Platyhelminth Venom Allergen-Like (VAL) proteins: revealing structural diversity, class-specific features and biological associations across the phylum

Science.gov (United States)

CHALMERS, IAIN W.; HOFFMANN, KARL F.

2012-01-01

SUMMARY During platyhelminth infection, a cocktail of proteins is released by the parasite to aid invasion, initiate feeding, facilitate adaptation and mediate modulation of the host immune response. Included amongst these proteins is the Venom Allergen-Like (VAL) family, part of the larger sperm coating protein/Tpx-1/Ag5/PR-1/Sc7 (SCP/TAPS) superfamily. To explore the significance of this protein family during Platyhelminthes development and host interactions, we systematically summarize all published proteomic, genomic and immunological investigations of the VAL protein family to date. By conducting new genomic and transcriptomic interrogations to identify over 200 VAL proteins (228) from species in all 4 traditional taxonomic classes (Trematoda, Cestoda, Monogenea and Turbellaria), we further expand our knowledge related to platyhelminth VAL diversity across the phylum. Subsequent phylogenetic and tertiary structural analyses reveal several class-specific VAL features, which likely indicate a range of roles mediated by this protein family. Our comprehensive analysis of platyhelminth VALs represents a unifying synopsis for understanding diversity within this protein family and a firm context in which to initiate future functional characterization of these enigmatic members. PMID:22717097

Structural features that predict real-value fluctuations of globular proteins.

Science.gov (United States)

Jamroz, Michal; Kolinski, Andrzej; Kihara, Daisuke

2012-05-01

It is crucial to consider dynamics for understanding the biological function of proteins. We used a large number of molecular dynamics (MD) trajectories of nonhomologous proteins as references and examined static structural features of proteins that are most relevant to fluctuations. We examined correlation of individual structural features with fluctuations and further investigated effective combinations of features for predicting the real value of residue fluctuations using the support vector regression (SVR). It was found that some structural features have higher correlation than crystallographic B-factors with fluctuations observed in MD trajectories. Moreover, SVR that uses combinations of static structural features showed accurate prediction of fluctuations with an average Pearson's correlation coefficient of 0.669 and a root mean square error of 1.04 Å. This correlation coefficient is higher than the one observed in predictions by the Gaussian network model (GNM). An advantage of the developed method over the GNMs is that the former predicts the real value of fluctuation. The results help improve our understanding of relationships between protein structure and fluctuation. Furthermore, the developed method provides a convienient practial way to predict fluctuations of proteins using easily computed static structural features of proteins. Copyright © 2012 Wiley Periodicals, Inc.

VVER-specific features regarding core degradation - Status Report

International Nuclear Information System (INIS)

Hozer, Z.; Trambauer, K.; Duspiva, J.

1999-01-01

The objective of this report is to compare VVER reactors to pressurised water reactors (PWRs) of Western design from the point of view of core degradation phenomena using the terminology which was applied to the systematisation of severe accident phenomena in earlier CSNI reports. In the following the acronym 'PWR' is used for a PWR of Western design. The basic design features are described and the most important parameters are summarised in order to identify the differences between the two reactor types. In some specific cases the comparison shows more similarities with boiling water reactors (BWRs) than with PWRs. The known VVER experimental support is also summarised. RBMKs are not included in this report, as this reactor type is not operated in OECD countries, furthermore its design is completely different from those of VVERs and PWRs. The scope of this report is limited to in-vessel severe fuel damage phenomena. Neither thermal hydraulic processes involving no core degradation, nor containment phenomena, are discussed in detail. The VVER (water-cooled water-moderated power reactor) is a pressurised light water reactor of Soviet design. It operates on the same principles as a Western PWR reactor and uses similar technological systems. The primary coolant is pressurised water, which heats up in the reactor core and steam is produced on the secondary side of steam generators. The comparison of basic geometrical and technological parameters pointed out some differences between a PWR and a VVER, but it should be noted that differences exist even between two Western PWRs of different design. The VVER reactors are special types of PWRs, the most important design features of which are the horizontal steam generators and the hexagonal core structure. Similarity between PWR and VVER reactors was found in the comparison of dominant accidents sequences leading to core melt. The accident progression sequence consists of the same steps for VVERs and PWRs. The larger water

FeatureMap3D - a tool to map protein features and sequence conservation onto homologous structures in the PDB

DEFF Research Database (Denmark)

Wernersson, Rasmus; Rapacki, Krzysztof; Stærfeldt, Hans Henrik

2006-01-01

FeatureMap3D is a web-based tool that maps protein features onto 3D structures. The user provides sequences annotated with any feature of interest, such as post-translational modifications, protease cleavage sites or exonic structure and FeatureMap3D will then search the Protein Data Bank (PDB) f...

Specific features of a single-pulse sliding discharge in neon near the threshold for spark breakdown

Science.gov (United States)

Trusov, K. K.

2017-08-01

Experimental data on the spatial structure of a single-pulse sliding discharge in neon at voltages below, equal to, and above the threshold for spark breakdown are discussed. The experiments were carried at gas pressures of 30 and 100 kPa and different polarities of the discharge voltage. Photographs of the plasma structure in two discharge chambers with different dimensions of the discharge zone and different thicknesses of an alumina dielectric plate on the surface of which the discharge develops are inspected. Common features of the prebreakdown discharge and its specific features depending on the voltage polarity and gas pressure are analyzed. It is shown that, at voltages below the threshold for spark breakdown, a low-current glow discharge with cathode and anode spots develops in the electrode gap. Above the breakdown threshold, regardless of the voltage polarity, spark channels directed from the cathode to the anode develop against the background of a low-current discharge.

Analysis of Specific Features of the Ukrainian Market of Natural Gas Production and Consumption

Directory of Open Access Journals (Sweden)

Lelyuk Oleksiy V.

2013-11-01

Full Text Available The article provides results of the study of specific features of the Ukrainian market of natural gas production and consumption. It analyses dynamics of the specific weight of Ukraine in general volumes of natural gas consumption in the world, dynamics of natural gas consumption in Ukraine during 1990 – 2012 and dependence of natural gas consumption on GDP volumes by the purchasing power parity. It studies the structure of natural gas consumption by regions in 2012 and sectors of economy, resource base of natural gas in Ukraine and also dynamics of established resources of natural gas in Ukraine and dynamics of natural gas production. It analyses base rates of growth of natural gas resources and production in Ukraine. It considers dynamics of import of natural gas into Ukraine and its import prices and also the structure of natural gas import. It identifies the balance of the natural gas market in Ukraine. On the basis of the conducted analysis the article proves that Ukraine is a gas-deficit country of the world, which depends on natural gas import supplies.

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

Science.gov (United States)

Jee, Benjamin D; Wiley, Jennifer

2014-01-01

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

Crystal Structure of a UDP-glucose-specific Glycosyltransferase from a Mycobacterium Species

Energy Technology Data Exchange (ETDEWEB)

Fulton, Zara; McAlister, Adrian; Wilce, Matthew C.J.; Brammananth, Rajini; Zaker-Tabrizi, Leyla; Perugini, Matthew A.; Bottomley, Stephen P.; Coppel, Ross L.; Crellin, Paul K.; Rossjohn, Jamie; Beddoe, Travis (Monash); (Melbourne)

2008-10-24

Glycosyltransferases (GTs) are a large and ubiquitous family of enzymes that specifically transfer sugar moieties to a range of substrates. Mycobacterium tuberculosis contains a large number of GTs, many of which are implicated in cell wall synthesis, yet the majority of these GTs remain poorly characterized. Here, we report the high resolution crystal structures of an essential GT (MAP2569c) from Mycobacterium avium subsp. paratuberculosis (a close homologue of Rv1208 from M. tuberculosis) in its apo- and ligand-bound forms. The structure adopted the GT-A fold and possessed the characteristic DXD motif that coordinated an Mn{sup 2+} ion. Atypical of most GTs characterized to date, MAP2569c exhibited specificity toward the donor substrate, UDP-glucose. The structure of this ligated complex revealed an induced fit binding mechanism and provided a basis for this unique specificity. Collectively, the structural features suggested that MAP2569c may adopt a 'retaining' enzymatic mechanism, which has implications for the classification of other GTs in this large superfamily.

Subsurface structures of buried features in the lunar Procellarum region

Science.gov (United States)

Wang, Wenrui; Heki, Kosuke

2017-07-01

The Gravity Recovery and Interior Laboratory (GRAIL) mission unraveled numbers of features showing strong gravity anomalies without prominent topographic signatures in the lunar Procellarum region. These features, located in different geologic units, are considered to have complex subsurface structures reflecting different evolution processes. By using the GRAIL level-1 data, we estimated the free-air and Bouguer gravity anomalies in several selected regions including such intriguing features. With the three-dimensional inversion technique, we recovered subsurface density structures in these regions.

Enteroclysis in adult celiac disease: diagnostic value of specific radiographic features

International Nuclear Information System (INIS)

Lomoschitz, F.; Schima, W.; Schober, E.; Turetschek, K.; Kaider, A.; Vogelsang, H.

2003-01-01

The purpose of this study was to compare the diagnostic accuracy of various radiographic findings at enteroclysis in adult patients with untreated celiac disease. Twenty-seven adult patients underwent enteroclysis because of unspecific intestinal symptoms before definitive biopsy proof of celiac disease. Enteroclysis of 123 subjects with similar clinical presentation, including abdominal pain, diarrhea, occult intestinal bleeding, and weight loss, who had a definitive diagnosis other than celiac disease, served as controls. The radiographic features previously described in the literature as indicative of adult celiac disease (i.e., fold thickening, decrease of jejunal folds, increase of ileal folds, small bowel dilatation, flocculation) were evaluated in blinded fashion in all studies and the subjective likelihood of diagnosis of celiac disease was assessed. Assessing every finding separately, each feature proved to have a high specificity (78-100%) but low sensitivity (19-59%) for celiac disease. Reversal of jejunoileal fold pattern was the single best feature (specificity 100%, 95% CI 97-100%; sensitivity 59%, 95% CI 40-78%); however, combination of criteria enables establishment of the diagnosis of celiac disease quite accurately (specificity 100%, 95% CI 98-100%; sensitivity 78%, 95% CI 58-91%). Reversal of jejunoileal fold pattern as a single finding as well as combination at least three of the following features, i.e., fold thickening, decrease of jejunal folds (''colonization''), increase of ileal folds (''jejunization''), dilatation, and flocculation, make enteroclysis an accurate tool for diagnosis of celiac disease in adult patients with suspected intestinal disease. (orig.)

SPECIFIC FEATURES OF DEVELOPMENT OF ORGANIC PRODUCTS MARKET IN UKRAINE

Directory of Open Access Journals (Sweden)

T. Kharchenko

2013-08-01

Full Text Available The article is dedicated to the development of new and improvement of existing theoretical and methodological basis of forming and developing the market of organic products, its correspondence to the present-day situation, determination of problems and ways of their solving, introduction in practical activity of Ukrainian enterprises. The main objective of the article is to determine the specific features of forming and developing organic products market in Ukraine, and the perspective directions of its development based on analysis and practice of functioning of such markets in the world. The environmentally sound products market in the world is being analyzed, some information on the countries with the most commodity turnover of organic products, structure of international market of organic products, volumes of sales of organic products in the European countries is provided. As a result of studying the modern trends of economic development the authors reach a conclusion on problems of standard introduction, investigate the European norms and requirements for organic products. The conducted research allows distinguishing the basic features of Ukrainian market of organic products: it quickly grows, which makes it especially appealing for the participants of market relations, however entry into this market requires considerable capital investments and is characterized by high risk; criteria for qualifying products as environmentally sound products are unstructured and unclear. The potential for growth of organic products market in Ukraine is examined.

Application of Specific Features of Industrial Products when Forming and Developing Brands of Industrial Enterprises

Directory of Open Access Journals (Sweden)

Yatsentiuk Stanislav V.

2014-03-01

Full Text Available The article analyses and structures approaches and principles of formulation of industrial products. It offers classification of goods and markets of industrial products by their characteristics and participants. It identifies main participants that make decisions at B2C and B2B markets and characterises their specific features and motivation when making decisions on purchase of products of industrial enterprises. It studies and analyses indicators of development of domestic markets of consumer goods and market of industrial products and dynamics of development of their relation in retrospective view.

Structural and phylogenetic analysis of Rhodobacter capsulatus NifF: uncovering general features of nitrogen-fixation (nif)-flavodoxins.

Science.gov (United States)

Pérez-Dorado, Inmaculada; Bortolotti, Ana; Cortez, Néstor; Hermoso, Juan A

2013-01-09

Analysis of the crystal structure of NifF from Rhodobacter capsulatus and its homologues reported so far reflects the existence of unique structural features in nif flavodoxins: a leucine at the re face of the isoalloxazine, an eight-residue insertion at the C-terminus of the 50's loop and a remarkable difference in the electrostatic potential surface with respect to non-nif flavodoxins. A phylogenetic study on 64 sequences from 52 bacterial species revealed four clusters, including different functional prototypes, correlating the previously defined as "short-chain" with the firmicutes flavodoxins and the "long-chain" with gram-negative species. The comparison of Rhodobacter NifF structure with other bacterial flavodoxin prototypes discloses the concurrence of specific features of these functional electron donors to nitrogenase.

Specific features of auxiliary water supply at underground NPPs

International Nuclear Information System (INIS)

Pergamenshchik, B.K.; Pavlov, A.S.

1991-01-01

Specific features of auxiliary water supply systems for underground NPPs related to peculiarities of NPP basis equipment arrangement, are considered. Circulation water supply scheme, in which water cooling storage basin (cooling towers) with operational area corresponding to NPP power is on the surface and has traditional design, is proposed. Sufficiently high efficiency of the arrangement proposed is proved

Automatic selective feature retention in patient specific elastic surface registration

CSIR Research Space (South Africa)

Jansen van Rensburg, GJ

2011-01-01

Full Text Available The accuracy with which a recent elastic surface registration algorithm deforms the complex geometry of a skull is examined. This algorithm is then coupled to a line based algorithm as is frequently used in patient specific feature registration...

Crystal Structure of Human Dual-Specificity Tyrosine-Regulated Kinase 3 Reveals New Structural Features and Insights into its Auto-phosphorylation.

Science.gov (United States)

Kim, Kuglae; Cha, Jeong Seok; Cho, Yong-Soon; Kim, Hoyoung; Chang, Nienping; Kim, Hye-Jung; Cho, Hyun-Soo

2018-04-07

Dual-specificity tyrosine-regulated kinases (DYRKs) auto-phosphorylate a critical tyrosine residue in their activation loop and phosphorylate their substrate on serine and threonine residues. The auto-phosphorylation occurs intramolecularly and is a one-off event. DYRK3 is selectively expressed at a high level in hematopoietic cells and attenuates erythroblast development, leading to anemia. In the present study, we determined the crystal structure of the mature form of human DYRK3 in complex with harmine, an ATP competitive inhibitor. The crystal structure revealed a phosphorylation site, residue S350, whose phosphorylation increases the stability of DYRK3 and enhances its kinase activity. In addition, our structural and biochemical assays suggest that the N-terminal auto-phosphorylation accessory domain stabilizes the DYRK3 protein, followed by auto-phosphorylation of the tyrosine of the activation loop, which is important for kinase activity. Finally, our docking analysis provides information for the design of novel and potent therapeutics to treat anemia. Copyright © 2018 Elsevier Ltd. All rights reserved.

Enteroclysis in adult celiac disease: diagnostic value of specific radiographic features

Energy Technology Data Exchange (ETDEWEB)

Lomoschitz, F.; Schima, W.; Schober, E.; Turetschek, K. [Department of Radiology and Ludwig Boltzmann Institute for Clinical and Experimental Radiologic Research, University of Vienna, Waehringer Guertel 18-20, 1090 Vienna (Austria); Kaider, A. [Department of Medical Computer Sciences, University of Vienna, Waehringer Guertel 18-20, 1090 Vienna (Austria); Vogelsang, H. [Department of Internal Medicine IV, Division of Gastroenterology, University of Vienna, Waehringer Guertel 18-20, 1090 Vienna (Austria)

2003-04-01

The purpose of this study was to compare the diagnostic accuracy of various radiographic findings at enteroclysis in adult patients with untreated celiac disease. Twenty-seven adult patients underwent enteroclysis because of unspecific intestinal symptoms before definitive biopsy proof of celiac disease. Enteroclysis of 123 subjects with similar clinical presentation, including abdominal pain, diarrhea, occult intestinal bleeding, and weight loss, who had a definitive diagnosis other than celiac disease, served as controls. The radiographic features previously described in the literature as indicative of adult celiac disease (i.e., fold thickening, decrease of jejunal folds, increase of ileal folds, small bowel dilatation, flocculation) were evaluated in blinded fashion in all studies and the subjective likelihood of diagnosis of celiac disease was assessed. Assessing every finding separately, each feature proved to have a high specificity (78-100%) but low sensitivity (19-59%) for celiac disease. Reversal of jejunoileal fold pattern was the single best feature (specificity 100%, 95% CI 97-100%; sensitivity 59%, 95% CI 40-78%); however, combination of criteria enables establishment of the diagnosis of celiac disease quite accurately (specificity 100%, 95% CI 98-100%; sensitivity 78%, 95% CI 58-91%). Reversal of jejunoileal fold pattern as a single finding as well as combination at least three of the following features, i.e., fold thickening, decrease of jejunal folds (''colonization''), increase of ileal folds (''jejunization''), dilatation, and flocculation, make enteroclysis an accurate tool for diagnosis of celiac disease in adult patients with suspected intestinal disease. (orig.)

Structural and Phylogenetic Analysis of Rhodobacter capsulatus NifF: Uncovering General Features of Nitrogen-fixation (nif-Flavodoxins

Directory of Open Access Journals (Sweden)

Inmaculada Pérez-Dorado

2013-01-01

Full Text Available Analysis of the crystal structure of NifF from Rhodobacter capsulatus and its homologues reported so far reflects the existence of unique structural features in nif flavodoxins: a leucine at the re face of the isoalloxazine, an eight-residue insertion at the C-terminus of the 50’s loop and a remarkable difference in the electrostatic potential surface with respect to non-nif flavodoxins. A phylogenetic study on 64 sequences from 52 bacterial species revealed four clusters, including different functional prototypes, correlating the previously defined as “short-chain” with the firmicutes flavodoxins and the “long-chain” with gram-negative species. The comparison of Rhodobacter NifF structure with other bacterial flavodoxin prototypes discloses the concurrence of specific features of these functional electron donors to nitrogenase.

Feature-Specific Event-Related Potential Effects to Action- and Sound-Related Verbs during Visual Word Recognition.

Science.gov (United States)

Popp, Margot; Trumpp, Natalie M; Kiefer, Markus

2016-01-01

Grounded cognition theories suggest that conceptual representations essentially depend on modality-specific sensory and motor systems. Feature-specific brain activation across different feature types such as action or audition has been intensively investigated in nouns, while feature-specific conceptual category differences in verbs mainly focused on body part specific effects. The present work aimed at assessing whether feature-specific event-related potential (ERP) differences between action and sound concepts, as previously observed in nouns, can also be found within the word class of verbs. In Experiment 1, participants were visually presented with carefully matched sound and action verbs within a lexical decision task, which provides implicit access to word meaning and minimizes strategic access to semantic word features. Experiment 2 tested whether pre-activating the verb concept in a context phase, in which the verb is presented with a related context noun, modulates subsequent feature-specific action vs. sound verb processing within the lexical decision task. In Experiment 1, ERP analyses revealed a differential ERP polarity pattern for action and sound verbs at parietal and central electrodes similar to previous results in nouns. Pre-activation of the meaning of verbs in the preceding context phase in Experiment 2 resulted in a polarity-reversal of feature-specific ERP effects in the lexical decision task compared with Experiment 1. This parallels analogous earlier findings for primed action and sound related nouns. In line with grounded cognitions theories, our ERP study provides evidence for a differential processing of action and sound verbs similar to earlier observation for concrete nouns. Although the localizational value of ERPs must be viewed with caution, our results indicate that the meaning of verbs is linked to different neural circuits depending on conceptual feature relevance.

Ethnocultural features of a linguistic persona: the specifics of the ...

African Journals Online (AJOL)

Ethnocultural features of a linguistic persona: the specifics of the representation of universal emotional concepts. ... The paper pays special attention to the ethnocultural content of emotional and lexical units, which indicate the ethnic identity of a linguistic persona and reflect typical, historically developed signs of the ethnic ...

Specific features of physical development in extremely premature infants

Directory of Open Access Journals (Sweden)

G. A. Alyamovskaya

2015-01-01

Full Text Available The literature review deals with the specilic features of physical development in extremely premature infants weighing less than 1500 g at birth. It describes the regularities of an increment in basic physical development parameters (weight, height, and head circumference within the first year of life. Genetic factors, the specific features of a neonatal period, comorbidity, and different feeding types are shown to affect the increment rates of the physical development parameters. Emphasis is placed on the early initiation of enteral feeding and on the long-term use of fortified foods in low birthweight premature babies for the correction of energy deficiency resulting from preterm birth. The review shows that there is a relationship of the long-term outcomes of physical and psychomotor developments in low birthweight premature babies.

Degree of contribution (DoC) feature selection algorithm for structural brain MRI volumetric features in depression detection.

Science.gov (United States)

Kipli, Kuryati; Kouzani, Abbas Z

2015-07-01

Accurate detection of depression at an individual level using structural magnetic resonance imaging (sMRI) remains a challenge. Brain volumetric changes at a structural level appear to have importance in depression biomarkers studies. An automated algorithm is developed to select brain sMRI volumetric features for the detection of depression. A feature selection (FS) algorithm called degree of contribution (DoC) is developed for selection of sMRI volumetric features. This algorithm uses an ensemble approach to determine the degree of contribution in detection of major depressive disorder. The DoC is the score of feature importance used for feature ranking. The algorithm involves four stages: feature ranking, subset generation, subset evaluation, and DoC analysis. The performance of DoC is evaluated on the Duke University Multi-site Imaging Research in the Analysis of Depression sMRI dataset. The dataset consists of 115 brain sMRI scans of 88 healthy controls and 27 depressed subjects. Forty-four sMRI volumetric features are used in the evaluation. The DoC score of forty-four features was determined as the accuracy threshold (Acc_Thresh) was varied. The DoC performance was compared with that of four existing FS algorithms. At all defined Acc_Threshs, DoC outperformed the four examined FS algorithms for the average classification score and the maximum classification score. DoC has a good ability to generate reduced-size subsets of important features that could yield high classification accuracy. Based on the DoC score, the most discriminant volumetric features are those from the left-brain region.

Linguistic Features and Schematic Textual Structure in Look-Good Advertisements in the Indian Print Media in English

Science.gov (United States)

Singh, Sukhdev; Bedi, Navkiran Kaur

2013-01-01

Every text has a communicative purpose that it performs by dividing itself into generic stages. These stages are assigned specific goals and have differing linguistic structures. This paper makes an attempt to investigate whether there is a definable co-relation between linguistic features and stages in the genre of look-good advertisements. It…

STRUCTURAL FEATURES OF PLANT CHITINASES AND CHITIN-BINDING PROTEINS

NARCIS (Netherlands)

BEINTEMA, JJ

1994-01-01

Structural features of plant chitinases and chitin-binding proteins are discussed. Many of these proteins consist of multiple domains,of which the chitin-binding hevein domain is a predominant one. X-ray and NMR structures of representatives of the major classes of these proteins are available now,

Coordination Analysis Using Global Structural Constraints and Alignment-based Local Features

Science.gov (United States)

Hara, Kazuo; Shimbo, Masashi; Matsumoto, Yuji

We propose a hybrid approach to coordinate structure analysis that combines a simple grammar to ensure consistent global structure of coordinations in a sentence, and features based on sequence alignment to capture local symmetry of conjuncts. The weight of the alignment-based features, which in turn determines the score of coordinate structures, is optimized by perceptron training on a given corpus. A bottom-up chart parsing algorithm efficiently finds the best scoring structure, taking both nested or non-overlapping flat coordinations into account. We demonstrate that our approach outperforms existing parsers in coordination scope detection on the Genia corpus.

Features and Recursive Structure

Directory of Open Access Journals (Sweden)

Kuniya Nasukawa

2015-01-01

Full Text Available Based on the cross-linguistic tendency that weak vowels are realized with a central quality such as ə, ɨ, or ɯ, this paper attempts to account for this choice by proposing that the nucleus itself is one of the three monovalent vowel elements |A|, |I| and |U| which function as the building blocks of melodic structure. I claim that individual languages make a parametric choice to determine which of the three elements functions as the head of a nuclear expression. In addition, I show that elements can be freely concatenated to create melodic compounds. The resulting phonetic value of an element compound is determined by the specific elements it contains and by the head-dependency relations between those elements. This concatenation-based recursive mechanism of melodic structure can also be extended to levels above the segment, thus ultimately eliminating the need for syllabic constituents. This approach reinterprets the notion of minimalism in phonology by opposing the string-based flat structure.

Understanding Protein-Protein Interactions Using Local Structural Features

DEFF Research Database (Denmark)

Planas-Iglesias, Joan; Bonet, Jaume; García-García, Javier

2013-01-01

Protein-protein interactions (PPIs) play a relevant role among the different functions of a cell. Identifying the PPI network of a given organism (interactome) is useful to shed light on the key molecular mechanisms within a biological system. In this work, we show the role of structural features...... interacting and non-interacting protein pairs to classify the structural features that sustain the binding (or non-binding) behavior. Our study indicates that not only the interacting region but also the rest of the protein surface are important for the interaction fate. The interpretation...... to score the likelihood of the interaction between two proteins and to develop a method for the prediction of PPIs. We have tested our method on several sets with unbalanced ratios of interactions and non-interactions to simulate real conditions, obtaining accuracies higher than 25% in the most unfavorable...

General And Specific Features In Realizing An Essay In English Language – A Case Study Of Essay On Economic Themes

Directory of Open Access Journals (Sweden)

Daliana Ecaterina TASCOVICI

2016-04-01

Full Text Available The present paper wants to be a systematic and not only a theoretical approach on essays. This type of writing knows several points of view connecting its form, content, specific features and types, rules to be observed in its writing, structures or styles. As we know, it implies freedom of composition, originality, associations of surprising images and propensity for aphorism. We try to frame all its specifications within the economic essay, as economics is a field of exact utterance, where the speaker cannot play with the words and their meaning.

The future of primordial features with large-scale structure surveys

International Nuclear Information System (INIS)

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

2016-01-01

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

The future of primordial features with large-scale structure surveys

Energy Technology Data Exchange (ETDEWEB)

Chen, Xingang; Namjoo, Mohammad Hossein [Institute for Theory and Computation, Harvard-Smithsonian Center for Astrophysics, 60 Garden Street, Cambridge, MA 02138 (United States); Dvorkin, Cora [Department of Physics, Harvard University, Cambridge, MA 02138 (United States); Huang, Zhiqi [School of Physics and Astronomy, Sun Yat-Sen University, 135 Xingang Xi Road, Guangzhou, 510275 (China); Verde, Licia, E-mail: xingang.chen@cfa.harvard.edu, E-mail: dvorkin@physics.harvard.edu, E-mail: huangzhq25@sysu.edu.cn, E-mail: mohammad.namjoo@cfa.harvard.edu, E-mail: liciaverde@icc.ub.edu [ICREA and ICC-UB, University of Barcelona (IEEC-UB), Marti i Franques, 1, Barcelona 08028 (Spain)

2016-11-01

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

Metallacyclopentadienes: structural features and coordination in transition metal complexes

International Nuclear Information System (INIS)

Dolgushin, Fedor M; Yanovsky, Aleksandr I; Antipin, Mikhail Yu

2004-01-01

Results of structural studies of polynuclear transition metal complexes containing the metallacyclopentadiene fragment are overviewed. The structural features of the complexes in relation to the nature of the substituents in the organic moiety of the metallacycles, the nature of the transition metals and their ligand environment are analysed. The main structural characteristics corresponding to different modes of coordination of metallacyclopentadienes to one or two additional metal centres are revealed.

Sequence- and structure-dependent DNA base dynamics: Synthesis, structure, and dynamics of site and sequence specifically spin-labeled DNA

International Nuclear Information System (INIS)

Spaltenstein, A.; Robinson, B.H.; Hopkins, P.B.

1989-01-01

A nitroxide spin-labeled analogue of thymidine (1a), in which the methyl group is replaced by an acetylene-tethered nitroxide, was evaluated as a probe for structural and dynamics studies of sequence specifically spin-labeled DNA. Residue 1a was incorporated into synthetic deoxyoligonucleotides by using automated phosphite triester methods. 1 H NMR, CD, and thermal denaturation studies indicate that 1a (T) does not significantly alter the structure of 5'-d(CGCGAATT*CGCG) from that of the native dodecamer. EPR studies on monomer, single-stranded, and duplexed DNA show that 1a readily distinguishes environments of different rigidity. Comparison of the general line-shape features of the observed EPR spectra of several small duplexes (12-mer, 24-mer) with simulated EPR spectra assuming isotropic motion suggests that probe 1a monitors global tumbling of small duplexes. Increasing the length of the DNA oligomers results in significant deviation from isotropic motion, with line-shape features similar to those of calculated spectra of objects with isotropic rotational correlation times of 20-100 ns. EPR spectra of a spin-labeled GT mismatch and a T bulge in long DNAs are distinct from those of spin-labeled Watson-Crick paired DNAs, further demonstrating the value of EPR as a tool in the evaluation of local dynamic and structural features in macromolecules

Common Features in Electronic Structure of the Oxypnictide Superconductors from Photoemission Spectroscopy

International Nuclear Information System (INIS)

Xiao-Wen, Jia; Hai-Yun, Liu; Wen-Tao, Zhang; Lin, Zhao; Jian-Qiao, Meng; Guo-Dong, Liu; Xiao-Li, Dong; Zhi-An, Ren; Wei, Yi; Guang-Can, Che; Zhong-Xian, Zhao; Gang, Wu; Rong-Hua, Liu; Xian-Hui, Chen; Gen-Fu, Chen; Nan-Lin, Wang; Yong, Zhu; Xiao-Yang, Wang; Gui-Ling, Wang; Yong, Zhou

2008-01-01

High resolution photoemission measurements are carried out on non-superconducting LaFeAsO parent compound and various superconducting RFeAs(O 1-x F x ) (R=La, Ce and Pr) compounds. It is found that the parent LaFeAsO compound shows a metallic character. By extensive measurements, several common features are identified in the electronic structure of these Fe-based compounds: (1) 0.2 eV feature in the valence band, (2) a universal 13-16 meV feature, (3) near Ef spectral weight suppression with decreasing temperature. These universal features can provide important information about band structure, superconducting gap and pseudogap in these Fe-based materials

Structural Feature Ions for Distinguishing N- and O-Linked Glycan Isomers by LC-ESI-IT MS/MS

Science.gov (United States)

Everest-Dass, Arun V.; Abrahams, Jodie L.; Kolarich, Daniel; Packer, Nicolle H.; Campbell, Matthew P.

2013-06-01

Glycomics is the comprehensive study of glycan expression in an organism, cell, or tissue that relies on effective analytical technologies to understand glycan structure-function relationships. Owing to the macro- and micro-heterogeneity of oligosaccharides, detailed structure characterization has required an orthogonal approach, such as a combination of specific exoglycosidase digestions, LC-MS/MS, and the development of bioinformatic resources to comprehensively profile a complex biological sample. Liquid chromatography-electrospray ionization-mass spectrometry (LC-ESI-MS/MS) has emerged as a key tool in the structural analysis of oligosaccharides because of its high sensitivity, resolution, and robustness. Here, we present a strategy that uses LC-ESI-MS/MS to characterize over 200 N- and O-glycans from human saliva glycoproteins, complemented by sequential exoglycosidase treatment, to further verify the annotated glycan structures. Fragment-specific substructure diagnostic ions were collated from an extensive screen of the literature available on the detailed structural characterization of oligosaccharides and, together with other specific glycan structure feature ions derived from cross-ring and glycosidic-linkage fragmentation, were used to characterize the glycans and differentiate isomers. The availability of such annotated mass spectrometric fragmentation spectral libraries of glycan structures, together with such substructure diagnostic ions, will be key inputs for the future development of the automated elucidation of oligosaccharide structures from MS/MS data.

Structural and sequence features of two residue turns in beta-hairpins.

Science.gov (United States)

Madan, Bharat; Seo, Sung Yong; Lee, Sun-Gu

2014-09-01

Beta-turns in beta-hairpins have been implicated as important sites in protein folding. In particular, two residue β-turns, the most abundant connecting elements in beta-hairpins, have been a major target for engineering protein stability and folding. In this study, we attempted to investigate and update the structural and sequence properties of two residue turns in beta-hairpins with a large data set. For this, 3977 beta-turns were extracted from 2394 nonhomologous protein chains and analyzed. First, the distribution, dihedral angles and twists of two residue turn types were determined, and compared with previous data. The trend of turn type occurrence and most structural features of the turn types were similar to previous results, but for the first time Type II turns in beta-hairpins were identified. Second, sequence motifs for the turn types were devised based on amino acid positional potentials of two-residue turns, and their distributions were examined. From this study, we could identify code-like sequence motifs for the two residue beta-turn types. Finally, structural and sequence properties of beta-strands in the beta-hairpins were analyzed, which revealed that the beta-strands showed no specific sequence and structural patterns for turn types. The analytical results in this study are expected to be a reference in the engineering or design of beta-hairpin turn structures and sequences. © 2014 Wiley Periodicals, Inc.

Chinese wine classification system based on micrograph using combination of shape and structure features

Science.gov (United States)

Wan, Yi

2011-06-01

Chinese wines can be classification or graded by the micrographs. Micrographs of Chinese wines show floccules, stick and granule of variant shape and size. Different wines have variant microstructure and micrographs, we study the classification of Chinese wines based on the micrographs. Shape and structure of wines' particles in microstructure is the most important feature for recognition and classification of wines. So we introduce a feature extraction method which can describe the structure and region shape of micrograph efficiently. First, the micrographs are enhanced using total variation denoising, and segmented using a modified Otsu's method based on the Rayleigh Distribution. Then features are extracted using proposed method in the paper based on area, perimeter and traditional shape feature. Eight kinds total 26 features are selected. Finally, Chinese wine classification system based on micrograph using combination of shape and structure features and BP neural network have been presented. We compare the recognition results for different choices of features (traditional shape features or proposed features). The experimental results show that the better classification rate have been achieved using the combinational features proposed in this paper.

Top-down contingent feature-specific orienting with and without awareness of the visual input.

Science.gov (United States)

Ansorge, Ulrich; Horstmann, Gernot; Scharlau, Ingrid

2011-01-01

In the present article, the role of endogenous feature-specific orienting for conscious and unconscious vision is reviewed. We start with an overview of orienting. We proceed with a review of masking research, and the definition of the criteria of experimental protocols that demonstrate endogenous and exogenous orienting, respectively. Against this background of criteria, we assess studies of unconscious orienting and come to the conclusion that so far studies of unconscious orienting demonstrated endogenous feature-specific orienting. The review closes with a discussion of the role of unconscious orienting in action control.

A Feature-Based Structural Measure: An Image Similarity Measure for Face Recognition

Directory of Open Access Journals (Sweden)

Noor Abdalrazak Shnain

2017-08-01

Full Text Available Facial recognition is one of the most challenging and interesting problems within the field of computer vision and pattern recognition. During the last few years, it has gained special attention due to its importance in relation to current issues such as security, surveillance systems and forensics analysis. Despite this high level of attention to facial recognition, the success is still limited by certain conditions; there is no method which gives reliable results in all situations. In this paper, we propose an efficient similarity index that resolves the shortcomings of the existing measures of feature and structural similarity. This measure, called the Feature-Based Structural Measure (FSM, combines the best features of the well-known SSIM (structural similarity index measure and FSIM (feature similarity index measure approaches, striking a balance between performance for similar and dissimilar images of human faces. In addition to the statistical structural properties provided by SSIM, edge detection is incorporated in FSM as a distinctive structural feature. Its performance is tested for a wide range of PSNR (peak signal-to-noise ratio, using ORL (Olivetti Research Laboratory, now AT&T Laboratory Cambridge and FEI (Faculty of Industrial Engineering, São Bernardo do Campo, São Paulo, Brazil databases. The proposed measure is tested under conditions of Gaussian noise; simulation results show that the proposed FSM outperforms the well-known SSIM and FSIM approaches in its efficiency of similarity detection and recognition of human faces.

Contribution of transposable elements and distal enhancers to evolution of human-specific features of interphase chromatin architecture in embryonic stem cells.

Science.gov (United States)

Glinsky, Gennadi V

2018-03-01

Transposable elements have made major evolutionary impacts on creation of primate-specific and human-specific genomic regulatory loci and species-specific genomic regulatory networks (GRNs). Molecular and genetic definitions of human-specific changes to GRNs contributing to development of unique to human phenotypes remain a highly significant challenge. Genome-wide proximity placement analysis of diverse families of human-specific genomic regulatory loci (HSGRL) identified topologically associating domains (TADs) that are significantly enriched for HSGRL and designated rapidly evolving in human TADs. Here, the analysis of HSGRL, hESC-enriched enhancers, super-enhancers (SEs), and specific sub-TAD structures termed super-enhancer domains (SEDs) has been performed. In the hESC genome, 331 of 504 (66%) of SED-harboring TADs contain HSGRL and 68% of SEDs co-localize with HSGRL, suggesting that emergence of HSGRL may have rewired SED-associated GRNs within specific TADs by inserting novel and/or erasing existing non-coding regulatory sequences. Consequently, markedly distinct features of the principal regulatory structures of interphase chromatin evolved in the hESC genome compared to mouse: the SED quantity is 3-fold higher and the median SED size is significantly larger. Concomitantly, the overall TAD quantity is increased by 42% while the median TAD size is significantly decreased (p = 9.11E-37) in the hESC genome. Present analyses illustrate a putative global role for transposable elements and HSGRL in shaping the human-specific features of the interphase chromatin organization and functions, which are facilitated by accelerated creation of novel transcription factor binding sites and new enhancers driven by targeted placement of HSGRL at defined genomic coordinates. A trend toward the convergence of TAD and SED architectures of interphase chromatin in the hESC genome may reflect changes of 3D-folding patterns of linear chromatin fibers designed to enhance both

The influence of target structure on topographical features produced by ion beam sputtering

International Nuclear Information System (INIS)

Whitton, J.L.; Grant, W.A.

1981-01-01

Ion beam erosion of solid surfaces often results in the development of distinctive topographical features. The relationship between the type of features formed by ion erosion and target structure has been investigated. Single crystals of copper and nickel and the amorphous alloy Metglas have been bombarded to high doses (approx. >=10 19 ions cm -2 ) with 40 keV Ar + and P + . Topography changes were monitored using SEM and structural changes by TEM. Targets that retain their long range crystallinity show sharply defined, regular features that are related to the target structure. Targets that are highly disordered, either intrinsically or as a result of the ion bombardment, produce diffuse, smaller features. Those differences are observed at all stages in topographical evolution. (orig.)

Sensory memory of structure-from-motion is shape-specific.

Science.gov (United States)

Pastukhov, Alexander; Füllekrug, Jana; Braun, Jochen

2013-08-01

Perceptual priming can stabilize the phenomenal appearance of multistable visual displays (Leopold, Wilke, Maier, & Logothetis, Nature Neuroscience, 5, 605-609, 2002). Prior exposure to such displays induces a sensory memory of their appearance, which persists over long intervals and intervening stimulation, and which facilitates renewed perception of the same appearance. Here, we investigated perceptual priming for the apparent rotation in depth of ambiguous structure-from-motion (SFM) displays. Specifically, we generated SFM objects with different three-dimensional shapes and presented them in random order and with intervening blank periods. To assess perceptual priming, we established the probability that a perceived direction of rotation would persist between successive objects. In general, persistence was greatest between identical objects, intermediate between similar objects, and negligible between dissimilar objects. These results demonstrate unequivocally that sensory memory for apparent rotation is specific to three-dimensional shape, contrary to previous reports (e.g., Maier, Wilke, Logothetis, & Leopold, Current Biology, 13, 1076-1085, 2003). Because persistence did not depend on presentation order for any pair of objects, it provides a commutative measure for the similarity of object shapes. However, it is not clear exactly which features or aspects of object shape determine similarity. At least, we did not find simple, low-level features (such as volume overlap, heterogeneity, or rotational symmetry) that could have accounted for all observations. Accordingly, it seems that sensory memory of SFM (which underlies priming of ambiguous rotation) engages higher-level representations of object surface and shape.

Specific features of using programmed hardware in emergency protection systems of NPP

International Nuclear Information System (INIS)

Konoplev, N.P.; Pogorelov, I.V.; Kirsanov, A.V.

2005-01-01

The specific features of using the microprocessor-based technical means and programmed logic integrated circuits (PLIC) in WWER reactor protection systems are considered. The basic causes of occurring the failures in programmed technical means are analyzed. The features of using PLIC in reactor protection systems are discussed. The methods permitting to decrease the probability occurring the common mode failure of programmed technical means are proposed. It is concluded that at creating of reactor protection systems with the use of microprocessors and PLIC it is necessary to apply the principle of the functional diversity [ru

Linker histones: novel insights into structure-specific recognition of the nucleosome.

Science.gov (United States)

Cutter, Amber R; Hayes, Jeffrey J

2017-04-01

Linker histones (H1s) are a primary component of metazoan chromatin, fulfilling numerous functions, both in vitro and in vivo, including stabilizing the wrapping of DNA around the nucleosome, promoting folding and assembly of higher order chromatin structures, influencing nucleosome spacing on DNA, and regulating specific gene expression. However, many molecular details of how H1 binds to nucleosomes and recognizes unique structural features on the nucleosome surface remain undefined. Numerous, confounding studies are complicated not only by experimental limitations, but the use of different linker histone isoforms and nucleosome constructions. This review summarizes the decades of research that has resulted in several models of H1 association with nucleosomes, with a focus on recent advances that suggest multiple modes of H1 interaction in chromatin, while highlighting the remaining questions.

Perceptual learning of basic visual features remains task specific with Training-Plus-Exposure (TPE) training.

Science.gov (United States)

Cong, Lin-Juan; Wang, Ru-Jie; Yu, Cong; Zhang, Jun-Yun

2016-01-01

Visual perceptual learning is known to be specific to the trained retinal location, feature, and task. However, location and feature specificity can be eliminated by double-training or TPE training protocols, in which observers receive additional exposure to the transfer location or feature dimension via an irrelevant task besides the primary learning task Here we tested whether these new training protocols could even make learning transfer across different tasks involving discrimination of basic visual features (e.g., orientation and contrast). Observers practiced a near-threshold orientation (or contrast) discrimination task. Following a TPE training protocol, they also received exposure to the transfer task via performing suprathreshold contrast (or orientation) discrimination in alternating blocks of trials in the same sessions. The results showed no evidence for significant learning transfer to the untrained near-threshold contrast (or orientation) discrimination task after discounting the pretest effects and the suprathreshold practice effects. These results thus do not support a hypothetical task-independent component in perceptual learning of basic visual features. They also set the boundary of the new training protocols in their capability to enable learning transfer.

