polystyrene scintillator fiber array and monolithic polystyrene for neutron imaging and radiography.

PubMed

Simpson, R; Cutler, T E; Danly, C R; Espy, M A; Goglio, J H; Hunter, J F; Madden, A C; Mayo, D R; Merrill, F E; Nelson, R O; Swift, A L; Wilde, C H; Zocco, T G

2016-11-01

The neutron imaging diagnostic at the National Ignition Facility has been operating since 2011 generating neutron images of deuterium-tritium (DT) implosions at peak compression. The current design features a scintillating fiber array, which allows for high imaging resolution to discern small-scale structure within the implosion. In recent years, it has become clear that additional neutron imaging systems need to be constructed in order to provide 3D reconstructions of the DT source and these additional views need to be on a shorter line of sight. As a result, there has been increased effort to identify new image collection techniques that improve upon imaging resolution for these next generation neutron imaging systems, such as monolithic deuterated scintillators. This work details measurements performed at the Weapons Neutron Research Facility at Los Alamos National Laboratory that compares the radiographic abilities of the fiber scintillator with a monolithic scintillator, which may be featured in a future short line of sight neutron imaging systems.

Comparison of polystyrene scintillator fiber array and monolithic polystyrene for neutron imaging and radiography

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

Simpson, R., E-mail: raspberry@lanl.gov; Cutler, T. E.; Danly, C. R.

The neutron imaging diagnostic at the National Ignition Facility has been operating since 2011 generating neutron images of deuterium-tritium (DT) implosions at peak compression. The current design features a scintillating fiber array, which allows for high imaging resolution to discern small-scale structure within the implosion. In recent years, it has become clear that additional neutron imaging systems need to be constructed in order to provide 3D reconstructions of the DT source and these additional views need to be on a shorter line of sight. As a result, there has been increased effort to identify new image collection techniques that improvemore » upon imaging resolution for these next generation neutron imaging systems, such as monolithic deuterated scintillators. This work details measurements performed at the Weapons Neutron Research Facility at Los Alamos National Laboratory that compares the radiographic abilities of the fiber scintillator with a monolithic scintillator, which may be featured in a future short line of sight neutron imaging systems.« less

Comparison of polystyrene scintillator fiber array and monolithic polystyrene for neutron imaging and radiography

NASA Astrophysics Data System (ADS)

Simpson, R.; Cutler, T. E.; Danly, C. R.; Espy, M. A.; Goglio, J. H.; Hunter, J. F.; Madden, A. C.; Mayo, D. R.; Merrill, F. E.; Nelson, R. O.; Swift, A. L.; Wilde, C. H.; Zocco, T. G.

2016-11-01

The neutron imaging diagnostic at the National Ignition Facility has been operating since 2011 generating neutron images of deuterium-tritium (DT) implosions at peak compression. The current design features a scintillating fiber array, which allows for high imaging resolution to discern small-scale structure within the implosion. In recent years, it has become clear that additional neutron imaging systems need to be constructed in order to provide 3D reconstructions of the DT source and these additional views need to be on a shorter line of sight. As a result, there has been increased effort to identify new image collection techniques that improve upon imaging resolution for these next generation neutron imaging systems, such as monolithic deuterated scintillators. This work details measurements performed at the Weapons Neutron Research Facility at Los Alamos National Laboratory that compares the radiographic abilities of the fiber scintillator with a monolithic scintillator, which may be featured in a future short line of sight neutron imaging systems.

A super-cusp divertor configuration for tokamaks

NASA Astrophysics Data System (ADS)

Ryutov, D. D.

2015-10-01

> This study demonstrates a remarkable flexibility of advanced divertor configurations created with the remote poloidal field coils. The emphasis here is on the configurations with three poloidal field nulls in the divertor area. We are seeking the structures where all three nulls lie on the same separatrix, thereby creating two zones of a very strong flux expansion, as envisaged in the concept of Takase's cusp divertor. It turns out that the set of remote coils can indeed produce a cusp divertor, with additional advantages of: (i) a large stand-off distance between the divertor and the coils and (ii) a thorough control that these coils exert over the fine features of the configuration. In reference to these additional favourable properties acquired by the cusp divertor, the resulting configuration could be called `a super-cusp'. General geometrical features of the three-null configurations produced by remote coils are described. Issues on the way to practical applications include the need for a more sophisticated control system and possible constraints related to excessively high currents in the divertor coils.

HCMM imagery for the discrimination of rock types, the detection of geothermal energy sources and the assessment of soil moisture content in western Queensland and adjacent parts of New South Wales and South Australia

NASA Technical Reports Server (NTRS)

Cole, M. M. (Principal Investigator)

1980-01-01

The author has identified the following significant results. Day-visible and day-IR imagery of northwest Queensland show that large scale geological features like the Mitakoodi anticlinorium, which involves rocks of contrasting lithological type, can be delineated. North of Cloncurry, the contrasting lithological units of the Knapdale quartzite and bedded argillaceous limestones within the Proterozoic Corella sequence are clearly delineated in the area of the Dugald River Lode. Major structural features in the Mount Isa area are revealed on the day-visible cover. Which provides similar but less detailed information than the LANDSAT imagery. The day-IR cover provides less additional information for areas of outcropping bedrock than had been expected. Initial studies of the day-IR and night-IR cover for parts of South Australia suggest that they contain additional information on geology compared with day-visible cover.

Ocean Classification of Dynamical Structures Detected by SAR and Spectral Methods

NASA Astrophysics Data System (ADS)

Redondo, J. M.; Martinez-Benjamin, J. J.; Tellez, J. D.; Jorge, J.; Diez, M.; Sekula, E.

2016-08-01

We discuss a taxonomy of different dynamical features in the ocean surface and provide some eddy and front statistics, as well as describing some events detected by several satellites and even with additional cruise observations and measurements, in the North-west Mediterranean Sea area between 1996 and 2012. The structure of the flows are presented using self-similar traces that may be used to parametrize mixing at both limits of the Rossby Deformation Radius scale, RL. Results show the ability to identify different SAR signatures and at the same time provide calibrations for the different local configurations of vortices, spirals, Langmuir cells, oil spills and tensioactive slicks that eventually allow the study of the self-similar structure of the turbulence. Depending on the surface wind and wave level, and also on the fetch. the bathimetry, the spiral parameters and the resolution of vortical features change. Previous descriptions did not include the new wind and buoyancy features. SAR images also show the turbulence structure of the coastal area and the Regions of Fresh Water Influence (ROFI). It is noteworthy tt such complex coastal field-dependent behavior is strongly influenced by stratification and rotation of the turbulence spectrum is observed only in the range smaller than the local Rossby deformation radius, RL. The measures of diffusivity from buoy or tracer experiments are used to calibrate the behavior of different tracers and pollutants, both natural and man-made in the NW Mediterranean Sea. Thanks to different polarization and intensity levels in ASAR satellite imagery, these can be used to distinguish between natural and man-made sea surface features due to their distinct self-similar and fractal as a function of spill and slick parameters, environmental conditions and history of both oil releases and weather conditions. Eddy diffusivity map derived from SAR measurements of the ocean surface, performing a feature spatial correlation of the available images of the region are presented. Both the multi fractal discrimination of the local features and the diffusivity measurements are important to evaluate the state of the environment. The distribution of meso-scale vortices of size, the Rossby deformation scale and other dominant features can be used to distinguish features in the ocean surface. Multi-fractal analysis is then very usefull. The SAR images exhibited a large variation of natural features produced by winds, internal waves, the bathymetric distribution, by convection, rain, etc as all of these produce variations in the sea surface roughness so that the topological changes may be studied and classified. In a similar way bathimetry may be studied with the methodology described here using the coastline and the thalwegs as generators of local vertical vorticity.

Reduced-Order Modeling and Wavelet Analysis of Turbofan Engine Structural Response Due to Foreign Object Damage (FOD) Events

NASA Technical Reports Server (NTRS)

Turso, James; Lawrence, Charles; Litt, Jonathan

2004-01-01

The development of a wavelet-based feature extraction technique specifically targeting FOD-event induced vibration signal changes in gas turbine engines is described. The technique performs wavelet analysis of accelerometer signals from specified locations on the engine and is shown to be robust in the presence of significant process and sensor noise. It is envisioned that the technique will be combined with Kalman filter thermal/health parameter estimation for FOD-event detection via information fusion from these (and perhaps other) sources. Due to the lack of high-frequency FOD-event test data in the open literature, a reduced-order turbofan structural model (ROM) was synthesized from a finite element model modal analysis to support the investigation. In addition to providing test data for algorithm development, the ROM is used to determine the optimal sensor location for FOD-event detection. In the presence of significant noise, precise location of the FOD event in time was obtained using the developed wavelet-based feature.

Waveform Based Acoustic Emission Detection and Location of Matrix Cracking in Composites

NASA Technical Reports Server (NTRS)

Prosser, W. H.

1995-01-01

The operation of damage mechanisms in a material or structure under load produces transient acoustic waves. These acoustic waves are known as acoustic emission (AE). In composites they can be caused by a variety of sources including matrix cracking, fiber breakage, and delamination. AE signals can be detected and analyzed to determine the location of the acoustic source by triangulation. Attempts are also made to analyze the signals to determine the type and severity of the damage mechanism. AE monitoring has been widely used for both laboratory studies of materials, and for testing the integrity of structures in the field. In this work, an advanced, waveform based AE system was used in a study of transverse matrix cracking in cross-ply graphite/epoxy laminates. This AE system featured broad band, high fidelity sensors, and high capture rate digital acquisition and storage of acoustic signals. In addition, analysis techniques based on plate wave propagation models were employed. These features provided superior source location and noise rejection capabilities.

Reduced-Order Modeling and Wavelet Analysis of Turbofan Engine Structural Response Due to Foreign Object Damage "FOD" Events

NASA Technical Reports Server (NTRS)

Turso, James A.; Lawrence, Charles; Litt, Jonathan S.

2007-01-01

The development of a wavelet-based feature extraction technique specifically targeting FOD-event induced vibration signal changes in gas turbine engines is described. The technique performs wavelet analysis of accelerometer signals from specified locations on the engine and is shown to be robust in the presence of significant process and sensor noise. It is envisioned that the technique will be combined with Kalman filter thermal/ health parameter estimation for FOD-event detection via information fusion from these (and perhaps other) sources. Due to the lack of high-frequency FOD-event test data in the open literature, a reduced-order turbofan structural model (ROM) was synthesized from a finite-element model modal analysis to support the investigation. In addition to providing test data for algorithm development, the ROM is used to determine the optimal sensor location for FOD-event detection. In the presence of significant noise, precise location of the FOD event in time was obtained using the developed wavelet-based feature.

High resolution PFPE-based molding High resolution PFPE-based molding High resolution PFPE-based molding techniques for nanofabrication of high pattern density sub-20 nm features: A fundamental materials approach

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

Williams, Stuart S; Samulski, Edward; Lopez, Renee

2010-01-01

ABSTRACT. Described herein is the development and investigation of PFPE-based elastomers for high resolution replica molding applications. The modulus of the elastomeric materials was increased through synthetic and additive approaches while maintaining relatively low surface energies (<25 mN/m). Using practically relevant large area master templates, we show that the resolution of the molds is strongly dependant upon the elastomeric mold modulus. A composite mold approach was used to form flexible molds out of stiff, high modulus materials that allow for replication of sub-20 nm post structures. Sub-100 nm line grating master templates, formed using e-beam lithography, were used to determinemore » the experimental stability of the molding materials. It was observed that as the feature spacing decreased, high modulus composite molds were able to effectively replicate the nano-grating structures without cracking or tear-out defects that typically occur with high modulus elastomers.« less

Supramolecular features of 2-(chlorophenyl)-3-[(chlorobenzylidene)-amino]-2,3-dihydroquinazolin-4(1H)-ones: A combined experimental and computational study

NASA Astrophysics Data System (ADS)

Mandal, Arkalekha; Patel, Bhisma K.

