Enhancing Team Composition in Professional Networks: Problem Definitions and Fast Solutions

PubMed Central

Li, Liangyue; Tong, Hanghang; Cao, Nan; Ehrlich, Kate; Lin, Yu-Ru; Buchler, Norbou

2017-01-01

In this paper, we study ways to enhance the composition of teams based on new requirements in a collaborative environment. We focus on recommending team members who can maintain the team’s performance by minimizing changes to the team’s skills and social structure. Our recommendations are based on computing team-level similarity, which includes skill similarity, structural similarity as well as the synergy between the two. Current heuristic approaches are one-dimensional and not comprehensive, as they consider the two aspects independently. To formalize team-level similarity, we adopt the notion of graph kernel of attributed graphs to encompass the two aspects and their interaction. To tackle the computational challenges, we propose a family of fast algorithms by (a) designing effective pruning strategies, and (b) exploring the smoothness between the existing and the new team structures. Extensive empirical evaluations on real world datasets validate the effectiveness and efficiency of our algorithms. PMID:29104408

Biogenic manganese oxide nanoparticle formation by a multimeric multicopper oxidase Mnx.

PubMed

Romano, Christine A; Zhou, Mowei; Song, Yang; Wysocki, Vicki H; Dohnalkova, Alice C; Kovarik, Libor; Paša-Tolić, Ljiljana; Tebo, Bradley M

2017-09-29

Bacteria that produce Mn oxides are extraordinarily skilled engineers of nanomaterials that contribute significantly to global biogeochemical cycles. Their enzyme-based reaction mechanisms may be genetically tailored for environmental remediation applications or bioenergy production. However, significant challenges exist for structural characterization of the enzymes responsible for biomineralization. The active Mn oxidase in Bacillus sp. PL-12, Mnx, is a complex composed of a multicopper oxidase (MCO), MnxG, and two accessory proteins, MnxE and MnxF. MnxG shares sequence similarity with other, structurally characterized MCOs. MnxE and MnxF have no similarity to any characterized proteins. The ~200 kDa complex has been recalcitrant to crystallization, so its structure is unknown. Here, we show that native mass spectrometry defines the subunit topology and copper binding of Mnx, while high-resolution electron microscopy visualizes the protein and nascent Mn oxide minerals. These data provide critical structural information for understanding Mn biomineralization by such unexplored enzymes.Significant challenges exist for structural characterization of enzymes responsible for biomineralization. Here the authors show that native mass spectrometry and high resolution electron microscopy can define the subunit topology and copper binding of a manganese oxidizing complex, and describe early stage formation of its mineral products.

RAG-3D: A search tool for RNA 3D substructures

DOE PAGES

Zahran, Mai; Sevim Bayrak, Cigdem; Elmetwaly, Shereef; ...

2015-08-24

In this study, to address many challenges in RNA structure/function prediction, the characterization of RNA's modular architectural units is required. Using the RNA-As-Graphs (RAG) database, we have previously explored the existence of secondary structure (2D) submotifs within larger RNA structures. Here we present RAG-3D—a dataset of RNA tertiary (3D) structures and substructures plus a web-based search tool—designed to exploit graph representations of RNAs for the goal of searching for similar 3D structural fragments. The objects in RAG-3D consist of 3D structures translated into 3D graphs, cataloged based on the connectivity between their secondary structure elements. Each graph is additionally describedmore » in terms of its subgraph building blocks. The RAG-3D search tool then compares a query RNA 3D structure to those in the database to obtain structurally similar structures and substructures. This comparison reveals conserved 3D RNA features and thus may suggest functional connections. Though RNA search programs based on similarity in sequence, 2D, and/or 3D structural elements are available, our graph-based search tool may be advantageous for illuminating similarities that are not obvious; using motifs rather than sequence space also reduces search times considerably. Ultimately, such substructuring could be useful for RNA 3D structure prediction, structure/function inference and inverse folding.« less

RAG-3D: a search tool for RNA 3D substructures

PubMed Central

Zahran, Mai; Sevim Bayrak, Cigdem; Elmetwaly, Shereef; Schlick, Tamar

2015-01-01

To address many challenges in RNA structure/function prediction, the characterization of RNA's modular architectural units is required. Using the RNA-As-Graphs (RAG) database, we have previously explored the existence of secondary structure (2D) submotifs within larger RNA structures. Here we present RAG-3D—a dataset of RNA tertiary (3D) structures and substructures plus a web-based search tool—designed to exploit graph representations of RNAs for the goal of searching for similar 3D structural fragments. The objects in RAG-3D consist of 3D structures translated into 3D graphs, cataloged based on the connectivity between their secondary structure elements. Each graph is additionally described in terms of its subgraph building blocks. The RAG-3D search tool then compares a query RNA 3D structure to those in the database to obtain structurally similar structures and substructures. This comparison reveals conserved 3D RNA features and thus may suggest functional connections. Though RNA search programs based on similarity in sequence, 2D, and/or 3D structural elements are available, our graph-based search tool may be advantageous for illuminating similarities that are not obvious; using motifs rather than sequence space also reduces search times considerably. Ultimately, such substructuring could be useful for RNA 3D structure prediction, structure/function inference and inverse folding. PMID:26304547

RAG-3D: A search tool for RNA 3D substructures

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

Zahran, Mai; Sevim Bayrak, Cigdem; Elmetwaly, Shereef

In this study, to address many challenges in RNA structure/function prediction, the characterization of RNA's modular architectural units is required. Using the RNA-As-Graphs (RAG) database, we have previously explored the existence of secondary structure (2D) submotifs within larger RNA structures. Here we present RAG-3D—a dataset of RNA tertiary (3D) structures and substructures plus a web-based search tool—designed to exploit graph representations of RNAs for the goal of searching for similar 3D structural fragments. The objects in RAG-3D consist of 3D structures translated into 3D graphs, cataloged based on the connectivity between their secondary structure elements. Each graph is additionally describedmore » in terms of its subgraph building blocks. The RAG-3D search tool then compares a query RNA 3D structure to those in the database to obtain structurally similar structures and substructures. This comparison reveals conserved 3D RNA features and thus may suggest functional connections. Though RNA search programs based on similarity in sequence, 2D, and/or 3D structural elements are available, our graph-based search tool may be advantageous for illuminating similarities that are not obvious; using motifs rather than sequence space also reduces search times considerably. Ultimately, such substructuring could be useful for RNA 3D structure prediction, structure/function inference and inverse folding.« less

Self-similar conductance patterns in graphene Cantor-like structures.

PubMed

García-Cervantes, H; Gaggero-Sager, L M; Díaz-Guerrero, D S; Sotolongo-Costa, O; Rodríguez-Vargas, I

2017-04-04

Graphene has proven to be an ideal system for exotic transport phenomena. In this work, we report another exotic characteristic of the electron transport in graphene. Namely, we show that the linear-regime conductance can present self-similar patterns with well-defined scaling rules, once the graphene sheet is subjected to Cantor-like nanostructuring. As far as we know the mentioned system is one of the few in which a self-similar structure produces self-similar patterns on a physical property. These patterns are analysed quantitatively, by obtaining the scaling rules that underlie them. It is worth noting that the transport properties are an average of the dispersion channels, which makes the existence of scale factors quite surprising. In addition, that self-similarity be manifested in the conductance opens an excellent opportunity to test this fundamental property experimentally.

An efficient sequential strategy for realizing cross-gradient joint inversion: method and its application to 2-D cross borehole seismic traveltime and DC resistivity tomography

NASA Astrophysics Data System (ADS)

Gao, Ji; Zhang, Haijiang

2018-05-01

Cross-gradient joint inversion that enforces structural similarity between different models has been widely utilized in jointly inverting different geophysical data types. However, it is a challenge to combine different geophysical inversion systems with the cross-gradient structural constraint into one joint inversion system because they may differ greatly in the model representation, forward modelling and inversion algorithm. Here we propose a new joint inversion strategy that can avoid this issue. Different models are separately inverted using the existing inversion packages and model structure similarity is only enforced through cross-gradient minimization between two models after each iteration. Although the data fitting and structural similarity enforcing processes are decoupled, our proposed strategy is still able to choose appropriate models to balance the trade-off between geophysical data fitting and structural similarity. This is realized by using model perturbations from separate data inversions to constrain the cross-gradient minimization process. We have tested this new strategy on 2-D cross borehole synthetic seismic traveltime and DC resistivity data sets. Compared to separate geophysical inversions, our proposed joint inversion strategy fits the separate data sets at comparable levels while at the same time resulting in a higher structural similarity between the velocity and resistivity models.

H-bonding in liquid acetamide as studied by x-ray scattering

NASA Astrophysics Data System (ADS)

Nasr, Salah; Ghédira, Mounir; Cortès, Robert

1999-06-01

A structural investigation of liquid acetamide was performed at 346 K using x-ray scattering. The data are analyzed to yield the molecular structure factor and the distinct pair correlation function. Two H-bonds per molecule are found on average. The mean N⋯O distance is about 3.03 Å. The liquid structure can be described by some structural units similar to the ones existing either in the rhombohedral or in the orthorhombic crystalline form.

Non-cooperative Fisher-KPP systems: traveling waves and long-time behavior

NASA Astrophysics Data System (ADS)

Girardin, Léo

2018-01-01

This paper is concerned with non-cooperative parabolic reaction-diffusion systems which share structural similarities with the scalar Fisher-KPP equation. These similarities make it possible to prove, among other results, an extinction and persistence dichotomy and, when persistence occurs, the existence of a positive steady state, the existence of traveling waves with a half-line of possible speeds and a positive minimal speed and the equality between this minimal speed and the spreading speed for the Cauchy problem. Non-cooperative KPP systems can model various phenomena where the following three mechanisms occur: local diffusion in space, linear cooperation and superlinear competition.

Learning context-sensitive shape similarity by graph transduction.

PubMed

Bai, Xiang; Yang, Xingwei; Latecki, Longin Jan; Liu, Wenyu; Tu, Zhuowen

2010-05-01

Shape similarity and shape retrieval are very important topics in computer vision. The recent progress in this domain has been mostly driven by designing smart shape descriptors for providing better similarity measure between pairs of shapes. In this paper, we provide a new perspective to this problem by considering the existing shapes as a group, and study their similarity measures to the query shape in a graph structure. Our method is general and can be built on top of any existing shape similarity measure. For a given similarity measure, a new similarity is learned through graph transduction. The new similarity is learned iteratively so that the neighbors of a given shape influence its final similarity to the query. The basic idea here is related to PageRank ranking, which forms a foundation of Google Web search. The presented experimental results demonstrate that the proposed approach yields significant improvements over the state-of-art shape matching algorithms. We obtained a retrieval rate of 91.61 percent on the MPEG-7 data set, which is the highest ever reported in the literature. Moreover, the learned similarity by the proposed method also achieves promising improvements on both shape classification and shape clustering.

Géologie du synclinal de l'Itombwe (Zaïre oriental) et le problème de l'existence d'un sillon plissé pan-africain

NASA Astrophysics Data System (ADS)

Villeneuve, Michel

From the N.S. linear structure of the Itombwe syncline arise some problems in central Africa. Some authors considered it as a Kibarian structure and others as an isolated fold belt of Pan-African orogeny. This ambiguity is the result, in its greatest part, of the scarceness of field work and the lack of dating on the rocks of this syncline. A study on the central area showed the existence of two lithostructural units. The western area is correlated with a Kibarian structure while the eastern area had some similarities with the tectonic Pan-African troughts from NE of Zaïre and west of Uganda. The existence of an area folded during the Pan-African orogeny and in the same environment as the great African lakes area must be considered.

Lunar and Martian Sub-surface Habitat Structure Technology Development and Application

NASA Technical Reports Server (NTRS)

Boston, Penelope J.; Strong, Janet D.

2005-01-01

NASA's human exploration initiative poses great opportunity and great risk for manned missions to the Moon and Mars. Subsidace structures such as caves and lava tubes offer readily available and existing in-situ habitat options. Sub-surface dwellings can provide complete radiation, micro-meteorite and exhaust plume shielding and a moderate and constant temperature environment; they are, therefore, excellent pre-existing habitat risk mitigation elements. Technical challenges to subsurface habitat structure development include surface penetration (digging and mining equipment), environmental pressurization, and psychological environment enhancement requirements. Lunar and Martian environments and elements have many beneficial similarities. This will allow for lunar testing and design development of subsurface habitat structures for Martian application; however, significant differences between lunar and Martian environments and resource elements will mandate unique application development. Mars is NASA's ultimate exploration goal and is known to have many very large lava tubes. Other cave types are plausible. The Moon has unroofed rilles and lava tubes, but further research will, in the near future, define the extent of Lunar and Martian differences and similarities. This paper will discuss Lunar and Martian subsurface habitation technology development challenges and opportunities.

On small beams with large topological charge: II. Photons, electrons and gravitational waves

NASA Astrophysics Data System (ADS)

Krenn, Mario; Zeilinger, Anton

2018-06-01

Beams of light with a large topological charge significantly change their spatial structure when they are focused strongly. Physically, it can be explained by an emerging electromagnetic field component in the direction of propagation, which is neglected in the simplified scalar wave picture in optics. Here we ask: is this a specific photonic behavior, or can similar phenomena also be predicted for other species of particles? We show that the same modification of the spatial structure exists for relativistic electrons as well as for focused gravitational waves. However, this is for different physical reasons: for electrons, which are described by the Dirac equation, the spatial structure changes due to a spin–orbit coupling in the relativistic regime. In gravitational waves described with linearized general relativity, the curvature of space–time between the transverse and propagation direction leads to the modification of the spatial structure. Thus, this universal phenomenon exists for both massive and massless elementary particles with spin 1/2, 1 and 2. It would be very interesting whether other types of particles such as composite systems (neutrons or C60) or neutrinos show a similar behavior and how this phenomenon can be explained in a unified physical way.

Conflict between object structural and functional affordances in peripersonal space.

PubMed

Kalénine, Solène; Wamain, Yannick; Decroix, Jérémy; Coello, Yann

2016-10-01

Recent studies indicate that competition between conflicting action representations slows down planning of object-directed actions. The present study aims to assess whether similar conflict effects exist during manipulable object perception. Twenty-six young adults performed reach-to-grasp and semantic judgements on conflictual objects (with competing structural and functional gestures) and non-conflictual objects (with similar structural and functional gestures) presented at difference distances in a 3D virtual environment. Results highlight a space-dependent conflict between structural and functional affordances. Perceptual judgments on conflictual objects were slower that perceptual judgments on non-conflictual objects, but only when objects were presented within reach. Findings demonstrate that competition between structural and functional affordances during object perception induces a processing cost, and further show that object position in space can bias affordance competition. Copyright © 2016 Elsevier B.V. All rights reserved.

PSSP-RFE: accurate prediction of protein structural class by recursive feature extraction from PSI-BLAST profile, physical-chemical property and functional annotations.

PubMed

Li, Liqi; Cui, Xiang; Yu, Sanjiu; Zhang, Yuan; Luo, Zhong; Yang, Hua; Zhou, Yue; Zheng, Xiaoqi

2014-01-01

Protein structure prediction is critical to functional annotation of the massively accumulated biological sequences, which prompts an imperative need for the development of high-throughput technologies. As a first and key step in protein structure prediction, protein structural class prediction becomes an increasingly challenging task. Amongst most homological-based approaches, the accuracies of protein structural class prediction are sufficiently high for high similarity datasets, but still far from being satisfactory for low similarity datasets, i.e., below 40% in pairwise sequence similarity. Therefore, we present a novel method for accurate and reliable protein structural class prediction for both high and low similarity datasets. This method is based on Support Vector Machine (SVM) in conjunction with integrated features from position-specific score matrix (PSSM), PROFEAT and Gene Ontology (GO). A feature selection approach, SVM-RFE, is also used to rank the integrated feature vectors through recursively removing the feature with the lowest ranking score. The definitive top features selected by SVM-RFE are input into the SVM engines to predict the structural class of a query protein. To validate our method, jackknife tests were applied to seven widely used benchmark datasets, reaching overall accuracies between 84.61% and 99.79%, which are significantly higher than those achieved by state-of-the-art tools. These results suggest that our method could serve as an accurate and cost-effective alternative to existing methods in protein structural classification, especially for low similarity datasets.

Fractal and multifractal analyses of bipartite networks

NASA Astrophysics Data System (ADS)

Liu, Jin-Long; Wang, Jian; Yu, Zu-Guo; Xie, Xian-Hua

2017-03-01

Bipartite networks have attracted considerable interest in various fields. Fractality and multifractality of unipartite (classical) networks have been studied in recent years, but there is no work to study these properties of bipartite networks. In this paper, we try to unfold the self-similarity structure of bipartite networks by performing the fractal and multifractal analyses for a variety of real-world bipartite network data sets and models. First, we find the fractality in some bipartite networks, including the CiteULike, Netflix, MovieLens (ml-20m), Delicious data sets and (u, v)-flower model. Meanwhile, we observe the shifted power-law or exponential behavior in other several networks. We then focus on the multifractal properties of bipartite networks. Our results indicate that the multifractality exists in those bipartite networks possessing fractality. To capture the inherent attribute of bipartite network with two types different nodes, we give the different weights for the nodes of different classes, and show the existence of multifractality in these node-weighted bipartite networks. In addition, for the data sets with ratings, we modify the two existing algorithms for fractal and multifractal analyses of edge-weighted unipartite networks to study the self-similarity of the corresponding edge-weighted bipartite networks. The results show that our modified algorithms are feasible and can effectively uncover the self-similarity structure of these edge-weighted bipartite networks and their corresponding node-weighted versions.

Fractal and multifractal analyses of bipartite networks.

PubMed

Liu, Jin-Long; Wang, Jian; Yu, Zu-Guo; Xie, Xian-Hua

2017-03-31

Bipartite networks have attracted considerable interest in various fields. Fractality and multifractality of unipartite (classical) networks have been studied in recent years, but there is no work to study these properties of bipartite networks. In this paper, we try to unfold the self-similarity structure of bipartite networks by performing the fractal and multifractal analyses for a variety of real-world bipartite network data sets and models. First, we find the fractality in some bipartite networks, including the CiteULike, Netflix, MovieLens (ml-20m), Delicious data sets and (u, v)-flower model. Meanwhile, we observe the shifted power-law or exponential behavior in other several networks. We then focus on the multifractal properties of bipartite networks. Our results indicate that the multifractality exists in those bipartite networks possessing fractality. To capture the inherent attribute of bipartite network with two types different nodes, we give the different weights for the nodes of different classes, and show the existence of multifractality in these node-weighted bipartite networks. In addition, for the data sets with ratings, we modify the two existing algorithms for fractal and multifractal analyses of edge-weighted unipartite networks to study the self-similarity of the corresponding edge-weighted bipartite networks. The results show that our modified algorithms are feasible and can effectively uncover the self-similarity structure of these edge-weighted bipartite networks and their corresponding node-weighted versions.

Fractal and multifractal analyses of bipartite networks

PubMed Central

Liu, Jin-Long; Wang, Jian; Yu, Zu-Guo; Xie, Xian-Hua

2017-01-01

Bipartite networks have attracted considerable interest in various fields. Fractality and multifractality of unipartite (classical) networks have been studied in recent years, but there is no work to study these properties of bipartite networks. In this paper, we try to unfold the self-similarity structure of bipartite networks by performing the fractal and multifractal analyses for a variety of real-world bipartite network data sets and models. First, we find the fractality in some bipartite networks, including the CiteULike, Netflix, MovieLens (ml-20m), Delicious data sets and (u, v)-flower model. Meanwhile, we observe the shifted power-law or exponential behavior in other several networks. We then focus on the multifractal properties of bipartite networks. Our results indicate that the multifractality exists in those bipartite networks possessing fractality. To capture the inherent attribute of bipartite network with two types different nodes, we give the different weights for the nodes of different classes, and show the existence of multifractality in these node-weighted bipartite networks. In addition, for the data sets with ratings, we modify the two existing algorithms for fractal and multifractal analyses of edge-weighted unipartite networks to study the self-similarity of the corresponding edge-weighted bipartite networks. The results show that our modified algorithms are feasible and can effectively uncover the self-similarity structure of these edge-weighted bipartite networks and their corresponding node-weighted versions. PMID:28361962

NNvPDB: Neural Network based Protein Secondary Structure Prediction with PDB Validation.

PubMed

Sakthivel, Seethalakshmi; S K M, Habeeb

2015-01-01

The predicted secondary structural states are not cross validated by any of the existing servers. Hence, information on the level of accuracy for every sequence is not reported by the existing servers. This was overcome by NNvPDB, which not only reported greater Q3 but also validates every prediction with the homologous PDB entries. NNvPDB is based on the concept of Neural Network, with a new and different approach of training the network every time with five PDB structures that are similar to query sequence. The average accuracy for helix is 76%, beta sheet is 71% and overall (helix, sheet and coil) is 66%. http://bit.srmuniv.ac.in/cgi-bin/bit/cfpdb/nnsecstruct.pl.

A Weighted Multipath Measurement Based on Gene Ontology for Estimating Gene Products Similarity

PubMed Central

Liu, Lizhen; Dai, Xuemin; Song, Wei; Lu, Jingli

2014-01-01

Abstract Many different methods have been proposed for calculating the semantic similarity of term pairs based on gene ontology (GO). Most existing methods are based on information content (IC), and the methods based on IC are used more commonly than those based on the structure of GO. However, most IC-based methods not only fail to handle identical annotations but also show a strong bias toward well-annotated proteins. We propose a new method called weighted multipath measurement (WMM) for estimating the semantic similarity of gene products based on the structure of the GO. We not only considered the contribution of every path between two GO terms but also took the depth of the lowest common ancestors into account. We assigned different weights for different kinds of edges in GO graph. The similarity values calculated by WMM can be reused because they are only relative to the characteristics of GO terms. Experimental results showed that the similarity values obtained by WMM have a higher accuracy. We compared the performance of WMM with that of other methods using GO data and gene annotation datasets for yeast and humans downloaded from the GO database. We found that WMM is more suited for prediction of gene function than most existing IC-based methods and that it can distinguish proteins with identical annotations (two proteins are annotated with the same terms) from each other. PMID:25229994

A perspective on the structural studies of inner membrane electrochemical potential-driven transporters.

PubMed

Lemieux, M Joanne

2008-09-01

Electrochemical potential-driven transporters represent a vast array of proteins with varied substrate specificities. While diverse in size and substrate specificity, they are all driven by electrochemical potentials. Over the past five years there have been increasing numbers of X-ray structures reported for this family of transporters. Structural information is available for five subfamilies of electrochemical potential-driven transporters. No structural information exists for the remaining 91 subfamilies. In this review, the various subfamilies of electrochemical potential-driven transporters are discussed. The seven reported structures for the electrochemical potential-driven transporters and the methods for their crystallization are also presented. With a few exceptions, overall crystallization trends have been very similar for the transporters despite their differences in substrate specificity and topology. Also discussed is why the structural studies on these transporters were successful while others are not as fruitful. With the plethora of transporters with unknown structures, this review provides incentive for crystallization of transporters in the remaining subfamilies for which no structural information exists.

Modification of Existing Prestressed Girder Cross-Sections for the Optimal Structural Use of Ultra-High Performance Concrete

DOT National Transportation Integrated Search

2008-10-22

Ultra High Performance Concrete (UHPC) is a class of cementitious materials that share similar characteristics including very large compressive strengths, tensile strength greater than conventional concrete and high durability. The material consists ...

Hidden relationships between metalloproteins unveiled by structural comparison of their metal sites

NASA Astrophysics Data System (ADS)

Valasatava, Yana; Andreini, Claudia; Rosato, Antonio

2015-03-01

Metalloproteins account for a substantial fraction of all proteins. They incorporate metal atoms, which are required for their structure and/or function. Here we describe a new computational protocol to systematically compare and classify metal-binding sites on the basis of their structural similarity. These sites are extracted from the MetalPDB database of minimal functional sites (MFSs) in metal-binding biological macromolecules. Structural similarity is measured by the scoring function of the available MetalS2 program. Hierarchical clustering was used to organize MFSs into clusters, for each of which a representative MFS was identified. The comparison of all representative MFSs provided a thorough structure-based classification of the sites analyzed. As examples, the application of the proposed computational protocol to all heme-binding proteins and zinc-binding proteins of known structure highlighted the existence of structural subtypes, validated known evolutionary links and shed new light on the occurrence of similar sites in systems at different evolutionary distances. The present approach thus makes available an innovative viewpoint on metalloproteins, where the functionally crucial metal sites effectively lead the discovery of structural and functional relationships in a largely protein-independent manner.

Graph-based similarity concepts in virtual screening.

PubMed

Hutter, Michael C

2011-03-01

Applying similarity for finding new promising compounds is a key issue in drug design. Conversely, quantifying similarity between molecules has remained a difficult task despite the numerous approaches. Here, some general aspects along with recent developments regarding similarity criteria are collected. For the purpose of virtual screening, the compounds have to be encoded into a computer-readable format that permits a comparison, according to given similarity criteria, comprising the use of the 3D structure, fingerprints, graph-based and alignment-based approaches. Whereas finding the most common substructures is the most obvious method, more recent approaches take into account chemical modifications that appear throughout existing drugs, from various therapeutic categories and targets.

Topological relationships between brain and social networks.

PubMed

Sakata, Shuzo; Yamamori, Tetsuo

2007-01-01

Brains are complex networks. Previously, we revealed that specific connected structures are either significantly abundant or rare in cortical networks. However, it remains unknown whether systems from other disciplines have similar architectures to brains. By applying network-theoretical methods, here we show topological similarities between brain and social networks. We found that the statistical relevance of specific tied structures differs between social "friendship" and "disliking" networks, suggesting relation-type-specific topology of social networks. Surprisingly, overrepresented connected structures in brain networks are more similar to those in the friendship networks than to those in other networks. We found that balanced and imbalanced reciprocal connections between nodes are significantly abundant and rare, respectively, whereas these results are unpredictable by simply counting mutual connections. We interpret these results as evidence of positive selection of balanced mutuality between nodes. These results also imply the existence of underlying common principles behind the organization of brain and social networks.

Structure of the thermodynamic arrow of time in classical and quantum theories

NASA Astrophysics Data System (ADS)

Korzekwa, Kamil

2017-05-01

In this work we analyze the structure of the thermodynamic arrow of time, defined by transformations that leave the thermal equilibrium state unchanged, in classical (incoherent) and quantum (coherent) regimes. We note that in the infinite-temperature limit, the thermodynamic ordering of states in both regimes exhibits a lattice structure. This means that when energy does not matter and the only thermodynamic resource is given by information, the thermodynamic arrow of time has a very specific structure. Namely, for any two states at present there exists a unique state in the past consistent with them and with all possible joint pasts. Similarly, there also exists a unique state in the future consistent with those states and with all possible joint futures. We also show that the lattice structure in the classical regime is broken at finite temperatures, i.e., when energy is a relevant thermodynamic resource. Surprisingly, however, we prove that in the simplest quantum scenario of a two-dimensional system, this structure is preserved at finite temperatures. We provide the physical interpretation of these results by introducing and analyzing the history erasure process, and point out that quantum coherence may be a necessary resource for the existence of an optimal erasure process.

Shedding of dual structures in the wake of a surface-mounted low aspect ratio cone

NASA Astrophysics Data System (ADS)

Chen, Zixiang; Martinuzzi, Robert J.

2018-04-01

The periodic shedding of vortex pairs in the turbulent wake of a surface-mounted right cone of aspect ratio 0.867 protruding a thin turbulent boundary layer is investigated experimentally. A phase-averaged volumetric velocity field is reconstructed from planar stereoscopic particle image velocimetry. During a typical (phase-averaged) shedding cycle, counter-rotating base vortices alternately form. These are tilted and stretched to merge with stream-wise tip vortices. The merged structure sheds and is convected downstream. A synthesis of earlier observations suggests that a similar shedding process exists for other low aspect ratio tapered geometries and is more complex than the shedding patterns observed for cantilevered cylinders, despite similarities of the mean flow field structure.

Fabrication of biomimetic resorption lacunae-like structure on titanium surface and its osteoblast responses

NASA Astrophysics Data System (ADS)

Huo, Fangjun; Guo, Weihua; Wu, Hao; Wang, Yueting; He, Gang; Xie, Li; Tian, Weidong

2018-04-01

Biomimetic specific surface structure could improve biological behaviors of specific cells and eventual tissue integration. Featuring titanium surface with structures resembling bone resorption lacunae (RL) can be a promising approach to improve the osteoblast responses and osseointegration of implants. As a most common used dental implant surface, sandblasting and acid etching (SLA) surface has micro-sized structures with dimensions similar to RL, but great differences exist when it comes to shape and contour. In this work, by anodizing titanium substrate in a novel HCOONa/CH3COONa electrolyte, RL-like crater structures were fabricated with highly similar size, shape and contour. Compared with SLA, it was much more similar to RL structure in shape and contour. Furthermore, through subsequent alkali-heat treatment, nano-sized structures that overlaid the whole surface were obtained, which further mimic undercuts features inside the RL. The as-prepared surface was consisted of crystalline titania and exhibited super-hydrophilicity with good stability. In vitro evaluation results showed that the surface could significantly improve adhesion, proliferation and differentiation of MG63 cells in comparison with SLA. This new method may be a promising candidate for biomimetic modification of titanium implant to promote osseointegration.

Proteins as sponges: a statistical journey along protein structure organization principles.

PubMed

Paola, Luisa Di; Paci, Paola; Santoni, Daniele; Ruvo, Micol De; Giuliani, Alessandro

2012-02-27

The analysis of a large database of protein structures by means of topological and shape indexes inspired by complex network and fractal analysis shed light on some organizational principles of proteins. Proteins appear much more similar to "fractal" sponges than to closely packed spheres, casting doubts on the tenability of the hydrophobic core concept. Principal component analysis highlighted three main order parameters shaping the protein universe: (1) "size", with the consequent generation of progressively less dense and more empty structures at an increasing number of residues, (2) "microscopic structuring", linked to the existence of a spectrum going from the prevalence of heterologous (different hydrophobicity) to the prevalence of homologous (similar hydrophobicity) contacts, and (3) "fractal shape", an organizing protein data set along a continuum going from approximately linear to very intermingled structures. Perhaps the time has come for seriously taking into consideration the real relevance of time-honored principles like the hydrophobic core and hydrophobic effect.

GalaxyGPCRloop: Template-Based and Ab Initio Structure Sampling of the Extracellular Loops of G-Protein-Coupled Receptors.

PubMed

Won, Jonghun; Lee, Gyu Rie; Park, Hahnbeom; Seok, Chaok

2018-06-07

The second extracellular loops (ECL2s) of G-protein-coupled receptors (GPCRs) are often involved in GPCR functions, and their structures have important implications in drug discovery. However, structure prediction of ECL2 is difficult because of its long length and the structural diversity among different GPCRs. In this study, a new ECL2 conformational sampling method involving both template-based and ab initio sampling was developed. Inspired by the observation of similar ECL2 structures of closely related GPCRs, a template-based sampling method employing loop structure templates selected from the structure database was developed. A new metric for evaluating similarity of the target loop to templates was introduced for template selection. An ab initio loop sampling method was also developed to treat cases without highly similar templates. The ab initio method is based on the previously developed fragment assembly and loop closure method. A new sampling component that takes advantage of secondary structure prediction was added. In addition, a conserved disulfide bridge restraining ECL2 conformation was predicted and analytically incorporated into sampling, reducing the effective dimension of the conformational search space. The sampling method was combined with an existing energy function for comparison with previously reported loop structure prediction methods, and the benchmark test demonstrated outstanding performance.

Improving the measurement of semantic similarity by combining gene ontology and co-functional network: a random walk based approach.

PubMed

Peng, Jiajie; Zhang, Xuanshuo; Hui, Weiwei; Lu, Junya; Li, Qianqian; Liu, Shuhui; Shang, Xuequn

2018-03-19

Gene Ontology (GO) is one of the most popular bioinformatics resources. In the past decade, Gene Ontology-based gene semantic similarity has been effectively used to model gene-to-gene interactions in multiple research areas. However, most existing semantic similarity approaches rely only on GO annotations and structure, or incorporate only local interactions in the co-functional network. This may lead to inaccurate GO-based similarity resulting from the incomplete GO topology structure and gene annotations. We present NETSIM2, a new network-based method that allows researchers to measure GO-based gene functional similarities by considering the global structure of the co-functional network with a random walk with restart (RWR)-based method, and by selecting the significant term pairs to decrease the noise information. Based on the EC number (Enzyme Commission)-based groups of yeast and Arabidopsis, evaluation test shows that NETSIM2 can enhance the accuracy of Gene Ontology-based gene functional similarity. Using NETSIM2 as an example, we found that the accuracy of semantic similarities can be significantly improved after effectively incorporating the global gene-to-gene interactions in the co-functional network, especially on the species that gene annotations in GO are far from complete.

EEG Sleep Stages Classification Based on Time Domain Features and Structural Graph Similarity.

PubMed

Diykh, Mohammed; Li, Yan; Wen, Peng

2016-11-01

The electroencephalogram (EEG) signals are commonly used in diagnosing and treating sleep disorders. Many existing methods for sleep stages classification mainly depend on the analysis of EEG signals in time or frequency domain to obtain a high classification accuracy. In this paper, the statistical features in time domain, the structural graph similarity and the K-means (SGSKM) are combined to identify six sleep stages using single channel EEG signals. Firstly, each EEG segment is partitioned into sub-segments. The size of a sub-segment is determined empirically. Secondly, statistical features are extracted, sorted into different sets of features and forwarded to the SGSKM to classify EEG sleep stages. We have also investigated the relationships between sleep stages and the time domain features of the EEG data used in this paper. The experimental results show that the proposed method yields better classification results than other four existing methods and the support vector machine (SVM) classifier. A 95.93% average classification accuracy is achieved by using the proposed method.

Wind loads and competition for light sculpt trees into self-similar structures.

PubMed

Eloy, Christophe; Fournier, Meriem; Lacointe, André; Moulia, Bruno

2017-10-18

Trees are self-similar structures: their branch lengths and diameters vary allometrically within the tree architecture, with longer and thicker branches near the ground. These tree allometries are often attributed to optimisation of hydraulic sap transport and safety against elastic buckling. Here, we show that these allometries also emerge from a model that includes competition for light, wind biomechanics and no hydraulics. We have developed MECHATREE, a numerical model of trees growing and evolving on a virtual island. With this model, we identify the fittest growth strategy when trees compete for light and allocate their photosynthates to grow seeds, create new branches or reinforce existing ones in response to wind-induced loads. Strikingly, we find that selected trees species are self-similar and follow allometric scalings similar to those observed on dicots and conifers. This result suggests that resistance to wind and competition for light play an essential role in determining tree allometries.

Towards a 4{sup th} generation storage ring at the Canadian Light Source

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

Dallin, Les; Wurtz, Ward

2016-07-27

Demands from beamline scientists for more brilliant sources of synchrotron radiation have resulted in the emergence of 4{sup th} generation (diffraction-limited) storage rings. The practical development of the multi-bend achromat (MBA) concept by MAX IV lab has spurred many synchrotron light sources around the world to develop similar machines. For existing facilities two options are available: upgrading existing machines or building a new structure. The Canadian Light Source (CLS) has explored both options. For a new low emittance source in the existing CLS tunnel a decrease in electron energy would be required. A machine similar to the ALS upgrade couldmore » be contemplated. To achieve low emittance at our present energy of 2.9 GeV a new storage ring is desirable. Several options have been investigated. These designs use extremely strong focusing magnets to achieve extremely low emittances in compact lattice achromats.« less

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.

In situ damage detection in frame structures through coupled response measurements

NASA Astrophysics Data System (ADS)

Liu, D.; Gurgenci, H.; Veidt, M.

2004-05-01

Due to the existence of global modes and local modes of the neighbouring members, damage detection on a structure is more challenging than damage on isolated beams. Detection of an artificial circumferential crack on a joint in a frame-like welded structure is studied in this paper using coupled response measurements. Similarity to real engineering structures is maintained in the fabrication of the test frame. Both the chords and the branch members have hollow sections and the branch members have smaller sizes. The crack is created by a hacksaw on a joint where a branch meets the chord. The methodology is first demonstrated on a single hollow section beam. The test results are then presented for the damaged and undamaged frame. The existence of the damage is clearly observable from the experimental results. It is suggested that this approach offers the potential to detect damage in welded structures such as cranes, mining equipment, steel-frame bridges, naval and offshore structures.

Comparative analysis of chemical similarity methods for modular natural products with a hypothetical structure enumeration algorithm.

PubMed

Skinnider, Michael A; Dejong, Chris A; Franczak, Brian C; McNicholas, Paul D; Magarvey, Nathan A

2017-08-16

Natural products represent a prominent source of pharmaceutically and industrially important agents. Calculating the chemical similarity of two molecules is a central task in cheminformatics, with applications at multiple stages of the drug discovery pipeline. Quantifying the similarity of natural products is a particularly important problem, as the biological activities of these molecules have been extensively optimized by natural selection. The large and structurally complex scaffolds of natural products distinguish their physical and chemical properties from those of synthetic compounds. However, no analysis of the performance of existing methods for molecular similarity calculation specific to natural products has been reported to date. Here, we present LEMONS, an algorithm for the enumeration of hypothetical modular natural product structures. We leverage this algorithm to conduct a comparative analysis of molecular similarity methods within the unique chemical space occupied by modular natural products using controlled synthetic data, and comprehensively investigate the impact of diverse biosynthetic parameters on similarity search. We additionally investigate a recently described algorithm for natural product retrobiosynthesis and alignment, and find that when rule-based retrobiosynthesis can be applied, this approach outperforms conventional two-dimensional fingerprints, suggesting it may represent a valuable approach for the targeted exploration of natural product chemical space and microbial genome mining. Our open-source algorithm is an extensible method of enumerating hypothetical natural product structures with diverse potential applications in bioinformatics.

Statistical potential-based amino acid similarity matrices for aligning distantly related protein sequences.

PubMed

Tan, Yen Hock; Huang, He; Kihara, Daisuke

2006-08-15

Aligning distantly related protein sequences is a long-standing problem in bioinformatics, and a key for successful protein structure prediction. Its importance is increasing recently in the context of structural genomics projects because more and more experimentally solved structures are available as templates for protein structure modeling. Toward this end, recent structure prediction methods employ profile-profile alignments, and various ways of aligning two profiles have been developed. More fundamentally, a better amino acid similarity matrix can improve a profile itself; thereby resulting in more accurate profile-profile alignments. Here we have developed novel amino acid similarity matrices from knowledge-based amino acid contact potentials. Contact potentials are used because the contact propensity to the other amino acids would be one of the most conserved features of each position of a protein structure. The derived amino acid similarity matrices are tested on benchmark alignments at three different levels, namely, the family, the superfamily, and the fold level. Compared to BLOSUM45 and the other existing matrices, the contact potential-based matrices perform comparably in the family level alignments, but clearly outperform in the fold level alignments. The contact potential-based matrices perform even better when suboptimal alignments are considered. Comparing the matrices themselves with each other revealed that the contact potential-based matrices are very different from BLOSUM45 and the other matrices, indicating that they are located in a different basin in the amino acid similarity matrix space.

Prediction of Protein Structural Classes for Low-Similarity Sequences Based on Consensus Sequence and Segmented PSSM.

PubMed

Liang, Yunyun; Liu, Sanyang; Zhang, Shengli

2015-01-01

Prediction of protein structural classes for low-similarity sequences is useful for understanding fold patterns, regulation, functions, and interactions of proteins. It is well known that feature extraction is significant to prediction of protein structural class and it mainly uses protein primary sequence, predicted secondary structure sequence, and position-specific scoring matrix (PSSM). Currently, prediction solely based on the PSSM has played a key role in improving the prediction accuracy. In this paper, we propose a novel method called CSP-SegPseP-SegACP by fusing consensus sequence (CS), segmented PsePSSM, and segmented autocovariance transformation (ACT) based on PSSM. Three widely used low-similarity datasets (1189, 25PDB, and 640) are adopted in this paper. Then a 700-dimensional (700D) feature vector is constructed and the dimension is decreased to 224D by using principal component analysis (PCA). To verify the performance of our method, rigorous jackknife cross-validation tests are performed on 1189, 25PDB, and 640 datasets. Comparison of our results with the existing PSSM-based methods demonstrates that our method achieves the favorable and competitive performance. This will offer an important complementary to other PSSM-based methods for prediction of protein structural classes for low-similarity sequences.

Asymptotic structure and similarity solutions for three-dimensional turbulent boundary layers

NASA Technical Reports Server (NTRS)

Degani, A. T.; Walker, J. D. A.

1989-01-01

The asymptotic structure of the three-dimensional turbulent boundary layer is investigated in the limit of large Reynolds numbers. A self-consistent, but relatively complex, two-layer structure exists and the simplest situation, corresponding to a plane of symmetry, is considered in this paper as a first step. The adjustment of the streamwise velocity to relative rest, through an outer defect layer and then an inner wall layer, is similar to that in two-dimensional flow. The adjustment of the cross-streamwise velocity is more complicated and it is shown that two terms in the expansion are required to obtain useful results, and in particular to obtain the velocity skew angle at the wall near the symmetry plane. The conditions under which self-similarity is achieved near a plane of symmetry are investigated. A set of ordinary differential equations is developed which describe the streamwise and cross-streamwise velocities near a plane of symmetry in a self-similar flow through two orders of magnitude. Calculated numerical solutions of these equations yield trends which are consistent with experimental observations.

On Prolonging Network Lifetime through Load-Similar Node Deployment in Wireless Sensor Networks

PubMed Central

Li, Qiao-Qin; Gong, Haigang; Liu, Ming; Yang, Mei; Zheng, Jun

2011-01-01

This paper is focused on the study of the energy hole problem in the Progressive Multi-hop Rotational Clustered (PMRC)-structure, a highly scalable wireless sensor network (WSN) architecture. Based on an analysis on the traffic load distribution in PMRC-based WSNs, we propose a novel load-similar node distribution strategy combined with the Minimum Overlapping Layers (MOL) scheme to address the energy hole problem in PMRC-based WSNs. In this strategy, sensor nodes are deployed in the network area according to the load distribution. That is, more nodes shall be deployed in the range where the average load is higher, and then the loads among different areas in the sensor network tend to be balanced. Simulation results demonstrate that the load-similar node distribution strategy prolongs network lifetime and reduces the average packet latency in comparison with existing nonuniform node distribution and uniform node distribution strategies. Note that, besides the PMRC structure, the analysis model and the proposed load-similar node distribution strategy are also applicable to other multi-hop WSN structures. PMID:22163809

Crystal structures of the coil 2B fragment and the globular tail domain of human lamin B1

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

Ruan, Jianbin; Xu, Chao; Bian, Chuanbing

2012-07-18

We present here the crystal structures of human lamin B1 globular tail domain and coiled 2B domain, which adopt similar folds to Ig-like domain and coiled-coil domain of lamin A, respectively. Despite the overall similarity, we found an extra intermolecular disulfide bond in the lamin B1 coil 2B domain, which does not exist in lamin A/C. In addition, the structural analysis indicates that interactions at the lamin B1 homodimer interface are quite different from those of lamin A/C. Thus our research not only reveals the diversely formed homodimers among lamin family members, but also sheds light on understanding the importantmore » roles of lamin B1 in forming the nuclear lamina matrix.« less

Predicting the evolution of complex networks via similarity dynamics

NASA Astrophysics Data System (ADS)

Wu, Tao; Chen, Leiting; Zhong, Linfeng; Xian, Xingping

2017-01-01

Almost all real-world networks are subject to constant evolution, and plenty of them have been investigated empirically to uncover the underlying evolution mechanism. However, the evolution prediction of dynamic networks still remains a challenging problem. The crux of this matter is to estimate the future network links of dynamic networks. This paper studies the evolution prediction of dynamic networks with link prediction paradigm. To estimate the likelihood of the existence of links more accurate, an effective and robust similarity index is presented by exploiting network structure adaptively. Moreover, most of the existing link prediction methods do not make a clear distinction between future links and missing links. In order to predict the future links, the networks are regarded as dynamic systems in this paper, and a similarity updating method, spatial-temporal position drift model, is developed to simulate the evolutionary dynamics of node similarity. Then the updated similarities are used as input information for the future links' likelihood estimation. Extensive experiments on real-world networks suggest that the proposed similarity index performs better than baseline methods and the position drift model performs well for evolution prediction in real-world evolving networks.

Optimal Alignment of Structures for Finite and Periodic Systems.

PubMed

Griffiths, Matthew; Niblett, Samuel P; Wales, David J

2017-10-10

Finding the optimal alignment between two structures is important for identifying the minimum root-mean-square distance (RMSD) between them and as a starting point for calculating pathways. Most current algorithms for aligning structures are stochastic, scale exponentially with the size of structure, and the performance can be unreliable. We present two complementary methods for aligning structures corresponding to isolated clusters of atoms and to condensed matter described by a periodic cubic supercell. The first method (Go-PERMDIST), a branch and bound algorithm, locates the global minimum RMSD deterministically in polynomial time. The run time increases for larger RMSDs. The second method (FASTOVERLAP) is a heuristic algorithm that aligns structures by finding the global maximum kernel correlation between them using fast Fourier transforms (FFTs) and fast SO(3) transforms (SOFTs). For periodic systems, FASTOVERLAP scales with the square of the number of identical atoms in the system, reliably finds the best alignment between structures that are not too distant, and shows significantly better performance than existing algorithms. The expected run time for Go-PERMDIST is longer than FASTOVERLAP for periodic systems. For finite clusters, the FASTOVERLAP algorithm is competitive with existing algorithms. The expected run time for Go-PERMDIST to find the global RMSD between two structures deterministically is generally longer than for existing stochastic algorithms. However, with an earlier exit condition, Go-PERMDIST exhibits similar or better performance.

The Advantages of Hierarchical Linear Modeling. ERIC/AE Digest.

ERIC Educational Resources Information Center

Osborne, Jason W.

This digest introduces hierarchical data structure, describes how hierarchical models work, and presents three approaches to analyzing hierarchical data. Hierarchical, or nested data, present several problems for analysis. People or creatures that exist within hierarchies tend to be more similar to each other than people randomly sampled from the…

The molecular matching problem

NASA Technical Reports Server (NTRS)

Kincaid, Rex K.

1993-01-01

Molecular chemistry contains many difficult optimization problems that have begun to attract the attention of optimizers in the Operations Research community. Problems including protein folding, molecular conformation, molecular similarity, and molecular matching have been addressed. Minimum energy conformations for simple molecular structures such as water clusters, Lennard-Jones microclusters, and short polypeptides have dominated the literature to date. However, a variety of interesting problems exist and we focus here on a molecular structure matching (MSM) problem.

'Passive-roof' duplex geometry in the frontal structures of the Kirthar and Sulaiman mountain belts, Pakistan

NASA Astrophysics Data System (ADS)

Banks, C. J.; Warburton, J.

Exploration for hydrocarbons over the past few years has greatly improved our understanding of the geometry of frontal mountain belt structures. In this study we introduce and discuss the concept of the 'Passive-roof duplex', using as the main example the Kirthar and Sulaiman Ranges in the Baluchistan Province of Pakistan. Structures similar to those described here have been recognized previously in other mountain belts, and they appear to exist as a common feature in many more frontal regions of mountain belts. Our example of a Passive-roof duplex which we describe from Pakistan is compared briefly with similar structures reported by others. The Passive-roof duplex is here defined as a duplex whose roof thrust has backthrust sense ( Passive-roof thrust) and whose roof sequence (those rocks lying above the roof thrust) remains relatively 'stationary' during foreland directed piggy-back style propagation of horses within the duplex.

Coupling effect of nodes popularity and similarity on social network persistence

PubMed Central

Jin, Xiaogang; Jin, Cheng; Huang, Jiaxuan; Min, Yong

2017-01-01

Network robustness represents the ability of networks to withstand failures and perturbations. In social networks, maintenance of individual activities, also called persistence, is significant towards understanding robustness. Previous works usually consider persistence on pre-generated network structures; while in social networks, the network structure is growing with the cascading inactivity of existed individuals. Here, we address this challenge through analysis for nodes under a coevolution model, which characterizes individual activity changes under three network growth modes: following the descending order of nodes’ popularity, similarity or uniform random. We show that when nodes possess high spontaneous activities, a popularity-first growth mode obtains highly persistent networks; otherwise, with low spontaneous activities, a similarity-first mode does better. Moreover, a compound growth mode, with the consecutive joining of similar nodes in a short period and mixing a few high popularity nodes, obtains the highest persistence. Therefore, nodes similarity is essential for persistent social networks, while properly coupling popularity with similarity further optimizes the persistence. This demonstrates the evolution of nodes activity not only depends on network topology, but also their connective typology. PMID:28220840

Coupling effect of nodes popularity and similarity on social network persistence

NASA Astrophysics Data System (ADS)

Jin, Xiaogang; Jin, Cheng; Huang, Jiaxuan; Min, Yong

2017-02-01

Network robustness represents the ability of networks to withstand failures and perturbations. In social networks, maintenance of individual activities, also called persistence, is significant towards understanding robustness. Previous works usually consider persistence on pre-generated network structures; while in social networks, the network structure is growing with the cascading inactivity of existed individuals. Here, we address this challenge through analysis for nodes under a coevolution model, which characterizes individual activity changes under three network growth modes: following the descending order of nodes’ popularity, similarity or uniform random. We show that when nodes possess high spontaneous activities, a popularity-first growth mode obtains highly persistent networks; otherwise, with low spontaneous activities, a similarity-first mode does better. Moreover, a compound growth mode, with the consecutive joining of similar nodes in a short period and mixing a few high popularity nodes, obtains the highest persistence. Therefore, nodes similarity is essential for persistent social networks, while properly coupling popularity with similarity further optimizes the persistence. This demonstrates the evolution of nodes activity not only depends on network topology, but also their connective typology.

Coupling effect of nodes popularity and similarity on social network persistence.

PubMed

Jin, Xiaogang; Jin, Cheng; Huang, Jiaxuan; Min, Yong

2017-02-21

Network robustness represents the ability of networks to withstand failures and perturbations. In social networks, maintenance of individual activities, also called persistence, is significant towards understanding robustness. Previous works usually consider persistence on pre-generated network structures; while in social networks, the network structure is growing with the cascading inactivity of existed individuals. Here, we address this challenge through analysis for nodes under a coevolution model, which characterizes individual activity changes under three network growth modes: following the descending order of nodes' popularity, similarity or uniform random. We show that when nodes possess high spontaneous activities, a popularity-first growth mode obtains highly persistent networks; otherwise, with low spontaneous activities, a similarity-first mode does better. Moreover, a compound growth mode, with the consecutive joining of similar nodes in a short period and mixing a few high popularity nodes, obtains the highest persistence. Therefore, nodes similarity is essential for persistent social networks, while properly coupling popularity with similarity further optimizes the persistence. This demonstrates the evolution of nodes activity not only depends on network topology, but also their connective typology.

Integrated analysis of drug-induced gene expression profiles predicts novel hERG inhibitors.

PubMed

Babcock, Joseph J; Du, Fang; Xu, Kaiping; Wheelan, Sarah J; Li, Min

2013-01-01

Growing evidence suggests that drugs interact with diverse molecular targets mediating both therapeutic and toxic effects. Prediction of these complex interactions from chemical structures alone remains challenging, as compounds with different structures may possess similar toxicity profiles. In contrast, predictions based on systems-level measurements of drug effect may reveal pharmacologic similarities not evident from structure or known therapeutic indications. Here we utilized drug-induced transcriptional responses in the Connectivity Map (CMap) to discover such similarities among diverse antagonists of the human ether-à-go-go related (hERG) potassium channel, a common target of promiscuous inhibition by small molecules. Analysis of transcriptional profiles generated in three independent cell lines revealed clusters enriched for hERG inhibitors annotated using a database of experimental measurements (hERGcentral) and clinical indications. As a validation, we experimentally identified novel hERG inhibitors among the unannotated drugs in these enriched clusters, suggesting transcriptional responses may serve as predictive surrogates of cardiotoxicity complementing existing functional assays.

Integrated Analysis of Drug-Induced Gene Expression Profiles Predicts Novel hERG Inhibitors

PubMed Central

Babcock, Joseph J.; Du, Fang; Xu, Kaiping; Wheelan, Sarah J.; Li, Min

2013-01-01

Growing evidence suggests that drugs interact with diverse molecular targets mediating both therapeutic and toxic effects. Prediction of these complex interactions from chemical structures alone remains challenging, as compounds with different structures may possess similar toxicity profiles. In contrast, predictions based on systems-level measurements of drug effect may reveal pharmacologic similarities not evident from structure or known therapeutic indications. Here we utilized drug-induced transcriptional responses in the Connectivity Map (CMap) to discover such similarities among diverse antagonists of the human ether-à-go-go related (hERG) potassium channel, a common target of promiscuous inhibition by small molecules. Analysis of transcriptional profiles generated in three independent cell lines revealed clusters enriched for hERG inhibitors annotated using a database of experimental measurements (hERGcentral) and clinical indications. As a validation, we experimentally identified novel hERG inhibitors among the unannotated drugs in these enriched clusters, suggesting transcriptional responses may serve as predictive surrogates of cardiotoxicity complementing existing functional assays. PMID:23936032

Solution structure of the His12 --> Cys mutant of the N-terminal zinc binding domain of HIV-1 integrase complexed to cadmium.

PubMed Central

Cai, M.; Huang, Y.; Caffrey, M.; Zheng, R.; Craigie, R.; Clore, G. M.; Gronenborn, A. M.

1998-01-01

The solution structure of His12 --> Cys mutant of the N-terminal zinc binding domain (residues 1-55; IN(1-55)) of HIV-1 integrase complexed to cadmium has been solved by multidimensional heteronuclear NMR spectroscopy. The overall structure is very similar to that of the wild-type N-terminal domain complexed to zinc. In contrast to the wild-type domain, however, which exists in two interconverting conformational states arising from different modes of coordination of the two histidine side chains to the metal, the cadmium complex of the His12 --> Cys mutant exists in only a single form at low pH. The conformation of the polypeptide chain encompassing residues 10-18 is intermediate between the two forms of the wild-type complex. PMID:9865962

Sco X-1 - A galactic radio source with an extragalactic radio morphology

NASA Technical Reports Server (NTRS)

Geldzahler, B. J.; Corey, B. E.; Fomalont, E. B.; Hilldrup, K.

1981-01-01

VLA observations of radio emissions at 1465 and 4885 MHz, of Sco X-1 confirm the existence of a colinear triple structure. Evidence that the three components of Sco X-1 are physically associated is presented, including the morphology, spectrum, variability, volume emissivity and magnetic field strength. The possibility of a physical phenomenon occurring in Sco X-1 similar to that occurring in extragalactic radio sources is discussed, and two galactic sources are found having extended emission similar to that in extragalactic objects. The extended structure of Sco X-1 is also observed to be similar to that of the hot spots in luminous extragalactic sources, and a radio source 20 arcmin from Sco X-1 is found to lie nearly along the radio axis formed by the components of Sco X-1.

Fast and accurate non-sequential protein structure alignment using a new asymmetric linear sum assignment heuristic.

PubMed

Brown, Peter; Pullan, Wayne; Yang, Yuedong; Zhou, Yaoqi

2016-02-01

The three dimensional tertiary structure of a protein at near atomic level resolution provides insight alluding to its function and evolution. As protein structure decides its functionality, similarity in structure usually implies similarity in function. As such, structure alignment techniques are often useful in the classifications of protein function. Given the rapidly growing rate of new, experimentally determined structures being made available from repositories such as the Protein Data Bank, fast and accurate computational structure comparison tools are required. This paper presents SPalignNS, a non-sequential protein structure alignment tool using a novel asymmetrical greedy search technique. The performance of SPalignNS was evaluated against existing sequential and non-sequential structure alignment methods by performing trials with commonly used datasets. These benchmark datasets used to gauge alignment accuracy include (i) 9538 pairwise alignments implied by the HOMSTRAD database of homologous proteins; (ii) a subset of 64 difficult alignments from set (i) that have low structure similarity; (iii) 199 pairwise alignments of proteins with similar structure but different topology; and (iv) a subset of 20 pairwise alignments from the RIPC set. SPalignNS is shown to achieve greater alignment accuracy (lower or comparable root-mean squared distance with increased structure overlap coverage) for all datasets, and the highest agreement with reference alignments from the challenging dataset (iv) above, when compared with both sequentially constrained alignments and other non-sequential alignments. SPalignNS was implemented in C++. The source code, binary executable, and a web server version is freely available at: http://sparks-lab.org yaoqi.zhou@griffith.edu.au. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

A plasma membrane sucrose-binding protein that mediates sucrose uptake shares structural and sequence similarity with seed storage proteins but remains functionally distinct.

PubMed

Overvoorde, P J; Chao, W S; Grimes, H D

1997-06-20

Photoaffinity labeling of a soybean cotyledon membrane fraction identified a sucrose-binding protein (SBP). Subsequent studies have shown that the SBP is a unique plasma membrane protein that mediates the linear uptake of sucrose in the presence of up to 30 mM external sucrose when ectopically expressed in yeast. Analysis of the SBP-deduced amino acid sequence indicates it lacks sequence similarity with other known transport proteins. Data presented here, however, indicate that the SBP shares significant sequence and structural homology with the vicilin-like seed storage proteins that organize into homotrimers. These similarities include a repeated sequence that forms the basis of the reiterated domain structure characteristic of the vicilin-like protein family. In addition, analytical ultracentrifugation and nonreducing SDS-polyacrylamide gel electrophoresis demonstrate that the SBP appears to be organized into oligomeric complexes with a Mr indicative of the existence of SBP homotrimers and homodimers. The structural similarity shared by the SBP and vicilin-like proteins provides a novel framework to explore the mechanistic basis of SBP-mediated sucrose uptake. Expression of the maize Glb protein (a vicilin-like protein closely related to the SBP) in yeast demonstrates that a closely related vicilin-like protein is unable to mediate sucrose uptake. Thus, despite sequence and structural similarities shared by the SBP and the vicilin-like protein family, the SBP is functionally divergent from other members of this group.

InteGO2: A web tool for measuring and visualizing gene semantic similarities using Gene Ontology

DOE PAGES

Peng, Jiajie; Li, Hongxiang; Liu, Yongzhuang; ...

2016-08-31

Here, the Gene Ontology (GO) has been used in high-throughput omics research as a major bioinformatics resource. The hierarchical structure of GO provides users a convenient platform for biological information abstraction and hypothesis testing. Computational methods have been developed to identify functionally similar genes. However, none of the existing measurements take into account all the rich information in GO. Similarly, using these existing methods, web-based applications have been constructed to compute gene functional similarities, and to provide pure text-based outputs. Without a graphical visualization interface, it is difficult for result interpretation. As a result, we present InteGO2, a web toolmore » that allows researchers to calculate the GO-based gene semantic similarities using seven widely used GO-based similarity measurements. Also, we provide an integrative measurement that synergistically integrates all the individual measurements to improve the overall performance. Using HTML5 and cytoscape.js, we provide a graphical interface in InteGO2 to visualize the resulting gene functional association networks. In conclusion, InteGO2 is an easy-to-use HTML5 based web tool. With it, researchers can measure gene or gene product functional similarity conveniently, and visualize the network of functional interactions in a graphical interface.« less

InteGO2: a web tool for measuring and visualizing gene semantic similarities using Gene Ontology.

PubMed

Peng, Jiajie; Li, Hongxiang; Liu, Yongzhuang; Juan, Liran; Jiang, Qinghua; Wang, Yadong; Chen, Jin

2016-08-31

The Gene Ontology (GO) has been used in high-throughput omics research as a major bioinformatics resource. The hierarchical structure of GO provides users a convenient platform for biological information abstraction and hypothesis testing. Computational methods have been developed to identify functionally similar genes. However, none of the existing measurements take into account all the rich information in GO. Similarly, using these existing methods, web-based applications have been constructed to compute gene functional similarities, and to provide pure text-based outputs. Without a graphical visualization interface, it is difficult for result interpretation. We present InteGO2, a web tool that allows researchers to calculate the GO-based gene semantic similarities using seven widely used GO-based similarity measurements. Also, we provide an integrative measurement that synergistically integrates all the individual measurements to improve the overall performance. Using HTML5 and cytoscape.js, we provide a graphical interface in InteGO2 to visualize the resulting gene functional association networks. InteGO2 is an easy-to-use HTML5 based web tool. With it, researchers can measure gene or gene product functional similarity conveniently, and visualize the network of functional interactions in a graphical interface. InteGO2 can be accessed via http://mlg.hit.edu.cn:8089/ .

InteGO2: A web tool for measuring and visualizing gene semantic similarities using Gene Ontology

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

Peng, Jiajie; Li, Hongxiang; Liu, Yongzhuang

Here, the Gene Ontology (GO) has been used in high-throughput omics research as a major bioinformatics resource. The hierarchical structure of GO provides users a convenient platform for biological information abstraction and hypothesis testing. Computational methods have been developed to identify functionally similar genes. However, none of the existing measurements take into account all the rich information in GO. Similarly, using these existing methods, web-based applications have been constructed to compute gene functional similarities, and to provide pure text-based outputs. Without a graphical visualization interface, it is difficult for result interpretation. As a result, we present InteGO2, a web toolmore » that allows researchers to calculate the GO-based gene semantic similarities using seven widely used GO-based similarity measurements. Also, we provide an integrative measurement that synergistically integrates all the individual measurements to improve the overall performance. Using HTML5 and cytoscape.js, we provide a graphical interface in InteGO2 to visualize the resulting gene functional association networks. In conclusion, InteGO2 is an easy-to-use HTML5 based web tool. With it, researchers can measure gene or gene product functional similarity conveniently, and visualize the network of functional interactions in a graphical interface.« less

Robust hashing with local models for approximate similarity search.

PubMed

Song, Jingkuan; Yang, Yi; Li, Xuelong; Huang, Zi; Yang, Yang

2014-07-01

Similarity search plays an important role in many applications involving high-dimensional data. Due to the known dimensionality curse, the performance of most existing indexing structures degrades quickly as the feature dimensionality increases. Hashing methods, such as locality sensitive hashing (LSH) and its variants, have been widely used to achieve fast approximate similarity search by trading search quality for efficiency. However, most existing hashing methods make use of randomized algorithms to generate hash codes without considering the specific structural information in the data. In this paper, we propose a novel hashing method, namely, robust hashing with local models (RHLM), which learns a set of robust hash functions to map the high-dimensional data points into binary hash codes by effectively utilizing local structural information. In RHLM, for each individual data point in the training dataset, a local hashing model is learned and used to predict the hash codes of its neighboring data points. The local models from all the data points are globally aligned so that an optimal hash code can be assigned to each data point. After obtaining the hash codes of all the training data points, we design a robust method by employing l2,1 -norm minimization on the loss function to learn effective hash functions, which are then used to map each database point into its hash code. Given a query data point, the search process first maps it into the query hash code by the hash functions and then explores the buckets, which have similar hash codes to the query hash code. Extensive experimental results conducted on real-life datasets show that the proposed RHLM outperforms the state-of-the-art methods in terms of search quality and efficiency.

Boolean network inference from time series data incorporating prior biological knowledge.

PubMed

Haider, Saad; Pal, Ranadip

2012-01-01

Numerous approaches exist for modeling of genetic regulatory networks (GRNs) but the low sampling rates often employed in biological studies prevents the inference of detailed models from experimental data. In this paper, we analyze the issues involved in estimating a model of a GRN from single cell line time series data with limited time points. We present an inference approach for a Boolean Network (BN) model of a GRN from limited transcriptomic or proteomic time series data based on prior biological knowledge of connectivity, constraints on attractor structure and robust design. We applied our inference approach to 6 time point transcriptomic data on Human Mammary Epithelial Cell line (HMEC) after application of Epidermal Growth Factor (EGF) and generated a BN with a plausible biological structure satisfying the data. We further defined and applied a similarity measure to compare synthetic BNs and BNs generated through the proposed approach constructed from transitions of various paths of the synthetic BNs. We have also compared the performance of our algorithm with two existing BN inference algorithms. Through theoretical analysis and simulations, we showed the rarity of arriving at a BN from limited time series data with plausible biological structure using random connectivity and absence of structure in data. The framework when applied to experimental data and data generated from synthetic BNs were able to estimate BNs with high similarity scores. Comparison with existing BN inference algorithms showed the better performance of our proposed algorithm for limited time series data. The proposed framework can also be applied to optimize the connectivity of a GRN from experimental data when the prior biological knowledge on regulators is limited or not unique.

The Antarctic cold desert and the search for traces of life on Mars.

PubMed

Friedmann, E I

1986-01-01

The cryptoendolithic microorganisms that live inside rocks in the frigid Ross Desert of Antarctica can serve as a terrestrial model for what may have happened to life forms on Mars when the planet became dry and cold. Trace fossils of microbial rock colonization exist in Antarctica, and similar structures could have formed on Mars. In some respects, such trace fossils could be an easier target for life-detection systems than fossils of cellular structures.

The Antarctic cold desert and the search for traces of life on Mars

NASA Technical Reports Server (NTRS)

Friedmann, E. I.

1986-01-01

The cryptoendolithic microoganisms that live inside rocks in the frigid Ross Desert of Antarctica can serve as a terrestrial model for what may have happened to life forms on Mars when the planet became dry and cold. Trace fossils of microbial rock colonization exist in Antarctica, and similar structures could have formed on Mars. In some respects, such trace fossils could be an easier target for life-detection systems than fossils of cellular structures.

Similarity indices based on link weight assignment for link prediction of unweighted complex networks

NASA Astrophysics Data System (ADS)

Liu, Shuxin; Ji, Xinsheng; Liu, Caixia; Bai, Yi

2017-01-01

Many link prediction methods have been proposed for predicting the likelihood that a link exists between two nodes in complex networks. Among these methods, similarity indices are receiving close attention. Most similarity-based methods assume that the contribution of links with different topological structures is the same in the similarity calculations. This paper proposes a local weighted method, which weights the strength of connection between each pair of nodes. Based on the local weighted method, six local weighted similarity indices extended from unweighted similarity indices (including Common Neighbor (CN), Adamic-Adar (AA), Resource Allocation (RA), Salton, Jaccard and Local Path (LP) index) are proposed. Empirical study has shown that the local weighted method can significantly improve the prediction accuracy of these unweighted similarity indices and that in sparse and weakly clustered networks, the indices perform even better.

Low-resolution structure of Drosophila translin

PubMed Central

Kumar, Vinay; Gupta, Gagan D.

2012-01-01

Crystals of native Drosophila melanogaster translin diffracted to 7 Å resolution. Reductive methylation of the protein improved crystal quality. The native and methylated proteins showed similar profiles in size-exclusion chromatography analyses but the methylated protein displayed reduced DNA-binding activity. Crystals of the methylated protein diffracted to 4.2 Å resolution at BM14 of the ESRF synchrotron. Crystals with 49% solvent content belonged to monoclinic space group P21 with eight protomers in the asymmetric unit. Only 2% of low-resolution structures with similar low percentage solvent content were found in the PDB. The crystal structure, solved by molecular replacement method, refined to Rwork (Rfree) of 0.24 (0.29) with excellent stereochemistry. The crystal structure clearly shows that drosophila protein exists as an octamer, and not as a decamer as expected from gel-filtration elution profiles. The similar octameric quaternary fold in translin orthologs and in translin–TRAX complexes suggests an up-down dimer as the basic structural subunit of translin-like proteins. The drosophila oligomer displays asymmetric assembly and increased radius of gyration that accounts for the observed differences between the elution profiles of human and drosophila proteins on gel-filtration columns. This study demonstrates clearly that low-resolution X-ray structure can be useful in understanding complex biological oligomers. PMID:23650579

Towards methodical modelling: Differences between the structure and output dynamics of multiple conceptual models

NASA Astrophysics Data System (ADS)

Knoben, Wouter; Woods, Ross; Freer, Jim

2016-04-01

Conceptual hydrologic models consist of a certain arrangement of spatial and temporal dynamics consisting of stores, fluxes and transformation functions, depending on the modeller's choices and intended use. They have the advantages of being computationally efficient, being relatively easy model structures to reconfigure and having relatively low input data demands. This makes them well-suited for large-scale and large-sample hydrology, where appropriately representing the dominant hydrologic functions of a catchment is a main concern. Given these requirements, the number of parameters in the model cannot be too high, to avoid equifinality and identifiability issues. This limits the number and level of complexity of dominant hydrologic processes the model can represent. Specific purposes and places thus require a specific model and this has led to an abundance of conceptual hydrologic models. No structured overview of these models exists and there is no clear method to select appropriate model structures for different catchments. This study is a first step towards creating an overview of the elements that make up conceptual models, which may later assist a modeller in finding an appropriate model structure for a given catchment. To this end, this study brings together over 30 past and present conceptual models. The reviewed model structures are simply different configurations of three basic model elements (stores, fluxes and transformation functions), depending on the hydrologic processes the models are intended to represent. Differences also exist in the inner workings of the stores, fluxes and transformations, i.e. the mathematical formulations that describe each model element's intended behaviour. We investigate the hypothesis that different model structures can produce similar behavioural simulations. This can clarify the overview of model elements by grouping elements which are similar, which can improve model structure selection.

Some recent experimental results related to nuclear chirality

NASA Astrophysics Data System (ADS)

Timár, J.; Kuti, I.; Sohler, D.; Starosta, K.; Koike, T.; Paul, E. S.

2014-09-01

Detailed band structures of three chiral-candidate nuclei, 134Pr, 132La and 103Rh have been studied. The aim of the study was twofold. First, to try to explore the reasons behind the contradiction between the theoretically predicted chirality in these nuclei and the recently observed fingerprints that suggest non-chiral interpretation for the previous chiral candidate band doublets. Second, to search for multiple chiral bands of different types in these nuclei. In 134Pr a new πh11/2vh11/2 band has been observed besides the previously known chiral-candidate πh11/2vh11/2 doublet. This new band and the yrare πh11/2vh11/2 band show the expected features of a chiral doublet structure. This fact combined with the observed similarity between the band structures of 134Pr and 132La suggests that chirality might exist in these nuclei. The detailed study of the 103Rh band structure resulted in the observation of two new chiral-doublet looking structures besides the previously known one. This is indicative of possible existence of multiple chiral doublet structure in this nucleus.

