Detailed electromagnetic simulation for the structural color of butterfly wings.

PubMed

Lee, R Todd; Smith, Glenn S

2009-07-20

Many species of butterflies exhibit interesting optical phenomena due to structural color. The physical reason for this color is subwavelength features on the surface of a single scale. The exposed surface of a scale is covered with a ridge structure. The fully three-dimensional, periodic, finite-difference time-domain method is used to create a detailed electromagnetic model of a generic ridge. A novel method for presenting the three-dimensional observed color pattern is developed. Using these tools, the change in color that is a result of varying individual features of the scale is explored. Computational models are developed that are similar to three butterflies: Morpho rhetenor, Troides magellanus, and Ancyluris meliboeus.

Amorphous photonic crystals with only short-range order.

PubMed

Shi, Lei; Zhang, Yafeng; Dong, Biqin; Zhan, Tianrong; Liu, Xiaohan; Zi, Jian

2013-10-04

Distinct from conventional photonic crystals with both short- and long-range order, amorphous photonic crystals that possess only short-range order show interesting optical responses owing to their unique structural features. Amorphous photonic crystals exhibit unique light scattering and transport, which lead to a variety of interesting phenomena such as isotropic photonic bandgaps or pseudogaps, noniridescent structural colors, and light localization. Recent experimental and theoretical advances in the study of amorphous photonic crystals are summarized, focusing on their unique optical properties, artificial fabrication, bionspiration, and potential applications. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Real-time vibration-based structural damage detection using one-dimensional convolutional neural networks

NASA Astrophysics Data System (ADS)

Abdeljaber, Osama; Avci, Onur; Kiranyaz, Serkan; Gabbouj, Moncef; Inman, Daniel J.

2017-02-01

Structural health monitoring (SHM) and vibration-based structural damage detection have been a continuous interest for civil, mechanical and aerospace engineers over the decades. Early and meticulous damage detection has always been one of the principal objectives of SHM applications. The performance of a classical damage detection system predominantly depends on the choice of the features and the classifier. While the fixed and hand-crafted features may either be a sub-optimal choice for a particular structure or fail to achieve the same level of performance on another structure, they usually require a large computation power which may hinder their usage for real-time structural damage detection. This paper presents a novel, fast and accurate structural damage detection system using 1D Convolutional Neural Networks (CNNs) that has an inherent adaptive design to fuse both feature extraction and classification blocks into a single and compact learning body. The proposed method performs vibration-based damage detection and localization of the damage in real-time. The advantage of this approach is its ability to extract optimal damage-sensitive features automatically from the raw acceleration signals. Large-scale experiments conducted on a grandstand simulator revealed an outstanding performance and verified the computational efficiency of the proposed real-time damage detection method.

Metrics for comparing neuronal tree shapes based on persistent homology.

PubMed

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

2017-01-01

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

Metrics for comparing neuronal tree shapes based on persistent homology

PubMed Central

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

2017-01-01

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

Crystal structure of guanidinium hexafluoridovanadate(III), (CN3H6)3[VF6]: an unusual hybrid compound related to perovskite.

PubMed

Black, Cameron; Lightfoot, Philip

2017-03-01

Vanadium fluorides with novel crystal-chemical features and interesting physical properties can be prepared by solvothermal synthetic routes. The title compound, guanidinium hexafluoridovanadate(III), has a cubic structure (space group Pa-3), exhibiting isolated regular VF 6 octahedral units, which are hydrogen bonded to protonated guanidinium moieties. Although the VF 6 octahedral units are not linked directly together, there are structural similarities between this crystal structure and those of the wider family of perovskite materials, in particular, hybrid perovskites based on extended ligands such as cyanide. In this context, the octahedral tilt system of the present compound is of interest and demonstrates that unusual tilt systems can be mediated via `molecular' linkers which allow only supramolecular rather than covalent interactions.

a Robust Descriptor Based on Spatial and Frequency Structural Information for Visible and Thermal Infrared Image Matching

NASA Astrophysics Data System (ADS)

Fu, Z.; Qin, Q.; Wu, C.; Chang, Y.; Luo, B.

2017-09-01

Due to the differences of imaging principles, image matching between visible and thermal infrared images still exist new challenges and difficulties. Inspired by the complementary spatial and frequency information of geometric structural features, a robust descriptor is proposed for visible and thermal infrared images matching. We first divide two different spatial regions to the region around point of interest, using the histogram of oriented magnitudes, which corresponds to the 2-D structural shape information to describe the larger region and the edge oriented histogram to describe the spatial distribution for the smaller region. Then the two vectors are normalized and combined to a higher feature vector. Finally, our proposed descriptor is obtained by applying principal component analysis (PCA) to reduce the dimension of the combined high feature vector to make our descriptor more robust. Experimental results showed that our proposed method was provided with significant improvements in correct matching numbers and obvious advantages by complementing information within spatial and frequency structural information.

The future of primordial features with large-scale structure surveys

NASA Astrophysics Data System (ADS)

Chen, Xingang; Dvorkin, Cora; Huang, Zhiqi; Namjoo, Mohammad Hossein; Verde, Licia

2016-11-01

Primordial features are one of the most important extensions of the Standard Model of cosmology, providing a wealth of information on the primordial Universe, ranging from discrimination between inflation and alternative scenarios, new particle detection, to fine structures in the inflationary potential. We study the prospects of future large-scale structure (LSS) surveys on the detection and constraints of these features. We classify primordial feature models into several classes, and for each class we present a simple template of power spectrum that encodes the essential physics. We study how well the most ambitious LSS surveys proposed to date, including both spectroscopic and photometric surveys, will be able to improve the constraints with respect to the current Planck data. We find that these LSS surveys will significantly improve the experimental sensitivity on features signals that are oscillatory in scales, due to the 3D information. For a broad range of models, these surveys will be able to reduce the errors of the amplitudes of the features by a factor of 5 or more, including several interesting candidates identified in the recent Planck data. Therefore, LSS surveys offer an impressive opportunity for primordial feature discovery in the next decade or two. We also compare the advantages of both types of surveys.

The future of primordial features with large-scale structure surveys

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

Chen, Xingang; Namjoo, Mohammad Hossein; Dvorkin, Cora

2016-11-01

Primordial features are one of the most important extensions of the Standard Model of cosmology, providing a wealth of information on the primordial Universe, ranging from discrimination between inflation and alternative scenarios, new particle detection, to fine structures in the inflationary potential. We study the prospects of future large-scale structure (LSS) surveys on the detection and constraints of these features. We classify primordial feature models into several classes, and for each class we present a simple template of power spectrum that encodes the essential physics. We study how well the most ambitious LSS surveys proposed to date, including both spectroscopicmore » and photometric surveys, will be able to improve the constraints with respect to the current Planck data. We find that these LSS surveys will significantly improve the experimental sensitivity on features signals that are oscillatory in scales, due to the 3D information. For a broad range of models, these surveys will be able to reduce the errors of the amplitudes of the features by a factor of 5 or more, including several interesting candidates identified in the recent Planck data. Therefore, LSS surveys offer an impressive opportunity for primordial feature discovery in the next decade or two. We also compare the advantages of both types of surveys.« less

Crystallographic features of the approximant H (Mn7Si2V) phase in the Mn-Si-V alloy system

NASA Astrophysics Data System (ADS)

Nakayama, Kei; Komatsuzaki, Takumi; Koyama, Yasumasa

2018-07-01

The intermetallic compound H (Mn7Si2V) phase in the Mn-Si-V alloy system can be regarded as an approximant phase of the dodecagonal quasicrystal as one of the two-dimensional quasicrystals. To understand the features of the approximant H phase, in this study, the crystallographic features of both the H phase and the (σ → H) reaction in Mn-Si-V alloy samples were investigated, mainly by transmission electron microscopy. It was found that, in the H phase, there were characteristic structural disorders with respect to an array of a dodecagonal structural unit consisting of 19 dodecagonal atomic columns. Concretely, penetrated structural units consisting of two dodecagonal structural units were presumed to be typical of such disorders. An interesting feature of the (σ → H) reaction was that regions with a rectangular arrangement of penetrated structural units (RAPU) first appeared in the σ matrix as the initial state, and H regions were then nucleated in contact with RAPU regions. The subsequent conversion of RAPU regions into H regions eventually resulted in the formation of the approximant H state as the final state. Furthermore, atomic positions in both the H structure and the dodecagonal quasicrystal were examined using a simple plane-wave model with 12 plane waves.

Hai Long | NREL

Science.gov Websites

research interests are broadly in computational modeling for renewable energy generation and energy ions transport in fuel cell and bioenergetics enzymes, and functional membrane structure modeling and University Featured Publications Hydroxide Degradation Pathways for Imidazolium Cations: A DFT Study, J. Phys

Broadband locally resonant metamaterials with graded hierarchical architecture

NASA Astrophysics Data System (ADS)

Liu, Chenchen; Reina, Celia

2018-03-01

We investigate the effect of hierarchical designs on the bandgap structure of periodic lattice systems with inner resonators. A detailed parameter study reveals various interesting features of structures with two levels of hierarchy as compared with one level systems with identical static mass. In particular: (i) their overall bandwidth is approximately equal, yet bounded above by the bandwidth of the single-resonator system; (ii) the number of bandgaps increases with the level of hierarchy; and (iii) the spectrum of bandgap frequencies is also enlarged. Taking advantage of these features, we propose graded hierarchical structures with ultra-broadband properties. These designs are validated over analogous continuum models via finite element simulations, demonstrating their capability to overcome the bandwidth narrowness that is typical of resonant metamaterials.

Small is beautiful: features of the smallest insects and limits to miniaturization.

PubMed

Polilov, Alexey A

2015-01-07

Miniaturization leads to considerable reorganization of structures in insects, affecting almost all organs and tissues. In the smallest insects, comparable in size to unicellular organisms, modifications arise not only at the level of organs, but also at the cellular level. Miniaturization is accompanied by allometric changes in many organ systems. The consequences of miniaturization displayed by different insect taxa include both common and unique changes. Because the smallest insects are among the smallest metazoans and have the most complex organization among organisms of the same size, their peculiar structural features and the factors that limit their miniaturization are of considerable theoretical interest to general biology.

Epoxide-Opening Cascades in the Synthesis of Polycyclic Polyether Natural Products

PubMed Central

2009-01-01

The group of polycyclic polyether natural products is of special interest due to the fascinating structure and biological effects displayed by its members. The latter includes potentially therapeutic antibiotic, antifungal, and anticancer properties, as well as extreme lethality. The polycyclic structural features of this family can, in some cases, be traced to their biosynthetic origin, but in others that are less well understood, only to proposed biosynthetic pathways that feature dramatic, yet speculative, epoxide–opening cascades. In this review we summarize how such epoxide–opening cascade reactions have been used in the synthesis of polycyclic polyethers and related natural products. PMID:19572302

Enhancement of a Virtual Geology Field Guide of Georgia Initiative Using Gigapan© and ArcGIS Online's Story Map

NASA Astrophysics Data System (ADS)

Mobasher, K.; Turk, H. J.; Witherspoon, W.; Tate, L.; Hoynes, J.

2015-12-01

A GIS geology geodatabase of Georgia was developed using ArcGIS 10.2. The geodatabase for each physiographic provinces of Georgia contains fields designed to store information regarding geologic features. Using ArcGIS online, the virtual field guide is created which provides an interactive learning experience for students to allow in real time photography, description, mapping and sharing their observations with the instructor and peers. Gigapan© facilitates visualizing geologic features at different scales with high resolutions and in their larger surrounding context. The classroom applications of the Gigapan© are limitless when teaching students the entire range of geologic structures from showcasing crystalline structures of minerals to understanding the geological processes responsible for formation of an entire mountain range. The addition of the Story Map enhances the virtual experience when you want to present a geo-located story point narrative featuring images or videos. The virtual field component and supplementary Gigapan© imagery coupled with Story Map added significantly to the detailed realism of virtual field guide further allowing students to more fully understand geological concepts at various scales. These technologies peaked students interest and facilitated their learning and preparation to function more effectively in the geosciences by developing better observations and new skills. These technologies facilitated increased student engagement in the geosciences by sharing, enhancing and transferring lecture information to actual field knowledge and experiences. This enhanced interactive learning experience not only begins to allow students to understand and recognize geologic features in the field but also increased their collaboration, enthusiasm and interest in the discipline. The increased interest and collaboration occurred as students assisted in populating a geologic geodatabase of Georgia.

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.

Elastase kinetics and structural features of colorimetric and fluorescent peptides on cellulose nanocrystals

USDA-ARS?s Scientific Manuscript database

Human neutrophil elastase (HNE) and porcine pancreatic elastase (PPE) are serine proteases with destructive proteolytic activity. Because of this activity, there is considerable interest in elastase sensors. Herein we report the synthesis, characterization, and kinetic profiles of tri- and tetrapept...

TRANSAT-- method for detecting the conserved helices of functional RNA structures, including transient, pseudo-knotted and alternative structures.

PubMed

Wiebe, Nicholas J P; Meyer, Irmtraud M

2010-06-24

The prediction of functional RNA structures has attracted increased interest, as it allows us to study the potential functional roles of many genes. RNA structure prediction methods, however, assume that there is a unique functional RNA structure and also do not predict functional features required for in vivo folding. In order to understand how functional RNA structures form in vivo, we require sophisticated experiments or reliable prediction methods. So far, there exist only a few, experimentally validated transient RNA structures. On the computational side, there exist several computer programs which aim to predict the co-transcriptional folding pathway in vivo, but these make a range of simplifying assumptions and do not capture all features known to influence RNA folding in vivo. We want to investigate if evolutionarily related RNA genes fold in a similar way in vivo. To this end, we have developed a new computational method, Transat, which detects conserved helices of high statistical significance. We introduce the method, present a comprehensive performance evaluation and show that Transat is able to predict the structural features of known reference structures including pseudo-knotted ones as well as those of known alternative structural configurations. Transat can also identify unstructured sub-sequences bound by other molecules and provides evidence for new helices which may define folding pathways, supporting the notion that homologous RNA sequence not only assume a similar reference RNA structure, but also fold similarly. Finally, we show that the structural features predicted by Transat differ from those assuming thermodynamic equilibrium. Unlike the existing methods for predicting folding pathways, our method works in a comparative way. This has the disadvantage of not being able to predict features as function of time, but has the considerable advantage of highlighting conserved features and of not requiring a detailed knowledge of the cellular environment.

Environmental modeling and recognition for an autonomous land vehicle

NASA Technical Reports Server (NTRS)

Lawton, D. T.; Levitt, T. S.; Mcconnell, C. C.; Nelson, P. C.

1987-01-01

An architecture for object modeling and recognition for an autonomous land vehicle is presented. Examples of objects of interest include terrain features, fields, roads, horizon features, trees, etc. The architecture is organized around a set of data bases for generic object models and perceptual structures, temporary memory for the instantiation of object and relational hypotheses, and a long term memory for storing stable hypotheses that are affixed to the terrain representation. Multiple inference processes operate over these databases. Researchers describe these particular components: the perceptual structure database, the grouping processes that operate over this, schemas, and the long term terrain database. A processing example that matches predictions from the long term terrain model to imagery, extracts significant perceptual structures for consideration as potential landmarks, and extracts a relational structure to update the long term terrain database is given.

Curveslam: Utilizing Higher Level Structure In Stereo Vision-Based Navigation

DTIC Science & Technology

2012-01-01

consider their applica- tion to SLAM . The work of [31] [32] develops a spline-based SLAM framework, but this is only for application to LIDAR -based SLAM ...Existing approaches to visual Simultaneous Localization and Mapping ( SLAM ) typically utilize points as visual feature primitives to represent landmarks...regions of interest. Further, previous SLAM techniques that propose the use of higher level structures often place constraints on the environment, such as

Porous Structure Design of Polymeric Membranes for Gas Separation

DOE PAGES

Zhang, Jinshui; Schott, Jennifer Ann; Mahurin, Shannon Mark; ...

2017-04-04

High-performance polymeric membranes for gas separation are of interest for molecular-level separations in industrial-scale chemical, energy and environmental processes. To overcome the inherent trade-off relationship between permeability and selectivity, the creation of permanent microporosity in polymeric matrices is highly desirable because the porous structures can provide a high fractional free volume to facilitate gas transport through the dense layer. In this feature article, recent developments in the formation of porous polymeric membranes and potential strategies for pore structure design are reviewed.

Similar Ring Structures on Mars and Tibetan Plateau confirm recent tectonism on Martian Northern polar region

NASA Astrophysics Data System (ADS)

Anglés, A.; Li, Y. L.

2017-10-01

The polar regions of Mars feature layered deposits, some of which exist as enclosed zoning structures. These deposits raised strong interest since their discovery and still remain one of the most controversial features on Mars. Zoning structures that are enclosed only appear in the Northern polar region, where the disappearance of water bodies may have left behind huge deposits of evaporate salts. The origin of the layered deposits has been widely debated. Here we propose that the enclosed nature of the zoning structures indicates the result of recent tectonism. We compared similar structures at an analogue site located in the western Qaidam Basin of Tibetan Plateau, a unique tectonic setting with abundant saline deposits. The enclosed structures, which we term Ring Structures, in both the analogue site and in the Northern polar region of Mars, were formed by uplift induced pressurization and buoyancy of salts as the result of recent tectonic activity.

Prospects and limitations of full-text index structures in genome analysis

PubMed Central

Vyverman, Michaël; De Baets, Bernard; Fack, Veerle; Dawyndt, Peter

2012-01-01

The combination of incessant advances in sequencing technology producing large amounts of data and innovative bioinformatics approaches, designed to cope with this data flood, has led to new interesting results in the life sciences. Given the magnitude of sequence data to be processed, many bioinformatics tools rely on efficient solutions to a variety of complex string problems. These solutions include fast heuristic algorithms and advanced data structures, generally referred to as index structures. Although the importance of index structures is generally known to the bioinformatics community, the design and potency of these data structures, as well as their properties and limitations, are less understood. Moreover, the last decade has seen a boom in the number of variant index structures featuring complex and diverse memory-time trade-offs. This article brings a comprehensive state-of-the-art overview of the most popular index structures and their recently developed variants. Their features, interrelationships, the trade-offs they impose, but also their practical limitations, are explained and compared. PMID:22584621

Solar loading thermography: Time-lapsed thermographic survey and advanced thermographic signal processing for the inspection of civil engineering and cultural heritage structures

NASA Astrophysics Data System (ADS)

Ibarra-Castanedo, Clemente; Sfarra, Stefano; Klein, Matthieu; Maldague, Xavier

2017-05-01

The experimental results from infrared thermography surveys over two buildings externally exposed walls are presented. Data acquisition was performed on a static configuration by recording direct and indirect solar loading during several days and was processed using advanced signal processing techniques in order to increase signal-to-noise ratio and signature contrast of the elements of interest. It is demonstrated that it is possible to detect the thermal signature of large internal structures as well as surface features under such thermographic scenarios. Results from a long-wave microbolometer compared favorably to those from a mid-wave cooled infrared camera for the detection of large subsurface features from unprocessed images. In both cases, however, advanced signal processing greatly improved contrast of the internal features.

Earth observations during STS-58

NASA Image and Video Library

1993-10-22

STS058-88-017 (18 Oct-1 Nov 1993) --- The eye-catching "bullseye" of the Richat Structure adds interest to the barren Gres de Chinguetti Plateau in central Mauretania, northwest Africa. It represents domally uplifted, layered (sedimentary) rocks that have been eroded by water and wind into the present shape. Desert sands have invaded the feature from the south. The origin of the structure is unknown. It is not an impact structure, because field work showed that strata are undisturbed and flat-lying in the middle of the feature, and no shock-altered rock could be found. There is no evidence for a salt dome or shale diapir, nor is there any geophysical evidence for an underlying dome of dense igneous rock having about the same density as the sedimentary layers.

First-principles investigation of structural, elastic, lattice dynamical and thermodynamic properties of lithium sulfur under pressure

NASA Astrophysics Data System (ADS)

Saib, S.; Bouarissa, N.

2017-10-01

In this study we report on the influence of hydrostatic pressure on structural, elastic, lattice dynamical and thermal properties of Li2S in the anti-fluorite structure using ab initio pseudopotential approach based on the density functional perturbation theory. Our results are found to be in good agreement with those existing in the literature. The present phonon dispersion spectra, dielectric constants and Born effective charges may be seen as the first investigation for the material under load. The pressure dependence of all features of interest has been examined and discussed. Besides, the temperature dependence of the lattice parameter and bulk modulus is predicted. The generalized elastic stability criteria showed that the material of interest is mechanically unstable for pressures beyond 55 GPa.

The South Scandinavian crust: Structural complexities from seismic reflection and refraction profiling

NASA Astrophysics Data System (ADS)

Kinck, J. J.; Husebye, E. S.; Lund, C.-E.

1991-04-01

Pioneering work on mapping the Scandinavian crust commenced in the early 1960s and since then numerous profiling surveys have been undertaken, particularly as part of the on-going EUGENO-S project. However, the most significant contribution to mapping crustal structural details came from the M.V. Mobil Search cruises in the Skagerrak and off the West coast of Norway (16 s TWT reflection profiling). All past and present crustal profiling results have been integrated to produce detailed maps of Moho depths and crustal thicknesses for South Scandinavia. The thinnest crust is found in the North Sea and Skagerrak (approximately 20 km), while East-central Sweden features very thick crust (approximately 50 km). Other interesting features are the apparent correlation between crustal thinning and sedimentation/subsidence, magmatic activity, earthquake occurrences and the tectonic age of the crust. Moho depths and the crustal thicknesses clearly reflect the tectonic evolution and the present structural features of the region investigated.

Attentional Bias in Human Category Learning: The Case of Deep Learning.

PubMed

Hanson, Catherine; Caglar, Leyla Roskan; Hanson, Stephen José

2018-01-01

Category learning performance is influenced by both the nature of the category's structure and the way category features are processed during learning. Shepard (1964, 1987) showed that stimuli can have structures with features that are statistically uncorrelated (separable) or statistically correlated (integral) within categories. Humans find it much easier to learn categories having separable features, especially when attention to only a subset of relevant features is required, and harder to learn categories having integral features, which require consideration of all of the available features and integration of all the relevant category features satisfying the category rule (Garner, 1974). In contrast to humans, a single hidden layer backpropagation (BP) neural network has been shown to learn both separable and integral categories equally easily, independent of the category rule (Kruschke, 1993). This "failure" to replicate human category performance appeared to be strong evidence that connectionist networks were incapable of modeling human attentional bias. We tested the presumed limitations of attentional bias in networks in two ways: (1) by having networks learn categories with exemplars that have high feature complexity in contrast to the low dimensional stimuli previously used, and (2) by investigating whether a Deep Learning (DL) network, which has demonstrated humanlike performance in many different kinds of tasks (language translation, autonomous driving, etc.), would display human-like attentional bias during category learning. We were able to show a number of interesting results. First, we replicated the failure of BP to differentially process integral and separable category structures when low dimensional stimuli are used (Garner, 1974; Kruschke, 1993). Second, we show that using the same low dimensional stimuli, Deep Learning (DL), unlike BP but similar to humans, learns separable category structures more quickly than integral category structures. Third, we show that even BP can exhibit human like learning differences between integral and separable category structures when high dimensional stimuli (face exemplars) are used. We conclude, after visualizing the hidden unit representations, that DL appears to extend initial learning due to feature development thereby reducing destructive feature competition by incrementally refining feature detectors throughout later layers until a tipping point (in terms of error) is reached resulting in rapid asymptotic learning.

Computational approaches for predicting biomedical research collaborations.

PubMed

Zhang, Qing; Yu, Hong

2014-01-01

Biomedical research is increasingly collaborative, and successful collaborations often produce high impact work. Computational approaches can be developed for automatically predicting biomedical research collaborations. Previous works of collaboration prediction mainly explored the topological structures of research collaboration networks, leaving out rich semantic information from the publications themselves. In this paper, we propose supervised machine learning approaches to predict research collaborations in the biomedical field. We explored both the semantic features extracted from author research interest profile and the author network topological features. We found that the most informative semantic features for author collaborations are related to research interest, including similarity of out-citing citations, similarity of abstracts. Of the four supervised machine learning models (naïve Bayes, naïve Bayes multinomial, SVMs, and logistic regression), the best performing model is logistic regression with an ROC ranging from 0.766 to 0.980 on different datasets. To our knowledge we are the first to study in depth how research interest and productivities can be used for collaboration prediction. Our approach is computationally efficient, scalable and yet simple to implement. The datasets of this study are available at https://github.com/qingzhanggithub/medline-collaboration-datasets.

In silico studies on tryparedoxin peroxidase of Leishmania infantum: structural aspects.

PubMed

Singh, Bishal Kumar; Dubey, Vikash Kumar

2009-09-01

Tryparedoxin peroxidase (TryP) is a key enzyme of the trypanothione-dependent metabolism for removal of oxidative stress in leishmania. These enzymes function as antioxidants through their peroxidase and peroxynitrite reductase activities. Inhibitors of this enzyme are presumed to be antilesihmania drugs and structural studies are prerequisite of rational drug design. We have constructed three dimensional structure of TryP of Leishmania infantum using comparative modeling. Structural analysis reveals several interesting features. Moreover, it shows remarkable structural difference with human host glutathione peroxidase, an enzyme involved in similar function and TryP from Leishmania major.

OBSERVATIONS ON A CASE OF CYCLIC ALBUMINURIA.

PubMed

Mendel, L B; Hooker, D B

1901-10-01

The preceding observations record a new instance of the occurrence of cyclic albuminuria in an otherwise apparently healthy young man. The typical course of the proteid excretion from hour to hour under various conditions has been reviewed and its independence of the changes in diet or muscular work pointed out. No relationship between the volume of urine eliminated and the quantity of proteid excreted has been ascertained. The specific effect of the horizontal posture in dispelling the albuminuria is the most interesting feature observed. The attempt to refer this to attendant circulatory changes in the kidneys is, for the present, no more than an interesting speculation. See PDF for Structure See PDF for Structure.

UV absorption investigation of ferromagnetically filled ultra-thick carbon onions, carriers of the 217.5 nm Interstellar Absorption Feature

NASA Astrophysics Data System (ADS)

Boi, Filippo S.; Zhang, Xiaotian; Ivaturi, Sameera; Liu, Qianyang; Wen, Jiqiu; Wang, Shanling

2017-12-01

Carbon nano-onions (CNOs) are fullerene-like structures which consist of quasi-spherical closed carbon shells. These structures have become a subject of great interest thanks to their characteristic absorption feature of interstellar origin (at 217.5 nm, 4.6 μm-1). An additional extinction peak at 3.8 μm-1 has also been reported and attributed to absorption by graphitic residues between the as-grown CNOs. Here, we report the ultraviolet absorption properties of ultra-thick CNOs filled with FePt3 crystals, which also exhibit two main absorption peaks—features located at 4.58 μm-1 and 3.44 μm-1. The presence of this additional feature is surprising and is attributed to nonmagnetic graphite flakes produced as a by-product in the pyrolysis experiment (as confirmed by magnetic separation methods). Instead, the feature at 4.58 μm-1 is associated with the π-plasmonic resonance of the CNOs structures. The FePt3 filled CNOs were fabricated in situ by an advanced one-step fast process consisting in the direct sublimation and pyrolysis of two molecular precursors, namely, ferrocene and dichloro-cyclooctadiene-platinum in a chemical vapour deposition system. The morphological, structural, and magnetic properties of the as-grown filled CNOs were characterized by a means of scanning and transmission electron microscopy, X-ray diffraction, and magnetometry.

Pectin-modifying enzymes and pectin-derived materials: applications and impacts.

PubMed

Bonnin, Estelle; Garnier, Catherine; Ralet, Marie-Christine

2014-01-01

Pectins are complex branched polysaccharides present in primary cell walls. As a distinctive feature, they contain high amount of partly methyl-esterified galacturonic acid and low amount of rhamnose and carry arabinose and galactose as major neutral sugars. Due to their structural complexity, they are modifiable by many different enzymes, including hydrolases, lyases, and esterases. Their peculiar structure is the origin of their physicochemical properties. Among others, their remarkable gelling properties make them a key additive for food industries. Pectin-degrading enzymes and -modifying enzymes may be used in a wide variety of applications to modulate pectin properties or produce pectin derivatives and oligosaccharides with functional as well as nutritional interests. This paper reviews the scientific information available on pectin structure, pectin-modifying enzymes, and the use of enzymes to produce pectin with controlled structure or pectin-derived oligosaccharides, with functional or nutritional interesting properties.

3D High Resolution Mesh Deformation Based on Multi Library Wavelet Neural Network Architecture

NASA Astrophysics Data System (ADS)

Dhibi, Naziha; Elkefi, Akram; Bellil, Wajdi; Amar, Chokri Ben

2016-12-01

This paper deals with the features of a novel technique for large Laplacian boundary deformations using estimated rotations. The proposed method is based on a Multi Library Wavelet Neural Network structure founded on several mother wavelet families (MLWNN). The objective is to align features of mesh and minimize distortion with a fixed feature that minimizes the sum of the distances between all corresponding vertices. New mesh deformation method worked in the domain of Region of Interest (ROI). Our approach computes deformed ROI, updates and optimizes it to align features of mesh based on MLWNN and spherical parameterization configuration. This structure has the advantage of constructing the network by several mother wavelets to solve high dimensions problem using the best wavelet mother that models the signal better. The simulation test achieved the robustness and speed considerations when developing deformation methodologies. The Mean-Square Error and the ratio of deformation are low compared to other works from the state of the art. Our approach minimizes distortions with fixed features to have a well reconstructed object.

Parenchymal texture analysis in digital mammography: robust texture feature identification and equivalence across devices.

PubMed

Keller, Brad M; Oustimov, Andrew; Wang, Yan; Chen, Jinbo; Acciavatti, Raymond J; Zheng, Yuanjie; Ray, Shonket; Gee, James C; Maidment, Andrew D A; Kontos, Despina

2015-04-01

An analytical framework is presented for evaluating the equivalence of parenchymal texture features across different full-field digital mammography (FFDM) systems using a physical breast phantom. Phantom images (FOR PROCESSING) are acquired from three FFDM systems using their automated exposure control setting. A panel of texture features, including gray-level histogram, co-occurrence, run length, and structural descriptors, are extracted. To identify features that are robust across imaging systems, a series of equivalence tests are performed on the feature distributions, in which the extent of their intersystem variation is compared to their intrasystem variation via the Hodges-Lehmann test statistic. Overall, histogram and structural features tend to be most robust across all systems, and certain features, such as edge enhancement, tend to be more robust to intergenerational differences between detectors of a single vendor than to intervendor differences. Texture features extracted from larger regions of interest (i.e., [Formula: see text]) and with a larger offset length (i.e., [Formula: see text]), when applicable, also appear to be more robust across imaging systems. This framework and observations from our experiments may benefit applications utilizing mammographic texture analysis on images acquired in multivendor settings, such as in multicenter studies of computer-aided detection and breast cancer risk assessment.

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.

Biophysical Adaptations of Prokaryotic Voltage-Gated Sodium Channels.

PubMed

Vien, T N; DeCaen, P G

2016-01-01

This chapter describes the adaptive features found in voltage-gated sodium channels (NaVs) of prokaryotes and eukaryotes. These two families are distinct, having diverged early in evolutionary history but maintain a surprising degree of convergence in function. While prokaryotic NaVs are required for growth and motility, eukaryotic NaVs selectively conduct fast electrical currents for short- and long-range signaling across cell membranes in mammalian organs. Current interest in prokaryotic NaVs is stoked by their resolved high-resolution structures and functional features which are reminiscent of eukaryotic NaVs. In this chapter, comparisons between eukaryotic and prokaryotic NaVs are made to highlight the shared and unique aspects of ion selectivity, voltage sensitivity, and pharmacology. Examples of prokaryotic and eukaryotic NaV convergent evolution will be discussed within the context of their structural features. Copyright © 2016 Elsevier Inc. All rights reserved.

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

Mauna Iki and the Kaju Desert: Kilauea Volcano, Hawaii

NASA Technical Reports Server (NTRS)

Cruikshank, D. P.

1974-01-01

The Ka'u Desert lies southwest of Kilauea Volcano. The region contains some of the most interesting and best preserved volcanic features found in the islands. The structural setting and synopsis of recent volcanic activity on the Ka'u Desert are discussed here, and a field guide to Mauna Iki is provided.

Periodic and Aperiodic Close Packing: A Spontaneous Hard-Sphere Model.

ERIC Educational Resources Information Center

van de Waal, B. W.

1985-01-01

Shows how to make close-packed models from balloons and table tennis balls to illustrate structural features of clusters and organometallic cluster-compounds (which are of great interest in the study of chemical reactions). These models provide a very inexpensive and tactile illustration of the organization of matter for concrete operational…

The Narrative Process of Improving Vocational Classroom Practice

ERIC Educational Resources Information Center

Sharman, Kathleen Y.

2011-01-01

This research inquires into the use of stories by vocational teachers. These stories are of interest because they are a fundamental feature of both the subject content and the social structures of vocational classrooms. The trade experiences of vocational teachers are brought to the classroom through stories. These stories have a secondary effect…

First-Principles Prediction of Spin-Polarized Multiple Dirac Rings in Manganese Fluoride

NASA Astrophysics Data System (ADS)

Jiao, Yalong; Ma, Fengxian; Zhang, Chunmei; Bell, John; Sanvito, Stefano; Du, Aijun

2017-07-01

Spin-polarized materials with Dirac features have sparked great scientific interest due to their potential applications in spintronics. But such a type of structure is very rare and none has been fabricated. Here, we investigate the already experimentally synthesized manganese fluoride (MnF3 ) as a novel spin-polarized Dirac material by using first-principles calculations. MnF3 exhibits multiple Dirac cones in one spin orientation, while it behaves like a large gap semiconductor in the other spin channel. The estimated Fermi velocity for each cone is of the same order of magnitude as that in graphene. The 3D band structure further reveals that MnF3 possesses rings of Dirac nodes in the Brillouin zone. Such a spin-polarized multiple Dirac ring feature is reported for the first time in an experimentally realized material. Moreover, similar band dispersions can be also found in other transition metal fluorides (e.g., CoF3 , CrF3 , and FeF3 ). Our results highlight a new interesting single-spin Dirac material with promising applications in spintronics and information technologies.

First-Principles Prediction of Spin-Polarized Multiple Dirac Rings in Manganese Fluoride.

PubMed

Jiao, Yalong; Ma, Fengxian; Zhang, Chunmei; Bell, John; Sanvito, Stefano; Du, Aijun

2017-07-07

Spin-polarized materials with Dirac features have sparked great scientific interest due to their potential applications in spintronics. But such a type of structure is very rare and none has been fabricated. Here, we investigate the already experimentally synthesized manganese fluoride (MnF_{3}) as a novel spin-polarized Dirac material by using first-principles calculations. MnF_{3} exhibits multiple Dirac cones in one spin orientation, while it behaves like a large gap semiconductor in the other spin channel. The estimated Fermi velocity for each cone is of the same order of magnitude as that in graphene. The 3D band structure further reveals that MnF_{3} possesses rings of Dirac nodes in the Brillouin zone. Such a spin-polarized multiple Dirac ring feature is reported for the first time in an experimentally realized material. Moreover, similar band dispersions can be also found in other transition metal fluorides (e.g., CoF_{3}, CrF_{3}, and FeF_{3}). Our results highlight a new interesting single-spin Dirac material with promising applications in spintronics and information technologies.

Fuzzy Intervals for Designing Structural Signature: An Application to Graphic Symbol Recognition

NASA Astrophysics Data System (ADS)

Luqman, Muhammad Muzzamil; Delalandre, Mathieu; Brouard, Thierry; Ramel, Jean-Yves; Lladós, Josep

The motivation behind our work is to present a new methodology for symbol recognition. The proposed method employs a structural approach for representing visual associations in symbols and a statistical classifier for recognition. We vectorize a graphic symbol, encode its topological and geometrical information by an attributed relational graph and compute a signature from this structural graph. We have addressed the sensitivity of structural representations to noise, by using data adapted fuzzy intervals. The joint probability distribution of signatures is encoded by a Bayesian network, which serves as a mechanism for pruning irrelevant features and choosing a subset of interesting features from structural signatures of underlying symbol set. The Bayesian network is deployed in a supervised learning scenario for recognizing query symbols. The method has been evaluated for robustness against degradations & deformations on pre-segmented 2D linear architectural & electronic symbols from GREC databases, and for its recognition abilities on symbols with context noise i.e. cropped symbols.

2.4 Å resolution crystal structure of human TRAP1NM, the Hsp90 paralog in the mitochondrial matrix.

PubMed

Sung, Nuri; Lee, Jungsoon; Kim, Ji Hyun; Chang, Changsoo; Tsai, Francis T F; Lee, Sukyeong

2016-08-01

TRAP1 is an organelle-specific Hsp90 paralog that is essential for neoplastic growth. As a member of the Hsp90 family, TRAP1 is presumed to be a general chaperone facilitating the late-stage folding of Hsp90 client proteins in the mitochondrial matrix. Interestingly, TRAP1 cannot replace cytosolic Hsp90 in protein folding, and none of the known Hsp90 co-chaperones are found in mitochondria. Thus, the three-dimensional structure of TRAP1 must feature regulatory elements that are essential to the ATPase activity and chaperone function of TRAP1. Here, the crystal structure of a human TRAP1NM dimer is presented, featuring an intact N-domain and M-domain structure, bound to adenosine 5'-β,γ-imidotriphosphate (ADPNP). The crystal structure together with epitope-mapping results shows that the TRAP1 M-domain loop 1 contacts the neighboring subunit and forms a previously unobserved third dimer interface that mediates the specific interaction with mitochondrial Hsp70.

Environment and initial state engineered dynamics of quantum and classical correlations

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

Wang, Cheng-Zhi, E-mail: czczwang@outlook.com; Li, Chun-Xian; Guo, Yu

Based on an open exactly solvable system coupled to an environment with nontrivial spectral density, we connect the features of quantum and classical correlations with some features of the environment, initial states of the system, and the presence of initial system–environment correlations. Some interesting features not revealed before are observed by changing the structure of environment, the initial states of system, and the presence of initial system–environment correlations. The main results are as follows. (1) Quantum correlations exhibit temporary freezing and permanent freezing even at high temperature of the environment, for which the necessary and sufficient conditions are given bymore » three propositions. (2) Quantum correlations display a transition from temporary freezing to permanent freezing by changing the structure of environment. (3) Quantum correlations can be enhanced all the time, for which the condition is put forward. (4) The one-to-one dependency relationship between all kinds of dynamic behaviors of quantum correlations and the initial states of the system as well as environment structure is established. (5) In the presence of initial system–environment correlations, quantum correlations under local environment exhibit temporary multi-freezing phenomenon. While under global environment they oscillate, revive, and damp, an explanation for which is given. - Highlights: • Various interesting behaviors of quantum and classical correlations are observed in an open exactly solvable model. • The important effects of the bath structure on quantum and classical correlations are revealed. • The one-to-one correspondence between the type of dynamical behavior of quantum discord and the initial state is given. • Quantum correlations are given in the presence of initial qubits–bath correlations.« less

Discriminative analysis of schizophrenia using support vector machine and recursive feature elimination on structural MRI images.

PubMed

Lu, Xiaobing; Yang, Yongzhe; Wu, Fengchun; Gao, Minjian; Xu, Yong; Zhang, Yue; Yao, Yongcheng; Du, Xin; Li, Chengwei; Wu, Lei; Zhong, Xiaomei; Zhou, Yanling; Fan, Ni; Zheng, Yingjun; Xiong, Dongsheng; Peng, Hongjun; Escudero, Javier; Huang, Biao; Li, Xiaobo; Ning, Yuping; Wu, Kai

2016-07-01

Structural abnormalities in schizophrenia (SZ) patients have been well documented with structural magnetic resonance imaging (MRI) data using voxel-based morphometry (VBM) and region of interest (ROI) analyses. However, these analyses can only detect group-wise differences and thus, have a poor predictive value for individuals. In the present study, we applied a machine learning method that combined support vector machine (SVM) with recursive feature elimination (RFE) to discriminate SZ patients from normal controls (NCs) using their structural MRI data. We first employed both VBM and ROI analyses to compare gray matter volume (GMV) and white matter volume (WMV) between 41 SZ patients and 42 age- and sex-matched NCs. The method of SVM combined with RFE was used to discriminate SZ patients from NCs using significant between-group differences in both GMV and WMV as input features. We found that SZ patients showed GM and WM abnormalities in several brain structures primarily involved in the emotion, memory, and visual systems. An SVM with a RFE classifier using the significant structural abnormalities identified by the VBM analysis as input features achieved the best performance (an accuracy of 88.4%, a sensitivity of 91.9%, and a specificity of 84.4%) in the discriminative analyses of SZ patients. These results suggested that distinct neuroanatomical profiles associated with SZ patients might provide a potential biomarker for disease diagnosis, and machine-learning methods can reveal neurobiological mechanisms in psychiatric diseases.

Examining Brain Morphometry Associated with Self-Esteem in Young Adults Using Multilevel-ROI-Features-Based Classification Method

PubMed Central

Peng, Bo; Lu, Jieru; Saxena, Aditya; Zhou, Zhiyong; Zhang, Tao; Wang, Suhong; Dai, Yakang

2017-01-01

Purpose: This study is to exam self-esteem related brain morphometry on brain magnetic resonance (MR) images using multilevel-features-based classification method. Method: The multilevel region of interest (ROI) features consist of two types of features: (i) ROI features, which include gray matter volume, white matter volume, cerebrospinal fluid volume, cortical thickness, and cortical surface area, and (ii) similarity features, which are based on similarity calculation of cortical thickness between ROIs. For each feature type, a hybrid feature selection method, comprising of filter-based and wrapper-based algorithms, is used to select the most discriminating features. ROI features and similarity features are integrated by using multi-kernel support vector machines (SVMs) with appropriate weighting factor. Results: The classification performance is improved by using multilevel ROI features with an accuracy of 96.66%, a specificity of 96.62%, and a sensitivity of 95.67%. The most discriminating ROI features that are related to self-esteem spread over occipital lobe, frontal lobe, parietal lobe, limbic lobe, temporal lobe, and central region, mainly involving white matter and cortical thickness. The most discriminating similarity features are distributed in both the right and left hemisphere, including frontal lobe, occipital lobe, limbic lobe, parietal lobe, and central region, which conveys information of structural connections between different brain regions. Conclusion: By using ROI features and similarity features to exam self-esteem related brain morphometry, this paper provides a pilot evidence that self-esteem is linked to specific ROIs and structural connections between different brain regions. PMID:28588470

Examining Brain Morphometry Associated with Self-Esteem in Young Adults Using Multilevel-ROI-Features-Based Classification Method.

PubMed

Peng, Bo; Lu, Jieru; Saxena, Aditya; Zhou, Zhiyong; Zhang, Tao; Wang, Suhong; Dai, Yakang

2017-01-01

Purpose: This study is to exam self-esteem related brain morphometry on brain magnetic resonance (MR) images using multilevel-features-based classification method. Method: The multilevel region of interest (ROI) features consist of two types of features: (i) ROI features, which include gray matter volume, white matter volume, cerebrospinal fluid volume, cortical thickness, and cortical surface area, and (ii) similarity features, which are based on similarity calculation of cortical thickness between ROIs. For each feature type, a hybrid feature selection method, comprising of filter-based and wrapper-based algorithms, is used to select the most discriminating features. ROI features and similarity features are integrated by using multi-kernel support vector machines (SVMs) with appropriate weighting factor. Results: The classification performance is improved by using multilevel ROI features with an accuracy of 96.66%, a specificity of 96.62%, and a sensitivity of 95.67%. The most discriminating ROI features that are related to self-esteem spread over occipital lobe, frontal lobe, parietal lobe, limbic lobe, temporal lobe, and central region, mainly involving white matter and cortical thickness. The most discriminating similarity features are distributed in both the right and left hemisphere, including frontal lobe, occipital lobe, limbic lobe, parietal lobe, and central region, which conveys information of structural connections between different brain regions. Conclusion: By using ROI features and similarity features to exam self-esteem related brain morphometry, this paper provides a pilot evidence that self-esteem is linked to specific ROIs and structural connections between different brain regions.

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.

Development of multiple source data processing for structural analysis at a regional scale. [digital remote sensing in geology

NASA Technical Reports Server (NTRS)

Carrere, Veronique

1990-01-01

Various image processing techniques developed for enhancement and extraction of linear features, of interest to the structural geologist, from digital remote sensing, geologic, and gravity data, are presented. These techniques include: (1) automatic detection of linear features and construction of rose diagrams from Landsat MSS data; (2) enhancement of principal structural directions using selective filters on Landsat MSS, Spacelab panchromatic, and HCMM NIR data; (3) directional filtering of Spacelab panchromatic data using Fast Fourier Transform; (4) detection of linear/elongated zones of high thermal gradient from thermal infrared data; and (5) extraction of strong gravimetric gradients from digitized Bouguer anomaly maps. Processing results can be compared to each other through the use of a geocoded database to evaluate the structural importance of each lineament according to its depth: superficial structures in the sedimentary cover, or deeper ones affecting the basement. These image processing techniques were successfully applied to achieve a better understanding of the transition between Provence and the Pyrenees structural blocks, in southeastern France, for an improved structural interpretation of the Mediterranean region.

An image-processing method to detect sub-optical features based on understanding noise in intensity measurements.

PubMed

Bhatia, Tripta

2018-07-01

Accurate quantitative analysis of image data requires that we distinguish between fluorescence intensity (true signal) and the noise inherent to its measurements to the extent possible. We image multilamellar membrane tubes and beads that grow from defects in the fluid lamellar phase of the lipid 1,2-dioleoyl-sn-glycero-3-phosphocholine dissolved in water and water-glycerol mixtures by using fluorescence confocal polarizing microscope. We quantify image noise and determine the noise statistics. Understanding the nature of image noise also helps in optimizing image processing to detect sub-optical features, which would otherwise remain hidden. We use an image-processing technique "optimum smoothening" to improve the signal-to-noise ratio of features of interest without smearing their structural details. A high SNR renders desired positional accuracy with which it is possible to resolve features of interest with width below optical resolution. Using optimum smoothening, the smallest and the largest core diameter detected is of width [Formula: see text] and [Formula: see text] nm, respectively, discussed in this paper. The image-processing and analysis techniques and the noise modeling discussed in this paper can be used for detailed morphological analysis of features down to sub-optical length scales that are obtained by any kind of fluorescence intensity imaging in the raster mode.

Applying Gradient Descent in Convolutional Neural Networks

NASA Astrophysics Data System (ADS)

Cui, Nan

2018-04-01

With the development of the integrated circuit and computer science, people become caring more about solving practical issues via information technologies. Along with that, a new subject called Artificial Intelligent (AI) comes up. One popular research interest of AI is about recognition algorithm. In this paper, one of the most common algorithms, Convolutional Neural Networks (CNNs) will be introduced, for image recognition. Understanding its theory and structure is of great significance for every scholar who is interested in this field. Convolution Neural Network is an artificial neural network which combines the mathematical method of convolution and neural network. The hieratical structure of CNN provides it reliable computer speed and reasonable error rate. The most significant characteristics of CNNs are feature extraction, weight sharing and dimension reduction. Meanwhile, combining with the Back Propagation (BP) mechanism and the Gradient Descent (GD) method, CNNs has the ability to self-study and in-depth learning. Basically, BP provides an opportunity for backwardfeedback for enhancing reliability and GD is used for self-training process. This paper mainly discusses the CNN and the related BP and GD algorithms, including the basic structure and function of CNN, details of each layer, the principles and features of BP and GD, and some examples in practice with a summary in the end.

Childhood and Current Autistic Features in Adolescents with Schizotypal Personality Disorder

PubMed Central

Esterberg, Michelle L.; Trotman, Hanan D.; Brasfield, Joy L.; Compton, Michael T.; Walker, Elaine F.

2008-01-01

The diagnostic boundaries between autistic- and schizophrenia-spectrum disorders have varied over the years, and some overlap in diagnostic criteria persists. The present study examined childhood and current signs of autistic disorder (AD) in adolescents with schizotypal personality disorder (SPD) or other personality disorders, as well as healthy controls. A structured interview was administered to rate participants’ current symptoms. Participants’ guardians were interviewed with the Autism Diagnostic Inventory-Revised (ADI-R), a clinical assessment of childhood and current autistic signs. Compared to both the other personality-disordered and healthy groups, adolescents with SPD were rated as having significantly more impairment on childhood and current social functioning, and having more unusual interests and behaviors. For the entire sample, impaired childhood social functioning and unusual interests and behaviors were associated with higher negative symptom scores. Current impairments in social functioning, unusual interests and behaviors, and communication were also linked with greater negative symptoms. However, neither childhood nor current autistic features significantly predicted later conversion to an Axis I psychotic disorder over the course of three years of follow-up. The findings indicate that past and current autistic signs are more common in adolescents with SPD, but neither current nor childhood autistic features are linked with conversion to psychosis. PMID:18554872

Which Features Make Illustrations in Multimedia Learning Interesting?

ERIC Educational Resources Information Center

Magner, Ulrike Irmgard Elisabeth; Glogger, Inga; Renkl, Alexander

2016-01-01

How can illustrations motivate learners in multimedia learning? Which features make illustrations interesting? Beside the theoretical relevance of addressing these questions, these issues are practically relevant when instructional designers are to decide which features of illustrations can trigger situational interest irrespective of individual…

Molecular interactions within the halophilic, thermophilic, and mesophilic prokaryotic ribosomal complexes: clues to environmental adaptation.

PubMed

Mallik, Saurav; Kundu, Sudip

2015-01-01

Using the available crystal structures of 50S ribosomal subunits from three prokaryotic species: Escherichia coli (mesophilic), Thermus thermophilus (thermophilic), and Haloarcula marismortui (halophilic), we have analyzed different structural features of ribosomal RNAs (rRNAs), proteins, and of their interfaces. We have correlated these structural features with the environmental adaptation strategies of the corresponding species. While dense intra-rRNA packing is observed in thermophilic, loose intra-rRNA packing is observed in halophilic (both compared to mesophilic). Interestingly, protein-rRNA interfaces of both the extremophiles are densely packed compared to that of the mesophilic. The intersubunit bridge regions are almost devoid of cavities, probably ensuring the proper formation of each bridge (by not allowing any loosely packed region nearby). During rRNA binding, the ribosomal proteins experience some structural transitions. Here, we have analyzed the intrinsically disordered and ordered regions of the ribosomal proteins, which are subjected to such transitions. The intrinsically disordered and disorder-to-order transition sites of the thermophilic and mesophilic ribosomal proteins are simultaneously (i) highly conserved and (ii) slowly evolving compared to rest of the protein structure. Although high conservation is observed at such sites of halophilic ribosomal proteins, but slow rate of evolution is absent. Such differences between thermophilic, mesophilic, and halophilic can be explained from their environmental adaptation strategy. Interestingly, a universal biophysical principle evident by a linear relationship between the free energy of interface formation, interface area, and structural changes of r-proteins during assembly is always maintained, irrespective of the environmental conditions.

Chaos Theory as a Model for Managing Issues and Crises.

ERIC Educational Resources Information Center

Murphy, Priscilla

1996-01-01

Uses chaos theory to model public relations situations in which the salient feature is volatility of public perceptions. Discusses the premises of chaos theory and applies them to issues management, the evolution of interest groups, crises, and rumors. Concludes that chaos theory is useful as an analogy to structure image problems and to raise…

Extracting Intrinsic Functional Networks with Feature-Based Group Independent Component Analysis

ERIC Educational Resources Information Center

Calhoun, Vince D.; Allen, Elena

2013-01-01

There is increasing use of functional imaging data to understand the macro-connectome of the human brain. Of particular interest is the structure and function of intrinsic networks (regions exhibiting temporally coherent activity both at rest and while a task is being performed), which account for a significant portion of the variance in…

Automatic registration of Iphone images to LASER point clouds of the urban structures using shape features

NASA Astrophysics Data System (ADS)

Sirmacek, B.; Lindenbergh, R. C.; Menenti, M.

2013-10-01

Fusion of 3D airborne laser (LIDAR) data and terrestrial optical imagery can be applied in 3D urban modeling and model up-dating. The most challenging aspect of the fusion procedure is registering the terrestrial optical images on the LIDAR point clouds. In this article, we propose an approach for registering these two different data from different sensor sources. As we use iPhone camera images which are taken in front of the interested urban structure by the application user and the high resolution LIDAR point clouds of the acquired by an airborne laser sensor. After finding the photo capturing position and orientation from the iPhone photograph metafile, we automatically select the area of interest in the point cloud and transform it into a range image which has only grayscale intensity levels according to the distance from the image acquisition position. We benefit from local features for registering the iPhone image to the generated range image. In this article, we have applied the registration process based on local feature extraction and graph matching. Finally, the registration result is used for facade texture mapping on the 3D building surface mesh which is generated from the LIDAR point cloud. Our experimental results indicate possible usage of the proposed algorithm framework for 3D urban map updating and enhancing purposes.

The Visible Human Project: From Body to Bits.

PubMed

Ackerman, Michael J

2017-01-01

Atlases of anatomy have long been a mainstay for visualizing and identifying features of the human body [1]. Many are constructed of idealized illustrations rendered so that structures are presented as three-dimensional (3-D) pictures. Others have employed photographs of actual dissections. Still others are composed of collections of artist renderings of organs or areas of interest. All rely on a basically two-dimensional (2-D) graphic display to depict and allow for a better understanding of a complicated 3-D structure.

Step-by-step growth of complex oxide microstructures

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

Datskos, Panos G.; Cullen, David A.; Sharma, Jaswinder K.

The synthesis of complex and hybrid oxide microstructures is of fundamental interest and practical applications. However, the design and synthesis of such structures is a challenging task. A solution-phase process to synthesize complex silica and silica-titania hybrid microstructures was developed by exploiting the emulsion-droplet-based step-by-step growth featuring shape control. Lastly, the strategy is robust and can be extended to the preparation of complex hybrid structures consisting of two or more materials, with each having its own shape.

Step-by-step growth of complex oxide microstructures

DOE PAGES

Datskos, Panos G.; Cullen, David A.; Sharma, Jaswinder K.

2015-06-10

The synthesis of complex and hybrid oxide microstructures is of fundamental interest and practical applications. However, the design and synthesis of such structures is a challenging task. A solution-phase process to synthesize complex silica and silica-titania hybrid microstructures was developed by exploiting the emulsion-droplet-based step-by-step growth featuring shape control. Lastly, the strategy is robust and can be extended to the preparation of complex hybrid structures consisting of two or more materials, with each having its own shape.

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

Risky forward interest rates and swaptions: Quantum finance model and empirical results

NASA Astrophysics Data System (ADS)

Baaquie, Belal Ehsan; Yu, Miao; Bhanap, Jitendra

2018-02-01

Risk free forward interest rates (Diebold and Li, 2006 [1]; Jamshidian, 1991 [2 ]) - and their realization by US Treasury bonds as the leading exemplar - have been studied extensively. In Baaquie (2010), models of risk free bonds and their forward interest rates based on the quantum field theoretic formulation of the risk free forward interest rates have been discussed, including the empirical evidence supporting these models. The quantum finance formulation of risk free forward interest rates is extended to the case of risky forward interest rates. The examples of the Singapore and Malaysian forward interest rates are used as specific cases. The main feature of the quantum finance model is that the risky forward interest rates are modeled both a) as a stand-alone case as well as b) being driven by the US forward interest rates plus a spread - having its own term structure -above the US forward interest rates. Both the US forward interest rates and the term structure for the spread are modeled by a two dimensional Euclidean quantum field. As a precursor to the evaluation of put option of the Singapore coupon bond, the quantum finance model for swaptions is tested using empirical study of swaptions for the US Dollar -showing that the model is quite accurate. A prediction for the market price of the put option for the Singapore coupon bonds is obtained. The quantum finance model is generalized to study the Malaysian case and the Malaysian forward interest rates are shown to have anomalies absent for the US and Singapore case. The model's prediction for a Malaysian interest rate swap is obtained.

Effects of contact network structure on epidemic transmission trees: implications for data required to estimate network structure.

PubMed

Carnegie, Nicole Bohme

2018-01-30

Understanding the dynamics of disease spread is key to developing effective interventions to control or prevent an epidemic. The structure of the network of contacts over which the disease spreads has been shown to have a strong influence on the outcome of the epidemic, but an open question remains as to whether it is possible to estimate contact network features from data collected in an epidemic. The approach taken in this paper is to examine the distributions of epidemic outcomes arising from epidemics on networks with particular structural features to assess whether that structure could be measured from epidemic data and what other constraints might be needed to make the problem identifiable. To this end, we vary the network size, mean degree, and transmissibility of the pathogen, as well as the network feature of interest: clustering, degree assortativity, or attribute-based preferential mixing. We record several standard measures of the size and spread of the epidemic, as well as measures that describe the shape of the transmission tree in order to ascertain whether there are detectable signals in the final data from the outbreak. The results suggest that there is potential to estimate contact network features from transmission trees or pure epidemic data, particularly for diseases with high transmissibility or for which the relevant contact network is of low mean degree. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

Multimedia Classifier

NASA Astrophysics Data System (ADS)

Costache, G. N.; Gavat, I.

2004-09-01

Along with the aggressive growing of the amount of digital data available (text, audio samples, digital photos and digital movies joined all in the multimedia domain) the need for classification, recognition and retrieval of this kind of data became very important. In this paper will be presented a system structure to handle multimedia data based on a recognition perspective. The main processing steps realized for the interesting multimedia objects are: first, the parameterization, by analysis, in order to obtain a description based on features, forming the parameter vector; second, a classification, generally with a hierarchical structure to make the necessary decisions. For audio signals, both speech and music, the derived perceptual features are the melcepstral (MFCC) and the perceptual linear predictive (PLP) coefficients. For images, the derived features are the geometric parameters of the speaker mouth. The hierarchical classifier consists generally in a clustering stage, based on the Kohonnen Self-Organizing Maps (SOM) and a final stage, based on a powerful classification algorithm called Support Vector Machines (SVM). The system, in specific variants, is applied with good results in two tasks: the first, is a bimodal speech recognition which uses features obtained from speech signal fused to features obtained from speaker's image and the second is a music retrieval from large music database.

Predicting the performance of fingerprint similarity searching.

PubMed

Vogt, Martin; Bajorath, Jürgen

2011-01-01

Fingerprints are bit string representations of molecular structure that typically encode structural fragments, topological features, or pharmacophore patterns. Various fingerprint designs are utilized in virtual screening and their search performance essentially depends on three parameters: the nature of the fingerprint, the active compounds serving as reference molecules, and the composition of the screening database. It is of considerable interest and practical relevance to predict the performance of fingerprint similarity searching. A quantitative assessment of the potential that a fingerprint search might successfully retrieve active compounds, if available in the screening database, would substantially help to select the type of fingerprint most suitable for a given search problem. The method presented herein utilizes concepts from information theory to relate the fingerprint feature distributions of reference compounds to screening libraries. If these feature distributions do not sufficiently differ, active database compounds that are similar to reference molecules cannot be retrieved because they disappear in the "background." By quantifying the difference in feature distribution using the Kullback-Leibler divergence and relating the divergence to compound recovery rates obtained for different benchmark classes, fingerprint search performance can be quantitatively predicted.

Multi-object segmentation framework using deformable models for medical imaging analysis.

PubMed

Namías, Rafael; D'Amato, Juan Pablo; Del Fresno, Mariana; Vénere, Marcelo; Pirró, Nicola; Bellemare, Marc-Emmanuel

2016-08-01

Segmenting structures of interest in medical images is an important step in different tasks such as visualization, quantitative analysis, simulation, and image-guided surgery, among several other clinical applications. Numerous segmentation methods have been developed in the past three decades for extraction of anatomical or functional structures on medical imaging. Deformable models, which include the active contour models or snakes, are among the most popular methods for image segmentation combining several desirable features such as inherent connectivity and smoothness. Even though different approaches have been proposed and significant work has been dedicated to the improvement of such algorithms, there are still challenging research directions as the simultaneous extraction of multiple objects and the integration of individual techniques. This paper presents a novel open-source framework called deformable model array (DMA) for the segmentation of multiple and complex structures of interest in different imaging modalities. While most active contour algorithms can extract one region at a time, DMA allows integrating several deformable models to deal with multiple segmentation scenarios. Moreover, it is possible to consider any existing explicit deformable model formulation and even to incorporate new active contour methods, allowing to select a suitable combination in different conditions. The framework also introduces a control module that coordinates the cooperative evolution of the snakes and is able to solve interaction issues toward the segmentation goal. Thus, DMA can implement complex object and multi-object segmentations in both 2D and 3D using the contextual information derived from the model interaction. These are important features for several medical image analysis tasks in which different but related objects need to be simultaneously extracted. Experimental results on both computed tomography and magnetic resonance imaging show that the proposed framework has a wide range of applications especially in the presence of adjacent structures of interest or under intra-structure inhomogeneities giving excellent quantitative results.

MMDB: Entrez’s 3D-structure database

PubMed Central

Wang, Yanli; Anderson, John B.; Chen, Jie; Geer, Lewis Y.; He, Siqian; Hurwitz, David I.; Liebert, Cynthia A.; Madej, Thomas; Marchler, Gabriele H.; Marchler-Bauer, Aron; Panchenko, Anna R.; Shoemaker, Benjamin A.; Song, James S.; Thiessen, Paul A.; Yamashita, Roxanne A.; Bryant, Stephen H.

2002-01-01

Three-dimensional structures are now known within many protein families and it is quite likely, in searching a sequence database, that one will encounter a homolog with known structure. The goal of Entrez’s 3D-structure database is to make this information, and the functional annotation it can provide, easily accessible to molecular biologists. To this end Entrez’s search engine provides three powerful features. (i) Sequence and structure neighbors; one may select all sequences similar to one of interest, for example, and link to any known 3D structures. (ii) Links between databases; one may search by term matching in MEDLINE, for example, and link to 3D structures reported in these articles. (iii) Sequence and structure visualization; identifying a homolog with known structure, one may view molecular-graphic and alignment displays, to infer approximate 3D structure. In this article we focus on two features of Entrez’s Molecular Modeling Database (MMDB) not described previously: links from individual biopolymer chains within 3D structures to a systematic taxonomy of organisms represented in molecular databases, and links from individual chains (and compact 3D domains within them) to structure neighbors, other chains (and 3D domains) with similar 3D structure. MMDB may be accessed at http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Structure. PMID:11752307

Study of the electronic structure of electron accepting cyano-films: TCNQversusTCNE.

PubMed

Capitán, Maria J; Álvarez, Jesús; Navio, Cristina

2018-04-18

In this article, we perform systematic research on the electronic structure of two closely related organic electron acceptor molecules (TCNQ and TCNE), which are of technological interest due to their outstanding electronic properties. These studies have been performed from the experimental point of view by the use electron spectroscopies (XPS and UPS) and supported theoretically by the use of ab-initio DFT calculations. The cross-check between both molecules allows us to identify the characteristic electronic features of each part of the molecules and their contribution to the final electronic structure. We can describe the nature of the band gap of these materials, and we relate this with the appearance of the shake-up features in the core level spectra. A band bending and energy gap reduction of the aforementioned electronic structure in contact with a metal surface are seen in the experimental results as well in the theoretical calculations. This behavior implies that the TCNQ thin film accepts electrons from the metal substrate becoming a Schottky n-junction.

Patch-based automatic retinal vessel segmentation in global and local structural context.

PubMed

Cao, Shuoying; Bharath, Anil A; Parker, Kim H; Ng, Jeffrey

2012-01-01

In this paper, we extend our published work [1] and propose an automated system to segment retinal vessel bed in digital fundus images with enough adaptability to analyze images from fluorescein angiography. This approach takes into account both the global and local context and enables both vessel segmentation and microvascular centreline extraction. These tools should allow researchers and clinicians to estimate and assess vessel diameter, capillary blood volume and microvascular topology for early stage disease detection, monitoring and treatment. Global vessel bed segmentation is achieved by combining phase-invariant orientation fields with neighbourhood pixel intensities in a patch-based feature vector for supervised learning. This approach is evaluated against benchmarks on the DRIVE database [2]. Local microvascular centrelines within Regions-of-Interest (ROIs) are segmented by linking the phase-invariant orientation measures with phase-selective local structure features. Our global and local structural segmentation can be used to assess both pathological structural alterations and microemboli occurrence in non-invasive clinical settings in a longitudinal study.