2018-03-01

The molecular structures of two isomeric 2-(chlorophenyl)-3-[(chlorobenzylidene)-amino] substituted 2,3-dihydroquinazolin-4(1H)-ones have been determined via single crystal XRD. Both isomers contain chloro substitutions on each of the phenyl rings and as a result a broad spectrum of halogen mediated weak interactions are viable in their crystal structures. The crystal packing of these compounds is stabilized by strong N-H⋯O hydrogen bond and various weak, non-classical hydrogen bonds acting synergistically. Both the molecules contain a chiral center and the weak interactions observed in them are either chiral self-discriminatory or chiral self-recognizing in nature. The weak interactions and spectral features of the compounds have been studied through experimental as well as computational methods including DFT, MEP, NBO and Hiresfeld surface analyses. In addition, the effect of different weak interactions to dictate either chiral self-recognition or self-discrimination in crystal packing has been elucidated.

The cytopathology of Actinomyces, Nocardia, and their mimickers.

PubMed

McHugh, Kelsey E; Sturgis, Charles D; Procop, Gary W; Rhoads, Daniel D

2017-12-01

Nocardia species and Actinomyces species are 2 of the most commonly diagnosed filamentous bacteria in routine cytopathology practice. These genera share many overlapping cytomorphologic features, including their thin, beaded, branching, Gram-positive, GMS-positive filamentous structures that fragment at their peripheries into bacillary- and coccoid-appearing forms. Features that help distinguish between these 2 microorganisms include the width of their filamentous structures, the angles at which they branch, and their ability or lack thereof to retain a modified acid-fast stain. In addition to cytomorphologic overlap, overlap in clinical presentation is frequent with pulmonary and mucocutaneous presentations seen in both. Differentiating between Nocardia and Actinomyces is essential because patients with these infections require different approaches to medical management. Both antibiotic susceptibilities and the need for early surgical intervention as part of the treatment plan vary greatly among these 2 groups. This review focuses on the clinical presentation, cytomorphology and staining characteristics that can be useful in identifying and distinguishing between Nocardia and Actinomyces infections, as well as their mimickers. © 2017 Wiley Periodicals, Inc.

X-ray Raman spectroscopy of lithium-ion battery electrolyte solutions in a flow cell.

PubMed

Ketenoglu, Didem; Spiekermann, Georg; Harder, Manuel; Oz, Erdinc; Koz, Cevriye; Yagci, Mehmet C; Yilmaz, Eda; Yin, Zhong; Sahle, Christoph J; Detlefs, Blanka; Yavaş, Hasan

2018-03-01

The effects of varying LiPF 6 salt concentration and the presence of lithium bis(oxalate)borate additive on the electronic structure of commonly used lithium-ion battery electrolyte solvents (ethylene carbonate-dimethyl carbonate and propylene carbonate) have been investigated. X-ray Raman scattering spectroscopy (a non-resonant inelastic X-ray scattering method) was utilized together with a closed-circle flow cell. Carbon and oxygen K-edges provide characteristic information on the electronic structure of the electrolyte solutions, which are sensitive to local chemistry. Higher Li + ion concentration in the solvent manifests itself as a blue-shift of both the π* feature in the carbon edge and the carbonyl π* feature in the oxygen edge. While these oxygen K-edge results agree with previous soft X-ray absorption studies on LiBF 4 salt concentration in propylene carbonate, carbon K-edge spectra reveal a shift in energy, which can be explained with differing ionic conductivities of the electrolyte solutions.

THE FINE STRUCTURE OF GREEN BACTERIA

PubMed Central

Cohen-Bazire, Germaine; Pfennig, Norbert; Kunisawa, Riyo

1964-01-01

The fine structure of several strains of green bacteria belonging to the genus Chlorobium has been studied in thin sections with the electron microscope. In addition to having general cytological features typical of Gram-negative bacteria, the cells of these organisms always contain membranous mesosomal elements, connected with the cytoplasmic membrane, and an elaborate system of isolated cortical vesicles, some 300 to 400 A wide and 1000 to 1500 A long. The latter structures, chlorobium vesicles, have been isolated in a partly purified state by differential centrifugation of cell-free extracts. They are associated with a centrifugal fraction that has a very high specific chlorophyll content. In all probability, therefore, the chlorobium vesicles are the site of the photosynthetic apparatus of green bacteria. PMID:14195611

Chromophoric Nucleoside Analogues: Synthesis and Characterization of 6-Aminouracil-Based Nucleodyes.

PubMed

Freeman, Noam S; Moore, Curtis E; Wilhelmsson, L Marcus; Tor, Yitzhak

2016-06-03

Nucleodyes, visibly colored chromophoric nucleoside analogues, are reported. Design criteria are outlined and the syntheses of cytidine and uridine azo dye analogues derived from 6-aminouracil are described. Structural analysis shows that the nucleodyes are sound structural analogues of their native nucleoside counterparts, and photophysical studies demonstrate that the nucleodyes are sensitive to microenvironmental changes. Quantum chemical calculations are presented as a valuable complementary tool for the design of strongly absorbing nucleodyes, which overlap with the emission of known fluorophores. Förster critical distance (R0) calculations determine that the nucleodyes make good FRET pairs with both 2-aminopurine (2AP) and pyrrolocytosine (PyC). Additionally, unique tautomerization features exhibited by 5-(4-nitrophenylazo)-6-oxocytidine (8) are visualized by an extraordinary crystal structure.

ECE-imaging of the H-mode pedestal (invited).

PubMed

Tobias, B J; Austin, M E; Boom, J E; Burrell, K H; Classen, I G J; Domier, C W; Luhmann, N C; Nazikian, R; Snyder, P B

2012-10-01

A synthetic diagnostic has been developed that reproduces the highly structured electron cyclotron emission (ECE) spectrum radiated from the edge region of H-mode discharges. The modeled dependence on local perturbations of the equilibrium plasma pressure allows for interpretation of ECE data for diagnosis of local quantities. Forward modeling of the diagnostic response in this region allows for improved mapping of the observed fluctuations to flux surfaces within the plasma, allowing for the poloidal mode number of coherent structures to be resolved. In addition, other spectral features that are dependent on both T(e) and n(e) contain information about pedestal structure and the electron energy distribution of localized phenomena, such as edge filaments arising during edge-localized mode (ELM) activity.

Additive Technology: Update on Current Materials and Applications in Dentistry.

PubMed

Barazanchi, Abdullah; Li, Kai Chun; Al-Amleh, Basil; Lyons, Karl; Waddell, J Neil

2017-02-01

Additive manufacturing or 3D printing is becoming an alternative to subtractive manufacturing or milling in the area of computer-aided manufacturing. Research on material for use in additive manufacturing is ongoing, and a wide variety of materials are being used or developed for use in dentistry. Some materials, however, such as cobalt chromium, still lack sufficient research to allow definite conclusions about the suitability of their use in clinical dental practice. Despite this, due to the wide variety of machines that use additive manufacturing, there is much more flexibility in the build material and geometry when building structures compared with subtractive manufacturing. Overall additive manufacturing produces little material waste and is energy efficient when compared to subtractive manufacturing, due to passivity and the additive layering nature of the build process. Such features make the technique suitable to be used with fabricating structures out of hard to handle materials such as cobalt chromium. The main limitations of this technology include the appearance of steps due to layering of material and difficulty in fabricating certain material generally used in dentistry for use in 3D printing such as ceramics. The current pace of technological development, however, promises exciting possibilities. © 2016 by the American College of Prosthodontists.

Three-dimensional P-wave velocity structure in the greater Mount Rainier area from local earthquake tomography

NASA Astrophysics Data System (ADS)

Moran, Seth Charles

1997-08-01

One of the most striking features of seismicity in western Washington is the clustering of crustal earthquakes into one of several zones of concentrated seismicity. In this dissertation I explore the hypothesis that geologic structures, in conjunction with regional tectonic forces, are primarily responsible for controlling the location of seismicity in parts of western Washington. The primary tool for testing this hypothesis is a 3-dimensional image of the P-wave velocity structure of the greater Mount Rainier area that I derive using local earthquake tomography. I use P-wave arrival times from local earthquakes occurring between 1980 and 1996 recorded at short-period vertical component stations operated by the Pacific Northwest Seismograph Network (PNSN) and 18 temporary sites operated during a field experiment in 1995 and 1996. The tomographic methodology I use is similar to that described by Lees and Crosson (1989, 1990). In addition, I use the parameter separation method to decouple the hypocenter and velocity problems, don't use station corrections, and use ray-bending for 3-D raytracing, allowing for a full non-linear inversion. In the upper 4 km several low velocity features show good correlation with the Carbon River, Skate Creek, and Morton anticlines, as well as the Chehalis, Tacoma, and Seattle basins. There is also good correlation between high velocity features and surface exposures of several plutons. One seismic zone, the St. Helens Seismic Zone, correlates well with a planar low velocity feature. This correlation supports the idea that this seismic zone reflects a continuous structure roughly 50 km in length. A second zone, the Western Rainier Seismic Zone (WRSZ), does not correlate in any simple way with anomaly patterns, suggesting that the WRSZ does not represent a distinct fault. A 10 km-wide low velocity anomaly occurs 8 to 18 km beneath Mount Rainier, which I interpret to be due to a thermal aureole associated with the magmatic system beneath Mount Rainier. Volcano-tectonic earthquakes locate above this feature, and are interpreted to be caused by forces related to hydrothermal circulation and/or the cooling of magmatic bodies at depth.

Topology Optimization for Reducing Additive Manufacturing Processing Distortions

DTIC Science & Technology

2017-12-01

features that curl or warp under thermal load and are subsequently struck by the recoater blade /roller. Support structures act to wick heat away and...was run for 150 iterations. The material properties for all examples were Young’s modulus E = 1 GPa, Poisson’s ratio ν = 0.25, and thermal expansion...the element-birth model is significantly more computationally expensive for a full op- timization run . Consider, the computational complexity of a

Vessel Classification in Cosmo-Skymed SAR Data Using Hierarchical Feature Selection

NASA Astrophysics Data System (ADS)

Makedonas, A.; Theoharatos, C.; Tsagaris, V.; Anastasopoulos, V.; Costicoglou, S.

2015-04-01

SAR based ship detection and classification are important elements of maritime monitoring applications. Recently, high-resolution SAR data have opened new possibilities to researchers for achieving improved classification results. In this work, a hierarchical vessel classification procedure is presented based on a robust feature extraction and selection scheme that utilizes scale, shape and texture features in a hierarchical way. Initially, different types of feature extraction algorithms are implemented in order to form the utilized feature pool, able to represent the structure, material, orientation and other vessel type characteristics. A two-stage hierarchical feature selection algorithm is utilized next in order to be able to discriminate effectively civilian vessels into three distinct types, in COSMO-SkyMed SAR images: cargos, small ships and tankers. In our analysis, scale and shape features are utilized in order to discriminate smaller types of vessels present in the available SAR data, or shape specific vessels. Then, the most informative texture and intensity features are incorporated in order to be able to better distinguish the civilian types with high accuracy. A feature selection procedure that utilizes heuristic measures based on features' statistical characteristics, followed by an exhaustive research with feature sets formed by the most qualified features is carried out, in order to discriminate the most appropriate combination of features for the final classification. In our analysis, five COSMO-SkyMed SAR data with 2.2m x 2.2m resolution were used to analyse the detailed characteristics of these types of ships. A total of 111 ships with available AIS data were used in the classification process. The experimental results show that this method has good performance in ship classification, with an overall accuracy reaching 83%. Further investigation of additional features and proper feature selection is currently in progress.

The association between patella alta and the prevalence and worsening of structural features of patellofemoral joint osteoarthritis: The Multicenter Osteoarthritis Study

PubMed Central

Stefanik, J.J.; Zhu, Y.; Zumwalt, A.C.; Gross, K.D.; Clancy, M.; Lynch, J. A.; Frey Law, L.A.; Lewis, C.E.; Roemer, F.W.; Powers, C.M.; Guermazi, A.; Felson, D.T.