Using Comedy Improvisation Techniques to Support Dance Training

ERIC Educational Resources Information Center

Larimer, Amy

2012-01-01

Although contemporary dance improvisation techniques and comedy improvisation are seldom linked, the two forms evolved around the same time and have many similarities. Both forms exist in the moment, share a highly ephemeral nature, and make use of physical games and structures. Both forms teach students the skill of being present, so essential to…

75 FR 39307 - Self-Regulatory Organizations; EDGX Exchange, Inc.; Notice of Filing and Immediate Effectiveness...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-07-08

... rule change reflects a competitive pricing structure designed to incent market participants to direct..., and is similar to existing pricing for this order type on the International Securities Exchange, LLC... that it operates in a highly competitive market in which market participants can readily direct order...

Lexical Semantics and Irregular Inflection

PubMed Central

Huang, Yi Ting; Pinker, Steven

2010-01-01

Whether a word has an irregular inflection does not depend on its sound alone: compare lie-lay (recline) and lie-lied (prevaricate). Theories of morphology, particularly connectionist and symbolic models, disagree on which nonphonological factors are responsible. We test four possibilities: (1) Lexical effects, in which two lemmas differ in whether they specify an irregular form; (2) Semantic effects, in which the semantic features of a word become associated with regular or irregular forms; (3) Morphological structure effects, in which a word with a headless structure (e.g., a verb derived from a noun) blocks access to a stored irregular form; (4) Compositionality effects, in which the stored combination of an irregular word’s meaning (e.g., the verb’s inherent aspect) with the meaning of the inflection (e.g., pastness) doesn’t readily transfer to new senses with different combinations of such meanings. In four experiments, speakers were presented with existing and novel verbs and asked to rate their past-tense forms, semantic similarities, grammatical structure, and aspectual similarities. We found (1) an interaction between semantic and phonological similarity, coinciding with reported strategies of analogizing to known verbs and implicating lexical effects; (2) weak and inconsistent effects of semantic similarity; (3) robust effects of morphological structure, and (4) robust effects of aspectual compositionality. Results are consistent with theories of language that invoke lexical entries and morphological structure, and which differentiate the mode of storage of regular and irregular verbs. They also suggest how psycholinguistic processes have shaped vocabulary structure over history. PMID:21151703

Methodological advances in predicting flow-induced dynamics of plants using mechanical-engineering theory.

PubMed

de Langre, Emmanuel

2012-03-15

The modeling of fluid-structure interactions, such as flow-induced vibrations, is a well-developed field of mechanical engineering. Many methods exist, and it seems natural to apply them to model the behavior of plants, and potentially other cantilever-like biological structures, under flow. Overcoming this disciplinary divide, and the application of such models to biological systems, will significantly advance our understanding of ecological patterns and processes and improve our predictive capabilities. Nonetheless, several methodological issues must first be addressed, which I describe here using two practical examples that have strong similarities: one from agricultural sciences and the other from nuclear engineering. Very similar issues arise in both: individual and collective behavior, small and large space and time scales, porous modeling, standard and extreme events, trade-off between the surface of exchange and individual or collective risk of damage, variability, hostile environments and, in some aspects, evolution. The conclusion is that, although similar issues do exist, which need to be exploited in some detail, there is a significant gap that requires new developments. It is obvious that living plants grow in and adapt to their environment, which certainly makes plant biomechanics fundamentally distinct from classical mechanical engineering. Moreover, the selection processes in biology and in human engineering are truly different, making the issue of safety different as well. A thorough understanding of these similarities and differences is needed to work efficiently in the application of a mechanistic approach to ecology.

Identifying States of a Financial Market

NASA Astrophysics Data System (ADS)

Münnix, Michael C.; Shimada, Takashi; Schäfer, Rudi; Leyvraz, Francois; Seligman, Thomas H.; Guhr, Thomas; Stanley, H. Eugene

2012-09-01

The understanding of complex systems has become a central issue because such systems exist in a wide range of scientific disciplines. We here focus on financial markets as an example of a complex system. In particular we analyze financial data from the S&P 500 stocks in the 19-year period 1992-2010. We propose a definition of state for a financial market and use it to identify points of drastic change in the correlation structure. These points are mapped to occurrences of financial crises. We find that a wide variety of characteristic correlation structure patterns exist in the observation time window, and that these characteristic correlation structure patterns can be classified into several typical ``market states''. Using this classification we recognize transitions between different market states. A similarity measure we develop thus affords means of understanding changes in states and of recognizing developments not previously seen.

Identifying states of a financial market.

PubMed

Münnix, Michael C; Shimada, Takashi; Schäfer, Rudi; Leyvraz, Francois; Seligman, Thomas H; Guhr, Thomas; Stanley, H Eugene

2012-01-01

The understanding of complex systems has become a central issue because such systems exist in a wide range of scientific disciplines. We here focus on financial markets as an example of a complex system. In particular we analyze financial data from the S&P 500 stocks in the 19-year period 1992-2010. We propose a definition of state for a financial market and use it to identify points of drastic change in the correlation structure. These points are mapped to occurrences of financial crises. We find that a wide variety of characteristic correlation structure patterns exist in the observation time window, and that these characteristic correlation structure patterns can be classified into several typical "market states". Using this classification we recognize transitions between different market states. A similarity measure we develop thus affords means of understanding changes in states and of recognizing developments not previously seen.

Oscillatory interfacial instability between miscible fluids

NASA Astrophysics Data System (ADS)

Shevtsova, Valentina; Gaponenko, Yuri; Mialdun, Aliaksandr; Torregrosa, Marita; Yasnou, Viktar

Interfacial instabilities occurring between two fluids are of fundamental interest in fluid dynamics, biological systems and engineering applications such as liquid storage, solvent extraction, oil recovery and mixing. Horizontal vibrations applied to stratified layers of immiscible liquids may generate spatially periodic waving of the interface, stationary in the reference frame of the vibrated cell, referred to as a "frozen wave". We present experimental evidence that frozen wave instability exists between two ordinary miscible liquids of similar densities and viscosities. At the experiments and at the numerical model, two superimposed layers of ordinary liquids, water-alcohol of different concentrations, are placed in a closed cavity in a gravitationally stable configuration. The density and viscosity of these fluids are somewhat similar. Similar to the immiscible fluids this instability has a threshold. When the value of forcing is increased the amplitudes of perturbations grow continuously displaying a saw-tooth structure. The decrease of gravity drastically changes the structure of frozen waves.

Visualizing and Clustering Protein Similarity Networks: Sequences, Structures, and Functions.

PubMed

Mai, Te-Lun; Hu, Geng-Ming; Chen, Chi-Ming

2016-07-01

Research in the recent decade has demonstrated the usefulness of protein network knowledge in furthering the study of molecular evolution of proteins, understanding the robustness of cells to perturbation, and annotating new protein functions. In this study, we aimed to provide a general clustering approach to visualize the sequence-structure-function relationship of protein networks, and investigate possible causes for inconsistency in the protein classifications based on sequences, structures, and functions. Such visualization of protein networks could facilitate our understanding of the overall relationship among proteins and help researchers comprehend various protein databases. As a demonstration, we clustered 1437 enzymes by their sequences and structures using the minimum span clustering (MSC) method. The general structure of this protein network was delineated at two clustering resolutions, and the second level MSC clustering was found to be highly similar to existing enzyme classifications. The clustering of these enzymes based on sequence, structure, and function information is consistent with each other. For proteases, the Jaccard's similarity coefficient is 0.86 between sequence and function classifications, 0.82 between sequence and structure classifications, and 0.78 between structure and function classifications. From our clustering results, we discussed possible examples of divergent evolution and convergent evolution of enzymes. Our clustering approach provides a panoramic view of the sequence-structure-function network of proteins, helps visualize the relation between related proteins intuitively, and is useful in predicting the structure and function of newly determined protein sequences.

Pressure-induced amorphization of YVO₄:Eu³⁺ nanoboxes.

PubMed

Ruiz-Fuertes, J; Gomis, O; León-Luis, S F; Schrodt, N; Manjón, F J; Ray, S; Santamaría-Pérez, D; Sans, J A; Ortiz, H M; Errandonea, D; Ferrer-Roca, C; Segura, A; Martínez-García, D; Lavín, V; Rodríguez-Mendoza, U R; Muñoz, A

2016-01-15

A structural transformation from the zircon-type structure to an amorphous phase has been found in YVO4:Eu(3+) nanoboxes at high pressures above 12.7 GPa by means of x-ray diffraction measurements. However, the pair distribution function of the high-pressure phase shows that the local structure of the amorphous phase is similar to the scheelite-type YVO4. These results are confirmed both by Raman spectroscopy and Eu(3+) photoluminescence which detect the phase transition to a scheelite-type structure at 10.1 and 9.1 GPa, respectively. The irreversibility of the phase transition is observed with the three techniques after a maximum pressure in the upstroke of around 20 GPa. The existence of two (5)D0-->(7)F0 photoluminescence peaks confirms the existence of two local environments for Eu(3+), at least for the low-pressure phase. One environment is the expected for substituting Y(3+) and the other is likely a disordered environment possibly found at the surface of the nanoboxes.

One-step synthesis and structural features of CdS/montmorillonite nanocomposites.

PubMed

Han, Zhaohui; Zhu, Huaiyong; Bulcock, Shaun R; Ringer, Simon P

2005-02-24

A novel synthesis method was introduced for the nanocomposites of cadmium sulfide and montmorillonite. This method features the combination of an ion exchange process and an in situ hydrothermal decomposition process of a complex precursor, which is simple in contrast to the conventional synthesis methods that comprise two separate steps for similar nanocomposite materials. Cadmium sulfide species in the composites exist in the forms of pillars and nanoparticles, the crystallized sulfide particles are in the hexagonal phase, and the sizes change when the amount of the complex for the synthesis is varied. Structural features of the nanocomposites are similar to those of the clay host but changed because of the introduction of the sulfide into the clay.

Evidence for monoclinic distortion in the ground state phase of underdoped La 1.95Sr 0.05CuO 4: A single crystal neutron diffraction study

DOE PAGES

Singh, Anar; Schefer, Jurg; Sura, Ravi; ...

2016-03-24

The existing controversy about the symmetry of the crystal structure of the ground state of the critical doped La 1.95Sr 0.05CuO 4 has been resolved by analyzing the single crystal neutron diffraction data collected between 5 and 730 K. We observed small but significant intensities for "forbidden" reflections given by extinction rules of the orthorhombic Bmab space group at low temperatures. A careful investigation of neutron diffraction data reveals that the crystal structure of La 1.95Sr 0.05CuO 4 at 5 K is monoclinic with B2/m (2/m 1 1) space group. The monoclinic structure emerges from the orthorhombic structure in amore » continuous way; however, the structure is stable below similar to 120K which agrees with other observed phenomena. Lastly, our results on symmetry changes are crucial for the interpretation of physical properties also in other high temperature superconductors with similar structures.« less

In silico insights into protein-protein interactions and folding dynamics of the saposin-like domain of Solanum tuberosum aspartic protease.

PubMed

De Moura, Dref C; Bryksa, Brian C; Yada, Rickey Y

2014-01-01

The plant-specific insert is an approximately 100-residue domain found exclusively within the C-terminal lobe of some plant aspartic proteases. Structurally, this domain is a member of the saposin-like protein family, and is involved in plant pathogen defense as well as vacuolar targeting of the parent protease molecule. Similar to other members of the saposin-like protein family, most notably saposins A and C, the recently resolved crystal structure of potato (Solanum tuberosum) plant-specific insert has been shown to exist in a substrate-bound open conformation in which the plant-specific insert oligomerizes to form homodimers. In addition to the open structure, a closed conformation also exists having the classic saposin fold of the saposin-like protein family as observed in the crystal structure of barley (Hordeum vulgare L.) plant-specific insert. In the present study, the mechanisms of tertiary and quaternary conformation changes of potato plant-specific insert were investigated in silico as a function of pH. Umbrella sampling and determination of the free energy change of dissociation of the plant-specific insert homodimer revealed that increasing the pH of the system to near physiological levels reduced the free energy barrier to dissociation. Furthermore, principal component analysis was used to characterize conformational changes at both acidic and neutral pH. The results indicated that the plant-specific insert may adopt a tertiary structure similar to the characteristic saposin fold and suggest a potential new structural motif among saposin-like proteins. To our knowledge, this acidified PSI structure presents the first example of an alternative saposin-fold motif for any member of the large and diverse SAPLIP family.

In Silico Insights into Protein-Protein Interactions and Folding Dynamics of the Saposin-Like Domain of Solanum tuberosum Aspartic Protease

PubMed Central

De Moura, Dref C.; Bryksa, Brian C.; Yada, Rickey Y.

2014-01-01

The plant-specific insert is an approximately 100-residue domain found exclusively within the C-terminal lobe of some plant aspartic proteases. Structurally, this domain is a member of the saposin-like protein family, and is involved in plant pathogen defense as well as vacuolar targeting of the parent protease molecule. Similar to other members of the saposin-like protein family, most notably saposins A and C, the recently resolved crystal structure of potato (Solanum tuberosum) plant-specific insert has been shown to exist in a substrate-bound open conformation in which the plant-specific insert oligomerizes to form homodimers. In addition to the open structure, a closed conformation also exists having the classic saposin fold of the saposin-like protein family as observed in the crystal structure of barley (Hordeum vulgare L.) plant-specific insert. In the present study, the mechanisms of tertiary and quaternary conformation changes of potato plant-specific insert were investigated in silico as a function of pH. Umbrella sampling and determination of the free energy change of dissociation of the plant-specific insert homodimer revealed that increasing the pH of the system to near physiological levels reduced the free energy barrier to dissociation. Furthermore, principal component analysis was used to characterize conformational changes at both acidic and neutral pH. The results indicated that the plant-specific insert may adopt a tertiary structure similar to the characteristic saposin fold and suggest a potential new structural motif among saposin-like proteins. To our knowledge, this acidified PSI structure presents the first example of an alternative saposin-fold motif for any member of the large and diverse SAPLIP family. PMID:25188221

Identification of distant drug off-targets by direct superposition of binding pocket surfaces.

PubMed

Schumann, Marcel; Armen, Roger S

2013-01-01

Correctly predicting off-targets for a given molecular structure, which would have the ability to bind a large range of ligands, is both particularly difficult and important if they share no significant sequence or fold similarity with the respective molecular target ("distant off-targets"). A novel approach for identification of off-targets by direct superposition of protein binding pocket surfaces is presented and applied to a set of well-studied and highly relevant drug targets, including representative kinases and nuclear hormone receptors. The entire Protein Data Bank is searched for similar binding pockets and convincing distant off-target candidates were identified that share no significant sequence or fold similarity with the respective target structure. These putative target off-target pairs are further supported by the existence of compounds that bind strongly to both with high topological similarity, and in some cases, literature examples of individual compounds that bind to both. Also, our results clearly show that it is possible for binding pockets to exhibit a striking surface similarity, while the respective off-target shares neither significant sequence nor significant fold similarity with the respective molecular target ("distant off-target").

Identification of Distant Drug Off-Targets by Direct Superposition of Binding Pocket Surfaces

PubMed Central

Schumann, Marcel; Armen, Roger S.

2013-01-01

Correctly predicting off-targets for a given molecular structure, which would have the ability to bind a large range of ligands, is both particularly difficult and important if they share no significant sequence or fold similarity with the respective molecular target (“distant off-targets”). A novel approach for identification of off-targets by direct superposition of protein binding pocket surfaces is presented and applied to a set of well-studied and highly relevant drug targets, including representative kinases and nuclear hormone receptors. The entire Protein Data Bank is searched for similar binding pockets and convincing distant off-target candidates were identified that share no significant sequence or fold similarity with the respective target structure. These putative target off-target pairs are further supported by the existence of compounds that bind strongly to both with high topological similarity, and in some cases, literature examples of individual compounds that bind to both. Also, our results clearly show that it is possible for binding pockets to exhibit a striking surface similarity, while the respective off-target shares neither significant sequence nor significant fold similarity with the respective molecular target (“distant off-target”). PMID:24391782

Structural and Functional Similarities of Calcium Homeostasis Modulator 1 (CALHM1) Ion Channel with Connexins, Pannexins, and Innexins*

PubMed Central

Siebert, Adam P.; Ma, Zhongming; Grevet, Jeremy D.; Demuro, Angelo; Parker, Ian; Foskett, J. Kevin

2013-01-01

CALHM1 (calcium homeostasis modulator 1) forms a plasma membrane ion channel that mediates neuronal excitability in response to changes in extracellular Ca2+ concentration. Six human CALHM homologs exist with no homology to other proteins, although CALHM1 is conserved across >20 species. Here we demonstrate that CALHM1 shares functional and quaternary and secondary structural similarities with connexins and evolutionarily distinct innexins and their vertebrate pannexin homologs. A CALHM1 channel is a hexamer, comprised of six monomers, each of which possesses four transmembrane domains, cytoplasmic amino and carboxyl termini, an amino-terminal helix, and conserved extracellular cysteines. The estimated pore diameter of the CALHM1 channel is ∼14 Å, enabling permeation of large charged molecules. Thus, CALHMs, connexins, and pannexins and innexins are structurally related protein families with shared and distinct functional properties. PMID:23300080

Discovering relevance knowledge in data: a growing cell structures approach.

PubMed

Azuaje, F; Dubitzky, W; Black, N; Adamson, K

2000-01-01

Both information retrieval and case-based reasoning systems rely on effective and efficient selection of relevant data. Typically, relevance in such systems is approximated by similarity or indexing models. However, the definition of what makes data items similar or how they should be indexed is often nontrivial and time-consuming. Based on growing cell structure artificial neural networks, this paper presents a method that automatically constructs a case retrieval model from existing data. Within the case-based reasoning (CBR) framework, the method is evaluated for two medical prognosis tasks, namely, colorectal cancer survival and coronary heart disease risk prognosis. The results of the experiments suggest that the proposed method is effective and robust. To gain a deeper insight and understanding of the underlying mechanisms of the proposed model, a detailed empirical analysis of the models structural and behavioral properties is also provided.

Molecular Assembly of Clostridium botulinum progenitor M complex of type E.

PubMed

Eswaramoorthy, Subramaniam; Sun, Jingchuan; Li, Huilin; Singh, Bal Ram; Swaminathan, Subramanyam

2015-12-07

Clostridium botulinum neurotoxin (BoNT) is released as a progenitor complex, in association with a non-toxic-non-hemagglutinin protein (NTNH) and other associated proteins. We have determined the crystal structure of M type Progenitor complex of botulinum neurotoxin E [PTC-E(M)], a heterodimer of BoNT and NTNH. The crystal structure reveals that the complex exists as a tight, interlocked heterodimer of BoNT and NTNH. The crystal structure explains the mechanism of molecular assembly of the complex and reveals several acidic clusters at the interface responsible for association at low acidic pH and disassociation at basic/neutral pH. The similarity of the general architecture between the PTC-E(M) and the previously determined PTC-A(M) strongly suggests that the progenitor M complexes of all botulinum serotypes may have similar molecular arrangement, although the neurotoxins apparently can take very different conformation when they are released from the M complex.

Physical mechanisms of active control of sound transmission through rib stiffened double-panel structure

NASA Astrophysics Data System (ADS)

Ma, Xiyue; Chen, Kean; Ding, Shaohu; Yu, Haoxin

2016-06-01

This paper presents an analytical investigation on physical mechanisms of actively controlling sound transmission through a rib stiffened double-panel structure using point source in the cavity. The combined modal expansion and vibro-acoustic coupling methods are applied to establish the theoretical model of such active structure. Under the condition of minimizing radiated power of the radiating ribbed plate, the physical mechanisms are interpreted in detail from the point of view of modal couplings similar as that used in existed literatures. Results obtained demonstrate that the rule of sound energy transmission and the physical mechanisms for the rib stiffened double-panel structure are all changed, and affected by the coupling effects of the rib when compared with the analytical results obtained for unribbed double-panel case. By taking the coupling effects of the rib into considerations, the cavity modal suppression and rearrangement mechanisms obtained in existed investigations are modified and supplemented for the ribbed plate case, which gives a clear interpretation for the physical nature involved in the active rib stiffened double-panel structure.

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

Walton, B.T.

A chemical impurity isolated from commercially purchased acridine causes cricket embryos to develop extra compound eyes, branched antennae, extra antennae, and extra heads. Purified acridine does not produce similar duplications of cricket heads or head structures nor do the substituted acridines proflavine, acriflavine, or acridine orange. A dose-response relation exists such that the number and severity of abnormalities increase with increasing concentration of the teratogen.

The Structure of Intergenerational Relations in Rural China: A Latent Class Analysis

ERIC Educational Resources Information Center

Guo, Man; Chi, Iris; Silverstein, Merril

2012-01-01

Most existing typology studies of intergenerational relations have used samples in North America and Europe. The present study expands on previous research by determining whether similar family relation typologies could be found using a sample of Chinese rural elders. The data were derived from a survey of 1,224 older adults in China's rural Anhui…

Experiencing Past and Future Personal Events: Functional Neuroimaging Evidence on the Neural Bases of Mental Time Travel

ERIC Educational Resources Information Center

Botzung, Anne; Denkova, Ekaterina; Manning, Lilianne

2008-01-01

Functional MRI was used in healthy subjects to investigate the existence of common neural structures supporting re-experiencing the past and pre-experiencing the future. Past and future events evocation appears to involve highly similar patterns of brain activation including, in particular, the medial prefrontal cortex, posterior regions and the…

The Supreme Court, Civil Rights, and Preference Policies: Judicial Decision Making Processes in the United States and India.

ERIC Educational Resources Information Center

Parikh, Sunita

1990-01-01

Presents a comparative analysis of the U.S. and Indian Supreme Courts' roles in civil rights and preference policies. Despite structural and historical differences, similarities exist in the development of such policies. Both are more concerned with fidelity to constitutional and statutory interpretations than to personal ideological viewpoints.…

A Structure-Based Distance Metric for High-Dimensional Space Exploration with Multi-Dimensional Scaling

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

Lee, Hyun Jung; McDonnell, Kevin T.; Zelenyuk, Alla

2014-03-01

Although the Euclidean distance does well in measuring data distances within high-dimensional clusters, it does poorly when it comes to gauging inter-cluster distances. This significantly impacts the quality of global, low-dimensional space embedding procedures such as the popular multi-dimensional scaling (MDS) where one can often observe non-intuitive layouts. We were inspired by the perceptual processes evoked in the method of parallel coordinates which enables users to visually aggregate the data by the patterns the polylines exhibit across the dimension axes. We call the path of such a polyline its structure and suggest a metric that captures this structure directly inmore » high-dimensional space. This allows us to better gauge the distances of spatially distant data constellations and so achieve data aggregations in MDS plots that are more cognizant of existing high-dimensional structure similarities. Our MDS plots also exhibit similar visual relationships as the method of parallel coordinates which is often used alongside to visualize the high-dimensional data in raw form. We then cast our metric into a bi-scale framework which distinguishes far-distances from near-distances. The coarser scale uses the structural similarity metric to separate data aggregates obtained by prior classification or clustering, while the finer scale employs the appropriate Euclidean distance.« less

Global kinetic simulations of neoclassical toroidal viscosity in low-collisional perturbed tokamak plasmas

NASA Astrophysics Data System (ADS)

Matsuoka, Seikichi; Idomura, Yasuhiro; Satake, Shinsuke

2017-10-01

The neoclassical toroidal viscosity (NTV) caused by a non-axisymmetric magnetic field perturbation is numerically studied using two global kinetic simulations with different numerical approaches. Both simulations reproduce similar collisionality ( νb*) dependencies over wide νb * ranges. It is demonstrated that resonant structures in the velocity space predicted by the conventional superbanana-plateau theory exist in the small banana width limit, while the resonances diminish when the banana width becomes large. It is also found that fine scale structures are generated in the velocity space as νb* decreases in the large banana width simulations, leading to the νb* -dependency of the NTV. From the analyses of the particle orbit, it is found that the finite k∥ mode structure along the bounce motion appears owing to the finite orbit width, and it suffers from bounce phase mixing, suggesting the generation of the fine scale structures by the similar mechanism as the parallel phase mixing of passing particles.

Biogenic manganese oxide nanoparticle formation by a multimeric multicopper oxidase Mnx

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

Romano, Christine A.; Zhou, Mowei; Song, Yang

Bacteria that produce Mn oxides are extraordinarily skilled engineers of nanomaterials that contribute significantly to global biogeochemical cycles. Their enzyme-based reaction mechanisms may be genetically tailored for environmental remediation applications or bioenergy production. However, significant challenges exist for structural characterization of the enzymes responsible for biomineralization. The active Mn oxidase, Mnx, in Bacillus sp. PL-12 is a complex composed of a multicopper oxidase (MCO), MnxG, and two accessory proteins MnxE and MnxF. MnxG shares sequence similarity with other, structurally characterized MCOs. However, MnxE and MnxF have no similarity to any characterized proteins. The ~200 kDa complex has been recalcitrant tomore » crystallization, so its structure is unknown. In this study, native mass spectrometry defines the subunit topology and copper binding of the Mnx complex, while high resolution electron microscopy visualizes the protein and nascent Mn oxide minerals. These data provide critical structural information for conceptualizing how Mnx produces nanoparticulate Mn oxides.« less

Travelling wave effects in large space structures

NASA Technical Reports Server (NTRS)

Vonflotow, A.

1983-01-01

Several aspects of travelling waves in Large Space Structures(LSS) are discussed. The dynamic similarity among LSS's, electric power systems, microwave circuits and communications network is noted. The existence of time lag between actuation and response is illuminated with the aid of simple examples, and their prediction is demonstrated. To prevent echoes, communications lines have matched terminations; this idea is applied to the design of dampers of one dimensional structures. Periodic structures act as mechanical band pass filters. Implications of this behavior are examined on a simple example. It is noted that the implication is twofold; continuum models of periodic lattice structures may err considerably; on the other hand, it is possible to design favorable transmission (and resonance) characteristics into the structure.

Surface similarity-based molecular query-retrieval

PubMed Central

Singh, Rahul

2007-01-01

Background Discerning the similarity between molecules is a challenging problem in drug discovery as well as in molecular biology. The importance of this problem is due to the fact that the biochemical characteristics of a molecule are closely related to its structure. Therefore molecular similarity is a key notion in investigations targeting exploration of molecular structural space, query-retrieval in molecular databases, and structure-activity modelling. Determining molecular similarity is related to the choice of molecular representation. Currently, representations with high descriptive power and physical relevance like 3D surface-based descriptors are available. Information from such representations is both surface-based and volumetric. However, most techniques for determining molecular similarity tend to focus on idealized 2D graph-based descriptors due to the complexity that accompanies reasoning with more elaborate representations. Results This paper addresses the problem of determining similarity when molecules are described using complex surface-based representations. It proposes an intrinsic, spherical representation that systematically maps points on a molecular surface to points on a standard coordinate system (a sphere). Molecular surface properties such as shape, field strengths, and effects due to field super-positioningcan then be captured as distributions on the surface of the sphere. Surface-based molecular similarity is subsequently determined by computing the similarity of the surface-property distributions using a novel formulation of histogram-intersection. The similarity formulation is not only sensitive to the 3D distribution of the surface properties, but is also highly efficient to compute. Conclusion The proposed method obviates the computationally expensive step of molecular pose-optimisation, can incorporate conformational variations, and facilitates highly efficient determination of similarity by directly comparing molecular surfaces and surface-based properties. Retrieval performance, applications in structure-activity modeling of complex biological properties, and comparisons with existing research and commercial methods demonstrate the validity and effectiveness of the approach. PMID:17634096

fMRI Syntactic and Lexical Repetition Effects Reveal the Initial Stages of Learning a New Language.

PubMed

Weber, Kirsten; Christiansen, Morten H; Petersson, Karl Magnus; Indefrey, Peter; Hagoort, Peter

2016-06-29

When learning a new language, we build brain networks to process and represent the acquired words and syntax and integrate these with existing language representations. It is an open question whether the same or different neural mechanisms are involved in learning and processing a novel language compared with the native language(s). Here we investigated the neural repetition effects of repeating known and novel word orders while human subjects were in the early stages of learning a new language. Combining a miniature language with a syntactic priming paradigm, we examined the neural correlates of language learning on-line using functional magnetic resonance imaging. In left inferior frontal gyrus and posterior temporal cortex, the repetition of novel syntactic structures led to repetition enhancement, whereas repetition of known structures resulted in repetition suppression. Additional verb repetition led to an increase in the syntactic repetition enhancement effect in language-related brain regions. Similarly, the repetition of verbs led to repetition enhancement effects in areas related to lexical and semantic processing, an effect that continued to increase in a subset of these regions. Repetition enhancement might reflect a mechanism to build and strengthen a neural network to process novel syntactic structures and lexical items. By contrast, the observed repetition suppression points to overlapping neural mechanisms for native and new language constructions when these have sufficient structural similarities. Acquiring a second language entails learning how to interpret novel words and relations between words, and to integrate them with existing language knowledge. To investigate the brain mechanisms involved in this particularly human skill, we combined an artificial language learning task with a syntactic repetition paradigm. We show that the repetition of novel syntactic structures, as well as words in contexts, leads to repetition enhancement, whereas repetition of known structures results in repetition suppression. We thus propose that repetition enhancement might reflect a brain mechanism to build and strengthen a neural network to process novel syntactic regularities and novel words. Importantly, the results also indicate an overlap in neural mechanisms for native and new language constructions with sufficient structural similarities. Copyright © 2016 the authors 0270-6474/16/366872-09$15.00/0.

A Quantitative Comparison of the Similarity between Genes and Geography in Worldwide Human Populations

PubMed Central

Wang, Chaolong; Zöllner, Sebastian; Rosenberg, Noah A.

2012-01-01

Multivariate statistical techniques such as principal components analysis (PCA) and multidimensional scaling (MDS) have been widely used to summarize the structure of human genetic variation, often in easily visualized two-dimensional maps. Many recent studies have reported similarity between geographic maps of population locations and MDS or PCA maps of genetic variation inferred from single-nucleotide polymorphisms (SNPs). However, this similarity has been evident primarily in a qualitative sense; and, because different multivariate techniques and marker sets have been used in different studies, it has not been possible to formally compare genetic variation datasets in terms of their levels of similarity with geography. In this study, using genome-wide SNP data from 128 populations worldwide, we perform a systematic analysis to quantitatively evaluate the similarity of genes and geography in different geographic regions. For each of a series of regions, we apply a Procrustes analysis approach to find an optimal transformation that maximizes the similarity between PCA maps of genetic variation and geographic maps of population locations. We consider examples in Europe, Sub-Saharan Africa, Asia, East Asia, and Central/South Asia, as well as in a worldwide sample, finding that significant similarity between genes and geography exists in general at different geographic levels. The similarity is highest in our examples for Asia and, once highly distinctive populations have been removed, Sub-Saharan Africa. Our results provide a quantitative assessment of the geographic structure of human genetic variation worldwide, supporting the view that geography plays a strong role in giving rise to human population structure. PMID:22927824

A quantitative comparison of the similarity between genes and geography in worldwide human populations.

PubMed

Wang, Chaolong; Zöllner, Sebastian; Rosenberg, Noah A

2012-08-01

Multivariate statistical techniques such as principal components analysis (PCA) and multidimensional scaling (MDS) have been widely used to summarize the structure of human genetic variation, often in easily visualized two-dimensional maps. Many recent studies have reported similarity between geographic maps of population locations and MDS or PCA maps of genetic variation inferred from single-nucleotide polymorphisms (SNPs). However, this similarity has been evident primarily in a qualitative sense; and, because different multivariate techniques and marker sets have been used in different studies, it has not been possible to formally compare genetic variation datasets in terms of their levels of similarity with geography. In this study, using genome-wide SNP data from 128 populations worldwide, we perform a systematic analysis to quantitatively evaluate the similarity of genes and geography in different geographic regions. For each of a series of regions, we apply a Procrustes analysis approach to find an optimal transformation that maximizes the similarity between PCA maps of genetic variation and geographic maps of population locations. We consider examples in Europe, Sub-Saharan Africa, Asia, East Asia, and Central/South Asia, as well as in a worldwide sample, finding that significant similarity between genes and geography exists in general at different geographic levels. The similarity is highest in our examples for Asia and, once highly distinctive populations have been removed, Sub-Saharan Africa. Our results provide a quantitative assessment of the geographic structure of human genetic variation worldwide, supporting the view that geography plays a strong role in giving rise to human population structure.

SIMBAD : a sequence-independent molecular-replacement pipeline

DOE PAGES

Simpkin, Adam J.; Simkovic, Felix; Thomas, Jens M. H.; ...

2018-06-08

The conventional approach to finding structurally similar search models for use in molecular replacement (MR) is to use the sequence of the target to search against those of a set of known structures. Sequence similarity often correlates with structure similarity. Given sufficient similarity, a known structure correctly positioned in the target cell by the MR process can provide an approximation to the unknown phases of the target. An alternative approach to identifying homologous structures suitable for MR is to exploit the measured data directly, comparing the lattice parameters or the experimentally derived structure-factor amplitudes with those of known structures. Here,more » SIMBAD , a new sequence-independent MR pipeline which implements these approaches, is presented. SIMBAD can identify cases of contaminant crystallization and other mishaps such as mistaken identity (swapped crystallization trays), as well as solving unsequenced targets and providing a brute-force approach where sequence-dependent search-model identification may be nontrivial, for example because of conformational diversity among identifiable homologues. The program implements a three-step pipeline to efficiently identify a suitable search model in a database of known structures. The first step performs a lattice-parameter search against the entire Protein Data Bank (PDB), rapidly determining whether or not a homologue exists in the same crystal form. The second step is designed to screen the target data for the presence of a crystallized contaminant, a not uncommon occurrence in macromolecular crystallography. Solving structures with MR in such cases can remain problematic for many years, since the search models, which are assumed to be similar to the structure of interest, are not necessarily related to the structures that have actually crystallized. To cater for this eventuality, SIMBAD rapidly screens the data against a database of known contaminant structures. Where the first two steps fail to yield a solution, a final step in SIMBAD can be invoked to perform a brute-force search of a nonredundant PDB database provided by the MoRDa MR software. Through early-access usage of SIMBAD , this approach has solved novel cases that have otherwise proved difficult to solve.« less

SIMBAD : a sequence-independent molecular-replacement pipeline

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

Simpkin, Adam J.; Simkovic, Felix; Thomas, Jens M. H.

The conventional approach to finding structurally similar search models for use in molecular replacement (MR) is to use the sequence of the target to search against those of a set of known structures. Sequence similarity often correlates with structure similarity. Given sufficient similarity, a known structure correctly positioned in the target cell by the MR process can provide an approximation to the unknown phases of the target. An alternative approach to identifying homologous structures suitable for MR is to exploit the measured data directly, comparing the lattice parameters or the experimentally derived structure-factor amplitudes with those of known structures. Here,more » SIMBAD , a new sequence-independent MR pipeline which implements these approaches, is presented. SIMBAD can identify cases of contaminant crystallization and other mishaps such as mistaken identity (swapped crystallization trays), as well as solving unsequenced targets and providing a brute-force approach where sequence-dependent search-model identification may be nontrivial, for example because of conformational diversity among identifiable homologues. The program implements a three-step pipeline to efficiently identify a suitable search model in a database of known structures. The first step performs a lattice-parameter search against the entire Protein Data Bank (PDB), rapidly determining whether or not a homologue exists in the same crystal form. The second step is designed to screen the target data for the presence of a crystallized contaminant, a not uncommon occurrence in macromolecular crystallography. Solving structures with MR in such cases can remain problematic for many years, since the search models, which are assumed to be similar to the structure of interest, are not necessarily related to the structures that have actually crystallized. To cater for this eventuality, SIMBAD rapidly screens the data against a database of known contaminant structures. Where the first two steps fail to yield a solution, a final step in SIMBAD can be invoked to perform a brute-force search of a nonredundant PDB database provided by the MoRDa MR software. Through early-access usage of SIMBAD , this approach has solved novel cases that have otherwise proved difficult to solve.« less

Along-axis segmentation and isostasy in the Western rift, East Africa

NASA Astrophysics Data System (ADS)

Upcott, N. M.; Mukasa, R. K.; Ebinger, C. J.; Karner, G. D.

1996-02-01

Structural variations along the southern sectors of the Western rift, East Africa, have previously been described, but subsurface structures in the northern sector (Uganda, Zaire) are virtually unknown. Our aims are to investigate the along-axis segmentation of the northern sector, thereby adding to the structural picture of the Western rift, and to study the isostatic compensation of the varying rift morphology along the sector's length. This study describes the first gravity survey to be carried out on the shallow Lake Albert, forward models of these and existing gravity data, and the results from inverse modeling of existing aeromagnetic data designed to delimit border and transfer fault systems. Our tectonic model shows that the northern rift sector is segmented along-axis into five 25 to 65-km-wide, 80 to 100-km-long rift segments, characterized by closed-contour Bouguer anomaly lows, and bounded by steep gravity, aeromagnetic, and topographic/bathymetric gradients. Werner and Euler deconvolution results and gravity anomaly data reveal that some faulted basins are separated by structural highs and cross-rift ramps or faults and suggest sedimentary basin depths of 4-6 km. Forward modeling of structural and free-air gravity profiles across individual basins and flanks using a model that assumes flexural compensation also suggests sediment thicknesses of up to 5.5 km, similar to the estimates from magnetic data. The basin and flank morphology can be explained by 6-9 km of extension of a lithosphere with an effective elastic thickness (Te) of 25 km (equivalent to a flexural rigidity of 1.4 × 1023 N m), similar to results in other Western rift basins. Potential field data and lithospheric strength estimates in the Western rift system show small along-axis variations in lithospheric structure, regardless of the presence or absence of Cenozoic magmatism.

A novel numerical framework for self-similarity in plasticity: Wedge indentation in single crystals

NASA Astrophysics Data System (ADS)

Juul, K. J.; Niordson, C. F.; Nielsen, K. L.; Kysar, J. W.

2018-03-01

A novel numerical framework for analyzing self-similar problems in plasticity is developed and demonstrated. Self-similar problems of this kind include processes such as stationary cracks, void growth, indentation etc. The proposed technique offers a simple and efficient method for handling this class of complex problems by avoiding issues related to traditional Lagrangian procedures. Moreover, the proposed technique allows for focusing the mesh in the region of interest. In the present paper, the technique is exploited to analyze the well-known wedge indentation problem of an elastic-viscoplastic single crystal. However, the framework may be readily adapted to any constitutive law of interest. The main focus herein is the development of the self-similar framework, while the indentation study serves primarily as verification of the technique by comparing to existing numerical and analytical studies. In this study, the three most common metal crystal structures will be investigated, namely the face-centered cubic (FCC), body-centered cubic (BCC), and hexagonal close packed (HCP) crystal structures, where the stress and slip rate fields around the moving contact point singularity are presented.

Analysis of network motifs in cellular regulation: Structural similarities, input-output relations and signal integration.

PubMed

Straube, Ronny

2017-12-01

Much of the complexity of regulatory networks derives from the necessity to integrate multiple signals and to avoid malfunction due to cross-talk or harmful perturbations. Hence, one may expect that the input-output behavior of larger networks is not necessarily more complex than that of smaller network motifs which suggests that both can, under certain conditions, be described by similar equations. In this review, we illustrate this approach by discussing the similarities that exist in the steady state descriptions of a simple bimolecular reaction, covalent modification cycles and bacterial two-component systems. Interestingly, in all three systems fundamental input-output characteristics such as thresholds, ultrasensitivity or concentration robustness are described by structurally similar equations. Depending on the system the meaning of the parameters can differ ranging from protein concentrations and affinity constants to complex parameter combinations which allows for a quantitative understanding of signal integration in these systems. We argue that this approach may also be extended to larger regulatory networks. Copyright © 2017 Elsevier B.V. All rights reserved.

How State Education Agencies Acquire and Use Research in School Improvement Strategies. Policy Brief. RB-55

ERIC Educational Resources Information Center

Goertz, Margaret E.; Barnes, Carol; Massell, Diane

2013-01-01

Although studies of districts' and schools' use of research exist, little is known about how SEAs search for, select, and use research and other kinds of evidence in their school improvement strategies. While one might assume similarities in research use behaviors, both the organizational structures of SEAs and the population of external…

Systemic Operational Design: Improving Operational Planning for the Netherlands Armed Forces

DTIC Science & Technology

2006-05-25

This methodology is called Soft Systems Methodology . His methodology is a structured way of thinking in which not only a perceived problematic...Many similarities exist between Systemic Operational Design and Soft Systems Methodology , their epistemology is related. Furthermore, they both have...Systems Thinking: Managing Chaos and Complexity. Boston: Butterworth Heinemann, 1999. Checkland, Peter, and Jim Scholes. Soft Systems Methodology in

Visual Similarity of Words Alone Can Modulate Hemispheric Lateralization in Visual Word Recognition: Evidence from Modeling Chinese Character Recognition

ERIC Educational Resources Information Center

Hsiao, Janet H.; Cheung, Kit

2016-01-01

In Chinese orthography, the most common character structure consists of a semantic radical on the left and a phonetic radical on the right (SP characters); the minority, opposite arrangement also exists (PS characters). Recent studies showed that SP character processing is more left hemisphere (LH) lateralized than PS character processing.…

Mycorrhizas and soil ecosystem function of co-existing woody vegetation islands at the alpine tree line.

PubMed

Wang, Lixia; Otgonsuren, Burenjargal; Godbold, Douglas L

2017-01-01

Picea abies , Pinus mugo and Rhododendron ferrugineum co-exist at the alpine tree line, and can have different mycorrhizal communities. The activity and diversity of mycorrhizal fungi are considered to be important factors in regulation of soil function. At a tree line site and a lower elevation site in the Austrian Alps, the community structure of ectomycorrhiza on Picea abies and Pinus mugo was determined. The activity of surface enzymes was determined on ectomycorrhizal and ericoid mycorrhizal roots. In soils, the activity of a range of enzymes, nitrogen (N) mineralization and biomass decomposition were determined. The community structure of the ectomycorrhizal community of Picea abies and Pinus mugo differed strongly, but the average activity of surface enzymes of the ectomycorrhizal communities was similar. A lower root surface enzyme activity was determined on Rhododendron ferrugineum . Soil N-mineralization under Rhododendron ferrugineum was significantly lower than under Picea abies and Pinus mugo . In soil, the activity of a range of enzymes did not differ at the tree line but differed between the tree line and the lower elevation sites. The different ectomycorrhizal communities on Picea abies and Pinus mugo and ericoid mycorrhizas on Rhododendron ferrugineum support similar ecosystem functions in soil.

Detecting network communities beyond assortativity-related attributes

NASA Astrophysics Data System (ADS)

Liu, Xin; Murata, Tsuyoshi; Wakita, Ken

2014-07-01

In network science, assortativity refers to the tendency of links to exist between nodes with similar attributes. In social networks, for example, links tend to exist between individuals of similar age, nationality, location, race, income, educational level, religious belief, and language. Thus, various attributes jointly affect the network topology. An interesting problem is to detect community structure beyond some specific assortativity-related attributes ρ, i.e., to take out the effect of ρ on network topology and reveal the hidden community structures which are due to other attributes. An approach to this problem is to redefine the null model of the modularity measure, so as to simulate the effect of ρ on network topology. However, a challenge is that we do not know to what extent the network topology is affected by ρ and by other attributes. In this paper, we propose a distance modularity, which allows us to freely choose any suitable function to simulate the effect of ρ. Such freedom can help us probe the effect of ρ and detect the hidden communities which are due to other attributes. We test the effectiveness of distance modularity on synthetic benchmarks and two real-world networks.

Identification of Conserved Water Sites in Protein Structures for Drug Design.

PubMed

Jukič, Marko; Konc, Janez; Gobec, Stanislav; Janežič, Dušanka

2017-12-26

Identification of conserved waters in protein structures is a challenging task with applications in molecular docking and protein stability prediction. As an alternative to computationally demanding simulations of proteins in water, experimental cocrystallized waters in the Protein Data Bank (PDB) in combination with a local structure alignment algorithm can be used for reliable prediction of conserved water sites. We developed the ProBiS H2O approach based on the previously developed ProBiS algorithm, which enables identification of conserved water sites in proteins using experimental protein structures from the PDB or a set of custom protein structures available to the user. With a protein structure, a binding site, or an individual water molecule as a query, ProBiS H2O collects similar proteins from the PDB and performs local or binding site-specific superimpositions of the query structure with similar proteins using the ProBiS algorithm. It collects the experimental water molecules from the similar proteins and transposes them to the query protein. Transposed waters are clustered by their mutual proximity, which enables identification of discrete sites in the query protein with high water conservation. ProBiS H2O is a robust and fast new approach that uses existing experimental structural data to identify conserved water sites on the interfaces of protein complexes, for example protein-small molecule interfaces, and elsewhere on the protein structures. It has been successfully validated in several reported proteins in which conserved water molecules were found to play an important role in ligand binding with applications in drug design.

Comparison Between Terrestrial Explosion Crater Morphology in Floating Ice and Europan Chaos

NASA Technical Reports Server (NTRS)

Billings, S. E.; Kattenhorn, S. A.

2003-01-01

Craters created by explosives have been found to serve as valuable analogs to impact craters, within limits. Explosion craters have been created in floating terrestrial ice in experiments related to clearing ice from waterways. Features called chaos occur on the surface of Europa s floating ice shell. Chaos is defined as a region in which the background plains have been disrupted. Common features of chaos include rafted blocks of pre-existing terrain suspended in a matrix of smooth or hummocky material; low surface albedo; and structural control on chaos outline shape by pre-existing lineaments. All published models of chaos formation call on endogenic processes whereby chaos forms through thermal processes. Nonetheless, we note morphological similarities between terrestrial explosion craters and Europan chaos at a range of scales and consider whether some chaos may have formed by impact. We explore these similarities through geologic and morphologic mapping.

Beyond the Drake Equation: On the Probability of the Nature of Extraterrestrial Life Forms in Our Galaxy Today

NASA Astrophysics Data System (ADS)

Geller, Harold A.

2014-01-01

I will discuss my research into the issues associated with the nature of any extraterrestrials that may be encountered in the future in our galaxy. This research was sparked by statements made by Stephen Hawking in 2010 regarding his fear of emitting radiation from our Earth so that an extraterrestrial intelligent civilization may be alerted to our existence in the galaxy today. While addressing issues of extraterrestrial altruism, a probabilistic equation was developed which addresses the number of extraterrestrial intelligent life forms that may exist in our galaxy today, who could use our bodies for nourishment or reproductive purposes. The equation begins with the results from a Drake Equation calculation, and proceeds by addressing such biochemical parameters as the fraction of ETIs with: dextro sugar stereo-isomers; levo amino acid stereo-isomers; similar codon interpretation; chromosomal length and, similar cell membrane structure to allow egg penetration.

A morphometric analysis of cellular differentiation in caps of primary and lateral roots of Helianthus annuus

NASA Technical Reports Server (NTRS)

Moore, R.

1985-01-01

In order to determine if patterns of cell differentiation are similar in primary and lateral roots, I performed a morphometric analysis of the ultrastructure of calyptrogen, columella, and peripheral cells in primary and lateral roots of Helianthus annuus. Each cell type is characterized by a unique ultrastructure, and the ultrastructural changes characteristic of cellular differentiation in root caps are organelle specific. No major structural differences exist in the structures of the composite cell types, or in patterns of cell differentiation in caps of primary vs. lateral roots.

Increased Diversity of Libraries from Libraries: Chemoinformatic Analysis of Bis-Diazacyclic Libraries

PubMed Central

López-Vallejo, Fabian; Nefzi, Adel; Bender, Andreas; Owen, John R.; Nabney, Ian T.; Houghten, Richard A.; Medina-Franco, Jose L.

2011-01-01

Combinatorial libraries continue to play a key role in drug discovery. To increase structural diversity, several experimental methods have been developed. However, limited efforts have been performed so far to quantify the diversity of the broadly used diversity-oriented synthetic (DOS) libraries. Herein we report a comprehensive characterization of 15 bis-diazacyclic combinatorial libraries obtained through libraries from libraries, which is a DOS approach. Using MACCS keys, radial and different pharmacophoric fingerprints as well as six molecular properties, it was demonstrated the increased structural and property diversity of the libraries from libraries over the individual libraries. Comparison of the libraries to existing drugs, NCI Diversity and the Molecular Libraries Small Molecule Repository revealed the structural uniqueness of the combinatorial libraries (mean similarity < 0.5 for any fingerprint representation). In particular, bis-cyclic thiourea libraries were the most structurally dissimilar to drugs retaining drug-like character in property space. This study represents the first comprehensive quantification of the diversity of libraries from libraries providing a solid quantitative approach to compare and contrast the diversity of DOS libraries with existing drugs or any other compound collection. PMID:21294850

Finiteness of corner vortices

NASA Astrophysics Data System (ADS)

Kalita, Jiten C.; Biswas, Sougata; Panda, Swapnendu

2018-04-01

Till date, the sequence of vortices present in the solid corners of steady internal viscous incompressible flows was thought to be infinite. However, the already existing and most recent geometric theories on incompressible viscous flows that express vortical structures in terms of critical points in bounded domains indicate a strong opposition to this notion of infiniteness. In this study, we endeavor to bridge the gap between the two opposing stream of thoughts by diagnosing the assumptions of the existing theorems on such vortices. We provide our own set of proofs for establishing the finiteness of the sequence of corner vortices by making use of the continuum hypothesis and Kolmogorov scale, which guarantee a nonzero scale for the smallest vortex structure possible in incompressible viscous flows. We point out that the notion of infiniteness resulting from discrete self-similarity of the vortex structures is not physically feasible. Making use of some elementary concepts of mathematical analysis and our own construction of diametric disks, we conclude that the sequence of corner vortices is finite.

Curvature, metric and parametrization of origami tessellations: theory and application to the eggbox pattern.

PubMed

Nassar, H; Lebée, A; Monasse, L

2017-01-01

Origami tessellations are particular textured morphing shell structures. Their unique folding and unfolding mechanisms on a local scale aggregate and bring on large changes in shape, curvature and elongation on a global scale. The existence of these global deformation modes allows for origami tessellations to fit non-trivial surfaces thus inspiring applications across a wide range of domains including structural engineering, architectural design and aerospace engineering. The present paper suggests a homogenization-type two-scale asymptotic method which, combined with standard tools from differential geometry of surfaces, yields a macroscopic continuous characterization of the global deformation modes of origami tessellations and other similar periodic pin-jointed trusses. The outcome of the method is a set of nonlinear differential equations governing the parametrization, metric and curvature of surfaces that the initially discrete structure can fit. The theory is presented through a case study of a fairly generic example: the eggbox pattern. The proposed continuous model predicts correctly the existence of various fittings that are subsequently constructed and illustrated.

Curvature, metric and parametrization of origami tessellations: theory and application to the eggbox pattern

NASA Astrophysics Data System (ADS)

Nassar, H.; Lebée, A.; Monasse, L.

2017-01-01

Origami tessellations are particular textured morphing shell structures. Their unique folding and unfolding mechanisms on a local scale aggregate and bring on large changes in shape, curvature and elongation on a global scale. The existence of these global deformation modes allows for origami tessellations to fit non-trivial surfaces thus inspiring applications across a wide range of domains including structural engineering, architectural design and aerospace engineering. The present paper suggests a homogenization-type two-scale asymptotic method which, combined with standard tools from differential geometry of surfaces, yields a macroscopic continuous characterization of the global deformation modes of origami tessellations and other similar periodic pin-jointed trusses. The outcome of the method is a set of nonlinear differential equations governing the parametrization, metric and curvature of surfaces that the initially discrete structure can fit. The theory is presented through a case study of a fairly generic example: the eggbox pattern. The proposed continuous model predicts correctly the existence of various fittings that are subsequently constructed and illustrated.

How Molecular Size Impacts RMSD Applications in Molecular Dynamics Simulations.

PubMed

Sargsyan, Karen; Grauffel, Cédric; Lim, Carmay

2017-04-11

The root-mean-square deviation (RMSD) is a similarity measure widely used in analysis of macromolecular structures and dynamics. As increasingly larger macromolecular systems are being studied, dimensionality effects such as the "curse of dimensionality" (a diminishing ability to discriminate pairwise differences between conformations with increasing system size) may exist and significantly impact RMSD-based analyses. For such large bimolecular systems, whether the RMSD or other alternative similarity measures might suffer from this "curse" and lose the ability to discriminate different macromolecular structures had not been explicitly addressed. Here, we show such dimensionality effects for both weighted and nonweighted RMSD schemes. We also provide a mechanism for the emergence of the "curse of dimensionality" for RMSD from the law of large numbers by showing that the conformational distributions from which RMSDs are calculated become increasingly similar as the system size increases. Our findings suggest the use of weighted RMSD schemes for small proteins (less than 200 residues) and nonweighted RMSD for larger proteins when analyzing molecular dynamics trajectories.

A New Approach to Diagnose Parkinson's Disease Using a Structural Cooccurrence Matrix for a Similarity Analysis.

PubMed

de Souza, João W M; Alves, Shara S A; Rebouças, Elizângela de S; Almeida, Jefferson S; Rebouças Filho, Pedro P

2018-01-01

Parkinson's disease affects millions of people around the world and consequently various approaches have emerged to help diagnose this disease, among which we can highlight handwriting exams. Extracting features from handwriting exams is an important contribution of the computational field for the diagnosis of this disease. In this paper, we propose an approach that measures the similarity between the exam template and the handwritten trace of the patient following the exam template. This similarity was measured using the Structural Cooccurrence Matrix to calculate how close the handwritten trace of the patient is to the exam template. The proposed approach was evaluated using various exam templates and the handwritten traces of the patient. Each of these variations was used together with the Naïve Bayes, OPF, and SVM classifiers. In conclusion the proposed approach was proven to be better than the existing methods found in the literature and is therefore a promising tool for the diagnosis of Parkinson's disease.

simDEF: definition-based semantic similarity measure of gene ontology terms for functional similarity analysis of genes.

PubMed

Pesaranghader, Ahmad; Matwin, Stan; Sokolova, Marina; Beiko, Robert G

2016-05-01

Measures of protein functional similarity are essential tools for function prediction, evaluation of protein-protein interactions (PPIs) and other applications. Several existing methods perform comparisons between proteins based on the semantic similarity of their GO terms; however, these measures are highly sensitive to modifications in the topological structure of GO, tend to be focused on specific analytical tasks and concentrate on the GO terms themselves rather than considering their textual definitions. We introduce simDEF, an efficient method for measuring semantic similarity of GO terms using their GO definitions, which is based on the Gloss Vector measure commonly used in natural language processing. The simDEF approach builds optimized definition vectors for all relevant GO terms, and expresses the similarity of a pair of proteins as the cosine of the angle between their definition vectors. Relative to existing similarity measures, when validated on a yeast reference database, simDEF improves correlation with sequence homology by up to 50%, shows a correlation improvement >4% with gene expression in the biological process hierarchy of GO and increases PPI predictability by > 2.5% in F1 score for molecular function hierarchy. Datasets, results and source code are available at http://kiwi.cs.dal.ca/Software/simDEF CONTACT: ahmad.pgh@dal.ca or beiko@cs.dal.ca Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Disentangling the co-structure of multilayer interaction networks: degree distribution and module composition in two-layer bipartite networks.

PubMed

Astegiano, Julia; Altermatt, Florian; Massol, François

2017-11-13

Species establish different interactions (e.g. antagonistic, mutualistic) with multiple species, forming multilayer ecological networks. Disentangling network co-structure in multilayer networks is crucial to predict how biodiversity loss may affect the persistence of multispecies assemblages. Existing methods to analyse multilayer networks often fail to consider network co-structure. We present a new method to evaluate the modular co-structure of multilayer networks through the assessment of species degree co-distribution and network module composition. We focus on modular structure because of its high prevalence among ecological networks. We apply our method to two Lepidoptera-plant networks, one describing caterpillar-plant herbivory interactions and one representing adult Lepidoptera nectaring on flowers, thereby possibly pollinating them. More than 50% of the species established either herbivory or visitation interactions, but not both. These species were over-represented among plants and lepidopterans, and were present in most modules in both networks. Similarity in module composition between networks was high but not different from random expectations. Our method clearly delineates the importance of interpreting multilayer module composition similarity in the light of the constraints imposed by network structure to predict the potential indirect effects of species loss through interconnected modular networks.

Scalable and Axiomatic Ranking of Network Role Similarity

PubMed Central

Jin, Ruoming; Lee, Victor E.; Li, Longjie

2014-01-01

A key task in analyzing social networks and other complex networks is role analysis: describing and categorizing nodes according to how they interact with other nodes. Two nodes have the same role if they interact with equivalent sets of neighbors. The most fundamental role equivalence is automorphic equivalence. Unfortunately, the fastest algorithms known for graph automorphism are nonpolynomial. Moreover, since exact equivalence is rare, a more meaningful task is measuring the role similarity between any two nodes. This task is closely related to the structural or link-based similarity problem that SimRank addresses. However, SimRank and other existing similarity measures are not sufficient because they do not guarantee to recognize automorphically or structurally equivalent nodes. This paper makes two contributions. First, we present and justify several axiomatic properties necessary for a role similarity measure or metric. Second, we present RoleSim, a new similarity metric which satisfies these axioms and which can be computed with a simple iterative algorithm. We rigorously prove that RoleSim satisfies all these axiomatic properties. We also introduce Iceberg RoleSim, a scalable algorithm which discovers all pairs with RoleSim scores above a user-defined threshold θ. We demonstrate the interpretative power of RoleSim on both both synthetic and real datasets. PMID:25383066

Construction of ontology augmented networks for protein complex prediction.

PubMed

Zhang, Yijia; Lin, Hongfei; Yang, Zhihao; Wang, Jian

2013-01-01

Protein complexes are of great importance in understanding the principles of cellular organization and function. The increase in available protein-protein interaction data, gene ontology and other resources make it possible to develop computational methods for protein complex prediction. Most existing methods focus mainly on the topological structure of protein-protein interaction networks, and largely ignore the gene ontology annotation information. In this article, we constructed ontology augmented networks with protein-protein interaction data and gene ontology, which effectively unified the topological structure of protein-protein interaction networks and the similarity of gene ontology annotations into unified distance measures. After constructing ontology augmented networks, a novel method (clustering based on ontology augmented networks) was proposed to predict protein complexes, which was capable of taking into account the topological structure of the protein-protein interaction network, as well as the similarity of gene ontology annotations. Our method was applied to two different yeast protein-protein interaction datasets and predicted many well-known complexes. The experimental results showed that (i) ontology augmented networks and the unified distance measure can effectively combine the structure closeness and gene ontology annotation similarity; (ii) our method is valuable in predicting protein complexes and has higher F1 and accuracy compared to other competing methods.

Epsilon Eridani Inner Asteroid Belt

NASA Image and Video Library

2017-09-14

SCI2017_0004: Artist's illustration of the Epsilon Eridani system showing Epsilon Eridani b, right foreground, a Jupiter-mass planet orbiting its parent star at the outside edge of an asteroid belt. In the background can be seen another narrow asteroid or comet belt plus an outermost belt similar in size to our solar system's Kuiper Belt. The similarity of the structure of the Epsilon Eridani system to our solar system is remarkable, although Epsilon Eridani is much younger than our sun. SOFIA observations confirmed the existence of the asteroid belt adjacent to the orbit of the Jovian planet. Credit: NASA/SOFIA/Lynette Cook

Anatomical study of minor alterations in neonate vocal folds.

PubMed

Silva, Adriano Rezende; Machado, Almiro José; Crespo, Agrício Nubiato

2014-01-01

Minor structural alterations of the vocal fold cover are frequent causes of voice abnormalities. They may be difficult to diagnose, and are expressed in different manners. Cases of intracordal cysts, sulcus vocalis, mucosal bridge, and laryngeal micro-diaphragm form the group of minor structural alterations of the vocal fold cover investigated in the present study. The etiopathogenesis and epidemiology of these alterations are poorly known. To evaluate the existence and anatomical characterization of minor structural alterations in the vocal folds of newborns. 56 larynxes excised from neonates of both genders were studied. They were examined fresh, or defrosted after conservation via freezing, under a microscope at magnifications of 25× and 40×. The vocal folds were inspected and palpated by two examiners, with the aim of finding minor structural alterations similar to those described classically, and other undetermined minor structural alterations. Larynges presenting abnormalities were submitted to histological examination. Six cases of abnormalities were found in different larynges: one (1.79%) compatible with a sulcus vocalis and five (8.93%) compatible with a laryngeal micro-diaphragm. No cases of cysts or mucosal bridges were found. The observed abnormalities had characteristics similar to those described in other age groups. Abnormalities similar to sulcus vocalis or micro-diaphragm may be present at birth. Copyright © 2014 Associação Brasileira de Otorrinolaringologia e Cirurgia Cérvico-Facial. Published by Elsevier Editora Ltda. All rights reserved.

Structural Investigation of a Novel N-Acetyl Glucosamine Binding Chi-Lectin Which Reveals Evolutionary Relationship with Class III Chitinases

PubMed Central

Patil, Dipak N.; Datta, Manali; Dev, Aditya; Dhindwal, Sonali; Singh, Nirpendra; Dasauni, Pushpanjali; Kundu, Suman; Sharma, Ashwani K.; Tomar, Shailly; Kumar, Pravindra

2013-01-01

The glycosyl hydrolase 18 (GH18) family consists of active chitinases as well as chitinase like lectins/proteins (CLPs). The CLPs share significant sequence and structural similarities with active chitinases, however, do not display chitinase activity. Some of these proteins are reported to have specific functions and carbohydrate binding property. In the present study, we report a novel chitinase like lectin (TCLL) from Tamarindus indica. The crystal structures of native TCLL and its complex with N-acetyl glucosamine were determined. Similar to the other CLPs of the GH18 members, TCLL lacks chitinase activity due to mutations of key active site residues. Comparison of TCLL with chitinases and other chitin binding CLPs shows that TCLL has substitution of some chitin binding site residues and more open binding cleft due to major differences in the loop region. Interestingly, the biochemical studies suggest that TCLL is an N-acetyl glucosamine specific chi-lectin, which is further confirmed by the complex structure of TCLL with N-acetyl glucosamine complex. TCLL has two distinct N-acetyl glucosamine binding sites S1 and S2 that contain similar polar residues, although interaction pattern with N-acetyl glucosamine varies extensively among them. Moreover, TCLL structure depicts that how plants utilize existing structural scaffolds ingenuously to attain new functions. To date, this is the first structural investigation of a chi-lectin from plants that explore novel carbohydrate binding sites other than chitin binding groove observed in GH18 family members. Consequently, TCLL structure confers evidence for evolutionary link of lectins with chitinases. PMID:23717482

Evidence that Magnetic Navigation and Geomagnetic Imprinting Shape Spatial Genetic Variation in Sea Turtles.

PubMed

Brothers, J Roger; Lohmann, Kenneth J

2018-04-23

The canonical drivers of population genetic structure, or spatial genetic variation, are isolation by distance and isolation by environment. Isolation by distance predicts that neighboring populations will be genetically similar and geographically distant populations will be genetically distinct [1]. Numerous examples also exist of isolation by environment, a phenomenon in which populations that inhabit similar environments (e.g., same elevation, temperature, or vegetation) are genetically similar even if they are distant, whereas populations that inhabit different environments are genetically distinct even when geographically close [2-4]. These dual models provide a widely accepted conceptual framework for understanding population structure [5-8]. Here, we present evidence for an additional, novel process that we call isolation by navigation, in which the navigational mechanism used by a long-distance migrant influences population structure independently of isolation by either distance or environment. Specifically, we investigated the population structure of loggerhead sea turtles (Caretta caretta) [9], which return to nest on their natal beaches by seeking out unique magnetic signatures along the coast-a behavior known as geomagnetic imprinting [10-12]. Results reveal that spatial variation in Earth's magnetic field strongly predicts genetic differentiation between nesting beaches, even when environmental similarities and geographic proximity are taken into account. The findings provide genetic corroboration of geomagnetic imprinting [10, 13]. Moreover, they provide strong evidence that geomagnetic imprinting and magnetic navigation help shape the population structure of sea turtles and perhaps numerous other long-distance migrants that return to their natal areas to reproduce [13-17]. Copyright © 2018 Elsevier Ltd. All rights reserved.

Small Artery Elastin Distribution and Architecture-Focus on Three Dimensional Organization.

PubMed

Hill, Michael A; Nourian, Zahra; Ho, I-Lin; Clifford, Philip S; Martinez-Lemus, Luis; Meininger, Gerald A

2016-11-01

The distribution of ECM proteins within the walls of resistance vessels is complex both in variety of proteins and structural arrangement. In particular, elastin exists as discrete fibers varying in orientation across the adventitia and media as well as often resembling a sheet-like structure in the case of the IEL. Adding to the complexity is the tissue heterogeneity that exists in these structural arrangements. For example, small intracranial cerebral arteries lack adventitial elastin while similar sized arteries from skeletal muscle and intestinal mesentery exhibit a complex adventitial network of elastin fibers. With regard to the IEL, several vascular beds exhibit an elastin sheet with punctate holes/fenestrae while in others the IEL is discontinuous and fibrous in appearance. Importantly, these structural patterns likely sub-serve specific functional properties, including mechanosensing, control of external forces, mechanical properties of the vascular wall, cellular positioning, and communication between cells. Of further significance, these processes are altered in vascular disorders such as hypertension and diabetes mellitus where there is modification of ECM. This brief report focuses on the three-dimensional wall structure of small arteries and considers possible implications with regard to mechanosensing under physiological and pathophysiological conditions. © 2016 John Wiley & Sons Ltd.

Effects of proline cis-trans isomerization on TB domain secondary structure.

PubMed Central

Yuan, X.; Werner, J. M.; Knott, V.; Handford, P. A.; Campbell, I. D.; Downing, K.

1998-01-01

The transforming growth factor beta (TGF-beta) binding protein-like (TB) domain is found principally in proteins localized to extracellular matrix fibrils, including human fibrillin-1, the defective protein in the Marfan syndrome. Analysis of the nuclear magnetic resonance (NMR) data for the sixth TB module from human fibrillin-1 has revealed the existence of two stable conformers that differ in the isomerization states of two proline residues. Unusually, the two isoforms do not readily interconvert and are stable on the time scale of milliseconds. We have computed independent structures of the major and minor conformers of TB6 to assess how the domain fold adjusts to incorporate alternatively cis- or trans-prolines. Based on previous observations, it has been suggested that multiple conformers can only be accommodated in flexible regions of protein structure. In contrast, P22, which exists in trans in the major form and cis in the minor form of TB6, is in a rigid region of the domain, which is confirmed by backbone dynamics measurements. Overall, the structures of the major and minor conformers are similar. However, the secondary structure topologies of the two forms differ as a direct consequence of the changes in proline conformation. PMID:9792099

Polymorphism in 'L' shaped lipids: structure of N-, O-diacylethanolamines with mixed acyl chains.

PubMed

Tarafdar, Pradip K; Swamy, Musti J

2009-11-01

Although solid state polymorphism in lipids has been established by spectroscopic and calorimetric studies long ago, only in a few cases crystal structures of different polymorphs of the same compound have been reported, possibly due to difficulties in obtaining high quality single crystals of individual polymorphs. Recent studies show that N-, O-diacylethanolamines (DAEs) can be derived by the O-acylation of the stress-related lipids, the N-acylethanolamines under physiological conditions. In this study, two DAEs with mixed acyl chains, namely N-palmitoyl, O-octanoylethanolamine and N-palmitoyl, O-decanoylethanolamine have been synthesized and their three-dimensional structures were determined. Both the compounds were found to adopt 'L' shaped structures and exist in two polymorphic forms, alpha and beta. In the alpha form a mixed-type chain packing has been observed whereas in the beta form the chain packing is symmetric. Similar polymorphic forms are likely to exist in other 'L' shaped lipids such as 1,3-diacylglycerols and ceramides, where polymorphism has been detected earlier, but three-dimensional structures - which can give precise information about the packing at atomic resolution - have not been reported.

ProBiS-CHARMMing: Web Interface for Prediction and Optimization of Ligands in Protein Binding Sites.

PubMed

Konc, Janez; Miller, Benjamin T; Štular, Tanja; Lešnik, Samo; Woodcock, H Lee; Brooks, Bernard R; Janežič, Dušanka

2015-11-23

Proteins often exist only as apo structures (unligated) in the Protein Data Bank, with their corresponding holo structures (with ligands) unavailable. However, apoproteins may not represent the amino-acid residue arrangement upon ligand binding well, which is especially problematic for molecular docking. We developed the ProBiS-CHARMMing web interface by connecting the ProBiS ( http://probis.cmm.ki.si ) and CHARMMing ( http://www.charmming.org ) web servers into one functional unit that enables prediction of protein-ligand complexes and allows for their geometry optimization and interaction energy calculation. The ProBiS web server predicts ligands (small compounds, proteins, nucleic acids, and single-atom ligands) that may bind to a query protein. This is achieved by comparing its surface structure against a nonredundant database of protein structures and finding those that have binding sites similar to that of the query protein. Existing ligands found in the similar binding sites are then transposed to the query according to predictions from ProBiS. The CHARMMing web server enables, among other things, minimization and potential energy calculation for a wide variety of biomolecular systems, and it is used here to optimize the geometry of the predicted protein-ligand complex structures using the CHARMM force field and to calculate their interaction energies with the corresponding query proteins. We show how ProBiS-CHARMMing can be used to predict ligands and their poses for a particular binding site, and minimize the predicted protein-ligand complexes to obtain representations of holoproteins. The ProBiS-CHARMMing web interface is freely available for academic users at http://probis.nih.gov.