ROCK FRACTURES NEAR FAULTS: SPECIFIC FEATURES OF STRUCTURAL‐PARAGENETIC ANALYSIS

Directory of Open Access Journals (Sweden)

Yu. P. Burzunova

2017-01-01

Full Text Available The new approach to structural‐paragenetic analysis of near‐fault fractures [Seminsky, 2014, 2015] and specific features of its application are discussed. This approach was tested in studies of fracturing in West Pribaikalie and Central Mongolia. We give some recommendations concerning collection, selection and initial processing of the data on fractures and faults. The analysis technique is briefly described, and its distinctive details are specified. Under the new approach, we compare systems of natural fractures with the standard joint sets. By analysing the mass measurements of the orientations of joint sets in a fault zone, it becomes possible to reveal the characteristics of this fault zone, such as its structure, morphogenetic type, etc. The comparative analysis is based on the identification of the main fracture paragenesis near the faults. This paragenesis is represented by a triplet of mutually perpendicular joint sets. The technique uses the qualitative approach to establish the rank hierarchy of fractures and stress fields on the basis of genetic subordination. We collect and analyse the data on tectonic fractures identified from a number of indicators, the main of which are the geometric structure of the (systematic or chaotic fracture system, and shear type of fractures. The new technique can be applied to analyse other genetic types of fractures (primary, hypergenic, provided that tectonic stresses were significantly involved in fracturing, which is evidenced by the corresponding indicators. Methods for conducting geological and structural observations are uniform for all sites and points, and increasing the number of observation points provides for a more effective use of the new technique. In our paper, we give specific parameters for constructing circle fracture diagrams. All the maximums in the diagram are involved in the analysis for comparison with the standard patterns. Errors caused by random coincidence are minimized

Specificities of micro-structured reactors for hydrogen production and purification

Energy Technology Data Exchange (ETDEWEB)

Dupont, N.; Germani, G.; Van Veen, A.C.; Schuurman, Y.; Mirodatos, C. [Institut de Recherches sur la Catalyse - CNRS, 2, Avenue Albert Einstein, 69626 Villeurbanne Cedex (France); Schaefer, G. [Atotech Deutschland GmbH, PO Box 210780, 10507 Berlin (Germany)

2007-07-15

This paper presents the specificities of micro-structured reactors as compared to conventional fixed-bed reactors through two case studies devoted to (i) hydrogen production by methanol steam reforming, (ii) hydrogen purification by water-gas shift (WGS). Key features like catalyst coating stability, temperature and pressure management, effects of operating conditions (residence time, pressure drops, etc.) are well identified as controlling the micro-reactor performances for methanol reforming. These devices are also shown to be excellent tools for fast access to reaction kinetics as exemplified for the WGS reaction, subject to operating conditions carefully chosen to ensure proper hydrodynamics, in order to use conventional plug flow reactor models for extracting rate constants. (author)

Feature Extraction for Structural Dynamics Model Validation

Energy Technology Data Exchange (ETDEWEB)

Farrar, Charles [Los Alamos National Laboratory; Nishio, Mayuko [Yokohama University; Hemez, Francois [Los Alamos National Laboratory; Stull, Chris [Los Alamos National Laboratory; Park, Gyuhae [Chonnam Univesity; Cornwell, Phil [Rose-Hulman Institute of Technology; Figueiredo, Eloi [Universidade Lusófona; Luscher, D. J. [Los Alamos National Laboratory; Worden, Keith [University of Sheffield

2016-01-13

As structural dynamics becomes increasingly non-modal, stochastic and nonlinear, finite element model-updating technology must adopt the broader notions of model validation and uncertainty quantification. For example, particular re-sampling procedures must be implemented to propagate uncertainty through a forward calculation, and non-modal features must be defined to analyze nonlinear data sets. The latter topic is the focus of this report, but first, some more general comments regarding the concept of model validation will be discussed.

Specific features of the REDUCE system and calculation of QCD Feynman graphs

International Nuclear Information System (INIS)

Dulyan, L.S.

1990-01-01

The ways and methods used in calculation of one class of the QCD Feynman graphs with the help of the REDUCE system are described. It is shown how by introducing new constructions and operations the user could avoid difficulties connected with specific restrictions and features of the REDUCE system

Control-group feature normalization for multivariate pattern analysis of structural MRI data using the support vector machine.

Science.gov (United States)

Linn, Kristin A; Gaonkar, Bilwaj; Satterthwaite, Theodore D; Doshi, Jimit; Davatzikos, Christos; Shinohara, Russell T

2016-05-15

Normalization of feature vector values is a common practice in machine learning. Generally, each feature value is standardized to the unit hypercube or by normalizing to zero mean and unit variance. Classification decisions based on support vector machines (SVMs) or by other methods are sensitive to the specific normalization used on the features. In the context of multivariate pattern analysis using neuroimaging data, standardization effectively up- and down-weights features based on their individual variability. Since the standard approach uses the entire data set to guide the normalization, it utilizes the total variability of these features. This total variation is inevitably dependent on the amount of marginal separation between groups. Thus, such a normalization may attenuate the separability of the data in high dimensional space. In this work we propose an alternate approach that uses an estimate of the control-group standard deviation to normalize features before training. We study our proposed approach in the context of group classification using structural MRI data. We show that control-based normalization leads to better reproducibility of estimated multivariate disease patterns and improves the classifier performance in many cases. Copyright © 2016 Elsevier Inc. All rights reserved.

Heuristic algorithms for feature selection under Bayesian models with block-diagonal covariance structure.

Science.gov (United States)

Foroughi Pour, Ali; Dalton, Lori A

2018-03-21

Many bioinformatics studies aim to identify markers, or features, that can be used to discriminate between distinct groups. In problems where strong individual markers are not available, or where interactions between gene products are of primary interest, it may be necessary to consider combinations of features as a marker family. To this end, recent work proposes a hierarchical Bayesian framework for feature selection that places a prior on the set of features we wish to select and on the label-conditioned feature distribution. While an analytical posterior under Gaussian models with block covariance structures is available, the optimal feature selection algorithm for this model remains intractable since it requires evaluating the posterior over the space of all possible covariance block structures and feature-block assignments. To address this computational barrier, in prior work we proposed a simple suboptimal algorithm, 2MNC-Robust, with robust performance across the space of block structures. Here, we present three new heuristic feature selection algorithms. The proposed algorithms outperform 2MNC-Robust and many other popular feature selection algorithms on synthetic data. In addition, enrichment analysis on real breast cancer, colon cancer, and Leukemia data indicates they also output many of the genes and pathways linked to the cancers under study. Bayesian feature selection is a promising framework for small-sample high-dimensional data, in particular biomarker discovery applications. When applied to cancer data these algorithms outputted many genes already shown to be involved in cancer as well as potentially new biomarkers. Furthermore, one of the proposed algorithms, SPM, outputs blocks of heavily correlated genes, particularly useful for studying gene interactions and gene networks.

Using sequence-specific chemical and structural properties of DNA to predict transcription factor binding sites.

Directory of Open Access Journals (Sweden)

Amy L Bauer

2010-11-01

Full Text Available An important step in understanding gene regulation is to identify the DNA binding sites recognized by each transcription factor (TF. Conventional approaches to prediction of TF binding sites involve the definition of consensus sequences or position-specific weight matrices and rely on statistical analysis of DNA sequences of known binding sites. Here, we present a method called SiteSleuth in which DNA structure prediction, computational chemistry, and machine learning are applied to develop models for TF binding sites. In this approach, binary classifiers are trained to discriminate between true and false binding sites based on the sequence-specific chemical and structural features of DNA. These features are determined via molecular dynamics calculations in which we consider each base in different local neighborhoods. For each of 54 TFs in Escherichia coli, for which at least five DNA binding sites are documented in RegulonDB, the TF binding sites and portions of the non-coding genome sequence are mapped to feature vectors and used in training. According to cross-validation analysis and a comparison of computational predictions against ChIP-chip data available for the TF Fis, SiteSleuth outperforms three conventional approaches: Match, MATRIX SEARCH, and the method of Berg and von Hippel. SiteSleuth also outperforms QPMEME, a method similar to SiteSleuth in that it involves a learning algorithm. The main advantage of SiteSleuth is a lower false positive rate.

Feature-specific encoding flexibility in visual working memory.

Directory of Open Access Journals (Sweden)

Aki Kondo

Full Text Available The current study examined selective encoding in visual working memory by systematically investigating interference from task-irrelevant features. The stimuli were objects defined by three features (color, shape, and location, and during a delay period, any of the features could switch between two objects. Additionally, single- and whole-probe trials were randomized within experimental blocks to investigate effects of memory retrieval. A series of relevant-feature switch detection tasks, where one feature was task-irrelevant, showed that interference from the task-irrelevant feature was only observed in the color-shape task, suggesting that color and shape information could be successfully filtered out, but location information could not, even when location was a task-irrelevant feature. Therefore, although location information is added to object representations independent of task demands in a relatively automatic manner, other features (e.g., color, shape can be flexibly added to object representations.

Feature-specific encoding flexibility in visual working memory.

Science.gov (United States)

Kondo, Aki; Saiki, Jun

2012-01-01

The current study examined selective encoding in visual working memory by systematically investigating interference from task-irrelevant features. The stimuli were objects defined by three features (color, shape, and location), and during a delay period, any of the features could switch between two objects. Additionally, single- and whole-probe trials were randomized within experimental blocks to investigate effects of memory retrieval. A series of relevant-feature switch detection tasks, where one feature was task-irrelevant, showed that interference from the task-irrelevant feature was only observed in the color-shape task, suggesting that color and shape information could be successfully filtered out, but location information could not, even when location was a task-irrelevant feature. Therefore, although location information is added to object representations independent of task demands in a relatively automatic manner, other features (e.g., color, shape) can be flexibly added to object representations.

DroidEnsemble: Detecting Android Malicious Applications with Ensemble of String and Structural Static Features

KAUST Repository

Wang, Wei

2018-05-11

Android platform has dominated the Operating System of mobile devices. However, the dramatic increase of Android malicious applications (malapps) has caused serious software failures to Android system and posed a great threat to users. The effective detection of Android malapps has thus become an emerging yet crucial issue. Characterizing the behaviors of Android applications (apps) is essential to detecting malapps. Most existing work on detecting Android malapps was mainly based on string static features such as permissions and API usage extracted from apps. There also exists work on the detection of Android malapps with structural features, such as Control Flow Graph (CFG) and Data Flow Graph (DFG). As Android malapps have become increasingly polymorphic and sophisticated, using only one type of static features may result in false negatives. In this work, we propose DroidEnsemble that takes advantages of both string features and structural features to systematically and comprehensively characterize the static behaviors of Android apps and thus build a more accurate detection model for the detection of Android malapps. We extract each app’s string features, including permissions, hardware features, filter intents, restricted API calls, used permissions, code patterns, as well as structural features like function call graph. We then use three machine learning algorithms, namely, Support Vector Machine (SVM), k-Nearest Neighbor (kNN) and Random Forest (RF), to evaluate the performance of these two types of features and of their ensemble. In the experiments, We evaluate our methods and models with 1386 benign apps and 1296 malapps. Extensive experimental results demonstrate the effectiveness of DroidEnsemble. It achieves the detection accuracy as 95.8% with only string features and as 90.68% with only structural features. DroidEnsemble reaches the detection accuracy as 98.4% with the ensemble of both types of features, reducing 9 false positives and 12 false

Specific features of the Galician language and implications for speech technology development

OpenAIRE

2008-01-01

Specific features of the Galician language and implications for speech technology development correspondence: Corresponding author. (Banga, Eduardo Rodriguez) (Banga, Eduardo Rodriguez) Dpto. Filoloxia Galega. Universidade de Santiago. Santiago de Compostela. Spain - (Gonzalez, Manuel Gonzalez) Dpto. Teoria de la Se?al y Comunicaciones. Universidad de Vigo. Vigo. Spain - (Banga, Eduardo Rodriguez) SPAIN (Banga...

An Matching Method for Vehicle-borne Panoramic Image Sequence Based on Adaptive Structure from Motion Feature

Directory of Open Access Journals (Sweden)

ZHANG Zhengpeng

2015-10-01

Full Text Available Panoramic image matching method with the constraint condition of local structure from motion similarity feature is an important method, the process requires multivariable kernel density estimations for the structure from motion feature used nonparametric mean shift. Proper selection of the kernel bandwidth is a critical step for convergence speed and accuracy of matching method. Variable bandwidth with adaptive structure from motion feature for panoramic image matching method has been proposed in this work. First the bandwidth matrix is defined using the locally adaptive spatial structure of the sampling point in spatial domain and optical flow domain. The relaxation diffusion process of structure from motion similarity feature is described by distance weighting method of local optical flow feature vector. Then the expression form of adaptive multivariate kernel density function is given out, and discusses the solution of the mean shift vector, termination conditions, and the seed point selection method. The final fusions of multi-scale SIFT the features and structure features to establish a unified panoramic image matching framework. The sphere panoramic images from vehicle-borne mobile measurement system are chosen such that a comparison analysis between fixed bandwidth and adaptive bandwidth is carried out in detail. The results show that adaptive bandwidth is good for case with the inlier ratio changes and the object space scale changes. The proposed method can realize the adaptive similarity measure of structure from motion feature, improves the correct matching points and matching rate, experimental results have shown our method to be robust.

Structural conceptual models of water-conducting features at Aespoe

International Nuclear Information System (INIS)

Bossart, P.; Mazurek, M.; Hermansson, Jan

1998-01-01

Within the framework of the Fracture Classification and Characterization Project (FCC), water conducting features (WCF) in the Aespoe tunnel system and on the surface of Aespoe Island are being characterized over a range of scales. The larger-scale hierarchies of WCF are mostly constituted of fault arrays, i.e. brittle structures that accommodated episodes of shear strain. The smaller-scale WCF (contained within blocks 1 m. Structural evidence indicates that the fractures within the TRUE-1 block constitute an interconnected system with a pronounced anisotropy

Analysis of Conserved Structural Features of Selenoprotein K | Al ...

African Journals Online (AJOL)

Selenium plays important roles in human health and these roles may be exerted through its presence in selenoproteins. Among the 25 selenoproteins in human is selenoprotein K (SelK) whose exact function is still unclear. Here, we investigated the conserved structural features of SelK using bioinformatics as an approach ...

Specific features of modern multifunctional high-rise building construction

Science.gov (United States)

Manukhina, Lyubov; Samosudova, Natal'ja

2018-03-01

The article analyzes the main reasons for the development of high-rise building construction the most important of which-is a limitation of the urban areas and, consequently, the high price of land reserved for construction. New engineering and compositional solutions for the creation of new types of buildings are considered - complex technical designs of a large number of storeys completely meet the new requirements for safety and comfort. Some peculiarities of designing high-rise buildings and searching for optimal architectural and planning solutions are revealed since, with external architectural simplicity, high-rise buildings have complex structural and technological and space-planning solutions. We consider the specific features of a high-rise housing in various countries around the world, including Russia, such as the layout of the multi-storey residential buildings, depending on the climatic characteristics of the regions, assessment of the geological risk of the construction site, the choice of parameters and functional purpose of the sections of the territory of high-rise construction, location of the town-planning object for substantiating the overall dimensions of the building, assessment of changes aeration and engineering and hydrological conditions of the site. A special place in the article on the problems of improvement of the territory, the device of courtyards, landscaping, the device of playing and sports grounds. The main conclusion in the article is the following problem - when developing high-rise housing construction, the development of high-rise housing, and an increase in the population density in the territory of large cities of Russia, necessary to create a comfortable and safe level of residents living and not a decrease, but an improvement in the quality of the urban environment.

The research of structural features of astralens - nanodimensional carbon particles of fulleroid type

International Nuclear Information System (INIS)

Ponomarev, A.N.; Nikitin, V.A.; Rybalko, V.V.

2006-01-01

The article is focused on the research of structural features of astralens - nanodimensional carbonic particles of fulleroid type. Astralens are perspective nanomodificators of properties of materials of different types. The potentials os astralens as modificators depend on their characteristic structural features, and in the first place, on the distribution of nanoparticles by sizes. The typical dimensions of astralens are determined to be within the range of 15-75 nm [ru

Contingent capture can occur at specific feature values: behavioral and electrophysiological evidence.

Science.gov (United States)

Jiao, Jun; Zhao, Guang; Wang, Qi; Zhang, Kan; Li, Hong; Sun, Hong-Jin; Liu, Qiang

2013-02-01

The notion that attentional top-down control can be tuned to a stimulus feature is widely accepted. Although previous studies suggested that the stimulus-driven attentional capture could be contingent on top-down attentional control settings, it was uncertain whether contingent capture can occur at a specific feature value. Three experiments were conducted to address this issue using both behavioral and ERPs measures. Participants were required to respond to one color singleton in the search display (target) but refrain from responding to the search display containing another color singleton (nontarget). When target and nontarget belonged to different color categories (Experiment 1), only the target-color cue and within category irrelevant-color cue elicited the significant cue validity effect (i.e. RTs were shorter when the target was presented at the same location as the preceding cue rather than at a different location); they also lead to a robust N2pc effect, indicative of attention-capture. In addition, these two cue types had similar attention-capturing capacity. However, when target and nontarget belonged to the same color category (Experiments 2 and 3), only the target-color cue elicited the significant cue validity effect and the robust N2pc effect. The same within category irrelevant-color cue no longer elicited the cue validity effect, and the N2pc effect was also attenuated. Present findings suggest that contingent capture can occur at a specific feature value. Copyright © 2012 Elsevier B.V. All rights reserved.

Specific features of two diffraction schemes for a widely divergent X-ray beam

Energy Technology Data Exchange (ETDEWEB)

Avetyan, K. T.; Levonyan, L. V.; Semerjian, H. S.; Arakelyan, M. M., E-mail: marakelyan@ysu.am; Badalyan, O. M. [Yerevan State University (Armenia)

2015-03-15

We investigated the specific features of two diffraction schemes for a widely divergent X-ray beam that use a circular diaphragm 30–50 μm in diameter as a point source of characteristic radiation. In one of the schemes, the diaphragm was set in front of the crystal (the diaphragm-crystal (d-c) scheme); in the other, it was installed behind the crystal (the crystal-diaphragm (c-d) scheme). It was established that the diffraction image in the c-d scheme is a topographic map of the investigated crystal area. In the d-c scheme at L = 2l (l and L are the distances between the crystal and the diaphragm and between the photographic plate and the diaphragm, respectively), the branches of hyperbolas formed in this family of planes (hkl) by the characteristic K{sub α} and K{sub β} radiations, including higher order reflections, converge into one straight line. It is experimentally demonstrated that this convergence is very sensitive to structural inhomogeneities in the crystal under study.

Crystal structure and nanotopographical features on the surface of heat-treated and anodized porous titanium biomaterials produced using selective laser melting

Energy Technology Data Exchange (ETDEWEB)

Amin Yavari, S., E-mail: s.aminyavari@tudelft.nl [Faculty of Mechanical, Maritime, and Materials Engineering, Delft University of Technology (TU Delft), Mekelweg 2, 2628 CD Delft (Netherlands); FT Innovations BV, Braamsluiper 1, 5831 PW Boxmeer (Netherlands); Wauthle, R. [KU Leuven, Department of Mechanical Engineering, Section Production Engineering, Machine Design and Automation (PMA), Celestijnenlaan 300B, 3001 Leuven (Belgium); LayerWise NV, Kapeldreef 60, Leuven (Belgium); Böttger, A.J. [Faculty of Mechanical, Maritime, and Materials Engineering, Delft University of Technology (TU Delft), Mekelweg 2, 2628 CD Delft (Netherlands); Schrooten, J. [Department of Metallurgy and Materials Engineering, KU Leuven, Kasteelpark Arenberg 44 PB 2450, 3001 Heverlee (Belgium); Weinans, H. [Faculty of Mechanical, Maritime, and Materials Engineering, Delft University of Technology (TU Delft), Mekelweg 2, 2628 CD Delft (Netherlands); Department of Orthopedics and Department of Rheumatology, UMC Utrecht, Heidelberglaan 100, 3584 CX Utrecht (Netherlands); Zadpoor, A.A. [Faculty of Mechanical, Maritime, and Materials Engineering, Delft University of Technology (TU Delft), Mekelweg 2, 2628 CD Delft (Netherlands)

2014-01-30

Porous titanium biomaterials manufactured using additive manufacturing techniques such as selective laser melting are considered promising materials for orthopedic applications where the biomaterial needs to mimic the properties of bone. Despite their appropriate mechanical properties and the ample pore space they provide for bone ingrowth and osseointegration, porous titanium structures have an intrinsically bioinert surface and need to be subjected to surface bio-functionalizing procedures to enhance their in vivo performance. In this study, we used a specific anodizing process to build a hierarchical oxide layer on the surface of porous titanium structures made by selective laser melting of Ti6Al4V ELI powder. The hierarchical structure included both nanotopographical features (nanotubes) and micro-features (micropits). After anodizing, the biomaterial was heat treated in Argon at different temperatures ranging between 400 and 600 °C for either 1 or 2 h to improve its bioactivity. The effects of applied heat treatment on the crystal structure of TiO{sub 2} nanotubes and the nanotopographical features of the surface were studied using scanning electron microscopy and X-ray diffraction. It was shown that the transition from the initial crystal structure, i.e. anatase, to rutile occurs between 500 and 600 °C and that after 2 h of heat treatment at 600 °C the crystal structure is predominantly rutile. The nanotopographical features of the surface were found to be largely unchanged for heat treatments carried out at 500 °C or below, whereas they were partially or largely disrupted after heat treatment at 600 °C. The possible implications of these findings for the bioactivity of porous titanium structures are discussed.

[The specific microbiological and clinical features of acute otitis media].

Science.gov (United States)

Gurov, A V; Levina, Yu V; Guseva, A L; Elchueva, Z G; Efimova, S P; Gordienko, M V

The objective of the present study was to elucidate the specific features of the clinical course of acute otitis media as well as the peculiarities of the vestibular function and the microbial paysage associated with this pathological condition under the present-day conditions. The study included 135 patients presenting with acute otitis media (AOM) at different stages of the disease. The discharge obtained from the tympanic cavity of all the patients was examined with the use of polymerase chain reaction in real time, audiological and vestibulogical methods. The distinctive features of acute otitis medium associated with Streptococcus pneumoniae infection were found to be the intense pain syndrome with the symptoms of intoxication, well apparent inflammatory changes in the tympanic membrane as revealed by otoscopy, the increased frequency of sensorineural impairment of hearing, and the characteristic type B tympanometric curve. Typical of AOM associated with Haemophilus influenza infection are the mild pain syndrome, weak changes in the tympanic membrane as revealed by otoscopy, conductive hearing loss, and the type C tympanometric curve.

Structural features of subtype-selective EP receptor modulators.

Science.gov (United States)

Markovič, Tijana; Jakopin, Žiga; Dolenc, Marija Sollner; Mlinarič-Raščan, Irena

2017-01-01

Prostaglandin E2 is a potent endogenous molecule that binds to four different G-protein-coupled receptors: EP1-4. Each of these receptors is a valuable drug target, with distinct tissue localisation and signalling pathways. We review the structural features of EP modulators required for subtype-selective activity, as well as the structural requirements for improved pharmacokinetic parameters. Novel EP receptor subtype selective agonists and antagonists appear to be valuable drug candidates in the therapy of many pathophysiological states, including ulcerative colitis, glaucoma, bone healing, B cell lymphoma, neurological diseases, among others, which have been studied in vitro, in vivo and in early phase clinical trials. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

Structural features of nitroaromatics that determine mutagenic activity in Salmonella typhimurium

International Nuclear Information System (INIS)

Vance, W.A.; Levin, D.E.

1984-01-01

Seventeen structurally homologous nitroaromatics were tested for direct-acting mutagenic potency in nine strains of Salmonella typhimurium. The following four structural features were determined to have a strong influence on mutagenic activity: physical dimensions of the aromatic rings, isomeric position of the nitro group, conformation of the nitro group with respect to the plane of the aromatic rings, and ability to resonance-stabilize the utimate electrophile. Progressive addition of five- and six-membered rings to a nitrobenzene nucleus demonstrated that mutagenic activity was a direct function of size. Nitroaromatics with a nitro group oriented along the long axis of symmetry of the molecule were more potent mutagens that those with the nitro group oriented along the short axis. These results are discussed in light of the insertion-denaturation model for intercalation of certain DNA adducts. Finally, structural features that contribute to resonance stabilization of the reactive nitrenium ion enhance mutagenic potency. The predictive value of these structure-activity relationships should permit a first approximation in the assessment of mutagenic potency of nitroaromatics

In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features.

Science.gov (United States)

Ding, Yiliang; Tang, Yin; Kwok, Chun Kit; Zhang, Yu; Bevilacqua, Philip C; Assmann, Sarah M

2014-01-30

RNA structure has critical roles in processes ranging from ligand sensing to the regulation of translation, polyadenylation and splicing. However, a lack of genome-wide in vivo RNA structural data has limited our understanding of how RNA structure regulates gene expression in living cells. Here we present a high-throughput, genome-wide in vivo RNA structure probing method, structure-seq, in which dimethyl sulphate methylation of unprotected adenines and cytosines is identified by next-generation sequencing. Application of this method to Arabidopsis thaliana seedlings yielded the first in vivo genome-wide RNA structure map at nucleotide resolution for any organism, with quantitative structural information across more than 10,000 transcripts. Our analysis reveals a three-nucleotide periodic repeat pattern in the structure of coding regions, as well as a less-structured region immediately upstream of the start codon, and shows that these features are strongly correlated with translation efficiency. We also find patterns of strong and weak secondary structure at sites of alternative polyadenylation, as well as strong secondary structure at 5' splice sites that correlates with unspliced events. Notably, in vivo structures of messenger RNAs annotated for stress responses are poorly predicted in silico, whereas mRNA structures of genes related to cell function maintenance are well predicted. Global comparison of several structural features between these two categories shows that the mRNAs associated with stress responses tend to have more single-strandedness, longer maximal loop length and higher free energy per nucleotide, features that may allow these RNAs to undergo conformational changes in response to environmental conditions. Structure-seq allows the RNA structurome and its biological roles to be interrogated on a genome-wide scale and should be applicable to any organism.

SPECIFIC CONSTITUTIONAL FEATURES OF CHILDREN INFECTED WITH TUBERCULOSIS

Directory of Open Access Journals (Sweden)

Yu. A. Yarovaya

2017-01-01

Full Text Available In order to define specific constitutional features of the children infected with tuberculosis 222 children in the age from 1 to 14 years old have been examined: 106 children with active tuberculosis; 54 children with remaining post-tuberculosis changes; 62 children infected with tuberculous mycobacteria. The following types of diatheses were identified: lymphohypoplastic, allergic, neuroarthritic, exudative-catarrhal. It has been found out that among those with active tuberculosis the children suffering from lymphohypoplastic and neuroarthritic diatheses prevail (17.0 ± 3.7%, and allergic diathesis is less common (10.4 ± 3.0% cases. Children with lymphohypoplastic diathesis have a complicated course of tuberculosis (27.8 ± 10.6% and more intensive intoxication syndrome (55.6 ± 11.7%. The frequency of allergic diathesis is higher in the children with remaining post-tuberculosis changes (29.6 ± 6.2% and those infected with tuberculosis (33.8 ± 6.1% compared to children with active tuberculosis (10.4 ± 3.0%.

Burnout specific features in steam-water mixture annular flow in a tube

International Nuclear Information System (INIS)

Doroshchuk, V.E.

1981-01-01

Some unexplained burnout specific features in a steam-generating tube are analysed on the basis of experimental data. The following problems are considered: 1) the effect of the tube length and the state of the working medium (single-phase, two-phase) on burnout at the tube inlet; 2) the character of the specific thermal flow dependence at the moment of burnout appearance on the mass steam content q=f(x). It is found that the effect of the tube length on the burnout exists only in a relatively narrow range of the operating parameters. The run of the q=f(x) dependence is also explained [ru

Unique Structural Features of Influenza Virus H15 Hemagglutinin

Energy Technology Data Exchange (ETDEWEB)

Tzarum, Netanel; McBride, Ryan; Nycholat, Corwin M.; Peng, Wenjie; Paulson, James C.; Wilson, Ian A. (Scripps)

2017-04-12

Influenza A H15 viruses are members of a subgroup (H7-H10-H15) of group 2 hemagglutinin (HA) subtypes that include H7N9 and H10N8 viruses that were isolated from humans during 2013. The isolation of avian H15 viruses is, however, quite rare and, until recently, geographically restricted to wild shorebirds and waterfowl in Australia. The HAs of H15 viruses contain an insertion in the 150-loop (loop beginning at position 150) of the receptor-binding site common to this subgroup and a unique insertion in the 260-loop compared to any other subtype. Here, we show that the H15 HA has a high preference for avian receptor analogs by glycan array analyses. The H15 HA crystal structure reveals that it is structurally closest to H7N9 HA, but the head domain of the H15 trimer is wider than all other HAs due to a tilt and opening of the HA1 subunits of the head domain. The extended 150-loop of the H15 HA retains the conserved conformation as in H7 and H10 HAs. Furthermore, the elongated 260-loop increases the exposed HA surface and can contribute to antigenic variation in H15 HAs. Since avian-origin H15 HA viruses have been shown to cause enhanced disease in mammalian models, further characterization and immune surveillance of H15 viruses are warranted.

IMPORTANCEIn the last 2 decades, an apparent increase has been reported for cases of human infection by emerging avian influenza A virus subtypes, including H7N9 and H10N8 viruses isolated during 2013. H15 is the other member of the subgroup of influenza A virus group 2 hemagglutinins (HAs) that also include H7 and H10. H15 viruses have been restricted to Australia, but recent isolation of H15 viruses in western Siberia suggests that they could be spread more globally via the avian flyways that converge and emanate from this region. Here we report on characterization of the three-dimensional structure and receptor specificity of the H15 hemagglutinin, revealing distinct features and specificities that can

Structural similarity and category-specificity

DEFF Research Database (Denmark)

Gerlach, Christian; Law, Ian; Paulson, Olaf B

2004-01-01

It has been suggested that category-specific recognition disorders for natural objects may reflect that natural objects are more structurally (visually) similar than artefacts and therefore more difficult to recognize following brain damage. On this account one might expect a positive relationshi...

Features of construction of structures in long-term training acrobatics at the modern stage

Directory of Open Access Journals (Sweden)

N.V. Bachynska

2015-02-01

Full Text Available Purpose: the basic directions of the structure of long-term training in sports acrobatics are ground. The objectives of the study was to determine the leading requirements and criteria, the main stages of a multi-year training in acrobatics. Material : analysis of special scientific and methodical literature, revealing the specific features of the construction of long-term training in sports and gymnastics, acrobatic rock 'n' roll, a number of other sports. Results : general structure, goals, objectives and provisions of the basic stages of a multi-year training in sports acrobatics. Singled leading indicators and criteria for each of the main stages of long-term sports training in acrobatics. Recommended duration of training sessions and key requirements for the preparation of acrobats. Conclusions : outlines the main requirements and benchmarks that can guide the trainer in a training and competitive activity when working with acrobats all age groups and different sports qualification.

A systematic identification of species-specific protein succinylation sites using joint element features information

Directory of Open Access Journals (Sweden)

Hasan MM

2017-08-01

Full Text Available Md Mehedi Hasan,1 Mst Shamima Khatun,2 Md Nurul Haque Mollah,2 Cao Yong,3 Dianjing Guo1 1School of Life Sciences and the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territory, Hong Kong, People’s Republic of China; 2Laboratory of Bioinformatics, Department of Statistics, University of Rajshahi, Rajshahi, Bangladesh; 3Department of Mechanical Engineering and Automation, Harbin Institute of Technology, Shenzhen Graduate School, Shenzhen, People’s Republic of China Abstract: Lysine succinylation, an important type of protein posttranslational modification, plays significant roles in many cellular processes. Accurate identification of succinylation sites can facilitate our understanding about the molecular mechanism and potential roles of lysine succinylation. However, even in well-studied systems, a majority of the succinylation sites remain undetected because the traditional experimental approaches to succinylation site identification are often costly, time-consuming, and laborious. In silico approach, on the other hand, is potentially an alternative strategy to predict succinylation substrates. In this paper, a novel computational predictor SuccinSite2.0 was developed for predicting generic and species-specific protein succinylation sites. This predictor takes the composition of profile-based amino acid and orthogonal binary features, which were used to train a random forest classifier. We demonstrated that the proposed SuccinSite2.0 predictor outperformed other currently existing implementations on a complementarily independent dataset. Furthermore, the important features that make visible contributions to species-specific and cross-species-specific prediction of protein succinylation site were analyzed. The proposed predictor is anticipated to be a useful computational resource for lysine succinylation site prediction. The integrated species-specific online tool of SuccinSite2.0 is publicly

Accurate facade feature extraction method for buildings from three-dimensional point cloud data considering structural information

Science.gov (United States)

Wang, Yongzhi; Ma, Yuqing; Zhu, A.-xing; Zhao, Hui; Liao, Lixia

2018-05-01

Facade features represent segmentations of building surfaces and can serve as a building framework. Extracting facade features from three-dimensional (3D) point cloud data (3D PCD) is an efficient method for 3D building modeling. By combining the advantages of 3D PCD and two-dimensional optical images, this study describes the creation of a highly accurate building facade feature extraction method from 3D PCD with a focus on structural information. The new extraction method involves three major steps: image feature extraction, exploration of the mapping method between the image features and 3D PCD, and optimization of the initial 3D PCD facade features considering structural information. Results show that the new method can extract the 3D PCD facade features of buildings more accurately and continuously. The new method is validated using a case study. In addition, the effectiveness of the new method is demonstrated by comparing it with the range image-extraction method and the optical image-extraction method in the absence of structural information. The 3D PCD facade features extracted by the new method can be applied in many fields, such as 3D building modeling and building information modeling.

Evaluation of physical structural features on influencing enzymatic hydrolysis efficiency of micronized wood

Science.gov (United States)

Jinxue Jiang; Jinwu Wang; Xiao Zhang; Michael Wolcott

2016-01-01

Enzymatic hydrolysis of lignocellulosic biomass is highly dependent on the changes in structural features after pretreatment. Mechanical milling pretreatment is an effective approach to alter the physical structure of biomass and thus improve enzymatic hydrolysis. This study examined the influence of structural characteristics on the enzymatic hydrolysis of micronized...

The role of emotion in musical improvisation: an analysis of structural features.

Science.gov (United States)

McPherson, Malinda J; Lopez-Gonzalez, Monica; Rankin, Summer K; Limb, Charles J

2014-01-01

One of the primary functions of music is to convey emotion, yet how music accomplishes this task remains unclear. For example, simple correlations between mode (major vs. minor) and emotion (happy vs. sad) do not adequately explain the enormous range, subtlety or complexity of musically induced emotions. In this study, we examined the structural features of unconstrained musical improvisations generated by jazz pianists in response to emotional cues. We hypothesized that musicians would not utilize any universal rules to convey emotions, but would instead combine heterogeneous musical elements together in order to depict positive and negative emotions. Our findings demonstrate a lack of simple correspondence between emotions and musical features of spontaneous musical improvisation. While improvisations in response to positive emotional cues were more likely to be in major keys, have faster tempos, faster key press velocities and more staccato notes when compared to negative improvisations, there was a wide distribution for each emotion with components that directly violated these primary associations. The finding that musicians often combine disparate features together in order to convey emotion during improvisation suggests that structural diversity may be an essential feature of the ability of music to express a wide range of emotion.

Specific features of the flow structure in a reactive type turbine stage

Science.gov (United States)

Chernikov, V. A.; Semakina, E. Yu.

2017-04-01

The results of experimental studies of the gas dynamics for a reactive type turbine stage are presented. The objective of the studies is the measurement of the 3D flow fields in reference cross sections, experimental determination of the stage characteristics, and analysis of the flow structure for detecting the sources of kinetic energy losses. The integral characteristics of the studied stage are obtained by averaging the results of traversing the 3D flow over the area of the reference cross sections before and behind the stage. The averaging is performed using the conservation equations for mass, total energy flux, angular momentum with respect to the axis z of the turbine, entropy flow, and the radial projection of the momentum flux equation. The flow parameter distributions along the channel height behind the stage are obtained in the same way. More thorough analysis of the flow structure is performed after interpolation of the experimentally measured point parameter values and 3D flow velocities behind the stage. The obtained continuous velocity distributions in the absolute and relative coordinate systems are presented in the form of vector fields. The coordinates of the centers and the vectors of secondary vortices are determined using the results of point measurements of velocity vectors in the cross section behind the turbine stage and their subsequent interpolation. The approach to analysis of experimental data on aerodynamics of the turbine stage applied in this study allows one to find the detailed space structure of the working medium flow, including secondary coherent vortices at the root and peripheral regions of the air-gas part of the stage. The measured 3D flow parameter fields and their interpolation, on the one hand, point to possible sources of increased power losses, and, on the other hand, may serve as the basis for detailed testing of CFD models of the flow using both integral and local characteristics. The comparison of the numerical and

Structuring Formal Requirements Specifications for Reuse and Product Families

Science.gov (United States)

Heimdahl, Mats P. E.

2001-01-01

In this project we have investigated how formal specifications should be structured to allow for requirements reuse, product family engineering, and ease of requirements change, The contributions of this work include (1) a requirements specification methodology specifically targeted for critical avionics applications, (2) guidelines for how to structure state-based specifications to facilitate ease of change and reuse, and (3) examples from the avionics domain demonstrating the proposed approach.

Photonic crystals based on opals and inverse opals: synthesis and structural features

International Nuclear Information System (INIS)

Klimonsky, S O; Abramova, Vera V; Sinitskii, Alexander S; Tretyakov, Yuri D

2011-01-01

Methods of synthesis of photonic crystals based on opals and inverse opals are considered. Their structural features are discussed. Data on different types of structural defects and their influence on the optical properties of opaline materials are systematized. The possibilities of investigation of structural defects by optical spectroscopy, electron microscopy, microradian X-ray diffraction, laser diffraction and using an analysis of Kossel ring patterns are described. The bibliography includes 253 references.

Specific features of goal setting in road traffic safety

Science.gov (United States)

Kolesov, V. I.; Danilov, O. F.; Petrov, A. I.

2017-10-01

Road traffic safety (RTS) management is inherently a branch of cybernetics and therefore requires clear formalization of the task. The paper aims at identification of the specific features of goal setting in RTS management under the system approach. The paper presents the results of cybernetic modeling of the cause-to-effect mechanism of a road traffic accident (RTA); in here, the mechanism itself is viewed as a complex system. A designed management goal function is focused on minimizing the difficulty in achieving the target goal. Optimization of the target goal has been performed using the Lagrange principle. The created working algorithms have passed the soft testing. The key role of the obtained solution in the tactical and strategic RTS management is considered. The dynamics of the management effectiveness indicator has been analyzed based on the ten-year statistics for Russia.

Specific features of cytological and colposcopical pattern in pregnant women with benign cervix uteri pathology in anamnesis.

Science.gov (United States)

Bysaha, Nataliya Yu

2016-01-01

a tendency of increasing incidence of the cervix uteri precancer and cancer in women of reproductive age is noticed recently being related to the growth of number of the sexually-transmitted infections. The cervix uteri pathology incidence in women of fertile age is 20-25%. to study the specific features of the cytological and colposcopical pattern in pregnant patients with benign cervix uteri pathology in the anamnesis and the character of its change post partum. we have examined 195 women during their pregnancy and 3-5 months post partum. All pregnant women, alongside with generally accepted clinical and laboratory examinations, were subjected to the simple and extended colposcopy, cytology of the targeted smears and, according to indications, the histological studies of bioptate. according to the results of the colcoscopical studies and the signs of the cervix uteri pathology found, the patients were divided into several groups. A control group included 49 pregnant women. The clinical and instrumental examination of 146 women with cervix uteri pathology has been carried out both during pregnancy and post partum. the structure of the clinical forms of benign and premalignant changes in the cervix uteri epithelium in pregnant patients has been found. Specific features of the cytological and colposcopical pattern in pregnant patients with benign cervix uteri pathology in anamnesis have been studied. The relationship between the parity of pregnancy, delivery, route of delivery and regress of both benign and premalignant changes in the cervix uteri epithelium 3-5 months post partum has been determined.

Specific features of the electrical properties in partially graphitized porous biocarbons of beech wood

Science.gov (United States)

Popov, V. V.; Orlova, T. S.; Gutierrez-Pardo, A.; Ramirez-Rico, J.

2015-09-01

The electrical and galvanomagnetic properties of partially graphitized highly porous bioC(Ni) biocarbon matrices produced by pyrolysis (carbonization) of beech wood at temperatures T carb = 850-1600°C in the presence of a Ni-containing catalyst have been studied in comparison with their microstructural features. The temperature dependences of the resistivity, the magnetoresistance, and the Hall coefficient have been measured in the temperature range of 4.2-300 K in magnetic fields to 28 kOe. It has been shown that an additional graphite phase introduction into samples with T carb ≥ 1000°C results in an increase in the carrier mobility by a factor of 2-3, whereas the carrier (hole) concentration remains within ~1020 cm-3, as in biocarbons obtained without catalyst. An analysis of experimental data has demonstrated that the features of the conductivity and magnetoresistance of these samples are described by quantum corrections related to their structural features, i.e., the formation of a globular graphite phase of nano- and submicrometer sizes in the amorphous matrix. The quantum corrections to the conductivity decrease with increasing carbonization temperature, which indicates an increase in the degree of structure ordering and is in good agreement with microstructural data.

Quantification of Lignin and Its Structural Features in Plant Biomass Using

NARCIS (Netherlands)

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

2017-01-01

Understanding the mechanisms underlying plant biomass recalcitrance at the molecular level can only be achieved by accurate analyses of both the content and structural features of the molecules involved. Current quantification of lignin is, however, majorly based on unspecific gravimetric

Analysis of specific features of digital instrumentation and control systems and possibilities of accounting for them within PSA

International Nuclear Information System (INIS)

Hustak, S.

2002-10-01

The report is structured as follows: Basic information on the peculiarities of digital technology for the I and C system at an NPP (Digital signal; Digital communication; Communication protocols; Examples of practical tools for creation of I and C digital systems); Peculiarities of the digital I and C technology from the reliability viewpoint (Software as a new component of implementation of a system function; Problems with the assessment or demonstration of reliability of software components of an I and C system); Possibilities of accounting for the specific features of digital I and C technology within PSA (Relevant PSA components; Using PSA as a supporting tool in designing new NPPs; Categorization of NPP I and C system tasks with respect to the defence-in-depth principle). (P.A.)

[Specific features of gastroesophageal reflux disease associated with obesity and overweight].

Science.gov (United States)

Livzan, M A; Lapteva, I V; Krolevets, T S; Kiselev, I E

2016-01-01

To reveal the specific features of gastroesophageal reflux disease (GERD) associated with obesity and overweight, by investigating the clinical and endoscopic manifestations of the disease, 24-hour pH-metry scores, and leptin levels. A total of 131 patients with GERD were examined. The data about complaints and those from life and medical histories were collected; anthropometric measurements and the results of blood biochemical tests, esophagoduodenoscopy (EPDS), and pH-metry were assessed; and the serum levels of leptin and its receptor were estimated. The patients were allocated into a study group (104 obese and/or overweight patients) and a comparison one (27 normal weight people). Waist circumference, hip circumference, and blood glucose levels proved to be statistically significantly higher in the study group (pstudy group and 5.47 (3.35-7.68) ng/ml in the comparison group; the median levels of the receptors were 18.83 (14.98-25.11) ng/ml and 30.93 (24.68-33.53) ng/ml, respectively). This group showed a moderate negative correlation between these indicators (rs=-0.451; pstudy group displayed higher pH values in the gastric cardia and body (prefluxate having with a low pH value (refluxate having a pH below 4.0 (rs=0.543; preflux episodes longer than 5 minutes in the esophagus, and to the De Meester index for this indicator (rs=0.471; pdisease, which determines the specific features of the disease (alkaline or mixed refluxate) and the need for individualized therapy.

The role of emotion in musical improvisation: an analysis of structural features.

Directory of Open Access Journals (Sweden)

Malinda J McPherson

Full Text Available One of the primary functions of music is to convey emotion, yet how music accomplishes this task remains unclear. For example, simple correlations between mode (major vs. minor and emotion (happy vs. sad do not adequately explain the enormous range, subtlety or complexity of musically induced emotions. In this study, we examined the structural features of unconstrained musical improvisations generated by jazz pianists in response to emotional cues. We hypothesized that musicians would not utilize any universal rules to convey emotions, but would instead combine heterogeneous musical elements together in order to depict positive and negative emotions. Our findings demonstrate a lack of simple correspondence between emotions and musical features of spontaneous musical improvisation. While improvisations in response to positive emotional cues were more likely to be in major keys, have faster tempos, faster key press velocities and more staccato notes when compared to negative improvisations, there was a wide distribution for each emotion with components that directly violated these primary associations. The finding that musicians often combine disparate features together in order to convey emotion during improvisation suggests that structural diversity may be an essential feature of the ability of music to express a wide range of emotion.

Specific Features of Social Competence Development in the Future Music Teachers Working at Universities

Science.gov (United States)

Dzheksembekova, Menslu I.; Ibrayeva, Kamarsulu E.; Akhmetova, Aimkul K.; Urazalieva, Moldir A.; Sultangaliyeva, Elmira S.; Issametova, Klavdiya I.

2016-01-01

This paper aims at analyzing specific features of social competence of future music teachers and the development of specialized techniques in order to improve the quality of motivational and cognitive components of student social competence. The sample involved 660 undergraduate students. The authors used a number of research methods, such as…

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

Science.gov (United States)

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.

Minearl associated microbial communities from The Cedars, associate with specific geological features

Science.gov (United States)

Rowe, A. R.; Wanger, G. P.; Bhartia, R.