2010-01-01

Objective To examine the relationship between patella alta and the prevalence and worsening at follow-up of structural features of patellofemoral joint (PFJ) osteoarthritis (OA) on MRI. Methods The Multicenter Osteoarthritis (MOST) Study is a cohort study of persons aged 50-79 years with or at risk for knee OA. Patella alta was measured using the Insall-Salvati ratio (ISR) on the baseline lateral radiograph and cartilage damage, bone marrow lesions (BMLs), and subchondral bone attrition (SBA) were graded on MRI at baseline and at 30 months follow-up in the PFJ. We examined the association of the ISR with the prevalence and worsening of cartilage damage, BMLs, and SBA in the PFJ using logistic regression. Results 907 knees were studied (mean age 62, BMI 30, ISR 1.10), 63% from female subjects. Compared with knees in the lowest ISR quartile at baseline, those in the highest had 2.4 (95% CI 1.7, 3.3), 2.9 (2.0, 4.3), and 3.5 (2.3, 5.5) times the odds of having lateral PFJ cartilage damage, BMLs, and SBA respectively, and 1.5 (95% CI 1.1, 2.0), 1.3 (0.9, 1.8), and 2.2 (1.4, 3.4) times the odds of having medial PFJ cartilage damage, BMLs, and SBA respectively. Similarly, those with high ISRs were also at risk for worsening of cartilage damage and BMLs over time than those with low ISRs. Conclusion A high ISR, indicative of patella alta, is associated with structural features of OA in the PFJ. Additionally, the same knees have increased risk of worsening of these same features over time. PMID:20506169

The development of real-time stability supports visual working memory performance: Young children's feature binding can be improved through perceptual structure.

PubMed

Simmering, Vanessa R; Wood, Chelsey M

2017-08-01

Working memory is a basic cognitive process that predicts higher-level skills. A central question in theories of working memory development is the generality of the mechanisms proposed to explain improvements in performance. Prior theories have been closely tied to particular tasks and/or age groups, limiting their generalizability. The cognitive dynamics theory of visual working memory development has been proposed to overcome this limitation. From this perspective, developmental improvements arise through the coordination of cognitive processes to meet demands of different behavioral tasks. This notion is described as real-time stability, and can be probed through experiments that assess how changing task demands impact children's performance. The current studies test this account by probing visual working memory for colors and shapes in a change detection task that compares detection of changes to new features versus swaps in color-shape binding. In Experiment 1, 3- to 4-year-old children showed impairments specific to binding swaps, as predicted by decreased real-time stability early in development; 5- to 6-year-old children showed a slight advantage on binding swaps, but 7- to 8-year-old children and adults showed no difference across trial types. Experiment 2 tested the proposed explanation of young children's binding impairment through added perceptual structure, which supported the stability and precision of feature localization in memory-a process key to detecting binding swaps. This additional structure improved young children's binding swap detection, but not new-feature detection or adults' performance. These results provide further evidence for the cognitive dynamics and real-time stability explanation of visual working memory development. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Enriching 3D optical surface scans with prior knowledge: tissue thickness computation by exploiting local neighborhoods.

PubMed

Wissel, Tobias; Stüber, Patrick; Wagner, Benjamin; Bruder, Ralf; Schweikard, Achim; Ernst, Floris

2016-04-01

Patient immobilization and X-ray-based imaging provide neither a convenient nor a very accurate way to ensure low repositioning errors or to compensate for motion in cranial radiotherapy. We therefore propose an optical tracking device that exploits subcutaneous structures as landmarks in addition to merely spatial registration. To develop such head tracking algorithms, precise and robust computation of these structures is necessary. Here, we show that the tissue thickness can be predicted with high accuracy and moreover exploit local neighborhood information within the laser spot grid on the forehead to further increase this estimation accuracy. We use statistical learning with Support Vector Regression and Gaussian Processes to learn a relationship between optical backscatter features and an MR tissue thickness ground truth. We compare different kernel functions for the data of five different subjects. The incident angle of the laser on the forehead as well as local neighborhoods is incorporated into the feature space. The latter represent the backscatter features from four neighboring laser spots. We confirm that the incident angle has a positive effect on the estimation error of the tissue thickness. The root-mean-square error falls even below 0.15 mm when adding the complete neighborhood information. This prior knowledge also leads to a smoothing effect on the reconstructed skin patch. Learning between different head poses yields similar results. The partial overlap of the point clouds makes the trade-off between novel information and increased feature space dimension obvious and hence feature selection by e.g., sequential forward selection necessary.

Design and Analysis of Wind Turbine Rotors Using Hinged Structures and Rods

NASA Astrophysics Data System (ADS)

Lu, Hongya; Zeng, Pan; Lei, Liping

2018-03-01

Light weight and high stiffness are key design factors in ensuring cost effectiveness and reliability of wind turbines, especially for the inboard region of the rotor blades. In this study, several novel designs were developed to improve the mechanical performance of the rotor. Experiments were performed on an isolated blade incorporating the new features of a hinged structure and rods. The results validated the effectiveness of these features at alleviating the root-bending moment of the blade under varying wind loads and enhancing the stiffness of the blade. A numerical investigation was carried out to further examine the bending moment distribution, shear and axial force, and rod tension of these novel rotor designs under uniform loads. Longitudinal geometrical variations of the blade were considered in the model. Results showed that two designs realized a favorable bending moment distribution and improved the modal frequencies of the edgewise modes: bisymmetrical rods on a single-hinged structure and interveined symmetrical rods on a cantilevered structure. However, these designs have different deformation mechanisms. In addition, the first group of edgewise modal frequencies of these two designs were improved compared with the traditional rotor design. Their potential values in the application to the design of a lightweight, high-stiffness, and reliable wind turbine rotor were discussed.

Investigating the cognitive structure of stereotypes: Generic beliefs about groups predict social judgments better than statistical beliefs.

PubMed

Hammond, Matthew D; Cimpian, Andrei

2017-05-01

Stereotypes are typically defined as beliefs about groups, but this definition is underspecified. Beliefs about groups can be generic or statistical. Generic beliefs attribute features to entire groups (e.g., men are strong), whereas statistical beliefs encode the perceived prevalence of features (e.g., how common it is for men to be strong). In the present research, we sought to determine which beliefs-generic or statistical-are more central to the cognitive structure of stereotypes. Specifically, we tested whether generic or statistical beliefs are more influential in people's social judgments, on the assumption that greater functional importance indicates greater centrality in stereotype structure. Relative to statistical beliefs, generic beliefs about social groups were significantly stronger predictors of expectations (Studies 1-3) and explanations (Study 4) for unfamiliar individuals' traits. In addition, consistent with prior evidence that generic beliefs are cognitively simpler than statistical beliefs, generic beliefs were particularly predictive of social judgments for participants with more intuitive (vs. analytic) cognitive styles and for participants higher (vs. lower) in authoritarianism, who tend to view outgroups in simplistic, all-or-none terms. The present studies suggest that generic beliefs about groups are more central than statistical beliefs to the cognitive structure of stereotypes. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Ancestral multipartite units in light-responsive plant promoters have structural features correlating with specific phototransduction pathways.

PubMed Central

Argüello-Astorga, G R; Herrera-Estrella, L R

1996-01-01

Regulation of plant gene transcription by light is mediated by multipartite cis-regulatory units. Previous attempts to identify structural features that are common to all light-responsive elements (LREs) have been unsuccessful. To address the question of what is needed to confer photoresponsiveness to a promoter, the upstream sequences from more than 110 light-regulated plant genes were analyzed by a new, phylogenetic-structural method. As a result, 30 distinct conserved DNA module arrays (CMAs) associated with light-responsive promoter regions were identified. Several of these CMAs have remained invariant throughout the evolutionary radiation of angiosperms and are conserved between homologous genes as well as between members of different gene families. The identified CMAs share a gene superfamily-specific core that correlates with the particular phytochrome-dependent transduction pathway that controls their expression, i.e. ACCTA(A/C)C(A/C) for the cGMP-dependent phenylpropanoid metabolism-associated genes, and GATA(A/T)GR for the Ca2+/calmodulin-dependent photosynthesis-associated nuclear genes. In addition to suggesting a general model for the functional and structural organization of LREs, the data obtained in this study indicate that angiosperm LREs probably evolved from complex cis-acting elements involved in regulatory processes other than photoregulation in gymnosperms. PMID:8938415

Advanced Metallic Thermal Protection System Development

NASA Technical Reports Server (NTRS)

Blosser, M. L.; Chen, R. R.; Schmidt, I. H.; Dorsey, J. T.; Poteet, C. C.; Bird, R. K.

2002-01-01

A new Adaptable, Robust, Metallic, Operable, Reusable (ARMOR) thermal protection system (TPS) concept has been designed, analyzed, and fabricated. In addition to the inherent tailorable robustness of metallic TPS, ARMOR TPS offers improved features based on lessons learned from previous metallic TPS development efforts. A specific location on a single-stage-to-orbit reusable launch vehicle was selected to develop loads and requirements needed to design prototype ARMOR TPS panels. The design loads include ascent and entry heating rate histories, pressures, acoustics, and accelerations. Additional TPS design issues were identified and discussed. An iterative sizing procedure was used to size the ARMOR TPS panels for thermal and structural loads as part of an integrated TPS/cryogenic tank structural wall. The TPS panels were sized to maintain acceptable temperatures on the underlying structure and to operate under the design structural loading. Detailed creep analyses were also performed on critical components of the ARMOR TPS panels. A lightweight, thermally compliant TPS support system (TPSS) was designed to connect the TPS to the cryogenic tank structure. Four 18-inch-square ARMOR TPS panels were fabricated. Details of the fabrication process are presented. Details of the TPSS for connecting the ARMOR TPS panels to the externally stiffened cryogenic tank structure are also described. Test plans for the fabricated hardware are presented.

Direct methods in protein crystallography.

PubMed

Karle, J

1989-11-01

It is pointed out that the 'direct methods' of phase determination for small-structure crystallography do not have immediate applicability to macromolecular structures. The term 'direct methods in macromolecular crystallography' is suggested to categorize a spectrum of approaches to macromolecular structure determination in which the analyses are characterized by the use of two-phase and higher-order-phase invariants. The evaluation of the invariants is generally obtained by the use of heavy-atom techniques. The results of a number of the more recent algebraic and probabilistic studies involving isomorphous replacement and anomalous dispersion thus become valid subjects for discussion here. These studies are described and suggestions are also presented concerning future applicability. Additional discussion concerns the special techniques of filtering, the use of non-crystallographic symmetry, some features of maximum entropy and attempts to apply phase-determining formulas to the refinement of macromolecular structure. It is noted that, in addition to the continuing remarkable progress in macromolecular crystallography based on the traditional applications of isomorphous replacement and anomalous dispersion, recent valuable advances have been made in the application of non-crystallographic symmetry, in particular, to virus structures and in applications of filtering. Good progress has also been reported in the application of exact linear algebra to multiple-wavelength anomalous-dispersion investigations of structures containing anomalous scatterers of only moderate scattering power.

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

PubMed

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

2016-05-01

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

REVIEWS OF TOPICAL PROBLEMS: Prediction and discovery of new structures in spiral galaxies

NASA Astrophysics Data System (ADS)

Fridman, Aleksei M.