Drug Repositioning by Kernel-Based Integration of Molecular Structure, Molecular Activity, and Phenotype Data

PubMed Central

Wang, Yongcui; Chen, Shilong; Deng, Naiyang; Wang, Yong

2013-01-01

Computational inference of novel therapeutic values for existing drugs, i.e., drug repositioning, offers the great prospect for faster and low-risk drug development. Previous researches have indicated that chemical structures, target proteins, and side-effects could provide rich information in drug similarity assessment and further disease similarity. However, each single data source is important in its own way and data integration holds the great promise to reposition drug more accurately. Here, we propose a new method for drug repositioning, PreDR (Predict Drug Repositioning), to integrate molecular structure, molecular activity, and phenotype data. Specifically, we characterize drug by profiling in chemical structure, target protein, and side-effects space, and define a kernel function to correlate drugs with diseases. Then we train a support vector machine (SVM) to computationally predict novel drug-disease interactions. PreDR is validated on a well-established drug-disease network with 1,933 interactions among 593 drugs and 313 diseases. By cross-validation, we find that chemical structure, drug target, and side-effects information are all predictive for drug-disease relationships. More experimentally observed drug-disease interactions can be revealed by integrating these three data sources. Comparison with existing methods demonstrates that PreDR is competitive both in accuracy and coverage. Follow-up database search and pathway analysis indicate that our new predictions are worthy of further experimental validation. Particularly several novel predictions are supported by clinical trials databases and this shows the significant prospects of PreDR in future drug treatment. In conclusion, our new method, PreDR, can serve as a useful tool in drug discovery to efficiently identify novel drug-disease interactions. In addition, our heterogeneous data integration framework can be applied to other problems. PMID:24244318

Helical Peierls distortion: Formation of helices of polyketone and polyisocyanide

NASA Astrophysics Data System (ADS)

Cui, Chang-Xing; Kertesz, Miklos

1990-06-01

A new type of Peierls-like distortion, the formation of a helix due to the existence of partially filled crossing bands, is reported for polyketone and polyisocyanide. The torsional potential curves, optimized geometries, band structures and phonon dispersion curves are derived. A comparison with the well-known Peierls-distorted all-trans polyacetylene indicates close similarity between the two types of Peierls distortions.

15 CFR Appendix B to Subpart R of... - Minor Projects for Purposes of § 922.193(a)(2)(iii)

Code of Federal Regulations, 2011 CFR

2011-01-01

... will be constructed of clean, non-polluting materials, which do not impair the use of the adjacent... water and drift material. (b) Spring piles and pile clusters when their design and purpose is usual for... in length and is located in an area on the body of water where other similar structures already exist...

IUPAC Periodic Table of the Isotopes

USGS Publications Warehouse

Holden, N.E.; Coplen, T.B.; Böhlke, J.K.; Wieser, M.E.; Singleton, G.; Walczyk, T.; Yoneda, S.; Mahaffy, P.G.; Tarbox, L.V.

2011-01-01

For almost 150 years, the Periodic Table of the Elements has served as a guide to the world of elements by highlighting similarities and differences in atomic structure and chemical properties. To introduce students, teachers, and society to the existence and importance of isotopes of the chemical elements, an IUPAC Periodic Table of the Isotopes (IPTI) has been prepared and can be found as a supplement to this issue.

Lexical Collocation and Topic Occurrence in Well-Written Editorials: A Study in Form.

ERIC Educational Resources Information Center

Addison, James C., Jr.

To explore the concept of lexical collocation, or relationships between words, a study was conducted based on three assumptions: (1) that a text structure for a unit of discourse was analogous to that existing at the level of the sentence, (2) that such a text form could be discovered if a large enough sample of generically similar texts was…

Objective Quality Assessment for Color-to-Gray Image Conversion.

PubMed

Ma, Kede; Zhao, Tiesong; Zeng, Kai; Wang, Zhou

2015-12-01

Color-to-gray (C2G) image conversion is the process of transforming a color image into a grayscale one. Despite its wide usage in real-world applications, little work has been dedicated to compare the performance of C2G conversion algorithms. Subjective evaluation is reliable but is also inconvenient and time consuming. Here, we make one of the first attempts to develop an objective quality model that automatically predicts the perceived quality of C2G converted images. Inspired by the philosophy of the structural similarity index, we propose a C2G structural similarity (C2G-SSIM) index, which evaluates the luminance, contrast, and structure similarities between the reference color image and the C2G converted image. The three components are then combined depending on image type to yield an overall quality measure. Experimental results show that the proposed C2G-SSIM index has close agreement with subjective rankings and significantly outperforms existing objective quality metrics for C2G conversion. To explore the potentials of C2G-SSIM, we further demonstrate its use in two applications: 1) automatic parameter tuning for C2G conversion algorithms and 2) adaptive fusion of C2G converted images.

Discrimination of Isomers of Released N- and O-Glycans Using Diagnostic Product Ions in Negative Ion PGC-LC-ESI-MS/MS

NASA Astrophysics Data System (ADS)

Ashwood, Christopher; Lin, Chi-Hung; Thaysen-Andersen, Morten; Packer, Nicolle H.

2018-03-01

Profiling cellular protein glycosylation is challenging due to the presence of highly similar glycan structures that play diverse roles in cellular physiology. As the anomericity and the exact linkage type of a single glycosidic bond can influence glycan function, there is a demand for improved and automated methods to confirm detailed structural features and to discriminate between structurally similar isomers, overcoming a significant bottleneck in the analysis of data generated by glycomics experiments. We used porous graphitized carbon-LC-ESI-MS/MS to separate and detect released N- and O-glycan isomers from mammalian model glycoproteins using negative mode resonance activation CID-MS/MS. By interrogating similar fragment spectra from closely related glycan isomers that differ only in arm position and sialyl linkage, product fragment ions for discrimination between these features were discovered. Using the Skyline software, at least two diagnostic fragment ions of high specificity were validated for automated discrimination of sialylation and arm position in N-glycan structures, and sialylation in O-glycan structures, complementing existing structural diagnostic ions. These diagnostic ions were shown to be useful for isomer discrimination using both linear and 3D ion trap mass spectrometers when analyzing complex glycan mixtures from cell lysates. Skyline was found to serve as a useful tool for automated assessment of glycan isomer discrimination. This platform-independent workflow can potentially be extended to automate the characterization and quantitation of other challenging glycan isomers. [Figure not available: see fulltext.

A comparison of Gemini and ERTS imagery obtained over southern Morocco

NASA Technical Reports Server (NTRS)

Blodget, H. W.; Anderson, A. T.

1973-01-01

A mosaic constructed from three ERTS MSS band 5 images enlarged to 1:500,000 compares favorably with a similar scale geologic map of southern Morocco, and a near-similar scale Gemini 5 photo pair. A comparative plot of lineations and generalized geology on the three formats show that a significantly greater number of probable fractures are visible on the ERTS imagery than on the Gemini photography, and that both orbital formats show several times more lineaments than were previously mapped. A plot of mineral occurrences on the structural overlays indicates that definite structure-mineralization relationships exist; this finding is used to define underdeveloped areas which are prospective for mineralization. More detailed mapping is possible using MSS imagery than on Gemini 5 photographs, and in addition, the ERTS format is not restricted to limited coverage.

Structural Similitude and Scaling Laws

NASA Technical Reports Server (NTRS)

Simitses, George J.

1998-01-01

Aircraft and spacecraft comprise the class of aerospace structures that require efficiency and wisdom in design, sophistication and accuracy in analysis and numerous and careful experimental evaluations of components and prototype, in order to achieve the necessary system reliability, performance and safety. Preliminary and/or concept design entails the assemblage of system mission requirements, system expected performance and identification of components and their connections as well as of manufacturing and system assembly techniques. This is accomplished through experience based on previous similar designs, and through the possible use of models to simulate the entire system characteristics. Detail design is heavily dependent on information and concepts derived from the previous steps. This information identifies critical design areas which need sophisticated analyses, and design and redesign procedures to achieve the expected component performance. This step may require several independent analysis models, which, in many instances, require component testing. The last step in the design process, before going to production, is the verification of the design. This step necessitates the production of large components and prototypes in order to test component and system analytical predictions and verify strength and performance requirements under the worst loading conditions that the system is expected to encounter in service. Clearly then, full-scale testing is in many cases necessary and always very expensive. In the aircraft industry, in addition to full-scale tests, certification and safety necessitate large component static and dynamic testing. Such tests are extremely difficult, time consuming and definitely absolutely necessary. Clearly, one should not expect that prototype testing will be totally eliminated in the aircraft industry. It is hoped, though, that we can reduce full-scale testing to a minimum. Full-scale large component testing is necessary in other industries as well, Ship building, automobile and railway car construction all rely heavily on testing. Regardless of the application, a scaled-down (by a large factor) model (scale model) which closely represents the structural behavior of the full-scale system (prototype) can prove to be an extremely beneficial tool. This possible development must be based on the existence of certain structural parameters that control the behavior of a structural system when acted upon by static and/or dynamic loads. If such structural parameters exist, a scaled-down replica can be built, which will duplicate the response of the full-scale system. The two systems are then said to be structurally similar. The term, then, that best describes this similarity is structural similitude. Similarity of systems requires that the relevant system parameters be identical and these systems be governed by a unique set of characteristic equations. Thus, if a relation or equation of variables is written for a system, it is valid for all systems which are similar to it. Each variable in a model is proportional to the corresponding variable of the prototype. This ratio, which plays an essential role in predicting the relationship between the model and its prototype, is called the scale factor.

A Novel Botulinum Neurotoxin, Previously Reported as Serotype H, Has a Hybrid-Like Structure With Regions of Similarity to the Structures of Serotypes A and F and Is Neutralized With Serotype A Antitoxin

PubMed Central

Maslanka, Susan E.; Lúquez, Carolina; Dykes, Janet K.; Tepp, William H.; Pier, Christina L.; Pellett, Sabine; Raphael, Brian H.; Kalb, Suzanne R.; Barr, John R.; Rao, Agam; Johnson, Eric A.

2016-01-01

Botulism is a potentially fatal paralytic disease caused by the action of botulinum neurotoxin (BoNT) on nerve cells. There are 7 known serotypes (A–G) of BoNT and up to 40 genetic variants. Clostridium botulinum strain IBCA10-7060 was recently reported to produce BoNT serotype B (BoNT/B) and a novel BoNT, designated as BoNT/H. The BoNT gene (bont) sequence of BoNT/H was compared to known bont sequences. Genetic analysis suggested that BoNT/H has a hybrid-like structure containing regions of similarity to the structures of BoNT/A1 and BoNT/F5. This novel BoNT was serologically characterized by the mouse neutralization assay and a neuronal cell–based assay. The toxic effects of this hybrid-like BoNT were completely eliminated by existing serotype A antitoxins, including those contained in multivalent therapeutic antitoxin products that are the mainstay of human botulism treatment. PMID:26068781

The structure and evolution of ancient impact basins on Mars

NASA Technical Reports Server (NTRS)

Schultz, P. H.; Schultz, R. A.; Rogers, J.

1982-01-01

It is pointed out that characteristic styles of degradation and modification of obvious Martian basins make it possible to recognize more subtle expressions. This approach is seen as providing not only additional basins to the existing inventory but also fundamental clues for initial impact basin structure and stratigraphy. It also reveals the long-lasting influence of basin formation on the crust of Mars in spite of extensive erosion and resurfacing. Consideration is given to five clear examples of modified impact basins, and regions around each that have undergone similar processes (fracturing, collapse, channeling) are delineated. These processes among the different basins are then compared, and similar zones of modification are correlated with concentric basin rings. Consideration is then given to the implications of these observations for current models of basin formation and to the role of impact basins in controlling regional tectonics. The results indicate that large multiring impact scars leave a major but sometimes subtle imprint on the geologic structure of stable crustal regions on Mars.

Molecular assembly of Clostridium botulinum progenitor M complex of type E

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

Eswaramoorthy, Subramaniam; Sun, Jingchuan; Li, Huilin

2015-12-07

Clostridium botulinum neurotoxin (BoNT) is released as a progenitor complex, in association with a non-toxic-non-hemagglutinin protein (NTNH) and other associated proteins. We have determined the crystal structure of M type Progenitor complex of botulinum neurotoxin E [PTC-E(M)], a heterodimer of BoNT and NTNH. The crystal structure reveals that the complex exists as a tight, interlocked heterodimer of BoNT and NTNH. The crystal structure explains the mechanism of molecular assembly of the complex and reveals several acidic clusters at the interface responsible for association at low acidic pH and disassociation at basic/neutral pH. Furthermore, the similarity of the general architecture betweenmore » the PTC-E(M) and the previously determined PTC-A(M) strongly suggests that the progenitor M complexes of all botulinum serotypes may have similar molecular arrangement, although the neurotoxins apparently can take very different conformation when they are released from the M complex.« less

The sound insulations of studio doors. Part 1: Door blanks

NASA Astrophysics Data System (ADS)

Plumb, G. D.; Clark, R.

The sound insulations of a range of different door blanks were measured. The results were compared with the sound insulations of existing BBC door blanks. The new doors were made from medium density fiberboard (MDF) which is more stable than the blockboard used in existing studio doors. Consequently, they should require less maintenance and adjustment and should have a longer lifespan. The doors had higher sound insulations for their weight than existing designs, which might permit savings in the costs of the surrounding building structures. Overall construction costs of the door blanks themselves are likely to be similar to those of existing designs. A companion Report (BBC RD 1994/15) describes sound insulation measurements made on plant-on door seals. The intention of this work was to simplify the construction of the door frame and the fitting of the seals to reduce costs.

An Integrated Geophysical and Tectonic Study of the Structure and Evolution of the Crust in the Snake River Plain Region, Pacific Northwest

NASA Astrophysics Data System (ADS)

Keller, G. R.; Khatiwada, M.

2016-12-01

The Snake River Plain region in the Pacific Northwest of North America has been the target of a number of recent studies that have revealed further complexities in its structure and tectonic evolution. Based on surface morphology and Late Cenozoic volcanic activity, the Snake River Plain consists of an eastern and western arm (ESRP and WSRP) that are similar in many respects but also quite different in other respects. Thus, its origin, evolution, structural complexities, the role of extension and magmatism in its formation, and the tectonic drivers are still subjects of debate. Numerous seismic studies have specifically focused on the structure of the ESRP and Yellowstone area. However, crustal-scale studies of the WSRP are limited. We added new gravity data to the existing coverage in the WSRP region and undertook a regional, integrated analysis approach that included magnetic, seismic reflection and refraction profiling, receiver function results, geological and geospatial data, and interpreted well logs. Our integrated geophysical modeling focused on the structure of the WSRP. We generated two crustal models across it at locations where the most existing geophysical and geological constraints were available. We observed both differences and similarities in the structure of the WSRP and ESRP. Although, the shallow crustal structures are different, a mid-crustal mafic intrusion is a major source of the high gravity anomaly values. Within the context of recent studies in the surrounding region, the intersection of the two arms of the Snake River Plain emerges as a major element of a complex tectonic intersection that includes the High Lava Plains of eastern Oregon, the Northern Nevada Rift, a southwestern extension of the ESRP into northern Nevada, as well as, faulting and volcanism extending northwestward to connect with the Columbia River Basalts region.

Investigation of the cluster formation in lithium niobate crystals by computer modeling method

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

Voskresenskii, V. M.; Starodub, O. R., E-mail: ol-star@mail.ru; Sidorov, N. V.

The processes occurring upon the formation of energetically equilibrium oxygen-octahedral clusters in the ferroelectric phase of a stoichiometric lithium niobate (LiNbO{sub 3}) crystal have been investigated by the computer modeling method within the semiclassical atomistic model. An energetically favorable cluster size (at which a structure similar to that of a congruent crystal is organized) is shown to exist. A stoichiometric cluster cannot exist because of the electroneutrality loss. The most energetically favorable cluster is that with a Li/Nb ratio of about 0.945, a value close to the lithium-to-niobium ratio for a congruent crystal.

Stochastic HKMDHE: A multi-objective contrast enhancement algorithm

NASA Astrophysics Data System (ADS)

Pratiher, Sawon; Mukhopadhyay, Sabyasachi; Maity, Srideep; Pradhan, Asima; Ghosh, Nirmalya; Panigrahi, Prasanta K.

2018-02-01

This contribution proposes a novel extension of the existing `Hyper Kurtosis based Modified Duo-Histogram Equalization' (HKMDHE) algorithm, for multi-objective contrast enhancement of biomedical images. A novel modified objective function has been formulated by joint optimization of the individual histogram equalization objectives. The optimal adequacy of the proposed methodology with respect to image quality metrics such as brightness preserving abilities, peak signal-to-noise ratio (PSNR), Structural Similarity Index (SSIM) and universal image quality metric has been experimentally validated. The performance analysis of the proposed Stochastic HKMDHE with existing histogram equalization methodologies like Global Histogram Equalization (GHE) and Contrast Limited Adaptive Histogram Equalization (CLAHE) has been given for comparative evaluation.

Young and Older Adults' Gender Stereotype in Multitasking

PubMed Central

Strobach, Tilo; Woszidlo, Alesia

2015-01-01

In the present study, we investigated discrepancies between two components of stereotyping by means of the popular notion that women are better at multitasking behaviors: the cognitive structure in individuals (personal belief) and the perceived consensus regarding certain beliefs (perceived belief of groups). With focus on this notion, we examined whether there was empirical evidence for the stereotype's existence and whether and how it was shared among different age groups. Data were collected from 241 young (n = 129) and older (n = 112) German individuals. The reported perceptions of gender effects at multitasking were substantial and thus demonstrated the existence of its stereotype. Importantly, in young and older adults, this stereotype existed in the perception of attributed characteristics by members of a collective (perceived belief of groups). When contrasting this perceived belief of groups and the personal belief, older adults showed a similar level of conformation of the gender stereotype while young adults were able to differentiate between these perspectives. Thus, young adults showed a discrepancy between the stereotype's components cognitive structure in individuals and perceived consensus regarding certain beliefs. PMID:26733913

Young and Older Adults' Gender Stereotype in Multitasking.

PubMed

Strobach, Tilo; Woszidlo, Alesia

2015-01-01

In the present study, we investigated discrepancies between two components of stereotyping by means of the popular notion that women are better at multitasking behaviors: the cognitive structure in individuals (personal belief) and the perceived consensus regarding certain beliefs (perceived belief of groups). With focus on this notion, we examined whether there was empirical evidence for the stereotype's existence and whether and how it was shared among different age groups. Data were collected from 241 young (n = 129) and older (n = 112) German individuals. The reported perceptions of gender effects at multitasking were substantial and thus demonstrated the existence of its stereotype. Importantly, in young and older adults, this stereotype existed in the perception of attributed characteristics by members of a collective (perceived belief of groups). When contrasting this perceived belief of groups and the personal belief, older adults showed a similar level of conformation of the gender stereotype while young adults were able to differentiate between these perspectives. Thus, young adults showed a discrepancy between the stereotype's components cognitive structure in individuals and perceived consensus regarding certain beliefs.

Elastic properties of iron-based superconductor SrFe2(As1-xPx)2

NASA Astrophysics Data System (ADS)

Horikoshi, Keita; Imai, Jo; Nakanishi, Yoshiki; Nakamura, Mitsuteru; Kobayashi, Tatsuya; Adachi, Toru; Miyasaka, Shigeki; Tajima, Setsuko; Yoshizawa, Masahito

2018-05-01

We have measured the transverse elastic constants C44 and C66 of iron-based superconductor SrFe2(As1-xPx)2 (Sr122) single crystals as a function of temperature. Under-doped samples show elastic anomalies towards the structural/magnetic transition temperature. Optimal sample shows an upturn at the superconducting transition temperature in both C44 and C66. These behavior is similar to Ba122, while only C66 shows anomaly for Ba122. The elastic anomalies were analyzed by Jahn-Teller formula, and it was found that the Jahn-Teller energy of C44 is much larger than that of C66. This indicates that monoclinic structural fluctuations exist inherently in Sr122 in addition to the known tetragonal fluctuations. Co-existence of these diverse fluctuations and their cooperation are a key to investigate the mechanism and properties of superconductivity in iron based superconductors.

Correlations between contouring similarity metrics and simulated treatment outcome for prostate radiotherapy

NASA Astrophysics Data System (ADS)

Roach, D.; Jameson, M. G.; Dowling, J. A.; Ebert, M. A.; Greer, P. B.; Kennedy, A. M.; Watt, S.; Holloway, L. C.

2018-02-01

Many similarity metrics exist for inter-observer contouring variation studies, however no correlation between metric choice and prostate cancer radiotherapy dosimetry has been explored. These correlations were investigated in this study. Two separate trials were undertaken, the first a thirty-five patient cohort with three observers, the second a five patient dataset with ten observers. Clinical and planning target volumes (CTV and PTV), rectum, and bladder were independently contoured by all observers in each trial. Structures were contoured on T2-weighted MRI and transferred onto CT following rigid registration for treatment planning in the first trial. Structures were contoured directly on CT in the second trial. STAPLE and majority voting volumes were generated as reference gold standard volumes for each structure for the two trials respectively. VMAT treatment plans (78 Gy to PTV) were simulated for observer and gold standard volumes, and dosimetry assessed using multiple radiobiological metrics. Correlations between contouring similarity metrics and dosimetry were calculated using Spearman’s rank correlation coefficient. No correlations were observed between contouring similarity metrics and dosimetry for CTV within either trial. Volume similarity correlated most strongly with radiobiological metrics for PTV in both trials, including TCPPoisson (ρ  =  0.57, 0.65), TCPLogit (ρ  =  0.39, 0.62), and EUD (ρ  =  0.43, 0.61) for each respective trial. Rectum and bladder metric correlations displayed no consistency for the two trials. PTV volume similarity was found to significantly correlate with rectum normal tissue complication probability (ρ  =  0.33, 0.48). Minimal to no correlations with dosimetry were observed for overlap or boundary contouring metrics. Future inter-observer contouring variation studies for prostate cancer should incorporate volume similarity to provide additional insights into dosimetry during analysis.

Application of nonlinear least-squares regression to ground-water flow modeling, west-central Florida

USGS Publications Warehouse

Yobbi, D.K.

2000-01-01

A nonlinear least-squares regression technique for estimation of ground-water flow model parameters was applied to an existing model of the regional aquifer system underlying west-central Florida. The regression technique minimizes the differences between measured and simulated water levels. Regression statistics, including parameter sensitivities and correlations, were calculated for reported parameter values in the existing model. Optimal parameter values for selected hydrologic variables of interest are estimated by nonlinear regression. Optimal estimates of parameter values are about 140 times greater than and about 0.01 times less than reported values. Independently estimating all parameters by nonlinear regression was impossible, given the existing zonation structure and number of observations, because of parameter insensitivity and correlation. Although the model yields parameter values similar to those estimated by other methods and reproduces the measured water levels reasonably accurately, a simpler parameter structure should be considered. Some possible ways of improving model calibration are to: (1) modify the defined parameter-zonation structure by omitting and/or combining parameters to be estimated; (2) carefully eliminate observation data based on evidence that they are likely to be biased; (3) collect additional water-level data; (4) assign values to insensitive parameters, and (5) estimate the most sensitive parameters first, then, using the optimized values for these parameters, estimate the entire data set.

Time-lapse imaging reveals highly dynamic structural maturation of postnatally born dentate granule cells in organotypic entorhino-hippocampal slice cultures

PubMed Central

Radic, Tijana; Jungenitz, Tassilo; Singer, Mathias; Beining, Marcel; Cuntz, Hermann; Vlachos, Andreas; Deller, Thomas; Schwarzacher, Stephan W.

2017-01-01

Neurogenesis of hippocampal granule cells (GCs) persists throughout mammalian life and is important for learning and memory. How newborn GCs differentiate and mature into an existing circuit during this time period is not yet fully understood. We established a method to visualize postnatally generated GCs in organotypic entorhino-hippocampal slice cultures (OTCs) using retroviral (RV) GFP-labeling and performed time-lapse imaging to study their morphological development in vitro. Using anterograde tracing we could, furthermore, demonstrate that the postnatally generated GCs in OTCs, similar to adult born GCs, grow into an existing entorhino-dentate circuitry. RV-labeled GCs were identified and individual cells were followed for up to four weeks post injection. Postnatally born GCs exhibited highly dynamic structural changes, including dendritic growth spurts but also retraction of dendrites and phases of dendritic stabilization. In contrast, older, presumably prenatally born GCs labeled with an adeno-associated virus (AAV), were far less dynamic. We propose that the high degree of structural flexibility seen in our preparations is necessary for the integration of newborn granule cells into an already existing neuronal circuit of the dentate gyrus in which they have to compete for entorhinal input with cells generated and integrated earlier. PMID:28256620

Financing Opportunities for Renewable Energy Development in Alaska

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

Ardani, K.; Hillman, D.; Busche, S.

2013-04-01

This technical report provides an overview of existing and potential financing structures for renewable energy project development in Alaska with a focus on four primary sources of project funding: government financed or supported (the most commonly used structure in Alaska today), developer equity capital, commercial debt, and third-party tax-equity investment. While privately funded options currently have limited application in Alaska, their implementation is theoretically possible based on successful execution in similar circumstances elsewhere. This report concludes that while tax status is a key consideration in determining appropriate financing structure, there are opportunities for both taxable and tax-exempt entities to participatemore » in renewable energy project development.« less

Structural properties and glass transition in Aln clusters

NASA Astrophysics Data System (ADS)

Sun, D. Y.; Gong, X. G.

1998-02-01

We have studied the structural and dynamical properties of several Aln clusters by the molecular-dynamics method combined with simulated annealing. The well-fitted glue potential is used to describe the interatomic interaction. The obtained atomic structures for n=13, 55, and 147 are in agreement with results from ab initio calculations. Our results have demonstrated that the disordered cluster Al43 can be considered as a glass cluster. The obtained thermal properties of glass cluster Al43 are clearly different from the results for high-symmetry clusters, its melting behavior has properties similar to those of a glass solid. The present studies also show that the surface melting behavior does not exist in the studied Aln clusters.

Common substructure in otoacoustic emission spectra of land vertebrates

NASA Astrophysics Data System (ADS)

Manley, Geoffrey A.; Köppl, Christine; Bergevin, Christopher

2015-12-01

In humans, a similar spectral periodicity is found in all otoacoustic emission types and in threshold fine structure. This may reflect travelling wave phase and reflectance from "structural roughness" in the organ of Corti, or entrainment and suppressive interactions between emissions. To further understand these phenomena, we have examined spontaneous otoacoustic emission (SOAE) spectra in 9 lizard species and the barn owl and find a comparable periodicity. Importantly, the frequency spacing between SOAE peaks was independent of the physical spacing and of the frequency space constants in hearing organs. In 9 lizard species, median spectral gaps lay between 219 and 461 Hz, with no correlation to papillar length (0.3 to 2.1 mm). Similarly in much longer organs: In humans (35 mm), SOAE spectral gaps vary up to 220 Hz at 4 kHz; in the barn owl (11 mm), the median SOAE peak spacing was 395Hz. In the barn owl, a very large space constant between 5 and 10 kHz (5 mm/octave) contrasts with stable SOAE spacing between 1 and 11 kHz. Similar SOAE spectral gaps across all species suggests they represent a basic frequency grating revealing local phase-dependent interactions between active hair cells, a feature not determined by macro-structural anatomy. Emission spectral spacing is independent of cochlear length, of the frequency space constant, of the existence of travelling waves or of a tectorial membrane. Our data suggest that there are greater similarities between frequency selectivity reflected at the level of the hair cells' spontaneous mechanical output (OAEs) than there are at the level of the auditory nerve, where macro-structural anatomy links hair-cell activity differentially to the neural output. Apparently, all hair-cell arrays show a similar frequency substructure not directly replicated in neural tuning.

Fellowships in community pharmacy research: Experiences of five schools and colleges of pharmacy.

PubMed

Snyder, Margie E; Frail, Caitlin K; Gernant, Stephanie A; Bacci, Jennifer L; Coley, Kim C; Colip, Lauren M; Ferreri, Stefanie P; Hagemeier, Nicholas E; McGivney, Melissa Somma; Rodis, Jennifer L; Smith, Megan G; Smith, Randall B

2016-01-01

To describe common facilitators, challenges, and lessons learned in 5 schools and colleges of pharmacy in establishing community pharmacy research fellowships. Five schools and colleges of pharmacy in the United States. Schools and colleges of pharmacy with existing community partnerships identified a need and ability to develop opportunities for pharmacists to engage in advanced research training. Community pharmacy fellowships, each structured as 2 years long and in combination with graduate coursework, have been established at the University of Pittsburgh, Purdue University, East Tennessee State University, University of North Carolina at Chapel Hill, and The Ohio State University. Program directors from each of the 5 community pharmacy research fellowships identified common themes pertaining to program structure, outcomes, and lessons learned to assist others planning similar programs. Common characteristics across the programs include length of training, prerequisites, graduate coursework, mentoring structure, and immersion into a pharmacist patient care practice. Common facilitators have been the existence of strong community pharmacy partnerships, creating a fellowship advisory team, and networking. A common challenge has been recruitment, with many programs experiencing at least one year without filling the fellowship position. All program graduates (n = 4) have been successful in securing pharmacy faculty positions. Five schools and colleges of pharmacy share similar experiences in implementing community pharmacy research fellowships. Early outcomes show promise for this training pathway in growing future pharmacist-scientists focused on community pharmacy practice. Copyright © 2016 American Pharmacists Association®. Published by Elsevier Inc. All rights reserved.

Fellowships in Community Pharmacy Research: Experiences of Five Schools and Colleges of Pharmacy

PubMed Central

Snyder, Margie E.; Frail, Caitlin K.; Gernant, Stephanie A.; Bacci, Jennifer L.; Coley, Kim C.; Colip, Lauren M.; Ferreri, Stefanie P.; Hagemeier, Nicholas E.; McGivney, Melissa Somma; Rodis, Jennifer L.; Smith, Megan G.; Smith, Randall B.

2017-01-01

Objective To describe common facilitators, challenges, and lessons learned of five schools and colleges of pharmacy in establishing community pharmacy research fellowships. Setting Five schools and colleges of pharmacy in the United States. Practice Description Schools and colleges of pharmacy with existing community partnerships identified a need and ability to develop opportunities for pharmacists to engage in advanced research training. Practice Innovation Community pharmacy fellowships, each structured as two years in length and in combination with graduate coursework, have been established at the University of Pittsburgh, Purdue University, East Tennessee State University, University of North Carolina at Chapel Hill and The Ohio State University. Evaluation Program directors from each of the five community pharmacy research fellowships identified common themes pertaining to program structure, outcomes, and lessons learned to assist others planning similar programs. Results Common characteristics across the programs include length of training, pre-requisites, graduate coursework, mentoring structure, and immersion into a pharmacist patient care practice. Common facilitators have been the existence of strong community pharmacy partnerships, creating a fellowship advisory team, and networking. A common challenge has been recruitment, with many programs experiencing at least one year without filling the fellowship position. All program graduates (n=4) have been successful in securing pharmacy faculty positions. Conclusion Five schools and colleges of pharmacy share similar experiences in implementing community pharmacy research fellowships. Early outcomes show promise for this training pathway in growing future pharmacist-scientists focused on community pharmacy practice. PMID:27083852

Magnonic band structure in a Co/Pd stripe domain system investigated by Brillouin light scattering and micromagnetic simulations

NASA Astrophysics Data System (ADS)

Banerjee, Chandrima; Gruszecki, Pawel; Klos, Jaroslaw W.; Hellwig, Olav; Krawczyk, Maciej; Barman, Anjan

2017-07-01

By combining Brillouin light scattering and micromagnetic simulations, we studied the spin-wave (SW) dynamics of a Co/Pd thin film multilayer, which features a stripe domain structure at remanence. The periodic up and down domains are separated by corkscrew type domain walls. The existence of these domains causes a scattering of the otherwise bulk and surface SW modes, which form mode families, similar to a one-dimensional magnonic crystal. The dispersion relation and mode profiles of SWs are measured for the transferred wave vector parallel and perpendicular to the domain axis.

Automatic Keyframe Summarization of User-Generated Video

DTIC Science & Technology

2014-06-01

using the framework presented in this paper. 12 Scenery Technology has been developed that classifies the genre of a video. Here, video genres are...types of videos that shares similarities in content and structure. Many genres of video footage exist. Some examples include news, sports, movies...cartoons, and commercials. Rasheed et al. [42] classify video genres (comedy, action, drama, and horror) with low-level video statistics, such as average

Metric learning with spectral graph convolutions on brain connectivity networks.

PubMed

Ktena, Sofia Ira; Parisot, Sarah; Ferrante, Enzo; Rajchl, Martin; Lee, Matthew; Glocker, Ben; Rueckert, Daniel

2018-04-01

Graph representations are often used to model structured data at an individual or population level and have numerous applications in pattern recognition problems. In the field of neuroscience, where such representations are commonly used to model structural or functional connectivity between a set of brain regions, graphs have proven to be of great importance. This is mainly due to the capability of revealing patterns related to brain development and disease, which were previously unknown. Evaluating similarity between these brain connectivity networks in a manner that accounts for the graph structure and is tailored for a particular application is, however, non-trivial. Most existing methods fail to accommodate the graph structure, discarding information that could be beneficial for further classification or regression analyses based on these similarities. We propose to learn a graph similarity metric using a siamese graph convolutional neural network (s-GCN) in a supervised setting. The proposed framework takes into consideration the graph structure for the evaluation of similarity between a pair of graphs, by employing spectral graph convolutions that allow the generalisation of traditional convolutions to irregular graphs and operates in the graph spectral domain. We apply the proposed model on two datasets: the challenging ABIDE database, which comprises functional MRI data of 403 patients with autism spectrum disorder (ASD) and 468 healthy controls aggregated from multiple acquisition sites, and a set of 2500 subjects from UK Biobank. We demonstrate the performance of the method for the tasks of classification between matching and non-matching graphs, as well as individual subject classification and manifold learning, showing that it leads to significantly improved results compared to traditional methods. Copyright © 2017 Elsevier Inc. All rights reserved.

Visualizing spatial population structure with estimated effective migration surfaces

PubMed Central

Petkova, Desislava; Novembre, John; Stephens, Matthew

2015-01-01

Genetic data often exhibit patterns broadly consistent with “isolation by distance” – a phenomenon where genetic similarity decays with geographic distance. In a heterogeneous habitat this may occur more quickly in some regions than others: for example, barriers to gene flow can accelerate differentiation between neighboring groups. We use the concept of “effective migration” to model the relationship between genetics and geography: in this paradigm, effective migration is low in regions where genetic similarity decays quickly. We present a method to visualize variation in effective migration across the habitat from geographically indexed genetic data. Our approach uses a population genetic model to relate effective migration rates to expected genetic dissimilarities. We illustrate its potential and limitations using simulations and data from elephant, human and A. thaliana populations. The resulting visualizations highlight important spatial features of population structure that are difficult to discern using existing methods for summarizing genetic variation. PMID:26642242

Comparison of 3D quantitative structure-activity relationship methods: Analysis of the in vitro antimalarial activity of 154 artemisinin analogues by hypothetical active-site lattice and comparative molecular field analysis

NASA Astrophysics Data System (ADS)

Woolfrey, John R.; Avery, Mitchell A.; Doweyko, Arthur M.

1998-03-01

Two three-dimensional quantitative structure-activity relationship (3D-QSAR) methods, comparative molecular field analysis (CoMFA) and hypothetical active site lattice (HASL), were compared with respect to the analysis of a training set of 154 artemisinin analogues. Five models were created, including a complete HASL and two trimmed versions, as well as two CoMFA models (leave-one-out standard CoMFA and the guided-region selection protocol). Similar r2 and q2 values were obtained by each method, although some striking differences existed between CoMFA contour maps and the HASL output. Each of the four predictive models exhibited a similar ability to predict the activity of a test set of 23 artemisinin analogues, although some differences were noted as to which compounds were described well by either model.

"Nonspecific" cholinesterase and acetylcholinesterase in rat tissues: molecular forms, structural and catalytic properties, and significance of the two enzyme systems.

PubMed Central

Vigny, M; Gisiger, V; Massoulié, J

1978-01-01

"Nonspecific" cholinesterase (acylcholine acylhydrolase; EC 3.1.1.8) from various rat tissues has been found to exist in several stable molecular forms that appear as exact counterparts of molecular forms of acetylcholinesterase (acetylcholine hydrolase; EC 3.1.1.7). The sedimentation pattern of cholinesterase was similar to that of acetylcholinesterase with a small but significant shift between the sedimentation coefficients of the corresponding forms. Extraction yields in different media also demonstrated a close parallelism between the two enzyme systems. Other properties, such as thermal stability and catalytic characteristics, indicated both differences and similarities. In spite of the structural resemblance implied by their physicochemical properties, cholinesterase did not crossreact with antibodies against acetylcholinesterase. The nature of the relationships revealed by these studies and their bearing on the physiological significance of cholinesterases are discussed. PMID:78492

Local Orthorhombicity in the Magnetic C 4 Phase of the Hole-Doped Iron-Arsenide Superconductor Sr 1 - x Na x Fe 2 As 2

DOE PAGES

Frandsen, Benjamin A.; Taddei, Keith M.; Yi, Ming; ...

2017-10-30

We report on temperature-dependent pair distribution function measurements of Sr 1-xNa xFe 2As 2, an iron-based superconductor system that contains a magnetic phase with reentrant tetragonal symmetry, known as the magnetic C 4 phase. Quantitative refinements indicate that the instantaneous local structure in the C 4 phase comprises fluctuating orthorhombic regions with a length scale of similar to 2 nm, despite the tetragonal symmetry of the average static structure. Additionally, local orthorhombic fluctuations exist on a similar length scale at temperatures well into the paramagnetic tetragonal phase. Furthermore, these results highlight the exceptionally large nematic susceptibility of iron-based superconductors andmore » have significant implications for the magnetic C 4 phase and the neighboring C 2 and superconducting phases.« less

Local Orthorhombicity in the Magnetic C 4 Phase of the Hole-Doped Iron-Arsenide Superconductor Sr 1 - x Na x Fe 2 As 2

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

Frandsen, Benjamin A.; Taddei, Keith M.; Yi, Ming

We report on temperature-dependent pair distribution function measurements of Sr 1-xNa xFe 2As 2, an iron-based superconductor system that contains a magnetic phase with reentrant tetragonal symmetry, known as the magnetic C 4 phase. Quantitative refinements indicate that the instantaneous local structure in the C 4 phase comprises fluctuating orthorhombic regions with a length scale of similar to 2 nm, despite the tetragonal symmetry of the average static structure. Additionally, local orthorhombic fluctuations exist on a similar length scale at temperatures well into the paramagnetic tetragonal phase. Furthermore, these results highlight the exceptionally large nematic susceptibility of iron-based superconductors andmore » have significant implications for the magnetic C 4 phase and the neighboring C 2 and superconducting phases.« less

Binding ligand prediction for proteins using partial matching of local surface patches.

PubMed

Sael, Lee; Kihara, Daisuke

2010-01-01

Functional elucidation of uncharacterized protein structures is an important task in bioinformatics. We report our new approach for structure-based function prediction which captures local surface features of ligand binding pockets. Function of proteins, specifically, binding ligands of proteins, can be predicted by finding similar local surface regions of known proteins. To enable partial comparison of binding sites in proteins, a weighted bipartite matching algorithm is used to match pairs of surface patches. The surface patches are encoded with the 3D Zernike descriptors. Unlike the existing methods which compare global characteristics of the protein fold or the global pocket shape, the local surface patch method can find functional similarity between non-homologous proteins and binding pockets for flexible ligand molecules. The proposed method improves prediction results over global pocket shape-based method which was previously developed by our group.

Binding Ligand Prediction for Proteins Using Partial Matching of Local Surface Patches

PubMed Central

Sael, Lee; Kihara, Daisuke

2010-01-01

Functional elucidation of uncharacterized protein structures is an important task in bioinformatics. We report our new approach for structure-based function prediction which captures local surface features of ligand binding pockets. Function of proteins, specifically, binding ligands of proteins, can be predicted by finding similar local surface regions of known proteins. To enable partial comparison of binding sites in proteins, a weighted bipartite matching algorithm is used to match pairs of surface patches. The surface patches are encoded with the 3D Zernike descriptors. Unlike the existing methods which compare global characteristics of the protein fold or the global pocket shape, the local surface patch method can find functional similarity between non-homologous proteins and binding pockets for flexible ligand molecules. The proposed method improves prediction results over global pocket shape-based method which was previously developed by our group. PMID:21614188

Water in a Soft Confinement: Structure of Water in Amorphous Sorbitol.

PubMed

Shalaev, Evgenyi; Soper, Alan K

2016-07-28

The structure of water in 70 wt % sorbitol-30 wt % water mixture is investigated by wide-angle neutron scattering (WANS) as a function of temperature. WANS data are analyzed using empirical potential structure refinement to obtain the site-site radial distribution functions (RDFs). Orientational structure of water is represented using OW-OW-OW triangles distributions and a tetrahedrality parameter, q, while water-water correlation function is used to estimate size of water clusters. Water structure in the sorbitol matrix is compared with that of water confined in nanopores of MCM41. The results indicate the existence of voids in the sorbitol matrix with the length scale of approximately 5 Å, which are filled by water. At 298 K, positional water structure in these voids is similar to that of water in MCM41, whereas there is a difference in the tetrahedral (orientational) arrangement. Cooling to 213 K strengthens tetrahedrality, with the orientational order of water in sorbitol becoming similar to that of confined water in MCM41 at 210 K, whereas further cooling to 100 K does not introduce any additional changes in the tetrahedrality. The results obtained allow us to propose, for the first time, that such confinement of water in a sorbitol matrix is the main reason for the lack of ice formation in this system.

Query3d: a new method for high-throughput analysis of functional residues in protein structures.

PubMed

Ausiello, Gabriele; Via, Allegra; Helmer-Citterich, Manuela

2005-12-01

The identification of local similarities between two protein structures can provide clues of a common function. Many different methods exist for searching for similar subsets of residues in proteins of known structure. However, the lack of functional and structural information on single residues, together with the low level of integration of this information in comparison methods, is a limitation that prevents these methods from being fully exploited in high-throughput analyses. Here we describe Query3d, a program that is both a structural DBMS (Database Management System) and a local comparison method. The method conserves a copy of all the residues of the Protein Data Bank annotated with a variety of functional and structural information. New annotations can be easily added from a variety of methods and known databases. The algorithm makes it possible to create complex queries based on the residues' function and then to compare only subsets of the selected residues. Functional information is also essential to speed up the comparison and the analysis of the results. With Query3d, users can easily obtain statistics on how many and which residues share certain properties in all proteins of known structure. At the same time, the method also finds their structural neighbours in the whole PDB. Programs and data can be accessed through the PdbFun web interface.

Query3d: a new method for high-throughput analysis of functional residues in protein structures

PubMed Central

Ausiello, Gabriele; Via, Allegra; Helmer-Citterich, Manuela

2005-01-01

Background The identification of local similarities between two protein structures can provide clues of a common function. Many different methods exist for searching for similar subsets of residues in proteins of known structure. However, the lack of functional and structural information on single residues, together with the low level of integration of this information in comparison methods, is a limitation that prevents these methods from being fully exploited in high-throughput analyses. Results Here we describe Query3d, a program that is both a structural DBMS (Database Management System) and a local comparison method. The method conserves a copy of all the residues of the Protein Data Bank annotated with a variety of functional and structural information. New annotations can be easily added from a variety of methods and known databases. The algorithm makes it possible to create complex queries based on the residues' function and then to compare only subsets of the selected residues. Functional information is also essential to speed up the comparison and the analysis of the results. Conclusion With Query3d, users can easily obtain statistics on how many and which residues share certain properties in all proteins of known structure. At the same time, the method also finds their structural neighbours in the whole PDB. Programs and data can be accessed through the PdbFun web interface. PMID:16351754

Evaluating the efficacy of a structure-derived amino acid substitution matrix in detecting protein homologs by BLAST and PSI-BLAST.

PubMed

Goonesekere, Nalin Cw

2009-01-01

The large numbers of protein sequences generated by whole genome sequencing projects require rapid and accurate methods of annotation. The detection of homology through computational sequence analysis is a powerful tool in determining the complex evolutionary and functional relationships that exist between proteins. Homology search algorithms employ amino acid substitution matrices to detect similarity between proteins sequences. The substitution matrices in common use today are constructed using sequences aligned without reference to protein structure. Here we present amino acid substitution matrices constructed from the alignment of a large number of protein domain structures from the structural classification of proteins (SCOP) database. We show that when incorporated into the homology search algorithms BLAST and PSI-blast, the structure-based substitution matrices enhance the efficacy of detecting remote homologs.

Similarity measure and domain adaptation in multiple mixture model clustering: An application to image processing.

PubMed

Leong, Siow Hoo; Ong, Seng Huat

2017-01-01

This paper considers three crucial issues in processing scaled down image, the representation of partial image, similarity measure and domain adaptation. Two Gaussian mixture model based algorithms are proposed to effectively preserve image details and avoids image degradation. Multiple partial images are clustered separately through Gaussian mixture model clustering with a scan and select procedure to enhance the inclusion of small image details. The local image features, represented by maximum likelihood estimates of the mixture components, are classified by using the modified Bayes factor (MBF) as a similarity measure. The detection of novel local features from MBF will suggest domain adaptation, which is changing the number of components of the Gaussian mixture model. The performance of the proposed algorithms are evaluated with simulated data and real images and it is shown to perform much better than existing Gaussian mixture model based algorithms in reproducing images with higher structural similarity index.

Similarity measure and domain adaptation in multiple mixture model clustering: An application to image processing

PubMed Central

Leong, Siow Hoo

2017-01-01

This paper considers three crucial issues in processing scaled down image, the representation of partial image, similarity measure and domain adaptation. Two Gaussian mixture model based algorithms are proposed to effectively preserve image details and avoids image degradation. Multiple partial images are clustered separately through Gaussian mixture model clustering with a scan and select procedure to enhance the inclusion of small image details. The local image features, represented by maximum likelihood estimates of the mixture components, are classified by using the modified Bayes factor (MBF) as a similarity measure. The detection of novel local features from MBF will suggest domain adaptation, which is changing the number of components of the Gaussian mixture model. The performance of the proposed algorithms are evaluated with simulated data and real images and it is shown to perform much better than existing Gaussian mixture model based algorithms in reproducing images with higher structural similarity index. PMID:28686634

Fluid-structure finite-element vibrational analysis

NASA Technical Reports Server (NTRS)

Feng, G. C.; Kiefling, L.

1974-01-01

A fluid finite element has been developed for a quasi-compressible fluid. Both kinetic and potential energy are expressed as functions of nodal displacements. Thus, the formulation is similar to that used for structural elements, with the only differences being that the fluid can possess gravitational potential, and the constitutive equations for fluid contain no shear coefficients. Using this approach, structural and fluid elements can be used interchangeably in existing efficient sparse-matrix structural computer programs such as SPAR. The theoretical development of the element formulations and the relationships of the local and global coordinates are shown. Solutions of fluid slosh, liquid compressibility, and coupled fluid-shell oscillation problems which were completed using a temporary digital computer program are shown. The frequency correlation of the solutions with classical theory is excellent.

Apomorphine effects on frog locomotor behavior.

PubMed

Chu, Joanne; Wilczynski, Walter

2007-05-16

The neuroanatomical pathways of the DA systems have been shown to be largely conserved across many vertebrate taxa. It is less certain whether the structural similarities seen between mammals and amphibians reflect a similar functional homology. DA is well known for its role in facilitating motor behaviors in mammals. We examined whether a similar role for DA exists in amphibians using the Northern Leopard Frog (Rana pipiens). We investigated the effects of the nonspecific DA agonist, apomorphine (APO) on a complex motor task that included two distinct components known to be differentially modulated by DA in mammals: swimming and climbing. We demonstrated that a high single dose of APO (20 mg/kg, body weight) strongly increased the amount of time spent completing the motor task. Furthermore, we showed that although APO did not significantly alter several aspects of swimming behavior, two aspects of climbing behavior were disrupted. Both climbing speed and climbing ability were impaired by APO treatment. These results increase our understanding of DA function in amphibians and add to our understanding of structure-function homologies of dopamine function across vertebrate taxa.

Do plant cell walls have a code?

PubMed

Tavares, Eveline Q P; Buckeridge, Marcos S

2015-12-01

A code is a set of rules that establish correspondence between two worlds, signs (consisting of encrypted information) and meaning (of the decrypted message). A third element, the adaptor, connects both worlds, assigning meaning to a code. We propose that a Glycomic Code exists in plant cell walls where signs are represented by monosaccharides and phenylpropanoids and meaning is cell wall architecture with its highly complex association of polymers. Cell wall biosynthetic mechanisms, structure, architecture and properties are addressed according to Code Biology perspective, focusing on how they oppose to cell wall deconstruction. Cell wall hydrolysis is mainly focused as a mechanism of decryption of the Glycomic Code. Evidence for encoded information in cell wall polymers fine structure is highlighted and the implications of the existence of the Glycomic Code are discussed. Aspects related to fine structure are responsible for polysaccharide packing and polymer-polymer interactions, affecting the final cell wall architecture. The question whether polymers assembly within a wall display similar properties as other biological macromolecules (i.e. proteins, DNA, histones) is addressed, i.e. do they display a code? Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

A shortest-path graph kernel for estimating gene product semantic similarity.

PubMed

Alvarez, Marco A; Qi, Xiaojun; Yan, Changhui

2011-07-29

Existing methods for calculating semantic similarity between gene products using the Gene Ontology (GO) often rely on external resources, which are not part of the ontology. Consequently, changes in these external resources like biased term distribution caused by shifting of hot research topics, will affect the calculation of semantic similarity. One way to avoid this problem is to use semantic methods that are "intrinsic" to the ontology, i.e. independent of external knowledge. We present a shortest-path graph kernel (spgk) method that relies exclusively on the GO and its structure. In spgk, a gene product is represented by an induced subgraph of the GO, which consists of all the GO terms annotating it. Then a shortest-path graph kernel is used to compute the similarity between two graphs. In a comprehensive evaluation using a benchmark dataset, spgk compares favorably with other methods that depend on external resources. Compared with simUI, a method that is also intrinsic to GO, spgk achieves slightly better results on the benchmark dataset. Statistical tests show that the improvement is significant when the resolution and EC similarity correlation coefficient are used to measure the performance, but is insignificant when the Pfam similarity correlation coefficient is used. Spgk uses a graph kernel method in polynomial time to exploit the structure of the GO to calculate semantic similarity between gene products. It provides an alternative to both methods that use external resources and "intrinsic" methods with comparable performance.

Combination of 2D/3D ligand-based similarity search in rapid virtual screening from multimillion compound repositories. Selection and biological evaluation of potential PDE4 and PDE5 inhibitors.

PubMed

Dobi, Krisztina; Hajdú, István; Flachner, Beáta; Fabó, Gabriella; Szaszkó, Mária; Bognár, Melinda; Magyar, Csaba; Simon, István; Szisz, Dániel; Lőrincz, Zsolt; Cseh, Sándor; Dormán, György

2014-05-28

Rapid in silico selection of target focused libraries from commercial repositories is an attractive and cost effective approach. If structures of active compounds are available rapid 2D similarity search can be performed on multimillion compound databases but the generated library requires further focusing by various 2D/3D chemoinformatics tools. We report here a combination of the 2D approach with a ligand-based 3D method (Screen3D) which applies flexible matching to align reference and target compounds in a dynamic manner and thus to assess their structural and conformational similarity. In the first case study we compared the 2D and 3D similarity scores on an existing dataset derived from the biological evaluation of a PDE5 focused library. Based on the obtained similarity metrices a fusion score was proposed. The fusion score was applied to refine the 2D similarity search in a second case study where we aimed at selecting and evaluating a PDE4B focused library. The application of this fused 2D/3D similarity measure led to an increase of the hit rate from 8.5% (1st round, 47% inhibition at 10 µM) to 28.5% (2nd round at 50% inhibition at 10 µM) and the best two hits had 53 nM inhibitory activities.

Structural Health Monitoring in Composite Structures by Fiber-Optic Sensors.

PubMed

Güemes, Alfredo; Fernández-López, Antonio; F Díaz-Maroto, Patricia; Lozano, Angel; Sierra-Perez, Julian

2018-04-04

Fiber-optic sensors cannot measure damage; to get information about damage from strain measurements, additional strategies are needed, and several alternatives are available in the existing literature. This paper discusses two independent procedures. The first is based on detecting new strains appearing around a damage spot. The structure does not need to be under loads, the technique is very robust, and damage detectability is high, but it requires sensors to be located very close to the damage, so it is a local technique. The second approach offers wider coverage of the structure; it is based on identifying the changes caused by damage on the strain field in the whole structure for similar external loads. Damage location does not need to be known a priori, and detectability is dependent upon the sensor's network density, the damage size, and the external loads. Examples of application to real structures are given.

Structural Health Monitoring in Composite Structures by Fiber-Optic Sensors †

PubMed Central

Güemes, Alfredo; Díaz-Maroto, Patricia F.; Lozano, Angel; Sierra-Perez, Julian

2018-01-01

Fiber-optic sensors cannot measure damage; to get information about damage from strain measurements, additional strategies are needed, and several alternatives are available in the existing literature. This paper discusses two independent procedures. The first is based on detecting new strains appearing around a damage spot. The structure does not need to be under loads, the technique is very robust, and damage detectability is high, but it requires sensors to be located very close to the damage, so it is a local technique. The second approach offers wider coverage of the structure; it is based on identifying the changes caused by damage on the strain field in the whole structure for similar external loads. Damage location does not need to be known a priori, and detectability is dependent upon the sensor’s network density, the damage size, and the external loads. Examples of application to real structures are given. PMID:29617345

Structure-Based Mutagenesis of Sulfolobus Turreted Icosahedral Virus B204 Reveals Essential Residues in the Virion-Associated DNA-Packaging ATPase.

PubMed

Dellas, Nikki; Snyder, Jamie C; Dills, Michael; Nicolay, Sheena J; Kerchner, Keshia M; Brumfield, Susan K; Lawrence, C Martin; Young, Mark J

2015-12-23

Sulfolobus turreted icosahedral virus (STIV), an archaeal virus that infects the hyperthermoacidophile Sulfolobus solfataricus, is one of the most well-studied viruses of the domain Archaea. STIV shares structural, morphological, and sequence similarities with viruses from other domains of life, all of which are thought to belong to the same viral lineage. Several of these common features include a conserved coat protein fold, an internal lipid membrane, and a DNA-packaging ATPase. B204 is the ATPase encoded by STIV and is thought to drive packaging of viral DNA during the replication process. Here, we report the crystal structure of B204 along with the biochemical analysis of B204 mutants chosen based on structural information and sequence conservation patterns observed among members of the same viral lineage and the larger FtsK/HerA superfamily to which B204 belongs. Both in vitro ATPase activity assays and transfection assays with mutant forms of B204 confirmed the essentiality of conserved and nonconserved positions. We also have identified two distinct particle morphologies during an STIV infection that differ in the presence or absence of the B204 protein. The biochemical and structural data presented here are not only informative for the STIV replication process but also can be useful in deciphering DNA-packaging mechanisms for other viruses belonging to this lineage. STIV is a virus that infects a host from the domain Archaea that replicates in high-temperature, acidic environments. While STIV has many unique features, there exist several striking similarities between this virus and others that replicate in different environments and infect a broad range of hosts from Bacteria and Eukarya. Aside from structural features shared by viruses from this lineage, there exists a significant level of sequence similarity between the ATPase genes carried by these different viruses; this gene encodes an enzyme thought to provide energy that drives DNA packaging into the virion during infection. The experiments described here highlight the elements of this enzyme that are essential for proper function and also provide supporting evidence that B204 is present in the mature STIV virion. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Robust inference of population structure for ancestry prediction and correction of stratification in the presence of relatedness.

PubMed

Conomos, Matthew P; Miller, Michael B; Thornton, Timothy A

2015-05-01

Population structure inference with genetic data has been motivated by a variety of applications in population genetics and genetic association studies. Several approaches have been proposed for the identification of genetic ancestry differences in samples where study participants are assumed to be unrelated, including principal components analysis (PCA), multidimensional scaling (MDS), and model-based methods for proportional ancestry estimation. Many genetic studies, however, include individuals with some degree of relatedness, and existing methods for inferring genetic ancestry fail in related samples. We present a method, PC-AiR, for robust population structure inference in the presence of known or cryptic relatedness. PC-AiR utilizes genome-screen data and an efficient algorithm to identify a diverse subset of unrelated individuals that is representative of all ancestries in the sample. The PC-AiR method directly performs PCA on the identified ancestry representative subset and then predicts components of variation for all remaining individuals based on genetic similarities. In simulation studies and in applications to real data from Phase III of the HapMap Project, we demonstrate that PC-AiR provides a substantial improvement over existing approaches for population structure inference in related samples. We also demonstrate significant efficiency gains, where a single axis of variation from PC-AiR provides better prediction of ancestry in a variety of structure settings than using 10 (or more) components of variation from widely used PCA and MDS approaches. Finally, we illustrate that PC-AiR can provide improved population stratification correction over existing methods in genetic association studies with population structure and relatedness. © 2015 WILEY PERIODICALS, INC.

Structure-wise discrimination of cytosine, thymine, and uracil by proteins in terms of their nonbonded interactions.

PubMed

Usha, S; Selvaraj, S

2014-01-01

The molecular recognition and discrimination of very similar ligand moieties by proteins are important subjects in protein-ligand interaction studies. Specificity in the recognition of molecules is determined by the arrangement of protein and ligand atoms in space. The three pyrimidine bases, viz. cytosine, thymine, and uracil, are structurally similar, but the proteins that bind to them are able to discriminate them and form interactions. Since nonbonded interactions are responsible for molecular recognition processes in biological systems, our work attempts to understand some of the underlying principles of such recognition of pyrimidine molecular structures by proteins. The preferences of the amino acid residues to contact the pyrimidine bases in terms of nonbonded interactions; amino acid residue-ligand atom preferences; main chain and side chain atom contributions of amino acid residues; and solvent-accessible surface area of ligand atoms when forming complexes are analyzed. Our analysis shows that the amino acid residues, tyrosine and phenyl alanine, are highly involved in the pyrimidine interactions. Arginine prefers contacts with the cytosine base. The similarities and differences that exist between the interactions of the amino acid residues with each of the three pyrimidine base atoms in our analysis provide insights that can be exploited in designing specific inhibitors competitive to the ligands.

40 CFR 165.87 - Design and capacity requirements for existing structures.

Code of Federal Regulations, 2013 CFR

2013-07-01

... existing containment structure: (1) The containment structure must be constructed of steel, reinforced... existing structures. 165.87 Section 165.87 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Structures § 165.87 Design and capacity requirements for existing structures. (a) For all existing...

40 CFR 165.87 - Design and capacity requirements for existing structures.

Code of Federal Regulations, 2011 CFR

2011-07-01

... existing containment structure: (1) The containment structure must be constructed of steel, reinforced... existing structures. 165.87 Section 165.87 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Structures § 165.87 Design and capacity requirements for existing structures. (a) For all existing...

40 CFR 165.87 - Design and capacity requirements for existing structures.

Code of Federal Regulations, 2012 CFR

2012-07-01

... existing containment structure: (1) The containment structure must be constructed of steel, reinforced... existing structures. 165.87 Section 165.87 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Structures § 165.87 Design and capacity requirements for existing structures. (a) For all existing...

40 CFR 165.87 - Design and capacity requirements for existing structures.

Code of Federal Regulations, 2014 CFR

2014-07-01

... existing containment structure: (1) The containment structure must be constructed of steel, reinforced... existing structures. 165.87 Section 165.87 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Structures § 165.87 Design and capacity requirements for existing structures. (a) For all existing...

Feasibility of Artificial Attention at Beyond-Human-Scales

DTIC Science & Technology

2012-04-01

2012-5091 3.0 RELATED WORK Studies of human attention have a long history . Early efforts that continue today are empirical investigations of the...Cleared 21 Sep 12, 88ABW-2012-5091 provide observability of the Artificial Attention agent view direction sampling history . 4. Center and surround...at this point that a new data structure called a sampling history is necessary. A sampling history exists per process and is similar to the sampling

Guided Socialization: Using U.S. Influence to Establish an Inter Elite Culture of Cooperation in East Asia

DTIC Science & Technology

2014-04-01

the use of bilateral agreements and alliances to isolate and power balance in East Asia constitutes a schizophrenic presentation of strategy...military posture, despite prohibitions in the Japanese constitution .17 Importantly, this process is not limited to Japan. Nationalist and anti- Great...though some motivation exists to create an effective East Asian economic order, similar in structure to NAFTA , powerful East Asian actors

The Mitosis and Neurodevelopment Proteins NDE1 and NDEL1 Form Dimers, Tetramers, and Polymers with a Folded Back Structure in Solution*

PubMed Central

Soares, Dinesh C.; Bradshaw, Nicholas J.; Zou, Juan; Kennaway, Christopher K.; Hamilton, Russell S.; Chen, Zhuo A.; Wear, Martin A.; Blackburn, Elizabeth A.; Bramham, Janice; Böttcher, Bettina; Millar, J. Kirsty; Barlow, Paul N.; Walkinshaw, Malcolm D.; Rappsilber, Juri; Porteous, David J.

2012-01-01

Paralogs NDE1 (nuclear distribution element 1) and NDEL1 (NDE-like 1) are essential for mitosis and neurodevelopment. Both proteins are predicted to have similar structures, based upon high sequence similarity, and they co-complex in mammalian cells. X-ray diffraction studies and homology modeling suggest that their N-terminal regions (residues 8–167) adopt continuous, extended α-helical coiled-coil structures, but no experimentally derived information on the structure of their C-terminal regions or the architecture of the full-length proteins is available. In the case of NDE1, no biophysical data exists. Here we characterize the structural architecture of both full-length proteins utilizing negative stain electron microscopy along with our established paradigm of chemical cross-linking followed by tryptic digestion, mass spectrometry, and database searching, which we enhance using isotope labeling for mixed NDE1-NDEL1. We determined that full-length NDE1 forms needle-like dimers and tetramers in solution, similar to crystal structures of NDEL1, as well as chain-like end-to-end polymers. The C-terminal domain of each protein, required for interaction with key protein partners dynein and DISC1 (disrupted-in-schizophrenia 1), includes a predicted disordered region that allows a bent back structure. This facilitates interaction of the C-terminal region with the N-terminal coiled-coil domain and is in agreement with previous results showing N- and C-terminal regions of NDEL1 and NDE1 cooperating in dynein interaction. It sheds light on recently identified mutations in the NDE1 gene that cause truncation of the encoded protein. Additionally, analysis of mixed NDE1-NDEL1 complexes demonstrates that NDE1 and NDEL1 can interact directly. PMID:22843697

Mn induced 1 × 2 reconstruction in the τ-MnAl(0 0 1) surface

NASA Astrophysics Data System (ADS)

Guerrero-Sánchez, J.; Takeuchi, Noboru

2018-05-01

We report on first principles total energy calculations to describe the structural, electronic and magnetic properties of MnAl(0 0 1) surfaces. We have concentrated in structural models having 1 × 1 and 1 × 2 periodicities, since recent experiments of the similar MnGa(0 0 1) surface have found 1 × 1 and 1 × 2 reconstructions. Our calculations show the existence of two stable structures for different ranges of chemical potential. A 1 × 1 surface is stable for Al-rich conditions, whereas a Mn-induced 1 × 2 reconstruction appears after increasing the Mn chemical potential up to Mn-rich conditions. It is important to notice that experimentally, Mn rich conditions are important for improved magnetic properties. The Mn layers in both structures have ferromagnetic arrangements, but they are aligned antiferromagnetically with the almost no magnetic Al atoms. Moreover, the on top Mn atoms, which produce the 1 × 2 reconstruction, align antiferromagnetically with the second layer Mn atoms. These findings are similar to those obtained experimentally in MnGa thin films grown by molecular beam epitaxy. Therefore, this method could also be used to grow the proposed MnAl films.

Find structural aspects of anthozoan desmocyte development (phylum Cnidaria).

PubMed

Tidball, J G

1982-01-01

The fine structural changes associated with the differentiation of skeletogenic cells into cells specialized in binding soft tissues onto skeletal structures are described in the gorgonian coral, Leptogorgia virgulata (Lam.). These binding cells are called desmocytes. The sequence of events in desmocyte development includes: growth of the plasma membrane, invagination of the mesoglea-end of the cell, expansion of the axis-end of the cell, loss of organelles involved in skeletogenesis, proliferation of double vesicles and transformation of double vesicles into cytoskeletal rods. Double vesicles appear either cup-shaped or as a vesicle within a vesicle in sectioned material. These observations of desmocyte development are compared to previous light microscopical observations desmocyte development in diverse forms of anthozoans. Similarities in desmocyte development throughout the class include invagination of the differentiating cell, formation of a pectinate mesogleal margin and formation of an array of cytoskeletal rods at the axis-end of the cell. Comparison with available information on the development and fine structure of desmocytes in the cnidarian classes Scyphozoa and Hydrozoa shows these similarities do not extend across class boundaries and, therefore, common ancestry between the three classes of cnidarian desmocytes seems remote if, indeed, such an ancestral cell existed at all.

Mars Life? - Microscopic Tubular Structures

NASA Technical Reports Server (NTRS)

1996-01-01

This electron microscope image shows extremely tiny tubular structures that are possible microscopic fossils of bacteria-like organisms that may have lived on Mars more than 3.6 billion years ago. A two-year investigation by a NASA research team found organic molecules, mineral features characteristic of biological activity and possible microscopic fossils such as these inside of an ancient Martian rock that fell to Earth as a meteorite. The largest possible fossils are less than 1/100th the diameter of a human hair in size while most are ten times smaller. The fossil-like structures were found in carbonate minerals formed along pre-existing fractures in the meteorite in a fashion similar to the way fossils occur in limestone on Earth, although on a microscopic scale.

A folded viral noncoding RNA blocks host cell exoribonucleases through a conformationally dynamic RNA structure.

PubMed

Steckelberg, Anna-Lena; Akiyama, Benjamin M; Costantino, David A; Sit, Tim L; Nix, Jay C; Kieft, Jeffrey S

2018-06-19

Folded RNA elements that block processive 5' → 3' cellular exoribonucleases (xrRNAs) to produce biologically active viral noncoding RNAs have been discovered in flaviviruses, potentially revealing a new mode of RNA maturation. However, whether this RNA structure-dependent mechanism exists elsewhere and, if so, whether a singular RNA fold is required, have been unclear. Here we demonstrate the existence of authentic RNA structure-dependent xrRNAs in dianthoviruses, plant-infecting viruses unrelated to animal-infecting flaviviruses. These xrRNAs have no sequence similarity to known xrRNAs; thus, we used a combination of biochemistry and virology to characterize their sequence requirements and mechanism of stopping exoribonucleases. By solving the structure of a dianthovirus xrRNA by X-ray crystallography, we reveal a complex fold that is very different from that of the flavivirus xrRNAs. However, both versions of xrRNAs contain a unique topological feature, a pseudoknot that creates a protective ring around the 5' end of the RNA structure; this may be a defining structural feature of xrRNAs. Single-molecule FRET experiments reveal that the dianthovirus xrRNAs undergo conformational changes and can use "codegradational remodeling," exploiting the exoribonucleases' degradation-linked helicase activity to help form their resistant structure; such a mechanism has not previously been reported. Convergent evolution has created RNA structure-dependent exoribonuclease resistance in different contexts, which establishes it as a general RNA maturation mechanism and defines xrRNAs as an authentic functional class of RNAs.

Assessment of semantic similarity between proteins using information content and topological properties of the Gene Ontology graph.

PubMed

Dutta, Pritha; Basu, Subhadip; Kundu, Mahantapas

2017-03-31

The semantic similarity between two interacting proteins can be estimated by combining the similarity scores of the GO terms associated with the proteins. Greater number of similar GO annotations between two proteins indicates greater interaction affinity. Existing semantic similarity measures make use of the GO graph structure, the information content of GO terms, or a combination of both. In this paper, we present a hybrid approach which utilizes both the topological features of the GO graph and information contents of the GO terms. More specifically, we 1) consider a fuzzy clustering of the GO graph based on the level of association of the GO terms, 2) estimate the GO term memberships to each cluster center based on the respective shortest path lengths, and 3) assign weightage to GO term pairs on the basis of their dissimilarity with respect to the cluster centers. We test the performance of our semantic similarity measure against seven other previously published similarity measures using benchmark protein-protein interaction datasets of Homo sapiens and Saccharomyces cerevisiae based on sequence similarity, Pfam similarity, area under ROC curve and F1 measure.

Urban Public Health: Is There a Pyramid?

PubMed Central

Su, Meirong; Chen, Bin; Yang, Zhifeng; Cai, Yanpeng; Wang, Jiao

2013-01-01

Early ecologists identified a pyramidal trophic structure in terms of number, biomass and energy transfer. In 1943, the psychologist Maslow put forward a pyramid model to describe layers of human needs. It is indicated that the pyramid principle is universally applicable in natural, humanistic and social disciplines. Here, we report that a pyramid structure also exists in urban public health (UPH). Based on 18 indicators, the UPH states of four cities (Beijing, Tokyo, New York, and London) are compared from the point of view of five aspects, namely physical health, living conditions, social security, environmental quality, and education and culture. A pyramid structure was found in each city when focusing on 2000–2009 data. The pyramid of Beijing is relatively similar to that of Tokyo, and the pyramids of New York and London are similar to each other. A general development trend in UPH is proposed and represented by different pyramid modes. As a basic conjecture, the UPH pyramid model can be verified and developed with data of more cities over a longer period, and be used to promote healthy urban development. PMID:23358233

Urban public health: is there a pyramid?

PubMed

Su, Meirong; Chen, Bin; Yang, Zhifeng; Cai, Yanpeng; Wang, Jiao

2013-01-28

Early ecologists identified a pyramidal trophic structure in terms of number, biomass and energy transfer. In 1943, the psychologist Maslow put forward a pyramid model to describe layers of human needs. It is indicated that the pyramid principle is universally applicable in natural, humanistic and social disciplines. Here, we report that a pyramid structure also exists in urban public health (UPH). Based on 18 indicators, the UPH states of four cities (Beijing, Tokyo, New York, and London) are compared from the point of view of five aspects, namely physical health, living conditions, social security, environmental quality, and education and culture. A pyramid structure was found in each city when focusing on 2000-2009 data. The pyramid of Beijing is relatively similar to that of Tokyo, and the pyramids of New York and London are similar to each other. A general development trend in UPH is proposed and represented by different pyramid modes. As a basic conjecture, the UPH pyramid model can be verified and developed with data of more cities over a longer period, and be used to promote healthy urban development.