2017-12-01

The Cedars, an area of active serpentinization located in the Russian River area of Northern California, represents one of the few terrestrial areas on Earth undergoing active serpentinization. One of the products of the serpentinization reaction is the formation of hydroxyl radicals making the springs of the Cedars some of the most alkaline natural waters on Earth. These waters, with very high pH (pH>11), low EH and, low concentrations of electron acceptors are extremely inhospitible; however microbial life has found a way to thrive and a distinct microbial community is observed in the spring waters. Previous work with environmental samples and pure culture isolates [3] derived from The Cedars has suggested the importance of minearal association to these characteristic microbes. Here we show the results combined spectroscopic and molecular studies on aseries of mineral colonization experiemnts performed with a pure culture Cedar's isolate (Serpentenamonas str. A1) and in situ at CS spring. Centimeter scale, polished coupons of a variety of mminerals were prepared in the lab, spectroscopically characterized (Green Raman, DUV Raman, and DUV Fluorescence maps) and deployed into the springs for three months. The coupons were recovered and the distribution of the microbes on the minerals was mapped using a deep-UV native fluorescent mapping sustem that allows for non-destructive mapping of organics and microbes on surfaces. Subsequently the DNA from the minerals was extracted for community structure analysis. The MOSAIC (i.e. deep UV Fluorescence) showed extensicve colonization of the minerals and in some cases we were able to correlate microbial assemblages with specific geological features. In one example, organisms tended to associate strongly with carbonate features on Chromite mineral surfaces (Figure 1). The 16s rDNA revealed the microbial assemblages from each slide was dominated by active Cedars community memebers (i.e., Serpentinamonas and Silanimonas species

Critical Features of Fragment Libraries for Protein Structure Prediction.

Science.gov (United States)

Trevizani, Raphael; Custódio, Fábio Lima; Dos Santos, Karina Baptista; Dardenne, Laurent Emmanuel

2017-01-01

The use of fragment libraries is a popular approach among protein structure prediction methods and has proven to substantially improve the quality of predicted structures. However, some vital aspects of a fragment library that influence the accuracy of modeling a native structure remain to be determined. This study investigates some of these features. Particularly, we analyze the effect of using secondary structure prediction guiding fragments selection, different fragments sizes and the effect of structural clustering of fragments within libraries. To have a clearer view of how these factors affect protein structure prediction, we isolated the process of model building by fragment assembly from some common limitations associated with prediction methods, e.g., imprecise energy functions and optimization algorithms, by employing an exact structure-based objective function under a greedy algorithm. Our results indicate that shorter fragments reproduce the native structure more accurately than the longer. Libraries composed of multiple fragment lengths generate even better structures, where longer fragments show to be more useful at the beginning of the simulations. The use of many different fragment sizes shows little improvement when compared to predictions carried out with libraries that comprise only three different fragment sizes. Models obtained from libraries built using only sequence similarity are, on average, better than those built with a secondary structure prediction bias. However, we found that the use of secondary structure prediction allows greater reduction of the search space, which is invaluable for prediction methods. The results of this study can be critical guidelines for the use of fragment libraries in protein structure prediction.

Contribution of Sequence Motif, Chromatin State, and DNA Structure Features to Predictive Models of Transcription Factor Binding in Yeast.

Science.gov (United States)

Tsai, Zing Tsung-Yeh; Shiu, Shin-Han; Tsai, Huai-Kuang

2015-08-01

Transcription factor (TF) binding is determined by the presence of specific sequence motifs (SM) and chromatin accessibility, where the latter is influenced by both chromatin state (CS) and DNA structure (DS) properties. Although SM, CS, and DS have been used to predict TF binding sites, a predictive model that jointly considers CS and DS has not been developed to predict either TF-specific binding or general binding properties of TFs. Using budding yeast as model, we found that machine learning classifiers trained with either CS or DS features alone perform better in predicting TF-specific binding compared to SM-based classifiers. In addition, simultaneously considering CS and DS further improves the accuracy of the TF binding predictions, indicating the highly complementary nature of these two properties. The contributions of SM, CS, and DS features to binding site predictions differ greatly between TFs, allowing TF-specific predictions and potentially reflecting different TF binding mechanisms. In addition, a "TF-agnostic" predictive model based on three DNA "intrinsic properties" (in silico predicted nucleosome occupancy, major groove geometry, and dinucleotide free energy) that can be calculated from genomic sequences alone has performance that rivals the model incorporating experiment-derived data. This intrinsic property model allows prediction of binding regions not only across TFs, but also across DNA-binding domain families with distinct structural folds. Furthermore, these predicted binding regions can help identify TF binding sites that have a significant impact on target gene expression. Because the intrinsic property model allows prediction of binding regions across DNA-binding domain families, it is TF agnostic and likely describes general binding potential of TFs. Thus, our findings suggest that it is feasible to establish a TF agnostic model for identifying functional regulatory regions in potentially any sequenced genome.

Contribution of Sequence Motif, Chromatin State, and DNA Structure Features to Predictive Models of Transcription Factor Binding in Yeast.

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Zing Tsung-Yeh Tsai

2015-08-01

Full Text Available Transcription factor (TF binding is determined by the presence of specific sequence motifs (SM and chromatin accessibility, where the latter is influenced by both chromatin state (CS and DNA structure (DS properties. Although SM, CS, and DS have been used to predict TF binding sites, a predictive model that jointly considers CS and DS has not been developed to predict either TF-specific binding or general binding properties of TFs. Using budding yeast as model, we found that machine learning classifiers trained with either CS or DS features alone perform better in predicting TF-specific binding compared to SM-based classifiers. In addition, simultaneously considering CS and DS further improves the accuracy of the TF binding predictions, indicating the highly complementary nature of these two properties. The contributions of SM, CS, and DS features to binding site predictions differ greatly between TFs, allowing TF-specific predictions and potentially reflecting different TF binding mechanisms. In addition, a "TF-agnostic" predictive model based on three DNA "intrinsic properties" (in silico predicted nucleosome occupancy, major groove geometry, and dinucleotide free energy that can be calculated from genomic sequences alone has performance that rivals the model incorporating experiment-derived data. This intrinsic property model allows prediction of binding regions not only across TFs, but also across DNA-binding domain families with distinct structural folds. Furthermore, these predicted binding regions can help identify TF binding sites that have a significant impact on target gene expression. Because the intrinsic property model allows prediction of binding regions across DNA-binding domain families, it is TF agnostic and likely describes general binding potential of TFs. Thus, our findings suggest that it is feasible to establish a TF agnostic model for identifying functional regulatory regions in potentially any sequenced genome.

Crystal structure analysis reveals functional flexibility in the selenocysteine-specific tRNA from mouse.

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Oleg M Ganichkin

Full Text Available Selenocysteine tRNAs (tRNA(Sec exhibit a number of unique identity elements that are recognized specifically by proteins of the selenocysteine biosynthetic pathways and decoding machineries. Presently, these identity elements and the mechanisms by which they are interpreted by tRNA(Sec-interacting factors are incompletely understood.We applied rational mutagenesis to obtain well diffracting crystals of murine tRNA(Sec. tRNA(Sec lacking the single-stranded 3'-acceptor end ((ΔGCCARNA(Sec yielded a crystal structure at 2.0 Å resolution. The global structure of (ΔGCCARNA(Sec resembles the structure of human tRNA(Sec determined at 3.1 Å resolution. Structural comparisons revealed flexible regions in tRNA(Sec used for induced fit binding to selenophosphate synthetase. Water molecules located in the present structure were involved in the stabilization of two alternative conformations of the anticodon stem-loop. Modeling of a 2'-O-methylated ribose at position U34 of the anticodon loop as found in a sub-population of tRNA(Secin vivo showed how this modification favors an anticodon loop conformation that is functional during decoding on the ribosome. Soaking of crystals in Mn(2+-containing buffer revealed eight potential divalent metal ion binding sites but the located metal ions did not significantly stabilize specific structural features of tRNA(Sec.We provide the most highly resolved structure of a tRNA(Sec molecule to date and assessed the influence of water molecules and metal ions on the molecule's conformation and dynamics. Our results suggest how conformational changes of tRNA(Sec support its interaction with proteins.

SPECIFIC FEATURES OF ANTI-TUBERCULOSIS CHEMOTHERAPY TOLERANCE IN THE LIGHT OF PSYCHOLOGICAL STATUS OF PATIENTS

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N. V. Zolotova

2017-01-01

Full Text Available Specific features of psychological state were studied in 295 pulmonary tuberculosis patients with satisfactory tolerance to anti-tuberculosis medications and 75 patients poorly tolerating the treatment.Before the treatment start the patients who later demonstrated adverse reactions to treatment were diagnosed with more intense neurotic and hypochondriac personal features, destructive reactions and higher level of emotional tension and frustration – all the above promote dysregulation of the host adaptation. The research demonstrated the need to consider psychological aspects when studying the tolerance to anti-tuberculosis chemotherapy. 

Process Features in Writing: Internal Structure and Incremental Value over Product Features. Research Report. ETS RR-15-27

Science.gov (United States)

Zhang, Mo; Deane, Paul

2015-01-01

In educational measurement contexts, essays have been evaluated and formative feedback has been given based on the end product. In this study, we used a large sample collected from middle school students in the United States to investigate the factor structure of the writing process features gathered from keystroke logs and the association of that…

Common structural features of cholesterol binding sites in crystallized soluble proteins.

Science.gov (United States)

Bukiya, Anna N; Dopico, Alejandro M

2017-06-01

Cholesterol-protein interactions are essential for the architectural organization of cell membranes and for lipid metabolism. While cholesterol-sensing motifs in transmembrane proteins have been identified, little is known about cholesterol recognition by soluble proteins. We reviewed the structural characteristics of binding sites for cholesterol and cholesterol sulfate from crystallographic structures available in the Protein Data Bank. This analysis unveiled key features of cholesterol-binding sites that are present in either all or the majority of sites: i ) the cholesterol molecule is generally positioned between protein domains that have an organized secondary structure; ii ) the cholesterol hydroxyl/sulfo group is often partnered by Asn, Gln, and/or Tyr, while the hydrophobic part of cholesterol interacts with Leu, Ile, Val, and/or Phe; iii ) cholesterol hydrogen-bonding partners are often found on α-helices, while amino acids that interact with cholesterol's hydrophobic core have a slight preference for β-strands and secondary structure-lacking protein areas; iv ) the steroid's C21 and C26 constitute the "hot spots" most often seen for steroid-protein hydrophobic interactions; v ) common "cold spots" are C8-C10, C13, and C17, at which contacts with the proteins were not detected. Several common features we identified for soluble protein-steroid interaction appear evolutionarily conserved. Copyright © 2017 by the American Society for Biochemistry and Molecular Biology, Inc.

Relevance feature selection of modal frequency-ambient condition pattern recognition in structural health assessment for reinforced concrete buildings

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He-Qing Mu

2016-08-01

Full Text Available Modal frequency is an important indicator for structural health assessment. Previous studies have shown that this indicator is substantially affected by the fluctuation of ambient conditions, such as temperature and humidity. Therefore, recognizing the pattern between modal frequency and ambient conditions is necessary for reliable long-term structural health assessment. In this article, a novel machine-learning algorithm is proposed to automatically select relevance features in modal frequency-ambient condition pattern recognition based on structural dynamic response and ambient condition measurement. In contrast to the traditional feature selection approaches by examining a large number of combinations of extracted features, the proposed algorithm conducts continuous relevance feature selection by introducing a sophisticated hyperparameterization on the weight parameter vector controlling the relevancy of different features in the prediction model. The proposed algorithm is then utilized for structural health assessment for a reinforced concrete building based on 1-year daily measurements. It turns out that the optimal model class including the relevance features for each vibrational mode is capable to capture the pattern between the corresponding modal frequency and the ambient conditions.

SPECIFIC FEATURES OF THE SOCIAL INTELLIGENCE OF THE TEENAGERS MAKING USE OF SMOKING BLENDS

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Anna Leonidovna Plotnikova

2016-02-01

Full Text Available In this article one can find the results of the research of the teenagers social intelligence at the age of 14-15 years old, making use of narcotic smoking blends. Some specific features of their social intelligence, development level of empathy and communicative skills in comparison with nonsmoking peers are given.Purpose: to find and describe specific features of the social intelligence of the teenagers at the age of 14-15 years old making use of the narcotic smoking blends in comparison with nonsmoking peers.Method: testing, Mann – Whitney U Test.Results: the teenagers making use of narcotic smoking blends have a low level of the social intelligence, communicative skills and empathic abilities. Such elements of the social intelligence as the ability to foresee the behavioral consequences in a concrete situation (prognostic competence and the ability to logical generalization of non-verbal reactions of a person are worse developed in comparison with nonsmoking peers. There are no significant differences between smoking girls and smoking boys.Areas of use: resocialization and rehabilitation of the addicted teenagers

Features Of Household Lexics, Their Characteristics And Structural Analysis In The Modern English Language

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Aygun Yusifova

2014-04-01

Full Text Available The present paper aims to analyze the most inherent features and characteristics of household lexis in English. Special emphasis has been placed on their names of the objects used in everyday life, kitchen utensils, animal and birds. Lexical units concerning ceremonies, habits and traditions are also among the scope of the paper. Moreover, the study deals with the structural features of the units under consideration. It is believed that the thematic-semantic characterization of every-day lexis can have both pedagogical and linguistic implications, especially when dealing with comparative structures.

Reductio ad discrimen: Where features come from

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Elizabeth Cowper

2015-04-01

Full Text Available This paper addresses two fundamental questions about the nature of formal features in phonology and morphosyntax: what is their expressive power, and where do they come from? To answer these questions, we begin with the most restrictive possible hypothesis (all features are privative, and are wholly dictated by Universal Grammar, with no room for cross-linguistic variation, and examine the extent to which empirical evidence from a variety of languages compels a retreat from this position. We argue that there is little to be gained by positing a universal set of specific features, and propose instead that the crucial contribution of UG is the language learner's ability to construct features by identifying correlations between contrasts at different levels of linguistic structure. This view resonates with current research on how the interaction between UG and external 'third factors' shapes the structure of language, while at the same time harking back to the Saussurean notion that contrast is the central function of linguistic representations.

Automatic feature learning using multichannel ROI based on deep structured algorithms for computerized lung cancer diagnosis.

Science.gov (United States)

Sun, Wenqing; Zheng, Bin; Qian, Wei

2017-10-01

This study aimed to analyze the ability of extracting automatically generated features using deep structured algorithms in lung nodule CT image diagnosis, and compare its performance with traditional computer aided diagnosis (CADx) systems using hand-crafted features. All of the 1018 cases were acquired from Lung Image Database Consortium (LIDC) public lung cancer database. The nodules were segmented according to four radiologists' markings, and 13,668 samples were generated by rotating every slice of nodule images. Three multichannel ROI based deep structured algorithms were designed and implemented in this study: convolutional neural network (CNN), deep belief network (DBN), and stacked denoising autoencoder (SDAE). For the comparison purpose, we also implemented a CADx system using hand-crafted features including density features, texture features and morphological features. The performance of every scheme was evaluated by using a 10-fold cross-validation method and an assessment index of the area under the receiver operating characteristic curve (AUC). The observed highest area under the curve (AUC) was 0.899±0.018 achieved by CNN, which was significantly higher than traditional CADx with the AUC=0.848±0.026. The results from DBN was also slightly higher than CADx, while SDAE was slightly lower. By visualizing the automatic generated features, we found some meaningful detectors like curvy stroke detectors from deep structured schemes. The study results showed the deep structured algorithms with automatically generated features can achieve desirable performance in lung nodule diagnosis. With well-tuned parameters and large enough dataset, the deep learning algorithms can have better performance than current popular CADx. We believe the deep learning algorithms with similar data preprocessing procedure can be used in other medical image analysis areas as well. Copyright © 2017. Published by Elsevier Ltd.

Structural characterization of a D-isomer specific 2-hydroxyacid dehydrogenase from Lactobacillus delbrueckii ssp. bulgaricus.

Science.gov (United States)

Holton, Simon J; Anandhakrishnan, Madhankumar; Geerlof, Arie; Wilmanns, Matthias

2013-02-01

Hydroxyacid dehydrogenases, responsible for the stereospecific conversion of 2-keto acids to 2-hydroxyacids in lactic acid producing bacteria, have a range of biotechnology applications including antibiotic synthesis, flavor development in dairy products and the production of valuable synthons. The genome of Lactobacillus delbrueckii ssp. bulgaricus, a member of the heterogeneous group of lactic acid bacteria, encodes multiple hydroxyacid dehydrogenases whose structural and functional properties remain poorly characterized. Here, we report the apo and coenzyme NAD⁺ complexed crystal structures of the L. bulgaricusD-isomer specific 2-hydroxyacid dehydrogenase, D2-HDH. Comparison with closely related members of the NAD-dependent dehydrogenase family reveals that whilst the D2-HDH core fold is structurally conserved, the substrate-binding site has a number of non-canonical features that may influence substrate selection and thus dictate the physiological function of the enzyme. Copyright © 2012 Elsevier Inc. All rights reserved.

Structural features that optimize high temperature superconductivity

International Nuclear Information System (INIS)

Jorgensen, J.D.; Argonne Nat. Lab., IL; Hinks, D.G.; Argonne Nat. Lab., IL; Chmaissem, O.; Argonne Nat. Lab., IL; Argyriou, D.N.; Argonne Nat. Lab., IL; Mitchell, J.F.; Argonne Nat. Lab., IL; Dabrowski, B.

1996-01-01

Studies of a large number of compounds have provided a consistent picture of what structural features give rise to the highest T c 's in copper-oxide superconductors. For example, various defects can be introduced into the blocking layer to provide the optimum carrier concentration, but defects that form in or adjacent to the CuO 2 layers will lower T c and eventually destroy superconductivity. After these requirements are satisfied, the highest T c 's are observed for compounds (such as the HgBa 2 Ca n-1 Cu n O 2n+2+x family) that have flat and square CuO 2 planes and long apical Cu-O bonds. This conclusion is confirmed by the study of materials in which the flatness of the CuO 2 plane can be varied in a systematic way. In more recent work, attention has focused on how the structure can be modified, for example, by chemical substitution, to improve flux pinning properties. Two strategies are being investigated: (1) Increasing the coupling of pancake vortices to form vortex lines by shortening or ''metallizing'' the blocking layer; and (2) the formation of defects that pin flux. (orig.)

Constitution-specific features of perspiration and skin visco-elasticity in SCM.

Science.gov (United States)

Kim, Young-Min; Ku, Boncho; Jung, Chang Jin; Kim, Jaeuk U; Jeon, Young Ju; Kim, Keun Ho; Kim, Jong Yeol

2014-01-15

Human skin properties have been used as an important diagnostic component in traditional medicine as they change with health conditions. Sasang constitutional medicine (SCM) puts emphasis on the recognition of the constitution-specific skin features prior to the diagnostic decision of health. In this work, in search of skin-characteristics effectively reflecting SCM features, we compared several skin properties such as perspiration, visco-elasticity, elasticity, and elasticity hysteresis, in several candidate body parts. We conducted a clinical study in which a total of 111 healthy females aged 50 - 70 years participated with their Sasang constitution (SC) types determined objectively by the Sasang constitutional analytic tool. Perspiration on the skin surface was estimated by using a capacitance sensor to measure the amount of moisture on the palm, forehead, and philtrum before and after a heating stimulus. We acquired the visco-elasticity, elasticity, and elasticity hysteresis at the forearm by Dermalab's elasticity sensing device. An analysis of covariance (ANCOVA) was conducted to evaluate the effect of SC on the nine skin features acquired. The visco-elasticity of the forearm of the Soeum-in (SE) group was significantly lower than that of the Taeeum-in (TE) group (F = 68.867, p elasticity hysteresis of the SE group was higher than that of the TE group (F = 10.364, p elasticity, elasticity hysteresis, perspiration on the forehead and philtrum. Our findings are based on a novel interpretation of the SCM literature and will contribute to developing the constitutional health status evaluation system in SCM.

USER EMOTION IDENTIFICATION IN TWITTER USING SPECIFIC FEATURES: HASHTAG, EMOJI, EMOTICON, AND ADJECTIVE TERM

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Yuita Arum Sari

2014-08-01

Full Text Available Abstract Twitter is a social media application, which can give a sign for identifying user emotion. Identification of user emotion can be utilized in commercial domain, health, politic, and security problems. The problem of emotion identification in twit is the unstructured short text messages which lead the difficulty to figure out main features. In this paper, we propose a new framework for identifying the tendency of user emotions using specific features, i.e. hashtag, emoji, emoticon, and adjective term. Preprocessing is applied in the first phase, and then user emotions are identified by means of classification method using kNN. The proposed method can achieve good results, near ground truth, with accuracy of 92%.

Structural damage identification using damping: a compendium of uses and features

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Cao, M. S.; Sha, G. G.; Gao, Y. F.; Ostachowicz, W.

2017-04-01

The vibration responses of structures under controlled or ambient excitation can be used to detect structural damage by correlating changes in structural dynamic properties extracted from responses with damage. Typical dynamic properties refer to modal parameters: natural frequencies, mode shapes, and damping. Among these parameters, natural frequencies and mode shapes have been investigated extensively for their use in damage characterization by associating damage with reduction in local stiffness of structures. In contrast, the use of damping as a dynamic property to represent structural damage has not been comprehensively elucidated, primarily due to the complexities of damping measurement and analysis. With advances in measurement technologies and analysis tools, the use of damping to identify damage is becoming a focus of increasing attention in the damage detection community. Recently, a number of studies have demonstrated that damping has greater sensitivity for characterizing damage than natural frequencies and mode shapes in various applications, but damping-based damage identification is still a research direction ‘in progress’ and is not yet well resolved. This situation calls for an overall survey of the state-of-the-art and the state-of-the-practice of using damping to detect structural damage. To this end, this study aims to provide a comprehensive survey of uses and features of applying damping in structural damage detection. First, we present various methods for damping estimation in different domains including the time domain, the frequency domain, and the time-frequency domain. Second, we investigate the features and applications of damping-based damage detection methods on the basis of two predominant infrastructure elements, reinforced concrete structures and fiber-reinforced composites. Third, we clarify the influential factors that can impair the capability of damping to characterize damage. Finally, we recommend future research directions

Face processing in chronic alcoholism: a specific deficit for emotional features.

Science.gov (United States)

Maurage, P; Campanella, S; Philippot, P; Martin, S; de Timary, P

2008-04-01

It is well established that chronic alcoholism is associated with a deficit in the decoding of emotional facial expression (EFE). Nevertheless, it is still unclear whether this deficit is specifically for emotions or due to a more general impairment in visual or facial processing. This study was designed to clarify this issue using multiple control tasks and the subtraction method. Eighteen patients suffering from chronic alcoholism and 18 matched healthy control subjects were asked to perform several tasks evaluating (1) Basic visuo-spatial and facial identity processing; (2) Simple reaction times; (3) Complex facial features identification (namely age, emotion, gender, and race). Accuracy and reaction times were recorded. Alcoholic patients had a preserved performance for visuo-spatial and facial identity processing, but their performance was impaired for visuo-motor abilities and for the detection of complex facial aspects. More importantly, the subtraction method showed that alcoholism is associated with a specific EFE decoding deficit, still present when visuo-motor slowing down is controlled for. These results offer a post hoc confirmation of earlier data showing an EFE decoding deficit in alcoholism by strongly suggesting a specificity of this deficit for emotions. This may have implications for clinical situations, where emotional impairments are frequently observed among alcoholic subjects.

The Specific Features of the Course of Critical Conditions in Miners

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V. V. Moroz

2012-01-01

Full Text Available Objective: to improve treatment results in miners, by studying the specific features of the course of their critical conditions caused by severe traumatic injuries, and to develop differentiated intensive therapeutic regimens for detected abnormalities. Subjects and methods. A total of 1107 subjects were examined during the study. Central hemodynamic function was explored in 371 healthy miners with various lengths of underground mining; a control group included 30 healthy volunteers unexposed to occupational hazards. Examinations were made in 386 severe brain injury victims, including 218 victims with no length of underground work and 115 injured miners with an underground work length of more than 5 years. A control group comprised 53 apparently healthy donors. One hundred and twenty-two miners with severe thermal injury were examined. A control group consisted of 39 apparently healthy volunteers. One hundred and six victims with acute respiratory distress syndrome in the presence of severe concomitant injury were examined under mechanical ventilation. Sixty-three injured miners formed a study group; a comparison group included 43 subjects with no length of underground mining. Conclusion. Upon longer exposure to occupational hazards, the prenosological changes occur in the miners' organs and systems, which display a regular phasic pattern, fit in the picture of general adjustment syndrome, and determine the specific features of critical conditions. The peculiarities of the critical conditions caused by severe traumatic injuries in miners are the early development and high frequency of complications, the more severe course and late recovery of the body's lost functions, unlike the victims unexposed to occupational hazards. Differentiated intensive therapy for critical conditions in miners with severe traumatic injuries makes it possible to improve treatment results and to reduce death rates. 

Specificity of Structural Assessment of Knowledge

Science.gov (United States)

Trumpower, David L.; Sharara, Harold; Goldsmith, Timothy E.

2010-01-01

This study examines the specificity of information provided by structural assessment of knowledge (SAK). SAK is a technique which uses the Pathfinder scaling algorithm to transform ratings of concept relatedness into network representations (PFnets) of individuals' knowledge. Inferences about individuals' overall domain knowledge based on the…

The impact of the structural features of the rock mass on seismicity in Polish coal mines

Science.gov (United States)

Patyńska, Renata

2017-11-01

The article presents seismic activity induced in the coal mines of the Upper Silesian Coal Basin (GZW) in relation to the locations of the occurrence of rockbursts. The comparison of these measurements with the structural features of the rock mass of coal mines indicates the possibility of estimating the so-called Unitary Energy Expenditure (UEE) in a specific time. The obtained values of UEE were compared with the distribution of seismic activity in GZW mines. The level of seismic activity in the analysed period changed and depended on the intensity of mining works and diverse mining and geological conditions. Five regions, where tremors occurred (Bytom Trough, Main Saddle, Main Trough, Kazimierz Trough, and Jejkowice and Chwałowice Trough) which belong to various structural units of the Upper Silesia were analyzed. It was found out that rock bursts were recorded only in three regions: Main Saddle, Bytom Trough, and Jejkowice and Chwałowice Trough.

Features of Inner Structure of Placer Gold of the North-Eastern Part Siberian Platform

Science.gov (United States)

Gerasimov, Boris; Zhuravlev, Anatolii; Ivanov, Alexey

2017-12-01

Mineral and raw material base of placer and ore gold is based on prognosis evaluation, which allows to define promising areas regarding gold-bearing deposit prospecting. But there are some difficulties in gold primary source predicting and prospecting at the North-east Siberian platform, because the studied area is overlapped by thick cover of the Cenozoic deposits, where traditional methods of gold deposit prospecting are ineffective. In this connection, detailed study of typomorphic features of placer gold is important, because it contains key genetic information, necessary for development of mineralogical criteria of prognosis evaluation of ore gold content. Authors studied mineralogical-geochemical features of placer gold of the Anabar placer area for 15 years, with a view to identify indicators of gold, typical for different formation types of primary sources. This article presents results of these works. In placer regions, where primary sources of gold are not identified, there is need to study typomorphic features of placer gold, because it contains important genetic information, necessary for the development of mineralogical criteria of prognosis evaluation of ore gold content. Inner structures of gold from the Anabar placer region are studied, as one of the diagnostic typomorphic criteria as described in prominent method, developed by N.V. Petrovskaya [1980]. Etching of gold was carried out using reagent: HCl + HNO3 + FeCl3 × 6H2O + CrO3 +thioureat + water. Identified inner structures wer studied in details by means of scanning electron microscope JEOL JSM-6480LV. Two types of gold are identified according to the features of inner structure of placer gold of the Anabar region. First type - medium-high karat fine, well processed gold with significantly changed inner structure. This gold is allochthonous, which was redeposited many times from ancient intermediate reservoirs to younger deposits. Second type - low-medium karat, poorly rounded gold with

[The prevalence, causes and specific features of voice disturbances in teachers].

Science.gov (United States)

Orlova, O S; Vasilenko, Iu S; Zakharova, A F; Samokhvalova, L O; Kozlova, P A

2000-01-01

The paper analyzes voice disturbances, their causes and specific features in teachers based on the questionnaires filled by 934 general educational school teachers. The teachers have been found to associate voice disturbances not only with changes in the voice timbre, but with different subjective feelings that make their professional activity difficult. The major factors that cause voice disturbances are the voice overloads that differ in teachers of different specialities, their inability to use the voice, psychoemotional stresses, and frequent colds, as well as a combination of several factors. The incidence of vocal apparatus diseases does not tend to decrease, which makes it necessary to implement combined medical and pedagogical prophylactic measures to prevent dysphonia.

A feature-based approach to modeling protein-DNA interactions.

Directory of Open Access Journals (Sweden)

Eilon Sharon

Full Text Available Transcription factor (TF binding to its DNA target site is a fundamental regulatory interaction. The most common model used to represent TF binding specificities is a position specific scoring matrix (PSSM, which assumes independence between binding positions. However, in many cases, this simplifying assumption does not hold. Here, we present feature motif models (FMMs, a novel probabilistic method for modeling TF-DNA interactions, based on log-linear models. Our approach uses sequence features to represent TF binding specificities, where each feature may span multiple positions. We develop the mathematical formulation of our model and devise an algorithm for learning its structural features from binding site data. We also developed a discriminative motif finder, which discovers de novo FMMs that are enriched in target sets of sequences compared to background sets. We evaluate our approach on synthetic data and on the widely used TF chromatin immunoprecipitation (ChIP dataset of Harbison et al. We then apply our algorithm to high-throughput TF ChIP data from mouse and human, reveal sequence features that are present in the binding specificities of mouse and human TFs, and show that FMMs explain TF binding significantly better than PSSMs. Our FMM learning and motif finder software are available at http://genie.weizmann.ac.il/.

Specific-structured lipids: nutritional perspectives and production potentials

DEFF Research Database (Denmark)

Xu, Xuebing; Høy, Carl-Erik; Balchen, Steen

1997-01-01

Structured lipids are referring to any triacylglycerols containing both long chain fatty acids (mostly essential fatty acids) and medium or short chain fatty acids. In case of specific-structured lipids (SSLs), each group of fatty acids locates specifically at sn-2 or -1.3 positions of the glycerol...... backbone. Recently the nutritional perspectives of this kind of lipids attract many interests. This causes an increasing interest in the production of them by lipase-catalyzed interesterification. One of the advantages of lipase method over chemical ones is that SSLs can be produced with particular fatty...

Feature-based morphometry: discovering group-related anatomical patterns.

Science.gov (United States)

Toews, Matthew; Wells, William; Collins, D Louis; Arbel, Tal

2010-02-01

This paper presents feature-based morphometry (FBM), a new fully data-driven technique for discovering patterns of group-related anatomical structure in volumetric imagery. In contrast to most morphometry methods which assume one-to-one correspondence between subjects, FBM explicitly aims to identify distinctive anatomical patterns that may only be present in subsets of subjects, due to disease or anatomical variability. The image is modeled as a collage of generic, localized image features that need not be present in all subjects. Scale-space theory is applied to analyze image features at the characteristic scale of underlying anatomical structures, instead of at arbitrary scales such as global or voxel-level. A probabilistic model describes features in terms of their appearance, geometry, and relationship to subject groups, and is automatically learned from a set of subject images and group labels. Features resulting from learning correspond to group-related anatomical structures that can potentially be used as image biomarkers of disease or as a basis for computer-aided diagnosis. The relationship between features and groups is quantified by the likelihood of feature occurrence within a specific group vs. the rest of the population, and feature significance is quantified in terms of the false discovery rate. Experiments validate FBM clinically in the analysis of normal (NC) and Alzheimer's (AD) brain images using the freely available OASIS database. FBM automatically identifies known structural differences between NC and AD subjects in a fully data-driven fashion, and an equal error classification rate of 0.80 is achieved for subjects aged 60-80 years exhibiting mild AD (CDR=1). Copyright (c) 2009 Elsevier Inc. All rights reserved.

Phylogeny of isolates of Prunus necrotic ringspot virus from the Ilarvirus Ringtest and identification of group-specific features.

Science.gov (United States)

Hammond, R W

2003-06-01

Isolates of Prunus necrotic ringspot virus (PNRSV) were examined to establish the level of naturally occurring sequence variation in the coat protein (CP) gene and to identify group-specific genome features that may prove valuable for the generation of diagnostic reagents. Phylogenetic analysis of a 452 bp sequence of 68 virus isolates, 20 obtained from the European Union Ilarvirus Ringtest held in October 1998, confirmed the clustering of the isolates into three distinct groups. Although no correlation was found between the sequence and host or geographic origin, there was a general trend for severe isolates to cluster into one group. Group-specific features have been identified for discrimination between virus strains.

Hidden Markov model-derived structural alphabet for proteins: the learning of protein local shapes captures sequence specificity.

Science.gov (United States)

Camproux, A C; Tufféry, P

2005-08-05

Understanding and predicting protein structures depend on the complexity and the accuracy of the models used to represent them. We have recently set up a Hidden Markov Model to optimally compress protein three-dimensional conformations into a one-dimensional series of letters of a structural alphabet. Such a model learns simultaneously the shape of representative structural letters describing the local conformation and the logic of their connections, i.e. the transition matrix between the letters. Here, we move one step further and report some evidence that such a model of protein local architecture also captures some accurate amino acid features. All the letters have specific and distinct amino acid distributions. Moreover, we show that words of amino acids can have significant propensities for some letters. Perspectives point towards the prediction of the series of letters describing the structure of a protein from its amino acid sequence.

The structure of Lactococcus lactis thioredoxin reductase reveals molecular features of photo-oxidative damage

DEFF Research Database (Denmark)

Skjoldager, Nicklas; Bang, Maria Blanner; Rykær, Martin

2017-01-01

The NADPH-dependent homodimeric flavoenzyme thioredoxin reductase (TrxR) provides reducing equivalents to thioredoxin, a key regulator of various cellular redox processes. Crystal structures of photo-inactivated thioredoxin reductase (TrxR) from the Gram-positive bacterium Lactococcus lactis have...... been determined. These structures reveal novel molecular features that provide further insight into the mechanisms behind the sensitivity of this enzyme toward visible light. We propose that a pocket on the si-face of the isoalloxazine ring accommodates oxygen that reacts with photo-excited FAD...... thus be a widespread feature among bacterial TrxR with the described characteristics, which affords applications in clinical photo-therapy of drug-resistant bacteria....

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

Science.gov (United States)

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.

Organizational structure features supporting knowledge management processes

OpenAIRE

Claver-Cortés, Enrique; Zaragoza Sáez, Patrocinio del Carmen; Pertusa-Ortega, Eva

2007-01-01

Purpose – The idea that knowledge management can be a potential source of competitive advantage has gained strength in the last few years. However, a number of business actions are needed to generate an appropriate environment and infrastructure for knowledge creation, transfer and application. Among these actions there stands out the design of an organizational structure, the link of which with knowledge management is the main concern here. More specifically, the present paper has as its aim...

Specific features of waveguide recombination in laser structures with asymmetric barrier layers

Energy Technology Data Exchange (ETDEWEB)

Polubavkina, Yu. S., E-mail: polubavkina@mail.ru; Zubov, F. I.; Moiseev, E. I.; Kryzhanovskaya, N. V.; Maximov, M. V. [Russian Academy of Sciences, St. Petersburg National Research Academic University (Russian Federation); Semenova, E. S.; Yvind, K. [Technical University of Denmark, DTU Fotonik (Denmark); Asryan, L. V. [Virginia Polytechnic Institute and State University (United States); Zhukov, A. E. [Russian Academy of Sciences, St. Petersburg National Research Academic University (Russian Federation)

2017-02-15

The spatial distribution of the intensity of the emission caused by recombination appearing at a high injection level (up to 30 kA/cm{sup 2}) in the waveguide layer of a GaAs/AlGaAs laser structure with GaInP and AlGaInAs asymmetric barrier layers is studied by means of near-field scanning optical microscopy. It is found that the waveguide luminescence in such a laser, which is on the whole less intense as compared to that observed in a similar laser without asymmetric barriers, is non-uniformly distributed in the waveguide, so that the distribution maximum is shifted closer to the p-type cladding layer. This can be attributed to the ability of the GaInP barrier adjoining the quantum well on the side of the n-type cladding layer to suppress the hole transport.

Specific features of waveguide recombination in laser structures with asymmetric barrier layers

DEFF Research Database (Denmark)

Polubavkina, Yu; Zubov, F. I.; Moiseev, E.

2017-01-01

microscopy. It is found that the waveguide luminescence in such a laser, which is on the whole less intense as compared to that observed in a similar laser without asymmetric barriers, is non-uniformly distributed in the waveguide, so that the distribution maximum is shifted closer to the p-type cladding......The spatial distribution of the intensity of the emission caused by recombination appearing at a high injection level (up to 30 kA/cm2) in the waveguide layer of a GaAs/AlGaAs laser structure with GaInP and AlGaInAs asymmetric barrier layers is studied by means of near-field scanning optical...... layer. This can be attributed to the ability of the GaInP barrier adjoining the quantum well on the side of the n-type cladding layer to suppress the hole transport....

Specific features of the WWER Uranium-Gadolinium fuel behavior at BOL

International Nuclear Information System (INIS)

Shcheglov, A.; Proselkov, V.; Volkov, B.

2013-01-01

The calculated-experimental analysis of the WWER fuel behavior with 5%wt of gadolinium oxide at the beginning of life (BOL) is presented. The results are based on the data on fuel centerline temperature measurements, gas media pressure inside the cladding and fuel elongation obtained during irradiation of the test fuel rods in HBWR (Halden). Computer analysis of experimental data is performed with TOPRA-2, version 2 code. It is shown that specific features of the uranium-gadolinium fuel behavior at the early of life is due to presence of burnable absorber influencing the average linear heat rating, radial power distribution and lower thermal conductivity. In particular, the analysis of “late” relocation effect on the maximum Gd fuel temperature is presented. (authors)

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

Science.gov (United States)

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

2017-06-01

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

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

Science.gov (United States)

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

2017-10-17

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

Paralog-Specific Patterns of Structural Disorder and Phosphorylation in the Vertebrate SH3-SH2-Tyrosine Kinase Protein Family.

Science.gov (United States)

Dos Santos, Helena G; Siltberg-Liberles, Jessica

2016-09-19

One of the largest multigene families in Metazoa are the tyrosine kinases (TKs). These are important multifunctional proteins that have evolved as dynamic switches that perform tyrosine phosphorylation and other noncatalytic activities regulated by various allosteric mechanisms. TKs interact with each other and with other molecules, ultimately activating and inhibiting different signaling pathways. TKs are implicated in cancer and almost 30 FDA-approved TK inhibitors are available. However, specific binding is a challenge when targeting an active site that has been conserved in multiple protein paralogs for millions of years. A cassette domain (CD) containing SH3-SH2-Tyrosine Kinase domains reoccurs in vertebrate nonreceptor TKs. Although part of the CD function is shared between TKs, it also presents TK specific features. Here, the evolutionary dynamics of sequence, structure, and phosphorylation across the CD in 17 TK paralogs have been investigated in a large-scale study. We establish that TKs often have ortholog-specific structural disorder and phosphorylation patterns, while secondary structure elements, as expected, are highly conserved. Further, domain-specific differences are at play. Notably, we found the catalytic domain to fluctuate more in certain secondary structure elements than the regulatory domains. By elucidating how different properties evolve after gene duplications and which properties are specifically conserved within orthologs, the mechanistic understanding of protein evolution is enriched and regions supposedly critical for functional divergence across paralogs are highlighted. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Hydrotalcites: relation between structural features, basicity and activity in the Wittig reaction

NARCIS (Netherlands)

Sychev, M.V.; Prihod'ko, R.V.; Erdmann, K.; Mangel, A.; Santen, van R.A.

2001-01-01

Carbonate hydrotalcitrs (HTls) were prepared by coprecipitation of metal nitrate salts and Na2CO3. The structural features of noncalcined, calcined and reconstructed materials were characterized by XRD, Al-27 MAS NMR, AAS and N-2 adsorption. If was shown that reconstruction of the calcined HTls due

COMPETITIVE FEATURES IN THE MARKET STRUCTURE OF HOUSING PROPERTY WITH REGARD TO REGIONAL DEFINITIONS

Directory of Open Access Journals (Sweden)

Kostyantyn Pavlov

2017-09-01

Full Text Available The subject of research. Given the steady demand for residential real estate, the low solvency of the population, and unbalanced development of individual segments of the regional housing market, competition issues and the mechanism of its operation, today is very relevant. Real estate is one of the components of the national economy because it carries more than half of total world wealth and its stable functioning is one of the most complex processes of market transformations occurring in the country. Active functioning property markets are a prerequisite for the sustainable development of cities and regions of the country. This development is the basis for the effective management of regional and implemented in the system of national governance and local governance. In modern terms, Ukraine is at the stage of the market system, one of which is real estate market. From the way, the subject of study is a competitive relationship, and especially their formation in the regional real estate market. Methodology. In order to carry out a thorough study, there was elaborated numerous scientific literature authored by leading scientists of Ukraine, Europe, and the former Soviet Union camp to define the concepts of “competition”, “regional market”, “real estate”, “residential property”. According to the research of current problems and competitive features in the structure of the real estate market on the basis of regional specificity, a logical systematization of these concepts is made. Results of the research allowed us to “carry” a clear parallel between the correlation of factors and competitive impact on the regional real estate market of the potential buyers, the developer and manufacturer of products directly to real estate as an object relationship. Practical implications. The article is to study the specific competitive position in the regional real estate market in Ukraine and also features of exposure to it by consumers

Stream specificity and asymmetries in feature binding and content-addressable access in visual encoding and memory.

Science.gov (United States)

Huynh, Duong L; Tripathy, Srimant P; Bedell, Harold E; Ögmen, Haluk

2015-01-01

Human memory is content addressable-i.e., contents of the memory can be accessed using partial information about the bound features of a stored item. In this study, we used a cross-feature cuing technique to examine how the human visual system encodes, binds, and retains information about multiple stimulus features within a set of moving objects. We sought to characterize the roles of three different features (position, color, and direction of motion, the latter two of which are processed preferentially within the ventral and dorsal visual streams, respectively) in the construction and maintenance of object representations. We investigated the extent to which these features are bound together across the following processing stages: during stimulus encoding, sensory (iconic) memory, and visual short-term memory. Whereas all features examined here can serve as cues for addressing content, their effectiveness shows asymmetries and varies according to cue-report pairings and the stage of information processing and storage. Position-based indexing theories predict that position should be more effective as a cue compared to other features. While we found a privileged role for position as a cue at the stimulus-encoding stage, position was not the privileged cue at the sensory and visual short-term memory stages. Instead, the pattern that emerged from our findings is one that mirrors the parallel processing streams in the visual system. This stream-specific binding and cuing effectiveness manifests itself in all three stages of information processing examined here. Finally, we find that the Leaky Flask model proposed in our previous study is applicable to all three features.

Specific features of RBMK severe accidents progression and approach to the accident management

International Nuclear Information System (INIS)

Vasilevskij, V.P.; Nikitin, Yu.M.; Petrov, A.A.; Potapov, A.A.; Cherkashov, Yu.M.

2001-01-01

Fundamental construction features of the LWGR facilities (absence of common external containment shell, disintegrated circulation circuit and multichannel reactor core, positive vapor reactivity coefficient, high mass of thermally capacious graphite moderator) predetermining development of assumed heavy non-projected accidents and handling them are treated. Rating the categories of the reactor core damages for non-projected accidents and accident types producing specific grope of damages is given. Passing standard non-projected accidents, possible methods of attack accident consequences, as well as methods of calculated analysis of non-projected accidents are demonstrated [ru

Structural and spectroscopic features of proton hydrates in the crystalline state. Solid-state DFT study on HCl and triflic acid hydrates

Science.gov (United States)

Vener, M. V.; Chernyshov, I. Yu.; Rykounov, A. A.; Filarowski, A.