2007-02-01

A review is given of the last 20 years of published research into the nature, origin mechanisms, and observed features of spiral-vortex structures found in galaxies. The so-called rotating shallow water experiments are briefly discussed, carried out with a facility designed by the present author and built at the Russian Scientific Center 'Kurchatov Institute' to model the origin of galactic spiral structures. The discovery of new vortex-anticyclone structures in these experiments stimulated searching for them astronomically using the RAS Special Astrophysical Observatory's 6-meter BTA optical telescope, formerly the world's and now Europe's largest. Seven years after the pioneering experiments, Afanasyev and the present author discovered the predicted giant anticyclones in the galaxy Mrk 1040 by using BTA. Somewhat later, the theoretical prediction of giant cyclones in spiral galaxies was made, also to be verified by BTA afterwards. To use the observed line-of-sight velocity field for reconstructing the 3D velocity vector distribution in a galactic disk, a method for solving a problem from the class of ill-posed astrophysical problems was developed by the present author and colleagues. In addition to the vortex structure, other new features were discovered — in particular, slow bars (another theoretical prediction), for whose discovery an observational test capable of distinguishing them from their earlier-studied normal (fast) counterparts was designed.

Structure and origin of Australian ring and dome features with reference to the search for asteroid impact events

NASA Astrophysics Data System (ADS)

Glikson, Andrew

2018-01-01

Ring, dome and crater features on the Australian continent and shelf include (A) 38 structures of confirmed or probable asteroid and meteorite impact origin and (B) numerous buried and exposed ring, dome and crater features of undefined origin. A large number of the latter include structural and geophysical elements consistent with impact structures, pending test by field investigations and/or drilling. This paper documents and briefly describes 43 ring and dome features with the aim of appraising their similarities and differences from those of impact structures. Discrimination between impact structures and igneous plugs, volcanic caldera and salt domes require field work and/or drilling. Where crater-like morphological patterns intersect pre-existing linear structural features and contain central morphological highs and unique thrust and fault patterns an impact connection needs to tested in the field. Hints of potential buried impact structures may be furnished by single or multi-ring TMI patterns, circular TMI quiet zones, corresponding gravity patterns, low velocity and non-reflective seismic zones.

PredPPCrys: accurate prediction of sequence cloning, protein production, purification and crystallization propensity from protein sequences using multi-step heterogeneous feature fusion and selection.

PubMed

Wang, Huilin; Wang, Mingjun; Tan, Hao; Li, Yuan; Zhang, Ziding; Song, Jiangning

2014-01-01

X-ray crystallography is the primary approach to solve the three-dimensional structure of a protein. However, a major bottleneck of this method is the failure of multi-step experimental procedures to yield diffraction-quality crystals, including sequence cloning, protein material production, purification, crystallization and ultimately, structural determination. Accordingly, prediction of the propensity of a protein to successfully undergo these experimental procedures based on the protein sequence may help narrow down laborious experimental efforts and facilitate target selection. A number of bioinformatics methods based on protein sequence information have been developed for this purpose. However, our knowledge on the important determinants of propensity for a protein sequence to produce high diffraction-quality crystals remains largely incomplete. In practice, most of the existing methods display poorer performance when evaluated on larger and updated datasets. To address this problem, we constructed an up-to-date dataset as the benchmark, and subsequently developed a new approach termed 'PredPPCrys' using the support vector machine (SVM). Using a comprehensive set of multifaceted sequence-derived features in combination with a novel multi-step feature selection strategy, we identified and characterized the relative importance and contribution of each feature type to the prediction performance of five individual experimental steps required for successful crystallization. The resulting optimal candidate features were used as inputs to build the first-level SVM predictor (PredPPCrys I). Next, prediction outputs of PredPPCrys I were used as the input to build second-level SVM classifiers (PredPPCrys II), which led to significantly enhanced prediction performance. Benchmarking experiments indicated that our PredPPCrys method outperforms most existing procedures on both up-to-date and previous datasets. In addition, the predicted crystallization targets of currently non-crystallizable proteins were provided as compendium data, which are anticipated to facilitate target selection and design for the worldwide structural genomics consortium. PredPPCrys is freely available at http://www.structbioinfor.org/PredPPCrys.

Imaging pigment chemistry in melanocytic conjunctival lesions with pump-probe microscopy

NASA Astrophysics Data System (ADS)

Wilson, Jesse W.; Vajzovic, Lejla; Robles, Francisco E.; Cummings, Thomas J.; Mruthyunjaya, Prithvi; Warren, Warren S.

2013-03-01

We extend nonlinear pump-probe microscopy, recently demonstrated to image the microscopic distribution of eumelanin and pheomelanin in unstained skin biopsy sections, to the case of melanocytic conjunctival lesions. The microscopic distribution of pigmentation chemistry serves as a functional indicator of melanocyte activity. In these conjunctival specimens (benign nevi, primary acquired melanoses, and conjunctival melanoma), we have observed pump-probe spectroscopic signatures of eumelanin, pheomelanin, hemoglobin, and surgical ink, in addition to important structural features that differentiate benign from malignant lesions. We will also discuss prospects for an in vivo `optical biopsy' to provide additional information before having to perform invasive procedures.

Magnetic properties of the honeycomb oxide Na 2 Co 2 TeO 6

DOE PAGES

Lefrançois, E.; Songvilay, M.; Robert, J.; ...

2016-12-14

We have studied the magnetic properties of Na 2 Co 2 TeO 6 , which features a honeycomb lattice of magnetic Co 2 + ions, through macroscopic characterization and neutron diffraction on a powder sample. We also show that this material orders in a zigzag antiferromagnetic structure. Additionally by allowing a linear magnetoelectric coupling, this magnetic arrangement displays very peculiar spatial magnetic correlations, larger in the honeycomb planes than between the planes, which do not evolve with the temperature. We have investigated this behavior by classical Monte Carlo calculations using the J 1 - J 2 - Jmore » 3 model on a honeycomb lattice with a small interplane interaction. Furthermore, our model reproduces the experimental neutron structure factor, although its absence of temperature evolution must be due to additional ingredients, such as chemical disorder or quantum fluctuations enhanced by the proximity to a phase boundary.« less

Phosphorus K4 Crystal: A New Stable Allotrope

PubMed Central

Liu, Jie; Zhang, Shunhong; Guo, Yaguang; Wang, Qian

2016-01-01

The intriguing properties of phosphorene motivate scientists to further explore the structures and properties of phosphorus materials. Here, we report a new allotrope named K4 phosphorus composed of three-coordinated phosphorus atoms in non-layered structure which is not only dynamically and mechanically stable, but also possesses thermal stability comparable to that of the orthorhombic black phosphorus (A17). Due to its unique configuration, K4 phosphorus exhibits exceptional properties: it possesses a band gap of 1.54 eV which is much larger than that of black phosphorus (0.30 eV), and it is stiffer than black phosphorus. The band gap of the newly predicted phase can be effectively tuned by appling hydrostastic pressure. In addition, K4 phosphorus exibits a good light absorption in visible and near ultraviolet region. These findings add additional features to the phosphorus family with new potential applications in nanoelectronics and nanomechanics. PMID:27857232

Replication fidelity assessment of large area sub-μm structured polymer surfaces using scatterometry

NASA Astrophysics Data System (ADS)

Calaon, M.; Madsen, M. H.; Weirich, J.; Hansen, H. N.; Tosello, G.; Hansen, P. E.; Garnaes, J.; Tang, P. T.

2015-12-01

The present study addresses one of the key challenges in the product quality control of transparent structured polymer substrates, the replication fidelity of sub-μm structures over a large area. Additionally the work contributes to the development of new techniques focused on in-line characterization of large nanostructured surfaces using scatterometry. In particular an approach to quantify the replication fidelity of high volume manufacturing processes such as polymer injection moulding is presented. Both periodic channels and semi-spherical structures were fabricated on nickel shims used for later injection moulding of Cyclic-olefin-copolymer (COC) substrate were the sub-μm features where ultimately transferred. The scatterometry system was validated using calibrated atomic force microscopy measurements and a model based on scalar diffraction theory employed to calculate the expected angular distribution of the reflected and the transmitted intensity for the nickel surfaces and structured COC and, respectively.

Structural classification of CDR-H3 revisited: a lesson in antibody modeling.

PubMed

Kuroda, Daisuke; Shirai, Hiroki; Kobori, Masato; Nakamura, Haruki

2008-11-15

Among the six complementarity-determining regions (CDRs) in the variable domains of an antibody, the third CDR of the heavy chain (CDR-H3), which lies in the center of the antigen-binding site, plays a particularly important role in antigen recognition. CDR-H3 shows significant variability in its length, sequence, and structure. Although difficult, model building of this segment is the most critical step in antibody modeling. Since our first proposal of the "H3-rules," which classify CDR-H3 structure based on amino acid sequence, the number of experimentally determined antibody structures has increased. Here, we revise these H3-rules and propose an improved classification scheme for CDR-H3 structure modeling. In addition, we determine the common features of CDR-H3 in antibody drugs as well as discuss the concept of "antibody druggability," which can be applied as an indicator of antibody evaluation during drug discovery.

Structural and Mechanistic Insights into C-P Bond Hydrolysis by Phosphonoacetate Hydrolase

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

Agarwal, Vinayak; Borisova, Svetlana A.; Metcalf, William W.

2011-12-22

Bacteria have evolved pathways to metabolize phosphonates as a nutrient source for phosphorus. In Sinorhizobium meliloti 1021, 2-aminoethylphosphonate is catabolized to phosphonoacetate, which is converted to acetate and inorganic phosphate by phosphonoacetate hydrolase (PhnA). Here we present detailed biochemical and structural characterization of PhnA that provides insights into the mechanism of C-P bond cleavage. The 1.35 {angstrom} resolution crystal structure reveals a catalytic core similar to those of alkaline phosphatases and nucleotide pyrophosphatases but with notable differences, such as a longer metal-metal distance. Detailed structure-guided analysis of active site residues and four additional cocrystal structures with phosphonoacetate substrate, acetate, phosphonoformatemore » inhibitor, and a covalently bound transition state mimic provide insight into active site features that may facilitate cleavage of the C-P bond. These studies expand upon the array of reactions that can be catalyzed by enzymes of the alkaline phosphatase superfamily.« less

High Quality Facade Segmentation Based on Structured Random Forest, Region Proposal Network and Rectangular Fitting

NASA Astrophysics Data System (ADS)

Rahmani, K.; Mayer, H.

2018-05-01

In this paper we present a pipeline for high quality semantic segmentation of building facades using Structured Random Forest (SRF), Region Proposal Network (RPN) based on a Convolutional Neural Network (CNN) as well as rectangular fitting optimization. Our main contribution is that we employ features created by the RPN as channels in the SRF.We empirically show that this is very effective especially for doors and windows. Our pipeline is evaluated on two datasets where we outperform current state-of-the-art methods. Additionally, we quantify the contribution of the RPN and the rectangular fitting optimization on the accuracy of the result.

The morphologic universe of melanoma.

PubMed

Jaimes, Natalia; Marghoob, Ashfaq A

2013-10-01

Differentiating dysplastic nevi from melanoma remains one of the main objectives of dermoscopy. Melanomas tend not to manifest any of the benign patterns described for nevi and instead usually display chaotic dermoscopic morphologies. Melanomas located on the face, chronically sun-damaged skin, volar surfaces, nails, and mucosal surfaces have additional features that can assist in their identification. However, some melanomas lack any defined dermoscopic structures. These so-called featureless melanomas can be identified via digital surveillance. This article reviews the melanoma-specific structures as a function of anatomic location (ie, melanomas on nonglabrous skin, face, volar surfaces, mucosae, and nails). Copyright © 2013 Elsevier Inc. All rights reserved.

Compact optical filter for dual-wavelength fluorescence-spectrometry based on enhanced transmission through metallic nano-slit array

NASA Astrophysics Data System (ADS)

Hu, X.; Zhan, L.; Xia, Y.

2009-03-01

A novel optical filter based on enhanced transmission through metallic nano-slit is proposed for dual-wavelength fluorescence-spectrometry. A special structure, sampled-period slit array, is utilized to meet the requirement of dual-wavelength transmission in this system. Structure parameters on the transmission property are analyzed by means of Fourier transformation. With the features both to enhance the fluorescence generation and to enhance light transmission, in addition with the feasibility for miniaturization, integration on one chip, and mass production, the proposed filters are promising for the realization of dual-wavelength fluorescence-spectrometry in micro-total-analysis-system.