Temporal Organization of Sound Information in Auditory Memory.

PubMed

Song, Kun; Luo, Huan

2017-01-01

Memory is a constructive and organizational process. Instead of being stored with all the fine details, external information is reorganized and structured at certain spatiotemporal scales. It is well acknowledged that time plays a central role in audition by segmenting sound inputs into temporal chunks of appropriate length. However, it remains largely unknown whether critical temporal structures exist to mediate sound representation in auditory memory. To address the issue, here we designed an auditory memory transferring study, by combining a previously developed unsupervised white noise memory paradigm with a reversed sound manipulation method. Specifically, we systematically measured the memory transferring from a random white noise sound to its locally temporal reversed version on various temporal scales in seven experiments. We demonstrate a U-shape memory-transferring pattern with the minimum value around temporal scale of 200 ms. Furthermore, neither auditory perceptual similarity nor physical similarity as a function of the manipulating temporal scale can account for the memory-transferring results. Our results suggest that sounds are not stored with all the fine spectrotemporal details but are organized and structured at discrete temporal chunks in long-term auditory memory representation.

Salient Object Detection via Structured Matrix Decomposition.

PubMed

Peng, Houwen; Li, Bing; Ling, Haibin; Hu, Weiming; Xiong, Weihua; Maybank, Stephen J

2016-05-04

Low-rank recovery models have shown potential for salient object detection, where a matrix is decomposed into a low-rank matrix representing image background and a sparse matrix identifying salient objects. Two deficiencies, however, still exist. First, previous work typically assumes the elements in the sparse matrix are mutually independent, ignoring the spatial and pattern relations of image regions. Second, when the low-rank and sparse matrices are relatively coherent, e.g., when there are similarities between the salient objects and background or when the background is complicated, it is difficult for previous models to disentangle them. To address these problems, we propose a novel structured matrix decomposition model with two structural regularizations: (1) a tree-structured sparsity-inducing regularization that captures the image structure and enforces patches from the same object to have similar saliency values, and (2) a Laplacian regularization that enlarges the gaps between salient objects and the background in feature space. Furthermore, high-level priors are integrated to guide the matrix decomposition and boost the detection. We evaluate our model for salient object detection on five challenging datasets including single object, multiple objects and complex scene images, and show competitive results as compared with 24 state-of-the-art methods in terms of seven performance metrics.

Structure of the exotic He 9 nucleus from the no-core shell model with continuum

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

Vorabbi, Matteo; Calci, Angelo; Navratil, Petr

2018-03-13

Here, the exotic 9He nucleus, which presents one of the most extreme neutron-to-proton ratios, belongs to the N = 7 isotonic chain famous for the phenomenon of ground-state parity inversion with decreasing number of protons. Consequently, it would be expected to have an unnatural (positive) parity ground state similar to 11Be and 10Li. Despite many experimental and theoretical investigations, its structure remains uncertain. Apart from the fact that it is unbound, other properties including the spin and parity of its ground state, and the very existence of additional low-lying resonances are still a matter of debate

Factor structure of the Brief Negative Symptom Scale.

PubMed

Strauss, Gregory P; Hong, L Elliot; Gold, James M; Buchanan, Robert W; McMahon, Robert P; Keller, William R; Fischer, Bernard A; Catalano, Lauren T; Culbreth, Adam J; Carpenter, William T; Kirkpatrick, Brian

2012-12-01

The current study examined the factor structure of the Brief Negative Symptom Scale (BNSS), a next-generation negative symptom rating instrument developed in response to the NIMH-sponsored Consensus Development Conference on Negative Symptoms. Participants included 146 individuals with a DSM-IV diagnosis of schizophrenia or schizoaffective disorder. Principal axis factoring indicated two distinct factors explaining 68.7% of the variance. Similar to previous findings, the factors reflected motivation and pleasure and emotional expressivity. These findings provide further support for the construct validity of the BNSS, and for the existence of these two negative symptom factors. Copyright © 2012 Elsevier B.V. All rights reserved.

Post-traumatic stress symptoms and structure among orphan and vulnerable children and adolescents in Zambia.

PubMed

Familiar, Itziar; Murray, Laura; Gross, Alden; Skavenski, Stephanie; Jere, Elizabeth; Bass, Judith

2014-11-01

Scant information exists on PTSD symptoms and structure in youth from developing countries. We describe the symptom profile and exposure to trauma experiences among 343 orphan and vulnerable children and adolescents from Zambia. We distinguished profiles of post-traumatic stress symptoms using latent class analysis. Average number of trauma-related symptoms (21.6; range 0-38) was similar across sex and age. Latent class model suggested 3 classes varying by level of severity: low (31% of the sample), medium (45% of the sample), and high (24% of the sample) symptomatology. Results suggest that PTSD is a continuously distributed latent trait.

Physics of smectic membranes

NASA Astrophysics Data System (ADS)

Pieranski, P.; Beliard, L.; Tournellec, J.-Ph.; Leoncini, X.; Furtlehner, C.; Dumoulin, H.; Riou, E.; Jouvin, B.; Fénerol, J.-P.; Palaric, Ph.; Heuving, J.; Cartier, B.; Kraus, I.

1993-03-01

Due to their layered structure, smectic liquid crystals can form membranes, similar to soap bubbles, that can be spanned on frames. Such smectic membranes have been used extensively as samples in many structural X-ray studies of smectic liquid crystals. In this context they have been considered as very convenient and highly perfect samples but little attention has been paid to the reasons for their existence and to the process of their formation. Our aim here is to address a first list of questions, which are the most urgent to answer. We will also describe experiments and models that have been conceived especially in order to understand the physics of these fascinating systems.

Structure and origin of Australian ring and dome features with reference to the search for asteroid impact events

NASA Astrophysics Data System (ADS)

Glikson, Andrew

2018-01-01

Ring, dome and crater features on the Australian continent and shelf include (A) 38 structures of confirmed or probable asteroid and meteorite impact origin and (B) numerous buried and exposed ring, dome and crater features of undefined origin. A large number of the latter include structural and geophysical elements consistent with impact structures, pending test by field investigations and/or drilling. This paper documents and briefly describes 43 ring and dome features with the aim of appraising their similarities and differences from those of impact structures. Discrimination between impact structures and igneous plugs, volcanic caldera and salt domes require field work and/or drilling. Where crater-like morphological patterns intersect pre-existing linear structural features and contain central morphological highs and unique thrust and fault patterns an impact connection needs to tested in the field. Hints of potential buried impact structures may be furnished by single or multi-ring TMI patterns, circular TMI quiet zones, corresponding gravity patterns, low velocity and non-reflective seismic zones.

FINE STRUCTURES AND OVERLYING LOOPS OF CONFINED SOLAR FLARES

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

Yang, Shuhong; Zhang, Jun; Xiang, Yongyuan, E-mail: shuhongyang@nao.cas.cn

2014-10-01

Using the Hα observations from the New Vacuum Solar Telescope at the Fuxian Solar Observatory, we focus on the fine structures of three confined flares and the issue why all the three flares are confined instead of eruptive. All the three confined flares take place successively at the same location and have similar morphologies, so can be termed homologous confined flares. In the simultaneous images obtained by the Solar Dynamics Observatory, many large-scale coronal loops above the confined flares are clearly observed in multi-wavelengths. At the pre-flare stage, two dipoles emerge near the negative sunspot, and the dipolar patches aremore » connected by small loops appearing as arch-shaped Hα fibrils. There exists a reconnection between the small loops, and thus the Hα fibrils change their configuration. The reconnection also occurs between a set of emerging Hα fibrils and a set of pre-existing large loops, which are rooted in the negative sunspot, a nearby positive patch, and some remote positive faculae, forming a typical three-legged structure. During the flare processes, the overlying loops, some of which are tracked by activated dark materials, do not break out. These direct observations may illustrate the physical mechanism of confined flares, i.e., magnetic reconnection between the emerging loops and the pre-existing loops triggers flares and the overlying loops prevent the flares from being eruptive.« less

Cross-over between discrete and continuous protein structure space: insights into automatic classification and networks of protein structures.

PubMed

Pascual-García, Alberto; Abia, David; Ortiz, Angel R; Bastolla, Ugo

2009-03-01

Structural classifications of proteins assume the existence of the fold, which is an intrinsic equivalence class of protein domains. Here, we test in which conditions such an equivalence class is compatible with objective similarity measures. We base our analysis on the transitive property of the equivalence relationship, requiring that similarity of A with B and B with C implies that A and C are also similar. Divergent gene evolution leads us to expect that the transitive property should approximately hold. However, if protein domains are a combination of recurrent short polypeptide fragments, as proposed by several authors, then similarity of partial fragments may violate the transitive property, favouring the continuous view of the protein structure space. We propose a measure to quantify the violations of the transitive property when a clustering algorithm joins elements into clusters, and we find out that such violations present a well defined and detectable cross-over point, from an approximately transitive regime at high structure similarity to a regime with large transitivity violations and large differences in length at low similarity. We argue that protein structure space is discrete and hierarchic classification is justified up to this cross-over point, whereas at lower similarities the structure space is continuous and it should be represented as a network. We have tested the qualitative behaviour of this measure, varying all the choices involved in the automatic classification procedure, i.e., domain decomposition, alignment algorithm, similarity score, and clustering algorithm, and we have found out that this behaviour is quite robust. The final classification depends on the chosen algorithms. We used the values of the clustering coefficient and the transitivity violations to select the optimal choices among those that we tested. Interestingly, this criterion also favours the agreement between automatic and expert classifications. As a domain set, we have selected a consensus set of 2,890 domains decomposed very similarly in SCOP and CATH. As an alignment algorithm, we used a global version of MAMMOTH developed in our group, which is both rapid and accurate. As a similarity measure, we used the size-normalized contact overlap, and as a clustering algorithm, we used average linkage. The resulting automatic classification at the cross-over point was more consistent than expert ones with respect to the structure similarity measure, with 86% of the clusters corresponding to subsets of either SCOP or CATH superfamilies and fewer than 5% containing domains in distinct folds according to both SCOP and CATH. Almost 15% of SCOP superfamilies and 10% of CATH superfamilies were split, consistent with the notion of fold change in protein evolution. These results were qualitatively robust for all choices that we tested, although we did not try to use alignment algorithms developed by other groups. Folds defined in SCOP and CATH would be completely joined in the regime of large transitivity violations where clustering is more arbitrary. Consistently, the agreement between SCOP and CATH at fold level was lower than their agreement with the automatic classification obtained using as a clustering algorithm, respectively, average linkage (for SCOP) or single linkage (for CATH). The networks representing significant evolutionary and structural relationships between clusters beyond the cross-over point may allow us to perform evolutionary, structural, or functional analyses beyond the limits of classification schemes. These networks and the underlying clusters are available at http://ub.cbm.uam.es/research/ProtNet.php.

The US business cycle: power law scaling for interacting units with complex internal structure

NASA Astrophysics Data System (ADS)

Ormerod, Paul

2002-11-01

In the social sciences, there is increasing evidence of the existence of power law distributions. The distribution of recessions in capitalist economies has recently been shown to follow such a distribution. The preferred explanation for this is self-organised criticality. Gene Stanley and colleagues propose an alternative, namely that power law scaling can arise from the interplay between random multiplicative growth and the complex structure of the units composing the system. This paper offers a parsimonious model of the US business cycle based on similar principles. The business cycle, along with long-term growth, is one of the two features which distinguishes capitalism from all previously existing societies. Yet, economics lacks a satisfactory theory of the cycle. The source of cycles is posited in economic theory to be a series of random shocks which are external to the system. In this model, the cycle is an internal feature of the system, arising from the level of industrial concentration of the agents and the interactions between them. The model-in contrast to existing economic theories of the cycle-accounts for the key features of output growth in the US business cycle in the 20th century.

The universal existence of myodural bridge in mammals: an indication of a necessary function.

PubMed

Zheng, Nan; Yuan, Xiao-Ying; Chi, Yan-Yan; Liu, Pei; Wang, Bing; Sui, Jia-Ying; Han, Seung-Ho; Yu, Sheng-Bo; Sui, Hong-Jin

2017-08-15

The "myodural bridge" was described in literatures as a dense fibrous tissue connecting the sub-occipital musculature with the spinal dura mater in human studies. Now the concept of "myodural bridge" was perceived as an exact anatomical structure presumably essential for critical physiological functions in human body, and might exist in other mammals as well. To determine the existence of the "myodural bridge" in other mammals and to lay a foundation for the functional study, we examined representatives in five different mammalian orders. Based on the anatomical dissections, P45 plastinated sections and histological sections, we found that a dense fibrous tissue connected the rectus capitisdorsalis minor and the spinal dura mater through the dorsal atlanto-occipital interspace with or without the medium of the posterior atlanto-occipital membrane. These observed connective tissues were very similar to the "myodural bridge" previously described in humans. We proposed that the "myodural bridge", as an evolutionally conserved structure, presents in many other mammals. Moreover, we believed that the "myodural bridge" might be a homologous organ in mammals. Thus, this study could provide an insight for our understanding the physiological significance of the "myodural bridge", especially in human.

Making big sense from big data in toxicology by read-across.

PubMed

Hartung, Thomas

2016-01-01

Modern information technologies have made big data available in safety sciences, i.e., extremely large data sets that may be analyzed only computationally to reveal patterns, trends and associations. This happens by (1) compilation of large sets of existing data, e.g., as a result of the European REACH regulation, (2) the use of omics technologies and (3) systematic robotized testing in a high-throughput manner. All three approaches and some other high-content technologies leave us with big data--the challenge is now to make big sense of these data. Read-across, i.e., the local similarity-based intrapolation of properties, is gaining momentum with increasing data availability and consensus on how to process and report it. It is predominantly applied to in vivo test data as a gap-filling approach, but can similarly complement other incomplete datasets. Big data are first of all repositories for finding similar substances and ensure that the available data is fully exploited. High-content and high-throughput approaches similarly require focusing on clusters, in this case formed by underlying mechanisms such as pathways of toxicity. The closely connected properties, i.e., structural and biological similarity, create the confidence needed for predictions of toxic properties. Here, a new web-based tool under development called REACH-across, which aims to support and automate structure-based read-across, is presented among others.

A network medicine approach to quantify distance between hereditary disease modules on the interactome

NASA Astrophysics Data System (ADS)

Caniza, Horacio; Romero, Alfonso E.; Paccanaro, Alberto

2015-12-01

We introduce a MeSH-based method that accurately quantifies similarity between heritable diseases at molecular level. This method effectively brings together the existing information about diseases that is scattered across the vast corpus of biomedical literature. We prove that sets of MeSH terms provide a highly descriptive representation of heritable disease and that the structure of MeSH provides a natural way of combining individual MeSH vocabularies. We show that our measure can be used effectively in the prediction of candidate disease genes. We developed a web application to query more than 28.5 million relationships between 7,574 hereditary diseases (96% of OMIM) based on our similarity measure.

Shakespearean tragedies dynamics: identifying a generic structure in Shakespeare's four major tragedies

NASA Astrophysics Data System (ADS)

Domínguez-Rué, Emma; Mrotzek, Maximilian

2012-10-01

Many interpretations of Shakespearean tragedy have been conducted, mostly following the principles of interpretation in literary study. In our paper, four tragedies by William Shakespeare - Hamlet, King Lear, Othello, and Macbeth - were analysed systemically to find out whether they inhabit a common structure. Using the plot structure as the basis for our analysis, we identified the most important system elements, their connections, and interactive behaviour using causal loop diagrams (CLDs). Our results revealed that all four tragedies basically conform to Senge's archetypal structure 'shifting the burden', adding the action of the heroine or villain and the characters' boundaries of perception. The results suggest that, even though characters and settings vary highly, these tragedies have similar structures and archetypal solutions exist to overcome the problem. Furthermore, we propose that CLDs and systems archetypes are a reasonable hermeneutic tool to analyse not only Shakespearean tragedies but also other literary works.

Modular prediction of protein structural classes from sequences of twilight-zone identity with predicting sequences.

PubMed

Mizianty, Marcin J; Kurgan, Lukasz

2009-12-13

Knowledge of structural class is used by numerous methods for identification of structural/functional characteristics of proteins and could be used for the detection of remote homologues, particularly for chains that share twilight-zone similarity. In contrast to existing sequence-based structural class predictors, which target four major classes and which are designed for high identity sequences, we predict seven classes from sequences that share twilight-zone identity with the training sequences. The proposed MODular Approach to Structural class prediction (MODAS) method is unique as it allows for selection of any subset of the classes. MODAS is also the first to utilize a novel, custom-built feature-based sequence representation that combines evolutionary profiles and predicted secondary structure. The features quantify information relevant to the definition of the classes including conservation of residues and arrangement and number of helix/strand segments. Our comprehensive design considers 8 feature selection methods and 4 classifiers to develop Support Vector Machine-based classifiers that are tailored for each of the seven classes. Tests on 5 twilight-zone and 1 high-similarity benchmark datasets and comparison with over two dozens of modern competing predictors show that MODAS provides the best overall accuracy that ranges between 80% and 96.7% (83.5% for the twilight-zone datasets), depending on the dataset. This translates into 19% and 8% error rate reduction when compared against the best performing competing method on two largest datasets. The proposed predictor provides accurate predictions at 58% accuracy for membrane proteins class, which is not considered by majority of existing methods, in spite that this class accounts for only 2% of the data. Our predictive model is analyzed to demonstrate how and why the input features are associated with the corresponding classes. The improved predictions stem from the novel features that express collocation of the secondary structure segments in the protein sequence and that combine evolutionary and secondary structure information. Our work demonstrates that conservation and arrangement of the secondary structure segments predicted along the protein chain can successfully predict structural classes which are defined based on the spatial arrangement of the secondary structures. A web server is available at http://biomine.ece.ualberta.ca/MODAS/.

Modular prediction of protein structural classes from sequences of twilight-zone identity with predicting sequences

PubMed Central

2009-01-01

Background Knowledge of structural class is used by numerous methods for identification of structural/functional characteristics of proteins and could be used for the detection of remote homologues, particularly for chains that share twilight-zone similarity. In contrast to existing sequence-based structural class predictors, which target four major classes and which are designed for high identity sequences, we predict seven classes from sequences that share twilight-zone identity with the training sequences. Results The proposed MODular Approach to Structural class prediction (MODAS) method is unique as it allows for selection of any subset of the classes. MODAS is also the first to utilize a novel, custom-built feature-based sequence representation that combines evolutionary profiles and predicted secondary structure. The features quantify information relevant to the definition of the classes including conservation of residues and arrangement and number of helix/strand segments. Our comprehensive design considers 8 feature selection methods and 4 classifiers to develop Support Vector Machine-based classifiers that are tailored for each of the seven classes. Tests on 5 twilight-zone and 1 high-similarity benchmark datasets and comparison with over two dozens of modern competing predictors show that MODAS provides the best overall accuracy that ranges between 80% and 96.7% (83.5% for the twilight-zone datasets), depending on the dataset. This translates into 19% and 8% error rate reduction when compared against the best performing competing method on two largest datasets. The proposed predictor provides accurate predictions at 58% accuracy for membrane proteins class, which is not considered by majority of existing methods, in spite that this class accounts for only 2% of the data. Our predictive model is analyzed to demonstrate how and why the input features are associated with the corresponding classes. Conclusions The improved predictions stem from the novel features that express collocation of the secondary structure segments in the protein sequence and that combine evolutionary and secondary structure information. Our work demonstrates that conservation and arrangement of the secondary structure segments predicted along the protein chain can successfully predict structural classes which are defined based on the spatial arrangement of the secondary structures. A web server is available at http://biomine.ece.ualberta.ca/MODAS/. PMID:20003388

Structure and function of SemiSWEET and SWEET sugar transporters.

PubMed

Feng, Liang; Frommer, Wolf B

2015-08-01

SemiSWEETs and SWEETs have emerged as unique sugar transporters. First discovered in plants with the help of fluorescent biosensors, homologs exist in all kingdoms of life. Bacterial and plant homologs transport hexoses and sucrose, whereas animal SWEETs transport glucose. Prokaryotic SemiSWEETs are small and comprise a parallel homodimer of an approximately 100 amino acid-long triple helix bundle (THB). Duplicated THBs are fused to create eukaryotic SWEETs in a parallel orientation via an inversion linker helix, producing a similar configuration to that of SemiSWEET dimers. Structures of four SemiSWEETs have been resolved in three states: open outside, occluded, and open inside, indicating alternating access. As we discuss here, these atomic structures provide a basis for exploring the evolution of structure-function relations in this new class of transporters. Copyright © 2015 Elsevier Ltd. All rights reserved.

Different Structural Changes Occur in the Blue- and Green-Absorbing Proteorhodopsin During the Primary Photoreaction†

PubMed Central

Amsden, Jason J.; Kralj, Joel M.; Bergo, Vladislav B.; Spudich, Elena N.; Spudich, John L.; Rothschild, Kenneth J.

2013-01-01

We examine the structural changes during the primary photoreaction in blue-absorbing proteorhodopsin (BPR), a light-driven retinylidene proton pump, using low-temperature FTIR difference spectroscopy. Comparison of the light induced BPR difference spectrum recorded at 80 K to that of green-absorbing proteorhodopsin (GPR) reveals that there are several differences in the BPR and GPR primary photoreactions despite the similar structure of the retinal chromophore and all-trans → 13-cis isomerization. Strong bands near 1700 cm−1 assigned previously to a change in hydrogen bonding of Asn230 in GPR are still present in BPR but in addition bands in the same region are assigned on the basis of site-directed mutagenesis to changes occurring in Gln105. In the amide II region bands are assigned on the basis of total-N15 labeling to structural changes of the protein backbone, although no such bands were previously observed for GPR. A band at 3642 cm−1 in BPR, assigned to the OH stretching mode of a water molecule on the basis of H218O substitution, appears at a different frequency than a band at 3626 cm−1 previously assigned to a water molecule in GPR. However, the substitution of Gln105 for Leu105 in BPR leads to the appearance of both bands at 3642 and 3626 cm−1 indicating the waters assigned in BPR and GPR exist in separate distinct locations and can coexist in the GPR-like Q105L mutant of BPR. These results indicate that there exist significant differences in the conformational changes occurring in these two types proteorhodopsin during the initial photoreaction despite their similar chromophores structures, which might reflect a different arrangement of water in the active site as well as substitution of a hydrophilic for hydrophobic residue at residue 105. PMID:18842006

[Detection of hydrodynamically operative tissue in the substantia spongiosa of the femoral head in Bos taurus and Ovis aries].

PubMed

Copf, F; Czarnetzki, A; Lierse, W; Dolenc, A

1990-12-01

The authors show the presence of CC-Tensulae in Bos taurus and Ovis aries. They define CC-Tensulae as tense membranes in openings between the trabeculae of spongy bone. These structures were interpreted in man as a hydrodynamic subsystem which serves the flow and the impulses of mechanical forces. The authors point especially to the similarity that exists between their findings and what has been seen in man.

Algorithm-Dependent Generalization Bounds for Multi-Task Learning.

PubMed

Liu, Tongliang; Tao, Dacheng; Song, Mingli; Maybank, Stephen J

2017-02-01

Often, tasks are collected for multi-task learning (MTL) because they share similar feature structures. Based on this observation, in this paper, we present novel algorithm-dependent generalization bounds for MTL by exploiting the notion of algorithmic stability. We focus on the performance of one particular task and the average performance over multiple tasks by analyzing the generalization ability of a common parameter that is shared in MTL. When focusing on one particular task, with the help of a mild assumption on the feature structures, we interpret the function of the other tasks as a regularizer that produces a specific inductive bias. The algorithm for learning the common parameter, as well as the predictor, is thereby uniformly stable with respect to the domain of the particular task and has a generalization bound with a fast convergence rate of order O(1/n), where n is the sample size of the particular task. When focusing on the average performance over multiple tasks, we prove that a similar inductive bias exists under certain conditions on the feature structures. Thus, the corresponding algorithm for learning the common parameter is also uniformly stable with respect to the domains of the multiple tasks, and its generalization bound is of the order O(1/T), where T is the number of tasks. These theoretical analyses naturally show that the similarity of feature structures in MTL will lead to specific regularizations for predicting, which enables the learning algorithms to generalize fast and correctly from a few examples.

Cardiovascular dynamics of Canadian Indigenous peoples.

PubMed

Foulds, Heather J A; Bredin, Shannon S D; Warburton, Darren E R

2018-12-01

Limited understanding of Indigenous adults' cardiovascular structure and function exists despite high rates of cardiovascular disease. This investigation characterised cardiovascular structure and function among young Indigenous adults and compared to age- and sex-matched European descendants. Echocardiographic assessments included apical two- and four-chamber images, parasternal short-axis images and Doppler. Analyses included cardiac volumes, dimensions, velocities and strains. Cardiovascular structure and function were similar between Indigenous (n=10, 25 ± 3 years, 4 women) and European-descendant (n=10, 24 ± 4 years, 4 women,) adults, though European descendants demonstrated greater systemic vascular resistance (18.19 ± 3.94 mmHg∙min -1 ∙L -1 vs. 15.36 ± 2.97 mmHg∙min -1 ∙L -1 , p=0.03). Among Indigenous adults, women demonstrated greater arterial elastance (0.80 ± 0.15 mmHg·mL -1 ·m -2 vs. 0.55 ± 0.17 mmHg·mL -1 ·m -2 , p=0.02) and possibly greater systemic vascular resistance (17.51 ± 2.20 mmHg∙min -1 ∙L -1 vs. 13.93 ± 2.61 mmHg∙min -1 ∙L -1 , p=0.07). Indigenous men had greater cardiac size, dimensions and output, though body size differences accounted for cardiac size differences. Similar cardiac rotation and strains were observed across sexes. Arterial elastance and cardiac size were different between Indigenous men and women while cardiovascular structure and function may be similar between Indigenous and European descendants.

Genetic diversity based on 28S rDNA sequences among populations of Culex quinquefasciatus collected at different locations in Tamil Nadu, India.

PubMed

Sakthivelkumar, S; Ramaraj, P; Veeramani, V; Janarthanan, S

2015-09-01

The basis of the present study was to distinguish the existence of any genetic variability among populations of Culex quinquefasciatus which would be a valuable tool in the management of mosquito control programmes. In the present study, population of Cx. quinquefasciatus collected at different locations in Tamil Nadu were analyzed for their genetic variation based on 28S rDNA D2 region nucleotide sequences. A high degree of genetic polymorphism was detected in the sequences of D2 region of 28S rDNA on the predicted secondary structures in spite of high nucleotide sequence similarity. The findings based on secondary structure using rDNA sequences suggested the existence of a complex genotypic diversity of Cx. quinquefasciatus population collected at different locations of Tamil Nadu, India. This complexity in genetic diversity in a single mosquito population collected at different locations is considered an important issue towards their influence and nature of vector potential of these mosquitoes.

Electronic and optoelectronic device applications based on ReS2

NASA Astrophysics Data System (ADS)

Liu, Erfu; Long, Mingsheng; Wang, Yaojia; Pan, Yiming; Ho, Chinghwa; Wang, Baigeng; Miao, Feng

Rhenium disulfide (ReS2) is a unique semiconducting TMD with distorted 1T structure and weak interlayer coupling. We have previously investigated its in-plane anisotropic property and electronic applications on FET and digital inverters. In this talk, we will present high responsivity phototransistors based on few-layer ReS2. Depending on the back gate voltage, source drain bias and incident optical light intensity, the maximum attainable photoresponsivity can reach as high as 88,600 A W-1, which is one of the highest value among individual two-dimensional materials with similar device structures. Such high photoresponsivity is attributed to the increased light absorption as well as the gain enhancement due to the existence of trap states in the few-layer ReS2 flakes. The existence of trap states is proved by temperature dependent transport measurements. It further enables the detection of weak signals. Our studies underscore ReS2 as a promising material for future electronic and sensitive optoelectronic applications.

Evidence of C-F-P and aromatic π-F-P weak interactions in imidazolium ionic liquids and its consequences

NASA Astrophysics Data System (ADS)

Panja, Sumit Kumar; Srivastava, Nitin; Srivastava, Jyoti; Prasad, Namburi Eswara; Noothalapati, Hemanth; Shigeto, Shinsuke; Saha, Satyen

2018-04-01

A simple change from alkyl group to alkene in side chain of imidazolium cation with same anion resulted in a drastic impact on physical properties (e.g., melting point) from bmimPF6 IL to cmimPF6 IL. The underlying reasons have been elucidated by structural and interaction studies with the help of DSC, SCXRD, vibrational and multi-nuclear NMR spectroscopic techniques. Experiments reveal existence of new weak interactions involving the carbon and π cloud of the imidazolium aromatic ring with fluoride of PF6 anion (i.e., C2-F-P and π-F-P) in cmimPF6 but are absent in structurally similar prototype IL, bmimPF6. Though weak, these interactions helped to form ladder type supramolecular arrangement, resulting in quite high melting point for cmimPF6 IL compared to bmimPF6 IL. These findings emphasize that an IL system can behave uniquely because of the existence of uncommon weak interactions.

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

PubMed

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

2012-01-01

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

CombAlign: a code for generating a one-to-many sequence alignment from a set of pairwise structure-based sequence alignments.

PubMed

Zhou, Carol L Ecale

2015-01-01

In order to better define regions of similarity among related protein structures, it is useful to identify the residue-residue correspondences among proteins. Few codes exist for constructing a one-to-many multiple sequence alignment derived from a set of structure or sequence alignments, and a need was evident for creating such a tool for combining pairwise structure alignments that would allow for insertion of gaps in the reference structure. This report describes a new Python code, CombAlign, which takes as input a set of pairwise sequence alignments (which may be structure based) and generates a one-to-many, gapped, multiple structure- or sequence-based sequence alignment (MSSA). The use and utility of CombAlign was demonstrated by generating gapped MSSAs using sets of pairwise structure-based sequence alignments between structure models of the matrix protein (VP40) and pre-small/secreted glycoprotein (sGP) of Reston Ebolavirus and the corresponding proteins of several other filoviruses. The gapped MSSAs revealed structure-based residue-residue correspondences, which enabled identification of structurally similar versus differing regions in the Reston proteins compared to each of the other corresponding proteins. CombAlign is a new Python code that generates a one-to-many, gapped, multiple structure- or sequence-based sequence alignment (MSSA) given a set of pairwise sequence alignments (which may be structure based). CombAlign has utility in assisting the user in distinguishing structurally conserved versus divergent regions on a reference protein structure relative to other closely related proteins. CombAlign was developed in Python 2.6, and the source code is available for download from the GitHub code repository.

Super-massive binary black holes in galaxies. Dynamical models and observed structures in Arp 5, 87, 214, 240, and NGC 4027, 6946

NASA Astrophysics Data System (ADS)

Anosova, Joanna P.

2017-06-01

On 14 Sept, 2015 The LIGO reported the first direct detection of gravitational waves and the first direct observation of a binary black hole. These observations demonstrate the existence of binary black holes in stellar systems predicted by Einstein in his general theory of relativity a century earlier.A lot of violent and complicated phenomena take place on different scales in the Universe. Many of them may be caused by multiple centers of gravitational attraction: planetary rings, accretion discs of various scales, peculiar structures of single galaxies and interacting galaxies. In this work, we show that various features of celestial objects can be understood by assuming the existence of two dominant centers of gravity in stellar systems.We study numerically the dynamical evolution of models with the central super-massive binary black holes and extended shells with numerous low-mass particles inside and around the orbits of binaries. These particles could be star clusters or gas and dust complexes. We consider several tens of thousands of initial conditions for the general three-body problem and compile them. We studied the dynamical evolution of all spherical shells together and separately. Our method permits us to study the individual trajectories of particles, their close double and triple approaches, and inspect the time-depending structures in the models. Multiple runs of the models allow us to classify the numerous strong triple interactions of the binary components with low-mass particles; frequently, the "gravitational slingshot" effect occurs in the center of systems. Such strong interactions of bodies are results in various structures with "dumb-bell" bars, close and open spirals, different types of flows, jets etc. These structures are often very similar the observed structures of galaxies.We found some combinations of the initial conditions and model parameters that produce at some time similar structures as that found in the galaxies Arp 5, 87, 214, 240, and NGC 4027, 6946. Our Figures show results of such comparison and the past and future evolution of our models.

Understanding the local context and its possible influences on shaping, implementing and running social accountability initiatives for maternal health services in rural Democratic Republic of the Congo: a contextual factor analysis.

PubMed

Mafuta, Eric M; Hogema, Lisanne; Mambu, Thérèse N M; Kiyimbi, Pontien B; Indebe, Berthys P; Kayembe, Patrick K; De Cock Buning, Tjard; Dieleman, Marjolein A

2016-11-09

Social accountability has to be configured according to the context in which it operates. This paper aimed to identify local contextual factors in two health zones in the Democratic Republic of the Congo and discuss their possible influences on shaping, implementing and running social accountability initiatives. Data on local socio-cultural characteristics, the governance context, and socio-economic conditions related to social accountability enabling factors were collected in the two health zones using semi-structured interviews and document reviews, and were analyzed using thematic analysis. The contexts of the two health zones were similar and characterized by the existence of several community groups, similarly structured and using similar decision-making processes. They were not involved in the health sector's activities and had no link with the health committee, even though they acknowledged its existence. They were not networked as they focused on their own activities and did not have enough capacity in terms of social mobilization or exerting pressure on public authorities or providers. Women were not perceived as marginalized as they often occupied other positions in the community besides carrying out domestic tasks and participated in community groups. However, they were still subject to the local male dominance culture, which restrains their involvement in decision-making, as they tend to be less educated, unemployed and suffer from a lack of resources or specific skills. The socio-economic context is characterized by subsistence activities and a low employment rate, which limits the community members' incomes and increases their dependence on external support. The governance context was characterized by imperfect implementation of political decentralization. Community groups advocating community rights are identified as "political" and are not welcomed. The community groups seemed not to be interested in the health center's information and had no access to media as it is non-existent. The local contexts in the two health zones seemed not to be supportive of the operation of social accountability initiatives. However, they offer starting points for social accountability initiatives if better use is made of existing contextual factors, for instance by making community groups work together and improving their capacities in terms of knowledge and information.

The “unreasonable effectiveness” of stratigraphic and geomorphic experiments

NASA Astrophysics Data System (ADS)

Paola, Chris; Straub, Kyle; Mohrig, David; Reinhardt, Liam

2009-12-01

The growth of quantitative analysis and prediction in Earth-surface science has been accompanied by growth in experimental stratigraphy and geomorphology. Experimenters have grown increasingly bold in targeting landscape elements from channel reaches up to the entire erosional networks and depositional basins, often using very small facilities. The experiments produce spatial structure and kinematics that, although imperfect, compare well with natural systems despite differences of spatial scale, time scale, material properties, and number of active processes. Experiments have been particularly useful in studying a wide range of forms of self-organized (autogenic) complexity that occur in morphodynamic systems. Autogenic dynamics creates much of the spatial structure we see in the landscape and in preserved strata, and is strongly associated with sediment storage and release. The observed consistency between experimental and field systems despite large differences in governing dimensionless numbers is what we mean by "unreasonable effectiveness". We suggest that unreasonable experimental effectiveness arises from natural scale independence. We generalize existing ideas to relate internal similarity, in which a small part of a system is similar to the larger system, to external similarity, in which a small copy of a system is similar to the larger system. We propose that internal similarity implies external similarity, though not the converse. The external similarity of landscape experiments to natural landscapes suggests that natural scale independence may be even more characteristic of morphodynamics than it is of better studied cases such as turbulence. We urge a shift in emphasis in experimental stratigraphy and geomorphology away from classical dynamical scaling and towards a quantitative understanding of the origins and limits of scale independence. Other research areas with strong growth potential in experimental surface dynamics include physical-biotic interactions, cohesive effects, stochastic processes, the interplay of structural and geomorphic self-organization, extraction of quantitative process information from landscape and stratigraphic records, and closer interaction between experimentation and theory.

Improved cosine similarity measures of simplified neutrosophic sets for medical diagnoses.

PubMed

Ye, Jun

2015-03-01

In pattern recognition and medical diagnosis, similarity measure is an important mathematical tool. To overcome some disadvantages of existing cosine similarity measures of simplified neutrosophic sets (SNSs) in vector space, this paper proposed improved cosine similarity measures of SNSs based on cosine function, including single valued neutrosophic cosine similarity measures and interval neutrosophic cosine similarity measures. Then, weighted cosine similarity measures of SNSs were introduced by taking into account the importance of each element. Further, a medical diagnosis method using the improved cosine similarity measures was proposed to solve medical diagnosis problems with simplified neutrosophic information. The improved cosine similarity measures between SNSs were introduced based on cosine function. Then, we compared the improved cosine similarity measures of SNSs with existing cosine similarity measures of SNSs by numerical examples to demonstrate their effectiveness and rationality for overcoming some shortcomings of existing cosine similarity measures of SNSs in some cases. In the medical diagnosis method, we can find a proper diagnosis by the cosine similarity measures between the symptoms and considered diseases which are represented by SNSs. Then, the medical diagnosis method based on the improved cosine similarity measures was applied to two medical diagnosis problems to show the applications and effectiveness of the proposed method. Two numerical examples all demonstrated that the improved cosine similarity measures of SNSs based on the cosine function can overcome the shortcomings of the existing cosine similarity measures between two vectors in some cases. By two medical diagnoses problems, the medical diagnoses using various similarity measures of SNSs indicated the identical diagnosis results and demonstrated the effectiveness and rationality of the diagnosis method proposed in this paper. The improved cosine measures of SNSs based on cosine function can overcome some drawbacks of existing cosine similarity measures of SNSs in vector space, and then their diagnosis method is very suitable for handling the medical diagnosis problems with simplified neutrosophic information and demonstrates the effectiveness and rationality of medical diagnoses. Copyright © 2014 Elsevier B.V. All rights reserved.

Late-time cosmological phase transitions

NASA Technical Reports Server (NTRS)

Schramm, David N.

1991-01-01

It is shown that the potential galaxy formation and large scale structure problems of objects existing at high redshifts (Z approx. greater than 5), structures existing on scales of 100 M pc as well as velocity flows on such scales, and minimal microwave anisotropies ((Delta)T/T) (approx. less than 10(exp -5)) can be solved if the seeds needed to generate structure form in a vacuum phase transition after decoupling. It is argued that the basic physics of such a phase transition is no more exotic than that utilized in the more traditional GUT scale phase transitions, and that, just as in the GUT case, significant random Gaussian fluctuations and/or topological defects can form. Scale lengths of approx. 100 M pc for large scale structure as well as approx. 1 M pc for galaxy formation occur naturally. Possible support for new physics that might be associated with such a late-time transition comes from the preliminary results of the SAGE solar neutrino experiment, implying neutrino flavor mixing with values similar to those required for a late-time transition. It is also noted that a see-saw model for the neutrino masses might also imply a tau neutrino mass that is an ideal hot dark matter candidate. However, in general either hot or cold dark matter can be consistent with a late-time transition.

Radio Frequency Plasma Synthesis of Boron Nitride Nanotubes (BNNTs) for Structural Applications: Part I

NASA Technical Reports Server (NTRS)

Hales, Stephen J.; Alexa, Joel A.; Jensen, Brian J.; Thomsen, Donald L.

2016-01-01

It is evident that nanotubes, such as carbon, boron nitride and even silicon, offer great potential for many aerospace applications. The opportunity exists to harness the extremely high strength and stiffness exhibited by high-purity, low-defect nanotubes in structural materials. Even though the technology associated with carbon nanotube (CNT) development is mature, the mechanical property benefits have yet to be fully realized. Boron nitride nanotubes (BNNTs) offer similar structural benefits, but exhibit superior chemical and thermal stability. A broader range of potential structural applications results, particularly as reinforcing agents for metal- and ceramic- based composites. However, synthesis of BNNTs is more challenging than CNTs mainly because of the higher processing temperatures required, and mass production techniques have yet to emerge. A promising technique is radio frequency plasma spray (RFPS), which is an inductively coupled, very high temperature process. The lack of electrodes and the self- contained, inert gas environment lend themselves to an ultraclean product. It is the aim of this White Paper to survey the state of the art with regard to nano-material production by analyzing the pros and cons of existing methods. The intention is to combine the best concepts and apply the NASA Langley Research Center (LaRC) RFPS facility to reliably synthesize large quantities of consistent, high-purity BNNTs.

From Bridges and Rockets, Lessons for Software Systems

NASA Technical Reports Server (NTRS)

Holloway, C. Michael

2004-01-01

Although differences exist between building software systems and building physical structures such as bridges and rockets, enough similarities exist that software engineers can learn lessons from failures in traditional engineering disciplines. This paper draws lessons from two well-known failures the collapse of the Tacoma Narrows Bridge in 1940 and the destruction of the space shuttle Challenger in 1986 and applies these lessons to software system development. The following specific applications are made: (1) the verification and validation of a software system should not be based on a single method, or a single style of methods; (2) the tendency to embrace the latest fad should be overcome; and (3) the introduction of software control into safety-critical systems should be done cautiously.

An anatomy lesson and the quality of intermittence

PubMed Central

van Tellingen, C.

2007-01-01

Not only in the second century AD but also at the end of the second millennium, there was much debate on the structural and functional characteristics of the heart in different-sized mammals. Galen commented on the dissection of the heart of an elephant, whereas Meijler, a Dutch cardiologist, set out on a whale-ECG expedition to prove pre-existing assumptions too. The chain of thoughts is remarkably similar, in as far as human nature is driven by the aspiration to fill in the voids in pre-existing learning. As appreciation for our heritage of knowledge has somewhat receded into the background, a plea is made for reappraisal and the quality of being intermittent. (Neth Heart J 2007;15:239-41.) PMID:22279427

Adolescent cocaine exposure simplifies orbitofrontal cortical dendritic arbors

PubMed Central

DePoy, Lauren M.; Perszyk, Riley E.; Zimmermann, Kelsey S.; Koleske, Anthony J.; Gourley, Shannon L.

2014-01-01

Cocaine and amphetamine remodel dendritic spines within discrete cortico-limbic brain structures including the orbitofrontal cortex (oPFC). Whether dendrite structure is similarly affected, and whether pre-existing cellular characteristics influence behavioral vulnerabilities to drugs of abuse, remain unclear. Animal models provide an ideal venue to address these issues because neurobehavioral phenotypes can be defined both before, and following, drug exposure. We exposed mice to cocaine from postnatal days 31–35, corresponding to early adolescence, using a dosing protocol that causes impairments in an instrumental reversal task in adulthood. We then imaged and reconstructed excitatory neurons in deep-layer oPFC. Prior cocaine exposure shortened and simplified arbors, particularly in the basal region. Next, we imaged and reconstructed orbital neurons in a developmental-genetic model of cocaine vulnerability—the p190rhogap+/– mouse. p190RhoGAP is an actin cytoskeleton regulatory protein that stabilizes dendrites and dendritic spines, and p190rhogap+/– mice develop rapid and robust locomotor activation in response to cocaine. Despite this, oPFC dendritic arbors were intact in drug-naïve p190rhogap+/– mice. Together, these findings provide evidence that adolescent cocaine exposure has long-term effects on dendrite structure in the oPFC, and they suggest that cocaine-induced modifications in dendrite structure may contribute to the behavioral effects of cocaine more so than pre-existing structural abnormalities in this cell population. PMID:25452728

Identifying the Critical Links in Road Transportation Networks: Centrality-based approach utilizing structural properties

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

Chinthavali, Supriya

Surface transportation road networks share structural properties similar to other complex networks (e.g., social networks, information networks, biological networks, and so on). This research investigates the structural properties of road networks for any possible correlation with the traffic characteristics such as link flows those determined independently. Additionally, we define a criticality index for the links of the road network that identifies the relative importance in the network. We tested our hypotheses with two sample road networks. Results show that, correlation exists between the link flows and centrality measures of a link of the road (dual graph approach is followed) andmore » the criticality index is found to be effective for one test network to identify the vulnerable nodes.« less

Ordered mixed-layer structures in the Mighei carbonaceous chondrite matrix

NASA Technical Reports Server (NTRS)

Mackinnon, I. D. R.

1982-01-01

High resolution transmission electron microscopy of the Mighei carbonaceous chondrite matrix has revealed the presence of a new mixed layer structure material. This mixed-layer material consists of an ordered arrangement of serpentine-type (S) and brucite-type (B) layers in the sequence SBBSBB. Electron diffraction and imaging techniques show that the basal periodicity is approximately 17 A. Discrete crystals of SBB-type material are typically curved, of small size (less than 1 micron) and show structural variations similar to the serpentine group minerals. Mixed-layer material also occurs in association with planar serpentine. Characteristics of SBB-type material are not consistent with known terrestrial mixed-layer clay minerals. Evidence for formation by a condensation event or by subsequent alteration of pre-existing material is not yet apparent.

A comprehensive comparison of network similarities for link prediction and spurious link elimination

NASA Astrophysics Data System (ADS)

Zhang, Peng; Qiu, Dan; Zeng, An; Xiao, Jinghua

2018-06-01

Identifying missing interactions in complex networks, known as link prediction, is realized by estimating the likelihood of the existence of a link between two nodes according to the observed links and nodes' attributes. Similar approaches have also been employed to identify and remove spurious links in networks which is crucial for improving the reliability of network data. In network science, the likelihood for two nodes having a connection strongly depends on their structural similarity. The key to address these two problems thus becomes how to objectively measure the similarity between nodes in networks. In the literature, numerous network similarity metrics have been proposed and their accuracy has been discussed independently in previous works. In this paper, we systematically compare the accuracy of 18 similarity metrics in both link prediction and spurious link elimination when the observed networks are very sparse or consist of inaccurate linking information. Interestingly, some methods have high prediction accuracy, they tend to perform low accuracy in identification spurious interaction. We further find that methods can be classified into several cluster according to their behaviors. This work is useful for guiding future use of these similarity metrics for different purposes.

Theoretical and experimental characterization of the DUal-BAse transistor (DUBAT)

NASA Astrophysics Data System (ADS)

Wu, Chung-Yu; Wu, Ching-Yuan

1980-11-01

A new A-type integrated voltage controlled differential negative resistance device using an extra effective base region to form a lateral pnp (npn) bipolar transistor beside the original base region of a vertical npn (pnp) bipolar junction transistor, and so called the DUal BAse Transistor (DUBAT), is studied both experimentally and theoretically, The DUBAT has three terminals and is fully comparible with the existing bipolar integrated circuits technologies. Based upon the equivalent circuit of the DUBAT, a simple first-order analytical theory is developed, and important device parameters, such as: the I-V characteristic, the differential negative resistance, and the peak and valley points, are also characterized. One of the proposed integrated structures of the DUBAT, which is similar in structure to I 2L but with similar high density and a normally operated vertical npn transistor, has been successfully fabricated and studied. Comparisons between the experimental data and theoretical analyses are made, and show in satisfactory agreements.

OAS proteins and cGAS: unifying concepts in sensing and responding to cytosolic nucleic acids.

PubMed

Hornung, Veit; Hartmann, Rune; Ablasser, Andrea; Hopfner, Karl-Peter

2014-08-01

Recent discoveries in the field of innate immunity have highlighted the existence of a family of nucleic acid-sensing proteins that have similar structural and functional properties. These include the well-known oligoadenylate synthase (OAS) family proteins and the recently identified OAS homologue cyclic GMP-AMP (cGAMP) synthase (cGAS). The OAS proteins and cGAS are template-independent nucleotidyltransferases that, once activated by double-stranded nucleic acids in the cytosol, produce unique classes of 2'-5'-linked second messenger molecules, which - through distinct mechanisms - have crucial antiviral functions. 2'-5'-linked oligoadenylates limit viral propagation through the activation of the enzyme RNase L, which degrades host and viral RNA, and 2'-5'-linked cGAMP activates downstream signalling pathways to induce de novo antiviral gene expression. In this Progress article, we describe the striking functional and structural similarities between OAS proteins and cGAS, and highlight their roles in antiviral immunity.

Hydrothermal synthesis of pollucite, analcime and their solid solutions and analysis of their properties

NASA Astrophysics Data System (ADS)

Jing, Zhenzi; Cai, Kunchuan; Li, Yan; Fan, Junjie; Zhang, Yi; Miao, Jiajun; Chen, Yuqian; Jin, Fangming

2017-05-01

Pollucite, as a perfect long-term potential host for radioactive Cs immobilization, barely exists in pure form naturally but in an isomorphism form between pollucite and analcime due to coexistence of Cs and Na. Pollucite could be hydrothermally synthesized with Cs-polluted soil or clay minerals which contain Cs and Na, and it is necessary to study the properties of the synthesis if Cs and Na contained. Pure pollucite, analcime and their solid solutions were hydrothermally synthesized with chemicals, and it was found that the most formed pollucite analcime solid solutions with Cs/(Cs + Na) ratios of 2/6-5/6 had very similar properties in mineral composition, morphology and size, structural water (Cs cations) and coordination environment to pollucite. This also suggests that even coexistence of Cs and Na in nature, pollucite favors to form due to site preference for Cs over Na, which leads to the property and the structure of the most solid solutions similar to that of pollucite.

Leveraging disjoint communities for detecting overlapping community structure

NASA Astrophysics Data System (ADS)

Chakraborty, Tanmoy

2015-05-01

Network communities represent mesoscopic structure for understanding the organization of real-world networks, where nodes often belong to multiple communities and form overlapping community structure in the network. Due to non-triviality in finding the exact boundary of such overlapping communities, this problem has become challenging, and therefore huge effort has been devoted to detect overlapping communities from the network. In this paper, we present PVOC (Permanence based Vertex-replication algorithm for Overlapping Community detection), a two-stage framework to detect overlapping community structure. We build on a novel observation that non-overlapping community structure detected by a standard disjoint community detection algorithm from a network has high resemblance with its actual overlapping community structure, except the overlapping part. Based on this observation, we posit that there is perhaps no need of building yet another overlapping community finding algorithm; but one can efficiently manipulate the output of any existing disjoint community finding algorithm to obtain the required overlapping structure. We propose a new post-processing technique that by combining with any existing disjoint community detection algorithm, can suitably process each vertex using a new vertex-based metric, called permanence, and thereby finds out overlapping candidates with their community memberships. Experimental results on both synthetic and large real-world networks show that PVOC significantly outperforms six state-of-the-art overlapping community detection algorithms in terms of high similarity of the output with the ground-truth structure. Thus our framework not only finds meaningful overlapping communities from the network, but also allows us to put an end to the constant effort of building yet another overlapping community detection algorithm.

Crystal structure of cbbF from Zymomonas mobilis and its functional implication

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

Hwang, Hyo-Jeong; Park, Suk-Youl; Kim, Jeong-Sun, E-mail: jsunkim@chonnam.ac.kr

2014-02-28

Highlights: • The crystal structure of one cbbF from Zymomonas mobilis was revealed. • Scores of residues form two secondary structures with a non-polar protruded residue. • It exists as a dimeric form in solution. - Abstract: A phosphate group at the C1-atom of inositol-monophosphate (IMP) and fructose-1,6-bisphosphate (FBP) is hydrolyzed by a phosphatase IMPase and FBPase in a metal-dependent way, respectively. The two enzymes are almost indiscernible from each other because of their highly similar sequences and structures. Metal ions are bound to residues on the β1- and β2-strands and one mobile loop. However, FBP has another phosphate andmore » FBPases exist as a higher oligomeric state, which may discriminate FBPases from IMPases. There are three genes annotated as FBPases in Zymomonas mobilis, termed also cbbF (ZmcbbF). The revealed crystal structure of one ZmcbbF shows a globular structure formed by five stacked layers. Twenty-five residues in the middle of the sequence form an α-helix and a β-strand, which occupy one side of the catalytic site. A non-polar Leu residue among them is protruded to the active site, pointing out unfavorable access of a bulky charged group to this side. In vitro assays have shown its dimeric form in solution. Interestingly, two β-strands of β1 and β2 are disordered in the ZmcbbF structure. These data indicate that ZmcbbF might structurally belong to IMPase, and imply that its active site would be reorganized in a yet unreported way.« less

GPU-Q-J, a fast method for calculating root mean square deviation (RMSD) after optimal superposition

PubMed Central

2011-01-01

Background Calculation of the root mean square deviation (RMSD) between the atomic coordinates of two optimally superposed structures is a basic component of structural comparison techniques. We describe a quaternion based method, GPU-Q-J, that is stable with single precision calculations and suitable for graphics processor units (GPUs). The application was implemented on an ATI 4770 graphics card in C/C++ and Brook+ in Linux where it was 260 to 760 times faster than existing unoptimized CPU methods. Source code is available from the Compbio website http://software.compbio.washington.edu/misc/downloads/st_gpu_fit/ or from the author LHH. Findings The Nutritious Rice for the World Project (NRW) on World Community Grid predicted de novo, the structures of over 62,000 small proteins and protein domains returning a total of 10 billion candidate structures. Clustering ensembles of structures on this scale requires calculation of large similarity matrices consisting of RMSDs between each pair of structures in the set. As a real-world test, we calculated the matrices for 6 different ensembles from NRW. The GPU method was 260 times faster that the fastest existing CPU based method and over 500 times faster than the method that had been previously used. Conclusions GPU-Q-J is a significant advance over previous CPU methods. It relieves a major bottleneck in the clustering of large numbers of structures for NRW. It also has applications in structure comparison methods that involve multiple superposition and RMSD determination steps, particularly when such methods are applied on a proteome and genome wide scale. PMID:21453553

Overload-based cascades on multiplex networks and effects of inter-similarity

PubMed Central

Zhou, Dong

2017-01-01

Although cascading failures caused by overload on interdependent/interconnected networks have been studied in the recent years, the effect of overlapping links (inter-similarity) on robustness to such cascades in coupled networks is not well understood. This is an important issue since shared links exist in many real-world coupled networks. In this paper, we propose a new model for load-based cascading failures in multiplex networks. We leverage it to compare different network structures, coupling schemes, and overload rules. More importantly, we systematically investigate the impact of inter-similarity on the robustness of the whole system under an initial intentional attack. Surprisingly, we find that inter-similarity can have a negative impact on robustness to overload cascades. To the best of our knowledge, we are the first to report the competition between the positive and the negative impacts of overlapping links on the robustness of coupled networks. These results provide useful suggestions for designing robust coupled traffic systems. PMID:29252988

The registration of non-cooperative moving targets laser point cloud in different view point

NASA Astrophysics Data System (ADS)

Wang, Shuai; Sun, Huayan; Guo, Huichao

2018-01-01

Non-cooperative moving target multi-view cloud registration is the key technology of 3D reconstruction of laser threedimension imaging. The main problem is that the density changes greatly and noise exists under different acquisition conditions of point cloud. In this paper, firstly, the feature descriptor is used to find the most similar point cloud, and then based on the registration algorithm of region segmentation, the geometric structure of the point is extracted by the geometric similarity between point and point, The point cloud is divided into regions based on spectral clustering, feature descriptors are created for each region, searching to find the most similar regions in the most similar point of view cloud, and then aligning the pair of point clouds by aligning their minimum bounding boxes. Repeat the above steps again until registration of all point clouds is completed. Experiments show that this method is insensitive to the density of point clouds and performs well on the noise of laser three-dimension imaging.

A mutational analysis and molecular dynamics simulation of quinolone resistance proteins QnrA1 and QnrC from Proteus mirabilis.

PubMed

Guo, Qinglan; Weng, Jingwei; Xu, Xiaogang; Wang, Minghua; Wang, Xiaoying; Ye, Xinyu; Wang, Wenning; Wang, Minggui

2010-10-08

The first report on the transferable, plasmid-mediated quinolone-resistance determinant qnrA1 was in 1998. Since then, qnr alleles have been discovered worldwide in clinical strains of Gram-negative bacilli. Qnr proteins confer quinolone resistance, and belong to the pentapeptide repeat protein (PRP) family. Several PRP crystal structures have been solved, but little is known about the functional significance of their structural arrangement. We conducted random and site-directed mutagenesis on qnrA1 and on qnrC, a newly identified quinolone-resistance gene from Proteus mirabilis. Many of the Qnr mutants lost their quinolone resistance function. The highly conserved hydrophobic Leu or Phe residues at the center of the pentapeptide repeats are known as i sites, and loss-of-function mutations included replacement of the i site hydrophobic residues with charged residues, replacing the i-2 site, N-terminal to the i residues, with bulky side-chain residues, introducing Pro into the β-helix coil, deletion of the N- and C-termini, and excision of a central coil. Molecular dynamics simulations and homology modeling demonstrated that QnrC overall adopts a stable β-helix fold and shares more similarities with MfpA than with other PRP structures. Based on homology modeling and molecular dynamics simulation, the dysfunctional point mutations introduced structural deformations into the quadrilateral β-helix structure of PRPs. Of the pentapeptides of QnrC, two-thirds adopted a type II β-turn, while the rest adopted type IV turns. A gap exists between coil 2 and coil 3 in the QnrC model structure, introducing a structural flexibility that is similar to that seen in MfpA. The hydrophobic core and the β-helix backbone conformation are important for maintaining the quinolone resistance property of Qnr proteins. QnrC may share structural similarity with MfpA.

Mean dyadic Green's function for a two layer random medium

NASA Technical Reports Server (NTRS)

Zuniga, M. A.

1981-01-01

The mean dyadic Green's function for a two-layer random medium with arbitrary three-dimensional correlation functions has been obtained with the zeroth-order solution to the Dyson equation by applying the nonlinear approximation. The propagation of the coherent wave in the random medium is similar to that in an anisotropic medium with different propagation constants for the characteristic transverse electric and transverse magnetic polarizations. In the limit of a laminar structure, two propagation constants for each polarization are found to exist.

Scaffold hopping identifies 6,8-disubstituted purines as novel anaplastic lymphoma kinase inhibitors.

PubMed

Schlütke, Laura; Immer, Markus; Preu, Lutz; Totzke, Frank; Schächtele, Christoph; Kubbutat, Michael H G; Kunick, Conrad

2018-05-01

Rearrangements of anaplastic lymphoma kinase (ALK) are associated with several cancer diseases. Due to resistance development against existing ALK-inhibitors, new, structurally unrelated inhibitors are required. By a scaffold hopping strategy, 6,8-disubstituted purines were designed as analogues of similar ALK-inhibiting thieno[3,2-d]pyrimidines. While the new title compounds indeed inhibited ALK and several ALK mutants in submicromolar concentrations, they retained poor water solubility. Copyright © 2017 Elsevier B.V. All rights reserved.

Designing Roads and Retaining Structures for Nangarhar Province, Afghanistan

DTIC Science & Technology

2011-01-01

exist, typically using burnt brick masonry, with or without a frame, and with a reinforced concrete foundation, columns, stairs, and roofs. These...is 20 ×10 ×5 or 6 cm. The bricks are held in place with a mud mortar. Burnt bricks are placed at the top of two layers of a wall to protect against...conglomerate rocks appeared to be fragmental, such that the pieces are similar to broken concrete . The sandstone is characterized by a gritty sandpaper feel

Simulations of laminar boundary-layer flow encountering large-scale surface indentions

NASA Astrophysics Data System (ADS)

Beratlis, N.; Balaras, E.; Squires, K.; Vizard, A.

2016-03-01

The transition from laminar to turbulent flow over dimples and grooves has been investigated through a series of direct numerical simulations. Emphasis has been given to the mechanism of transition and the momentum transport in the post-dimple boundary layer. It has been found that the dimple geometry plays an important role in the evolution of the turbulent boundary layer downstream. The mechanism of transition in all cases is that of the reorientation of the spanwise vorticity into streamwise oriented structures resembling hairpin vortices commonly encountered in wall bounded turbulent flows. Although qualitatively the transition mechanism amongst the three different cases is similar, important quantitative differences exist. It was shown that two-dimensional geometries like a groove are more stable than three-dimensional geometries like a dimple. In addition, it was found that the cavity geometry controls the initial thickness of the boundary layer and practically results in a shift of the virtual origin of the turbulent boundary layer. Important differences in the momentum transport downstream of the dimples exist but in all cases the boundary layer grows in a self-similar manner.

NoFold: RNA structure clustering without folding or alignment.

PubMed

Middleton, Sarah A; Kim, Junhyong

2014-11-01

Structures that recur across multiple different transcripts, called structure motifs, often perform a similar function-for example, recruiting a specific RNA-binding protein that then regulates translation, splicing, or subcellular localization. Identifying common motifs between coregulated transcripts may therefore yield significant insight into their binding partners and mechanism of regulation. However, as most methods for clustering structures are based on folding individual sequences or doing many pairwise alignments, this results in a tradeoff between speed and accuracy that can be problematic for large-scale data sets. Here we describe a novel method for comparing and characterizing RNA secondary structures that does not require folding or pairwise alignment of the input sequences. Our method uses the idea of constructing a distance function between two objects by their respective distances to a collection of empirical examples or models, which in our case consists of 1973 Rfam family covariance models. Using this as a basis for measuring structural similarity, we developed a clustering pipeline called NoFold to automatically identify and annotate structure motifs within large sequence data sets. We demonstrate that NoFold can simultaneously identify multiple structure motifs with an average sensitivity of 0.80 and precision of 0.98 and generally exceeds the performance of existing methods. We also perform a cross-validation analysis of the entire set of Rfam families, achieving an average sensitivity of 0.57. We apply NoFold to identify motifs enriched in dendritically localized transcripts and report 213 enriched motifs, including both known and novel structures. © 2014 Middleton and Kim; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

An efficicient data structure for three-dimensional vertex based finite volume method

NASA Astrophysics Data System (ADS)

Akkurt, Semih; Sahin, Mehmet

2017-11-01

A vertex based three-dimensional finite volume algorithm has been developed using an edge based data structure.The mesh data structure of the given algorithm is similar to ones that exist in the literature. However, the data structures are redesigned and simplied in order to fit requirements of the vertex based finite volume method. In order to increase the cache efficiency, the data access patterns for the vertex based finite volume method are investigated and these datas are packed/allocated in a way that they are close to each other in the memory. The present data structure is not limited with tetrahedrons, arbitrary polyhedrons are also supported in the mesh without putting any additional effort. Furthermore, the present data structure also supports adaptive refinement and coarsening. For the implicit and parallel implementation of the FVM algorithm, PETSc and MPI libraries are employed. The performance and accuracy of the present algorithm are tested for the classical benchmark problems by comparing the CPU time for the open source algorithms.

DEM modeling of flexible structures against granular material avalanches

NASA Astrophysics Data System (ADS)

Lambert, Stéphane; Albaba, Adel; Nicot, François; Chareyre, Bruno

2016-04-01

This article presents the numerical modeling of flexible structures intended to contain avalanches of granular and coarse material (e.g. rock slide, a debris slide). The numerical model is based on a discrete element method (YADE-Dem). The DEM modeling of both the flowing granular material and the flexible structure are detailed before presenting some results. The flowing material consists of a dry polydisperse granular material accounting for the non-sphericity of real materials. The flexible structure consists in a metallic net hanged on main cables, connected to the ground via anchors, on both sides of the channel, including dissipators. All these components were modeled as flexible beams or wires, with mechanical parameters defined from literature data. The simulation results are presented with the aim of investigating the variability of the structure response depending on different parameters related to the structure (inclination of the fence, with/without brakes, mesh size opening), but also to the channel (inclination). Results are then compared with existing recommendations in similar fields.

Post-traumatic stress symptoms and structure among orphan and vulnerable children and adolescents in Zambia

PubMed Central

Familiar, Itziar; Murray, Laura; Gross, Alden; Skavenski, Stephanie; Jere, Elizabeth; Bass, Judith

2014-01-01

Background Scant information exists on PTSD symptoms and structure in youth from developing countries. Methods We describe the symptom profile and exposure to trauma experiences among 343 orphan and vulnerable children and adolescents from Zambia. We distinguished profiles of post-traumatic stress symptoms using latent class analysis. Results Average number of trauma-related symptoms (21.6; range 0-38) was similar across sex and age. Latent class model suggested 3 classes varying by level of severity: low (31% of the sample), medium (45% of the sample), and high (24% of the sample) symptomatology. Conclusions Results suggest that PTSD is a continuously distributed latent trait. PMID:25382359

Trace fossils of microbial colonization on Mars: Criteria for search and for sample return

NASA Technical Reports Server (NTRS)

Friedmann, E. I.

1988-01-01

The recent discovery of microbial trace-fossil formation in the frigid Ross Desert of Antarctica suggests that early primitive life on Mars may have left behind similar signatures. These trace fossils are apparent as chemical or physical changes in rock (or sediment) structure (or chemistry) caused by the activity of organisms. Life on Mars, if it ever existed, almost certainly did not evolve above the level of microorganisms, and this should be considered in search for fossil life. For the reasons detailed here, microbial trace fossils seem to be a better and more realistic target for search than would be true microbial fossils (remnants of cellular structures).

Bifurcation analysis of nephron pressure and flow regulation

NASA Astrophysics Data System (ADS)

Barfred, Mikael; Mosekilde, Erik; Holstein-Rathlou, Niels-Henrik

1996-09-01

One- and two-dimensional continuation techniques are applied to study the bifurcation structure of a model of renal flow and pressure control. Integrating the main physiological mechanisms by which the individual nephron regulates the incoming blood flow, the model describes the interaction between the tubuloglomerular feedback and the response of the afferent arteriole. It is shown how a Hopf bifurcation leads the system to perform self-sustained oscillations if the feedback gain becomes sufficiently strong, and how a further increase of this parameter produces a folded structure of overlapping period-doubling cascades. Similar phenomena arise in response to increasing blood pressure. The numerical analyses are supported by existing experimental results on anesthetized rats.

The dynamics of single protein molecules is non-equilibrium and self-similar over thirteen decades in time

NASA Astrophysics Data System (ADS)

Hu, Xiaohu; Hong, Liang; Dean Smith, Micholas; Neusius, Thomas; Cheng, Xiaolin; Smith, Jeremy C.

2016-02-01

Internal motions of proteins are essential to their function. The time dependence of protein structural fluctuations is highly complex, manifesting subdiffusive, non-exponential behaviour with effective relaxation times existing over many decades in time, from ps up to ~102 s (refs ,,,). Here, using molecular dynamics simulations, we show that, on timescales from 10-12 to 10-5 s, motions in single proteins are self-similar, non-equilibrium and exhibit ageing. The characteristic relaxation time for a distance fluctuation, such as inter-domain motion, is observation-time-dependent, increasing in a simple, power-law fashion, arising from the fractal nature of the topology and geometry of the energy landscape explored. Diffusion over the energy landscape follows a non-ergodic continuous time random walk. Comparison with single-molecule experiments suggests that the non-equilibrium self-similar dynamical behaviour persists up to timescales approaching the in vivo lifespan of individual protein molecules.

Effect law of Damage Characteristics of Rock Similar Material with Pre-Existing Cracks

NASA Astrophysics Data System (ADS)

Li, S. G.; Cheng, X. Y.; Liu, C.

2017-11-01

In order to further study the failure mechanism for rock similar materials, this study established the damage model based on accumulative AE events, investigated the damage characteristics for rock similar material samples with pre-existing cracks of varying width under uniaxial compression load. The equipment used in this study is the self-developed YYW-II strain controlled unconfined compression apparatus and the PCIE-8 acoustic emission (AE) monitoring system. The influences of the width of the pre-existing cracks to the damage characteristics of rock similar materials are analyzed. Results show that, (1) the damage model can better describe the damage characteristics of rock similar materials; (2) the tested samples have three stages during failure: initial damage stage, stable development of damage stage, and accelerated development of damage stage; (3) with the width of pre-existing cracks vary from 3mm to 5mm, the damage of rock similar materials increases gradually. The outcomes of this study provided additional values to the research of the failure mechanism for geotechnical similar material models.

Characterization and crystal structure of lysine insensitive Corynebacterium glutamicum dihydrodipicolinate synthase (cDHDPS) protein

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

Rice, E.A.; Bannon, G.A.; Glenn, K.C.

2008-11-21

The lysine insensitive Corynebacterium glutamicum dihydrodipicolinate synthase enzyme (cDHDPS) was recently successfully introduced into maize plants to enhance the level of lysine in the grain. To better understand lysine insensitivity of the cDHDPS, we expressed, purified, kinetically characterized the protein, and solved its X-ray crystal structure. The cDHDPS enzyme has a fold and overall structure that is highly similar to other DHDPS proteins. A noteworthy feature of the active site is the evidence that the catalytic lysine residue forms a Schiff base adduct with pyruvate. Analyses of the cDHDPS structure in the vicinity of the putative binding site for S-lysinemore » revealed that the allosteric binding site in the Escherichia coli DHDPS protein does not exist in cDHDPS due to three non-conservative amino acids substitutions, and this is likely why cDHDPS is not feedback inhibited by lysine.« less

Beyond syntactic priming: evidence for activation of alternative syntactic structures.

PubMed

Vasilyeva, Marina; Waterfall, Heidi

2012-03-01

Priming methodology was previously used to investigate children's ability to represent abstract syntactic forms. Existing evidence indicates that following exposure to a particular syntactic structure (such as the passive voice), English-speaking children increase their production of that structure with new lexical items. In the present work, we utilize priming methodology to explore whether exposure to passive primes may increase children's production of sentences that have a different structure but share a similar purpose in discourse. We report three studies, two involving English- and Russian-speaking children, and a third involving Russian-speaking adults. Unlike English, Russian offers a variety of syntactic forms that emphasize the patient of a transitive action, thus fulfilling the discourse function of the passive. We found that English speakers increased the use of the particular syntactic form presented in the prime, whereas Russian speakers increased their production of several different syntactic forms used to emphasize the patient of the action.

Measuring self-concept among African-Americans: validating the factor structure of the self-perception profile for adolescents.

PubMed

Powell-Young, Yolanda M; Spruill, Ida J

2011-12-01

The purpose of this investigation was to examine the reliability and factor structure of the Harter Self-Perception Profile for Adolescents (SPPA) with African-Americans. While the SPPA has demonstrated strong psychometric properties with European-Americans, limited information exists with African-Americans. Three hundred and ten (N = 310) female adolescents, from 14 through 18 years of age, completed the SPPA. Estimations of internal consistency reliability with Cronbach's alpha (alpha), item suitability with Pearson (gamma) correlations, and evaluation of factor structure fit utilizing principle axis extraction with oblimin (oblique) rotation were conducted. When compared with Harter's normative data, psychometric properties of the SPPA varied significantly with the current sample. Findings suggested cautious interpretation of data generated with demographically similar cohorts. Further study is warranted to ascertain the factor structure that is most relevant for use with African-American adolescents.