2018-01-01

Crystalline HCl and CF3SO3H hydrates serve as excellent model systems for protonated water and perfluorosulphonic acid membranes, respectively. They contain characteristic H3O+, H5О+2, H7О+3 and H3O+(H2O)3 (the Eigen cation) structures. The properties of these cations in the crystalline hydrates of strong monobasic acids are studied by solid-state density function theory (DFT). Simultaneous consideration of the HCl and CF3SO3H hydrates reveals the impact of the size of a counter ion and the crystalline environment on the structure and infrared active bands of the simplest proton hydrates. The H7O+3 structure is very sensitive to the size of the counter ion and symmetry of the local environment. This makes it virtually impossible to identify the specific features of H7O+3 in molecular crystals. The H3O+ ion can be treated as the Eigen-like cation in the crystalline state. Structural, infrared and electron-density features of H5О+2 and the Eigen cation are virtually insensitive to the size of the counter ion and the symmetry of the local crystalline environment. These cations can be considered as the simplest stable proton hydrates in the condensed phase. Finally, the influence of the Grimme correction on the structure and harmonic frequencies of the molecular crystals with short (strong) intermolecular O-H···O bonds is discussed.

Pose Estimation using Local Structure-Specific Shape and Appearance Context

DEFF Research Database (Denmark)

Buch, Anders Glent; Kraft, Dirk; Kämäräinen, Joni-Kristian

2013-01-01

information for both edge and texture structures. This is achieved by defining feature space relations which describe the neighborhood of a descriptor. By quantitative evaluations, we show that our descriptors provide high discriminative power compared to state of the art approaches. In addition, we show how...

Three-Dimensional Elastomeric Scaffolds Designed with Cardiac-Mimetic Structural and Mechanical Features

Science.gov (United States)

Neal, Rebekah A.; Jean, Aurélie; Park, Hyoungshin; Wu, Patrick B.; Hsiao, James; Engelmayr, George C.; Langer, Robert

2013-01-01

Tissue-engineered constructs, at the interface of material science, biology, engineering, and medicine, have the capacity to improve outcomes for cardiac patients by providing living cells and degradable biomaterials that can regenerate the native myocardium. With an ultimate goal of both delivering cells and providing mechanical support to the healing heart, we designed three-dimensional (3D) elastomeric scaffolds with (1) stiffnesses and anisotropy mimicking explanted myocardial specimens as predicted by finite-element (FE) modeling, (2) systematically varied combinations of rectangular pore pattern, pore aspect ratio, and strut width, and (3) structural features approaching tissue scale. Based on predicted mechanical properties, three scaffold designs were selected from eight candidates for fabrication from poly(glycerol sebacate) by micromolding from silicon wafers. Large 20×20 mm scaffolds with high aspect ratio features (5:1 strut height:strut width) were reproducibly cast, cured, and demolded at a relatively high throughput. Empirically measured mechanical properties demonstrated that scaffolds were cardiac mimetic and validated FE model predictions. Two-layered scaffolds providing fully interconnected pore networks were fabricated by layer-by-layer assembly. C2C12 myoblasts cultured on one-layered scaffolds exhibited specific patterns of cell elongation and interconnectivity that appeared to be guided by the scaffold pore pattern. Neonatal rat heart cells cultured on two-layered scaffolds for 1 week were contractile, both spontaneously and in response to electrical stimulation, and expressed sarcomeric α-actinin, a cardiac biomarker. This work not only demonstrated several scaffold designs that promoted functional assembly of rat heart cells, but also provided the foundation for further computational and empirical investigations of 3D elastomeric scaffolds for cardiac tissue engineering. PMID:23190320

Georeferenced Point Clouds: A Survey of Features and Point Cloud Management

Directory of Open Access Journals (Sweden)

Johannes Otepka

2013-10-01

Full Text Available This paper presents a survey of georeferenced point clouds. Concentration is, on the one hand, put on features, which originate in the measurement process themselves, and features derived by processing the point cloud. On the other hand, approaches for the processing of georeferenced point clouds are reviewed. This includes the data structures, but also spatial processing concepts. We suggest a categorization of features into levels that reflect the amount of processing. Point clouds are found across many disciplines, which is reflected in the versatility of the literature suggesting specific features.

A pursuit of lineage-specific and niche-specific proteome features in the world of archaea.

Science.gov (United States)

Roy Chowdhury, Anindya; Dutta, Chitra

2012-06-12

Archaea evoke interest among researchers for two enigmatic characteristics -a combination of bacterial and eukaryotic components in their molecular architectures and an enormous diversity in their life-style and metabolic capabilities. Despite considerable research efforts, lineage- specific/niche-specific molecular features of the whole archaeal world are yet to be fully unveiled. The study offers the first large-scale in silico proteome analysis of all archaeal species of known genome sequences with a special emphasis on methanogenic and sulphur-metabolising archaea. Overall amino acid usage in archaea is dominated by GC-bias. But the environmental factors like oxygen requirement or thermal adaptation seem to play important roles in selection of residues with no GC-bias at the codon level. All methanogens, irrespective of their thermal/salt adaptation, show higher usage of Cys and have relatively acidic proteomes, while the proteomes of sulphur-metabolisers have higher aromaticity and more positive charges. Despite of exhibiting thermophilic life-style, korarchaeota possesses an acidic proteome. Among the distinct trends prevailing in COGs (Cluster of Orthologous Groups of proteins) distribution profiles, crenarchaeal organisms display higher intra-order variations in COGs repertoire, especially in the metabolic ones, as compared to euryarchaea. All methanogens are characterised by a presence of 22 exclusive COGs. Divergences in amino acid usage, aromaticity/charge profiles and COG repertoire among methanogens and sulphur-metabolisers, aerobic and anaerobic archaea or korarchaeota and nanoarchaeota, as elucidated in the present study, point towards the presence of distinct molecular strategies for niche specialization in the archaeal world.

A pursuit of lineage-specific and niche-specific proteome features in the world of archaea

Directory of Open Access Journals (Sweden)

Roy Chowdhury Anindya

2012-06-01

Full Text Available Abstract Background Archaea evoke interest among researchers for two enigmatic characteristics –a combination of bacterial and eukaryotic components in their molecular architectures and an enormous diversity in their life-style and metabolic capabilities. Despite considerable research efforts, lineage- specific/niche-specific molecular features of the whole archaeal world are yet to be fully unveiled. The study offers the first large-scale in silico proteome analysis of all archaeal species of known genome sequences with a special emphasis on methanogenic and sulphur-metabolising archaea. Results Overall amino acid usage in archaea is dominated by GC-bias. But the environmental factors like oxygen requirement or thermal adaptation seem to play important roles in selection of residues with no GC-bias at the codon level. All methanogens, irrespective of their thermal/salt adaptation, show higher usage of Cys and have relatively acidic proteomes, while the proteomes of sulphur-metabolisers have higher aromaticity and more positive charges. Despite of exhibiting thermophilic life-style, korarchaeota possesses an acidic proteome. Among the distinct trends prevailing in COGs (Cluster of Orthologous Groups of proteins distribution profiles, crenarchaeal organisms display higher intra-order variations in COGs repertoire, especially in the metabolic ones, as compared to euryarchaea. All methanogens are characterised by a presence of 22 exclusive COGs. Conclusions Divergences in amino acid usage, aromaticity/charge profiles and COG repertoire among methanogens and sulphur-metabolisers, aerobic and anaerobic archaea or korarchaeota and nanoarchaeota, as elucidated in the present study, point towards the presence of distinct molecular strategies for niche specialization in the archaeal world.

Structural features of Fab fragments of rheumatoid factor IgM-RF in solution

International Nuclear Information System (INIS)

Volkov, V. V.; Lapuk, V. A.; Shtykova, E. V.; Stepina, N. D.; Dembo, K. A.; Sokolova, A. V.; Amarantov, S. V.; Timofeev, V. P.; Ziganshin, R. Kh.; Varlamova, E. Yu.

2008-01-01

The structural features of the Fab fragments of monoclonal (Waldenstroem's disease) immunoglobulin M (IgM) and rheumatoid immunoglobulin M (IgM-RF) were studied by a complex of methods, including small-angle X-ray scattering (SAXS), electron spin resonance (ESR), and mass spectrometry (MS). The Fab-RF fragment was demonstrated to be much more flexible in the region of interdomain contacts, the molecular weights and the shapes of the Fab and Fab-RF macromolecules in solution being only slightly different. According to the ESR data, the rotational correlation time for a spin label introduced into the peptide sequence for Fab is twice as large as that for Fab-RF (21±2 and 11±1 ns, respectively), whereas the molecular weights of these fragments differ by only 0.5% (mass-spectrometric data), which correlates with the results of molecular-shape modeling by small-angle X-ray scattering. The conclusion about the higher flexibility of the Fab-RF fragment contributes to an understanding of the specificity of interactions between the rheumatoid factor and the antigens of the own organism.

“Focal thyroid inferno” on color Doppler ultrasonography: A specific feature of focal Hashimoto's thyroiditis

International Nuclear Information System (INIS)

Fu, Xianshui; Guo, Limei; Zhang, Huabin; Ran, Weiqiang; Fu, Peng; Li, Zhiqiang; Chen, Wen; Jiang, Ling; Wang, Jinrui; Jia, Jianwen

2012-01-01

Purpose: To evaluate color-Doppler features predictive of focal Hashimoto's thyroiditis. Materials and methods: A total of 521 patients with 561 thyroid nodules that underwent surgeries or gun biopsies were included in this study. These nodules were divided into three groups: focal Hashimoto's thyroiditis (104 nodules in 101 patients), benignity other than focal Hashimoto's thyroiditis (73 nodules in 70 patients), and malignancy (358 nodules in 350 patients). On color Doppler sonography, four vascularity types were determined as: hypovascularity, marked internal flow, marked peripheral flow and focal thyroid inferno. The χ 2 test was performed to seek the potential vascularity type with the predictive ability of certain thyroid pathology. Furthermore, the gray-scale features of each nodule were also studied. Results: The vascularity type I (hypovascularity) was more often seen in focal Hashimoto's thyroiditis than other benignity and malignancy (46% vs. 20.5% and 19%). While the type II (marked internal flow) showed the opposite tendency (26.9% [focal Hashimoto's thyroiditis] vs. 45.2% [other benignity] and 52.8% [malignancy]). However, type III (marked peripheral flow) was unable to predict any thyroid pathology. Importantly, type IV (focal thyroid inferno) was exclusive to focal Hashimoto's thyroiditis. All 8 type IV nodules appeared to be solid, hypoechoic, and well-defined. Using “focal thyroid inferno” as an indicator of FHT, the diagnostic sensitivity and specificity were 7.7% and 100% respectively. Conclusions: The vascularity type of “focal thyroid inferno” is specific for focal Hashimoto thyroiditis. Recognition of this particular feature may avoid unnecessary interventional procedures for some solid hypoechoic thyroid nodules suspicious of malignancy.

Deep Convolutional Neural Networks: Structure, Feature Extraction and Training

Directory of Open Access Journals (Sweden)

Namatēvs Ivars

2017-12-01

Full Text Available Deep convolutional neural networks (CNNs are aimed at processing data that have a known network like topology. They are widely used to recognise objects in images and diagnose patterns in time series data as well as in sensor data classification. The aim of the paper is to present theoretical and practical aspects of deep CNNs in terms of convolution operation, typical layers and basic methods to be used for training and learning. Some practical applications are included for signal and image classification. Finally, the present paper describes the proposed block structure of CNN for classifying crucial features from 3D sensor data.

SPECIFIC FEATURES OF ANESTHESIA IN PATIENTS WITH MYASTHENIA GRAVIS.

Science.gov (United States)

Spasojevic, Ivana; Hajdukovic, Danica; Komarcevic, Milena; Petrovic, Stanislava; Jovanovic, Jelena; Ciric, Aleksandra

2016-09-01

Myasthenia gravis is an autoimmune disease caused by antibodies leading to the destruction of nicotinic acetylcholine receptors on the neuromuscular junction. It is characterized by muscle weakness that gets aggravated with physical activity and improves at rest. Myasthenia Gravis Foundation of America made the clinical classification of Myasthenia gravis which is still in use today. "Tensilon test" is still the gold standard for the diagnosis of Myasthenia gravis. In addition to this test repeated muscular stimulation can be used as well as the analysis of specific autoantibodies. Treatment of Myasthenia Gravis. In conservative treatment of Mysthenia gravis anticholinesterases, immunosuppressants and plasmapheresis can be used. If conservative treatment does not lead to the desired remission, surgical treatment is indicated. The most accepted indication for thymectomy is the presence of thymoma with generalized form of Myasthenia gravis in adults. How to Distinguish Myasthenic From Cholinergic Crisis.'The following is important to make a difference between these two crises: knowledge of the events that preceded the crisis, the size of pupils as well as the presence of muscarinic signs and tensilon test. Specific Features of Anesthesia in Patients with Myasthienia Gravis. Mechanism of the disease development is the reason'for the increased sensitivity or resistance of these patients to certain types of drugs used in anesthesia. Protocol of Perioperative Anesthesia in Patients with Myasthenia Gravis. Based on 35 years of experience in the surgical treatment of patients with Myasthenia gravis anesthesiologists at the Department of Thoracic Surgery, Institute for Pulmonary Diseases of Vojvodina. made the protocol of anesthesia and perioperative treatment for these patients. Anesthesiologists may have to deal with a patient with myasthenia gravis in different types of surgical interventions. The protocol for anesthesia and perioperative management of these patients

Structure of a year cycle of athletes training in aerobics (woman with various psychophysiological and functional features

Directory of Open Access Journals (Sweden)

T.V. Shepelenko

2018-02-01

Full Text Available Purpose : to develop structure of training process creation in a year cycle of qualified athletes’ preparation in aerobics (woman. Material : qualified athletes in aerobics participated in a research (n=46, age 20-22 years, height is 168±2, 4 cm, body weight is 62±4, 2 kg. Athletes were divided into experimental group (n=24 and control group (n=22. It was determined the level of special preparation: performance of standard combinations of basic aerobic steps. Results . The general principles of training programs preparation are developed. Programs include basic and variable components. The basic component of programs represents the standardized structure of means and methods selection of athletes’ preparation. The variable component of programs contained special means and methods differ on character and volume. One of the main parts of a variable component is the psychophysical training. It is based on performance of special sets of exercises in combination with mental figurative representations of motor nature. Conclusions . It is appropriate to carry out planning of training process in a year cycle of preparation considering specific features of factorial structure of athletes’ preparation.

nRC: non-coding RNA Classifier based on structural features.

Science.gov (United States)

Fiannaca, Antonino; La Rosa, Massimo; La Paglia, Laura; Rizzo, Riccardo; Urso, Alfonso

2017-01-01

Non-coding RNA (ncRNA) are small non-coding sequences involved in gene expression regulation of many biological processes and diseases. The recent discovery of a large set of different ncRNAs with biologically relevant roles has opened the way to develop methods able to discriminate between the different ncRNA classes. Moreover, the lack of knowledge about the complete mechanisms in regulative processes, together with the development of high-throughput technologies, has required the help of bioinformatics tools in addressing biologists and clinicians with a deeper comprehension of the functional roles of ncRNAs. In this work, we introduce a new ncRNA classification tool, nRC (non-coding RNA Classifier). Our approach is based on features extraction from the ncRNA secondary structure together with a supervised classification algorithm implementing a deep learning architecture based on convolutional neural networks. We tested our approach for the classification of 13 different ncRNA classes. We obtained classification scores, using the most common statistical measures. In particular, we reach an accuracy and sensitivity score of about 74%. The proposed method outperforms other similar classification methods based on secondary structure features and machine learning algorithms, including the RNAcon tool that, to date, is the reference classifier. nRC tool is freely available as a docker image at https://hub.docker.com/r/tblab/nrc/. The source code of nRC tool is also available at https://github.com/IcarPA-TBlab/nrc.

The sequence, structure and evolutionary features of HOTAIR in mammals

Science.gov (United States)

2011-01-01

. Conclusions HOTAIR exists in mammals, has poorly conserved sequences and considerably conserved structures, and has evolved faster than nearby HoxC genes. Exons of HOTAIR show distinct evolutionary features, and a 239 bp domain in the 1804 bp exon6 is especially conserved. These features, together with the absence of some exons and sequences in mouse, rat and kangaroo, suggest ab initio generation of HOTAIR in marsupials. Structure prediction identifies two fragments in the 5' end exon1 and the 3' end domain B of exon6, with sequence and structure invariably occurring in various predicted structures of exon1, the domain B of exon6 and the full HOTAIR. PMID:21496275

Specific features of NDT data and processing algorithms: new remedies to old ills

International Nuclear Information System (INIS)

Georgel, B.

1994-01-01

Non destructive testing data from in-service inspections have specific features that require the most sophisticated techniques of signal and image processing. Each step in the overall information extraction process must be optimized by using recent approaches such like data decomposition and modelization, compression, sensor fusion and knowledge based systems. This can be achieved by means of wavelet transform, inverse problems formulation, standard compression algorithms, combined detection and estimation, neural networks and expert systems. These techniques are briefly presented through a number of Electricite de France applications or through recent literature results. (author). 1 fig., 20 refs

Mine layout, geological features and seismic hazard.

CSIR Research Space (South Africa)

Van Aswegen, G

1993-01-01

Full Text Available – Applied Structure Stability Analysis .................................................27 4.2. Modelled System Stiffness ...........................................................................................28 4.2.1. Instability and System Stiffness... with the potential for large(r) dynamic rockmass instability in response to deep level mining, e.g.: • tectonic stresses, depth, mechanical strength of intact rock, • the existence and the frequency of intermediate and larger geological features, specifically...

Proteínas quinases: características estruturais e inibidores químicos Kinase protein: structural features and chemical inhibitors

Directory of Open Access Journals (Sweden)

Bárbara V. Silva

2009-01-01

Full Text Available Protein kinases are one of the largest protein families and they are responsible for regulation of a great number of signal transduction pathways in cells, through the phosphorylation of serine, threonine, or tyrosine residues. Deregulation of these enzymes is associated with several diseases including cancer, diabetes and inflammation. For this reason, specific inhibition of tyrosine or serine/threonine kinases may represent an interesting therapeutic approach. The most important types of protein kinases, their structural features and chemical inhibitors are discussed in this paper. Emphasis is given to the small-molecule drugs that target the ATP-binding sites of these enzymes.

Standardized Technical Specifications for Westinghouse PWRs

International Nuclear Information System (INIS)

1978-01-01

This Standard Technical Specification (STS) has been structured for the broadest possible use on Westinghouse plants currently being reviewed for an Operating License. Accordingly, the document contains specifications applicable to plants (1) with either 3 or 4 loops and (2) with and without loop stop valves. In addition, four separate and discrete containment specification sections are provided for each of the following containment types: Atmospheric, Ice Condenser, Sub-Atmospheric, and Dual. Optional specifications are provided for those features and systems which may be included in individual plant designs but are not generic in their scope of application. Alternate specifications are provided in a limited number of cases to cover situations where alternate specification requirements are necessary on a generic basis because of design differences. The format of the STS addresses the categories required by 10 CFR 50 and consists of six sections covering the areas of: Definitions, Safety Limits and Limiting Safety System Settings, Limiting Conditions for Operation, Surveillance Requirements, Design Features, and Administrative Controls

Camouflaging in a complex environment--octopuses use specific features of their surroundings for background matching.

Directory of Open Access Journals (Sweden)

Noam Josef

Full Text Available Living under intense predation pressure, octopuses evolved an effective and impressive camouflaging ability that exploits features of their surroundings to enable them to "blend in." To achieve such background matching, an animal may use general resemblance and reproduce characteristics of its entire surroundings, or it may imitate a specific object in its immediate environment. Using image analysis algorithms, we examined correlations between octopuses and their backgrounds. Field experiments show that when camouflaging, Octopus cyanea and O. vulgaris base their body patterns on selected features of nearby objects rather than attempting to match a large field of view. Such an approach enables the octopus to camouflage in partly occluded environments and to solve the problem of differences in appearance as a function of the viewing inclination of the observer.

Understanding specificity in metabolic pathways-Structural biology of human nucleotide metabolism

International Nuclear Information System (INIS)

Welin, Martin; Nordlund, Paer

2010-01-01

Interactions are the foundation of life at the molecular level. In the plethora of activities in the cell, the evolution of enzyme specificity requires the balancing of appropriate substrate affinity with a negative selection, in order to minimize interactions with other potential substrates in the cell. To understand the structural basis for enzyme specificity, the comparison of structural and biochemical data between enzymes within pathways using similar substrates and effectors is valuable. Nucleotide metabolism is one of the largest metabolic pathways in the human cell and is of outstanding therapeutic importance since it activates and catabolises nucleoside based anti-proliferative drugs and serves as a direct target for anti-proliferative drugs. In recent years the structural coverage of the enzymes involved in human nucleotide metabolism has been dramatically improved and is approaching completion. An important factor has been the contribution from the Structural Genomics Consortium (SGC) at Karolinska Institutet, which recently has solved 33 novel structures of enzymes and enzyme domains in human nucleotide metabolism pathways and homologs thereof. In this review we will discuss some of the principles for substrate specificity of enzymes in human nucleotide metabolism illustrated by a selected set of enzyme families where a detailed understanding of the structural determinants for specificity is now emerging.

Structure-specific endonucleases

DEFF Research Database (Denmark)

Minocherhomji, Sheroy; Hickson, Ian D

2014-01-01

Fragile sites are conserved loci predisposed to form breaks in metaphase chromosomes. The inherent instability of these loci is associated with chromosomal rearrangements in cancers and is a feature of cells from patients with chromosomal instability syndromes. One class of fragile sites, the com...

Subsurface mapping of Rustenburg Layered Suite (RLS), Bushveld Complex, South Africa: Inferred structural features using borehole data and spatial analysis

Science.gov (United States)

Bamisaiye, O. A.; Eriksson, P. G.; Van Rooy, J. L.; Brynard, H. M.; Foya, S.; Billay, A. Y.; Nxumalo, V.

2017-08-01

Faults and other structural features within the mafic-ultramafic layers of the Bushveld Complex have been a major issue mainly for exploration and mine planning. This study employed a new approach in detecting faults with both regional and meter scale offsets, which was not possible with the usually applied structure contour mapping. Interpretations of faults from structural and isopach maps were previously based on geological experience, while meter-scale faults were virtually impossible to detect from such maps. Spatial analysis was performed using borehole data primarily. This resulted in the identification of previously known structures and other hitherto unsuspected structural features. Consequently, the location, trends, and geometry of faults and some regional features within the Rustenburg Layered Suite (RLS) that might not be easy to detect through field mapping are adequately described in this study.

Design, construction and operation features of high-rise structures

Science.gov (United States)

Mylnik, Alexey; Mylnik, Vladimir; Zubeeva, Elena; Mukhamedzhanova, Olga

2018-03-01

The article considers design, construction and operation features of high-rise facilities. The analysis of various situations, that come from improper designing, construction and operation of unique facilities, is carried out. The integrated approach is suggested, when the problems of choosing acceptable constructional solutions related to the functional purpose, architectural solutions, methods of manufacturing and installation, operating conditions for unique buildings and structures are being tackled. A number of main causes for the emergency destruction of objects under construction and operation is considered. A number of measures are proposed on the basis of factor classification in order to efficiently prevent the situations, when various negative options of design loads and emergency impacts occur.

Consumers’ Preferences for Electronic Nicotine Delivery System Product Features: A Structured Content Analysis

Directory of Open Access Journals (Sweden)

Christine E. Kistler

2017-06-01

Full Text Available To inform potential governmental regulations, we aimed to develop a list of electronic nicotine delivery system (ENDS product features important to U.S. consumers by age and gender. We employed qualitative data methods. Participants were eligible if they had used an ENDS at least once. Groups were selected by age and gender (young adult group aged 18–25, n = 11; middle-age group aged 26–64, n = 9; and women’s group aged 26–64, n = 9. We conducted five individual older adult interviews (aged 68–80. Participants discussed important ENDS features. We conducted a structured content analysis of the group and interview responses. Of 34 participants, 68% were white and 56% were female. Participants mentioned 12 important ENDS features, including: (1 user experience; (2 social acceptability; (3 cost; (4 health risks/benefits; (5 ease of use; (6 flavors; (7 smoking cessation aid; (8 nicotine content; (9 modifiability; (10 ENDS regulation; (11 bridge between tobacco cigarettes; (12 collectability. The most frequently mentioned ENDS feature was modifiability for young adults, user experience for middle-age and older adults, and flavor for the women’s group. This study identified multiple features important to ENDS consumers. Groups differed in how they viewed various features by age and gender. These results can inform ongoing regulatory efforts.

Obstructive sleep apnea screening by integrating snore feature classes

International Nuclear Information System (INIS)

Abeyratne, U R; De Silva, S; Hukins, C; Duce, B

2013-01-01

Obstructive sleep apnea (OSA) is a serious sleep disorder with high community prevalence. More than 80% of OSA suffers remain undiagnosed. Polysomnography (PSG) is the current reference standard used for OSA diagnosis. It is expensive, inconvenient and demands the extensive involvement of a sleep technologist. At present, a low cost, unattended, convenient OSA screening technique is an urgent requirement. Snoring is always almost associated with OSA and is one of the earliest nocturnal symptoms. With the onset of sleep, the upper airway undergoes both functional and structural changes, leading to spatially and temporally distributed sites conducive to snore sound (SS) generation. The goal of this paper is to investigate the possibility of developing a snore based multi-feature class OSA screening tool by integrating snore features that capture functional, structural, and spatio-temporal dependences of SS. In this paper, we focused our attention to the features in voiced parts of a snore, where quasi-repetitive packets of energy are visible. Individual snore feature classes were then optimized using logistic regression for optimum OSA diagnostic performance. Consequently, all feature classes were integrated and optimized to obtain optimum OSA classification sensitivity and specificity. We also augmented snore features with neck circumference, which is a one-time measurement readily available at no extra cost. The performance of the proposed method was evaluated using snore recordings from 86 subjects (51 males and 35 females). Data from each subject consisted of 6–8 h long sound recordings, made concurrently with routine PSG in a clinical sleep laboratory. Clinical diagnosis supported by standard PSG was used as the reference diagnosis to compare our results against. Our proposed techniques resulted in a sensitivity of 93±9% with specificity 93±9% for females and sensitivity of 92±6% with specificity 93±7% for males at an AHI decision threshold of 15 events

Light-harvesting features revealed by the structure of plant Photosystem I

CERN Document Server

Ben-Shem, A; Nelson, N; 10.1023/B:PRES.0000036881.23512.42

2004-01-01

Oxygenic photosynthesis is driven by two multi-subunit membrane protein complexes, Photosystem I and Photosystem II. In plants and green algae, both complexes are composed of two moieties: a reaction center (RC), where light-induced charge translocation occurs, and a peripheral antenna that absorbs light and funnels its energy to the reaction center. The peripheral antenna of PS I (LHC I) is composed of four gene products (Lhca 1-4) that are unique among the chlorophyll a/b binding proteins in their pronounced long-wavelength absorbance and in their assembly into dimers. The recently determined structure of plant Photosystem I provides the first relatively high- resolution structural model of a super-complex containing a reaction center and its peripheral antenna. We describe some of the structural features responsible for the unique properties of LHC I and discuss the advantages of the particular LHC I dimerization mode over monomeric or trimeric forms. In addition, we delineate some of the interactions betw...

The Roles of Feature-Specific Task Set and Bottom-Up Salience in Attentional Capture: An ERP Study

Science.gov (United States)

Eimer, Martin; Kiss, Monika; Press, Clare; Sauter, Disa

2009-01-01

We investigated the roles of top-down task set and bottom-up stimulus salience for feature-specific attentional capture. Spatially nonpredictive cues preceded search arrays that included a color-defined target. For target-color singleton cues, behavioral spatial cueing effects were accompanied by cue-induced N2pc components, indicative of…

Purification of specific structured lipids by distillation: Effects on acyl migration

DEFF Research Database (Denmark)

Xu, Xuebing; Skands, A.; Adler-Nissen, Jens

2001-01-01

The cause and effects of acyl migration during the purification of specific structured lipids by distillation were studied in a conventional batch deodorizer with stripping steam. The mixture of specific structured lipids produced by lipase-catalyzed acidolysis between rapeseed oil and capric acid...... influenced the rate of acyl migration, and their combinations made the effect more severe. However, diacylglycerols were found to be the main reason for acyl migration. In the distillation of the specific structured lipid product mixture, distillation temperature and time were the main factors to determine...... the degree of acyl migration and the extent of separation of free fatty acids. The results indicate that more efficient separation technology should be used to improve the quality of the purified structured lipids. in order to reduce the distillation temperature, vacuum should be made as low as possible...

Damage and noise sensitivity evaluation of autoregressive features extracted from structure vibration

International Nuclear Information System (INIS)

Yao, Ruigen; Pakzad, Shamim N

2014-01-01

In the past few decades many types of structural damage indices based on structural health monitoring signals have been proposed, requiring performance evaluation and comparison studies on these indices in a quantitative manner. One tool to help accomplish this objective is analytical sensitivity analysis, which has been successfully used to evaluate the influences of system operational parameters on observable characteristics in many fields of study. In this paper, the sensitivity expressions of two damage features, namely the Mahalanobis distance of autoregressive coefficients and the Cosh distance of autoregressive spectra, will be derived with respect to both structural damage and measurement noise level. The effectiveness of the proposed methods is illustrated in a numerical case study on a 10-DOF system, where their results are compared with those from direct simulation and theoretical calculation. (paper)

Porous silicon structures with high surface area/specific pore size

Science.gov (United States)

Northrup, M.A.; Yu, C.M.; Raley, N.F.

1999-03-16

Fabrication and use of porous silicon structures to increase surface area of heated reaction chambers, electrophoresis devices, and thermopneumatic sensor-actuators, chemical preconcentrates, and filtering or control flow devices. In particular, such high surface area or specific pore size porous silicon structures will be useful in significantly augmenting the adsorption, vaporization, desorption, condensation and flow of liquids and gases in applications that use such processes on a miniature scale. Examples that will benefit from a high surface area, porous silicon structure include sample preconcentrators that are designed to adsorb and subsequently desorb specific chemical species from a sample background; chemical reaction chambers with enhanced surface reaction rates; and sensor-actuator chamber devices with increased pressure for thermopneumatic actuation of integrated membranes. Examples that benefit from specific pore sized porous silicon are chemical/biological filters and thermally-activated flow devices with active or adjacent surfaces such as electrodes or heaters. 9 figs.

Detecting Structural Features in Metallic Glass via Synchrotron Radiation Experiments Combined with Simulations

Directory of Open Access Journals (Sweden)

Gu-Qing Guo

2015-11-01

Full Text Available Revealing the essential structural features of metallic glasses (MGs will enhance the understanding of glass-forming mechanisms. In this work, a feasible scheme is provided where we performed the state-of-the-art synchrotron-radiation based experiments combined with simulations to investigate the microstructures of ZrCu amorphous compositions. It is revealed that in order to stabilize the amorphous state and optimize the topological and chemical distribution, besides the icosahedral or icosahedral-like clusters, other types of clusters also participate in the formation of the microstructure in MGs. This cluster-level co-existing feature may be popular in this class of glassy materials.

Structural basis for the site-specific incorporation of lysine derivatives into proteins.

Directory of Open Access Journals (Sweden)

Veronika Flügel

Full Text Available Posttranslational modifications (PTMs of proteins determine their structure-function relationships, interaction partners, as well as their fate in the cell and are crucial for many cellular key processes. For instance chromatin structure and hence gene expression is epigenetically regulated by acetylation or methylation of lysine residues in histones, a phenomenon known as the 'histone code'. Recently it was shown that these lysine residues can furthermore be malonylated, succinylated, butyrylated, propionylated and crotonylated, resulting in significant alteration of gene expression patterns. However the functional implications of these PTMs, which only differ marginally in their chemical structure, is not yet understood. Therefore generation of proteins containing these modified amino acids site specifically is an important tool. In the last decade methods for the translational incorporation of non-natural amino acids using orthogonal aminoacyl-tRNA synthetase (aaRS:tRNAaaCUA pairs were developed. A number of studies show that aaRS can be evolved to use non-natural amino acids and expand the genetic code. Nevertheless the wild type pyrrolysyl-tRNA synthetase (PylRS from Methanosarcina mazei readily accepts a number of lysine derivatives as substrates. This enzyme can further be engineered by mutagenesis to utilize a range of non-natural amino acids. Here we present structural data on the wild type enzyme in complex with adenylated ε-N-alkynyl-, ε-N-butyryl-, ε-N-crotonyl- and ε-N-propionyl-lysine providing insights into the plasticity of the PylRS active site. This shows that given certain key features in the non-natural amino acid to be incorporated, directed evolution of this enzyme is not necessary for substrate tolerance.

Architecture Of Uzbekistan Of The Ancient Period Style Features And Composition Laws

Directory of Open Access Journals (Sweden)

Nurmukhamedova Shoira Zahidovna

2015-08-01

Full Text Available Specific features of the development of architecture in Uzbekistan in ancient period are considered in the paper. The author emphasizes the role of building materials and structures studies the composition of ancient settlements in Khorezm and Bactria reveals a high level of military architecture and planning principles of residential and castle structures.

Tissue-specific features of the X chromosome and nucleolus spatial dynamics in a malaria mosquito, Anopheles atroparvus.

Science.gov (United States)

Bondarenko, Semen M; Artemov, Gleb N; Sharakhov, Igor V; Stegniy, Vladimir N

2017-01-01

Spatial organization of chromosome territories is important for maintenance of genomic stability and regulation of gene expression. Recent studies have shown tissue-specific features of chromosome attachments to the nuclear envelope in various organisms including malaria mosquitoes. However, other spatial characteristics of nucleus organization, like volume and shape of chromosome territories, have not been studied in Anopheles. We conducted a thorough analysis of tissue-specific features of the X chromosome and nucleolus volume and shape in follicular epithelium and nurse cells of the Anopheles atroparvus ovaries using a modern open-source software. DNA of the polytene X chromosome from ovarian nurse cells was obtained by microdissection and was used as a template for amplification with degenerate oligo primers. A fluorescently labeled X chromosome painting probe was hybridized with formaldehyde-fixed ovaries of mosquitoes using a 3D-FISH method. The nucleolus was stained by immunostaining with an anti-fibrillarin antibody. The analysis was conducted with TANGO-a software for a chromosome spatial organization analysis. We show that the volume and position of the X chromosome have tissue-specific characteristics. Unlike nurse cell nuclei, the growth of follicular epithelium nuclei is not accompanied with the proportional growth of the X chromosome. However, the shape of the X chromosome does not differ between the tissues. The dynamics of the X chromosome attachment regions location is tissue-specific and it is correlated with the process of nucleus growth in follicular epithelium and nurse cells.

Island-specific preferences of tourists for environmental features: implications of climate change for tourism dependent states

Energy Technology Data Exchange (ETDEWEB)

Uyarra, M.C.; Cote, I.M. [East Anglia Univ., Norwich (United Kingdom). Centre for Ecology, Evolution and Conservation; Gill, J.A. [East Anglia Univ., Norwich (United Kingdom). School of Environmental Sciences; Tyndall Centre for Climate Change Research, Norwich (United Kingdom); Tinch, R.T. [East Anglia Univ., Norwich (United Kingdom). School of Environmental Sciences; Macaulay Land Use Research Inst., Aberdeen (United Kingdom); Viner, D. [East Anglia Univ., Norwich (United Kingdom). Climate Research Unit; Watkinson, A.R. [East Anglia Univ., Norwich (United Kingdom). Centre for Ecology, Evolution and Conservation; East Anglia Univ., Norwich (United Kingdom). School of Environmental Sciences

2005-03-15

Climate change may affect important environmental components of holiday destinations, which might have repercussions for tourism-dependent economies. This study documents the importance of environmental attributes in determining the choice and holiday enjoyment of tourists visiting Bonaire and Barbados, two Caribbean islands with markedly different tourism markets and infrastructure. Three hundred and sixteen and 338 participants from Bonaire and Barbados, respectively, completed standardized questionnaires. Warm temperatures, clear waters and low health risks were the most important environmental features determining holiday destination choice. However, tourists in Bonaire thereafter prioritized marine wildlife attributes (i.e. coral and fish diversity and abundance) over other environmental features, whereas tourists in Barbados exhibited stronger preferences for terrestrial features, particularly beach characteristics. The willingness of tourists to revisit these islands was strongly linked to the state of the preferred environmental attributes. More than 80% of tourists in Bonaire and Barbados would be unwilling to return for the same holiday price in the event, respectively, of coral bleaching as a result of elevated sea surface temperatures and reduced beach area as a result of sea level rise. Climate change might have a significant impact on Caribbean tourism economy through alteration of environmental features important to destination selection. Island-specific management strategies, such as focusing resources on the protection of key marine or terrestrial features, may provide a means of reducing the environmental and economic impacts of climate change. (author)

Guiding exploration in conformational feature space with Lipschitz underestimation for ab-initio protein structure prediction.

Science.gov (United States)

Hao, Xiaohu; Zhang, Guijun; Zhou, Xiaogen

2018-04-01

Computing conformations which are essential to associate structural and functional information with gene sequences, is challenging due to the high dimensionality and rugged energy surface of the protein conformational space. Consequently, the dimension of the protein conformational space should be reduced to a proper level, and an effective exploring algorithm should be proposed. In this paper, a plug-in method for guiding exploration in conformational feature space with Lipschitz underestimation (LUE) for ab-initio protein structure prediction is proposed. The conformational space is converted into ultrafast shape recognition (USR) feature space firstly. Based on the USR feature space, the conformational space can be further converted into Underestimation space according to Lipschitz estimation theory for guiding exploration. As a consequence of the use of underestimation model, the tight lower bound estimate information can be used for exploration guidance, the invalid sampling areas can be eliminated in advance, and the number of energy function evaluations can be reduced. The proposed method provides a novel technique to solve the exploring problem of protein conformational space. LUE is applied to differential evolution (DE) algorithm, and metropolis Monte Carlo(MMC) algorithm which is available in the Rosetta; When LUE is applied to DE and MMC, it will be screened by the underestimation method prior to energy calculation and selection. Further, LUE is compared with DE and MMC by testing on 15 small-to-medium structurally diverse proteins. Test results show that near-native protein structures with higher accuracy can be obtained more rapidly and efficiently with the use of LUE. Copyright © 2018 Elsevier Ltd. All rights reserved.

The Advantage of Playing Home in NBA: Microscopic, Team-Specific and Evolving Features.

Science.gov (United States)

Ribeiro, Haroldo V; Mukherjee, Satyam; Zeng, Xiao Han T

2016-01-01

The idea that the success rate of a team increases when playing home is broadly accepted and documented for a wide variety of sports. Investigations on the so-called "home advantage phenomenon" date back to the 70's and ever since has attracted the attention of scholars and sport enthusiasts. These studies have been mainly focused on identifying the phenomenon and trying to correlate it with external factors such as crowd noise and referee bias. Much less is known about the effects of home advantage in the "microscopic" dynamics of the game (within the game) or possible team-specific and evolving features of this phenomenon. Here we present a detailed study of these previous features in the National Basketball Association (NBA). By analyzing play-by-play events of more than sixteen thousand games that span thirteen NBA seasons, we have found that home advantage affects the microscopic dynamics of the game by increasing the scoring rates and decreasing the time intervals between scores of teams playing home. We verified that these two features are different among the NBA teams, for instance, the scoring rate of the Cleveland Cavaliers team is increased ≈0.16 points per minute (on average the seasons 2004-05 to 2013-14) when playing home, whereas for the New Jersey Nets (now the Brooklyn Nets) this rate increases in only ≈0.04 points per minute. We further observed that these microscopic features have evolved over time in a non-trivial manner when analyzing the results team-by-team. However, after averaging over all teams some regularities emerge; in particular, we noticed that the average differences in the scoring rates and in the characteristic times (related to the time intervals between scores) have slightly decreased over time, suggesting a weakening of the phenomenon. This study thus adds evidence of the home advantage phenomenon and contributes to a deeper understanding of this effect over the course of games.

The Advantage of Playing Home in NBA: Microscopic, Team-Specific and Evolving Features.

Directory of Open Access Journals (Sweden)

Haroldo V Ribeiro

Full Text Available The idea that the success rate of a team increases when playing home is broadly accepted and documented for a wide variety of sports. Investigations on the so-called "home advantage phenomenon" date back to the 70's and ever since has attracted the attention of scholars and sport enthusiasts. These studies have been mainly focused on identifying the phenomenon and trying to correlate it with external factors such as crowd noise and referee bias. Much less is known about the effects of home advantage in the "microscopic" dynamics of the game (within the game or possible team-specific and evolving features of this phenomenon. Here we present a detailed study of these previous features in the National Basketball Association (NBA. By analyzing play-by-play events of more than sixteen thousand games that span thirteen NBA seasons, we have found that home advantage affects the microscopic dynamics of the game by increasing the scoring rates and decreasing the time intervals between scores of teams playing home. We verified that these two features are different among the NBA teams, for instance, the scoring rate of the Cleveland Cavaliers team is increased ≈0.16 points per minute (on average the seasons 2004-05 to 2013-14 when playing home, whereas for the New Jersey Nets (now the Brooklyn Nets this rate increases in only ≈0.04 points per minute. We further observed that these microscopic features have evolved over time in a non-trivial manner when analyzing the results team-by-team. However, after averaging over all teams some regularities emerge; in particular, we noticed that the average differences in the scoring rates and in the characteristic times (related to the time intervals between scores have slightly decreased over time, suggesting a weakening of the phenomenon. This study thus adds evidence of the home advantage phenomenon and contributes to a deeper understanding of this effect over the course of games.

Local appearance features for robust MRI brain structure segmentation across scanning protocols

DEFF Research Database (Denmark)

Achterberg, H.C.; Poot, Dirk H. J.; van der Lijn, Fedde

2013-01-01

Segmentation of brain structures in magnetic resonance images is an important task in neuro image analysis. Several papers on this topic have shown the benefit of supervised classification based on local appearance features, often combined with atlas-based approaches. These methods require...... a representative annotated training set and therefore often do not perform well if the target image is acquired on a different scanner or with a different acquisition protocol than the training images. Assuming that the appearance of the brain is determined by the underlying brain tissue distribution...... with substantially different imaging protocols and on different scanners. While a combination of conventional appearance features trained on data from a different scanner with multiatlas segmentation performed poorly with an average Dice overlap of 0.698, the local appearance model based on the new acquisition...

Specific features of early post-stroke seizures

Directory of Open Access Journals (Sweden)

Tatyana Valeryevna Danilova

2012-01-01

Full Text Available The paper presents the results of examining 101 patients (68 men and 33 women aged 48 to 89 years with seizures in the first 7 days of stroke. A control group comprised 97 patients who had experienced ischemic stroke without seizures. Early seizures more frequently occurred in the cardioembolic subtype of stroke as simple partial seizures. The neuroimaging features of ischemic foci were revealed and the cerebrovascular responsiveness was evaluated in different vascular basins in these patients.

Human lactoferricin derived di-peptides deploying loop structures induce apoptosis specifically in cancer cells through targeting membranous phosphatidylserine.

Science.gov (United States)

Riedl, Sabrina; Leber, Regina; Rinner, Beate; Schaider, Helmut; Lohner, Karl; Zweytick, Dagmar

2015-11-01

Host defense-derived peptides have emerged as a novel strategy for the development of alternative anticancer therapies. In this study we report on characteristic features of human lactoferricin (hLFcin) derivatives which facilitate specific killing of cancer cells of melanoma, glioblastoma and rhabdomyosarcoma compared with non-specific derivatives and the synthetic peptide RW-AH. Changes in amino acid sequence of hLFcin providing 9-11 amino acids stretched derivatives LF11-316, -318 and -322 only yielded low antitumor activity. However, the addition of the repeat (di-peptide) and the retro-repeat (di-retro-peptide) sequences highly improved cancer cell toxicity up to 100% at 20 μM peptide concentration. Compared to the complete parent sequence hLFcin the derivatives showed toxicity on the melanoma cell line A375 increased by 10-fold and on the glioblastoma cell line U-87mg by 2-3-fold. Reduced killing velocity, apoptotic blebbing, activation of caspase 3/7 and formation of apoptotic DNA fragments proved that the active and cancer selective peptides, e.g. R-DIM-P-LF11-322, trigger apoptosis, whereas highly active, though non-selective peptides, such as DIM-LF11-318 and RW-AH seem to kill rapidly via necrosis inducing membrane lyses. Structural studies revealed specific toxicity on cancer cells by peptide derivatives with loop structures, whereas non-specific peptides comprised α-helical structures without loop. Model studies with the cancer membrane mimic phosphatidylserine (PS) gave strong evidence that PS only exposed by cancer cells is an important target for specific hLFcin derivatives. Other negatively charged membrane exposed molecules as sialic acid, heparan and chondroitin sulfate were shown to have minor impact on peptide activity. Copyright © 2015. Published by Elsevier B.V.