A novel asymmetric chair-like hydroxyl-bridged tetra-copper compound: Synthesis, supramolecular structure and magnetic property

NASA Astrophysics Data System (ADS)

Wang, Xiao-Feng; Du, Ke-Jie; Wang, Hong-Qing; Zhang, Xue-Li; Nie, Chang-Ming

2017-06-01

A new polynuclear Cu(II) compound, [Cu4(bpy)4(OH)4(H2O)(BTC)]NO3·8H2O (1), was prepared by self-assembly from the solution of copper(II) nitrate and two kinds of ligands, 2,2‧-bipyridine (bpy) and benzene-tricarboxylic acid (H3BTC). Single crystal structure analysis reveals that 1 features a rare asymmetric chair-like hydroxyl-bridged tetra-copper cluster: [Cu4(OH)4] core along with one H2O and one BTC3- occupied each terminal coordinated site. In addition, the magnetic property has been investigated.

Uranus - Disk structure within the 7300-A methane band

NASA Technical Reports Server (NTRS)

Price, M. J.; Franz, O. G.

1979-01-01

Orthogonal narrow-band (100 A) photoelectric slit scan photometry of Uranus has been used to infer the basic two-dimensional structure of the disk within the 7300-A methane band. Numerical image reconstruction and restoration techniques have been applied to quantitatively estimate the degrees of polar and limb brightening on the planet. Through partial removal of atmospheric smearing, an effective spatial resolution of approximately 0.9 arcsec has been achieved. Peak polar, limb, and central intensities on the disk are in the respective proportions 3:2:1. In addition, the bright polar feature is displaced from the geometric pole towards the equator of the planet.

Phellilane L, Sesquiterpene Metabolite of Phellinus linteus: Isolation, Structure Elucidation, and Asymmetric Total Synthesis.

PubMed

Ota, Koichiro; Yamazaki, Ikuma; Saigoku, Takahiro; Fukui, Mei; Miyata, Tomoki; Kamaike, Kazuo; Shirahata, Tatsuya; Mizuno, Fumi; Asada, Yoshihisa; Hirotani, Masao; Ino, Chieko; Yoshikawa, Takafumi; Kobayashi, Yoshinori; Miyaoka, Hiroaki

2017-12-01

A new cyclopropane-containing sesquiterpenoid, phellilane L (1), was isolated from the medicinal mushroom Phellinus linteus ("Meshimakobu" in Japanese), a member of the Hymenochaetaceae family and a well-known fungus that is widely used in East Asia. The planar structure of 1 was determined on the basis of spectroscopic analysis. The authors achieved the first total synthesis of 1. Our protecting group-free synthesis features a highly stereoselective one-pot synthesis involving an intermolecular alkylation/cyclization/lactonization strategy for construction of the key cyclopropane-γ-lactone intermediate. Additionally, our synthesis determined the absolute configuration of phellilane L (1).

The preparation and characterization of a lithium borate glass prepared by the gel technique

NASA Technical Reports Server (NTRS)

Weinberg, M. C.; Neilson, G. F.; Smith, G. L.; Dunn, B.; Moore, G. S.; Mackenzie, J. D.

1985-01-01

The preparation of an amorphous lithium borate gel by the metal organic procedure is described. In addition, a preliminary evaluation of the behavior of the gel upon heating is given. In particular the crystallization tendency of the gel is studied with the aid of DTA and X-ray diffraction, and the structural changes in the gel are monitored with the aid of IR spectroscopy. The glass produced from the lithium borate gel is compared to both the gel precursor material and a glass of similar composition prepared by conventional techniques. Specifically, the relevant water contents, crystallization behavior, and structural features are contrasted.

Experimental shock deformation in zircon: a transmission electron microscopic study

NASA Astrophysics Data System (ADS)

Leroux, H.; Reimold, W. U.; Koeberl, C.; Hornemann, U.; Doukhan, J.-C.

1999-06-01

In recent years, apparently shock-induced and, thus, impact-characteristic microdeformations, in the form of planar microdeformation features and so-called strawberry (granular) texture, have been observed in zircons in rocks from confirmed impact structures and from the K/ T boundary. The nature of the planar microdeformations in this mineral is, however, still unknown, and critical information is needed regarding the shock pressure range in which these deformation effects are produced. We experimentally shock deformed two series of thin zircon (ZrSiO 4) target plates, cut perpendicular to the c-axis, at shock pressures of 20, 40, and 60 GPa. The recovered samples were characterized by optical and scanning electron microscopy. In addition, one sample series was studied by transmission electron microscopy (TEM). Microdeformation effects observed at 20 GPa include pervasive micro-cleavage and dislocation patterns. Plastic deformation is indicated by a high density of straight dislocations in glide configuration. The dominant glide systems are <100>{010}. Micro-cleavages, induced by shear stresses during the compression stage, occur mostly in the {100} planes. The large density of dislocations at crack tips shows that plastic deformation was initiated by the micro-cracking processs. At 40 GPa, the sample was partly transformed from the zircon (z) to a scheelite (CaWO 4)-type (s) structure. Planar deformation features (PDFs) containing an amorphous phase of zircon composition are present in the not yet transformed zircon relics. The phase with scheelite structure, initiated in the {100} planes of zircon, consists of thin (0.1 to several μm) bands that crosscut the zircon matrix. The phase transformation is displacive (martensitic) and can be related by {100} z // {112} s and [001] z // <110> s. The scheelite structure phase is densely twinned, with twins in the (112) plane. The 60-GPa sample consists completely of the scheelite structure phase. Crosscutting and displacing relationships between twins and PDFs demonstrate that PDFs are formed in the zircon structure, i.e., before the phase transformation to the scheelite structure occurred, most likely at the shock front. Crystallographic orientations of optically visible planar features in zircon, in comparison with orientations of planar defects at the TEM scale, suggest that the optically visible features are more likely planar microfractures than PDFs.

Structural changes of macula and optic disk of the fellow eye in patients with nonarteritic anterior ischemic optic neuropathy.

PubMed

Duman, R; Yavas, G F; Veliyev, I; Dogan, M; Duman, R

2018-05-10

The aim was to assess the ganglion cell complex (GCC) thickness, retinal nerve fiber layer (RNFL) thickness and optic disk features in the affected eyes (AE) and unaffected fellow eyes (FE) of subjects with unilateral nonarteritic anterior ischemic optic neuropathy (NAION) and to compare with healthy control eyes (CE) using spectral domain-optical coherence tomography (SD-OCT). This study included 28 patients and age, sex and refraction-matched 28 control subjects. Mean GCC thickness and peripapillary RNFL thickness in four quadrants measured by cirrus SD-OCT were evaluated in both AE and FE of patients and CE. In addition, optic disk measurements obtained with OCT were evaluated. Mean GCC thickness was significantly lower in AE compared with both FE and CE (P < 0.001), and mean GCC thickness in FE was significantly lower than CE (P = 0.022). In addition, mean RNFL thickness in superior and nasal quadrants significantly decreased in FE compared with CE (P = 0.020 and 0.010, respectively). Furthermore, AE had significantly greater optic disk cupping compared with both FE and CE (P < 0.001). GCC and RNFL thickness decreased significantly at late stages of NAION, in both AE and FE compared with CE, suggesting that some subclinical structural changes may occur in FE despite lack of obvious visual symptoms. In addition, there was no significant difference in optic disk features between the CE and FE. And significantly greater optic disk cupping in the AE compared with both FE and CE supports the acquired enlargement of cupping after the onset of NAION.

Model of community emergence in weighted social networks

NASA Astrophysics Data System (ADS)

Kumpula, J. M.; Onnela, J.-P.; Saramäki, J.; Kertész, J.; Kaski, K.

2009-04-01

Over the years network theory has proven to be rapidly expanding methodology to investigate various complex systems and it has turned out to give quite unparalleled insight to their structure, function, and response through data analysis, modeling, and simulation. For social systems in particular the network approach has empirically revealed a modular structure due to interplay between the network topology and link weights between network nodes or individuals. This inspired us to develop a simple network model that could catch some salient features of mesoscopic community and macroscopic topology formation during network evolution. Our model is based on two fundamental mechanisms of network sociology for individuals to find new friends, namely cyclic closure and focal closure, which are mimicked by local search-link-reinforcement and random global attachment mechanisms, respectively. In addition we included to the model a node deletion mechanism by removing all its links simultaneously, which corresponds for an individual to depart from the network. Here we describe in detail the implementation of our model algorithm, which was found to be computationally efficient and produce many empirically observed features of large-scale social networks. Thus this model opens a new perspective for studying such collective social phenomena as spreading, structure formation, and evolutionary processes.

CLICK: The new USGS center for LIDAR information coordination and knowledge

USGS Publications Warehouse

Stoker, Jason M.; Greenlee, Susan K.; Gesch, Dean B.; Menig, Jordan C.

2006-01-01

Elevation data is rapidly becoming an important tool for the visualization and analysis of geographic information. The creation and display of three-dimensional models representing bare earth, vegetation, and structures have become major requirements for geographic research in the past few years. Light Detection and Ranging (lidar) has been increasingly accepted as an effective and accurate technology for acquiring high-resolution elevation data for bare earth, vegetation, and structures. Lidar is an active remote sensing system that records the distance, or range, of a laser fi red from an airborne or space borne platform such as an airplane, helicopter or satellite to objects or features on the Earth’s surface. By converting lidar data into bare ground topography and vegetation or structural morphologic information, extremely accurate, high-resolution elevation models can be derived to visualize and quantitatively represent scenes in three dimensions. In addition to high-resolution digital elevation models (Evans et al., 2001), other lidar-derived products include quantitative estimates of vegetative features such as canopy height, canopy closure, and biomass (Lefsky et al., 2002), and models of urban areas such as building footprints and three-dimensional city models (Maas, 2001).

AUTO-MUTE 2.0: A Portable Framework with Enhanced Capabilities for Predicting Protein Functional Consequences upon Mutation.

PubMed

Masso, Majid; Vaisman, Iosif I

2014-01-01

The AUTO-MUTE 2.0 stand-alone software package includes a collection of programs for predicting functional changes to proteins upon single residue substitutions, developed by combining structure-based features with trained statistical learning models. Three of the predictors evaluate changes to protein stability upon mutation, each complementing a distinct experimental approach. Two additional classifiers are available, one for predicting activity changes due to residue replacements and the other for determining the disease potential of mutations associated with nonsynonymous single nucleotide polymorphisms (nsSNPs) in human proteins. These five command-line driven tools, as well as all the supporting programs, complement those that run our AUTO-MUTE web-based server. Nevertheless, all the codes have been rewritten and substantially altered for the new portable software, and they incorporate several new features based on user feedback. Included among these upgrades is the ability to perform three highly requested tasks: to run "big data" batch jobs; to generate predictions using modified protein data bank (PDB) structures, and unpublished personal models prepared using standard PDB file formatting; and to utilize NMR structure files that contain multiple models.

The newly expanded KSC Visitors Complex features a new ticket plaza, information center, exhibits an

NASA Technical Reports Server (NTRS)

1999-01-01

A host robot, Starquester 2000, helps describe for visitors the accomplishments of unsung space heroes - space probes - and their role in space exploration. The walk-through Robot Scouts exhibit is part of the $13 million expansion to KSC's Visitor Complex. Other additions include a walk-through Robot Scouts exhibit, a wildlife exhibit, and the film Quest for Life in a new 300-seat theater, plus an International Space Station-themed ticket plaza, featuring a structure of overhanging solar panels and astronauts performing assembly tasks. Inaugurated three decades ago, the Visitor Complex is now one of the top five tourist attractions in Florida. It is located on S.R. 407, east of I-95, within the Merritt Island National Wildlife Refuge.

Visual Pattern Analysis in Histopathology Images Using Bag of Features

NASA Astrophysics Data System (ADS)

Cruz-Roa, Angel; Caicedo, Juan C.; González, Fabio A.