Hierarchical Multi-atlas Label Fusion with Multi-scale Feature Representation and Label-specific Patch Partition

PubMed Central

Wu, Guorong; Kim, Minjeong; Sanroma, Gerard; Wang, Qian; Munsell, Brent C.; Shen, Dinggang

2014-01-01

Multi-atlas patch-based label fusion methods have been successfully used to improve segmentation accuracy in many important medical image analysis applications. In general, to achieve label fusion a single target image is first registered to several atlas images, after registration a label is assigned to each target point in the target image by determining the similarity between the underlying target image patch (centered at the target point) and the aligned image patch in each atlas image. To achieve the highest level of accuracy during the label fusion process it’s critical the chosen patch similarity measurement accurately captures the tissue/shape appearance of the anatomical structure. One major limitation of existing state-of-the-art label fusion methods is that they often apply a fixed size image patch throughout the entire label fusion procedure. Doing so may severely affect the fidelity of the patch similarity measurement, which in turn may not adequately capture complex tissue appearance patterns expressed by the anatomical structure. To address this limitation, we advance state-of-the-art by adding three new label fusion contributions: First, each image patch now characterized by a multi-scale feature representation that encodes both local and semi-local image information. Doing so will increase the accuracy of the patch-based similarity measurement. Second, to limit the possibility of the patch-based similarity measurement being wrongly guided by the presence of multiple anatomical structures in the same image patch, each atlas image patch is further partitioned into a set of label-specific partial image patches according to the existing labels. Since image information has now been semantically divided into different patterns, these new label-specific atlas patches make the label fusion process more specific and flexible. Lastly, in order to correct target points that are mislabeled during label fusion, a hierarchically approach is used to improve the label fusion results. In particular, a coarse-to-fine iterative label fusion approach is used that gradually reduces the patch size. To evaluate the accuracy of our label fusion approach, the proposed method was used to segment the hippocampus in the ADNI dataset and 7.0 tesla MR images, sub-cortical regions in LONI LBPA40 dataset, mid-brain regions in SATA dataset from MICCAI 2013 segmentation challenge, and a set of key internal gray matter structures in IXI dataset. In all experiments, the segmentation results of the proposed hierarchical label fusion method with multi-scale feature representations and label-specific atlas patches are more accurate than several well-known state-of-the-art label fusion methods. PMID:25463474

The Crystal Structure and RNA-Binding of an Orthomyxovirus Nucleoprotein

PubMed Central

Zheng, Wenjie; Olson, John; Vakharia, Vikram; Tao, Yizhi Jane

2013-01-01

Genome packaging for viruses with segmented genomes is often a complex problem. This is particularly true for influenza viruses and other orthomyxoviruses, whose genome consists of multiple negative-sense RNAs encapsidated as ribonucleoprotein (RNP) complexes. To better understand the structural features of orthomyxovirus RNPs that allow them to be packaged, we determined the crystal structure of the nucleoprotein (NP) of a fish orthomyxovirus, the infectious salmon anemia virus (ISAV) (genus Isavirus). As the major protein component of the RNPs, ISAV-NP possesses a bi-lobular structure similar to the influenza virus NP. Because both RNA-free and RNA-bound ISAV NP forms stable dimers in solution, we were able to measure the NP RNA binding affinity as well as the stoichiometry using recombinant proteins and synthetic oligos. Our RNA binding analysis revealed that each ISAV-NP binds ∼12 nts of RNA, shorter than the 24–28 nts originally estimated for the influenza A virus NP based on population average. The 12-nt stoichiometry was further confirmed by results from electron microscopy and dynamic light scattering. Considering that RNPs of ISAV and the influenza viruses have similar morphologies and dimensions, our findings suggest that NP-free RNA may exist on orthomyxovirus RNPs, and selective RNP packaging may be accomplished through direct RNA-RNA interactions. PMID:24068932

Partially collapsed cristobalite structure in the non molecular phase V in CO2

PubMed Central

Santoro, Mario; Gorelli, Federico A.; Bini, Roberto; Haines, Julien; Cambon, Olivier; Levelut, Claire; Montoya, Javier A.; Scandolo, Sandro

2012-01-01

Non molecular CO2 has been an important subject of study in high pressure physics and chemistry for the past decade opening up a unique area of carbon chemistry. The phase diagram of CO2 includes several non molecular phases above 30 GPa. Among these, the first discovered was CO2-V which appeared silica-like. Theoretical studies suggested that the structure of CO2-V is related to that of β-cristobalite with tetrahedral carbon coordination similar to silicon in SiO2, but reported experimental structural studies have been controversial. We have investigated CO2-V obtained from molecular CO2 at 40–50 GPa and T > 1500 K using synchrotron X-ray diffraction, optical spectroscopy, and computer simulations. The structure refined by the Rietveld method is a partially collapsed variant of SiO2 β-cristobalite, space group , in which the CO4 tetrahedra are tilted by 38.4° about the c-axis. The existence of CO4 tetrahedra (average O-C-O angle of 109.5°) is thus confirmed. The results add to the knowledge of carbon chemistry with mineral phases similar to SiO2 and potential implications for Earth and planetary interiors. PMID:22431594

Porous titanium manufactured by a novel powder tapping method using spherical salt bead space holders: Characterisation and mechanical properties.

PubMed

Jia, Jiangang; Siddiq, Abdur R; Kennedy, Andrew R

2015-08-01

Porous Ti with open porosity in the range of 70-80% has been made using Ti powder and a particulate leaching technique using porous, spherical, NaCl beads. By incorporating the Ti powder into a pre-existing network of salt beads, by tapping followed by compaction, salt dissolution and "sintering", porous structures with uniform density, pore and strut sizes and a predictable level of connectivity have been produced, showing a significant improvement on the structures made by conventional powder mixing processes. Parts made using beads with sizes in the range of 0.5-1.0 mm show excellent promise as porous metals for medical devices, showing structures and porosities similar to those of commercial porous metals used in this sector, with inter-pore connections that are similar to trabecular bone. The elastic modulus (0.86 GPa) is lower than those for commercial porous metals and more closely matches that of trabecular bone and good compressive yield strength is retained (21 MPa). The ability to further tailor the structure, in terms of the density and the size of the pores and interconnections has also been demonstrated by immersion of the porous components in acid. Copyright © 2015 Elsevier Ltd. All rights reserved.

Survey on Sentence Similarity Evaluation using Deep Learning

NASA Astrophysics Data System (ADS)

Ramaprabha, J.; Das, Sayan; Mukerjee, Pronay

2018-04-01

Two questions asking the same thing can have di erent set of vocabulary set and syntactic structure. Which makes detecting the semantics equivalence between the sentences challenging. In online user forums like Quora, Stack Over ow, Stack Exchange, etc. its important to maintain high quality knowledge base by ensuring each unique question exists only once. Writers shouldn't have to write the same answer to each of the similar question and the reader must get a single page of the question they are looking for. For example, consider questions like What are the best ways to lose weight?, How can a person reduce weight?, and What are elective weight loss plans? to be duplicate questions because they all have the same intent.

Guidelines for transoesophageal echocardiographic probe cleaning and disinfection from the British Society of Echocardiography.

PubMed

Kanagala, P; Bradley, C; Hoffman, P; Steeds, R P

2011-10-01

The clinical utility of transoesophageal echocardiography (TOE) is well established. Being a semi-invasive procedure, however, the potential for transmission of infection between sequential patients exists. This has implications for the protection of both patients and medical staff. Guidelines for disinfection during gastrointestinal endoscopy (GIE) have been in place for many years.(1,2) Unfortunately, similar guidance is lacking with respect to TOE. Although traversing the same body cavities and sharing many similarities with upper GIE, there are fundamental structural and procedural differences with TOE which merit special consideration in establishing a decontamination protocol. This document provides recommendations for TOE probe decontamination based on the available evidence, expert opinion, and modification of the current British Society of Gastroenterology guidelines.

Structural classification of small, disulfide-rich protein domains.

PubMed

Cheek, Sara; Krishna, S Sri; Grishin, Nick V

2006-05-26

Disulfide-rich domains are small protein domains whose global folds are stabilized primarily by the formation of disulfide bonds and, to a much lesser extent, by secondary structure and hydrophobic interactions. Disulfide-rich domains perform a wide variety of roles functioning as growth factors, toxins, enzyme inhibitors, hormones, pheromones, allergens, etc. These domains are commonly found both as independent (single-domain) proteins and as domains within larger polypeptides. Here, we present a comprehensive structural classification of approximately 3000 small, disulfide-rich protein domains. We find that these domains can be arranged into 41 fold groups on the basis of structural similarity. Our fold groups, which describe broader structural relationships than existing groupings of these domains, bring together representatives with previously unacknowledged similarities; 18 of the 41 fold groups include domains from several SCOP folds. Within the fold groups, the domains are assembled into families of homologs. We define 98 families of disulfide-rich domains, some of which include newly detected homologs, particularly among knottin-like domains. On the basis of this classification, we have examined cases of convergent and divergent evolution of functions performed by disulfide-rich proteins. Disulfide bonding patterns in these domains are also evaluated. Reducible disulfide bonding patterns are much less frequent, while symmetric disulfide bonding patterns are more common than expected from random considerations. Examples of variations in disulfide bonding patterns found within families and fold groups are discussed.

Clustering network layers with the strata multilayer stochastic block model.

PubMed

Stanley, Natalie; Shai, Saray; Taylor, Dane; Mucha, Peter J

2016-01-01

Multilayer networks are a useful data structure for simultaneously capturing multiple types of relationships between a set of nodes. In such networks, each relational definition gives rise to a layer. While each layer provides its own set of information, community structure across layers can be collectively utilized to discover and quantify underlying relational patterns between nodes. To concisely extract information from a multilayer network, we propose to identify and combine sets of layers with meaningful similarities in community structure. In this paper, we describe the "strata multilayer stochastic block model" (sMLSBM), a probabilistic model for multilayer community structure. The central extension of the model is that there exist groups of layers, called "strata", which are defined such that all layers in a given stratum have community structure described by a common stochastic block model (SBM). That is, layers in a stratum exhibit similar node-to-community assignments and SBM probability parameters. Fitting the sMLSBM to a multilayer network provides a joint clustering that yields node-to-community and layer-to-stratum assignments, which cooperatively aid one another during inference. We describe an algorithm for separating layers into their appropriate strata and an inference technique for estimating the SBM parameters for each stratum. We demonstrate our method using synthetic networks and a multilayer network inferred from data collected in the Human Microbiome Project.

First principles study of structural, vibrational and electronic properties of graphene-like MX 2 (M=Mo, Nb, W, Ta; X=S, Se, Te) monolayers

NASA Astrophysics Data System (ADS)

Ding, Yi; Wang, Yanli; Ni, Jun; Shi, Lin; Shi, Siqi; Tang, Weihua

2011-05-01

Using first principles calculations, we investigate the structural, vibrational and electronic structures of the monolayer graphene-like transition-metal dichalcogenide (MX 2) sheets. We find the lattice parameters and stabilities of the MX 2 sheets are mainly determined by the chalcogen atoms, while the electronic properties depend on the metal atoms. The NbS 2 and TaS 2 sheets have comparable energetic stabilities to the synthesized MoS 2 and WS 2 ones. The molybdenum and tungsten dichalcogenide (MoX 2 and WX 2) sheets have similar lattice parameters, vibrational modes, and electronic structures. These analogies also exist between the niobium and tantalum dichalcogenide (NbX 2 and TaX 2) sheets. However, the NbX 2 and TaX 2 sheets are metals, while the MoX 2 and WX 2 ones are semiconductors with direct-band gaps. When the Nb and Ta atoms are doped into the MoS 2 and WS 2 sheets, a semiconductor-to-metal transition occurs. Comparing to the bulk compounds, these monolayer sheets have similar structural parameters and properties, but their vibrational and electronic properties are varied and have special characteristics. Our results suggest that the graphene-like MX 2 sheets have potential applications in nano-electronics and nano-devices.

Clustering network layers with the strata multilayer stochastic block model

PubMed Central

Stanley, Natalie; Shai, Saray; Taylor, Dane; Mucha, Peter J.

2016-01-01

Multilayer networks are a useful data structure for simultaneously capturing multiple types of relationships between a set of nodes. In such networks, each relational definition gives rise to a layer. While each layer provides its own set of information, community structure across layers can be collectively utilized to discover and quantify underlying relational patterns between nodes. To concisely extract information from a multilayer network, we propose to identify and combine sets of layers with meaningful similarities in community structure. In this paper, we describe the “strata multilayer stochastic block model” (sMLSBM), a probabilistic model for multilayer community structure. The central extension of the model is that there exist groups of layers, called “strata”, which are defined such that all layers in a given stratum have community structure described by a common stochastic block model (SBM). That is, layers in a stratum exhibit similar node-to-community assignments and SBM probability parameters. Fitting the sMLSBM to a multilayer network provides a joint clustering that yields node-to-community and layer-to-stratum assignments, which cooperatively aid one another during inference. We describe an algorithm for separating layers into their appropriate strata and an inference technique for estimating the SBM parameters for each stratum. We demonstrate our method using synthetic networks and a multilayer network inferred from data collected in the Human Microbiome Project. PMID:28435844

Population genetics and evaluation of genetic evidence for subspecies in the Semipalmated Sandpiper (Calidris pusilla)

USGS Publications Warehouse

Miller, Mark P.; Gratto-Trevor, Cheri; Haig, Susan M.; Mizrahi, David S.; Mitchell, Melanie M.; Mullins, Thomas D.

2013-01-01

Semipalmated Sandpipers (Calidris pusilla) are among the most common North American shorebirds. Breeding in Arctic North America, this species displays regional differences in migratory pathways and possesses longitudinal bill length variation. Previous investigations suggested that genetic structure may occur within Semipalmated Sandpipers and that three subspecies corresponding to western, central, and eastern breeding groups exist. In this study, mitochondrial control region sequences and nuclear microsatellite loci were used to analyze DNA of birds (microsatellites: n = 120; mtDNA: n = 114) sampled from seven North American locations. Analyses designed to quantify genetic structure and diversity patterns, evaluate genetic evidence for population size changes, and determine if genetic data support the existence of Semipalmated Sandpiper subspecies were performed. Genetic structure based only on the mtDNA data was observed, whereas the microsatellite loci provided no evidence of genetic differentiation. Differentiation among locations and regions reflected allele frequency differences rather than separate phylogenetic groups, and similar levels of genetic diversity were noted. Combined, the two data sets provided no evidence to support the existence of subspecies and were not useful for determining migratory connectivity between breeding sites and wintering grounds. Birds from western and central groups displayed signatures of population expansions, whereas the eastern group was more consistent with a stable overall population. Results of this analysis suggest that the eastern group was the source of individuals that colonized the central and western regions currently utilized by Semipalmated Sandpipers.

Crystal structure of a dimeric mannose-specific agglutinin from garlic: quaternary association and carbohydrate specificity.

PubMed

Chandra, N R; Ramachandraiah, G; Bachhawat, K; Dam, T K; Surolia, A; Vijayan, M

1999-01-22

A mannose-specific agglutinin, isolated from garlic bulbs, has been crystallized in the presence of a large excess of alpha-d-mannose, in space group C2 and cell dimensions, a=203.24, b=43.78, c=79.27 A, beta=112.4 degrees, with two dimers in the asymmetric unit. X-ray diffraction data were collected up to a nominal resolution of 2.4 A and the structure was solved by molecular replacement. The structure, refined to an R-factor of 22.6 % and an Rfree of 27.8 % reveals a beta-prism II fold, similar to that in the snowdrop lectin, comprising three antiparallel four-stranded beta-sheets arranged as a 12-stranded beta-barrel, with an approximate internal 3-fold symmetry. This agglutinin is, however, a dimer unlike snowdrop lectin which exists as a tetramer, despite a high degree of sequence similarity between them. A comparison of the two structures reveals a few substitutions in the garlic lectin which stabilise it into a dimer and prevent tetramer formation. Three mannose molecules have been identified on each subunit. In addition, electron density is observed for another possible mannose molecule per dimer resulting in a total of seven mannose molecules in each dimer. Although the mannose binding sites and the overall structure are similar in the subunits of snowdrop and garlic lectin, their specificities to glycoproteins such as GP120 vary considerably. These differences appear, in part, to be a direct consequence of the differences in oligomerisation, implying that variation in quaternary association may be a mode of achieving oligosaccharide specificity in bulb lectins. Copyright 1998 Academic Press.

Theoretical exploration of various lithium peroxide crystal structures in a Li-air battery

DOE PAGES

Lau, Kah; Qiu, Dantong; Luo, Xiangyi; ...

2015-01-14

We describe a series of metastable Li₂O₂ crystal structures involving different orientations and displacements of the O₂²⁻ peroxy ions based on the known Li₂O₂ crystal structure. Within the vicinity of the chemical potential ΔG ~ 0.20 eV/Li from the thermodynamic ground state of the Li₂O₂ crystal structure (i.e., Föppl structure), all of these newly found metastable Li₂O₂ crystal structures are found to be insulating and high-k materials, and they have a common unique signature of an O₂²⁻ O-O vibration mode (ω ~ 799–865 cm⁻¹), which is in the range of that commonly observed in Li-air battery experiments, regardless of themore » random O₂²⁻ orientations and the symmetry in the crystal lattice. From XRD patterns analysis, the commercially available Li₂O₂ powder is confirmed to be the thermodynamic ground state Föppl-like structure. However, for Li₂O₂ compounds that are grown electrochemically under the environment of Li-O₂ cells, we found that the XRD patterns alone are not sufficient for structural identification of these metastable Li₂O₂ crystalline phases due to the poor crystallinity of the sample. In addition, the commonly known Raman signal of O₂²⁻ vibration mode is also found to be insufficient to validate the possible existence of these newly predicted Li₂O₂ crystal structures, as all of them similarly share the similar O₂²⁻ vibration mode. However considering that the discharge voltage in most Li-O₂ cells are typically several tenths of an eV below the thermodynamic equilibrium for the formation of ground state Föppl structure, the formation of these metastable Li₂O₂ crystal structures appears to be thermodynamically feasible.« less

Evolutionary conservation of sequence and secondary structures inCRISPR repeats

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

Kunin, Victor; Sorek, Rotem; Hugenholtz, Philip

Clustered Regularly Interspaced Palindromic Repeats (CRISPRs) are a novel class of direct repeats, separated by unique spacer sequences of similar length, that are present in {approx}40% of bacterial and all archaeal genomes analyzed to date. More than 40 gene families, called CRISPR-associated sequences (CAS), appear in conjunction with these repeats and are thought to be involved in the propagation and functioning of CRISPRs. It has been proposed that the CRISPR/CAS system samples, maintains a record of, and inactivates invasive DNA that the cell has encountered, and therefore constitutes a prokaryotic analog of an immune system. Here we analyze CRISPR repeatsmore » identified in 195 microbial genomes and show that they can be organized into multiple clusters based on sequence similarity. All individual repeats in any given cluster were inferred to form characteristic RNA secondary structure, ranging from non-existent to pronounced. Stable secondary structures included G:U base pairs and exhibited multiple compensatory base changes in the stem region, indicating evolutionary conservation and functional importance. We also show that the repeat-based classification corresponds to, and expands upon, a previously reported CAS gene-based classification including specific relationships between CRISPR and CAS subtypes.« less

Anti-infectious drug repurposing using an integrated chemical genomics and structural systems biology approach.

PubMed

Ng, Clara; Hauptman, Ruth; Zhang, Yinliang; Bourne, Philip E; Xie, Lei

2014-01-01

The emergence of multi-drug and extensive drug resistance of microbes to antibiotics poses a great threat to human health. Although drug repurposing is a promising solution for accelerating the drug development process, its application to anti-infectious drug discovery is limited by the scope of existing phenotype-, ligand-, or target-based methods. In this paper we introduce a new computational strategy to determine the genome-wide molecular targets of bioactive compounds in both human and bacterial genomes. Our method is based on the use of a novel algorithm, ligand Enrichment of Network Topological Similarity (ligENTS), to map the chemical universe to its global pharmacological space. ligENTS outperforms the state-of-the-art algorithms in identifying novel drug-target relationships. Furthermore, we integrate ligENTS with our structural systems biology platform to identify drug repurposing opportunities via target similarity profiling. Using this integrated strategy, we have identified novel P. falciparum targets of drug-like active compounds from the Malaria Box, and suggest that a number of approved drugs may be active against malaria. This study demonstrates the potential of an integrative chemical genomics and structural systems biology approach to drug repurposing.

Macroclimatic change expected to transform coastal wetland ecosystems this century

USGS Publications Warehouse

Gabler, Christopher A.; Osland, Michael J.; Grace, James B.; Stagg, Camille L.; Day, Richard H.; Hartley, Stephen B.; Enwright, Nicholas M.; From, Andrew; McCoy, Meagan L.; McLeod, Jennie L.

2017-01-01

Coastal wetlands, existing at the interface between land and sea, are highly vulnerable to climate change. Macroclimate (for example, temperature and precipitation regimes) greatly influences coastal wetland ecosystem structure and function. However, research on climate change impacts in coastal wetlands has concentrated primarily on sea-level rise and largely ignored macroclimatic drivers, despite their power to transform plant community structure and modify ecosystem goods and services. Here, we model wetland plant community structure based on macroclimate using field data collected across broad temperature and precipitation gradients along the northern Gulf of Mexico coast. Our analyses quantify strongly nonlinear temperature thresholds regulating the potential for marsh-to-mangrove conversion. We also identify precipitation thresholds for dominance by various functional groups, including succulent plants and unvegetated mudflats. Macroclimate-driven shifts in foundation plant species abundance will have large effects on certain ecosystem goods and services. Based on current and projected climatic conditions, we project that transformative ecological changes are probable throughout the region this century, even under conservative climate scenarios. Coastal wetland ecosystems are functionally similar worldwide, so changes in this region are indicative of potential future changes in climatically similar regions globally.

Efficient Design and Analysis of Lightweight Reinforced Core Sandwich and PRSEUS Structures

NASA Technical Reports Server (NTRS)

Bednarcyk, Brett A.; Yarrington, Phillip W.; Lucking, Ryan C.; Collier, Craig S.; Ainsworth, James J.; Toubia, Elias A.

2012-01-01

Design, analysis, and sizing methods for two novel structural panel concepts have been developed and incorporated into the HyperSizer Structural Sizing Software. Reinforced Core Sandwich (RCS) panels consist of a foam core with reinforcing composite webs connecting composite facesheets. Boeing s Pultruded Rod Stitched Efficient Unitized Structure (PRSEUS) panels use a pultruded unidirectional composite rod to provide axial stiffness along with integrated transverse frames and stitching. Both of these structural concepts are ovencured and have shown great promise applications in lightweight structures, but have suffered from the lack of efficient sizing capabilities similar to those that exist for honeycomb sandwich, foam sandwich, hat stiffened, and other, more traditional concepts. Now, with accurate design methods for RCS and PRSEUS panels available in HyperSizer, these concepts can be traded and used in designs as is done with the more traditional structural concepts. The methods developed to enable sizing of RCS and PRSEUS are outlined, as are results showing the validity and utility of the methods. Applications include several large NASA heavy lift launch vehicle structures.

Evaluating the Influence of the Microsatellite Marker Set on the Genetic Structure Inferred in Pyrus communis L.

PubMed Central

Urrestarazu, Jorge; Royo, José B.; Santesteban, Luis G.; Miranda, Carlos

2015-01-01

Fingerprinting information can be used to elucidate in a robust manner the genetic structure of germplasm collections, allowing a more rational and fine assessment of genetic resources. Bayesian model-based approaches are nowadays majorly preferred to infer genetic structure, but it is still largely unresolved how marker sets should be built in order to obtain a robust inference. The objective was to evaluate, in Pyrus germplasm collections, the influence of the SSR marker set size on the genetic structure inferred, also evaluating the influence of the criterion used to select those markers. Inferences were performed considering an increasing number of SSR markers that ranged from just two up to 25, incorporated one at a time into the analysis. The influence of the number of SSR markers used was evaluated comparing the number of populations and the strength of the signal detected, and also the similarity of the genotype assignments to populations between analyses. In order to test if those results were influenced by the criterion used to select the SSRs, several choosing scenarios based on the discrimination power or the fixation index values of the SSRs were tested. Our results indicate that population structure could be inferred accurately once a certain SSR number threshold was reached, which depended on the underlying structure within the genotypes, but the method used to select the markers included on each set appeared not to be very relevant. The minimum number of SSRs required to provide robust structure inferences and adequate measurements of the differentiation, even when low differentiation levels exist within populations, was proved similar to that of the complete list of recommended markers for fingerprinting. When a SSR set size similar to the minimum marker sets recommended for fingerprinting it is used, only major divisions or moderate (F ST>0.05) differentiation of the germplasm are detected. PMID:26382618

Tertiary model of a plant cellulose synthase

PubMed Central

Sethaphong, Latsavongsakda; Haigler, Candace H.; Kubicki, James D.; Zimmer, Jochen; Bonetta, Dario; DeBolt, Seth; Yingling, Yaroslava G.

2013-01-01

A 3D atomistic model of a plant cellulose synthase (CESA) has remained elusive despite over forty years of experimental effort. Here, we report a computationally predicted 3D structure of 506 amino acids of cotton CESA within the cytosolic region. Comparison of the predicted plant CESA structure with the solved structure of a bacterial cellulose-synthesizing protein validates the overall fold of the modeled glycosyltransferase (GT) domain. The coaligned plant and bacterial GT domains share a six-stranded β-sheet, five α-helices, and conserved motifs similar to those required for catalysis in other GT-2 glycosyltransferases. Extending beyond the cross-kingdom similarities related to cellulose polymerization, the predicted structure of cotton CESA reveals that plant-specific modules (plant-conserved region and class-specific region) fold into distinct subdomains on the periphery of the catalytic region. Computational results support the importance of the plant-conserved region and/or class-specific region in CESA oligomerization to form the multimeric cellulose–synthesis complexes that are characteristic of plants. Relatively high sequence conservation between plant CESAs allowed mapping of known mutations and two previously undescribed mutations that perturb cellulose synthesis in Arabidopsis thaliana to their analogous positions in the modeled structure. Most of these mutation sites are near the predicted catalytic region, and the confluence of other mutation sites supports the existence of previously undefined functional nodes within the catalytic core of CESA. Overall, the predicted tertiary structure provides a platform for the biochemical engineering of plant CESAs. PMID:23592721

Sustainability on the urban scale: Proposal of a structure of indicators for the Spanish context

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

Braulio-Gonzalo, Marta, E-mail: braulio@uji.es; Bovea, María Dolores, E-mail: bovea@uji.es; Ruá, María José, E-mail: rua@uji.es

Some efforts to assess sustainability on the urban scale have been made and different tools for measuring the impact on and caused by cities have emerged. However, the sustainability concept varies from region to region, and indicators to measure it should be suitable for the context-specific conditions of the region under study. After doing a comprehensive review of the indicators included in 13 tools developed to assess urban sustainability of cities, this article proposes a new structure of indicators adapted to a Mediterranean city in Spain. The proposed structure is based on a two-level scheme that consists in 14 categoriesmore » and 63 subcategories, which agglutinate urban sustainability indicators according to their purpose. This structure suggests a set of comprehensible qualitative and quantitative indicators that are easily applicable on neighbourhood or city scales. Given the similar features of Mediterranean countries in terms of environmental and socio-economic aspects, the proposed structure could be extrapolated to other countries with climatic and cultural similarities. Otherwise, the system is a useful tool in the decision-making process to help the different stakeholders involved in new urban developments and regeneration projects in existing neighbourhoods, such as developers, urban planners and public administrations. - Highlights: • Comprehensive review of 13 urban sustainability assessment tools • Proposal of a two-level structure to cluster urban sustainability indicators • Inclusion of sustainability criteria for urban planning projects and interventions.« less

Beyond common features: The role of roles in determining similarity1

PubMed Central

Jones, Matt; Love, Bradley C.

2007-01-01

Historically, accounts of object representation and perceived similarity have focused on intrinsic features. Although more recent accounts have explored how objects, scenes, and situations containing common relational structures come to be perceived as similar, less is known about how the perceived similarity of parts or objects embedded within these relational systems is affected. The current studies test the hypothesis that objects situated in common relational systems come to be perceived as more similar. Similarity increases most for objects playing the same role within a relation (e.g., predator), but also increases for objects playing different roles within the same relation (e.g., the predator or prey role in the hunts relation) regardless of whether the objects participate in the same instance of the relation. This pattern of results can be captured by extending existing models that extract meaning from text corpora so that they are sensitive to the verb-specific thematic roles that objects fill. Alternative explanations based on analogical and inferential processes are also considered, as well as the implications of the current findings to research in language processing, personality and person perception, decision making, and category learning. PMID:17094958

Functional Inference of Complex Anatomical Tendinous Networks at a Macroscopic Scale via Sparse Experimentation

PubMed Central

Saxena, Anupam; Lipson, Hod; Valero-Cuevas, Francisco J.

2012-01-01

In systems and computational biology, much effort is devoted to functional identification of systems and networks at the molecular-or cellular scale. However, similarly important networks exist at anatomical scales such as the tendon network of human fingers: the complex array of collagen fibers that transmits and distributes muscle forces to finger joints. This network is critical to the versatility of the human hand, and its function has been debated since at least the 16th century. Here, we experimentally infer the structure (both topology and parameter values) of this network through sparse interrogation with force inputs. A population of models representing this structure co-evolves in simulation with a population of informative future force inputs via the predator-prey estimation-exploration algorithm. Model fitness depends on their ability to explain experimental data, while the fitness of future force inputs depends on causing maximal functional discrepancy among current models. We validate our approach by inferring two known synthetic Latex networks, and one anatomical tendon network harvested from a cadaver's middle finger. We find that functionally similar but structurally diverse models can exist within a narrow range of the training set and cross-validation errors. For the Latex networks, models with low training set error [<4%] and resembling the known network have the smallest cross-validation errors [∼5%]. The low training set [<4%] and cross validation [<7.2%] errors for models for the cadaveric specimen demonstrate what, to our knowledge, is the first experimental inference of the functional structure of complex anatomical networks. This work expands current bioinformatics inference approaches by demonstrating that sparse, yet informative interrogation of biological specimens holds significant computational advantages in accurate and efficient inference over random testing, or assuming model topology and only inferring parameters values. These findings also hold clues to both our evolutionary history and the development of versatile machines. PMID:23144601

Functional inference of complex anatomical tendinous networks at a macroscopic scale via sparse experimentation.

PubMed

Saxena, Anupam; Lipson, Hod; Valero-Cuevas, Francisco J

2012-01-01

In systems and computational biology, much effort is devoted to functional identification of systems and networks at the molecular-or cellular scale. However, similarly important networks exist at anatomical scales such as the tendon network of human fingers: the complex array of collagen fibers that transmits and distributes muscle forces to finger joints. This network is critical to the versatility of the human hand, and its function has been debated since at least the 16(th) century. Here, we experimentally infer the structure (both topology and parameter values) of this network through sparse interrogation with force inputs. A population of models representing this structure co-evolves in simulation with a population of informative future force inputs via the predator-prey estimation-exploration algorithm. Model fitness depends on their ability to explain experimental data, while the fitness of future force inputs depends on causing maximal functional discrepancy among current models. We validate our approach by inferring two known synthetic Latex networks, and one anatomical tendon network harvested from a cadaver's middle finger. We find that functionally similar but structurally diverse models can exist within a narrow range of the training set and cross-validation errors. For the Latex networks, models with low training set error [<4%] and resembling the known network have the smallest cross-validation errors [∼5%]. The low training set [<4%] and cross validation [<7.2%] errors for models for the cadaveric specimen demonstrate what, to our knowledge, is the first experimental inference of the functional structure of complex anatomical networks. This work expands current bioinformatics inference approaches by demonstrating that sparse, yet informative interrogation of biological specimens holds significant computational advantages in accurate and efficient inference over random testing, or assuming model topology and only inferring parameters values. These findings also hold clues to both our evolutionary history and the development of versatile machines.

Identifying Drug-Target Interactions with Decision Templates.

PubMed

Yan, Xiao-Ying; Zhang, Shao-Wu

2018-01-01

During the development process of new drugs, identification of the drug-target interactions wins primary concerns. However, the chemical or biological experiments bear the limitation in coverage as well as the huge cost of both time and money. Based on drug similarity and target similarity, chemogenomic methods can be able to predict potential drug-target interactions (DTIs) on a large scale and have no luxurious need about target structures or ligand entries. In order to reflect the cases that the drugs having variant structures interact with common targets and the targets having dissimilar sequences interact with same drugs. In addition, though several other similarity metrics have been developed to predict DTIs, the combination of multiple similarity metrics (especially heterogeneous similarities) is too naïve to sufficiently explore the multiple similarities. In this paper, based on Gene Ontology and pathway annotation, we introduce two novel target similarity metrics to address above issues. More importantly, we propose a more effective strategy via decision template to integrate multiple classifiers designed with multiple similarity metrics. In the scenarios that predict existing targets for new drugs and predict approved drugs for new protein targets, the results on the DTI benchmark datasets show that our target similarity metrics are able to enhance the predictive accuracies in two scenarios. And the elaborate fusion strategy of multiple classifiers has better predictive power than the naïve combination of multiple similarity metrics. Compared with other two state-of-the-art approaches on the four popular benchmark datasets of binary drug-target interactions, our method achieves the best results in terms of AUC and AUPR for predicting available targets for new drugs (S2), and predicting approved drugs for new protein targets (S3).These results demonstrate that our method can effectively predict the drug-target interactions. The software package can freely available at https://github.com/NwpuSY/DT_all.git for academic users. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Observing Flux Rope Formation During the Impulsive Phase of a Solar Eruption

NASA Astrophysics Data System (ADS)

Cheng, Xin; Zhang, J.; Yang, L.; Ding, M.

2011-05-01

Magnetic flux rope is believed to be an important structural component of coronal mass ejections (CMEs). While there exist much observational evidence of the flux rope post the eruption, e.g., as seen in remote-sensing coronagraph images or in-situ solar wind data, the direct observation of flux ropes during CME impulsive phase has been rare or non-exist. In this Letter, we present an unambiguous observation of a flux rope still in the formation phase in the low corona. The CME of interest occurred above the east limb on 2010 November 03 with footpoints partially blocked. The flux rope was seen as a blob of hot plasma in AIA 131 A passband (peak temperature 11 MK) rising from the core of the source active region, rapidly moving outward and stretching upward the surrounding background magnetic field. The stretched magnetic field seemed to curve-in, similar to the classical magnetic reconnection scenario in eruptive flares. The flux rope was also seen as a dark cavity in AIA 211 A passpand (2.0 MK) and 171 A passband (0.6 MK); in these relatively cool temperature bands, a bright rim clearly enclosed the dark cavity. The bright rim likely represents the pile-up of the surrounding coronal plasma compressed by the expanding flux rope. The composite structure seen in AIA multiple temperature bands is very similar to that in the corresponding coronagraph images, which consists of a bright leading edge and a dark cavity, commonly believed to be a flux rope.

A taxonomy of state public health preparedness units: an empirical examination of organizational structure.

PubMed

Menachemi, Nir; Yeager, Valerie A; Duncan, W Jack; Katholi, Charles R; Ginter, Peter M

2012-01-01

State public health preparedness units (SPHPUs) were developed in response to federal funding to improve response to disasters: a responsibility that had not traditionally been within the purview of public health. The SPHPUs were created within the existing public health organizational structure, and their placement may have implications for how the unit functions, how communication takes place, and ultimately how well the key responsibilities are performed. This study empirically identifies a taxonomy of similarly structured SPHPUs and examines whether this structure is associated with state geographic, demographic, and threat-vulnerability characteristics. Data representing each SPHPU were extracted from publically available sources, including organizational charts and emergency preparedness plans for 2009. A cross-sectional segmentation analysis was conducted of variables representing structural attributes. Fifty state public health departments. Variables representing "span of control" and "hierarchal levels" were extracted from organizational charts. Structural "complexity" and "centralization" were extracted from state emergency preparedness documents and other secondary sources. On average, 6.6 people report to the same manager as the SPHPU director; 2.1 levels separate the SPHPU director from the state health officer; and a mean of 13.5 agencies collaborate with SPHPU during a disaster. Despite considerable variability in how SPHPUs had been structured, results of the cluster and principal component analysis identified 7 similarly structured groups. Neither the taxonomic groups nor the individual variables representing structure were found to be associated with state characteristics, including threat vulnerabilities. Our finding supports the hypothesis that SPHPUs are seemingly inadvertently (eg, not strategically) organized. This taxonomy provides the basis for which future research can examine how SPHPU structure relates to performance measures and preparedness strategies.

High resolution 3-D shear wave velocity structure in South China from surface wave tomography

NASA Astrophysics Data System (ADS)

Ning, S.; Guo, Z.; Chen, Y. J.

2017-12-01

Using continuous data from a total of 638 seismic stations, including 484 from CEArray between 2008 and 2013 and 154 from SINOPROBE between 2014 and 2015, we perform both ambient noise and earthquake Rayleigh wave tomography across South China. Combining Rayleigh wave phase velocity between 6and 40s periods from ambient noise tomography and Rayleigh wave phase velocity between 20and 140s from teleseismic two-plane-wave tomography, we obtain phase velocity maps between 6 and140 s periods. We then invert Rayleigh wave phase velocity to construct a 3-D shear wave velocity structure of South China by Markov Chain Monte Carlo method. Similar to other inversion results, our results correspond topography well. Moreover, our results also reveal that velocity structure of the eastern South China in mantle depth is similar to eastern North China, the core of the western South China, Sichuan Block (SB),still exists thick lithosphere. However, owing to much more data employed and some data quality control techniques in this research, our results reveal more detailed structures. Along Qinling-Dabie Orogenic Belt (QDOB), North-South Gravity Lineament (NSGL) and the Sichuan-Yunnan Rhombic Block (SYRB), there are obvious high speed anomalies in depths of 10-20 km, which possibly imply ancient intrusions. Moreover, it seems that Tancheng-Lujiang Fault Zone (TLFZ) has already cut through QDOB, forming a deep fracture cutting through the crust of the whole China continent. Although SB still exists thick lithosphere, there are indications for thermal erosion. At the same time, the lithosphere of the central SYRB seems to be experiencing delamination process, obviously forming a barrier to prevent the hot Tibetan Plateau (TP) mantle material from flowing further southeast. Upwelling hot mantle material possibly triggered by this delamination process might be the cause of the Emeishan Large Igneous Province. There exists an intercontinental low velocity layer in the crust of the TP, which not only extend to the northern part, but the whole SYRB, and further rifle through the vast region between the SYRB and the SB. Its scope corresponds well with topography high in there, which forms a strong evidence for the Lower Crustal Flow model in Eastern Tibet claimed by Royden et al. (Science, 1997).

The Phenomenology of Small-Scale Turbulence

NASA Astrophysics Data System (ADS)

Sreenivasan, K. R.; Antonia, R. A.

I have sometimes thought that what makes a man's work classic is often just this multiplicity [of interpretations], which invites and at the same time resists our craving for a clear understanding. Wright (1982, p. 34), on Wittgenstein's philosophy Small-scale turbulence has been an area of especially active research in the recent past, and several useful research directions have been pursued. Here, we selectively review this work. The emphasis is on scaling phenomenology and kinematics of small-scale structure. After providing a brief introduction to the classical notions of universality due to Kolmogorov and others, we survey the existing work on intermittency, refined similarity hypotheses, anomalous scaling exponents, derivative statistics, intermittency models, and the structure and kinematics of small-scale structure - the latter aspect coming largely from the direct numerical simulation of homogeneous turbulence in a periodic box.

Structure-wise discrimination of adenine and guanine by proteins on the basis of their nonbonded interactions.

PubMed

Usha, S; Selvaraj, S

2015-01-01

We have analyzed the nonbonded interactions of the structurally similar moieties, adenine and guanine forming complexes with proteins. The results comprise (a) the amino acid-ligand atom preferences, (b) solvent accessibility of ligand atoms before and after complex formation with proteins, and (c) preferred amino acid residue atoms involved in the interactions. We have observed that the amino acid preferences involved in the hydrogen bonding interactions vary for adenine and guanine. The structural variation between the purine atoms is clearly reflected by their burial tendency in the solvent environment. Correlation of the mean amino acid preference values show the variation that exists between adenine and guanine preferences of all the amino acid residues. All our observations provide evidence for the discriminating nature of the proteins in recognizing adenine and guanine.

High pressure–low temperature phase diagram of barium: Simplicity versus complexity

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

Desgreniers, Serge; Tse, John S., E-mail: John.Tse@usask.ca; State Key Laboratory of Superhard Materials, Jilin University, 130012 Changchun

2015-11-30

Barium holds a distinctive position among all elements studied upon densification. Indeed, it was the first example shown to violate the long-standing notion that high compression of simple metals should preserve or yield close-packed structures. From modest pressure conditions at room temperature, barium transforms at higher pressures from its simple structures to the extraordinarily complex atomic arrangements of the incommensurate and self-hosting Ba-IV phases. By a detailed mapping of the pressure/temperature structures of barium, we demonstrate the existence of another crystalline arrangement of barium, Ba-VI, at low temperature and high pressure. The simple structure of Ba-VI is unlike that ofmore » complex Ba-IV, the phase encountered in a similar pressure range at room temperature. First-principles calculations predict Ba-VI to be stable at high pressure and superconductive. The results illustrate the complexity of the low temperature-high pressure phase diagram of barium and the significant effect of temperature on structural phase transformations.« less

Controlled replication of butterfly wings for achieving tunable photonic properties.

PubMed

Huang, Jingyun; Wang, Xudong; Wang, Zhong Lin

2006-10-01

The fine structure of the wing scale of a Morpho Peleides butterfly was examined carefully, and the entire configuration was completely replicated by a uniform Al(2)O(3) coating through a low-temperature ALD process. An inverted structure was achieved by removing the butterfly wing template at high temperature, forming a polycrystalline Al(2)O(3) shell structure with precisely controlled thickness. Other than the copy of the morphology of the structure, the optical property, such as the existence of PBG, was also inherited by the alumina replica. Reflection peaks at the violet/blue range were detected on both original wings and their replica, while a simple alumina coating shifted the reflection peak to longer wavelength because of the change of periodicity and refraction index. The alumina replicas also exhibited similar functional structures as waveguide and beam splitter, which may be used as the building blocks for photonic ICs with high reproducibility and lower fabrication cost compared to traditional lithography techniques.

Self-organizing Large-scale Structures in Earth's Foreshock Waves

NASA Astrophysics Data System (ADS)

Ganse, U.; Pfau-Kempf, Y.; Turc, L.; Hoilijoki, S.; von Alfthan, S.; Vainio, R. O.; Palmroth, M.

2017-12-01

Earth's foreshock is populated by plasma waves in the ULF regime, assumed to be caused by wave instabilities of shock-reflected particle beams. While in-situ observation of these waves has provided plentiful data of their amplitudes, frequencies, obliquities and relation to local plasma conditions, global-scale structures are hard to grasp from observation data alone. The hybrid-Vlasov simulation system Vlasiator, designed for kinetic modeling of the Earth's magnetosphere, has been employed to study foreshock formation under radial and near-radial IMF conditions on global scales. Structures arising in the foreshock can be comprehensively studied and directly compared to observation results. Our modeling results show that foreshock waves present emergent large-scale structures, in which regions of waves with similar phase exist. At the interfaces of these regions ("spines") we observe high wave obliquity, higher beam densities and lower beam velocities than inside them. We characterize these apparently self-organizing structures through the interplay between wave- and beam properties and present the microphysical mechanisms involved in their creation.

Surface-enhanced Raman spectroscopy of hexabenzobenzene, C24H12, an analogue of a graphene nanostructure

NASA Astrophysics Data System (ADS)

Owens, Frank J.

2018-05-01

While large scale fabrication of graphene nanoribbons remains a challenge, there exist materials which can be fabricated in quantities such as hexabenzobenzene,HBZB, (C24H12) and which have a two-dimensional (2D) carbon structure similar to graphene nanostructures. Using a 632 nm laser, no Raman spectra could be obtained from the solid material because of a strong luminescence produced by the laser. However, surface-enhanced Raman spectroscopy enabled the measurement of some of the Raman active modes. The G and D modes, which are characteristic fingerprints of a 2D graphene structure, were observed at 1331 and 1600 cm-1, respectively. Density functional theory at the B3LYP/6-31G* level was used to calculate the minimum energy structure and the Raman active vibrational frequencies of HBZB. The calculated minimum energy structure was 2D having D6h symmetry in agreement with the experimental structure in the liquid phase. The calculated frequencies were in good agreement with the measured values.

Structure-directing weak phosphoryl XH...O=P (X = C, N) hydrogen bonds in cyclic oxazaphospholidines and oxazaphosphinanes.

PubMed

van der Lee, A; Rolland, M; Marat, X; Virieux, D; Volle, J N; Pirat, J L

2008-04-01

The structures of six cyclic oxazaphospholidines and three cyclic oxazaphosphinanes have been determined and their supramolecular structures have been compared. The molecules differ with respect to the functional groups attached to the central five- or six-membered rings, but have one phosphoryl group in common. The predominant feature in the supramolecular structures is the existence of relatively weak intermolecular phosphoryl XH...O=P (X = C, N) hydrogen bonds, creating in nearly all cases linear zigzag or double molecular chains. The molecular chains are in general linked to each other via very weak CH...pi or usual hydrogen-bond interactions. A survey of the Cambridge Structural Database on similar XH...O=P interactions shows a very large flexibility of the XH...O angle, which is in agreement with the DFT calculation reported elsewhere. The strength of the XH...O=P interaction can therefore be considered as relatively weak to moderately strong, and is expected to play at least a role in the formation of secondary substructures.

The role of OH…O and CH…O hydrogen bonds and H…H interactions in ethanol/methanol-water heterohexamers.

PubMed

Mejía, Sol M; Espinal, Juan F; Mills, Matthew J L; Mondragón, Fanor

2016-08-01

Bioethanol is one of the world's most extensively produced biofuels. However, it is difficult to purify due to the formation of the ethanol-water azeotrope. Knowledge of the azeotrope structure at the molecular level can help to improve existing purification methods. In order to achieve a better understanding of this azeotrope structure, the characterization of (ethanol)5-water heterohexamers was carried out by analyzing the results of electronic structure calculations performed at the B3LYP/6-31+G(d) level. Hexamerization energies were found to range between -36.8 and -25.8 kcal/mol. Topological analysis of the electron density confirmed the existence of primary (OH…O) hydrogen bonds (HBs), secondary (CH…O) HBs, and H…H interactions in these clusters. Comparison with three different solvated alcohol systems featuring the same types of atom-atom interactions permitted the following order of stability to be determined: (methanol)5-water > (methanol)6 > (ethanol)5-water > (ethanol)6. These findings, together with accompanying geometric and spectroscopic analyses, show that similar cooperative effects exist among the primary HBs for structures with the same arrangement of primary HBs, regardless of the nature of the molecules involved. This result provides an indication that the molecular ratio can be considered to determine the unusual behavior of the ethanol-water system. The investigation also highlights the presence of several types of weak interaction in addition to primary HBs. Graphical Abstract Water-ethanol clusters exhibit a variety of interaction types between their atoms, such as primary OH...O (blue), secondary CH...O (green) and H...H (yellow) interactions as revealed by Quantum Chemical Topology.

Assessment of modal-pushover-based scaling procedure for nonlinear response history analysis of ordinary standard bridges

USGS Publications Warehouse

Kalkan, E.; Kwong, N.

2012-01-01

The earthquake engineering profession is increasingly utilizing nonlinear response history analyses (RHA) to evaluate seismic performance of existing structures and proposed designs of new structures. One of the main ingredients of nonlinear RHA is a set of ground motion records representing the expected hazard environment for the structure. When recorded motions do not exist (as is the case in the central United States) or when high-intensity records are needed (as is the case in San Francisco and Los Angeles), ground motions from other tectonically similar regions need to be selected and scaled. The modal-pushover-based scaling (MPS) procedure was recently developed to determine scale factors for a small number of records such that the scaled records provide accurate and efficient estimates of “true” median structural responses. The adjective “accurate” refers to the discrepancy between the benchmark responses and those computed from the MPS procedure. The adjective “efficient” refers to the record-to-record variability of responses. In this paper, the accuracy and efficiency of the MPS procedure are evaluated by applying it to four types of existing Ordinary Standard bridges typical of reinforced concrete bridge construction in California. These bridges are the single-bent overpass, multi-span bridge, curved bridge, and skew bridge. As compared with benchmark analyses of unscaled records using a larger catalog of ground motions, it is demonstrated that the MPS procedure provided an accurate estimate of the engineering demand parameters (EDPs) accompanied by significantly reduced record-to-record variability of the EDPs. Thus, it is a useful tool for scaling ground motions as input to nonlinear RHAs of Ordinary Standard bridges.

Documentation for assessment of modal pushover-based scaling procedure for nonlinear response history analysis of "ordinary standard" bridges

USGS Publications Warehouse

Kalkan, Erol; Kwong, Neal S.

2010-01-01

The earthquake engineering profession is increasingly utilizing nonlinear response history analyses (RHA) to evaluate seismic performance of existing structures and proposed designs of new structures. One of the main ingredients of nonlinear RHA is a set of ground-motion records representing the expected hazard environment for the structure. When recorded motions do not exist (as is the case for the central United States), or when high-intensity records are needed (as is the case for San Francisco and Los Angeles), ground motions from other tectonically similar regions need to be selected and scaled. The modal-pushover-based scaling (MPS) procedure recently was developed to determine scale factors for a small number of records, such that the scaled records provide accurate and efficient estimates of 'true' median structural responses. The adjective 'accurate' refers to the discrepancy between the benchmark responses and those computed from the MPS procedure. The adjective 'efficient' refers to the record-to-record variability of responses. Herein, the accuracy and efficiency of the MPS procedure are evaluated by applying it to four types of existing 'ordinary standard' bridges typical of reinforced-concrete bridge construction in California. These bridges are the single-bent overpass, multi span bridge, curved-bridge, and skew-bridge. As compared to benchmark analyses of unscaled records using a larger catalog of ground motions, it is demonstrated that the MPS procedure provided an accurate estimate of the engineering demand parameters (EDPs) accompanied by significantly reduced record-to-record variability of the responses. Thus, the MPS procedure is a useful tool for scaling ground motions as input to nonlinear RHAs of 'ordinary standard' bridges.

Empirical development of ground acceleration, velocity, and displacement for accidental explosions at J5 or the proposed large altitude rocket cell at Arnold Engineering Development Center

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

Davis, B.C.

This study is an assessment of the ground shock which may be generated in the event of an accidental explosion at J5 or the Proposed Large Altitude Rocket Cell (LARC) at the Arnold Engineering Development Center (AEDC). The assessment is accomplished by reviewing existing empirical relationships for predicting ground motion from ground shock. These relationships are compared with data for surface explosions at sites with similar geology and with yields similar to expected conditions at AEDC. Empirical relationships are developed from these data and a judgment made whether to use existing empirical relationships or the relationships developed in this study.more » An existing relationship (Lipner et al.) is used to predict velocity; the empirical relationships developed in the course of this study are used to predict acceleration and displacement. The ground motions are presented in table form and as contour plots. Included also is a discussion of damage criteria from blast and earthquake studies. This report recommends using velocity rather than acceleration as an indicator of structural blast damage. It is recommended that v = 2 ips (v = .167 fps) be used as the damage threshold value (no major damage for v less than or equal to 2 ips). 13 references, 25 figures, 6 tables.« less

RNA-TVcurve: a Web server for RNA secondary structure comparison based on a multi-scale similarity of its triple vector curve representation.

PubMed

Li, Ying; Shi, Xiaohu; Liang, Yanchun; Xie, Juan; Zhang, Yu; Ma, Qin

2017-01-21

RNAs have been found to carry diverse functionalities in nature. Inferring the similarity between two given RNAs is a fundamental step to understand and interpret their functional relationship. The majority of functional RNAs show conserved secondary structures, rather than sequence conservation. Those algorithms relying on sequence-based features usually have limitations in their prediction performance. Hence, integrating RNA structure features is very critical for RNA analysis. Existing algorithms mainly fall into two categories: alignment-based and alignment-free. The alignment-free algorithms of RNA comparison usually have lower time complexity than alignment-based algorithms. An alignment-free RNA comparison algorithm was proposed, in which novel numerical representations RNA-TVcurve (triple vector curve representation) of RNA sequence and corresponding secondary structure features are provided. Then a multi-scale similarity score of two given RNAs was designed based on wavelet decomposition of their numerical representation. In support of RNA mutation and phylogenetic analysis, a web server (RNA-TVcurve) was designed based on this alignment-free RNA comparison algorithm. It provides three functional modules: 1) visualization of numerical representation of RNA secondary structure; 2) detection of single-point mutation based on secondary structure; and 3) comparison of pairwise and multiple RNA secondary structures. The inputs of the web server require RNA primary sequences, while corresponding secondary structures are optional. For the primary sequences alone, the web server can compute the secondary structures using free energy minimization algorithm in terms of RNAfold tool from Vienna RNA package. RNA-TVcurve is the first integrated web server, based on an alignment-free method, to deliver a suite of RNA analysis functions, including visualization, mutation analysis and multiple RNAs structure comparison. The comparison results with two popular RNA comparison tools, RNApdist and RNAdistance, showcased that RNA-TVcurve can efficiently capture subtle relationships among RNAs for mutation detection and non-coding RNA classification. All the relevant results were shown in an intuitive graphical manner, and can be freely downloaded from this server. RNA-TVcurve, along with test examples and detailed documents, are available at: http://ml.jlu.edu.cn/tvcurve/ .

Innovative Strategies to Develop Chemical Categories Using a Combination of Structural and Toxicological Properties.

PubMed

Batke, Monika; Gütlein, Martin; Partosch, Falko; Gundert-Remy, Ursula; Helma, Christoph; Kramer, Stefan; Maunz, Andreas; Seeland, Madeleine; Bitsch, Annette

2016-01-01

Interest is increasing in the development of non-animal methods for toxicological evaluations. These methods are however, particularly challenging for complex toxicological endpoints such as repeated dose toxicity. European Legislation, e.g., the European Union's Cosmetic Directive and REACH, demands the use of alternative methods. Frameworks, such as the Read-across Assessment Framework or the Adverse Outcome Pathway Knowledge Base, support the development of these methods. The aim of the project presented in this publication was to develop substance categories for a read-across with complex endpoints of toxicity based on existing databases. The basic conceptual approach was to combine structural similarity with shared mechanisms of action. Substances with similar chemical structure and toxicological profile form candidate categories suitable for read-across. We combined two databases on repeated dose toxicity, RepDose database, and ELINCS database to form a common database for the identification of categories. The resulting database contained physicochemical, structural, and toxicological data, which were refined and curated for cluster analyses. We applied the Predictive Clustering Tree (PCT) approach for clustering chemicals based on structural and on toxicological information to detect groups of chemicals with similar toxic profiles and pathways/mechanisms of toxicity. As many of the experimental toxicity values were not available, this data was imputed by predicting them with a multi-label classification method, prior to clustering. The clustering results were evaluated by assessing chemical and toxicological similarities with the aim of identifying clusters with a concordance between structural information and toxicity profiles/mechanisms. From these chosen clusters, seven were selected for a quantitative read-across, based on a small ratio of NOAEL of the members with the highest and the lowest NOAEL in the cluster (< 5). We discuss the limitations of the approach. Based on this analysis we propose improvements for a follow-up approach, such as incorporation of metabolic information and more detailed mechanistic information. The software enables the user to allocate a substance in a cluster and to use this information for a possible read- across. The clustering tool is provided as a free web service, accessible at http://mlc-reach.informatik.uni-mainz.de.

Modeling the marine magnetic field of Bahía de Banderas, Mexico, confirms the half-graben structure of the bay

NASA Astrophysics Data System (ADS)

Alvarez, Román; López-Loera, Héctor; Arzate, Jorge

2010-06-01

An existing aeromagnetic survey flown on the central, western portion of Mexico did not include an important tectonic structure: Bahía de Banderas. The bay has an extension of approximately 1400 km 2 and is located within the Puerto Vallarta batholith, a granitic structure of Cretaceous origin. We report here the additional gathering of 5523 magnetic values on the bay, in order to complement the existing land aeromagnetic information; this allowed modeling the structure of the bay from the magnetic viewpoint. A late Miocene age has been proposed for the bay making it roughly contemporaneous with the first stages of separation of Baja California from mainland Mexico. Initially proposed as a graben, it was subsequently shown that its structure actually corresponds to a half-graben of the fault growth type, with reverse drag geometry; it appears to have been developed in response to an extensional process in the ˜ N-S direction. Valle de Banderas neighbors the bay constituting its eastern land continuation; it has also been proposed as a graben and it is also likely the result of an extensional process. However, it seems to be a structure more recently formed, probably around 5 Ma. The different time origin of the bay and of the valley is strengthened by the different alignment of the valley axis, where Ameca River flows and discharges into the bay, of around 30° from the trace of Banderas fault. The magnetic responses of the valley, aeromagnetic and terrestrial, support the existence of an extensional process. Upward and downward continuations of the magnetic fields show that Sierra de Vallejo and Sierra de Zapotán, to the NW of the valley, are deeply rooted structures and their magnetic responses are similar to those obtained in the Puerto Vallarta batholith; these characteristics support a common origin for them. Three magnetic profiles trending NNW are modeled across Bahía de Banderas. The models identify the structure as a half-graben with a listric main fault and reverse drag geometry, just as it was previously obtained elsewhere by an independent modeling process.

Habitat fragmentation effects on the orchid bee communities in remnant forests of southeastern Brazil.

PubMed

Knoll, Fátima do Rosário Naschenveng; Penatti, N C

2012-10-01

The effect of habitat fragmentation on the structure of orchid bee communities was analyzed by the investigation of the existence of a spatial structure in the richness and abundance of Euglossini species and by determining the relationship between these data and environmental factors. The surveys were carried out in four different forest fragments and one university campus. Richness, abundance, and diversity of species were analyzed in relation to abiotic (size of the area, extent of the perimeter, perimeter/area ratio, and shape index) and biotic characteristics (vegetation index of the fragment and of the matrix of each of the locations studied). We observed a highly significant positive correlation between the diversity index and the vegetation index of the fragment, landscape and shape index. Our analysis demonstrated that the observed variation could be explained mainly by the vegetation index and the size of the fragment. Variations in relative abundance showed a tendency toward an aggregated spatial distribution between the fragments studied, as well as between the sampling stations within the same habitat, demonstrating the existence of a spatial structure on a small scale in the populations of Euglossini. This distribution will determine the composition of species that coexist in the area after fragmentation. These data help in understanding the differences and similarities in the structure of communities of Euglossini resulting from forest fragmentation.

Legal regime of human activities in outer space law

NASA Technical Reports Server (NTRS)

Golda, Carlo

1994-01-01

Current developments in space activities increasingly involve the presence of humans on board spacecraft and, in the near future, on the Moon, on Mars, on board Space Stations, etc. With respect to these challenges, the political and legal issues connected to the status of astronauts are largely unclear and require a new doctrinal attention. In the same way, many legal and political questions remain open in the structure of future space crews: the need for international standards in the definition and training of astronauts, etc.; but, first of all, an international uniform legal definition of astronauts. Moreover, the legal structure for human life and operations in outer space can be a new and relevant paradigm for the definition of similar rules in all the situations and environments in which humans are involved in extreme frontiers. The present article starts from an overview on the existing legal and political definitions of 'astronauts', moving to the search of a more useful definition. This is followed by an analysis of the concrete problems created by human space activities, and the legal and political responses to them (the need for a code of conduct; the structure of the crew and the existing rules in the US and ex-USSR; the new legal theories on the argument; the definition and structure of a code of conduct; the next legal problems in fields such as privacy law, communications law, business law, criminal law, etc.).

Structure-activity correlations in a nickel-borate oxygen evolution catalyst.

PubMed

Bediako, D Kwabena; Lassalle-Kaiser, Benedikt; Surendranath, Yogesh; Yano, Junko; Yachandra, Vittal K; Nocera, Daniel G

2012-04-18

An oxygen evolution catalyst that forms as a thin film from Ni(aq)(2+) solutions containing borate electrolyte (Ni-B(i)) has been studied by in situ X-ray absorption spectroscopy. A dramatic increase in catalytic rate, induced by anodic activation of the electrodeposited films, is accompanied by structure and oxidation state changes. Coulometric measurements correlated with X-ray absorption near-edge structure spectra of the active catalyst show that the nickel centers in activated films possess an average oxidation state of +3.6, indicating that a substantial proportion of nickel centers exist in a formal oxidation state of Ni(IV). In contrast, nickel centers in nonactivated films exist predominantly as Ni(III). Extended X-ray absorption fine structure reveals that activated catalyst films comprise bis-oxo/hydroxo-bridged nickel centers organized into sheets of edge-sharing NiO(6) octahedra. Diminished long-range ordering in catalyst films is due to their ostensibly amorphous nature. Nonactivated films display a similar oxidic nature but exhibit a distortion in the local coordination geometry about nickel centers, characteristic of Jahn-Teller distorted Ni(III) centers. Our findings indicate that the increase in catalytic activity of films is accompanied by changes in oxidation state and structure that are reminiscent of those observed for conversion of β-NiOOH to γ-NiOOH and consequently challenge the long-held notion that the β-NiOOH phase is a more efficient oxygen-evolving catalyst. © 2012 American Chemical Society

Resilient 3D hierarchical architected metamaterials

PubMed Central

Meza, Lucas R.; Zelhofer, Alex J.; Clarke, Nigel; Mateos, Arturo J.; Kochmann, Dennis M.; Greer, Julia R.

2015-01-01

Hierarchically designed structures with architectural features that span across multiple length scales are found in numerous hard biomaterials, like bone, wood, and glass sponge skeletons, as well as manmade structures, like the Eiffel Tower. It has been hypothesized that their mechanical robustness and damage tolerance stem from sophisticated ordering within the constituents, but the specific role of hierarchy remains to be fully described and understood. We apply the principles of hierarchical design to create structural metamaterials from three material systems: (i) polymer, (ii) hollow ceramic, and (iii) ceramic–polymer composites that are patterned into self-similar unit cells in a fractal-like geometry. In situ nanomechanical experiments revealed (i) a nearly theoretical scaling of structural strength and stiffness with relative density, which outperforms existing nonhierarchical nanolattices; (ii) recoverability, with hollow alumina samples recovering up to 98% of their original height after compression to ≥50% strain; (iii) suppression of brittle failure and structural instabilities in hollow ceramic hierarchical nanolattices; and (iv) a range of deformation mechanisms that can be tuned by changing the slenderness ratios of the beams. Additional levels of hierarchy beyond a second order did not increase the strength or stiffness, which suggests the existence of an optimal degree of hierarchy to amplify resilience. We developed a computational model that captures local stress distributions within the nanolattices under compression and explains some of the underlying deformation mechanisms as well as validates the measured effective stiffness to be interpreted as a metamaterial property. PMID:26330605

Resilient 3D hierarchical architected metamaterials.

PubMed

Meza, Lucas R; Zelhofer, Alex J; Clarke, Nigel; Mateos, Arturo J; Kochmann, Dennis M; Greer, Julia R

2015-09-15

Hierarchically designed structures with architectural features that span across multiple length scales are found in numerous hard biomaterials, like bone, wood, and glass sponge skeletons, as well as manmade structures, like the Eiffel Tower. It has been hypothesized that their mechanical robustness and damage tolerance stem from sophisticated ordering within the constituents, but the specific role of hierarchy remains to be fully described and understood. We apply the principles of hierarchical design to create structural metamaterials from three material systems: (i) polymer, (ii) hollow ceramic, and (iii) ceramic-polymer composites that are patterned into self-similar unit cells in a fractal-like geometry. In situ nanomechanical experiments revealed (i) a nearly theoretical scaling of structural strength and stiffness with relative density, which outperforms existing nonhierarchical nanolattices; (ii) recoverability, with hollow alumina samples recovering up to 98% of their original height after compression to ≥ 50% strain; (iii) suppression of brittle failure and structural instabilities in hollow ceramic hierarchical nanolattices; and (iv) a range of deformation mechanisms that can be tuned by changing the slenderness ratios of the beams. Additional levels of hierarchy beyond a second order did not increase the strength or stiffness, which suggests the existence of an optimal degree of hierarchy to amplify resilience. We developed a computational model that captures local stress distributions within the nanolattices under compression and explains some of the underlying deformation mechanisms as well as validates the measured effective stiffness to be interpreted as a metamaterial property.

Molecular and structural characteristics in toxic algae cultures of Ostreopsis ovata and Ostreopsis spp. evidenced by FTIR and FTNIR spectroscopy

NASA Astrophysics Data System (ADS)

Mecozzi, Mauro; Pietroletti, Marco; Tornambè, Andrea

2011-05-01

In this article we investigated the compositional and structural characteristics of the principal biomolecules such as carbohydrates, proteins, lipids, nucleic acids and chlorophyll pigments present in biofilm cultures of Ostreopsis spp. and in batch cultures of Ostreopsis ovata. Our approach based on the use of infrared (FTIR) and near infrared (FTNIR) spectroscopy showed the marked differences existing between biofilm cultures and batch cultures. FTIR spectroscopy showed the higher contents of polysaccharides and chlorophyll pigments in O. ovata from batch cultures with respect to Ostreopsis spp. Second derivative FTIR spectroscopy showed different features concerning the secondary structure of proteins because in O. ovata samples the beta sheet and beta turn structures were observed whereas in Ostreopsis spp. samples the alpha helix structure was the most evident. FTNIR spectroscopy showed other structural differences observed existing between O. ovata and Ostreopsis spp. mainly related to hydrogen bond interactions determining more packed structures in the nucleus of O. ovata. In addition, the interpretation of FTIR and FTNIR spectral information was also supported by the application of two statistical methods, the independent component analysis (ICA) and the spectral cross correlation analysis (SCCA). ICA was used as spectral deconvolution technique to separate the effects of the interference bicarbonate ion from algal FTIR spectra so to verify the high similar qualitative composition of the three biofilm samples of Ostreopsis spp. At last, SCCA applied to FTIR and FTNIR spectra was useful to evidence some structural differences involving -CH and CH 2 groups of aliphatic chains in O. ovata and Ostreopsis spp. samples. Though preliminary, these results agree with some previous studies suggesting that the presence of different ecophysiological characteristics in O. ovata and Ostreopsis spp. depending on the parameters related to the condition growth.

Greek classicism in living structure? Some deductive pathways in animal morphology.

PubMed

Zweers, G A

1985-01-01

Classical temples in ancient Greece show two deterministic illusionistic principles of architecture, which govern their functional design: geometric proportionalism and a set of illusion-strengthening rules in the proportionalism's "stochastic margin". Animal morphology, in its mechanistic-deductive revival, applies just one architectural principle, which is not always satisfactory. Whether a "Greek Classical" situation occurs in the architecture of living structure is to be investigated by extreme testing with deductive methods. Three deductive methods for explanation of living structure in animal morphology are proposed: the parts, the compromise, and the transformation deduction. The methods are based upon the systems concept for an organism, the flow chart for a functionalistic picture, and the network chart for a structuralistic picture, whereas the "optimal design" serves as the architectural principle for living structure. These methods show clearly the high explanatory power of deductive methods in morphology, but they also make one open end most explicit: neutral issues do exist. Full explanation of living structure asks for three entries: functional design within architectural and transformational constraints. The transformational constraint brings necessarily in a stochastic component: an at random variation being a sort of "free management space". This variation must be a variation from the deterministic principle of the optimal design, since any transformation requires space for plasticity in structure and action, and flexibility in role fulfilling. Nevertheless, finally the question comes up whether for animal structure a similar situation exists as in Greek Classical temples. This means that the at random variation, that is found when the optimal design is used to explain structure, comprises apart from a stochastic part also real deviations being yet another deterministic part. This deterministic part could be a set of rules that governs actualization in the "free management space".

Molecular dynamics simulations of domain motions of substrate-free S-adenosyl- L-homocysteine hydrolase in solution.

PubMed

Hu, Chen; Fang, Jianwen; Borchardt, Ronald T; Schowen, Richard L; Kuczera, Krzysztof

2008-04-01

S-Adenosyl-L-homocysteine hydrolase (SAHH) is an enzyme regulating intracellular methylation reactions. The homotetrameric SAHH exists in an open conformation in absence of substrate, while enzyme:inhibitor complexes crystallize in the closed conformation, in which the ligands are engulfed by the protein due to an 18 degrees domain reorientation within each of the four subunits. We present a microscopic description of the structure and dynamics of the substrate-free, NAD(+)-bound SAHH in solution, based on a 15-ns molecular dynamics simulation in explicit solvent. In the trajectory, the four cofactor-binding domains formed a relatively rigid core with structure very similar to the crystal conformation. The four substrate-binding domains, located at the protein exterior, also retained internal structures similar to the crystal, while undergoing large amplitude rigid-body reorientations. The trajectory domain motions exhibited two interesting properties. First, within each subunit the domains fluctuated between open and closed conformations, while at the tetramer level 80% of the domain motions were perpendicular to the direction of the open-to-closed structural transition. Second, the domain reorientations in solution could be represented as a sum of two components, faster, with 20-50 ps correlation time and 3-4 degrees amplitude, and slower, with 8-23 ns correlation time and amplitude of 14-22 degrees . The faster motion is similar to the 1.5 cm(-1) frequency hinge-bending vibrations found in our recent normal mode analysis (Wang et al., Biochemistry 2005;44:7228-7239). The slower motion agrees with fluorescence anisotropy decay measurements, which detected a 10-20 ns domain reorientation of ca. 26 degrees amplitude in the substrate-free enzyme (Wang et al., Biochemistry 2006;45:7778-7786). Our simulations are thus in excellent agreement with experimental data. The simulations allow us to assign the observed nanosecond fluorescence anisotropy signal to fluctuations in domain orientations, and indicate that the microscopic mechanism of the motion involves rotational diffusion within a cone of 10-20 degrees . Overall, our simulation results complement the existing experimental data and provide important new insights into SAHH domain motions in solution, which play a crucial role in the catalytic mechanism of SAHH. (c) 2007 Wiley-Liss, Inc.