Polymer-directed synthesis of metal oxide-containing nanomaterials for electrochemical energy storage

NASA Astrophysics Data System (ADS)

Mai, Yiyong; Zhang, Fan; Feng, Xinliang

2013-12-01

Metal oxide-containing nanomaterials (MOCNMs) of controllable structures at the nano-scale have attracted considerable interest because of their great potential applications in electrochemical energy storage devices, such as lithium-ion batteries (LIBs) and supercapacitors. Among many structure-directing agents, polymers and macromolecules, including block copolymers (BCPs) and graphene, exhibit distinct advantages in the template-assisted synthesis of MOCNMs. In this feature article, we introduce the controlled preparation of MOCNMs employing BCPs and graphene as structure-directing agents. Typical synthetic strategies are presented for the control of structures and sizes as well as the improvement of physical properties and electrochemical performance of MOCNMs in LIBs and supercapacitors.

Polymer-directed synthesis of metal oxide-containing nanomaterials for electrochemical energy storage.

PubMed

Mai, Yiyong; Zhang, Fan; Feng, Xinliang

2014-01-07

Metal oxide-containing nanomaterials (MOCNMs) of controllable structures at the nano-scale have attracted considerable interest because of their great potential applications in electrochemical energy storage devices, such as lithium-ion batteries (LIBs) and supercapacitors. Among many structure-directing agents, polymers and macromolecules, including block copolymers (BCPs) and graphene, exhibit distinct advantages in the template-assisted synthesis of MOCNMs. In this feature article, we introduce the controlled preparation of MOCNMs employing BCPs and graphene as structure-directing agents. Typical synthetic strategies are presented for the control of structures and sizes as well as the improvement of physical properties and electrochemical performance of MOCNMs in LIBs and supercapacitors.

Phagraphene: A Low-Energy Graphene Allotrope Composed of 5-6-7 Carbon Rings with Distorted Dirac Cones.

PubMed

Wang, Zhenhai; Zhou, Xiang-Feng; Zhang, Xiaoming; Zhu, Qiang; Dong, Huafeng; Zhao, Mingwen; Oganov, Artem R

2015-09-09

Using systematic evolutionary structure searching we propose a new carbon allotrope, phagraphene [fæ'græfi:n], standing for penta-hexa-hepta-graphene, because the structure is composed of 5-6-7 carbon rings. This two-dimensional (2D) carbon structure is lower in energy than most of the predicted 2D carbon allotropes due to its sp(2)-binding features and density of atomic packing comparable to graphene. More interestingly, the electronic structure of phagraphene has distorted Dirac cones. The direction-dependent cones are further proved to be robust against external strain with tunable Fermi velocities.

Execution of deep dipole geoelectrical soundings in areas of geothermal interest. Final report

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

Patella, D.

It is suggested that deep geoelectrical problems may be resolved by carrying out dipole soundings in the field and applying a quantitative interpretation in the Schlumberger domain. The 'transformation' of original field dipole sounding curves into equivalent Schlumberger curves is outlined for the cases of layered structures and arbitrary underground structures. Theoretical apparent resistivity curves are derived for soundings over bidimensional structures. Following a summary of the geological features of the Travale-Radicondoli geothermal area of Italy, the dipole sounding method employed for this field study and the means of collecting and analyzing the data, are outlined.

Antifeedant activity of quassinoids.

PubMed

Leskinen, V; Polonsky, J; Bhatnagar, S

1984-10-01

The antifeedant activity of 13 quassinoids of different structural types has been studied against the Mexican bean beetle (Epilachna varivestis Mulsant) 4th instar larvae and the southern armyworm (Spodoptera eridania Crawer) 5th instar larvae. All quassinoids tested displayed significant activity against the Mexican bean beetle and, thus, do not reveal a simple structure-activity relationship. Five quassinoids were active against the southern armyworm. Interestingly, four of these-bruceantin (I), glaucarubinone (VI), isobruceine A (VIII), and simalikalactone D (XI)-possess the required structural features for antineoplastic activity. The noncytotoxic quassin (X) is an exception; it is active against both pests.

Engineered biomimicry: polymeric replication of surface features found on insects

NASA Astrophysics Data System (ADS)

Pulsifer, Drew P.; Lakhtakia, Akhlesh; Martín-Palma, Raúl J.; Pantano, Carlo G.

2011-04-01

By combining the modified conformal-evaporated-film-by-rotation (M-CEFR) technique with nickel electroforming, we have produced master negatives of nonplanar biotemplates. An approximately 250-nm-thick conformal coating of nanocrystaline nickel is deposited on a surface structure of interest found in class Insecta, and the coating is then reinforced with a roughly 60-μm-thick structural layer of nickel by electroforming. This structural layer endows the M-CEFR coating with the mechanical robustness necessary for casting or stamping multiple polymer replicas of the biotemplate. We have made master negatives of blowfly corneas, beetle elytrons, and butterfly wings.

Obtaining environmental measures to facilitate vertebrate habitat modeling

USGS Publications Warehouse

Karl, J.W.; Wright, N.M.; Heglund, P.J.; Scott, J.M.

1999-01-01

Published literature generally lacks habitat information needed to adequately model the habitats of most wildlife species at large scales (>1:100,000). We searched in primary and secondary literature for occurrence of several potentially useful habitat measures for 20 species of interest to the Idaho Department of Fish and Game. We found adequate information for modeling only the habitats of certain game species and species of special interest. We suggest that many more researchers could collect simple habitat information regarding vegetation composition and structure, topographic features, soils, temperature, and distance to special landscape features such that current research expenses would not be increased significantly. We recommend that habitat data be consistently reported in peer-reviewed literature or deposited into a central data repository. This will not only help fill the gaps in our current knowledge of wildlife but also place it in a format that is readily accessible by the scientific community.

Earth observations and photography experiment: Summary of significant results

NASA Technical Reports Server (NTRS)

El-Baz, F.

1978-01-01

Observation and photographic data from the Apollo Soyuz Test Project are analyzed. The discussion is structured according to the fields of investigation including: geology, desert studies, oceanography, hydrology, and meteorology. The data were obtained by: (1) visual observations of selected Earth features, (2) hand-held camera photography to document observations, and (3) stereo mapping photography of areas of significant scientific interest.

A Structured Grid Based Solution-Adaptive Technique for Complex Separated Flows

NASA Technical Reports Server (NTRS)

Thornburg, Hugh; Soni, Bharat K.; Kishore, Boyalakuntla; Yu, Robert

1996-01-01

The objective of this work was to enhance the predictive capability of widely used computational fluid dynamic (CFD) codes through the use of solution adaptive gridding. Most problems of engineering interest involve multi-block grids and widely disparate length scales. Hence, it is desirable that the adaptive grid feature detection algorithm be developed to recognize flow structures of different type as well as differing intensity, and adequately address scaling and normalization across blocks. In order to study the accuracy and efficiency improvements due to the grid adaptation, it is necessary to quantify grid size and distribution requirements as well as computational times of non-adapted solutions. Flow fields about launch vehicles of practical interest often involve supersonic freestream conditions at angle of attack exhibiting large scale separate vortical flow, vortex-vortex and vortex-surface interactions, separated shear layers and multiple shocks of different intensity. In this work, a weight function and an associated mesh redistribution procedure is presented which detects and resolves these features without user intervention. Particular emphasis has been placed upon accurate resolution of expansion regions and boundary layers. Flow past a wedge at Mach=2.0 is used to illustrate the enhanced detection capabilities of this newly developed weight function.

Regional information guidance system based on hypermedia concept

NASA Astrophysics Data System (ADS)

Matoba, Hiroshi; Hara, Yoshinori; Kasahara, Yutako

1990-08-01

A regional information guidance system has been developed on an image workstation. Two main features of this system are hypermedia data structure and friendly visual interface realized by the full-color frame memory system. As the hypermedia data structure manages regional information such as maps, pictures and explanations of points of interest, users can retrieve those information one by one, next to next according to their interest change. For example, users can retrieve explanation of a picture through the link between pictures and text explanations. Users can also traverse from one document to another by using keywords as cross reference indices. The second feature is to utilize a full-color, high resolution and wide space frame memory for visual interface design. This frame memory system enables real-time operation of image data and natural scene representation. The system also provides half tone representing function which enables fade-in/out presentations. This fade-in/out functions used in displaying and erasing menu and image data, makes visual interface soft for human eyes. The system we have developed is a typical example of multimedia applications. We expect the image workstation will play an important role as a platform for multimedia applications.

Complementary spectroscopic studies of materials of security interest

NASA Astrophysics Data System (ADS)

Burnett, Andrew; Fan, Wenhui; Upadhya, Prashanth; Cunningham, John; Edwards, Howell; Munshi, Tasnim; Hargreaves, Michael; Linfield, Edmund; Davies, Giles

2006-09-01

We demonstrate that, through coherent measurement of the transmitted terahertz frequency electric fields, broadband (0.3 - 8 THz) time-domain spectroscopy can be used to measure far-infrared vibrational modes of a range of drugs-of-abuse and high explosives that are of interest to the forensic and security services. Our results indicate that absorption features in these materials are highly sensitive to the structural and spatial arrangement of the molecules. Terahertz frequency spectra are also compared with high-resolution low-frequency Raman spectra to assist in understanding the low-frequency inter- and intra-molecular vibrational modes of the molecules.

Biomimetics: lessons from nature--an overview.

PubMed

Bhushan, Bharat

2009-04-28

Nature has developed materials, objects and processes that function from the macroscale to the nanoscale. These have gone through evolution over 3.8 Gyr. The emerging field of biomimetics allows one to mimic biology or nature to develop nanomaterials, nanodevices and processes. Properties of biological materials and surfaces result from a complex interplay between surface morphology and physical and chemical properties. Hierarchical structures with dimensions of features ranging from the macroscale to the nanoscale are extremely common in nature to provide properties of interest. Molecular-scale devices, superhydrophobicity, self-cleaning, drag reduction in fluid flow, energy conversion and conservation, high adhesion, reversible adhesion, aerodynamic lift, materials and fibres with high mechanical strength, biological self-assembly, antireflection, structural coloration, thermal insulation, self-healing and sensory-aid mechanisms are some of the examples found in nature that are of commercial interest. This paper provides a broad overview of the various objects and processes of interest found in nature and applications under development or available in the marketplace.

Tuning transport properties on graphene multiterminal structures by mechanical deformations

NASA Astrophysics Data System (ADS)

Latge, Andrea; Torres, Vanessa; Faria, Daiara

The realization of mechanical strain on graphene structures is viewed as a promise route to tune electronic and transport properties such as changing energy band-gaps and promoting localization of states. Using continuum models, mechanical deformations are described by effective gauge fields, mirrored as pseudomagnetic fields that may reach quite high values. Interesting symmetry features are developed due to out of plane deformations on graphene; lift sublattice symmetry was predicted and observed in centrosymmetric bumps and strained nanobubbles. Here we discuss the effects of Gaussian-like strain on a hexagonal graphene flake connected to three leads, modeled as perfect graphene nanoribbons. The Green function formalism is used within a tight-binding approximation. For this particular deformation sharp resonant states are achieved depending on the strained structure details. We also study a fold-strained structure in which the three leads are deformed extending up to the very center of the hexagonal flake. We show that conductance suppressions can be controlled by the strain intensity and important transport features are modeled by the electronic band structure of the leads.

New Features in the Lipid A Structure of Brucella suis and Brucella abortus Lipopolysaccharide

NASA Astrophysics Data System (ADS)

Casabuono, Adriana C.; Czibener, Cecilia; Del Giudice, Mariela G.; Valguarnera, Ezequiel; Ugalde, Juan E.; Couto, Alicia S.

2017-12-01

Brucellaceae are Gram-negative bacteria that cause brucellosis, one of the most distributed worldwide zoonosis, transmitted to humans by contact with either infected animals or their products. The lipopolysaccharide exposed on the cell surface has been intensively studied and is considered a major virulence factor of Brucella. In the last years, structural studies allowed the determination of new structures in the core oligosaccharide and the O-antigen of this lipopolysaccharide. In this work, we have reinvestigated the lipid A structure isolated from B. suis and B. abortus lipopolysaccharides. A detailed study by MALDI-TOF mass spectrometry in the positive and negative ion modes of the lipid A moieties purified from both species was performed. Interestingly, a new feature was detected: the presence of a pyrophosphorylethanolamine residue substituting the backbone. LID-MS/MS analysis of some of the detected ions allowed assurance that the Lipid A structure composed by the diGlcN3N disaccharide, mainly hexa-acylated and penta-acylated, bearing one phosphate and one pyrophosphorylethanolamine residue. [Figure not available: see fulltext.

2.4 Å resolution crystal structure of human TRAP1 NM , the Hsp90 paralog in the mitochondrial matrix

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

Sung, Nuri; Lee, Jungsoon; Kim, Ji-Hyun

2016-07-13

TRAP1 is an organelle-specific Hsp90 paralog that is essential for neoplastic growth. As a member of the Hsp90 family, TRAP1 is presumed to be a general chaperone facilitating the late-stage folding of Hsp90 client proteins in the mitochondrial matrix. Interestingly, TRAP1 cannot replace cytosolic Hsp90 in protein folding, and none of the known Hsp90 co-chaperones are found in mitochondria. Thus, the three-dimensional structure of TRAP1 must feature regulatory elements that are essential to the ATPase activity and chaperone function of TRAP1. Here, the crystal structure of a human TRAP1 NMdimer is presented, featuring an intact N-domain and M-domain structure, boundmore » to adenosine 5'-β,γ-imidotriphosphate (ADPNP). The crystal structure together with epitope-mapping results shows that the TRAP1 M-domain loop 1 contacts the neighboring subunit and forms a previously unobserved third dimer interface that mediates the specific interaction with mitochondrial Hsp70.« less

New Features in the Lipid A Structure of Brucella suis and Brucella abortus Lipopolysaccharide.

PubMed

Casabuono, Adriana C; Czibener, Cecilia; Del Giudice, Mariela G; Valguarnera, Ezequiel; Ugalde, Juan E; Couto, Alicia S

2017-12-01

Brucellaceae are Gram-negative bacteria that cause brucellosis, one of the most distributed worldwide zoonosis, transmitted to humans by contact with either infected animals or their products. The lipopolysaccharide exposed on the cell surface has been intensively studied and is considered a major virulence factor of Brucella. In the last years, structural studies allowed the determination of new structures in the core oligosaccharide and the O-antigen of this lipopolysaccharide. In this work, we have reinvestigated the lipid A structure isolated from B. suis and B. abortus lipopolysaccharides. A detailed study by MALDI-TOF mass spectrometry in the positive and negative ion modes of the lipid A moieties purified from both species was performed. Interestingly, a new feature was detected: the presence of a pyrophosphorylethanolamine residue substituting the backbone. LID-MS/MS analysis of some of the detected ions allowed assurance that the Lipid A structure composed by the diGlcN3N disaccharide, mainly hexa-acylated and penta-acylated, bearing one phosphate and one pyrophosphorylethanolamine residue. Graphical abstract ᅟ.

An international standard for observation data

NASA Astrophysics Data System (ADS)

Cox, Simon

2010-05-01

A generic information model for observations and related features supports data exchange both within and between different scientific and technical communities. Observations and Measurements (O&M) formalizes a neutral terminology for observation data and metadata. It was based on a model developed for medical observations, and draws on experience from geology and mineral exploration, in-situ monitoring, remote sensing, intelligence, biodiversity studies, ocean observations and climate simulations. Hundreds of current deployments of Sensor Observation Services (SOS), covering multiple disciplines, provide validation of the O&M model. A W3C Incubator group on 'Semantic Sensor Networks' is now using O&M as one of the bases for development of a formal ontology for sensor networks. O&M defines the information describing observation acts and their results, including the following key terms: observation, result, observed-property, feature-of-interest, procedure, phenomenon-time, and result-time. The model separates of the (meta-)data associated with the observation procedure, the observed feature, and the observation event itself. Observation results may take various forms, including scalar quantities, categories, vectors, grids, or any data structure required to represent the value of some property of some observed feature. O&M follows the ISO/TC 211 General Feature Model so non-geometric properties must be associated with typed feature instances. This requires formalization of information that may be trivial when working within some earth-science sub-disciplines (e.g. temperature, pressure etc. are associated with the atmosphere or ocean, and not just a location) but is critical to cross-disciplinary applications. It also allows the same structure and terminology to be used for in-situ, ex-situ and remote sensing observations, as well as for simulations. For example: a stream level observation is an in-situ monitoring application where the feature-of-interest is a reach, the observed property is water-level, and the result is a time-series of heights; stream quality is usually determined by ex-situ observation where the feature-of-interest is a specimen that is recovered from the stream, the observed property is water-quality, and the result is a set of measures of various parameters, or an assessment derived from these; on the other hand, distribution of surface temperature of a water body is typically determined through remote-sensing, where at observation time the procedure is located distant from the feature-of-interest, and the result is an image or grid. Observations usually involve sampling of an ultimate feature-of-interest. In the environmental sciences common sampling strategies are used. Spatial sampling is classified primarily by topological dimension (point, curve, surface, volume) and is supported by standard processing and visualisation tools. Specimens are used for ex-situ processing in most disciplines. Sampling features are often part of complexes (e.g. specimens are sub-divided; specimens are retrieved from points along a transect; sections are taken across tracts), so relationships between instances must be recorded. And observational campaigns involve collections of sampling features. The sampling feature model is a core part of O&M, and application experience has shown that describing the relationships between sampling features and observations is generally critical to successful use of the model. O&M was developed through Open Geospatial Consortium (OGC) as part of the Sensor Web Enablement (SWE) initiative. Other SWE standards include SensorML, SOS, Sensor Planning Service (SPS). The OGC O&M standard (Version 1) had two parts: part 1 describes observation events, and part 2 provides a schema sampling features. A revised version of O&M (Version 2) is to be published in a single document as ISO 19156. O&M Version 1 included an XML encoding for data exchange, which is used as the payload for SOS responses. The new version will provide a UML model only. Since an XML encoding may be generated following a rule, such as that presented in ISO 19136 (GML 3.2), it is not included in the standard directly. O&M Version 2 thus supports multiple physical implementations and versions.

LDRD final report :

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

Brost, Randolph C.; McLendon, William Clarence,

2013-01-01

Modeling geospatial information with semantic graphs enables search for sites of interest based on relationships between features, without requiring strong a priori models of feature shape or other intrinsic properties. Geospatial semantic graphs can be constructed from raw sensor data with suitable preprocessing to obtain a discretized representation. This report describes initial work toward extending geospatial semantic graphs to include temporal information, and initial results applying semantic graph techniques to SAR image data. We describe an efficient graph structure that includes geospatial and temporal information, which is designed to support simultaneous spatial and temporal search queries. We also report amore » preliminary implementation of feature recognition, semantic graph modeling, and graph search based on input SAR data. The report concludes with lessons learned and suggestions for future improvements.« less

Inorganic anion-dependent assembly of zero-, one-, two- and three-dimensional Cu(II)/Ag(I) complexes under the guidance of the HSAB theory: Synthesis, structure, and magnetic property

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

Liu, Yaru; Xing, Zhiyan; Zhang, Xiao

To systematically explore the influence of inorganic anions on building coordination complexes, five novel complexes based on 1-(benzotriazole-1-methyl)−2-propylimidazole (bpmi), [Cu(bpmi){sub 2}(Ac){sub 2}]·H{sub 2}O (1), [Cu(bpmi){sub 2}(H{sub 2}O){sub 2}]·2NO{sub 3}·2H{sub 2}O (2), [Cu(bpmi)(N{sub 3}){sub 2}] (3), [Ag(bpmi)(NO{sub 3})] (4) and [Cu{sub 3}(bpmi){sub 2}(SCN){sub 4}(DMF)] (5) (Ac{sup −}=CH{sub 3}COO{sup −}, DMF=N,N-Dimethylformamide) are synthesized through rationally introducing Cu(II) salts and Ag(I) salt with different inorganic anions. X-ray single-crystal analyses reveal that these complexes show interesting structural features from mononuclear (1), one-dimensional (2 and 3), two-dimensional (4) to three-dimensional (5) under the influence of inorganic anions with different basicities. The structural variation can bemore » explained by the hard-soft-acid-base (HSAB) theory. Magnetic susceptibility measurement indicates that complex 3 exhibits an antiferromagnetic coupling between adjacent Cu(II) ions. - Graphical abstract: Five new Cu(II)/Ag(I) complexes show interesting structural features from mononuclear, one-dimension, two-dimension to three-dimension under the influence of inorganic anions. The structural variation can be explained by the HSAB theory. - Highlights: • Five inorganic anion-dependent complexes are synthesized. • Structural variation can be explained by the hard-soft-acid-base (HSAB) theory. • The magnetic property of complex has been studied.« less

Disease Prediction based on Functional Connectomes using a Scalable and Spatially-Informed Support Vector Machine

PubMed Central

Watanabe, Takanori; Kessler, Daniel; Scott, Clayton; Angstadt, Michael; Sripada, Chandra

2014-01-01

Substantial evidence indicates that major psychiatric disorders are associated with distributed neural dysconnectivity, leading to strong interest in using neuroimaging methods to accurately predict disorder status. In this work, we are specifically interested in a multivariate approach that uses features derived from whole-brain resting state functional connectomes. However, functional connectomes reside in a high dimensional space, which complicates model interpretation and introduces numerous statistical and computational challenges. Traditional feature selection techniques are used to reduce data dimensionality, but are blind to the spatial structure of the connectomes. We propose a regularization framework where the 6-D structure of the functional connectome (defined by pairs of points in 3-D space) is explicitly taken into account via the fused Lasso or the GraphNet regularizer. Our method only restricts the loss function to be convex and margin-based, allowing non-differentiable loss functions such as the hinge-loss to be used. Using the fused Lasso or GraphNet regularizer with the hinge-loss leads to a structured sparse support vector machine (SVM) with embedded feature selection. We introduce a novel efficient optimization algorithm based on the augmented Lagrangian and the classical alternating direction method, which can solve both fused Lasso and GraphNet regularized SVM with very little modification. We also demonstrate that the inner subproblems of the algorithm can be solved efficiently in analytic form by coupling the variable splitting strategy with a data augmentation scheme. Experiments on simulated data and resting state scans from a large schizophrenia dataset show that our proposed approach can identify predictive regions that are spatially contiguous in the 6-D “connectome space,” offering an additional layer of interpretability that could provide new insights about various disease processes. PMID:24704268

Laser-induced patterns on metals and polymers for biomimetic surface engineering

NASA Astrophysics Data System (ADS)

Kietzig, Anne-Marie; Lehr, Jorge; Matus, Luke; Liang, Fang

2014-03-01

One common feature of many functional surfaces found in nature is their modular composition often exhibiting several length scales. Prominent natural examples for extreme behaviors can be named in various plant leaf (rose, peanut, lotus) or animal toe surfaces (Gecko, tree frog). Influence factors of interest are the surface's chemical composition, its microstructure, its organized or random roughness and hence the resulting surface wetting and adhesion character. Femtosecond (fs) laser micromachining offers a possibility to render all these factors in one single processing step on metallic and polymeric surfaces. Exemplarily, studies on Titanium and PTFE are shown, where the dependence of the resulting feature sizes on lasing intensity is investigated. While Ti surfaces show rigid surface patterns of micrometer scaled features with superimposed nanostructures, PTFE exhibits elastic hairy structures of nanometric diameter, which upon a certain threshold tend to bundle to larger features. Both surface patterns can be adjusted to mimic specific wetting and flow behaviour as seen on natural examples. Therefore, fs-laser micromachining is suggested as an interesting industrially scalable technique to pattern and fine-tune the surface wettability of a surface to the desired extends in one process step. Possible applications can be seen with surfaces, which require specific wetting, fouling, icing, friction or cell adhesion behaviour.

Characterizing trabecular bone structure for assessing vertebral fracture risk on volumetric quantitative computed tomography

NASA Astrophysics Data System (ADS)

Nagarajan, Mahesh B.; Checefsky, Walter A.; Abidin, Anas Z.; Tsai, Halley; Wang, Xixi; Hobbs, Susan K.; Bauer, Jan S.; Baum, Thomas; Wismüller, Axel

2015-03-01

While the proximal femur is preferred for measuring bone mineral density (BMD) in fracture risk estimation, the introduction of volumetric quantitative computed tomography has revealed stronger associations between BMD and spinal fracture status. In this study, we propose to capture properties of trabecular bone structure in spinal vertebrae with advanced second-order statistical features for purposes of fracture risk assessment. For this purpose, axial multi-detector CT (MDCT) images were acquired from 28 spinal vertebrae specimens using a whole-body 256-row CT scanner with a dedicated calibration phantom. A semi-automated method was used to annotate the trabecular compartment in the central vertebral slice with a circular region of interest (ROI) to exclude cortical bone; pixels within were converted to values indicative of BMD. Six second-order statistical features derived from gray-level co-occurrence matrices (GLCM) and the mean BMD within the ROI were then extracted and used in conjunction with a generalized radial basis functions (GRBF) neural network to predict the failure load of the specimens; true failure load was measured through biomechanical testing. Prediction performance was evaluated with a root-mean-square error (RMSE) metric. The best prediction performance was observed with GLCM feature `correlation' (RMSE = 1.02 ± 0.18), which significantly outperformed all other GLCM features (p < 0.01). GLCM feature correlation also significantly outperformed MDCTmeasured mean BMD (RMSE = 1.11 ± 0.17) (p< 10-4). These results suggest that biomechanical strength prediction in spinal vertebrae can be significantly improved through characterization of trabecular bone structure with GLCM-derived texture features.

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.

Features of the normal choriocapillaris with OCT-angiography: Density estimation and textural properties.

PubMed

Montesano, Giovanni; Allegrini, Davide; Colombo, Leonardo; Rossetti, Luca M; Pece, Alfredo

2017-01-01

The main objective of our work is to perform an in depth analysis of the structural features of normal choriocapillaris imaged with OCT Angiography. Specifically, we provide an optimal radius for a circular Region of Interest (ROI) to obtain a stable estimate of the subfoveal choriocapillaris density and characterize its textural properties using Markov Random Fields. On each binarized image of the choriocapillaris OCT Angiography we performed simulated measurements of the subfoveal choriocapillaris densities with circular Regions of Interest (ROIs) of different radii and with small random displacements from the center of the Foveal Avascular Zone (FAZ). We then calculated the variability of the density measure with different ROI radii. We then characterized the textural features of choriocapillaris binary images by estimating the parameters of an Ising model. For each image we calculated the Optimal Radius (OR) as the minimum ROI radius required to obtain a standard deviation in the simulation below 0.01. The density measured with the individual OR was 0.52 ± 0.07 (mean ± STD). Similar density values (0.51 ± 0.07) were obtained using a fixed ROI radius of 450 μm. The Ising model yielded two parameter estimates (β = 0.34 ± 0.03; γ = 0.003 ± 0.012; mean ± STD), characterizing pixel clustering and white pixel density respectively. Using the estimated parameters to synthetize new random textures via simulation we obtained a good reproduction of the original choriocapillaris structural features and density. In conclusion, we developed an extensive characterization of the normal subfoveal choriocapillaris that might be used for flow analysis and applied to the investigation pathological alterations.

Lithium halide monolayers: Structural, electronic and optical properties by first principles study

NASA Astrophysics Data System (ADS)

Safari, Mandana; Maskaneh, Pegah; Moghadam, Atousa Dashti; Jalilian, Jaafar

2016-09-01

Using first principle study, we investigate the structural, electronic and optical properties of lithium halide monolayers (LiF, LiCl, LiBr). In contrast to graphene and other graphene-like structures that form hexagonal rings in plane, these compounds can form and stabilize in cubic shape interestingly. The type of band structure in these insulators is identified as indirect type and ionic nature of their bonds are illustrated as well. The optical properties demonstrate extremely transparent feature for them as a result of wide band gap in the visible range; also their electron transitions are indicated for achieving a better vision on the absorption mechanism in these kinds of monolayers.

Lamb wave detection of limpet mines on ship hulls.

PubMed

Bingham, Jill; Hinders, Mark; Friedman, Adam

2009-12-01

This paper describes the use of ultrasonic guided waves for identifying the mass loading due to underwater limpet mines on ship hulls. The Dynamic Wavelet Fingerprint Technique (DFWT) is used to render the guided wave mode information in two-dimensional binary images because the waveform features of interest are too subtle to identify in time domain. The use of wavelets allows both time and scale features from the original signals to be retained, and image processing can be used to automatically extract features that correspond to the arrival times of the guided wave modes. For further understanding of how the guided wave modes propagate through the real structures, a parallel processing, 3D elastic wave simulation is developed using the finite integration technique (EFIT). This full field, technique models situations that are too complex for analytical solutions, such as built up 3D structures. The simulations have produced informative visualizations of the guided wave modes in the structures as well as mimicking directly the output from sensors placed in the simulation space for direct comparison to experiments. Results from both drydock and in-water experiments with dummy mines are also shown.

Regional shape-based feature space for segmenting biomedical images using neural networks

NASA Astrophysics Data System (ADS)

Sundaramoorthy, Gopal; Hoford, John D.; Hoffman, Eric A.

1993-07-01

In biomedical images, structure of interest, particularly the soft tissue structures, such as the heart, airways, bronchial and arterial trees often have grey-scale and textural characteristics similar to other structures in the image, making it difficult to segment them using only gray- scale and texture information. However, these objects can be visually recognized by their unique shapes and sizes. In this paper we discuss, what we believe to be, a novel, simple scheme for extracting features based on regional shapes. To test the effectiveness of these features for image segmentation (classification), we use an artificial neural network and a statistical cluster analysis technique. The proposed shape-based feature extraction algorithm computes regional shape vectors (RSVs) for all pixels that meet a certain threshold criteria. The distance from each such pixel to a boundary is computed in 8 directions (or in 26 directions for a 3-D image). Together, these 8 (or 26) values represent the pixel's (or voxel's) RSV. All RSVs from an image are used to train a multi-layered perceptron neural network which uses these features to 'learn' a suitable classification strategy. To clearly distinguish the desired object from other objects within an image, several examples from inside and outside the desired object are used for training. Several examples are presented to illustrate the strengths and weaknesses of our algorithm. Both synthetic and actual biomedical images are considered. Future extensions to this algorithm are also discussed.

Volumetric quantitative characterization of human patellar cartilage with topological and geometrical features on phase-contrast X-ray computed tomography.

PubMed

Nagarajan, Mahesh B; Coan, Paola; Huber, Markus B; Diemoz, Paul C; Wismüller, Axel

2015-11-01

Phase-contrast X-ray computed tomography (PCI-CT) has attracted significant interest in recent years for its ability to provide significantly improved image contrast in low absorbing materials such as soft biological tissue. In the research context of cartilage imaging, previous studies have demonstrated the ability of PCI-CT to visualize structural details of human patellar cartilage matrix and capture changes to chondrocyte organization induced by osteoarthritis. This study evaluates the use of geometrical and topological features for volumetric characterization of such chondrocyte patterns in the presence (or absence) of osteoarthritic damage. Geometrical features derived from the scaling index method (SIM) and topological features derived from Minkowski Functionals were extracted from 1392 volumes of interest (VOI) annotated on PCI-CT images of ex vivo human patellar cartilage specimens. These features were subsequently used in a machine learning task with support vector regression to classify VOIs as healthy or osteoarthritic; classification performance was evaluated using the area under the receiver operating characteristic curve (AUC). Our results show that the classification performance of SIM-derived geometrical features (AUC: 0.90 ± 0.09) is significantly better than Minkowski Functionals volume (AUC: 0.54 ± 0.02), surface (AUC: 0.72 ± 0.06), mean breadth (AUC: 0.74 ± 0.06) and Euler characteristic (AUC: 0.78 ± 0.04) (p < 10(-4)). These results suggest that such geometrical features can provide a detailed characterization of the chondrocyte organization in the cartilage matrix in an automated manner, while also enabling classification of cartilage as healthy or osteoarthritic with high accuracy. Such features could potentially serve as diagnostic imaging markers for evaluating osteoarthritis progression and its response to different therapeutic intervention strategies.

Ultra high molecular weight polyethylene: Optical features at millimeter wavelengths

NASA Astrophysics Data System (ADS)

D'Alessandro, G.; Paiella, A.; Coppolecchia, A.; Castellano, M. G.; Colantoni, I.; de Bernardis, P.; Lamagna, L.; Masi, S.

2018-05-01

The next generation of experiments for the measurement of the Cosmic Microwave Background (CMB) requires more and more the use of advanced materials, with specific physical and structural properties. An example is the material used for receiver's cryostat windows and internal lenses. The large throughput of current CMB experiments requires a large diameter (of the order of 0.5 m) of these parts, resulting in heavy structural and optical requirements on the material to be used. Ultra High Molecular Weight (UHMW) polyethylene (PE) features high resistance to traction and good transmissivity in the frequency range of interest. In this paper, we discuss the possibility of using UHMW PE for windows and lenses in experiments working at millimeter wavelengths, by measuring its optical properties: emissivity, transmission and refraction index. Our measurements show that the material is well suited to this purpose.

Differential role of molten globule and protein folding in distinguishing unique features of botulinum neurotoxin.

PubMed

Kumar, Raj; Kukreja, Roshan V; Cai, Shuowei; Singh, Bal R

2014-06-01

Botulinum neurotoxins (BoNTs) are proteins of great interest not only because of their extreme toxicity but also paradoxically for their therapeutic applications. All the known serotypes (A-G) have varying degrees of longevity and potency inside the neuronal cell. Differential chemical modifications such as phosphorylation and ubiquitination have been suggested as possible mechanisms for their longevity, but the molecular basis of the longevity remains unclear. Since the endopeptidase domain (light chain; LC) of toxin apparently survives inside the neuronal cells for months, it is important to examine the structural features of this domain to understand its resistance to intracellular degradation. Published crystal structures (both botulinum neurotoxins and endopeptidase domain) have not provided adequate explanation for the intracellular longevity of the domain. Structural features obtained from spectroscopic analysis of LCA and LCB were similar, and a PRIME (PReImminent Molten Globule Enzyme) conformation appears to be responsible for their optimal enzymatic activity at 37°C. LCE, on the other hand, was although optimally active at 37°C, but its active conformation differed from the PRIME conformation of LCA and LCB. This study establishes and confirms our earlier finding that an optimally active conformation of these proteins in the form of PRIME exists for the most poisonous poison, botulinum neurotoxin. There are substantial variations in the structural and functional characteristics of these active molten globule related structures among the three BoNT endopeptidases examined. These differential conformations of LCs are important in understanding the fundamental structural features of proteins, and their possible connection to intracellular longevity could provide significant clues for devising new countermeasures and effective therapeutics. Copyright © 2014 Elsevier B.V. All rights reserved.

Electronic band structure of 4d and 5d transition metal trichalcogenides

NASA Astrophysics Data System (ADS)

Sugita, Yusuke; Miyake, Takashi; Motome, Yukitoshi

2018-05-01

Transition metal trichalcogenides (TMTs), a family of van der Waals materials, have gained increasing interests from the discovery of magnetism in few-layer forms. Although TMTs with 3d transition metal elements have been studied extensively, much less is explored for the 4d and 5d cases, where the interesting interplay between electron correlations and the relativistic spin-orbit coupling is expected. Using ab initio calculations, we here investigate the electronic property of TMTs with 4d and 5d transition metal elements. We show that the band structures exhibit multiple node-like features near the Fermi level. These are the remnant of multiple Dirac cones that were recently discovered in the monolayer cases. Our results indicate that the peculiar two-dimensional multiple Dirac cones are concealed even in the layered bulk systems.

Rhetorical Structure and Linguistic Features of Case Presentations in Case Reports in Taiwanese and International Medical Journals

ERIC Educational Resources Information Center

Hung, Hsuan; Chen, Pi-Ching; Tsai, Jing-Jane

2012-01-01

The case presentation is the core section of a medical case report. Issues in the teaching of case report writing have recently been the subject of great interest in medical education, especially in the era of globalization. Given that Taiwanese medical students, residents and junior physicians are requested to write case reports in English and…

Operation HARDTACK 1, 1958

DTIC Science & Technology

1982-12-01

parts of the weapon development and ef fects studies each had particular features that led to the possibility of radiation exposure. RADIOLOGICAL...exposures of DOD personnel for interested former partici- pants and for use In public health research and Federal policy studies . Information from...StriActu(𔃾 ard Equipment 128 Program 4 Bif(,4#crical Studies 133 Program 5 -- Aircrdft Structures 133 Program 6 Test of Service fqipmont and Materials 137

Texture analysis of ultrahigh field T2*-weighted MR images of the brain: application to Huntington's disease.

PubMed

Doan, Nhat Trung; van den Bogaard, Simon J A; Dumas, Eve M; Webb, Andrew G; van Buchem, Mark A; Roos, Raymund A C; van der Grond, Jeroen; Reiber, Johan H C; Milles, Julien

2014-03-01

To develop a framework for quantitative detection of between-group textural differences in ultrahigh field T2*-weighted MR images of the brain. MR images were acquired using a three-dimensional (3D) T2*-weighted gradient echo sequence on a 7 Tesla MRI system. The phase images were high-pass filtered to remove phase wraps. Thirteen textural features were computed for both the magnitude and phase images of a region of interest based on 3D Gray-Level Co-occurrence Matrix, and subsequently evaluated to detect between-group differences using a Mann-Whitney U-test. We applied the framework to study textural differences in subcortical structures between premanifest Huntington's disease (HD), manifest HD patients, and controls. In premanifest HD, four phase-based features showed a difference in the caudate nucleus. In manifest HD, 7 magnitude-based features showed a difference in the pallidum, 6 phase-based features in the caudate nucleus, and 10 phase-based features in the putamen. After multiple comparison correction, significant differences were shown in the putamen in manifest HD by two phase-based features (both adjusted P values=0.04). This study provides the first evidence of textural heterogeneity of subcortical structures in HD. Texture analysis of ultrahigh field T2*-weighted MR images can be useful for noninvasive monitoring of neurodegenerative diseases. Copyright © 2013 Wiley Periodicals, Inc.

Biological features of hepatitis B virus isolates from patients based on full-length genomic analysis.

PubMed

Wen, Yu-Mei; Wang, Yong-Xiang

2009-01-01

The mechanisms for HBV persistence and the pathogenesis of chronic HB have been shown mainly due to defects in host immune responses. However, HBV isolates with different biological features may also contribute to different clinical outcomes and epidemiological implications in viral hepatitis B (HB). This review presents interesting biological features of HBV isolates based on the structural and functional analysis of full-length HBV isolates from various patients. Among isolates from children after failure of HB vaccination, 129L mutant at the 'a' determinant was found with normal binding efficiency to anti-HBs, but with reduced immunogenicity, which could initiate persistent HBV infections. Isolates from fulminant hepatitis (FH) B patients were not all highly replicative, but differences in capacities of anti-HBs induction could be involved in the pathogenesis of FH. The high replicative competency of isolates from hepatocellular carcinoma (HCC) patients could result in enhanced immune-mediated cytopathic effects against HBV viral proteins, and increased transactivating activity by the X protein. The mechanism of a double-spliced variant in enhancing replication of the wild-type virus is presented. The importance of integrating structural and functional analysis to reveal biological features of HBV isolates in viral pathogenesis is discussed.

Equivalent circuit models for interpreting impedance perturbation spectroscopy data

NASA Astrophysics Data System (ADS)

Smith, R. Lowell

2004-07-01

As in-situ structural integrity monitoring disciplines mature, there is a growing need to process sensor/actuator data efficiently in real time. Although smaller, faster embedded processors will contribute to this, it is also important to develop straightforward, robust methods to reduce the overall computational burden for practical applications of interest. This paper addresses the use of equivalent circuit modeling techniques for inferring structure attributes monitored using impedance perturbation spectroscopy. In pioneering work about ten years ago significant progress was associated with the development of simple impedance models derived from the piezoelectric equations. Using mathematical modeling tools currently available from research in ultrasonics and impedance spectroscopy is expected to provide additional synergistic benefits. For purposes of structural health monitoring the objective is to use impedance spectroscopy data to infer the physical condition of structures to which small piezoelectric actuators are bonded. Features of interest include stiffness changes, mass loading, and damping or mechanical losses. Equivalent circuit models are typically simple enough to facilitate the development of practical analytical models of the actuator-structure interaction. This type of parametric structure model allows raw impedance/admittance data to be interpreted optimally using standard multiple, nonlinear regression analysis. One potential long-term outcome is the possibility of cataloging measured viscoelastic properties of the mechanical subsystems of interest as simple lists of attributes and their statistical uncertainties, whose evolution can be followed in time. Equivalent circuit models are well suited for addressing calibration and self-consistency issues such as temperature corrections, Poisson mode coupling, and distributed relaxation processes.

Aesthetics-based classification of geological structures in outcrops for geotourism purposes: a tentative proposal

NASA Astrophysics Data System (ADS)

Mikhailenko, Anna V.; Nazarenko, Olesya V.; Ruban, Dmitry A.; Zayats, Pavel P.

2017-03-01

The current growth in geotourism requires an urgent development of classifications of geological features on the basis of criteria that are relevant to tourist perceptions. It appears that structure-related patterns are especially attractive for geotourists. Consideration of the main criteria by which tourists judge beauty and observations made in the geodiversity hotspot of the Western Caucasus allow us to propose a tentative aesthetics-based classification of geological structures in outcrops, with two classes and four subclasses. It is possible to distinguish between regular and quasi-regular patterns (i.e., striped and lined and contorted patterns) and irregular and complex patterns (paysage and sculptured patterns). Typical examples of each case are found both in the study area and on a global scale. The application of the proposed classification permits to emphasise features of interest to a broad range of tourists. Aesthetics-based (i.e., non-geological) classifications are necessary to take into account visions and attitudes of visitors.

Design of an activity landscape view taking compound-based feature probabilities into account.

PubMed

Zhang, Bijun; Vogt, Martin; Bajorath, Jürgen

2014-09-01

Activity landscapes (ALs) of compound data sets are rationalized as graphical representations that integrate similarity and potency relationships between active compounds. ALs enable the visualization of structure-activity relationship (SAR) information and are thus computational tools of interest for medicinal chemistry. For AL generation, similarity and potency relationships are typically evaluated in a pairwise manner and major AL features are assessed at the level of compound pairs. In this study, we add a conditional probability formalism to AL design that makes it possible to quantify the probability of individual compounds to contribute to characteristic AL features. Making this information graphically accessible in a molecular network-based AL representation is shown to further increase AL information content and helps to quickly focus on SAR-informative compound subsets. This feature probability-based AL variant extends the current spectrum of AL representations for medicinal chemistry applications.

Radiation biology of HZE particles

NASA Technical Reports Server (NTRS)

Nelson, Gregory A.

1990-01-01

The biological effects of heavy charged particle (HZE) radiation are of particular interest to travellers and planners for long duration space flights where exposure levels represent a potential health hazard. The unique feature of HZE radiation is the structured pattern of its energy deposition in targets which may be related to charge, velocity, or rate of energy loss. There are many consequences of this feature to biological endpoints when compared to effects of ionizing photons. Dose vs response and dose rate kinetics are modified, DNA and cellular repair systems are altered in their abilities to cope with damage and, the qualitative features of damage are unique for different ions. These features must be incorporated into any risk assessment system for radiation health management. HZE induced mutation, cell inactivation and altered organogenesis will be discussed emphasizing studies with the nematode Caenorhabditis elegans and cultured cells. Observations from radiobiology experiments in space will also be reviewed along with plans for future space-based studies.

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.

Structural features of phosphate accumulations in the Gantour basin - Morocco : Application of GIS

NASA Astrophysics Data System (ADS)

Mohamed, Laadraoui; El Hassane, Boumaggard; Essaid, Jourani

2010-05-01

The Moroccan Atlantic margin raises a lot of interest because of its potential resources in phosphates. It also holds in its Mesetien part one of the largest phosphatic deposit in the world. The authors present the results of their researches on structural environments of the phosphatic sedimentary sequences in the Gantour deposit in western Morocco. These investigations are mainly based on field data, data recorded from work done by the OCP (Office Chérifien des Phosphates) group, the interpretation of industrial seismic profiles and the application of GIS. Our aim are devoted to the apprehension of the geometry and the cinematic of these basins which are contemporaneous to the Central Atlantic Rifting, as well as the determination of the list of factors liable to the genesis of these phosphatic basins. Other data of field observations (cartography, study of structural features,...) permit to identify the general structure of the prospect. Sedimentation of phosphated deposits is strained by the presence of two wrench faulting systems oriented N20¬40E, N80¬120E and N140¬160E.

Molecular determinants of enzyme cold adaptation: comparative structural and computational studies of cold- and warm-adapted enzymes.

PubMed

Papaleo, Elena; Tiberti, Matteo; Invernizzi, Gaetano; Pasi, Marco; Ranzani, Valeria

2011-11-01

The identification of molecular mechanisms underlying enzyme cold adaptation is a hot-topic both for fundamental research and industrial applications. In the present contribution, we review the last decades of structural computational investigations on cold-adapted enzymes in comparison to their warm-adapted counterparts. Comparative sequence and structural studies allow the definition of a multitude of adaptation strategies. Different enzymes carried out diverse mechanisms to adapt to low temperatures, so that a general theory for enzyme cold adaptation cannot be formulated. However, some common features can be traced in dynamic and flexibility properties of these enzymes, as well as in their intra- and inter-molecular interaction networks. Interestingly, the current data suggest that a family-centered point of view is necessary in the comparative analyses of cold- and warm-adapted enzymes. In fact, enzymes belonging to the same family or superfamily, thus sharing at least the three-dimensional fold and common features of the functional sites, have evolved similar structural and dynamic patterns to overcome the detrimental effects of low temperatures.

Feature tracking cardiac magnetic resonance imaging: A review of a novel non-invasive cardiac imaging technique

PubMed Central

Rahman, Zia Ur; Sethi, Pooja; Murtaza, Ghulam; Virk, Hafeez Ul Hassan; Rai, Aitzaz; Mahmod, Masliza; Schoondyke, Jeffrey; Albalbissi, Kais

2017-01-01

Cardiovascular disease is a leading cause of morbidity and mortality globally. Early diagnostic markers are gaining popularity for better patient care disease outcomes. There is an increasing interest in noninvasive cardiac imaging biomarkers to diagnose subclinical cardiac disease. Feature tracking cardiac magnetic resonance imaging is a novel post-processing technique that is increasingly being employed to assess global and regional myocardial function. This technique has numerous applications in structural and functional diagnostics. It has been validated in multiple studies, although there is still a long way to go for it to become routine standard of care. PMID:28515849

Modeling Protein Expression and Protein Signaling Pathways

PubMed Central

Telesca, Donatello; Müller, Peter; Kornblau, Steven M.; Suchard, Marc A.; Ji, Yuan

2015-01-01

High-throughput functional proteomic technologies provide a way to quantify the expression of proteins of interest. Statistical inference centers on identifying the activation state of proteins and their patterns of molecular interaction formalized as dependence structure. Inference on dependence structure is particularly important when proteins are selected because they are part of a common molecular pathway. In that case, inference on dependence structure reveals properties of the underlying pathway. We propose a probability model that represents molecular interactions at the level of hidden binary latent variables that can be interpreted as indicators for active versus inactive states of the proteins. The proposed approach exploits available expert knowledge about the target pathway to define an informative prior on the hidden conditional dependence structure. An important feature of this prior is that it provides an instrument to explicitly anchor the model space to a set of interactions of interest, favoring a local search approach to model determination. We apply our model to reverse-phase protein array data from a study on acute myeloid leukemia. Our inference identifies relevant subpathways in relation to the unfolding of the biological process under study. PMID:26246646

Semantic memory: a feature-based analysis and new norms for Italian.

PubMed

Montefinese, Maria; Ambrosini, Ettore; Fairfield, Beth; Mammarella, Nicola

2013-06-01

Semantic norms for properties produced by native speakers are valuable tools for researchers interested in the structure of semantic memory and in category-specific semantic deficits in individuals following brain damage. The aims of this study were threefold. First, we sought to extend existing semantic norms by adopting an empirical approach to category (Exp. 1) and concept (Exp. 2) selection, in order to obtain a more representative set of semantic memory features. Second, we extensively outlined a new set of semantic production norms collected from Italian native speakers for 120 artifactual and natural basic-level concepts, using numerous measures and statistics following a feature-listing task (Exp. 3b). Finally, we aimed to create a new publicly accessible database, since only a few existing databases are publicly available online.

FIGENIX: Intelligent automation of genomic annotation: expertise integration in a new software platform

PubMed Central

Gouret, Philippe; Vitiello, Vérane; Balandraud, Nathalie; Gilles, André; Pontarotti, Pierre; Danchin, Etienne GJ

2005-01-01

Background Two of the main objectives of the genomic and post-genomic era are to structurally and functionally annotate genomes which consists of detecting genes' position and structure, and inferring their function (as well as of other features of genomes). Structural and functional annotation both require the complex chaining of numerous different software, algorithms and methods under the supervision of a biologist. The automation of these pipelines is necessary to manage huge amounts of data released by sequencing projects. Several pipelines already automate some of these complex chaining but still necessitate an important contribution of biologists for supervising and controlling the results at various steps. Results Here we propose an innovative automated platform, FIGENIX, which includes an expert system capable to substitute to human expertise at several key steps. FIGENIX currently automates complex pipelines of structural and functional annotation under the supervision of the expert system (which allows for example to make key decisions, check intermediate results or refine the dataset). The quality of the results produced by FIGENIX is comparable to those obtained by expert biologists with a drastic gain in terms of time costs and avoidance of errors due to the human manipulation of data. Conclusion The core engine and expert system of the FIGENIX platform currently handle complex annotation processes of broad interest for the genomic community. They could be easily adapted to new, or more specialized pipelines, such as for example the annotation of miRNAs, the classification of complex multigenic families, annotation of regulatory elements and other genomic features of interest. PMID:16083500

VMD-SS: A graphical user interface plug-in to calculate the protein secondary structure in VMD program.

PubMed

Yahyavi, Masoumeh; Falsafi-Zadeh, Sajad; Karimi, Zahra; Kalatarian, Giti; Galehdari, Hamid

2014-01-01

The investigation on the types of secondary structure (SS) of a protein is important. The evolution of secondary structures during molecular dynamics simulations is a useful parameter to analyze protein structures. Therefore, it is of interest to describe VMD-SS (a software program) for the identification of secondary structure elements and its trajectories during simulation for known structures available at the Protein Data Bank (PDB). The program helps to calculate (1) percentage SS, (2) SS occurrence in each residue, (3) percentage SS during simulation, and (4) percentage residues in all SS types during simulation. The VMD-SS plug-in was designed using TCL script and stride to calculate secondary structure features. The database is available for free at http://science.scu.ac.ir/HomePage.aspx?TabID=13755.

Study of Varying Boundary Layer Height on Turret Flow Structures

DTIC Science & Technology

2011-06-01

fluid dynamics. The difficulties of the problem arise in modeling several complex flow features including separation, reattachment, three-dimensional...impossible. In this case, the approach is to create a model to calculate the properties of interest. The main issue with resolving turbulent flows...operation and their effect is modeled through subgrid scale models . As a result, the the most important turbulent scales are resolved and the

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

Zhong,Z.; Bennett, D.; Chapman, D.

We explored diffraction enhanced imaging (DEI) in both planar and computed tomography (CT) modes for early detection of beta amyloid deposition, a hallmark feature in Alzheimer's disease (AD). Since amyloid plaques precede clinical symptoms by years, their early detection is of great interest. These findings were correlated with results from synchrotron infrared microspectroscopic imaging and X-ray fluorescence microscopy, to determine the secondary structure of the amyloid beta protein and metal concentration in the amyloid plaques, respectively.

A novel method for unsteady flow field segmentation based on stochastic similarity of direction

NASA Astrophysics Data System (ADS)

Omata, Noriyasu; Shirayama, Susumu

2018-04-01

Recent developments in fluid dynamics research have opened up the possibility for the detailed quantitative understanding of unsteady flow fields. However, the visualization techniques currently in use generally provide only qualitative insights. A method for dividing the flow field into physically relevant regions of interest can help researchers quantify unsteady fluid behaviors. Most methods at present compare the trajectories of virtual Lagrangian particles. The time-invariant features of an unsteady flow are also frequently of interest, but the Lagrangian specification only reveals time-variant features. To address these challenges, we propose a novel method for the time-invariant spatial segmentation of an unsteady flow field. This segmentation method does not require Lagrangian particle tracking but instead quantitatively compares the stochastic models of the direction of the flow at each observed point. The proposed method is validated with several clustering tests for 3D flows past a sphere. Results show that the proposed method reveals the time-invariant, physically relevant structures of an unsteady flow.

Dynamic response of underpasses for high-speed train lines

NASA Astrophysics Data System (ADS)

Vega, J.; Fraile, A.; Alarcon, E.; Hermanns, L.

2012-11-01

Underpasses are common in modern railway lines. Wildlife corridors and drainage conduits often fall into this category of partially buried structures. Their dynamic behavior has received far less attention than that of other structures such as bridges, but their large number makes their study an interesting challenge from the viewpoint of safety and cost savings. Here, we present a complete study of a culvert, including on-site measurements and numerical modeling. The studied structure belongs to the high-speed railway line linking Segovia and Valladolid in Spain. The line was opened to traffic in 2004. On-site measurements were performed for the structure by recording the dynamic response at selected points of the structure during the passage of high-speed trains at speeds ranging between 200 and 300 km/h. The measurements provide not only reference values suitable for model fitting, but also a good insight into the main features of the dynamic behavior of this structure. Finite element techniques were used to model the dynamic behavior of the structure and its key features. Special attention is paid to vertical accelerations, the values of which should be limited to avoid track instability according to Eurocode. This study furthers our understanding of the dynamic response of railway underpasses to train loads.

On the relationship between the dynamic behavior and nanoscale staggered structure of the bone

NASA Astrophysics Data System (ADS)

Qwamizadeh, Mahan; Zhang, Zuoqi; Zhou, Kun; Zhang, Yong Wei

2015-05-01

Bone, a typical load-bearing biological material, composed of ordinary base materials such as organic protein and inorganic mineral arranged in a hierarchical architecture, exhibits extraordinary mechanical properties. Up to now, most of previous studies focused on its mechanical properties under static loading. However, failure of the bone occurs often under dynamic loading. An interesting question is: Are the structural sizes and layouts of the bone related or even adapted to the functionalities demanded by its dynamic performance? In the present work, systematic finite element analysis was performed on the dynamic response of nanoscale bone structures under dynamic loading. It was found that for a fixed mineral volume fraction and unit cell area, there exists a nanoscale staggered structure at some specific feature size and layout which exhibits the fastest attenuation of stress waves. Remarkably, these specific feature sizes and layouts are in excellent agreement with those experimentally observed in the bone at the same scale, indicating that the structural size and layout of the bone at the nanoscale are evolutionarily adapted to its dynamic behavior. The present work points out the importance of dynamic effect on the biological evolution of load-bearing biological materials.

Classification of damage in structural systems using time series analysis and supervised and unsupervised pattern recognition techniques

NASA Astrophysics Data System (ADS)

Omenzetter, Piotr; de Lautour, Oliver R.

2010-04-01

Developed for studying long, periodic records of various measured quantities, time series analysis methods are inherently suited and offer interesting possibilities for Structural Health Monitoring (SHM) applications. However, their use in SHM can still be regarded as an emerging application and deserves more studies. In this research, Autoregressive (AR) models were used to fit experimental acceleration time histories from two experimental structural systems, a 3- storey bookshelf-type laboratory structure and the ASCE Phase II SHM Benchmark Structure, in healthy and several damaged states. The coefficients of the AR models were chosen as damage sensitive features. Preliminary visual inspection of the large, multidimensional sets of AR coefficients to check the presence of clusters corresponding to different damage severities was achieved using Sammon mapping - an efficient nonlinear data compression technique. Systematic classification of damage into states based on the analysis of the AR coefficients was achieved using two supervised classification techniques: Nearest Neighbor Classification (NNC) and Learning Vector Quantization (LVQ), and one unsupervised technique: Self-organizing Maps (SOM). This paper discusses the performance of AR coefficients as damage sensitive features and compares the efficiency of the three classification techniques using experimental data.

An Analysis of Cassini Observations Regarding the Structure of Jupiter's Equatorial Atmosphere

NASA Technical Reports Server (NTRS)

Choi, David S.; Simon-Miller, Amy A.

2012-01-01

A variety of intriguing atmospheric phenomena reside on both sides of Jupiter's equator. 5-micron bright hot spots and opaque plumes prominently exhibit dynamic behavior to the north, whereas compact, dark chevron-shaped features and isolated anticyclonic disturbances periodically occupy the southern equatorial latitudes. All of these phenomena are associated with the vertical and meridional perturbations of Rossby waves disturbing the mean atmospheric state. As previous observational analysis and numerical simulations have investigated the dynamics of the region, an examination of the atmosphere's vertical structure though radiative transfer analysis is necessary for improved understanding of this unique environment. Here we present preliminary analysis of a multispectral Cassini imaging data set acquired during the spacecraft's flyby of Jupiter in 2000. We evaluated multiple methane and continuum spectral channels at available viewing angles to improve constraints on the vertical structure of the haze and cloud layers comprising these interesting features. Our preliminary results indicate distinct differences in the structure for both hemispheres. Upper troposphere hazes and cloud layers are prevalent in the northern equatorial latitudes, but are not present in corresponding southern latitudes. Continued analysis will further constrain the precise structure present in these phenomena and the differences between them.

Structural and spectroscopic investigation of new luminescent hybrid materials based on calix[4]arene-tetracarboxylate and Ln3+ ions (Ln = Gd, Tb or Eu)

NASA Astrophysics Data System (ADS)

Viana, R. S.; Oliveira, C. A. F.; Chojnacki, J.; Barros, B. S.; Alves-Jr, S.; Kulesza, J.

2017-07-01

Lanthanide-calixarene hybrid materials are of particular interest due to the combination of the interesting properties of the ligand cavity-like structure and the luminescent features of lanthanides. The aim of this study was to synthesize and investigate the photophysical properties of Eu3+, Tb3+ and Gd3+ hybrids based on calix[4]arene-tetracarboxylate. The preparation of two structurally different Tb3+ compounds (calix-TA-SC-Tb and calix-TA-Tb) was dictated by the ligand to metal molar ratio and the synthesis time. Analysis of calix-TA-SC-Tb monocrystals revealed the formation of a mononuclear complex of C2 symmetry containing Tb3+ coordinated by four calixarene ionized groups and formate anion encapsulated within the upper cavity. Syntheses of other hybrids failed in producing high-quality crystals and the structures could not be solved. The solid-state luminescent properties of hybrids were evaluated, and the structure/property relationship was investigated. Based on the emission and excitation spectra, the energy diagrams for calix-TA-Eu, calix-TA-Tb and calix-TA-Gd were proposed.

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.

Automatic structured grid generation using Gridgen (some restrictions apply)

NASA Technical Reports Server (NTRS)

Chawner, John R.; Steinbrenner, John P.

1995-01-01

The authors have noticed in the recent grid generation literature an emphasis on the automation of structured grid generation. The motivation behind such work is clear; grid generation is easily the most despised task in the grid-analyze-visualize triad of computational analysis (CA). However, because grid generation is closely coupled to both the design and analysis software and because quantitative measures of grid quality are lacking, 'push button' grid generation usually results in a compromise between speed, control, and quality. Overt emphasis on automation obscures the substantive issues of providing users with flexible tools for generating and modifying high quality grids in a design environment. In support of this paper's tongue-in-cheek title, many features of the Gridgen software are described. Gridgen is by no stretch of the imagination an automatic grid generator. Despite this fact, the code does utilize many automation techniques that permit interesting regenerative features.

The dielectric signature of glass density

NASA Astrophysics Data System (ADS)

Rams-Baron, M.; Wojnarowska, Z.; Knapik-Kowalczuk, J.; Jurkiewicz, K.; Burian, A.; Wojtyniak, M.; Pionteck, J.; Jaworska, M.; Rodríguez-Tinoco, C.; Paluch, M.

2017-09-01

At present, we are witnessing a renewed interest in the properties of densified glasses prepared by isobaric cooling of a liquid at elevated pressure. As high-pressure densification emerges as a promising approach in the development of glasses with customized features, understanding and controlling their unique properties represent a contemporary scientific and technological goal. The results presented herein indicate that the applied high-pressure preparation route leads to a glassy state with higher density (˜1%) and a reduced free volume of about 7%. We show that these subtle structural changes remarkably influence the dielectric response and spectral features of β-relaxation in etoricoxib glass. Our study, combining dynamical and structural techniques, reveal that β-relaxation in etoricoxib is extremely sensitive to the variations in molecular packing and can be used to probe the changes in glass density. Such connection is technologically relevant and may advance further progress in the field.

Comparative NEXAFS study of the selected icefish hard tissues and hydroxyapatite

NASA Astrophysics Data System (ADS)

Petrova, O. V.; Nekipelov, S. V.; Sivkov, D. V.; Mingaleva, A. E.; Nikolaev, A.; Frank-Kamenetskaya, O. V.; Bazhenov, V. V.; Vyalikh, D. V.; Molodtsov, S. L.; Sivkov, V. N.; Ehrlich, H.

2017-11-01

The structure of native Champsocephalus gunnari icefish otoliths, scales, teeth, bones and pristine hydroxyapatite (HA) were examined using Near Edge X-ray Absorption Fine Structure (NEXAFS) spectroscopy. NEXAFS Cls-absorption spectra of the selected icefish hard tissues indicate that otoliths contain anion [CO3]2-. NEXAFS P2p-spectra clearly indicate the absence of phosphorus atoms only within otoliths and scales samples. However, the icefish teeth and bones P2p-spectra demonstrate identical spectral feature typical for the HA. NEXAFS Ca2p-spectra of the icefish hard tissues studied also shows features, which are in good correspondence with HA spectra. Interestingly, there is a red shift ≈ 0.1 eV of the 2p1/2,3/2 → 3d transition energies in NEXAFS Ca2p-spectra of teethes and bones of the C. gunnari in comparison to HA.

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.

Energetic rationale for an unexpected and abrupt reversal of guanidinium chloride-induced unfolding of peptide deformylase.

PubMed

Berg, Alexander K; Manokaran, Sumathra; Eiler, Daniel; Kooren, Joel; Mallik, Sanku; Srivastava, D K

2008-01-01

Peptide deformylase (PDF) catalyzes the removal of formyl group from the N-terminal methionine residues of nascent proteins in prokaryotes, and this enzyme is a high priority target for antibiotic design. In pursuit of delineating the structural-functional features of Escherichia coli PDF (EcPDF), we investigated the mechanistic pathway for the guanidinium chloride (GdmCl)-induced unfolding of the enzyme by monitoring the secondary structural changes via CD spectroscopy. The experimental data revealed that EcPDF is a highly stable enzyme, and it undergoes slow denaturation in the presence of varying concentrations of GdmCl. The most interesting aspect of these studies has been the abrupt reversal of the unfolding pathway at low to moderate concentrations of the denaturant, but not at high concentration. An energetic rationale for such an unprecedented feature in protein chemistry is offered.

Improved binding affinity and interesting selectivities of aminopyrimidine-bearing carbohydrate receptors in comparison with their aminopyridine analogues.

PubMed

Lippe, Jan; Seichter, Wilhelm; Mazik, Monika

2015-12-28

Due to the problems with the exact prediction of the binding properties of an artificial carbohydrate receptor, the identification of characteristic structural features, having the ability to influence the binding properties in a predictable way, is of high importance. The purpose of our investigation was to examine whether the previously observed higher affinity of 2-aminopyrimidine-bearing carbohydrate receptors in comparison with aminopyridine substituted analogues represents a general tendency of aminopyrimidine-bearing compounds. Systematic binding studies on new compounds consisting of 2-aminopyrimidine groups confirmed such a tendency and allowed the identification of interesting structure-activity relationships. Receptors having different symmetries showed systematic preferences for specific glycosides, which are remarkable for such simple receptor systems. Particularly suitable receptor architectures for the recognition of selected glycosides were identified and represent a valuable base for further developments in this field.

Contrast Invariant Interest Point Detection by Zero-Norm LoG Filter.