This paper presents a framework to analyse visual patterns in a collection of medical images in a two stage procedure. First, a set of representative visual patterns from the image collection is obtained by constructing a visual-word dictionary under a bag-of-features approach. Second, an analysis of the relationships between visual patterns and semantic concepts in the image collection is performed. The most important visual patterns for each semantic concept are identified using correlation analysis. A matrix visualization of the structure and organization of the image collection is generated using a cluster analysis. The experimental evaluation was conducted on a histopathology image collection and results showed clear relationships between visual patterns and semantic concepts, that in addition, are of easy interpretation and understanding.

Biofuels combustion.

PubMed

Westbrook, Charles K

2013-01-01

This review describes major features of current research in renewable fuels derived from plants and from fatty acids. Recent and ongoing fundamental studies of biofuel molecular structure, oxidation reactions, and biofuel chemical properties are reviewed, in addition to combustion applications of biofuels in the major types of engines in which biofuels are used. Biofuels and their combustion are compared with combustion features of conventional petroleum-based fuels. Two main classes of biofuels are described, those consisting of small, primarily alcohol, fuels (particularly ethanol, n-butanol, and iso-pentanol) that are used primarily to replace or supplement gasoline and those derived from fatty acids and used primarily to replace or supplement conventional diesel fuels. Research efforts on so-called second- and third-generation biofuels are discussed briefly.

Hallerman-Streiff-like syndrome presenting with laterality and cardiac defects.

PubMed

Morice-Picard, Fanny; Marlin, Sandrine; Rooryck, Caroline; Fayon, Mickael; Thambo, Jeao-Benoît; Demarquez, Jean-Louis; Fauroux, Brigitte; Denoyelle, Francoise; Lacombe, Didier

2009-04-01

We report two patients considered to have an atypical presentation of Hallerman-Streiff syndrome (HSS) associated with laterality and cardiac defects. Clinical features include typical facial gestalt, atrophy of the skin, and hypotrichosis. Ophthalmologic abnormalities, normally present in HSS, are only found in one of the two patients. Both of them have respiratory problems secondary to the classical narrow upper airway described in this syndrome. Both these patients have laterality defects and one has additional structural cardiac malformations. Cardiac defects have occasionally been reported in the HSS literature, but are not considered as a classical feature of the syndrome. Situs inversus has never been reported in this syndrome. Almost all HSS cases have been sporadic and their origin and inheritance pattern remain unknown.

Structure-function analysis of the auxilin J-domain reveals an extended Hsc70 interaction interface.

PubMed

Jiang, Jianwen; Taylor, Alexander B; Prasad, Kondury; Ishikawa-Brush, Yumiko; Hart, P John; Lafer, Eileen M; Sousa, Rui

2003-05-20

J-domains are widespread protein interaction modules involved in recruiting and stimulating the activity of Hsp70 family chaperones. We have determined the crystal structure of the J-domain of auxilin, a protein which is involved in uncoating clathrin-coated vesicles. Comparison to the known structures of J-domains from four other proteins reveals that the auxilin J-domain is the most divergent of all J-domain structures described to date. In addition to the canonical J-domain features described previously, the auxilin J-domain contains an extra N-terminal helix and a long loop inserted between helices I and II. The latter loop extends the positively charged surface which forms the Hsc70 binding site, and is shown by directed mutagenesis and surface plasmon resonance to contain side chains important for binding to Hsc70.

Voltage-Gated Potassium Channels: A Structural Examination of Selectivity and Gating

PubMed Central

Kim, Dorothy M.; Nimigean, Crina M.

2016-01-01

Voltage-gated potassium channels play a fundamental role in the generation and propagation of the action potential. The discovery of these channels began with predictions made by early pioneers, and has culminated in their extensive functional and structural characterization by electrophysiological, spectroscopic, and crystallographic studies. With the aid of a variety of crystal structures of these channels, a highly detailed picture emerges of how the voltage-sensing domain reports changes in the membrane electric field and couples this to conformational changes in the activation gate. In addition, high-resolution structural and functional studies of K+ channel pores, such as KcsA and MthK, offer a comprehensive picture on how selectivity is achieved in K+ channels. Here, we illustrate the remarkable features of voltage-gated potassium channels and explain the mechanisms used by these machines with experimental data. PMID:27141052

Design of plate directional heat transmission structure based on layered thermal metamaterials

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

Sun, L. K.; Yu, Z. F.; Huang, J., E-mail: slk-0-1999@163.com

2016-02-15

Invisibility cloaks based on transformation optics are often closed structures; however, such a structure limits the kinds of objects that can be placed in the cloak. In this work, we adopt a transformation thermodynamics approach to design an “open cloak”, called a plate directional heat transmission structure, which is capable of guiding heat fluxes to the flank region of the metamaterial device. The most fascinating and unique feature of the device is that the lower surface can remain at a lower temperature compared with the SiO{sub 2} aerogel thermal insulation material. Our results are expected to markedly enhance capabilities inmore » thermal protection, thermal-energy utilization, and domains beyond. In addition to the theoretical analysis, the present design is demonstrated in numerical simulations based on finite element calculations.« less

The impact of aging on epithelial barriers.

PubMed

Parrish, Alan R

2017-10-02

The epithelium has many critical roles in homeostasis, including an essential responsibility in establishing tissue barriers. In addition to the fundamental role in separating internal from external environment, epithelial barriers maintain nutrient, fluid, electrolyte and metabolic waste balance in multiple organs. While, by definition, barrier function is conserved, the structure of the epithelium varies across organs. For example, the skin barrier is a squamous layer of cells with distinct structural features, while the lung barrier is composed of a very thin single cell to minimize diffusion space. With the increased focus on age-dependent alterations in organ structure and function, there is an emerging interest in the impact of age on epithelial barriers. This review will focus on the impact of aging on the epithelial barrier of several organs, including the skin, lung, gastrointestinal tract and the kidney, at a structural and functional level.

Evolution of salt and hydrocarbon migration: Sweet Lake area, Cameron Parish, Louisiana

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

Spencer, J.A.; Sharpe, C.L.

The interpretation of seismic, gravity, and well data in northern Cameron Parish, Louisiana suggest that lateral salt flow has influenced the area`s structural evolution, depositional patterns, and hydrocarbon migration. Sweet Lake Field has produced over 46 MMBO and 15 BCFG from Middle Miocene deltaic sands. The structural closure is a downthrown anticline on a fault controlled by the underlying salt feature. Sweet Lake Field overlies an allochthonous salt mass that was probably once part of an ancestral salt ridge extending from Hackberry to Big Lake fields. Nine wells encountering top of salt and several seismic lines define a detached saltmore » feature underlying over twenty square miles at depths from 8500-18,000 ft. Salt withdrawal in the East Hackberry-Big Lake area influenced the depositional patterns of the Oligocene lower Hackberry channel systems. Progradation of thick Middle Oligocene Camerina (A) and Miogypsinoides sands into the area caused salt thinning and withdrawal resulting in the development and orientation of the large Marginulina-Miogypsinoides growth fault northwest of Sweet Lake. Additional evidence for the southeast trend of the salt is a well approximately two miles southeast of Sweet Lake which encountered salt at approximately 19,800 ft. High quality 2-D and 3-D seismic data will continue to enhance the regional understanding of the evolving salt structures in the onshore Gulf Coast and the local understanding of hydrocarbon migration. Additional examples of lateral salt flow will be recognized and some may prove to have subsalt hydrocarbon potential.« less

GeoSciML version 3: A GML application for geologic information

NASA Astrophysics Data System (ADS)

International Union of Geological Sciences., I. C.; Richard, S. M.

2011-12-01

After 2 years of testing and development, XML schema for GeoSciML version 3 are now ready for application deployment. GeoSciML draws from many geoscience data modelling efforts to establish a common suite of feature types to represent information associated with geologic maps (materials, structures, and geologic units) and observations including structure data, samples, and chemical analyses. After extensive testing and use case analysis, in December 2008 the CGI Interoperability Working Group (IWG) released GeoSciML 2.0 as an application schema for basic geological information. GeoSciML 2.0 is in use to deliver geologic data by the OneGeology Europe portal, the Geological Survey of Canada Groundwater Information Network (wet GIN), and the Auscope Mineral Resources portal. GeoSciML to version 3.0 is updated to OGC Geography Markup Language v3.2, re-engineered patterns for association of element values with controlled vocabulary concepts, incorporation of ISO19156 Observation and Measurement constructs for representing numeric and categorical values and for representing analytical data, incorporation of EarthResourceML to represent mineral occurrences and mines, incorporation of the GeoTime model to represent GSSP and stratigraphic time scale, and refactoring of the GeoSciML namespace to follow emerging ISO practices for decoupling of dependencies between standardized namespaces. These changes will make it easier for data providers to link to standard vocabulary and registry services. The depth and breadth of GeoSciML remains largely unchanged, covering the representation of geologic units, earth materials and geologic structures. ISO19156 elements and patterns are used to represent sampling features such as boreholes and rock samples, as well as geochemical and geochronologic measurements. Geologic structures include shear displacement structures (brittle faults and ductile shears), contacts, folds, foliations, lineations and structures with no preferred orientation (e.g. 'miarolitic cavities'). The Earth material package allows for the description of both individual components, such as minerals, and compound materials, such as rocks or unconsolidated materials. Provision is made for alteration, weathering, metamorphism, particle geometry, fabric, and petrophysical descriptions. Mapped features describe the shape of the geological features using standard GML geometries, such as polygons, lines, points or 3D volumes. Geological events provide the age, process and environment of formation of geological features. The Earth Resource section includes features to represent mineral occurrences and mines and associated human activities independently. This addition allows description of resources and reserves that can comply with national and internationally accepted reporting codes. GeoSciML v3 is under consideration as the data model for INSPIRE annex 2 geologic reporting in Europe.

Piezoelectric energy harvesting from an L-shaped beam-mass structure

NASA Astrophysics Data System (ADS)

Erturk, Alper; Renno, Jamil M.; Inman, Daniel J.

2008-03-01

Cantilevered piezoelectric harvesters have been extensively considered in the energy harvesting literature. Mostly, a traditional cantilevered beam with one or more piezoceramic layers is located on a vibrating host structure. Motion of the host structure results in vibrations of the harvester beam and that yields an alternating voltage output. As an alternative to classical cantilevered beams, this paper presents a novel harvesting device; a flexible L-shaped beam-mass structure that can be tuned to have a two-to-one internal resonance to a primary resonance ω II ≅ 2ω I which is not possible for classical cantilevers). The L-shaped structure has been well investigated in the literature of nonlinear dynamics since the two-to-one internal resonance, along with the consideration of quadratic nonlinearities, may yield modal energy exchange (for excitation frequency ω≅ ω Ior the so-called saturation phenomenon (for ω≅ω II). As a part of our ongoing research on piezoelectric energy harvesting, we are investigating the possibility of improving the electrical outputs in energy harvesting by employing these features of the L-shaped structure. This paper aims to introduce the idea, describes the important features of the L-shaped harvester configuration and develops a linear distributed parameter model for predicting the electromechanically coupled response. In addition, this work proposes a direct application of the L-shaped piezoelectric energy harvester configuration for use as landing gears in unmanned air vehicle applications.

An unconventional family 1 uracil DNA glycosylase in Nitratifractor salsuginis.