Luminescence of silicon dioxide different polymorph modification: Silica glass, α-quartz, stishovite, coesite

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

Trukhin, A. N., E-mail: truhins@cfi.lu.lv

2014-10-21

Stishovite, coesite, oxygen deficient silica glass as well as irradiated α-quartz, exhibit two luminescence bands: a blue one and an UV one both excitable in the range within optical gap. There are similarities in spectral position and in luminescence decay kinetics among centers in these materials. The interpretation was done on the model of Oxygen Deficient Centers (ODC) [1]. The ODC(II) or twofold coordinated silicon and ODC(I) are distinguished. ODC(I) is object of controversial interpretation. The Si-Si oxygen vacancy [2] and complex defect including latent twofold coordinated silicon [3] are proposed. Remarkably, this luminescence center does not exist in asmore » grown crystalline α-quartz. However, destructive irradiation of α-quartz crystals with fast neutrons, γ rays, or dense electron beams [4–6] creates ODC(I) like defect. In tetrahedron structured coesite the self trapped exciton (STE) luminescence observed with high energetic yield (∼30%) like in α-quartz crystals. STE in coesite coexists with oxygen deficient-like center. In octahedron structured stishovite STE was not found and only ODC exists.« less

Enhancement of axial momentum lost to the radial wall by the upstream magnetic field in a helicon source

NASA Astrophysics Data System (ADS)

Takahashi, Kazunori; Ando, Akira

2017-05-01

Individual measurements of forces exerted to an upstream back wall, a radial source wall, and a magnetic field of a helicon plasma thruster, which has two solenoids upstream and downstream of a radiofrequency antenna, are precisely measured. Two different structures of magnetic field lines in the source are tested, where the solenoid current is supplied to either only the downstream solenoid or to both the solenoids. It is observed that the high density plasma exists upstream of the rf antenna when both the solenoids are powered, while the maximum density exists near the rf antenna when only the downstream solenoid is powered. Although the force exerted to the back wall is increased for the two solenoids case, the axial momentum lost to the radial wall is simultaneously enhanced; then the total force exerted to the whole structure of the thruster is found to be very similar for the two magnetic field configurations. It is shown that the individual force measurement provides useful information on the plasma momentum interacting with the physical boundaries and the magnetic fields.

Open-source platform to benchmark fingerprints for ligand-based virtual screening

PubMed Central

2013-01-01

Similarity-search methods using molecular fingerprints are an important tool for ligand-based virtual screening. A huge variety of fingerprints exist and their performance, usually assessed in retrospective benchmarking studies using data sets with known actives and known or assumed inactives, depends largely on the validation data sets used and the similarity measure used. Comparing new methods to existing ones in any systematic way is rather difficult due to the lack of standard data sets and evaluation procedures. Here, we present a standard platform for the benchmarking of 2D fingerprints. The open-source platform contains all source code, structural data for the actives and inactives used (drawn from three publicly available collections of data sets), and lists of randomly selected query molecules to be used for statistically valid comparisons of methods. This allows the exact reproduction and comparison of results for future studies. The results for 12 standard fingerprints together with two simple baseline fingerprints assessed by seven evaluation methods are shown together with the correlations between methods. High correlations were found between the 12 fingerprints and a careful statistical analysis showed that only the two baseline fingerprints were different from the others in a statistically significant way. High correlations were also found between six of the seven evaluation methods, indicating that despite their seeming differences, many of these methods are similar to each other. PMID:23721588

Quartz and feldspar glasses produced by natural and experimental shock.

NASA Technical Reports Server (NTRS)

Stoeffler, D.; Hornemann, U.

1972-01-01

Refractive index, density, and infrared absorption studies of naturally and experimentally shocked-produced glasses formed from quartz, plagioclase, and alkali-feldspar confirm the existence of two main groups of amorphous forms of the framework silicates: solid-state and liquid-state glasses. These were apparently formed as metastable release products of high-pressure-phases above and below the glass transition temperatures. Solid-state glasses exhibit a series of structural states with increasing disorder caused by increasing shock pressures and temperatures. They gradually merge into the structural state of fused minerals similar to that of synthetic glasses quenched from a melt. Shock-fused alkali feldspars can, however, be distinguished from their laboratory-fused counterparts by infrared absorption and by higher density.

Role of damping in spin Seebeck effect in yttrium iron garnet thin films

PubMed Central

Chang, Houchen; Praveen Janantha, P. A.; Ding, Jinjun; Liu, Tao; Cline, Kevin; Gelfand, Joseph N.; Li, Wei; Marconi, Mario C.; Wu, Mingzhong

2017-01-01

The role of damping in the spin Seebeck effect (SSE) was studied experimentally for the first time. The experiments used Y3Fe5O12 (YIG)/Pt bilayered structures where the YIG films exhibit very similar structural and static magnetic properties but very different damping. The data show that a decrease in the damping gives rise to an increase in the SSE coefficient, which is qualitatively consistent with some of the theoretical models. This response also shows quasi-linear behavior, which was not predicted explicitly by previous studies. The data also indicate that the SSE coefficient shows no notable correlations with the enhanced damping due to spin pumping, which can be understood in the frame of two existing models. PMID:28435873

First-Principles Study of Antimony Doping Effects on the Iron-Based Superconductor CaFe(SbxAs1-x)2

NASA Astrophysics Data System (ADS)

Nagai, Yuki; Nakamura, Hiroki; Machida, Masahiko; Kuroki, Kazuhiko

2015-09-01

We study antimony doping effects on the iron-based superconductor CaFe(SbxAs1-x)2 by using the first-principles calculation. The calculations reveal that the substitution of a doped antimony atom into As of the chainlike As layers is more stable than that into FeAs layers. This prediction can be checked by experiments. Our results suggest that doping homologous elements into the chainlike As layers, which only exist in the novel 112 system, is responsible for rising up the critical temperature. We discuss antimony doping effects on the electronic structure. It is found that the calculated band structures with and without the antimony doping are similar to each other within our framework.

Generative model selection using a scalable and size-independent complex network classifier

NASA Astrophysics Data System (ADS)

Motallebi, Sadegh; Aliakbary, Sadegh; Habibi, Jafar

2013-12-01

Real networks exhibit nontrivial topological features, such as heavy-tailed degree distribution, high clustering, and small-worldness. Researchers have developed several generative models for synthesizing artificial networks that are structurally similar to real networks. An important research problem is to identify the generative model that best fits to a target network. In this paper, we investigate this problem and our goal is to select the model that is able to generate graphs similar to a given network instance. By the means of generating synthetic networks with seven outstanding generative models, we have utilized machine learning methods to develop a decision tree for model selection. Our proposed method, which is named "Generative Model Selection for Complex Networks," outperforms existing methods with respect to accuracy, scalability, and size-independence.

Reproductive habitat selection in alien and native populations of the genus Discoglossus

NASA Astrophysics Data System (ADS)

Escoriza, Daniel; Boix, Dani

2014-08-01

The existence of suitable breeding habitats is an important factor explaining the regional presence of an anuran species. This study examined patterns of habitat selection in populations of three species of the genus Discoglossus: Discoglossusgalganoi (south-western Iberian Peninsula), Discoglossusscovazzi (Morocco) and Discoglossuspictus (three different areas were included in the study: Sicily, Tunisia and north-eastern Iberian Peninsula). The populations of D. pictus on the Iberian Peninsula are allochthonous, and analysis of these patterns may provide insights into the processes that regulate the invasion phase. The hypotheses tested were: (i) congeneric species show the same patterns of habitat selection, and alien species have been established following these patterns; (ii) there are differences in species associations between assemblages structured deterministically and by chance, i.e. native versus invaded assemblages. The larval habitats of three species of this genus were characterized by measuring physical and chemical parameters of the water bodies. We examined the covariation between the presence of Discoglossus species and the species richness of sympatric anurans, and investigated a possible relationship between morphological similarity (as a proxy of functional group) and overlap in habitat use. The results showed that congeneric species are morphologically conservative and also select very similar types of aquatic habitat. The alien population and other sympatric species showed a high degree of overlap in habitat use, which was greater than that observed in the native assemblage with a similar functional richness. Species associations were not structured on the basis of morphological similarity in any of the assemblages. Among native populations, the presence of Discoglossus was either negatively correlated or not significantly correlated with species richness. Only the alien population showed a positive correlation between its presence and species richness, which suggests a loss of assemblage structure.

Evaluation of Basalt Fibre Composites for Marine Applications

NASA Astrophysics Data System (ADS)

Davies, P.; Verbouwe, W.

2018-04-01

Basalt fibres offer potential for use in marine structures, but few data exist to evaluate the influence of seawater immersion on their mechanical behaviour. This paper provides the results from a study in which basalt fibre reinforced epoxy composites were aged in natural seawater at different temperatures. Tests were performed under quasi-static and cyclic loading, first in the as-received state then after saturation in natural seawater. Results are compared to those for an E-glass reinforced composite with the same epoxy matrix. They indicate similar mechanical performance for both materials after seawater saturation.

An Optimal Seed Based Compression Algorithm for DNA Sequences

PubMed Central

Gopalakrishnan, Gopakumar; Karunakaran, Muralikrishnan

2016-01-01

This paper proposes a seed based lossless compression algorithm to compress a DNA sequence which uses a substitution method that is similar to the LempelZiv compression scheme. The proposed method exploits the repetition structures that are inherent in DNA sequences by creating an offline dictionary which contains all such repeats along with the details of mismatches. By ensuring that only promising mismatches are allowed, the method achieves a compression ratio that is at par or better than the existing lossless DNA sequence compression algorithms. PMID:27555868

Ising model of financial markets with many assets

NASA Astrophysics Data System (ADS)

Eckrot, A.; Jurczyk, J.; Morgenstern, I.

2016-11-01

Many models of financial markets exist, but most of them simulate single asset markets. We study a multi asset Ising model of a financial market. Each agent has two possible actions (buy/sell) for every asset. The agents dynamically adjust their coupling coefficients according to past market returns and external news. This leads to fat tails and volatility clustering independent of the number of assets. We find that a separation of news into different channels leads to sector structures in the cross correlations, similar to those found in real markets.

Trilobite spines and beetle horns: sexual selection in the Palaeozoic?

PubMed Central

Knell, Robert J; Fortey, Richard A

2005-01-01

Raphiophorid trilobites commonly bore median cephalic protuberances such as spines or bulbs, showing a remarkable variety of form. It is unlikely that their primary function was for protection or in hydrodynamics. A case is made that they were secondary sexual features, by comparison with similar morphological structures developed on rhinoceros beetles and other arthropods. This interpretation is supported by four lines of evidence: their ontogeny, their diversity, the existence of plausible examples of sexual dimorphs in some cases and the fact that they show positive allometry. PMID:17148165

Trilobite spines and beetle horns: sexual selection in the Palaeozoic?

PubMed

Knell, Robert J; Fortey, Richard A

2005-06-22

Raphiophorid trilobites commonly bore median cephalic protuberances such as spines or bulbs, showing a remarkable variety of form. It is unlikely that their primary function was for protection or in hydrodynamics. A case is made that they were secondary sexual features, by comparison with similar morphological structures developed on rhinoceros beetles and other arthropods. This interpretation is supported by four lines of evidence: their ontogeny, their diversity, the existence of plausible examples of sexual dimorphs in some cases and the fact that they show positive allometry.

On a bender—BARs, ESCRTs, COPs, and finally getting your coat

PubMed Central

Sali, Andrej; Rout, Michael P.

2011-01-01

Tremendous variety in form and function is displayed among the intracellular membrane systems of different eukaryotes. Until recently, few clues existed as to how these internal membrane systems had originated and diversified. However, proteomic, structural, and comparative genomics studies together have revealed extensive similarities among many of the protein complexes used in controlling the morphology and trafficking of intracellular membranes. These new insights have had a profound impact on our understanding of the evolutionary origins of the internal architecture of the eukaryotic cell. PMID:21670211

Dihydronaphthalenone Carboxylates - Spectral Characteristics and Structure

NASA Astrophysics Data System (ADS)

Bakalova, Sn.; Georgieva, A.; Nikolov, P.; Stanoeva, E.

1997-05-01

The absorption and luminescence characteristics of a group of newly synthesized methyl esters of 2-alkyl (p-substituted-aryl) -aminomethylene-3,4-dihydro-1(2 H)-naphthalenone-4-carboxylic acids have been investigated. The studied compounds may exist in three tautomeric forms. On the basis of comparison of their electronic spectra to those of similar substances, the observed substituent effect on the position of the UV-VIS absorption bands, the IR spectra and the results of PPP-SCF-CI quantum-chemical calculations it is concluded that the keto tautomer predominates in solution.

Network structures between strategies in iterated prisoners' dilemma games

NASA Astrophysics Data System (ADS)

Kim, Young Jin; Roh, Myungkyoon; Son, Seung-Woo

2014-02-01

We use replicator dynamics to study an iterated prisoners' dilemma game with memory. In this study, we investigate the characteristics of all 32 possible strategies with a single-step memory by observing the results when each strategy encounters another one. Based on these results, we define similarity measures between the 32 strategies and perform a network analysis of the relationship between the strategies by constructing a strategies network. Interestingly, we find that a win-lose circulation, like rock-paper-scissors, exists between strategies and that the circulation results from one unusual strategy.

Genomic analysis of coxsackieviruses A1, A19, A22, enteroviruses 113 and 104: viruses representing two clades with distinct tropism within enterovirus C

PubMed Central

Haq, Saddef; Sameroff, Stephen; Howie, Stephen R. C.; Lipkin, W. Ian

2013-01-01

Coxsackieviruses (CV) A1, CV-A19 and CV-A22 have historically comprised a distinct phylogenetic clade within Enterovirus (EV) C. Several novel serotypes that are genetically similar to these three viruses have been recently discovered and characterized. Here, we report the coding sequence analysis of two genotypes of a previously uncharacterized serotype EV-C113 from Bangladesh and demonstrate that it is most similar to CV-A22 and EV-C116 within the capsid region. We sequenced novel genotypes of CV-A1, CV-A19 and CV-A22 from Bangladesh and observed a high rate of recombination within this group. We also report genomic analysis of the rarely reported EV-C104 circulating in the Gambia in 2009. All available EV-C104 sequences displayed a high degree of similarity within the structural genes but formed two clusters within the non-structural genes. One cluster included the recently reported EV-C117, suggesting an ancestral recombination between these two serotypes. Phylogenetic analysis of all available complete genome sequences indicated the existence of two subgroups within this distinct Enterovirus C clade: one has been exclusively recovered from gastrointestinal samples, while the other cluster has been implicated in respiratory disease. PMID:23761409

Frustration-induced internal stresses are responsible for quasilocalized modes in structural glasses

NASA Astrophysics Data System (ADS)

Lerner, Edan; Bouchbinder, Eran

2018-03-01

It has been recently shown [E. Lerner, G. Düring, and E. Bouchbinder, Phys. Rev. Lett. 117, 035501 (2016), 10.1103/PhysRevLett.117.035501] that the nonphononic vibrational modes of structural glasses at low frequencies ω are quasilocalized and follow a universal density of states D (ω ) ˜ω4 . Here we show that the gapless nature of the observed density of states depends on the existence of internal stresses that generically emerge in glasses due to frustration, thus elucidating a basic element underlying this universal behavior. Similarly to jammed particulate packings, low-frequency modes in structural glasses emerge from a balance between a local elasticity term and an internal stress term in the dynamical matrix, where the difference between them is orders of magnitude smaller than their typical magnitude. By artificially reducing the magnitude of internal stresses in a computer glass former in three dimensions, we show that a gap is formed in the density of states below which no vibrational modes exist, thus demonstrating the crucial importance of internal stresses. Finally, we show that while better annealing the glass upon cooling from the liquid state significantly reduces its internal stresses, the self-organizational processes during cooling render the gapless D (ω ) ˜ω4 density of state unaffected.

Convex blind image deconvolution with inverse filtering

NASA Astrophysics Data System (ADS)

Lv, Xiao-Guang; Li, Fang; Zeng, Tieyong

2018-03-01

Blind image deconvolution is the process of estimating both the original image and the blur kernel from the degraded image with only partial or no information about degradation and the imaging system. It is a bilinear ill-posed inverse problem corresponding to the direct problem of convolution. Regularization methods are used to handle the ill-posedness of blind deconvolution and get meaningful solutions. In this paper, we investigate a convex regularized inverse filtering method for blind deconvolution of images. We assume that the support region of the blur object is known, as has been done in a few existing works. By studying the inverse filters of signal and image restoration problems, we observe the oscillation structure of the inverse filters. Inspired by the oscillation structure of the inverse filters, we propose to use the star norm to regularize the inverse filter. Meanwhile, we use the total variation to regularize the resulting image obtained by convolving the inverse filter with the degraded image. The proposed minimization model is shown to be convex. We employ the first-order primal-dual method for the solution of the proposed minimization model. Numerical examples for blind image restoration are given to show that the proposed method outperforms some existing methods in terms of peak signal-to-noise ratio (PSNR), structural similarity (SSIM), visual quality and time consumption.

Emergent quasicrystals in strongly correlated systems

NASA Astrophysics Data System (ADS)

Sagi, Eran; Nussinov, Zohar

2016-07-01

Commensurability is of paramount importance in numerous strongly interacting electronic systems. In the fractional quantum Hall effect, a rich cascade of increasingly narrow plateaux appear at larger denominator filling fractions. Rich commensurate structures also emerge, at certain filling fractions, in high temperature superconductors and other electronic systems. A natural question concerns the character of these and other electronic systems at irrational filling fractions. Here we demonstrate that quasicrystalline structures naturally emerge in these situations, and trigger behaviors not typically expected of periodic systems. We first show that irrationally filled quantum Hall systems cross over into quasiperiodically ordered configuration in the thin-torus limit. Using known properties of quasicrystals, we argue that these states are unstable against the effects of disorder, in agreement with the existence of quantum Hall plateaux. We then study analogous physical situations in a system of cold Rydberg atoms placed on an optical lattice. Such an experimental setup is generally disorder free, and can therefore be used to detect the emergent quasicrystals we predict. We discuss similar situations in the Falicov-Kimball model, where known exact results can be used to establish quasicrystalline structures in one and two dimensions. We briefly speculate on possible relations between our theoretical findings and the existence of glassy dynamics and other features of strongly correlated electronic systems.

Unexpected structural and magnetic depth dependence of YIG thin films

NASA Astrophysics Data System (ADS)

Cooper, J. F. K.; Kinane, C. J.; Langridge, S.; Ali, M.; Hickey, B. J.; Niizeki, T.; Uchida, K.; Saitoh, E.; Ambaye, H.; Glavic, A.

2017-09-01

We report measurements on yttrium iron garnet (YIG) thin films grown on both gadolinium gallium garnet (GGG) and yttrium aluminum garnet (YAG) substrates, with and without thin Pt top layers. We provide three principal results: the observation of an interfacial region at the Pt/YIG interface, we place a limit on the induced magnetism of the Pt layer, and confirm the existence of an interfacial layer at the GGG/YIG interface. Polarized neutron reflectometry (PNR) was used to give depth dependence of both the structure and magnetism of these structures. We find that a thin film of YIG on GGG is best described by three distinct layers: an interfacial layer near the GGG, around 5 nm thick and nonmagnetic, a magnetic "bulk" phase, and a nonmagnetic and compositionally distinct thin layer near the surface. We theorize that the bottom layer, which is independent of the film thickness, is caused by Gd diffusion. The top layer is likely to be extremely important in inverse spin Hall effect measurements, and is most likely Y2O3 or very similar. Magnetic sensitivity in the PNR to any induced moment in the Pt is increased by the existence of the Y2O3 layer; any moment is found to be less than 0.02 μB/atom .

47 CFR 17.17 - Existing structures.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 47 Telecommunication 1 2010-10-01 2010-10-01 false Existing structures. 17.17 Section 17.17... STRUCTURES Federal Aviation Administration Notification Criteria § 17.17 Existing structures. (a) The requirements found in § 17.23 relating to painting and lighting of antenna structures shall not apply to those...

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

Diaz, A.; Valdez, V; Rudino-Pinera, E

Neurospora crassa has two large-subunit catalases, CAT-1 and CAT-3. CAT-1 is associated with non-growing cells and accumulates particularly in asexual spores; CAT-3 is associated with growing cells and is induced under different stress conditions. It is our interest to elucidate the structure-function relationships in large-subunit catalases. Here we have determined the CAT-3 crystal structure and compared it with the previously determined CAT-1 structure. Similar to CAT-1, CAT-3 hydrogen peroxide (H{sub 2}O{sub 2}) saturation kinetics exhibited two components, consistent with the existence of two active sites: one saturated in the millimolar range and the other in the molar range. In themore » CAT-1 structure, we found three interesting features related to its unusual kinetics: (a) a constriction in the channel that conveys H{sub 2}O{sub 2} to the active site; (b) a covalent bond between the tyrosine, which forms the fifth coordination bound to the iron of the heme, and a vicinal cysteine; (c) oxidation of the pyrrole ring III to form a cis-hydroxyl group in C5 and a cis-{gamma}-spirolactone in C6. The site of heme oxidation marks the starts of the central channel that communicates to the central cavity and the shortest way products can exit the active site. CAT-3 has a similar constriction in its major channel, which could function as a gating system regulated by the H{sub 2}O{sub 2} concentration before the gate. CAT-3 functional tyrosine is not covalently bonded, but has instead the electron relay mechanism described for the human catalase to divert electrons from it. Pyrrole ring III in CAT-3 is not oxidized as it is in other large-subunit catalases whose structure has been determined. Different in CAT-3 from these enzymes is an occupied central cavity. Results presented here indicate that CAT-3 and CAT-1 enzymes represent a functional group of catalases with distinctive structural characteristics that determine similar kinetics.« less

Structural characterization of a family of cytochromes c{sub 7} involved in Fe(III) respiration by Geobacter sulfurreducens.

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

Pokkuluri, P. R.; Londer, Y. Y.; Yang, X.

2010-02-01

Periplasmic cytochromes c{sub 7} are important in electron transfer pathway(s) in Fe(III) respiration by Geobacter sulfurreducens. The genome of G. sulfurreducens encodes a family of five 10-kDa, three-heme cytochromes c{sub 7}. The sequence identity between the five proteins (designated PpcA, PpcB, PpcC, PpcD, and PpcE) varies between 45% and 77%. Here, we report the high-resolution structures of PpcC, PpcD, and PpcE determined by X-ray diffraction. This new information made it possible to compare the sequences and structures of the entire family. The triheme cores are largely conserved but are not identical. We observed changes, due to different crystal packing, inmore » the relative positions of the hemes between two molecules in the crystal. The overall protein fold of the cytochromes is similar. The structure of PpcD differs most from that of the other homologs, which is not obvious from the sequence comparisons of the family. Interestingly, PpcD is the only cytochrome c{sub 7} within the family that has higher abundance when G. sulfurreducens is grown on insoluble Fe(III) oxide compared to ferric citrate. The structures have the highest degree of conservation around 'heme IV'; the protein surface around this heme is positively charged in all of the proteins, and therefore all cytochromes c{sub 7} could interact with similar molecules involving this region. The structures and surface characteristics of the proteins near the other two hemes, 'heme I' and 'heme III', differ within the family. The above observations suggest that each of the five cytochromes c{sub 7} could interact with its own redox partner via an interface involving the regions of heme I and/or heme III; this provides a possible rationalization for the existence of five similar proteins in G. sulfurreducens.« less

Ancient wet aeolian environments on Earth: Clues to presence of fossil/live microorganisms on Mars

USGS Publications Warehouse

Mahaney, W.C.; Milner, M.W.; Netoff, D.I.; Malloch, D.; Dohm, J.M.; Baker, V.R.; Miyamoto, H.; Hare, T.M.; Komatsu, G.

2004-01-01

Ancient wet aeolian (wet-sabkha) environments on Earth, represented in the Entrada and Navajo sandstones of Utah, contain pipe structures considered to be the product of gas/water release under pressure. The sediments originally had considerable porosity allowing the ingress of living plant structures, microorganisms, clay minerals, and fine-grained primary minerals of silt and sand size from the surface downward in the sedimentary column. Host rock material is of a similar size and porosity and presumably the downward migration of fine-grained material would have been possible prior to lithogenesis and final cementation. Recent field emission scanning electron microscopy (FESEM) and EDS (energy-dispersive spectrometry) examination of sands from fluidized pipes in the Early Jurassic Navajo Sandstone reveal the presence of fossil forms resembling fungal filaments, some bearing hyphopodium-like structures similar to those produced by modern tropical leaf parasites. The tropical origin of the fungi is consistent with the paleogeography of the sandstone, which was deposited in a tropical arid environment. These fossil fungi are silicized, with minor amounts of CaCO3 and Fe, and in some cases a Si/Al ratio similar to smectite. They exist as pseudomorphs, totally depleted in nitrogen, adhering to the surfaces of fine-grained sands, principally quartz and orthoclase. Similar wet aeolian paleoenvironments are suspected for Mars, especially following catastrophic sediment-charged floods of enormous magnitudes that are believed to have contributed to rapid formation of large water bodies in the northern plains, ranging from lakes to oceans. These events are suspected to have contributed to a high frequency of constructional landforms (also known as pseudocraters) related to trapped volatiles and water-enriched sediment underneath a thick blanket of materials that were subsequently released to the martian surface, forming piping structures at the near surface and constructional landforms at the surface. This constructional process on Mars may help unravel the complex history of some of the piping structures observed on Earth; on Earth, evidence for the constructional landforms has been all but erased and the near-surface piping structures exposed through millions of years of differential erosion and topographic inversion now occur as high-standing promontories. If the features on both Earth and Mars formed by similar processes, especially involving water and other volatiles, and since the piping structures of Earth provided suitable environments for life to thrive in, the martian features in the northern plains should be considered as prime targets for physico/mineral/chemical/microbiological analyses once the astrobiological exploration of the red planet begins in earnest. ?? 2004 Elsevier Inc. All rights reserved.

Ancient wet aeolian environments on Earth: clues to presence of fossil/live microorganisms on Mars

NASA Astrophysics Data System (ADS)

Mahaney, William C.; Milner, Michael W.; Netoff, D. I.; Malloch, David; Dohm, James M.; Baker, Victor R.; Miyamoto, Hideaki; Hare, Trent M.; Komatsu, Goro

2004-09-01

Ancient wet aeolian (wet-sabkha) environments on Earth, represented in the Entrada and Navajo sandstones of Utah, contain pipe structures considered to be the product of gas/water release under pressure. The sediments originally had considerable porosity allowing the ingress of living plant structures, microorganisms, clay minerals, and fine-grained primary minerals of silt and sand size from the surface downward in the sedimentary column. Host rock material is of a similar size and porosity and presumably the downward migration of fine-grained material would have been possible prior to lithogenesis and final cementation. Recent field emission scanning electron microscopy (FESEM) and EDS (energy-dispersive spectrometry) examination of sands from fluidized pipes in the Early Jurassic Navajo Sandstone reveal the presence of fossil forms resembling fungal filaments, some bearing hyphopodium-like structures similar to those produced by modern tropical leaf parasites. The tropical origin of the fungi is consistent with the paleogeography of the sandstone, which was deposited in a tropical arid environment. These fossil fungi are silicized, with minor amounts of CaCO 3 and Fe, and in some cases a Si/Al ratio similar to smectite. They exist as pseudomorphs, totally depleted in nitrogen, adhering to the surfaces of fine-grained sands, principally quartz and orthoclase. Similar wet aeolian paleoenvironments are suspected for Mars, especially following catastrophic sediment-charged floods of enormous magnitudes that are believed to have contributed to rapid formation of large water bodies in the northern plains, ranging from lakes to oceans. These events are suspected to have contributed to a high frequency of constructional landforms (also known as pseudocraters) related to trapped volatiles and water-enriched sediment underneath a thick blanket of materials that were subsequently released to the martian surface, forming piping structures at the near surface and constructional landforms at the surface. This constructional process on Mars may help unravel the complex history of some of the piping structures observed on Earth; on Earth, evidence for the constructional landforms has been all but erased and the near-surface piping structures exposed through millions of years of differential erosion and topographic inversion now occur as high-standing promontories. If the features on both Earth and Mars formed by similar processes, especially involving water and other volatiles, and since the piping structures of Earth provided suitable environments for life to thrive in, the martian features in the northern plains should be considered as prime targets for physico/mineral/chemical/microbiological analyses once the astrobiological exploration of the red planet begins in earnest.

High-pressure NMR reveals close similarity between cold and alcohol protein denaturation in ubiquitin.

PubMed

Vajpai, Navratna; Nisius, Lydia; Wiktor, Maciej; Grzesiek, Stephan

2013-01-29

Proteins denature not only at high, but also at low temperature as well as high pressure. These denatured states are not easily accessible for experiment, because usually heat denaturation causes aggregation, whereas cold or pressure denaturation occurs at temperatures well below the freezing point of water or pressures above 5 kbar, respectively. Here we have obtained atomic details of the pressure-assisted, cold-denatured state of ubiquitin at 2,500 bar and 258 K by high-resolution NMR techniques. Under these conditions, a folded, native-like and a disordered state exist in slow exchange. Secondary chemical shifts show that the disordered state has structural propensities for a native-like N-terminal β-hairpin and α-helix and a nonnative C-terminal α-helix. These propensities are very similar to the previously described alcohol-denatured (A-)state. Similar to the A-state, (15)N relaxation data indicate that the secondary structure elements move as independent segments. The close similarity of pressure-assisted, cold-denatured, and alcohol-denatured states with native and nonnative secondary elements supports a hierarchical mechanism of folding and supports the notion that similar to alcohol, pressure and cold reduce the hydrophobic effect. Indeed, at nondenaturing concentrations of methanol, a complete transition from the native to the A-state can be achieved at ambient temperature by varying the pressure from 1 to 2,500 bar. The methanol-assisted pressure transition is completely reversible and can also be induced in protein G. This method should allow highly detailed studies of protein-folding transitions in a continuous and reversible manner.

Evolution of birds: ichthyosaur integumental fibers conform to dromaeosaur protofeathers.

PubMed

Lingham-Soliar, Theagarten

2003-09-01

Filamentous integumentary structures have been reported as protofeathers in dromaeosaurs (non-avian dinosaurs). This hypothesis is considered against data on the complex architecture of dermal and subdermal collagenous fibers widely prevalent in living and extinct animals. Ichthyosaur integumental fibers, as dromaeosaur "protofeathers", are the most external structures preserved. Marked similarities are shown in branching patterns of these fibers compared with those of the dromaeosaur Sinornithosaurus; hence distinguishing between aberrant and primary features is difficult. Analysis of a pterosaur specimen shows that bent and straight fibers on the wings have functional implications. The fibers conform to the twofold shape of collagen and contradict the notion that bent integumental structures in the dinosaur Sinosauropteryx indicate softness and pliability. A suggestion also concerning Sinosauropteryx is that integumental structures with darker edges, compared with the middle, imply that they were hollow. Investigation of a similar condition in an ichthyosaur shows that it is more likely a consequence of mineralization. Dermal collagen fibers in, for example, sharks, dolphins, snakes, and turtles are shown to be grouped in bundles of varying sizes. Degradation of the dermis results in the breakdown of the fiber bundles and formation of myriad patterns of the disrupted fibers, as noted in decomposed dolphin skin. The overall findings of the study are that the thesis of dinosaur "protofeathers" requires more substantial support than exists at present.

Structural behavior of ZnCr 2S 4 spinel under pressure

DOE PAGES

Efthimiopoulos, I.; Lochbiler, T.; Tsurkan, V.; ...

2016-12-15

Here, the series of Cr-chalcogenide spinels ACr 2X 4 (A = Zn, Cd, Hg; X = S, Se) exhibits a rich phase diagram upon compression, as revealed by our recent investigations. There exist, however, some open questions regarding the role of cations in the observed structural transitions. In order to address these queries, we have performed X-ray diffraction and Raman spectroscopic studies on the ZnCr 2S 4 spinel up to 42 GPa, chosen mainly due to the similarity of the Zn 2+ and Cr 3+ cationic radii. Two reversible structural transitions were identified at 22 and 33 GPa, into a I4 1/ amd and an orthorhombic phase, respectively. Close comparison with the behavior of relevant Cr-spinels revealed that the structural transitions are mainly governed by the competition of the magnetic exchange interactions present in these systems, and not by steric effects. In addition, careful inspection of the starting Fdmore » $$\\bar{3}$$m phase revealed a previously unnoticed isostructural transition. The latter is intimately related to changes in the electronic properties of these systems, as evidenced by our Raman studies. Our results provide insights for tuning the physical and chemical properties of these materials, even under moderate compression, as well as promoting the understanding of similar pressure-induced effects in relevant systems.« less

Fast metabolite identification with Input Output Kernel Regression.

PubMed

Brouard, Céline; Shen, Huibin; Dührkop, Kai; d'Alché-Buc, Florence; Böcker, Sebastian; Rousu, Juho

2016-06-15

An important problematic of metabolomics is to identify metabolites using tandem mass spectrometry data. Machine learning methods have been proposed recently to solve this problem by predicting molecular fingerprint vectors and matching these fingerprints against existing molecular structure databases. In this work we propose to address the metabolite identification problem using a structured output prediction approach. This type of approach is not limited to vector output space and can handle structured output space such as the molecule space. We use the Input Output Kernel Regression method to learn the mapping between tandem mass spectra and molecular structures. The principle of this method is to encode the similarities in the input (spectra) space and the similarities in the output (molecule) space using two kernel functions. This method approximates the spectra-molecule mapping in two phases. The first phase corresponds to a regression problem from the input space to the feature space associated to the output kernel. The second phase is a preimage problem, consisting in mapping back the predicted output feature vectors to the molecule space. We show that our approach achieves state-of-the-art accuracy in metabolite identification. Moreover, our method has the advantage of decreasing the running times for the training step and the test step by several orders of magnitude over the preceding methods. celine.brouard@aalto.fi Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

T-RMSD: a fine-grained, structure-based classification method and its application to the functional characterization of TNF receptors.

PubMed

Magis, Cedrik; Stricher, François; van der Sloot, Almer M; Serrano, Luis; Notredame, Cedric

2010-07-16

This study addresses the relation between structural and functional similarity in proteins. We introduce a novel method named tree based on root mean square deviation (T-RMSD), which uses distance RMSD (dRMSD) variations to build fine-grained structure-based classifications of proteins. The main improvement of the T-RMSD over similar methods, such as Dali, is its capacity to produce the equivalent of a bootstrap value for each cluster node. We validated our approach on two domain families studied extensively for their role in many biological and pathological pathways: the small GTPase RAS superfamily and the cysteine-rich domains (CRDs) associated with the tumor necrosis factor receptors (TNFRs) family. Our analysis showed that T-RMSD is able to automatically recover and refine existing classifications. In the case of the small GTPase ARF subfamily, T-RMSD can distinguish GTP- from GDP-bound states, while in the case of CRDs it can identify two new subgroups associated with well defined functional features (ligand binding and formation of ligand pre-assembly complex). We show how hidden Markov models (HMMs) can be built on these new groups and propose a methodology to use these models simultaneously in order to do fine-grained functional genomic annotation without known 3D structures. T-RMSD, an open source freeware incorporated in the T-Coffee package, is available online. 2010 Elsevier Ltd. All rights reserved.

Fast metabolite identification with Input Output Kernel Regression

PubMed Central

Brouard, Céline; Shen, Huibin; Dührkop, Kai; d'Alché-Buc, Florence; Böcker, Sebastian; Rousu, Juho

2016-01-01

Motivation: An important problematic of metabolomics is to identify metabolites using tandem mass spectrometry data. Machine learning methods have been proposed recently to solve this problem by predicting molecular fingerprint vectors and matching these fingerprints against existing molecular structure databases. In this work we propose to address the metabolite identification problem using a structured output prediction approach. This type of approach is not limited to vector output space and can handle structured output space such as the molecule space. Results: We use the Input Output Kernel Regression method to learn the mapping between tandem mass spectra and molecular structures. The principle of this method is to encode the similarities in the input (spectra) space and the similarities in the output (molecule) space using two kernel functions. This method approximates the spectra-molecule mapping in two phases. The first phase corresponds to a regression problem from the input space to the feature space associated to the output kernel. The second phase is a preimage problem, consisting in mapping back the predicted output feature vectors to the molecule space. We show that our approach achieves state-of-the-art accuracy in metabolite identification. Moreover, our method has the advantage of decreasing the running times for the training step and the test step by several orders of magnitude over the preceding methods. Availability and implementation: Contact: celine.brouard@aalto.fi Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27307628

Detecting Lung and Colorectal Cancer Recurrence Using Structured Clinical/Administrative Data to Enable Outcomes Research and Population Health Management.

PubMed

Hassett, Michael J; Uno, Hajime; Cronin, Angel M; Carroll, Nikki M; Hornbrook, Mark C; Ritzwoller, Debra

2017-12-01

Recurrent cancer is common, costly, and lethal, yet we know little about it in community-based populations. Electronic health records and tumor registries contain vast amounts of data regarding community-based patients, but usually lack recurrence status. Existing algorithms that use structured data to detect recurrence have limitations. We developed algorithms to detect the presence and timing of recurrence after definitive therapy for stages I-III lung and colorectal cancer using 2 data sources that contain a widely available type of structured data (claims or electronic health record encounters) linked to gold-standard recurrence status: Medicare claims linked to the Cancer Care Outcomes Research and Surveillance study, and the Cancer Research Network Virtual Data Warehouse linked to registry data. Twelve potential indicators of recurrence were used to develop separate models for each cancer in each data source. Detection models maximized area under the ROC curve (AUC); timing models minimized average absolute error. Algorithms were compared by cancer type/data source, and contrasted with an existing binary detection rule. Detection model AUCs (>0.92) exceeded existing prediction rules. Timing models yielded absolute prediction errors that were small relative to follow-up time (<15%). Similar covariates were included in all detection and timing algorithms, though differences by cancer type and dataset challenged efforts to create 1 common algorithm for all scenarios. Valid and reliable detection of recurrence using big data is feasible. These tools will enable extensive, novel research on quality, effectiveness, and outcomes for lung and colorectal cancer patients and those who develop recurrence.

Crystal structure of Rv2258c from Mycobacterium tuberculosis H37Rv, an S-adenosyl-l-methionine-dependent methyltransferase.

PubMed

Im, Ha Na; Kim, Hyoun Sook; An, Doo Ri; Jang, Jun Young; Kim, Jieun; Yoon, Hye-Jin; Yang, Jin Kuk; Suh, Se Won

2016-03-01

The Mycobacterium tuberculosis Rv2258c protein is an S-adenosyl-L-methionine (SAM)-dependent methyltransferase (MTase). Here, we have determined its crystal structure in three forms: a ligand-unbound form, a binary complex with sinefungin (SFG), and a binary complex with S-adenosyl-L-homocysteine (SAH). The monomer structure of Rv2258c consists of two domains which are linked by a long α-helix. The N-terminal domain is essential for dimerization and the C-terminal domain has the Class I MTase fold. Rv2258c forms a homodimer in the crystal, with the N-terminal domains facing each other. It also exists as a homodimer in solution. A DALI structural similarity search with Rv2258c reveals that the overall structure of Rv2258c is very similar to small-molecule SAM-dependent MTases. Rv2258c interacts with the bound SFG (or SAH) in an extended conformation maintained by a network of hydrogen bonds and stacking interactions. Rv2258c has a relatively large hydrophobic cavity for binding of the methyl-accepting substrate, suggesting that bulky nonpolar molecules with aromatic rings might be targeted for methylation by Rv2258c in M. tuberculosis. However, the ligand-binding specificity and the biological role of Rv2258c remain to be elucidated due to high variability of the amino acid residues defining the substrate-binding site. Copyright © 2016 Elsevier Inc. All rights reserved.

The players may change but the game remains: network analyses of ruminal microbiomes suggest taxonomic differences mask functional similarity

PubMed Central

Taxis, Tasia M.; Wolff, Sara; Gregg, Sarah J.; Minton, Nicholas O.; Zhang, Chiqian; Dai, Jingjing; Schnabel, Robert D.; Taylor, Jeremy F.; Kerley, Monty S.; Pires, J. Chris; Lamberson, William R.; Conant, Gavin C.

2015-01-01

By mapping translated metagenomic reads to a microbial metabolic network, we show that ruminal ecosystems that are rather dissimilar in their taxonomy can be considerably more similar at the metabolic network level. Using a new network bi-partition approach for linking the microbial network to a bovine metabolic network, we observe that these ruminal metabolic networks exhibit properties consistent with distinct metabolic communities producing similar outputs from common inputs. For instance, the closer in network space that a microbial reaction is to a reaction found in the host, the lower will be the variability of its enzyme copy number across hosts. Similarly, these microbial enzymes that are nearby to host nodes are also higher in copy number than are more distant enzymes. Collectively, these results demonstrate a widely expected pattern that, to our knowledge, has not been explicitly demonstrated in microbial communities: namely that there can exist different community metabolic networks that have the same metabolic inputs and outputs but differ in their internal structure. PMID:26420832

The Development of Layered Photonic Band Gap Structures Using a Micro-Transfer Molding Technique

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

Sutherland, Kevin Jerome

Photonic band gap (PBG) crystals are periodic dielectric structures that manipulate electromagnetic radiation in a manner similar to semiconductor devices manipulating electrons. Whereas a semiconductor material exhibits an electronic band gap in which electrons cannot exist, similarly, a photonic crystal containing a photonic band gap does not allow the propagation of specific frequencies of electromagnetic radiation. This phenomenon results from the destructive Bragg diffraction interference that a wave propagating at a specific frequency will experience because of the periodic change in dielectric permitivity. This gives rise to a variety of optical applications for improving the efficiency and effectiveness of opto-electronicmore » devices. These applications are reviewed later. Several methods are currently used to fabricate photonic crystals, which are also discussed in detail. This research involves a layer-by-layer micro-transfer molding ({mu}TM) and stacking method to create three-dimensional FCC structures of epoxy or titania. The structures, once reduced significantly in size can be infiltrated with an organic gain media and stacked on a semiconductor to improve the efficiency of an electronically pumped light-emitting diode. Photonic band gap structures have been proven to effectively create a band gap for certain frequencies of electro-magnetic radiation in the microwave and near-infrared ranges. The objective of this research project was originally two-fold: to fabricate a three dimensional (3-D) structure of a size scaled to prohibit electromagnetic propagation within the visible wavelength range, and then to characterize that structure using laser dye emission spectra. As a master mold has not yet been developed for the micro transfer molding technique in the visible range, the research was limited to scaling down the length scale as much as possible with the current available technology and characterizing these structures with other methods.« less

Design Oriented Structural Modeling for Airplane Conceptual Design Optimization

NASA Technical Reports Server (NTRS)

Livne, Eli

1999-01-01

The main goal for research conducted with the support of this grant was to develop design oriented structural optimization methods for the conceptual design of airplanes. Traditionally in conceptual design airframe weight is estimated based on statistical equations developed over years of fitting airplane weight data in data bases of similar existing air- planes. Utilization of such regression equations for the design of new airplanes can be justified only if the new air-planes use structural technology similar to the technology on the airplanes in those weight data bases. If any new structural technology is to be pursued or any new unconventional configurations designed the statistical weight equations cannot be used. In such cases any structural weight estimation must be based on rigorous "physics based" structural analysis and optimization of the airframes under consideration. Work under this grant progressed to explore airframe design-oriented structural optimization techniques along two lines of research: methods based on "fast" design oriented finite element technology and methods based on equivalent plate / equivalent shell models of airframes, in which the vehicle is modelled as an assembly of plate and shell components, each simulating a lifting surface or nacelle / fuselage pieces. Since response to changes in geometry are essential in conceptual design of airplanes, as well as the capability to optimize the shape itself, research supported by this grant sought to develop efficient techniques for parametrization of airplane shape and sensitivity analysis with respect to shape design variables. Towards the end of the grant period a prototype automated structural analysis code designed to work with the NASA Aircraft Synthesis conceptual design code ACS= was delivered to NASA Ames.

Evidence for monoclinic distortion in the ground state phase of underdoped La{sub 1.95}Sr{sub 0.05}CuO{sub 4}: A single crystal neutron diffraction study

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

Singh, Anar, E-mail: singhanar@gmail.com; Schefer, Jürg; Frontzek, Matthias

2016-03-28

The existing controversy about the symmetry of the crystal structure of the ground state of the critical doped La{sub 1.95}Sr{sub 0.05}CuO{sub 4} has been resolved by analyzing the single crystal neutron diffraction data collected between 5 and 730 K. We observed small but significant intensities for “forbidden” reflections given by extinction rules of the orthorhombic Bmab space group at low temperatures. A careful investigation of neutron diffraction data reveals that the crystal structure of La{sub 1.95}Sr{sub 0.05}CuO{sub 4} at 5 K is monoclinic with B2/m (2/m 1 1) space group. The monoclinic structure emerges from the orthorhombic structure in a continuous way;more » however, the structure is stable below ∼120 K which agrees with other observed phenomena. Our results on symmetry changes are crucial for the interpretation of physical properties also in other high temperature superconductors with similar structures.« less

SPONTANEOUS FORMATION OF SURFACE MAGNETIC STRUCTURE FROM LARGE-SCALE DYNAMO IN STRONGLY STRATIFIED CONVECTION

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

Masada, Youhei; Sano, Takayoshi, E-mail: ymasada@auecc.aichi-edu.ac.jp, E-mail: sano@ile.osaka-u.ac.jp

We report the first successful simulation of spontaneous formation of surface magnetic structures from a large-scale dynamo by strongly stratified thermal convection in Cartesian geometry. The large-scale dynamo observed in our strongly stratified model has physical properties similar to those in earlier weakly stratified convective dynamo simulations, indicating that the α {sup 2}-type mechanism is responsible for the dynamo. In addition to the large-scale dynamo, we find that large-scale structures of the vertical magnetic field are spontaneously formed in the convection zone (CZ) surface only in cases with a strongly stratified atmosphere. The organization of the vertical magnetic field proceedsmore » in the upper CZ within tens of convective turnover time and band-like bipolar structures recurrently appear in the dynamo-saturated stage. We consider several candidates to be possibly be the origin of the surface magnetic structure formation, and then suggest the existence of an as-yet-unknown mechanism for the self-organization of the large-scale magnetic structure, which should be inherent in the strongly stratified convective atmosphere.« less

Effective evaluation of privacy protection techniques in visible and thermal imagery

NASA Astrophysics Data System (ADS)

Nawaz, Tahir; Berg, Amanda; Ferryman, James; Ahlberg, Jörgen; Felsberg, Michael

2017-09-01

Privacy protection may be defined as replacing the original content in an image region with a (less intrusive) content having modified target appearance information to make it less recognizable by applying a privacy protection technique. Indeed, the development of privacy protection techniques also needs to be complemented with an established objective evaluation method to facilitate their assessment and comparison. Generally, existing evaluation methods rely on the use of subjective judgments or assume a specific target type in image data and use target detection and recognition accuracies to assess privacy protection. An annotation-free evaluation method that is neither subjective nor assumes a specific target type is proposed. It assesses two key aspects of privacy protection: "protection" and "utility." Protection is quantified as an appearance similarity, and utility is measured as a structural similarity between original and privacy-protected image regions. We performed an extensive experimentation using six challenging datasets (having 12 video sequences), including a new dataset (having six sequences) that contains visible and thermal imagery. The new dataset is made available online for the community. We demonstrate effectiveness of the proposed method by evaluating six image-based privacy protection techniques and also show comparisons of the proposed method over existing methods.

Molecular Dynamics Information Improves cis-Peptide-Based Function Annotation of Proteins.

PubMed

Das, Sreetama; Bhadra, Pratiti; Ramakumar, Suryanarayanarao; Pal, Debnath

2017-08-04

cis-Peptide bonds, whose occurrence in proteins is rare but evolutionarily conserved, are implicated to play an important role in protein function. This has led to their previous use in a homology-independent, fragment-match-based protein function annotation method. However, proteins are not static molecules; dynamics is integral to their activity. This is nicely epitomized by the geometric isomerization of cis-peptide to trans form for molecular activity. Hence we have incorporated both static (cis-peptide) and dynamics information to improve the prediction of protein molecular function. Our results show that cis-peptide information alone cannot detect functional matches in cases where cis-trans isomerization exists but 3D coordinates have been obtained for only the trans isomer or when the cis-peptide bond is incorrectly assigned as trans. On the contrary, use of dynamics information alone includes false-positive matches for cases where fragments with similar secondary structure show similar dynamics, but the proteins do not share a common function. Combining the two methods reduces errors while detecting the true matches, thereby enhancing the utility of our method in function annotation. A combined approach, therefore, opens up new avenues of improving existing automated function annotation methodologies.

Strengthening the reliability and credibility of observational epidemiology studies by creating an Observational Studies Register.

PubMed

Swaen, Gerard M H; Carmichael, Neil; Doe, John

2011-05-01

To evaluate the need for the creation of a system in which observational epidemiology studies are registered; an Observational Studies Register (OSR). The current scientific process for observational epidemiology studies is described. Next, a parallel is made with the clinical trials area, where the creation of clinical trial registers has greatly restored and improved their credibility and reliability. Next, the advantages and disadvantages of an OSR are compared. The advantages of an OSR outweigh its disadvantages. The creation of an OSR, similar to the existing Clinical Trials Registers, will improve the assessment of publication bias and will provide an opportunity to compare the original study protocol with the results reported in the publication. Reliability, credibility, and transparency of observational epidemiology studies are strengthened by the creation of an OSR. We propose a structured, collaborative, and coordinated approach for observational epidemiology studies that can provide solutions for existing weaknesses and will strengthen credibility and reliability, similar to the approach currently used in clinical trials, where Clinical Trials Registers have played a key role in strengthening their scientific value. Copyright © 2011 Elsevier Inc. All rights reserved.

The three-dimensional turbulent boundary layer near a plane of symmetry

NASA Technical Reports Server (NTRS)

Degani, A. T.; Smith, F. T.; Walker, J. D. A.

1992-01-01

The asymptotic structure of the three-dimensional turbulent boundary layer near a plane of symmetry is considered in the limit of large Reynolds number. A self-consistent two-layer structure is shown to exist wherein the streamwise velocity is brought to rest through an outer defect layer and an inner wall layer in a manner similar to that in two-dimensional boundary layers. The cross-stream velocity distribution is more complex and two terms in the asymptotic expansion are required to yield a complete profile which is shown to exhibit a logarithmic region. The flow in the inner wall layer is demonstrated to be collateral to leading order; pressure-gradient effects are formally of higher order but can cause the velocity profile to skew substantially near the wall at the large but finite Reynolds numbers encountered in practice. The governing set of ordinary differential equations describing a self-similar flow is derived. The calculated numerical solutions of these equations are matched asymptotically to an inner wall-layer solution and the results show trends that are consistent with experimental observations.

Evidence for a dwarf galaxy remnant around M82 from deep Hubble Space Telescope imaging

NASA Astrophysics Data System (ADS)

Suwannajak, Chutipong; Sarajedini, Ata

2018-01-01

We present HST/ACS photometry of an over-dense region of stars in the southern halo of the edge-on galaxy M82. The structure is located at a projected distance of 5 kpc from the disk of the galaxy, and its color-magnitude diagram reveals a population of predominantly young stars, which are largely absent from the surrounding halo. Their ages are similar to those of the young stars formed in the tidal debris between M81, M82, and NGC3077 as a result of their interactions. We derive the mean metallicity of the surrounding stars, which are considered to be the halo population of M82, to be similar to that of the red giant branch (RGB) population of the halo of M81. However, the mean metallicity of the RGB in the over-dense structure is significantly more metal-rich than the halo. We theorize that this over-density existed as a dwarf galaxy prior to its interaction with M82 with the young stars forming later from the gas remaining in its main body.

A research for Class II defect Bored Pile’s Accept Criteria: A case of Penang Second Marine bridge

NASA Astrophysics Data System (ADS)

Huang, Kang

2018-03-01

The aim of this preliminary research is to study the accept criteria of class II bored pile with subtle defect. According to a detailed comparison of the existed different standards, Chinese ones are more applicable especially for the large diameter bored piles. Through the concrete coring at pile No P25-03 of this case and the comparison to the actual calculation, the Class II pile’s defects were very minor. Comparison was also made for the effects on pile structural capacities before and after repair of the defects. the feasible repair proposal may bring forward to more defects to the piles. The Class II piles don’t need any further repairation when piles have typical of similar character and sonic logging test result with P25-03‘s one. For other Class II piles with some differences in characters, verification is needed through further concrete coring on the pile. The recommendation of this research could be adopted for the similar huge marine structures which installed large diameter bored piles.

Geometry Of Discrete Sets With Applications To Pattern Recognition

NASA Astrophysics Data System (ADS)

Sinha, Divyendu

1990-03-01

In this paper we present a new framework for discrete black and white images that employs only integer arithmetic. This framework is shown to retain the essential characteristics of the framework for Euclidean images. We propose two norms and based on them, the permissible geometric operations on images are defined. The basic invariants of our geometry are line images, structure of image and the corresponding local property of strong attachment of pixels. The permissible operations also preserve the 3x3 neighborhoods, area, and perpendicularity. The structure, patterns, and the inter-pattern gaps in a discrete image are shown to be conserved by the magnification and contraction process. Our notions of approximate congruence, similarity and symmetry are similar, in character, to the corresponding notions, for Euclidean images [1]. We mention two discrete pattern recognition algorithms that work purely with integers, and which fit into our framework. Their performance has been shown to be at par with the performance of traditional geometric schemes. Also, all the undesired effects of finite length registers in fixed point arithmetic that plague traditional algorithms, are non-existent in this family of algorithms.

The properties of fast and slow oblique solitons in a magnetized plasma

NASA Astrophysics Data System (ADS)

McKenzie, J. F.; Doyle, T. B.

2002-01-01

This work builds on a recent treatment by McKenzie and Doyle [Phys. Plasmas 8, 4367 (2001)], on oblique solitons in a cold magnetized plasma, to include the effects of plasma thermal pressure. Conservation of total momentum in the direction of wave propagation immediately shows that if the flow is supersonic, compressive (rarefactive) changes in the magnetic pressure induce decelerations (accelerations) in the flow speed, whereas if the flow is subsonic, compressive (rarefactive) changes in the magnetic pressure induce accelerations (decelerations) in the flow speed. Such behavior is characteristic of a Bernoulli-type plasma momentum flux which exhibits a minimum at the plasma sonic point. The plasma energy flux (kinetic plus enthalpy) also shows similar Bernoulli-type behavior. This transonic effect is manifest in the spatial structure equation for the flow speed (in the direction of propagation) which shows that soliton structures may exist if the wave speed lies either (i) in the range between the fast and Alfven speeds or (ii) between the sound and slow mode speed. These conditions follow from the requirement that a defined, characteristic "soliton parameter" m exceeds unity. It is in this latter slow soliton regime that the effects of plasma pressure are most keenly felt. The equilibrium points of the structure equation define the center of the wave. The structure of both fast and slow solitons is elucidated through the properties of the energy integral function of the structure equation. In particular, the slow soliton, which owes its existence to plasma pressure, may have either a compressive or rarefactive nature, and exhibits a rich structure, which is revealed through the spatial structure of the longitudinal speed and its corresponding transverse velocity hodograph.

Long-range dipolar order and dispersion forces in polar liquids

NASA Astrophysics Data System (ADS)

Besford, Quinn Alexander; Christofferson, Andrew Joseph; Liu, Maoyuan; Yarovsky, Irene

2017-11-01

Complex solvation phenomena, such as specific ion effects, occur in polar liquids. Interpretation of these effects in terms of structure and dispersion forces will lead to a greater understanding of solvation. Herein, using molecular dynamics, we probe the structure of polar liquids through specific dipolar pair correlation functions that contribute to the potential of mean force that is "felt" between thermally rotating dipole moments. It is shown that unique dipolar order exists at separations at least up to 20 Å for all liquids studied. When the structural order is compared with a dipolar dispersion force that arises from local co-operative enhancement of dipole moments, a strong agreement is found. Lifshitz theory of dispersion forces was compared with the structural order, where the theory is validated for all liquids that do not have significant local dipole correlations. For liquids that do have significant local dipole correlations, specifically liquid water, Lifshitz theory underestimates the dispersion force by a factor of 5-10, demonstrating that the force that leads to the increased structure in liquid water is missed by Lifshitz theory of van der Waals forces. We apply similar correlation functions to an ionic aqueous system, where long-range order between water's dipole moment and a single chloride ion is found to exist at 20 Å of separation, revealing a long-range perturbation of water's structure by an ion. Furthermore, we found that waters within the 1st, 2nd, and 3rd solvation shells of a chloride ion exhibit significantly enhanced dipolar interactions, particularly with waters at larger distances of separation. Our results provide a link between structures, dispersion forces, and specific ion effects, which may lead to a more robust understanding of solvation.

Community structure, trophic position and reproductive mode of soil and bark-living oribatid mites in an alpine grassland ecosystem.

PubMed

Fischer, Barbara M; Schatz, Heinrich; Maraun, Mark

2010-11-01

The community structure, stable isotope ratios ((15)N/(14)N, (13)C/(12)C) and reproductive mode of oribatid mites (Acari, Oribatida) were investigated in four habitats (upper tree bark, lower tree bark, dry grassland soil, forest soil) at two sites in the Central Alps (Tyrol, Austria). We hypothesized that community structure and trophic position of oribatid mites of dry grassland soils and bark of trees are similar since these habitats have similar abiotic characteristics (open, dry) compared with forest soil. Further, we hypothesized that derived taxa of oribatid mites reproducing sexually dominate on the bark of trees since species in this habitat consume living resources such as lichens. In contrast to our hypothesis, the community structure of oribatid mites differed among grassland, forest and bark indicating the existence of niche differentiation in the respective oribatid mite species. In agreement with our hypothesis, sexually reproducing taxa of oribatid mites dominated on the bark of trees whereas parthenogenetic species were more frequent in soil. Several species of bark-living oribatid mites had stable isotope signatures that were similar to lichens indicating that they feed on lichens. However, nine species that frequently occurred on tree bark did not feed on lichens according to their stable isotope signatures. No oribatid mite species could be ascribed to moss feeding. We conclude that sexual reproduction served as preadaptation for oribatid mites allowing them to exploit new habitats and new resources on the bark of trees. Abiotic factors likely are of limited importance for bark-living oribatid mites since harsh abiotic conditions are assumed to favor parthenogenesis.

Spatial Genetic Structure of the Abundant and Widespread Peatmoss Sphagnum magellanicum Brid.

PubMed Central

Kyrkjeeide, Magni Olsen; Hassel, Kristian; Flatberg, Kjell Ivar; Shaw, A. Jonathan; Yousefi, Narjes; Stenøien, Hans K.

2016-01-01

Spore-producing organisms have small dispersal units enabling them to become widespread across continents. However, barriers to gene flow and cryptic speciation may exist. The common, haploid peatmoss Sphagnum magellanicum occurs in both the Northern and Southern hemisphere, and is commonly used as a model in studies of peatland ecology and peatmoss physiology. Even though it will likely act as a rich source in functional genomics studies in years to come, surprisingly little is known about levels of genetic variability and structuring in this species. Here, we assess for the first time how genetic variation in S. magellanicum is spatially structured across its full distribution range (Northern Hemisphere and South America). The morphologically similar species S. alaskense was included for comparison. In total, 195 plants were genotyped at 15 microsatellite loci. Sequences from two plastid loci (trnG and trnL) were obtained from 30 samples. Our results show that S. alaskense and almost all plants of S. magellanicum in the northern Pacific area are diploids and share the same gene pool. Haploid plants occur in South America, Europe, eastern North America, western North America, and southern Asia, and five genetically differentiated groups with different distribution ranges were found. Our results indicate that S. magellanicum consists of several distinct genetic groups, seemingly with little or no gene flow among them. Noteworthy, the geographical separation of diploids and haploids is strikingly similar to patterns found within other haploid Sphagnum species spanning the Northern Hemisphere. Our results confirm a genetic division between the Beringian and the Atlantic that seems to be a general pattern in Sphagnum taxa. The pattern of strong genetic population structuring throughout the distribution range of morphologically similar plants need to be considered in future functional genomic studies of S. magellanicum. PMID:26859563

Spatial Genetic Structure of the Abundant and Widespread Peatmoss Sphagnum magellanicum Brid.

PubMed

Kyrkjeeide, Magni Olsen; Hassel, Kristian; Flatberg, Kjell Ivar; Shaw, A Jonathan; Yousefi, Narjes; Stenøien, Hans K

2016-01-01

Spore-producing organisms have small dispersal units enabling them to become widespread across continents. However, barriers to gene flow and cryptic speciation may exist. The common, haploid peatmoss Sphagnum magellanicum occurs in both the Northern and Southern hemisphere, and is commonly used as a model in studies of peatland ecology and peatmoss physiology. Even though it will likely act as a rich source in functional genomics studies in years to come, surprisingly little is known about levels of genetic variability and structuring in this species. Here, we assess for the first time how genetic variation in S. magellanicum is spatially structured across its full distribution range (Northern Hemisphere and South America). The morphologically similar species S. alaskense was included for comparison. In total, 195 plants were genotyped at 15 microsatellite loci. Sequences from two plastid loci (trnG and trnL) were obtained from 30 samples. Our results show that S. alaskense and almost all plants of S. magellanicum in the northern Pacific area are diploids and share the same gene pool. Haploid plants occur in South America, Europe, eastern North America, western North America, and southern Asia, and five genetically differentiated groups with different distribution ranges were found. Our results indicate that S. magellanicum consists of several distinct genetic groups, seemingly with little or no gene flow among them. Noteworthy, the geographical separation of diploids and haploids is strikingly similar to patterns found within other haploid Sphagnum species spanning the Northern Hemisphere. Our results confirm a genetic division between the Beringian and the Atlantic that seems to be a general pattern in Sphagnum taxa. The pattern of strong genetic population structuring throughout the distribution range of morphologically similar plants need to be considered in future functional genomic studies of S. magellanicum.

Structural and functional studies of a family of Dictyostelium discoideum developmentally regulated, prestalk genes coding for small proteins.

PubMed

Vicente, Juan J; Galardi-Castilla, María; Escalante, Ricardo; Sastre, Leandro

2008-01-03

The social amoeba Dictyostelium discoideum executes a multicellular development program upon starvation. This morphogenetic process requires the differential regulation of a large number of genes and is coordinated by extracellular signals. The MADS-box transcription factor SrfA is required for several stages of development, including slug migration and spore terminal differentiation. Subtractive hybridization allowed the isolation of a gene, sigN (SrfA-induced gene N), that was dependent on the transcription factor SrfA for expression at the slug stage of development. Homology searches detected the existence of a large family of sigN-related genes in the Dictyostelium discoideum genome. The 13 most similar genes are grouped in two regions of chromosome 2 and have been named Group1 and Group2 sigN genes. The putative encoded proteins are 87-89 amino acids long. All these genes have a similar structure, composed of a first exon containing a 13 nucleotides long open reading frame and a second exon comprising the remaining of the putative coding region. The expression of these genes is induced at10 hours of development. Analyses of their promoter regions indicate that these genes are expressed in the prestalk region of developing structures. The addition of antibodies raised against SigN Group 2 proteins induced disintegration of multi-cellular structures at the mound stage of development. A large family of genes coding for small proteins has been identified in D. discoideum. Two groups of very similar genes from this family have been shown to be specifically expressed in prestalk cells during development. Functional studies using antibodies raised against Group 2 SigN proteins indicate that these genes could play a role during multicellular development.

Generalized Structured Component Analysis with Uniqueness Terms for Accommodating Measurement Error

PubMed Central

Hwang, Heungsun; Takane, Yoshio; Jung, Kwanghee

2017-01-01

Generalized structured component analysis (GSCA) is a component-based approach to structural equation modeling (SEM), where latent variables are approximated by weighted composites of indicators. It has no formal mechanism to incorporate errors in indicators, which in turn renders components prone to the errors as well. We propose to extend GSCA to account for errors in indicators explicitly. This extension, called GSCAM, considers both common and unique parts of indicators, as postulated in common factor analysis, and estimates a weighted composite of indicators with their unique parts removed. Adding such unique parts or uniqueness terms serves to account for measurement errors in indicators in a manner similar to common factor analysis. Simulation studies are conducted to compare parameter recovery of GSCAM and existing methods. These methods are also applied to fit a substantively well-established model to real data. PMID:29270146

The Effect of a Helix-Coil Transition on the Extension Elasticity

NASA Astrophysics Data System (ADS)

Buhot, Arnaud; Halperin, Avi

2000-03-01

The secondary structure of a polymer affects its deformation behavior in accordance with the Le Chatelier principle. An important example of such secondary structure is the alpha helix encountered in polypeptides. Similar structure was recently proposed for PEO in aqueous media. Our discussion concerns the coupling of the cooperative helix-coil transition and the extension elasticity. In particular, we analyze the extension of a long single chain by use of optical tweezers or AFM. We consider chains that exist in the coil-state when unperturbed. The transition nevertheless occurs because the extension favors the low entropy helical state. As a result, the corresponding force law exhibits a plateau. The analysis of this situation involves two ingredients: (I) the stretching free energy penalty for a rod-coil mutiblock copolymer (II) the entropy associated with the possible placements of the rod and coil blocks.

Metagenomic analysis reveals significant changes of microbial compositions and protective functions during drinking water treatment.

PubMed

Chao, Yuanqing; Ma, Liping; Yang, Ying; Ju, Feng; Zhang, Xu-Xiang; Wu, Wei-Min; Zhang, Tong

2013-12-19

The metagenomic approach was applied to characterize variations of microbial structure and functions in raw (RW) and treated water (TW) in a drinking water treatment plant (DWTP) at Pearl River Delta, China. Microbial structure was significantly influenced by the treatment processes, shifting from Gammaproteobacteria and Betaproteobacteria in RW to Alphaproteobacteria in TW. Further functional analysis indicated the basic metabolic functions of microorganisms in TW did not vary considerably. However, protective functions, i.e. glutathione synthesis genes in 'oxidative stress' and 'detoxification' subsystems, significantly increased, revealing the surviving bacteria may have higher chlorine resistance. Similar results were also found in glutathione metabolism pathway, which identified the major reaction for glutathione synthesis and supported more genes for glutathione metabolism existed in TW. This metagenomic study largely enhanced our knowledge about the influences of treatment processes, especially chlorination, on bacterial community structure and protective functions (e.g. glutathione metabolism) in ecosystems of DWTPs.

A deformation of Sasakian structure in the presence of torsion and supergravity solutions

NASA Astrophysics Data System (ADS)

Houri, Tsuyoshi; Takeuchi, Hiroshi; Yasui, Yukinori

2013-07-01

A deformation of Sasakian structure in the presence of totally skew-symmetric torsion is discussed on odd-dimensional manifolds whose metric cones are Kähler with torsion. It is shown that such a geometry inherits similar properties to those of Sasakian geometry. As their example, we present an explicit expression of local metrics. It is also demonstrated that our example of the metrics admits the existence of hidden symmetry described by non-trivial odd-rank generalized closed conformal Killing-Yano tensors. Furthermore, using these metrics as an ansatz, we construct exact solutions in five-dimensional minimal gauged/ungauged supergravity and 11-dimensional supergravity. Finally, the global structures of the solutions are discussed. We obtain regular metrics on compact manifolds in five dimensions, which give natural generalizations of Sasaki-Einstein manifolds Yp, q and La, b, c. We also briefly discuss regular metrics on non-compact manifolds in 11 dimensions.

Fragment approach to the electronic structure of τ -boron allotrope

NASA Astrophysics Data System (ADS)

Karmodak, Naiwrit; Jemmis, Eluvathingal D.

2017-04-01

The presence of nonconventional bonding features is an intriguing part of elemental boron. The recent addition of τ boron to the family of three-dimensional boron allotropes is no exception. We provide an understanding of the electronic structure of τ boron using a fragment molecular approach, where the effect of symmetry reduction on skeletal bands of B12 and the B57 fragments are examined qualitatively by analyzing the projected density of states of these fragments. In spite of the structural resemblance to β boron, the reduction of symmetry from a rhombohedral space group to the orthorhombic one destabilizes the bands and reduces the electronic requirements. This suggests the presence of the partially occupied boron sites, as seen for a β boron unit cell, and draws the possibility for the existence of different energetically similar polymorphs. τ boron has a lower binding energy than β boron.

Structural characteristics of the shock-induced boundary layer separation extended to the leading edge

NASA Astrophysics Data System (ADS)

Tao, Y.; Liu, W. D.; Fan, X. Q.; Zhao, Y. L.

2017-07-01

For a better understanding of the local unstart of supersonic/hypersonic inlet, a series of experiments has been conducted to investigate the shock-induced boundary layer separation extended to the leading edge. Using the nanoparticle-based planar laser scattering, we recorded the fine structures of these interactions under different conditions and paid more attention to their structural characteristics. According to their features, these interactions could be divided into four types. Specifically, Type A wave pattern is similar to the classic shock wave/turbulent boundary layer interaction, and Type B wave configuration consists of an overall Mach reflection above the large scale separation bubble. Due to the gradual decrease in the size of the separation bubble, the separation bubble was replaced by several vortices (Type C wave pattern). Besides, for Type D wave configuration which exists in the local unstart inlet, there appears to be some flow spillage around the leading edge.

Chromosome ends: different sequences may provide conserved functions.

PubMed

Louis, Edward J; Vershinin, Alexander V

2005-07-01

The structures of specific chromosome regions, centromeres and telomeres, present a number of puzzles. As functions performed by these regions are ubiquitous and essential, their DNA, proteins and chromatin structure are expected to be conserved. Recent studies of centromeric DNA from human, Drosophila and plant species have demonstrated that a hidden universal centromere-specific sequence is highly unlikely. The DNA of telomeres is more conserved consisting of a tandemly repeated 6-8 bp Arabidopsis-like sequence in a majority of organisms as diverse as protozoan, fungi, mammals and plants. However, there are alternatives to short DNA repeats at the ends of chromosomes and for telomere elongation by telomerase. Here we focus on the similarities and diversity that exist among the structural elements, DNA sequences and proteins, that make up terminal domains (telomeres and subtelomeres), and how organisms use these in different ways to fulfil the functions of end-replication and end-protection. Copyright (c) 2005 Wiley Periodicals, Inc.