PubMed

Zhenwei Miao; Xudong Jiang; Kim-Hui Yap

2016-01-01

The Laplacian of Gaussian (LoG) filter is widely used in interest point detection. However, low-contrast image structures, though stable and significant, are often submerged by the high-contrast ones in the response image of the LoG filter, and hence are difficult to be detected. To solve this problem, we derive a generalized LoG filter, and propose a zero-norm LoG filter. The response of the zero-norm LoG filter is proportional to the weighted number of bright/dark pixels in a local region, which makes this filter be invariant to the image contrast. Based on the zero-norm LoG filter, we develop an interest point detector to extract local structures from images. Compared with the contrast dependent detectors, such as the popular scale invariant feature transform detector, the proposed detector is robust to illumination changes and abrupt variations of images. Experiments on benchmark databases demonstrate the superior performance of the proposed zero-norm LoG detector in terms of the repeatability and matching score of the detected points as well as the image recognition rate under different conditions.

Isotropic and Anisotropic Growth of Metal-Organic Framework (MOF) on MOF: Logical Inference on MOF Structure Based on Growth Behavior and Morphological Feature.

PubMed

Choi, Sora; Kim, Taeho; Ji, Hoyeon; Lee, Hee Jung; Oh, Moonhyun

2016-11-02

The growth of one metal-organic framework (MOF) on another MOF for constructing a heterocompositional hybrid MOF is an interesting research topic because of the curiosity regarding the occurrence of this phenomenon and the value of hybrid MOFs as multifunctional materials or routes for fine-tuning MOF properties. In particular, the anisotropic growth of MOF on MOF is fascinating for the development of MOFs possessing atypical shapes and heterostructures or abnormal properties. Herein, we clarify the understanding of growth behavior of a secondary MOF on an initial MOF template, such as isotropic or anisotropic ways associated with their cell parameters. The isotropic growth of MIL-68-Br on the MIL-68 template results in the formation of core-shell-type MIL-68@MIL-68-Br. However, the unique anisotropic growth of a secondary MOF (MOF-NDC) on the MIL-68 template results in semitubular particles, and structural features of this unknown secondary MOF are successfully speculated for the first time on the basis of its unique growth behavior and morphological characteristics. Finally, the validation of this structural speculation is verified by the powder X-ray diffraction and the selected area electron diffraction studies. The results suggests that the growth behavior and morphological features of MOFs should be considered to be important factors for understanding the MOFs' structures.

FT IR spectral investigations of toxic material dibrom using DFT

NASA Astrophysics Data System (ADS)

Parvathy, M.; Gopika, M. S.; Mary, B. L. Bincy; Nimmi, D. E.; Praveen, S. G.; Binoy, J.

2018-05-01

Since, dibrom is widely used organophosphate pesticide, the exploration of its structural features is of immense research interest, and can be effectively carried out using infrared spectroscopy aided by DFT simulation. The present work aims to investigate the interrelation between carbon-halogen bond strength and electronegativity halogen. The resonance of phosphate in dibrom and the deviation from resonant structure due to bridging of oxygen by electron donating methyl group has been investigated in detail. The molecular docking study has been performed to explore the bioactivity of dibrom and to assess the strength of interaction of dibrom towards DNA and BSA.

Three-dimensional {Co(3+)-Zn2+} and {Co(3+)-Cd2+} networks originated from carboxylate-rich building blocks: syntheses, structures, and heterogeneous catalysis.

PubMed

Kumar, Girijesh; Gupta, Rajeev

2013-10-07

The present work shows the utilization of Co(3+) complexes appended with either para- or meta-arylcarboxylic acid groups as the molecular building blocks for the construction of three-dimensional {Co(3+)-Zn(2+)} and {Co(3+)-Cd(2+)} heterobimetallic networks. The structural characterizations of these networks show several interesting features including well-defined pores and channels. These networks function as heterogeneous and reusable catalysts for the regio- and stereoselective ring-opening reactions of various epoxides and size-selective cyanation reactions of assorted aldehydes.

Active Polymers — Emergent Conformational and Dynamical Properties: A Brief Review

NASA Astrophysics Data System (ADS)

Winkler, Roland G.; Elgeti, Jens; Gompper, Gerhard

2017-10-01

Active matter exhibits a wealth of emerging nonequilibrium behaviours. A paradigmatic example is the interior of cells, where active components, such as the cytoskeleton, are responsible for its structural organization and the dynamics of the various components. Of particular interest are the properties of polymers and filaments. The intimate coupling of thermal and active noise, hydrodynamic interactions, and polymer conformations implies the emergence of novel structural and dynamical features. In this article, we review recent theoretical and simulation developments and results for the structural and dynamical properties of polymers exposed to activity. Two- and three-dimensional filaments are considered propelled by different mechanisms such as active Brownian particles or hydrodynamically-coupled force dipoles.

Legume Lectins: Proteins with Diverse Applications

PubMed Central

Lagarda-Diaz, Irlanda; Guzman-Partida, Ana Maria; Vazquez-Moreno, Luz

2017-01-01

Lectins are a diverse class of proteins distributed extensively in nature. Among these proteins; legume lectins display a variety of interesting features including antimicrobial; insecticidal and antitumor activities. Because lectins recognize and bind to specific glycoconjugates present on the surface of cells and intracellular structures; they can serve as potential target molecules for developing practical applications in the fields of food; agriculture; health and pharmaceutical research. This review presents the current knowledge of the main structural characteristics of legume lectins and the relationship of structure to the exhibited specificities; provides an overview of their particular antimicrobial; insecticidal and antitumor biological activities and describes possible applications based on the pattern of recognized glyco-targets. PMID:28604616

Landmark-based deep multi-instance learning for brain disease diagnosis.

PubMed

Liu, Mingxia; Zhang, Jun; Adeli, Ehsan; Shen, Dinggang

2018-01-01

In conventional Magnetic Resonance (MR) image based methods, two stages are often involved to capture brain structural information for disease diagnosis, i.e., 1) manually partitioning each MR image into a number of regions-of-interest (ROIs), and 2) extracting pre-defined features from each ROI for diagnosis with a certain classifier. However, these pre-defined features often limit the performance of the diagnosis, due to challenges in 1) defining the ROIs and 2) extracting effective disease-related features. In this paper, we propose a landmark-based deep multi-instance learning (LDMIL) framework for brain disease diagnosis. Specifically, we first adopt a data-driven learning approach to discover disease-related anatomical landmarks in the brain MR images, along with their nearby image patches. Then, our LDMIL framework learns an end-to-end MR image classifier for capturing both the local structural information conveyed by image patches located by landmarks and the global structural information derived from all detected landmarks. We have evaluated our proposed framework on 1526 subjects from three public datasets (i.e., ADNI-1, ADNI-2, and MIRIAD), and the experimental results show that our framework can achieve superior performance over state-of-the-art approaches. Copyright © 2017 Elsevier B.V. All rights reserved.

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

Extraction of object skeletons in multispectral imagery by the orthogonal regression fitting

NASA Astrophysics Data System (ADS)

Palenichka, Roman M.; Zaremba, Marek B.

2003-03-01

Accurate and automatic extraction of skeletal shape of objects of interest from satellite images provides an efficient solution to such image analysis tasks as object detection, object identification, and shape description. The problem of skeletal shape extraction can be effectively solved in three basic steps: intensity clustering (i.e. segmentation) of objects, extraction of a structural graph of the object shape, and refinement of structural graph by the orthogonal regression fitting. The objects of interest are segmented from the background by a clustering transformation of primary features (spectral components) with respect to each pixel. The structural graph is composed of connected skeleton vertices and represents the topology of the skeleton. In the general case, it is a quite rough piecewise-linear representation of object skeletons. The positions of skeleton vertices on the image plane are adjusted by means of the orthogonal regression fitting. It consists of changing positions of existing vertices according to the minimum of the mean orthogonal distances and, eventually, adding new vertices in-between if a given accuracy if not yet satisfied. Vertices of initial piecewise-linear skeletons are extracted by using a multi-scale image relevance function. The relevance function is an image local operator that has local maximums at the centers of the objects of interest.

Knowledge-based segmentation and feature analysis of hand and wrist radiographs

NASA Astrophysics Data System (ADS)

Efford, Nicholas D.

1993-07-01

The segmentation of hand and wrist radiographs for applications such as skeletal maturity assessment is best achieved by model-driven approaches incorporating anatomical knowledge. The reasons for this are discussed, and a particular frame-based or 'blackboard' strategy for the simultaneous segmentation of the hand and estimation of bone age via the TW2 method is described. The new approach is structured for optimum robustness and computational efficiency: features of interest are detected and analyzes in order of their size and prominence in the image, the largest and most distinctive being dealt with first, and the evidence generated by feature analysis is used to update a model of hand anatomy and hence guide later stages of the segmentation. Closed bone boundaries are formed by a hybrid technique combining knowledge-based, one-dimensional edge detection with model-assisted heuristic tree searching.

Pb0.65Mn2.85Ga3S8 and Pb0.72Mn2.84Ga2.95Se8: Two Quaternary Metal Chalcognides with Open-Tunnel-Framework Structures Displaying Intense Second Harmonic Generation Responses and Interesting Magnetic Properties.

PubMed

Zhou, Molin; Jiang, Xingxing; Guo, Yangwu; Lin, Zheshuai; Yao, Jiyong; Wu, Yicheng

2017-07-17

By combining different nonlinear optical-active structural chromophores with transition metal Mn into a crystal structure, two novel quaternary metal chalcogenides Pb 0.65 Mn 2.85 Ga 3 S 8 (1) and Pb 0.72 Mn 2.84 Ga 2.95 Se 8 (2) were successfully synthesized. Compounds 1 and 2 are isostructural, and they represent a new structure type that crystallizes in the space group P6̅ (No. 174) in the hexagonal system. Their structures feature an interesting three-dimensional open-tunnel framework composed of bridged infinite chains with Pb 2+ cations filling in the biggest tunnels. Interestingly, both 1 and 2 demonstrate intense second harmonic generation responses at 2.09 μm that is about 1.5 and 4.4 times, respectively, of that of the benchmark material AgGaS 2 . However, 1 and 2 possess different optical diffuse reflectance spectra: 1 displays an evident multiband absorption characteristic with two distinguishing absorption edges of 738 and 551 nm, corresponding to two band gaps of 1.68 and 2.25 eV, respectively, while 2 exhibits only one sharp edge, and the corresponding band gap was estimated to be 1.65 eV. Moreover, apart from the considerable structural similarity between 1 and 2, the dc temperature dependent susceptibility measurements indicate that compound 1 is paramagnetic, while compound 2 exhibits spin-glass-like behavior.

Features of nanostructures sputtering

NASA Astrophysics Data System (ADS)

Kapustin, S. N.; Matveev, V. I.; Eseev, M. K.

2017-09-01

The research of ion sputtering of nanoparticles is interesting both from the fundamental point of view - for researching the interior structure of nanoobjects, and the economical one - nanostructures often play the role of functional supplements in composite materials under the radiation pressure. This process should be taken into account while creating objects decorated by nanoclusters during ion implantation. Polyatomic clusters obtained as a result of ion bombing could be used as nanodisperse catalysts or quantum points.

Flow Field Analysis of Fully Coupled Computations of a Flexible Wing undergoing Stall Flutter

DTIC Science & Technology

2016-01-01

unsteady aerodynamic loads due to structural displacements. In terms of actuation , most, if not all, active ∗Research Associate, Department of...flutter suppression techniques, conventional trailing edge flap actuators with a bandwidth of 10 Hz5 was used. Interestingly, the frequencies associated...influence of the flow features on the aeroelastic instability are quantified. Finally, the influence of actuation through a blowing port at 75% span is

Challenging the state-of-the-art in protein structure prediction: Highlights of experimental target structures for the 10th Critical Assessment of Techniques for Protein Structure Prediction Experiment CASP10

PubMed Central

Kryshtafovych, Andriy; Moult, John; Bales, Patrick; Bazan, J. Fernando; Biasini, Marco; Burgin, Alex; Chen, Chen; Cochran, Frank V.; Craig, Timothy K.; Das, Rhiju; Fass, Deborah; Garcia-Doval, Carmela; Herzberg, Osnat; Lorimer, Donald; Luecke, Hartmut; Ma, Xiaolei; Nelson, Daniel C.; van Raaij, Mark J.; Rohwer, Forest; Segall, Anca; Seguritan, Victor; Zeth, Kornelius; Schwede, Torsten

2014-01-01

For the last two decades, CASP has assessed the state of the art in techniques for protein structure prediction and identified areas which required further development. CASP would not have been possible without the prediction targets provided by the experimental structural biology community. In the latest experiment, CASP10, over 100 structures were suggested as prediction targets, some of which appeared to be extraordinarily difficult for modeling. In this paper, authors of some of the most challenging targets discuss which specific scientific question motivated the experimental structure determination of the target protein, which structural features were especially interesting from a structural or functional perspective, and to what extent these features were correctly reproduced in the predictions submitted to CASP10. Specifically, the following targets will be presented: the acid-gated urea channel, a difficult to predict trans-membrane protein from the important human pathogen Helicobacter pylori; the structure of human interleukin IL-34, a recently discovered helical cytokine; the structure of a functionally uncharacterized enzyme OrfY from Thermoproteus tenax formed by a gene duplication and a novel fold; an ORFan domain of mimivirus sulfhydryl oxidase R596; the fibre protein gp17 from bacteriophage T7; the Bacteriophage CBA-120 tailspike protein; a virus coat protein from metagenomic samples of the marine environment; and finally an unprecedented class of structure prediction targets based on engineered disulfide-rich small proteins. PMID:24318984

Passion fruit-like nano-architectures: a general synthesis route

NASA Astrophysics Data System (ADS)

Cassano, D.; David, J.; Luin, S.; Voliani, V.

2017-03-01

Noble metal nanostructures have demonstrated a number of intriguing features for both medicine and catalysis. However, accumulation issues have prevented their clinical translation, while their use in catalysis has shown serious efficiency and stability hurdles. Here we introduce a simple and robust synthetic protocol for passion fruit-like nano-architectures composed by a silica shell embedding polymeric arrays of ultrasmall noble metal nanoparticles. These nano-architectures show interesting features for both oncology and catalysis. They avoid the issue of persistence in organism thanks to their fast biodegradation in renal clearable building blocks. Furthermore, their calcination results in yolk-shell structures composed by naked metal or alloy nanospheres shielded from aggregation by a silica shell.

Passion fruit-like nano-architectures: a general synthesis route

PubMed Central

Cassano, D.; David, J.; Luin, S.; Voliani, V.

2017-01-01

Noble metal nanostructures have demonstrated a number of intriguing features for both medicine and catalysis. However, accumulation issues have prevented their clinical translation, while their use in catalysis has shown serious efficiency and stability hurdles. Here we introduce a simple and robust synthetic protocol for passion fruit-like nano-architectures composed by a silica shell embedding polymeric arrays of ultrasmall noble metal nanoparticles. These nano-architectures show interesting features for both oncology and catalysis. They avoid the issue of persistence in organism thanks to their fast biodegradation in renal clearable building blocks. Furthermore, their calcination results in yolk-shell structures composed by naked metal or alloy nanospheres shielded from aggregation by a silica shell. PMID:28256565

New displacement-based methods for optimal truss topology design

NASA Technical Reports Server (NTRS)

Bendsoe, Martin P.; Ben-Tal, Aharon; Haftka, Raphael T.

1991-01-01

Two alternate methods for maximum stiffness truss topology design are presented. The ground structure approach is used, and the problem is formulated in terms of displacements and bar areas. This large, nonconvex optimization problem can be solved by a simultaneous analysis and design approach. Alternatively, an equivalent, unconstrained, and convex problem in the displacements only can be formulated, and this problem can be solved by a nonsmooth, steepest descent algorithm. In both methods, the explicit solving of the equilibrium equations and the assembly of the global stiffness matrix are circumvented. A large number of examples have been studied, showing the attractive features of topology design as well as exposing interesting features of optimal topologies.

[Psychopathologic traits of patients addicted to heroin].

PubMed

Cabal Bravo, J C; Bobes García, J; Vázquez Fernández, A; González-Quirós Corujo, P; Bousoño García, M; García Prieto, A; González García-Portilla, P

1989-01-01

The aim of our work is the search for some differential psychopathologic features in the heroin addict personality, through the 16 PF of Cattell (A form), which we try to contrast with other contributions from studies carried out up to the present. Moreover, other parameters of demographic and socioeconomic interest have been evaluated. Through the results we have gotten, it seems that there is a larger number of psychopathologic elements in the personality of the heroin addict, such as greater introversion, frustration, culpability, radicalism, self-sufficiency, anxiety, over-excitement, actions influenced by their feelings, and a minor acceptance of the rules of the group, though these features do not constitute a standard structure of personality.

Object Synthesis in Conway's Game of Life and Other Cellular Automata

NASA Astrophysics Data System (ADS)

Niemiec, Mark D.

Of the very large number of cellular automata rules in existence, a relatively small number of rules may be considered interesting. Some of the features that make such rules interesting permit patterns to expand, contract, separate into multiple sub-patterns, or combine with other patterns. Such rules generally include still-lifes, oscillators, spaceships, spaceship guns, and puffer trains. Such structures can often be used to construct more complicated computational circuitry, and rules that contain them can often be shown to be computationally universal. Conway's Game of Life is one rule that has been well-studied for several decades, and has been shown to be very fruitful in this regard.

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

Establish and Evaluate Ada Runtime Features of Interest for Real-Time Systems

DTIC Science & Technology

1989-02-15

Runtime Features of Interest for Real - Time Systems -,-. CLEARED POR :)E,4 pUEL tCATLON SEP 2 0 19E19 ,CETM ORP t ’R RE LOO O Nt-U~HM- ANDQ SECURITY...ESTABLISH AND EVALUATE py ADA RUNTIME FEATURES OF INTEREST FOR REAL - TIME SYSTEMS CONTRACT NUMBER: MDA 903-87-D-0056 IITRI PROJECT NUMBER: T06168 PREPARED...2 2.0 SELECTION PROCESS OVERVIEW .................................... 3 2.1 REAL - TIME SYSTEMS IDENTIFICATION ........................... 4 2.2

Influence of landscape structure on reef fish assemblages

USGS Publications Warehouse

Grober-Dunsmore, R.; Frazer, T.K.; Beets, J.P.; Lindberg, W.J.; Zwick, P.; Funicelli, N.A.

2008-01-01

Management of tropical marine environments calls for interdisciplinary studies and innovative methodologies that consider processes occurring over broad spatial scales. We investigated relationships between landscape structure and reef fish assemblage structure in the US Virgin Islands. Measures of landscape structure were transformed into a reduced set of composite indices using principal component analyses (PCA) to synthesize data on the spatial patterning of the landscape structure of the study reefs. However, composite indices (e.g., habitat diversity) were not particularly informative for predicting reef fish assemblage structure. Rather, relationships were interpreted more easily when functional groups of fishes were related to individual habitat features. In particular, multiple reef fish parameters were strongly associated with reef context. Fishes responded to benthic habitat structure at multiple spatial scales, with various groups of fishes each correlated to a unique suite of variables. Accordingly, future experiments should be designed to test functional relationships based on the ecology of the organisms of interest. Our study demonstrates that landscape-scale habitat features influence reef fish communities, illustrating promise in applying a landscape ecology approach to better understand factors that structure coral reef ecosystems. Furthermore, our findings may prove useful in design of spatially-based conservation approaches such as marine protected areas (MPAs), because landscape-scale metrics may serve as proxies for areas with high species diversity and abundance within the coral reef landscape. ?? 2007 Springer Science+Business Media B.V.

Divalent ions are potential permeating blockers of the non-selective NaK ion channel: combined QM and MD based investigations.

PubMed

Sadhu, Biswajit; Sundararajan, Mahesh; Bandyopadhyay, Tusar

2017-10-18

The bacterial NaK ion channel is distinctly different from other known ion channels due to its inherent non-selective feature. One of the unexplored and rather interesting features is its ability to permeate divalent metal ions (such as Ca 2+ and Ba 2+ ) and not monovalent alkali metal ions. Several intriguing questions about the energetics and structural aspects still remain unanswered. For instance, what causes Ca 2+ to permeate as well as block the selectivity filter (SF) of the NaK ion channel and act as a "permeating blocker"? How and at what energetic cost does another chemical congener, Sr 2+ , as well as Ba 2+ , a potent blocker of the K + ion channel, permeate through the SF of the NaK ion channel? Finally, how do their translocation energetics differ from those of monovalent ions such as K + ? Here, in an attempt to address these outstanding issues, we elucidate the structure, binding and selectivity of divalent ions (Ca 2+ , Sr 2+ and Ba 2+ ) as they permeate through the SF of the NaK ion channel using all-atom molecular dynamics simulations and density functional theory based calculations. We unveil mechanistic insight into this translocation event using well-tempered metadynamics simulations in a polarizable environment using the mean-field model of water and incorporating electronic continuum corrections for ions via charge rescaling. The results show that, akin to K + coordination, Sr 2+ and Ba 2+ bind at the SF in a very similar fashion and remain octa-coordinated at all sites. Interestingly, differing from its local hydration structure, Ca 2+ interacts with eight carbonyls to remain at the middle of the S3 site. Furthermore, the binding of divalent metals at SF binding sites is more favorable than the binding of K + . However, their permeation through the extracellular entrance faces a considerably higher energetic barrier compared to that for K + , which eventually manifests their inherent blocking feature.

Image-based overlay measurement using subsurface ultrasonic resonance force microscopy

NASA Astrophysics Data System (ADS)

Tamer, M. S.; van der Lans, M. J.; Sadeghian, H.

2018-03-01

Image Based Overlay (IBO) measurement is one of the most common techniques used in Integrated Circuit (IC) manufacturing to extract the overlay error values. The overlay error is measured using dedicated overlay targets which are optimized to increase the accuracy and the resolution, but these features are much larger than the IC feature size. IBO measurements are realized on the dedicated targets instead of product features, because the current overlay metrology solutions, mainly based on optics, cannot provide sufficient resolution on product features. However, considering the fact that the overlay error tolerance is approaching 2 nm, the overlay error measurement on product features becomes a need for the industry. For sub-nanometer resolution metrology, Scanning Probe Microscopy (SPM) is widely used, though at the cost of very low throughput. The semiconductor industry is interested in non-destructive imaging of buried structures under one or more layers for the application of overlay and wafer alignment, specifically through optically opaque media. Recently an SPM technique has been developed for imaging subsurface features which can be potentially considered as a solution for overlay metrology. In this paper we present the use of Subsurface Ultrasonic Resonance Force Microscopy (SSURFM) used for IBO measurement. We used SSURFM for imaging the most commonly used overlay targets on a silicon substrate and photoresist. As a proof of concept we have imaged surface and subsurface structures simultaneously. The surface and subsurface features of the overlay targets are fabricated with programmed overlay errors of +/-40 nm, +/-20 nm, and 0 nm. The top layer thickness changes between 30 nm and 80 nm. Using SSURFM the surface and subsurface features were successfully imaged and the overlay errors were extracted, via a rudimentary image processing algorithm. The measurement results are in agreement with the nominal values of the programmed overlay errors.

Direct femtosecond laser surface structuring of crystalline silicon at 400 nm

NASA Astrophysics Data System (ADS)

Nivas, Jijil JJ; Anoop, K. K.; Bruzzese, Riccardo; Philip, Reji; Amoruso, Salvatore

2018-03-01

We have analyzed the effects of the laser pulse wavelength (400 nm) on femtosecond laser surface structuring of silicon. The features of the produced surface structures are investigated as a function of the number of pulses, N, and compared with the surface textures produced by more standard near-infrared (800 nm) laser pulses at a similar level of excitation. Our experimental findings highlight the importance of the light wavelength for the formation of the supra-wavelength grooves, and, for a large number of pulses (N ≈ 1000), the generation of other periodic structures (stripes) at 400 nm, which are not observed at 800 nm. These results provide interesting information on the generation of various surface textures, addressing the effect of the laser pulse wavelength on the generation of grooves and stripes.

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.

Epidemic outbreaks in growing scale-free networks with local structure

NASA Astrophysics Data System (ADS)

Ni, Shunjiang; Weng, Wenguo; Shen, Shifei; Fan, Weicheng

2008-09-01

The class of generative models has already attracted considerable interest from researchers in recent years and much expanded the original ideas described in BA model. Most of these models assume that only one node per time step joins the network. In this paper, we grow the network by adding n interconnected nodes as a local structure into the network at each time step with each new node emanating m new edges linking the node to the preexisting network by preferential attachment. This successfully generates key features observed in social networks. These include power-law degree distribution pk∼k, where μ=(n-1)/m is a tuning parameter defined as the modularity strength of the network, nontrivial clustering, assortative mixing, and modular structure. Moreover, all these features are dependent in a similar way on the parameter μ. We then study the susceptible-infected epidemics on this network with identical infectivity, and find that the initial epidemic behavior is governed by both of the infection scheme and the network structure, especially the modularity strength. The modularity of the network makes the spreading velocity much lower than that of the BA model. On the other hand, increasing the modularity strength will accelerate the propagation velocity.

Binary classification of items of interest in a repeatable process

DOEpatents

Abell, Jeffrey A.; Spicer, John Patrick; Wincek, Michael Anthony; Wang, Hui; Chakraborty, Debejyo

2014-06-24

A system includes host and learning machines in electrical communication with sensors positioned with respect to an item of interest, e.g., a weld, and memory. The host executes instructions from memory to predict a binary quality status of the item. The learning machine receives signals from the sensor(s), identifies candidate features, and extracts features from the candidates that are more predictive of the binary quality status relative to other candidate features. The learning machine maps the extracted features to a dimensional space that includes most of the items from a passing binary class and excludes all or most of the items from a failing binary class. The host also compares the received signals for a subsequent item of interest to the dimensional space to thereby predict, in real time, the binary quality status of the subsequent item of interest.

Local structural effects in Sr 3NiRhO 6 across magnetic transitions

DOE PAGES

Singh, Navneet; Khalid, S.; Bindu, R.

2016-04-06

Here, we investigate the temperature dependence of the structural parameters of quasi-one-dimensional Sr 3NiRhO 6 across the region of magnetic phase transitions using Ni K-edge and Sr K-edge x-ray absorption spectroscopy (XAS). The features in the x-ray absorption near-edge region are identified using multiple scattering calculations. The temperature-dependent extended x-ray absorption fine structure (EXAFS) studies show that the setting of the intra-chain super exchange interaction starts at ~200 K, which is well above the first transition temperature (45 K) revealed by magnetic susceptibility studies. The onset of the inter-chain super–super exchange interaction appears to be at ~125 K. Interestingly, themore » role played by direct exchange interaction between the Ni 3d and Rh 4d states in stabilising the magnetic interaction is less significant. The present results shed light on the generic features exhibited by isostructural compounds and may help in identifying the magnetic exchange pathways useful for understanding the unusual properties exhibited by such compounds.« less

Characterization of ultrafast laser-ablation plasma plumes at various Ar ambient pressures

DOE PAGES

Diwakar, P. K.; Harilal, S. S.; Phillips, M. C.; ...

2015-07-30

Expansion dynamics and internal plume structures of fs laser ablated brass plasma in Ar at various pressure levels ranging from vacuum to atmospheric were studied using multitude of diagnostic tools including time resolved and time integrated 2-dimensional imaging, optical time of flight measurements and visible emission spectroscopy. Temporal evolution of excited Cu and Zn species in the plume were imaged using band pass interference filters and compared its hydrodynamic expansion features with spectrally integrated images of the plume. 2D imaging coupled with monochromatic line selection showed several interesting features at various pressure levels which include velocity differences among the plumemore » species, emission intensity distribution, plasma temperature, electron density etc. Plume confinement, enhanced signal intensity, and dual peak structures in time-of-flight profiles were observed at intermediate pressure range of ~10 Torr. Optimum signal to background ratio was also observed in this pressure range. As a result, possible mechanisms for observed changes in plume shape, optical emission intensity and dual peak structures in time-of-flight profiles were discussed.« less

Psychology of knowledge representation.

PubMed

Grimm, Lisa R

2014-05-01

Every cognitive enterprise involves some form of knowledge representation. Humans represent information about the external world and internal mental states, like beliefs and desires, and use this information to meet goals (e.g., classification or problem solving). Unfortunately, researchers do not have direct access to mental representations. Instead, cognitive scientists design experiments and implement computational models to develop theories about the mental representations present during task performance. There are several main types of mental representation and corresponding processes that have been posited: spatial, feature, network, and structured. Each type has a particular structure and a set of processes that are capable of accessing and manipulating information within the representation. The structure and processes determine what information can be used during task performance and what information has not been represented at all. As such, the different types of representation are likely used to solve different kinds of tasks. For example, structured representations are more complex and computationally demanding, but are good at representing relational information. Researchers interested in human psychology would benefit from considering how knowledge is represented in their domain of inquiry. For further resources related to this article, please visit the WIREs website. The author has declared no conflicts of interest for this article. © 2014 John Wiley & Sons, Ltd.

Cointegration and why it works for SHM

NASA Astrophysics Data System (ADS)

Cross, Elizabeth J.; Worden, Keith

2012-08-01

One of the most fundamental problems in Structural Health Monitoring (SHM) is that of projecting out operational and environmental variations from measured feature data. The reason for this is that algorithms used for SHM to detect changes in structural condition should not raise alarms if the structure of interest changes because of benign operational or environmental variations. This is sometimes called the data normalisation problem. Many solutions to this problem have been proposed over the years, but a new approach that uses cointegration, a concept from the field of econometrics, appears to provide a very promising solution. The theory of cointegration is mathematically complex and its use is based on the holding of a number of assumptions on the time series to which it is applied. An interesting observation that has emerged from its applications to SHM data is that the approach works very well even though the aforementioned assumptions do not hold in general. The objective of the current paper is to discuss how the cointegration assumptions break down individually in the context of SHM and to explain why this does not invalidate the application of the algorithm.

Three-dimensional micro/nano-scale structure fabricated by combination of non-volatile polymerizable RTIL and FIB irradiation

PubMed Central

Kuwabata, Susumu; Minamimoto, Hiro; Inoue, Kosuke; Imanishi, Akihito; Hosoya, Ken; Uyama, Hiroshi; Torimoto, Tsukasa; Tsuda, Tetsuya; Seki, Shu

2014-01-01

Room-temperature ionic liquid (RTIL) has been widely investigated as a nonvolatile solvent as well as a unique liquid material because of its interesting features, e.g., negligible vapor pressure and high thermal stability. Here we report that a non-volatile polymerizable RTIL is a useful starting material for the fabrication of micro/nano-scale polymer structures with a focused-ion-beam (FIB) system operated under high-vacuum condition. Gallium-ion beam irradiation to the polymerizable 1-allyl-3-ethylimidazolium bis((trifluoromethane)sulfonyl)amide RTIL layer spread on a Si wafer induced a polymerization reaction without difficulty. What is interesting to note is that we have succeeded in provoking the polymerization reaction anywhere on the Si wafer substrate by using FIB irradiation with a raster scanning mode. By this finding, two- and three-dimensional micro/nano-scale polymer structure fabrications were possible at the resolution of 500,000 dpi. Even intricate three-dimensional micro/nano-figures with overhang and hollow moieties could be constructed at the resolution of approximately 100 nm. PMID:24430465

Enabling optical metrology on small 5×5μm2 in-cell targets to support flexible sampling and higher order overlay and CD control for advanced logic devices nodes

NASA Astrophysics Data System (ADS)

Salerno, Antonio; de la Fuente, Isabel; Hsu, Zack; Tai, Alan; Chang, Hammer; McNamara, Elliott; Cramer, Hugo; Li, Daoping

2018-03-01

In next generation Logic devices, overlay control requirements shrink to sub 2.5nm level on-product overlay. Historically on-product overlay has been defined by the overlay capability of after-develop in-scribe targets. However, due to design and dimension, the after development metrology targets are not completely representative for the final overlay of the device. In addition, they are confined to the scribe-lane area, which limits the sampling possibilities. To address these two issues, metrology on structures matching the device structure and which can be sampled with high density across the device is required. Conventional after-etch CDSEM techniques on logic devices present difficulties in discerning the layers of interest, potential destructive charging effects and finally, they are limited by the long measurement times[1] [2] [3] . All together, limit the sampling densities and making CDSEM less attractive for control applications. Optical metrology can overcome most of these limitations. Such measurement, however, does require repetitive structures. This requirement is not fulfilled by logic devices, as the features vary in pitch and CD over the exposure field. The solution is to use small targets, with a maximum pad size of 5x5um2 , which can easily be placed in the logic cell area. These targets share the process and architecture of the device features of interest, but with a modified design that replicates as close as possible the device layout, allowing for in-device metrology for both CD and Overlay. This solution enables measuring closer to the actual product feature location and, not being limited to scribe-lanes, it opens the possibility of higher-density sampling schemes across the field. In summary, these targets become the facilitator of in-device metrology (IDM), that is, enabling the measurements both in-device Overlay and the CD parameters of interest and can deliver accurate, high-throughput, dense and after-etch measurements for Logic. Overlay improvements derived from a high-densely sampled Overlay map measured with 5x5 um2 In Device Metrology (IDM) targets were investigated on a customer Logic application. In this work we present both the main design aspects of the 5x5 um2 IDM targets, as well as the results on the improved Overlay performance.

Comparison between flood prone areas' geomorphic features in the Abruzzo region

NASA Astrophysics Data System (ADS)

Orlando, D.; Giglioni, M.; Magnaldi, S.

2017-07-01

Flood risk maps are one of the main non-structural measures for risk mitigation, but, as the risk knowledge degree is directly proportional to the community interest and financial capability, many sites are devoid of flood inundation areas studies. Recently many authors have investigated the capability of flood prone areas individuation with geomorphological DIGITAL ELEVATION MODEL(DEM) based approaches. These approaches highlight the role of geomorphic features derived from DEM, in this case slope, curvature, elevation, and topographic wetness index, to preliminary inundated areas' identification, without using hydraulic simulations. The present studies aim to analyze the geomorphic features of different hazard levels that lie under the identified inundated areas that have been carried out by the Abruzzo Region Basin Authority. The Aterno-Pescara and Foro river basins have been investigated. The results show that the characteristics of the flooded areas can be clearly distinguished from those of the entire basin,however, the difficultly of geomorphic features in individuatingthe areas of different hazard classifications is obvious.

A priori Prediction of Neoadjuvant Chemotherapy Response and Survival in Breast Cancer Patients using Quantitative Ultrasound

PubMed Central

Tadayyon, Hadi; Sannachi, Lakshmanan; Gangeh, Mehrdad J.; Kim, Christina; Ghandi, Sonal; Trudeau, Maureen; Pritchard, Kathleen; Tran, William T.; Slodkowska, Elzbieta; Sadeghi-Naini, Ali; Czarnota, Gregory J.

2017-01-01

Quantitative ultrasound (QUS) can probe tissue structure and analyze tumour characteristics. Using a 6-MHz ultrasound system, radiofrequency data were acquired from 56 locally advanced breast cancer patients prior to their neoadjuvant chemotherapy (NAC) and QUS texture features were computed from regions of interest in tumour cores and their margins as potential predictive and prognostic indicators. Breast tumour molecular features were also collected and used for analysis. A multiparametric QUS model was constructed, which demonstrated a response prediction accuracy of 88% and ability to predict patient 5-year survival rates (p = 0.01). QUS features demonstrated superior performance in comparison to molecular markers and the combination of QUS and molecular markers did not improve response prediction. This study demonstrates, for the first time, that non-invasive QUS features in the core and margin of breast tumours can indicate breast cancer response to neoadjuvant chemotherapy (NAC) and predict five-year recurrence-free survival. PMID:28401902

A priori Prediction of Neoadjuvant Chemotherapy Response and Survival in Breast Cancer Patients using Quantitative Ultrasound.

PubMed

Tadayyon, Hadi; Sannachi, Lakshmanan; Gangeh, Mehrdad J; Kim, Christina; Ghandi, Sonal; Trudeau, Maureen; Pritchard, Kathleen; Tran, William T; Slodkowska, Elzbieta; Sadeghi-Naini, Ali; Czarnota, Gregory J

2017-04-12

Quantitative ultrasound (QUS) can probe tissue structure and analyze tumour characteristics. Using a 6-MHz ultrasound system, radiofrequency data were acquired from 56 locally advanced breast cancer patients prior to their neoadjuvant chemotherapy (NAC) and QUS texture features were computed from regions of interest in tumour cores and their margins as potential predictive and prognostic indicators. Breast tumour molecular features were also collected and used for analysis. A multiparametric QUS model was constructed, which demonstrated a response prediction accuracy of 88% and ability to predict patient 5-year survival rates (p = 0.01). QUS features demonstrated superior performance in comparison to molecular markers and the combination of QUS and molecular markers did not improve response prediction. This study demonstrates, for the first time, that non-invasive QUS features in the core and margin of breast tumours can indicate breast cancer response to neoadjuvant chemotherapy (NAC) and predict five-year recurrence-free survival.

A cooperative game framework for detecting overlapping communities in social networks

NASA Astrophysics Data System (ADS)

Jonnalagadda, Annapurna; Kuppusamy, Lakshmanan

2018-02-01

Community detection in social networks is a challenging and complex task, which received much attention from researchers of multiple domains in recent years. The evolution of communities in social networks happens merely due to the self-interest of the nodes. The interesting feature of community structure in social networks is the multi membership of the nodes resulting in overlapping communities. Assuming the nodes of the social network as self-interested players, the dynamics of community formation can be captured in the form of a game. In this paper, we propose a greedy algorithm, namely, Weighted Graph Community Game (WGCG), in order to model the interactions among the self-interested nodes of the social network. The proposed algorithm employs the Shapley value mechanism to discover the inherent communities of the underlying social network. The experimental evaluation on the real-world and synthetic benchmark networks demonstrates that the performance of the proposed algorithm is superior to the state-of-the-art overlapping community detection algorithms.

The application of data mining and cloud computing techniques in data-driven models for structural health monitoring

NASA Astrophysics Data System (ADS)

Khazaeli, S.; Ravandi, A. G.; Banerji, S.; Bagchi, A.

2016-04-01

Recently, data-driven models for Structural Health Monitoring (SHM) have been of great interest among many researchers. In data-driven models, the sensed data are processed to determine the structural performance and evaluate the damages of an instrumented structure without necessitating the mathematical modeling of the structure. A framework of data-driven models for online assessment of the condition of a structure has been developed here. The developed framework is intended for automated evaluation of the monitoring data and structural performance by the Internet technology and resources. The main challenges in developing such framework include: (a) utilizing the sensor measurements to estimate and localize the induced damage in a structure by means of signal processing and data mining techniques, and (b) optimizing the computing and storage resources with the aid of cloud services. The main focus in this paper is to demonstrate the efficiency of the proposed framework for real-time damage detection of a multi-story shear-building structure in two damage scenarios (change in mass and stiffness) in various locations. Several features are extracted from the sensed data by signal processing techniques and statistical methods. Machine learning algorithms are deployed to select damage-sensitive features as well as classifying the data to trace the anomaly in the response of the structure. Here, the cloud computing resources from Amazon Web Services (AWS) have been used to implement the proposed framework.

Mediastinal lymph node detection and station mapping on chest CT using spatial priors and random forest

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

Liu, Jiamin; Hoffman, Joanne; Zhao, Jocelyn

2016-07-15

Purpose: To develop an automated system for mediastinal lymph node detection and station mapping for chest CT. Methods: The contextual organs, trachea, lungs, and spine are first automatically identified to locate the region of interest (ROI) (mediastinum). The authors employ shape features derived from Hessian analysis, local object scale, and circular transformation that are computed per voxel in the ROI. Eight more anatomical structures are simultaneously segmented by multiatlas label fusion. Spatial priors are defined as the relative multidimensional distance vectors corresponding to each structure. Intensity, shape, and spatial prior features are integrated and parsed by a random forest classifiermore » for lymph node detection. The detected candidates are then segmented by the following curve evolution process. Texture features are computed on the segmented lymph nodes and a support vector machine committee is used for final classification. For lymph node station labeling, based on the segmentation results of the above anatomical structures, the textual definitions of mediastinal lymph node map according to the International Association for the Study of Lung Cancer are converted into patient-specific color-coded CT image, where the lymph node station can be automatically assigned for each detected node. Results: The chest CT volumes from 70 patients with 316 enlarged mediastinal lymph nodes are used for validation. For lymph node detection, their system achieves 88% sensitivity at eight false positives per patient. For lymph node station labeling, 84.5% of lymph nodes are correctly assigned to their stations. Conclusions: Multiple-channel shape, intensity, and spatial prior features aggregated by a random forest classifier improve mediastinal lymph node detection on chest CT. Using the location information of segmented anatomic structures from the multiatlas formulation enables accurate identification of lymph node stations.« less

MSClique: Multiple Structure Discovery through the Maximum Weighted Clique Problem.

PubMed

Sanroma, Gerard; Penate-Sanchez, Adrian; Alquézar, René; Serratosa, Francesc; Moreno-Noguer, Francesc; Andrade-Cetto, Juan; González Ballester, Miguel Ángel

2016-01-01

We present a novel approach for feature correspondence and multiple structure discovery in computer vision. In contrast to existing methods, we exploit the fact that point-sets on the same structure usually lie close to each other, thus forming clusters in the image. Given a pair of input images, we initially extract points of interest and extract hierarchical representations by agglomerative clustering. We use the maximum weighted clique problem to find the set of corresponding clusters with maximum number of inliers representing the multiple structures at the correct scales. Our method is parameter-free and only needs two sets of points along with their tentative correspondences, thus being extremely easy to use. We demonstrate the effectiveness of our method in multiple-structure fitting experiments in both publicly available and in-house datasets. As shown in the experiments, our approach finds a higher number of structures containing fewer outliers compared to state-of-the-art methods.

Development of students' interest in particle physics as effect of participating in a Masterclass

NASA Astrophysics Data System (ADS)

Gedigk, Kerstin; Pospiech, Gesche

2016-05-01

The International Hands On Particle Physics Masterclasses are enjoying increasing popularity worldwide every year. In Germany a national program was brought to live in 2010, which offers these appreciated events to whole classes or courses of high school students all over the year. These events were evaluated concerning the issues of students' interest in particle physics and their perception of the events. How several interest variables interact with each other and the perception of the events is answered by structural equation modelling (sect. 5.2). The results give information about the events' effects on the students' interest development in particle physics, show which event features are important ( e.g. the authenticity) and give information about practical approaches to improve the effects of the Masterclasses. Section 5.3 deals with a group of participants which have a high interest in particle physics 6-8 weeks after the participation. The number of these students is remarkable large, with 26% of all participants. The investigation of this group shows that the Masterclass participation has the same positive effect on both sexes and all levels of physics education.

Correlating Intravital Multi-Photon Microscopy to 3D Electron Microscopy of Invading Tumor Cells Using Anatomical Reference Points

PubMed Central

Karreman, Matthia A.; Mercier, Luc; Schieber, Nicole L.; Shibue, Tsukasa; Schwab, Yannick; Goetz, Jacky G.

2014-01-01

Correlative microscopy combines the advantages of both light and electron microscopy to enable imaging of rare and transient events at high resolution. Performing correlative microscopy in complex and bulky samples such as an entire living organism is a time-consuming and error-prone task. Here, we investigate correlative methods that rely on the use of artificial and endogenous structural features of the sample as reference points for correlating intravital fluorescence microscopy and electron microscopy. To investigate tumor cell behavior in vivo with ultrastructural accuracy, a reliable approach is needed to retrieve single tumor cells imaged deep within the tissue. For this purpose, fluorescently labeled tumor cells were subcutaneously injected into a mouse ear and imaged using two-photon-excitation microscopy. Using near-infrared branding, the position of the imaged area within the sample was labeled at the skin level, allowing for its precise recollection. Following sample preparation for electron microscopy, concerted usage of the artificial branding and anatomical landmarks enables targeting and approaching the cells of interest while serial sectioning through the specimen. We describe here three procedures showing how three-dimensional (3D) mapping of structural features in the tissue can be exploited to accurately correlate between the two imaging modalities, without having to rely on the use of artificially introduced markers of the region of interest. The methods employed here facilitate the link between intravital and nanoscale imaging of invasive tumor cells, enabling correlating function to structure in the study of tumor invasion and metastasis. PMID:25479106

Universal structures in some mean field spin glasses and an application

NASA Astrophysics Data System (ADS)

Bolthausen, Erwin; Kistler, Nicola

2008-12-01

We discuss a spin glass reminiscent of the random energy model (REM), which allows, in particular, to recast the Parisi minimization into a more classical Gibbs variational principle, thereby shedding some light into the physical meaning of the order parameter of the Parisi theory. As an application, we study the impact of an extensive cavity field on Derrida's REM: Despite its simplicity, this model displays some interesting features such as ultrametricity and chaos in temperature.

On the ground state of Yang-Mills theory

NASA Astrophysics Data System (ADS)

Bakry, Ahmed S.; Leinweber, Derek B.; Williams, Anthony G.

2011-08-01

We investigate the overlap of the ground state meson potential with sets of mesonic-trial wave functions corresponding to different gluonic distributions. We probe the transverse structure of the flux tube through the creation of non-uniform smearing profiles for the string of glue connecting two color sources in Wilson loop operator. The non-uniformly UV-regulated flux-tube operators are found to optimize the overlap with the ground state and display interesting features in the ground state overlap.

A Rejoinder.

PubMed

Nesselroade, John R; Molenaar, Peter C M

2016-01-01

Three commentaries on the Nesselroade and Molenaar target article in this issue are responded to in the interest of elaborating and defending the points of view expressed in our article. The commentaries feature philosophy of science, general structural modeling, and broad behavioral research perspectives. Responding to the commentaries afforded us the opportunity to clarify further matters that we deem critical to the fundamental matter of measurement in behavioral science, especially as it emphasizes (properly, we believe) the individual as the primary unit of analysis.

High performance mode locking characteristics of single section quantum dash lasers.

PubMed

Rosales, Ricardo; Murdoch, S G; Watts, R T; Merghem, K; Martinez, Anthony; Lelarge, Francois; Accard, Alain; Barry, L P; Ramdane, Abderrahim

2012-04-09

Mode locking features of single section quantum dash based lasers are investigated. Particular interest is given to the static spectral phase profile determining the shape of the mode locked pulses. The phase profile dependence on cavity length and injection current is experimentally evaluated, demonstrating the possibility of efficiently using the wide spectral bandwidth exhibited by these quantum dash structures for the generation of high peak power sub-picosecond pulses with low radio frequency linewidths.

Anomalies in, and Crystallization of Supercooled Water and Aqueous Solutions.

DTIC Science & Technology

1984-03-01

and to an extent novel situations, by D. L. Fields. The first study has been on water contained in the newly developed microemulsions in which there...feature of this microemulsion is March 8, 1984 ..... ...... ....... % *~.~- * -7- * •that the only-OH groups present derive from the water component. Our...interest in this subject has been two-fold. (1) To obtain information on the structure of water in the microemulsion form, (2) attempt to use the

Structural sensitivity of x-ray Bragg projection ptychography to domain patterns in epitaxial thin films

NASA Astrophysics Data System (ADS)

Hruszkewycz, S. O.; Zhang, Q.; Holt, M. V.; Highland, M. J.; Evans, P. G.; Fuoss, P. H.

2016-10-01

Bragg projection ptychography (BPP) is a coherent diffraction imaging technique capable of mapping the spatial distribution of the Bragg structure factor in nanostructured thin films. Here, we show that, because these images are projections, the structural sensitivity of the resulting images depends on the film thickness and the aspect ratio and orientation of the features of interest and that image interpretation depends on these factors. We model changes in contrast in the BPP reconstructions of simulated PbTiO3 ferroelectric thin films with meandering 180∘ stripe domains as a function of film thickness, discuss their origin, and comment on the implication of these factors on the design of BPP experiments of general nanostructured films.

The biology and chemistry of the zoanthamine alkaloids.

PubMed

Behenna, Douglas C; Stockdill, Jennifer L; Stoltz, Brian M

2008-01-01

Marine natural products have long played an important role in natural products chemistry and drug discovery. Mirroring the rich variety and complicated interactions of the marine environment, the substances isolated from sea creatures tend to be incredibly diverse in both molecular structure and biological activity. The natural products isolated from the polyps of marine zoanthids are no exception. The zoanthamine alkaloids, the first of which were isolated over 20 years ago, are of particular interest to the synthetic community because they feature a novel structural framework and exhibit a broad range of biological activities. In this Review, we summarize the major contributions to understanding the zoanthamine natural products with regard to their isolation and structure determination, as well as studies on their biological activity and total synthesis.

Intricate Hollow Structures: Controlled Synthesis and Applications in Energy Storage and Conversion.

PubMed

Zhou, Liang; Zhuang, Zechao; Zhao, Huihui; Lin, Mengting; Zhao, Dongyuan; Mai, Liqiang

2017-05-01

Intricate hollow structures garner tremendous interest due to their aesthetic beauty, unique structural features, fascinating physicochemical properties, and widespread applications. Here, the recent advances in the controlled synthesis are discussed, as well as applications of intricate hollow structures with regard to energy storage and conversion. The synthetic strategies toward complex multishelled hollow structures are classified into six categories, including well-established hard- and soft-templating methods, as well as newly emerging approaches based on selective etching of "soft@hard" particles, Ostwald ripening, ion exchange, and thermally induced mass relocation. Strategies for constructing structures beyond multishelled hollow structures, such as bubble-within-bubble, tube-in-tube, and wire-in-tube structures, are also covered. Niche applications of intricate hollow structures in lithium-ion batteries, Li-S batteries, supercapacitors, Li-O 2 batteries, dye-sensitized solar cells, photocatalysis, and fuel cells are discussed in detail. Some perspectives on the future research and development of intricate hollow structures are also provided. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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.

A no-reference bitstream-based perceptual model for video quality estimation of videos affected by coding artifacts and packet losses

NASA Astrophysics Data System (ADS)

Pandremmenou, K.; Shahid, M.; Kondi, L. P.; Lövström, B.

2015-03-01

In this work, we propose a No-Reference (NR) bitstream-based model for predicting the quality of H.264/AVC video sequences, affected by both compression artifacts and transmission impairments. The proposed model is based on a feature extraction procedure, where a large number of features are calculated from the packet-loss impaired bitstream. Many of the features are firstly proposed in this work, and the specific set of the features as a whole is applied for the first time for making NR video quality predictions. All feature observations are taken as input to the Least Absolute Shrinkage and Selection Operator (LASSO) regression method. LASSO indicates the most important features, and using only them, it is possible to estimate the Mean Opinion Score (MOS) with high accuracy. Indicatively, we point out that only 13 features are able to produce a Pearson Correlation Coefficient of 0.92 with the MOS. Interestingly, the performance statistics we computed in order to assess our method for predicting the Structural Similarity Index and the Video Quality Metric are equally good. Thus, the obtained experimental results verified the suitability of the features selected by LASSO as well as the ability of LASSO in making accurate predictions through sparse modeling.

Myosin MyTH4-FERM structures highlight important principles of convergent evolution.

PubMed

Planelles-Herrero, Vicente José; Blanc, Florian; Sirigu, Serena; Sirkia, Helena; Clause, Jeffrey; Sourigues, Yannick; Johnsrud, Daniel O; Amigues, Beatrice; Cecchini, Marco; Gilbert, Susan P; Houdusse, Anne; Titus, Margaret A

2016-05-24

Myosins containing MyTH4-FERM (myosin tail homology 4-band 4.1, ezrin, radixin, moesin, or MF) domains in their tails are found in a wide range of phylogenetically divergent organisms, such as humans and the social amoeba Dictyostelium (Dd). Interestingly, evolutionarily distant MF myosins have similar roles in the extension of actin-filled membrane protrusions such as filopodia and bind to microtubules (MT), suggesting that the core functions of these MF myosins have been highly conserved over evolution. The structures of two DdMyo7 signature MF domains have been determined and comparison with mammalian MF structures reveals that characteristic features of MF domains are conserved. However, across millions of years of evolution conserved class-specific insertions are seen to alter the surfaces and the orientation of subdomains with respect to each other, likely resulting in new sites for binding partners. The MyTH4 domains of Myo10 and DdMyo7 bind to MT with micromolar affinity but, surprisingly, their MT binding sites are on opposite surfaces of the MyTH4 domain. The structural analysis in combination with comparison of diverse MF myosin sequences provides evidence that myosin tail domain features can be maintained without strict conservation of motifs. The results illustrate how tuning of existing features can give rise to new structures while preserving the general properties necessary for myosin tails. Thus, tinkering with the MF domain enables it to serve as a multifunctional platform for cooperative recruitment of various partners, allowing common properties such as autoinhibition of the motor and microtubule binding to arise through convergent evolution.

A flexible pressure responsive device based on the interaction between silver nanoparticles and an aluminum reflector

NASA Astrophysics Data System (ADS)

Rankin, Alasdair; McGarry, Steven

2018-01-01

The unique and tunable optical properties of metal nanoparticles have attracted intense and sustained academic attention in recent years. In tandem with the demand for low-cost responsive materials, one particular topic of interest is the development of mechanically responsive device structures. This work describes the design, fabrication, and testing of a mechanically responsive plasmonic device structure that has been integrated onto a standard commercial plastic substrate. With a low actuation force and a visually perceivable color shift, this device would be attractive for applications requiring responsive features that can be activated by the human hand.

Martian Clouds Data Workshop

NASA Technical Reports Server (NTRS)

Lee, Steven (Editor)

1987-01-01

The major topics covered were a discussion of the structure of relational data base systems and features of the Britton Lee Relational Data Base Management System (RDBMS); a discussion of the workshop's objectives, approach, and research scenarios; and an overview of the Atmospheres Node User's Guide, which details the datasets stored on the Britton Lee, the structure of the query and data analysis system, and examples of the exact menu screens encountered. Also discussed were experience with the system, review of the system performance, and a strategy to produce queries and performance data retrievals of mutual interest. The goals were defined as examining correlations between cloud occurrence, water vapor abundance, and surface properties.

Clues for biomimetics from natural composite materials

PubMed Central

Lapidot, Shaul; Meirovitch, Sigal; Sharon, Sigal; Heyman, Arnon; Kaplan, David L; Shoseyov, Oded

2013-01-01

Bio-inspired material systems are derived from different living organisms such as plants, arthropods, mammals and marine organisms. These biomaterial systems from nature are always present in the form of composites, with molecular-scale interactions optimized to direct functional features. With interest in replacing synthetic materials with natural materials due to biocompatibility, sustainability and green chemistry issues, it is important to understand the molecular structure and chemistry of the raw component materials to also learn from their natural engineering, interfaces and interactions leading to durable and highly functional material architectures. This review will focus on applications of biomaterials in single material forms, as well as biomimetic composites inspired by natural organizational features. Examples of different natural composite systems will be described, followed by implementation of the principles underlying their composite organization into artificial bio-inspired systems for materials with new functional features for future medicine. PMID:22994958

Clues for biomimetics from natural composite materials.

PubMed

Lapidot, Shaul; Meirovitch, Sigal; Sharon, Sigal; Heyman, Arnon; Kaplan, David L; Shoseyov, Oded

2012-09-01

Bio-inspired material systems are derived from different living organisms such as plants, arthropods, mammals and marine organisms. These biomaterial systems from nature are always present in the form of composites, with molecular-scale interactions optimized to direct functional features. With interest in replacing synthetic materials with natural materials due to biocompatibility, sustainability and green chemistry issues, it is important to understand the molecular structure and chemistry of the raw component materials to also learn from their natural engineering, interfaces and interactions leading to durable and highly functional material architectures. This review will focus on applications of biomaterials in single material forms, as well as biomimetic composites inspired by natural organizational features. Examples of different natural composite systems will be described, followed by implementation of the principles underlying their composite organization into artificial bio-inspired systems for materials with new functional features for future medicine.

Summary of an integrated ERTS-1 project and its results at the Missouri Geological Survey

NASA Technical Reports Server (NTRS)

Martin, J. A.; Allen, W. H.; Rath, D. L.; Rueff, A.

1974-01-01

Use of the ERTS imagery involved the recognition and interpretation of various ground patterns. Analysis and application are tied to ongoing programs. Specific studies utilizing the imagery and NASA aircraft photography are: a statewide lake and dam inventory; assessment of flooding and floodprone areas along the Missouri portion of the Mississippi and Missouri Rivers; land-use classification for several counties; structural features in selected areas; and Pleistocene features in northern Missouri. Though it has been suggested that repetitive coverage is not necessary for geologic studies, it is this specific feature along with the synoptic view of large portions of the State that provided the potential for the utilization of the ERTS imagery in Missouri. Other State agencies, Departments of Conservation, Agriculture, and Community Affairs, have expressed interest in the potential application of ERTS data in their respective fields.

Nonequilibrium critical behavior of model statistical systems and methods for the description of its features

NASA Astrophysics Data System (ADS)

Prudnikov, V. V.; Prudnikov, P. V.; Mamonova, M. V.

2017-11-01

This paper reviews features in critical behavior of far-from-equilibrium macroscopic systems and presents current methods of describing them by referring to some model statistical systems such as the three-dimensional Ising model and the two-dimensional XY model. The paper examines the critical relaxation of homogeneous and structurally disordered systems subjected to abnormally strong fluctuation effects involved in ordering processes in solids at second-order phase transitions. Interest in such systems is due to the aging properties and fluctuation-dissipation theorem violations predicted for and observed in systems slowly evolving from a nonequilibrium initial state. It is shown that these features of nonequilibrium behavior show up in the magnetic properties of magnetic superstructures consisting of alternating nanoscale-thick magnetic and nonmagnetic layers and can be observed not only near the film’s critical ferromagnetic ordering temperature Tc, but also over the wide temperature range T ⩽ Tc.

Scanning electron microscope cathodoluminescence imaging of subgrain boundaries, twins and planar deformation features in quartz

NASA Astrophysics Data System (ADS)

Hamers, M. F.; Pennock, G. M.; Drury, M. R.

2017-04-01

The study of deformation features has been of great importance to determine deformation mechanisms in quartz. Relevant microstructures in both growth and deformation processes include dislocations, subgrains, subgrain boundaries, Brazil and Dauphiné twins and planar deformation features (PDFs). Dislocations and twin boundaries are most commonly imaged using a transmission electron microscope (TEM), because these cannot directly be observed using light microscopy, in contrast to PDFs. Here, we show that red-filtered cathodoluminescence imaging in a scanning electron microscope (SEM) is a useful method to visualise subgrain boundaries, Brazil and Dauphiné twin boundaries. Because standard petrographic thin sections can be studied in the SEM, the observed structures can be directly and easily correlated to light microscopy studies. In contrast to TEM preparation methods, SEM techniques are non-destructive to the area of interest on a petrographic thin section.

Radiobiological studies with the nematode Caenorhabditis elegans. Genetic and developmental effects of high LET radiation

NASA Technical Reports Server (NTRS)

Nelson, G. A.; Schubert, W. W.; Marshall, T. M.

1992-01-01

The biological effects of heavy charged particle (HZE) radiation are of particular interest to travellers and planners for long-duration space flights where exposure levels represent a potential health hazard. The unique feature of HZE radiation is the structured pattern of its energy deposition in targets. There are many consequences of this feature to biological endpoints when compared with effects of ionizing photons. Dose vs response and dose-rate kinetics may be modified, DNA and cellular repair systems may be altered in their abilities to cope with damage, and the qualitative features of damage may be unique for different ions. The nematode Caenorhabditis elegans is being used to address these and related questions associated with exposure to radiation. HZE-induced mutation, chromosome aberration, cell inactivation and altered organogenesis are discussed along with plans for radiobiological experiments in space.

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.

Optimizing students' motivation in inquiry-based learning environments: The role of instructional practices

NASA Astrophysics Data System (ADS)

Kempler, Toni M.

The influence of inquiry science instruction on the motivation of 1360 minority inner-city seventh graders was examined. The project-based curriculum incorporates motivating features like real world questions, collaboration, technology, and lesson variety. Students design investigations, collect and analyze data, and create artifacts; challenging tasks require extensive use of learning and metacognitive strategies. Study 1 used Structural Equation Modeling to investigate student perceptions of the prevalence of project-based features, including real world connections, collaboration, academic press, and work norms, and their relation to interest, efficacy, cognitive engagement, and achievement. Perceptions of features related to different motivational outcomes, indicating the importance of using differentiated rather than single measures to study motivation in context. Cognitive engagement was enhanced by interest and efficacy but did not influence achievement, perhaps because students were not proficient strategy users and were new to inquiry. Study 2 examined the relationship between instructional practices and motivation. The 23 teachers in study 1 were observed six times during one unit. Observations focused on curriculum congruence, content accuracy, contextualization, sense making, and management and climate. A majority of teacher enactment was congruent with the curriculum, indicating that students experienced motivating features of project-based science. Hierarchical Linear Modeling showed that contextualization accounted for between-teacher variance in student interest, efficacy, and cognitive engagement; Teachers encouraged motivation through extended real world examples that related material to students' experiences. Cluster analysis was used to determine how patterns of practice affected motivation. Unexpectedly these patterns did not differentially relate to cognitive engagement. Findings showed that interest and efficacy were enhanced when teachers used particular sense making practices. These teachers provided explicit scaffolding for accomplishing complex tasks with questioning and feedback that highlighted key points. Teachers also used effective management practices and maintained a positive classroom climate. In contrast, a pattern of practice where teachers used questioning and feedback to press students to make connections and synthesize concepts without scaffolding support diminished motivation, because students may have needed more help to deal with challenge. Implications from both studies suggest inquiry teachers need to use explicit scaffolding and academic press together, with effective management practices, to support motivation.

Nanoscale organization in the fluorinated room temperature ionic liquid: Tetraethyl ammonium (trifluoromethanesulfonyl)(nonafluorobutylsulfonyl)imide

NASA Astrophysics Data System (ADS)

Lo Celso, F.; Appetecchi, G. B.; Jafta, C. J.; Gontrani, L.; Canongia Lopes, J. N.; Triolo, A.; Russina, O.

2018-05-01

Fluorinated Room Temperature Ionic Liquids (FRTILs) are a branch of ionic liquids that is the object of growing interest for a wide range of potential applications, due to the synergic combination of specifically ionic features and those properties that stem from fluorous tails. So far limited experimental work exists on the micro- and mesoscopic structural organization in this class of compounds. Such a work is however necessary to fully understand morphological details at atomistic level that would have strong implications in terms of bulk properties. Here we use the synergy between X-ray and neutron scattering together with molecular dynamics simulations to access structural details of a technologically relevant FRTIL that is characterised by an anion bearing a long enough fluorinated tail to develop specific morphological features. In particular, we find the first experimental evidence that in FRTILs bearing an asymmetric bis(perfluoroalkyl)sulfonyl-imide anion, fluorous side chains tend to be spatially segregated into nm-scale spatial heterogeneities. This feature together with the well-established micro-segregation of side alkyl chains in conventional RTILs leads to the concept of triphilic ILs, whose technological applications are yet to be fully developed.

Segmentation and feature extraction of cervical spine x-ray images

NASA Astrophysics Data System (ADS)

Long, L. Rodney; Thoma, George R.

1999-05-01

As part of an R&D project in mixed text/image database design, the National Library of Medicine has archived a collection of 17,000 digitized x-ray images of the cervical and lumbar spine which were collected as part of the second National Health and Nutrition Examination Survey (NHANES II). To make this image data available and usable to a wide audience, we are investigating techniques for indexing the image content by automated or semi-automated means. Indexing of the images by features of interest to researchers in spine disease and structure requires effective segmentation of the vertebral anatomy. This paper describes work in progress toward this segmentation of the cervical spine images into anatomical components of interest, including anatomical landmarks for vertebral location, and segmentation and identification of individual vertebrae. Our work includes developing a reliable method for automatically fixing an anatomy-based coordinate system in the images, and work to adaptively threshold the images, using methods previously applied by researchers in cardioangiography. We describe the motivation for our work and present our current results in both areas.