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

Science.gov (United States)

Derby, Brian

2010-08-01

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

Key structural features of nonsteroidal ligands for binding and activation of the androgen receptor.

Science.gov (United States)

Yin, Donghua; He, Yali; Perera, Minoli A; Hong, Seoung Soo; Marhefka, Craig; Stourman, Nina; Kirkovsky, Leonid; Miller, Duane D; Dalton, James T

2003-01-01

The purposes of the present studies were to examine the androgen receptor (AR) binding ability and in vitro functional activity of multiple series of nonsteroidal compounds derived from known antiandrogen pharmacophores and to investigate the structure-activity relationships (SARs) of these nonsteroidal compounds. The AR binding properties of sixty-five nonsteroidal compounds were assessed by a radioligand competitive binding assay with the use of cytosolic AR prepared from rat prostates. The AR agonist and antagonist activities of high-affinity ligands were determined by the ability of the ligand to regulate AR-mediated transcriptional activation in cultured CV-1 cells, using a cotransfection assay. Nonsteroidal compounds with diverse structural features demonstrated a wide range of binding affinity for the AR. Ten compounds, mainly from the bicalutamide-related series, showed a binding affinity superior to the structural pharmacophore from which they were derived. Several SARs regarding nonsteroidal AR binding were revealed from the binding data, including stereoisomeric conformation, steric effect, and electronic effect. The functional activity of high-affinity ligands ranged from antagonist to full agonist for the AR. Several structural features were found to be determinative of agonist and antagonist activities. The nonsteroidal AR agonists identified from the present studies provided a pool of candidates for further development of selective androgen receptor modulators (SARMs) for androgen therapy. Also, these studies uncovered or confirmed numerous important SARs governing AR binding and functional properties by nonsteroidal molecules, which would be valuable in the future structural optimization of SARMs.

Analysis of Specific Features of International Standards of Personnel Security of an Enterprise

Directory of Open Access Journals (Sweden)

Otenko Iryna P.

2014-03-01

Full Text Available The article marks out components of personnel security of an enterprise, outlines processes of personnel management, which correspond with conditions of security of life and labour, competent, socially protected professional activity, availability of the acting system of motivation and stimulation, and possibilities for corporate conflicts resolution. The article presents basic standards, rules and legislative acts that regulate ensuring personnel security. It analyses specific features of application of standards with respect to: life security and labour protection culture at an enterprise, including managerial systems and practice, behaviour of personnel at working places and also intellectual component of personnel security, which envisages that personnel has knowledge and competences that assist in achievement of strategic goals of an enterprise.

Specific features of NH3 and plasma-assisted MBE in the fabrication of III-N HEMT heterostructures

International Nuclear Information System (INIS)

Alexeev, A. N.; Krasovitsky, D. M.; Petrov, S. I.; Chaly, V. P.; Mamaev, V. V.; Sidorov, V. G.

2015-01-01

The specific features of how nitride HEMT heterostructures are produced by NH 3 and plasma-assisted (PA) molecular-beam epitaxy (MBE) are considered. It is shown that the use of high-temperature AlN/AlGaN buffer layers grown with ammonia at extremely high temperatures (up to 1150°C) can drastically improve the structural perfection of the active GaN layers and reduce the dislocation density in these layers to values of 9 × 10 8 −1 × 10 9 cm −2 . The use of buffer layers of this kind makes it possible to obtain high-quality GaN/AlGaN heterostructures by both methods. At the same time, in contrast to ammonia MBE which is difficult to apply at T < 500°C (because of the low efficiency of ammonia decomposition), PA MBE is rather effective at low temperatures, e.g., for the growth of InAlN layers lattice-matched with GaN. The results obtained in the MBE growth of AlN/AlGaN/GaN/InAlN heterostructures by both PA-MBE and NH 3 -MBE with an extremely high ammonia flux are demonstrated

Perceptual learning is specific to the trained structure of information.

Science.gov (United States)

Cohen, Yamit; Daikhin, Luba; Ahissar, Merav

2013-12-01

What do we learn when we practice a simple perceptual task? Many studies have suggested that we learn to refine or better select the sensory representations of the task-relevant dimension. Here we show that learning is specific to the trained structural regularities. Specifically, when this structure is modified after training with a fixed temporal structure, performance regresses to pretraining levels, even when the trained stimuli and task are retained. This specificity raises key questions as to the importance of low-level sensory modifications in the learning process. We trained two groups of participants on a two-tone frequency discrimination task for several days. In one group, a fixed reference tone was consistently presented in the first interval (the second tone was higher or lower), and in the other group the same reference tone was consistently presented in the second interval. When following training, these temporal protocols were switched between groups, performance of both groups regressed to pretraining levels, and further training was needed to attain postlearning performance. ERP measures, taken before and after training, indicated that participants implicitly learned the temporal regularity of the protocol and formed an attentional template that matched the trained structure of information. These results are consistent with Reverse Hierarchy Theory, which posits that even the learning of simple perceptual tasks progresses in a top-down manner, hence can benefit from temporal regularities at the trial level, albeit at the potential cost that learning may be specific to these regularities.

Innovations in individual feature history management - The significance of feature-based temporal model

Science.gov (United States)

Choi, J.; Seong, J.C.; Kim, B.; Usery, E.L.

2008-01-01

A feature relies on three dimensions (space, theme, and time) for its representation. Even though spatiotemporal models have been proposed, they have principally focused on the spatial changes of a feature. In this paper, a feature-based temporal model is proposed to represent the changes of both space and theme independently. The proposed model modifies the ISO's temporal schema and adds new explicit temporal relationship structure that stores temporal topological relationship with the ISO's temporal primitives of a feature in order to keep track feature history. The explicit temporal relationship can enhance query performance on feature history by removing topological comparison during query process. Further, a prototype system has been developed to test a proposed feature-based temporal model by querying land parcel history in Athens, Georgia. The result of temporal query on individual feature history shows the efficiency of the explicit temporal relationship structure. ?? Springer Science+Business Media, LLC 2007.

Association between MRI structural features and cognitive measures in pediatric multiple sclerosis

Science.gov (United States)

Amoroso, N.; Bellotti, R.; Fanizzi, A.; Lombardi, A.; Monaco, A.; Liguori, M.; Margari, L.; Simone, M.; Viterbo, R. G.; Tangaro, S.

2017-09-01

Multiple sclerosis (MS) is an inflammatory and demyelinating disease associated with neurodegenerative processes that lead to brain structural changes. The disease affects mostly young adults, but 3-5% of cases has a pediatric onset (POMS). Magnetic Resonance Imaging (MRI) is generally used for diagnosis and follow-up in MS patients, however the most common MRI measures (e.g. new or enlarging T2-weighted lesions, T1-weighted gadolinium- enhancing lesions) have often failed as surrogate markers of MS disability and progression. MS is clinically heterogenous with symptoms that can include both physical changes (such as visual loss or walking difficulties) and cognitive impairment. 30-50% of POMS experience prominent cognitive dysfunction. In order to investigate the association between cognitive measures and brain morphometry, in this work we present a fully automated pipeline for processing and analyzing MRI brain scans. Relevant anatomical structures are segmented with FreeSurfer; besides, statistical features are computed. Thus, we describe the data referred to 12 patients with early POMS (mean age at MRI: 15.5 +/- 2.7 years) with a set of 181 structural features. The major cognitive abilities measured are verbal and visuo-spatial learning, expressive language and complex attention. Data was collected at the Department of Basic Sciences, Neurosciences and Sense Organs, University of Bari, and exploring different abilities like the verbal and visuo-spatial learning, expressive language and complex attention. Different regression models and parameter configurations are explored to assess the robustness of the results, in particular Generalized Linear Models, Bayes Regression, Random Forests, Support Vector Regression and Artificial Neural Networks are discussed.

Structural features of the San Andreas fault at Tejon Pass, California

Science.gov (United States)

Dewers, T. A.; Reches, Z.; Brune, J. N.

2002-12-01

We mapped a 2 km belt along the San Andreas fault (SAF) in the Tejon Pass area where road cuts provide fresh exposures of the fault zone and surrounding rocks. Our 1:2,000 structural mapping is focused on analysis of faulting processes and is complementary to regional mapping at 1:12,000 scale by Ramirez (M.Sc., UC Santa Barbara, 1984). The dominant rock units are the Hungry Valley Formation of Pliocene age (clastic sediments) exposed south of the SAF, and the Tejon Lookout granite (Cretaceous) and Neenach Volcanic Formation exposed north of it. Ramirez (1983) deduced ~220 km of post-Miocene lateral slip. The local trend of the SAF is about N60W and it includes at least three main, subparallel segments that form a 200 m wide zone. The traces of the segments are quasi-linear, discontinuous, and they are stepped with respect to each other, forming at least five small pull-aparts and sag ponds in the mapping area. The three segments were not active semi-contemporaneously and the southern segment is apparently the oldest. The largest pull-apart, 60-70 m wide, displays young (Quaternary?) silt and shale layers. We found two rock bodies that are suspected as fault-rocks. One is a 1-2 m thick sheet-like body that separates the Tejon Lookout granite from young (Recent?) clastic rocks. In the field, it appears as a gouge zone composed of poorly cemented, dark clay size grains; however, the microstructure of this rock does not reveal clear shear features. The second body is the 80-120 m wide zone of Tejon Lookout granite that extends for less than 1 km along the SAF in the mapped area. It is characterized by three structural features: (1) pulverization into friable, granular material by multitude of grain-crossing fractures; (2) abundance of dip-slip small faults that are gently dipping toward and away from the SAF; and (3) striking lack of evidence for shear parallel to the SAF. The relationships between these features and the large right-lateral shear along the SAF are

The Role of Emotion in Musical Improvisation: An Analysis of Structural Features

OpenAIRE

McPherson, Malinda J.; Lopez-Gonzalez, Monica; Rankin, Summer K.; Limb, Charles J.

2014-01-01

One of the primary functions of music is to convey emotion, yet how music accomplishes this task remains unclear. For example, simple correlations between mode (major vs. minor) and emotion (happy vs. sad) do not adequately explain the enormous range, subtlety or complexity of musically induced emotions. In this study, we examined the structural features of unconstrained musical improvisations generated by jazz pianists in response to emotional cues. We hypothesized that musicians would not u...

Classification of Vessels in Single-Pol COSMO-SkyMed Images Based on Statistical and Structural Features

Directory of Open Access Journals (Sweden)

Fan Wu

2015-05-01

Full Text Available Vessel monitoring is one of the most important maritime applications of Synthetic Aperture Radar (SAR data. Because of the dihedral reflections between the vessel hull and sea surface and the trihedral reflections among superstructures, vessels usually have strong backscattering in SAR images. Furthermore, in high-resolution SAR images, detailed information on vessel structures can be observed, allowing for vessel classification in high-resolution SAR images. This paper focuses on the feature analysis of merchant vessels, including bulk carriers, container ships and oil tankers, in 3 m resolution COSMO-SkyMed stripmap HIMAGE mode images and proposes a method for vessel classification. After preprocessing, a feature vector is estimated by calculating the average value of the kernel density estimation, three structural features and the mean backscattering coefficient. Support vector machine (SVM classifier is used for the vessel classification, and the results are compared with traditional methods, such as the K-nearest neighbor algorithm (K-NN and minimum distance classifier (MDC. In situ investigations are conducted during the SAR data acquisition. Corresponding Automatic Identification System (AIS reports are also obtained as ground truth to evaluate the effectiveness of the classifier. The preliminary results show that the combination of the average value of the kernel density estimation and mean backscattering coefficient has good ability for classifying the three types of vessels. When adding the three structural features, the results slightly improve. The result of the SVM classifier is better than that of K-NN and MDC. However, the SVM requires more time, when the parameters of the kernel are estimated.

Structural features of various kinds of carbon fibers as determined by small-angle X-ray scattering

Energy Technology Data Exchange (ETDEWEB)

Li, Denghua; Du, Sujun [Shanxi Transportation Research Institute, National and Local Joint Engineering Laboratory of Advanced Road Materials, Taiyuan (China); Lu, Chunxiang; Wu, Gangping; Yang, Yu; Wang, Lina [Chinese Academy of Sciences, National Engineering Laboratory for Carbon Fiber Technology, Institute of Coal Chemistry, Taiyuan (China)

2016-11-15

The structural features of polyacrylonitrile and pitch-based carbon fibers were analyzed from a comprehensive point of view by X-ray measurements and related techniques. The results indicated that the undulating graphite ribbon with embedded microvoid was the main structural unit for graphitic fibers. The void's parameters for these fibers could be obtained directly by small-angle X-ray scattering following the classic method deduced based on the typical two-phase system (i.e., Porod's law, Guinier's law and Debye's law). The non-graphitic fibers, however, were composed of two-dimensional turbostratic crystallites in the aggregation of microfibril and thus had a quasi two-phase structure (microfibril, interfibrillar amorphous structure and microvoid embedded within the microfibril). The extended Debye or Beaucage model in this case should be applied in order to obtain the structural parameters. It also revealed that the quasi two-phase system would complete its transformation to two-phase system during high-temperature graphitization. Therefore, the degree of graphitization was speculated to be the essential indicator distinguishing graphitic fibers from non-graphitic ones and would be helpful in understanding the transformation of structural features during the graphitization of carbon fibers. (orig.)

Molecular Features of Subtype-Specific Progression from Ductal Carcinoma In Situ to Invasive Breast Cancer

Directory of Open Access Journals (Sweden)

Robert Lesurf

2016-07-01

Full Text Available Breast cancer consists of at least five main molecular “intrinsic” subtypes that are reflected in both pre-invasive and invasive disease. Although previous studies have suggested that many of the molecular features of invasive breast cancer are established early, it is unclear what mechanisms drive progression and whether the mechanisms of progression are dependent or independent of subtype. We have generated mRNA, miRNA, and DNA copy-number profiles from a total of 59 in situ lesions and 85 invasive tumors in order to comprehensively identify those genes, signaling pathways, processes, and cell types that are involved in breast cancer progression. Our work provides evidence that there are molecular features associated with disease progression that are unique to the intrinsic subtypes. We additionally establish subtype-specific signatures that are able to identify a small proportion of pre-invasive tumors with expression profiles that resemble invasive carcinoma, indicating a higher likelihood of future disease progression.

Sustainable Corporate Social Media Marketing Based on Message Structural Features: Firm Size Plays a Significant Role as a Moderator

OpenAIRE

Moon Young Kang; Byungho Park

2018-01-01

Social media has been receiving attention as a cost-effective tool to build corporate brand image and to enrich customer relationships. This phenomenon calls for more attention to developing a model that measures the impact of structural features, used in corporate social media messages. Based on communication science, this study proposes a model to measure the impact of three essential message structural features (interactivity, formality, and immediacy) in corporate social media on customer...

[Specific features of surgical anatomy of the subhyoid region with special reference to tracheostomy].

Science.gov (United States)

Chernykh, A V; Mashkova, T A; Nerovnyĭ, A I; Maleev, Iu V

2010-01-01

Peculiarities of thyroid gland linear dimensions, volume, shape, and topographical features were investigated using the morphological material obtained from 426 human corpses of either gender with a view to using this information for planning and performing tracheostomy in residents of the Central Chernozem region, Russia. The study yielded new data on surgical anatomy of additional muscles of the subhyoid region, thyroid isthmus and pyramidal lobe. Rare and previously unknown variants of anatomical structure of the anterior cervical area are described that may play the role of risk factors of postoperative complications of tracheostomy. Relevant recommendations are provided for practicing otorhinolaryngologists.

The evaluation of multi-structure, multi-atlas pelvic anatomy features in a prostate MR lymphography CAD system

Science.gov (United States)

Meijs, M.; Debats, O.; Huisman, H.

2015-03-01

In prostate cancer, the detection of metastatic lymph nodes indicates progression from localized disease to metastasized cancer. The detection of positive lymph nodes is, however, a complex and time consuming task for experienced radiologists. Assistance of a two-stage Computer-Aided Detection (CAD) system in MR Lymphography (MRL) is not yet feasible due to the large number of false positives in the first stage of the system. By introducing a multi-structure, multi-atlas segmentation, using an affine transformation followed by a B-spline transformation for registration, the organ location is given by a mean density probability map. The atlas segmentation is semi-automatically drawn with ITK-SNAP, using Active Contour Segmentation. Each anatomic structure is identified by a label number. Registration is performed using Elastix, using Mutual Information and an Adaptive Stochastic Gradient optimization. The dataset consists of the MRL scans of ten patients, with lymph nodes manually annotated in consensus by two expert readers. The feature map of the CAD system consists of the Multi-Atlas and various other features (e.g. Normalized Intensity and multi-scale Blobness). The voxel-based Gentleboost classifier is evaluated using ROC analysis with cross validation. We show in a set of 10 studies that adding multi-structure, multi-atlas anatomical structure likelihood features improves the quality of the lymph node voxel likelihood map. Multiple structure anatomy maps may thus make MRL CAD more feasible.

Informational economy: specific features and challenges of monopolization

OpenAIRE

Kotsofana, T.

2013-01-01

The article discusses the features of the informational economy, as well as some issues with which this economy is facing today. In particular, contemporary forms of monopoly, its causes and consequences, changing trends towards monopolization and monopolization of markets due to the high degree of automation and information of the socio-economic life were analyzed.

Detection and analysis of unusual features in the structural model and structure-factor data of a birch pollen allergen

International Nuclear Information System (INIS)

Rupp, Bernhard

2012-01-01

The structure factors deposited with PDB entry 3k78 show properties inconsistent with experimentally observed diffraction data, and without uncertainty represent calculated structure factors. The refinement of the model against these structure factors leads to an isomorphous structure different from the deposited model with an implausibly small R value (0.019). Physically improbable features in the model of the birch pollen structure Bet v 1d are faithfully reproduced in electron density generated with the deposited structure factors, but these structure factors themselves exhibit properties that are characteristic of data calculated from a simple model and are inconsistent with the data and error model obtained through experimental measurements. The refinement of the model against these structure factors leads to an isomorphous structure different from the deposited model with an implausibly small R value (0.019). The abnormal refinement is compared with normal refinement of an isomorphous variant structure of Bet v 1l. A variety of analytical tools, including the application of Diederichs plots, Rσ plots and bulk-solvent analysis are discussed as promising aids in validation. The examination of the Bet v 1d structure also cautions against the practice of indicating poorly defined protein chain residues through zero occupancies. The recommendation to preserve diffraction images is amplified

An Approach for Patient-Specific Multi-domain Vascular Mesh Generation Featuring Spatially Varying Wall Thickness Modeling

OpenAIRE

Raut, Samarth S.; Liu, Peng; Finol, Ender A.

2015-01-01

In this work, we present a computationally efficient image-derived volume mesh generation approach for vasculatures that implements spatially varying patient-specific wall thickness with a novel inward extrusion of the wall surface mesh. Multi-domain vascular meshes with arbitrary numbers, locations, and patterns of both iliac bifurcations and thrombi can be obtained without the need to specify features or landmark points as input. In addition, the mesh output is coordinate-frame independent ...

Working memory templates are maintained as feature-specific perceptual codes.

Science.gov (United States)

Sreenivasan, Kartik K; Sambhara, Deepak; Jha, Amishi P

2011-07-01

Working memory (WM) representations serve as templates that guide behavior, but the neural basis of these templates remains elusive. We tested the hypothesis that WM templates are maintained by biasing activity in sensoriperceptual neurons that code for features of items being held in memory. Neural activity was recorded using event-related potentials (ERPs) as participants viewed a series of faces and responded when a face matched a target face held in WM. Our prediction was that if activity in neurons coding for the features of the target is preferentially weighted during maintenance of the target, then ERP activity evoked by a nontarget probe face should be commensurate with the visual similarity between target and probe. Visual similarity was operationalized as the degree of overlap in visual features between target and probe. A face-sensitive ERP response was modulated by target-probe similarity. Amplitude was largest for probes that were similar to the target, and decreased monotonically as a function of decreasing target-probe similarity. These results indicate that neural activity is weighted in favor of visual features that comprise an actively held memory representation. As such, our findings support the notion that WM templates rely on neural populations involved in forming percepts of memory items.

Templated Synthesis of Single-Walled Carbon Nanotubes with Specific Structure.

Science.gov (United States)

Yang, Feng; Wang, Xiao; Li, Meihui; Liu, Xiyan; Zhao, Xiulan; Zhang, Daqi; Zhang, Yan; Yang, Juan; Li, Yan

2016-04-19

Single-walled carbon nanotubes (SWNTs) have shown great potential in various applications attributed to their unique structure-dependent properties. Therefore, the controlled preparation of chemically and structurally pristine SWNTs is a crucial issue for their advanced applications (e.g., nanoelectronics) and has been a great challenge for two decades. Epitaxial growth from well-defined seeds has been shown to be a promising strategy to control the structure of SWNTs. Segments of carbon nanotubes, including short pipes from cutting of preformed nanotubes and caps from opening of fullerenes or cyclodehydrogenation of polycyclic hydrocarbon precursors, have been used as the seeds to grow SWNTs. Single-chirality SWNTs were obtained with both presorted chirality-pure SWNT segments and end caps obtained from polycyclic hydrocarbon molecules with designed structure. The main challenges of nanocarbon-segment-seeded processes are the stability of the seeds, yield, and efficiency. Catalyst-mediated SWNT growth is believed to be more efficient. The composition and morphology of the catalyst nanoparticles have been widely reported to affect the chirality distribution of SWNTs. However, chirality-specific SWNT growth is hard to achieve by alternating catalysts. The specificity of enzyme-catalyzed reactions brings us an awareness of the essentiality of a unique catalyst structure for the chirality-selective growth of SWNTs. Only catalysts with the desired atomic arrangements in their crystal planes can act as structural templates for chirality-specific growth of SWNTs. We have developed a new family of catalysts, tungsten-based intermetallic compounds, which have high melting points and very special crystal structures, to facilitate the growth of SWNTs with designed chirality. By the use of W6Co7 catalysts, (12,6) SWNTs were directly grown with purity higher than 92%. Both high-resolution transmission electron microscopy measurements and density functional theory simulations

SU-D-204-01: A Methodology Based On Machine Learning and Quantum Clustering to Predict Lung SBRT Dosimetric Endpoints From Patient Specific Anatomic Features

Energy Technology Data Exchange (ETDEWEB)

Lafata, K; Ren, L; Wu, Q; Kelsey, C; Hong, J; Cai, J; Yin, F [Duke University Medical Center, Durham, NC (United States)

2016-06-15

Purpose: To develop a data-mining methodology based on quantum clustering and machine learning to predict expected dosimetric endpoints for lung SBRT applications based on patient-specific anatomic features. Methods: Ninety-three patients who received lung SBRT at our clinic from 2011–2013 were retrospectively identified. Planning information was acquired for each patient, from which various features were extracted using in-house semi-automatic software. Anatomic features included tumor-to-OAR distances, tumor location, total-lung-volume, GTV and ITV. Dosimetric endpoints were adopted from RTOG-0195 recommendations, and consisted of various OAR-specific partial-volume doses and maximum point-doses. First, PCA analysis and unsupervised quantum-clustering was used to explore the feature-space to identify potentially strong classifiers. Secondly, a multi-class logistic regression algorithm was developed and trained to predict dose-volume endpoints based on patient-specific anatomic features. Classes were defined by discretizing the dose-volume data, and the feature-space was zero-mean normalized. Fitting parameters were determined by minimizing a regularized cost function, and optimization was performed via gradient descent. As a pilot study, the model was tested on two esophageal dosimetric planning endpoints (maximum point-dose, dose-to-5cc), and its generalizability was evaluated with leave-one-out cross-validation. Results: Quantum-Clustering demonstrated a strong separation of feature-space at 15Gy across the first-and-second Principle Components of the data when the dosimetric endpoints were retrospectively identified. Maximum point dose prediction to the esophagus demonstrated a cross-validation accuracy of 87%, and the maximum dose to 5cc demonstrated a respective value of 79%. The largest optimized weighting factor was placed on GTV-to-esophagus distance (a factor of 10 greater than the second largest weighting factor), indicating an intuitively strong

Insights into Protein Sequence and Structure-Derived Features Mediating 3D Domain Swapping Mechanism using Support Vector Machine Based Approach

Directory of Open Access Journals (Sweden)

Khader Shameer

2010-06-01

Full Text Available 3-dimensional domain swapping is a mechanism where two or more protein molecules form higher order oligomers by exchanging identical or similar subunits. Recently, this phenomenon has received much attention in the context of prions and neuro-degenerative diseases, due to its role in the functional regulation, formation of higher oligomers, protein misfolding, aggregation etc. While 3-dimensional domain swap mechanism can be detected from three-dimensional structures, it remains a formidable challenge to derive common sequence or structural patterns from proteins involved in swapping. We have developed a SVM-based classifier to predict domain swapping events using a set of features derived from sequence and structural data. The SVM classifier was trained on features derived from 150 proteins reported to be involved in 3D domain swapping and 150 proteins not known to be involved in swapped conformation or related to proteins involved in swapping phenomenon. The testing was performed using 63 proteins from the positive dataset and 63 proteins from the negative dataset. We obtained 76.33% accuracy from training and 73.81% accuracy from testing. Due to high diversity in the sequence, structure and functions of proteins involved in domain swapping, availability of such an algorithm to predict swapping events from sequence and structure-derived features will be an initial step towards identification of more putative proteins that may be involved in swapping or proteins involved in deposition disease. Further, the top features emerging in our feature selection method may be analysed further to understand their roles in the mechanism of domain swapping.

Specific features of the domain structure of (Gd1-xNdx)2(MoO4)3 crystals

International Nuclear Information System (INIS)

Bryzgalov, A.N.; Slepchenko, B.M.; Virachev, B.P.

1989-01-01

Formation of the domain structures by sample transfer into thermodynamically metastable state using a simultaneous effect of electric field and temperature change is investigated in Gd 1.7 Nd 0.3 (MoO 4 ) 3 monocrystals (GMO). Some new results obtained under investigations into GMO domain structure using neodymium by means of hydrothermal etching and polarization-optical method are presented

Features of CRISPR-Cas Regulation Key to Highly Efficient and Temporally-Specific crRNA Production

Directory of Open Access Journals (Sweden)

Andjela Rodic

2017-11-01

Full Text Available Bacterial immune systems, such as CRISPR-Cas or restriction-modification (R-M systems, affect bacterial pathogenicity and antibiotic resistance by modulating horizontal gene flow. A model system for CRISPR-Cas regulation, the Type I-E system from Escherichia coli, is silent under standard laboratory conditions and experimentally observing the dynamics of CRISPR-Cas activation is challenging. Two characteristic features of CRISPR-Cas regulation in E. coli are cooperative transcription repression of cas gene and CRISPR array promoters, and fast non-specific degradation of full length CRISPR transcripts (pre-crRNA. In this work, we use computational modeling to understand how these features affect the system expression dynamics. Signaling which leads to CRISPR-Cas activation is currently unknown, so to bypass this step, we here propose a conceptual setup for cas expression activation, where cas genes are put under transcription control typical for a restriction-modification (R-M system and then introduced into a cell. Known transcription regulation of an R-M system is used as a proxy for currently unknown CRISPR-Cas transcription control, as both systems are characterized by high cooperativity, which is likely related to similar dynamical constraints of their function. We find that the two characteristic CRISPR-Cas control features are responsible for its temporally-specific dynamical response, so that the system makes a steep (switch-like transition from OFF to ON state with a time-delay controlled by pre-crRNA degradation rate. We furthermore find that cooperative transcription regulation qualitatively leads to a cross-over to a regime where, at higher pre-crRNA processing rates, crRNA generation approaches the limit of an infinitely abrupt system induction. We propose that these dynamical properties are associated with rapid expression of CRISPR-Cas components and efficient protection of bacterial cells against foreign DNA. In terms of synthetic

Specifics of Gender Manifestation of Prosocial and Antisocial Features in Human Behavior

Directory of Open Access Journals (Sweden)

Shatyr Yuliya Aleksandrovna

2014-12-01

Full Text Available The paper presents an analysis of the gender factors in the formation of prosociality – asociality in humans. A set of indicators reflecting the quantitative and qualitative terms motivational prerequisites of social behavior is presented. The estimation actualization needs are characterized as the beginning of the centripetal and focused on the involvement of the individual in society. Comparative analysis and accentuation of personality traits identified predominance of cycles, emotive and exaltation on the background of male domination of reactive aggression and masculinity. Assessment of the severity of empathy revealed the advantage of emotional and intuitive channels in the group of women relative to men. Undertaken study allowed to determine the presence of specific features of the formation of prosocial behavior of women, where the key element is the dominance of emotional factors initiation of social behavior, and situational mode, reactive response.

Structural basis for IL-1α recognition by a modified DNA aptamer that specifically inhibits IL-1α signaling

Energy Technology Data Exchange (ETDEWEB)

Ren, Xiaoming; Gelinas, Amy D.; von Carlowitz, Ira; Janjic, Nebojsa; Pyle, Anna Marie (Yale); (SomaLogic)

2017-10-09

IL-1α is an essential cytokine that contributes to inflammatory responses and is implicated in various forms of pathogenesis and cancer. Here we report a naphthyl modified DNA aptamer that specifically binds IL-1α and inhibits its signaling pathway. By solving the crystal structure of the IL-1α/aptamer, we provide a high-resolution structure of this critical cytokine and we reveal its functional interaction interface with high-affinity ligands. The non-helical aptamer, which represents a highly compact nucleic acid structure, contains a wealth of new conformational features, including an unknown form of G-quadruplex. The IL-1α/aptamer interface is composed of unusual polar and hydrophobic elements, along with an elaborate hydrogen bonding network that is mediated by sodium ion. IL-1α uses the same interface to interact with both the aptamer and its cognate receptor IL-1RI, thereby suggesting a novel route to immunomodulatory therapeutics.

Building theory-based concepts: four-year-olds preferentially seek explanations for features of kinds.

Science.gov (United States)

Cimpian, Andrei; Petro, Gina

2014-05-01

Is the structure of human concepts continuous across development, or does it undergo qualitative transformations? Extensive evidence with adults has demonstrated that they are motivated to understand why categories have the features they do. To investigate whether young children display a similar motivation-an issue that bears on the question of continuity vs. transformation in conceptual structure-we conducted three studies involving 4-year-olds (N=90) and adults (N=124). Experiments 1 and 2 suggested that 4-year-olds indeed display a strong motivation to explain why categories have the features they do. Specifically, when provided with the option of asking "why?" about features of novel categories vs. features of individuals from other novel categories, children preferred to ask "why?" about the category features. Moreover, children's explanatory preference was specific to facts about categories per se and did not extend to facts that were merely presented in the context of multiple category instances. Experiment 3 also ruled out the possibility that the category facts were preferred because these facts were more surprising. In sum, these three studies reveal an early-emerging motivation to make sense of the categories encountered in the world and, more generally, speak to the richness of children's conceptual representations. Copyright © 2014 Elsevier B.V. All rights reserved.

Structural basis for substrate specificities of cellular deoxyribonucleoside kinases

DEFF Research Database (Denmark)

Johansson, K.; Ramaswamy, S.; Ljungcrantz, C.

2001-01-01

Deoxyribonucleoside kinases phosphorylate deoxyribonucleosides and activate a number of medically important nucleoside analogs. Here we report the structure of the Drosophila deoxyribonucleoside kinase with deoxycytidine bound at the nucleoside binding site and that of the human deoxyguanosine ki......; this is apparently due to the presence of Arg 118, which provides favorable hydrogen bonding interactions with the substrate. The two new structures provide an explanation for the substrate specificity of cellular deoxyribonucleoside kinases....

The General and the Specific in the Psychological ModelsElites

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N B Karabuschenko

2008-12-01

Full Text Available The article discloses the general and specific features of the psychology of the political, business and cultural-intellectual elites, reflecting the basic structural components of the psychological concept of elites.

Identification of Subtype-Specific Prognostic Genes for Early-Stage Lung Adenocarcinoma and Squamous Cell Carcinoma Patients Using an Embedded Feature Selection Algorithm.

Directory of Open Access Journals (Sweden)

Suyan Tian

Full Text Available The existence of fundamental differences between lung adenocarcinoma (AC and squamous cell carcinoma (SCC in their underlying mechanisms motivated us to postulate that specific genes might exist relevant to prognosis of each histology subtype. To test on this research hypothesis, we previously proposed a simple Cox-regression model based feature selection algorithm and identified successfully some subtype-specific prognostic genes when applying this method to real-world data. In this article, we continue our effort on identification of subtype-specific prognostic genes for AC and SCC, and propose a novel embedded feature selection method by extending Threshold Gradient Descent Regularization (TGDR algorithm and minimizing on a corresponding negative partial likelihood function. Using real-world datasets and simulated ones, we show these two proposed methods have comparable performance whereas the new proposal is superior in terms of model parsimony. Our analysis provides some evidence on the existence of such subtype-specific prognostic genes, more investigation is warranted.

Spatial features register: toward standardization of spatial features

Science.gov (United States)

Cascio, Janette

1994-01-01

As the need to share spatial data increases, more than agreement on a common format is needed to ensure that the data is meaningful to both the importer and the exporter. Effective data transfer also requires common definitions of spatial features. To achieve this, part 2 of the Spatial Data Transfer Standard (SDTS) provides a model for a spatial features data content specification and a glossary of features and attributes that fit this model. The model provides a foundation for standardizing spatial features. The glossary now contains only a limited subset of hydrographic and topographic features. For it to be useful, terms and definitions must be included for other categories, such as base cartographic, bathymetric, cadastral, cultural and demographic, geodetic, geologic, ground transportation, international boundaries, soils, vegetation, water, and wetlands, and the set of hydrographic and topographic features must be expanded. This paper will review the philosophy of the SDTS part 2 and the current plans for creating a national spatial features register as one mechanism for maintaining part 2.

MRI features of extraskeletal myxoid chondrosarcoma

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Tateishi, Ukihide; Arai, Yasuaki [National Cancer Center Hospital, Division of Diagnostic Radiology, Tokyo (Japan); Hasegawa, Tadashi [Sapporo Medical University School of Medicine, Department of Clinical Pathology, Sapporo (Japan); Nojima, Takayuki [Kanazawa Medical University, Department of Pathology, Ishikawa (Japan); Takegami, Tsutomu [Kanazawa Medical University, Medical Research Institute, Ishikawa (Japan)

2006-01-01

To describe the MRI features of extraskeletal myxoid chondrosarcoma in comparison with clinicopathologic findings. The study comprised 12 male subjects and seven female subjects with a mean age of 53 years (range 16-76 years). MRI findings, evaluated by two radiologists with agreement by consensus, were compared for histopathologic features. The tumor size ranged from 2.0 cm to 20.0 cm (mean 8.9 cm). Fusion gene transcripts could be detected in 13 (68%) of the 19 cases: EWS-CHN in nine cases, TAF2N-CHN in three, and TFG-TCH in one. There were six fusion-negative cases. Signal characteristics on T1-weighted and T2-weighted MR images were non-specific with regard to each cytogenetic variant. Peripheral enhancement was seen more frequently in tumors with the EWS-CHN variant than in those with other cytogenetic variants. The characteristic pattern of enhancement corresponded to the presence of fibrous septa and peripheral areas of high cellularity within lobules, by correlation with pathologic findings. All cases with TAF2N-CHN or TFG-TCH variants showed invasion of extracompartmental structure, bone, or vessels. Extraskeletal myxoid chondrosarcoma is an uncommon soft-tissue malignancy that may be recognized by MRI features of multi-lobular soft-tissue mass often invading extracompartmental, bony, and vascular structures. (orig.)

Revealing the Structural Complexity of Component Interactions of Topic-Specific PCK when Planning to Teach

Science.gov (United States)

Mavhunga, Elizabeth

2018-04-01

Teaching pedagogical content knowledge (PCK) at a topic-specific level requires clarity on the content-specific nature of the components employed, as well as the specific features that bring about the desirable depth in teacher explanations. Such understanding is often hazy; yet, it influences the nature of teacher tasks and learning opportunities afforded to pre-service teachers in a teaching program. The purpose of this study was twofold: firstly, to illuminate the emerging complexity when content-specific components of PCK interact when planning to teach a chemistry topic; and secondly, to identify the kinds of teacher tasks that promote the emergence of such complexity. Data collected were content representations (CoRes) in chemical equilibrium accompanied by expanded lesson outlines from 15 pre-service teachers in their final year of study towards a first degree in teaching (B Ed). The analysis involved extraction of episodes that exhibited component interaction by using a qualitative in-depth analysis method. The results revealed the structure in which the components of PCK in a topic interact among each other to be linear, interwoven, or a combination of the two. The interwoven interactions contained multiple components that connected explanations on different aspects of a concept, all working in a complementary manner. The most sophisticated component interactions emerged from teacher tasks on descriptions of a lesson sequence and a summary of a lesson. Recommendations in this study highlight core practices for making pedagogical transformation of topic content knowledge more accessible.

Imaging specific cellular glycan structures using glycosyltransferases via click chemistry.

Science.gov (United States)

Wu, Zhengliang L; Person, Anthony D; Anderson, Matthew; Burroughs, Barbara; Tatge, Timothy; Khatri, Kshitij; Zou, Yonglong; Wang, Lianchun; Geders, Todd; Zaia, Joseph; Sackstein, Robert

2018-02-01

Heparan sulfate (HS) is a polysaccharide fundamentally important for biologically activities. T/Tn antigens are universal carbohydrate cancer markers. Here, we report the specific imaging of these carbohydrates using a mesenchymal stem cell line and human umbilical vein endothelial cells (HUVEC). The staining specificities were demonstrated by comparing imaging of different glycans and validated by either removal of target glycans, which results in loss of signal, or installation of target glycans, which results in gain of signal. As controls, representative key glycans including O-GlcNAc, lactosaminyl glycans and hyaluronan were also imaged. HS staining revealed novel architectural features of the extracellular matrix (ECM) of HUVEC cells. Results from T/Tn antigen staining suggest that O-GalNAcylation is a rate-limiting step for O-glycan synthesis. Overall, these highly specific approaches for HS and T/Tn antigen imaging should greatly facilitate the detection and functional characterization of these biologically important glycans. © The Author(s) 2017. Published by Oxford University Press.

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

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Bo Peng

2017-05-01

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

Potential-specific structure at the hematite-electrolyte interface

Energy Technology Data Exchange (ETDEWEB)

McBriarty, Martin E.; Stubbs, Joanne; Eng, Peter; Rosso, Kevin M.

2018-02-21

The atomic-scale structure of interfaces between metal oxides and aqueous electrolytes controls their catalytic, geochemical, and corrosion behavior. Measurements that probe these interfaces in situ provide important details of ion and solvent arrangements, but atomically precise structural models do not exist for common oxide-electrolyte interfaces far from equilibrium. Using a novel cell, we measured the structure of the hematite (a-Fe₂O₃) (110$\\bar{2}$)-electrolyte interface under controlled electrochemical bias using synchrotron crystal truncation rod X ray scattering. At increasingly cathodic potentials, charge-compensating protonation of surface oxygen groups increases the coverage of specifically bound water while adjacent water layers displace outwardly and became disordered. Returning to open circuit potential leaves the surface in a persistent metastable protonation state. The flux of current and ions at applied potential is thus regulated by a unique interfacial electrolyte environment, suggesting that electrical double layer models should be adapted to the dynamically changing interfacial structure far from equilibrium.

Featureous: infrastructure for feature-centric analysis of object-oriented software

DEFF Research Database (Denmark)

Olszak, Andrzej; Jørgensen, Bo Nørregaard

2010-01-01

The decentralized nature of collaborations between objects in object-oriented software makes it difficult to understand how user-observable program features are implemented and how their implementations relate to each other. It is worthwhile to improve this situation, since feature-centric program...... understanding and modification are essential during software evolution and maintenance. In this paper, we present an infrastructure built on top of the NetBeans IDE called Featureous that allows for rapid construction of tools for feature-centric analysis of object-oriented software. Our infrastructure...... encompasses a lightweight feature location mechanism, a number of analytical views and an API allowing for addition of third-party extensions. To form a common conceptual framework for future feature-centric extensions, we propose to structure feature centric analysis along three dimensions: perspective...

The development of real-time stability supports visual working memory performance: Young children's feature binding can be improved through perceptual structure.

Science.gov (United States)

Simmering, Vanessa R; Wood, Chelsey M

2017-08-01

Working memory is a basic cognitive process that predicts higher-level skills. A central question in theories of working memory development is the generality of the mechanisms proposed to explain improvements in performance. Prior theories have been closely tied to particular tasks and/or age groups, limiting their generalizability. The cognitive dynamics theory of visual working memory development has been proposed to overcome this limitation. From this perspective, developmental improvements arise through the coordination of cognitive processes to meet demands of different behavioral tasks. This notion is described as real-time stability, and can be probed through experiments that assess how changing task demands impact children's performance. The current studies test this account by probing visual working memory for colors and shapes in a change detection task that compares detection of changes to new features versus swaps in color-shape binding. In Experiment 1, 3- to 4-year-old children showed impairments specific to binding swaps, as predicted by decreased real-time stability early in development; 5- to 6-year-old children showed a slight advantage on binding swaps, but 7- to 8-year-old children and adults showed no difference across trial types. Experiment 2 tested the proposed explanation of young children's binding impairment through added perceptual structure, which supported the stability and precision of feature localization in memory-a process key to detecting binding swaps. This additional structure improved young children's binding swap detection, but not new-feature detection or adults' performance. These results provide further evidence for the cognitive dynamics and real-time stability explanation of visual working memory development. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Specific Features in Accessing European Funding

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Elena Alexandra CĂLDĂRARU

2011-12-01

Full Text Available Abstract: European Funds are the European Union financial instruments in order to assist Member States in reducing the existing disparities between regions and between countries, and for harmonization with the economic, social and cultural European standards. This paper intends to present some general characteristics applicable to the most important financing programs, and also to outline certain features of the main financing lines, referring to investment projects development and their implementation, based on the Applicant Guides analysis. The paper treats institutional, legal, financial, technical, social and environmental aspects and outlines proposals and recommendations to achieve a better EU funds absorption and also a higher success rate of initiated projects. In knowledge-based economy circumstances, training consultancy specialists, that represent the intellectual capital in this area, will ensure the professional management of the developing process, submission and ongoing competitive projects, and will help enhance the funds absorption at national level. Thus, the European support for investments in ensuring sustainable growth will help overcoming the difficulties encountered by our country, and will sustain the Romanian economy recovery.

Numerical Simulation of Flow Features and Energy Exchange Physics in Near-Wall Region with Fluid-Structure Interaction

Science.gov (United States)

Zhang, Lixiang; Wang, Wenquan; Guo, Yakun

Large eddy simulation is used to explore flow features and energy exchange physics between turbulent flow and structure vibration in the near-wall region with fluid-structure interaction (FSI). The statistical turbulence characteristics in the near-wall region of a vibrating wall, such as the skin frictional coefficient, velocity, pressure, vortices, and the coherent structures have been studied for an aerofoil blade passage of a true three-dimensional hydroturbine. The results show that (i) FSI greatly strengthens the turbulence in the inner region of y+ < 25; and (ii) the energy exchange mechanism between the flow and the vibration depends strongly on the vibration-induced vorticity in the inner region. The structural vibration provokes a frequent action between the low- and high-speed streaks to balance the energy deficit caused by the vibration. The velocity profile in the inner layer near the vibrating wall has a significant distinctness, and the viscosity effect of the fluid in the inner region decreases due to the vibration. The flow features in the inner layer are altered by a suitable wall vibration.

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

Science.gov (United States)

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

2015-05-19

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

The Discourse Structure and Linguistic Features of Research Article Abstracts in English by Indonesian Academics

Science.gov (United States)

Arsyad, Safnil

2014-01-01

To effectively teach university lecturers or students to write a good research article (RA) abstract for publication in international journals, instructors need to know the present characteristics of abstracts written published in such journals. This study examines the discourse structure and linguistic features of RA abstracts written in English…

Structural Basis for Specific Inhibition of tRNA Synthetase by an ATP Competitive Inhibitor.