Universal scaling of the distribution of land in urban areas

NASA Astrophysics Data System (ADS)

Riascos, A. P.

2017-09-01

In this work, we explore the spatial structure of built zones and green areas in diverse western cities by analyzing the probability distribution of areas and a coefficient that characterize their respective shapes. From the analysis of diverse datasets describing land lots in urban areas, we found that the distribution of built-up areas and natural zones in cities obey inverse power laws with a similar scaling for the cities explored. On the other hand, by studying the distribution of shapes of lots in urban regions, we are able to detect global differences in the spatial structure of the distribution of land. Our findings introduce information about spatial patterns that emerge in the structure of urban settlements; this knowledge is useful for the understanding of urban growth, to improve existing models of cities, in the context of sustainability, in studies about human mobility in urban areas, among other applications.

Large-scale oscillation of structure-related DNA sequence features in human chromosome 21

NASA Astrophysics Data System (ADS)

Li, Wentian; Miramontes, Pedro

2006-08-01

Human chromosome 21 is the only chromosome in the human genome that exhibits oscillation of the (G+C) content of a cycle length of hundreds kilobases (kb) ( 500kb near the right telomere). We aim at establishing the existence of a similar periodicity in structure-related sequence features in order to relate this (G+C)% oscillation to other biological phenomena. The following quantities are shown to oscillate with the same 500kb periodicity in human chromosome 21: binding energy calculated by two sets of dinucleotide-based thermodynamic parameters, AA/TT and AAA/TTT bi- and tri-nucleotide density, 5'-TA-3' dinucleotide density, and signal for 10- or 11-base periodicity of AA/TT or AAA/TTT. These intrinsic quantities are related to structural features of the double helix of DNA molecules, such as base-pair binding, untwisting or unwinding, stiffness, and a putative tendency for nucleosome formation.

The similarity of life across the universe

PubMed Central

Cockell, Charles S.

2016-01-01

Is the hypothesis correct that if life exists elsewhere in the universe, it would have forms and structures unlike anything we could imagine? From the subatomic level in cellular energy acquisition to the assembly and even behavior of organisms at the scale of populations, life on Earth exhibits characteristics that suggest it is a universal norm for life at all levels of hierarchy. These patterns emerge from physical and biochemical limitations. Their potentially universal nature is supported by recent data on the astrophysical abundance and availability of carbon compounds and water. Within these constraints, biochemical and biological variation is certainly possible, but it is limited. If life exists elsewhere, life on Earth, rather than being a contingent product of one specific experiment in biological evolution, is likely to reflect common patterns for the assembly of living matter. PMID:27255694

Probing disorder in isometric pyrochlore and related complex oxides

NASA Astrophysics Data System (ADS)

Shamblin, Jacob; Feygenson, Mikhail; Neuefeind, Joerg; Tracy, Cameron L.; Zhang, Fuxiang; Finkeldei, Sarah; Bosbach, Dirk; Zhou, Haidong; Ewing, Rodney C.; Lang, Maik

2016-05-01

There has been an increased focus on understanding the energetics of structures with unconventional ordering (for example, correlated disorder that is heterogeneous across different length scales). In particular, compounds with the isometric pyrochlore structure, A2B2O7, can adopt a disordered, isometric fluorite-type structure, (A, B)4O7, under extreme conditions. Despite the importance of the disordering process there exists only a limited understanding of the role of local ordering on the energy landscape. We have used neutron total scattering to show that disordered fluorite (induced intrinsically by composition/stoichiometry or at far-from-equilibrium conditions produced by high-energy radiation) consists of a local orthorhombic structural unit that is repeated by a pseudo-translational symmetry, such that orthorhombic and isometric arrays coexist at different length scales. We also show that inversion in isometric spinel occurs by a similar process. This insight provides a new basis for understanding order-to-disorder transformations important for applications such as plutonium immobilization, fast ion conduction, and thermal barrier coatings.

Thermal denaturation of the BRCT tandem repeat region of human tumour suppressor gene product BRCA1.

PubMed

Pyrpassopoulos, Serapion; Ladopoulou, Angela; Vlassi, Metaxia; Papanikolau, Yannis; Vorgias, Constantinos E; Yannoukakos, Drakoulis; Nounesis, George

2005-04-01

Reduced stability of the tandem BRCT domains of human BReast CAncer 1 (BRCA1) due to missense mutations may be critical for loss of function in DNA repair and damage-induced checkpoint control. In the present thermal denaturation study of the BRCA1 BRCT region, high-precision differential scanning calorimetry (DSC) and circular dichroism (CD) spectroscopy provide evidence for the existence of a denatured state that is structurally very similar to the native. Consistency between theoretical structure-based estimates of the enthalpy (DeltaH) and heat capacity change (DeltaCp) and the calorimetric results is obtained when considering partial thermal unfolding contained in the region of the conserved hydrophobic pocket formed at the interface of the two BRCT repeats. The structural integrity of this region has been shown to be crucial for the interaction of BRCA1 with phosphorylated peptides. In addition, cancer-causing missense mutations located at the inter-BRCT-repeat interface have been linked to the destabilization of the tandem BRCT structure.

Natural snowfall reveals large-scale flow structures in the wake of a 2.5-MW wind turbine.

PubMed

Hong, Jiarong; Toloui, Mostafa; Chamorro, Leonardo P; Guala, Michele; Howard, Kevin; Riley, Sean; Tucker, James; Sotiropoulos, Fotis

2014-06-24

To improve power production and structural reliability of wind turbines, there is a pressing need to understand how turbines interact with the atmospheric boundary layer. However, experimental techniques capable of quantifying or even qualitatively visualizing the large-scale turbulent flow structures around full-scale turbines do not exist today. Here we use snowflakes from a winter snowstorm as flow tracers to obtain velocity fields downwind of a 2.5-MW wind turbine in a sampling area of ~36 × 36 m(2). The spatial and temporal resolutions of the measurements are sufficiently high to quantify the evolution of blade-generated coherent motions, such as the tip and trailing sheet vortices, identify their instability mechanisms and correlate them with turbine operation, control and performance. Our experiment provides an unprecedented in situ characterization of flow structures around utility-scale turbines, and yields significant insights into the Reynolds number similarity issues presented in wind energy applications.

Crystal Structure and Proteomics Analysis of Empty Virus-like Particles of Cowpea Mosaic Virus

PubMed Central

Huynh, Nhung T.; Hesketh, Emma L.; Saxena, Pooja; Meshcheriakova, Yulia; Ku, You-Chan; Hoang, Linh T.; Johnson, John E.; Ranson, Neil A.; Lomonossoff, George P.; Reddy, Vijay S.

2016-01-01

SUMMARY Empty virus-like particles (eVLPs) of Cowpea mosaic virus (CPMV) are currently being utilized as reagents in various biomedical and nanotechnology applications. Here, we report the crystal structure of CPMV eVLPs determined using X-ray crystallography at 2.3 Å resolution and compare it with previously reported cryo-electron microscopy (cryo-EM) of eVLPs and virion crystal structures. Although the X-ray and cryo-EM structures of eVLPs are mostly similar, there exist significant differences at the C terminus of the small (S) subunit. The intact C terminus of the S subunit plays a critical role in enabling the efficient assembly of CPMV virions and eVLPs, but undergoes proteolysis after particle formation. In addition, we report the results of mass spectrometry-based proteomics analysis of coat protein subunits from CPMV eVLPs and virions that identify the C termini of S subunits undergo proteolytic cleavages at multiple sites instead of a single cleavage site as previously observed. PMID:27021160

PROFESS: a PROtein Function, Evolution, Structure and Sequence database

PubMed Central

Triplet, Thomas; Shortridge, Matthew D.; Griep, Mark A.; Stark, Jaime L.; Powers, Robert; Revesz, Peter

2010-01-01

The proliferation of biological databases and the easy access enabled by the Internet is having a beneficial impact on biological sciences and transforming the way research is conducted. There are ∼1100 molecular biology databases dispersed throughout the Internet. To assist in the functional, structural and evolutionary analysis of the abundant number of novel proteins continually identified from whole-genome sequencing, we introduce the PROFESS (PROtein Function, Evolution, Structure and Sequence) database. Our database is designed to be versatile and expandable and will not confine analysis to a pre-existing set of data relationships. A fundamental component of this approach is the development of an intuitive query system that incorporates a variety of similarity functions capable of generating data relationships not conceived during the creation of the database. The utility of PROFESS is demonstrated by the analysis of the structural drift of homologous proteins and the identification of potential pancreatic cancer therapeutic targets based on the observation of protein–protein interaction networks. Database URL: http://cse.unl.edu/∼profess/ PMID:20624718

Structural analysis and antimicrobial activity of 2[1H]-pyrimidinethione/selenone derivatives

NASA Astrophysics Data System (ADS)

Żesławska, Ewa; Korona-Głowniak, Izabela; Szczesio, Małgorzata; Olczak, Andrzej; Żylewska, Alicja; Tejchman, Waldemar; Malm, Anna

2017-08-01

Four new crystal structures of sulfur and selenium analogues of 2[1H]-pyrimidinone derivatives were determined with the use of X-ray diffraction method. The molecular geometry and intermolecular interactions of the investigated molecules were analyzed in order to find the structural features and geometrical parameters, which can be responsible for antimicrobial activities. The influence of chalcogen substituents (sulfur and selenium) on the crystal packing was also studied. The main differences in the molecular structures exist in mutual arrangement of two aromatic rings. The intermolecular interactions in all investigated compounds are similar. Furthermore, the in vitro antibacterial and antifungal activities for these compounds were evaluated. Preliminary investigations have identified two highly potent antibacterial compounds containing selenium atom, which display selectivity towards staphylococci and micrococci. This selectivity was not observed for a control compound used as a drug, namely vancomycin. These compounds possess also good antifungal activity. This is the first report of biological activities of 2[1H]-pyrimidineselenone derivatives.

The dynamics of single protein molecules is non-equilibrium and self-similar over thirteen decades in time

DOE PAGES

Hu, Xiaohu; Hong, Liang; Smith, Micholas Dean; ...

2015-11-23

Here, internal motions of proteins are essential to their function. The time dependence of protein structural fluctuations is highly complex, manifesting subdiffusive, non-exponential behavior with effective relaxation times existing over many decades in time, from ps up to ~10 2s (refs 1-4). Here, using molecular dynamics simulations, we show that, on timescales from 10 –12 to 10 –5s, motions in single proteins are self-similar, non-equilibrium and exhibit ageing. The characteristic relaxation time for a distance fluctuation, such as inter-domain motion, is observation-time-dependent, increasing in a simple, power-law fashion, arising from the fractal nature of the topology and geometry of themore » energy landscape explored. Diffusion over the energy landscape follows a non-ergodic continuous time random walk. Comparison with single-molecule experiments suggests that the non-equilibrium self-similar dynamical behavior persists up to timescales approaching the in vivo lifespan of individual protein molecules.« less

Similarity searching and scaffold hopping in synthetically accessible combinatorial chemistry spaces.

PubMed

Boehm, Markus; Wu, Tong-Ying; Claussen, Holger; Lemmen, Christian

2008-04-24

Large collections of combinatorial libraries are an integral element in today's pharmaceutical industry. It is of great interest to perform similarity searches against all virtual compounds that are synthetically accessible by any such library. Here we describe the successful application of a new software tool CoLibri on 358 combinatorial libraries based on validated reaction protocols to create a single chemistry space containing over 10 (12) possible products. Similarity searching with FTrees-FS allows the systematic exploration of this space without the need to enumerate all product structures. The search result is a set of virtual hits which are synthetically accessible by one or more of the existing reaction protocols. Grouping these virtual hits by their synthetic protocols allows the rapid design and synthesis of multiple follow-up libraries. Such library ideas support hit-to-lead design efforts for tasks like follow-up from high-throughput screening hits or scaffold hopping from one hit to another attractive series.

Shared attention increases mood infusion.

PubMed

Shteynberg, Garriy; Hirsh, Jacob B; Galinsky, Adam D; Knight, Andrew P

2014-02-01

The current research explores how awareness of shared attention influences attitude formation. We theorized that sharing the experience of an object with fellow group members would increase elaborative processing, which in turn would intensify the effects of participant mood on attitude formation. Four experiments found that observing the same object as similar others produced more positive ratings among those in a positive mood, but more negative ratings among those in a negative mood. Participant mood had a stronger influence on evaluations when an object had purportedly been viewed by similar others than when (a) that same object was being viewed by dissimilar others, (b) similar others were viewing a different object, (c) different others were viewing a different object, or (d) the object was viewed alone with no others present. Study 4 demonstrated that these effects were driven by heightened cognitive elaboration of the attended object in the shared attention condition. These findings support the theoretical conjecture that an object attended with one's ingroup is subject to broader encoding in relation to existing knowledge structures.

Shared memories reveal shared structure in neural activity across individuals

PubMed Central

Chen, J.; Leong, Y.C.; Honey, C.J.; Yong, C.H.; Norman, K.A.; Hasson, U.

2016-01-01

Our lives revolve around sharing experiences and memories with others. When different people recount the same events, how similar are their underlying neural representations? Participants viewed a fifty-minute movie, then verbally described the events during functional MRI, producing unguided detailed descriptions lasting up to forty minutes. As each person spoke, event-specific spatial patterns were reinstated in default-network, medial-temporal, and high-level visual areas. Individual event patterns were both highly discriminable from one another and similar between people, suggesting consistent spatial organization. In many high-order areas, patterns were more similar between people recalling the same event than between recall and perception, indicating systematic reshaping of percept into memory. These results reveal the existence of a common spatial organization for memories in high-level cortical areas, where encoded information is largely abstracted beyond sensory constraints; and that neural patterns during perception are altered systematically across people into shared memory representations for real-life events. PMID:27918531

Visual Similarity of Words Alone Can Modulate Hemispheric Lateralization in Visual Word Recognition: Evidence From Modeling Chinese Character Recognition.

PubMed

Hsiao, Janet H; Cheung, Kit

2016-03-01

In Chinese orthography, the most common character structure consists of a semantic radical on the left and a phonetic radical on the right (SP characters); the minority, opposite arrangement also exists (PS characters). Recent studies showed that SP character processing is more left hemisphere (LH) lateralized than PS character processing. Nevertheless, it remains unclear whether this is due to phonetic radical position or character type frequency. Through computational modeling with artificial lexicons, in which we implement a theory of hemispheric asymmetry in perception but do not assume phonological processing being LH lateralized, we show that the difference in character type frequency alone is sufficient to exhibit the effect that the dominant type has a stronger LH lateralization than the minority type. This effect is due to higher visual similarity among characters in the dominant type than the minority type, demonstrating the modulation of visual similarity of words on hemispheric lateralization. Copyright © 2015 Cognitive Science Society, Inc.

Comparative Study on Code-based Linear Evaluation of an Existing RC Building Damaged during 1998 Adana-Ceyhan Earthquake

NASA Astrophysics Data System (ADS)

Toprak, A. Emre; Gülay, F. Gülten; Ruge, Peter

2008-07-01

Determination of seismic performance of existing buildings has become one of the key concepts in structural analysis topics after recent earthquakes (i.e. Izmit and Duzce Earthquakes in 1999, Kobe Earthquake in 1995 and Northridge Earthquake in 1994). Considering the need for precise assessment tools to determine seismic performance level, most of earthquake hazardous countries try to include performance based assessment in their seismic codes. Recently, Turkish Earthquake Code 2007 (TEC'07), which was put into effect in March 2007, also introduced linear and non-linear assessment procedures to be applied prior to building retrofitting. In this paper, a comparative study is performed on the code-based seismic assessment of RC buildings with linear static methods of analysis, selecting an existing RC building. The basic principles dealing the procedure of seismic performance evaluations for existing RC buildings according to Eurocode 8 and TEC'07 will be outlined and compared. Then the procedure is applied to a real case study building is selected which is exposed to 1998 Adana-Ceyhan Earthquake in Turkey, the seismic action of Ms = 6.3 with a maximum ground acceleration of 0.28 g It is a six-storey RC residential building with a total of 14.65 m height, composed of orthogonal frames, symmetrical in y direction and it does not have any significant structural irregularities. The rectangular shaped planar dimensions are 16.40 m×7.80 m = 127.90 m2 with five spans in x and two spans in y directions. It was reported that the building had been moderately damaged during the 1998 earthquake and retrofitting process was suggested by the authorities with adding shear-walls to the system. The computations show that the performing methods of analysis with linear approaches using either Eurocode 8 or TEC'07 independently produce similar performance levels of collapse for the critical storey of the structure. The computed base shear value according to Eurocode is much higher than the requirements of the Turkish Earthquake Code while the selected ground conditions represent the same characteristics. The main reason is that the ordinate of the horizontal elastic response spectrum for Eurocode 8 is increased by the soil factor. In TEC'07 force-based linear assessment, the seismic demands at cross-sections are to be checked with residual moment capacities; however, the chord rotations of primary ductile elements must be checked for Eurocode safety verifications. On the other hand, the demand curvatures from linear methods of analysis of Eurocode 8 together with TEC'07 are almost similar.

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

George, G.N.; Coyle, C.L.; Hales, B.J.

Evidence for the existence of a vanadium-containing nitrogenase has existed for more than half a century, but progress in understanding this enzyme has only come recently. In 1980, Bishop and co-workers proposed that an alternative nitrogen-fixing enzyme exists in Azotobacter vinelandii and subsequently proposed that vanadium was involved. In 1986, Robson et al. demonstrated clearly that the alternate nitrogenase from Azotobacter chroococcum, Acl*, contained vanadium instead of molybdenum. Hales et al. have shown the vanadium is also found in the Azotobacter vinelandii alternative component I, Avl'. The molybdenum and vanadium nitrogenase proteins are similar in many respects. Like the molybdenummore » enzyme, both Acl* and Avl' exhibit an EPR spectrum characteristic of a species with an S = 3/2 ground state; Avl' also contains the so-called P-clusters. Additionally Acl* has recently been shown to possess an N-methylformamide soluble cofactor, FeVco, analogous to the well-known iron-molybdenum cofactor FeMoco. Arber et al. have reported X-ray absorption spectra for the Acl* enzyme and interpreted the EXAFS as evidence for a V-Fe-S cluster. The local vanadium structure is proposed to resemble a recently synthesized cubane-like VFe/sub 3/S/sub 4/ cluster, and analogies are drawn with the EXAFS-derived structure reported for the molybdenum nitrogenases. The authors report herein an X-ray absorption spectroscopic study of A. vinelandii vanadium nitrogenase, Avl', which supports and extends the work of Arber et al.« less

Bottom-up Formation of Carbon-Based Structures with Multilevel Hierarchy from MOF-Guest Polyhedra.

PubMed

Wang, Tiesheng; Kim, Hyun-Kyung; Liu, Yingjun; Li, Weiwei; Griffiths, James T; Wu, Yue; Laha, Sourav; Fong, Kara D; Podjaski, Filip; Yun, Chao; Kumar, R Vasant; Lotsch, Bettina V; Cheetham, Anthony K; Smoukov, Stoyan K

2018-05-16

Three-dimensional carbon-based structures have proven useful for tailoring material properties in structural mechanical and energy storage applications. One approach to obtain them has been by carbonization of selected metal-organic frameworks (MOFs) with catalytic metals, but this is not applicable to most common MOF structures. Here, we present a strategy to transform common MOFs, by guest inclusions and high-temperature MOF-guest interactions, into complex carbon-based, diatom-like, hierarchical structures (named for the morphological similarities with the naturally existing diatomaceous species). As an example, we introduce metal salt guests into HKUST-1-type MOFs to generate a family of carbon-based nano-diatoms with two to four levels of structural hierarchy. We report control of the morphology by simple changes in the chemistry of the MOF and guest, with implications for the formation mechanisms. We demonstrate that one of these structures has unique advantages as a fast-charging lithium-ion battery anode. The tunability of composition should enable further studies of reaction mechanisms and result in the growth of a myriad of unprecedented carbon-based structures from the enormous variety of currently available MOF-guest candidates.

Specific features of the atomic structure of metallic layers of multilayered (CoFeZr/SiO2)32 and (CoFeZr/ a-Si)40 nanostructures with different interlayers

NASA Astrophysics Data System (ADS)

Domashevskaya, E. P.; Guda, A. A.; Chernyshev, A. V.; Sitnikov, V. G.

2017-02-01

Multilayered nanostructures (MN) were prepared by ion-beam successive sputtering from two targets, one of which was a metallic Co45Fe45Zr10 alloy plate and another target was a quartz (SiO2) or silicon plate on the surface of a rotating glass-ceramic substrate in an argon atmosphere. The Co and Fe K edges X-ray absorption fine structure of XANES in the (CoFeZr/SiO2)32 sample with oxide interlayers was similar to XANES of metallic Fe foil. This indicated the existence in metallic layers of multilayered CoFeZr nanocrystals with a local environment similar to the atomic environment in solid solutions on the base of bcc Fe structure, which is also confirmed by XRD data. XANES near the Co and Fe K edges absorption in another multilayered nanostructure with silicon interlayers (CoFeZr/ a-Si)40 differs from XANES of MN with dielectric SiO2 interlayer, which demonstrates a dominant influence of the Fe-Si and Co-Si bonds in the local environment of 3 d Co and Fe metals when they form CoFeSi-type silicide phases in thinner bilayers of this MN.

Synthetic cannabinoids: In silico prediction of the cannabinoid receptor 1 affinity by a quantitative structure-activity relationship model.

PubMed

Paulke, Alexander; Proschak, Ewgenij; Sommer, Kai; Achenbach, Janosch; Wunder, Cora; Toennes, Stefan W

2016-03-14

The number of new synthetic psychoactive compounds increase steadily. Among the group of these psychoactive compounds, the synthetic cannabinoids (SCBs) are most popular and serve as a substitute of herbal cannabis. More than 600 of these substances already exist. For some SCBs the in vitro cannabinoid receptor 1 (CB1) affinity is known, but for the majority it is unknown. A quantitative structure-activity relationship (QSAR) model was developed, which allows the determination of the SCBs affinity to CB1 (expressed as binding constant (Ki)) without reference substances. The chemically advance template search descriptor was used for vector representation of the compound structures. The similarity between two molecules was calculated using the Feature-Pair Distribution Similarity. The Ki values were calculated using the Inverse Distance Weighting method. The prediction model was validated using a cross validation procedure. The predicted Ki values of some new SCBs were in a range between 20 (considerably higher affinity to CB1 than THC) to 468 (considerably lower affinity to CB1 than THC). The present QSAR model can serve as a simple, fast and cheap tool to get a first hint of the biological activity of new synthetic cannabinoids or of other new psychoactive compounds. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Lead(ii) soaps: crystal structures, polymorphism, and solid and liquid mesophases.

PubMed

Martínez-Casado, F J; Ramos-Riesco, M; Rodríguez-Cheda, J A; Redondo-Yélamos, M I; Garrido, L; Fernández-Martínez, A; García-Barriocanal, J; da Silva, I; Durán-Olivencia, M; Poulain, A

2017-07-05

The long-chain members of the lead(ii) alkanoate series or soaps, from octanoate to octadecanoate, have been thoroughly characterized by means of XRD, PDF analysis, DSC, FTIR, ssNMR and other techniques, in all their phases and mesophases. The crystal structures at room temperature of all of the members of the series are now solved, showing the existence of two polymorphic forms in the room temperature crystal phase, different to short and long-chain members. Only nonanoate and decanoate present both forms, and this polymorphism is proven to be monotropic. At higher temperature, these compounds present a solid mesophase, defined as rotator, a liquid crystal phase and a liquid phase, all of which have a similar local arrangement. Since some lead(ii) soaps appear as degradation compounds in oil paintings, the solved crystal structures of lead(ii) soaps can now be used as fingerprints for their detection using X-ray diffraction. Pair distribution function analysis on these compounds is very similar in the same phases and mesophases for the different members, showing the same short range order. This observation suggests that this technique could also be used in the detection of these compounds in disordered phases or in the initial stages of formation in paintings.

Thermally stable solids based on endohedrally doped ZnS clusters.

PubMed

Matxain, Jon M; Piris, Mario; Lopez, Xabier; Ugalde, Jesus M

2009-01-01

The existence of inorganic, hollow, fullerene-like ZnS clusters has been theoretically predicted and then recently confirmed experimentally. These clusters were observed to trap alkali metals and halogens because the ionization energies (IE) of alkali metals are very similar to the electron affinities (EA) of halogens. This opens the possibility of forming molecular solids composed of these fullerene building blocks because the energy released due to the difference between the IE and EA would be very small. Herein we have focused on assembling bare Zn(12)S(12) and endohedral X@Zn(12)S(12)-Y@Zn(12)S(12) dimers (X = Na, K; Y = Cl, Br) by considering the square-faces-square orientation of every two adjacent clusters, which leads to a fcc cubic crystal structure in the solid. The structures were fully optimized in all cases, and their thermal stability was confirmed by ab initio thermal molecular dynamics calculations. The optimum lattice parameter of the solids was found to be around 13.8 A, which corresponds to distances of about 2.5 A between monomers, which is typical of covalent Zn-S bonds. The resulting solids are nanoporous materials similar to B(12)N(12). Due to their nanoporous structure, these zeolite-shaped solids could be used in heterogeneous catalysis and as storage materials and molecular sieves.

Anti-GM1 antibodies as a model of the immune response to self-glycans.

PubMed

Nores, Gustavo A; Lardone, Ricardo D; Comín, Romina; Alaniz, María E; Moyano, Ana L; Irazoqui, Fernando J

2008-03-01

Glycans are a class of molecules with high structural variability, frequently found in the plasma membrane facing the extracellular space. Because of these characteristics, glycans are often considered as recognition molecules involved in cell social functions, and as targets of pathogenic factors. Induction of anti-glycan antibodies is one of the early events in immunological defense against bacteria that colonize the body. Because of this natural infection, antibodies recognizing a variety of bacterial glycans are found in sera of adult humans and animals. The immune response to glycans is restricted by self-tolerance, and no antibodies to self-glycans should exist in normal subjects. However, antibodies recognizing structures closely related to self-glycans do exist, and can lead to production of harmful anti-self antibodies. Normal human sera contain low-affinity anti-GM1 IgM-antibodies. Similar antibodies with higher affinity or different isotype are found in some neuropathy patients. Two hypotheses have been developed to explain the origin of disease-associated anti-GM1 antibodies. According to the "molecular mimicry" hypothesis, similarity between GM1 and Campylobacter jejuni lipopolysaccharide carrying a GM1-like glycan is the cause of Guillain-Barré syndrome associated with anti-GM1 IgG-antibodies. According to the "binding site drift" hypothesis, IgM-antibodies associated with disease originate through changes in the binding site of normally occurring anti-GM1 antibodies. We now present an "integrated" hypothesis, combining the "mimicry" and "drift" concepts, which satisfactorily explains most of the published data on anti-GM1 antibodies.

Effect of inherited structures on strike-slip plate boundaries: insight from analogue modelling of the central Levant Fracture System, Lebanon

NASA Astrophysics Data System (ADS)

Ghalayini, Ramadan; Daniel, Jean-Marc; Homberg, Catherine; Nader, Fadi

2015-04-01

Analogue sandbox modeling is a tool to simulate deformation style and structural evolution of sedimentary basins. The initial goal is to test what is the effect of inherited and crustal structures on the propagation, evolution, and final geometry of major strike-slip faults at the boundary between two tectonic plates. For this purpose, we have undertaken a series of analogue models to validate and reproduce the structures of the Levant Fracture System, a major NNE-SSW sinistral strike-slip fault forming the boundary between the Arabian and African plates. Onshore observations and recent high quality 3D seismic data in the Levant Basin offshore Lebanon demonstrated that Mesozoic ENE striking normal faults were reactivated into dextral strike-slip faults during the Late Miocene till present day activity of the plate boundary which shows a major restraining bend in Lebanon with a ~ 30°clockwise rotation in its trend. Experimental parameters consisted of a silicone layer at the base simulating the ductile crust, overlain by intercalated quartz sand and glass sand layers. Pre-existing structures were simulated by creating a graben in the silicone below the sand at an oblique (>60°) angle to the main throughgoing strike-slip fault. The latter contains a small stepover at depth to create transpression during sinistral strike-slip movement and consequently result in mountain building similarly to modern day Lebanon. Strike-slip movement and compression were regulated by steady-speed computer-controlled engines and the model was scanned using a CT-scanner continuously while deforming to have a final 4D model of the system. Results showed that existing normal faults were reactivated into dextral strike-slip faults as the sinistral movement between the two plates accumulated. Notably, the resulting restraining bend is asymmetric and segmented into two different compartments with differing geometries. One compartment shows a box fold anticline, while the second shows an asymmetric anticline. Thus, analogue modeling has validated observation in seismic data and onshore geology whereby Mount Lebanon and adjacent folds exhibit similar compartmentalization and geometric dissimilarities along the Levant Fracture System. We suggest that the presence of inherited structures will affect to a certain extent the geometry of restraining bends and control the evolution of large strike-slip faults passing through.

A new multi-scale method to reveal hierarchical modular structures in biological networks.

PubMed

Jiao, Qing-Ju; Huang, Yan; Shen, Hong-Bin

2016-11-15

Biological networks are effective tools for studying molecular interactions. Modular structure, in which genes or proteins may tend to be associated with functional modules or protein complexes, is a remarkable feature of biological networks. Mining modular structure from biological networks enables us to focus on a set of potentially important nodes, which provides a reliable guide to future biological experiments. The first fundamental challenge in mining modular structure from biological networks is that the quality of the observed network data is usually low owing to noise and incompleteness in the obtained networks. The second problem that poses a challenge to existing approaches to the mining of modular structure is that the organization of both functional modules and protein complexes in networks is far more complicated than was ever thought. For instance, the sizes of different modules vary considerably from each other and they often form multi-scale hierarchical structures. To solve these problems, we propose a new multi-scale protocol for mining modular structure (named ISIMB) driven by a node similarity metric, which works in an iteratively converged space to reduce the effects of the low data quality of the observed network data. The multi-scale node similarity metric couples both the local and the global topology of the network with a resolution regulator. By varying this resolution regulator to give different weightings to the local and global terms in the metric, the ISIMB method is able to fit the shape of modules and to detect them on different scales. Experiments on protein-protein interaction and genetic interaction networks show that our method can not only mine functional modules and protein complexes successfully, but can also predict functional modules from specific to general and reveal the hierarchical organization of protein complexes.

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.

Text Mining for Protein Docking

PubMed Central

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

2015-01-01

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

Inference of Population Structure using Dense Haplotype Data

PubMed Central

Lawson, Daniel John; Hellenthal, Garrett

2012-01-01

The advent of genome-wide dense variation data provides an opportunity to investigate ancestry in unprecedented detail, but presents new statistical challenges. We propose a novel inference framework that aims to efficiently capture information on population structure provided by patterns of haplotype similarity. Each individual in a sample is considered in turn as a recipient, whose chromosomes are reconstructed using chunks of DNA donated by the other individuals. Results of this “chromosome painting” can be summarized as a “coancestry matrix,” which directly reveals key information about ancestral relationships among individuals. If markers are viewed as independent, we show that this matrix almost completely captures the information used by both standard Principal Components Analysis (PCA) and model-based approaches such as STRUCTURE in a unified manner. Furthermore, when markers are in linkage disequilibrium, the matrix combines information across successive markers to increase the ability to discern fine-scale population structure using PCA. In parallel, we have developed an efficient model-based approach to identify discrete populations using this matrix, which offers advantages over PCA in terms of interpretability and over existing clustering algorithms in terms of speed, number of separable populations, and sensitivity to subtle population structure. We analyse Human Genome Diversity Panel data for 938 individuals and 641,000 markers, and we identify 226 populations reflecting differences on continental, regional, local, and family scales. We present multiple lines of evidence that, while many methods capture similar information among strongly differentiated groups, more subtle population structure in human populations is consistently present at a much finer level than currently available geographic labels and is only captured by the haplotype-based approach. The software used for this article, ChromoPainter and fineSTRUCTURE, is available from http://www.paintmychromosomes.com/. PMID:22291602

De Novo Protein Structure Prediction

NASA Astrophysics Data System (ADS)

Hung, Ling-Hong; Ngan, Shing-Chung; Samudrala, Ram

An unparalleled amount of sequence data is being made available from large-scale genome sequencing efforts. The data provide a shortcut to the determination of the function of a gene of interest, as long as there is an existing sequenced gene with similar sequence and of known function. This has spurred structural genomic initiatives with the goal of determining as many protein folds as possible (Brenner and Levitt, 2000; Burley, 2000; Brenner, 2001; Heinemann et al., 2001). The purpose of this is twofold: First, the structure of a gene product can often lead to direct inference of its function. Second, since the function of a protein is dependent on its structure, direct comparison of the structures of gene products can be more sensitive than the comparison of sequences of genes for detecting homology. Presently, structural determination by crystallography and NMR techniques is still slow and expensive in terms of manpower and resources, despite attempts to automate the processes. Computer structure prediction algorithms, while not providing the accuracy of the traditional techniques, are extremely quick and inexpensive and can provide useful low-resolution data for structure comparisons (Bonneau and Baker, 2001). Given the immense number of structures which the structural genomic projects are attempting to solve, there would be a considerable gain even if the computer structure prediction approach were applicable to a subset of proteins.

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.

An integrative approach for measuring semantic similarities using gene ontology.

PubMed

Peng, Jiajie; Li, Hongxiang; Jiang, Qinghua; Wang, Yadong; Chen, Jin

2014-01-01

Gene Ontology (GO) provides rich information and a convenient way to study gene functional similarity, which has been successfully used in various applications. However, the existing GO based similarity measurements have limited functions for only a subset of GO information is considered in each measure. An appropriate integration of the existing measures to take into account more information in GO is demanding. We propose a novel integrative measure called InteGO2 to automatically select appropriate seed measures and then to integrate them using a metaheuristic search method. The experiment results show that InteGO2 significantly improves the performance of gene similarity in human, Arabidopsis and yeast on both molecular function and biological process GO categories. InteGO2 computes gene-to-gene similarities more accurately than tested existing measures and has high robustness. The supplementary document and software are available at http://mlg.hit.edu.cn:8082/.

Crystal structure and mutational analysis of aminoacylhistidine dipeptidase from Vibrio alginolyticus reveal a new architecture of M20 metallopeptidases.

PubMed

Chang, Chin-Yuan; Hsieh, Yin-Cheng; Wang, Ting-Yi; Chen, Yi-Chin; Wang, Yu-Kuo; Chiang, Ting-Wei; Chen, Yi-Ju; Chang, Cheng-Hsiang; Chen, Chun-Jung; Wu, Tung-Kung

2010-12-10

Aminoacylhistidine dipeptidases (PepD, EC 3.4.13.3) belong to the family of M20 metallopeptidases from the metallopeptidase H clan that catalyze a broad range of dipeptide and tripeptide substrates, including L-carnosine and L-homocarnosine. Homocarnosine has been suggested as a precursor for the neurotransmitter γ-aminobutyric acid (GABA) and may mediate the antiseizure effects of GABAergic therapies. Here, we report the crystal structure of PepD from Vibrio alginolyticus and the results of mutational analysis of substrate-binding residues in the C-terminal as well as substrate specificity of the PepD catalytic domain-alone truncated protein PepD(CAT). The structure of PepD was found to exist as a homodimer, in which each monomer comprises a catalytic domain containing two zinc ions at the active site center for its hydrolytic function and a lid domain utilizing hydrogen bonds between helices to form the dimer interface. Although the PepD is structurally similar to PepV, which exists as a monomer, putative substrate-binding residues reside in different topological regions of the polypeptide chain. In addition, the lid domain of the PepD contains an "extra" domain not observed in related M20 family metallopeptidases with a dimeric structure. Mutational assays confirmed both the putative di-zinc allocations and the architecture of substrate recognition. In addition, the catalytic domain-alone truncated PepD(CAT) exhibited substrate specificity to l-homocarnosine compared with that of the wild-type PepD, indicating a potential value in applications of PepD(CAT) for GABAergic therapies or neuroprotection.

Uneven Expressive Language Development in Mandarin-Exposed Preschool Children with ASD: Comparing Vocabulary, Grammar, and the Decontextualized Use of Language via the PCDI-Toddler Form.

PubMed

Su, Yi Esther; Naigles, Letitia R; Su, Lin-Yan

2018-05-21

Data from children with ASD who are learning Indo-European languages indicate that (a) they vary hugely in their expressive language skills and (b) their pragmatic/socially-based language is more impaired than their structural language. We investigate whether similar patterns of language development exist for Mandarin-exposed children with ASD. Parent report data of the Putonghua Communicative Development Inventory-Toddler Form were collected from 160 17-83-month-old children with ASD. These children with ASD demonstrated similar levels of variability as Western children with ASD. In particular, they could be divided into three distinct subgroups (high verbal, middle verbal, low verbal), all of which manifested relative strengths in lexical and grammatical language compared to pragmatic usage of decontextualized language.

Beyond testosterone cypionate: evidence behind the use of nandrolone in male health and wellness

PubMed Central

Pan, Michael M.

2016-01-01

Characterized by low serum testosterone levels and diverse symptoms, male hypogonadism is a common condition. Current medical treatment focuses on testosterone supplementation using multiple modalities such as injections, gels and pellets. Interestingly, while testosterone is considered an anabolic androgenic steroid, it has not been saddled with the social stigma that other, similar medications have. The goal of this review is to highlight an anabolic steroid, 19-nortestosterone (i.e., nandrolone, deca-durabolin) and illustrate prospective therapeutic applications for male health. Containing a chemical structure similar to testosterone, nandrolone has a higher myotrophic: androgenic ratio resulting in improved effects on muscle mass. Animal models have suggested application in the improvement of joint healing following rotator cuff repair. Minimal literature exists regarding the use of nandrolone and, as such, further human studies are required. PMID:27141449

Beyond testosterone cypionate: evidence behind the use of nandrolone in male health and wellness.

PubMed

Pan, Michael M; Kovac, Jason R

2016-04-01

Characterized by low serum testosterone levels and diverse symptoms, male hypogonadism is a common condition. Current medical treatment focuses on testosterone supplementation using multiple modalities such as injections, gels and pellets. Interestingly, while testosterone is considered an anabolic androgenic steroid, it has not been saddled with the social stigma that other, similar medications have. The goal of this review is to highlight an anabolic steroid, 19-nortestosterone (i.e., nandrolone, deca-durabolin) and illustrate prospective therapeutic applications for male health. Containing a chemical structure similar to testosterone, nandrolone has a higher myotrophic: androgenic ratio resulting in improved effects on muscle mass. Animal models have suggested application in the improvement of joint healing following rotator cuff repair. Minimal literature exists regarding the use of nandrolone and, as such, further human studies are required.

FUNDAMENTAL DIFFERENCES BETWEEN NATURAL ANTIBODIES AND POLYREACTIVE IMMUNOGLOBULINS.

PubMed

Bobrovnik, S A; Demchenko, M A; Komisarenko, S V

2015-01-01

A problem of similarity and differences between so-called polyreactive immunoglobulins (PRIGs) and natural antibodies (NAbs), capable of cross-reacting with some structurally dissimilar antigens, has been considered. The analysis of mechanisms of an unspecific interaction between PRIGs or NAbs and antigens evidences for the fact that essential differences exist between these substances. These differences permit classifying the abovementioned substances as different types of immunoglobulin molecules. The major difference between PRIGs and NAbs may include both the mechanisms of the above mentioned immunoglobulin molecules binding to antigens and their interaction affinity, as well as an absolutely different influence of some low-molecular substances on the efficiency of the interaction with antigens. Relying on the obtained data it can be assumed that, since PRIGs and NAbs have fundamental differences, they may perform not only similar but also different functions of the immune system.

Generative model selection using a scalable and size-independent complex network classifier

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

Motallebi, Sadegh, E-mail: motallebi@ce.sharif.edu; Aliakbary, Sadegh, E-mail: aliakbary@ce.sharif.edu; Habibi, Jafar, E-mail: jhabibi@sharif.edu

2013-12-15

Real networks exhibit nontrivial topological features, such as heavy-tailed degree distribution, high clustering, and small-worldness. Researchers have developed several generative models for synthesizing artificial networks that are structurally similar to real networks. An important research problem is to identify the generative model that best fits to a target network. In this paper, we investigate this problem and our goal is to select the model that is able to generate graphs similar to a given network instance. By the means of generating synthetic networks with seven outstanding generative models, we have utilized machine learning methods to develop a decision tree formore » model selection. Our proposed method, which is named “Generative Model Selection for Complex Networks,” outperforms existing methods with respect to accuracy, scalability, and size-independence.« less

Ligand regulation of a constitutively dimeric EGF receptor

NASA Astrophysics Data System (ADS)

Freed, Daniel M.; Alvarado, Diego; Lemmon, Mark A.

2015-06-01

Ligand-induced receptor dimerization has traditionally been viewed as the key event in transmembrane signalling by epidermal growth factor receptors (EGFRs). Here we show that the Caenorhabditis elegans EGFR orthologue LET-23 is constitutively dimeric, yet responds to its ligand LIN-3 without changing oligomerization state. SAXS and mutational analyses further reveal that the preformed dimer of the LET-23 extracellular region is mediated by its domain II dimerization arm and resembles other EGFR extracellular dimers seen in structural studies. Binding of LIN-3 induces only minor structural rearrangements in the LET-23 dimer to promote signalling. Our results therefore argue that EGFR can be regulated by allosteric changes within an existing receptor dimer--resembling signalling by insulin receptor family members, which share similar extracellular domain compositions but form covalent dimers.

NMR crystallography of 2-acylamino-6-[1 H]-pyridones: Solid-state NMR, GIPAW computational, and single crystal X-ray diffraction studies

NASA Astrophysics Data System (ADS)

Ośmiałowski, Borys; Kolehmainen, Erkki; Ikonen, Satu; Ahonen, Kari; Löfman, Miika

2011-12-01

2-Acylamino-6-[1 H]-pyridones [acyl = RCO, where R = methyl ( 1), ethyl ( 2), iso-propyl ( 3), tert-butyl ( 4), and 1-adamantyl ( 5)] have been synthesized and characterized by NMR spectroscopy. From three congeners, 2, 3 and 5, also single crystal X-ray structures have been solved. For these derivatives GIPAW calculations acts as a "bridge" between solid-state NMR data and calculated chemical shifts based on X-ray determined geometry. In crystals all three compounds exist as pyridone tautomers possessing similar six-membered ring structure stabilized by intramolecular C dbnd O⋯HN hydrogen bond. Theoretical GIPAW calculated and experimental 13C and 15N CPMAS NMR shifts are in excellent agreement with each other.

Three-dimensional convection of binary mixtures in porous media.

PubMed

Umla, R; Augustin, M; Huke, B; Lücke, M

2011-11-01

We investigate convection patterns of binary mixtures with a positive separation ratio in porous media. As setup, we choose the Rayleigh-Bénard system of a fluid layer heated from below. Results are obtained by a multimode Galerkin method. Using this method, we compute square and crossroll patterns, and we analyze their structural, bifurcation, and stability properties. Evidence is provided that, for a strong enough Soret effect, both structures exist as stable forms of convection. Some of their properties are found to be similar to square and crossroll convection in the system without porous medium. However, there are also qualitative differences. For example, squares can be destabilized by oscillatory perturbations with square symmetry in porous media, and their velocity isolines are deformed in the so-called Soret regime.

Application of Landsat imagery to problems of petroleum exploration in Qaidam Basin, China

USGS Publications Warehouse

Bailey, G.B.; Anderson, P.D.

1982-01-01

Tertiary and Quaternary nonmarine, petroleum-bearing sedimentary rocks have been extensively deformed by compressive forces. These forces created many folds which are current targets of Chinese exploration programs. Image-derived interpretations of folds, strike-slip faults, thrust faults, normal or reverse faults, and fractures compared very favorably, in terms of locations and numbers mapped, with Chinese data compiled from years of extensive field mapping. Many potential hydrocarbon trapping structures were precisely located. Orientations of major structural trends defined from Landsat imagery correlate well with those predicted for the area based on global tectonic theory. These correlations suggest that similar orientations exist in the eastern half of the basin where folded rocks are mostly obscured by unconsolidated surface sediments and where limited exploration has occurred.--Modified journal abstract.

[Scale Relativity Theory in living beings morphogenesis: fratal, determinism and chance].

PubMed

Chaline, J

2012-10-01

The Scale Relativity Theory has many biological applications from linear to non-linear and, from classical mechanics to quantum mechanics. Self-similar laws have been used as model for the description of a huge number of biological systems. Theses laws may explain the origin of basal life structures. Log-periodic behaviors of acceleration or deceleration can be applied to branching macroevolution, to the time sequences of major evolutionary leaps. The existence of such a law does not mean that the role of chance in evolution is reduced, but instead that randomness and contingency may occur within a framework which may itself be structured in a partly statistical way. The scale relativity theory can open new perspectives in evolution. Copyright © 2012 Elsevier Masson SAS. All rights reserved.

First Comparative Analysis of the Community Structures and Carbon Metabolic Pathways of the Bacteria Associated with Alvinocaris longirostris in a Hydrothermal Vent of Okinawa Trough.

PubMed

Sun, Qing-Lei; Zeng, Zhi-Gang; Chen, Shuai; Sun, Li

2016-01-01

Alvinocaris longirostris is a species of shrimp existing in the hydrothermal fields of Okinawa Trough. To date the structure and function of the microbial community associated with A. longirostris are essentially unknown. In this study, by employment of the techniques of high through-put sequencing and clone library construction and analysis, we compared for the first time the community structures and metabolic profiles of microbes associated with the gill and gut of A. longirostris in a hydrothermal field of Okinawa Trough. Fourteen phyla were detected in the gill and gut communities, of which 11 phyla were shared by both tissues. Proteobacteria made up a substantial proportion in both tissues, while Firmicutes was abundant only in gut. Although gill and gut communities were similar in bacterial diversities, the bacterial community structures in these two tissues were significantly different. Further, we discovered for the first time the existence in the gill and gut communities of A. longirostris the genes (cbbM and aclB) encoding the key enzymes of Calvin-Benson-Bassham (CBB) cycle and the reductive tricarboxylic acid (rTCA) cycle, and that both cbbM and aclB were significantly more abundant in gill than in gut. Taken together, these results provide the first evidence that at least two carbon fixation pathways are present in both the gill and the gut communities of A. longirostris, and that the communities in different tissues likely differ in autotrophic productivity.

Performance Evaluation and Improvement of Ferroelectric Field-Effect Transistor Memory

NASA Astrophysics Data System (ADS)

Yu, Hyung Suk

Flash memory is reaching scaling limitations rapidly due to reduction of charge in floating gates, charge leakage and capacitive coupling between cells which cause threshold voltage fluctuations, short retention times, and interference. Many new memory technologies are being considered as alternatives to flash memory in an effort to overcome these limitations. Ferroelectric Field-Effect Transistor (FeFET) is one of the main emerging candidates because of its structural similarity to conventional FETs and fast switching speed. Nevertheless, the performance of FeFETs have not been systematically compared and analyzed against other competing technologies. In this work, we first benchmark the intrinsic performance of FeFETs and other memories by simulations in order to identify the strengths and weaknesses of FeFETs. To simulate realistic memory applications, we compare memories on an array structure. For the comparisons, we construct an accurate delay model and verify it by benchmarking against exact HSPICE simulations. Second, we propose an accurate model for FeFET memory window since the existing model has limitations. The existing model assumes symmetric operation voltages but it is not valid for the practical asymmetric operation voltages. In this modeling, we consider practical operation voltages and device dimensions. Also, we investigate realistic changes of memory window over time and retention time of FeFETs. Last, to improve memory window and subthreshold swing, we suggest nonplanar junctionless structures for FeFETs. Using the suggested structures, we study the dimensional dependences of crucial parameters like memory window and subthreshold swing and also analyze key interference mechanisms.

Co-existence of Anaerobic Ammonium Oxidation Bacteria and Denitrifying Anaerobic Methane Oxidation Bacteria in Sewage Sludge: Community Diversity and Seasonal Dynamics.

PubMed

Xu, Sai; Lu, Wenjing; Mustafa, Muhammad Farooq; Caicedo, Luis Miguel; Guo, Hanwen; Fu, Xindi; Wang, Hongtao

2017-11-01

Anaerobic ammonium oxidation (ANAMMOX) and denitrifying anaerobic methane oxidation (DAMO) have been recently discovered as relevant processes in the carbon and nitrogen cycles of wastewater treatment plants. In this study, the seasonal dynamics of ANAMMOX and DAMO bacterial community structures and their abundance in sewage sludge collected from wastewater treatment plants were analysed. Results indicated that ANAMMOX and DAMO bacteria co-existed in sewage sludge in different seasons and their abundance was positively correlated (P < 0.05). The high abundance of ANAMMOX and DAMO bacteria in autumn and winter indicated that these seasons were the preferred time to favour the growth of ANAMMOX and DAMO bacteria. The community structure of ANNAMOX and DAMO bacteria could also shift with seasonal changes. The "Candidatus Brocadia" genus of ANAMMOX bacteria was mainly recovered in spring and summer, and an unknown cluster was primarily detected in autumn and winter. Similar patterns of seasonal variation in the community structure of DAMO bacteria were also observed. Group B was the dominant in spring and summer, whereas in autumn and winter, group A and group B presented almost the same proportion. The redundancy analysis revealed that pH and nitrate were the most significant factors affecting community structures of these two groups (P < 0.01). This study reported the diversity of ANAMMOX and DAMO in wastewater treatment plants that may be the basis for new nitrogen removal technologies.

Spin Polarized Transport in Multilayer Structures with Complex Magnetic Configurations

NASA Astrophysics Data System (ADS)

Sahakyan, Avag; Poghosyan, Anahit; Movsesyan, Ruzan; Kocharian, Armen

The spin transport and spin polarization in a new class of multilayer structures are investigated for non-collinear and noncoplanar magnetic configurations containing repetitive magnetic layers. The magnetic configuration of the structure dictates the existence of certain degrees of freedom that determines magnetic transport and polarization properties. We consider magnetic structures in magnetic multilayers with canted spin configurations separated by non-magnetic quantum well so that the exchange interaction between the neighbor barriers can be ignored. Configurations of magnetizations in barriers include some structures consisting of two ''ferromagnetic'' or ''antiferromagnetic'' domains twisted relative to each other by a certain angle (angle noncollinearity). The similar system, formed from two noncollinear domains separated by canted ''magnetic defect'' is also considered. The above mentioned properties of these systems depend strongly on the type of magnetic configuration and variation of certain degrees of freedom. Simple theoretical approach with the transfer matrix method is carried out to understand and predict the magnetic properties of the multilayer systems. The work at California University Los Angeles was supported by the National Science Foundation-Partnerships for Research and Education in Materials under Grant DMR-1523588.

Flow field topology of transient mixing driven by buoyancy

NASA Technical Reports Server (NTRS)

Duval, Walter M B.

2004-01-01

Transient mixing driven by buoyancy occurs through the birth of a symmetric Rayleigh-Taylor morphology (RTM) structure for large length scales. Beyond its critical bifurcation the RTM structure exhibits self-similarity and occurs on smaller and smaller length scales. The dynamics of the RTM structure, its nonlinear growth and internal collision, show that its genesis occurs from an explosive bifurcation which leads to the overlap of resonance regions in phase space. This event shows the coexistence of regular and chaotic regions in phase space which is corroborated with the existence of horseshoe maps. A measure of local chaos given by the topological entropy indicates that as the system evolves there is growth of uncertainty. Breakdown of the dissipative RTM structure occurs during the transition from explosive to catastrophic bifurcation; this event gives rise to annihilation of the separatrices which drives overlap of resonance regions. The global bifurcation of explosive and catastrophic events in phase space for the large length scale of the RTM structure serves as a template for which mixing occurs on smaller and smaller length scales. Copyright 2004 American Institute of Physics.

VLA Observation of Seyfert Galaxy MRK 6

NASA Astrophysics Data System (ADS)

Xu, C.; Baum, S. A.; O'Dea, C.; Colbert, E. J. M.

1997-12-01

We have obtained deep radio observation of the Seyfert 1.5 galaxy Mrk6 with all VLA configurations at 6 and 20 cm. We confirm the existence of two pairs of diffuse low surface brightness radio lobes at different scales and orientations. The larger pair of lobes extend ( ~ 40" or 20 kpc) ~ 30(deg) NW-SE, and is evidence of starburst-driven superwind as suggested in Baum et. al (1993). The outer lobes are roughly perpendicular to a set of inner lobes which extend ( ~ 4" or 2 kpc) E-W and are in turn perpendicular to the inner jets imaged by Kukula et. al (1996). Both pairs of lobes appear to have shell-like structures, as implied by the observed anti-symmetric emission morphology which might be due to limb brightening as a result of increasing optical depth at the line of sight. The width of each structure is comparable to the length of the next smaller structure suggesting a "self-similar" (and possibly dynamical) relationship between these structures. These nested "bubble-like" structures with different orientations pose a challenge to the current paradigm of energy transport in Seyfert galaxies.

Local structure order in Pd 78Cu 6Si 16 liquid

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

Yue, G. Q.; Zhang, Y.; Sun, Y.

2015-02-05

The short-range order (SRO) in Pd 78Cu 6Si 16 liquid was studied by high energy x-ray diffraction and ab initio molecular dynamics (MD) simulations. The calculated pair correlation functions at different temperatures agree well with the experimental results. The partial pair correlation functions from ab intio MD simulations indicate that Si atoms prefer to be uniformly distributed while Cu atoms tend to aggregate. By performing structure analysis using Honeycutt-Andersen index, Voronoi tessellation, and atomic cluster alignment method, we show that the icosahedron and face-centered cubic SRO increase upon cooling. The dominant SRO is the Pd-centered Pd 9Si 2 motif, namelymore » the structure of which motif is similar to the structure of Pd-centered clusters in the Pd 9Si 2 crystal. The study further confirms the existence of trigonal prism capped with three half-octahedra that is reported as a structural unit in Pd-based amorphous alloys. The majority of Cu-centered clusters are icosahedra, suggesting that the presence of Cu is benefit to promote the glass forming ability.« less

Secondary flow vortical structures in a 180∘ elastic curved vessel with torsion under steady and pulsatile inflow conditions

NASA Astrophysics Data System (ADS)

Najjari, Mohammad Reza; Plesniak, Michael W.

2018-01-01

Secondary flow structures in a 180∘ curved pipe model of an artery are studied using particle image velocimetry. Both steady and pulsatile inflow conditions are investigated. In planar curved pipes with steady flow, multiple (two, four, six) vortices are detected. For pulsatile flow, various pairs of vortices, i.e., Dean, deformed-Dean, Lyne-type, and split-Dean, are present in the cross section of the pipe at 90∘ into the bend. The effects of nonplanar curvature (torsion) and vessel dilatation on these vortical structures are studied. Torsion distorts the symmetric secondary flows (which exist in planar curvatures) and can result in formation of more complex vortical structures. For example, the split-Dean and Lyne-type vortices with same rotation direction originating from opposite sides of the cross section tend to merge together in pulsatile flow. The vortical structures in elastic vessels with dilatation (0.61%-3.23%) are also investigated and the results are compared with rigid model results. It was found that the secondary flow structures in rigid and elastic models are similar, and hence the local compliance of the vessel does not affect the morphology of secondary flow structures.

Deep faulting and structural reactivation beneath the southern Illinois basin

USGS Publications Warehouse

McBride, J.H.; Leetaru, H.E.; Bauer, R.A.; Tingey, B.E.; Schmidt, S.E.A.

2007-01-01

The investigation of deep fault structure and seismogenesis within "stable" continental interiors has been hindered by the paucity of detailed subsurface information and by low levels of seismicity. Outstanding seismotectonic questions for these areas include whether pre-existing structures govern the release of seismic energy as earthquakes, can reactivation of such structures be recognized, and to what extent have Precambrian basement structures exerted long-lived controls on the development of overlying Phanerozoic features. The southern portion of the Illinois basin provides a premier area in which to study the relation between contemporary seismicity and pre-existing structures due to the frequency of seismic events, the concentration of available geophysical data, and the wealth of borehole information. We have integrated the study of this information in order to create a 2.5-dimensional picture of the earth for local seismogenic depths (0-15 km) for a study area of moderate 20th century earthquake activity. The area is located along the western flanks of two of the major structures within the Illinois basin, the Wabash Valley fault system (WVFS) and the La Salle anticlinal belt (LSA). The results of reprocessing seismic reflection profiles, combined with earthquake hypocenter parameters, suggest three distinct seismotectonic environments in the upper crust. First, we have delineated a fault pattern that appears to correspond to the steep nodal plane of a strike-slip mechanism event (1974.04.03; mb = 4.7). The fault pattern is interpreted to be a deeply buried rift zone or zone of intense normal faulting underpinning a major Paleozoic depocenter of the Illinois basin (Fairfield basin). Second, a similar event (1987.06.10; mb = 5.2) and its well-located aftershocks define a narrow zone of deformation that occurs along and parallel to the frontal thrust of the LSA. Third, the hypocenter of the largest event in the study area (1968.11.09; mb = 5.5) may be spatially associated with a prominent zone of dipping middle crustal reflections, just west of the WVFS, which have been interpreted as a deeply buried blind thrust. The proposed correlation of pre-existing structures with earthquakes having consistently oriented structural parameters supports the reactivation of old deformation zones by contemporary stresses as previously proposed by earlier workers. However, the degree to which deformation has propagated upward from Precambrian basement into the Paleozoic rocks varied significantly even over a small study area. The societal value of associating an earthquake with a specific pre-existing deformation zone in the seismogenic crust is to improve the assessment of seismic hazard or to assess the integrity of a stratigraphic formation, being considered as a target for natural gas storage or carbon sequestration. ?? 2007 Elsevier B.V. All rights reserved.

Exploring the sequence-structure protein landscape in the glycosyltransferase family

PubMed Central

Zhang, Ziding; Kochhar, Sunil; Grigorov, Martin

2003-01-01

To understand the molecular basis of glycosyltransferases’ (GTFs) catalytic mechanism, extensive structural information is required. Here, fold recognition methods were employed to assign 3D protein shapes (folds) to the currently known GTF sequences, available in public databases such as GenBank and Swissprot. First, GTF sequences were retrieved and classified into clusters, based on sequence similarity only. Intracluster sequence similarity was chosen sufficiently high to ensure that the same fold is found within a given cluster. Then, a representative sequence from each cluster was selected to compose a subset of GTF sequences. The members of this reduced set were processed by three different fold recognition methods: 3D-PSSM, FUGUE, and GeneFold. Finally, the results from different fold recognition methods were analyzed and compared to sequence-similarity search methods (i.e., BLAST and PSI-BLAST). It was established that the folds of about 70% of all currently known GTF sequences can be confidently assigned by fold recognition methods, a value which is higher than the fold identification rate based on sequence comparison alone (48% for BLAST and 64% for PSI-BLAST). The identified folds were submitted to 3D clustering, and we found that most of the GTF sequences adopt the typical GTF A or GTF B folds. Our results indicate a lack of evidence that new GTF folds (i.e., folds other than GTF A and B) exist. Based on cases where fold identification was not possible, we suggest several sequences as the most promising targets for a structural genomics initiative focused on the GTF protein family. PMID:14500887

The Tropical Convective Spectrum. Part 1; Archetypal Vertical Structures

NASA Technical Reports Server (NTRS)

Boccippio, Dennis J.; Petersen, Walter A.; Cecil, Daniel J.

2005-01-01

A taxonomy of tropical convective and stratiform vertical structures is constructed through cluster analysis of 3 yr of Tropical Rainfall Measuring Mission (TRMM) "warm-season" (surface temperature greater than 10 C) precipitation radar (PR) vertical profiles, their surface rainfall, and associated radar-based classifiers (convective/ stratiform and brightband existence). Twenty-five archetypal profile types are identified, including nine convective types, eight stratiform types, two mixed types, and six anvil/fragment types (nonprecipitating anvils and sheared deep convective profiles). These profile types are then hierarchically clustered into 10 similar families, which can be further combined, providing an objective and physical reduction of the highly multivariate PR data space that retains vertical structure information. The taxonomy allows for description of any storm or local convective spectrum by the profile types or families. The analysis provides a quasi-independent corroboration of the TRMM 2A23 convective/ stratiform classification. The global frequency of occurrence and contribution to rainfall for the profile types are presented, demonstrating primary rainfall contribution by midlevel glaciated convection (27%) and similar depth decaying/stratiform stages (28%-31%). Profiles of these types exhibit similar 37- and 85-GHz passive microwave brightness temperatures but differ greatly in their frequency of occurrence and mean rain rates, underscoring the importance to passive microwave rain retrieval of convective/stratiform discrimination by other means, such as polarization or texture techniques, or incorporation of lightning observations. Close correspondence is found between deep convective profile frequency and annualized lightning production, and pixel-level lightning occurrence likelihood directly tracks the estimated mean ice water path within profile types.

The Effect of Naturally Occurring Chronic Kidney Disease on the Micro-Structural and Mechanical Properties of Bone

PubMed Central

Meltzer, Hagar; Milrad, Moran; Brenner, Ori; Atkins, Ayelet; Shahar, Ron

2014-01-01

Chronic kidney disease (CKD) is a growing public health concern worldwide, and is associated with marked increase of bone fragility. Previous studies assessing the effect of CKD on bone quality were based on biopsies from human patients or on laboratory animal models. Such studies provide information of limited relevance due to the small size of the samples (biopsies) or the non-physiologic CKD syndrome studied (rodent models with artificially induced CKD). Furthermore, the type, architecture, structure and biology of the bone of rodents are remarkably different from human bones; therefore similar clinicopathologic circumstances may affect their bones differently. We describe the effects of naturally occurring CKD with features resembling human CKD on the skeleton of cats, whose bone biology, structure and composition are remarkably similar to those of humans. We show that CKD causes significant increase of resorption cavity density compared with healthy controls, as well as significantly lower cortical mineral density, cortical cross-sectional area and cortical cross-sectional thickness. Young's modulus, yield stress, and ultimate stress of the cortical bone material were all significantly decreased in the skeleton of CKD cats. Cancellous bone was also affected, having significantly lower trabecular thickness and bone volume over total volume in CKD cats compared with controls. This study shows that naturally occurring CKD has deleterious effects on bone quality and strength. Since many similarities exist between human and feline CKD patients, including the clinicopathologic features of the syndrome and bone microarchitecture and biology, these results contribute to better understanding of bone abnormalities associated with CKD. PMID:25333360

Improved pose and affinity predictions using different protocols tailored on the basis of data availability

NASA Astrophysics Data System (ADS)

Prathipati, Philip; Nagao, Chioko; Ahmad, Shandar; Mizuguchi, Kenji

2016-09-01

The D3R 2015 grand drug design challenge provided a set of blinded challenges for evaluating the applicability of our protocols for pose and affinity prediction. In the present study, we report the application of two different strategies for the two D3R protein targets HSP90 and MAP4K4. HSP90 is a well-studied target system with numerous co-crystal structures and SAR data. Furthermore the D3R HSP90 test compounds showed high structural similarity to existing HSP90 inhibitors in BindingDB. Thus, we adopted an integrated docking and scoring approach involving a combination of both pharmacophoric and heavy atom similarity alignments, local minimization and quantitative structure activity relationships modeling, resulting in the reasonable prediction of pose [with the root mean square deviation (RMSD) values of 1.75 Å for mean pose 1, 1.417 Å for the mean best pose and 1.85 Å for the mean all poses] and affinity (ROC AUC = 0.702 at 7.5 pIC50 cut-off and R = 0.45 for 180 compounds). The second protein, MAP4K4, represents a novel system with limited SAR and co-crystal structure data and little structural similarity of the D3R MAP4K4 test compounds to known MAP4K4 ligands. For this system, we implemented an exhaustive pose and affinity prediction protocol involving docking and scoring using the PLANTS software which considers side chain flexibility together with protein-ligand fingerprints analysis assisting in pose prioritization. This protocol through fares poorly in pose prediction (with the RMSD values of 4.346 Å for mean pose 1, 4.69 Å for mean best pose and 4.75 Å for mean all poses) and produced reasonable affinity prediction (AUC = 0.728 at 7.5 pIC50 cut-off and R = 0.67 for 18 compounds, ranked 1st among 80 submissions).

Phase Behavior and Equations of State of the Actinide Oxides

NASA Astrophysics Data System (ADS)

Chidester, B.; Pardo, O. S.; Panero, W. R.; Fischer, R. A.; Thompson, E. C.; Heinz, D. L.; Prescher, C.; Prakapenka, V. B.; Campbell, A.

2017-12-01

The distribution of the long-lived heat-producing actinide elements U and Th in the deep Earth has important implications for the dynamics of the mantle and possibly the energy budget of Earth's core. The low shear velocities of the Large Low-Shear Velocity Provinces (LLSVPs) on the core-mantle boundary suggests that these regions are at least partially molten and may contain concentrated amounts of the radioactive elements, as well as other large cations such as the rare Earth elements. As such, by exploring the phase behavior of actinide-bearing minerals at extreme conditions, some insight into the mineralogy, formation, and geochemical and geodynamical effects of these regions can be gained. We have performed in situ high-pressure, high-temperature synchrotron X-ray diffraction experiments and calculations on two actinide oxide materials, UO2 and ThO2, to determine their phase behavior at the extreme conditions of the lower mantle. Experiments on ThO2 reached 60 GPa and 2500 K, and experiments on UO2 reached 95 GPa and 2500 K. We find that ThO2 exists in the fluorite-type structure to 20 GPa at high temperatures, at which point it transforms to the high-pressure cotunnite-type structure and remains thus up to 60 GPa. At room temperature, an anomalous expansion of the fluorite structure is observed prior to the transition, and may signal anion sub-lattice disorder. Similarly, UO2 exists in the fluorite-type structure at ambient conditions and up to 28 GPa at high temperatures. Above these pressures, we have observed a previously unidentified phase of UO2 with a tetragonal structure as the lower-temperature phase and the cotunnite-type phase at higher temperatures. Above 78 GPa, UO2 undergoes another transition or possible dissociation into two separate oxide phases. These phase diagrams suggest that the actinides could exist as oxides in solid solution with other analogous phases (e.g. ZrO2) in the cotunnite-type structure throughout much of Earth's lower mantle.

bpRNA: large-scale automated annotation and analysis of RNA secondary structure.

PubMed

Danaee, Padideh; Rouches, Mason; Wiley, Michelle; Deng, Dezhong; Huang, Liang; Hendrix, David

2018-05-09

While RNA secondary structure prediction from sequence data has made remarkable progress, there is a need for improved strategies for annotating the features of RNA secondary structures. Here, we present bpRNA, a novel annotation tool capable of parsing RNA structures, including complex pseudoknot-containing RNAs, to yield an objective, precise, compact, unambiguous, easily-interpretable description of all loops, stems, and pseudoknots, along with the positions, sequence, and flanking base pairs of each such structural feature. We also introduce several new informative representations of RNA structure types to improve structure visualization and interpretation. We have further used bpRNA to generate a web-accessible meta-database, 'bpRNA-1m', of over 100 000 single-molecule, known secondary structures; this is both more fully and accurately annotated and over 20-times larger than existing databases. We use a subset of the database with highly similar (≥90% identical) sequences filtered out to report on statistical trends in sequence, flanking base pairs, and length. Both the bpRNA method and the bpRNA-1m database will be valuable resources both for specific analysis of individual RNA molecules and large-scale analyses such as are useful for updating RNA energy parameters for computational thermodynamic predictions, improving machine learning models for structure prediction, and for benchmarking structure-prediction algorithms.

A novel manifold-manifold distance index applied to looseness state assessment of viscoelastic sandwich structures

NASA Astrophysics Data System (ADS)

Sun, Chuang; Zhang, Zhousuo; Guo, Ting; Luo, Xue; Qu, Jinxiu; Zhang, Chenxuan; Cheng, Wei; Li, Bing

2014-06-01

Viscoelastic sandwich structures (VSS) are widely used in mechanical equipment; their state assessment is necessary to detect structural states and to keep equipment running with high reliability. This paper proposes a novel manifold-manifold distance-based assessment (M2DBA) method for assessing the looseness state in VSSs. In the M2DBA method, a manifold-manifold distance is viewed as a health index. To design the index, response signals from the structure are firstly acquired by condition monitoring technology and a Hankel matrix is constructed by using the response signals to describe state patterns of the VSS. Thereafter, a subspace analysis method, that is, principal component analysis (PCA), is performed to extract the condition subspace hidden in the Hankel matrix. From the subspace, pattern changes in dynamic structural properties are characterized. Further, a Grassmann manifold (GM) is formed by organizing a set of subspaces. The manifold is mapped to a reproducing kernel Hilbert space (RKHS), where support vector data description (SVDD) is used to model the manifold as a hypersphere. Finally, a health index is defined as the cosine of the angle between the hypersphere centers corresponding to the structural baseline state and the looseness state. The defined health index contains similarity information existing in the two structural states, so structural looseness states can be effectively identified. Moreover, the health index is derived by analysis of the global properties of subspace sets, which is different from traditional subspace analysis methods. The effectiveness of the health index for state assessment is validated by test data collected from a VSS subjected to different degrees of looseness. The results show that the health index is a very effective metric for detecting the occurrence and extension of structural looseness. Comparison results indicate that the defined index outperforms some existing state-of-the-art ones.

Social network supported process recommender system.

PubMed

Ye, Yanming; Yin, Jianwei; Xu, Yueshen

2014-01-01

Process recommendation technologies have gained more and more attention in the field of intelligent business process modeling to assist the process modeling. However, most of the existing technologies only use the process structure analysis and do not take the social features of processes into account, while the process modeling is complex and comprehensive in most situations. This paper studies the feasibility of social network research technologies on process recommendation and builds a social network system of processes based on the features similarities. Then, three process matching degree measurements are presented and the system implementation is discussed subsequently. Finally, experimental evaluations and future works are introduced.