Dendrimer Nanoscaffolds for Potential Theranostics of Prostate Cancer with a Focus on Radiochemistry

PubMed Central

Lo, Su-Tang; Kumar, Amit; Hsieh, Jer-Tsong; Sun, Xiankai

2013-01-01

Dendrimers are a class of structurally defined macromolecules featured with a central core, a low-density interior formed by repetitive branching units, and a high-density exterior terminated with surface functional groups. In contrast to their polymeric counterparts, dendrimers are nano-sized and symmetrically shaped, which can be reproducibly synthesized in a large scale with monodispersity. These unique features have made dendrimers of increasing interest for drug delivery and other biomedical applications as a nanoscaffold system. Intended to address the potential use of dendrimers for the development of theranostic agents, which combines therapeutics and diagnostics in a single entity for personalized medicine, this review focuses on the reported methodologies of using dendrimer nanoscaffolds for targeted imaging and therapy of prostate cancer. Of particular interest, relevant chemistry strategies are discussed due to their important roles in the design and synthesis of diagnostic and therapeutic dendrimer-based nanoconjugates and potential theranostic agents, targeted or non-targeted. Given the developing status of nanoscaffolded theranostics, major challenges and potential hurdles are discussed along with the examples representing current advances. PMID:23294202

Incorporation of local structure into kriging models for the prediction of atomistic properties in the water decamer.

PubMed

Davie, Stuart J; Di Pasquale, Nicodemo; Popelier, Paul L A

2016-10-15

Machine learning algorithms have been demonstrated to predict atomistic properties approaching the accuracy of quantum chemical calculations at significantly less computational cost. Difficulties arise, however, when attempting to apply these techniques to large systems, or systems possessing excessive conformational freedom. In this article, the machine learning method kriging is applied to predict both the intra-atomic and interatomic energies, as well as the electrostatic multipole moments, of the atoms of a water molecule at the center of a 10 water molecule (decamer) cluster. Unlike previous work, where the properties of small water clusters were predicted using a molecular local frame, and where training set inputs (features) were based on atomic index, a variety of feature definitions and coordinate frames are considered here to increase prediction accuracy. It is shown that, for a water molecule at the center of a decamer, no single method of defining features or coordinate schemes is optimal for every property. However, explicitly accounting for the structure of the first solvation shell in the definition of the features of the kriging training set, and centring the coordinate frame on the atom-of-interest will, in general, return better predictions than models that apply the standard methods of feature definition, or a molecular coordinate frame. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.

Computerized bone analysis of hand radiographs

NASA Astrophysics Data System (ADS)

Pietka, Ewa; McNitt-Gray, Michael F.; Hall, Theodore R.; Huang, H. K.

1992-06-01

A computerized approach to the problem of skeletal maturity is presented. The analysis of a computed radiography (CR) hand image results in obtaining features, that can be used to assess the skeletal age of pediatric patients. It is performed on a standard left hand radiograph. First, epiphyseal regions of interest (EROI) are located. Then, within each EROI the distals, middles, and proximals are separated. This serves as a basis to locate the extremities of epiphyses and metaphyses. Next, the diameters of epiphyses and metaphyses are calculated. Finally, an epiphyseal diameter and metaphyseal diameter ratio is calculated. A pilot study indicated that these features are sensitive to the changes of the anatomical structure of a growing hand and can be used in the skeletal age assessment.

Challenging the state of the art in protein structure prediction: Highlights of experimental target structures for the 10th Critical Assessment of Techniques for Protein Structure Prediction Experiment CASP10.

PubMed

Kryshtafovych, Andriy; Moult, John; Bales, Patrick; Bazan, J Fernando; Biasini, Marco; Burgin, Alex; Chen, Chen; Cochran, Frank V; Craig, Timothy K; Das, Rhiju; Fass, Deborah; Garcia-Doval, Carmela; Herzberg, Osnat; Lorimer, Donald; Luecke, Hartmut; Ma, Xiaolei; Nelson, Daniel C; van Raaij, Mark J; Rohwer, Forest; Segall, Anca; Seguritan, Victor; Zeth, Kornelius; Schwede, Torsten

2014-02-01

For the last two decades, CASP has assessed the state of the art in techniques for protein structure prediction and identified areas which required further development. CASP would not have been possible without the prediction targets provided by the experimental structural biology community. In the latest experiment, CASP10, more than 100 structures were suggested as prediction targets, some of which appeared to be extraordinarily difficult for modeling. In this article, authors of some of the most challenging targets discuss which specific scientific question motivated the experimental structure determination of the target protein, which structural features were especially interesting from a structural or functional perspective, and to what extent these features were correctly reproduced in the predictions submitted to CASP10. Specifically, the following targets will be presented: the acid-gated urea channel, a difficult to predict transmembrane protein from the important human pathogen Helicobacter pylori; the structure of human interleukin (IL)-34, a recently discovered helical cytokine; the structure of a functionally uncharacterized enzyme OrfY from Thermoproteus tenax formed by a gene duplication and a novel fold; an ORFan domain of mimivirus sulfhydryl oxidase R596; the fiber protein gene product 17 from bacteriophage T7; the bacteriophage CBA-120 tailspike protein; a virus coat protein from metagenomic samples of the marine environment; and finally, an unprecedented class of structure prediction targets based on engineered disulfide-rich small proteins. Copyright © 2013 The Authors. Wiley Periodicals, Inc.

Geology of the Bighorn Mountains

USGS Publications Warehouse

Darton, N.H.

1906-01-01

There are extensive, forests in the mountains, which are now included in a Government forest reserve, but their timber is not of great value. Much of the area below timber line contains an abundance of luxuriant grasses and other plants, which afford excellent pasturage for stock, and large herds of sheep and cattle are ranged in the region during the short summer season. Game is moderately abundant, and most of the streams contain large numbers of trout. The region is one of great interest geologically on account of its variety of sedimentary rocks, interesting structure, and remarkably instructive glacial features. The central area, with its high peaks, presents alpine scenery of notable character. Doubtless in the future the region will be extensively visited by tourists, hunters, and geologists.

Best interests decisions: professional practices in health and social care.

PubMed

Williams, Val; Boyle, Geraldine; Jepson, Marcus; Swift, Paul; Williamson, Toby; Heslop, Pauline

2014-01-01

This paper reports on data collected in 2011 from a national study about the operation of the best interests principle, a key feature of the Mental Capacity Act (MCA) 2005 for England and Wales. The objective was to provide a picture of current professional practices in best interests decision-making. Four contrasting sample sites were selected, in which National Health Service trusts, social care and other organisations were recruited to participate. A multimethod design was followed, including an online survey with 385 participants, followed by qualitative research through a telephone survey of 68 participants, and face-to-face semi-structured interviews following up 25 best interests cases, with different perspectives on the process in 12 of those cases. The current paper reports only on the qualitative findings. The findings indicate that the MCA was successful in providing a structure for these practitioners, and that the five principles of the MCA were in general adhered to. A variety of perceived risks led to best interests processes being undertaken, and a typical scenario was for a period of hospitalisation or ill health to trigger a best interests decision process about a social care and or a life decision. The study supported previous research in finding the notion of capacity the most difficult aspect of the MCA, and it provides evidence of some specific capacity assessment practices, including problematic ones relating to 'insight'. Best interests decisions were often made by consensus, with practitioners taking on different roles within the process. Meetings played a key part, but other ways of involving people lacking capacity and significant others were also important. It was recommended that the issues highlighted in this research could be clarified further in the Code of Practice, or within risk guidance. © 2013 John Wiley & Sons Ltd.

Exploring Hot Gas at Junctions of Galaxy Filaments

NASA Astrophysics Data System (ADS)

Mitsuishi, Ikuyuki; Yamasaki, Noriko; Kawahara, Hajime; Sekiya, Norio; Sasaki, Shin; Sousbie, Thierry

Because galaxies are forced to follow the strong gravitational potential created by the underlying cosmic web of the dark matter, their distribution reflects its filamentary structures. By identifying the filamentary structures, one can therefore recover a map of the network that drives structure formation. Filamentary junctions are regions of particular interest as they identify places where mergers and other interesting astrophysical phenomena have high chances to occur. We identified the galaxy filaments by our original method (Sousbie (2011) & Sousbie et al. (2011)) and X-ray pointing observations were conducted for the six fields locating in the junctions of the galaxy filaments where no specific diffuse X-ray emissions had previously been detected so far. We discovered significant X-ray signals in their images and spectra of the all regions. Spectral analysis demonstrated that six sources originate from diffuse emissions associated with optically bright galaxies, group-scale, or cluster-scale X-ray halos with kT˜1-4 keV, while the others are compact object origin. Interestingly, all of the newly discovered three intracluster media show peculiar features such as complex or elongated morphologies in X-ray and/or optical and hot spot involved in ongoing merger events (Kawahara et al. (2011) & Mitsuishi et al. (2014)). In this conference, results of follow-up radio observations for the merging groups as well as the details of the X-ray observations will be reported.

Finding regions of interest in pathological images: an attentional model approach

NASA Astrophysics Data System (ADS)

Gómez, Francisco; Villalón, Julio; Gutierrez, Ricardo; Romero, Eduardo

2009-02-01

This paper introduces an automated method for finding diagnostic regions-of-interest (RoIs) in histopathological images. This method is based on the cognitive process of visual selective attention that arises during a pathologist's image examination. Specifically, it emulates the first examination phase, which consists in a coarse search for tissue structures at a "low zoom" to separate the image into relevant regions.1 The pathologist's cognitive performance depends on inherent image visual cues - bottom-up information - and on acquired clinical medicine knowledge - top-down mechanisms -. Our pathologist's visual attention model integrates the latter two components. The selected bottom-up information includes local low level features such as intensity, color, orientation and texture information. Top-down information is related to the anatomical and pathological structures known by the expert. A coarse approximation to these structures is achieved by an oversegmentation algorithm, inspired by psychological grouping theories. The algorithm parameters are learned from an expert pathologist's segmentation. Top-down and bottom-up integration is achieved by calculating a unique index for each of the low level characteristics inside the region. Relevancy is estimated as a simple average of these indexes. Finally, a binary decision rule defines whether or not a region is interesting. The method was evaluated on a set of 49 images using a perceptually-weighted evaluation criterion, finding a quality gain of 3dB when comparing to a classical bottom-up model of attention.

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.

Regional magnetic and gravity features of the Gibson Dome area and surrounding region, Paradox Basin, Utah : a preliminary report

USGS Publications Warehouse

Hildenbrand, T.G.; Kucks, R.P.

1983-01-01

Analyses of regional gravity and magnetic anomaly maps have been carried out to assist in the evaluation of the Gibson Dome area as a possible repository site for high-level radioactive waste. Derivative, wavelength-filtered, and trend maps were compiled to aid in properly locating major geophysical trends corresponding to faults, folds, and lithologic boundaries. The anomaly maps indicate that Paradox Basin is characterized by a heterogeneous Precambrian basement, essentially a metamorphic complex of gneisses and schist intruded by granitic rocks and mafic to ultramafic bodies. Interpreted Precambrian structures trend predominantly northwest and northeast although east-west trending features are evident. Prominent gravity lows define the salt anticlines. Structural and lithologic trends in the Gibson Dome area are closely examined. Of greatest interest is a series of circular magnetic highs trending west-northwest into the Gibson Dome area. Further study of the exact definition and geologic significance of this series of anomalies is warranted.

Insights using the molecular model of Lipoxygenase from Finger millet (Eleusine coracana (L.)).

PubMed

Tiwari, Apoorv; Avashthi, Himanshu; Jha, Richa; Srivastava, Ambuj; Kumar Garg, Vijay; Wasudev Ramteke, Pramod; Kumar, Anil

2016-01-01

Lipoxygenase-1 (LOX-1) protein provides defense against pests and pathogens and its presence have been positively correlated with plant resistance against pathogens. Linoleate is a known substrate of lipoxygenase and it induces necrosis leading to the accumulation of isoflavonoid phytoalexins in plant leaves. Therefore, it is of interest to study the structural features of LOX-1 from Finger millet. However, the structure ofLOX-1 from Finger millet is not yet known. A homology model of LOX-1 from Finger millet is described. Domain architecture study suggested the presence of two domains namely PLAT (Phospho Lipid Acyl Transferase) and lipoxygenase. Molecular docking models of linoleate with lipoxygenase from finger millet, rice and sorghum are reported. The features of docked models showed that finger millet have higher pathogen resistance in comparison to other cereal crops. This data is useful for the molecular cloning of fulllength LOX-1 gene for validating its role in improving plant defense against pathogen infection and for various other biological processes.

Enhanced water repellency of surfaces coated with multiscale carbon structures

NASA Astrophysics Data System (ADS)

Marchalot, Julien; Ramos, Stella. M. M.; Pirat, Christophe; Journet, Catherine

2018-01-01

Low cost and well characterized superhydrophobic surfaces are frequently required for industrial applications. Materials are commonly structured at the micro or nano scale. Surfaces decorated with nanotube derivatives synthesized by plasma enhanced chemical vapor deposition (PECVD) are of particular interest, since suitable modifications in the growth parameters can lead to numerous designs. In this article, we present surfaces that are selected for their specific wetting features with patterns ranging from dense forests to jungles with concave (re-entrant) surface such as flake-like multiscale roughness. Once these surfaces are functionalized adequately, their wetting properties are investigated. Their ability to sustain a superhydrophobic state for sessile water drops is examined. Finally, we propose a design to achieve a robust so-called ;Fakir; state, even for micrometer-sized drops, whereas with classic nanotubes forests it is not achievable. Thus, the drop remains on the apex of the protrusions with a high contact angle and a low contact angle hysteresis, while the surface features demonstrate good mechanical resistance against capillary forces.

Hit to lead account of the discovery of a new class of inhibitors of Pim kinases and crystallographic studies revealing an unusual kinase binding mode.

PubMed

Qian, Kevin; Wang, Lian; Cywin, Charles L; Farmer, Bennett T; Hickey, Eugene; Homon, Carol; Jakes, Scott; Kashem, Mohammed A; Lee, George; Leonard, Scott; Li, Jun; Magboo, Ronald; Mao, Wang; Pack, Edward; Peng, Charlene; Prokopowicz, Anthony; Welzel, Morgan; Wolak, John; Morwick, Tina

2009-04-09

A series of inhibitors of Pim-2 kinase identified by high-throughput screening is described. Details of the hit validation and lead generation process and structure-activity relationship (SAR) studies are presented. Disclosure of an unconventional binding mode for 1, as revealed by X-ray crystallography using the highly homologous Pim-1 protein, is also presented, and observed binding features are shown to correlate with the Pim-2 SAR. While highly selective within the kinase family, the series shows similar potency for both Pim-1 and Pim-2, which was expected on the basis of homology, but unusual in light of reports in the literature documenting a bias for Pim-1. A rationale for these observations based on Pim-1 and Pim-2 K(M(ATP)) values is suggested. Some interesting cross reactivity with casein kinase-2 was also identified, and structural features which may contribute to the association are discussed.

Engineering Hollow Carbon Architecture for High-Performance K-Ion Battery Anode.

PubMed

Bin, De-Shan; Lin, Xi-Jie; Sun, Yong-Gang; Xu, Yan-Song; Zhang, Ke; Cao, An-Min; Wan, Li-Jun

2018-05-31

K-ion batteries (KIBs) are now drawing increasing research interest as an inexpensive alternative to Li-ion batteries (LIBs). However, due to the large size of K + , stable electrode materials capable of sustaining the repeated K + intercalation/deintercalation cycles are extremely deficient especially if a satisfactory reversible capacity is expected. Herein, we demonstrated that the structural engineering of carbon into a hollow interconnected architecture, a shape similar to the neuron-cell network, promised high conceptual and technological potential for a high-performance KIB anode. Using melamine-formaldehyde resin as the starting material, we identify an interesting glass blowing effect of this polymeric precursor during its carbonization, which features a skeleton-softening process followed by its spontaneous hollowing. When used as a KIB anode, the carbon scaffold with interconnected hollow channels can ensure a resilient structure for a stable potassiation/depotassiation process and deliver an extraordinary capacity (340 mAh g -1 at 0.1 C) together with a superior cycling stability (no obvious fading over 150 cycles at 0.5 C).

Diatom Valve Three-Dimensional Representation: A New Imaging Method Based on Combined Microscopies

PubMed Central

Ferrara, Maria Antonietta; De Tommasi, Edoardo; Coppola, Giuseppe; De Stefano, Luca; Rea, Ilaria; Dardano, Principia

2016-01-01

The frustule of diatoms, unicellular microalgae, shows very interesting photonic features, generally related to its complicated and quasi-periodic micro- and nano-structure. In order to simulate light propagation inside and through this natural structure, it is important to develop three-dimensional (3D) models for synthetic replica with high spatial resolution. In this paper, we present a new method that generates images of microscopic diatoms with high definition, by merging scanning electron microscopy and digital holography microscopy or atomic force microscopy data. Starting from two digital images, both acquired separately with standard characterization procedures, a high spatial resolution (Δz = λ/20, Δx = Δy ≅ 100 nm, at least) 3D model of the object has been generated. Then, the two sets of data have been processed by matrix formalism, using an original mathematical algorithm implemented on a commercially available software. The developed methodology could be also of broad interest in the design and fabrication of micro-opto-electro-mechanical systems. PMID:27690008

Strong Correlation and Topological States in Orbital-Active Dirac Materials

NASA Astrophysics Data System (ADS)

Xu, Shenglong; Wu, Congjun

Two dimensional Dirac materials, starting with graphene, have drawn tremendous research interests in the past decade. Instead of focusing on the pz orbital as in graphene, we go a step further and study its two orbitals counterpart, namely the px and py orbitals on a honeycomb lattice. The model applies to both optical lattices and several solid state systems including organic material, fluoridated tin film, BiX/SBX (X=H.F.CI.Br). In the band structure, besides the well known Dirac points in the graphene band structure, the orbital degrees of freedom give rise to flat bands as well as quadratic band touching points. These new features provide an even wider playground for searching exotic states of matter. With help of mean field theory and functional renormalization group (FRG) method, we explore the effects of interaction on the system and investigate the consequential interesting states such as ferromagnetism, Wigner crystallization, quantum anomalous Hall states and f-wave superconductivity.

Spun-wrapped aligned nanofiber (SWAN) lithography for fabrication of micro/nano-structures on 3D objects

NASA Astrophysics Data System (ADS)

Ye, Zhou; Nain, Amrinder S.; Behkam, Bahareh

2016-06-01

Fabrication of micro/nano-structures on irregularly shaped substrates and three-dimensional (3D) objects is of significant interest in diverse technological fields. However, it remains a formidable challenge thwarted by limited adaptability of the state-of-the-art nanolithography techniques for nanofabrication on non-planar surfaces. In this work, we introduce Spun-Wrapped Aligned Nanofiber (SWAN) lithography, a versatile, scalable, and cost-effective technique for fabrication of multiscale (nano to microscale) structures on 3D objects without restriction on substrate material and geometry. SWAN lithography combines precise deposition of polymeric nanofiber masks, in aligned single or multilayer configurations, with well-controlled solvent vapor treatment and etching processes to enable high throughput (>10-7 m2 s-1) and large-area fabrication of sub-50 nm to several micron features with high pattern fidelity. Using this technique, we demonstrate whole-surface nanopatterning of bulk and thin film surfaces of cubes, cylinders, and hyperbola-shaped objects that would be difficult, if not impossible to achieve with existing methods. We demonstrate that the fabricated feature size (b) scales with the fiber mask diameter (D) as b1.5 ~ D. This scaling law is in excellent agreement with theoretical predictions using the Johnson, Kendall, and Roberts (JKR) contact theory, thus providing a rational design framework for fabrication of systems and devices that require precisely designed multiscale features.Fabrication of micro/nano-structures on irregularly shaped substrates and three-dimensional (3D) objects is of significant interest in diverse technological fields. However, it remains a formidable challenge thwarted by limited adaptability of the state-of-the-art nanolithography techniques for nanofabrication on non-planar surfaces. In this work, we introduce Spun-Wrapped Aligned Nanofiber (SWAN) lithography, a versatile, scalable, and cost-effective technique for fabrication of multiscale (nano to microscale) structures on 3D objects without restriction on substrate material and geometry. SWAN lithography combines precise deposition of polymeric nanofiber masks, in aligned single or multilayer configurations, with well-controlled solvent vapor treatment and etching processes to enable high throughput (>10-7 m2 s-1) and large-area fabrication of sub-50 nm to several micron features with high pattern fidelity. Using this technique, we demonstrate whole-surface nanopatterning of bulk and thin film surfaces of cubes, cylinders, and hyperbola-shaped objects that would be difficult, if not impossible to achieve with existing methods. We demonstrate that the fabricated feature size (b) scales with the fiber mask diameter (D) as b1.5 ~ D. This scaling law is in excellent agreement with theoretical predictions using the Johnson, Kendall, and Roberts (JKR) contact theory, thus providing a rational design framework for fabrication of systems and devices that require precisely designed multiscale features. Electronic supplementary information (ESI) available: SWAN lithography on silicon; comparison of SWAN lithography and state-of-the-art nanopatterning methods; replica molding using SWAN lithography fabricated template; PDMS nanofluidic device, gold nanopattern characterization. See DOI: 10.1039/c6nr03323g

The development of a center cell structure in bonded aluminum for the Ferrari 408 research vehicle

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

Seeds, A.; Nardini, D.; Cassese, F.

1989-01-01

In F408 research vehicle has enabled Ferrari Engineering to evaluate new forms of transmission, suspension, bodywork and structure for future production vehicles. As Alcan worked with Ferrari Engineering to adapt its Aluminum Structured Vehicle Technology (ASVT) to develop a bonded version of a central section of the structure (center cell). This paper begins with an outline of the major F408 project objectives and indicates the performance and manufacturing advantages for the features of interest, particularly the center cell structure. The paper describes the development stages of the bonded aluminum center cell. It shows that the performance and manufacturing objectives weremore » met with a substantial weight-saving and improvement in stiffness compared to laser-welded stainless steel. The paper concludes with a summary of the other technical innovations and developments in the F408 vehicle.« less

Engineering the electronic structure of graphene superlattices via Fermi velocity modulation

NASA Astrophysics Data System (ADS)

Lima, Jonas R. F.

2017-01-01

Graphene superlattices have attracted much research interest in the last years, since it is possible to manipulate the electronic properties of graphene in these structures. It has been verified that extra Dirac points appear in the electronic structure of the system. The electronic structure in the vicinity of these points has been studied for a gapless and gapped graphene superlattice and for a graphene superlattice with a spatially modulated energy gap. In each case a different behavior was obtained. In this work we show that via Fermi velocity engineering it is possible to tune the electronic properties of a graphene superlattice to match all the previous cases studied. We also obtained new features of the system never observed before, reveling that the electronic structure of graphene is very sensitive to the modulation of the Fermi velocity. The results obtained here are relevant for the development of novel graphene-based electronic devices.

A comparative study of two polymorphs of L-aspartic acid hydrochloride.

PubMed

Benali-Cherif, Rim; Takouachet, Radhwane; Bendeif, El-Eulmi; Benali-Cherif, Nourredine

2014-07-01

Two polymorphs of L-aspartic acid hydrochloride, C4H8NO4(+)·Cl(-), were obtained from the same aqueous solution. Their crystal structures have been determined from single-crystal data collected at 100 K. The crystal structures revealed three- and two-dimensional hydrogen-bonding networks for the triclinic and orthorhombic polymorphs, respectively. The cations and anions are connected to one another via N-H···Cl and O-H···Cl interactions and form alternating cation-anion layer-like structures. The two polymorphs share common structural features; however, the conformations of the L-aspartate cations and the crystal packings are different. Furthermore, the molecular packing of the orthorhombic polymorph contains more interesting interactions which seems to be a favourable factor for more efficient charge transfer within the crystal.

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.

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.

Low-Temperature Synthesis of New Ternary Chalcogenide Compounds of Copper, Gold, and Mercury Using Alkali Metal Polychalcogenide Fluxes

NASA Astrophysics Data System (ADS)

Park, Younbong

In last two decades great efforts have been exerted to find new materials with interesting optical, electrical, and catalytic properties. Metal chalcogenides have been studied extensively because of their interesting physical properties and rich structural chemistry, among the potential materials. Prior to this work, most known metal chalcogenides had been synthesized at high temperature (T > 500^circC). Intermediate temperature synthesis in solid state chemistry was seldom pursued because of the extremely slow diffusion rates between reactants. This intermediate temperature regime could be a new synthesis condition if one looks for new materials with unusual structural features and properties. Metastable or kinetically stable compounds can be stabilized in this intermediate temperature regime, in contrast to the thermodynamically stable high temperature compounds. Molten salts, especially alkali metal polychalcogenide fluxes, can provide a route for exploring new chalcogenide materials at intermediate temperatures. These fluxes are very reactive and melt as low as 145^circC (mp of K_2S_4). Using these fluxes as reaction media, we have encountered many novel chalcogenide compounds with unusual structures and interesting electrical properties (semiconductors to metallic conductors). Low-dimensional polychalcogenide compounds of alpha-ACuQ_4 (A = K, Cs; Q = S, Se), beta -KCuS_4, KAuQ_5 (Q = S, Se), K_3AuSe_ {13}, Na_3AuSe _8, and CsAuSe_3 exhibit the beautiful structural diversity and bonding flexibility of the polychalcogenide ligands. In addition, many novel chalcogenide compounds of Cu, Hg, and Au with low-dimensional structures. The preparation of novel mixed -valence Cu compounds, K_2Cu _5Te_5, Cs _3Cu_8Te_ {10}, Na_3Cu _4Se_4, K _3Cu_8S_4 Te_2, and KCu_4 S_2Te, which show interesting metallic properties, especially underscores the enormous potential of the molten salt method for the synthesis of new chalcogenide materials with interesting physical properties. The materials prepared in this study can be classified as a new class of chalcogenide compounds due to their unique structures. In this dissertation the synthesis, characterization with emphasis on structures, charge transport properties, and magnetic susceptibilities of the materials will be illustrated.

RelFinder: Revealing Relationships in RDF Knowledge Bases

NASA Astrophysics Data System (ADS)

Heim, Philipp; Hellmann, Sebastian; Lehmann, Jens; Lohmann, Steffen; Stegemann, Timo

The Semantic Web has recently seen a rise of large knowledge bases (such as DBpedia) that are freely accessible via SPARQL endpoints. The structured representation of the contained information opens up new possibilities in the way it can be accessed and queried. In this paper, we present an approach that extracts a graph covering relationships between two objects of interest. We show an interactive visualization of this graph that supports the systematic analysis of the found relationships by providing highlighting, previewing, and filtering features.

Constraints on modified gravity models from white dwarfs

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

Banerjee, Srimanta; Singh, Tejinder P.; Shankar, Swapnil, E-mail: srimanta.banerjee@tifr.res.in, E-mail: swapnil.shankar@cbs.ac.in, E-mail: tpsingh@tifr.res.in

Modified gravity theories can introduce modifications to the Poisson equation in the Newtonian limit. As a result, we expect to see interesting features of these modifications inside stellar objects. White dwarf stars are one of the most well studied stars in stellar astrophysics. We explore the effect of modified gravity theories inside white dwarfs. We derive the modified stellar structure equations and solve them to study the mass-radius relationships for various modified gravity theories. We also constrain the parameter space of these theories from observations.

Stereoselective Synthesis of Functionalized Bicyclic Scaffolds by Passerini 3-Center-2-Component Reactions of Cyclic Ketoacids.

PubMed

Cioc, Răzvan C; Estévez, Verónica; van der Niet, Daan J; Vande Velde, Christophe M L; Turrini, Nikolaus G; Hall, Mélanie; Faber, Kurt; Ruijter, Eelco; Orru, Romano V A

2017-03-03

We report the use of bifunctional starting materials (ketoacids) in a diastereoselective Passerini three-center-two-component reaction. Study of the reaction scope revealed the required structural features for stereoselectivity in the isocyanide addition. In this system, an interesting isomerization of the primary Passerini product - the α-carboxamido lactone - into an atypical product, an α-hydroxy imide, was found to occur under acidic conditions. Furthermore, enantioenriched Passerini products can be generated from an enantioenriched ketoacid obtained by chemoenzymatic synthesis.

Synthetic and semi-synthetic chondroitin sulfate oligosaccharides, polysaccharides, and glycomimetics.

PubMed

Bedini, Emiliano; Parrilli, Michelangelo

2012-07-15

Chondroitin sulfate (CS) is a sulfated polysaccharide involved in a myriad of biological processes. Due to the variable sulfation pattern of CS polymer chains, the need to study in detail structure-activity relationships regarding CS biomedical features has provoked much interest in obtaining synthetic CS species. This paper reviews two decades of synthetic and semi-synthetic CS oligosaccharides, polysaccharides, and glycomimetics obtained by chemical, chemoenzymatic, enzymatic, and microbiological-chemical strategies. Copyright © 2012 Elsevier Ltd. All rights reserved.

Binary classification of items of interest in a repeatable process

DOEpatents

Abell, Jeffrey A; Spicer, John Patrick; Wincek, Michael Anthony; Wang, Hui; Chakraborty, Debejyo

2015-01-06

A system includes host and learning machines. Each machine has a processor in electrical communication with at least one sensor. Instructions for predicting a binary quality status of an item of interest during a repeatable process are recorded in memory. The binary quality status includes passing and failing binary classes. The learning machine receives signals from the at least one sensor and identifies candidate features. Features are extracted from the candidate features, each more predictive of the binary quality status. The extracted features are mapped to a dimensional space having a number of dimensions proportional to the number of extracted features. The dimensional space includes most of the passing class and excludes at least 90 percent of the failing class. Received signals are compared to the boundaries of the recorded dimensional space to predict, in real time, the binary quality status of a subsequent item of interest.

Psychopathy and interests: Implications of psychopathic personality traits for vocational and avocational preferences.

PubMed

Nagel, Madeline G; Watts, Ashley L; Murphy, Brett A; Lilienfeld, Scott O

2018-06-21

General personality traits and interests, both vocational and avocational, have long been considered intertwined constructs. Nevertheless, the linkages between personality disorder features, such as psychopathy, and interests are poorly understood. This study bridges this gap by examining how psychopathic traits relate to vocational and avocational interests, and to what extent these associations are distinctive to psychopathy as opposed to a broader pattern of general and abnormal personality traits. In a sample of 426 community participants, Psychopathic Personality Inventory-Revised Fearless Dominance features of psychopathy were associated with interest in a broad swath of vocational and avocational interests, whereas Self-Centered Impulsivity features were associated with realistic, artistic, enterprising, and conventional interests; most zero-order associations were in the small to medium range. Coldheartedness and the factors derived from the Levenson Self-Report Psychopathy Scale were largely unrelated to interests, although there were several notable exceptions. Narcissistic traits, as well as HEXACO (Honesty-Humility, Emotionality, Extraversion, Agreeableness, Conscientiousness, and Openness) Honesty-Humility, Extraversion, and Openness to Experience, were also related broadly to interests. The patterns of interests associated with personality disorder traits may ultimately bear practical implications for interventions as individuals seek out positions or hobbies that suit their traits. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

Feature-Based Statistical Analysis of Combustion Simulation Data

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

Bennett, J; Krishnamoorthy, V; Liu, S

2011-11-18

We present a new framework for feature-based statistical analysis of large-scale scientific data and demonstrate its effectiveness by analyzing features from Direct Numerical Simulations (DNS) of turbulent combustion. Turbulent flows are ubiquitous and account for transport and mixing processes in combustion, astrophysics, fusion, and climate modeling among other disciplines. They are also characterized by coherent structure or organized motion, i.e. nonlocal entities whose geometrical features can directly impact molecular mixing and reactive processes. While traditional multi-point statistics provide correlative information, they lack nonlocal structural information, and hence, fail to provide mechanistic causality information between organized fluid motion and mixing andmore » reactive processes. Hence, it is of great interest to capture and track flow features and their statistics together with their correlation with relevant scalar quantities, e.g. temperature or species concentrations. In our approach we encode the set of all possible flow features by pre-computing merge trees augmented with attributes, such as statistical moments of various scalar fields, e.g. temperature, as well as length-scales computed via spectral analysis. The computation is performed in an efficient streaming manner in a pre-processing step and results in a collection of meta-data that is orders of magnitude smaller than the original simulation data. This meta-data is sufficient to support a fully flexible and interactive analysis of the features, allowing for arbitrary thresholds, providing per-feature statistics, and creating various global diagnostics such as Cumulative Density Functions (CDFs), histograms, or time-series. We combine the analysis with a rendering of the features in a linked-view browser that enables scientists to interactively explore, visualize, and analyze the equivalent of one terabyte of simulation data. We highlight the utility of this new framework for combustion science; however, it is applicable to many other science domains.« less

A reduced amino acid alphabet for understanding and designing protein adaptation to mutation.

PubMed

Etchebest, C; Benros, C; Bornot, A; Camproux, A-C; de Brevern, A G

2007-11-01

Protein sequence world is considerably larger than structure world. In consequence, numerous non-related sequences may adopt similar 3D folds and different kinds of amino acids may thus be found in similar 3D structures. By grouping together the 20 amino acids into a smaller number of representative residues with similar features, sequence world simplification may be achieved. This clustering hence defines a reduced amino acid alphabet (reduced AAA). Numerous works have shown that protein 3D structures are composed of a limited number of building blocks, defining a structural alphabet. We previously identified such an alphabet composed of 16 representative structural motifs (5-residues length) called Protein Blocks (PBs). This alphabet permits to translate the structure (3D) in sequence of PBs (1D). Based on these two concepts, reduced AAA and PBs, we analyzed the distributions of the different kinds of amino acids and their equivalences in the structural context. Different reduced sets were considered. Recurrent amino acid associations were found in all the local structures while other were specific of some local structures (PBs) (e.g Cysteine, Histidine, Threonine and Serine for the alpha-helix Ncap). Some similar associations are found in other reduced AAAs, e.g Ile with Val, or hydrophobic aromatic residues Trp with Phe and Tyr. We put into evidence interesting alternative associations. This highlights the dependence on the information considered (sequence or structure). This approach, equivalent to a substitution matrix, could be useful for designing protein sequence with different features (for instance adaptation to environment) while preserving mainly the 3D fold.

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.

Antibody-protein interactions: benchmark datasets and prediction tools evaluation

PubMed Central

Ponomarenko, Julia V; Bourne, Philip E

2007-01-01

Background The ability to predict antibody binding sites (aka antigenic determinants or B-cell epitopes) for a given protein is a precursor to new vaccine design and diagnostics. Among the various methods of B-cell epitope identification X-ray crystallography is one of the most reliable methods. Using these experimental data computational methods exist for B-cell epitope prediction. As the number of structures of antibody-protein complexes grows, further interest in prediction methods using 3D structure is anticipated. This work aims to establish a benchmark for 3D structure-based epitope prediction methods. Results Two B-cell epitope benchmark datasets inferred from the 3D structures of antibody-protein complexes were defined. The first is a dataset of 62 representative 3D structures of protein antigens with inferred structural epitopes. The second is a dataset of 82 structures of antibody-protein complexes containing different structural epitopes. Using these datasets, eight web-servers developed for antibody and protein binding sites prediction have been evaluated. In no method did performance exceed a 40% precision and 46% recall. The values of the area under the receiver operating characteristic curve for the evaluated methods were about 0.6 for ConSurf, DiscoTope, and PPI-PRED methods and above 0.65 but not exceeding 0.70 for protein-protein docking methods when the best of the top ten models for the bound docking were considered; the remaining methods performed close to random. The benchmark datasets are included as a supplement to this paper. Conclusion It may be possible to improve epitope prediction methods through training on datasets which include only immune epitopes and through utilizing more features characterizing epitopes, for example, the evolutionary conservation score. Notwithstanding, overall poor performance may reflect the generality of antigenicity and hence the inability to decipher B-cell epitopes as an intrinsic feature of the protein. It is an open question as to whether ultimately discriminatory features can be found. PMID:17910770

Manifestly covariant classical correlation dynamics I. General theory

NASA Astrophysics Data System (ADS)

Lin, Shiru; Wang, Yanchao; Chen, Zhongfang

2018-06-01

By means of density functional theory (DFT) computations and particle-swarm optimization (PSO) structure searches, we herein predict five low-lying energy structures of two-dimensional (2D) aluminum monoxide (AlO) nanosheets. Their high cohesive energy, absence of imaginary phonon dispersion, and good thermal stability make them feasible targets for experimental realization. These monolayers exhibit diverse structural topologies, for instance, PmA- and Pmm-AlO possess buckled four- and six-membered AlO rings, whereas P62-, PmB-, and P6 m-AlO have pores of varied sizes. Interestingly, the most energetically preferred monolayers, PmA- and Pmm-AlO, feature wide band gaps (2.45 and 5.13 eV, respectively), which are promising for green and blue light-emitting devices (LEDs) and photodetectors.

An Investigation for Ground State Features of Some Structural Fusion Materials

NASA Astrophysics Data System (ADS)

Aytekin, H.; Tel, E.; Baldik, R.; Aydin, A.

2011-02-01

Environmental concerns associated with fossil fuels are creating increased interest in alternative non-fossil energy sources. Nuclear fusion can be one of the most attractive sources of energy from the viewpoint of safety and minimal environmental impact. When considered in all energy systems, the requirements for performance of structural materials in a fusion reactor first wall, blanket or diverter, are arguably more demanding or difficult than for other energy system. The development of fusion materials for the safety of fusion power systems and understanding nuclear properties is important. In this paper, ground state properties for some structural fusion materials as 27Al, 51V, 52Cr, 55Mn, and 56Fe are investigated using Skyrme-Hartree-Fock method. The obtained results have been discussed and compared with the available experimental data.

Planar optics with patterned chiral liquid crystals

NASA Astrophysics Data System (ADS)

Kobashi, Junji; Yoshida, Hiroyuki; Ozaki, Masanori

2016-06-01

Reflective metasurfaces based on metallic and dielectric nanoscatterers have attracted interest owing to their ability to control the phase of light. However, because such nanoscatterers require subwavelength features, the fabrication of elements that operate in the visible range is challenging. Here, we show that chiral liquid crystals with a self-organized helical structure enable metasurface-like, non-specular reflection in the visible region. The phase of light that is Bragg-reflected off the helical structure can be controlled over 0-2π depending on the spatial phase of the helical structure; thus planar elements with arbitrary reflected wavefronts can be created via orientation control. The circular polarization selectivity and external field tunability of Bragg reflection open a wide variety of potential applications for this family of functional devices, from optical isolators to wearable displays.

Classifying Structures in the ISM with Machine Learning Techniques

NASA Astrophysics Data System (ADS)

Beaumont, Christopher; Goodman, A. A.; Williams, J. P.

2011-01-01

The processes which govern molecular cloud evolution and star formation often sculpt structures in the ISM: filaments, pillars, shells, outflows, etc. Because of their morphological complexity, these objects are often identified manually. Manual classification has several disadvantages; the process is subjective, not easily reproducible, and does not scale well to handle increasingly large datasets. We have explored to what extent machine learning algorithms can be trained to autonomously identify specific morphological features in molecular cloud datasets. We show that the Support Vector Machine algorithm can successfully locate filaments and outflows blended with other emission structures. When the objects of interest are morphologically distinct from the surrounding emission, this autonomous classification achieves >90% accuracy. We have developed a set of IDL-based tools to apply this technique to other datasets.

Review on Material Synthesis and Characterization of Sodium (Na) Super-Ionic Conductor (NASICON)

NASA Astrophysics Data System (ADS)

Kimpa, M. I.; Mayzan, M. Z. H.; Yabagi, J. A.; Nmaya, M. M.; Isah, K. U.; Agam, M. A.

2018-04-01

Sodium (Na) Super Ionic Conductor (NASICON) has general formula Na1+ x Zr2P3- xSi x O12 (0 ≤x ≤ 3) derived from its parent compound, sodium zirconium phosphate NaZr2(PO4)3 (NZP) which belong to a rhombohedral crystal structure. This material consists of three-dimensional structure with interesting features such as low thermal expansion coefficient, thermal stability, gas sensor and nuclear waste immobilization that make it viable for industrial applications. Current study presents comprehensive studies on the synthesis and essential characteristics required to understand the theory behind the mechanism that justifies the study of NASICON structure and its application such as lithium ion rechargeable battery, gas sensor, and nuclear waste immobilization and so on.

Structural sensitivity of x-ray Bragg projection ptychography to domain patterns in epitaxial thin films

DOE PAGES

Hruszkewycz, S. O.; Zhang, Q.; Holt, M. V.; ...

2016-10-04

Bragg projection ptychography (BPP) is a coherent diffraction imaging technique capable of mapping the spatial distribution of the Bragg structure factor in nanostructured thin films. Here, we show that, because these images are projections, the structural sensitivity of the resulting images depends on the film thickness and the aspect ratio and orientation of the features of interest and that image interpretation depends on these factors. Lastly, we model changes in contrast in the BPP reconstructions of simulated PbTiO 3 ferroelectric thin films with meandering 180° stripe domains as a function of film thickness, discuss their origin, and comment on themore » implication of these factors on the design of BPP experiments of general nanostructured films.« less

A quark model analysis of the transversity distribution

NASA Astrophysics Data System (ADS)

Scopetta, Sergio; Vento, Vicente

1998-04-01

The feasibility of measuring chiral-odd parton distribution functions in polarized Drell-Yan and semi-inclusive experiments has renewed theoretical interest in their study. Models of hadron structure have proven successful in describing the gross features of the chiral-even structure functions. Similar expectations motivated our study of the transversity parton distributions in the Isgur-Karl and MIT bag models. We confirm, by performing a NLO calculation, the diverse low x behaviors of the transversity and spin structure functions at the experimental scale and show that it is fundamentally a consequence of the different behaviors under evolution of these functions. The inequalities of Soffer establish constraints between data and model calculations of the chiral-odd transversity function. The approximate compatibility of our model calculations with these constraints confers credibility to our estimates.

A structural route to tuning the orbital structure of nickelates

NASA Astrophysics Data System (ADS)

Kumah, Divine; Disa, Ankit; Malashevich, Andrei; Chen, Hanghui; Ismail-Beigi, Sohrab; Walker, Fred; Ahn, Charles

2014-03-01

The rare-earth nickelates display a range of interesting magnetic and electronic phenomena arising from the strong coupling of the atomic-scale structural properties of these systems to the charge and orbital degrees of freedom. We report on modifying the orbital polarization in nickelate based heterostructures, motivated by the goal of emulating high-Tc cuprate behavior in the nickelates. Using a combination of synchrotron diffraction structural and spectroscopic characterization and first principles theory, we show how the design of a structure that splits the relative electronic occupation of Ni d x2-y2 and Ni d 3z2-r2 orbitals, is achieved in three-component heterostructures. These structures are comprised of LaTiO3/LaNiO3/LaAlO3 and are grown using molecular beam epitaxy. The key features of the theoretically proposed structure, including an internal polar field, a electron transfer from Ti to Ni, and a orbital polarization of the Ni-eg states, are experimentally studied.

Time to face the fats: what can mass spectrometry reveal about the structure of lipids and their interactions with proteins?

PubMed

Brown, Simon H J; Mitchell, Todd W; Oakley, Aaron J; Pham, Huong T; Blanksby, Stephen J

2012-09-01

Since the 1950s, X-ray crystallography has been the mainstay of structural biology, providing detailed atomic-level structures that continue to revolutionize our understanding of protein function. From recent advances in this discipline, a picture has emerged of intimate and specific interactions between lipids and proteins that has driven renewed interest in the structure of lipids themselves and raised intriguing questions as to the specificity and stoichiometry in lipid-protein complexes. Herein we demonstrate some of the limitations of crystallography in resolving critical structural features of ligated lipids and thus determining how these motifs impact protein binding. As a consequence, mass spectrometry must play an important and complementary role in unraveling the complexities of lipid-protein interactions. We evaluate recent advances and highlight ongoing challenges towards the twin goals of (1) complete structure elucidation of low, abundant, and structurally diverse lipids by mass spectrometry alone, and (2) assignment of stoichiometry and specificity of lipid interactions within protein complexes.

Time to Face the Fats: What Can Mass Spectrometry Reveal about the Structure of Lipids and Their Interactions with Proteins?

NASA Astrophysics Data System (ADS)

Brown, Simon H. J.; Mitchell, Todd W.; Oakley, Aaron J.; Pham, Huong T.; Blanksby, Stephen J.

2012-09-01

Since the 1950s, X-ray crystallography has been the mainstay of structural biology, providing detailed atomic-level structures that continue to revolutionize our understanding of protein function. From recent advances in this discipline, a picture has emerged of intimate and specific interactions between lipids and proteins that has driven renewed interest in the structure of lipids themselves and raised intriguing questions as to the specificity and stoichiometry in lipid-protein complexes. Herein we demonstrate some of the limitations of crystallography in resolving critical structural features of ligated lipids and thus determining how these motifs impact protein binding. As a consequence, mass spectrometry must play an important and complementary role in unraveling the complexities of lipid-protein interactions. We evaluate recent advances and highlight ongoing challenges towards the twin goals of (1) complete structure elucidation of low, abundant, and structurally diverse lipids by mass spectrometry alone, and (2) assignment of stoichiometry and specificity of lipid interactions within protein complexes.

Density functional theory for prediction of far-infrared vibrational frequencies: molecular crystals of astrophysical interest

NASA Astrophysics Data System (ADS)

Ennis, C.; Auchettl, R.; Appadoo, D. R. T.; Robertson, E. G.

2017-11-01

Solid-state density functional theory code has been implemented for the structure optimization of crystalline methanol, acetaldehyde and acetic acid and for the calculation of infrared frequencies. The results are compared to thin film spectra obtained from low-temperature experiments performed at the Australian Synchrotron. Harmonic frequency calculations of the internal modes calculated at the B3LYP-D3/m-6-311G(d) level shows higher deviation from infrared experiment than more advanced theory applied to the gas phase. Importantly for the solid-state, the simulation of low-frequency molecular lattice modes closely resembles the observed far-infrared features after application of a 0.92 scaling factor. This allowed experimental peaks to be assigned to specific translation and libration modes, including acetaldehyde and acetic acid lattice features for the first time. These frequency calculations have been performed without the need for supercomputing resources that are required for large molecular clusters using comparable levels of theory. This new theoretical approach will find use for the rapid characterization of intermolecular interactions and bonding in crystals, and the assignment of far-infrared spectra for crystalline samples such as pharmaceuticals and molecular ices. One interesting application may be for the detection of species of prebiotic interest on the surfaces of Kuiper-Belt and Trans-Neptunian Objects. At such locations, the three small organic molecules studied here could reside in their crystalline phase. The far-infrared spectra for their low-temperature solid phases are collected under planetary conditions, allowing us to compile and assign their most intense spectral features to assist future far-infrared surveys of icy Solar system surfaces.

Closed-Loop Process Control for Electron Beam Freeform Fabrication and Deposition Processes

NASA Technical Reports Server (NTRS)

Taminger, Karen M. (Inventor); Hofmeister, William H. (Inventor); Martin, Richard E. (Inventor); Hafley, Robert A. (Inventor)

2013-01-01

A closed-loop control method for an electron beam freeform fabrication (EBF(sup 3)) process includes detecting a feature of interest during the process using a sensor(s), continuously evaluating the feature of interest to determine, in real time, a change occurring therein, and automatically modifying control parameters to control the EBF(sup 3) process. An apparatus provides closed-loop control method of the process, and includes an electron gun for generating an electron beam, a wire feeder for feeding a wire toward a substrate, wherein the wire is melted and progressively deposited in layers onto the substrate, a sensor(s), and a host machine. The sensor(s) measure the feature of interest during the process, and the host machine continuously evaluates the feature of interest to determine, in real time, a change occurring therein. The host machine automatically modifies control parameters to the EBF(sup 3) apparatus to control the EBF(sup 3) process in a closed-loop manner.

3D Texture Features Mining for MRI Brain Tumor Identification

NASA Astrophysics Data System (ADS)

Rahim, Mohd Shafry Mohd; Saba, Tanzila; Nayer, Fatima; Syed, Afraz Zahra

2014-03-01

Medical image segmentation is a process to extract region of interest and to divide an image into its individual meaningful, homogeneous components. Actually, these components will have a strong relationship with the objects of interest in an image. For computer-aided diagnosis and therapy process, medical image segmentation is an initial mandatory step. Medical image segmentation is a sophisticated and challenging task because of the sophisticated nature of the medical images. Indeed, successful medical image analysis heavily dependent on the segmentation accuracy. Texture is one of the major features to identify region of interests in an image or to classify an object. 2D textures features yields poor classification results. Hence, this paper represents 3D features extraction using texture analysis and SVM as segmentation technique in the testing methodologies.

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.

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.

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

Roth, Friedrich, E-mail: Friedrich.Roth@cfel.de; Knupfer, Martin, E-mail: M.Knupfer@ifw-dresden.de

We report the doping induced changes of the electronic structure of tetracene and pentacene probed by electron energy-loss spectroscopy in transmission. A comparison between the dynamic response of undoped and potassium-intercalated tetracene and pentacene emphasizes the appearance of a new excitation feature in the former gap upon potassium addition. Interestingly, the momentum dependency of this new excitation shows a negative dispersion. Moreover, the analysis of the C 1s and K 2p core-level excitation results in a significantly lower doping level compared to potassium doped picene, a recently discovered superconductor. Therefore, the present electronic structure investigations open a new pathway to better understandmore » the exceptional differences between acenes and phenacene and their divergent behavior upon alkali doping.« less

Femtosecond laser-induced ripple patterns for homogenous nanostructuring of pyrolytic carbon heart valve implant

NASA Astrophysics Data System (ADS)

Stępak, Bogusz; Dzienny, Paulina; Franke, Volker; Kunicki, Piotr; Gotszalk, Teodor; Antończak, Arkadiusz

2018-04-01

Laser-induced periodic surface structures (LIPSS) are highly periodic wavy surface features which are frequently smaller than incident light wavelength that bring possibility of nanostructuring of many materials. In this paper the possibility of using them to homogeneously structure the surface of artificial heart valve made of PyC was examined. By changing laser irradiation parameters such like energy density and pulse separation the most suitable conditions were established for 1030 nm wavelength. A wide spectrum of periodicities and geometries was obtained. Interesting side effects like creating a thin shell-like layer were observed. Modified surfaces were examined using EDX and Raman spectroscopy to determine change in elemental composition of surface.

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.

Modeling shape and topology of low-resolution density maps of biological macromolecules.

PubMed Central

De-Alarcón, Pedro A; Pascual-Montano, Alberto; Gupta, Amarnath; Carazo, Jose M

2002-01-01

In the present work we develop an efficient way of representing the geometry and topology of volumetric datasets of biological structures from medium to low resolution, aiming at storing and querying them in a database framework. We make use of a new vector quantization algorithm to select the points within the macromolecule that best approximate the probability density function of the original volume data. Connectivity among points is obtained with the use of the alpha shapes theory. This novel data representation has a number of interesting characteristics, such as 1) it allows us to automatically segment and quantify a number of important structural features from low-resolution maps, such as cavities and channels, opening the possibility of querying large collections of maps on the basis of these quantitative structural features; 2) it provides a compact representation in terms of size; 3) it contains a subset of three-dimensional points that optimally quantify the densities of medium resolution data; and 4) a general model of the geometry and topology of the macromolecule (as opposite to a spatially unrelated bunch of voxels) is easily obtained by the use of the alpha shapes theory. PMID:12124252

Network motif frequency vectors reveal evolving metabolic network organisation.

PubMed

Pearcy, Nicole; Crofts, Jonathan J; Chuzhanova, Nadia

2015-01-01

At the systems level many organisms of interest may be described by their patterns of interaction, and as such, are perhaps best characterised via network or graph models. Metabolic networks, in particular, are fundamental to the proper functioning of many important biological processes, and thus, have been widely studied over the past decade or so. Such investigations have revealed a number of shared topological features, such as a short characteristic path-length, large clustering coefficient and hierarchical modular structure. However, the extent to which evolutionary and functional properties of metabolism manifest via this underlying network architecture remains unclear. In this paper, we employ a novel graph embedding technique, based upon low-order network motifs, to compare metabolic network structure for 383 bacterial species categorised according to a number of biological features. In particular, we introduce a new global significance score which enables us to quantify important evolutionary relationships that exist between organisms and their physical environments. Using this new approach, we demonstrate a number of significant correlations between environmental factors, such as growth conditions and habitat variability, and network motif structure, providing evidence that organism adaptability leads to increased complexities in the resultant metabolic networks.

Genotype-environment interaction and sociology: contributions and complexities.

PubMed

Seabrook, Jamie A; Avison, William R

2010-05-01

Genotype-environment interaction (G x E) refers to situations in which genetic effects connected to a phenotype are dependent upon variability in the environment, or when genes modify an organism's sensitivity to particular environmental features. Using a typology suggested in the G x E literature, we provide an overview of recent papers that show how social context can trigger a genetic vulnerability, compensate for a genetic vulnerability, control behaviors for which a genetic vulnerability exists, and improve adaptation via proximal causes. We argue that to improve their understanding of social structure, sociologists can take advantage of research in behavior genetics by assessing the impact of within-group variance of various health outcomes and complex human behaviors that are explainable by genotype, environment and their interaction. Insights from life course sociology can aid in ensuring that the dynamic nature of the environment in G x E has been accounted for. Identification of an appropriate entry point for sociologists interested in G x E research could begin with the choice of an environmental feature of interest, a genetic factor of interest, and/or behavior of interest. Optimizing measurement in order to capture the complexity of G x E is critical. Examining the interaction between poorly measured environmental factors and well measured genetic variables will overestimate the effects of genetic variables while underestimating the effect of environmental influences, thereby distorting the interaction between genotype and environment. Although the expense of collecting environmental data is very high, reliable and precise measurement of an environmental pathogen enhances a study's statistical power. Copyright 2010 Elsevier Ltd. All rights reserved.

Prostate segmentation in MR images using discriminant boundary features.

PubMed

Yang, Meijuan; Li, Xuelong; Turkbey, Baris; Choyke, Peter L; Yan, Pingkun

2013-02-01

Segmentation of the prostate in magnetic resonance image has become more in need for its assistance to diagnosis and surgical planning of prostate carcinoma. Due to the natural variability of anatomical structures, statistical shape model has been widely applied in medical image segmentation. Robust and distinctive local features are critical for statistical shape model to achieve accurate segmentation results. The scale invariant feature transformation (SIFT) has been employed to capture the information of the local patch surrounding the boundary. However, when SIFT feature being used for segmentation, the scale and variance are not specified with the location of the point of interest. To deal with it, the discriminant analysis in machine learning is introduced to measure the distinctiveness of the learned SIFT features for each landmark directly and to make the scale and variance adaptive to the locations. As the gray values and gradients vary significantly over the boundary of the prostate, separate appearance descriptors are built for each landmark and then optimized. After that, a two stage coarse-to-fine segmentation approach is carried out by incorporating the local shape variations. Finally, the experiments on prostate segmentation from MR image are conducted to verify the efficiency of the proposed algorithms.

Model-Free Conditional Independence Feature Screening For Ultrahigh Dimensional Data.

PubMed

Wang, Luheng; Liu, Jingyuan; Li, Yong; Li, Runze

2017-03-01

Feature screening plays an important role in ultrahigh dimensional data analysis. This paper is concerned with conditional feature screening when one is interested in detecting the association between the response and ultrahigh dimensional predictors (e.g., genetic makers) given a low-dimensional exposure variable (such as clinical variables or environmental variables). To this end, we first propose a new index to measure conditional independence, and further develop a conditional screening procedure based on the newly proposed index. We systematically study the theoretical property of the proposed procedure and establish the sure screening and ranking consistency properties under some very mild conditions. The newly proposed screening procedure enjoys some appealing properties. (a) It is model-free in that its implementation does not require a specification on the model structure; (b) it is robust to heavy-tailed distributions or outliers in both directions of response and predictors; and (c) it can deal with both feature screening and the conditional screening in a unified way. We study the finite sample performance of the proposed procedure by Monte Carlo simulations and further illustrate the proposed method through two real data examples.

A Local DCT-II Feature Extraction Approach for Personal Identification Based on Palmprint

NASA Astrophysics Data System (ADS)

Choge, H. Kipsang; Oyama, Tadahiro; Karungaru, Stephen; Tsuge, Satoru; Fukumi, Minoru

Biometric applications based on the palmprint have recently attracted increased attention from various researchers. In this paper, a method is presented that differs from the commonly used global statistical and structural techniques by extracting and using local features instead. The middle palm area is extracted after preprocessing for rotation, position and illumination normalization. The segmented region of interest is then divided into blocks of either 8×8 or 16×16 pixels in size. The type-II Discrete Cosine Transform (DCT) is applied to transform the blocks into DCT space. A subset of coefficients that encode the low to medium frequency components is selected using the JPEG-style zigzag scanning method. Features from each block are subsequently concatenated into a compact feature vector and used in palmprint verification experiments with palmprints from the PolyU Palmprint Database. Results indicate that this approach achieves better results than many conventional transform-based methods, with an excellent recognition accuracy above 99% and an Equal Error Rate (EER) of less than 1.2% in palmprint verification.

Towards physical implementation of an optical add-drop multiplexer (OADM) based upon properties of 12-fold photonic quasicrystals

NASA Astrophysics Data System (ADS)

Gauthier, Robert C.; Mnaymneh, Khaled

2005-09-01

The key feature that gives photonic crystals (PhCs) their ability to form photonic band gaps (PBGs) analogous to electronic band gaps of semiconductors is their translation symmetries. In recent years, however, it has been found that structures that possess only rotational symmetries can also have PBGs. In addition, these structures, known as Photonic Quasicrystals (PhQs), have other interesting qualities that set them apart of their translational cousins. One interesting feature is how defect states can be created in PhQs. If the rotational symmetry is disturbed, defect states analogous to defects states that are created in PhCs can be obtained. Simulation results of these defect states and other propagation properties of planar 12-fold photonic quasicrystal patterns, and its physical implementations in Silicon-On-Insulator (SOI) are presented. The main mechanisms required to make any optical multiplexing system is propagation; stop bands and add/drop ports. With the rotationally symmetry of the PhQ causing the stop bands, line defects facilitating propagation and now these specially design defect states acting as add/drop ports, a physical implementation of an OADM can be presented. Theoretical, practical and manufacturing benefits of PhQs are discussed. Simulated transmission plots are shown for various fill factors, dielectric contrast and propagation direction. It is shown that low index waveguides can be produced using the quasi-crystal photonic crystal pattern. Fabrication steps and results are shown.

User preferences for a text message-based smoking cessation intervention.

PubMed

Bock, Beth C; Heron, Kristin E; Jennings, Ernestine G; Magee, Joshua C; Morrow, Kathleen M

2013-04-01

Younger adults are more likely to smoke and less likely to seek treatment than older smokers. They are also frequent users of communication technology. In the current study, we conducted focus groups to obtain feedback about preferences for a text message-based smoking cessation program from potential users. Participants (N = 21, M age = 25.6 years, age range = 20-33 years) were current or recently quit smokers (M cigarettes/day = 12.8) who used text messaging. Participants completed questionnaires and participated in a 2-hour focus group. Focus groups were conducted using an a priori semistructured interview guide to promote discussion of the content and functionality of the intervention. Major themes from analysis of the focus groups included support for the acceptability of a text-based cessation program, suggestions for a more technologically broad-based program, and adjustments to the program structure. Participants recommended including social networking functions, user control of program output through an online profile, and text message features to promote interaction with the system. Interestingly, many participants suggested the program should begin on individuals' identified quit day, challenging the procedures used in most cessation programs, which begin by preparing participants for a future quit date. Overall, younger adult smokers appear to be interested in participating in a smoking cessation program that uses text messages and web-based elements. Qualitative feedback regarding the perceived optimal features and structure of a technology-based intervention challenged traditional methods of implementing smoking cessation interventions and will inform the development of future programs.

Very high resolution Earth observation features for monitoring plant and animal community structure across multiple spatial scales in protected areas

NASA Astrophysics Data System (ADS)

Mairota, Paola; Cafarelli, Barbara; Labadessa, Rocco; Lovergine, Francesco; Tarantino, Cristina; Lucas, Richard M.; Nagendra, Harini; Didham, Raphael K.

2015-05-01

Monitoring the status and future trends in biodiversity can be prohibitively expensive using ground-based surveys. Consequently, significant effort is being invested in the use of satellite remote sensing to represent aspects of the proximate mechanisms (e.g., resource availability) that can be related to biodiversity surrogates (BS) such as species community descriptors. We explored the potential of very high resolution (VHR) satellite Earth observation (EO) features as proxies for habitat structural attributes that influence spatial variation in habitat quality and biodiversity change. In a semi-natural grassland mosaic of conservation concern in southern Italy, we employed a hierarchical nested sampling strategy to collect field and VHR-EO data across three spatial extent levels (landscape, patch and plot). Species incidence and abundance data were collected at the plot level for plant, insect and bird functional groups. Spectral and textural VHR-EO image features were derived from a Worldview-2 image. Three window sizes (grains) were tested for analysis and computation of textural features, guided by the perception limits of different organisms. The modelled relationships between VHR-EO features and BS responses differed across scales, suggesting that landscape, patch and plot levels are respectively most appropriate when dealing with birds, plants and insects. This research demonstrates the potential of VHR-EO for biodiversity mapping and habitat modelling, and highlights the importance of identifying the appropriate scale of analysis for specific taxonomic groups of interest. Further, textural features are important in the modelling of functional group-specific indices which represent BS in high conservation value habitat types, and provide a more direct link to species interaction networks and ecosystem functioning, than provided by traditional taxonomic diversity indices.

Classification of Alzheimer's disease and prediction of mild cognitive impairment-to-Alzheimer's conversion from structural magnetic resource imaging using feature ranking and a genetic algorithm.

PubMed

Beheshti, Iman; Demirel, Hasan; Matsuda, Hiroshi

2017-04-01

We developed a novel computer-aided diagnosis (CAD) system that uses feature-ranking and a genetic algorithm to analyze structural magnetic resonance imaging data; using this system, we can predict conversion of mild cognitive impairment (MCI)-to-Alzheimer's disease (AD) at between one and three years before clinical diagnosis. The CAD system was developed in four stages. First, we used a voxel-based morphometry technique to investigate global and local gray matter (GM) atrophy in an AD group compared with healthy controls (HCs). Regions with significant GM volume reduction were segmented as volumes of interest (VOIs). Second, these VOIs were used to extract voxel values from the respective atrophy regions in AD, HC, stable MCI (sMCI) and progressive MCI (pMCI) patient groups. The voxel values were then extracted into a feature vector. Third, at the feature-selection stage, all features were ranked according to their respective t-test scores and a genetic algorithm designed to find the optimal feature subset. The Fisher criterion was used as part of the objective function in the genetic algorithm. Finally, the classification was carried out using a support vector machine (SVM) with 10-fold cross validation. We evaluated the proposed automatic CAD system by applying it to baseline values from the Alzheimer's Disease Neuroimaging Initiative (ADNI) dataset (160 AD, 162 HC, 65 sMCI and 71 pMCI subjects). The experimental results indicated that the proposed system is capable of distinguishing between sMCI and pMCI patients, and would be appropriate for practical use in a clinical setting. Copyright © 2017 Elsevier Ltd. All rights reserved.

3D Seismic Interpretation of a Plio-Pleistocene Mass Transport Deposit in the Deepwater Taranaki Basin of New Zealand

NASA Astrophysics Data System (ADS)

Rusconi, Francisco Jose

A series of Plio-Pleistocene mass transport deposits (MTD) have been identified in the deepwater Taranaki Basin, in New Zealand, using the Romney 3D seismic survey, which covers an area of approximately 2000 km2. One of these MTDs has been chosen for description and interpretation based on high confidence mapping of its boundary surfaces. The deposit exhibits an array of interesting features similar to those documented by researchers elsewhere plus a unique basal feature unlike those previously observed. The basal shear surface exhibits erosional features such as grooves, "monkey fingers", and glide tracks. Internally, the MTD is typically characterized by low impedance, chaotic, semi-transparent reflectors surrounding isolated coherent packages of seismic facies interpreted as intact blocks rafted within the mass transport complex. Distally, the deposit presents outrunner blocks and pressure ridges. The new element described in this work consists of a composite feature that includes a protruding obstacle ("shield block") on the paleo-seafloor that acted as a barrier to subsequent flows as they advanced downslope. These blocks disrupt the incoming flow and result in elongate, downflow negative features ("erosional shadow scours"), which are then infilled by the mass transport deposit, and are preserved as elongate isochore thicks. Kinematic evidence provided by various structures suggests that the MTD flow direction was SE-NW toward bathyal depths. The features presented and the absence of extensional headwall structures, such as local arcuate glide planes and rotated slide blocks, suggest that this part of the deposit belongs to the translational to distal domain of the MTD, and its source area is expected to be somewhere toward the SE in a paleo continental slope.