Science.gov (United States)

Fang, Pengfei; Han, Hongyan; Wang, Jing; Chen, Kaige; Chen, Xin; Guo, Min

2015-06-18

Pharmaceutical inhibitors of aminoacyl-tRNA synthetases demand high species and family specificity. The antimalarial ATP-mimetic cladosporin selectively inhibits Plasmodium falciparum LysRS (PfLysRS). How the binding to a universal ATP site achieves the specificity is unknown. Here we report three crystal structures of cladosporin with human LysRS, PfLysRS, and a Pf-like human LysRS mutant. In all three structures, cladosporin occupies the class defining ATP-binding pocket, replacing the adenosine portion of ATP. Three residues holding the methyltetrahydropyran moiety of cladosporin are critical for the specificity of cladosporin against LysRS over other class II tRNA synthetase families. The species-exclusive inhibition of PfLysRS is linked to a structural divergence beyond the active site that mounts a lysine-specific stabilizing response to binding cladosporin. These analyses reveal that inherent divergence of tRNA synthetase structural assembly may allow for highly specific inhibition even through the otherwise universal substrate binding pocket and highlight the potential for structure-driven drug development. Copyright © 2015 Elsevier Ltd. All rights reserved.

Evaluating The State Of Financial Globalization:Ukraine’s Specific Features

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Natalia Stukalo

2006-03-01

Full Text Available This article presents a system for evaluating the state of financial globalization in a given country. It identifies the contemporary distinctive features of globalization in the area of finance. It also systematizes available globalization indicators at all levels of the financial system. It collects and analyzes statistical data with regard to key financial globalization indicators for Ukraine and Russia as countries that will soon become members of the World Trade Organization. Based on this analysis, the article provides an overview of the contemporary distinctive features of the financial sector in these counties in the context of globalization.

Sensitivity and specificity of ultrasonographic features of gout in intercritical and chronic phase.

Science.gov (United States)

Das, Shyamashis; Ghosh, Alakendu; Ghosh, Parasar; Lahiri, Debasish; Sinhamahapatra, Pradyot; Basu, Kaushik

2017-07-01

This study aimed to assess the sensitivity and specificity of ultrasonographic features of gout in intercritical and chronic stages and compared ultrasonographic features of gout between patients with persistent high serum uric acid (SUA) and patients with low SUA. Adult patients with gout confirmed by demonstration of monosodium urate crystals were recruited, if they were in intercritical or chronic stage clinically. Ultrasonographic examination of the first metatarsophalangeal joints (MTPJs) and the knee joints of both sides were done by a blinded rheumatologist trained in musculoskeletal ultrasound. Sixty-two patients with gout and 30 control subjects were examined. The double contour sign (DCS) was found in 71 (57.3%) first MTPJs and tophi were found in 54 (43.5%) first MTPJs. DCS was present in 43 (69.4%) gout patients but none in the control group (P gout patients were 69.4% (56.4-80.4%) and 100% (88.3-100%), respectively, while of tophi they were 66.1% (53-77.7%) and 100% (88.3-100%), respectively. The sensitivity of DCS increased to 100% in high the SUA subgroup (SUA ≥ 7 mg/dL). The low SUA (SUA gout subgroup showed significantly higher occurrence of erosions (40%) and tophi (50%) in first MTP joints than the control group. MSUS is useful for diagnosis of gout in intercritical or chronic stages, especially in patients with persistently high SUA level. © 2016 Asia Pacific League of Associations for Rheumatology and John Wiley & Sons Australia, Ltd.

Phenotype- and genotype-specific structural alterations in spasmodic dysphonia.

Science.gov (United States)

Bianchi, Serena; Battistella, Giovanni; Huddleston, Hailey; Scharf, Rebecca; Fleysher, Lazar; Rumbach, Anna F; Frucht, Steven J; Blitzer, Andrew; Ozelius, Laurie J; Simonyan, Kristina

2017-04-01

Spasmodic dysphonia is a focal dystonia characterized by involuntary spasms in the laryngeal muscles that occur selectively during speaking. Although hereditary trends have been reported in up to 16% of patients, the causative etiology of spasmodic dysphonia is unclear, and the influences of various phenotypes and genotypes on disorder pathophysiology are poorly understood. In this study, we examined structural alterations in cortical gray matter and white matter integrity in relationship to different phenotypes and putative genotypes of spasmodic dysphonia to elucidate the structural component of its complex pathophysiology. Eighty-nine patients with spasmodic dysphonia underwent high-resolution magnetic resonance imaging and diffusion-weighted imaging to examine cortical thickness and white matter fractional anisotropy in adductor versus abductor forms (distinct phenotypes) and in sporadic versus familial cases (distinct genotypes). Phenotype-specific abnormalities were localized in the left sensorimotor cortex and angular gyrus and the white matter bundle of the right superior corona radiata. Genotype-specific alterations were found in the left superior temporal gyrus, supplementary motor area, and the arcuate portion of the left superior longitudinal fasciculus. Our findings suggest that phenotypic differences in spasmodic dysphonia arise at the level of the primary and associative areas of motor control, whereas genotype-related pathophysiological mechanisms may be associated with dysfunction of regions regulating phonological and sensory processing. Identification of structural alterations specific to disorder phenotype and putative genotype provides an important step toward future delineation of imaging markers and potential targets for novel therapeutic interventions for spasmodic dysphonia. © 2017 International Parkinson and Movement Disorder Society. © 2017 International Parkinson and Movement Disorder Society.

Identification of S-glutathionylation sites in species-specific proteins by incorporating five sequence-derived features into the general pseudo-amino acid composition.

Science.gov (United States)

Zhao, Xiaowei; Ning, Qiao; Ai, Meiyue; Chai, Haiting; Yang, Guifu

2016-06-07

As a selective and reversible protein post-translational modification, S-glutathionylation generates mixed disulfides between glutathione (GSH) and cysteine residues, and plays an important role in regulating protein activity, stability, and redox regulation. To fully understand S-glutathionylation mechanisms, identification of substrates and specific S-Glutathionylated sites is crucial. Experimental identification of S-glutathionylated sites is labor-intensive and time consuming, so establishing an effective computational method is much desirable due to their convenient and fast speed. Therefore, in this study, a new bioinformatics tool named SSGlu (Species-Specific identification of Protein S-glutathionylation Sites) was developed to identify species-specific protein S-glutathionylated sites, utilizing support vector machines that combine multiple sequence-derived features with a two-step feature selection. By 5-fold cross validation, the performance of SSGlu was measured with an AUC of 0.8105 and 0.8041 for Homo sapiens and Mus musculus, respectively. Additionally, SSGlu was compared with the existing methods, and the higher MCC and AUC of SSGlu demonstrated that SSGlu was very promising to predict S-glutathionylated sites. Furthermore, a site-specific analysis showed that S-glutathionylation intimately correlated with the features derived from its surrounding sites. The conclusions derived from this study might help to understand more of the S-glutathionylation mechanism and guide the related experimental validation. For public access, SSGlu is freely accessible at http://59.73.198.144:8080/SSGlu/. Copyright © 2016 Elsevier Ltd. All rights reserved.

[Specific features of nesting bird populations in forest-meadow-field landscapes of Meshchovsk Opolye reflect the diversity of their biotope connections].

Science.gov (United States)

Kut'in, S D; Konstantinov, V M

2008-01-01

Studies on specific features of nesting bird populations in patchy landscapes were performed in Meshchovsk Opolye, Kaluga Region, from 1981 to 1990. Indices of similarity between the avifaunas of agricultural fields, lowland bogs, and small-leaved forests markedly differed from parameters of their population density in rank and value. In the series of biotopes differing in the relative amount of woodland, from central areas of small-leaved forests to forest margins and then to forest islands gradually decreasing in size, the birds segregated into two distinct groups, one characteristic of forest margins and large forest islands and the other characteristic of small and very small forest islands. Specific features of bird density distribution in forest-meadow-field landscapes of Meshchovsk Opolye reflected heterogeneity of their populations manifested in diverse connections with nesting biotopes.

Feature Binding in Zebrafish

Directory of Open Access Journals (Sweden)

P Neri

2012-07-01

Full Text Available Binding operations are primarily ascribed to cortex or similarly complex avian structures. My experiments show that the zebrafish, a lower vertebrate lacking cortex, supports visual feature binding of form and motion for the purpose of social behavior. These results challenge the notion that feature binding may require highly evolved neural structures and demonstrate that the nervous system of lower vertebrates can afford unexpectedly complex computations.

Standard technical specifications for Babcock and Wilcox pressurized water reactors

International Nuclear Information System (INIS)

1978-06-01

The Standard Technical Specification (STS) has been structured for the broadest possible use on B and W NSSS plants currently being reviewed for an Operating License. Two separate and discrete containment specification sections are provided for each of the following containment types: Atmospheric, and Dual. Optional specifications are provided for those features and systems which may be included in individual plant designs but are not generic in their scope of application. Alternate specifications are provided in a limited number of cases to cover situations where alternate specification requirements are necessary on a generic basis because of design differences. The format of the STS addresses the categories required by 10 CFR 50 and consists of six sections covering the areas of: Definitions, Safety Limits and Limiting Safety System Settings, Limiting Conditions for Operation, Surveillance Requirements, Design Features, and Administrative Controls

SPECIFIC DEGRADATION STRUCTURE FEATURES AND MECHANICAL PROPERTIES OF FURNACE AND HEAT POWER EQUIPMENT ELEMENTS AFTER LONG-TERM OPERATION

Directory of Open Access Journals (Sweden)

F. I. Panteleenko

2012-01-01

Full Text Available The paper presents results of investigations on structure and mechanical properties of technological equipment elements made of heat-resistant steels. A scale of chrome and molybdenum steel microstructure degradation based on evaluation of  coagulated carbide size and material mechanical properties (a point from 0-operation without time limits, up to 4-operation prohibition has been proposed in the paper. It has been  established that an analysis of  steel microstructure directly on equipment elements by means of a portable microscope is an efficient express method for evaluation of equipment condition and structures due to control of material structure degradation rate of a diagnosed object.

Relevance of echo-structure and texture features

DEFF Research Database (Denmark)

Karemore, Gopal; Mullick, Jhinuk Basu; KV, Dr. Rajagopal

2010-01-01

Aim: Echostructure is an essential parameter for the evaluation of circumscribed lesions and can be described as a texture feature on ultrasound images. Present study evaluates the possibility of distinguishing between benign and malignant breast tumors using various texture features. Materials...... and Methods: 58 cases of breast tumor (29 each from benign and malignant) were documented under standardized conditions using a linear array machine and 7.5 MHz transducer. In each sonographic image, ROI of tumor was marked and then subjected to the evaluation of tumor status using five parameters of second...... performance ROC= 0.78(pbenign and malignant tumors. It also reveals that when evaluating images of a breast tumor...

Protein functional features are reflected in the patterns of mRNA translation speed.

Science.gov (United States)

López, Daniel; Pazos, Florencio

2015-07-09

The degeneracy of the genetic code makes it possible for the same amino acid string to be coded by different messenger RNA (mRNA) sequences. These "synonymous mRNAs" may differ largely in a number of aspects related to their overall translational efficiency, such as secondary structure content and availability of the encoded transfer RNAs (tRNAs). Consequently, they may render different yields of the translated polypeptides. These mRNA features related to translation efficiency are also playing a role locally, resulting in a non-uniform translation speed along the mRNA, which has been previously related to some protein structural features and also used to explain some dramatic effects of "silent" single-nucleotide-polymorphisms (SNPs). In this work we perform the first large scale analysis of the relationship between three experimental proxies of mRNA local translation efficiency and the local features of the corresponding encoded proteins. We found that a number of protein functional and structural features are reflected in the patterns of ribosome occupancy, secondary structure and tRNA availability along the mRNA. One or more of these proxies of translation speed have distinctive patterns around the mRNA regions coding for certain protein local features. In some cases the three patterns follow a similar trend. We also show specific examples where these patterns of translation speed point to the protein's important structural and functional features. This support the idea that the genome not only codes the protein functional features as sequences of amino acids, but also as subtle patterns of mRNA properties which, probably through local effects on the translation speed, have some consequence on the final polypeptide. These results open the possibility of predicting a protein's functional regions based on a single genomic sequence, and have implications for heterologous protein expression and fine-tuning protein function.

Fundamental structural aspects and features in the bioengineering of the gas exchangers: comparative perspectives.

Science.gov (United States)

Maina, J N

2002-01-01

Over its life, an organism's survival and success are determined by the inventory of vital adaptations that its progenitors have creatively appropriated, devised and harnessed along the evolutionary pathway. Such conserved attributes provide the armamentarium necessary for withstanding the adverse effects of natural selection. Refinements of the designs of the respiratory organs have been critical for survival and phylogenetic advancement of animal life. Gas exchangers have changed in direct response to the respiratory needs of whole organisms in different environmental states and conditions. Nowhere else is the dictum that in biology 'there are no rules but only necessities' more manifest than in the evolutionary biology of the gas exchangers. The constructions have been continually fashioned and refined to meet specific needs. Solutions to common respiratory needs have been typified by profound structural convergence. Over the evolutionary continuum, as shifts in environmental situations occurred, infinitely many designs should theoretically have emerged. Moreover, without specific selective pressures and preference for certain designs, considering that there are only two naturally occurring respirable fluid media (air and water), air-lungs, water-lungs, air-gills and water-gills would have formed to similar extents. Factors such as body size, phylogenetic level of development, respiratory medium utilized and habitats occupied have permutatively prescribed the design of the gas exchangers. The construction of the modern gas exchangers has eventuated through painstaking cost-benefit analysis. Trade-offs and compromises have decreed only a limited number of structurally feasible and functionally competent outcomes. The morphological congruity (analogy) of the gas exchangers indicates that similar selective pressures have compelled the designs. Solutions to metabolic demands for molecular O2 have only differed in details. Passive physical diffusion, for example, is

Structural Determinants of Specific Lipid Binding to Potassium Channels

NARCIS (Netherlands)

Weingarth, M.H.|info:eu-repo/dai/nl/330985655; Prokofyev, A.; van der Cruijsen, E.A.W.|info:eu-repo/dai/nl/330826743; Nand, D.|info:eu-repo/dai/nl/337731403; Bonvin, A.M.J.J.|info:eu-repo/dai/nl/113691238; Pongs, O.; Baldus, M.|info:eu-repo/dai/nl/314410864

2013-01-01

We have investigated specific lipid binding to the pore domain of potassium channels KcsA and chimeric KcsAKv1.3 on the structural and functional level using extensive coarse-grained and atomistic molecular dynamics simulations, solid-state NMR, and single channel measurements. We show that, while

GANN: Genetic algorithm neural networks for the detection of conserved combinations of features in DNA

Directory of Open Access Journals (Sweden)

Beiko Robert G

2005-02-01

Full Text Available Abstract Background The multitude of motif detection algorithms developed to date have largely focused on the detection of patterns in primary sequence. Since sequence-dependent DNA structure and flexibility may also play a role in protein-DNA interactions, the simultaneous exploration of sequence- and structure-based hypotheses about the composition of binding sites and the ordering of features in a regulatory region should be considered as well. The consideration of structural features requires the development of new detection tools that can deal with data types other than primary sequence. Results GANN (available at http://bioinformatics.org.au/gann is a machine learning tool for the detection of conserved features in DNA. The software suite contains programs to extract different regions of genomic DNA from flat files and convert these sequences to indices that reflect sequence and structural composition or the presence of specific protein binding sites. The machine learning component allows the classification of different types of sequences based on subsamples of these indices, and can identify the best combinations of indices and machine learning architecture for sequence discrimination. Another key feature of GANN is the replicated splitting of data into training and test sets, and the implementation of negative controls. In validation experiments, GANN successfully merged important sequence and structural features to yield good predictive models for synthetic and real regulatory regions. Conclusion GANN is a flexible tool that can search through large sets of sequence and structural feature combinations to identify those that best characterize a set of sequences.

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

Science.gov (United States)

2016-01-01

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

Inflation in Modern Russia: Theoretical Foundations, Specific Features of Manifestation and Regional Dimension

Directory of Open Access Journals (Sweden)

Vladimir Vladimirovich Ilyashenko

2017-06-01

Full Text Available The purpose of the article is to characterize the development and specific features of inflation in Russia on the basis of its theoretical justification and practical analysis. The article discusses the monetarist and Keynesian approaches to the characterization of inflation. The paper shows that the equation of exchange from the quantity theory of money, which is the basis of the monetarist theory of inflation, does not allow to make an unambiguous conclusion about the direct relationship between money supply and price level in the economy. The authors give the theoretical substantiation of cost-push inflation from the position of microeconomic theory, which is denied by the representatives of the monetarist school. We characterize the specific features of inflation in the period of market transformations in Russia. The article shows the considerable role of the cost factors of cost-push inflation: the monopolization of the economy, rise in the prices of energy and raw materials. There is an absence of the direct relationship between inflation and money supply growth in large part of the period of the 2000. The authors determine the dependence between the exchange rate and inflation in the Russian economy, which is most evident during periods of significant devaluation of the national currency, as a rule, associated with a significant increase in world oil prices. The paper notes that the significant decline in aggregate demand that occurred in Russia in recent years have reduced the level of inflation in 2016. Despite this, the reduction of inflation and its transformation to slow cost-push inflation was combined with negative consequences for the economy: the decrease of investments and production development, reduction of the living standards of the population. The authors conducted the analysis of inflation on the level of the subjects of the Russian Federation, which has confirmed the significant role of causes of cost-push inflation in

Homerinių himnų struktūros bruožai | Structural Features of the Homeric Hymns

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Naglis Kardelis

2012-01-01

shadow of some subordinate or even minor, if not marginal, deities.In the fourth chapter of the article, the author focuses on the structural framework of typical indi­vidual hymns of different length. During this stage of the research, the author posits five typical groups of the hymns according to their length and briefly dis­cusses the specific features of the hymns belonging to these five groups in terms of their form, content, and a correlation between their form and content.At the end of the article, the conclusion is made that some kind of a quantitative approach to the Ho­meric Hymns, for example, such as presented in this paper, if correctly conducted and creatively interpret­ed, might present us valuable fresh insights into the structural nature of the corpus of the Homeric Hymns as a whole, as well as shed some light on the prob­lems of the structure of individual hymns. As a con­sequence of these deeper insights, we find ourselves in a situation where we should abandon all talk about the so-called structural chaos of the Homeric Hymns.

Some structural aspects of language are more stable than others: a comparison of seven methods.

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Dan Dediu

Full Text Available Understanding the patterns and causes of differential structural stability is an area of major interest for the study of language change and evolution. It is still debated whether structural features have intrinsic stabilities across language families and geographic areas, or if the processes governing their rate of change are completely dependent upon the specific context of a given language or language family. We conducted an extensive literature review and selected seven different approaches to conceptualising and estimating the stability of structural linguistic features, aiming at comparing them using the same dataset, the World Atlas of Language Structures. We found that, despite profound conceptual and empirical differences between these methods, they tend to agree in classifying some structural linguistic features as being more stable than others. This suggests that there are intrinsic properties of such structural features influencing their stability across methods, language families and geographic areas. This finding is a major step towards understanding the nature of structural linguistic features and their interaction with idiosyncratic, lineage- and area-specific factors during language change and evolution.

SoftSearch: integration of multiple sequence features to identify breakpoints of structural variations.

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Steven N Hart

Full Text Available BACKGROUND: Structural variation (SV represents a significant, yet poorly understood contribution to an individual's genetic makeup. Advanced next-generation sequencing technologies are widely used to discover such variations, but there is no single detection tool that is considered a community standard. In an attempt to fulfil this need, we developed an algorithm, SoftSearch, for discovering structural variant breakpoints in Illumina paired-end next-generation sequencing data. SoftSearch combines multiple strategies for detecting SV including split-read, discordant read-pair, and unmated pairs. Co-localized split-reads and discordant read pairs are used to refine the breakpoints. RESULTS: We developed and validated SoftSearch using real and synthetic datasets. SoftSearch's key features are 1 not requiring secondary (or exhaustive primary alignment, 2 portability into established sequencing workflows, and 3 is applicable to any DNA-sequencing experiment (e.g. whole genome, exome, custom capture, etc.. SoftSearch identifies breakpoints from a small number of soft-clipped bases from split reads and a few discordant read-pairs which on their own would not be sufficient to make an SV call. CONCLUSIONS: We show that SoftSearch can identify more true SVs by combining multiple sequence features. SoftSearch was able to call clinically relevant SVs in the BRCA2 gene not reported by other tools while offering significantly improved overall performance.

A Comparison of Supervised Machine Learning Algorithms and Feature Vectors for MS Lesion Segmentation Using Multimodal Structural MRI

Science.gov (United States)

Sweeney, Elizabeth M.; Vogelstein, Joshua T.; Cuzzocreo, Jennifer L.; Calabresi, Peter A.; Reich, Daniel S.; Crainiceanu, Ciprian M.; Shinohara, Russell T.

2014-01-01

Machine learning is a popular method for mining and analyzing large collections of medical data. We focus on a particular problem from medical research, supervised multiple sclerosis (MS) lesion segmentation in structural magnetic resonance imaging (MRI). We examine the extent to which the choice of machine learning or classification algorithm and feature extraction function impacts the performance of lesion segmentation methods. As quantitative measures derived from structural MRI are important clinical tools for research into the pathophysiology and natural history of MS, the development of automated lesion segmentation methods is an active research field. Yet, little is known about what drives performance of these methods. We evaluate the performance of automated MS lesion segmentation methods, which consist of a supervised classification algorithm composed with a feature extraction function. These feature extraction functions act on the observed T1-weighted (T1-w), T2-weighted (T2-w) and fluid-attenuated inversion recovery (FLAIR) MRI voxel intensities. Each MRI study has a manual lesion segmentation that we use to train and validate the supervised classification algorithms. Our main finding is that the differences in predictive performance are due more to differences in the feature vectors, rather than the machine learning or classification algorithms. Features that incorporate information from neighboring voxels in the brain were found to increase performance substantially. For lesion segmentation, we conclude that it is better to use simple, interpretable, and fast algorithms, such as logistic regression, linear discriminant analysis, and quadratic discriminant analysis, and to develop the features to improve performance. PMID:24781953

THE GEOMORPHOLOGIC FEATURES OF INTRUSIVE MAGMATIC STRUCTURES FROM BÂRGĂU MOUNTAINS (EASTERN CARPATHIANS, ROMANIA

Directory of Open Access Journals (Sweden)

Ioan Bâca

2016-08-01

Full Text Available Igneous intrusive structures from Bârgău Mountains belong to the group of central Neogene volcanic chain of the Eastern Carpathians of Romania. The evolution of the relief developed on these structures are three main stages: the stage of injection of structures (Pannonian, the stage of uncovering of igneous intrusive bodies from Oligo-Miocene sedimentary cover (Pliocene, and the stage of subaerial modeling of magmatic bodies (Pliocene-current.In those circumstances, the geodiversity of intrusive magmatic structures from Bârgău Mountains is represented by several types of landforms such as: polycyclic landforms (erosional levels, structural landforms (the configuration of igneous intrusive structures, petrographic landforms (andesites, lithological contact, fluvial landforms (valleys, slopes, ridges, periglacial landforms (cryogenic and crionival landforms, biogenic and anthropogenic landforms. This study highlights certain features of the landforms modeled on igneous intrusive bodies with the aim of developing some strategy for tourism recovery by local and county authorities.

Modelling energy demand of developing countries: Are the specific features adequately captured?

International Nuclear Information System (INIS)

Bhattacharyya, Subhes C.; Timilsina, Govinda R.

2010-01-01

This paper critically reviews existing energy demand forecasting methodologies highlighting the methodological diversities and developments over the past four decades in order to investigate whether the existing energy demand models are appropriate for capturing the specific features of developing countries. The study finds that two types of approaches, econometric and end-use accounting, are commonly used in the existing energy demand models. Although energy demand models have greatly evolved since the early seventies, key issues such as the poor-rich and urban-rural divides, traditional energy resources and differentiation between commercial and non-commercial energy commodities are often poorly reflected in these models. While the end-use energy accounting models with detailed sectoral representations produce more realistic projections as compared to the econometric models, they still suffer from huge data deficiencies especially in developing countries. Development and maintenance of more detailed energy databases, further development of models to better reflect developing country context and institutionalizing the modelling capacity in developing countries are the key requirements for energy demand modelling to deliver richer and more reliable input to policy formulation in developing countries.

Modelling energy demand of developing countries: Are the specific features adequately captured?

Energy Technology Data Exchange (ETDEWEB)

Bhattacharyya, Subhes C. [CEPMLP, University of Dundee, Dundee DD1 4HN (United Kingdom); Timilsina, Govinda R. [Development Research Group, The World Bank, Washington DC (United States)

2010-04-15

This paper critically reviews existing energy demand forecasting methodologies highlighting the methodological diversities and developments over the past four decades in order to investigate whether the existing energy demand models are appropriate for capturing the specific features of developing countries. The study finds that two types of approaches, econometric and end-use accounting, are commonly used in the existing energy demand models. Although energy demand models have greatly evolved since the early seventies, key issues such as the poor-rich and urban-rural divides, traditional energy resources and differentiation between commercial and non-commercial energy commodities are often poorly reflected in these models. While the end-use energy accounting models with detailed sectoral representations produce more realistic projections as compared to the econometric models, they still suffer from huge data deficiencies especially in developing countries. Development and maintenance of more detailed energy databases, further development of models to better reflect developing country context and institutionalizing the modelling capacity in developing countries are the key requirements for energy demand modelling to deliver richer and more reliable input to policy formulation in developing countries. (author)

The role of specific features of the electronic structure in electrical resistivity of band ferromagnets Co2Fe Z ( Z = Al, Si, Ga, Ge, In, Sn, Sb)

Science.gov (United States)

Kourov, N. I.; Marchenkov, V. V.; Perevozchikova, Yu. A.; Weber, H. W.

2017-05-01

The electrical resistivity ρ( T) of the band ferromagnets Co2FeZ (where Z = Al, Si, Ga, Ge, In, Sn, and Sb are s- and p-elements of Mendeleev's Periodic Table) has been investigated in the temperature range 4.2 K < T < 1100 K. It has been shown that the dependences ρ( T) of these alloys in a magnetically ordered state at temperatures T < T C are predominantly determined by the specific features of the electronic spectrum in the vicinity of the Fermi level. The processes of charge carrier scattering affect the behavior of the electrical resistivity ρ( T) only in the vicinity of the Curie temperature T C and above, as well as in the low-temperature range (at T ≪ T C).

Between technical features and analytic capabilities

DEFF Research Database (Denmark)

Madsen, Anders Koed

2015-01-01

Digital social analytics is a subset of Big Data methods that is used to understand the social environment in which people and organizations have to act. This paper presents an analysis of eight projects that are experimenting with the use of these methods for various purposes. It shows that two...... specific technological features influence the work with such methods in all the cases. The first concerns the need to distribute choices about the structure of data to third-party actors and the second concerns the need to balance machine intelligence and human intuition when automating the analysis...

Specific features of NH{sub 3} and plasma-assisted MBE in the fabrication of III-N HEMT heterostructures

Energy Technology Data Exchange (ETDEWEB)

Alexeev, A. N. [NTO ZAO (Russian Federation); Krasovitsky, D. M. [Svetlana-Rost ZAO (Russian Federation); Petrov, S. I., E-mail: petrov@semiteq.ru [NTO ZAO (Russian Federation); Chaly, V. P.; Mamaev, V. V. [Svetlana-Rost ZAO (Russian Federation); Sidorov, V. G. [St. Petersburg State Polytechnic University (Russian Federation)

2015-01-15

The specific features of how nitride HEMT heterostructures are produced by NH{sub 3} and plasma-assisted (PA) molecular-beam epitaxy (MBE) are considered. It is shown that the use of high-temperature AlN/AlGaN buffer layers grown with ammonia at extremely high temperatures (up to 1150°C) can drastically improve the structural perfection of the active GaN layers and reduce the dislocation density in these layers to values of 9 × 10{sup 8}−1 × 10{sup 9} cm{sup −2}. The use of buffer layers of this kind makes it possible to obtain high-quality GaN/AlGaN heterostructures by both methods. At the same time, in contrast to ammonia MBE which is difficult to apply at T < 500°C (because of the low efficiency of ammonia decomposition), PA MBE is rather effective at low temperatures, e.g., for the growth of InAlN layers lattice-matched with GaN. The results obtained in the MBE growth of AlN/AlGaN/GaN/InAlN heterostructures by both PA-MBE and NH{sub 3}-MBE with an extremely high ammonia flux are demonstrated.

Distill: a suite of web servers for the prediction of one-, two- and three-dimensional structural features of proteins

Directory of Open Access Journals (Sweden)

Walsh Ian

2006-09-01

Full Text Available Abstract Background We describe Distill, a suite of servers for the prediction of protein structural features: secondary structure; relative solvent accessibility; contact density; backbone structural motifs; residue contact maps at 6, 8 and 12 Angstrom; coarse protein topology. The servers are based on large-scale ensembles of recursive neural networks and trained on large, up-to-date, non-redundant subsets of the Protein Data Bank. Together with structural feature predictions, Distill includes a server for prediction of Cα traces for short proteins (up to 200 amino acids. Results The servers are state-of-the-art, with secondary structure predicted correctly for nearly 80% of residues (currently the top performance on EVA, 2-class solvent accessibility nearly 80% correct, and contact maps exceeding 50% precision on the top non-diagonal contacts. A preliminary implementation of the predictor of protein Cα traces featured among the top 20 Novel Fold predictors at the last CASP6 experiment as group Distill (ID 0348. The majority of the servers, including the Cα trace predictor, now take into account homology information from the PDB, when available, resulting in greatly improved reliability. Conclusion All predictions are freely available through a simple joint web interface and the results are returned by email. In a single submission the user can send protein sequences for a total of up to 32k residues to all or a selection of the servers. Distill is accessible at the address: http://distill.ucd.ie/distill/.

Structure in galactic soft X-ray features

International Nuclear Information System (INIS)

Davelaar, J.

1979-01-01

Observations are described of the soft X-ray background in a part of the northern hemisphere in the energy range 0.06 - 3.0 keV. The X-ray instruments, placed onboard a sounding rocket, are a one-dimensional focusing collector with multi-cell proportional counters in the focal plane and eight large area counters on deployable panels. A description of the instruments and their preflight calibration is given. Precautions were taken to prevent UV sensitivity of the X-ray instruments. The observation program, which consisted of a number of pre-programmed slow scans, is outlined. The spectral date on the soft X-ray background in these and previous observations showed that at least two components of different temperature are present. A low temperature component of approximately (3-10)x10 5 is found all over the sky. Components of higher temperature approximately 3x10 6 K are found in regions of soft X-ray enhancement; The North Polar Spur has been observed in two scans at the galactic latitude b=25 0 and b=75 0 . The X-ray ridge structure is found to be strongly energy dependent. The low energy data ( 0 reveals two separate emission features on the ridge, both probably of finite extensions (approximately equal to 0 0 .5). A wider X-ray ridge (approximately equal to 10 0 ) is observed above 0.4 keV. (Auth.)

Specific features of domestic banks activity in the factoring services market

Directory of Open Access Journals (Sweden)

Trygub Olena V.

2014-01-01

Full Text Available The article analyses specific features of formation and development of the domestic factoring market. In the result of the study the article establishes that development of factoring in Ukraine took place due to active participation of banking institutions in this process and nowadays they are leaders in the domestic factoring services market due to possessing significant competitive advantages if compared with non-banking companies that specialise in factoring. The article detects that nowadays the banks are not only offerers of factoring services and finance factoring operations of other market participants, but also take an active part in establishment of factoring branches and are consumers of factoring services. In order to accelerate development of international factoring in Ukraine, the article offers such forms of state support of banks, which render factoring services to domestic exporters. The article recommends to focus banks’ attention, under modern conditions that are characterised with volatility of financial markets, on factoring servicing of those clients, whom they have long business relations with, without jeopardising themselves through provision of factoring services to a big number of small debtors. The article provides schemes of banks’ co-operation in the sphere of “non-classic” factoring with accredited factoring companies.

Structural Evidence for Regulation and Specificity of Flaviviral Proteases and Evolution of the Flaviviridae Fold

Energy Technology Data Exchange (ETDEWEB)

Aleshin,A.; Shiryaev, S.; Strongin, A.; Liddington, R.

2007-01-01

Pathogenic members of the flavivirus family, including West Nile Virus (WNV) and Dengue Virus (DV), are growing global threats for which there are no specific treatments. The two-component flaviviral enzyme NS2B-NS3 cleaves the viral polyprotein precursor within the host cell, a process that is required for viral replication. Here, we report the crystal structure of WNV NS2B-NS3pro both in a substrate-free form and in complex with the trypsin inhibitor aprotinin/BPTI. We show that aprotinin binds in a substrate-mimetic fashion in which the productive conformation of the protease is fully formed, providing evidence for an 'induced fit' mechanism of catalysis and allowing us to rationalize the distinct substrate specificities of WNV and DV proteases. We also show that the NS2B cofactor of WNV can adopt two very distinct conformations and that this is likely to be a general feature of flaviviral proteases, providing further opportunities for regulation. Finally, by comparing the flaviviral proteases with the more distantly related Hepatitis C virus, we provide insights into the evolution of the Flaviviridae fold. Our work should expedite the design of protease inhibitors to treat a range of flaviviral infections.

Feature Inference Learning and Eyetracking

Science.gov (United States)

Rehder, Bob; Colner, Robert M.; Hoffman, Aaron B.

2009-01-01

Besides traditional supervised classification learning, people can learn categories by inferring the missing features of category members. It has been proposed that feature inference learning promotes learning a category's internal structure (e.g., its typical features and interfeature correlations) whereas classification promotes the learning of…

Structural health monitoring for ship structures

Energy Technology Data Exchange (ETDEWEB)

Farrar, Charles [Los Alamos National Laboratory; Park, Gyuhae [Los Alamos National Laboratory; Angel, Marian [Los Alamos National Laboratory; Bement, Matthew [Los Alamos National Laboratory; Salvino, Liming [NSWC, CADEROCK

2009-01-01

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

Assessment of inservice conditions of safety-related nuclear plant structures

International Nuclear Information System (INIS)

Ashar, H.; Bagchi, G.

1995-06-01

The report is a compilation from a number of sources of information related to the condition Of structures and civil engineering features at operating nuclear power plants in the United States. The most significant information came from the hands-on inspection of the six old plants (licensed prior to 1977) performed by the staff of the Civil Engineering and Geosciences Branch (ECGB) in the Division of Engineering of the Office of Nuclear Reactor Regulation. For the containment structures, most of the information related to the degraded conditions came from the licensees as part of the Licensing Event Report System (10 CFR 50.73), or as part of the requirement under limiting condition of operation of the plant-specific Technical Specifications. Most of the information related to the degradation of other Structures and civil engineering features was extracted from the industry survey, the reported incidents, and the plant visits. The report discusses the condition of the structures and civil engineering features at operating nuclear power plants and provides information that would help detect, alleviate, and correct the degraded conditions of the structures and civil engineering features

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

Science.gov (United States)

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

2017-10-10

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

Iterative feature refinement for accurate undersampled MR image reconstruction

Science.gov (United States)

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

2016-05-01

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

Iterative feature refinement for accurate undersampled MR image reconstruction

International Nuclear Information System (INIS)

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

2016-01-01

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

'Focal thyroid inferno' on color Doppler ultrasonography: A specific feature of focal Hashimoto's thyroiditis

Energy Technology Data Exchange (ETDEWEB)

Fu, Xianshui, E-mail: fuxs1968@163.com [Department of Ultrasound, Peking University Third Hospital, 49 Huayuanbeilu Road, Beijing 100191 (China); Guo, Limei, E-mail: guolimei@bjmu.edu.cn [Department of Pathology, Peking University Third Hospital, 49 Huayuanbeilu Road, Beijing 100191 (China); Zhang, Huabin, E-mail: huabinzhang@bjmu.edu.cn [Department of Ultrasound, Peking University Third Hospital, 49 Huayuanbeilu Road, Beijing 100191 (China); Ran, Weiqiang, E-mail: ranwq-sina@vip.sina.com [Department of Ultrasound, Peking University Third Hospital, 49 Huayuanbeilu Road, Beijing 100191 (China); Fu, Peng, E-mail: fupeng01@gmail.com [Department of Ultrasound, Peking University Third Hospital, 49 Huayuanbeilu Road, Beijing 100191 (China); Li, Zhiqiang, E-mail: lizhq126@126.com [Department of Ultrasound, Peking University Third Hospital, 49 Huayuanbeilu Road, Beijing 100191 (China); Chen, Wen, E-mail: wendy7989@sina.com [Department of Ultrasound, Peking University Third Hospital, 49 Huayuanbeilu Road, Beijing 100191 (China); Jiang, Ling, E-mail: papayaling@yahoo.com.cn [Department of Ultrasound, Peking University Third Hospital, 49 Huayuanbeilu Road, Beijing 100191 (China); Wang, Jinrui, E-mail: jinrui_wang@sina.com [Department of Ultrasound, Peking University Third Hospital, 49 Huayuanbeilu Road, Beijing 100191 (China); Jia, Jianwen, E-mail: drjia88@sohu.com [Department of Ultrasound, Peking University Third Hospital, 49 Huayuanbeilu Road, Beijing 100191 (China)

2012-11-15

Purpose: To evaluate color-Doppler features predictive of focal Hashimoto's thyroiditis. Materials and methods: A total of 521 patients with 561 thyroid nodules that underwent surgeries or gun biopsies were included in this study. These nodules were divided into three groups: focal Hashimoto's thyroiditis (104 nodules in 101 patients), benignity other than focal Hashimoto's thyroiditis (73 nodules in 70 patients), and malignancy (358 nodules in 350 patients). On color Doppler sonography, four vascularity types were determined as: hypovascularity, marked internal flow, marked peripheral flow and focal thyroid inferno. The {chi}{sup 2} test was performed to seek the potential vascularity type with the predictive ability of certain thyroid pathology. Furthermore, the gray-scale features of each nodule were also studied. Results: The vascularity type I (hypovascularity) was more often seen in focal Hashimoto's thyroiditis than other benignity and malignancy (46% vs. 20.5% and 19%). While the type II (marked internal flow) showed the opposite tendency (26.9% [focal Hashimoto's thyroiditis] vs. 45.2% [other benignity] and 52.8% [malignancy]). However, type III (marked peripheral flow) was unable to predict any thyroid pathology. Importantly, type IV (focal thyroid inferno) was exclusive to focal Hashimoto's thyroiditis. All 8 type IV nodules appeared to be solid, hypoechoic, and well-defined. Using 'focal thyroid inferno' as an indicator of FHT, the diagnostic sensitivity and specificity were 7.7% and 100% respectively. Conclusions: The vascularity type of 'focal thyroid inferno' is specific for focal Hashimoto thyroiditis. Recognition of this particular feature may avoid unnecessary interventional procedures for some solid hypoechoic thyroid nodules suspicious of malignancy.

STRUCTURAL AND DESIGN SPECIFICS OF SPACE GRID SYSTEMS

Directory of Open Access Journals (Sweden)

G. M. Gasii

2017-01-01

Full Text Available The aim of the study is to identify main trends in the development of space grid structures. In order to reach the purpose it is necessary to conduct a review of the known structural concepts, nodal connections and specifics of the space grid structures and to make conclusions on feasibility improvement of the considered structural concepts that make it possible to develop new solutions without disadvantages residing in the analogues. Analysis of papers written by foreign and national scientists and devoted to theoretical, numerical and experimental studies of stress-strain state, influence of different factors on it and geometrical optimization and designing of space grid structures has been conducted in order to achieve the objectives. Space grid structures and, in particular, flat double-layer grid and most frequent nodes have been studied in the paper. The paper contains a short review of the history on development of space grid structures. It has been found that a rapid development of structural designs was caused by scientific and technical progress and, in particular, improvement of physical and mechanical properties of materials, development of calculation methods, application of software systems for simulating behavior of the structure under load, which significantly increased the calculation accuracy and reduced complexity of design. It has been also established that main parameters that have influence on effectiveness of a structural design are geometric dimensions of its modular elements, ratio of its depth to the span. The world experience on development of connection components has been studied in the paper. The paper presents general classification of nodal connections. Main advantages and disadvantages of existing space grid structures are highlighted and it allows to determine possible methods for their improvement. Theoretical research has permitted to establish that the main direction of spatial grid structures improvement

Structural and Kinetic Properties of the Aldehyde Dehydrogenase NahF, a Broad Substrate Specificity Enzyme for Aldehyde Oxidation.

Science.gov (United States)

Coitinho, Juliana B; Pereira, Mozart S; Costa, Débora M A; Guimarães, Samuel L; Araújo, Simara S; Hengge, Alvan C; Brandão, Tiago A S; Nagem, Ronaldo A P

2016-09-27

The salicylaldehyde dehydrogenase (NahF) catalyzes the oxidation of salicylaldehyde to salicylate using NAD(+) as a cofactor, the last reaction of the upper degradation pathway of naphthalene in Pseudomonas putida G7. The naphthalene is an abundant and toxic compound in oil and has been used as a model for bioremediation studies. The steady-state kinetic parameters for oxidation of aliphatic or aromatic aldehydes catalyzed by 6xHis-NahF are presented. The 6xHis-NahF catalyzes the oxidation of aromatic aldehydes with large kcat/Km values close to 10(6) M(-1) s(-1). The active site of NahF is highly hydrophobic, and the enzyme shows higher specificity for less polar substrates than for polar substrates, e.g., acetaldehyde. The enzyme shows α/β folding with three well-defined domains: the oligomerization domain, which is responsible for the interlacement between the two monomers; the Rossmann-like fold domain, essential for nucleotide binding; and the catalytic domain. A salicylaldehyde molecule was observed in a deep pocket in the crystal structure of NahF where the catalytic C284 and E250 are present. Moreover, the residues G150, R157, W96, F99, F274, F279, and Y446 were thought to be important for catalysis and specificity for aromatic aldehydes. Understanding the molecular features responsible for NahF activity allows for comparisons with other aldehyde dehydrogenases and, together with structural information, provides the information needed for future mutational studies aimed to enhance its stability and specificity and further its use in biotechnological processes.

Infective endocarditis: the specific features of its course, the criteria for diagnosis, differential diagnosis (part II

Directory of Open Access Journals (Sweden)

B S Belov

2008-01-01

Full Text Available Infective endocarditis (IE is today characterized by polyetiology due to a wide range of pathogens. The paper describes the specific features of the clinical picture of the disease in relation to the etiological agent, which have, in some cases, a crucial role in the choice of empiric antibiotic therapy. Significant clinical polymorphism, obscure symptoms, and monosyndromic onset as guises all enhance the importance of the differential diagnosis of IE, at its early stages in particular. Basic approaches to differentiating IE from the diseases in which differentially diagnostic problems arise to the utmost are outlined.

Students' Demand for Smartphones: Structural Relationships of Product Features, Brand Name, Product Price and Social Infuence

Science.gov (United States)

Suki, Norazah Mohd

2013-01-01

Purpose: The study aims to examine structural relationships of product features, brand name, product price and social influence with demand for Smartphones among Malaysian students'. Design/methodology/approach: Data collected from 320 valid pre-screened university students studying at the pubic higher learning institution in Federal Territory of…

Featureous: an Integrated Approach to Location, Analysis and Modularization of Features in Java Applications

DEFF Research Database (Denmark)

Olszak, Andrzej

, it is essential that features are properly modularized within the structural organization of software systems. Nevertheless, in many object-oriented applications, features are not represented explicitly. Consequently, features typically end up scattered and tangled over multiple source code units......, such as architectural layers, packages and classes. This lack of modularization is known to make application features difficult to locate, to comprehend and to modify in isolation from one another. To overcome these problems, this thesis proposes Featureous, a novel approach to location, analysis and modularization...... quantitative and qualitative results suggest that Featureous succeeds at efficiently locating features in unfamiliar codebases, at aiding feature-oriented comprehension and modification, and at improving modularization of features using Java packages....

Detection and analysis of diamond fingerprinting feature and its application

Energy Technology Data Exchange (ETDEWEB)

Li Xin; Huang Guoliang; Li Qiang; Chen Shengyi, E-mail: tshgl@tsinghua.edu.cn [Department of Biomedical Engineering, the School of Medicine, Tsinghua University, Beijing, 100084 (China)

2011-01-01

Before becoming a jewelry diamonds need to be carved artistically with some special geometric features as the structure of the polyhedron. There are subtle differences in the structure of this polyhedron in each diamond. With the spatial frequency spectrum analysis of diamond surface structure, we can obtain the diamond fingerprint information which represents the 'Diamond ID' and has good specificity. Based on the optical Fourier Transform spatial spectrum analysis, the fingerprinting identification of surface structure of diamond in spatial frequency domain was studied in this paper. We constructed both the completely coherent diamond fingerprinting detection system illuminated by laser and the partially coherent diamond fingerprinting detection system illuminated by led, and analyzed the effect of the coherence of light source to the diamond fingerprinting feature. We studied rotation invariance and translation invariance of the diamond fingerprinting and verified the feasibility of real-time and accurate identification of diamond fingerprint. With the profit of this work, we can provide customs, jewelers and consumers with a real-time and reliable diamonds identification instrument, which will curb diamond smuggling, theft and other crimes, and ensure the healthy development of the diamond industry.