PubMed

Li, Jing; Chen, Ran; Yang, Ye; Zhang, Zhemin; Fang, Guang-Chen; Xie, Wei; Cao, Weiguo

2017-12-01

The uracil DNA glycosylase superfamily consists of at least six families with a diverse specificity toward DNA base damage. Family 1 uracil N-glycosylase (UNG) exhibits exclusive specificity on uracil-containing DNA. Here, we report a family 1 UNG homolog from Nitratifractor salsuginis with distinct biochemical features that differentiate it from conventional family 1 UNGs. Globally, the crystal structure of N. salsuginisUNG shows a few additional secondary structural elements. Biochemical and enzyme kinetic analysis, coupled with structural determination, molecular modeling, and molecular dynamics simulations, shows that N. salsuginisUNG contains a salt bridge network that plays an important role in DNA backbone interactions. Disruption of the amino acid residues involved in the salt bridges greatly impedes the enzymatic activity. A tyrosine residue in motif 1 (GQDPY) is one of the distinct sequence features setting family 1 UNG apart from other families. The crystal structure of Y81G mutant indicates that several subtle changes may account for its inactivity. Unlike the conventional family 1 UNG enzymes, N. salsuginisUNG is not inhibited by Ugi, a potent inhibitor specific for family 1 UNG. This study underscores the diversity of paths that a uracil DNA glycosylase may take to acquire its unique structural and biochemical properties during evolution. Structure data are available in the PDB under accession numbers 5X3G and 5X3H. © 2017 Federation of European Biochemical Societies.

Design and Synthesis of Archaea-Inspired Tetraether Lipids

NASA Astrophysics Data System (ADS)

Koyanagi, Takaoki

Maintaining the correct ion homeostasis across membranes is a major challenge in both nature and artificial systems. Archaea, have evolved to solve membrane permeability problems to survive in extreme environments by incorporating unique structural features found in their lipid. Specifically, inclusion of phytanyl side chains, ether glycerol linkages, tethering of lipids, cycloalkanes, and different polar lipid headgroups into their lipid membrane are believed to contribute to membrane stability. We sought to gain a better understanding of the functional benefits attributed to these structural features to membrane stability to design a new class of synthetic Archaea inspired lipid membranes that can be used to overcome limitations (i.e. unstable in serum environment, high background leakage, and prone to hydrolysis) found in current lipid based technologies. Leakage experiments revealed liposomes made from GMGTPC (glycerol monoalkyl glycerol tetraether lipid with phosphatidylcholine headgroup) demonstrated a two order magnitude reduction in membrane leakage to small ions when compared with liposomes made from EggPC. Additionally, liposomes composed of GMGTPC-CH (cyclohexane integrated) lipid displayed an additional 40% decrease in membrane leakage to small ions when compared with liposomes made from GMGTPC lipids. Furthermore, leakage experiments revealed a higher degree of tolerance to headgroup modifications to membrane leakage for liposomes made from GMGT lipid analogs when compared with liposomes made from POPC. After designing an optimal tetraether lipid scaffold that incorporates key Archaeal structural features for membrane leakage, we explored to integrate strategies employed by eukaryotes to improve membrane properties (i.e. addition of cholesterol). Liposomes made from the hybrid lipid, GcGTPC-CH, displayed a five-fold decrease in membrane leakage when compared with liposomes made from GMGTPC-CH, while maintaining functional membrane properties similar to membranes made from diacyl lipids. Lastly, we engineered a thiol responsive hybrid lipid, GcGT(S-S)PC-CH, that demonstrated similar membrane stability in serum as GcGTPC-CH. Gratifyingly, doxorubicin loaded liposomes composed of GcGT(S-S)PC-CH liposomes displayed a 4 or 20-fold increase in toxicity to HeLa cells when compared with liposomes made from GcGTPC-CH or Doxil, respectively. This work represents a first step towards development of stimuli-responsive tetraether lipids that may offer advantages in membrane properties to be used in cancer therapy.

Shape Adaptive, Robust Iris Feature Extraction from Noisy Iris Images

PubMed Central

Ghodrati, Hamed; Dehghani, Mohammad Javad; Danyali, Habibolah

2013-01-01

In the current iris recognition systems, noise removing step is only used to detect noisy parts of the iris region and features extracted from there will be excluded in matching step. Whereas depending on the filter structure used in feature extraction, the noisy parts may influence relevant features. To the best of our knowledge, the effect of noise factors on feature extraction has not been considered in the previous works. This paper investigates the effect of shape adaptive wavelet transform and shape adaptive Gabor-wavelet for feature extraction on the iris recognition performance. In addition, an effective noise-removing approach is proposed in this paper. The contribution is to detect eyelashes and reflections by calculating appropriate thresholds by a procedure called statistical decision making. The eyelids are segmented by parabolic Hough transform in normalized iris image to decrease computational burden through omitting rotation term. The iris is localized by an accurate and fast algorithm based on coarse-to-fine strategy. The principle of mask code generation is to assign the noisy bits in an iris code in order to exclude them in matching step is presented in details. An experimental result shows that by using the shape adaptive Gabor-wavelet technique there is an improvement on the accuracy of recognition rate. PMID:24696801

Shape adaptive, robust iris feature extraction from noisy iris images.

PubMed

Ghodrati, Hamed; Dehghani, Mohammad Javad; Danyali, Habibolah

2013-10-01

In the current iris recognition systems, noise removing step is only used to detect noisy parts of the iris region and features extracted from there will be excluded in matching step. Whereas depending on the filter structure used in feature extraction, the noisy parts may influence relevant features. To the best of our knowledge, the effect of noise factors on feature extraction has not been considered in the previous works. This paper investigates the effect of shape adaptive wavelet transform and shape adaptive Gabor-wavelet for feature extraction on the iris recognition performance. In addition, an effective noise-removing approach is proposed in this paper. The contribution is to detect eyelashes and reflections by calculating appropriate thresholds by a procedure called statistical decision making. The eyelids are segmented by parabolic Hough transform in normalized iris image to decrease computational burden through omitting rotation term. The iris is localized by an accurate and fast algorithm based on coarse-to-fine strategy. The principle of mask code generation is to assign the noisy bits in an iris code in order to exclude them in matching step is presented in details. An experimental result shows that by using the shape adaptive Gabor-wavelet technique there is an improvement on the accuracy of recognition rate.

Category inference as a function of correlational structure, category discriminability, and number of available cues.

PubMed

Lancaster, Matthew E; Shelhamer, Ryan; Homa, Donald

2013-04-01

Two experiments investigated category inference when categories were composed of correlated or uncorrelated dimensions and the categories overlapped minimally or moderately. When the categories minimally overlapped, the dimensions were strongly correlated with the category label. Following a classification learning phase, subsequent transfer required the selection of either a category label or a feature when one, two, or three features were missing. Experiments 1 and 2 differed primarily in the number of learning blocks prior to transfer. In each experiment, the inference of the category label or category feature was influenced by both dimensional and category correlations, as well as their interaction. The number of cues available at test impacted performance more when the dimensional correlations were zero and category overlap was high. However, a minimal number of cues were sufficient to produce high levels of inference when the dimensions were highly correlated; additional cues had a positive but reduced impact, even when overlap was high. Subjects were generally more accurate in inferring the category label than a category feature regardless of dimensional correlation, category overlap, or number of cues available at test. Whether the category label functioned as a special feature or not was critically dependent upon these embedded correlations, with feature inference driven more strongly by dimensional correlations.

Reconstruction of biofilm images: combining local and global structural parameters

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

Resat, Haluk; Renslow, Ryan S.; Beyenal, Haluk

2014-10-20

Digitized images can be used for quantitative comparison of biofilms grown under different conditions. Using biofilm image reconstruction, it was previously found that biofilms with a completely different look can have nearly identical structural parameters and that the most commonly utilized global structural parameters were not sufficient to uniquely define these biofilms. Here, additional local and global parameters are introduced to show that these parameters considerably increase the reliability of the image reconstruction process. Assessment using human evaluators indicated that the correct identification rate of the reconstructed images increased from 50% to 72% with the introduction of the new parametersmore » into the reconstruction procedure. An expanded set of parameters especially improved the identification of biofilm structures with internal orientational features and of structures in which colony sizes and spatial locations varied. Hence, the newly introduced structural parameter sets helped to better classify the biofilms by incorporating finer local structural details into the reconstruction process.« less

Structural insights into substrate and inhibitor binding sites in human indoleamine 2,3-dioxygenase 1

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

Lewis-Ballester, Ariel; Pham, Khoa N.; Batabyal, Dipanwita

Human indoleamine 2,3-dioxygenase 1 (hIDO1) is an attractive cancer immunotherapeutic target owing to its role in promoting tumoral immune escape. However, drug development has been hindered by limited structural information. Here, we report the crystal structures of hIDO1 in complex with its substrate, Trp, an inhibitor, epacadostat, and/or an effector, indole ethanol (IDE). The data reveal structural features of the active site (Sa) critical for substrate activation; in addition, they disclose a new inhibitor-binding mode and a distinct small molecule binding site (Si). Structure-guided mutation of a critical residue, F270, to glycine perturbs the Si site, allowing structural determination ofmore » an inhibitory complex, where both the Sa and Si sites are occupied by Trp. The Si site offers a novel target site for allosteric inhibitors and a molecular explanation for the previously baffling substrate-inhibition behavior of the enzyme. Taken together, the data open exciting new avenues for structure-based drug design.« less

Is adermatoglyphia an additional feature of Kindler Syndrome?

PubMed

Almeida, Hiram Larangeira de; Goetze, Fernanda Mendes; Fong, Kenneth; Lai-Cheong, Joey; McGrath, John

2015-01-01

A typical feature of Kindler Syndrome is skin fragility; this condition in currently classified as a form of epidermolysis bullosa. We describe a rarely reported feature of two cases, one sporadic and one familial; both patients noticed acquired adermatoglyphia. The loss of dermatoglyphics could be an additional feature of this syndrome.

Development of National Map ontologies for organization and orchestration of hydrologic observations

NASA Astrophysics Data System (ADS)

Lieberman, J. E.

2014-12-01

Feature layers in the National Map program (TNM) are a fundamental context for much of the data collection and analysis conducted by the USGS and other governmental and nongovernmental organizations. Their computational usefulness, though, has been constrained by the lack of formal relationships besides superposition between TNM layers, as well as limited means of representing how TNM datasets relate to additional attributes, datasets, and activities. In the field of Geospatial Information Science, there has been a growing recognition of the value of semantic representation and technology for addressing these limitations, particularly in the face of burgeoning information volume and heterogeneity. Fundamental to this approach is the development of formal ontologies for concepts related to that information that can be processed computationally to enhance creation and discovery of new geospatial knowledge. They offer a means of making much of the presently innate knowledge about relationships in and between TNM features accessible for machine processing and distributed computation.A full and comprehensive ontology of all knowledge represented by TNM features is still impractical. The work reported here involves elaboration and integration of a number of small ontology design patterns (ODP's) that represent limited, discrete, but commonly accepted and broadly applicable physical theories for the behavior of TNM features representing surface water bodies and landscape surfaces and the connections between them. These ontology components are validated through use in applications for discovery and aggregation of water science observational data associated with National Hydrography Data features, features from the National Elevation Dataset (NED) and Water Boundary Dataset (WBD) that constrain water occurrence in the continental US. These applications emphasize workflows which are difficult or impossible to automate using existing data structures. Evaluation of the usefulness of the developed ontology components includes both solicitation of feedback on prototype applications, and provision of a query / mediation service for feature-linked data to facilitate development of additional third-party applications.

Catalogue of the morphological features in the Spitzer Survey of Stellar Structure in Galaxies (S4G)

NASA Astrophysics Data System (ADS)

Herrera-Endoqui, M.; Díaz-García, S.; Laurikainen, E.; Salo, H.