The Cutplane - A tool for interactive solid modeling

NASA Technical Reports Server (NTRS)

Edwards, Laurence; Kessler, William; Leifer, Larry

1988-01-01

A geometric modeling system which incorporates a new concept for intuitively and unambiguously specifying and manipulating points or features in three dimensional space is presented. The central concept, the Cutplane, consists of a plane that moves through space under control of a mouse or similar input device. The intersection of the plane and any object is highlighted, and only this highlighted section can be selected for manipulation. Selection is accomplished with a crosshair that is constrained to remain within the plane, so that the relationship between the crosshair and the feature of interest is immediately evident. Although the idea of a section view is not new, previously it has been used as a way to reveal hidden structure, not as a means of manipulating objects or indicating spatial position, as is proposed here.

Identifying significant environmental features using feature recognition.

DOT National Transportation Integrated Search

2015-10-01

The Department of Environmental Analysis at the Kentucky Transportation Cabinet has expressed an interest in feature-recognition capability because it may help analysts identify environmentally sensitive features in the landscape, : including those r...

SU-F-R-18: Updates to the Computational Environment for Radiological Research for Image Analysis

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

Apte, Aditya P.; Deasy, Joseph O.

2016-06-15

Purpose: To present new tools in CERR for Texture Analysis and Visualization. Method: (1) Quantitative Image Analysis: We added the ability to compute Haralick texture features based on local neighbourhood. The Texture features depend on many parameters used in their derivation. For example: (a) directionality, (b) quantization of image, (c) patch-size for the neighborhood, (d) handling of the edge voxels within the region of interest, (e) Averaging co-occurance matrix vs texture features for different directions etc. A graphical user interface was built to set these parameters and then visualize their impact on the resulting texture maps. The entire functionality wasmore » written in Matlab. Array indexing was used to speed up the texture calculation. The computation speed is very competitive with the ITK library. Moreover, our implementation works with multiple CPUs and the computation time can be further reduced by using multiple processor threads. In order to reduce the Haralick texture maps into scalar features, we propose the use of Texture Volume Histograms. This lets users make use of the entire distribution of texture values within the region of interest rather than using just the mean and the standard deviations. (2) Qualitative/Visualization tools: The derived texture maps are stored as a new scan (derived) within CERR’s planC data structure. A display that compares various scans was built to show the raw image and the derived texture maps side-by-side. These images are positionally linked and can be navigated together. CERR’s graphics handling was updated and sped-up to be compatible with the newer Matlab versions. As a result, the users can use (a) different window levels and colormaps for different viewports, (b) click-and-drag or use mouse scroll-wheel to navigate slices. Results: The new features and updates are available via https://www.github.com/adityaapte/cerr . Conclusion: Features added to CERR increase its utility in Radiomics and Outcomes modeling.« less

Generation algorithm of craniofacial structure contour in cephalometric images

NASA Astrophysics Data System (ADS)

Mondal, Tanmoy; Jain, Ashish; Sardana, H. K.

2010-02-01

Anatomical structure tracing on cephalograms is a significant way to obtain cephalometric analysis. Computerized cephalometric analysis involves both manual and automatic approaches. The manual approach is limited in accuracy and repeatability. In this paper we have attempted to develop and test a novel method for automatic localization of craniofacial structure based on the detected edges on the region of interest. According to the grey scale feature at the different region of the cephalometric images, an algorithm for obtaining tissue contour is put forward. Using edge detection with specific threshold an improved bidirectional contour tracing approach is proposed by an interactive selection of the starting edge pixels, the tracking process searches repetitively for an edge pixel at the neighborhood of previously searched edge pixel to segment images, and then craniofacial structures are obtained. The effectiveness of the algorithm is demonstrated by the preliminary experimental results obtained with the proposed method.

Basaltic Ring Structures as an Analog for Ring Features in Athabasca Valles, Mars

NASA Technical Reports Server (NTRS)

Jaeger, W. L.; Keszthelyi, L. P.; Burr, D. M.; Emery, J. P.; Baker, V. R.; McEwen, A. S.; Miyamoto, H.

2005-01-01

Basaltic ring structures (BRSs) are enigmatic, quasi-circular landforms in eastern Washington State that were first recognized in 1965. They remained a subject of geologic scrutiny through the 1970 s and subsequently faded from the spotlight, but recent Mars Orbiter Camera (MOC) images showing morphologically similar structures in Athabasca Valles, Mars, have sparked renewed interest in BRSs. The only known BRSs occur in the Channeled Scabland, a region where catastrophic Pleistocene floods from glacial Lake Missoula eroded into the Miocene flood basalts of the Columbia Plateau. The geologic setting of the martian ring structures (MRSs) is similar; Athabasca Valles is a young channel system that formed when catastrophic aqueous floods carved into a volcanic substrate. This study investigates the formation of terrestrial BRSs and examines the extent to which they are appropriate analogs for the MRSs in Athabasca Valles.

Structure Elucidation of Coxsackievirus A16 in Complex with GPP3 Informs a Systematic Review of Highly Potent Capsid Binders to Enteroviruses.

PubMed

De Colibus, Luigi; Wang, Xiangxi; Tijsma, Aloys; Neyts, Johan; Spyrou, John A B; Ren, Jingshan; Grimes, Jonathan M; Puerstinger, Gerhard; Leyssen, Pieter; Fry, Elizabeth E; Rao, Zihe; Stuart, David I

2015-10-01

The replication of enterovirus 71 (EV71) and coxsackievirus A16 (CVA16), which are the major cause of hand, foot and mouth disease (HFMD) in children, can be inhibited by the capsid binder GPP3. Here, we present the crystal structure of CVA16 in complex with GPP3, which clarifies the role of the key residues involved in interactions with the inhibitor. Based on this model, in silico docking was performed to investigate the interactions with the two next-generation capsid binders NLD and ALD, which we show to be potent inhibitors of a panel of enteroviruses with potentially interesting pharmacological properties. A meta-analysis was performed using the available structural information to obtain a deeper insight into those structural features required for capsid binders to interact effectively and also those that confer broad-spectrum anti-enterovirus activity.

Momentum-based morphometric analysis with application to Parkinson's disease

NASA Astrophysics Data System (ADS)

Chen, Jingyun; Khan, Ali R.; McKeown, Martin J.; Beg, Mirza F.

2011-03-01

We apply the initial momentum shape representation of diffeomorphic metric mapping from a template region of interest (ROI) to a given ROI as a morphometic marker in Parkinson's disease. We used a three-step segmentation-registrationmomentum process to derive feature vectors from ROIs in a group of 42 subjects consisting of 19 Parkinson's Disease (PD) subjects and 23 normal control (NC) subjects. Significant group differences between PD and NC subjects were detected in four basal ganglia structures including the caudate, putamen, thalamus and globus pallidus. The magnitude of regionally significant between-group differences detected ranged between 34-75%. Visualization of the different structural deformation pattern between-groups revealed that some parts of basal ganglia structure actually hypertrophy, presumably as a compensatory response to more widespread atrophy. Our results of both hypertrophy and atrophy in the same structures further demonstrate the importance of morphological measures as opposed to overall volume in the assessment of neurodegenerative disease.

Shock-absorbing and failure mechanisms of WS2 and MoS2 nanoparticles with fullerene-like structures under shock wave pressure.

PubMed

Zhu, Yan Qiu; Sekine, Toshimori; Li, Yan Hui; Fay, Michael W; Zhao, Yi Min; Patrick Poa, C H; Wang, Wen Xin; Roe, Martin J; Brown, Paul D; Fleischer, Niles; Tenne, Reshef

2005-11-23

The excellent shock-absorbing performance of WS2 and MoS2 nanoparticles with inorganic fullerene-like structures (IFs) under very high shock wave pressures of 25 GPa is described. The combined techniques of X-ray diffraction, Raman spectroscopy, X-ray photoelectron spectroscopy, thermal analysis, and transmission electron microscopy have been used to evaluate the diverse, intriguing features of shock recovered IFs, of interest for their tribological applications, thereby allowing improved understanding of their antishock behavior and structure-property relationships. Two possible failure mechanisms are proposed and discussed. The supershock-absorbing ability of the IF-WS2 enables them to survive pressures up to 25 GPa accompanied with concurrent temperatures of up to 1000 degrees C without any significant structural degradation or phase change making them probably the strongest cage molecules now known.

Resonances and bound states in the continuum on periodic arrays of slightly noncircular cylinders

NASA Astrophysics Data System (ADS)

Hu, Zhen; Lu, Ya Yan

2018-02-01

Optical bound states in the continuum (BICs), especially those on periodic structures, have interesting properties and potentially important applications. Existing theoretical and numerical studies for optical BICs are mostly for idealized structures with simple and perfect geometric features, such as circular holes, rectangular cylinders and spheres. Since small distortions are always present in actual fabricated structures, we perform a high accuracy numerical study for BICs and resonances on a simple periodic structure with small distortions, i.e., periodic arrays of slightly noncircular cylinders. Our numerical results confirm that symmetries are important not only for the so-called symmetry-protected BICs, but also for the majority of propagating BICs which do not have a symmetry mismatch with the outgoing radiation waves. Typically, the BICs continue to exist if the small distortions keep the relevant symmetries, and they become resonant modes with finite quality factors if the small distortions break a required symmetry.

Structural characteristics and tectonics of northeastern Tellus Regio and Meni Tessera

NASA Technical Reports Server (NTRS)

Toermaenen, T.

1992-01-01

The Tellus Regio-Meni Tessera region is an interesting highland area characterized by large areas of complex ridged terrain or tessera terrain. The area was previously studied from the Venera 15/16 data, typical characteristics of complex tessera terrain of Tellus Regio were analyzed, and a formation mechanism was proposed. Apparent depths of compensation of approximately 30-50 km were calculated from Pioneer Venus gravity and topography data. These values indicate predominant Airy compensation for the area. Regional stresses and lithospheric structures were defined from analysis of surface structures, topography, and gravity data. In this work we concentrate on northeastern Tellus Regio and Meni Tessera, which are situated north and west of Tellus Regio. Structural features and relationships are analyzed in order to interpret tectonic history of the area. Study area was divided into three subareas: northeastern Tellus Regio, Meni Tessera, and the deformed plain between them.

The Cyborg Astrobiologist: scouting red beds for uncommon features with geological significance

NASA Astrophysics Data System (ADS)

McGuire, Patrick Charles; Díaz-Martínez, Enrique; Ormö, Jens; Gómez-Elvira, Javier; Rodríguez-Manfredi, José Antonio; Sebastián-Martínez, Eduardo; Ritter, Helge; Haschke, Robert; Oesker, Markus; Ontrup, Jörg

2005-04-01

The `Cyborg Astrobiologist' has undergone a second geological field trial, at a site in northern Guadalajara, Spain, near Riba de Santiuste. The site at Riba de Santiuste is dominated by layered deposits of red sandstones. The Cyborg Astrobiologist is a wearable computer and video camera system that has demonstrated a capability to find uncommon interest points in geological imagery in real time in the field. In this second field trial, the computer vision system of the Cyborg Astrobiologist was tested at seven different tripod positions, on three different geological structures. The first geological structure was an outcrop of nearly homogeneous sandstone, which exhibits oxidized-iron impurities in red areas and an absence of these iron impurities in white areas. The white areas in these `red beds' have turned white because the iron has been removed. The iron removal from the sandstone can proceed once the iron has been chemically reduced, perhaps by a biological agent. In one instance the computer vision system found several (iron-free) white spots to be uncommon and therefore interesting, as well as several small and dark nodules. The second geological structure was another outcrop some 600 m to the east, with white, textured mineral deposits on the surface of the sandstone, at the bottom of the outcrop. The computer vision system found these white, textured mineral deposits to be interesting. We acquired samples of the mineral deposits for geochemical analysis in the laboratory. This laboratory analysis of the crust identifies a double layer, consisting of an internal millimetre-size layering of calcite and an external centimetre-size efflorescence of gypsum. The third geological structure was a 50 cm thick palaeosol layer, with fossilized root structures of some plants. The computer vision system also found certain areas of these root structures to be interesting. A quasi-blind comparison of the Cyborg Astrobiologist's interest points for these images with the interest points determined afterwards by a human geologist shows that the Cyborg Astrobiologist concurred with the human geologist 68% of the time (true-positive rate), with a 32% false-positive rate and a 32% false-negative rate. The performance of the Cyborg Astrobiologist's computer vision system was by no means perfect, so there is plenty of room for improvement. However, these tests validate the image-segmentation and uncommon-mapping technique that we first employed at a different geological site (Rivas Vaciamadrid) with somewhat different properties for the imagery.

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

PubMed

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

2015-11-01

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

Shell-corona microgels from double interpenetrating networks.

PubMed

Rudyak, Vladimir Yu; Gavrilov, Alexey A; Kozhunova, Elena Yu; Chertovich, Alexander V

2018-04-18

Polymer microgels with a dense outer shell offer outstanding features as universal carriers for different guest molecules. In this paper, microgels formed by an interpenetrating network comprised of collapsed and swollen subnetworks are investigated using dissipative particle dynamics (DPD) computer simulations, and it is found that such systems can form classical core-corona structures, shell-corona structures, and core-shell-corona structures, depending on the subchain length and molecular mass of the system. The core-corona structures consisting of a dense core and soft corona are formed at small microgel sizes when the subnetworks are able to effectively separate in space. The most interesting shell-corona structures consist of a soft cavity in a dense shell surrounded with a loose corona, and are found at intermediate gel sizes; the area of their existence depends on the subchain length and the corresponding mesh size. At larger molecular masses the collapsing network forms additional cores inside the soft cavity, leading to the core-shell-corona structure.

Analysis of the electron density features of small boron clusters and the effects of doping with C, P, Al, Si, and Zn: Magic B7P and B8Si clusters

NASA Astrophysics Data System (ADS)

Saha, P.; Rahane, A. B.; Kumar, V.; Sukumar, N.

2016-05-01

Boron atomic clusters show several interesting and unusual size-dependent features due to the small covalent radius, electron deficiency, and higher coordination number of boron as compared to carbon. These include aromaticity and a diverse array of structures such as quasi-planar, ring or tubular shaped, and fullerene-like. In the present work, we have analyzed features of the computed electron density distributions of small boron clusters having up to 11 boron atoms, and investigated the effect of doping with C, P, Al, Si, and Zn atoms on their structural and physical properties, in order to understand the bonding characteristics and discern trends in bonding and stability. We find that in general there are covalent bonds as well as delocalized charge distribution in these clusters. We associate the strong stability of some of these planar/quasiplanar disc-type clusters with the electronic shell closing with effectively twelve delocalized valence electrons using a disc-shaped jellium model. {{{{B}}}9}-, B10, B7P, and B8Si, in particular, are found to be exceptional with very large gaps between the highest occupied molecular orbital and the lowest unoccupied molecular orbital, and these are suggested to be magic clusters.

Network analysis of named entity co-occurrences in written texts

NASA Astrophysics Data System (ADS)

Amancio, Diego Raphael

2016-06-01

The use of methods borrowed from statistics and physics to analyze written texts has allowed the discovery of unprecedent patterns of human behavior and cognition by establishing links between models features and language structure. While current models have been useful to unveil patterns via analysis of syntactical and semantical networks, only a few works have probed the relevance of investigating the structure arising from the relationship between relevant entities such as characters, locations and organizations. In this study, we represent entities appearing in the same context as a co-occurrence network, where links are established according to a null model based on random, shuffled texts. Computational simulations performed in novels revealed that the proposed model displays interesting topological features, such as the small world feature, characterized by high values of clustering coefficient. The effectiveness of our model was verified in a practical pattern recognition task in real networks. When compared with traditional word adjacency networks, our model displayed optimized results in identifying unknown references in texts. Because the proposed representation plays a complementary role in characterizing unstructured documents via topological analysis of named entities, we believe that it could be useful to improve the characterization of written texts (and related systems), specially if combined with traditional approaches based on statistical and deeper paradigms.

Global Organization of a Positive-strand RNA Virus Genome

PubMed Central

Wu, Baodong; Grigull, Jörg; Ore, Moriam O.; Morin, Sylvie; White, K. Andrew

2013-01-01

The genomes of plus-strand RNA viruses contain many regulatory sequences and structures that direct different viral processes. The traditional view of these RNA elements are as local structures present in non-coding regions. However, this view is changing due to the discovery of regulatory elements in coding regions and functional long-range intra-genomic base pairing interactions. The ∼4.8 kb long RNA genome of the tombusvirus tomato bushy stunt virus (TBSV) contains these types of structural features, including six different functional long-distance interactions. We hypothesized that to achieve these multiple interactions this viral genome must utilize a large-scale organizational strategy and, accordingly, we sought to assess the global conformation of the entire TBSV genome. Atomic force micrographs of the genome indicated a mostly condensed structure composed of interconnected protrusions extending from a central hub. This configuration was consistent with the genomic secondary structure model generated using high-throughput selective 2′-hydroxyl acylation analysed by primer extension (i.e. SHAPE), which predicted different sized RNA domains originating from a central region. Known RNA elements were identified in both domain and inter-domain regions, and novel structural features were predicted and functionally confirmed. Interestingly, only two of the six long-range interactions known to form were present in the structural model. However, for those interactions that did not form, complementary partner sequences were positioned relatively close to each other in the structure, suggesting that the secondary structure level of viral genome structure could provide a basic scaffold for the formation of different long-range interactions. The higher-order structural model for the TBSV RNA genome provides a snapshot of the complex framework that allows multiple functional components to operate in concert within a confined context. PMID:23717202

Structural and functional features of lysine acetylation of plant and animal tubulins.

PubMed

Rayevsky, Alexey V; Sharifi, Mohsen; Samofalova, Dariya A; Karpov, Pavel A; Blume, Yaroslav B

2017-10-10

The study of the genome and the proteome of different species and representatives of distinct kingdoms, especially detection of proteome via wide-scaled analyses has various challenges and pitfalls. Attempts to combine all available information together and isolate some common features for determination of the pathway and their mechanism of action generally have a highly complicated nature. However, microtubule (MT) monomers are highly conserved protein structures, and microtubules are structurally conserved from Homo sapiens to Arabidopsis thaliana. The interaction of MT elements with microtubule-associated proteins and post-translational modifiers is fully dependent on protein interfaces, and almost all MT modifications are well described except acetylation. Crystallography and interactome data using different approaches were combined to identify conserved proteins important in acetylation of microtubules. Application of computational methods and comparative analysis of binding modes generated a robust predictive model of acetylation of the ϵ-amino group of Lys40 in α-tubulins. In turn, the model discarded some probable mechanisms of interaction between elements of interest. Reconstruction of unresolved protein structures was carried out with modeling by homology to the existing crystal structure (PDBID: 1Z2B) from B. taurus using Swiss-model server, followed by a molecular dynamics simulation. Docking of the human tubulin fragment with Lys40 into the active site of α-tubulin acetyltransferase, reproduces the binding mode of peptidomimetic from X-ray structure (PDBID: 4PK3). © 2017 International Federation for Cell Biology.

Ab initio RNA folding by discrete molecular dynamics: From structure prediction to folding mechanisms

PubMed Central

Ding, Feng; Sharma, Shantanu; Chalasani, Poornima; Demidov, Vadim V.; Broude, Natalia E.; Dokholyan, Nikolay V.

2008-01-01

RNA molecules with novel functions have revived interest in the accurate prediction of RNA three-dimensional (3D) structure and folding dynamics. However, existing methods are inefficient in automated 3D structure prediction. Here, we report a robust computational approach for rapid folding of RNA molecules. We develop a simplified RNA model for discrete molecular dynamics (DMD) simulations, incorporating base-pairing and base-stacking interactions. We demonstrate correct folding of 150 structurally diverse RNA sequences. The majority of DMD-predicted 3D structures have <4 Å deviations from experimental structures. The secondary structures corresponding to the predicted 3D structures consist of 94% native base-pair interactions. Folding thermodynamics and kinetics of tRNAPhe, pseudoknots, and mRNA fragments in DMD simulations are in agreement with previous experimental findings. Folding of RNA molecules features transient, non-native conformations, suggesting non-hierarchical RNA folding. Our method allows rapid conformational sampling of RNA folding, with computational time increasing linearly with RNA length. We envision this approach as a promising tool for RNA structural and functional analyses. PMID:18456842

3D porous polyurethanes featured by different mechanical properties: Characterization and interaction with skeletal muscle cells.

PubMed

Vannozzi, Lorenzo; Ricotti, Leonardo; Santaniello, Tommaso; Terencio, Tercio; Oropesa-Nunez, Reinier; Canale, Claudio; Borghi, Francesca; Menciassi, Arianna; Lenardi, Cristina; Gerges, Irini

2017-11-01

The fabrication of biomaterials for interaction with muscle cells has attracted significant interest in the last decades. However, 3D porous scaffolds featured by a relatively low stiffness (almost matching the natural muscle one) and highly stable in response to cyclic loadings are not available at present, in this context. This work describes 3D polyurethane-based porous scaffolds featured by different mechanical properties. Biomaterial stiffness was finely tuned by varying the cross-linking degree of the starting foam. Compression tests revealed, for the softest material formulation, stiffness values close to the ones possessed by natural skeletal muscles. The materials were also characterized in terms of local nanoindenting, rheometric properties and long-term stability through cyclic compressions, in a strain range reflecting the contraction extent of natural muscles. Preliminary in vitro tests revealed a preferential adhesion of C2C12 skeletal muscle cells over the softer, rougher and more porous structures. All the material formulations showed low cytotoxicity. Copyright © 2017 Elsevier Ltd. All rights reserved.

ELUCIDATING BRAIN CONNECTIVITY NETWORKS IN MAJOR DEPRESSIVE DISORDER USING CLASSIFICATION-BASED SCORING.

PubMed

Sacchet, Matthew D; Prasad, Gautam; Foland-Ross, Lara C; Thompson, Paul M; Gotlib, Ian H

2014-04-01

Graph theory is increasingly used in the field of neuroscience to understand the large-scale network structure of the human brain. There is also considerable interest in applying machine learning techniques in clinical settings, for example, to make diagnoses or predict treatment outcomes. Here we used support-vector machines (SVMs), in conjunction with whole-brain tractography, to identify graph metrics that best differentiate individuals with Major Depressive Disorder (MDD) from nondepressed controls. To do this, we applied a novel feature-scoring procedure that incorporates iterative classifier performance to assess feature robustness. We found that small-worldness , a measure of the balance between global integration and local specialization, most reliably differentiated MDD from nondepressed individuals. Post-hoc regional analyses suggested that heightened connectivity of the subcallosal cingulate gyrus (SCG) in MDDs contributes to these differences. The current study provides a novel way to assess the robustness of classification features and reveals anomalies in large-scale neural networks in MDD.

Cluster Analysis of Weighted Bipartite Networks: A New Copula-Based Approach

PubMed Central

Chessa, Alessandro; Crimaldi, Irene; Riccaboni, Massimo; Trapin, Luca

2014-01-01

In this work we are interested in identifying clusters of “positional equivalent” actors, i.e. actors who play a similar role in a system. In particular, we analyze weighted bipartite networks that describes the relationships between actors on one side and features or traits on the other, together with the intensity level to which actors show their features. We develop a methodological approach that takes into account the underlying multivariate dependence among groups of actors. The idea is that positions in a network could be defined on the basis of the similar intensity levels that the actors exhibit in expressing some features, instead of just considering relationships that actors hold with each others. Moreover, we propose a new clustering procedure that exploits the potentiality of copula functions, a mathematical instrument for the modelization of the stochastic dependence structure. Our clustering algorithm can be applied both to binary and real-valued matrices. We validate it with simulations and applications to real-world data. PMID:25303095

Diverse Electron and Ion Acceleration Characteristics Observed Over Jupiter's Main Aurora

NASA Astrophysics Data System (ADS)

Mauk, B. H.; Haggerty, D. K.; Paranicas, C.; Clark, G.; Kollmann, P.; Rymer, A. M.; Peachey, J. M.; Bolton, S. J.; Levin, S. M.; Adriani, A.; Allegrini, F.; Bagenal, F.; Bonfond, B.; Connerney, J. E. P.; Ebert, R. W.; Gladstone, G. R.; Kurth, W. S.; McComas, D. J.; Ranquist, D.; Valek, P.

2018-02-01

Two new Juno-observed particle features of Jupiter's main aurora demonstrate substantial diversity of processes generating Jupiter's mysterious auroral emissions. It was previously speculated that sometimes-observed potential-driven aurora (up to 400 kV) can turn into broadband stochastic acceleration (dominating at Jupiter) by means of instability. Here direct evidence for such a process is revealed with a "mono-energetic" electron inverted-V rising in energy to 200 keV, transforming into a region of broadband acceleration with downward energy fluxes tripling to 3,000 mW/m2, and then transforming back into a mono-energetic structure ramping down from 200 keV. But a second feature of interest observed nearby is unlikely to have operated in the same way. Here a downward accelerated proton inverted-V, with inferred potentials to 300-400 kV, occurred simultaneously with downward accelerated broadband electrons with downward energy fluxes as high as any observed ( 3,000 mW/m2). This latter feature has no known precedent with Earth auroral observations.

Geospatial-temporal semantic graph representations of trajectories from remote sensing and geolocation data

DOEpatents

Perkins, David Nikolaus; Brost, Randolph; Ray, Lawrence P.

2017-08-08

Various technologies for facilitating analysis of large remote sensing and geolocation datasets to identify features of interest are described herein. A search query can be submitted to a computing system that executes searches over a geospatial temporal semantic (GTS) graph to identify features of interest. The GTS graph comprises nodes corresponding to objects described in the remote sensing and geolocation datasets, and edges that indicate geospatial or temporal relationships between pairs of nodes in the nodes. Trajectory information is encoded in the GTS graph by the inclusion of movable nodes to facilitate searches for features of interest in the datasets relative to moving objects such as vehicles.

Superconductivity in Weyl semimetal candidate MoTe2.

PubMed

Qi, Yanpeng; Naumov, Pavel G; Ali, Mazhar N; Rajamathi, Catherine R; Schnelle, Walter; Barkalov, Oleg; Hanfland, Michael; Wu, Shu-Chun; Shekhar, Chandra; Sun, Yan; Süß, Vicky; Schmidt, Marcus; Schwarz, Ulrich; Pippel, Eckhard; Werner, Peter; Hillebrand, Reinald; Förster, Tobias; Kampert, Erik; Parkin, Stuart; Cava, R J; Felser, Claudia; Yan, Binghai; Medvedev, Sergey A

2016-03-14

Transition metal dichalcogenides have attracted research interest over the last few decades due to their interesting structural chemistry, unusual electronic properties, rich intercalation chemistry and wide spectrum of potential applications. Despite the fact that the majority of related research focuses on semiconducting transition-metal dichalcogenides (for example, MoS2), recently discovered unexpected properties of WTe2 are provoking strong interest in semimetallic transition metal dichalcogenides featuring large magnetoresistance, pressure-driven superconductivity and Weyl semimetal states. We investigate the sister compound of WTe2, MoTe2, predicted to be a Weyl semimetal and a quantum spin Hall insulator in bulk and monolayer form, respectively. We find that bulk MoTe2 exhibits superconductivity with a transition temperature of 0.10 K. Application of external pressure dramatically enhances the transition temperature up to maximum value of 8.2 K at 11.7 GPa. The observed dome-shaped superconductivity phase diagram provides insights into the interplay between superconductivity and topological physics.

Superconductivity in Weyl semimetal candidate MoTe2

PubMed Central

Qi, Yanpeng; Naumov, Pavel G.; Ali, Mazhar N.; Rajamathi, Catherine R.; Schnelle, Walter; Barkalov, Oleg; Hanfland, Michael; Wu, Shu-Chun; Shekhar, Chandra; Sun, Yan; Süß, Vicky; Schmidt, Marcus; Schwarz, Ulrich; Pippel, Eckhard; Werner, Peter; Hillebrand, Reinald; Förster, Tobias; Kampert, Erik; Parkin, Stuart; Cava, R. J.; Felser, Claudia; Yan, Binghai; Medvedev, Sergey A.

2016-01-01

Transition metal dichalcogenides have attracted research interest over the last few decades due to their interesting structural chemistry, unusual electronic properties, rich intercalation chemistry and wide spectrum of potential applications. Despite the fact that the majority of related research focuses on semiconducting transition-metal dichalcogenides (for example, MoS2), recently discovered unexpected properties of WTe2 are provoking strong interest in semimetallic transition metal dichalcogenides featuring large magnetoresistance, pressure-driven superconductivity and Weyl semimetal states. We investigate the sister compound of WTe2, MoTe2, predicted to be a Weyl semimetal and a quantum spin Hall insulator in bulk and monolayer form, respectively. We find that bulk MoTe2 exhibits superconductivity with a transition temperature of 0.10 K. Application of external pressure dramatically enhances the transition temperature up to maximum value of 8.2 K at 11.7 GPa. The observed dome-shaped superconductivity phase diagram provides insights into the interplay between superconductivity and topological physics. PMID:26972450

Groups of adjacent contour segments for object detection.

PubMed

Ferrari, V; Fevrier, L; Jurie, F; Schmid, C

2008-01-01

We present a family of scale-invariant local shape features formed by chains of k connected, roughly straight contour segments (kAS), and their use for object class detection. kAS are able to cleanly encode pure fragments of an object boundary, without including nearby clutter. Moreover, they offer an attractive compromise between information content and repeatability, and encompass a wide variety of local shape structures. We also define a translation and scale invariant descriptor encoding the geometric configuration of the segments within a kAS, making kAS easy to reuse in other frameworks, for example as a replacement or addition to interest points. Software for detecting and describing kAS is released on lear.inrialpes.fr/software. We demonstrate the high performance of kAS within a simple but powerful sliding-window object detection scheme. Through extensive evaluations, involving eight diverse object classes and more than 1400 images, we 1) study the evolution of performance as the degree of feature complexity k varies and determine the best degree; 2) show that kAS substantially outperform interest points for detecting shape-based classes; 3) compare our object detector to the recent, state-of-the-art system by Dalal and Triggs [4].

The Decoding Toolbox (TDT): a versatile software package for multivariate analyses of functional imaging data

PubMed Central

Hebart, Martin N.; Görgen, Kai; Haynes, John-Dylan

2015-01-01

The multivariate analysis of brain signals has recently sparked a great amount of interest, yet accessible and versatile tools to carry out decoding analyses are scarce. Here we introduce The Decoding Toolbox (TDT) which represents a user-friendly, powerful and flexible package for multivariate analysis of functional brain imaging data. TDT is written in Matlab and equipped with an interface to the widely used brain data analysis package SPM. The toolbox allows running fast whole-brain analyses, region-of-interest analyses and searchlight analyses, using machine learning classifiers, pattern correlation analysis, or representational similarity analysis. It offers automatic creation and visualization of diverse cross-validation schemes, feature scaling, nested parameter selection, a variety of feature selection methods, multiclass capabilities, and pattern reconstruction from classifier weights. While basic users can implement a generic analysis in one line of code, advanced users can extend the toolbox to their needs or exploit the structure to combine it with external high-performance classification toolboxes. The toolbox comes with an example data set which can be used to try out the various analysis methods. Taken together, TDT offers a promising option for researchers who want to employ multivariate analyses of brain activity patterns. PMID:25610393

Structural zooming research and development of an interactive computer graphical interface for stress analysis of cracks

NASA Technical Reports Server (NTRS)

Gerstle, Walter

1989-01-01

Engineering problems sometimes involve the numerical solution of boundary value problems over domains containing geometric feature with widely varying scales. Often, a detailed solution is required at one or more of these features. Small details in large structures may have profound effects upon global performance. Conversely, large-scale conditions may effect local performance. Many man-hours and CPU-hours are currently spent in modeling such problems. With the structural zooming technique, it is now possible to design an integrated program which allows the analyst to interactively focus upon a small region of interest, to modify the local geometry, and then to obtain highly accurate responses in that region which reflect both the properties of the overall structure and the local detail. A boundary integral equation analysis program, called BOAST, was recently developed for the stress analysis of cracks. This program can accurately analyze two-dimensional linear elastic fracture mechanics problems with far less computational effort than existing finite element codes. An interactive computer graphical interface to BOAST was written. The graphical interface would have several requirements: it would be menu-driven, with mouse input; all aspects of input would be entered graphically; the results of a BOAST analysis would be displayed pictorially but also the user would be able to probe interactively to get numerical values of displacement and stress at desired locations within the analysis domain; the entire procedure would be integrated into a single, easy to use package; and it would be written using calls to the graphic package called HOOPS. The program is nearing completion. All of the preprocessing features are working satisfactorily and were debugged. The postprocessing features are under development, and rudimentary postprocessing should be available by the end of the summer. The program was developed and run on a VAX workstation, and must be ported to the SUN workstation. This activity is currently underway.

Solid Lipid Nanoparticles and Nanostructured Lipid Carriers: Structure, Preparation and Application

PubMed Central

Naseri, Neda; Valizadeh, Hadi; Zakeri-Milani, Parvin

2015-01-01

Lipid nanoparticles (LNPs) have attracted special interest during last few decades. Solid lipid nanoparticles (SLNs) and nanostructured lipid carriers (NLCs) are two major types of Lipid-based nanoparticles. SLNs were developed to overcome the limitations of other colloidal carriers, such as emulsions, liposomes and polymeric nanoparticles because they have advantages like good release profile and targeted drug delivery with excellent physical stability. In the next generation of the lipid nanoparticle, NLCs are modified SLNs which improve the stability and capacity loading. Three structural models of NLCs have been proposed. These LNPs have potential applications in drug delivery field, research, cosmetics, clinical medicine, etc. This article focuses on features, structure and innovation of LNPs and presents a wide discussion about preparation methods, advantages, disadvantages and applications of LNPs by focusing on SLNs and NLCs. PMID:26504751

Non-dispersive conservative regularisation of nonlinear shallow water (and isentropic Euler equations)

NASA Astrophysics Data System (ADS)

Clamond, Didier; Dutykh, Denys

2018-02-01

A new regularisation of the shallow water (and isentropic Euler) equations is proposed. The regularised equations are non-dissipative, non-dispersive and posses a variational structure; thus, the mass, the momentum and the energy are conserved. Hence, for instance, regularised hydraulic jumps are smooth and non-oscillatory. Another particularly interesting feature of this regularisation is that smoothed 'shocks' propagates at exactly the same speed as the original discontinuous ones. The performance of the new model is illustrated numerically on some dam-break test cases, which are classical in the hyperbolic realm.

Scattering by ensembles of small particles experiment, theory and application

NASA Technical Reports Server (NTRS)

Gustafson, B. A. S.

1980-01-01

A hypothetical self consistent picture of evolution of prestellar intertellar dust through a comet phase leads to predictions about the composition of the circum-solar dust cloud. Scattering properties of thus resulting conglomerates with a bird's-nest type of structure are investigated using a micro-wave analogue technique. Approximate theoretical methods of general interest are developed which compared favorably with the experimental results. The principal features of scattering of visible radiation by zodiacal light particles are reasonably reproduced. A component which is suggestive of (ALPHA)-meteoroids is also predicted.

Brainhack: a collaborative workshop for the open neuroscience community.

PubMed

Cameron Craddock, R; S Margulies, Daniel; Bellec, Pierre; Nolan Nichols, B; Alcauter, Sarael; A Barrios, Fernando; Burnod, Yves; J Cannistraci, Christopher; Cohen-Adad, Julien; De Leener, Benjamin; Dery, Sebastien; Downar, Jonathan; Dunlop, Katharine; R Franco, Alexandre; Seligman Froehlich, Caroline; J Gerber, Andrew; S Ghosh, Satrajit; J Grabowski, Thomas; Hill, Sean; Sólon Heinsfeld, Anibal; Matthew Hutchison, R; Kundu, Prantik; R Laird, Angela; Liew, Sook-Lei; J Lurie, Daniel; G McLaren, Donald; Meneguzzi, Felipe; Mennes, Maarten; Mesmoudi, Salma; O'Connor, David; H Pasaye, Erick; Peltier, Scott; Poline, Jean-Baptiste; Prasad, Gautam; Fraga Pereira, Ramon; Quirion, Pierre-Olivier; Rokem, Ariel; S Saad, Ziad; Shi, Yonggang; C Strother, Stephen; Toro, Roberto; Q Uddin, Lucina; D Van Horn, John; W Van Meter, John; C Welsh, Robert; Xu, Ting

2016-01-01

Brainhack events offer a novel workshop format with participant-generated content that caters to the rapidly growing open neuroscience community. Including components from hackathons and unconferences, as well as parallel educational sessions, Brainhack fosters novel collaborations around the interests of its attendees. Here we provide an overview of its structure, past events, and example projects. Additionally, we outline current innovations such as regional events and post-conference publications. Through introducing Brainhack to the wider neuroscience community, we hope to provide a unique conference format that promotes the features of collaborative, open science.

Nanostructured MnO2 as Electrode Materials for Energy Storage

PubMed Central

Mauger, Alain

2017-01-01

Manganese dioxides, inorganic materials which have been used in industry for more than a century, now find great renewal of interest for storage and conversion of energy applications. In this review article, we report the properties of MnO2 nanomaterials with different morphologies. Techniques used for the synthesis, structural, physical properties, and electrochemical performances of periodic and aperiodic frameworks are discussed. The effect of the morphology of nanosized MnO2 particles on their fundamental features is evidenced. Applications as electrodes in lithium batteries and supercapacitors are examined. PMID:29149066

PolySac3DB: an annotated data base of 3 dimensional structures of polysaccharides.

PubMed

Sarkar, Anita; Pérez, Serge

2012-11-14

Polysaccharides are ubiquitously present in the living world. Their structural versatility makes them important and interesting components in numerous biological and technological processes ranging from structural stabilization to a variety of immunologically important molecular recognition events. The knowledge of polysaccharide three-dimensional (3D) structure is important in studying carbohydrate-mediated host-pathogen interactions, interactions with other bio-macromolecules, drug design and vaccine development as well as material science applications or production of bio-ethanol. PolySac3DB is an annotated database that contains the 3D structural information of 157 polysaccharide entries that have been collected from an extensive screening of scientific literature. They have been systematically organized using standard names in the field of carbohydrate research into 18 categories representing polysaccharide families. Structure-related information includes the saccharides making up the repeat unit(s) and their glycosidic linkages, the expanded 3D representation of the repeat unit, unit cell dimensions and space group, helix type, diffraction diagram(s) (when applicable), experimental and/or simulation methods used for structure description, link to the abstract of the publication, reference and the atomic coordinate files for visualization and download. The database is accompanied by a user-friendly graphical user interface (GUI). It features interactive displays of polysaccharide structures and customized search options for beginners and experts, respectively. The site also serves as an information portal for polysaccharide structure determination techniques. The web-interface also references external links where other carbohydrate-related resources are available. PolySac3DB is established to maintain information on the detailed 3D structures of polysaccharides. All the data and features are available via the web-interface utilizing the search engine and can be accessed at http://polysac3db.cermav.cnrs.fr.

Selective structural source identification

NASA Astrophysics Data System (ADS)

Totaro, Nicolas

2018-04-01

In the field of acoustic source reconstruction, the inverse Patch Transfer Function (iPTF) has been recently proposed and has shown satisfactory results whatever the shape of the vibrating surface and whatever the acoustic environment. These two interesting features are due to the virtual acoustic volume concept underlying the iPTF methods. The aim of the present article is to show how this concept of virtual subsystem can be used in structures to reconstruct the applied force distribution. Some virtual boundary conditions can be applied on a part of the structure, called virtual testing structure, to identify the force distribution applied in that zone regardless of the presence of other sources outside the zone under consideration. In the present article, the applicability of the method is only demonstrated on planar structures. However, the final example show how the method can be applied to a complex shape planar structure with point welded stiffeners even in the tested zone. In that case, if the virtual testing structure includes the stiffeners the identified force distribution only exhibits the positions of external applied forces. If the virtual testing structure does not include the stiffeners, the identified force distribution permits to localize the forces due to the coupling between the structure and the stiffeners through the welded points as well as the ones due to the external forces. This is why this approach is considered here as a selective structural source identification method. It is demonstrated that this approach clearly falls in the same framework as the Force Analysis Technique, the Virtual Fields Method or the 2D spatial Fourier transform. Even if this approach has a lot in common with these latters, it has some interesting particularities like its low sensitivity to measurement noise.

An evaluation of applicability of seismic refraction method in identifying shallow archaeological features A case study at archaeological site

NASA Astrophysics Data System (ADS)

Jahangardi, Morteza; Hafezi Moghaddas, Naser; Keivan Hosseini, Sayyed; Garazhian, Omran

2015-04-01

We applied the seismic refraction method at archaeological site, Tepe Damghani located in Sabzevar, NE of Iran, in order to determine the structures of archaeological interests. This pre-historical site has special conditions with respect to geographical location and geomorphological setting, so it is an urban archaeological site, and in recent years it has been used as an agricultural field. In spring and summer of 2012, the third season of archaeological excavation was carried out. Test trenches of excavations in this site revealed that cultural layers were often disturbed adversely due to human activities such as farming and road construction in recent years. Conditions of archaeological cultural layers in southern and eastern parts of Tepe are slightly better, for instance, in test trench 3×3 m²1S03, third test trench excavated in the southern part of Tepe, an adobe in situ architectural structure was discovered that likely belongs to cultural features of a complex with 5 graves. After conclusion of the third season of archaeological excavation, all of the test trenches were filled with the same soil of excavated test trenches. Seismic refraction method was applied with12 channels of P geophones in three lines with a geophone interval of 0.5 meter and a 1.5 meter distance between profiles on test trench 1S03. The goal of this operation was evaluation of applicability of seismic method in identification of archaeological features, especially adobe wall structures. Processing of seismic data was done with the seismic software, SiesImager. Results were presented in the form of seismic section for every profile, so that identification of adobe wall structures was achieved hardly. This could be due to that adobe wall had been built with the same materials of the natural surrounding earth. Thus, there is a low contrast and it has an inappropriate effect on seismic processing and identifying of archaeological features. Hence the result could be that application of the seismic method in order to determine the archaeological features, having the same conditions, is not affordable and efficient in comparison to GPR or magnetic methods which yield more desirable results.

Family physicians' interests in special features of electronic publication

PubMed Central

Torre, Dario M.; Wright, Scott M.; Wilson, Renee F.; Diener-West, Marie; Bass, Eric B.

2003-01-01

Objective: Because many of the medical journals read by family physicians now have an electronic version, the authors conducted a survey to determine the interest of family physicians in specific features of electronic journal publications. Setting and Participants: We surveyed 175 family physicians randomly selected from the American Academy of Family Physicians. Results: The response rate was 63%. About half of family physicians reported good to excellent computer proficiency, and about one quarter used online journals sometimes or often. Many respondents reported high interest in having links to: an electronic medical text (48% for original articles, 56% for review articles), articles' list of references (52% for original articles, 56% for review articles), and health-related Websites (48% for original and review articles). Conclusion: Primary care–oriented journals should consider the interests of family physicians when developing and offering electronic features for their readers. PMID:12883561

Anatomy and clinical significance of the uncinate process and uncovertebral joint: A comprehensive review.

PubMed

Hartman, Jeffrey

2014-04-01

The uncinate process and its associated uncovertebral articulation are features unique to the cervical spine. This review examines the morphology of these unique structures with particular emphasis on the regional anatomy, development and clinical significance. Five electronic databases were utilized in the literature search and additional relevant citations were retrieved from the references. A total of 74 citations were included for review. This literature review found that the uncinate processes and uncovertebral articulations are rudimentary at birth and develop and evolve with age. With degeneration they become clinically apparent with compression of related structures; most importantly affecting the spinal nerve root and vertebral artery. The articulations have also been found to precipitate torticollis when edematous and be acutely damaged in severe head and neck injuries. The uncinate processes are also important in providing stability and guiding the motion of the cervical spine. This review is intended to re-examine an often overlooked region of the cervical spine as not only an interesting anatomical feature but also a clinically relevant one. Copyright © 2014 Wiley Periodicals, Inc.

Hierarchical Feedback Modules and Reaction Hubs in Cell Signaling Networks

PubMed Central

Xu, Jianfeng; Lan, Yueheng

2015-01-01

Despite much effort, identification of modular structures and study of their organizing and functional roles remain a formidable challenge in molecular systems biology, which, however, is essential in reaching a systematic understanding of large-scale cell regulation networks and hence gaining capacity of exerting effective interference to cell activity. Combining graph theoretic methods with available dynamics information, we successfully retrieved multiple feedback modules of three important signaling networks. These feedbacks are structurally arranged in a hierarchical way and dynamically produce layered temporal profiles of output signals. We found that global and local feedbacks act in very different ways and on distinct features of the information flow conveyed by signal transduction but work highly coordinately to implement specific biological functions. The redundancy embodied with multiple signal-relaying channels and feedback controls bestow great robustness and the reaction hubs seated at junctions of different paths announce their paramount importance through exquisite parameter management. The current investigation reveals intriguing general features of the organization of cell signaling networks and their relevance to biological function, which may find interesting applications in analysis, design and control of bio-networks. PMID:25951347

Volumetric data analysis using Morse-Smale complexes

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

Natarajan, V; Pascucci, V

2005-10-13

The 3D Morse-Smale complex is a fundamental topological construct that partitions the domain of a real-valued function into regions having uniform gradient flow behavior. In this paper, we consider the construction and selective presentation of cells of the Morse-Smale complex and their use in the analysis and visualization of scientific datasets. We take advantage of the fact that cells of different dimension often characterize different types of features present in the data. For example, critical points pinpoint changes in topology by showing where components of the level sets are created, destroyed or modified in genus. Edges of the Morse-Smale complexmore » extract filament-like features that are not explicitly modeled in the original data. Interactive selection and rendering of portions of the Morse-Smale complex introduces fundamental data management challenges due to the unstructured nature of the complex even for structured inputs. We describe a data structure that stores the Morse-Smale complex and allows efficient selective traversal of regions of interest. Finally, we illustrate the practical use of this approach by applying it to cryo-electron microscopy data of protein molecules.« less

Evaluating molecular cobalt complexes for the conversion of N2 to NH3.

PubMed

Del Castillo, Trevor J; Thompson, Niklas B; Suess, Daniel L M; Ung, Gaël; Peters, Jonas C

2015-10-05

Well-defined molecular catalysts for the reduction of N2 to NH3 with protons and electrons remain very rare despite decades of interest and are currently limited to systems featuring molybdenum or iron. This report details the synthesis of a molecular cobalt complex that generates superstoichiometric yields of NH3 (>200% NH3 per Co-N2 precursor) via the direct reduction of N2 with protons and electrons. While the NH3 yields reported herein are modest by comparison to those of previously described iron and molybdenum systems, they intimate that other metals are likely to be viable as molecular N2 reduction catalysts. Additionally, a comparison of the featured tris(phosphine)borane Co-N2 complex with structurally related Co-N2 and Fe-N2 species shows how remarkably sensitive the N2 reduction performance of potential precatalysts is. These studies enable consideration of the structural and electronic effects that are likely relevant to N2 conversion activity, including the π basicity, charge state, and geometric flexibility.

Tuberculosis: finding a new potential antimycobacterium derivative in a aldehyde-arylhydrazone-oxoquinoline series.

PubMed

da C Santos, Fernanda; Castro, Helena C; Lourenço, Maria Cristina S; Abreu, Paula A; Batalha, Pedro N; Cunha, Anna C; Carvalho, Guilherme S L; Rodrigues, Carlos R; Medeiros, Cid A; Souza, Simone D; Ferreira, Vitor F; de Souza, Maria C B V

2012-10-01

Tuberculosis (TB) is a contagious disease caused by Mycobacterium tuberculosis, which remains a serious public health problem. The emergence of resistant bacterial strains has continuously increased and new treatment options are currently in need. In this work, we identified a new potential aldehyde-arylhydrazone-oxoquinoline derivative (4e) with interesting chemical structural features that may be important for designing new anti-TB agents. This 1-ethyl-N'-[(1E)-(5-nitro-2-furyl)methylene]-4-oxo-1,4-dihydroquinoline-3-carbohydrazide (4e) presented an in vitro active profile against M. tuberculosis H37Rv strain (minimum inhibitory concentration, MIC = 6.25 μg/mL) better than other acylhydrazones described in the literature (MIC = 12.5 μg/mL) and close to other antitubercular agents currently on the market. The theoretical analysis showed the importance of several structural features that together with the 5-nitro-2-furyl group generated this active compound (4e). This new compound and the analysis of its molecular properties may be useful for designing new and more efficient antibacterial drugs.

What amyloidoses may tell us about normal protein folding: The Alzheimer's disease story

NASA Astrophysics Data System (ADS)

Teplow, David B.

2002-03-01

Alzheimer's disease (AD) is a progressive, neurodegenerative disorder characterized by severe neuronal injury and death. A prominent histopathologic feature of AD is disseminated parenchymal and vascular amyloid deposition. The fibrils in these deposits are composed of the amyloid β-protein (Aβ), a peptide of 4 kDa mass. In vitro and in vivo studies of Aβ fibril formation have shown that both oligomeric and polymeric Aβ assemblies have neurotoxic activity. Understanding how these assemblies form thus could be of direct therapeutic relevance. However, the aggregation and fibril-forming propensities of Aβ have complicated structure determination. Nevertheless, careful morphologic, spectroscopic, protein chemical, and physiologic analyses of the time-dependent changes in Aβ conformation, assembly state, and biological activity which occur during fibrillogenesis have significantly advanced our understanding of this clinically important process. Here, I will discuss recent findings about the pathway(s) of Aβ folding and assembly and about key structural features of Aβ which control the associated kinetics. Interestingly, the amyloidogenic folding pathway of Aβ is in some respects the mirror image of that through which natively folded amyloidogenic proteins proceed.

Empirical Reference Distributions for Networks of Different Size

PubMed Central

Smith, Anna; Calder, Catherine A.; Browning, Christopher R.

2016-01-01

Network analysis has become an increasingly prevalent research tool across a vast range of scientific fields. Here, we focus on the particular issue of comparing network statistics, i.e. graph-level measures of network structural features, across multiple networks that differ in size. Although “normalized” versions of some network statistics exist, we demonstrate via simulation why direct comparison is often inappropriate. We consider normalizing network statistics relative to a simple fully parameterized reference distribution and demonstrate via simulation how this is an improvement over direct comparison, but still sometimes problematic. We propose a new adjustment method based on a reference distribution constructed as a mixture model of random graphs which reflect the dependence structure exhibited in the observed networks. We show that using simple Bernoulli models as mixture components in this reference distribution can provide adjusted network statistics that are relatively comparable across different network sizes but still describe interesting features of networks, and that this can be accomplished at relatively low computational expense. Finally, we apply this methodology to a collection of ecological networks derived from the Los Angeles Family and Neighborhood Survey activity location data. PMID:27721556

Structural and biochemical insights into 7β-hydroxysteroid dehydrogenase stereoselectivity.

PubMed

Savino, Simone; Ferrandi, Erica Elisa; Forneris, Federico; Rovida, Stefano; Riva, Sergio; Monti, Daniela; Mattevi, Andrea

2016-06-01

Hydroxysteroid dehydrogenases are of great interest as biocatalysts for transformations involving steroid substrates. They feature a high degree of stereo- and regio-selectivity, acting on a defined atom with a specific configuration of the steroid nucleus. The crystal structure of 7β-hydroxysteroid dehydrogenase from Collinsella aerofaciens reveals a loop gating active-site accessibility, the bases of the specificity for NADP(+) , and the general architecture of the steroid binding site. Comparison with 7α-hydroxysteroid dehydrogenase provides a rationale for the opposite stereoselectivity. The presence of a C-terminal extension reshapes the substrate site of the β-selective enzyme, possibly leading to an inverted orientation of the bound substrate. Proteins 2016; 84:859-865. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Wiener-Hammerstein system identification - an evolutionary approach

NASA Astrophysics Data System (ADS)

Naitali, Abdessamad; Giri, Fouad

2016-01-01

The problem of identifying parametric Wiener-Hammerstein (WH) systems is addressed within the evolutionary optimisation context. Specifically, a hybrid culture identification method is developed that involves model structure adaptation using genetic recombination and model parameter learning using particle swarm optimisation. The method enjoys three interesting features: (1) the risk of premature convergence of model parameter estimates to local optima is significantly reduced, due to the constantly maintained diversity of model candidates; (2) no prior knowledge is needed except for upper bounds on the system structure indices; (3) the method is fully autonomous as no interaction is needed with the user during the optimum search process. The performances of the proposed method will be illustrated and compared to alternative methods using a well-established WH benchmark.

Robust weak anti-localisation effect in strongly textured nanocrystalline Bi2Se3 samples

NASA Astrophysics Data System (ADS)

Pereira, V. M. M.; Henriques, M. S. C.; Paixão, J. A.

2018-05-01

Topological insulators are a quantum state of matter that has recently created a great interest among the scientific community, with Bi2Se3 being one of the most extensively studied materials. Here, we demonstrate that polycrystalline nanostructured samples of Bi2Se3 preserve the existence of topological surface states, where electrons cannot be localised. The nanosheet crystals were synthesised by a microwave-assisted method and their structure, composition and morphology thoroughly characterised. The transport properties of a textured polycrystalline sample with strong preferred orientation along the c-axis were measured, showing the presence of the weak anti-localisation effect and Shubnikov-de Haas oscillations. These features are robust against the presence of non-magnetic impurities and structural defects.

Phase structure of completely asymptotically free SU(Nc) models with quarks and scalar quarks

NASA Astrophysics Data System (ADS)

Hansen, F. F.; Janowski, T.; Langæble, K.; Mann, R. B.; Sannino, F.; Steele, T. G.; Wang, Z. W.

2018-03-01

We determine the phase diagram of completely asymptotically free SU (Nc) gauge theories featuring Ns complex scalars and Nf Dirac quarks transforming according to the fundamental representation of the gauge group. The analysis is performed at the maximum known order in perturbation theory. We unveil a very rich dynamics and associated phase structure. Intriguingly, we discover that the completely asymptotically free conditions guarantee that the infrared dynamics displays long-distance conformality, and in a regime when perturbation theory is applicable. We conclude our analysis by determining the quantum corrected potential of the model and summarizing the possible patterns of radiative symmetry breaking. These models are of potential phenomenological interest as either elementary or composite ultraviolet finite extensions of the standard model.

U-shaped relationship between current and pitch in helicene molecules

NASA Astrophysics Data System (ADS)

Guo, Yan-Dong; Yan, Xiao-Hong; Xiao, Yang; Liu, Chun-Sheng

2015-11-01

The helicene is constructed by twisted benzene or other aromatic rings, exhibiting a helical structure. Using first-principles calculations, we investigate the electronic transport of helicenes under stretching or compressing. Interestingly, a U-shaped curve of the current against d (the pitch of a helicene) is observed. Further analysis shows that, it is the result of the nonmonotonic change of HOMO-LUMO gap with d. The change of overlap between orbitals induced by conformational deformation is found to be the underlying mechanism. Moreover, the U-curve phenomenon is an intrinsic feature of the helicene molecules, being robust to the electrode materials or doping. This U-curve behavior is expected to be extended to helical graphene or other related structures, showing great application potential.

U-shaped relationship between current and pitch in helicene molecules.

PubMed

Guo, Yan-Dong; Yan, Xiao-Hong; Xiao, Yang; Liu, Chun-Sheng

2015-11-19

The helicene is constructed by twisted benzene or other aromatic rings, exhibiting a helical structure. Using first-principles calculations, we investigate the electronic transport of helicenes under stretching or compressing. Interestingly, a U-shaped curve of the current against d (the pitch of a helicene) is observed. Further analysis shows that, it is the result of the nonmonotonic change of HOMO-LUMO gap with d. The change of overlap between orbitals induced by conformational deformation is found to be the underlying mechanism. Moreover, the U-curve phenomenon is an intrinsic feature of the helicene molecules, being robust to the electrode materials or doping. This U-curve behavior is expected to be extended to helical graphene or other related structures, showing great application potential.

The myosin mesa and a possible unifying hypothesis for the molecular basis of human hypertrophic cardiomyopathy

PubMed Central

Spudich, James A.

2015-01-01

No matter how many times one explores the structure of the myosin molecule, there is always something new to discover. Here, I describe the myosin mesa, a structural feature of the motor domain that has the characteristics of a binding domain for another protein, possibly myosin-binding protein C (MyBP-C). Interestingly, many well-known hypertrophic cardiomyopathy (HCM) mutations lie along this surface and may affect the putative interactions proposed here. A potential unifying hypothesis for the molecular basis of human hypertrophic cardiomyopathy is discussed here. It involves increased power output of the cardiac muscle as a result of HCM mutations causing the release of inhibition by myosin binding protein C. PMID:25619247

High-pressure crystal structures of an insensitive energetic crystal: 1,1-diamino-2,2-dinitroethene

DOE PAGES

Dreger, Zbigniew A.; Stash, Adam I.; Yu, Zhi -Gang; ...

2015-12-03

Understanding the insensitivity/stability of insensitive high explosive crystals requires detailed structural information at high pressures and high temperatures of interest. Synchrotron single crystal x-ray diffraction experiments were used to determine the high-pressure structures of 1,1-diamino-2,2-dinitroethene (FOX-7), a prototypical insensitive high explosive. The phase transition around 4.5 GPa was investigated and the structures were determined at 4.27 GPa (α’-phase) and 5.9 GPa (ε-phase). The α’-phase (monoclinic, P2 1/ n), structurally indistinguishable from the ambient α-phase, transforms to the new ε-phase (triclinic, P1). The most notable features of the ε-phase, compared to the α’-phase, are: formation of planar layers and flattening ofmore » molecules. Density functional theory (DFT-D2) calculations complemented the experimental results. Furthermore, the results presented here are important for understanding the molecular and crystalline attributes governing the high-pressure insensitivity/stability of insensitive high explosive crystals.« less

High-pressure crystal structures of an insensitive energetic crystal: 1,1-diamino-2,2-dinitroethene

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

Dreger, Zbigniew A.; Stash, Adam I.; Yu, Zhi -Gang

Understanding the insensitivity/stability of insensitive high explosive crystals requires detailed structural information at high pressures and high temperatures of interest. Synchrotron single crystal x-ray diffraction experiments were used to determine the high-pressure structures of 1,1-diamino-2,2-dinitroethene (FOX-7), a prototypical insensitive high explosive. The phase transition around 4.5 GPa was investigated and the structures were determined at 4.27 GPa (α’-phase) and 5.9 GPa (ε-phase). The α’-phase (monoclinic, P2 1/ n), structurally indistinguishable from the ambient α-phase, transforms to the new ε-phase (triclinic, P1). The most notable features of the ε-phase, compared to the α’-phase, are: formation of planar layers and flattening ofmore » molecules. Density functional theory (DFT-D2) calculations complemented the experimental results. Furthermore, the results presented here are important for understanding the molecular and crystalline attributes governing the high-pressure insensitivity/stability of insensitive high explosive crystals.« less

Three-dimensional structure and multistable optical switching of triple-twisted particle-like excitations in anisotropic fluids.

PubMed

Smalyukh, Ivan I; Lansac, Yves; Clark, Noel A; Trivedi, Rahul P

2010-02-01

Control of structures in soft materials with long-range order forms the basis for applications such as displays, liquid-crystal biosensors, tunable lenses, distributed feedback lasers, muscle-like actuators and beam-steering devices. Bistable, tristable and multistable switching of well-defined structures of molecular alignment is of special interest for all of these applications. Here we describe the facile optical creation and multistable switching of localized configurations in the molecular orientation field of a chiral nematic anisotropic fluid. These localized chiro-elastic particle-like excitations--dubbed 'triple-twist torons'--are generated by vortex laser beams and embed the localized three-dimensional (3D) twist into a uniform background. Confocal polarizing microscopy and computer simulations reveal their equilibrium internal structures, manifesting both skyrmion-like and Hopf fibration features. Robust generation of torons at predetermined locations combined with both optical and electrical reversible switching can lead to new ways of multistable structuring of complex photonic architectures in soft materials.

Computer-aided diagnosis for phase-contrast X-ray computed tomography: quantitative characterization of human patellar cartilage with high-dimensional geometric features.

PubMed

Nagarajan, Mahesh B; Coan, Paola; Huber, Markus B; Diemoz, Paul C; Glaser, Christian; Wismüller, Axel

2014-02-01

Phase-contrast computed tomography (PCI-CT) has shown tremendous potential as an imaging modality for visualizing human cartilage with high spatial resolution. Previous studies have demonstrated the ability of PCI-CT to visualize (1) structural details of the human patellar cartilage matrix and (2) changes to chondrocyte organization induced by osteoarthritis. This study investigates the use of high-dimensional geometric features in characterizing such chondrocyte patterns in the presence or absence of osteoarthritic damage. Geometrical features derived from the scaling index method (SIM) and statistical features derived from gray-level co-occurrence matrices were extracted from 842 regions of interest (ROI) annotated on PCI-CT images of ex vivo human patellar cartilage specimens. These features were subsequently used in a machine learning task with support vector regression to classify ROIs as healthy or osteoarthritic; classification performance was evaluated using the area under the receiver-operating characteristic curve (AUC). SIM-derived geometrical features exhibited the best classification performance (AUC, 0.95 ± 0.06) and were most robust to changes in ROI size. These results suggest that such geometrical features can provide a detailed characterization of the chondrocyte organization in the cartilage matrix in an automated and non-subjective manner, while also enabling classification of cartilage as healthy or osteoarthritic with high accuracy. Such features could potentially serve as imaging markers for evaluating osteoarthritis progression and its response to different therapeutic intervention strategies.

Global Failure Modes in Composite Structures for High Altitudes

NASA Technical Reports Server (NTRS)

Knauss, W. G.

2004-01-01

This report summarizes the accomplishments under the referenced grant. The work described was started under the guidance and supervision of the late Dr. James Stames as the technical contact. It was aimed at investigating the development of analysis tools to deal with the problem of rupture in reinforced structural skin of future composites-based aircraft. It was of particular interest to assess methods by which failure features reminiscent of cracks in metallic structures would develop and propagate in fiber reinforced structures in interaction with the reinforcing frame. To eventually achieve that goal it was necessary to first understand the stress or strain distribution at the front of such features so that interactions between such features and reinforcing agents could be assessed computationally. Thus the major emphasis here was on the assessment of damage front and methods on how to assess or characterize it. During the conduct of this research program Dr. Stames changed to a different NASA- internal assignment, which divorced him of the direct supervision of this grant. A student who was approximately % into the completion of his Ph.D. research needed to finish this work, and NASA funds were made available under Dr. Damodar Ambur, the successor Branch Manager for Dr. James Starnes, for the completion of this work. The current grant was the thus a new and fmal support increment for completion of the started research. Final reports for previous funding have been completed and submitted. Because of the interconnection of this last phase of the investigation with previous work it is deemed useful to make the Ph.D. thesis by Luis Gonzales the body of this report.

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

Two Types of 2D Layered Iodoargentates Based on Trimeric [Ag3I7] Secondary Building Units and Hexameric [Ag6I12] Ternary Building Units: Syntheses, Crystal Structures, and Efficient Visible Light Responding Photocatalytic Properties.

PubMed

Lei, Xiao-Wu; Yue, Cheng-Yang; Zhao, Jian-Qiang; Han, Yong-Fang; Yang, Jiang-Tao; Meng, Rong-Rong; Gao, Chuan-Sheng; Ding, Hao; Wang, Chun-Yan; Chen, Wan-Dong; Hong, Mao-Chun

2015-11-16

With mixed transition-metal-complex, alkali-metal, or organic cations as structure-directing agents, a series of novel two-dimensional (2D) layered inorganic-organic hybrid iodoargentates, namely, Kx[TM(2,2-bipy)3]2Ag6I11 (TM = Mn (1), Fe (2), Co (3), Ni (4), Zn (5); x = 0.89-1) and [(Ni(2,2-bipy)3][H-2,2-bipy]Ag3I6 (6), have been solvothermally synthesized and structurally characterized. All the title compounds feature 2D microporous layers composed by [Ag3I7] secondary building units based on AgI4 tetrahedra. Differently, the [Ag3I7] trimers are directly interconnected via corner-sharing to form the 2D [Ag6I11](5-) layer in compounds 1-5, whereas two neighboring [Ag3I7] trimers are initially condensed into a hexameric [Ag6I12] ternary building unit as a new node, which further self-assembles, leading to the 2D [Ag6I10](4-) layer in compound 6. The UV-vis diffuse-reflectance measurements reveal that all the compounds possess proper semiconductor behaviors with tunable band gaps of 1.66-2.75 eV, which lead to highly efficient photocatalytic degradation activities over organic pollutants under visible light irradiation compared to that of N-dotted P25. Interestingly, all the samples feature distinct photodegradative speeds at the same reaction conditions, and compound 1 features the highest photocatalytic activity among the title phases. The luminescence properties, band structures, and thermal stabilities were also studied.