Crystal structure and novel recognition motif of rho ADP-ribosylating C3 exoenzyme from Clostridium botulinum: structural insights for recognition specificity and catalysis.

Science.gov (United States)

Han, S; Arvai, A S; Clancy, S B; Tainer, J A

2001-01-05

Clostridium botulinum C3 exoenzyme inactivates the small GTP-binding protein family Rho by ADP-ribosylating asparagine 41, which depolymerizes the actin cytoskeleton. C3 thus represents a major family of the bacterial toxins that transfer the ADP-ribose moiety of NAD to specific amino acids in acceptor proteins to modify key biological activities in eukaryotic cells, including protein synthesis, differentiation, transformation, and intracellular signaling. The 1.7 A resolution C3 exoenzyme structure establishes the conserved features of the core NAD-binding beta-sandwich fold with other ADP-ribosylating toxins despite little sequence conservation. Importantly, the central core of the C3 exoenzyme structure is distinguished by the absence of an active site loop observed in many other ADP-ribosylating toxins. Unlike the ADP-ribosylating toxins that possess the active site loop near the central core, the C3 exoenzyme replaces the active site loop with an alpha-helix, alpha3. Moreover, structural and sequence similarities with the catalytic domain of vegetative insecticidal protein 2 (VIP2), an actin ADP-ribosyltransferase, unexpectedly implicates two adjacent, protruding turns, which join beta5 and beta6 of the toxin core fold, as a novel recognition specificity motif for this newly defined toxin family. Turn 1 evidently positions the solvent-exposed, aromatic side-chain of Phe209 to interact with the hydrophobic region of Rho adjacent to its GTP-binding site. Turn 2 evidently both places the Gln212 side-chain for hydrogen bonding to recognize Rho Asn41 for nucleophilic attack on the anomeric carbon of NAD ribose and holds the key Glu214 catalytic side-chain in the adjacent catalytic pocket. This proposed bipartite ADP-ribosylating toxin turn-turn (ARTT) motif places the VIP2 and C3 toxin classes into a single ARTT family characterized by analogous target protein recognition via turn 1 aromatic and turn 2 hydrogen-bonding side-chain moieties. Turn 2 centrally anchors

Principal Feature Analysis: A Multivariate Feature Selection Method for fMRI Data

Directory of Open Access Journals (Sweden)

Lijun Wang

2013-01-01

Full Text Available Brain decoding with functional magnetic resonance imaging (fMRI requires analysis of complex, multivariate data. Multivoxel pattern analysis (MVPA has been widely used in recent years. MVPA treats the activation of multiple voxels from fMRI data as a pattern and decodes brain states using pattern classification methods. Feature selection is a critical procedure of MVPA because it decides which features will be included in the classification analysis of fMRI data, thereby improving the performance of the classifier. Features can be selected by limiting the analysis to specific anatomical regions or by computing univariate (voxel-wise or multivariate statistics. However, these methods either discard some informative features or select features with redundant information. This paper introduces the principal feature analysis as a novel multivariate feature selection method for fMRI data processing. This multivariate approach aims to remove features with redundant information, thereby selecting fewer features, while retaining the most information.

Porous Structure of Road Concrete

OpenAIRE

Пшембаев, М. К.; Гиринский, В. В.; Ковалев, Я. Н.; Яглов, В. Н.; Будниченко, С. С.

2016-01-01

Having a great number of concrete structure classifications it is recommended to specify the following three principal types: microstructure – cement stone structure; mesostructure – structure of cement-sand mortar in concrete; macrostucture – two-component system that consists of mortar and coarse aggregate. Every mentioned-above structure has its own specific features which are related to the conditions of their formation. Thus, microstructure of cement stone can be characterized by such st...

A highly specific phage defense system is a conserved feature of the Vibrio cholerae mobilome.

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Brendan J O'Hara

2017-06-01

Full Text Available Vibrio cholerae-specific bacteriophages are common features of the microbial community during cholera infection in humans. Phages impose strong selective pressure that favors the expansion of phage-resistant strains over their vulnerable counterparts. The mechanisms allowing virulent V. cholerae strains to defend against the ubiquitous threat of predatory phages have not been established. Here, we show that V. cholerae PLEs (phage-inducible chromosomal island-like elements are widespread genomic islands dedicated to phage defense. Analysis of V. cholerae isolates spanning a 60-year collection period identified five unique PLEs. Remarkably, we found that all PLEs (regardless of geographic or temporal origin respond to infection by a myovirus called ICP1, the most prominent V. cholerae phage found in cholera patient stool samples from Bangladesh. We found that PLE activity reduces phage genome replication and accelerates cell lysis following ICP1 infection, killing infected host cells and preventing the production of progeny phage. PLEs are mobilized by ICP1 infection and can spread to neighboring cells such that protection from phage predation can be horizontally acquired. Our results reveal that PLEs are a persistent feature of the V. cholerae mobilome that are adapted to providing protection from a single predatory phage and advance our understanding of how phages influence pathogen evolution.

A highly specific phage defense system is a conserved feature of the Vibrio cholerae mobilome.

Science.gov (United States)

O'Hara, Brendan J; Barth, Zachary K; McKitterick, Amelia C; Seed, Kimberley D

2017-06-01

Vibrio cholerae-specific bacteriophages are common features of the microbial community during cholera infection in humans. Phages impose strong selective pressure that favors the expansion of phage-resistant strains over their vulnerable counterparts. The mechanisms allowing virulent V. cholerae strains to defend against the ubiquitous threat of predatory phages have not been established. Here, we show that V. cholerae PLEs (phage-inducible chromosomal island-like elements) are widespread genomic islands dedicated to phage defense. Analysis of V. cholerae isolates spanning a 60-year collection period identified five unique PLEs. Remarkably, we found that all PLEs (regardless of geographic or temporal origin) respond to infection by a myovirus called ICP1, the most prominent V. cholerae phage found in cholera patient stool samples from Bangladesh. We found that PLE activity reduces phage genome replication and accelerates cell lysis following ICP1 infection, killing infected host cells and preventing the production of progeny phage. PLEs are mobilized by ICP1 infection and can spread to neighboring cells such that protection from phage predation can be horizontally acquired. Our results reveal that PLEs are a persistent feature of the V. cholerae mobilome that are adapted to providing protection from a single predatory phage and advance our understanding of how phages influence pathogen evolution.

Contrasted structuring effects of mesoscale features on the seabird community in the Mozambique Channel

Science.gov (United States)

Jaquemet, S.; Ternon, J. F.; Kaehler, S.; Thiebot, J. B.; Dyer, B.; Bemanaja, E.; Marteau, C.; Le Corre, M.

2014-02-01

The Mozambique Channel (western Indian Ocean) is a dynamic environment characterised by strong mesoscale features, which influence all biological components of the pelagic ecosystem. We investigated the distribution, abundance and feeding behaviour of seabirds in the Mozambique Channel in relation to physical and biological environmental variables, with a specific interest in mesoscale features. Seabird censuses were conducted in summer and winter during 7 cruises in the southern and northern Mozambique Channel. Tropical species accounted for 49% of the 37 species identified and 97% of the individuals, and species from the sub-Antarctic region constituted 30% of the identifications. The typically tropical sooty tern (Onychoprion fuscata) was the dominant species during all cruises, and overall accounted for 74% of the species observations and 85% of counted birds. Outputs of Generalised Linear Models at the scale of the Mozambique Channel suggested that higher densities of flying and feeding birds occurred in areas with lower sea surface temperatures and lower surface chlorophyll a concentrations. Most of the flocks of feeding birds did not associate with surface schools of fish or marine mammals, but when they did, these flocks were larger, especially when associated with tuna. While tropical species seemed to favour cyclonic eddies, frontal and divergence zones, non-tropical species were more frequently recorded over shelf waters. Sooty terns foraged preferentially in cyclonic eddies where zooplankton, micronekton and tuna schools were abundant. Among other major tropical species, frigatebirds (Fregata spp.) predominated in frontal zones between eddies, where tuna schools also frequently occurred and where geostrophic currents were the strongest. Red-footed boobies (Sula sula) concentrated in divergence zones characterised by low sea level anomalies, low geostrophic currents, and high zooplankton biomass close to the surface. Our results highlight the importance

Use cases and DEMO: aligning functional features of ICT-infrastructure to business processes.

Science.gov (United States)

Maij, E; Toussaint, P J; Kalshoven, M; Poerschke, M; Zwetsloot-Schonk, J H M

2002-11-12

The proper alignment of functional features of the ICT-infrastructure to business processes is a major challenge in health care organisations. This alignment takes into account that the organisational structure not only shapes the ICT-infrastructure, but that the inverse also holds. To solve the alignment problem, relevant features of the ICT-infrastructure should be derived from the organisational structure and the influence of this envisaged ICT to the work practices should be pointed out. The objective of our study was to develop a method to solve this alignment problem. In a previous study we demonstrated the appropriateness of the business process modelling methodology Dynamic Essential Modelling of Organizations (DEMO). A proven and widely used modelling language for expressing functional features is Unified Modelling Language (UML). In the context of a specific case study at the University Medical Centre Utrecht in the Netherlands we investigated if the combined use of DEMO and UML could solve the alignment problem. The study demonstrated that the DEMO models were suited as a starting point in deriving system functionality by using the use case concept of UML. Further, the case study demonstrated that in using this approach for the alignment problem, insight is gained into the mutual influence of ICT-infrastructure and organisation structure: (a) specification of independent, re-usable components-as a set of related functionalities-is realised, and (b) a helpful representation of the current and future work practice is provided for in relation to the envisaged ICT support.

Specific features of band structure and optical anisotropy of Cu{sub 2}CdGeSe{sub 4} quaternary compounds

Energy Technology Data Exchange (ETDEWEB)

Brik, M.G., E-mail: brik@fi.tartu.ee [College of Mathematics and Physics, Chongqing University of Posts and Telecommunications, Chongqing 400065 (China); Institute of Physics, University of Tartu, Riia 142, Tartu 51014 (Estonia); Institute of Physics, Jan Dlugosz University, Armii Krajowej 13/15, PL-42200 Czestochowa (Poland); Parasyuk, O.V. [Department of Chemistry, Eastern European National University, Voli 13, Lutsk 43025 (Ukraine); Myronchuk, G.L. [Department of Physics, Eastern European National University, Voli 13, Lutsk 43025 (Ukraine); Kityk, I.V. [Institute of Materials Science and Engineering, Technical University of Czestochowa, Al. Armii Krajowej 19, 42-200 Czestochowa (Poland)

2014-09-15

Complex theoretical and experimental studies of the band structure and optical functions of a new Cu{sub 2}CdGeSe{sub 4} quaternary crystal are reported. The benchmark band structure calculations were performed using the first-principles methods. As a result, the structural, electronic, optical and elastic properties of Cu{sub 2}CdGeSe{sub 4} were calculated in the general gradient approximation (GGA) and local density approximation (LDA). The calculated dielectric function and optical absorption spectra exhibit some anisotropic behavior. Detailed analysis of the band energy dispersion and effective space charge density helped in establishing the origin of the band structure anisotropy. All calculated properties are compared with the experimental data. An additional comparison with a similar crystal of Cu{sub 2}CdGeSe{sub 4} allowed to reveal the role played by the anions (S or Se) in formation of the optical properties of these two materials. - Highlights: • The structural, electronic, optical properties of Cu{sub 2}CdGeSe{sub 4} were calculated. • Pressure effects on these properties were modeled. • Comparison with a similar compound of Cu{sub 2}CdGeS{sub 4} was performed.

The Structure of Neurexin 1[alpha] Reveals Features Promoting a Role as Synaptic Organizer

Energy Technology Data Exchange (ETDEWEB)

Chen, Fang; Venugopal, Vandavasi; Murray, Beverly; Rudenko, Gabby (Michigan)

2014-10-02

{alpha}-Neurexins are essential synaptic adhesion molecules implicated in autism spectrum disorder and schizophrenia. The {alpha}-neurexin extracellular domain consists of six LNS domains interspersed by three EGF-like repeats and interacts with many different proteins in the synaptic cleft. To understand how {alpha}-neurexins might function as synaptic organizers, we solved the structure of the neurexin 1{alpha} extracellular domain (n1{alpha}) to 2.65 {angstrom}. The L-shaped molecule can be divided into a flexible repeat I (LNS1-EGF-A-LNS2), a rigid horseshoe-shaped repeat II (LNS3-EGF-B-LNS4) with structural similarity to so-called reelin repeats, and an extended repeat III (LNS5-EGF-B-LNS6) with controlled flexibility. A 2.95 {angstrom} structure of n1{alpha} carrying splice insert SS3 in LNS4 reveals that SS3 protrudes as a loop and does not alter the rigid arrangement of repeat II. The global architecture imposed by conserved structural features enables {alpha}-neurexins to recruit and organize proteins in distinct and variable ways, influenced by splicing, thereby promoting synaptic function.

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

Science.gov (United States)

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

2017-12-01

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

Endotoxin Structures in the Psychrophiles Psychromonas marina and Psychrobacter cryohalolentis Contain Distinctive Acyl Features

Directory of Open Access Journals (Sweden)

Charles R. Sweet

2014-07-01

Full Text Available Lipid A is the essential component of endotoxin (Gram-negative lipopolysaccharide, a potent immunostimulatory compound. As the outer surface of the outer membrane, the details of lipid A structure are crucial not only to bacterial pathogenesis but also to membrane integrity. This work characterizes the structure of lipid A in two psychrophiles, Psychromonas marina and Psychrobacter cryohalolentis, and also two mesophiles to which they are related using MALDI-TOF MS and fatty acid methyl ester (FAME GC-MS. P. marina lipid A is strikingly similar to that of Escherichia coli in organization and total acyl size, but incorporates an unusual doubly unsaturated tetradecadienoyl acyl residue. P. cryohalolentis also shows structural organization similar to a closely related mesophile, Acinetobacter baumannii, however it has generally shorter acyl constituents and shows many acyl variants differing by single methylene (-CH2- units, a characteristic it shares with the one previously reported psychrotolerant lipid A structure. This work is the first detailed structural characterization of lipid A from an obligate psychrophile and the second from a psychrotolerant species. It reveals distinctive structural features of psychrophilic lipid A in comparison to that of related mesophiles which suggest constitutive adaptations to maintain outer membrane fluidity in cold environments.

Production of specific-structured lipids by enzymatic interesterification in a pilot continuous enzyme bed reactor

DEFF Research Database (Denmark)

Xu, Xuebing; Balchen, Steen; Høy, Carl-Erik

1998-01-01

Production of specific-structured lipids (interesterified lipids with a specific structure) by enzymatic interesterification was carried out in a continuous enzyme bed pilot scale reactor. Commercial immobilized lipase (Lipozyme IM) was used and investigations of acyl migration, pressure drop...

[Specific features of 2-methyl hydroxybenzene and 3-methyl hydroxybenzene distribution in the organism of warm-blooded animals].

Science.gov (United States)

Shormanov, B K; Grishenko, V K; Astashkina, A P; Elizarova, M K

2013-01-01

The present work was designed to study the specific features of 2-methyl hydroxybezene and 3-methyl hydroxybenzene distribution after intragastric administration of these toxicants to warm-blooded animals (rats). They were detected in the unmetabolized form in the internal organs and blood of the animals. The levels of 2-methyl hydroxybezene were especially high in the stomach and blood whereas the maximum content of 3-methyl hydroxybenzene was found in brain, blood, small intestines of the poisoned rats.

Light field morphing using 2D features.

Science.gov (United States)

Wang, Lifeng; Lin, Stephen; Lee, Seungyong; Guo, Baining; Shum, Heung-Yeung

2005-01-01

We present a 2D feature-based technique for morphing 3D objects represented by light fields. Existing light field morphing methods require the user to specify corresponding 3D feature elements to guide morph computation. Since slight errors in 3D specification can lead to significant morphing artifacts, we propose a scheme based on 2D feature elements that is less sensitive to imprecise marking of features. First, 2D features are specified by the user in a number of key views in the source and target light fields. Then the two light fields are warped view by view as guided by the corresponding 2D features. Finally, the two warped light fields are blended together to yield the desired light field morph. Two key issues in light field morphing are feature specification and warping of light field rays. For feature specification, we introduce a user interface for delineating 2D features in key views of a light field, which are automatically interpolated to other views. For ray warping, we describe a 2D technique that accounts for visibility changes and present a comparison to the ideal morphing of light fields. Light field morphing based on 2D features makes it simple to incorporate previous image morphing techniques such as nonuniform blending, as well as to morph between an image and a light field.

The GOAL-to-HAL/S translator specification. [for space shuttle

Science.gov (United States)

Stanten, S. F.; Flanders, J. H.

1973-01-01

The specification sets forth a technical framework within which to deal with the transfer of specific GOAL features to HAL/S. Key technical features of the translator are described which communicate with the data bank, handle repeat statements, and deal with software interrupts. GOAL programs, databank information, and GOAL system subroutines are integrated into one GOAL in HAL/S. This output is fully compatible HAL/S source ready for insertion into the HAL/S compiler. The Translator uses a PASS1 to establish all the global data needed for the HAL/S output program. Individual GOAL statements are translated in PASS2. The specification document makes extensive use of flowcharts to specify exactly how each variation of each GOAL statement is to be translated. The specification also deals with definitions and assumptions, executive support structure and implementation. An appendix, entitled GOAL-to-HAL Mapping, provides examples of translated GOAL statements.

Coastal Geographic Structures in Coastal-Marine Environmental Management

Science.gov (United States)

Baklanov, P. Ya.; Ganzei, K. S.; Ermoshin, V. V.

2018-01-01

It has been proposed to distinguish the coastal geographic structures consisting of a spatial combination of three interconnected and mutually conditioned parts (coastal-territorial, coastal, coastal-marine), which are interlinked with each other by the cumulative effect of real-energy flows. Distinguishing specific resource features of the coastal structures, by which they play a connecting role in the complex coastalmarine management, has been considered. The main integral resource feature of the coastal structures is their connecting functions, which form transitional parts mutually connecting the coastal-territorial and coastalmarine environmental management.

Influence of major structural features of tocopherols and tocotrienols on their omega-oxidation by tocopherol-omega-hydroxylase.

Science.gov (United States)

Sontag, Timothy J; Parker, Robert S

2007-05-01

Human cytochrome P450 4F2 (CYP4F2) catalyzes the initial omega-hydroxylation reaction in the metabolism of tocopherols and tocotrienols to carboxychromanols and is, to date, the only enzyme shown to metabolize vitamin E. The objective of this study was to characterize this activity, particularly the influence of key features of tocochromanol substrate structure. The influence of the number and positions of methyl groups on the chromanol ring, and of stereochemistry and saturation of the side chain, were explored using HepG2 cultures and microsomal reaction systems. Human liver microsomes and microsomes selectively expressing recombinant human CYP4F2 exhibited substrate activity patterns similar to those of HepG2 cells. Although activity was strongly associated with substrate accumulation by cells or microsomes, substantial differences in specific activities between substrates remained under conditions of similar microsomal membrane substrate concentration. Methylation at C5 of the chromanol ring was associated with markedly low activity. Tocotrienols exhibited much higher Vmax values than their tocopherol counterparts. Side chain stereochemistry had no effect on omega-hydroxylation of alpha-tocopherol (alpha-TOH) by any system. Kinetic analysis of microsomal CYP4F2 activity revealed Michaelis-Menten kinetics for alpha-TOH but allosteric cooperativity for other vitamers, especially tocotrienols. Additionally, alpha-TOH was a positive effector of omega-hydroxylation of other vitamers. These results indicate that CYP4F2-mediated tocopherol-omega-hydroxylation is a central feature underlying the different biological half-lives, and therefore biopotencies, of the tocopherols and tocotrienols.

PROSPER: an integrated feature-based tool for predicting protease substrate cleavage sites.

Directory of Open Access Journals (Sweden)

Jiangning Song

Full Text Available The ability to catalytically cleave protein substrates after synthesis is fundamental for all forms of life. Accordingly, site-specific proteolysis is one of the most important post-translational modifications. The key to understanding the physiological role of a protease is to identify its natural substrate(s. Knowledge of the substrate specificity of a protease can dramatically improve our ability to predict its target protein substrates, but this information must be utilized in an effective manner in order to efficiently identify protein substrates by in silico approaches. To address this problem, we present PROSPER, an integrated feature-based server for in silico identification of protease substrates and their cleavage sites for twenty-four different proteases. PROSPER utilizes established specificity information for these proteases (derived from the MEROPS database with a machine learning approach to predict protease cleavage sites by using different, but complementary sequence and structure characteristics. Features used by PROSPER include local amino acid sequence profile, predicted secondary structure, solvent accessibility and predicted native disorder. Thus, for proteases with known amino acid specificity, PROSPER provides a convenient, pre-prepared tool for use in identifying protein substrates for the enzymes. Systematic prediction analysis for the twenty-four proteases thus far included in the database revealed that the features we have included in the tool strongly improve performance in terms of cleavage site prediction, as evidenced by their contribution to performance improvement in terms of identifying known cleavage sites in substrates for these enzymes. In comparison with two state-of-the-art prediction tools, PoPS and SitePrediction, PROSPER achieves greater accuracy and coverage. To our knowledge, PROSPER is the first comprehensive server capable of predicting cleavage sites of multiple proteases within a single substrate

Enhanced regulatory sequence prediction using gapped k-mer features.

Science.gov (United States)

Ghandi, Mahmoud; Lee, Dongwon; Mohammad-Noori, Morteza; Beer, Michael A

2014-07-01

Oligomers of length k, or k-mers, are convenient and widely used features for modeling the properties and functions of DNA and protein sequences. However, k-mers suffer from the inherent limitation that if the parameter k is increased to resolve longer features, the probability of observing any specific k-mer becomes very small, and k-mer counts approach a binary variable, with most k-mers absent and a few present once. Thus, any statistical learning approach using k-mers as features becomes susceptible to noisy training set k-mer frequencies once k becomes large. To address this problem, we introduce alternative feature sets using gapped k-mers, a new classifier, gkm-SVM, and a general method for robust estimation of k-mer frequencies. To make the method applicable to large-scale genome wide applications, we develop an efficient tree data structure for computing the kernel matrix. We show that compared to our original kmer-SVM and alternative approaches, our gkm-SVM predicts functional genomic regulatory elements and tissue specific enhancers with significantly improved accuracy, increasing the precision by up to a factor of two. We then show that gkm-SVM consistently outperforms kmer-SVM on human ENCODE ChIP-seq datasets, and further demonstrate the general utility of our method using a Naïve-Bayes classifier. Although developed for regulatory sequence analysis, these methods can be applied to any sequence classification problem.

Enhanced regulatory sequence prediction using gapped k-mer features.

Directory of Open Access Journals (Sweden)

Mahmoud Ghandi

2014-07-01

Full Text Available Oligomers of length k, or k-mers, are convenient and widely used features for modeling the properties and functions of DNA and protein sequences. However, k-mers suffer from the inherent limitation that if the parameter k is increased to resolve longer features, the probability of observing any specific k-mer becomes very small, and k-mer counts approach a binary variable, with most k-mers absent and a few present once. Thus, any statistical learning approach using k-mers as features becomes susceptible to noisy training set k-mer frequencies once k becomes large. To address this problem, we introduce alternative feature sets using gapped k-mers, a new classifier, gkm-SVM, and a general method for robust estimation of k-mer frequencies. To make the method applicable to large-scale genome wide applications, we develop an efficient tree data structure for computing the kernel matrix. We show that compared to our original kmer-SVM and alternative approaches, our gkm-SVM predicts functional genomic regulatory elements and tissue specific enhancers with significantly improved accuracy, increasing the precision by up to a factor of two. We then show that gkm-SVM consistently outperforms kmer-SVM on human ENCODE ChIP-seq datasets, and further demonstrate the general utility of our method using a Naïve-Bayes classifier. Although developed for regulatory sequence analysis, these methods can be applied to any sequence classification problem.

Automated measurement of CT noise in patient images with a novel structure coherence feature

International Nuclear Information System (INIS)

Chun, Minsoo; Kim, Jong Hyo; Choi, Young Hun

2015-01-01

While the assessment of CT noise constitutes an important task for the optimization of scan protocols in clinical routine, the majority of noise measurements in practice still rely on manual operation, hence limiting their efficiency and reliability. This study presents an algorithm for the automated measurement of CT noise in patient images with a novel structure coherence feature. The proposed algorithm consists of a four-step procedure including subcutaneous fat tissue selection, the calculation of structure coherence feature, the determination of homogeneous ROIs, and the estimation of the average noise level. In an evaluation with 94 CT scans (16 517 images) of pediatric and adult patients along with the participation of two radiologists, ROIs were placed on a homogeneous fat region at 99.46% accuracy, and the agreement of the automated noise measurements with the radiologists’ reference noise measurements (PCC  =  0.86) was substantially higher than the within and between-rater agreements of noise measurements (PCC within   =  0.75, PCC between   =  0.70). In addition, the absolute noise level measurements matched closely the theoretical noise levels generated by a reduced-dose simulation technique. Our proposed algorithm has the potential to be used for examining the appropriateness of radiation dose and the image quality of CT protocols for research purposes as well as clinical routine. (paper)

An object-oriented feature-based design system face-based detection of feature interactions

International Nuclear Information System (INIS)

Ariffin Abdul Razak

1999-01-01

This paper presents an object-oriented, feature-based design system which supports the integration of design and manufacture by ensuring that part descriptions fully account for any feature interactions. Manufacturing information is extracted from the feature descriptions in the form of volumes and Tool Access Directions, TADs. When features interact, both volumes and TADs are updated. This methodology has been demonstrated by developing a prototype system in which ACIS attributes are used to record feature information within the data structure of the solid model. The system implemented in the C++ programming language and embedded in a menu-driven X-windows user interface to the ACIS 3D Toolkit. (author)

Oxide-ion and proton conducting electrolyte materials for clean energy applications: structural and mechanistic features.

Science.gov (United States)

Malavasi, Lorenzo; Fisher, Craig A J; Islam, M Saiful

2010-11-01

This critical review presents an overview of the various classes of oxide materials exhibiting fast oxide-ion or proton conductivity for use as solid electrolytes in clean energy applications such as solid oxide fuel cells. Emphasis is placed on the relationship between structural and mechanistic features of the crystalline materials and their ion conduction properties. After describing well-established classes such as fluorite- and perovskite-based oxides, new materials and structure-types are presented. These include a variety of molybdate, gallate, apatite silicate/germanate and niobate systems, many of which contain flexible structural networks, and exhibit different defect properties and transport mechanisms to the conventional materials. It is concluded that the rich chemistry of these important systems provides diverse possibilities for developing superior ionic conductors for use as solid electrolytes in fuel cells and related applications. In most cases, a greater atomic-level understanding of the structures, defects and conduction mechanisms is achieved through a combination of experimental and computational techniques (217 references).

IgE to penicillins with different specificities can be identified by a multiepitope macromolecule: Bihaptenic penicillin structures and IgE specificities.

Science.gov (United States)

Ariza, A; Barrionuevo, E; Mayorga, C; Montañez, M I; Perez-Inestrosa, E; Ruiz-Sánchez, A; Rodríguez-Guéant, R M; Fernández, T D; Guéant, J L; Torres, M J; Blanca, M

2014-04-01

Quantitation of specific IgE by immunoassay is a recommended in vitro test for the diagnosis of immediate hypersensitivity reactions to betalactams (BLs), particularly when skin test results are negative. IgE antibodies that recognize the common nuclear structure of all BLs or the specific side chain structure can be mainly distinguished by immunoassays. The aim of this study was to develop an immunoassay system to detect IgE antibodies with different specificities. Cellulose discs conjugated with benzylpenicillin (BP), amoxicillin (AX) or both drugs, with poly-l-lysine (PLL) as carrier molecule, were used as solid phases in the radioallergosorbent test (RAST). Direct and inhibition radioimmunoassay studies were made to verify the structures recognized by serum IgE antibodies from penicillin-allergic patients. Our results indicated that the addition of both haptens did not decrease the capacity to capture IgE when serum specific to either BP or AX was used, at least in terms of sensitivity. In addition, the inclusion of two haptens improved significantly the levels of IgE detection in patients who recognized both BP and AX. Therefore, the use of a solid phase with a carrier molecule conjugated with two determinants (AX and BP) is helpful to recognize IgE antibodies against either of these determinants and is useful for screening sera with different specificities. Copyright © 2014 Elsevier B.V. All rights reserved.

On the Structural Context and Identification of Enzyme Catalytic Residues

Directory of Open Access Journals (Sweden)

Yu-Tung Chien

2013-01-01

Full Text Available Enzymes play important roles in most of the biological processes. Although only a small fraction of residues are directly involved in catalytic reactions, these catalytic residues are the most crucial parts in enzymes. The study of the fundamental and unique features of catalytic residues benefits the understanding of enzyme functions and catalytic mechanisms. In this work, we analyze the structural context of catalytic residues based on theoretical and experimental structure flexibility. The results show that catalytic residues have distinct structural features and context. Their neighboring residues, whether sequence or structure neighbors within specific range, are usually structurally more rigid than those of noncatalytic residues. The structural context feature is combined with support vector machine to identify catalytic residues from enzyme structure. The prediction results are better or comparable to those of recent structure-based prediction methods.

Learning Transferable Features with Deep Adaptation Networks

OpenAIRE

Long, Mingsheng; Cao, Yue; Wang, Jianmin; Jordan, Michael I.

2015-01-01

Recent studies reveal that a deep neural network can learn transferable features which generalize well to novel tasks for domain adaptation. However, as deep features eventually transition from general to specific along the network, the feature transferability drops significantly in higher layers with increasing domain discrepancy. Hence, it is important to formally reduce the dataset bias and enhance the transferability in task-specific layers. In this paper, we propose a new Deep Adaptation...

Line-feature-based calibration method of structured light plane parameters for robot hand-eye system

Science.gov (United States)

Qi, Yuhan; Jing, Fengshui; Tan, Min

2013-03-01

For monocular-structured light vision measurement, it is essential to calibrate the structured light plane parameters in addition to the camera intrinsic parameters. A line-feature-based calibration method of structured light plane parameters for a robot hand-eye system is proposed. Structured light stripes are selected as calibrating primitive elements, and the robot moves from one calibrating position to another with constraint in order that two misaligned stripe lines are generated. The images of stripe lines could then be captured by the camera fixed at the robot's end link. During calibration, the equations of two stripe lines in the camera coordinate system are calculated, and then the structured light plane could be determined. As the robot's motion may affect the effectiveness of calibration, so the robot's motion constraints are analyzed. A calibration experiment and two vision measurement experiments are implemented, and the results reveal that the calibration accuracy can meet the precision requirement of robot thick plate welding. Finally, analysis and discussion are provided to illustrate that the method has a high efficiency fit for industrial in-situ calibration.

[The characters and specific features of new human embryonic stem cells lines].

Science.gov (United States)

Krylova, T A; Kol'tsova, A M; Zenin, V V; Gordeeva, O F; Musorina, A S; Goriachaia, T S; Shlykova, S A; Kamenetskaia, Iu K; Pinaev, G P; Polianskaia, G G

2009-01-01

Four continuous human embryonic stem cell lines (SC1, SC2, SC3 and SC4), derived from the blastocysts has been described. The cell lines were cultivated on mitotically inactivated human feeder cells. The cell lines SC1 and SC2 have passed through 150 population doublings and the cell lines SC3 and SC4 -- near 120 populations doublings, which exceeds Hayflick limit sufficiently. These cell lines maintain high activity of alkaline phosphatase, expression of transcription factor OCT-4 and cell surface antigens (SSEA-4, TRA-1-60 and TRA-1-81), confirming their ESC status and human specificity. Immunofluorescent detection of antigens, characteristic of ectoderm, endoderm and mesoderm confirms the ability of these cells to retain their pluripotency under in vitro condition. PCR analysis revealed expression of six genes specific for pluripotent cells (OCT-4, NANOG, DPPA3/STELLA, TDGF/CRIPTO and LEFTYA). Correlation between the level of proliferative activity and the character of DNA-bound fluorescent staining was found. Fluorescent dyes, Hoechst 33342 and PI, produced diffuse staining of the nuclei in slowly proliferating cells of the SC1 and SC2 lines. In contrast, in actively proliferating cells of the SC3 and SC4 lines, the clear staining of the nuclei was observed. Upon changing the cultivation condition, proliferative activity of SC3 and SC4 lines decreased and became similar to that of SC1 and SC2 lines. The character of the fluorescent staining of all these lines was also shown to be similar. These results show that quality of the fluorescent staining with Hoechst 33342 and PI reflects the level of proliferation. Possible causes and mechanisms of this feature of human ESC are discussed.

Complete fold annotation of the human proteome using a novel structural feature space.

Science.gov (United States)

Middleton, Sarah A; Illuminati, Joseph; Kim, Junhyong

2017-04-13

Recognition of protein structural fold is the starting point for many structure prediction tools and protein function inference. Fold prediction is computationally demanding and recognizing novel folds is difficult such that the majority of proteins have not been annotated for fold classification. Here we describe a new machine learning approach using a novel feature space that can be used for accurate recognition of all 1,221 currently known folds and inference of unknown novel folds. We show that our method achieves better than 94% accuracy even when many folds have only one training example. We demonstrate the utility of this method by predicting the folds of 34,330 human protein domains and showing that these predictions can yield useful insights into potential biological function, such as prediction of RNA-binding ability. Our method can be applied to de novo fold prediction of entire proteomes and identify candidate novel fold families.

Structural features in Ni-Al alloys

International Nuclear Information System (INIS)

Abylkalykova, R.B.; Kveglis, L.I.; Rakhimova, U.A.; Nasokhova, Sh.B.; Tazhibaeva, G.B.

2007-01-01

Purpose of the work is study of structural transformations under diverse memory effect in Ni-Al alloys. Examination were conducted in following composition samples: Ni -75 at.% and Al - 25 at.%. The work is devoted to clarification reasons both formation atom-ordered structures in inter-grain boundaries of bulk samples under temperature action and static load. Revealed inter-grain inter-boundary layers in Ni-Al alloy both bulk and surface state have complicated structure

Language identification using excitation source features

CERN Document Server

Rao, K Sreenivasa

2015-01-01

This book discusses the contribution of excitation source information in discriminating language. The authors focus on the excitation source component of speech for enhancement of language identification (LID) performance. Language specific features are extracted using two different modes: (i) Implicit processing of linear prediction (LP) residual and (ii) Explicit parameterization of linear prediction residual. The book discusses how in implicit processing approach, excitation source features are derived from LP residual, Hilbert envelope (magnitude) of LP residual and Phase of LP residual; and in explicit parameterization approach, LP residual signal is processed in spectral domain to extract the relevant language specific features. The authors further extract source features from these modes, which are combined for enhancing the performance of LID systems. The proposed excitation source features are also investigated for LID in background noisy environments. Each chapter of this book provides the motivatio...

Antidepressant Specificity of Serotonin Transporter Suggested by Three LeuT-SSRI Structures

Energy Technology Data Exchange (ETDEWEB)

Zhou, Z.; Zhen, J; Karpowich, N; Law, C; Reith, M; Wang, D

2009-01-01

Sertraline and fluoxetine are selective serotonin re-uptake inhibitors (SSRIs) that are widely prescribed to treat depression. They exert their effects by inhibiting the presynaptic plasma membrane serotonin transporter (SERT). All SSRIs possess halogen atoms at specific positions, which are key determinants for the drugs' specificity for SERT. For the SERT protein, however, the structural basis of its specificity for SSRIs is poorly understood. Here we report the crystal structures of LeuT, a bacterial SERT homolog, in complex with sertraline, R-fluoxetine or S-fluoxetine. The SSRI halogens all bind to exactly the same pocket within LeuT. Mutation at this halogen-binding pocket (HBP) in SERT markedly reduces the transporter's affinity for SSRIs but not for tricyclic antidepressants. Conversely, when the only nonconserved HBP residue in both norepinephrine and dopamine transporters is mutated into that found in SERT, their affinities for all the three SSRIs increase uniformly. Thus, the specificity of SERT for SSRIs is dependent largely on interaction of the drug halogens with the protein's HBP.

Specific β-turns precede PPIIL structures binding to allele-specific HLA-DRβ1* PBRs in fully-protective malaria vaccine components

Science.gov (United States)

Bermudez, Adriana; Alba, Martha P.; Vanegas, Magnolia; Patarroyo, Manuel A.; Patarroyo, Manuel E.

2018-04-01

The 3D structural analysis of 62 peptides derived from highly pathogenic Plasmodium falciparum malaria parasite proteins involved in host cell invasion led to finding a striking association between particular β-turn types located in the N-terminal peripheral flanking residue region (preceding the polyproline II left-handed structures fitting into the HLA-DRβ* allele family) and modified immune protection-inducing protein structure induced long-lasting protective immunity. This is the first time association between two different secondary structures associated with a specific immunological function has been described: full, long-lasting protective immunity.

Standard technical specifications for General Electric boiling water reactors

International Nuclear Information System (INIS)

1979-08-01

This Standard Technical Specification (STS) has been structured for the broadest possible use on General Electric plants currently being reviewed for an Operating License. Optional specifications are provided for those features and systems which may be included in individual plant designs but are not generic in their scope of application. This revision of the GE-STS does not typically include requirements which may be added or revised as a result of the NRC staff's further review of the Three Mile Island incident

The changes of macroscopic features and microscopic structures of water under influence of magnetic field

International Nuclear Information System (INIS)

Pang Xiaofeng; Deng Bo

2008-01-01

Influences of magnetic field on microscopic structures and macroscopic properties of water are studied by the spectrum techniques of infrared, Raman, visible, ultraviolet lights and X-ray. From these investigations, we know that the magnetic fields change the distribution of molecules and electrons, cause displacements and polarization of molecules and atoms, result in changes of dipole-moment transition and vibrational states of molecules and variation of transition probability of electrons, but does not alter the constitution of molecules and atoms. These are helpful in seeking the mechanism of magnetization of water. Meanwhile, we also measure the changed rules of the surface tension force, soaking effect or angle of contact, viscosity, rheology features, refraction index, dielectric constant and electric conductivity of magnetized water relative to that of pure water. The results show that the magnetic fields increase the soaking degree and hydrophobicity of water to materials, depress its surface-tension force, diminish the viscosity of war, enhance the feature of plastic flowing of water, and increase the refraction index, dielectric constant and electric conductivity of water after magnetization. These changes are caused by the above changes of microscopic structures under the action of magnetic field. Therefore, our studies are significant in science and has practical value of applications

DAFS study of site-specific local structure of Mn in manganese ferrite films

International Nuclear Information System (INIS)

Kravtsov, E.; Haskel, D.; Cady, A.; Yang, A.; Vittoria, C.; Zuo, X.; Harris, V.G.

2006-01-01

Manganese ferrite (MnFe 2 O 4 ) is a well-known magnetic material widely used in electronics for many years. It is well established that its magnetic behavior is strongly influenced by local structural properties of Mn ions, which are distributed between crystallographically inequivalent tetrahedral and octahedral sites in the unit cell. In order to understand and be able to tune properties of these structures, it is necessary to have detailed site-specific structural information on the system. Here we report on the application of diffraction-anomalous fine structure (DAFS) spectroscopy to resolve site-specific Mn local structures in manganese ferrite films. The DAFS measurements were done at undulator beamline 4-ID-D of the Advanced Photon Source at Argonne National Laboratory. The DAFS spectra (Fig. 1) were measured at several Bragg reflections in the vicinity of the Mn absorption K-edge, having probed separately contributions from tetrahedrally and octahedrally coordinated Mn sites. The DAFS data analysis done with an iterative Kramers-Kroenig algorithm made it possible to solve separately the local structure around different inequivalent Mn sites in the unit cell. The reliability of the data treatment was checked carefully, and it was showed that the site-specific structural parameters obtained with DAFS allow us to describe fluorescence EXAFS spectrum measured independently. Fig. 2 shows individual site contributions to the imaginary part of the resonant scattering amplitude obtained from the treatment of the data of Fig. 1. The analysis of the refined site-specific absorption spectra was done using EXAFS methods based on theoretical standards. We provided direct evidence for the tetrahedral Mn-O bond distance being increased relative to the corresponding Fe-O distance in bulk manganese ferrites. The first coordination shell number was found to be reduced significantly for Mn atoms at these sites. This finding is consistent with the well-known tendency of Mn

Specific features of the determination of the pellet-cladding gap of the fuel rods by non-destructive method

International Nuclear Information System (INIS)

Amosov, S.V.; Pavlov, S.V.

2002-01-01

This report describes the specific features of determining the pellet-cladding gap of the irradiated WWER-1000 fuel rods by nondestructive method. The method is based on the elastic radial deformation of the cladding up to its contact with the fuel. The value of deformation of cladding till its contacting fuel when radial force changes from F max to 0 is proposed as a measuring parameter for determination of the diametrical gap. Because of the features of compression method, the obtained gap value is not analog of the gap measured on micrograph of the fuel rod cross-section. Results of metallography can provide only qualitative evaluation of its method efficiency. Comparison of the values determined by non-destructive method and metallography for WWER-1000 fuel rods with burnup from 25 to 55 MWd/kg U testified that the results of compression method can be used as a low estimate of the pellet-cladding gap value. (author)

Topographic features over the continental shelf off Visakhapatnam

Digital Repository Service at National Institute of Oceanography (India)

Rao, T.C.S.; Machado, T.; Murthy, K.S.R.

water depth and the continental shelfedge several interesting topographic features such as Terraces, Karstic structures associated with pinnacles and troughs and smooth dome shaped reef structures are recorded. The nature of these features...

Specific Features of Chip Making and Work-piece Surface Layer Formation in Machining Thermal Coatings

Directory of Open Access Journals (Sweden)

V. M. Yaroslavtsev

2016-01-01

Full Text Available A wide range of unique engineering structural and performance properties inherent in metallic composites characterizes wear- and erosion-resistant high-temperature coatings made by thermal spraying methods. This allows their use both in manufacturing processes to enhance the wear strength of products, which have to operate under the cyclic loading, high contact pressures, corrosion and high temperatures and in product renewal.Thermal coatings contribute to the qualitative improvement of the technical level of production and product restoration using the ceramic composite materials. However, the possibility to have a significantly increased product performance, reduce their factory labour hours and materials/output ratio in manufacturing and restoration is largely dependent on the degree of the surface layer quality of products at their finishing stage, which is usually provided by different kinds of machining.When machining the plasma-sprayed thermal coatings, a removing process of the cut-off layer material is determined by its distinctive features such as a layered structure, high internal stresses, low ductility material, high tendency to the surface layer strengthening and rehardening, porosity, high abrasive properties, etc. When coatings are machined these coating properties result in specific characteristics of chip formation and conditions for formation of the billet surface layer.The chip formation of plasma-sprayed coatings was studied at micro-velocities using an experimental tool-setting microscope-based setup, created in BMSTU. The setup allowed simultaneous recording both the individual stages (phases of the chip formation process and the operating force factors.It is found that formation of individual chip elements comes with the multiple micro-cracks that cause chipping-off the small particles of material. The emerging main crack in the cut-off layer of material leads to separation of the largest chip element. Then all the stages

Solution structure of the second bromodomain of Brd2 and its specific interaction with acetylated histone tails

Directory of Open Access Journals (Sweden)

Wu Jihui

2007-09-01

Full Text Available Abstract Background Brd2 is a transcriptional regulator and belongs to BET family, a less characterized novel class of bromodomain-containing proteins. Brd2 contains two tandem bromodomains (BD1 and BD2, 46% sequence identity in the N-terminus and a conserved motif named ET (extra C-terminal domain at the C-terminus that is also present in some other bromodomain proteins. The two bromodomains have been shown to bind the acetylated histone H4 and to be responsible for mitotic retention on chromosomes, which is probably a distinctive feature of BET family proteins. Although the crystal structure of Brd2 BD1 is reported, no structure features have been characterized for Brd2 BD2 and its interaction with acetylated histones. Results Here we report the solution structure of human Brd2 BD2 determined by NMR. Although the overall fold resembles the bromodomains from other proteins, significant differences can be found in loop regions, especially in the ZA loop in which a two amino acids insertion is involved in an uncommon π-helix, termed πD. The helix πD forms a portion of the acetyl-lysine binding site, which could be a structural characteristic of Brd2 BD2 and other BET bromodomains. Unlike Brd2 BD1, BD2 is monomeric in solution. With NMR perturbation studies, we have mapped the H4-AcK12 peptide binding interface on Brd2 BD2 and shown that the binding was with low affinity (2.9 mM and in fast exchange. Using NMR and mutational analysis, we identified several residues important for the Brd2 BD2-H4-AcK12 peptide interaction and probed the potential mechanism for the specific recognition of acetylated histone codes by Brd2 BD2. Conclusion Brd2 BD2 is monomeric in solution and dynamically interacts with H4-AcK12. The additional secondary elements in the long ZA loop may be a common characteristic of BET bromodomains. Surrounding the ligand-binding cavity, five aspartate residues form a negatively charged collar that serves as a secondary binding site

The structural basis of Arf effector specificity: the crystal structure of ARF6 in a complex with JIP4.