2015-10-01

Context. A catalogue of the features for the complete Spitzer Survey of Stellar Structure in Galaxies (S4G), including 2352 nearby galaxies, is presented. The measurements are made using 3.6 μm images, largely tracing the old stellar population; at this wavelength the effects of dust are also minimal. The measured features are the sizes, ellipticities, and orientations of bars, rings, ringlenses, and lenses. Measured in a similar manner are also barlenses (lens-like structures embedded in the bars), which are not lenses in the usual sense, being rather the more face-on counterparts of the boxy/peanut structures in the edge-on view. In addition, pitch angles of spiral arm segments are measured for those galaxies where they can be reliably traced. More than one pitch angle may appear for a single galaxy. All measurements are made in a human-supervised manner so that attention is paid to each galaxy. Aims: We create a catalogue of morphological features in the complete S4G. Methods: We used isophotal analysis, unsharp masking, and fitting ellipses to measured structures. Results: We find that the sizes of the inner rings and lenses normalized to barlength correlate with the galaxy mass: the normalized sizes increase toward the less massive galaxies; it has been suggested that this is related to the larger dark matter content in the bar region in these systems. Bars in the low mass galaxies are also less concentrated, likely to be connected to the mass cut-off in the appearance of the nuclear rings and lenses. We also show observational evidence that barlenses indeed form part of the bar, and that a large fraction of the inner lenses in the non-barred galaxies could be former barlenses in which the thin outer bar component has dissolved. Full Tables 2 and 3 are only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (ftp://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/582/A86

Breccia dikes from the Beaverhead Impact structure, southwest Montana

NASA Technical Reports Server (NTRS)

Fiske, P. S.; Hougen, S. B.; Hargraves, R. B.

1992-01-01

While shatter cones are generally accepted as indicators of meteorite impact, older petrologic features are not widely recognized in the geologic community. Breccia dikes are one such feature. They are found in many large impact structures occurring over an area at least as extensively as shatter cones. Breccia dikes will survive moderate degrees of metamorphism and tectonism, unlike many other microscopic features (shocked quartz grains, high-pressure polymorphs, etc.) and even large-scale features such as annular or bowl-shaped topographic features. Thus, they are important diagnostic criteria, especially for large, poorly preserved impact structures. The Beaverhead Impact structure is a recently discovered, deeply eroded impact structure in southwestern Montana. The remains of the structure are delineated by the occurrence of shatter cones, found in an area greater than 200 sq km, occurring within the Cabin thrust plate, part of the Cretaceous Sevier fold and thrust system. The distribution of shatter cones is further truncated by Tertiary normal faults. The present remains represent an allochthonous fragment of a larger structure.

Improved explanation of human intelligence using cortical features with second order moments and regression.

PubMed

Park, Hyunjin; Yang, Jin-ju; Seo, Jongbum; Choi, Yu-yong; Lee, Kun-ho; Lee, Jong-min

2014-04-01

Cortical features derived from magnetic resonance imaging (MRI) provide important information to account for human intelligence. Cortical thickness, surface area, sulcal depth, and mean curvature were considered to explain human intelligence. One region of interest (ROI) of a cortical structure consisting of thousands of vertices contained thousands of measurements, and typically, one mean value (first order moment), was used to represent a chosen ROI, which led to a potentially significant loss of information. We proposed a technological improvement to account for human intelligence in which a second moment (variance) in addition to the mean value was adopted to represent a chosen ROI, so that the loss of information would be less severe. Two computed moments for the chosen ROIs were analyzed with partial least squares regression (PLSR). Cortical features for 78 adults were measured and analyzed in conjunction with the full-scale intelligence quotient (FSIQ). Our results showed that 45% of the variance of the FSIQ could be explained using the combination of four cortical features using two moments per chosen ROI. Our results showed improvement over using a mean value for each ROI, which explained 37% of the variance of FSIQ using the same set of cortical measurements. Our results suggest that using additional second order moments is potentially better than using mean values of chosen ROIs for regression analysis to account for human intelligence. Copyright © 2014 Elsevier Ltd. All rights reserved.

The impact of jackpots on EGM gambling behavior: a review.

PubMed

Rockloff, Matthew J; Hing, Nerilee

2013-12-01

This paper reviews literature on how jackpots influence Electronic Gaming Machine (EGM) gambling behaviour. Most of the available evidence addresses the motivational effect of the mere presence of EGM jackpots on play, as actual wins are relatively rare for individual gamblers. The review identifies a distinction between rational, biased and irrational motivations that attract people to EGM jackpots. The evidence suggests that EGM jackpots should generate additional consumption on EGMs above machines that do not have such lottery-like features. Rational motivations are likely to lead to consumer surplus, whereas biased and irrational motivations are likely to contribute to excessive consumption. Moreover, there is evidence that excessive gambling consumption is strongly associated with gambling-related harm. Future research should identify how the structural features of different types of jackpots; such as progressive, deterministic, hidden, mystery, linked and wide-area jackpots; may differentially appeal to rational, biased and irrational gambling motivations. Jackpots are common feature of EGM games, and therefore it is important to have a better understanding of how jackpot features influence play on the machines.

Classification of a wetland area along the upper Mississippi River with aerial videography

USGS Publications Warehouse

Jennings, C.A.; Vohs, P.A.; Dewey, M.R.

1992-01-01

We evaluated the use of aerial videography for classifying wetland habitats along the upper Mississippi River and found the prompt availability of habitat feature maps to be the major advantage of the video imagery technique. We successfully produced feature maps from digitized video images that generally agreed with the known distribution and areal coverages of the major habitat types independently identified and quantified with photointerpretation techniques. However, video images were not sufficiently detailed to allow us to consistently discriminate among the classes of aquatic macrophytes present or to quantify their areal coverage. Our inability to consistently distinguish among emergent, floating, and submergent macrophytes from the feature maps may have been related to the structural complexity of the site, to our limited vegetation sampling, and to limitations in video imagery. We expect that careful site selection (i.e., the desired level of resolution is available from video imagery) and additional vegetation samples (e.g., along a transect) will allow improved assignment of spectral values to specific plant types and enhance plant classification from feature maps produced from video imagery.

Landscape determinants of fine-scale genetic structure of a small rodent in a heterogeneous landscape (Hluhluwe-iMfolozi Park, South Africa)

PubMed Central

Russo, Isa-Rita M.; Sole, Catherine L.; Barbato, Mario; von Bramann, Ullrich; Bruford, Michael W.

2016-01-01

Small mammals provide ecosystem services, acting, for example, as pollinators and seed dispersers. In addition, they are also disease reservoirs that can be detrimental to human health and they can also act as crop pests. Knowledge of their dispersal preferences is therefore useful for population management and landscape planning. Genetic data were used alongside landscape data to examine the influence of the landscape on the demographic connectedness of the Natal multimammate mouse (Mastomys natalensis) and to identify landscape characteristics that influence the genetic structure of this species across a spatially and temporally varying environment. The most significant landscape features shaping gene flow were aspect, vegetation cover, topographic complexity (TC) and rivers, with western facing slopes, topographic complexity and rivers restricting gene flow. In general, thicket vegetation was correlated with increased gene flow. Identifying features of the landscape that facilitate movement/dispersal in M. natalensis potentially has application for other small mammals in similar ecosystems. As the primary reservoir host of the zoonotic Lassa virus, a landscape genetics approach may have applications in determining areas of high disease risk to humans. Identifying these landscape features may also be important in crop management due to damage by rodent pests. PMID:27406468

Landscape determinants of fine-scale genetic structure of a small rodent in a heterogeneous landscape (Hluhluwe-iMfolozi Park, South Africa).

PubMed

Russo, Isa-Rita M; Sole, Catherine L; Barbato, Mario; von Bramann, Ullrich; Bruford, Michael W

2016-07-13

Small mammals provide ecosystem services, acting, for example, as pollinators and seed dispersers. In addition, they are also disease reservoirs that can be detrimental to human health and they can also act as crop pests. Knowledge of their dispersal preferences is therefore useful for population management and landscape planning. Genetic data were used alongside landscape data to examine the influence of the landscape on the demographic connectedness of the Natal multimammate mouse (Mastomys natalensis) and to identify landscape characteristics that influence the genetic structure of this species across a spatially and temporally varying environment. The most significant landscape features shaping gene flow were aspect, vegetation cover, topographic complexity (TC) and rivers, with western facing slopes, topographic complexity and rivers restricting gene flow. In general, thicket vegetation was correlated with increased gene flow. Identifying features of the landscape that facilitate movement/dispersal in M. natalensis potentially has application for other small mammals in similar ecosystems. As the primary reservoir host of the zoonotic Lassa virus, a landscape genetics approach may have applications in determining areas of high disease risk to humans. Identifying these landscape features may also be important in crop management due to damage by rodent pests.

Automated Interpretation of Subcellular Patterns in Fluorescence Microscope Images for Location Proteomics

PubMed Central

Chen, Xiang; Velliste, Meel; Murphy, Robert F.

2010-01-01

Proteomics, the large scale identification and characterization of many or all proteins expressed in a given cell type, has become a major area of biological research. In addition to information on protein sequence, structure and expression levels, knowledge of a protein’s subcellular location is essential to a complete understanding of its functions. Currently subcellular location patterns are routinely determined by visual inspection of fluorescence microscope images. We review here research aimed at creating systems for automated, systematic determination of location. These employ numerical feature extraction from images, feature reduction to identify the most useful features, and various supervised learning (classification) and unsupervised learning (clustering) methods. These methods have been shown to perform significantly better than human interpretation of the same images. When coupled with technologies for tagging large numbers of proteins and high-throughput microscope systems, the computational methods reviewed here enable the new subfield of location proteomics. This subfield will make critical contributions in two related areas. First, it will provide structured, high-resolution information on location to enable Systems Biology efforts to simulate cell behavior from the gene level on up. Second, it will provide tools for Cytomics projects aimed at characterizing the behaviors of all cell types before, during and after the onset of various diseases. PMID:16752421

Recent improvements to Binding MOAD: a resource for protein–ligand binding affinities and structures

PubMed Central

Ahmed, Aqeel; Smith, Richard D.; Clark, Jordan J.; Dunbar, James B.; Carlson, Heather A.

2015-01-01

For over 10 years, Binding MOAD (Mother of All Databases; http://www.BindingMOAD.org) has been one of the largest resources for high-quality protein–ligand complexes and associated binding affinity data. Binding MOAD has grown at the rate of 1994 complexes per year, on average. Currently, it contains 23 269 complexes and 8156 binding affinities. Our annual updates curate the data using a semi-automated literature search of the references cited within the PDB file, and we have recently upgraded our website and added new features and functionalities to better serve Binding MOAD users. In order to eliminate the legacy application server of the old platform and to accommodate new changes, the website has been completely rewritten in the LAMP (Linux, Apache, MySQL and PHP) environment. The improved user interface incorporates current third-party plugins for better visualization of protein and ligand molecules, and it provides features like sorting, filtering and filtered downloads. In addition to the field-based searching, Binding MOAD now can be searched by structural queries based on the ligand. In order to remove redundancy, Binding MOAD records are clustered in different families based on 90% sequence identity. The new Binding MOAD, with the upgraded platform, features and functionalities, is now equipped to better serve its users. PMID:25378330

Exploration of interaction zones of β-tubulin colchicine binding domain of helminths and binding mechanism of anthelmintics.

PubMed

Ranjan, Prabodh; Kumar, Sivakumar Prasanth; Kari, Vijayakrishna; Jha, Prakash Chandra

2017-06-01

Numerous studies postulated the possible modes of anthelmintic activity by targeting alternate or extended regions of colchicine binding domain of helminth β-tubulin. We present three interaction zones (zones vide -1 to -3) in the colchicine binding domain of Haemonchus contortus (a helminth) β-tubulin homology model and developed zone-wise structure-based pharmacophore models coupled with molecular docking technique to unveil the binding hypotheses. The resulted ten structure-based hypotheses were then refined to essential three point pharmacophore features that captured recurring and crucial non-covalent receptor contacts and proposed three characteristics necessary for optimal zone-2 binding: a conserved pair of H bond acceptor (HBA to form H bond with Asn226 residue) and an aliphatic moiety of molecule separated by 3.75±0.44Å. Further, an aliphatic or a heterocyclic group distant (11.75±1.14Å) to the conserved aliphatic site formed the third feature component in the zone-2 specific anthelmintic pharmacophore model. Alternatively, an additional HBA can be substituted as a third component to establish H bonding with Asn204. We discern that selective zone-2 anthelmintics can be designed effectively by closely adapting the pharmacophore feature patterns and its geometrical constraints. Copyright © 2017 Elsevier Ltd. All rights reserved.