Energetics of drug-DNA interactions.

PubMed

Chaires, J B

1997-01-01

Understanding the thermodynamics of drug binding to DNA is of both practical and fundamental interest. The practical interest lies in the contribution that thermodynamics can make to the rational design process for the development of new DNA targeted drugs. Thermodynamics offer key insights into the molecular forces that drive complex formation that cannot be obtained by structural or computational studies alone. The fundamental interest in these interactions lies in what they can reveal about the general problems of parsing and predicting ligand binding free energies. For these problems, drug-DNA interactions offer several distinct advantages, among them being that the structures of many drug-DNA complexes are known at high resolution and that such structures reveal that in many cases the drug acts as a rigid body, with little conformational change upon binding. Complete thermodynamic profiles (delta G, delta H, delta S, delta Cp) for numerous drug-DNA interactions have been obtained, with the help of high-sensitivity microcalorimetry. The purpose of this article is to offer a perspective on the interpretation of these thermodynamics parameters, and in particular how they might be correlated with known structural features. Obligatory conformational changes in the DNA to accommodate intercalators and the loss of translational and rotational freedom upon complex formation both present unfavorable free energy barriers for binding. Such barriers must be overcome by favorable free energy contributions from the hydrophobic transfer of ligand from solution into the binding site, polyelectrolyte contributions from coupled ion release, and molecular interactions (hydrogen and ionic bonds, van der Waals interactions) that form within the binding site. Theoretical and semiempirical tools that allow estimates of these contributions to be made will be discussed, and their use in dissecting experimental data illustrated. This process, even at the current level of approximation, can shed considerable light on the drug-DNA binding process.

Ynamides in Ring Forming Transformations

PubMed Central

WANG, XIAO-NA; YEOM, HYUN-SUK; FANG, LI-CHAO; HE, SHUZHONG; MA, ZHI-XIONG; KEDROWSKI, BRANT L.; HSUNG, RICHARD P.

2013-01-01

Conspectus The ynamide functional group activates carbon-carbon triple bonds through an attached nitrogen atom that bears an electron-withdrawing group. As a result, the alkyne has both electrophilic and nucleophilic properties. Through the selection of the electron-withdrawing group attached to nitrogen chemists can modulate the electronic properties and reactivity of ynamides, making these groups versatile synthetic building blocks. The reactions of ynamides also lead directly to nitrogen-containing products, which provides access to important structural motifs found in natural products and molecules of medicinal interest. Therefore, researchers have invested increasing time and research in the chemistry of ynamides in recent years. This Account surveys and assesses new organic transformations involving ynamides developed in our laboratory and in others around the world. We showcase the synthetic power of ynamides for rapid assembly of complex molecular structures. Among the recent reports of ynamide transformations, ring-forming reactions provide a powerful tool for generating molecular complexity quickly. In addition to their synthetic utility, such reactions are mechanistically interesting. Therefore, we focus primarily on the cyclization chemistry of ynamides. This Account highlights ynamide reactions that are useful in the rapid synthesis of cyclic and polycyclic structural manifolds. We discuss the mechanisms active in the ring formations and describe representative examples that demonstrate the scope of these reactions and provide mechanistic insights. In this discussion we feature examples of ynamide reactions involving radical cyclizations, ring-closing metathesis, transition metal and non-transition metal mediated cyclizations, cycloaddition reactions, and rearrangements. The transformations presented rapidly introduce structural complexity and include nitrogen within, or in close proximity to, a newly formed ring (or rings). Thus, ynamides have emerged as powerful synthons for nitrogen-containing heterocycles and nitrogen-substituted rings, and we hope this Account will promote continued interest in the chemistry of ynamides. PMID:24164363

Three Dimensional Aerosol Climatology over India and the North Indian Ocean

NASA Astrophysics Data System (ADS)

Adams, A.; Zhang, C.

2013-12-01

Numerical models are indispensable tools to study aerosol effects on climate, including both aerosol direct and indirect radiative effects and their role in precipitation. But, agreement among the models has not been achieved, and thus it is not possible to accurately and confidently attain estimates of aerosol effects on climate. The lack of reliable knowledge on global three-dimensional (3D) aerosol climatology has prevented us from assessing the degree to which the disagreement in their aerosol climatic effects may come from differences of aerosol vertical structures in their simulations. To that end, we created a six year, global 3D extinction coefficient dataset for each aerosol species identifiable by the Level 2, Version 3, 5 km Aerosol Profile product from Cloud-Aerosol Lidar with Orthogonal Polarization (CALIOP) onboard Cloud-Aerosol Lidar and Infrared Pathfinder Satellite Observation (CALIPSO) as a tool to improve 3D model representations. Here we describe the 3D structure of aerosol in the Middle East, India, and the Northern Indian Ocean and some of the interesting dynamical features responsible for the vertical structure and external mixing of aerosol species. One interesting feature in the 3D structure during boreal summer is a well-defined EC core located 0 - 10°N, 40°E - 90°E (Somalia across the Indian subcontinent), centered at 3 km. This is controlled by a shallow meridional circulation about the core. Additionally, the Somali Low-Level Jet exists at this location, but is usually located below the core (~850 mb). Another interesting feature is a strong EC core located 0 - 15°N, 60°E - 90°E below 0.5 km. Polluted dust (external mixture of dust and smoke) and marine aerosol are collocated in this area with maximum AODs of ~0.5 and ~0.2 respectively. Due to the wind stress over ocean, collocation of aerosol species, altitude, and lack of transport pathway for polluted dust, it is possible that this is an example of aerosol misclassification by the CALIPSO algorithm, probably misclassifying marine aerosol as polluted dust. The origin of much of the polluted dust, the most prominent aerosol species in the region, is the mixing of dust and smoke from Africa. Low-level southerly winds south of 10°N transport smoke northward while northerly winds north of 10°N transport dust southward and upward due to orographic lifting. At their area of convergence, zonal wind transports the now elevated polluted dust eastward toward the Indian subcontinent. Subsidence and monsoon circulation reversal during boreal winter and fall limit vertical and horizontal aerosol transport from the India, particularly in the highly populated and always polluted Indo¬-Gangetic Plain. Polluted dust, polluted continental (non-elevated smoke), and smoke aerosols are confined near the surface and located over high population density areas and known biomass burning locations. Himalayan topography is an obvious barrier for the northward extent of aerosol. However, it also acts to create a meridional circulation limiting the southward extent of aerosol. Although transport pathways and the spatial structure of aerosol are well documented in the 2D sense, understanding the mechanisms controlling the vertical structure in concert with observation of the structure will be a valuable tool in reducing the uncertainty of aerosol effects in model simulations.

Flat Terahertz Reflective Focusing Metasurface with Scanning Ability.

PubMed

Yi, Huan; Qu, Shi-Wei; Chen, Bao-Jie; Bai, Xue; Ng, Kung Bo; Chan, Chi Hou

2017-06-14

The ability to manipulate the propagation properties of electromagnetic waves, e.g., divergence, focusing, holography or deflection, is very significant in terahertz applications. Metasurfaces with flat structures are attractive for achieving such manipulations in terahertz band, as they feature low profile, lightweight, and ease of design and installation. Several types of terahertz reflective or transmitting metasurfaces with focusing function have been implemented recently, but none of them can provide scanning ability with controllable focus. Here, a flat reflective metasurface featuring controllable focal shift is proposed and experimentally demonstrated. Furthermore, the principle of designing a focus scanning reflective metasurface is presented and the focusing characteristics are discussed, including focus scanning along a line parallel or orthogonal to the metasurface with a large bandwidth. These interesting properties indicate that this flat reflective metasurface could play a key role in many terahertz imaging and detection systems.

Vortex line topology during vortex tube reconnection

NASA Astrophysics Data System (ADS)

McGavin, P.; Pontin, D. I.

2018-05-01

This paper addresses reconnection of vortex tubes, with particular focus on the topology of the vortex lines (field lines of the vorticity). This analysis of vortex line topology reveals key features of the reconnection process, such as the generation of many small flux rings, formed when reconnection occurs in multiple locations in the vortex sheet between the tubes. Consideration of three-dimensional reconnection principles leads to a robust measurement of the reconnection rate, even once instabilities break the symmetry. It also allows us to identify internal reconnection of vortex lines within the individual vortex tubes. Finally, the introduction of a third vortex tube is shown to render the vortex reconnection process fully three-dimensional, leading to a fundamental change in the topological structure of the process. An additional interesting feature is the generation of vorticity null points.

Generalized Weyl-Wigner map and Vey quantum mechanics

NASA Astrophysics Data System (ADS)

Dias, Nuno Costa; Prata, João Nuno

2001-12-01

The Weyl-Wigner map yields the entire structure of Moyal quantum mechanics directly from the standard operator formulation. The covariant generalization of Moyal theory, also known as Vey quantum mechanics, was presented in the literature many years ago. However, a derivation of the formalism directly from standard operator quantum mechanics, clarifying the relation between the two formulations, is still missing. In this article we present a covariant generalization of the Weyl order prescription and of the Weyl-Wigner map and use them to derive Vey quantum mechanics directly from the standard operator formulation. The procedure displays some interesting features: it yields all the key ingredients and provides a more straightforward interpretation of the Vey theory including a direct implementation of unitary operator transformations as phase space coordinate transformations in the Vey idiom. These features are illustrated through a simple example.

Time-domain terahertz spectroscopy and applications on drugs and explosives

NASA Astrophysics Data System (ADS)

Fan, W. H.; Zhao, W.; Cheng, G. H.; Burnett, A. D.; Upadhya, P. C.; Cunningham, J. E.; Linfield, E. H.; Davies, A. G.

2008-03-01

Many materials of interest to the forensic and security services, such as explosives, drugs and biological agents, exhibit characteristic spectral features in the terahertz (THz) frequency range. These spectral features originate from inter-molecular interactions, involving collective motions of molecules. Broadband THz time-domain spectroscopy (THz-TDS) system have been used to analyze a number of drugs-of-abuse and explosives that are of interest to the forensic and security services. These samples ranged from crystalline powders, pressed into pellets, to thin sheets of plastic explosives, and all being measured in transmission geometry in the frequency range 0.1 - 8 THz. To well understand the nature of the observed spectral features and the effects of thermal broadening on these far-infrared signatures, temperature-dependent THz-TDS measurements have also been performed at temperatures as low as 4 K, especially for two types of cocaine. Well-resolved low-frequency absorption peaks were observed in the frequency range 0.1 - 3 THz with high resolution. Some of absorption peaks were found clearly to become more intense and shift to higher frequencies as the temperature was reduced. The results confirm that the low-frequency collective modes are highly sensitive to the structural and spatial arrangement of molecules. Furthermore, a number of common postal packaging materials made from paper, cardboard, even several types of plastic, have been tested with drug sample to assess the ability of THz-TDS in a hostile detection environment.

Functional nucleic acid-based hydrogels for bioanalytical and biomedical applications

PubMed Central

Mo, Liuting; Lu, Chun-Hua; Fu, Ting

2016-01-01

Hydrogels are crosslinked hydrophilic polymers that can absorb a large amount of water. By their hydrophilic, biocompatible and highly tunable nature, hydrogels can be tailored for applications in bioanalysis and biomedicine. Of particular interest are DNA-based hydrogels owing to the unique features of nucleic acids. Since the discovery of DNA double helical structure, interest in DNA has expanded beyond its genetic role to applications in nanotechnology and materials science. In particular, DNA-based hydrogels present such remarkable features as stability, flexibility, precise programmability, stimuli-responsive DNA conformations, facile synthesis and modification. Moreover, functional nucleic acids (FNAs) have allowed the construction of hydrogels based on aptamers, DNAzymes, i-motif nanostructures, siRNAs and CpG oligodeoxynucleotides to provide additional molecular recognition, catalytic activities and therapeutic potential, making them key players in biological analysis and biomedical applications. To date, a variety of applications have been demonstrated with FNA-based hydrogels, including biosensing, environmental analysis, controlled drug release, cell adhesion and targeted cancer therapy. In this review, we focus on advances in the development of FNA-based hydrogels, which have fully incorporated both the unique features of FNAs and DNA-based hydrogels. We first introduce different strategies for constructing DNA-based hydrogels. Subsequently, various types of FNAs and the most recent developments of FNA-based hydrogels for bioanalytical and biomedical applications are described with some selected examples. Finally, the review provides an insight into the remaining challenges and future perspectives of FNA-based hydrogels. PMID:26758955

Interesting features of transmission across locally periodic delta potentials

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

Dharani, M., E-mail: m-dharani@blr.amrita.edu, E-mail: mdharu@yahoo.co.in; Shastry, C. S.

2016-05-23

We study the theory of transmission of electrons through N delta potential barriers as well as wells. Some of the interesting features like the correlation between resonance peak positions and box states, number of peaks in transmission band and bound states are analyzed for locally periodic attractive, repulsive and pair of attractive and repulsive potentials.

Utilizing Ion-Mobility Data to Estimate Molecular Masses

NASA Technical Reports Server (NTRS)

Duong, Tuan; Kanik, Isik

2008-01-01

A method is being developed for utilizing readings of an ion-mobility spectrometer (IMS) to estimate molecular masses of ions that have passed through the spectrometer. The method involves the use of (1) some feature-based descriptors of structures of molecules of interest and (2) reduced ion mobilities calculated from IMS readings as inputs to (3) a neural network. This development is part of a larger effort to enable the use of IMSs as relatively inexpensive, robust, lightweight instruments to identify, via molecular masses, individual compounds or groups of compounds (especially organic compounds) that may be present in specific environments or samples. Potential applications include detection of organic molecules as signs of life on remote planets, modeling and detection of biochemicals of interest in the pharmaceutical and agricultural industries, and detection of chemical and biological hazards in industrial, homeland-security, and industrial settings.

Patient portal readiness among postpartum patients in a safety net setting.

PubMed

Wieland, Daryl; Gibeau, Anne; Dewey, Caitlin; Roshto, Melanie; Frankel, Hilary

2017-07-05

Maternity patients interact with the healthcare system over an approximately ten-month interval, requiring multiple visits, acquiring pregnancy-specific education, and sharing health information among providers. Many features of a web-based patient portal could help pregnant women manage their interactions with the healthcare system; however, it is unclear whether pregnant women in safety-net settings have the resources, skills or interest required for portal adoption. In this study of postpartum patients in a safety net hospital, we aimed to: (1) determine if patients have the technical resources and skills to access a portal, (2) gain insight into their interest in health information, and (3) identify the perceived utility of portal features and potential barriers to adoption. We developed a structured questionnaire to collect demographics from postpartum patients and measure use of technology and the internet, self-reported literacy, interest in health information, awareness of portal functions, and perceived barriers to use. The questionnaire was administered in person to women in an inpatient setting. Of the 100 participants surveyed, 95% reported routine internet use and 56% used it to search for health information. Most participants had never heard of a patient portal, yet 92% believed that the portal functions were important. The two most appealing functions were to check results and manage appointments. Most participants in this study have the required resources such as a device and familiarity with the internet to access a patient portal including an interest in interacting with a healthcare institution via electronic means. Pregnancy is a critical episode of care where active engagement with the healthcare system can influence outcomes. Healthcare systems and portal developers should consider ways to tailor a portal to address the specific health needs of a maternity population including those in a safety net setting.

Comparing large covariance matrices under weak conditions on the dependence structure and its application to gene clustering.

PubMed

Chang, Jinyuan; Zhou, Wen; Zhou, Wen-Xin; Wang, Lan

2017-03-01

Comparing large covariance matrices has important applications in modern genomics, where scientists are often interested in understanding whether relationships (e.g., dependencies or co-regulations) among a large number of genes vary between different biological states. We propose a computationally fast procedure for testing the equality of two large covariance matrices when the dimensions of the covariance matrices are much larger than the sample sizes. A distinguishing feature of the new procedure is that it imposes no structural assumptions on the unknown covariance matrices. Hence, the test is robust with respect to various complex dependence structures that frequently arise in genomics. We prove that the proposed procedure is asymptotically valid under weak moment conditions. As an interesting application, we derive a new gene clustering algorithm which shares the same nice property of avoiding restrictive structural assumptions for high-dimensional genomics data. Using an asthma gene expression dataset, we illustrate how the new test helps compare the covariance matrices of the genes across different gene sets/pathways between the disease group and the control group, and how the gene clustering algorithm provides new insights on the way gene clustering patterns differ between the two groups. The proposed methods have been implemented in an R-package HDtest and are available on CRAN. © 2016, The International Biometric Society.

Structural features of Aspergillus niger β-galactosidase define its activity against glycoside linkages.

PubMed

Rico-Díaz, Agustín; Ramírez-Escudero, Mercedes; Vizoso-Vázquez, Ángel; Cerdán, M Esperanza; Becerra, Manuel; Sanz-Aparicio, Julia

2017-06-01

β-Galactosidases are biotechnologically interesting enzymes that catalyze the hydrolysis or transgalactosylation of β-galactosides. Among them, the Aspergillus niger β-galactosidase (AnβGal) belongs to the glycoside hydrolase family 35 (GH35) and is widely used in the industry due to its high hydrolytic activity which is used to degrade lactose. We present here its three-dimensional structure in complex with different oligosaccharides, to illustrate the structural determinants of the broad specificity of the enzyme against different glycoside linkages. Remarkably, the residues Phe264, Tyr304, and Trp806 make a dynamic hydrophobic platform that accommodates the sugar at subsite +1 suggesting a main role on the recognition of structurally different substrates. Moreover, complexes with the trisaccharides show two potential subsites +2 depending on the substrate type. This feature and the peculiar shape of its wide cavity suggest that AnβGal might accommodate branched substrates from the complex net of polysaccharides composing the plant material in its natural environment. Relevant residues were selected and mutagenesis analyses were performed to evaluate their role in the catalytic performance and the hydrolase/transferase ratio of AnβGal. Thus, we generated mutants with improved transgalactosylation activity. In particular, the variant Y304F/Y355H/N357G/W806F displays a higher level of galacto-oligosaccharides production than the Aspergillus oryzae β-galactosidase, which is the preferred enzyme in the industry owing to its high transferase activity. Our results provide new knowledge on the determinants modulating specificity and the catalytic performance of fungal GH35 β-galactosidases. In turn, this fundamental background gives novel tools for the future improvement of these enzymes, which represent an interesting target for rational design. Structural data are available in PDB database under the accession numbers 5IFP (native form), 5IHR (in complex with 6GalGlu), 5IFT (in complex with 3GalGlu), 5JUV (in complex with 6GalGal), 5MGC (in complex with 4GalLac), and 5MGD (in complex with 6GalLac). © 2017 Federation of European Biochemical Societies.

Structural Distortions under pressure and doping in superconducting BaFe2As2

NASA Astrophysics Data System (ADS)

Kimber, Simon

2010-03-01

The discovery of a new family of high-TC materials, the iron arsenides, has led to a resurgence of interest in superconductivity. Several important traits of these materials are now apparent: for example, layers of iron tetrahedrally coordinated by arsenic are crucial structural ingredients. The structure and properties of chemically substituted samples are known to be intimately linked; however, until recently (1), remarkably little was known about this relationship when high pressure is used to induce superconductivity in undoped compounds. Here we show that the key structural features in BaFe2As2 show the same behaviour under pressure as found in chemically substituted samples. Using experimentally derived structural data, we show that the electronic structure evolves similarly in both cases. Our results show that, in contrast to the cuprates, structural distortions are more important than charge doping in the iron arsenides. This work was performed at the Helmholtz-Zentrum Berlin in collaboration with Ames Laboratory, Goethe-Universit"at Frankfurt, JCNS J"ulich and the Institute Laue-Langevin. (1) S.A.J. Kimber et al, Nature Materials,

The crystal structure of Erwinia amylovora levansucrase provides a snapshot of the products of sucrose hydrolysis trapped into the active site.

PubMed

Wuerges, Jochen; Caputi, Lorenzo; Cianci, Michele; Boivin, Stephane; Meijers, Rob; Benini, Stefano

2015-09-01

Levansucrases are members of the glycoside hydrolase family and catalyse both the hydrolysis of the substrate sucrose and the transfer of fructosyl units to acceptor molecules. In the presence of sufficient sucrose, this may either lead to the production of fructooligosaccharides or fructose polymers. Aim of this study is to rationalise the differences in the polymerisation properties of bacterial levansucrases and in particular to identify structural features that determine different product spectrum in the levansucrase of the Gram-negative bacterium Erwinia amylovora (Ea Lsc, EC 2.4.1.10) as compared to Gram-positive bacteria such as Bacillus subtilis levansucrase. Ea is an enterobacterial pathogen responsible for the Fire Blight disease in rosaceous plants (e.g., apple and pear) with considerable interest for the agricultural industry. The crystal structure of Ea Lsc was solved at 2.77 Å resolution and compared to those of other fructosyltransferases from Gram-positive and Gram-negative bacteria. We propose the structural features, determining the different reaction products, to reside in just a few loops at the rim of the active site funnel. Moreover we propose that loop 8 may have a role in product length determination in Gluconacetobacter diazotrophicus LsdA and Microbacterium saccharophilum FFase. The Ea Lsc structure shows for the first time the products of sucrose hydrolysis still bound in the active site. Copyright © 2015 Elsevier Inc. All rights reserved.

Stormtime coupling of the ring current, plasmasphere, and topside ionosphere: Electromagnetic and plasma disturbances

NASA Astrophysics Data System (ADS)

Mishin, E. V.; Burke, W. J.

2005-07-01

We compare plasma and field disturbances observed in the ring current/plasmasphere overlap region and in the conjugate ionosphere during the magnetic storm of 5 June 1991. Data come from the Combined Release and Radiation Effects Satellite (CRRES) flying in a geostationary transfer orbit and three satellites of the Defense Meteorological Satellite Program (DMSP) series in Sun-synchronous polar orbits. In the region between ring current nose structures and the electron plasma sheet, CRRES detected wave-like features in local electric and magnetic fields, embedded in structured cold plasmas. Mapped to the ionosphere, these fields should reflect structuring within subauroral plasma streams (SAPS). Indeed, during the period of interest, DMSP F8, F9, and F10 satellites observed highly structured SAPS in the evening ionosphere at topside altitudes. They were collocated with precipitating ring current ions, enhanced fluxes of suprathermal electrons and ions, elevated electron temperatures, and irregular plasma density troughs. Overall, these events are similar to electromagnetic structures observed by DMSP satellites within SAPS during recent geomagnetic storms (Mishin et al., 2003, 2004). Their features can be explained in terms of Alfvén and fast magnetosonic perturbations. We developed a scenario for the formation of elevated electron temperatures at the equatorward side of the SAPS. It includes a lower-hybrid drift instability driven by diamagnetic currents, consistent with strong lower- and upper-hybrid plasma wave activity and intense fluxes of the low-energy electrons and ions near the ring current's inner edge.

Chinese lexical networks: The structure, function and formation

NASA Astrophysics Data System (ADS)

Li, Jianyu; Zhou, Jie; Luo, Xiaoyue; Yang, Zhanxin

2012-11-01

In this paper Chinese phrases are modeled using complex networks theory. We analyze statistical properties of the networks and find that phrase networks display some important features: not only small world and the power-law distribution, but also hierarchical structure and disassortative mixing. These statistical traits display the global organization of Chinese phrases. The origin and formation of such traits are analyzed from a macroscopic Chinese culture and philosophy perspective. It is interesting to find that Chinese culture and philosophy may shape the formation and structure of Chinese phrases. To uncover the structural design principles of networks, network motif patterns are studied. It is shown that they serve as basic building blocks to form the whole phrase networks, especially triad 38 (feed forward loop) plays a more important role in forming most of the phrases and other motifs. The distinct structure may not only keep the networks stable and robust, but also be helpful for information processing. The results of the paper can give some insight into Chinese language learning and language acquisition. It strengthens the idea that learning the phrases helps to understand Chinese culture. On the other side, understanding Chinese culture and philosophy does help to learn Chinese phrases. The hub nodes in the networks show the close relationship with Chinese culture and philosophy. Learning or teaching the hub characters, hub-linking phrases and phrases which are meaning related based on motif feature should be very useful and important for Chinese learning and acquisition.

You are lost without a map: Navigating the sea of protein structures.

PubMed

Lamb, Audrey L; Kappock, T Joseph; Silvaggi, Nicholas R

2015-04-01

X-ray crystal structures propel biochemistry research like no other experimental method, since they answer many questions directly and inspire new hypotheses. Unfortunately, many users of crystallographic models mistake them for actual experimental data. Crystallographic models are interpretations, several steps removed from the experimental measurements, making it difficult for nonspecialists to assess the quality of the underlying data. Crystallographers mainly rely on "global" measures of data and model quality to build models. Robust validation procedures based on global measures now largely ensure that structures in the Protein Data Bank (PDB) are largely correct. However, global measures do not allow users of crystallographic models to judge the reliability of "local" features in a region of interest. Refinement of a model to fit into an electron density map requires interpretation of the data to produce a single "best" overall model. This process requires inclusion of most probable conformations in areas of poor density. Users who misunderstand this can be misled, especially in regions of the structure that are mobile, including active sites, surface residues, and especially ligands. This article aims to equip users of macromolecular models with tools to critically assess local model quality. Structure users should always check the agreement of the electron density map and the derived model in all areas of interest, even if the global statistics are good. We provide illustrated examples of interpreted electron density as a guide for those unaccustomed to viewing electron density. Copyright © 2014 Elsevier B.V. All rights reserved.

Acoustic measurements of the spatial and temporal structure of the near-bottom boundary layer in the 1990-1991 STRESS experiment

NASA Astrophysics Data System (ADS)

Lynch, James F.; Irish, James D.; Gross, Thomas F.; Wiberg, Patricia L.; Newhall, Arthur E.; Traykovski, Peter A.; Warren, Joseph D.

1997-08-01

As part of the 1990-1991 Sediment TRansport Events on Shelves and Slopes (STRESS) experiment, a 5 MHz Acoustic BackScatter System (ABSS) was deployed in 90 m of water to measure vertical profiles of near-bottom suspended sediment concentration. By looking at the vertical profile of concentration from 0 to 50 cm above bottom (cmab) with 1 cm vertical resolution, the ABSS was able to examine the detailed structure of the bottom boundary layer created by combined wave and current stresses. The acoustic profiles clearly showed the wave-current boundary layer, which extends to (order) 10 cmab. The profiles also showed evidence of an "intermediate" boundary layer, also influenced by combined wave and current stresses, just above the wave-current boundary layer. This paper examines the boundary-layer structure by comparing acoustic data obtained by the authors to a 1-D eddy viscosity model formulation. Specifically, these data are compared to a simple extension of the Grant-Glenn-Madsen model formulation. Also of interest is the appearance of apparently 3-D "advective plume" structures in these data. This is an interesting feature in a site which was initially chosen to be a good example of (temporally averaged) 1-D bottom boundary-layer dynamics. Computer modeling and sector-scanning sonar images are presented to justify the plausibility of observing 3-D structure at the STRESS site. 1997 Elsevier Science Ltd

Validation of experimental molecular crystal structures with dispersion-corrected density functional theory calculations.

PubMed

van de Streek, Jacco; Neumann, Marcus A

2010-10-01

This paper describes the validation of a dispersion-corrected density functional theory (d-DFT) method for the purpose of assessing the correctness of experimental organic crystal structures and enhancing the information content of purely experimental data. 241 experimental organic crystal structures from the August 2008 issue of Acta Cryst. Section E were energy-minimized in full, including unit-cell parameters. The differences between the experimental and the minimized crystal structures were subjected to statistical analysis. The r.m.s. Cartesian displacement excluding H atoms upon energy minimization with flexible unit-cell parameters is selected as a pertinent indicator of the correctness of a crystal structure. All 241 experimental crystal structures are reproduced very well: the average r.m.s. Cartesian displacement for the 241 crystal structures, including 16 disordered structures, is only 0.095 Å (0.084 Å for the 225 ordered structures). R.m.s. Cartesian displacements above 0.25 A either indicate incorrect experimental crystal structures or reveal interesting structural features such as exceptionally large temperature effects, incorrectly modelled disorder or symmetry breaking H atoms. After validation, the method is applied to nine examples that are known to be ambiguous or subtly incorrect.

Multisensor satellite observations of meso- and submesoscale surface circulation in the Liguro-Provençal Basin

NASA Astrophysics Data System (ADS)

Karimova, Svetlana; Alvera-Azcarate, Aida

2017-04-01

Despite great efforts being paid to studying circulation of the Western Mediterranean Basin and the factors triggering bioproductivity of its marine ecosystem, the evidence provided by satellite imagery has not been fully analysed yet. In the present paper, we concentrate our attention on mesoscale and submesoscale circulation features of the Liguro-Provençal Basin captured by satellite radiometer, spectroradiometer, and radar images. Using such a dataset makes it possible to observe the circulation features from a wide spatial range, from the basin scale through mesoscale to the scales of a few kilometers. Mesoscale features in this study are being mostly observed with thermal infrared imagery retrieved by AVHRR and AATSR sensors. Special attention in the work was paid to an analysis of the data coming from a geostationary satellite, namely ones provided by SEVIRI. Due to their uniquely high temporal resolution, such imagery allows observing circulation features in their evolution. During the winter blooming events, surface circulation at meso- to submesoscales in the region of interest was additionally highlighted by images obtained in the visible range. Full spatial resolution images provided by Envisat MERIS, Sentinel-2 MSI, and Landsat TM/ETM+/OLI made the greatest contribution to this part. The smallest scales (namely submesoscale) are being observed with synthetic aperture radar (SAR) imagery provided by Envisat ASAR and Sentinel-1 SAR. During an analysis of SAR images, it was noted that there was strikingly great amount of biogenic surfactants on the water surface in the region of interest. Apparently, low biological productivity typical for the Western Mediterranean ecosystem is not a limiting factor for the formation of surfactant films seen in SAR imagery. This finding though requires further consideration in some other researches, and hereafter we just benefited from the presence of surfactants, because they behave as good tracers of surface currents. Even though the region of interest belongs to the areas with low mean eddy kinetic energy, analysis of the images listed above revealed that the Liguro-Provençal Basin was showing a surprisingly high eddy activity among submesoscale and mesoscale features. However, the typical size of eddies in this area was smaller than that in the southern part of the Western Mediterranean. The general impression retrieved from the observations performed is that the main contributors to generation of observed mesoscale vortical structures are (i) the instability of the main currents in the region of interest and especially frontal instability at the Liguro-Provençal front and (ii) instabilities caused by the coastline inhomogeneity, especially in the eastern part of the Basin. Submesoscale eddy activity seems to be developed to its full extent during the periods when the mesoscale activity in the region of interest is not so prominent. This study is supported by the University of Liege and the EU in the context of the FP7-PEOPLE-COFUND-BeIPD project. Satellite imagery is provided by the European Space Agency.

Fusion genes with ALK as recurrent partner in ependymoma-like gliomas: a new brain tumor entity?

PubMed Central

Olsen, Thale Kristin; Panagopoulos, Ioannis; Meling, Torstein R.; Micci, Francesca; Gorunova, Ludmila; Thorsen, Jim; Due-Tønnessen, Bernt; Scheie, David; Lund-Iversen, Marius; Krossnes, Bård; Saxhaug, Cathrine; Heim, Sverre; Brandal, Petter

2015-01-01

Background We have previously characterized 19 ependymal tumors using Giemsa banding and high-resolution comparative genomic hybridization. The aim of this study was to analyze these tumors searching for fusion genes. Methods RNA sequencing was performed in 12 samples. Potential fusion transcripts were assessed by seed count and structural chromosomal aberrations. Transcripts of interest were validated using fluorescence in situ hybridization and PCR followed by direct sequencing. Results RNA sequencing identified rearrangements of the anaplastic lymphoma kinase gene (ALK) in 2 samples. Both tumors harbored structural aberrations involving the ALK locus 2p23. Tumor 1 had an unbalanced t(2;14)(p23;q22) translocation which led to the fusion gene KTN1-ALK. Tumor 2 had an interstitial del(2)(p16p23) deletion causing the fusion of CCDC88A and ALK. In both samples, the breakpoint of ALK was located between exons 19 and 20. Both patients were infants and both tumors were supratentorial. The tumors were well demarcated from surrounding tissue and had both ependymal and astrocytic features but were diagnosed and treated as ependymomas. Conclusions By combining karyotyping and RNA sequencing, we identified the 2 first ever reported ALK rearrangements in CNS tumors. Such rearrangements may represent the hallmark of a new entity of pediatric glioma characterized by both ependymal and astrocytic features. Our findings are of particular importance because crizotinib, a selective ALK inhibitor, has demonstrated effect in patients with lung cancer harboring ALK rearrangements. Thus, ALK emerges as an interesting therapeutic target in patients with ependymal tumors carrying ALK fusions. PMID:25795305

Dendrimers as Carriers for siRNA Delivery and Gene Silencing: A Review

PubMed Central

Huang, Weizhe; He, Ziying

2013-01-01

RNA interference (RNAi) was first literaturally reported in 1998 and has become rapidly a promising tool for therapeutic applications in gene therapy. In a typical RNAi process, small interfering RNAs (siRNA) are used to specifically downregulate the expression of the targeted gene, known as the term “gene silencing.” One key point for successful gene silencing is to employ a safe and efficient siRNA delivery system. In this context, dendrimers are emerging as potential nonviral vectors to deliver siRNA for RNAi purpose. Dendrimers have attracted intense interest since their emanating research in the 1980s and are extensively studied as efficient DNA delivery vectors in gene transfer applications, due to their unique features based on the well-defined and multivalent structures. Knowing that DNA and RNA possess a similar structure in terms of nucleic acid framework and the electronegative nature, one can also use the excellent DNA delivery properties of dendrimers to develop effective siRNA delivery systems. In this review, the development of dendrimer-based siRNA delivery vectors is summarized, focusing on the vector features (siRNA delivery efficiency, cytotoxicity, etc.) of different types of dendrimers and the related investigations on structure-activity relationship to promote safe and efficient siRNA delivery system. PMID:24288498

Figure-Ground Segmentation Using Factor Graphs

PubMed Central

Shen, Huiying; Coughlan, James; Ivanchenko, Volodymyr

2009-01-01

Foreground-background segmentation has recently been applied [26,12] to the detection and segmentation of specific objects or structures of interest from the background as an efficient alternative to techniques such as deformable templates [27]. We introduce a graphical model (i.e. Markov random field)-based formulation of structure-specific figure-ground segmentation based on simple geometric features extracted from an image, such as local configurations of linear features, that are characteristic of the desired figure structure. Our formulation is novel in that it is based on factor graphs, which are graphical models that encode interactions among arbitrary numbers of random variables. The ability of factor graphs to express interactions higher than pairwise order (the highest order encountered in most graphical models used in computer vision) is useful for modeling a variety of pattern recognition problems. In particular, we show how this property makes factor graphs a natural framework for performing grouping and segmentation, and demonstrate that the factor graph framework emerges naturally from a simple maximum entropy model of figure-ground segmentation. We cast our approach in a learning framework, in which the contributions of multiple grouping cues are learned from training data, and apply our framework to the problem of finding printed text in natural scenes. Experimental results are described, including a performance analysis that demonstrates the feasibility of the approach. PMID:20160994

The structure of intense vorticity in homogeneous isotropic turbulence

NASA Technical Reports Server (NTRS)

Jimenez, J.; Wray, A. A.; Saffman, P. G.; Rogallo, R. S.

1992-01-01

The structure of the intense vorticity regions is studied in numerically simulated homogeneous, isotropic, equilibrium turbulent flow fields at four different Reynolds numbers in the range Re(sub lambda) = 36-171. In accordance with previous investigators, this vorticity is found to be organized in coherent, cylindrical or ribbon-like, vortices ('worms'). A statistical study suggests that they are just especially intense features of the background, O(omega'), vorticity. Their radii scale with the Kolmogorov microscale and their lengths with the integral scale of the flow. An interesting observation is that the Reynolds number based on the circulation of the intense vortices, gamma/nu, increases monotonically with Re(sub lambda), raising the question of the stability of the structures in the limit of Re(sub lambda) approaching infinity. One and two-dimensional statistics of vorticity and strain are presented; they are non-gaussian, and the behavior of their tails depends strongly on the Reynolds number. There is no evidence of convergence to a limiting distribution in our range of Re(sub lambda), even though the energy spectra and the energy dissipation rate show good asymptotic properties in the higher Reynolds number cases. Evidence is presented to show that worms are natural features of the flow and that they do not depend on the particular forcing scheme.

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.

Surveying the interest of individuals with upper limb loss in novel prosthetic control techniques.

PubMed

Engdahl, Susannah M; Christie, Breanne P; Kelly, Brian; Davis, Alicia; Chestek, Cynthia A; Gates, Deanna H

2015-06-13

Novel techniques for the control of upper limb prostheses may allow users to operate more complex prostheses than those that are currently available. Because many of these techniques are surgically invasive, it is important to understand whether individuals with upper limb loss would accept the associated risks in order to use a prosthesis. An online survey of individuals with upper limb loss was conducted. Participants read descriptions of four prosthetic control techniques. One technique was noninvasive (myoelectric) and three were invasive (targeted muscle reinnervation, peripheral nerve interfaces, cortical interfaces). Participants rated how likely they were to try each technique if it offered each of six different functional features. They also rated their general interest in each of the six features. A two-way repeated measures analysis of variance with Greenhouse-Geisser corrections was used to examine the effect of the technique type and feature on participants' interest in each technique. Responses from 104 individuals were analyzed. Many participants were interested in trying the techniques - 83 % responded positively toward myoelectric control, 63 % toward targeted muscle reinnervation, 68 % toward peripheral nerve interfaces, and 39 % toward cortical interfaces. Common concerns about myoelectric control were weight, cost, durability, and difficulty of use, while the most common concern about the invasive techniques was surgical risk. Participants expressed greatest interest in basic prosthesis features (e.g., opening and closing the hand slowly), as opposed to advanced features like fine motor control and touch sensation. The results of these investigations may be used to inform the development of future prosthetic technologies that are appealing to individuals with upper limb loss.

On application of kernel PCA for generating stimulus features for fMRI during continuous music listening.

PubMed

Tsatsishvili, Valeri; Burunat, Iballa; Cong, Fengyu; Toiviainen, Petri; Alluri, Vinoo; Ristaniemi, Tapani

2018-06-01

There has been growing interest towards naturalistic neuroimaging experiments, which deepen our understanding of how human brain processes and integrates incoming streams of multifaceted sensory information, as commonly occurs in real world. Music is a good example of such complex continuous phenomenon. In a few recent fMRI studies examining neural correlates of music in continuous listening settings, multiple perceptual attributes of music stimulus were represented by a set of high-level features, produced as the linear combination of the acoustic descriptors computationally extracted from the stimulus audio. NEW METHOD: fMRI data from naturalistic music listening experiment were employed here. Kernel principal component analysis (KPCA) was applied to acoustic descriptors extracted from the stimulus audio to generate a set of nonlinear stimulus features. Subsequently, perceptual and neural correlates of the generated high-level features were examined. The generated features captured musical percepts that were hidden from the linear PCA features, namely Rhythmic Complexity and Event Synchronicity. Neural correlates of the new features revealed activations associated to processing of complex rhythms, including auditory, motor, and frontal areas. Results were compared with the findings in the previously published study, which analyzed the same fMRI data but applied linear PCA for generating stimulus features. To enable comparison of the results, methodology for finding stimulus-driven functional maps was adopted from the previous study. Exploiting nonlinear relationships among acoustic descriptors can lead to the novel high-level stimulus features, which can in turn reveal new brain structures involved in music processing. Copyright © 2018 Elsevier B.V. All rights reserved.

The Centre for Speech, Language and the Brain (CSLB) concept property norms.

PubMed

Devereux, Barry J; Tyler, Lorraine K; Geertzen, Jeroen; Randall, Billi

2014-12-01

Theories of the representation and processing of concepts have been greatly enhanced by models based on information available in semantic property norms. This information relates both to the identity of the features produced in the norms and to their statistical properties. In this article, we introduce a new and large set of property norms that are designed to be a more flexible tool to meet the demands of many different disciplines interested in conceptual knowledge representation, from cognitive psychology to computational linguistics. As well as providing all features listed by 2 or more participants, we also show the considerable linguistic variation that underlies each normalized feature label and the number of participants who generated each variant. Our norms are highly comparable with the largest extant set (McRae, Cree, Seidenberg, & McNorgan, 2005) in terms of the number and distribution of features. In addition, we show how the norms give rise to a coherent category structure. We provide these norms in the hope that the greater detail available in the Centre for Speech, Language and the Brain norms should further promote the development of models of conceptual knowledge. The norms can be downloaded at www.csl.psychol.cam.ac.uk/propertynorms.

Introducing natural thermoplastic shellac to microfluidics: A green fabrication method for point-of-care devices

PubMed Central

Lausecker, R.; Badilita, V.; Wallrabe, U.

2016-01-01

We present a sustainable fabrication method for cheap point-of-care microfluidic systems, employing hot embossing of natural shellac as a key feature of an energy-efficient fabrication method that exclusively uses renewable materials as consumables. Shellac is a low-cost renewable biomaterial that features medium hydrophilicity (e.g., a water contact angle of ca. 73°) and a high chemical stability with respect to common solvents such as cyclohexane or toluene, rendering it an interesting candidate for low-cost microfluidics and a competitor to well-known systems such as paper-based or polydimethylsiloxane-based microfluidics. Moreover, its high replication accuracy for small features down to 30 μm lateral feature size and its ability to form smooth surfaces (surface roughness Ra = 29 nm) at low embossing temperatures (glass transition temperature Tg = 42.2 °C) enable energy-efficient hot embossing of microfluidic structures. Proof-of-concept for the implementation of shellac hot embossing as a green fabrication method for microfluidic systems is demonstrated through the successful fabrication of a microfluidic test setup and the assessment of its resource consumption. PMID:27478525

Language as a whole - A new framework for linguistic knowledge integration. Comment on "Approaching human language with complex networks" by Cong and Liu

NASA Astrophysics Data System (ADS)

Chen, Xinying

2014-12-01

Researchers have been talking about the language system theoretically for many years [1]. A well accepted assumption is that language is a complex adaptive system [2] which is hierarchical [3] and contains multiple levels along the meaning-form dimension [4]. Over the last decade or so, driven by the availability of digital language data and the popularity of statistical approach, many researchers interested in theoretical questions have started to try to quantitatively describe microscopic linguistic features in a certain level of a language system by using authentic language data. Despite the fruitful findings, one question remains unclear. That is, how does a whole language system look like? For answering this question, network approach, an analysis method emphasizes the macro features of structures, has been introduced into linguistic studies [5]. By analyzing the static and dynamic linguistics networks constructed from authentic language data, many macro and micro linguistic features, such as lexical, syntactic or semantic features have been discovered and successfully applied in linguistic typographical studies so that the huge potential of linguistic networks research has revealed [6].

Structural analysis of secretory phospholipase A2 from Clonorchis sinensis: therapeutic implications for hepatic fibrosis.

PubMed

Hariprasad, Gururao; Kaur, Punit; Srinivasan, Alagiri; Singh, Tej Pal; Kumar, Manoj

2012-07-01

Hepatic fibrosis is a common complication of the infection by the parasite, Clonorchis sinensis. There is a high incidence of this disease in the Asian countries with an increased risk of conversion to cancer. A secretory phospholipase A(2) (PLA(2)) enzyme from the parasite is implicated in the pathology. This is an attractive drug target in the light of extensive structural characterization of this class of enzyme. In this study, the structure of the enzyme was modeled based on its sequence homology to the group III bee venom PLA(2). On analysis, the overall structure essentially is comprised of three helices, two sets of β-wings and an elongated C-terminal extension. The structure is stabilized by four disulfide bonds. The structure is comprised of a calcium binding loop, active site and a substrate binding hydrophobic channel. The active site of the enzyme shows the classical features of PLA(2) with the participation of the three residues: histidine-aspartic acid-tyrosine in hydrogen bond formation. This is an interesting variation from the house keeping group III PLA(2) enzyme of human which has a histidine-aspartic acid and phenylalanine arrangement at the active site. This difference is therefore an important structural parameter that can be exploited to design specific inhibitor molecules against the pathogen PLA(2). Likewise, there are certain unique structural features in the hydrophobic channel and the putative membrane binding surface of the PLA(2) from Clonorchis sinensis that not only help understand the mechanism of action but also provide knowledge for a targeted therapy of liver fibrosis caused by the parasite.

The RNA Newton polytope and learnability of energy parameters.

PubMed

Forouzmand, Elmirasadat; Chitsaz, Hamidreza

2013-07-01

Computational RNA structure prediction is a mature important problem that has received a new wave of attention with the discovery of regulatory non-coding RNAs and the advent of high-throughput transcriptome sequencing. Despite nearly two score years of research on RNA secondary structure and RNA-RNA interaction prediction, the accuracy of the state-of-the-art algorithms are still far from satisfactory. So far, researchers have proposed increasingly complex energy models and improved parameter estimation methods, experimental and/or computational, in anticipation of endowing their methods with enough power to solve the problem. The output has disappointingly been only modest improvements, not matching the expectations. Even recent massively featured machine learning approaches were not able to break the barrier. Why is that? The first step toward high-accuracy structure prediction is to pick an energy model that is inherently capable of predicting each and every one of known structures to date. In this article, we introduce the notion of learnability of the parameters of an energy model as a measure of such an inherent capability. We say that the parameters of an energy model are learnable iff there exists at least one set of such parameters that renders every known RNA structure to date the minimum free energy structure. We derive a necessary condition for the learnability and give a dynamic programming algorithm to assess it. Our algorithm computes the convex hull of the feature vectors of all feasible structures in the ensemble of a given input sequence. Interestingly, that convex hull coincides with the Newton polytope of the partition function as a polynomial in energy parameters. To the best of our knowledge, this is the first approach toward computing the RNA Newton polytope and a systematic assessment of the inherent capabilities of an energy model. The worst case complexity of our algorithm is exponential in the number of features. However, dimensionality reduction techniques can provide approximate solutions to avoid the curse of dimensionality. We demonstrated the application of our theory to a simple energy model consisting of a weighted count of A-U, C-G and G-U base pairs. Our results show that this simple energy model satisfies the necessary condition for more than half of the input unpseudoknotted sequence-structure pairs (55%) chosen from the RNA STRAND v2.0 database and severely violates the condition for ~ 13%, which provide a set of hard cases that require further investigation. From 1350 RNA strands, the observed 3D feature vector for 749 strands is on the surface of the computed polytope. For 289 RNA strands, the observed feature vector is not on the boundary of the polytope but its distance from the boundary is not more than one. A distance of one essentially means one base pair difference between the observed structure and the closest point on the boundary of the polytope, which need not be the feature vector of a structure. For 171 sequences, this distance is larger than two, and for only 11 sequences, this distance is larger than five. The source code is available on http://compbio.cs.wayne.edu/software/rna-newton-polytope.

The vital role of the American Journal of Psychology in the early and continuing history of mental chronometry.

PubMed

O'Shea, Geoffrey; Bashore, Theodore R

2012-01-01

The American Journal of Psychology (AJP) was founded in 1887 by G. Stanley Hall during what Edwin G. Boring (1950) called the Period of Mental Chronometry and, consistent with the prevailing interests of the time, featured articles of relevance to scientists in this research domain. Contained in the early volumes of AJP were several articles that examined what have become some of the enduring issues faced by researchers studying the structure and timing of mental processing using reaction time (RT) procedures. Collectively, RT research published in AJP during its early years contributed to establishing mental chronometry as an important subfield of psychology. From 1900 to 1950 interest in mental chronometry waned, during what has been called its Dark Age. Nonetheless, interest in the effects of factors such as age and intelligence on total RT continued unabated. Numerous articles pertinent to these effects appeared in AJP. Finally, with the publication of Neisser's (1963) seminal work on visual search, AJP played an important role in reviving interest in mental chronometry in the latter half of the 20th century and continues in its 125th year of existence to contribute pertinent articles on contemporary research in mental chronometry.

Using airborne LiDAR in geoarchaeological contexts: Assessment of an automatic tool for the detection and the morphometric analysis of grazing archaeological structures (French Massif Central).

NASA Astrophysics Data System (ADS)

Roussel, Erwan; Toumazet, Jean-Pierre; Florez, Marta; Vautier, Franck; Dousteyssier, Bertrand

2014-05-01

Airborne laser scanning (ALS) of archaeological regions of interest is nowadays a widely used and established method for accurate topographic and microtopographic survey. The penetration of the vegetation cover by the laser beam allows the reconstruction of reliable digital terrain models (DTM) of forested areas where traditional prospection methods are inefficient, time-consuming and non-exhaustive. The ALS technology provides the opportunity to discover new archaeological features hidden by vegetation and provides a comprehensive survey of cultural heritage sites within their environmental context. However, the post-processing of LiDAR points clouds produces a huge quantity of data in which relevant archaeological features are not easily detectable with common visualizing and analysing tools. Undoubtedly, there is an urgent need for automation of structures detection and morphometric extraction techniques, especially for the "archaeological desert" in densely forested areas. This presentation deals with the development of automatic detection procedures applied to archaeological structures located in the French Massif Central, in the western forested part of the Puy-de-Dôme volcano between 950 and 1100 m a.s.l.. These unknown archaeological sites were discovered by the March 2011 ALS mission and display a high density of subcircular depressions with a corridor access. The spatial organization of these depressions vary from isolated to aggregated or aligned features. Functionally, they appear to be former grazing constructions built from the medieval to the modern period. Similar grazing structures are known in other locations of the French Massif Central (Sancy, Artense, Cézallier) where the ground is vegetation-free. In order to develop a reliable process of automatic detection and mapping of these archaeological structures, a learning zone has been delineated within the ALS surveyed area. The grazing features were mapped and typical morphometric attributes were calculated based on 2 methods: (i) The mapping of the archaeological structures by a human operator using common visualisation tools (DTM, multi-direction hillshading & local relief models) within a GIS environment; (ii) The automatic detection and mapping performed by a recognition algorithm based on a user defined geometric pattern of the grazing structures. The efficiency of the automatic tool has been assessed by comparing the number of structures detected and the morphometric attributes calculated by the two methods. Our results indicate that the algorithm is efficient for the detection and the location of grazing structures. Concerning the morphometric results, there is still a discrepancy between automatic and expert calculations, due to both the expert mapping choices and the algorithm calibration.

Uncertainty quantification in structural health monitoring: Applications on cultural heritage buildings

NASA Astrophysics Data System (ADS)

Lorenzoni, Filippo; Casarin, Filippo; Caldon, Mauro; Islami, Kleidi; Modena, Claudio

2016-01-01

In the last decades the need for an effective seismic protection and vulnerability reduction of cultural heritage buildings and sites determined a growing interest in structural health monitoring (SHM) as a knowledge-based assessment tool to quantify and reduce uncertainties regarding their structural performance. Monitoring can be successfully implemented in some cases as an alternative to interventions or to control the medium- and long-term effectiveness of already applied strengthening solutions. The research group at the University of Padua, in collaboration with public administrations, has recently installed several SHM systems on heritage structures. The paper reports the application of monitoring strategies implemented to avoid (or at least minimize) the execution of strengthening interventions/repairs and control the response as long as a clear worsening or damaging process is detected. Two emblematic case studies are presented and discussed: the Roman Amphitheatre (Arena) of Verona and the Conegliano Cathedral. Both are excellent examples of on-going monitoring activities, performed through static and dynamic approaches in combination with automated procedures to extract meaningful structural features from collected data. In parallel to the application of innovative monitoring techniques, statistical models and data processing algorithms have been developed and applied in order to reduce uncertainties and exploit monitoring results for an effective assessment and protection of historical constructions. Processing software for SHM was implemented to perform the continuous real time treatment of static data and the identification of modal parameters based on the structural response to ambient vibrations. Statistical models were also developed to filter out the environmental effects and thermal cycles from the extracted features.

Pressure-decoupled magnetic and structural transitions of the parent compound of iron-based 122 superconductors BaFe2As2

PubMed Central

Wu, J. J.; Lin, Jung-Fu; Wang, X. C.; Liu, Q. Q.; Zhu, J. L.; Xiao, Y. M.; Chow, P.; Jin, Changqing

2013-01-01

The recent discovery of iron ferropnictide superconductors has received intensive concern in connection with magnetically involved superconductors. Prominent features of ferropnictide superconductors are becoming apparent: the parent compounds exhibit an antiferromagnetic ordered spin density wave (SDW) state, the magnetic-phase transition is always accompanied by a crystal structural transition, and superconductivity can be induced by suppressing the SDW phase via either chemical doping or applied external pressure to the parent state. These features generated considerable interest in the interplay between magnetism and structure in chemically doped samples, showing crystal structure transitions always precede or coincide with magnetic transition. Pressure-tuned transition, on the other hand, would be more straightforward to superconducting mechanism studies because there are no disorder effects caused by chemical doping; however, remarkably little is known about the interplay in the parent compounds under controlled pressure due to the experimental challenge of in situ measuring both of magnetic and crystal structure evolution at high pressure and low temperatures. Here we show from combined synchrotron Mössbauer and X-ray diffraction at high pressures that the magnetic ordering surprisingly precedes the structural transition at high pressures in the parent compound BaFe2As2, in sharp contrast to the chemical-doping case. The results can be well understood in terms of the spin fluctuations in the emerging nematic phase before the long-range magnetic order that sheds light on understanding how the parent compound evolves from a SDW state to a superconducting phase, a key scientific inquiry of iron-based superconductors. PMID:24101468

Sutures and an Anomalous Deep Lithospheric Electrical Resistor in the Southeastern United States as Revealed by EarthScope Magnetotelluric Data

NASA Astrophysics Data System (ADS)

Murphy, B. S.; Egbert, G. D.

2016-12-01

We use newly acquired long-period magnetotelluric data to examine lithospheric structure beneath the modern Southern Appalachian Mountains and the adjacent Piedmont. The New York-Alabama Lineament is clearly visible both in inverse models and in the data themselves as a major Appalachian-parallel, mid- to lower-crustal conductive feature. This observation supports geologically-based interpretations of the NY-AL Lineament as a major Grenville suture. We also discern several other suture zones in our inverse models, including the Central Piedmont Suture. Interestingly, we do not observe any geoelectric signature of the Suwannee Suture. Most strikingly, we find a zone of exceptionally high resistivity (>1000 μm) that extends to a depth of more than 200 km beneath the modern Piedmont. This resistive block abuts more conductive lithosphere ( 100 μm, as would be expected for Phanerozoic lithosphere) to the northwest. The boundary between these two distinct domains coincides with the modern Appalachian topographic escarpment to within our resolution. The high resistivity values would seem to require completely dry, highly depleted lithosphere at anomalously cold temperatures; however, corresponding seismically fast lithospheric mantle that would be expected for such a structure has not been observed in any previous studies. The exact nature of this feature therefore remains uncertain at present. Regardless, as it is a persistent feature in inversions and it is also readily apparent in the impedance data, this geoelectric structure likely holds important implications for the past, present, and future tectonic evolution of the Southeastern United States.

Tie2 and Eph Receptor Tyrosine Kinase Activation and Signaling

PubMed Central

Barton, William A.; Dalton, Annamarie C.; Seegar, Tom C.M.; Himanen, Juha P.

2014-01-01

The Eph and Tie cell surface receptors mediate a variety of signaling events during development and in the adult organism. As other receptor tyrosine kinases, they are activated on binding of extracellular ligands and their catalytic activity is tightly regulated on multiple levels. The Eph and Tie receptors display some unique characteristics, including the requirement of ligand-induced receptor clustering for efficient signaling. Interestingly, both Ephs and Ties can mediate different, even opposite, biological effects depending on the specific ligand eliciting the response and on the cellular context. Here we discuss the structural features of these receptors, their interactions with various ligands, as well as functional implications for downstream signaling initiation. The Eph/ephrin structures are already well reviewed and we only provide a brief overview on the initial binding events. We go into more detail discussing the Tie-angiopoietin structures and recognition. PMID:24478383

Temporal Structure of Volatility Fluctuations

NASA Astrophysics Data System (ADS)

Wang, Fengzhong; Yamasaki, Kazuko; Stanley, H. Eugene; Havlin, Shlomo

Volatility fluctuations are of great importance for the study of financial markets, and the temporal structure is an essential feature of fluctuations. To explore the temporal structure, we employ a new approach based on the return interval, which is defined as the time interval between two successive volatility values that are above a given threshold. We find that the distribution of the return intervals follows a scaling law over a wide range of thresholds, and over a broad range of sampling intervals. Moreover, this scaling law is universal for stocks of different countries, for commodities, for interest rates, and for currencies. However, further and more detailed analysis of the return intervals shows some systematic deviations from the scaling law. We also demonstrate a significant memory effect in the return intervals time organization. We find that the distribution of return intervals is strongly related to the correlations in the volatility.

Methods for isolation of marine-derived endophytic fungi and their bioactive secondary products.

PubMed

Kjer, Julia; Debbab, Abdessamad; Aly, Amal H; Proksch, Peter

2010-03-01

Marine-derived fungi have been shown in recent years to produce a plethora of new bioactive secondary metabolites, some of them featuring new carbon frameworks hitherto unprecedented in nature. These compounds are of interest as new lead structures for medicine as well as for plant protection. The aim of this protocol is to give a detailed description of methods useful for the isolation and cultivation of fungi associated with various marine organisms (sponges, algae and mangrove plants) for the extraction, characterization and structure elucidation of biologically active secondary metabolites produced by these marine-derived endophytic fungi, and for the preliminary evaluation of their pharmacological properties based on rapid 'in house' screening systems. Some results exemplifying the positive outcomes of the protocol are given at the end. From sampling in marine environment to completion of the structure elucidation and bioactivity screening, a period of at least 3 months has to be scheduled.

Tetrametallic molecular catalysts for photochemical water oxidation.

PubMed

Sartorel, Andrea; Bonchio, Marcella; Campagna, Sebastiano; Scandola, Franco

2013-03-21

Among molecular water oxidation catalysts (WOCs), those featuring a reactive set of four multi-redox transition metals can leverage an extraordinary interplay of electronic and structural properties. These are of particular interest, owing to their close structural, and possibly functional, relationship to the oxygen evolving complex of natural photosynthesis. In this review, special attention is given to two classes of tetrametallic molecular WOCs: (i) M(4)O(4) cubane-type structures stabilized by simple organic ligands, and (ii) systems in which a tetranuclear metal core is stabilized by coordination of two polyoxometalate (POM) ligands. Recent work in this rapidly evolving field is reviewed, with particular emphasis on photocatalytic aspects. Special attention is given to studies addressing the mechanistic complexity of these systems, sometimes overlooked in the rush for oxygen evolving performance. The complementary role of molecular WOCs and their relationship with bulk oxides and heterogeneous catalysis are discussed.

Geophysical Data Define Boundaries and Sub-Regions of the Northern Gulf of Mexico Basin: Structural Histories and Causes are Hypothesized.

NASA Astrophysics Data System (ADS)

Kinsland, G. L.

2017-12-01

Within the last several years new types of geophysical data of the southern margin of the North American Craton and the Northern Gulf of Mexico Basin (NGoMB) have become available, e.g., results from the USArray experiment, high resolution satellite gravity data of the GoM itself and new heat flow data. These data when combined with previously existing geophysical data (gravity, magnetic and seismic) and shallow structural data offer new insights into the boundaries and sub-regions of the NGoMB. I offer hypotheses for the development of the structures of the buried crust and upper mantle which cause these features. Of particular interest might be my suggestion that the NGoMB might have extended in a southeasterly direction prior to the counter-clockwise rotation of the Yucatan Peninsula which ultimately resulted in the GoM.

Controlled nucleation and growth of CdS nanoparticles in a polymer matrix.

PubMed

Di Luccio, Tiziana; Laera, Anna Maria; Tapfer, Leander; Kempter, Susanne; Kraus, Robert; Nickel, Bert

2006-06-29

In-situ synchrotron X-ray diffraction (XRD) was used to monitor the thermal decomposition (thermolysis) of Cd thiolates precursors embedded in a polymer matrix and the nucleation of CdS nanoparticles. A thiolate precursor/polymer solid foil was heated to 300 degrees C in the X-ray diffraction setup of beamline W1.1 at Hasylab, and the diffraction curves were each recorded at 10 degrees C. At temperatures above 240 degrees C, the precursor decomposition is complete and CdS nanoparticles grow within the polymer matrix forming a nanocomposite with interesting optical properties. The nanoparticle structural properties (size and crystal structure) depend on the annealing temperature. Transmission electron microscopy (TEM) and photoluminescence (PL) analyses were used to characterize the nanoparticles. A possible mechanism driving the structural transformation of the precursor is inferred from the diffraction features arising at the different temperatures.

The flavivirus capsid protein: Structure, function and perspectives towards drug design.

PubMed

Oliveira, Edson R A; Mohana-Borges, Ronaldo; de Alencastro, Ricardo B; Horta, Bruno A C

2017-01-02

Flaviviruses, such as dengue and zika viruses, are etiologic agents transmitted to humans mainly by arthropods and are of great epidemiological interest. The flavivirus capsid protein is a structural element required for the viral nucleocapsid assembly that presents the classical function of sheltering the viral genome. After decades of research, many reports have shown its different functionalities and influence over cell normal functioning. The subcellular distribution of this protein, which involves accumulation around lipid droplets and nuclear localization, also corroborates with its multi-functional characteristic. As flavivirus diseases are still in need of global control and in view of the possible key functionalities that the capsid protein promotes over flavivirus biology, novel considerations arise towards anti-flavivirus drug research. This review covers the main aspects concerning structural and functional features of the flavivirus C protein, ultimately, highlighting prospects in drug discovery based on this viral target. Copyright © 2016 Elsevier B.V. All rights reserved.

Constitutively active mutants of the alpha 1B-adrenergic receptor: role of highly conserved polar amino acids in receptor activation.

PubMed Central

Scheer, A; Fanelli, F; Costa, T; De Benedetti, P G; Cotecchia, S

1996-01-01

Site-directed mutagenesis and molecular dynamics simulations of the alpha 1B-adrenergic receptor (AR) were combined to explore the potential molecular changes correlated with the transition from R (inactive state) to R (active state). Using molecular dynamics analysis we compared the structural/dynamic features of constitutively active mutants with those of the wild type and of an inactive alpha 1B-AR to build a theoretical model which defines the essential features of R and R. The results of site-directed mutagenesis were in striking agreement with the predictions of the model supporting the following hypothesis. (i) The equilibrium between R and R depends on the equilibrium between the deprotonated and protonated forms, respectively, of D142 of the DRY motif. In fact, replacement of D142 with alanine confers high constitutive activity to the alpha 1B-AR. (ii) The shift of R143 of the DRY sequence out of a conserved 'polar pocket' formed by N63, D91, N344 and Y348 is a feature common to all the active structures, suggesting that the role of R143 is fundamental for mediating receptor activation. Disruption of these intramolecular interactions by replacing N63 with alanine constitutively activates the alpha 1B-AR. Our findings might provide interesting generalities about the activation process of G protein-coupled receptors. Images PMID:8670860

Text Extraction from Scene Images by Character Appearance and Structure Modeling

PubMed Central

Yi, Chucai; Tian, Yingli

2012-01-01

In this paper, we propose a novel algorithm to detect text information from natural scene images. Scene text classification and detection are still open research topics. Our proposed algorithm is able to model both character appearance and structure to generate representative and discriminative text descriptors. The contributions of this paper include three aspects: 1) a new character appearance model by a structure correlation algorithm which extracts discriminative appearance features from detected interest points of character samples; 2) a new text descriptor based on structons and correlatons, which model character structure by structure differences among character samples and structure component co-occurrence; and 3) a new text region localization method by combining color decomposition, character contour refinement, and string line alignment to localize character candidates and refine detected text regions. We perform three groups of experiments to evaluate the effectiveness of our proposed algorithm, including text classification, text detection, and character identification. The evaluation results on benchmark datasets demonstrate that our algorithm achieves the state-of-the-art performance on scene text classification and detection, and significantly outperforms the existing algorithms for character identification. PMID:23316111

A correlational and experimental examination of reality television viewing and interest in cosmetic surgery.