[Amiodarone and thyroid].

PubMed

Capraro, Joël; Thalmann, Sébastien

2011-06-01

Amiodarone is a widely used antiarrythmic drug and can lead either to hypothyroidism or hyperthyroidism due to its molecular structure which is similar to levothyroxin. Amiodarone induced hypothyroidism can be treated easely with hormonal subsitution. Hyperthyroidism is more challenging. There exist two forms of amiodarone-induced Hyperthyroidism (AIT): AIT type 1 is directly related to the iodine compound of amiodarone and responds to thyreostatic therapy. Type 2 is a consequence of the direct toxicity of amiodarone to the thyroid gland and is treated primarily with glucocorticoids. However, this differentiation often is impossible in clinical settings and a pragmatic approach is needed.

The Evolution of the Brain, the Human Nature of Cortical Circuits, and Intellectual Creativity

PubMed Central

DeFelipe, Javier

2011-01-01

The tremendous expansion and the differentiation of the neocortex constitute two major events in the evolution of the mammalian brain. The increase in size and complexity of our brains opened the way to a spectacular development of cognitive and mental skills. This expansion during evolution facilitated the addition of microcircuits with a similar basic structure, which increased the complexity of the human brain and contributed to its uniqueness. However, fundamental differences even exist between distinct mammalian species. Here, we shall discuss the issue of our humanity from a neurobiological and historical perspective. PMID:21647212

Counting spanning trees on fractal graphs and their asymptotic complexity

NASA Astrophysics Data System (ADS)

Anema, Jason A.; Tsougkas, Konstantinos

2016-09-01

Using the method of spectral decimation and a modified version of Kirchhoff's matrix-tree theorem, a closed form solution to the number of spanning trees on approximating graphs to a fully symmetric self-similar structure on a finitely ramified fractal is given in theorem 3.4. We show how spectral decimation implies the existence of the asymptotic complexity constant and obtain some bounds for it. Examples calculated include the Sierpiński gasket, a non-post critically finite analog of the Sierpiński gasket, the Diamond fractal, and the hexagasket. For each example, the asymptotic complexity constant is found.

The Other Shoe: An Early Operant Conditioning Chamber for Pigeons.

PubMed

Sakagami, Takayuki; Lattal, Kennon A

2016-05-01

We describe an early operant conditioning chamber fabricated by Harvard University instrument maker Ralph Gerbrands and shipped to Japan in 1952 in response to a request of Professor B. F. Skinner by Japanese psychologists. It is a rare example, perhaps the earliest still physically existing, of such a chamber for use with pigeons. Although the overall structure and many of the components are similar to contemporary pigeon chambers, several differences are noted and contrasted to evolutionary changes in this most important laboratory tool in the experimental analysis of behavior. The chamber also is testimony to the early internationalization of behavior analysis.

On the Development and Use of Large Chemical Similarity Networks, Informatics Best Practices and Novel Chemical Descriptors Towards Materials Quantitative Structure Property Relationships

NASA Astrophysics Data System (ADS)

Krein, Michael

After decades of development and use in a variety of application areas, Quantitative Structure Property Relationships (QSPRs) and related descriptor-based statistical learning methods have achieved a level of infamy due to their misuse. The field is rife with past examples of overtrained models, overoptimistic performance assessment, and outright cheating in the form of explicitly removing data to fit models. These actions do not serve the community well, nor are they beneficial to future predictions based on established models. In practice, in order to select combinations of descriptors and machine learning methods that might work best, one must consider the nature and size of the training and test datasets, be aware of existing hypotheses about the data, and resist the temptation to bias structure representation and modeling to explicitly fit the hypotheses. The definition and application of these best practices is important for obtaining actionable modeling outcomes, and for setting user expectations of modeling accuracy when predicting the endpoint values of unknowns. A wide variety of statistical learning approaches, descriptor types, and model validation strategies are explored herein, with the goals of helping end users understand the factors involved in creating and using QSPR models effectively, and to better understand relationships within the data, especially by looking at the problem space from multiple perspectives. Molecular relationships are commonly envisioned in a continuous high-dimensional space of numerical descriptors, referred to as chemistry space. Descriptor and similarity metric choice influence the partitioning of this space into regions corresponding to local structural similarity. These regions, known as domains of applicability, are most likely to be successfully modeled by a QSPR. In Chapter 2, the network topology and scaling relationships of several chemistry spaces are thoroughly investigated. Chemistry spaces studied include the ZINC data set, a qHTS PubChem bioassay, as well as the protein binding sites from the PDB. The characteristics of these networks are compared and contrasted with those of the bioassay Structure Activity Landscape Index (SALI) subnetwork, which maps discontinuities or cliffs in the structure activity landscape. Mapping this newly generated information over underlying chemistry space networks generated using different descriptors demonstrates local modeling capacity and can guide the choice of better local representations of chemistry space. Chapter 2 introduces and demonstrates this novel concept, which also enables future work in visualization and interpretation of chemical spaces. Initially, it was discovered that there were no community-available tools to leverage best-practice ideas to comprehensively build, compare, and interpret QSPRs. The Yet Another Modeling System (YAMS) tool performs a series of balanced, rational decisions in dataset preprocessing and parameter/feature selection over a choice of modeling methods. To date, YAMS is the only community-available informatics tool that performs such decisions consistently between methods while also providing multiple model performance comparisons and detailed descriptor importance information. The focus of the tool is thus to convey rich information about model quality and predictions that help to "close the loop" between modeling and experimental efforts, for example, in tailoring nanocomposite properties. Polymer nanocomposites (PNC) are complex material systems encompassing many potential structures, chemistries, and self assembled morphologies that could significantly impact commercial and military applications. There is a strong desire to characterize and understand the tradespace of nanocomposites, to identify the important factors relating nanostructure to materials properties and determine an effective way to control materials properties at the manufacturing scale. Due to the complexity of the systems, existing design approaches rely heavily on trial-and-error learning. By leveraging existing experimental data, Materials Quantitative Structure-Property Relationships (MQSPRs) relate molecular structures to the polar and dispersive components of corresponding surface tensions. In turn, existing theories relate polymer and nanofiller polar and dispersive surface tension components to the dispersion state and interfacial polymer relaxation times. These quantities may, in the future, be used as input to continuum mechanics approaches shown able to predict the thermomechanical response of nanocomposites. For a polymer dataset and a particle dataset, multiple structural representations and descriptor sets are benchmarked, including a set of high performance surface-property descriptors developed as part of this work. The systematic variation of structural representations as part of the informatics approach reveals important insight in modeling polymers, and should become common practice when defining new problem spaces.

Highly-stretchable 3D-architected Mechanical Metamaterials

NASA Astrophysics Data System (ADS)

Jiang, Yanhui; Wang, Qiming

2016-09-01

Soft materials featuring both 3D free-form architectures and high stretchability are highly desirable for a number of engineering applications ranging from cushion modulators, soft robots to stretchable electronics; however, both the manufacturing and fundamental mechanics are largely elusive. Here, we overcome the manufacturing difficulties and report a class of mechanical metamaterials that not only features 3D free-form lattice architectures but also poses ultrahigh reversible stretchability (strain > 414%), 4 times higher than that of the existing counterparts with the similar complexity of 3D architectures. The microarchitected metamaterials, made of highly stretchable elastomers, are realized through an additive manufacturing technique, projection microstereolithography, and its postprocessing. With the fabricated metamaterials, we reveal their exotic mechanical behaviors: Under large-strain tension, their moduli follow a linear scaling relationship with their densities regardless of architecture types, in sharp contrast to the architecture-dependent modulus power-law of the existing engineering materials; under large-strain compression, they present tunable negative-stiffness that enables ultrahigh energy absorption efficiencies. To harness their extraordinary stretchability and microstructures, we demonstrate that the metamaterials open a number of application avenues in lightweight and flexible structure connectors, ultraefficient dampers, 3D meshed rehabilitation structures and stretchable electronics with designed 3D anisotropic conductivity.

Highly-stretchable 3D-architected Mechanical Metamaterials.

PubMed

Jiang, Yanhui; Wang, Qiming

2016-09-26

Soft materials featuring both 3D free-form architectures and high stretchability are highly desirable for a number of engineering applications ranging from cushion modulators, soft robots to stretchable electronics; however, both the manufacturing and fundamental mechanics are largely elusive. Here, we overcome the manufacturing difficulties and report a class of mechanical metamaterials that not only features 3D free-form lattice architectures but also poses ultrahigh reversible stretchability (strain > 414%), 4 times higher than that of the existing counterparts with the similar complexity of 3D architectures. The microarchitected metamaterials, made of highly stretchable elastomers, are realized through an additive manufacturing technique, projection microstereolithography, and its postprocessing. With the fabricated metamaterials, we reveal their exotic mechanical behaviors: Under large-strain tension, their moduli follow a linear scaling relationship with their densities regardless of architecture types, in sharp contrast to the architecture-dependent modulus power-law of the existing engineering materials; under large-strain compression, they present tunable negative-stiffness that enables ultrahigh energy absorption efficiencies. To harness their extraordinary stretchability and microstructures, we demonstrate that the metamaterials open a number of application avenues in lightweight and flexible structure connectors, ultraefficient dampers, 3D meshed rehabilitation structures and stretchable electronics with designed 3D anisotropic conductivity.

Movement and effects of spilled oil over the outer continental shelf; inadequacy of existent data for the Baltimore Canyon Trough area

USGS Publications Warehouse

Knebel, Harley J.

1974-01-01

A deductive approach to the problem of determining the movement and effects of spilled oil over the Outer Continental Shelf requires that the potential paths of oil be determined first, in order that critical subareas may be defined for later studies. The paths of spilled oil, in turn, depend primarily on the temporal and spatial variability of four factors: the thermohaline structure of the waters, the circulation of the water, the winds, and the distribution of suspended matter. A review of the existent data concerning these factors for the Baltimore Canyon Trough area (a relatively well studied segment of the Continental Shelf) reveals that the movement and dispersal of potential oil spills cannot be reliably predicted. Variations in the thermohaline structure of waters and in the distribution of suspended matter are adequately known; the uncertainty is due to insufficient wind and storm statistics and to the lack of quantitative understanding of the relationship between the nontidal drift and its basic driving mechanisms. Similar inadequacies should be anticipated for other potentially leasable areas of the shelf because an understanding of the movement of spilled oil has not been the underlying aim of most previous studies.

Coherent delocalization: views of entanglement in different scenarios

NASA Astrophysics Data System (ADS)

León-Montiel, R. de J.; Vallés, A.; Moya-Cessa, H. M.; Torres, J. P.

2015-08-01

The concept of entanglement was originally introduced to explain correlations existing between two spatially separated systems, that cannot be described using classical ideas. Interestingly, in recent years, it has been shown that similar correlations can be observed when considering different degrees of freedom of a single system, even a classical one. Surprisingly, it has also been suggested that entanglement might be playing a relevant role in certain biological processes, such as the functioning of pigment-proteins that constitute light-harvesting complexes of photosynthetic bacteria. The aim of this work is to show that the presence of entanglement in all of these different scenarios should not be unexpected, once it is realized that the very same mathematical structure can describe all of them. We show this by considering three different, realistic cases in which the only condition for entanglement to exist is that a single excitation is coherently delocalized between the different subsystems that compose the system of interest.

Gene refashioning through innovative shifting of reading frames in mosses.

PubMed

Guan, Yanlong; Liu, Li; Wang, Qia; Zhao, Jinjie; Li, Ping; Hu, Jinyong; Yang, Zefeng; Running, Mark P; Sun, Hang; Huang, Jinling

2018-04-19

Early-diverging land plants such as mosses are known for their outstanding abilities to grow in various terrestrial habitats, incorporating tremendous structural and physiological innovations, as well as many lineage-specific genes. How these genes and functional innovations evolved remains unclear. In this study, we show that a dual-coding gene YAN/AltYAN in the moss Physcomitrella patens evolved from a pre-existing hemerythrin gene. Experimental evidence indicates that YAN/AltYAN is involved in fatty acid and lipid metabolism, as well as oil body and wax formation. Strikingly, both the recently evolved dual-coding YAN/AltYAN and the pre-existing hemerythrin gene might have similar physiological effects on oil body biogenesis and dehydration resistance. These findings bear important implications in understanding the mechanisms of gene origination and the strategies of plants to fine-tune their adaptation to various habitats.

Survey on large scale system control methods

NASA Technical Reports Server (NTRS)

Mercadal, Mathieu

1987-01-01

The problem inherent to large scale systems such as power network, communication network and economic or ecological systems were studied. The increase in size and flexibility of future spacecraft has put those dynamical systems into the category of large scale systems, and tools specific to the class of large systems are being sought to design control systems that can guarantee more stability and better performance. Among several survey papers, reference was found to a thorough investigation on decentralized control methods. Especially helpful was the classification made of the different existing approaches to deal with large scale systems. A very similar classification is used, even though the papers surveyed are somehow different from the ones reviewed in other papers. Special attention is brought to the applicability of the existing methods to controlling large mechanical systems like large space structures. Some recent developments are added to this survey.

On the Importance of Both Dimensional and Discrete Models of Emotion.

PubMed

Harmon-Jones, Eddie; Harmon-Jones, Cindy; Summerell, Elizabeth

2017-09-29

We review research on the structure and functions of emotions that has benefitted from a serious consideration of both discrete and dimensional perspectives on emotion. To illustrate this point, we review research that demonstrates: (1) how affective valence within discrete emotions differs as a function of individuals and situations, and how these differences relate to various functions; (2) that anger (and other emotional states) should be considered as a discrete emotion but there are dimensions around and within anger; (3) that similarities exist between approach-related positive and negative discrete emotions and they have unique motivational functions; (4) that discrete emotions and broad dimensions of emotions both have unique functions; and (5) evidence that a "new" discrete emotion with discrete functions exists within a broader emotion family. We hope that this consideration of both discrete and dimensional perspectives on emotion will assist in understanding the functions of emotions.

On the Importance of Both Dimensional and Discrete Models of Emotion

PubMed Central

Harmon-Jones, Eddie

2017-01-01

We review research on the structure and functions of emotions that has benefitted from a serious consideration of both discrete and dimensional perspectives on emotion. To illustrate this point, we review research that demonstrates: (1) how affective valence within discrete emotions differs as a function of individuals and situations, and how these differences relate to various functions; (2) that anger (and other emotional states) should be considered as a discrete emotion but there are dimensions around and within anger; (3) that similarities exist between approach-related positive and negative discrete emotions and they have unique motivational functions; (4) that discrete emotions and broad dimensions of emotions both have unique functions; and (5) evidence that a “new” discrete emotion with discrete functions exists within a broader emotion family. We hope that this consideration of both discrete and dimensional perspectives on emotion will assist in understanding the functions of emotions. PMID:28961185

Tchebichef moment based restoration of Gaussian blurred images.

PubMed

Kumar, Ahlad; Paramesran, Raveendran; Lim, Chern-Loon; Dass, Sarat C

2016-11-10

With the knowledge of how edges vary in the presence of a Gaussian blur, a method that uses low-order Tchebichef moments is proposed to estimate the blur parameters: sigma (σ) and size (w). The difference between the Tchebichef moments of the original and the reblurred images is used as feature vectors to train an extreme learning machine for estimating the blur parameters (σ,w). The effectiveness of the proposed method to estimate the blur parameters is examined using cross-database validation. The estimated blur parameters from the proposed method are used in the split Bregman-based image restoration algorithm. A comparative analysis of the proposed method with three existing methods using all the images from the LIVE database is carried out. The results show that the proposed method in most of the cases performs better than the three existing methods in terms of the visual quality evaluated using the structural similarity index.

Commentary on: Are we overpathologizing everyday life? A tenable blueprint for behavioral addiction research. On the slippery slopes: The case of gambling addiction.

PubMed

Clark, Luke

2015-09-01

Billieux et al. (2015) propose that the recent proliferation of behavioral addictions has been driven by deficiencies in the underlying research strategy. This commentary considers how pathological gambling (now termed gambling disorder) traversed these challenges to become the first recognized behavioral addiction in the DSM-5. Ironically, many similar issues continue to exist in research on gambling disorder, including question-marks over the validity of tolerance, heterogeneity in gambling motives, and the under-specification of neuroimaging biomarkers. Nevertheless, I contend that the case for gambling disorder as a behavioral addiction has been bolstered by the existence of clear and consistent functional impairment (primarily in the form of debt), coupled with the development of a public health approach that has given emphasis to product features (i.e. the structural characteristics of gambling forms) as much as individual dispositions (the 'addictive personality').

Nontrivial Critical Fixed Point for Replica-Symmetry-Breaking Transitions.

PubMed

Charbonneau, Patrick; Yaida, Sho

2017-05-26

The transformation of the free-energy landscape from smooth to hierarchical is one of the richest features of mean-field disordered systems. A well-studied example is the de Almeida-Thouless transition for spin glasses in a magnetic field, and a similar phenomenon-the Gardner transition-has recently been predicted for structural glasses. The existence of these replica-symmetry-breaking phase transitions has, however, long been questioned below their upper critical dimension, d_{u}=6. Here, we obtain evidence for the existence of these transitions in d

Study of structural reliability of existing concrete structures

NASA Astrophysics Data System (ADS)

Druķis, P.; Gaile, L.; Valtere, K.; Pakrastiņš, L.; Goremikins, V.

2017-10-01

Structural reliability of buildings has become an important issue after the collapse of a shopping center in Riga 21.11.2013, caused the death of 54 people. The reliability of a building is the practice of designing, constructing, operating, maintaining and removing buildings in ways that ensure maintained health, ward suffered injuries or death due to use of the building. Evaluation and improvement of existing buildings is becoming more and more important. For a large part of existing buildings, the design life has been reached or will be reached in the near future. The structures of these buildings need to be reassessed in order to find out whether the safety requirements are met. The safety requirements provided by the Eurocodes are a starting point for the assessment of safety. However, it would be uneconomical to require all existing buildings and structures to comply fully with these new codes and corresponding safety levels, therefore the assessment of existing buildings differs with each design situation. This case study describes the simple and practical procedure of determination of minimal reliability index β of existing concrete structures designed by different codes than Eurocodes and allows to reassess the actual reliability level of different structural elements of existing buildings under design load.

Direct experimental observation of mesoscopic fluorous domains in fluorinated room temperature ionic liquids

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

Lo Celso, F.; Yoshida, Y.; Castiglione, F.

Fluorinated room temperature ionic liquids (FRTILs) represent a class of solvent media that are attracting great attention due to their IL-specific properties as well as features stemming from their fluorous nature. Medium-to-long fluorous tails constitute a well-defined apolar moiety in the otherwise polar environment. Similarly to the case of alkyl tails, such chains are expected to result in the formation of self-assembled fluorous domains. So far, however, no direct experimental observation has been made of the existence of such structural heterogeneities on the nm scale. We report here the first experimental evidence of the existence of mesoscopic spatial segregation ofmore » fluorinated domains, on the basis of highly complementary X-ray and neutron scattering data sets (highlighting the importance of the latter probe) and NMR spectroscopy. Data are interpreted using atomistic molecular dynamics simulations, emphasizing the existence of a self-assembly mechanism that delivers segregated fluorous domains, where preferential solubilisation of fluorinated compounds can occur, thus paving the way for several smart applications.« less

Origin and early evolution of photosynthesis

NASA Technical Reports Server (NTRS)

Blankenship, R. E.

1992-01-01

Photosynthesis was well-established on the earth at least 3.5 thousand million years ago, and it is widely believed that these ancient organisms had similar metabolic capabilities to modern cyanobacteria. This requires that development of two photosystems and the oxygen evolution capability occurred very early in the earth's history, and that a presumed phase of evolution involving non-oxygen evolving photosynthetic organisms took place even earlier. The evolutionary relationships of the reaction center complexes found in all the classes of currently existing organisms have been analyzed using sequence analysis and biophysical measurements. The results indicate that all reaction centers fall into two basic groups, those with pheophytin and a pair of quinones as early acceptors, and those with iron sulfur clusters as early acceptors. No simple linear branching evolutionary scheme can account for the distribution patterns of reaction centers in existing photosynthetic organisms, and lateral transfer of genetic information is considered as a likely possibility. Possible scenarios for the development of primitive reaction centers into the heterodimeric protein structures found in existing reaction centers and for the development of organisms with two linked photosystems are presented.

Evidence for Possible Exposed Water Ice Deposits in Martian Low Latitude Chasms and Chaos

NASA Technical Reports Server (NTRS)

Leovy, C.; Wood, S. E.; Catling, D.; Montgomery, D. R.; Moore, J.; Barnhart, C.; Ginder, E.; Louie, M.

2004-01-01

A light-toned interior layer deposit (ILD) on the floor of the deep martian depression Juventae Chasma is found to have a relatively high thermal inertia approx. 500 J m(exp -2) s(exp -1/2) K(exp -1). This could imply rock, but is also similar to the average value of thermal inertia found for north polar layered deposits. Furthermore, ILD-B is found to exhibit a bluff and terrace structure . A terrace structure arises naturally in model simulations of the sublimation of large ice deposits. Such a staircase terrain, of course, is a further characteristic of north polar layered terrain. Morphological similarity, thermal inertia in the range of thermal inertias of the north polar cap layered terrain, and relatively high albedo lead us to propose that the ILD-B may consist of residual water ice partially covered by, and perhaps mixed with, varying amounts of dust or sand. Other ILDs (A-C) are also found in Juventae Chasma. While these ILDs lack the close morphological resemblance to the north polar cap, they share many other common features and appear to be part of the same formation. Similar ILDs are found in chaotic terrain elsewhere in the martian tropics. This leads us to propose that water ice may exist in the martian tropics today and may be implicit in the formation of chaotic terrain.

The similarity between N-terminal targeting signals for protein import into different organelles and its evolutionary relevance

PubMed Central

Kunze, Markus; Berger, Johannes

2015-01-01

The proper distribution of proteins between the cytosol and various membrane-bound compartments is crucial for the functionality of eukaryotic cells. This requires the cooperation between protein transport machineries that translocate diverse proteins from the cytosol into these compartments and targeting signal(s) encoded within the primary sequence of these proteins that define their cellular destination. The mechanisms exerting protein translocation differ remarkably between the compartments, but the predominant targeting signals for mitochondria, chloroplasts and the ER share the N-terminal position, an α-helical structural element and the removal from the core protein by intraorganellar cleavage. Interestingly, similar properties have been described for the peroxisomal targeting signal type 2 mediating the import of a fraction of soluble peroxisomal proteins, whereas other peroxisomal matrix proteins encode the type 1 targeting signal residing at the extreme C-terminus. The structural similarity of N-terminal targeting signals poses a challenge to the specificity of protein transport, but allows the generation of ambiguous targeting signals that mediate dual targeting of proteins into different compartments. Dual targeting might represent an advantage for adaptation processes that involve a redistribution of proteins, because it circumvents the hierarchy of targeting signals. Thus, the co-existence of two equally functional import pathways into peroxisomes might reflect a balance between evolutionary constant and flexible transport routes. PMID:26441678

Distinct Correlation Structure Supporting a Rate-Code for Sound Localization in the Owl’s Auditory Forebrain

PubMed Central

2017-01-01

Abstract While a topographic map of auditory space exists in the vertebrate midbrain, it is absent in the forebrain. Yet, both brain regions are implicated in sound localization. The heterogeneous spatial tuning of adjacent sites in the forebrain compared to the midbrain reflects different underlying circuitries, which is expected to affect the correlation structure, i.e., signal (similarity of tuning) and noise (trial-by-trial variability) correlations. Recent studies have drawn attention to the impact of response correlations on the information readout from a neural population. We thus analyzed the correlation structure in midbrain and forebrain regions of the barn owl’s auditory system. Tetrodes were used to record in the midbrain and two forebrain regions, Field L and the downstream auditory arcopallium (AAr), in anesthetized owls. Nearby neurons in the midbrain showed high signal and noise correlations (RNCs), consistent with shared inputs. As previously reported, Field L was arranged in random clusters of similarly tuned neurons. Interestingly, AAr neurons displayed homogeneous monotonic azimuth tuning, while response variability of nearby neurons was significantly less correlated than the midbrain. Using a decoding approach, we demonstrate that low RNC in AAr restricts the potentially detrimental effect it can have on information, assuming a rate code proposed for mammalian sound localization. This study harnesses the power of correlation structure analysis to investigate the coding of auditory space. Our findings demonstrate distinct correlation structures in the auditory midbrain and forebrain, which would be beneficial for a rate-code framework for sound localization in the nontopographic forebrain representation of auditory space. PMID:28674698

Challenges of sulfur SAD phasing as a routine method in macromolecular crystallography.

PubMed

Doutch, James; Hough, Michael A; Hasnain, S Samar; Strange, Richard W

2012-01-01

The sulfur SAD phasing method allows the determination of protein structures de novo without reference to derivatives such as Se-methionine. The feasibility for routine automated sulfur SAD phasing using a number of current protein crystallography beamlines at several synchrotrons was examined using crystals of trimeric Achromobacter cycloclastes nitrite reductase (AcNiR), which contains a near average proportion of sulfur-containing residues and two Cu atoms per subunit. Experiments using X-ray wavelengths in the range 1.9-2.4 Å show that we are not yet at the level where sulfur SAD is routinely successful for automated structure solution and model building using existing beamlines and current software tools. On the other hand, experiments using the shortest X-ray wavelengths available on existing beamlines could be routinely exploited to solve and produce unbiased structural models using the similarly weak anomalous scattering signals from the intrinsic metal atoms in proteins. The comparison of long-wavelength phasing (the Bijvoet ratio for nine S atoms and two Cu atoms is ~1.25% at ~2 Å) and copper phasing (the Bijvoet ratio for two Cu atoms is 0.81% at ~0.75 Å) for AcNiR suggests that lower data multiplicity than is currently required for success should in general be possible for sulfur phasing if appropriate improvements to beamlines and data collection strategies can be implemented.

Unusual sugar specificity of banana lectin from Musa paradisiaca and its probable evolutionary origin. Crystallographic and modelling studies.

PubMed

Singh, D D; Saikrishnan, K; Kumar, Prashant; Surolia, A; Sekar, K; Vijayan, M

2005-10-01

The crystal structure of a complex of methyl-alpha-D-mannoside with banana lectin from Musa paradisiaca reveals two primary binding sites in the lectin, unlike in other lectins with beta-prism I fold which essentially consists of three Greek key motifs. It has been suggested that the fold evolved through successive gene duplication and fusion of an ancestral Greek key motif. In other lectins, all from dicots, the primary binding site exists on one of the three motifs in the three-fold symmetric molecule. Banana is a monocot, and the three motifs have not diverged enough to obliterate sequence similarity among them. Two Greek key motifs in it carry one primary binding site each. A common secondary binding site exists on the third Greek key. Modelling shows that both the primary sites can support 1-2, 1-3, and 1-6 linked mannosides with the second residue interacting in each case primarily with the secondary binding site. Modelling also readily leads to a bound branched mannopentose with the nonreducing ends of the two branches anchored at the two primary binding sites, providing a structural explanation for the lectin's specificity for branched alpha-mannans. A comparison of the dimeric banana lectin with other beta-prism I fold lectins, provides interesting insights into the variability in their quaternary structure.

River mainstem thermal regimes influence population structuring within an Appalachian brook trout population

USGS Publications Warehouse

Aunins, Aaron W.; Petty, J. Todd; King, Timothy L.; Schilz, Mariya; Mazik, Patricia M.

2015-01-01

Brook trout (Salvelinus fontinalis) often exist as highly differentiated populations, even at small spatial scales, due either to natural or anthropogenic sources of isolation and low rates of dispersal. In this study, we used molecular approaches to describe the unique population structure of brook trout inhabiting the Shavers Fork watershed, located in eastern West Virginia, and contrast it to nearby populations in tributaries of the upper Greenbrier River and North Fork South Branch Potomac Rivers. Bayesian and maximum likelihood clustering methods identified minimal population structuring among 14 collections of brook trout from throughout the mainstem and tributaries of Shavers Fork, highlighting the role of the cold-water mainstem for connectivity and high rates of effective migration among tributaries. In contrast, the Potomac and Greenbrier River collections displayed distinct levels of population differentiation among tributaries, presumably resulting from tributary isolation by warm-water mainstems. Our results highlight the importance of protecting and restoring cold-water mainstem habitats as part of region-wide brook trout conservation efforts. In addition, our results from Shavers Fork provide a contrast to previous genetic studies that characterize Appalachian brook trout as fragmented isolates rather than well-mixed populations. Additional study is needed to determine whether the existence of brook trout as genetically similar populations among tributaries is truly unique and whether connectivity among brook trout populations can potentially be restored within other central Appalachian watersheds.

Risk Classification with an Adaptive Naive Bayes Kernel Machine Model.

PubMed

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

2015-04-22

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

BAYESIAN PROTEIN STRUCTURE ALIGNMENT.

PubMed

Rodriguez, Abel; Schmidler, Scott C

The analysis of the three-dimensional structure of proteins is an important topic in molecular biochemistry. Structure plays a critical role in defining the function of proteins and is more strongly conserved than amino acid sequence over evolutionary timescales. A key challenge is the identification and evaluation of structural similarity between proteins; such analysis can aid in understanding the role of newly discovered proteins and help elucidate evolutionary relationships between organisms. Computational biologists have developed many clever algorithmic techniques for comparing protein structures, however, all are based on heuristic optimization criteria, making statistical interpretation somewhat difficult. Here we present a fully probabilistic framework for pairwise structural alignment of proteins. Our approach has several advantages, including the ability to capture alignment uncertainty and to estimate key "gap" parameters which critically affect the quality of the alignment. We show that several existing alignment methods arise as maximum a posteriori estimates under specific choices of prior distributions and error models. Our probabilistic framework is also easily extended to incorporate additional information, which we demonstrate by including primary sequence information to generate simultaneous sequence-structure alignments that can resolve ambiguities obtained using structure alone. This combined model also provides a natural approach for the difficult task of estimating evolutionary distance based on structural alignments. The model is illustrated by comparison with well-established methods on several challenging protein alignment examples.

Phenotypic and genetic structure of traits delineating personality disorder.

PubMed

Livesley, W J; Jang, K L; Vernon, P A

1998-10-01

The evidence suggests that personality traits are hierarchically organized with more specific or lower-order traits combining to form more generalized higher-order traits. Agreement exists across studies regarding the lower-order traits that delineate personality disorder but not the higher-order traits. This study seeks to identify the higher-order structure of personality disorder by examining the phenotypic and genetic structures underlying lower-order traits. Eighteen lower-order traits were assessed using the Dimensional Assessment of Personality Disorder-Basic Questionnaire in samples of 656 personality disordered patients, 939 general population subjects, and a volunteer sample of 686 twin pairs. Principal components analysis yielded 4 components, labeled Emotional Dysregulation, Dissocial Behavior, Inhibitedness, and Compulsivity, that were similar across the 3 samples. Multivariate genetic analyses also yielded 4 genetic and environmental factors that were remarkably similar to the phenotypic factors. Analysis of the residual heritability of the lower-order traits when the effects of the higher-order factors were removed revealed a substantial residual heritable component for 12 of the 18 traits. The results support the following conclusions. First, the stable structure of traits across clinical and nonclinical samples is consistent with dimensional representations of personality disorders. Second, the higher-order traits of personality disorder strongly resemble dimensions of normal personality. This implies that a dimensional classification should be compatible with normative personality. Third, the residual heritability of the lower-order traits suggests that the personality phenotypes are based on a large number of specific genetic components.

Structure and variability of symbiotic assemblages associated with feather stars (Crinoidea: Comatulida) Himerometra robustipinna

NASA Astrophysics Data System (ADS)

Britayev, T. A.; Beksheneva, L. F.; Deart, Yu. V.; Mekhova, E. S.

2016-09-01

The paper considers the influence of the geographical position and local conditions on the structure and abundance of symbiotic communities (SCs) associated with the crinoid Himerometra robustipinna. Two water areas at the coast of Vietnam (Nhatrang Bay and the Anthoy Archipelago; our data), Hansa Bay (Papua, New Guinea; Deyen et al., 2006), and the Great Barrier Reef (Australia; Fabricius and Dale, 1993) were compared. We found a similarity in the contribution from the main taxa to the structure of SCs between geographically distant water areas—Nhatrang Bay, Hansa Bay, and the Great Barrier Reef (GBR)—and strong differences between the two Vietnamese water areas. A possible reason for the differences in the SC structure in these water areas is not their geographical location, but the environmental conditions, which are more stable in the seaward part of Nhatrang Bay and less stable in the Anthoy Archipelago. The abundances of symbionts in the water areas of the coast of Vietnam are similar to each other and strongly different from Hansa Bay and the GBR. We suppose that a factor regulating the abundance of symbionts is their consumption by predatory fishes. A low abundance of fishes in the area of active coastal fishery (the coast of Vietnam) makes possible the existence of SCs with a high abundance. In Hansa Bay and the GBR where fishery pressure is low, a high number of predators leads to a low abundance of symbionts.

Primary structure of an adipokinetic neuropeptide from the rhinoceros beetle, Oryctes rhinoceros L (Coleoptera: Dynastidae).

PubMed

Ajay Kumar, A P; Gokuldas, M

2011-07-01

Neuropeptides play an important role in cellular communication in vertebrates. This is also true for insects in which many physiological, developmental and behavioral processes are affected by neuropeptides produced in neurosecretory cells of the retrocerebral complex. Small neuropeptides of the adipokinetic hormone/red pigment concentrating hormone family (AKH/RPCH) are one of the important groups of peptides that regulate physiological homeostasis. The present investigation was carried out to elucidate the primary structure of adipokinetic neuropeptides in the rhinoceros beetle, O. rhinoceros. In the present investigation, an adipokinetic neuropeptide from the coconut pest, Oryctes rhinoceros was isolated from corpora cardiaca by HPLC; the chromatographic fractions were tested for adipokinetic activity in the plant bug, Iphita limbata in vivo. Two UV absorbance peaks were found to be significantly active in elevating haemolymph lipid levels. MALDI-MS analysis of the extract indicated that the molecular mass, 1003.70 Da is similar to the already known AKH from another beetle, Melolontha melolontha. MALDI-MS/MS analysis confirmed that its primary structure is exactly similar to the structure reported for the Melme-AKH (pE-L-N-Y-S-P-D-W-NH2). The findings suggest that the distribution of AKH peptides has shown that there exists a taxonomic order or family specificity. This data can be used as additional information to aid in the construction of phylogenetic trees by means of computer programme and protein parsimony algorithms.

Characterization of protein and carbohydrate mid-IR spectral features in crop residues

NASA Astrophysics Data System (ADS)

Xin, Hangshu; Zhang, Yonggen; Wang, Mingjun; Li, Zhongyu; Wang, Zhibo; Yu, Peiqiang

2014-08-01

To the best of our knowledge, a few studies have been conducted on inherent structure spectral traits related to biopolymers of crop residues. The objective of this study was to characterize protein and carbohydrate structure spectral features of three field crop residues (rice straw, wheat straw and millet straw) in comparison with two crop vines (peanut vine and pea vine) by using Fourier transform infrared spectroscopy (FTIR) technique with attenuated total reflectance (ATR). Also, multivariate analyses were performed on spectral data sets within the regions mainly related to protein and carbohydrate in this study. The results showed that spectral differences existed in mid-IR peak intensities that are mainly related to protein and carbohydrate among these crop residue samples. With regard to protein spectral profile, peanut vine showed the greatest mid-IR band intensities that are related to protein amide and protein secondary structures, followed by pea vine and the rest three field crop straws. The crop vines had 48-134% higher spectral band intensity than the grain straws in spectral features associated with protein. Similar trends were also found in the bands that are mainly related to structural carbohydrates (such as cellulosic compounds). However, the field crop residues had higher peak intensity in total carbohydrates region than the crop vines. Furthermore, spectral ratios varied among the residue samples, indicating that these five crop residues had different internal structural conformation. However, multivariate spectral analyses showed that structural similarities still exhibited among crop residues in the regions associated with protein biopolymers and carbohydrate. Further study is needed to find out whether there is any relationship between spectroscopic information and nutrition supply in various kinds of crop residue when fed to animals.

[Spectroscopic Research on Slag Nanocrystal Glass Ceramics Containing Rare Earth Elements].

PubMed

Ouyang, Shun-li; Li, Bao-wei; Zhang, Xue-feng; Jia, Xiao-lin; Zhao, Ming; Deng, Lei-bo

2015-08-01

The research group prepared the high-performance slag nanocrystal glass ceramics by utilizing the valuable elements of the wastes in the Chinese Bayan Obo which are characterized by their symbiotic or associated existence. In this paper, inductively coupled plasma emission spectroscopy (ICP), X-ray diffraction (XRD), Raman spectroscopy (Raman) and scanning electron microscopy (SEM) are all used in the depth analysis for the composition and structure of the samples. The experiment results of ICP, XRD and SEM showed that the principal crystalline phase of the slag nanocrystal glass ceramics containing rare earth elements is diopside, its grain size ranges from 45 to 100 nm, the elements showed in the SEM scan are basically in consistent with the component analysis of ICP. Raman analysis indicated that its amorphous phase is a three-dimensional network structure composed by the structural unit of silicon-oxy tetrahedron with different non-bridging oxygen bonds. According to the further analysis, we found that the rare earth microelement has significant effect on the network structure. Compared the nanocrystal slag glass ceramic with the glass ceramics of similar ingredients, we found that generally, the Raman band wavenumber for the former is lower than the later. The composition difference between the glass ceramics and the slag nanocrystal with the similar ingredients mainly lies on the rare earth elements and other trace elements. Therefore, we think that the rare earth elements and other trace elements remains in the slag nanocrystal glass ceramics have a significant effect on the network structure of amorphous phase. The research method of this study provides an approach for the relationship among the composition, structure and performance of the glass ceramics.

Ontogeny of the Alligator Cartilago Transiliens and Its Significance for Sauropsid Jaw Muscle Evolution

PubMed Central

Tsai, Henry P.; Holliday, Casey M.

2011-01-01

The cartilago transiliens is a fibrocartilaginous structure within the jaw muscles of crocodylians. The cartilago transiliens slides between the pterygoid buttress and coronoid region of the lower jaw and connects two muscles historically identified as m. pseudotemporalis superficialis and m. intramandibularis. However, the position of cartilago transiliens, and its anatomical similarities to tendon organs suggest the structure may be a sesamoid linking a single muscle. Incompressible sesamoids often form inside tendons that wrap around bone. However, such structures rarely ossify in reptiles and have thus far received scant attention. We tested the hypothesis that the cartilago transiliens is a sesamoid developed within in one muscle by investigating its structure in an ontogenetic series of Alligator mississippiensis using dissection, 3D imaging, and polarizing and standard light microscopy. In all animals studied, the cartilago transiliens receives collagen fibers and tendon insertions from its two main muscular attachments. However, whereas collagen fibers were continuous within the cartilaginous nodule of younger animals, such continuity decreased in older animals, where the fibrocartilaginous core grew to displace the fibrous region. Whereas several neighboring muscles attached to the fibrous capsule in older individuals, only two muscles had significant contributions to the structure in young animals. Our results indicate that the cartilago transiliens is likely a sesamoid formed within a single muscle (i.e., m. pseudotemporalis superficialis) as it wraps around the pterygoid buttress. This tendon organ is ubiquitous among fossil crocodyliforms indicating it is a relatively ancient, conserved structure associated with the development of the large pterygoid flanges in this clade. Finally, these findings indicate that similar tendon organs exist among potentially homologous muscle groups in birds and turtles, thus impacting inferences of jaw muscle homology and evolution in sauropsids in general. PMID:21949795

Characterization of protein and carbohydrate mid-IR spectral features in crop residues.

PubMed

Xin, Hangshu; Zhang, Yonggen; Wang, Mingjun; Li, Zhongyu; Wang, Zhibo; Yu, Peiqiang

2014-08-14

To the best of our knowledge, a few studies have been conducted on inherent structure spectral traits related to biopolymers of crop residues. The objective of this study was to characterize protein and carbohydrate structure spectral features of three field crop residues (rice straw, wheat straw and millet straw) in comparison with two crop vines (peanut vine and pea vine) by using Fourier transform infrared spectroscopy (FTIR) technique with attenuated total reflectance (ATR). Also, multivariate analyses were performed on spectral data sets within the regions mainly related to protein and carbohydrate in this study. The results showed that spectral differences existed in mid-IR peak intensities that are mainly related to protein and carbohydrate among these crop residue samples. With regard to protein spectral profile, peanut vine showed the greatest mid-IR band intensities that are related to protein amide and protein secondary structures, followed by pea vine and the rest three field crop straws. The crop vines had 48-134% higher spectral band intensity than the grain straws in spectral features associated with protein. Similar trends were also found in the bands that are mainly related to structural carbohydrates (such as cellulosic compounds). However, the field crop residues had higher peak intensity in total carbohydrates region than the crop vines. Furthermore, spectral ratios varied among the residue samples, indicating that these five crop residues had different internal structural conformation. However, multivariate spectral analyses showed that structural similarities still exhibited among crop residues in the regions associated with protein biopolymers and carbohydrate. Further study is needed to find out whether there is any relationship between spectroscopic information and nutrition supply in various kinds of crop residue when fed to animals. Copyright © 2014 Elsevier B.V. All rights reserved.

A method for probing the mutational landscape of amyloid structure.

PubMed

O'Donnell, Charles W; Waldispühl, Jérôme; Lis, Mieszko; Halfmann, Randal; Devadas, Srinivas; Lindquist, Susan; Berger, Bonnie

2011-07-01

Proteins of all kinds can self-assemble into highly ordered β-sheet aggregates known as amyloid fibrils, important both biologically and clinically. However, the specific molecular structure of a fibril can vary dramatically depending on sequence and environmental conditions, and mutations can drastically alter amyloid function and pathogenicity. Experimental structure determination has proven extremely difficult with only a handful of NMR-based models proposed, suggesting a need for computational methods. We present AmyloidMutants, a statistical mechanics approach for de novo prediction and analysis of wild-type and mutant amyloid structures. Based on the premise of protein mutational landscapes, AmyloidMutants energetically quantifies the effects of sequence mutation on fibril conformation and stability. Tested on non-mutant, full-length amyloid structures with known chemical shift data, AmyloidMutants offers roughly 2-fold improvement in prediction accuracy over existing tools. Moreover, AmyloidMutants is the only method to predict complete super-secondary structures, enabling accurate discrimination of topologically dissimilar amyloid conformations that correspond to the same sequence locations. Applied to mutant prediction, AmyloidMutants identifies a global conformational switch between Aβ and its highly-toxic 'Iowa' mutant in agreement with a recent experimental model based on partial chemical shift data. Predictions on mutant, yeast-toxic strains of HET-s suggest similar alternate folds. When applied to HET-s and a HET-s mutant with core asparagines replaced by glutamines (both highly amyloidogenic chemically similar residues abundant in many amyloids), AmyloidMutants surprisingly predicts a greatly reduced capacity of the glutamine mutant to form amyloid. We confirm this finding by conducting mutagenesis experiments. Our tool is publically available on the web at http://amyloid.csail.mit.edu/. lindquist_admin@wi.mit.edu; bab@csail.mit.edu.

Effect of Angle on Flow-Induced Vibrations of Pinniped Vibrissae

PubMed Central

Murphy, Christin T.; Eberhardt, William C.; Calhoun, Benton H.; Mann, Kenneth A.; Mann, David A.

2013-01-01

Two types of vibrissal surface structures, undulated and smooth, exist among pinnipeds. Most Phocidae have vibrissae with undulated surfaces, while Otariidae, Odobenidae, and a few phocid species possess vibrissae with smooth surfaces. Variations in cross-sectional profile and orientation of the vibrissae also exist between pinniped species. These factors may influence the way that the vibrissae behave when exposed to water flow. This study investigated the effect that vibrissal surface structure and orientation have on flow-induced vibrations of pinniped vibrissae. Laser vibrometry was used to record vibrations along the whisker shaft from the undulated vibrissae of harbor seals (Phoca vitulina) and northern elephant seals (Mirounga angustirostris) and the smooth vibrissae of California sea lions (Zalophus californianus). Vibrations along the whisker shaft were measured in a flume tank, at three orientations (0°, 45°, 90°) to the water flow. The results show that vibration frequency and velocity ranges were similar for both undulated and smooth vibrissae. Angle of orientation, rather than surface structure, had the greatest effect on flow-induced vibrations. Vibration velocity was up to 60 times higher when the wide, flat aspect of the whisker faced into the flow (90°), compared to when the thin edge faced into the flow (0°). Vibration frequency was also dependent on angle of orientation. Peak frequencies were measured up to 270 Hz and were highest at the 0° orientation for all whiskers. Furthermore, CT scanning was used to quantify the three-dimensional structure of pinniped vibrissae that may influence flow interactions. The CT data provide evidence that all vibrissae are flattened in cross-section to some extent and that differences exist in the orientation of this profile with respect to the major curvature of the hair shaft. These data support the hypothesis that a compressed cross-sectional profile may play a key role in reducing self-noise of the vibrissae. PMID:23922834

Structural transformations and disordering in zirconolite (CaZrTi2O7) at high pressure.

PubMed

Salamat, Ashkan; McMillan, Paul F; Firth, Steven; Woodhead, Katherine; Hector, Andrew L; Garbarino, Gaston; Stennett, Martin C; Hyatt, Neil C

2013-02-04

There is interest in identifying novel materials for use in radioactive waste applications and studying their behavior under high pressure conditions. The mineral zirconolite (CaZrTi(2)O(7)) exists naturally in trace amounts in diamond-bearing deep-seated metamorphic/igneous environments, and it is also identified as a potential ceramic phase for radionuclide sequestration. However, it has been shown to undergo radiation-induced metamictization resulting in amorphous forms. In this study we probed the high pressure structural properties of this pyrochlore-like structure to study its phase transformations and possible amorphization behavior. Combined synchrotron X-ray diffraction and Raman spectroscopy studies reveal a series of high pressure phase transformations. Starting from the ambient pressure monoclinic structure, an intermediate phase with P2(1)/m symmetry is produced above 15.6 GPa via a first order transformation resulting in a wide coexistence range. Upon compression to above 56 GPa a disordered metastable phase III with a cotunnite-related structure appears that is recoverable to ambient conditions. We examine the similarity between the zirconolite behavior and the structural evolution of analogous pyrochlore systems under pressure.

On the inversion of the 1 Bu and 2 Ag electronic states in α,ω-diphenylpolyenes

NASA Astrophysics Data System (ADS)

Catalán, J.

2003-07-01

An alternative model to that of the inversion of the states 1Bu and 2Ag is proposed for interpreting the photophysics of the α,ω-diphenylpolyenes. This model is based upon the existence of two chemical structures with Bu symmetry, which may be ascribed to the same excited electronic state 1Bu. One of the two chemical structures corresponds to the Franck-Condon structure with conjugated single and double bonds for the polyene chain, and another consists of a nearly equivalent series of partial double bonds along the polyene chain. The latter relaxed structure is consistent with the observation of high torsional energy barriers and low photoisomerization quantum yields for diphenylhexatriene in the singlet excited state manifold. Interestingly, such a simple quantum model as that of the particle in a one-dimensional box provides quite an accurate description of the absorption spectroscopic properties of these major compounds. This is partly the result of the most stable structures for these compounds being of the all-trans type; such structures increase in length as additional ethylene units are added, which makes them very similar to a one-dimensional box becoming increasingly longer.

Semantic Similarity between Web Documents Using Ontology

NASA Astrophysics Data System (ADS)

Chahal, Poonam; Singh Tomer, Manjeet; Kumar, Suresh

2018-06-01

The World Wide Web is the source of information available in the structure of interlinked web pages. However, the procedure of extracting significant information with the assistance of search engine is incredibly critical. This is for the reason that web information is written mainly by using natural language, and further available to individual human. Several efforts have been made in semantic similarity computation between documents using words, concepts and concepts relationship but still the outcome available are not as per the user requirements. This paper proposes a novel technique for computation of semantic similarity between documents that not only takes concepts available in documents but also relationships that are available between the concepts. In our approach documents are being processed by making ontology of the documents using base ontology and a dictionary containing concepts records. Each such record is made up of the probable words which represents a given concept. Finally, document ontology's are compared to find their semantic similarity by taking the relationships among concepts. Relevant concepts and relations between the concepts have been explored by capturing author and user intention. The proposed semantic analysis technique provides improved results as compared to the existing techniques.

The players may change but the game remains: network analyses of ruminal microbiomes suggest taxonomic differences mask functional similarity.

PubMed

Taxis, Tasia M; Wolff, Sara; Gregg, Sarah J; Minton, Nicholas O; Zhang, Chiqian; Dai, Jingjing; Schnabel, Robert D; Taylor, Jeremy F; Kerley, Monty S; Pires, J Chris; Lamberson, William R; Conant, Gavin C

2015-11-16

By mapping translated metagenomic reads to a microbial metabolic network, we show that ruminal ecosystems that are rather dissimilar in their taxonomy can be considerably more similar at the metabolic network level. Using a new network bi-partition approach for linking the microbial network to a bovine metabolic network, we observe that these ruminal metabolic networks exhibit properties consistent with distinct metabolic communities producing similar outputs from common inputs. For instance, the closer in network space that a microbial reaction is to a reaction found in the host, the lower will be the variability of its enzyme copy number across hosts. Similarly, these microbial enzymes that are nearby to host nodes are also higher in copy number than are more distant enzymes. Collectively, these results demonstrate a widely expected pattern that, to our knowledge, has not been explicitly demonstrated in microbial communities: namely that there can exist different community metabolic networks that have the same metabolic inputs and outputs but differ in their internal structure. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Semantic Similarity between Web Documents Using Ontology

NASA Astrophysics Data System (ADS)

Chahal, Poonam; Singh Tomer, Manjeet; Kumar, Suresh

2018-03-01

The World Wide Web is the source of information available in the structure of interlinked web pages. However, the procedure of extracting significant information with the assistance of search engine is incredibly critical. This is for the reason that web information is written mainly by using natural language, and further available to individual human. Several efforts have been made in semantic similarity computation between documents using words, concepts and concepts relationship but still the outcome available are not as per the user requirements. This paper proposes a novel technique for computation of semantic similarity between documents that not only takes concepts available in documents but also relationships that are available between the concepts. In our approach documents are being processed by making ontology of the documents using base ontology and a dictionary containing concepts records. Each such record is made up of the probable words which represents a given concept. Finally, document ontology's are compared to find their semantic similarity by taking the relationships among concepts. Relevant concepts and relations between the concepts have been explored by capturing author and user intention. The proposed semantic analysis technique provides improved results as compared to the existing techniques.

Using Concept Maps to Monitor Knowledge Structure Changes in a Science Classroom

NASA Astrophysics Data System (ADS)

Cook, Leah J.

The aim of this research is to determine what differences may exist in students' structural knowledge while using a variety of concept mapping assessments. A concept map can be used as an assessment which connects concepts in a knowledge domain. A single assessment may not be powerful enough to establish how students' new knowledge relates to prior knowledge. More research is needed to establish how various aspects of the concept mapping task influence the output of map creation by students. Using multiple concept maps and pre-instruction and post-instruction VNOS instruments during a 16-week semester, this study was designed to investigate the impact of concept map training and the impact of assessment design on the created maps. Also, this study was designed to determine what differences can be observed between expert and novice maps and if similarities and differences exist between concept maps and an open-ended assessment. Participants created individual maps and the maps were analyzed for structural complexity, overall structure, and content. The concept maps were then compared by their timing, design, and scores. The results indicate that concept mapping training does significantly impact the shape and structure complexity of the map created by students. Additionally, these data support that students should be frequently reminded of appropriate concept mapping skills and opportunities so that good mapping skills will be utilized. Changing the assessment design does appear to be able to impact the overall structure and complexity of created maps, while narrowing the content focus of the map does not necessarily restrict the overall structure or the complexity. Furthermore, significant differences in structural complexity were observed between novice and expert mappers. The fluctuations of NOS concepts identified in student created maps may suggest why some students were still confused or had incorrect conceptions of NOS, despite explicit and reflective instruction throughout the semester.

Song hybridization events during revolutionary song change provide insights into cultural transmission in humpback whales

PubMed Central

Garland, Ellen C.; Rendell, Luke; Lamoni, Luca; Poole, M. Michael; Noad, Michael J.

2017-01-01

Cultural processes occur in a wide variety of animal taxa, from insects to cetaceans. The songs of humpback whales are one of the most striking examples of the transmission of a cultural trait and social learning in any nonhuman animal. To understand how songs are learned, we investigate rare cases of song hybridization, where parts of an existing song are spliced with a new one, likely before an individual totally adopts the new song. Song unit sequences were extracted from over 9,300 phrases recorded during two song revolutions across the South Pacific Ocean, allowing fine-scale analysis of composition and sequencing. In hybrid songs the current and new songs were spliced together in two specific ways: (i) singers placed a single hybrid phrase, in which content from both songs were combined, between the two song types when transitioning from one to the other, and/or (ii) singers spliced complete themes from the revolutionary song into the current song. Sequence analysis indicated that both processes were governed by structural similarity rules. Hybrid phrases or theme substitutions occurred at points in the songs where both songs contained “similar sounds arranged in a similar pattern.” Songs appear to be learned as segments (themes/phrase types), akin to birdsong and human language acquisition, and these can be combined in predictable ways if the underlying structural pattern is similar. These snapshots of song change provide insights into the mechanisms underlying song learning in humpback whales, and comparative perspectives on the evolution of human language and culture. PMID:28739940

Song hybridization events during revolutionary song change provide insights into cultural transmission in humpback whales.

PubMed

Garland, Ellen C; Rendell, Luke; Lamoni, Luca; Poole, M Michael; Noad, Michael J

2017-07-24

Cultural processes occur in a wide variety of animal taxa, from insects to cetaceans. The songs of humpback whales are one of the most striking examples of the transmission of a cultural trait and social learning in any nonhuman animal. To understand how songs are learned, we investigate rare cases of song hybridization, where parts of an existing song are spliced with a new one, likely before an individual totally adopts the new song. Song unit sequences were extracted from over 9,300 phrases recorded during two song revolutions across the South Pacific Ocean, allowing fine-scale analysis of composition and sequencing. In hybrid songs the current and new songs were spliced together in two specific ways: ( i ) singers placed a single hybrid phrase, in which content from both songs were combined, between the two song types when transitioning from one to the other, and/or ( ii ) singers spliced complete themes from the revolutionary song into the current song. Sequence analysis indicated that both processes were governed by structural similarity rules. Hybrid phrases or theme substitutions occurred at points in the songs where both songs contained "similar sounds arranged in a similar pattern." Songs appear to be learned as segments (themes/phrase types), akin to birdsong and human language acquisition, and these can be combined in predictable ways if the underlying structural pattern is similar. These snapshots of song change provide insights into the mechanisms underlying song learning in humpback whales, and comparative perspectives on the evolution of human language and culture.

Cloning of a cDNA encoding bovine mitochondrial NADP(+)-specific isocitrate dehydrogenase and structural comparison with its isoenzymes from different species.

PubMed Central

Huh, T L; Ryu, J H; Huh, J W; Sung, H C; Oh, I U; Song, B J; Veech, R L

1993-01-01

Mitochondrial NADP(+)-specific isocitrate dehydrogenase (IDP) was co-purified with the pyruvate dehydrogenase complex from bovine kidney mitochondria. The determination of its N-terminal 16-amino-acid sequence revealed that it is highly similar to the IDP from yeast. A cDNA clone (1.8 kb long) encoding this protein was isolated from a bovine kidney lambda gt11 cDNA library using a synthetic oligodeoxynucleotide. The deduced protein sequence of this cDNA clone rendered a precursor protein of 452 amino-acid residues (50,830 Da) and a mature protein of 413 amino-acid residues (46,519 Da). It is 100% identical to the internal tryptic peptide sequences of the autologous form from pig heart and 62% similar to that from yeast. However, it shares little similarity with the mitochondrial NAD(+)-specific isoenzyme from yeast. Structural analyses of the deduced proteins of IDP isoenzymes from different species indicated that similarity exists in certain regions, which may represent the common domains for the active sites or coenzyme-binding sites. In Northern-blot analysis, one species of mRNA (about 2.2 kb for both bovine and human) was hybridized with a 32P-labelled cDNA probe. Southern-blot analysis of genomic DNAs verified simple patterns of hybridization with this cDNA. These results strongly indicate that the mitochondrial IDP may be derived from a single gene family which does not appear to be closely related to that of the NAD(+)-specific isoenzyme. Images Figure 1 Figure 3 Figure 4 Figure 5 PMID:8318002

Structural evolution of the Nankai inner accretionary prism constrained by thermal structure and sedimentary age of deep borehole samples

NASA Astrophysics Data System (ADS)

Fukuchi, R.; Yamaguchi, A.; Ito, H.; Yamamoto, Y.; Ashi, J.

2017-12-01

The Nankai accretionary wedge has been developed by subduction of the Philippine Sea Plate beneath the Eurasian and Amur Plate, accompanying forearc basin development upon inner wedge. To evaluate the evolutionary processes of the Nankai inner accretionary wedge, we performed vitrinite reflectance analysis and detrital zircon U-Pb age dating using cuttings retrieved from the Integrated Ocean Drilling Program (IODP) Site C0002 located within the Kumano Basin and penetrates the inner accretionary wedge down to 3058.5 m below the seafloor (mbsf). Although Ro values of vitrinite reflectance tend to increase with depth, there are two reversals (1300-1500 mbsf and 2400-2600 mbsf) of Ro values. The youngest detrital zircon U-Pb age of the cuttings from 2600.5 mbsf is 7.41 Ma, which is obviously younger than shipboard nannofossil ages (9.56-10.54 Ma) at 2245.5 mbsf. Both Ro values and the youngest detrital zircon U-Pb ages show a reversal between 2400-2600 mbsf, suggesting the existence of a thrust fault with sufficient displacement to offset both paleothermal structure and sediment age. Despite similar depositonal age and paleogeothermal gradient, lithofacies in the hanging- and footwall of the 2400-2600 mbsf thrust fault are different; volcaniclastic sediments are rare in the footwall. The lack of volcaniclastic sediments corresponding to the Middle Shikoku Basin facies in the footwall of the thrust suggests that sediments below 2600 mbsf have similar sedimentation background to that of present off-Muroto input site sediments. Thus, our synthesized model of tectonic evolutionary process of deep portion of the Nankai inner accretionary wedge is as follows: 1) 4 Ma: hemipelagic sediments, which deposited similar environment of present off-Muroto input, have accreted ( 4 Ma corresponds to the age of unconformity between forearc basin and accretionary prism (Kinoshita et al., 2009)). 2) 2 Ma: The megasplay fault was activated (Strasser et al., 2009), and Site C0002 sediments moved into inner wedge. Moving direction of the Philippine Sea Plate became NNW to WNW (Kamata and Kodama, 1999). 3) present: inner accretionary wedge has been buried with formation of Kumano forearc basin. Sediments existed offshore of the 4 Ma source area of Site C0002 have moved to off-Muroto input with the motion of the Philippine Sea Plate.

The distribution of cigarette prices under different tax structures: findings from the International Tobacco Control Policy Evaluation (ITC) Project

PubMed Central

Shang, Ce; Chaloupka, Frank J; Zahra, Nahleen; Fong, Geoffrey T

2013-01-01

Background The distribution of cigarette prices has rarely been studied and compared under different tax structures. Descriptive evidence on price distributions by countries can shed light on opportunities for tax avoidance and brand switching under different tobacco tax structures, which could impact the effectiveness of increased taxation in reducing smoking. Objective This paper aims to describe the distribution of cigarette prices by countries and to compare these distributions based on the tobacco tax structure in these countries. Methods We employed data for 16 countries taken from the International Tobacco Control Policy Evaluation Project to construct survey-derived cigarette prices for each country. Self-reported prices were weighted by cigarette consumption and described using a comprehensive set of statistics. We then compared these statistics for cigarette prices under different tax structures. In particular, countries of similar income levels and countries that impose similar total excise taxes using different tax structures were paired and compared in mean and variance using a two-sample comparison test. Findings Our investigation illustrates that, compared with specific uniform taxation, other tax structures, such as ad valorem uniform taxation, mixed (a tax system using ad valorem and specific taxes) uniform taxation, and tiered tax structures of specific, ad valorem and mixed taxation tend to have price distributions with greater variability. Countries that rely heavily on ad valorem and tiered taxes also tend to have greater price variability around the median. Among mixed taxation systems, countries that rely more heavily on the ad valorem component tend to have greater price variability than countries that rely more heavily on the specific component. In countries with tiered tax systems, cigarette prices are skewed more towards lower prices than are prices under uniform tax systems. The analyses presented here demonstrate that more opportunities exist for tax avoidance and brand switching when the tax structure departs from a uniform specific tax. PMID:23792324

The distribution of cigarette prices under different tax structures: findings from the International Tobacco Control Policy Evaluation (ITC) Project.

PubMed

Shang, Ce; Chaloupka, Frank J; Zahra, Nahleen; Fong, Geoffrey T

2014-03-01

The distribution of cigarette prices has rarely been studied and compared under different tax structures. Descriptive evidence on price distributions by countries can shed light on opportunities for tax avoidance and brand switching under different tobacco tax structures, which could impact the effectiveness of increased taxation in reducing smoking. This paper aims to describe the distribution of cigarette prices by countries and to compare these distributions based on the tobacco tax structure in these countries. We employed data for 16 countries taken from the International Tobacco Control Policy Evaluation Project to construct survey-derived cigarette prices for each country. Self-reported prices were weighted by cigarette consumption and described using a comprehensive set of statistics. We then compared these statistics for cigarette prices under different tax structures. In particular, countries of similar income levels and countries that impose similar total excise taxes using different tax structures were paired and compared in mean and variance using a two-sample comparison test. Our investigation illustrates that, compared with specific uniform taxation, other tax structures, such as ad valorem uniform taxation, mixed (a tax system using ad valorem and specific taxes) uniform taxation, and tiered tax structures of specific, ad valorem and mixed taxation tend to have price distributions with greater variability. Countries that rely heavily on ad valorem and tiered taxes also tend to have greater price variability around the median. Among mixed taxation systems, countries that rely more heavily on the ad valorem component tend to have greater price variability than countries that rely more heavily on the specific component. In countries with tiered tax systems, cigarette prices are skewed more towards lower prices than are prices under uniform tax systems. The analyses presented here demonstrate that more opportunities exist for tax avoidance and brand switching when the tax structure departs from a uniform specific tax.

Self-similar solutions of stationary Navier-Stokes equations

NASA Astrophysics Data System (ADS)

Shi, Zuoshunhua

2018-02-01

In this paper, we mainly study the existence of self-similar solutions of stationary Navier-Stokes equations for dimension n = 3 , 4. For n = 3, if the external force is axisymmetric, scaling invariant, C 1 , α continuous away from the origin and small enough on the sphere S2, we shall prove that there exists a family of axisymmetric self-similar solutions which can be arbitrarily large in the class Cloc3 , α (R3 0). Moreover, for axisymmetric external forces without swirl, corresponding to this family, the momentum flux of the flow along the symmetry axis can take any real number. However, there are no regular (U ∈ Cloc3 , α (R3 0)) axisymmetric self-similar solutions provided that the external force is a large multiple of some scaling invariant axisymmetric F which cannot be driven by a potential. In the case of dimension 4, there always exists at least one self-similar solution to the stationary Navier-Stokes equations with any scaling invariant external force in L 4 / 3 , ∞ (R4).

Local ecological knowledge among Baka children: a case of “children's culture” ?

PubMed Central

Gallois, Sandrine; Duda, Romain; Reyes-García, Victoria

2016-01-01

Childhood is an extensive life period specific to the human species and a key stage for development. Considering the importance of childhood for cultural transmission, we test the existence of a 'children's culture', or child-specific knowledge and practices not necessarily shared with adults, among the Baka in Southeast Cameroon. Using structured questionnaires, we collected data among 69 children and 175 adults to assess the ability to name, identify, and conceptualize animals and wild edibles. We found that some of the ecological knowledge related to little mammals and birds reported by Baka children was not reported by adults. We also found similarities between children’s and adult’s knowledge, both regarding the content of knowledge and how knowledge is distributed. Thus, middle childhood children hold similar knowledge than adults, especially related to wild edibles. Moreover, as children age, they start shedding child-specific knowledge and holding more adult’s knowledge. Additionally and echoing the gendered knowledge distribution present in adulthood, since middle childhood there are differences in the knowledge hold by boys and girls. We discuss our results highlighting the existence of specific ecological knowledge held by Baka children, the overlap between children’s and adults’ knowledge, and the changes in children’s ecological knowledge as they move into adulthood. PMID:28386157

Towards Noise Tomography and Passive Monitoring Using Distributed Acoustic Sensing

NASA Astrophysics Data System (ADS)

Paitz, P.; Fichtner, A.

2017-12-01

Distributed Acoustic Sensing (DAS) has the potential to revolutionize the field of seismic data acquisition. Thanks to their cost-effectiveness, fiber-optic cables may have the capability of complementing conventional geophones and seismometers by filling a niche of applications utilizing large amounts of data. Therefore, DAS may serve as an additional tool to investigate the internal structure of the Earth and its changes over time; on scales ranging from hydrocarbon or geothermal reservoirs to the entire globe. An additional potential may be in the existence of large fibre networks deployed already for telecommunication purposes. These networks that already exist today could serve as distributed seismic antennas. We investigate theoretically how ambient noise tomography may be used with DAS data. For this we extend the theory of seismic interferometry to the measurement of strain. With numerical, 2D finite-difference examples we investigate the impact of source and receiver effects. We study the effect of heterogeneous source distributions and the cable orientation by assessing similarities and differences to the Green's function. We also compare the obtained interferometric waveforms from strain interferometry to displacement interferometric wave fields obtained with existing methods. Intermediate results show that the obtained interferometric waveforms can be connected to the Green's Functions and provide consistent information about the propagation medium. These simulations will be extended to reservoir scale subsurface structures. Future work will include the application of the theory to real-data examples. The presented research depicts the early stage of a combination of theoretical investigations, numerical simulations and real-world data applications. We will therefore evaluate the potentials and shortcomings of DAS in reservoir monitoring and seismology at the current state, with a long-term vision of global seismic tomography utilizing DAS data from existing fiber-optic cable networks.

Comparison and correlation of binding mode of ATP in the kinase domains of Hexokinase family

PubMed Central

Kumar, Yellapu Nanda; Kumar, Pasupuleti Santhosh; Sowjenya, Gopal; Rao, Valasani Koteswara; Yeswanth, Sthanikam; Prasad, Uppu Venkateswara; Pradeepkiran, Jangampalli Adi; Sarma, PVGK; Bhaskar, Matcha

2012-01-01

Hexokinases (HKs) are the enzymes that catalyses the ATP dependent phosphorylation of Hexose sugars to Hexose-6-Phosphate (Hex-6-P). There exist four different forms of HKs namely HK-I, HK-II, HK-III and HK-IV and all of them share a common ATP binding site core surrounded by more variable sequence that determine substrate affinities. Although they share a common binding site but they differ in their kinetic functions, hence the present study is aimed to analyze the binding mode of ATP. The analysis revealed that the four ATP binding domains are showing 13 identical, 7 similar and 6 dissimilar residues with similar structural conformation. Molecular docking of ATP into the kinase domains using Molecular Operating Environment (MOE) soft ware tool clearly showed the variation in the binding mode of ATP with variable docking scores. This probably explains the variable phosphorylation rates among hexokinases family. PMID:22829728

Beyond dark and bright: towards a more holistic understanding of inter-group networks.

PubMed

Hejnova, Petra

2010-01-01

Networks are becoming a popular organizational form for structuring human activities. To date, scholars have addressed networks in a variety of fields, including sociology, economics, public administration, criminology, political science, and international security. However, little has been done so far to systematically examine the similarities, differences, and connections between network forms of organization across different academic disciplines. This has important implications for both theory and practice. The lack of attention paid to organizational similarities and differences prevents the exchange of knowledge developed across fields. In turn, policy-makers cannot take full advantage of existing research, and may miss opportunities to improve the work of some networks and combat that of others. To address this gap in the literature, this paper uses the combination of organizational environments and organizational goals to develop a new typology of inter-group networks, and thus improve our understanding of how human behaviour is coordinated through networks.

Kinase Identification with Supervised Laplacian Regularized Least Squares

PubMed Central

Zhang, He; Wang, Minghui

2015-01-01

Phosphorylation is catalyzed by protein kinases and is irreplaceable in regulating biological processes. Identification of phosphorylation sites with their corresponding kinases contributes to the understanding of molecular mechanisms. Mass spectrometry analysis of phosphor-proteomes generates a large number of phosphorylated sites. However, experimental methods are costly and time-consuming, and most phosphorylation sites determined by experimental methods lack kinase information. Therefore, computational methods are urgently needed to address the kinase identification problem. To this end, we propose a new kernel-based machine learning method called Supervised Laplacian Regularized Least Squares (SLapRLS), which adopts a new method to construct kernels based on the similarity matrix and minimizes both structure risk and overall inconsistency between labels and similarities. The results predicted using both Phospho.ELM and an additional independent test dataset indicate that SLapRLS can more effectively identify kinases compared to other existing algorithms. PMID:26448296

Examining the Distribution, Modularity, and Community Structure in Article Networks for Systematic Reviews.

PubMed

Ji, Xiaonan; Machiraju, Raghu; Ritter, Alan; Yen, Po-Yin

2015-01-01

Systematic reviews (SRs) provide high quality evidence for clinical practice, but the article screening process is time and labor intensive. As SRs aim to identify relevant articles with a specific scope, we propose that a pre-defined article relationship, using similarity metrics, could accelerate this process. In this study, we established the article relationship using MEDLINE element similarities and visualized the article network with the Force Atlas layout. We also analyzed the article networks with graph diameter, closeness centrality, and module classes. The results revealed the distribution of articles and found that included articles tended to aggregate together in some module classes, providing further evidence of the existence of strong relationships among included articles. This approach can be utilized to facilitate the articles selection process through early identification of these dominant module classes. We are optimistic that the use of article network visualization can help better SR work prioritization.