PubMed

Markey, Charlotte N; Markey, Patrick M

2010-03-01

Two studies are presented that examine the influence of media messages about cosmetic surgery on youths' interest in altering their own physical appearance. In Study 1, 170 participants (59% female; M age=19.77 years) completed surveys assessing their impression of reality television shows featuring cosmetic surgery, appearance satisfaction, self-esteem, and their interest in cosmetic surgery. Results indicated that participants who reported favorable impressions of reality television shows featuring cosmetic surgery were more likely to indicate interest in pursuing surgery. One hundred and eighty-nine participants (51% female; M age=19.84 years) completed Study 2. Approximately half of the participants were exposed to a television message featuring a surgical make-over; the other half was exposed to a neutral message. Results indicated that participants who watched a television program about cosmetic surgery wanted to alter their own appearance using cosmetic surgery more than did participants who were not exposed to this program. Copyright 2009 Elsevier Ltd. All rights reserved.

What's New on MedlinePlus: Announcements and Special Features

MedlinePlus

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Salutogenic service user involvement in nursing research: a case study.

PubMed

Mjøsund, Nina Helen; Vinje, Hege Forbech; Eriksson, Monica; Haaland-Øverby, Mette; Jensen, Sven Liang; Kjus, Solveig; Norheim, Irene; Portaasen, Inger-Lill; Espnes, Geir Arild

2018-05-12

The aim was to explore the process of involving mental healthcare service users in a mental health promotion research project as research advisors and to articulate features of the collaboration which encouraged and empowered the advisors to make significant contributions to the research process and outcome. There is an increasing interest in evaluating aspects of service user involvement in nursing research. Few descriptions exist of features that enable meaningful service user involvement. We draw on experiences from conducting research which used the methodology interpretative phenomenological analysis to explore how persons with mental disorders perceived mental health. Aside from the participants in the project, five research advisors with service user experience were involved in the entire research process. We applied a case study design to explore the ongoing processes of service user involvement. Documents and texts produced while conducting the project (2012-2016), as well as transcripts from multistage focus group discussions with the research advisors, were analysed. The level of involvement was dynamic and varied throughout the different stages of the research process. Six features: leadership, meeting structure, role clarification, being members of a team, a focus on possibilities and being seen and treated as holistic individuals, were guiding principles for a salutogenic service user involvement. These features strengthened the advisors' perception of themselves as valuable and competent contributors. Significant contributions from research advisors were promoted by facilitating the process of involvement. A supporting structure and atmosphere were consistent with a salutogenic service user involvement. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Wavelength-scale light concentrator made by direct 3D laser writing of polymer metamaterials.

PubMed

Moughames, J; Jradi, S; Chan, T M; Akil, S; Battie, Y; Naciri, A En; Herro, Z; Guenneau, S; Enoch, S; Joly, L; Cousin, J; Bruyant, A

2016-10-04

We report on the realization of functional infrared light concentrators based on a thick layer of air-polymer metamaterial with controlled pore size gradients. The design features an optimum gradient index profile leading to light focusing in the Fresnel zone of the structures for two selected operating wavelength domains near 5.6 and 10.4 μm. The metamaterial which consists in a thick polymer containing air holes with diameters ranging from λ/20 to λ/8 is made using a 3D lithography technique based on the two-photon polymerization of a homemade photopolymer. Infrared imaging of the structures reveals a tight focusing for both structures with a maximum local intensity increase by a factor of 2.5 for a concentrator volume of 1.5 λ 3 , slightly limited by the residual absorption of the selected polymer. Such porous and flat metamaterial structures offer interesting perspectives to increase infrared detector performance at the pixel level for imaging or sensing applications.

Wavelength-scale light concentrator made by direct 3D laser writing of polymer metamaterials

PubMed Central

Moughames, J.; Jradi, S.; Chan, T. M.; Akil, S.; Battie, Y.; Naciri, A. En; Herro, Z.; Guenneau, S.; Enoch, S.; Joly, L.; Cousin, J.; Bruyant, A.

2016-01-01

We report on the realization of functional infrared light concentrators based on a thick layer of air-polymer metamaterial with controlled pore size gradients. The design features an optimum gradient index profile leading to light focusing in the Fresnel zone of the structures for two selected operating wavelength domains near 5.6 and 10.4 μm. The metamaterial which consists in a thick polymer containing air holes with diameters ranging from λ/20 to λ/8 is made using a 3D lithography technique based on the two-photon polymerization of a homemade photopolymer. Infrared imaging of the structures reveals a tight focusing for both structures with a maximum local intensity increase by a factor of 2.5 for a concentrator volume of 1.5 λ3, slightly limited by the residual absorption of the selected polymer. Such porous and flat metamaterial structures offer interesting perspectives to increase infrared detector performance at the pixel level for imaging or sensing applications. PMID:27698476

Atomic force microscopy study of the structure function relationships of the biofilm-forming bacterium Streptococcus mutans

NASA Astrophysics Data System (ADS)

Cross, Sarah E.; Kreth, Jens; Zhu, Lin; Qi, Fengxia; Pelling, Andrew E.; Shi, Wenyuan; Gimzewski, James K.

2006-02-01

Atomic force microscopy (AFM) has garnered much interest in recent years for its ability to probe the structure, function and cellular nanomechanics inherent to specific biological cells. In particular, we have used AFM to probe the important structure-function relationships of the bacterium Streptococcus mutans. S. mutans is the primary aetiological agent in human dental caries (tooth decay), and is of medical importance due to the virulence properties of these cells in biofilm initiation and formation, leading to increased tolerance to antibiotics. We have used AFM to characterize the unique surface structures of distinct mutants of S. mutans. These mutations are located in specific genes that encode surface proteins, thus using AFM we have resolved characteristic surface features for mutant strains compared to the wild type. Ultimately, our characterization of surface morphology has shown distinct differences in the local properties displayed by various S. mutans strains on the nanoscale, which is imperative for understanding the collective properties of these cells in biofilm formation.

Hypergraph topological quantities for tagged social networks.

PubMed

Zlatić, Vinko; Ghoshal, Gourab; Caldarelli, Guido

2009-09-01

Recent years have witnessed the emergence of a new class of social networks, which require us to move beyond previously employed representations of complex graph structures. A notable example is that of the folksonomy, an online process where users collaboratively employ tags to resources to impart structure to an otherwise undifferentiated database. In a recent paper, we proposed a mathematical model that represents these structures as tripartite hypergraphs and defined basic topological quantities of interest. In this paper, we extend our model by defining additional quantities such as edge distributions, vertex similarity and correlations as well as clustering. We then empirically measure these quantities on two real life folksonomies, the popular online photo sharing site Flickr and the bookmarking site CiteULike. We find that these systems share similar qualitative features with the majority of complex networks that have been previously studied. We propose that the quantities and methodology described here can be used as a standard tool in measuring the structure of tagged networks.

Hypergraph topological quantities for tagged social networks

NASA Astrophysics Data System (ADS)

Zlatić, Vinko; Ghoshal, Gourab; Caldarelli, Guido

2009-09-01

Recent years have witnessed the emergence of a new class of social networks, which require us to move beyond previously employed representations of complex graph structures. A notable example is that of the folksonomy, an online process where users collaboratively employ tags to resources to impart structure to an otherwise undifferentiated database. In a recent paper, we proposed a mathematical model that represents these structures as tripartite hypergraphs and defined basic topological quantities of interest. In this paper, we extend our model by defining additional quantities such as edge distributions, vertex similarity and correlations as well as clustering. We then empirically measure these quantities on two real life folksonomies, the popular online photo sharing site Flickr and the bookmarking site CiteULike. We find that these systems share similar qualitative features with the majority of complex networks that have been previously studied. We propose that the quantities and methodology described here can be used as a standard tool in measuring the structure of tagged networks.

Nuclear Structure in 78Ge

NASA Astrophysics Data System (ADS)

Forney, Anne M.; Walters, W. B.; Sethi, J.; Chiara, C. J.; Harker, J.; Janssens, R. V. F.; Zhu, S.; Carpenter, M.; Alcorta, M.; Gürdal, G.; Hoffman, C. R.; Kay, B. P.; Kondev, F. G.; Lauristen, T.; Lister, C. J.; McCutchan, E. A.; Rogers, A. M.; Seweryniak, D.

2017-01-01

Owing to the importance of the structure of 76Ge in interpreting double β decay studies, the structures of adjacent nuclei have been of considerable interest. Recently reported features for the structures of 72,74,76Ge indicate both shape coexistence and triaxiality. New data for the excited states of 78Ge will be reported arising from Gammasphere studies of multinucleon transfer reactions between a 76Ge beam and thick heavy targets at the ATLAS facility at Argonne National Laboratory. The previously known yrast band is extended to higher spins, candidate levels for a triaxial sequence have been observed, and the associated staggering determined. The staggering in 78Ge found in this work is not in agreement with theoretical work. Candidates for negative-parity states and seniority-four states will be discussed. This material is based upon work supported by the U.S. DOE under DE-AC02-06CH11357 and DE-FG02-94ER40834. Resources of ANL's ATLAS setup, a DOE Office of Science user facility, were used.

On the inner disc structure of MWC480: evidence for asymmetries?

NASA Astrophysics Data System (ADS)

Jamialahmadi, N.; Lopez, B.; Berio, Ph.; Matter, A.; Flament, S.; Fathivavsari, H.; Ratzka, T.; Sitko, M. L.; Spang, A.; Russell, R. W.

2018-01-01

Studying the physical conditions structuring the young circumstellar discs is required for understanding the onset of planet formation. Of particular interest is the protoplanetary disc surrounding the Herbig star MWC480. The structure and properties of the circumstellar disc of MWC480 are studied by infrared interferometry and interpreted from a modelling approach. New observations are driving this study, in particular, some recent Very Large Telescope Interferometer (VLTI)/MIDI data acquired in 2013 December. Our one-component disc model could not reproduce simultaneously all our data: the spectral energy distribution, the near-infrared Keck Interferometer data and the mid-infrared data obtained with the MIDI instrument. In order to explain all measurements, one possibility is to add an asymmetry in our one-component disc model with the assumption that the structure of the disc of MWC480 has not varied with time. Several scenarios are tested, and the one considering the presence of an azimuthal bright feature in the inner component of the disc model provides a better fit of the data.

What Do We Learn from Binding Features? Evidence for Multilevel Feature Integration

ERIC Educational Resources Information Center

Colzato, Lorenza S.; Raffone, Antonino; Hommel, Bernhard

2006-01-01

Four experiments were conducted to investigate the relationship between the binding of visual features (as measured by their after-effects on subsequent binding) and the learning of feature-conjunction probabilities. Both binding and learning effects were obtained, but they did not interact. Interestingly, (shape-color) binding effects…

Identification of upstream and intragenic regulatory elements that confer cell-type-restricted and differentiation-specific expression on the muscle creatine kinase gene

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

Sternberg, E.A.; Spizz, G.; Perry, W.M.

1988-07-01

Terminal differentiation of skeletal myobalsts is accompanied by induction of a series of tissue-specific gene products, which includes the muscle isoenzymte of creatine kinase (MCK). To begin to define the sequences and signals involved in MCK regulation in developing muscle cells, the mouse MCK gene has been isolated. Sequence analysis of 4,147 bases of DNA surrounding the transcription initiation site revealed several interesting structural features, some of which are common to other muscle-specific genes and to cellular and viral enhancers.

Towards a Quantum Game of Life

NASA Astrophysics Data System (ADS)

Flitney, Adrian P.; Abbott, Derek

Cellular automata provide a means of obtaining complex behaviour from a simple array of cells and a deterministic transition function. They supply a method of computation that dispenses with the need for manipulation of individual cells and they are computationally universal. Classical cellular automata have proved of great interest to computer scientists but the construction of quantum cellular automata pose particular difficulties. We present a version of John Conway's famous two-dimensional classical cellular automata Life that has some quantum-like features, including interference effects. Some basic structures in the new automata are given and comparisons are made with Conway's game.

Development of Yeast as an In Vivo Test Tube to Characterize a Broad Spectrum of p53 Mutations Associated with Breast Cancer

DTIC Science & Technology

2002-10-01

there is a mutation in the p53 gene itself (4, 5). Interestingly, -80% of p53 mutations are missense changes that lead to single amino acid...substitutions, a feature that distinguishes p53 from other tumor suppressor genes (e.g., APC, NF1, BRCAJ) (6). The incidence of p53 mutations and the types of...intronic promoter is contained within the human mutation hotspot maps of p53: correlation with p53 protein structural and mdm2 gene . Nucleic Acids Res

Sesterterpenes from a common marine sponge, Hyrtios erecta.

PubMed

Crews, P; Bescansa, P

1986-01-01

Eleven sesterterpenes have been characterized from the biotoxic extracts of Hyrtios erecta. Their structures and stereochemistry were established by spectral properties or results from chemical interconversions. Especially valuable for establishing stereochemical features were 13C-nmr methyl shift correlations and analysis of 1H-nmr couplings and chemical shifts. The new scalarane sesterterpenes included 2, 3, 7, 9, and 10a (but 9 and 10a might be artifacts), and they were accompanied by five previously described scalaranes, 1, 4, 5a, 6, and 8, along with hyrtial (11), a novel norsesterterpene. Many of these sesterterpenes exhibited interesting biological activity.

Features of polar cusp electron precipitation associated with a large magnetic storm

NASA Technical Reports Server (NTRS)

Berko, F. W.

1974-01-01

Measurements of precipitating electrons made by the OGO-4 satellite reveal several interesting phenomena in the polar cusp. Extremely high fluxes of 0.7 keV electrons were observed in the polar cusp ninety minutes following the sudden commencement of a very large magnetic storm. Structured, fairly high fluxes of 7.3 keV electrons were also observed in the cusp region, accompanied by very strong search coil magnetometer fluctuations, indicative of strong field-aligned currents. The observations confirm previously reported latitudinal shifts in the location of the polar cusp in response to southward interplanetary magnetic fields.

Analysis of drugs-of-abuse and explosives using terahertz time-domain and Raman spectroscopy

NASA Astrophysics Data System (ADS)

Burnett, Andrew; Fan, Wenhui; Upadhya, Prashanth; Cunningham, John; Linfield, Edmund; Davies, Giles; Edwards, Howell; Munshi, Tasnim; O'Neil, Andrew

2006-02-01

We demonstrate that, through coherent measurement of the transmitted terahertz electric fields, broadband (0.3-8THz) time-domain spectroscopy can be used to measure far-infrared vibrational modes of a range of illegal drugs and high explosives that are of interest to the forensic and security services. Our results show that these absorption features are highly sensitive to the structural and spatial arrangement of the molecules. Terahertz frequency spectra are also compared with high-resolution low-frequency Raman spectra to assist in understanding the low frequency inter- and intra-molecular vibrational modes of the molecules.

Overview of major hazards. Part 2: Source term; dispersion; combustion; blast, missiles, venting; fire; radiation; runaway reactions; toxic substances; dust explosions

NASA Astrophysics Data System (ADS)

Vilain, J.

Approaches to major hazard assessment and prediction are reviewed. Source term: (phenomenology/modeling of release, influence on early stages of dispersion); dispersion (atmospheric advection, diffusion and deposition, emphasis on dense/cold gases); combustion (flammable clouds and mists covering flash fires, deflagration, transition to detonation; mostly unconfined/partly confined situations); blast formation, propagation, interaction with structures; catastrophic fires (pool fires, torches and fireballs; highly reactive substances) runaway reactions; features of more general interest; toxic substances, excluding toxicology; and dust explosions (phenomenology and protective measures) are discussed.

Local Structure Fixation in the Composite Manufacturing Chain

NASA Astrophysics Data System (ADS)

Girdauskaite, Lina; Krzywinski, Sybille; Rödel, Hartmut; Wildasin-Werner, Andrea; Böhme, Ralf; Jansen, Irene

2010-12-01

Compared to metal materials, textile reinforced composites show interesting features, but also higher production costs because of low automation rate in the manufacturing chain at this time. Their applicability is also limited due to quality problems, which restrict the production of complex shaped dry textile preforms. New technologies, design concepts, and cost-effective manufacturing methods are needed in order to establish further fields of application. This paper deals with possible ways to improve the textile deformation process by locally applying a fixative to the structure parallel to the cut. This hinders unwanted deformation in the textile stock during the subsequent stacking and formation steps. It is found that suitable thermoplastic binders, applied in the appropriate manner do not restrict formation of the textile and have no negative influence on the mechanical properties of the composite.

The vacuole within

PubMed Central

Ellis, Kathryn; Hoffman, Brenton D.; Bagnat, Michel

2013-01-01

The notochord is an evolutionarily conserved structure that has long been known to play an important role in patterning during embryogenesis. Structurally, the notochord is composed of two cell layers: an outer epithelial-like sheath, and an inner core of cells that contain large fluid-filled vacuoles. We have recently shown these notochord vacuoles are lysosome-related organelles that form through Rab32a and vacuolar-type proton-ATPase-dependent acidification. Disruption of notochord vacuoles results in a shortened embryo along the anterior-posterior axis. Interestingly, we discovered that notochord vacuoles are also essential for proper spine morphogenesis and that vacuole defects lead to scoliosis of the spine. Here we discuss the cellular organization of the notochord and how key features of its architecture allow the notochord to function in embryonic axis elongation and spine formation. PMID:23887209

The prokaryotic zinc-finger: structure, function and comparison with the eukaryotic counterpart.

PubMed

Malgieri, Gaetano; Palmieri, Maddalena; Russo, Luigi; Fattorusso, Roberto; Pedone, Paolo V; Isernia, Carla

2015-12-01

Classical zinc finger (ZF) domains were thought to be confined to the eukaryotic kingdom until the transcriptional regulator Ros protein was identified in Agrobacterium tumefaciens. The Ros Cys2 His2 ZF binds DNA in a peculiar mode and folds in a domain significantly larger than its eukaryotic counterpart consisting of 58 amino acids (the 9-66 region) arranged in a βββαα topology, and stabilized by a conserved, extensive, 15-residue hydrophobic core. The prokaryotic ZF domain, then, shows some intriguing new features that make it interestingly different from its eukaryotic counterpart. This review will focus on the prokaryotic ZFs, summarizing and discussing differences and analogies with the eukaryotic domains and providing important insights into their structure/function relationships. © 2015 FEBS.

[Max Weber's illness--sociologic aspects of the depressive structure].

PubMed

Frommer, J; Frommer, S

1993-05-01

Between 1897 and 1902 the economist and sociologist Max Weber from Heidelberg suffered from a severe depressive crisis with multiple recurrences of its symptomatology in the following years. The biographic background of the disease process is examined. Questions regarding the specific diagnosis are discussed. Furthermore, his work shows that Weber was indirectly deeply concerned with the cultural, historical and social background conditions of depressive experience and behavior in the context of his study on Protestantic Ethics and the Spirit of Capitalism. Weber's definition of modern society as an iron cage, determined by Occidental Rationalism, shows that this cultural background demands a great amount of role conformity from the individual. Weber's theoretical approach should spark interest in the current psychopathological discussion of the characteristic structural features of a depressed personality.

Prokaryotic 2-component systems and the OmpR/PhoB superfamily.

PubMed

Nguyen, Minh-Phuong; Yoon, Joo-Mi; Cho, Man-Ho; Lee, Sang-Won

2015-11-01

In bacteria, 2-component regulatory systems (TCSs) are the critical information-processing pathways that link stimuli to specific adaptive responses. Signals perceived by membrane sensors, which are generally histidine kinases, are transmitted by response regulators (RRs) to allow cells to cope rapidly and effectively with environmental challenges. Over the past few decades, genes encoding components of TCSs and their responsive proteins have been identified, crystal structures have been described, and signaling mechanisms have been elucidated. Here, we review recent findings and interesting breakthroughs in bacterial TCS research. Furthermore, we discuss structural features, mechanisms of activation and regulation, and cross-regulation of RRs, with a focus on the largest RR family, OmpR/PhoB, to provide a comprehensive overview of these critically important signaling molecules.

Image-Guided Rendering with an Evolutionary Algorithm Based on Cloud Model

PubMed Central

2018-01-01

The process of creating nonphotorealistic rendering images and animations can be enjoyable if a useful method is involved. We use an evolutionary algorithm to generate painterly styles of images. Given an input image as the reference target, a cloud model-based evolutionary algorithm that will rerender the target image with nonphotorealistic effects is evolved. The resulting animations have an interesting characteristic in which the target slowly emerges from a set of strokes. A number of experiments are performed, as well as visual comparisons, quantitative comparisons, and user studies. The average scores in normalized feature similarity of standard pixel-wise peak signal-to-noise ratio, mean structural similarity, feature similarity, and gradient similarity based metric are 0.486, 0.628, 0.579, and 0.640, respectively. The average scores in normalized aesthetic measures of Benford's law, fractal dimension, global contrast factor, and Shannon's entropy are 0.630, 0.397, 0.418, and 0.708, respectively. Compared with those of similar method, the average score of the proposed method, except peak signal-to-noise ratio, is higher by approximately 10%. The results suggest that the proposed method can generate appealing images and animations with different styles by choosing different strokes, and it would inspire graphic designers who may be interested in computer-based evolutionary art. PMID:29805440

Automated detection of microaneurysms using robust blob descriptors

NASA Astrophysics Data System (ADS)

Adal, K.; Ali, S.; Sidibé, D.; Karnowski, T.; Chaum, E.; Mériaudeau, F.

2013-03-01

Microaneurysms (MAs) are among the first signs of diabetic retinopathy (DR) that can be seen as round dark-red structures in digital color fundus photographs of retina. In recent years, automated computer-aided detection and diagnosis (CAD) of MAs has attracted many researchers due to its low-cost and versatile nature. In this paper, the MA detection problem is modeled as finding interest points from a given image and several interest point descriptors are introduced and integrated with machine learning techniques to detect MAs. The proposed approach starts by applying a novel fundus image contrast enhancement technique using Singular Value Decomposition (SVD) of fundus images. Then, Hessian-based candidate selection algorithm is applied to extract image regions which are more likely to be MAs. For each candidate region, robust low-level blob descriptors such as Speeded Up Robust Features (SURF) and Intensity Normalized Radon Transform are extracted to characterize candidate MA regions. The combined features are then classified using SVM which has been trained using ten manually annotated training images. The performance of the overall system is evaluated on Retinopathy Online Challenge (ROC) competition database. Preliminary results show the competitiveness of the proposed candidate selection techniques against state-of-the art methods as well as the promising future for the proposed descriptors to be used in the localization of MAs from fundus images.

Three-dimensional sensor system using multistripe laser and stereo camera for environment recognition of mobile robots

NASA Astrophysics Data System (ADS)

Kim, Min Young; Cho, Hyung Suck; Kim, Jae H.

2002-10-01

In recent years, intelligent autonomous mobile robots have drawn tremendous interests as service robots for serving human or industrial robots for replacing human. To carry out the task, robots must be able to sense and recognize 3D space that they live or work. In this paper, we deal with the topic related to 3D sensing system for the environment recognition of mobile robots. For this, the structured lighting is basically utilized for a 3D visual sensor system because of the robustness on the nature of the navigation environment and the easy extraction of feature information of interest. The proposed sensing system is classified into a trinocular vision system, which is composed of the flexible multi-stripe laser projector, and two cameras. The principle of extracting the 3D information is based on the optical triangulation method. With modeling the projector as another camera and using the epipolar constraints which the whole cameras makes, the point-to-point correspondence between the line feature points in each image is established. In this work, the principle of this sensor is described in detail, and a series of experimental tests is performed to show the simplicity and efficiency and accuracy of this sensor system for 3D the environment sensing and recognition.

Comparative analysis of classification based algorithms for diabetes diagnosis using iris images.

PubMed

Samant, Piyush; Agarwal, Ravinder

2018-01-01

Photo-diagnosis is always an intriguing area for the researchers, with the advancement of image processing and computer machine vision techniques it have become more reliable and popular in recent years. The objective of this paper is to study the change in the features of iris, particularly irregularities in the pigmentation of certain areas of the iris with respect to diabetic health of an individual. Apart from the point that iris recognition concentrates on the overall structure of the iris, diagnostic techniques emphasises the local variations in the particular area of iris. Pre-image processing techniques have been applied to extract iris and thereafter, region of interest from the extracted iris have been cropped out. In order to observe the changes in the tissue pigmentation of region of interest, statistical, texture textural and wavelet features have been extracted. At the end, a comparison of accuracies of five different classifiers has been presented to classify two subject groups of diabetic and non-diabetic. Best classification accuracy has been calculated as 89.66% by the random forest classifier. Results have been shown the effectiveness and diagnostic significance of the proposed methodology. Presented piece of work offers a novel systemic perspective of non-invasive and automatic diabetic diagnosis.

Coordination of Leaf Photosynthesis, Transpiration, and Structural Traits in Rice and Wild Relatives (Genus Oryza)1[W][OA

PubMed Central

Giuliani, Rita; Koteyeva, Nuria; Voznesenskaya, Elena; Evans, Marc A.; Cousins, Asaph B.; Edwards, Gerald E.

2013-01-01

The genus Oryza, which includes rice (Oryza sativa and Oryza glaberrima) and wild relatives, is a useful genus to study leaf properties in order to identify structural features that control CO2 access to chloroplasts, photosynthesis, water use efficiency, and drought tolerance. Traits, 26 structural and 17 functional, associated with photosynthesis and transpiration were quantified on 24 accessions (representatives of 17 species and eight genomes). Hypotheses of associations within, and between, structure, photosynthesis, and transpiration were tested. Two main clusters of positively interrelated leaf traits were identified: in the first cluster were structural features, leaf thickness (Thickleaf), mesophyll (M) cell surface area exposed to intercellular air space per unit of leaf surface area (Smes), and M cell size; a second group included functional traits, net photosynthetic rate, transpiration rate, M conductance to CO2 diffusion (gm), stomatal conductance to gas diffusion (gs), and the gm/gs ratio. While net photosynthetic rate was positively correlated with gm, neither was significantly linked with any individual structural traits. The results suggest that changes in gm depend on covariations of multiple leaf (Smes) and M cell (including cell wall thickness) structural traits. There was an inverse relationship between Thickleaf and transpiration rate and a significant positive association between Thickleaf and leaf transpiration efficiency. Interestingly, high gm together with high gm/gs and a low Smes/gm ratio (M resistance to CO2 diffusion per unit of cell surface area exposed to intercellular air space) appear to be ideal for supporting leaf photosynthesis while preserving water; in addition, thick M cell walls may be beneficial for plant drought tolerance. PMID:23669746

Hotspot volcanism in the southern South Atlantic: Geophysical constraints on the evolution of the southern Walvis Ridge and the Discovery Seamounts

NASA Astrophysics Data System (ADS)

Jokat, Wilfried; Reents, Stefanie

2017-10-01

The southern Atlantic hosts a variety of magmatic structures, namely the Walvis Ridge, the Discovery Seamounts and the Shona Ridge, which are believed to be related to the evolution/movement of hotspots. Although the basement of the Walvis Ridge has been sampled at different locations, geophysical data are too sparse to provide sufficient information about its deeper structure to compare it with other hotspot tracks. The Discovery Seamounts represent a completely different type feature in a way that it cannot be connected to any onshore volcanic feature. However, geological sampling of the volcanic basement indicates that the petrology of the Discovery track is very similar to Gough Island and the southern branch of Walvis Ridge. Both structures erupted into already existing seafloor and so have been seismically investigated to document how/if an associated thermal anomaly might have modified the underlying and surrounding oceanic crust. Seismic lines for both structures indicate rather normal seismic velocity distributions for oceanic crust. Both, the Walvis Ridge and the largest volcano of the Discovery Seamounts have a maximum thickness in our research area of 13 km. An interesting difference between these structures is a high velocity cone (> 6 km/s) at 2.4 km depth in the central part of Discovery Seamount. This might indicate a primarily intrusional type of seamount such as has been reported for several similar structures. In contrast the Walvis Ridge velocity structure does not show evidences for a shallow intrusional cone, but seismic velocities typical for oceanic layer 3 at a more or less constant depth level along the entire profile. This might indicate that the ridge's present-day topography is built mainly by extrusive material.

Coordination of Leaf Photosynthesis, Transpiration, and Structural Traits in Rice and Wild Relatives (Genus Oryza).

PubMed

Giuliani, Rita; Koteyeva, Nuria; Voznesenskaya, Elena; Evans, Marc A; Cousins, Asaph B; Edwards, Gerald E

2013-07-01

The genus Oryza, which includes rice (Oryza sativa and Oryza glaberrima) and wild relatives, is a useful genus to study leaf properties in order to identify structural features that control CO(2) access to chloroplasts, photosynthesis, water use efficiency, and drought tolerance. Traits, 26 structural and 17 functional, associated with photosynthesis and transpiration were quantified on 24 accessions (representatives of 17 species and eight genomes). Hypotheses of associations within, and between, structure, photosynthesis, and transpiration were tested. Two main clusters of positively interrelated leaf traits were identified: in the first cluster were structural features, leaf thickness (Thick(leaf)), mesophyll (M) cell surface area exposed to intercellular air space per unit of leaf surface area (S(mes)), and M cell size; a second group included functional traits, net photosynthetic rate, transpiration rate, M conductance to CO(2) diffusion (g(m)), stomatal conductance to gas diffusion (g(s)), and the g(m)/g(s) ratio.While net photosynthetic rate was positively correlated with gm, neither was significantly linked with any individual structural traits. The results suggest that changes in gm depend on covariations of multiple leaf (S(mes)) and M cell (including cell wall thickness) structural traits. There was an inverse relationship between Thick(leaf) and transpiration rate and a significant positive association between Thick(leaf) and leaf transpiration efficiency. Interestingly, high g(m) together with high g(m)/g(s) and a low S(mes)/g(m) ratio (M resistance to CO(2) diffusion per unit of cell surface area exposed to intercellular air space) appear to be ideal for supporting leaf photosynthesis while preserving water; in addition, thick M cell walls may be beneficial for plant drought tolerance.

Large stationary wave features appearing repeatedly at the cloud top of Venus

NASA Astrophysics Data System (ADS)

Kouyama, Toru; Imamura, Takeshi; Taguchi, Makoto; Fukuhara, Tetsuya; Sato, Takao M.; Hashimoto, George L.; Futaguchi, Masahiko; Takamura, Mao; Yamada, Takeru; Satoh, Takehiko; Nakamura, Masato; Akatsuki Science Team

2017-10-01

At the first observation sequence after Akatsuki’s Venus orbiter re-insertion (VOI-R) on December 7, 2015, Akatsuki revealed an existence of a large-scale “bow-shaped” feature staying at almost same geographic location (above Aphrodite Terra) at the cloud top level with the Longwave Infrared Camera (LIR) and Ultra Violet Imager (UVI). It expanded ~10,000 km from south to north and bended to downstream side of the super-rotation of Venus. A numerical calculation in Fukuhara et al. (2017) suggested that a gravity wave generated in the lower atmosphere can propagate upward to the cloud top and reproduce the observed bow-shape structure. Because the wave can transport momentum to the upper atmosphere which possibly decelerates the super-rotation, it is an interesting topic whether the stationary wave event is regular or just an occasional event. For more than three Venus years, or four Venus solar days, Akatsuki has observed huge stationary wave features in LIR images again and again since the VOI-R. It has been confirmed that four high-altitude regions, east and west part of Aphrodite Terra, Atra Regio, and Beta Regio, accompany with the large stationary features. All four regions are located in lower latitudes (< 30°), while no clear stationary feature has been confirmed above Maxwell Mountain, which is the highest mountain but located at a high latitude (60°), indicating geographical and latitudinal dependencies of the generation of the stationary waves. Akatsuki also reveals the stationary features can be considered as "daily" phenomena in Venus atmosphere. At every timing when the four high-altitude regions were passing afternoon region of Venus, huge stationary waves became clearer. On the other hand, when the high mountains were located around mid-night and morning, stationary features were much weaker than that in afternoon, or cannot be confirmed, indicating strong local time dependency of the appearance. Since lower latitude has more incident solar flux and afternoon area experiences longer solar heating than morning area, the geographical and the local time dependencies indicate that interaction between mountains and solar heating or solar fixed atmospheric structure may cause the large-scale features.

Thermal characterization of QSH crashes in RFX-mod

NASA Astrophysics Data System (ADS)

Fassina, Alessandro; Gobbin, Marco; Franz, Paolo; Marrelli, Lionello; Ruzzon, Alberto

2012-10-01

QSH (Quasi Single Helicity) states have gained a growing interest in RFP research since they show improved confinement and transport features with respect to standard discharges. However, ITBs associated with QSH states can be obtained only in a transient way, and in general with a shorter lifetime with respect to that of the QSH phase [1]. In this work the analysis has essentially the purpose of confirming, with TS data, the Te dynamics seen with the double filter, multichord SXR spectrometer in [1]: TS data allow a better spatial definition of temperature profile and a more reliable description of plasma edge. Te profile features in rising and crashing phases are determined via ensemble averaging, possible precursors of thermal crashes are identified, while q(r) behavior is studied identifying the thermal structures associated with rational surfaces. [4pt] [1] Ruzzon et al, 39th EPS Conference, P2.023

Fingerprinting Breast Cancer vs. Normal Mammary Cells by Mass Spectrometric Analysis of Volatiles

NASA Astrophysics Data System (ADS)

He, Jingjing; Sinues, Pablo Martinez-Lozano; Hollmén, Maija; Li, Xue; Detmar, Michael; Zenobi, Renato

2014-06-01

There is increasing interest in the development of noninvasive diagnostic methods for early cancer detection, to improve the survival rate and quality of life of cancer patients. Identification of volatile metabolic compounds may provide an approach for noninvasive early diagnosis of malignant diseases. Here we analyzed the volatile metabolic signature of human breast cancer cell lines versus normal human mammary cells. Volatile compounds in the headspace of conditioned culture medium were directly fingerprinted by secondary electrospray ionization-mass spectrometry. The mass spectra were subsequently treated statistically to identify discriminating features between normal vs. cancerous cell types. We were able to classify different samples by using feature selection followed by principal component analysis (PCA). Additionally, high-resolution mass spectrometry allowed us to propose their chemical structures for some of the most discriminating molecules. We conclude that cancerous cells can release a characteristic odor whose constituents may be used as disease markers.

Application of Bottlebrush Block Copolymers as Photonic Crystals.

PubMed

Liberman-Martin, Allegra L; Chu, Crystal K; Grubbs, Robert H

2017-07-01

Brush block copolymers are a class of comb polymers that feature polymeric side chains densely grafted to a linear backbone. These polymers display interesting properties due to their dense functionality, low entanglement, and ability to rapidly self-assemble to highly ordered nanostructures. The ability to prepare brush polymers with precise structures has been enabled by advancements in controlled polymerization techniques. This Feature Article highlights the development of brush block copolymers as photonic crystals that can reflect visible to near-infrared wavelengths of light. Fabrication of these materials relies on polymer self-assembly processes to achieve nanoscale ordering, which allows for the rapid preparation of photonic crystals from common organic chemical feedstocks. The characteristic physical properties of brush block copolymers are discussed, along with methods for their preparation. Strategies to induce self-assembly at ambient temperatures and the use of blending techniques to tune photonic properties are emphasized. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Analysis of macrolinguistic aspects of narratives from individuals with Alzheimer's disease, mild cognitive impairment, and no cognitive impairment.

PubMed

Toledo, Cíntia Matsuda; Aluísio, Sandra Maria; Dos Santos, Leandro Borges; Brucki, Sonia Maria Dozzi; Trés, Eduardo Sturzeneker; de Oliveira, Maira Okada; Mansur, Letícia Lessa

2018-01-01

The depiction of features in discourse production promotes accurate diagnosis and helps to establish the therapeutic intervention in cognitive impairment and dementia. We aimed to identify alterations in the macrolinguistic aspects of discourse using a new computational tool. Sixty individuals, aged 60 years and older, were distributed in three different groups: mild Alzheimer's disease (mAD), amnestic mild cognitive impairment, and healthy controls. A narrative created by individuals was analyzed through the Coh-Metrix-Dementia program, extracting the features of interest automatically. mAD showed worse overall performance compared to the other groups: less informative discourse, greater impairment in global coherence, greater modalization, and inferior narrative structure. It was not possible to discriminate between amnestic mild cognitive impairment and healthy controls. Our results are in line with the literature, verifying a pathological change in the macrostructure of discourse in mAD.

DBAASP v.2: an enhanced database of structure and antimicrobial/cytotoxic activity of natural and synthetic peptides

PubMed Central

Pirtskhalava, Malak; Gabrielian, Andrei; Cruz, Phillip; Griggs, Hannah L.; Squires, R. Burke; Hurt, Darrell E.; Grigolava, Maia; Chubinidze, Mindia; Gogoladze, George; Vishnepolsky, Boris; Alekseev, Vsevolod; Rosenthal, Alex; Tartakovsky, Michael

2016-01-01

Antimicrobial peptides (AMPs) are anti-infectives that may represent a novel and untapped class of biotherapeutics. Increasing interest in AMPs means that new peptides (natural and synthetic) are discovered faster than ever before. We describe herein a new version of the Database of Antimicrobial Activity and Structure of Peptides (DBAASPv.2, which is freely accessible at http://dbaasp.org). This iteration of the database reports chemical structures and empirically-determined activities (MICs, IC50, etc.) against more than 4200 specific target microbes for more than 2000 ribosomal, 80 non-ribosomal and 5700 synthetic peptides. Of these, the vast majority are monomeric, but nearly 200 of these peptides are found as homo- or heterodimers. More than 6100 of the peptides are linear, but about 515 are cyclic and more than 1300 have other intra-chain covalent bonds. More than half of the entries in the database were added after the resource was initially described, which reflects the recent sharp uptick of interest in AMPs. New features of DBAASPv.2 include: (i) user-friendly utilities and reporting functions, (ii) a ‘Ranking Search’ function to query the database by target species and return a ranked list of peptides with activity against that target and (iii) structural descriptions of the peptides derived from empirical data or calculated by molecular dynamics (MD) simulations. The three-dimensional structural data are critical components for understanding structure–activity relationships and for design of new antimicrobial drugs. We created more than 300 high-throughput MD simulations specifically for inclusion in DBAASP. The resulting structures are described in the database by novel trajectory analysis plots and movies. Another 200+ DBAASP entries have links to the Protein DataBank. All of the structures are easily visualized directly in the web browser. PMID:26578581

Gold Raspberry-Like Colloidosomes Prepared at the Water-Nitromethane Interface.

PubMed

Smirnov, Evgeny; Peljo, Pekka; Girault, Hubert H

2018-02-27

In this study, we propose a simple shake-flask method to produce micron-size colloidosomes from a liquid-liquid interface functionalized with a gold nanoparticle (AuNP) film. A step-by-step extraction process of an organic phase partially miscible with water led to the formation of raspberry-like structures covered and protected by a gold nanofilm. The distinctive feature of the prepared colloidosomes is a very thin shell consisting of small AuNPs of 12 or 38 nm in diameter instead of several hundred nanometers reported previously. The interesting and remarkable property of the proposed approach is their reversibility: the colloidosomes may be easily transformed back to a nanofilm state simply by adding pure organic solvent. The obtained colloidosomes have a broadband absorbance spectrum, which makes them of great interest in applications such as photothermal therapy, surface-enhanced Raman spectroscopy studies, and microreactor vesicles for interfacial electrocatalysis.

Resonant tunneling diode based on band gap engineered graphene antidot structures

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

Palla, Penchalaiah, E-mail: penchalaiah.palla@vit.ac.in; Ethiraj, Anita S.; Raina, J. P.

The present work demonstrates the operation and performance of double barrier Graphene Antidot Resonant Tunnel Diode (DBGA-RTD). Non-Equilibrium Green’s Function (NEGF) frame work with tight-binding Hamiltonian and 2-D Poisson equations were solved self-consistently for device study. The interesting feature in this device is that it is an all graphene RTD with band gap engineered graphene antidot tunnel barriers. Another interesting new finding is that it shows negative differential resistance (NDR), which involves the resonant tunneling in the graphene quantum well through both the electron and hole bound states. The Graphene Antidot Lattice (GAL) barriers in this device efficiently improved themore » Peak to Valley Ratio to approximately 20 even at room temperature. A new fitting model is developed for the number of antidots and their corresponding effective barrier width, which will help in determining effective barrier width of any size of actual antidot geometry.« less

A tunable azine covalent organic framework platform for visible light-induced hydrogen generation

PubMed Central

Vyas, Vijay S.; Haase, Frederik; Stegbauer, Linus; Savasci, Gökcen; Podjaski, Filip; Ochsenfeld, Christian; Lotsch, Bettina V.

2015-01-01

Hydrogen evolution from photocatalytic reduction of water holds promise as a sustainable source of carbon-free energy. Covalent organic frameworks (COFs) present an interesting new class of photoactive materials, which combine three key features relevant to the photocatalytic process, namely crystallinity, porosity and tunability. Here we synthesize a series of water- and photostable 2D azine-linked COFs from hydrazine and triphenylarene aldehydes with varying number of nitrogen atoms. The electronic and steric variations in the precursors are transferred to the resulting frameworks, thus leading to a progressively enhanced light-induced hydrogen evolution with increasing nitrogen content in the frameworks. Our results demonstrate that by the rational design of COFs on a molecular level, it is possible to precisely adjust their structural and optoelectronic properties, thus resulting in enhanced photocatalytic activities. This is expected to spur further interest in these photofunctional frameworks where rational supramolecular engineering may lead to new material applications. PMID:26419805

ScMO(BO3) (M = Ca and Cd): new Sc-based oxyborates featuring interesting edge-sharing sandwich-like chains and UV cut-off edges.

PubMed

Ma, Ruru; Xu, Dongdong; Yang, Yun; Su, Xin; Lei, Binghua; Yang, Zhihua; Pan, Shilie

2017-11-07

Two new isostructural rare-earth oxyborates ScMO(BO 3 ) (M = Ca and Cd) with a three-dimensional (3D) cationic framework and parallel arranged [BO 3 ] triangles have been synthesized by the flux method. In the 3D cationic framework, an interesting sandwich-like basic building unit (BBU) is constructed by two [Ca(1)O 4 ] 6- chains and two [Sc(1)O 4 ] 5- chains. ScMO(BO 3 ) melt incongruently, which shows that title compounds can be grown by the flux method. The UV cut-off edges for ScCaO(BO 3 ) and ScCdO(BO 3 ) are 230 and 249 nm, respectively. In addition, the first-principles calculations are performed to gain further insights into the relationship between the microscopic electronic structures and associated optical properties.

Distinct Tertiary Lymphoid Structure Associations and Their Prognostic Relevance in HER2 Positive and Negative Breast Cancers.

PubMed

Liu, Xia; Tsang, Julia Y S; Hlaing, Thazin; Hu, Jintao; Ni, Yun-Bi; Chan, Siu Ki; Cheung, Sai Yin; Tse, Gary M

2017-11-01

The presence of tumor infiltrating lymphocytes (TIL) is associated with favorable prognosis. Recent evidence suggested that not only their density, but also the spatial organization as tertiary lymphoid structures (TLS), play a key role in determining patient survival. In a cohort of 248 breast cancers, the clinicopathologic association and prognostic role of TLS was examined. Tertiary lymphoid structures were associated with higher tumor grade, apocrine phenotype, necrosis, extensive in situ component, lymphovascular invasion (LVI), and high TIL. For biomarkers, TLS were associated with hormone receptors negativity, HER2 positivity, and c-kit expression. Tertiary lymphoid structures were significantly related to better disease-free survival (DFS) in HER2 positive (HER2+) breast cancers (log-rank = 4.054), which was not dependent on high TIL status. The combined TLS and TIL status was an independent favorable factor associated with DFS in those cases. Interestingly, tumor cell infiltration into the TLS was found in 41.9% of TLS positive cases. It was associated with LVI in HER2 negative (HER2-) TLS positive (particularly estrogen receptor positive [ER+] HER2-) cases. In the ER+ HER2- cases, tumor cell infiltration into TLS was also associated with increased pathologic nodal stage (pN) stage and nodal involvement. Tertiary lymphoid structures showed a similar relationship with clinicopathologic features and biomarkers as TIL. The presence of TLS, irrespective of TIL level, could be an important favorable prognostic indicator in HER2+ breast cancer patients. Given the significance of TLS in promoting effective antitumor immunity, further understanding of its organization and induction may provide new opportunities to improve the current immunotherapy strategies. Despite recent interest on the clinical value of tumor infiltrating lymphocyte (TIL), little was known on the clinical significance on their spatial organization as tertiary lymphoid structures (TLS). Although TLS showed similar relationships with clinicopathologic features and biomarkers as TIL, the prognostic value of TLS, particularly in HER2 positive cancers, was independent of TIL. Moreover, tumor infiltration could be present in TLS which appears to be related to tumor invasion in HER2 negative cancers. Overall, the results demonstrated the additional value for TLS in HER2 cancer subtypes. Further investigations and its standardized evaluation will enhance its use as standard practice. © AlphaMed Press 2017.

Testing of Haar-Like Feature in Region of Interest Detection for Automated Target Recognition (ATR) System

NASA Technical Reports Server (NTRS)

Zhang, Yuhan; Lu, Dr. Thomas

2010-01-01

The objectives of this project were to develop a ROI (Region of Interest) detector using Haar-like feature similar to the face detection in Intel's OpenCV library, implement it in Matlab code, and test the performance of the new ROI detector against the existing ROI detector that uses Optimal Trade-off Maximum Average Correlation Height filter (OTMACH). The ROI detector included 3 parts: 1, Automated Haar-like feature selection in finding a small set of the most relevant Haar-like features for detecting ROIs that contained a target. 2, Having the small set of Haar-like features from the last step, a neural network needed to be trained to recognize ROIs with targets by taking the Haar-like features as inputs. 3, using the trained neural network from the last step, a filtering method needed to be developed to process the neural network responses into a small set of regions of interests. This needed to be coded in Matlab. All the 3 parts needed to be coded in Matlab. The parameters in the detector needed to be trained by machine learning and tested with specific datasets. Since OpenCV library and Haar-like feature were not available in Matlab, the Haar-like feature calculation needed to be implemented in Matlab. The codes for Adaptive Boosting and max/min filters in Matlab could to be found from the Internet but needed to be integrated to serve the purpose of this project. The performance of the new detector was tested by comparing the accuracy and the speed of the new detector against the existing OTMACH detector. The speed was referred as the average speed to find the regions of interests in an image. The accuracy was measured by the number of false positives (false alarms) at the same detection rate between the two detectors.

Optimal contact definition for reconstruction of contact maps.

PubMed

Duarte, Jose M; Sathyapriya, Rajagopal; Stehr, Henning; Filippis, Ioannis; Lappe, Michael

2010-05-27

Contact maps have been extensively used as a simplified representation of protein structures. They capture most important features of a protein's fold, being preferred by a number of researchers for the description and study of protein structures. Inspired by the model's simplicity many groups have dedicated a considerable amount of effort towards contact prediction as a proxy for protein structure prediction. However a contact map's biological interest is subject to the availability of reliable methods for the 3-dimensional reconstruction of the structure. We use an implementation of the well-known distance geometry protocol to build realistic protein 3-dimensional models from contact maps, performing an extensive exploration of many of the parameters involved in the reconstruction process. We try to address the questions: a) to what accuracy does a contact map represent its corresponding 3D structure, b) what is the best contact map representation with regard to reconstructability and c) what is the effect of partial or inaccurate contact information on the 3D structure recovery. Our results suggest that contact maps derived from the application of a distance cutoff of 9 to 11A around the Cbeta atoms constitute the most accurate representation of the 3D structure. The reconstruction process does not provide a single solution to the problem but rather an ensemble of conformations that are within 2A RMSD of the crystal structure and with lower values for the pairwise average ensemble RMSD. Interestingly it is still possible to recover a structure with partial contact information, although wrong contacts can lead to dramatic loss in reconstruction fidelity. Thus contact maps represent a valid approximation to the structures with an accuracy comparable to that of experimental methods. The optimal contact definitions constitute key guidelines for methods based on contact maps such as structure prediction through contacts and structural alignments based on maximum contact map overlap.

Optimal contact definition for reconstruction of Contact Maps

PubMed Central

2010-01-01

Background Contact maps have been extensively used as a simplified representation of protein structures. They capture most important features of a protein's fold, being preferred by a number of researchers for the description and study of protein structures. Inspired by the model's simplicity many groups have dedicated a considerable amount of effort towards contact prediction as a proxy for protein structure prediction. However a contact map's biological interest is subject to the availability of reliable methods for the 3-dimensional reconstruction of the structure. Results We use an implementation of the well-known distance geometry protocol to build realistic protein 3-dimensional models from contact maps, performing an extensive exploration of many of the parameters involved in the reconstruction process. We try to address the questions: a) to what accuracy does a contact map represent its corresponding 3D structure, b) what is the best contact map representation with regard to reconstructability and c) what is the effect of partial or inaccurate contact information on the 3D structure recovery. Our results suggest that contact maps derived from the application of a distance cutoff of 9 to 11Å around the Cβ atoms constitute the most accurate representation of the 3D structure. The reconstruction process does not provide a single solution to the problem but rather an ensemble of conformations that are within 2Å RMSD of the crystal structure and with lower values for the pairwise average ensemble RMSD. Interestingly it is still possible to recover a structure with partial contact information, although wrong contacts can lead to dramatic loss in reconstruction fidelity. Conclusions Thus contact maps represent a valid approximation to the structures with an accuracy comparable to that of experimental methods. The optimal contact definitions constitute key guidelines for methods based on contact maps such as structure prediction through contacts and structural alignments based on maximum contact map overlap. PMID:20507547

Have personal statements become impersonal? An evaluation of personal statements in anesthesiology residency applications.

PubMed

Max, Bryan A; Gelfand, Brian; Brooks, Meredith R; Beckerly, Rena; Segal, Scott

2010-08-01

To evaluate personal statements submitted to a major academic anesthesiology program to determine the prevalence of common features and overall subjective quality, and to survey anesthesiology program directors as to how they utilized these statements during the resident selection process. Structured analysis of de-identified personal statements and Internet-based survey of program directors. Large academic anesthesiology training program. 670 applicant personal statements and academic anesthesiology program directors. Prevalence of 13 specific essay features and 8 quality ratings were calculated for the essays and correlated with other aspects of the residency application, as abstracted from the Electronic Residency Application Service (ERAS) files. A 6-question survey regarding use of personal statements was collected from program directors. 70 of 131 program directors queried responded to our survey. Interest in physiology and pharmacology, enjoyment of a hands-on specialty, and desire to comfort anxious patients were each mentioned in more than half of the essays. Candidates invited for an interview had essays that received higher quality ratings than essays of those not invited (P = 0.02 to P < 0.0001). Higher quality ratings were also strongly associated with graduation from a U.S. or Canadian medical school, applicant file screening score, female gender, and younger age. Interrater reliability was good (kappa 0.75-0.99 for structural features, and 0.45-0.65 for quality features). More than 90% of program directors found proper use of English to be a somewhat or very important feature of the essay. Only 41% found the personal statement to be very or somewhat important in selecting candidates for interview invitations. However, over 90% stated that they used the statements during actual interviews with invited applicants. The data showed a high prevalence of common features found within personal statements and a general ambivalence amongst those program directors for whom the statements were intended. Copyright 2010 Elsevier Inc. All rights reserved.

Effect of Heterogeneous Interest Similarity on the Spread of Information in Mobile Social Networks

NASA Astrophysics Data System (ADS)

Zhao, Narisa; Sui, Guoqin; Yang, Fan

2018-06-01

Mobile social networks (MSNs) are important platforms for spreading news. The fact that individuals usually forward information aligned with their own interests inevitably changes the dynamics of information spread. Thereby, first we present a theoretical model based on the discrete Markov chain and mean field theory to evaluate the effect of interest similarity on the information spread in MSNs. Meanwhile, individuals' interests are heterogeneous and vary with time. These two features result in interest shift behavior, and both features are considered in our model. A leveraging simulation demonstrates the accuracy of our model. Moreover, the basic reproduction number R0 is determined. Further extensive numerical analyses based on the model indicate that interest similarity has a critical impact on information spread at the early spreading stage. Specifically, the information always spreads more quickly and widely if the interest similarity between an individual and the information is higher. Finally, five actual data sets from Sina Weibo illustrate the validity of the model.

Interest point detection for hyperspectral imagery

NASA Astrophysics Data System (ADS)

Dorado-Muñoz, Leidy P.; Vélez-Reyes, Miguel; Roysam, Badrinath; Mukherjee, Amit

2009-05-01

This paper presents an algorithm for automated extraction of interest points (IPs)in multispectral and hyperspectral images. Interest points are features of the image that capture information from its neighbours and they are distinctive and stable under transformations such as translation and rotation. Interest-point operators for monochromatic images were proposed more than a decade ago and have since been studied extensively. IPs have been applied to diverse problems in computer vision, including image matching, recognition, registration, 3D reconstruction, change detection, and content-based image retrieval. Interest points are helpful in data reduction, and reduce the computational burden of various algorithms (like registration, object detection, 3D reconstruction etc) by replacing an exhaustive search over the entire image domain by a probe into a concise set of highly informative points. An interest operator seeks out points in an image that are structurally distinct, invariant to imaging conditions, stable under geometric transformation, and interpretable which are good candidates for interest points. Our approach extends ideas from Lowe's keypoint operator that uses local extrema of Difference of Gaussian (DoG) operator at multiple scales to detect interest point in gray level images. The proposed approach extends Lowe's method by direct conversion of scalar operations such as scale-space generation, and extreme point detection into operations that take the vector nature of the image into consideration. Experimental results with RGB and hyperspectral images which demonstrate the potential of the method for this application and the potential improvements of a fully vectorial approach over band-by-band approaches described in the literature.

Controlling destructive quantum interference in tunneling junctions comprising self-assembled monolayers via bond topology and functional groups† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c8sc00165k

PubMed Central

Zhang, Yanxi; Ye, Gang; Soni, Saurabh; Qiu, Xinkai; Krijger, Theodorus L.; Jonkman, Harry T.; Carlotti, Marco; Sauter, Eric; Zharnikov, Michael

2018-01-01

Quantum interference effects (QI) are of interest in nano-scale devices based on molecular tunneling junctions because they can affect conductance exponentially through minor structural changes. However, their utilization requires the prediction and deterministic control over the position and magnitude of QI features, which remains a significant challenge. In this context, we designed and synthesized three benzodithiophenes based molecular wires; one linearly-conjugated, one cross-conjugated and one cross-conjugated quinone. Using eutectic Ga–In (EGaIn) and CP-AFM, we compared them to a well-known anthraquinone in molecular junctions comprising self-assembled monolayers (SAMs). By combining density functional theory and transition voltage spectroscopy, we show that the presence of an interference feature and its position can be controlled independently by manipulating bond topology and electronegativity. This is the first study to separate these two parameters experimentally, demonstrating that the conductance of a tunneling junction depends on the position and depth of a QI feature, both of which can be controlled synthetically. PMID:29896382

Dynamic and structural features of a case of compulsive neurosis as revealed in dreams.

PubMed

Levitan, H L

Several examples of the manifest dreams reported by a patient with a compulsive neurosis are presented. An outstanding feature of the dreams was the sudden shift of the dreamer's self-representation from the role of criminal to the role of policeman. This shift is thought to parallel the oscillation between unconscious instinctual gratification and conscious attempts at reparation which is the main dynamic feature of the compulsive neurosis in waking life. The shift of orientation of the self reflects the operation of early defense mechanisms against the sadistic impulse. It also portrays graphically an early stage in the internalization process which leads ultimately to the creation of the superego. The repetitive nature of the dreams indicated that the patient had become fixated at this particular point in the course of his psychic development. It is interesting to note that like the Rat Man this patient suffered from a chronically undescended testicle. The real defect in the sexual apparatus in both patients may have been a factor which favored regression of the libido from the genital stage to the anal-sadistic stage.

Structural and Functional Analysis of the Human HDAC4 Catalytic Domain Reveals a Regulatory Structural Zinc-binding Domain*S⃞

PubMed Central

Bottomley, Matthew J.; Lo Surdo, Paola; Di Giovine, Paolo; Cirillo, Agostino; Scarpelli, Rita; Ferrigno, Federica; Jones, Philip; Neddermann, Petra; De Francesco, Raffaele; Steinkühler, Christian; Gallinari, Paola; Carfí, Andrea

2008-01-01

Histone deacetylases (HDACs) regulate chromatin status and gene expression, and their inhibition is of significant therapeutic interest. To date, no biological substrate for class IIa HDACs has been identified, and only low activity on acetylated lysines has been demonstrated. Here, we describe inhibitor-bound and inhibitor-free structures of the histone deacetylase-4 catalytic domain (HDAC4cd) and of an HDAC4cd active site mutant with enhanced enzymatic activity toward acetylated lysines. The structures presented, coupled with activity data, provide the molecular basis for the intrinsically low enzymatic activity of class IIa HDACs toward acetylated lysines and reveal active site features that may guide the design of class-specific inhibitors. In addition, these structures reveal a conformationally flexible structural zinc-binding domain conserved in all class IIa enzymes. Importantly, either the mutation of residues coordinating the structural zinc ion or the binding of a class IIa selective inhibitor prevented the association of HDAC4 with the N-CoR·HDAC3 repressor complex. Together, these data suggest a key role of the structural zinc-binding domain in the regulation of class IIa HDAC functions. PMID:18614528

Structural and functional analysis of the human HDAC4 catalytic domain reveals a regulatory structural zinc-binding domain.

PubMed

Bottomley, Matthew J; Lo Surdo, Paola; Di Giovine, Paolo; Cirillo, Agostino; Scarpelli, Rita; Ferrigno, Federica; Jones, Philip; Neddermann, Petra; De Francesco, Raffaele; Steinkühler, Christian; Gallinari, Paola; Carfí, Andrea

2008-09-26

Histone deacetylases (HDACs) regulate chromatin status and gene expression, and their inhibition is of significant therapeutic interest. To date, no biological substrate for class IIa HDACs has been identified, and only low activity on acetylated lysines has been demonstrated. Here, we describe inhibitor-bound and inhibitor-free structures of the histone deacetylase-4 catalytic domain (HDAC4cd) and of an HDAC4cd active site mutant with enhanced enzymatic activity toward acetylated lysines. The structures presented, coupled with activity data, provide the molecular basis for the intrinsically low enzymatic activity of class IIa HDACs toward acetylated lysines and reveal active site features that may guide the design of class-specific inhibitors. In addition, these structures reveal a conformationally flexible structural zinc-binding domain conserved in all class IIa enzymes. Importantly, either the mutation of residues coordinating the structural zinc ion or the binding of a class IIa selective inhibitor prevented the association of HDAC4 with the N-CoR.HDAC3 repressor complex. Together, these data suggest a key role of the structural zinc-binding domain in the regulation of class IIa HDAC functions.

Direct Femtosecond Laser Surface Structuring with Optical Vortex Beams Generated by a q-plate

PubMed Central

JJ Nivas, Jijil; He, Shutong; Rubano, Andrea; Vecchione, Antonio; Paparo, Domenico; Marrucci, Lorenzo; Bruzzese, Riccardo; Amoruso, Salvatore

2015-01-01

Creation of patterns and structures on surfaces at the micro- and nano-scale is a field of growing interest. Direct femtosecond laser surface structuring with a Gaussian-like beam intensity profile has already distinguished itself as a versatile method to fabricate surface structures on metals and semiconductors. Here we present an approach for direct femtosecond laser surface structuring based on optical vortex beams with different spatial distributions of the state of polarization, which are easily generated by means of a q-plate. The different states of an optical vortex beam carrying an orbital angular momentum ℓ = ±1 are used to demonstrate the fabrication of various regular surface patterns on silicon. The spatial features of the regular rippled and grooved surface structures are correlated with the state of polarization of the optical vortex beam. Moreover, scattered surface wave theory approach is used to rationalize the dependence of the surface structures on the local state of the laser beam characteristics (polarization and fluence). The present approach can be further extended to fabricate even more complex and unconventional surface structures by exploiting the possibilities offered by femtosecond optical vector fields. PMID:26658307

Sotos syndrome: An interesting disorder with gigantism.

PubMed

Nalini, A; Biswas, Arundhati

2008-07-01

We report the case of a 16-year-old boy diagnosed to have Sotos syndrome, with rare association of bilateral primary optic atrophy and epilepsy. He presented with accelerated linear growth, facial gestalt, distinctive facial features, seizures and progressive diminution of vision in both eyes. He had features of gigantism from early childhood. An MRI showed that brain and endocrine functions were normal. This case is of interest, as we have to be aware of this not so rare disorder. In addition to the classic features, there were two unusual associations with Sotos syndrome in the patient.

Factors in life science textbooks that may deter girls' interest in science

NASA Astrophysics Data System (ADS)

Potter, Ellen F.; Rosser, Sue V.

In order to examine factors that may deter girls' interest in science, five seventh-grade life science textbooks were analyzed for sexism in language, images, and curricular content, and for features of activities that have been found to be useful for motivating girls. Although overt sexism was not apparent, subtle forms of sexism in the selection of language, images, and curricular content were found. Activities had some features useful to girls, but other features were seldom included. Teachers may wish to use differences that were found among texts as one basis for text selection.

Sotos syndrome: An interesting disorder with gigantism

PubMed Central

Nalini, A.; Biswas, Arundhati

2008-01-01

We report the case of a 16-year-old boy diagnosed to have Sotos syndrome, with rare association of bilateral primary optic atrophy and epilepsy. He presented with accelerated linear growth, facial gestalt, distinctive facial features, seizures and progressive diminution of vision in both eyes. He had features of gigantism from early childhood. An MRI showed that brain and endocrine functions were normal. This case is of interest, as we have to be aware of this not so rare disorder. In addition to the classic features, there were two unusual associations with Sotos syndrome in the patient. PMID:19893668

Different Strokes for Different Folks: How Individual Interest Moderates the Effects of Situational Factors on Task Interest

ERIC Educational Resources Information Center

Durik, Amanda M.; Harackiewicz, Judith M.

2007-01-01

Individual interest was examined as a moderator of effects of situational factors designed to catch and hold task interest. In Study 1, 96 college students learned a math technique with materials enhanced with collative features (catch) versus not. Catch promoted motivation among participants with low individual interest in math (IIM) but hampered…

Wrinkle ridges on Venusian plains: Indicators of shallow crustal stress orientations at local and regional scales

NASA Technical Reports Server (NTRS)

Mcgill, George E.

1992-01-01

The plains regions of Venus exhibit a complex array of structural features, including deformation belts of various types, wrinkle ridges, grabens, and enigmatic radar-bright linears. Probably the most pervasive of these structures are the wrinkle ridges, which appear to be morphologically identical to their counterparts on the Moon and Mars. Almost all workers agree that wrinkle ridges result from horizontal compressive stresses in the crust; they either are explained as flexural fold structures, or alternatively as scarps or folds related to reverse faults. Wrinkle ridges generally are narrow, have small amplitudes, and commonly are closely spaced as well, characteristics that imply a shallow crustal origin. If wrinkle ridges are due to horizontally directed compressive stresses in the shallow crust, as generally has been inferred, then the trends of these features provide a means to map both local and regional orientations of principal stresses in the uppermost part of the venusian crust: maximum compressive stress is normal to the ridges, minimum compressive stress is normal to the topographic surface, and thus the wrinkle ridge trends trace the orientation of the intermediate principal stress. Because there are few plains areas on Venus totally devoid of wrinkle ridges, it should be possible to establish a number of interesting relationships on a near-global scale by mapping the trends of wrinkle ridges wherever they occur. The present study is addressing three questions: (1) Do the trends of wrinkle ridges define domains that are large relative to the sizes of individual plains regions? If so, can these domains be related to large-scale topographic or geologic features? (2) Are regional trends of wrinkle ridges affected by local features such as coronae? If so, is it possible to determine the relative ages of the far-field and local stresses from detailed study of trend inheritance or superposition relationships? (3) What is the relationship between wrinkle ridges and the larger ridges that make up ridge belts?

An Efficient Method to Detect Mutual Overlap of a Large Set of Unordered Images for Structure-From

NASA Astrophysics Data System (ADS)

Wang, X.; Zhan, Z. Q.; Heipke, C.

2017-05-01

Recently, low-cost 3D reconstruction based on images has become a popular focus of photogrammetry and computer vision research. Methods which can handle an arbitrary geometric setup of a large number of unordered and convergent images are of particular interest. However, determining the mutual overlap poses a considerable challenge. We propose a new method which was inspired by and improves upon methods employing random k-d forests for this task. Specifically, we first derive features from the images and then a random k-d forest is used to find the nearest neighbours in feature space. Subsequently, the degree of similarity between individual images, the image overlaps and thus images belonging to a common block are calculated as input to a structure-from-motion (sfm) pipeline. In our experiments we show the general applicability of the new method and compare it with other methods by analyzing the time efficiency. Orientations and 3D reconstructions were successfully conducted with our overlap graphs by sfm. The results show a speed-up of a factor of 80 compared to conventional pairwise matching, and of 8 and 2 compared to the VocMatch approach using 1 and 4 CPU, respectively.

Laser-assisted generation of periodic structures on a steel surface: A method for increasing microhardness

NASA Astrophysics Data System (ADS)

Razi, Sepehr; Ghasemi, Fatemeh

2018-02-01

Stainless steel grade 316L is a commonly used metal in various industrial applications because of its excellent resistance to corrosion and great welding and biocompatibility characteristics. Here, the laser-induced micro/nanostructures generation on the steel surface is investigated. A femtosecond ultrashort pulsed laser is selected in this regard, and various irradiation circumstances are considered for two groups of specimens possessing different initial roughness. It turns out that regular periodic ripples with spatial periodicities less than the laser wavelength are generated on both groups at irradiation fluences ≤ 2 J/cm2. Furthermore, it figures out that each ripple is composed of the closely created nano dimension structures. Vickers micro-hardness test is also utilized to examine the alterations of the surface hardness features. Moreover, variations of the surface chemistry are studied and discussions related to the most effective factors in surface hardness raise/decrease are presented. Results reveal the potential benefits of the femtosecond laser technique, such as its flexibility and ease of implementation in controlled modification of the surface features. Thus, it might be of interest to manufacturers looking for precise surface morphology, chemistry and hardness alterations.

Focused conformational sampling in proteins

NASA Astrophysics Data System (ADS)

Bacci, Marco; Langini, Cassiano; Vymětal, Jiří; Caflisch, Amedeo; Vitalis, Andreas

2017-11-01

A detailed understanding of the conformational dynamics of biological molecules is difficult to obtain by experimental techniques due to resolution limitations in both time and space. Computer simulations avoid these in theory but are often too short to sample rare events reliably. Here we show that the progress index-guided sampling (PIGS) protocol can be used to enhance the sampling of rare events in selected parts of biomolecules without perturbing the remainder of the system. The method is very easy to use as it only requires as essential input a set of several features representing the parts of interest sufficiently. In this feature space, new states are discovered by spontaneous fluctuations alone and in unsupervised fashion. Because there are no energetic biases acting on phase space variables or projections thereof, the trajectories PIGS generates can be analyzed directly in the framework of transition networks. We demonstrate the possibility and usefulness of such focused explorations of biomolecules with two loops that are part of the binding sites of bromodomains, a family of epigenetic "reader" modules. This real-life application uncovers states that are structurally and kinetically far away from the initial crystallographic structures and are also metastable. Representative conformations are intended to be used in future high-throughput virtual screening campaigns.

The 2D analytic signal for envelope detection and feature extraction on ultrasound images.

PubMed

Wachinger, Christian; Klein, Tassilo; Navab, Nassir

2012-08-01

The fundamental property of the analytic signal is the split of identity, meaning the separation of qualitative and quantitative information in form of the local phase and the local amplitude, respectively. Especially the structural representation, independent of brightness and contrast, of the local phase is interesting for numerous image processing tasks. Recently, the extension of the analytic signal from 1D to 2D, covering also intrinsic 2D structures, was proposed. We show the advantages of this improved concept on ultrasound RF and B-mode images. Precisely, we use the 2D analytic signal for the envelope detection of RF data. This leads to advantages for the extraction of the information-bearing signal from the modulated carrier wave. We illustrate this, first, by visual assessment of the images, and second, by performing goodness-of-fit tests to a Nakagami distribution, indicating a clear improvement of statistical properties. The evaluation is performed for multiple window sizes and parameter estimation techniques. Finally, we show that the 2D analytic signal allows for an improved estimation of local features on B-mode images. Copyright © 2012 Elsevier B.V. All rights reserved.

50-plus years of fungal viruses

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

Ghabrial, Said A., E-mail: saghab00@email.uky.edu; Castón, José R.; Jiang, Daohong

2015-05-15

Mycoviruses are widespread in all major taxa of fungi. They are transmitted intracellularly during cell division, sporogenesis, and/or cell-to-cell fusion (hyphal anastomosis), and thus their life cycles generally lack an extracellular phase. Their natural host ranges are limited to individuals within the same or closely related vegetative compatibility groups, although recent advances have established expanded experimental host ranges for some mycoviruses. Most known mycoviruses have dsRNA genomes packaged in isometric particles, but an increasing number of positive- or negative-strand ssRNA and ssDNA viruses have been isolated and characterized. Although many mycoviruses do not have marked effects on their hosts, thosemore » that reduce the virulence of their phytopathogenic fungal hosts are of considerable interest for development of novel biocontrol strategies. Mycoviruses that infect endophytic fungi and those that encode killer toxins are also of special interest. Structural analyses of mycoviruses have promoted better understanding of virus assembly, function, and evolution. - Highlights: • Historical perspective of fungal virus research. • Description, classification and diversity of fungal virus families. • Structural features of fungal virus particles. • Hypovirulence and exploitation of mycoviruses in biological control of plant pathogenic fungi.« less

Pseudo-Jahn-Teller Distortion in Two-Dimensional Phosphorus: Origin of Black and Blue Phases of Phosphorene and Band Gap Modulation by Molecular Charge Transfer.

PubMed

Chowdhury, Chandra; Jahiruddin, Sheik; Datta, Ayan

2016-04-07

Phosphorene (Pn) is stabilized as a layered material like graphite, yet it possess a natural direct band gap (Eg = 2.0 eV). Interestingly, unlike graphene, Pn exhibits a much richer phase diagram which includes distorted forms like the stapler-clip (black Pn, α form) and chairlike (blue Pn, β form) structures. The existence of these phases is attributed to pseudo-Jahn-Teller (PJT) instability of planar hexagonal P6(6-) rings. In both cases, the condition for vibronic instability of the planar P6(6-) rings is satisfied. Doping with electron donors like tetrathiafulvalene and tetraamino-tetrathiafulvalene and electron acceptors like tetracyanoquinodimethane and tetracyanoethylene convert blue Pn into N-type and black Pn into efficient P-type semiconductors, respectively. Interestingly, pristine blue Pn, an indirect gap semiconductor, gets converted into a direct gap semiconductor on electron or hole doping. Because of comparatively smaller undulation in blue Pn (with respect to black Pn), the van der Waals interactions between the dopants and blue Pn is stronger. PJT distortions for two-dimensional phosphorus provides a unified understanding of structural features and chemical reactivity in its different phases.

Integrated databanks access and sequence/structure analysis services at the PBIL.

PubMed

Perrière, Guy; Combet, Christophe; Penel, Simon; Blanchet, Christophe; Thioulouse, Jean; Geourjon, Christophe; Grassot, Julien; Charavay, Céline; Gouy, Manolo; Duret, Laurent; Deléage, Gilbert

2003-07-01

The World Wide Web server of the PBIL (Pôle Bioinformatique Lyonnais) provides on-line access to sequence databanks and to many tools of nucleic acid and protein sequence analyses. This server allows to query nucleotide sequence banks in the EMBL and GenBank formats and protein sequence banks in the SWISS-PROT and PIR formats. The query engine on which our data bank access is based is the ACNUC system. It allows the possibility to build complex queries to access functional zones of biological interest and to retrieve large sequence sets. Of special interest are the unique features provided by this system to query the data banks of gene families developed at the PBIL. The server also provides access to a wide range of sequence analysis methods: similarity search programs, multiple alignments, protein structure prediction and multivariate statistics. An originality of this server is the integration of these two aspects: sequence retrieval and sequence analysis. Indeed, thanks to the introduction of re-usable lists, it is possible to perform treatments on large sets of data. The PBIL server can be reached at: http://pbil.univ-lyon1.fr.

Correlative Raman spectroscopy and focused ion beam for targeted phase boundary analysis of titania polymorphs

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

Mangum, John S.; Chan, Lisa H.; Schmidt, Ute

Site-specific preparation of specimens using focused ion beam instruments for transmission electron microscopy is at the forefront of targeting regions of interest for nanoscale characterization. Typical methods of pinpointing desired features include electron backscatter diffraction for differentiating crystal structures and energy-dispersive X-Ray spectroscopy for probing compositional variations. Yet there are situations, notably in the titanium dioxide system, where these techniques can fail. Differentiating between the brookite and anatase polymorphs of titania is either excessively laborious or impossible with the aforementioned techniques. However, due to differences in bonding structure, Raman spectroscopy serves as an ideal candidate for polymorph differentiation. In thismore » work, a correlative approach utilizing Raman spectroscopy for targeted focused ion beam specimen preparation was employed. Dark field imaging and diffraction in the transmission electron microscope confirmed the region of interest located via Raman spectroscopy and demonstrated the validity of this new method. Correlative Raman spectroscopy, scanning electron microscopy, and focused ion beam is shown to be a promising new technique for identifying site-specific preparation of nanoscale specimens in cases where conventional approaches do not suffice.« less

Correlative Raman spectroscopy and focused ion beam for targeted phase boundary analysis of titania polymorphs.

PubMed

Mangum, John S; Chan, Lisa H; Schmidt, Ute; Garten, Lauren M; Ginley, David S; Gorman, Brian P

2018-05-01

Site-specific preparation of specimens using focused ion beam instruments for transmission electron microscopy is at the forefront of targeting regions of interest for nanoscale characterization. Typical methods of pinpointing desired features include electron backscatter diffraction for differentiating crystal structures and energy-dispersive X-Ray spectroscopy for probing compositional variations. Yet there are situations, notably in the titanium dioxide system, where these techniques can fail. Differentiating between the brookite and anatase polymorphs of titania is either excessively laborious or impossible with the aforementioned techniques. However, due to differences in bonding structure, Raman spectroscopy serves as an ideal candidate for polymorph differentiation. In this work, a correlative approach utilizing Raman spectroscopy for targeted focused ion beam specimen preparation was employed. Dark field imaging and diffraction in the transmission electron microscope confirmed the region of interest located via Raman spectroscopy and demonstrated the validity of this new method. Correlative Raman spectroscopy, scanning electron microscopy, and focused ion beam is shown to be a promising new technique for identifying site-specific preparation of nanoscale specimens in cases where conventional approaches do not suffice. Copyright © 2018 Elsevier B.V. All rights reserved.

Correlative Raman spectroscopy and focused ion beam for targeted phase boundary analysis of titania polymorphs

DOE PAGES

Mangum, John S.; Chan, Lisa H.; Schmidt, Ute; ...

2018-02-23

Site-specific preparation of specimens using focused ion beam instruments for transmission electron microscopy is at the forefront of targeting regions of interest for nanoscale characterization. Typical methods of pinpointing desired features include electron backscatter diffraction for differentiating crystal structures and energy-dispersive X-Ray spectroscopy for probing compositional variations. Yet there are situations, notably in the titanium dioxide system, where these techniques can fail. Differentiating between the brookite and anatase polymorphs of titania is either excessively laborious or impossible with the aforementioned techniques. However, due to differences in bonding structure, Raman spectroscopy serves as an ideal candidate for polymorph differentiation. In thismore » work, a correlative approach utilizing Raman spectroscopy for targeted focused ion beam specimen preparation was employed. Dark field imaging and diffraction in the transmission electron microscope confirmed the region of interest located via Raman spectroscopy and demonstrated the validity of this new method. Correlative Raman spectroscopy, scanning electron microscopy, and focused ion beam is shown to be a promising new technique for identifying site-specific preparation of nanoscale specimens in cases where conventional approaches do not suffice.« less

Special Relativity at the Quantum Scale

PubMed Central

Lam, Pui K.

2014-01-01

It has been suggested that the space-time structure as described by the theory of special relativity is a macroscopic manifestation of a more fundamental quantum structure (pre-geometry). Efforts to quantify this idea have come mainly from the area of abstract quantum logic theory. Here we present a preliminary attempt to develop a quantum formulation of special relativity based on a model that retains some geometric attributes. Our model is Feynman's “checker-board” trajectory for a 1-D relativistic free particle. We use this model to guide us in identifying (1) the quantum version of the postulates of special relativity and (2) the appropriate quantum “coordinates”. This model possesses a useful feature that it admits an interpretation both in terms of paths in space-time and in terms of quantum states. Based on the quantum version of the postulates, we derive a transformation rule for velocity. This rule reduces to the Einstein's velocity-addition formula in the macroscopic limit and reveals an interesting aspect of time. The 3-D case, time-dilation effect, and invariant interval are also discussed in term of this new formulation. This is a preliminary investigation; some results are derived, while others are interesting observations at this point. PMID:25531675

Special relativity at the quantum scale.

PubMed

Lam, Pui K

2014-01-01

It has been suggested that the space-time structure as described by the theory of special relativity is a macroscopic manifestation of a more fundamental quantum structure (pre-geometry). Efforts to quantify this idea have come mainly from the area of abstract quantum logic theory. Here we present a preliminary attempt to develop a quantum formulation of special relativity based on a model that retains some geometric attributes. Our model is Feynman's "checker-board" trajectory for a 1-D relativistic free particle. We use this model to guide us in identifying (1) the quantum version of the postulates of special relativity and (2) the appropriate quantum "coordinates". This model possesses a useful feature that it admits an interpretation both in terms of paths in space-time and in terms of quantum states. Based on the quantum version of the postulates, we derive a transformation rule for velocity. This rule reduces to the Einstein's velocity-addition formula in the macroscopic limit and reveals an interesting aspect of time. The 3-D case, time-dilation effect, and invariant interval are also discussed in term of this new formulation. This is a preliminary investigation; some results are derived, while others are interesting observations at this point.

Patterns of structural dynamics in RACK1 protein retained throughout evolution: A hydrogen-deuterium exchange study of three orthologs

PubMed Central

Tarnowski, Krzysztof; Fituch, Kinga; Szczepanowski, Roman H; Dadlez, Michal; Kaus-Drobek, Magdalena

2014-01-01

RACK1 is a member of the WD repeat family of proteins and is involved in multiple fundamental cellular processes. An intriguing feature of RACK1 is its ability to interact with at least 80 different protein partners. Thus, the structural features enabling such interactomic flexibility are of great interest. Several previous studies of the crystal structures of RACK1 orthologs described its detailed architecture and confirmed predictions that RACK1 adopts a seven-bladed β-propeller fold. However, this did not explain its ability to bind to multiple partners. We performed hydrogen-deuterium (H-D) exchange mass spectrometry on three orthologs of RACK1 (human, yeast, and plant) to obtain insights into the dynamic properties of RACK1 in solution. All three variants retained similar patterns of deuterium uptake, with some pronounced differences that can be attributed to RACK1's divergent biological functions. In all cases, the most rigid structural elements were confined to B-C turns and, to some extent, strands B and C, while the remaining regions retained much flexibility. We also compared the average rate constants for H-D exchange in different regions of RACK1 and found that amide protons in some regions exchanged at least 1000-fold faster than in others. We conclude that its evolutionarily retained structural architecture might have allowed RACK1 to accommodate multiple molecular partners. This was exemplified by our additional analysis of yeast RACK1 dimer, which showed stabilization, as well as destabilization, of several interface regions upon dimer formation. PMID:24591271

Understanding and Manipulating Electrostatic Fields at the Protein-Protein Interface Using Vibrational Spectroscopy and Continuum Electrostatics Calculations.

PubMed

Ritchie, Andrew W; Webb, Lauren J

2015-11-05

Biological function emerges in large part from the interactions of biomacromolecules in the complex and dynamic environment of the living cell. For this reason, macromolecular interactions in biological systems are now a major focus of interest throughout the biochemical and biophysical communities. The affinity and specificity of macromolecular interactions are the result of both structural and electrostatic factors. Significant advances have been made in characterizing structural features of stable protein-protein interfaces through the techniques of modern structural biology, but much less is understood about how electrostatic factors promote and stabilize specific functional macromolecular interactions over all possible choices presented to a given molecule in a crowded environment. In this Feature Article, we describe how vibrational Stark effect (VSE) spectroscopy is being applied to measure electrostatic fields at protein-protein interfaces, focusing on measurements of guanosine triphosphate (GTP)-binding proteins of the Ras superfamily binding with structurally related but functionally distinct downstream effector proteins. In VSE spectroscopy, spectral shifts of a probe oscillator's energy are related directly to that probe's local electrostatic environment. By performing this experiment repeatedly throughout a protein-protein interface, an experimental map of measured electrostatic fields generated at that interface is determined. These data can be used to rationalize selective binding of similarly structured proteins in both in vitro and in vivo environments. Furthermore, these data can be used to compare to computational predictions of electrostatic fields to explore the level of simulation detail that is necessary to accurately predict our experimental findings.

Computational study of the melting-freezing transition in the quantum hard-sphere system for intermediate densities. II. Structural features.

PubMed

Sesé, Luis M; Bailey, Lorna E

2007-04-28

The structural features of the quantum hard-sphere system in the region of the fluid-face-centered-cubic-solid transition, for reduced number densities 0.45

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

Hydrothermal Synthesis and Characterization of Novel Brackebuschite-Type Transition Metal Vanadates: Ba 2 M(VO 4 ) 2 (OH), M = V 3+ , Mn 3+ , and Fe 3+ , with Interesting Jahn–Teller and Spin-Liquid Behavior

DOE PAGES

Sanjeewa, Liurukara D.; McGuire, Michael A.; Garlea, Vasile O.; ...

2015-07-08

In a new series of transition metal vanadates, namely, Ba 2M(VO 4) 2(OH) (M = V 3+, Mn 3+, and Fe 3+), was synthesized as large single crystals hydrothermally in 5 M NaOH solution at 580 °C and 1 kbar. This new series of compounds is structurally reminiscent of the brackebuschite mineral type. The structure of Ba 2V(VO 4) 2(OH) is monoclinic in space group P2 1/m, a = 7.8783(2) Å, b = 6.1369(1) Å, c = 9.1836(2) Å, β = 113.07(3)°, V = 408.51(2) Å 3. Moreover, the other structures are similar and consist of one-dimensional trans edge-shared distortedmore » octahedral chains running along the b-axis. The vanadate groups bridge across edges of their tetrahedra. Structural analysis of the Ba 2Mn(VO 4) 2(OH) analogue yielded a new understanding of the Jahn–Teller effect in this structure type. Raman and infrared spectra were investigated to observe the fundamental vanadate and hydroxide vibrational modes. Finally, single-crystal temperature-dependent magnetic studies on Ba 2V(VO 4) 2(OH) reveal a broad feature over a wide temperature range with maximum at ~100 K indicating that an energy gap could exist between the antiferromagnetic singlet ground state and excited triplet states, making it potentially of interest for quantum magnetism studies.« less

Structural power and the evolution of collective fairness in social networks.

PubMed

Santos, Fernando P; Pacheco, Jorge M; Paiva, Ana; Santos, Francisco C

2017-01-01

From work contracts and group buying platforms to political coalitions and international climate and economical summits, often individuals assemble in groups that must collectively reach decisions that may favor each part unequally. Here we quantify to which extent our network ties promote the evolution of collective fairness in group interactions, modeled by means of Multiplayer Ultimatum Games (MUG). We show that a single topological feature of social networks-which we call structural power-has a profound impact on the tendency of individuals to take decisions that favor each part equally. Increased fair outcomes are attained whenever structural power is high, such that the networks that tie individuals allow them to meet the same partners in different groups, thus providing the opportunity to strongly influence each other. On the other hand, the absence of such close peer-influence relationships dismisses any positive effect created by the network. Interestingly, we show that increasing the structural power of a network leads to the appearance of well-defined modules-as found in human social networks that often exhibit community structure-providing an interaction environment that maximizes collective fairness.

Multiple-wavelength neutron holography with pulsed neutrons

PubMed Central

Hayashi, Kouichi; Ohoyama, Kenji; Happo, Naohisa; Matsushita, Tomohiro; Hosokawa, Shinya; Harada, Masahide; Inamura, Yasuhiro; Nitani, Hiroaki; Shishido, Toetsu; Yubuta, Kunio

2017-01-01

Local structures around impurities in solids provide important information for understanding the mechanisms of material functions, because most of them are controlled by dopants. For this purpose, the x-ray absorption fine structure method, which provides radial distribution functions around specific elements, is most widely used. However, a similar method using neutron techniques has not yet been developed. If one can establish a method of local structural analysis with neutrons, then a new frontier of materials science can be explored owing to the specific nature of neutron scattering—that is, its high sensitivity to light elements and magnetic moments. Multiple-wavelength neutron holography using the time-of-flight technique with pulsed neutrons has great potential to realize this. We demonstrated multiple-wavelength neutron holography using a Eu-doped CaF2 single crystal and obtained a clear three-dimensional atomic image around trivalent Eu substituted for divalent Ca, revealing an interesting feature of the local structure that allows it to maintain charge neutrality. The new holography technique is expected to provide new information on local structures using the neutron technique. PMID:28835917

Diverse Supramolecular Nanofiber Networks Assembled by Functional Low-Complexity Domains.

PubMed

An, Bolin; Wang, Xinyu; Cui, Mengkui; Gui, Xinrui; Mao, Xiuhai; Liu, Yan; Li, Ke; Chu, Cenfeng; Pu, Jiahua; Ren, Susu; Wang, Yanyi; Zhong, Guisheng; Lu, Timothy K; Liu, Cong; Zhong, Chao

2017-07-25

Self-assembling supramolecular nanofibers, common in the natural world, are of fundamental interest and technical importance to both nanotechnology and materials science. Despite important advances, synthetic nanofibers still lack the structural and functional diversity of biological molecules, and the controlled assembly of one type of molecule into a variety of fibrous structures with wide-ranging functional attributes remains challenging. Here, we harness the low-complexity (LC) sequence domain of fused in sarcoma (FUS) protein, an essential cellular nuclear protein with slow kinetics of amyloid fiber assembly, to construct random copolymer-like, multiblock, and self-sorted supramolecular fibrous networks with distinct structural features and fluorescent functionalities. We demonstrate the utilities of these networks in the templated, spatially controlled assembly of ligand-decorated gold nanoparticles, quantum dots, nanorods, DNA origami, and hybrid structures. Owing to the distinguishable nanoarchitectures of these nanofibers, this assembly is structure-dependent. By coupling a modular genetic strategy with kinetically controlled complex supramolecular self-assembly, we demonstrate that a single type of protein molecule can be used to engineer diverse one-dimensional supramolecular nanostructures with distinct functionalities.

PIV measurement of internal structure of diesel fuel spray

NASA Astrophysics Data System (ADS)

Cao, Z.-M.; Nishino, K.; Mizuno, S.; Torii, K.

2000-12-01

This paper reports particle image velocimetry (PIV) measurements of diesel fuel spray injected from a single-hole nozzle at injection pressures ranging from 30 to 70MPa, which are comparable to partial-load operating conditions of commercial diesel engines. The fuel is injected into a non-combusting environment pressurized up to 2.0MPa. A laser-induced fluorescent (LIF) technique is utilized to visualize internal structures of fuel sprays formed by densely-distributing droplets. A specially designed synchronization system is developed to acquire double-frame spray images at an arbitrary time delay after injection. A direct cross-correlation PIV technique is applied to measure instantaneous droplet velocity distribution. Unique large-scale structures in droplet concentration, called `branch-like structures' by Azetsu etal. (1990), are observed and shown to be associated with active vortical motions, which appear to be responsible for the mixing between droplets and the surrounding gas. It is found that the droplets tend to move out of the vortical structures and accumulate in the regions of low vorticity. Some other interesting features concerning droplet velocity fields are also presented.

PIV measurement of internal structure of diesel fuel spray

NASA Astrophysics Data System (ADS)

Cao, Z.-M.; Nishino, K.; Mizuno, S.; Torii, K.

This paper reports particle image velocimetry (PIV) measurements of diesel fuel spray injected from a single-hole nozzle at injection pressures ranging from 30 to 70MPa, which are comparable to partial-load operating conditions of commercial diesel engines. The fuel is injected into a non-combusting environment pressurized up to 2.0MPa. A laser-induced fluorescent (LIF) technique is utilized to visualize internal structures of fuel sprays formed by densely-distributing droplets. A specially designed synchronization system is developed to acquire double-frame spray images at an arbitrary time delay after injection. A direct cross-correlation PIV technique is applied to measure instantaneous droplet velocity distribution. Unique large-scale structures in droplet concentration, called `branch-like structures' by Azetsu etal. (1990), are observed and shown to be associated with active vortical motions, which appear to be responsible for the mixing between droplets and the surrounding gas. It is found that the droplets tend to move out of the vortical structures and accumulate in the regions of low vorticity. Some other interesting features concerning droplet velocity fields are also presented.

Multiple-wavelength neutron holography with pulsed neutrons.

PubMed

Hayashi, Kouichi; Ohoyama, Kenji; Happo, Naohisa; Matsushita, Tomohiro; Hosokawa, Shinya; Harada, Masahide; Inamura, Yasuhiro; Nitani, Hiroaki; Shishido, Toetsu; Yubuta, Kunio

2017-08-01

Local structures around impurities in solids provide important information for understanding the mechanisms of material functions, because most of them are controlled by dopants. For this purpose, the x-ray absorption fine structure method, which provides radial distribution functions around specific elements, is most widely used. However, a similar method using neutron techniques has not yet been developed. If one can establish a method of local structural analysis with neutrons, then a new frontier of materials science can be explored owing to the specific nature of neutron scattering-that is, its high sensitivity to light elements and magnetic moments. Multiple-wavelength neutron holography using the time-of-flight technique with pulsed neutrons has great potential to realize this. We demonstrated multiple-wavelength neutron holography using a Eu-doped CaF 2 single crystal and obtained a clear three-dimensional atomic image around trivalent Eu substituted for divalent Ca, revealing an interesting feature of the local structure that allows it to maintain charge neutrality. The new holography technique is expected to provide new information on local structures using the neutron technique.

Integration of real time kinematic satellite navigation with ground-penetrating radar surveys

USDA-ARS?s Scientific Manuscript database

Precision agriculture, environmental mapping, and construction benefit from subsurface imaging by revealing the spatial variability of underground features. Features surveyed of agricultural interest are bedrock depth, soil horizon thicknesses, and buried–object features such as drainage pipe. For t...

Optical properties of graphene-based materials in transparent polymer matrices

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

Bayrak, Osman; Demirci, Emrah, E-mail: E.Demirci@lboro.ac.uk; Silberschmidt, Vadim V.

2016-08-22

Different aspects of graphene-based materials (GBMs) and GBM-nanocomposites have been investigated due to their intriguing features; one of these features is their transparency. Transparency of GBMs has been of an interest to scientists and engineers mainly with regard to electronic devices. In this study, optical transmittance of structural, purpose-made nanocomposites reinforced with GBMs was analyzed to lay a foundation for optical microstructural characterization of nanocomposites in future studies. Two main types of GBM reinforcements were studied, graphene oxide (GO) and graphite nanoplates (GNPs). The nanocomposites investigated are GO/poly(vinyl alcohol), GO/sodium alginate, and GNP/epoxy with different volume fractions of GBMs. Togethermore » with UV-visible spectrophotometry, image-processing-assisted micro and macro photography were used to assess the transparency of GBMs embedded in the matrices. The micro and macro photography methods developed were proven to be an alternative way of measuring light transmittance of semi-transparent materials. It was found that there existed a linear relationship between light absorbance and a volume fraction of GBMs embedded in the same type of polymer matrices, provided that the nanocomposites of interest had the same thicknesses. This suggests that the GBM dispersion characteristics in the same type of polymer are similar and any possible change in crystal structure of polymer due to different volumetric contents of GBM does not have an effect on light transmittance of the matrices. The study also showed that the same types of GBMs could display different optical properties in different matrix materials. The results of this study will help to develop practical microstructural characterization techniques for GBM-based nanocomposites.« less

Syntheses, crystal structures and properties of series of 4d–4f ln(III)–Ag(I) heterometallic coordination polymers

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

Ran, Xing-Rui; Wang, Ning; Xie, Wei-Ping

2015-05-15

By control of the experimental parameters such as ligands, pH value and reacting temperature, series of three-dimensional (3D) 4d–4f Ln(III)–Ag(I) porous coordination polymers (PCPs) with interesting chain-layer construction, namely, ([Ln{sup III}Ag{sup I}(na)(ina)(ox)]·2(H{sub 2}O)){sub n} [Ln=Sm(1), Eu(2), Gd(3), Tb(4), Dy(5), Ho(6), Y(7), Yb(8)], have been successfully synthesized under hydrothermal conditions and structurally characterized. All the complexes are characterized by elemental analyses, FT-IR spectroscopy, Powder X-ray diffraction (PXRD) and thermogravimetric analyses (TGA). Furthermore, the luminescence properties of compounds 2 and 4 and the magsnetic properties of complexes 3 and 5 were also investigated in detail. - Graphical abstract: Series of three-dimensional (3D)more » 4d–4f Ln(III)–Ag(I) porous coordination polymers (PCPs) with interesting chain-layer construction which are featured by tetranuclear Ln{sub 2}Ag{sub 2} and ‘non-linear’ N–Ag–N linkages. - Highlights: • Complexes 1–8 are first built by three kinds of organic ligands based on nicotinic acid and isonicotinic acid. • PCPs 1–8 are featured by tetranuclear Ln{sub 2}Ag{sub 2} and ‘non-linear’ N–Ag–N linkages. • The total solvent-accessible volume of PCP 2 comprises 11.6% of the crystal volume after dislodging the free water molecules. • Complexes 2 and 4 exhibit characteristic lanthanide-centered luminescence, while compounds 3 and 5 show antiferromagnetic behaviors.« less

Global properties of physically interesting Lorentzian spacetimes

NASA Astrophysics Data System (ADS)

Nawarajan, Deloshan; Visser, Matt

Under normal circumstances most members of the general relativity community focus almost exclusively on the local properties of spacetime, such as the locally Euclidean structure of the manifold and the Lorentzian signature of the metric tensor. When combined with the classical Einstein field equations this gives an extremely successful empirical model of classical gravity and classical matter — at least as long as one does not ask too many awkward questions about global issues, (such as global topology and global causal structure). We feel however that this is a tactical error — even without invoking full-fledged “quantum gravity” we know that the standard model of particle physics is also an extremely good representation of some parts of empirical reality; and we had better be able to carry over all the good features of the standard model of particle physics — at least into the realm of semi-classical quantum gravity. Doing so gives us some interesting global features that spacetime should possess: On physical grounds spacetime should be space-orientable, time-orientable, and spacetime-orientable, and it should possess a globally defined tetrad (vierbein, or in general a globally defined vielbein/n-bein). So on physical grounds spacetime should be parallelizable. This strongly suggests that the metric is not the fundamental physical quantity; a very good case can be made for the tetrad being more fundamental than the metric. Furthermore, a globally-defined “almost complex structure” is almost unavoidable. Ideas along these lines have previously been mooted, but much is buried in the pre-arXiv literature and is either forgotten or inaccessible. We shall revisit these ideas taking a perspective very much based on empirical physical observation.

Probing Mantle Heterogeneity Across Spatial Scales

NASA Astrophysics Data System (ADS)

Hariharan, A.; Moulik, P.; Lekic, V.

2017-12-01

Inferences of mantle heterogeneity in terms of temperature, composition, grain size, melt and crystal structure may vary across local, regional and global scales. Probing these scale-dependent effects require quantitative comparisons and reconciliation of tomographic models that vary in their regional scope, parameterization, regularization and observational constraints. While a range of techniques like radial correlation functions and spherical harmonic analyses have revealed global features like the dominance of long-wavelength variations in mantle heterogeneity, they have limited applicability for specific regions of interest like subduction zones and continental cratons. Moreover, issues like discrepant 1-D reference Earth models and related baseline corrections have impeded the reconciliation of heterogeneity between various regional and global models. We implement a new wavelet-based approach that allows for structure to be filtered simultaneously in both the spectral and spatial domain, allowing us to characterize heterogeneity on a range of scales and in different geographical regions. Our algorithm extends a recent method that expanded lateral variations into the wavelet domain constructed on a cubed sphere. The isolation of reference velocities in the wavelet scaling function facilitates comparisons between models constructed with arbitrary 1-D reference Earth models. The wavelet transformation allows us to quantify the scale-dependent consistency between tomographic models in a region of interest and investigate the fits to data afforded by heterogeneity at various dominant wavelengths. We find substantial and spatially varying differences in the spectrum of heterogeneity between two representative global Vp models constructed using different data and methodologies. Applying the orthonormality of the wavelet expansion, we isolate detailed variations in velocity from models and evaluate additional fits to data afforded by adding such complexities to long-wavelength variations. Our method provides a way to probe and evaluate localized features in a multi-scale description of mantle heterogeneity.

"Radio-oncomics" : The potential of radiomics in radiation oncology.

PubMed

Peeken, Jan Caspar; Nüsslin, Fridtjof; Combs, Stephanie E

2017-10-01

Radiomics, a recently introduced concept, describes quantitative computerized algorithm-based feature extraction from imaging data including computer tomography (CT), magnetic resonance imaging (MRT), or positron-emission tomography (PET) images. For radiation oncology it offers the potential to significantly influence clinical decision-making and thus therapy planning and follow-up workflow. After image acquisition, image preprocessing, and defining regions of interest by structure segmentation, algorithms are applied to calculate shape, intensity, texture, and multiscale filter features. By combining multiple features and correlating them with clinical outcome, prognostic models can be created. Retrospective studies have proposed radiomics classifiers predicting, e. g., overall survival, radiation treatment response, distant metastases, or radiation-related toxicity. Besides, radiomics features can be correlated with genomic information ("radiogenomics") and could be used for tumor characterization. Distinct patterns based on data-based as well as genomics-based features will influence radiation oncology in the future. Individualized treatments in terms of dose level adaption and target volume definition, as well as other outcome-related parameters will depend on radiomics and radiogenomics. By integration of various datasets, the prognostic power can be increased making radiomics a valuable part of future precision medicine approaches. This perspective demonstrates the evidence for the radiomics concept in radiation oncology. The necessity of further studies to integrate radiomics classifiers into clinical decision-making and the radiation therapy workflow is emphasized.

An overview of wireless structural health monitoring for civil structures.

PubMed

Lynch, Jerome Peter

2007-02-15

Wireless monitoring has emerged in recent years as a promising technology that could greatly impact the field of structural monitoring and infrastructure asset management. This paper is a summary of research efforts that have resulted in the design of numerous wireless sensing unit prototypes explicitly intended for implementation in civil structures. Wireless sensing units integrate wireless communications and mobile computing with sensors to deliver a relatively inexpensive sensor platform. A key design feature of wireless sensing units is the collocation of computational power and sensors; the tight integration of computing with a wireless sensing unit provides sensors with the opportunity to self-interrogate measurement data. In particular, there is strong interest in using wireless sensing units to build structural health monitoring systems that interrogate structural data for signs of damage. After the hardware and the software designs of wireless sensing units are completed, the Alamosa Canyon Bridge in New Mexico is utilized to validate their accuracy and reliability. To improve the ability of low-cost wireless sensing units to detect the onset of structural damage, the wireless sensing unit paradigm is extended to include the capability to command actuators and active sensors.

Resolution Study of Marine CSEM Imaging of Subduction Zones

NASA Astrophysics Data System (ADS)

Gustafson, C.; Key, K.

2016-12-01

Marine controlled source electromagnetic (CSEM) data allow us to image seafloor electrical resistivity from which we can constrain the porosity and fluid content of the subsurface. In subduction zones, CSEM data can be used to constrain geologic structure, hydrogeology and fluid-tectonic processes. The scales of features we are interested in recovering with CSEM data range from large-scale features such as the incoming tectonic plate and subducting slab, to the narrow dipping plate boundary interface where slip occurs, to thin faults that cut the overriding forearc crust and shallow fluid seeps and mounds on the seafloor. Thus electrical structure is expected to vary on scales ranging from scales of meters to tens of kilometers. CSEM data collected by Scripps at the Middle America Trench in 2010 is the first and to-date the only application of the method for studying a subduction zone. The results from this pioneering data set highlight the types of new discoveries that are possible with CSEM data, such as imaging conductive bending faults and a water-rich channel of subducting sediments. In this work we explore the magnitude and scale of 2D resistivity structures that can be resolved with CSEM data through a suite of synthetic inversion studies. We build resistivity models that are representative of various known and hypothesized subduction zone plate boundary structures. We generate synthetic noisy data for these models and invert them using the freely available MARE2DEM inversion code. We compare the recovered models to the original models in order to determine which resistivity structures may be successfully identified using CSEM. We explore the potential effects of receiver spacing, frequency bandwidth and system noise levels on the ability of CSEM to recover these different subduction zone structures.

Automated sub-cortical brain structure segmentation combining spatial and deep convolutional features.

PubMed

Kushibar, Kaisar; Valverde, Sergi; González-Villà, Sandra; Bernal, Jose; Cabezas, Mariano; Oliver, Arnau; Lladó, Xavier

2018-06-15

Sub-cortical brain structure segmentation in Magnetic Resonance Images (MRI) has attracted the interest of the research community for a long time as morphological changes in these structures are related to different neurodegenerative disorders. However, manual segmentation of these structures can be tedious and prone to variability, highlighting the need for robust automated segmentation methods. In this paper, we present a novel convolutional neural network based approach for accurate segmentation of the sub-cortical brain structures that combines both convolutional and prior spatial features for improving the segmentation accuracy. In order to increase the accuracy of the automated segmentation, we propose to train the network using a restricted sample selection to force the network to learn the most difficult parts of the structures. We evaluate the accuracy of the proposed method on the public MICCAI 2012 challenge and IBSR 18 datasets, comparing it with different traditional and deep learning state-of-the-art methods. On the MICCAI 2012 dataset, our method shows an excellent performance comparable to the best participant strategy on the challenge, while performing significantly better than state-of-the-art techniques such as FreeSurfer and FIRST. On the IBSR 18 dataset, our method also exhibits a significant increase in the performance with respect to not only FreeSurfer and FIRST, but also comparable or better results than other recent deep learning approaches. Moreover, our experiments show that both the addition of the spatial priors and the restricted sampling strategy have a significant effect on the accuracy of the proposed method. In order to encourage the reproducibility and the use of the proposed method, a public version of our approach is available to download for the neuroimaging community. Copyright © 2018 The Authors. Published by Elsevier B.V. All rights reserved.

An “ADME Module” in the Adverse Outcome Pathway ...

EPA Pesticide Factsheets

The Adverse Outcome Pathway (AOP) framework has generated intense interest for its utility to organize knowledge on the toxicity mechanisms, starting from a molecular initiating event (MIE) to an adverse outcome across various levels of biological organization. While the AOP framework is designed to be chemical agnostic, it is widely recognized that considering chemicals’ absorption, distribution, metabolism, and excretion (ADME) behaviors is critical in applying the AOP framework in chemical-specific risk assessment. Currently, information being generated as part of the Organisation for Economic Co-operation and Development (OECD) AOP Development Programme is being consolidated into an AOP Knowledgebase (http://aopwiki.org). To enhance the use of this Knowledgebase in risk assessment, an ADME Module has been developed to contain the ADME information needed to connect MIEs and other key events in an AOP for specific chemicals. The conceptual structure of this module characterizes the potential of a chemical to reach the target MIE based on either its structure-based features or relative rates of ADME. The key features of this module include (1) a framework for connecting biology-based AOP to biochemical-based ADME and chemical/human activity-based exposure pathways; (2) links to qualitative tools (e.g., structure-based cheminformatic model) that screen for chemicals that could potentially reach the target MIE; (3) links to quantitative tools (e.g., dose-r

The effects of complex chemistry on triple flames

NASA Technical Reports Server (NTRS)

Echekki, T.; Chen, J. H.

1996-01-01

The structure, ignition, and stabilization mechanisms for a methanol (CH3OH)-air triple flame are studied using Direct Numerical Simulations (DNS). The methanol (CH3OH)-air triple flame is found to burn with an asymmetric shape due to the different chemical and transport processes characterizing the mixture. The excess fuel, methanol (CH3OH), on the rich premixed flame branch is replaced by more stable fuels CO and H2, which burn at the diffusion flame. On the lean premixed flame side, a higher concentration of O2 leaks through to the diffusion flame. The general structure of the triple point features the contribution of both differential diffusion of radicals and heat. A mixture fraction-temperature phase plane description of the triple flame structure is proposed to highlight some interesting features in partially premixed combustion. The effects of differential diffusion at the triple point add to the contribution of hydrodynamic effects in the stabilization of the triple flame. Differential diffusion effects are measured using two methods: a direct computation using diffusion velocities and an indirect computation based on the difference between the normalized mixture fractions of C and H. The mixture fraction approach does not clearly identify the effects of differential diffusion, in particular at the curved triple point, because of ambiguities in the contribution of carbon and hydrogen atoms' carrying species.

Measuring the Interestingness of Articles in a Limited User Environment Prospectus

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

Pon, Raymond K.

2007-04-18

Search engines, such as Google, assign scores to news articles based on their relevancy to a query. However, not all relevant articles for the query may be interesting to a user. For example, if the article is old or yields little new information, the article would be uninteresting. Relevancy scores do not take into account what makes an article interesting, which would vary from user to user. Although methods such as collaborative filtering have been shown to be effective in recommendation systems, in a limited user environment there are not enough users that would make collaborative filtering effective. I presentmore » a general framework for defining and measuring the ''interestingness'' of articles, called iScore, incorporating user-feedback including tracking multiple topics of interest as well as finding interesting entities or phrases in a complex relationship network. I propose and have shown the validity of the following: 1. Filtering based on only topic relevancy is insufficient for identifying interesting articles. 2. No single feature can characterize the interestingness of an article for a user. It is the combination of multiple features that yields higher quality results. For each user, these features have different degrees of usefulness for predicting interestingness. 3. Through user-feedback, a classifier can combine features to predict interestingness for the user. 4. Current evaluation corpora, such as TREC, do not capture all aspects of personalized news filtering systems necessary for system evaluation. 5. Focusing on only specific evolving user interests instead of all topics allows for more efficient resource utilization while yielding high quality recommendation results. 6. Multiple profile vectors yield significantly better results than traditional methods, such as the Rocchio algorithm, for identifying interesting articles. Additionally, the addition of tracking multiple topics as a new feature in iScore, can improve iScore's classification performance. 7. Multiple topic tracking yields better results than the best results from the last TREC adaptive filtering run. As future work, I will address the following hypothesis: Entities and the relationship among these entities using current information extraction technology can be utilized to identify entities of interest and relationships of interest, using a scheme such as PageRank. And I will address one of the following two hypotheses: 1. By addressing the multiple reading roles that a single user may have, classification results can be improved. 2. By tailoring the operating parameters of MTT, better classification results can be achieved.« less

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

Enclosure Transform for Interest Point Detection From Speckle Imagery.

PubMed

Yongjian Yu; Jue Wang

2017-03-01

We present a fast enclosure transform (ET) to localize complex objects of interest from speckle imagery. This approach explores the spatial confinement on regional features from a sparse image feature representation. Unrelated, broken ridge features surrounding an object are organized collaboratively, giving rise to the enclosureness of the object. Three enclosure likelihood measures are constructed, consisting of the enclosure force, potential energy, and encloser count. In the transform domain, the local maxima manifest the locations of objects of interest, for which only the intrinsic dimension is known a priori. The discrete ET algorithm is computationally efficient, being on the order of O(MN) using N measuring distances across an image of M ridge pixels. It involves easy and few parameter settings. We demonstrate and assess the performance of ET on the automatic detection of the prostate locations from supra-pubic ultrasound images. ET yields superior results in terms of positive detection rate, accuracy and coverage.

Systems and methods for predicting materials properties

DOEpatents

Ceder, Gerbrand; Fischer, Chris; Tibbetts, Kevin; Morgan, Dane; Curtarolo, Stefano

2007-11-06

Systems and methods for predicting features of materials of interest. Reference data are analyzed to deduce relationships between the input data sets and output data sets. Reference data includes measured values and/or computed values. The deduced relationships can be specified as equations, correspondences, and/or algorithmic processes that produce appropriate output data when suitable input data is used. In some instances, the output data set is a subset of the input data set, and computational results may be refined by optionally iterating the computational procedure. To deduce features of a new material of interest, a computed or measured input property of the material is provided to an equation, correspondence, or algorithmic procedure previously deduced, and an output is obtained. In some instances, the output is iteratively refined. In some instances, new features deduced for the material of interest are added to a database of input and output data for known materials.

Cross-population myelination covariance of human cerebral cortex.

PubMed

Ma, Zhiwei; Zhang, Nanyin

2017-09-01

Cross-population covariance of brain morphometric quantities provides a measure of interareal connectivity, as it is believed to be determined by the coordinated neurodevelopment of connected brain regions. Although useful, structural covariance analysis predominantly employed bulky morphological measures with mixed compartments, whereas studies of the structural covariance of any specific subdivisions such as myelin are rare. Characterizing myelination covariance is of interest, as it will reveal connectivity patterns determined by coordinated development of myeloarchitecture between brain regions. Using myelin content MRI maps from the Human Connectome Project, here we showed that the cortical myelination covariance was highly reproducible, and exhibited a brain organization similar to that previously revealed by other connectivity measures. Additionally, the myelination covariance network shared common topological features of human brain networks such as small-worldness. Furthermore, we found that the correlation between myelination covariance and resting-state functional connectivity (RSFC) was uniform within each resting-state network (RSN), but could considerably vary across RSNs. Interestingly, this myelination covariance-RSFC correlation was appreciably stronger in sensory and motor networks than cognitive and polymodal association networks, possibly due to their different circuitry structures. This study has established a new brain connectivity measure specifically related to axons, and this measure can be valuable to investigating coordinated myeloarchitecture development. Hum Brain Mapp 38:4730-4743, 2017. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Molecular Determinants of Cephalopod Muscles and Their Implication in Muscle Regeneration

PubMed Central

Zullo, Letizia; Fossati, Sara M.; Imperadore, Pamela; Nödl, Marie-Therese

2017-01-01

The ability to regenerate whole-body structures has been studied for many decades and is of particular interest for stem cell research due to its therapeutic potential. Several vertebrate and invertebrate species have been used as model systems to study pathways involved in regeneration in the past. Among invertebrates, cephalopods are considered as highly evolved organisms, which exhibit elaborate behavioral characteristics when compared to other mollusks including active predation, extraordinary manipulation, and learning abilities. These are enabled by a complex nervous system and a number of adaptations of their body plan, which were acquired over evolutionary time. Some of these novel features show similarities to structures present in vertebrates and seem to have evolved through a convergent evolutionary process. Octopus vulgaris (the common octopus) is a representative of modern cephalopods and is characterized by a sophisticated motor and sensory system as well as highly developed cognitive capabilities. Due to its phylogenetic position and its high regenerative power the octopus has become of increasing interest for studies on regenerative processes. In this paper we provide an overview over the current knowledge of cephalopod muscle types and structures and present a possible link between these characteristics and their high regenerative potential. This may help identify conserved molecular pathways underlying regeneration in invertebrate and vertebrate animal species as well as discover new leads for targeted tissue treatments in humans. PMID:28555185

Intelligence, Surveillance, and Reconnaissance Fusion for Coalition Operations

DTIC Science & Technology

2008-07-01

classification of the targets of interest. The MMI features extracted in this manner have two properties that provide a sound justification for...are generalizations of well- known feature extraction methods such as Principal Components Analysis (PCA) and Independent Component Analysis (ICA...augment (without degrading performance) a large class of generic fusion processes. Ontologies Classifications Feature extraction Feature analysis

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.

An Object-Oriented Approach for Analyzing CALIPSO's Profile Observations

NASA Astrophysics Data System (ADS)

Trepte, C. R.

2016-12-01

The CALIPSO satellite mission is a pioneering international partnership between NASA and the French Space Agency, CNES. Since launch on 28 April 2006, CALIPSO has been acquiring near-continuous lidar profile observations of clouds and aerosols in the Earth's atmosphere. Many studies have profitably used these observations to advance our understanding of climate, weather and air quality. For the most part, however, these studies have considered CALIPSO profile measurements independent from one another and have not related each to neighboring or family observations within a cloud element or aerosol feature. In this presentation we describe an alternative approach that groups measurements into objects visually identified from CALIPSO browse images. The approach makes use of the Visualization of CALIPSO (VOCAL) software tool that enables a user to outline a region of interest and save coordinates into a database. The selected features or objects can then be analyzed to explore spatial correlations over the feature's domain and construct bulk statistical properties for each structure. This presentation will show examples that examine cirrus and dust layers and will describe how this object-oriented approach can provide added insight into physical processes beyond conventional statistical treatments. It will further show results with combined measurements from other A-Train sensors to highlight advantages of viewing features in this manner.

The drug target genes show higher evolutionary conservation than non-target genes.

PubMed

Lv, Wenhua; Xu, Yongdeng; Guo, Yiying; Yu, Ziqi; Feng, Guanglong; Liu, Panpan; Luan, Meiwei; Zhu, Hongjie; Liu, Guiyou; Zhang, Mingming; Lv, Hongchao; Duan, Lian; Shang, Zhenwei; Li, Jin; Jiang, Yongshuai; Zhang, Ruijie

2016-01-26

Although evidence indicates that drug target genes share some common evolutionary features, there have been few studies analyzing evolutionary features of drug targets from an overall level. Therefore, we conducted an analysis which aimed to investigate the evolutionary characteristics of drug target genes. We compared the evolutionary conservation between human drug target genes and non-target genes by combining both the evolutionary features and network topological properties in human protein-protein interaction network. The evolution rate, conservation score and the percentage of orthologous genes of 21 species were included in our study. Meanwhile, four topological features including the average shortest path length, betweenness centrality, clustering coefficient and degree were considered for comparison analysis. Then we got four results as following: compared with non-drug target genes, 1) drug target genes had lower evolutionary rates; 2) drug target genes had higher conservation scores; 3) drug target genes had higher percentages of orthologous genes and 4) drug target genes had a tighter network structure including higher degrees, betweenness centrality, clustering coefficients and lower average shortest path lengths. These results demonstrate that drug target genes are more evolutionarily conserved than non-drug target genes. We hope that our study will provide valuable information for other researchers who are interested in evolutionary conservation of drug targets.

Features of a Health-Oriented Education Program during Daily Commutes: A Qualitative Study.

PubMed

Ramezankhani, Ali; Heydarabadi, Akbar Babaei; Ghaffari, Mohtasham; Mehrabi, Yadollah; Kazemi, Sadegh

2016-06-01

Today, despite scientific advances, many people spend more time and distance between home and their workplaces because of various economic and population reasons. The aim of this study was to identify features of an appropriate health education program during commutes for factory staff at Ardakan county (Yazd province, Iran). This qualitative study was conducted via the phenomenological method in 2014. The population of this study was members of the staff of Ardakan Steel Company. Nineteen specialists and 11 members of the factory's staff were invited to participate in the study, and data were collected using semi-structured interviews. The interviews took 20 to 40 minutes, and their content was analyzed using content analysis. Extraction of codes and themes and their placement in this study showed that an educational program during commutes should have nine features to have the desired effectiveness, i.e., the program must be audience-oriented, repeatable, participatory, technology-based, combinational, supportive, and motivational and interesting. Also, the program should have environmental and organizational support, and it must be evaluated for its effectiveness. Considering appropriate features of a health education program in educational situations, especially interventions related to daily commutes, is very important because the effectiveness of such health-oriented educational programs must be ensured.

Nonlocal atlas-guided multi-channel forest learning for human brain labeling

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

Ma, Guangkai; Gao, Yaozong; Wu, Guorong

Purpose: It is important for many quantitative brain studies to label meaningful anatomical regions in MR brain images. However, due to high complexity of brain structures and ambiguous boundaries between different anatomical regions, the anatomical labeling of MR brain images is still quite a challenging task. In many existing label fusion methods, appearance information is widely used. However, since local anatomy in the human brain is often complex, the appearance information alone is limited in characterizing each image point, especially for identifying the same anatomical structure across different subjects. Recent progress in computer vision suggests that the context features canmore » be very useful in identifying an object from a complex scene. In light of this, the authors propose a novel learning-based label fusion method by using both low-level appearance features (computed from the target image) and high-level context features (computed from warped atlases or tentative labeling maps of the target image). Methods: In particular, the authors employ a multi-channel random forest to learn the nonlinear relationship between these hybrid features and target labels (i.e., corresponding to certain anatomical structures). Specifically, at each of the iterations, the random forest will output tentative labeling maps of the target image, from which the authors compute spatial label context features and then use in combination with original appearance features of the target image to refine the labeling. Moreover, to accommodate the high inter-subject variations, the authors further extend their learning-based label fusion to a multi-atlas scenario, i.e., they train a random forest for each atlas and then obtain the final labeling result according to the consensus of results from all atlases. Results: The authors have comprehensively evaluated their method on both public LONI-LBPA40 and IXI datasets. To quantitatively evaluate the labeling accuracy, the authors use the dice similarity coefficient to measure the overlap degree. Their method achieves average overlaps of 82.56% on 54 regions of interest (ROIs) and 79.78% on 80 ROIs, respectively, which significantly outperform the baseline method (random forests), with the average overlaps of 72.48% on 54 ROIs and 72.09% on 80 ROIs, respectively. Conclusions: The proposed methods have achieved the highest labeling accuracy, compared to several state-of-the-art methods in the literature.« less

Nonlocal atlas-guided multi-channel forest learning for human brain labeling

PubMed Central

Ma, Guangkai; Gao, Yaozong; Wu, Guorong; Wu, Ligang; Shen, Dinggang

2016-01-01

Purpose: It is important for many quantitative brain studies to label meaningful anatomical regions in MR brain images. However, due to high complexity of brain structures and ambiguous boundaries between different anatomical regions, the anatomical labeling of MR brain images is still quite a challenging task. In many existing label fusion methods, appearance information is widely used. However, since local anatomy in the human brain is often complex, the appearance information alone is limited in characterizing each image point, especially for identifying the same anatomical structure across different subjects. Recent progress in computer vision suggests that the context features can be very useful in identifying an object from a complex scene. In light of this, the authors propose a novel learning-based label fusion method by using both low-level appearance features (computed from the target image) and high-level context features (computed from warped atlases or tentative labeling maps of the target image). Methods: In particular, the authors employ a multi-channel random forest to learn the nonlinear relationship between these hybrid features and target labels (i.e., corresponding to certain anatomical structures). Specifically, at each of the iterations, the random forest will output tentative labeling maps of the target image, from which the authors compute spatial label context features and then use in combination with original appearance features of the target image to refine the labeling. Moreover, to accommodate the high inter-subject variations, the authors further extend their learning-based label fusion to a multi-atlas scenario, i.e., they train a random forest for each atlas and then obtain the final labeling result according to the consensus of results from all atlases. Results: The authors have comprehensively evaluated their method on both public LONI_LBPA40 and IXI datasets. To quantitatively evaluate the labeling accuracy, the authors use the dice similarity coefficient to measure the overlap degree. Their method achieves average overlaps of 82.56% on 54 regions of interest (ROIs) and 79.78% on 80 ROIs, respectively, which significantly outperform the baseline method (random forests), with the average overlaps of 72.48% on 54 ROIs and 72.09% on 80 ROIs, respectively. Conclusions: The proposed methods have achieved the highest labeling accuracy, compared to several state-of-the-art methods in the literature. PMID:26843260

Palmprint verification using Lagrangian decomposition and invariant interest points

NASA Astrophysics Data System (ADS)

Gupta, P.; Rattani, A.; Kisku, D. R.; Hwang, C. J.; Sing, J. K.

2011-06-01

This paper presents a palmprint based verification system using SIFT features and Lagrangian network graph technique. We employ SIFT for feature extraction from palmprint images whereas the region of interest (ROI) which has been extracted from wide palm texture at the preprocessing stage, is considered for invariant points extraction. Finally, identity is established by finding permutation matrix for a pair of reference and probe palm graphs drawn on extracted SIFT features. Permutation matrix is used to minimize the distance between two graphs. The propsed system has been tested on CASIA and IITK palmprint databases and experimental results reveal the effectiveness and robustness of the system.

Medical smart textiles based on fiber optic technology: an overview.

PubMed

Massaroni, Carlo; Saccomandi, Paola; Schena, Emiliano

2015-04-13

The growing interest in the development of smart textiles for medical applications is driven by the aim to increase the mobility of patients who need a continuous monitoring of such physiological parameters. At the same time, the use of fiber optic sensors (FOSs) is gaining large acceptance as an alternative to traditional electrical and mechanical sensors for the monitoring of thermal and mechanical parameters. The potential impact of FOSs is related to their good metrological properties, their small size and their flexibility, as well as to their immunity from electromagnetic field. Their main advantage is the possibility to use textile based on fiber optic in a magnetic resonance imaging environment, where standard electronic sensors cannot be employed. This last feature makes FOSs suitable for monitoring biological parameters (e.g., respiratory and heartbeat monitoring) during magnetic resonance procedures. Research interest in combining FOSs and textiles into a single structure to develop wearable sensors is rapidly growing. In this review we provide an overview of the state-of-the-art of textiles, which use FOSs for monitoring of mechanical parameters of physiological interest. In particular we briefly describe the working principle of FOSs employed in this field and their relevant advantages and disadvantages. Also reviewed are their applications for the monitoring of mechanical parameters of physiological interest.

Medical Smart Textiles Based on Fiber Optic Technology: An Overview

PubMed Central

Massaroni, Carlo; Saccomandi, Paola; Schena, Emiliano

2015-01-01

The growing interest in the development of smart textiles for medical applications is driven by the aim to increase the mobility of patients who need a continuous monitoring of such physiological parameters. At the same time, the use of fiber optic sensors (FOSs) is gaining large acceptance as an alternative to traditional electrical and mechanical sensors for the monitoring of thermal and mechanical parameters. The potential impact of FOSs is related to their good metrological properties, their small size and their flexibility, as well as to their immunity from electromagnetic field. Their main advantage is the possibility to use textile based on fiber optic in a magnetic resonance imaging environment, where standard electronic sensors cannot be employed. This last feature makes FOSs suitable for monitoring biological parameters (e.g., respiratory and heartbeat monitoring) during magnetic resonance procedures. Research interest in combining FOSs and textiles into a single structure to develop wearable sensors is rapidly growing. In this review we provide an overview of the state-of-the-art of textiles, which use FOSs for monitoring of mechanical parameters of physiological interest. In particular we briefly describe the working principle of FOSs employed in this field and their relevant advantages and disadvantages. Also reviewed are their applications for the monitoring of mechanical parameters of physiological interest. PMID:25871010

Identification of muscle necrosis in the mdx mouse model of Duchenne muscular dystrophy using three-dimensional optical coherence tomography

NASA Astrophysics Data System (ADS)

Klyen, Blake R.; Shavlakadze, Thea; Radley-Crabb, Hannah G.; Grounds, Miranda D.; Sampson, David D.

2011-07-01

Three-dimensional optical coherence tomography (3D-OCT) was used to image the structure and pathology of skeletal muscle tissue from the treadmill-exercised mdx mouse model of human Duchenne muscular dystrophy. Optical coherence tomography (OCT) images of excised muscle samples were compared with co-registered hematoxylin and eosin-stained and Evans blue dye fluorescence histology. We show, for the first time, structural 3D-OCT images of skeletal muscle dystropathology well correlated with co-located histology. OCT could identify morphological features of interest and necrotic lesions within the muscle tissue samples based on intrinsic optical contrast. These findings demonstrate the utility of 3D-OCT for the evaluation of small-animal skeletal muscle morphology and pathology, particularly for studies of mouse models of muscular dystrophy.

In Situ Observations of PSCs Generated by Gravity Waves

NASA Technical Reports Server (NTRS)

Pfister, Leonhard; Bui, Paul; Mahoney, M. J.; Gandrud, Bruce; Hipskind, K. Stephen (Technical Monitor)

2000-01-01

During SOLVE, the bulk of the in-situ observations of PSCs are of large scale extended structures associated with synoptic scale cooling. The nature of these structures is also determined by layers of high relative NOy that have been stretched into thin layers by advective processes. Some of the in situ observations, however, are clearly correlated with gravity wave signatures. The first goal of this work is to examine these cases and evaluate gravity wave parameters. In particular, we are interested in the intrinsic periods of the waves and their temperature amplitude, which are key ingredients in the nucleation process. Secondly, we will examine some rudimentary properties of the particle size distributions and composition, comparing these with in situ observations of the more extended PSC features. Finally, we will attempt to ascertain the mechanism which generates the gravity waves.

Nanostructural hierarchy increases the strength of aluminium alloys.

PubMed

Liddicoat, Peter V; Liao, Xiao-Zhou; Zhao, Yonghao; Zhu, Yuntian; Murashkin, Maxim Y; Lavernia, Enrique J; Valiev, Ruslan Z; Ringer, Simon P

2010-09-07

Increasing the strength of metallic alloys while maintaining formability is an interesting challenge for enabling new generations of lightweight structures and technologies. In this paper, we engineer aluminium alloys to contain a hierarchy of nanostructures and possess mechanical properties that expand known performance boundaries-an aerospace-grade 7075 alloy exhibits a yield strength and uniform elongation approaching 1 GPa and 5%, respectively. The nanostructural architecture was observed using novel high-resolution microscopy techniques and comprises a solid solution, free of precipitation, featuring (i) a high density of dislocations, (ii) subnanometre intragranular solute clusters, (iii) two geometries of nanometre-scale intergranular solute structures and (iv) grain sizes tens of nanometres in diameter. Our results demonstrate that this novel architecture offers a design pathway towards a new generation of super-strong materials with new regimes of property-performance space.

Learning physical descriptors for materials science by compressed sensing

NASA Astrophysics Data System (ADS)

Ghiringhelli, Luca M.; Vybiral, Jan; Ahmetcik, Emre; Ouyang, Runhai; Levchenko, Sergey V.; Draxl, Claudia; Scheffler, Matthias

2017-02-01

The availability of big data in materials science offers new routes for analyzing materials properties and functions and achieving scientific understanding. Finding structure in these data that is not directly visible by standard tools and exploitation of the scientific information requires new and dedicated methodology based on approaches from statistical learning, compressed sensing, and other recent methods from applied mathematics, computer science, statistics, signal processing, and information science. In this paper, we explain and demonstrate a compressed-sensing based methodology for feature selection, specifically for discovering physical descriptors, i.e., physical parameters that describe the material and its properties of interest, and associated equations that explicitly and quantitatively describe those relevant properties. As showcase application and proof of concept, we describe how to build a physical model for the quantitative prediction of the crystal structure of binary compound semiconductors.

Emergence of Scale-Free Leadership Structure in Social Recommender Systems

PubMed Central

Zhou, Tao; Medo, Matúš; Cimini, Giulio; Zhang, Zi-Ke; Zhang, Yi-Cheng

2011-01-01

The study of the organization of social networks is important for the understanding of opinion formation, rumor spreading, and the emergence of trends and fashion. This paper reports empirical analysis of networks extracted from four leading sites with social functionality (Delicious, Flickr, Twitter and YouTube) and shows that they all display a scale-free leadership structure. To reproduce this feature, we propose an adaptive network model driven by social recommending. Artificial agent-based simulations of this model highlight a “good get richer” mechanism where users with broad interests and good judgments are likely to become popular leaders for the others. Simulations also indicate that the studied social recommendation mechanism can gradually improve the user experience by adapting to tastes of its users. Finally we outline implications for real online resource-sharing systems. PMID:21857891