Science.gov (United States)

Isabet, Tatiana; Montagnac, Guillaume; Regazzoni, Karine; Raynal, Bertrand; El Khadali, Fatima; England, Patrick; Franco, Michel; Chavrier, Philippe; Houdusse, Anne; Ménétrey, Julie

2009-09-16

The JNK-interacting proteins, JIP3 and JIP4, are specific effectors of the small GTP-binding protein ARF6. The interaction of ARF6-GTP with the second leucine zipper (LZII) domains of JIP3/JIP4 regulates the binding of JIPs to kinesin-1 and dynactin. Here, we report the crystal structure of ARF6-GTP bound to the JIP4-LZII at 1.9 A resolution. The complex is a heterotetramer with dyad symmetry arranged in an ARF6-(JIP4)(2)-ARF6 configuration. Comparison of the ARF6-JIP4 interface with the equivalent region of ARF1 shows the structural basis of JIP4's specificity for ARF6. Using site-directed mutagenesis and surface plasmon resonance, we further show that non-conserved residues at the switch region borders are the key structural determinants of JIP4 specificity. A structure-derived model of the association of the ARF6-JIP3/JIP4 complex with membranes shows that the JIP4-LZII coiled-coil should lie along the membrane to prevent steric hindrances, resulting in only one ARF6 molecule bound. Such a heterotrimeric complex gives insights to better understand the ARF6-mediated motor switch regulatory function.

Fall Detection Using Smartphone Audio Features.

Science.gov (United States)

Cheffena, Michael

2016-07-01

An automated fall detection system based on smartphone audio features is developed. The spectrogram, mel frequency cepstral coefficents (MFCCs), linear predictive coding (LPC), and matching pursuit (MP) features of different fall and no-fall sound events are extracted from experimental data. Based on the extracted audio features, four different machine learning classifiers: k-nearest neighbor classifier (k-NN), support vector machine (SVM), least squares method (LSM), and artificial neural network (ANN) are investigated for distinguishing between fall and no-fall events. For each audio feature, the performance of each classifier in terms of sensitivity, specificity, accuracy, and computational complexity is evaluated. The best performance is achieved using spectrogram features with ANN classifier with sensitivity, specificity, and accuracy all above 98%. The classifier also has acceptable computational requirement for training and testing. The system is applicable in home environments where the phone is placed in the vicinity of the user.

Conceptual structure within and between modalities

Directory of Open Access Journals (Sweden)

Katia eDilkina

2013-01-01

Full Text Available Current views of semantic memory share the assumption that conceptual representations are based on multi-modal experience, which activates distinct modality-specific brain regions. This proposition is widely accepted, yet little is known about how each modality contributes to conceptual knowledge and how the structure of this contribution varies across these multiple information sources. We used verbal feature lists, features from drawings and verbal co-occurrence statistics from latent semantic analysis to examine the informational structure in four domains of knowledge: perceptual, functional, encyclopedic and verbal. The goals of the analysis were three-fold: (1 to assess the structure within individual modalities; (2 to compare structures between modalities; and (3 to assess the degree to which concepts organize categorically or randomly.Our results indicated significant and unique structure in all four modalities: perceptually, concepts organize based on prominent features such as shape, size, color and parts; functionally, they group based on use and interaction; encyclopedically, they arrange based on commonality in location or behavior; and verbally, they group associatively or relationally. Visual/perceptual knowledge gives rise to the strongest hierarchical organization and is closest to classic taxonomic structure. Information is organized somewhat similarly in the perceptual and encyclopedic domains, which differs significantly from the structure in the functional and verbal domains. Notably, the verbal modality has the most unique organization, which is not at all categorical but also not random. The idiosyncrasy and complexity of conceptual structure across modalities begs the question of how all of these modality-specific experiences are fused together into coherent, multi-faceted yet unified concepts. Accordingly, both methodological and theoretical implications of the present findings are discussed.

Hybrid Electric Energy Storages: Their Specific Features and Application (Review)

Science.gov (United States)

Popel', O. S.; Tarasenko, A. B.

2018-05-01

The article presents a review of various aspects related to development and practical use of hybrid electric energy storages (i.e., those uniting different energy storage technologies and devices in an integrated system) in transport and conventional and renewable power engineering applications. Such devices, which were initially developed for transport power installations, are increasingly being used by other consumers characterized by pronounced nonuniformities of their load schedule. A range of tasks solved using such energy storages is considered. It is shown that, owing to the advent of new types of energy storages and the extended spectrum of their performance characteristics, new possibilities for combining different types of energy storages and for developing hybrid systems have become available. This, in turn, opens up the possibility of making energy storages with better mass and dimension characteristics and achieving essentially lower operational costs. The possibility to secure more comfortable (base) operating modes of primary sources of energy (heat engines and renewable energy source based power installations) and to achieve a higher capacity utilization factor are unquestionable merits of hybrid energy storages. Development of optimal process circuit solutions, as well as energy conversion and control devices facilitating the fullest utilization of the properties of each individual energy storage included in the hybrid system, is among the important lines of research carried out in this field in Russia and abroad. Our review of existing developments has shown that there are no universal technical solutions in this field (the specific features of a consumer have an essential effect on the process circuit solutions and on the composition of a hybrid energy storage), a circumstance that dictates the need to extend the scope of investigations in this promising field.

Structural and sequence variants in patients with Silver-Russell syndrome or similar features-Curation of a disease database

DEFF Research Database (Denmark)

Tümer, Zeynep; López-Hernández, Julia Angélica; Netchine, Irène

2018-01-01

data of these patients. The clinical features are scored according to the Netchine-Harbison clinical scoring system (NH-CSS), which has recently been accepted as standard by consensus. The structural and sequence variations are reviewed and where necessary redescribed according to recent...

The Specific Features of Congenital and Acquired Forms of Behavior in the Postresuscitative Period (Experimental Study

Directory of Open Access Journals (Sweden)

Yu. V. Zarzhetsky

2009-01-01

Full Text Available Academician of the USSR Academy of Medical Sciences V. A. Negovsky stated that there was an association of the pathogenesis of postresuscitative central nervous system (CNS lesions with the individual typological characteristics. Therefore the objective of the investigation was to study the early brain structural and functional changes in resuscitated rats, which were related to the baseline type of behavior. The investigation was carried out on outbred albino male rats. Circulation was stopped under ether anesthesia for 10 minutes via intrathoracic ligation of the cardiac vascular fascicle. Before clinical death simulation, the animals were divided by the types of behavior according to their behavioral activity in the elevated cross labyrinth or open field test. Postresuscitatively, the rats were found to preserve their individual typological features of behavior. At the same time the animals with baseline various behavioral patterns showed great differences in becoming familiar with a new environment. The study of conditioned reflex activities suggested the predominant impact of postresuscitative cerebral changes on different mechanisms responsible for active avoidance conditioning in rats with baseline different behavioral types. Examination of the CA1 and CA4 pyramidal cell neuronal populations of the hippocampus indicated that in the elevated cross labyrinth test, the resuscitated animals with a high baseline behavioral activity had more pronounced neurodystrophic and degenerative changes in the study brain regions than the rats with a low activity. The findings not only have supported V. A. Negovsky’s ideas on the association of the pathogenesis of postresuscitative cerebral disorders with the individual typological characteristics of the CNS, but also revealed differences in the neuropathophysiological mechanisms of these disorders, and ascertained the structural features of postresuscitative cerebral lesions in the animals with

Improving model predictions for RNA interference activities that use support vector machine regression by combining and filtering features

Directory of Open Access Journals (Sweden)

Peek Andrew S

2007-06-01

Full Text Available Abstract Background RNA interference (RNAi is a naturally occurring phenomenon that results in the suppression of a target RNA sequence utilizing a variety of possible methods and pathways. To dissect the factors that result in effective siRNA sequences a regression kernel Support Vector Machine (SVM approach was used to quantitatively model RNA interference activities. Results Eight overall feature mapping methods were compared in their abilities to build SVM regression models that predict published siRNA activities. The primary factors in predictive SVM models are position specific nucleotide compositions. The secondary factors are position independent sequence motifs (N-grams and guide strand to passenger strand sequence thermodynamics. Finally, the factors that are least contributory but are still predictive of efficacy are measures of intramolecular guide strand secondary structure and target strand secondary structure. Of these, the site of the 5' most base of the guide strand is the most informative. Conclusion The capacity of specific feature mapping methods and their ability to build predictive models of RNAi activity suggests a relative biological importance of these features. Some feature mapping methods are more informative in building predictive models and overall t-test filtering provides a method to remove some noisy features or make comparisons among datasets. Together, these features can yield predictive SVM regression models with increased predictive accuracy between predicted and observed activities both within datasets by cross validation, and between independently collected RNAi activity datasets. Feature filtering to remove features should be approached carefully in that it is possible to reduce feature set size without substantially reducing predictive models, but the features retained in the candidate models become increasingly distinct. Software to perform feature prediction and SVM training and testing on nucleic acid

Specific feature of magnetooptical images of stray fields of magnets of various geometrical shapes

Science.gov (United States)

Ivanov, V. E.; Koveshnikov, A. V.; Andreev, S. V.

2017-08-01

Specific features of magnetooptical images (MOIs) of stray fields near the faces of prismatic hard magnetic elements have been studied. Attention has primarily been focused on MOIs of fields near faces oriented perpendicular to the magnetic moment of hard magnetic elements. With regard to the polar sensitivity, MOIs have practically uniform brightness and geometrically they coincide with the figures of the bases of the elements. With regard to longitudinal sensitivity, MOIs consist of several sectors, the number of which is determined by the number of angles of the image. Each angle is divided by the bisectrix into two sectors of different brightnesses; therefore, the MOI of a triangular magnet consists of three sectors. A rectangle consists of four sectors separated by the bisectrices of the interior angles. In all types of figures, these lines converge at the center of the figure and form a singular point of the source or sink type.

Comparing writing style feature-based classification methods for estimating user reputations in social media.

Science.gov (United States)

Suh, Jong Hwan

2016-01-01

In recent years, the anonymous nature of the Internet has made it difficult to detect manipulated user reputations in social media, as well as to ensure the qualities of users and their posts. To deal with this, this study designs and examines an automatic approach that adopts writing style features to estimate user reputations in social media. Under varying ways of defining Good and Bad classes of user reputations based on the collected data, it evaluates the classification performance of the state-of-art methods: four writing style features, i.e. lexical, syntactic, structural, and content-specific, and eight classification techniques, i.e. four base learners-C4.5, Neural Network (NN), Support Vector Machine (SVM), and Naïve Bayes (NB)-and four Random Subspace (RS) ensemble methods based on the four base learners. When South Korea's Web forum, Daum Agora, was selected as a test bed, the experimental results show that the configuration of the full feature set containing content-specific features and RS-SVM combining RS and SVM gives the best accuracy for classification if the test bed poster reputations are segmented strictly into Good and Bad classes by portfolio approach. Pairwise t tests on accuracy confirm two expectations coming from the literature reviews: first, the feature set adding content-specific features outperform the others; second, ensemble learning methods are more viable than base learners. Moreover, among the four ways on defining the classes of user reputations, i.e. like, dislike, sum, and portfolio, the results show that the portfolio approach gives the highest accuracy.

Component Composition Using Feature Models

DEFF Research Database (Denmark)

Eichberg, Michael; Klose, Karl; Mitschke, Ralf

2010-01-01

interface description languages. If this variability is relevant when selecting a matching component then human interaction is required to decide which components can be bound. We propose to use feature models for making this variability explicit and (re-)enabling automatic component binding. In our...... approach, feature models are one part of service specifications. This enables to declaratively specify which service variant is provided by a component. By referring to a service's variation points, a component that requires a specific service can list the requirements on the desired variant. Using...... these specifications, a component environment can then determine if a binding of the components exists that satisfies all requirements. The prototypical environment Columbus demonstrates the feasibility of the approach....

Memory-Based Specification of Verbal Features for Classifying Animals into Super-Ordinate and Sub-Ordinate Categories

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Takahiro Soshi

2017-09-01

Full Text Available Accumulating evidence suggests that category representations are based on features. Distinguishing features are considered to define categories, because of all-or-none responses for objects in different categories; however, it is unclear how distinguishing features actually classify objects at various category levels. The present study included 75 animals within three classes (mammal, bird, and fish, along with 195 verbal features. Healthy adults participated in memory-based feature-animal matching verification tests. Analyses included a hierarchical clustering analysis, support vector machine, and independent component analysis to specify features effective for classifications. Quantitative and qualitative comparisons for significant features were conducted between super-ordinate and sub-ordinate levels. The number of significant features was larger for super-ordinate than sub-ordinate levels. Qualitatively, the proportion of biological features was larger than cultural/affective features in both the levels, while the proportion of affective features increased at the sub-ordinate level. To summarize, the two types of features differentially function to establish category representations.

Estimating perception of scene layout properties from global image features.

Science.gov (United States)

Ross, Michael G; Oliva, Aude

2010-01-08

The relationship between image features and scene structure is central to the study of human visual perception and computer vision, but many of the specifics of real-world layout perception remain unknown. We do not know which image features are relevant to perceiving layout properties, or whether those features provide the same information for every type of image. Furthermore, we do not know the spatial resolutions required for perceiving different properties. This paper describes an experiment and a computational model that provides new insights on these issues. Humans perceive the global spatial layout properties such as dominant depth, openness, and perspective, from a single image. This work describes an algorithm that reliably predicts human layout judgments. This model's predictions are general, not specific to the observers it trained on. Analysis reveals that the optimal spatial resolutions for determining layout vary with the content of the space and the property being estimated. Openness is best estimated at high resolution, depth is best estimated at medium resolution, and perspective is best estimated at low resolution. Given the reliability and simplicity of estimating the global layout of real-world environments, this model could help resolve perceptual ambiguities encountered by more detailed scene reconstruction schemas.

Structural basis of the substrate specificity of Bacillus cereus adenosine phosphorylase

Energy Technology Data Exchange (ETDEWEB)

Dessanti, Paola [Cornell University, Ithaca, NY 14853-1301 (United States); Università di Sassari, (Italy); Zhang, Yang [Cornell University, Ithaca, NY 14853-1301 (United States); Allegrini, Simone [Università di Sassari, (Italy); Tozzi, Maria Grazia [Università di Pisa, (Italy); Sgarrella, Francesco [Università di Sassari, (Italy); Ealick, Steven E., E-mail: see3@cornell.edu [Cornell University, Ithaca, NY 14853-1301 (United States)

2012-03-01

Adenosine phosphorylase from B. cereus shows a strong preference for adenosine over other 6-oxopurine nucleosides. Mutation of Asp204 to asparagine reduces the efficiency of adenosine cleavage but does not affect inosine cleavage, effectively reversing the substrate specificity. The structures of D204N complexes explain these observations. Purine nucleoside phosphorylases catalyze the phosphorolytic cleavage of the glycosidic bond of purine (2′-deoxy)nucleosides, generating the corresponding free base and (2′-deoxy)ribose 1-phosphate. Two classes of PNPs have been identified: homotrimers specific for 6-oxopurines and homohexamers that accept both 6-oxopurines and 6-aminopurines. Bacillus cereus adenosine phosphorylase (AdoP) is a hexameric PNP; however, it is highly specific for 6-aminopurines. To investigate the structural basis for the unique substrate specificity of AdoP, the active-site mutant D204N was prepared and kinetically characterized and the structures of the wild-type protein and the D204N mutant complexed with adenosine and sulfate or with inosine and sulfate were determined at high resolution (1.2–1.4 Å). AdoP interacts directly with the preferred substrate through a hydrogen-bond donation from the catalytically important residue Asp204 to N7 of the purine base. Comparison with Escherichia coli PNP revealed a more optimal orientation of Asp204 towards N7 of adenosine and a more closed active site. When inosine is bound, two water molecules are interposed between Asp204 and the N7 and O6 atoms of the nucleoside, thus allowing the enzyme to find alternative but less efficient ways to stabilize the transition state. The mutation of Asp204 to asparagine led to a significant decrease in catalytic efficiency for adenosine without affecting the efficiency of inosine cleavage.

STRUCTURAL AND CONTENT-RELATED SPECIFICITY OF PROGRAMME LITERARY CRITICISM TEXTS IN THE JOURNAL

Directory of Open Access Journals (Sweden)

Shilnikova Olga Gennadyevna

2015-06-01

Full Text Available The article specifies the notions of the structural, content-related, figurative, and functional characteristics of the texts which are traditionally referred to the group of informational genres of journalism. This lets us update the system of factors that influence the formation of the texts' genre specificity in the mass media. The analysis of programme literary criticism speeches published in the journals of N.M. Karamzin – Moskovsky Zhurnal, Vestnik Evropy – shows that not only rational and logical structures accomplish the constructive function in the text-formation mechanisms of such publications. The use of imaginative resources of journalistic and artistic discourses plays an important role in the implementation of the author's intentions. The supplementation of programme texts with the components non-typical of informational genres (lyrical and biographical fragments, expressive lexis, artistic and journalistic forms of the author's subjectivity expression is conditioned by organic interaction of several pragmatic goals in the texts, such as: informational, author's individual (Karamzin as a personality, and author's professional (Karamzin as an editor, writer, literary critic. These peculiarities together with a subtext contribute to the formation of new features of programme publications, which are not common for informational genres such as aesthetic function and multi-discursivity, reflected in semantic, expressive and vocabulary redundance. They also expand the range of possible effects on audience – cognitive, emotive, behavioral and communicative. As a result, a unique informational text of a programme type is formed. Therefore, a strict differentiation of genre forms of journal texts is only possible when taking into consideration all the possible text goals, as well as its role in the organization of common-journal discourse and publication policy.

Method to assess the temporal persistence of potential biometric features: Application to oculomotor, gait, face and brain structure databases

Science.gov (United States)

Nixon, Mark S.; Komogortsev, Oleg V.

2017-01-01

We introduce the intraclass correlation coefficient (ICC) to the biometric community as an index of the temporal persistence, or stability, of a single biometric feature. It requires, as input, a feature on an interval or ratio scale, and which is reasonably normally distributed, and it can only be calculated if each subject is tested on 2 or more occasions. For a biometric system, with multiple features available for selection, the ICC can be used to measure the relative stability of each feature. We show, for 14 distinct data sets (1 synthetic, 8 eye-movement-related, 2 gait-related, and 2 face-recognition-related, and one brain-structure-related), that selecting the most stable features, based on the ICC, resulted in the best biometric performance generally. Analyses based on using only the most stable features produced superior Rank-1-Identification Rate (Rank-1-IR) performance in 12 of 14 databases (p = 0.0065, one-tailed), when compared to other sets of features, including the set of all features. For Equal Error Rate (EER), using a subset of only high-ICC features also produced superior performance in 12 of 14 databases (p = 0. 0065, one-tailed). In general, then, for our databases, prescreening potential biometric features, and choosing only highly reliable features yields better performance than choosing lower ICC features or than choosing all features combined. We also determined that, as the ICC of a group of features increases, the median of the genuine similarity score distribution increases and the spread of this distribution decreases. There was no statistically significant similar relationships for the impostor distributions. We believe that the ICC will find many uses in biometric research. In case of the eye movement-driven biometrics, the use of reliable features, as measured by ICC, allowed to us achieve the authentication performance with EER = 2.01%, which was not possible before. PMID:28575030

Novel Fluorinated Indanone, Tetralone and Naphthone Derivatives: Synthesis and Unique Structural Features

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Joseph C. Sloop

2012-02-01

Full Text Available Several fluorinated and trifluoromethylated indanone, tetralone and naphthone derivatives have been prepared via Claisen condensations and selective fluorinations in yields ranging from 22–60%. In addition, we report the synthesis of new, selectively fluorinated bindones in yields ranging from 72–92%. Of particular interest is the fluorination and trifluoroacetylation regiochemistry observed in these fluorinated products. We also note unusual transformations including a novel one pot, dual trifluoroacetylation, trifluoroacetylnaphthone synthesis via a deacetylation as well as an acetyl-trifluoroacetyl group exchange. Solid-state structural features exhibited by these compounds were investigated using crystallographic methods. Crystallographic results, supported by spectroscopic data, show that trifluoroacetylated ketones prefer a chelated cis-enol form whereas fluorinated bindone products exist primarily as the cross-conjugated triketo form.

Demersal fish assemblages on seamounts and other rugged features in the northeastern Caribbean

Science.gov (United States)

Quattrini, Andrea M.; Demopoulos, Amanda W. J.; Singer, Randal; Roa-Varon, Adela; Chaytor, Jason D.

2017-05-01

Recent investigations of demersal fish communities in deepwater (>50 m) habitats have considerably increased our knowledge of the factors that influence the assemblage structure of fishes across mesophotic to deep-sea depths. While different habitat types influence deepwater fish distribution, whether different types of rugged seafloor features provide functionally equivalent habitat for fishes is poorly understood. In the northeastern Caribbean, different types of rugged features (e.g., seamounts, banks, canyons) punctuate insular margins, and thus create a remarkable setting in which to compare demersal fish communities across various features. Concurrently, several water masses are vertically layered in the water column, creating strong stratification layers corresponding to specific abiotic conditions. In this study, we examined differences among fish assemblages across different features (e.g., seamount, canyon, bank/ridge) and water masses at depths ranging from 98 to 4060 m in the northeastern Caribbean. We conducted 26 remotely operated vehicle dives across 18 sites, identifying 156 species of which 42% of had not been previously recorded from particular depths or localities in the region. While rarefaction curves indicated fewer species at seamounts than at other features in the NE Caribbean, assemblage structure was similar among the different types of features. Thus, similar to seamount studies in other regions, seamounts in the Anegada Passage do not harbor distinct communities from other types of rugged features. Species assemblages, however, differed among depths, with zonation generally corresponding to water mass boundaries in the region. High species turnover occurred at depths <1200 m, and may be driven by changes in water mass characteristics including temperature (4.8-24.4 °C) and dissolved oxygen (2.2-9.5 mg per l). Our study suggests the importance of water masses in influencing community structure of benthic fauna, while considerably adding

Does Gender-Specific Differential Item Functioning Affect the Structure in Vocational Interest Inventories?

Science.gov (United States)

Beinicke, Andrea; Pässler, Katja; Hell, Benedikt

2014-01-01

The study investigates consequences of eliminating items showing gender-specific differential item functioning (DIF) on the psychometric structure of a standard RIASEC interest inventory. Holland's hexagonal model was tested for structural invariance using a confirmatory methodological approach (confirmatory factor analysis and randomization…

Specific features of epilepsy in children with brain tumors

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G. V. Kalmykova

2015-01-01

Full Text Available Objective: to study the specific features of epilepsy in children and adolescents with brain tumors and to define the optimal tactics of management and antiepileptic therapy after surgical treatment. Patients and methods. Sixty-one patients aged 5 months to 15 years were examined. All the patients were diagnosed as having a brain tumor found in the presence of symptomatic epilepsy. They were all followed up for 5 years postsurgery or during their lifetime (in case of death. Comprehensive examination encompassing the assessment of history data and concomitant complaints, brain magnetic resonance imaging, video-EEC monitoring, and the neurological status (the presence of cognitive impairments and eye ground changes was done in all the cases. The probability of epileptic seizures in the clinical presentation of the disease, their semiology, and frequency were studied. Results and discussion. Epileptic seizures were the major complaint in all the patients at the first visit to their doctor. The disease occurred with status epilepticus in 9% of the patients. Different types of generalized seizures were more common (53%; p≥0.05. The tumor was located above the tentorium of the cerebellum in most examinees (77% and beneath it in the others (23%; p≤0.05. The significant clinical sign of a brain tumor in the epileptic children is focal neurological symptoms (72% of the cases. MRI was performed in children who had no focal neurological symptoms in the late periods. There was cerebrospinal fluid hypertension in 51% of the patients (p≥0.05 and cognitive impairments in 33% (p<0.05. The maximum number (74% of children with psycho-speech disorders and cognitive impairments were registered in the age group of 7–15 years. Eye ground changes characteristic of intracranial hypertension were identified in 19 epileptic children; they occurred in 27 patients more than 1 year after the onset of seizures. The late (few months-to-14 years diagnosis of a brain

Person Re-Identification by Camera Correlation Aware Feature Augmentation.

Science.gov (United States)

Chen, Ying-Cong; Zhu, Xiatian; Zheng, Wei-Shi; Lai, Jian-Huang

2018-02-01

The challenge of person re-identification (re-id) is to match individual images of the same person captured by different non-overlapping camera views against significant and unknown cross-view feature distortion. While a large number of distance metric/subspace learning models have been developed for re-id, the cross-view transformations they learned are view-generic and thus potentially less effective in quantifying the feature distortion inherent to each camera view. Learning view-specific feature transformations for re-id (i.e., view-specific re-id), an under-studied approach, becomes an alternative resort for this problem. In this work, we formulate a novel view-specific person re-identification framework from the feature augmentation point of view, called Camera coR relation Aware Feature augmenTation (CRAFT). Specifically, CRAFT performs cross-view adaptation by automatically measuring camera correlation from cross-view visual data distribution and adaptively conducting feature augmentation to transform the original features into a new adaptive space. Through our augmentation framework, view-generic learning algorithms can be readily generalized to learn and optimize view-specific sub-models whilst simultaneously modelling view-generic discrimination information. Therefore, our framework not only inherits the strength of view-generic model learning but also provides an effective way to take into account view specific characteristics. Our CRAFT framework can be extended to jointly learn view-specific feature transformations for person re-id across a large network with more than two cameras, a largely under-investigated but realistic re-id setting. Additionally, we present a domain-generic deep person appearance representation which is designed particularly to be towards view invariant for facilitating cross-view adaptation by CRAFT. We conducted extensively comparative experiments to validate the superiority and advantages of our proposed framework over state

Fundamental statistical features and self-similar properties of tagged networks

International Nuclear Information System (INIS)

Palla, Gergely; Farkas, Illes J; Pollner, Peter; Vicsek, Tamas; Derenyi, Imre

2008-01-01

We investigate the fundamental statistical features of tagged (or annotated) networks having a rich variety of attributes associated with their nodes. Tags (attributes, annotations, properties, features, etc) provide essential information about the entity represented by a given node, thus, taking them into account represents a significant step towards a more complete description of the structure of large complex systems. Our main goal here is to uncover the relations between the statistical properties of the node tags and those of the graph topology. In order to better characterize the networks with tagged nodes, we introduce a number of new notions, including tag-assortativity (relating link probability to node similarity), and new quantities, such as node uniqueness (measuring how rarely the tags of a node occur in the network) and tag-assortativity exponent. We apply our approach to three large networks representing very different domains of complex systems. A number of the tag related quantities display analogous behaviour (e.g. the networks we studied are tag-assortative, indicating possible universal aspects of tags versus topology), while some other features, such as the distribution of the node uniqueness, show variability from network to network allowing for pin-pointing large scale specific features of real-world complex networks. We also find that for each network the topology and the tag distribution are scale invariant, and this self-similar property of the networks can be well characterized by the tag-assortativity exponent, which is specific to each system.

Effect of processing on structural features of anodic aluminum oxides

Science.gov (United States)

Erdogan, Pembe; Birol, Yucel

2012-09-01

Morphological features of the anodic aluminum oxide (AAO) templates fabricated by electrochemical oxidation under different processing conditions were investigated. The selection of the polishing parameters does not appear to be critical as long as the aluminum substrate is polished adequately prior to the anodization process. AAO layers with a highly ordered pore distribution are obtained after anodizing in 0.6 M oxalic acid at 20 °C under 40 V for 5 minutes suggesting that the desired pore features are attained once an oxide layer develops on the surface. While the pore features are not affected much, the thickness of the AAO template increases with increasing anodization treatment time. Pore features are better and the AAO growth rate is higher at 20 °C than at 5 °C; higher under 45 V than under 40 V; higher with 0.6 M than with 0.3 M oxalic acid.

Sustainable Corporate Social Media Marketing Based on Message Structural Features: Firm Size Plays a Significant Role as a Moderator

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Moon Young Kang

2018-04-01

Full Text Available Social media has been receiving attention as a cost-effective tool to build corporate brand image and to enrich customer relationships. This phenomenon calls for more attention to developing a model that measures the impact of structural features, used in corporate social media messages. Based on communication science, this study proposes a model to measure the impact of three essential message structural features (interactivity, formality, and immediacy in corporate social media on customers’ purchase intentions, mediated by brand attitude and corporate trust. Especially, social media platforms are believed to provide a good marketing platform for small and medium enterprises (SMEs by providing access to huge audiences at a very low cost. The findings from this study based on a structural equation model suggest that brand attitude and corporate trust have larger impacts on purchase intention for SMEs than large firms. This implies that SMEs with little to no presence in the market should pay more attention to building corporate trust and brand attitude for their sustainable growth.

Specific features and techneiueq improving the reinforced s forenclosing structures for NPP with the RBMK-type reactors

International Nuclear Information System (INIS)

Kirillov, A.P.; Konviz, V.S.; Semenov, V.P.

1982-01-01

A study is made on a new technique of construction of NPP enclosing structures (walls and ceilings) by the assembled- monolith method. Its advantages over the monolith method are presented. The design philosophy of the assembled-monolith constructions is described. It is shown on the basis of the experience of Kursk and Chernobylsk NPP construction that during the introduction of assembled-monolith constructions of massive walls and ceilings the speed of reactor blocks construction increased practically twice

Categorical Structure among Shared Features in Networks of Early-Learned Nouns

Science.gov (United States)

Hills, Thomas T.; Maouene, Mounir; Maouene, Josita; Sheya, Adam; Smith, Linda

2009-01-01

The shared features that characterize the noun categories that young children learn first are a formative basis of the human category system. To investigate the potential categorical information contained in the features of early-learned nouns, we examine the graph-theoretic properties of noun-feature networks. The networks are built from the…

Structural basis for sequence-specific recognition of DNA by TAL effectors

KAUST Repository

Deng, Dong

2012-01-05

TAL (transcription activator-like) effectors, secreted by phytopathogenic bacteria, recognize host DNA sequences through a central domain of tandem repeats. Each repeat comprises 33 to 35 conserved amino acids and targets a specific base pair by using two hypervariable residues [known as repeat variable diresidues (RVDs)] at positions 12 and 13. Here, we report the crystal structures of an 11.5-repeat TAL effector in both DNA-free and DNA-bound states. Each TAL repeat comprises two helices connected by a short RVD-containing loop. The 11.5 repeats form a right-handed, superhelical structure that tracks along the sense strand of DNA duplex, with RVDs contacting the major groove. The 12th residue stabilizes the RVD loop, whereas the 13th residue makes a base-specific contact. Understanding DNA recognition by TAL effectors may facilitate rational design of DNA-binding proteins with biotechnological applications.

A comparative study of image low level feature extraction algorithms

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M.M. El-gayar

2013-07-01

Full Text Available Feature extraction and matching is at the base of many computer vision problems, such as object recognition or structure from motion. Current methods for assessing the performance of popular image matching algorithms are presented and rely on costly descriptors for detection and matching. Specifically, the method assesses the type of images under which each of the algorithms reviewed herein perform to its maximum or highest efficiency. The efficiency is measured in terms of the number of matches founds by the algorithm and the number of type I and type II errors encountered when the algorithm is tested against a specific pair of images. Current comparative studies asses the performance of the algorithms based on the results obtained in different criteria such as speed, sensitivity, occlusion, and others. This study addresses the limitations of the existing comparative tools and delivers a generalized criterion to determine beforehand the level of efficiency expected from a matching algorithm given the type of images evaluated. The algorithms and the respective images used within this work are divided into two groups: feature-based and texture-based. And from this broad classification only three of the most widely used algorithms are assessed: color histogram, FAST (Features from Accelerated Segment Test, SIFT (Scale Invariant Feature Transform, PCA-SIFT (Principal Component Analysis-SIFT, F-SIFT (fast-SIFT and SURF (speeded up robust features. The performance of the Fast-SIFT (F-SIFT feature detection methods are compared for scale changes, rotation, blur, illumination changes and affine transformations. All the experiments use repeatability measurement and the number of correct matches for the evaluation measurements. SIFT presents its stability in most situations although its slow. F-SIFT is the fastest one with good performance as the same as SURF, SIFT, PCA-SIFT show its advantages in rotation and illumination changes.

Auditory profiles of classical, jazz, and rock musicians: Genre-specific sensitivity to musical sound features

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Mari eTervaniemi

2016-01-01

Full Text Available When compared with individuals without explicit training in music, adult musicians have facilitated neural functions in several modalities. They also display structural changes in various brain areas, these changes corresponding to the intensity and duration of their musical training. Previous studies have focused on investigating musicians with training in Western classical music. However, musicians involved in different musical genres may display highly differentiated auditory profiles according to the demands set by their genre, i.e. varying importance of different musical sound features. This hypothesis was tested in a novel melody paradigm including deviants in tuning, timbre, rhythm, melody transpositions, and melody contour. Using this paradigm while the participants were watching a silent video and instructed to ignore the sounds, we compared classical, jazz, and rock musicians’ and non-musicians’ accuracy of neural encoding of the melody. In all groups of participants, all deviants elicited an MMN response, which is a cortical index of deviance discrimination. The strength of the MMN and the subsequent attentional P3a responses reflected the importance of various sound features in each music genre: these automatic brain responses were selectively enhanced to deviants in tuning (classical musicians, timing (classical and jazz musicians, transposition (jazz musicians, and melody contour (jazz and rock musicians. Taken together, these results indicate that musicians with different training history have highly specialized cortical reactivity to sounds which violate the neural template for melody content.

Auditory Profiles of Classical, Jazz, and Rock Musicians: Genre-Specific Sensitivity to Musical Sound Features.

Science.gov (United States)

Tervaniemi, Mari; Janhunen, Lauri; Kruck, Stefanie; Putkinen, Vesa; Huotilainen, Minna

2015-01-01

When compared with individuals without explicit training in music, adult musicians have facilitated neural functions in several modalities. They also display structural changes in various brain areas, these changes corresponding to the intensity and duration of their musical training. Previous studies have focused on investigating musicians with training in Western classical music. However, musicians involved in different musical genres may display highly differentiated auditory profiles according to the demands set by their genre, i.e., varying importance of different musical sound features. This hypothesis was tested in a novel melody paradigm including deviants in tuning, timbre, rhythm, melody transpositions, and melody contour. Using this paradigm while the participants were watching a silent video and instructed to ignore the sounds, we compared classical, jazz, and rock musicians' and non-musicians' accuracy of neural encoding of the melody. In all groups of participants, all deviants elicited an MMN response, which is a cortical index of deviance discrimination. The strength of the MMN and the subsequent attentional P3a responses reflected the importance of various sound features in each music genre: these automatic brain responses were selectively enhanced to deviants in tuning (classical musicians), timing (classical and jazz musicians), transposition (jazz musicians), and melody contour (jazz and rock musicians). Taken together, these results indicate that musicians with different training history have highly specialized cortical reactivity to sounds which violate the neural template for melody content.

Structural features of lignohumic acids

Czech Academy of Sciences Publication Activity Database

Novák, František; Šestauberová, Martina; Hrabal, R.

2015-01-01

Roč. 1093, August (2015), s. 179-185 ISSN 0022-2860 Institutional support: RVO:60077344 Keywords : C-13 NMR * FTIR * humic acids * lignohumate * lignosulfonate * structure Subject RIV: DF - Soil Science Impact factor: 1.780, year: 2015

Extra-zonal beech forests in Tuscany: structure, diversity and synecologic features

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Viciani D

2011-07-01

Full Text Available The present paper focuses on the structural, synecological and floristic diversity features of beech-dominated forest communities in four major areas of the Antiapenninic Tyrrhenian system in Tuscany: Metalliferous hills, mountains to the south of Mt. Amiata, volcanic area of the upper Lente valley and Mt. Cetona. These are relict woodlands of Holo-Pleistocene origin with a special ecological and conservation value due to their extrazonal location in lowland submediterranean areas. Results show substantial among-area differences in structure, synecology and plant species composition, but in general a potential for coppices to reach the tall forest stage, as demonstrated by the old-growth stands of Pietraporciana and Sassoforte. Compared with montane Apenninic beechwoods, the relatively rich flora of the studied communities include thermophilous species with a southern Apennine-Balkan distribution, making their syntaxonomical position unclear. Closer affinities are found with the calcicolous Beech Forests of the association and with the silicicolous ones of the . Based on the Natura 2000 system, all the examined communities belong to the priority Habitat “Apennine beech forests with and ” (code: 9210*. Due their relict nature, these biotopes appear vulnerable to climate changes and to a production-oriented forest management. Criteria of naturalistic silviculture should instead promote the dynamic development of these communities towards tall forests and their natural regeneration.

MNE SPECIFIC FACTORS OF CORPORATE CAPITAL STRUCTURE: COMPARATIVE ANALYSIS IN TERMS OF FINANCIAL RESOURCES DEMAND AND SUPPLY

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Sergiy Tsyganov

2015-11-01

Full Text Available This paper investigates corporate capital structure of multinational enterprises. Its core subject is focused on corporate capital structure defining factors that are specific for MNE rather than for domestic corporations. Substantial part of scientific literature concentrates on country specific and firm specific factors of corporate capital structure with most research devoted to domestic corporations. The main goal of our paper is to discover among plenty of corporate capital structure factors those that are specific for MNE and to develop a new approach for analyzing these factors in terms of financial resources demand and supply. There are some corporate capital structure factors that influence directly and some that have indirect influence while there is also another set of factors having both direct and indirect influence on indebtedness. Different theoretical and empirical research confirm different directions. Methodology of our study is based on analysis of two fundamental market driving forces that are demand and supply. Their influence on corporate capital structure is of a primary origin and that is why the suggested approach is to our mind theoretically significant and practically important. Demand factors imply that a corporation creates demand for financial resources and its capital structure is defined internally. Supply factors imply an external capital structure since it is created by external investors’ supply of financial resources. On empirical level, we use the primary data of corporate financial statements to analyze the leverage of MNE based in different countries and representing different industries. The key results of our study show that the main MNE specific factors of capital structure include such demand factors as multinationality level, assets tangibility and political risk. The first two are firm specific factors that can influence corporate capital structure either directly or indirectly according to

The Memory Is in the Details: Relations between Memory for the Specific Features of Events and Long-Term Recall during Infancy

Science.gov (United States)

Bauer, Patricia J.; Lukowski, Angela F.

2010-01-01

The second year of life is marked by pronounced changes in the length of time over which events are remembered. We tested whether the age-related differences are related to differences in memory for the specific features of events. In our study, 16- and 20-month-olds were tested for immediate and long-term recall of individual actions and temporal…

Linguo-cognitive and pragmatic features of the prosodic organization of English parables

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Musiienko Yulia

2017-06-01

Full Text Available This paper highlights the results of an investigation of the cognitive and pragmatic features of prosodic loading in English parables. The analysis of the prosodic organization of directive intentions in a parable was performed by applying systematization and classification of the pragmatic aspect, structural and semantic, functional and pragmatic specificity in order to examine the process of producing and understanding the texts of English parables.

Structural features and in-service inspection of the LTHR-200 pressure vessel

International Nuclear Information System (INIS)

Xiong Dunshi; He Shuyan; Liu Junjie; Yu Suyuan

1993-01-01

LTHR-200 is a low temperature district-heating reactor. It adopts double-shell design pressure vessel and metal containment. Because of the safety and structural features of the reactor, the in-service inspection of the pressure vessel can be simplified greatly. LTHR-200 is an integrated arrangement. Both its core components and the main heat exchangers are contained in the reactor pressure vessel. The coolant of the main loop is run by a full-power natural circulation and there need no main pumps and pipes. Thus, the reactor pressure vessel constitutes the pressure boundary of the reactor's main loop coolant. In regard to these features, a small-sized containment is designed for the reactor. The metal safety container with a small volume is placed closely around the reactor pressure vessel. Outside the metal containment, there is a large reinforced concrete construction for the reactor. Their main operation and design parameters are as follows: The pressure vessel: operation pressure = 2.4 MPa; design pressure = 3.0 MPa; design temperature = 250 deg C; 40 year fast neutron (E>1MeV) fluence in the belt-line region = < 10E16n/cm; internal diameter = 5000 mm; material SA516-70; shell thickness 65 mm; The metal containment: maximum operation pressure = 1.8 MPa; design pressure = 1.8 MPa; design temperature = 250 deg. C; upper internal diameter 7000 mm; lower internal diameter = 5600 mm; material = SA516-70; shell thickness, upper part = 80 mm; lower part = 50 mm. All penetrating pipes through the pressure vessel are located at the top penetration section of the shell. All the internal diameters of penetrating pipes are less than 50 mm. Inside and outside the metal containment wall respectively, isolating valves are connected to the reactor coolant pipe which passes through the containment. These two isolating valves use different driving methods. Every penetrating part of the reactor construction uses a proper form of structure according to safety requirements

Standard technical specifications for combustion engineering pressurized water reactors

International Nuclear Information System (INIS)

1979-08-01

This Standard Technical Specification (STS) has been structured for the broadest possible use on Combustion Engineering plants currently being reviewed for an Operating License. Two separate and discrete containment specification sections are provided for each of the following containment types: Atmospheric and Dual. Optional specifications are provided for those features and systems which may be included in individual plant designs but are not generic in their scope of application. Alternate specifications are provided in a limited number of cases to cover situations where alternate specification requirements are necessary on a generic basis because of design differences. This revision of STS does not typically include requirements which may be added or revised as a result of the NRC staff's further review of the Three Mile Island incident

Structural Basis for Specific Inhibition of tRNA Synthetase by an ATP Competitive Inhibitor

OpenAIRE

Fang, Pengfei; Han, Hongyan; Wang, Jing; Chen, Kaige; Chen, Xin; Guo, Min

2015-01-01

Pharmaceutical inhibitors of aminoacyl-tRNA synthetases demand high species and family specificity. The antimalarial ATP-mimetic cladosporin selectively inhibits P. falciparum LysRS (PfLysRS). How the binding to a universal ATP site achieves the specificity is unknown. Here we report 3 crystal structures of cladosporin with human LysRS, PfLysRS, and a Pf-like human LysRS mutant. In all 3 structures, cladosporin occupies the class defining ATP-binding pocket, replacing the adenosine portion of...

Site-specific local structure of Mn in artificial manganese ferrite films

International Nuclear Information System (INIS)

Kravtsov, E.; Haskel, D.; Cady, A.; Yang, A.; Vittoria, C.; Harris, V. G.; Zuo, X.

2006-01-01

Diffraction anomalous fine structure (DAFS) spectroscopy has been applied to resolve site-specific Mn local structure in manganese ferrite films grown under nonequilibrium conditions. The DAFS spectra were measured at a number of Bragg reflections in the vicinity of the Mn absorption K edge. The DAFS data analysis done with an iterative Kramers-Kroenig algorithm made it possible to solve separately the local structure around crystallographically inequivalent Mn sites in the unit cell with nominal octahedral and tetrahedral coordination. The strong preference for Mn to be tetrahedrally coordinated in this compound is not only manifested in the relative site occupancies but also in a strong reduction in coordination number for Mn ions at nominal octahedral sites

A Fast, Open EEG Classification Framework Based on Feature Compression and Channel Ranking

Directory of Open Access Journals (Sweden)

Jiuqi Han

2018-04-01

Full Text Available Superior feature extraction, channel selection and classification methods are essential for designing electroencephalography (EEG classification frameworks. However, the performance of most frameworks is limited by their improper channel selection methods and too specifical design, leading to high computational complexity, non-convergent procedure and narrow expansibility. In this paper, to remedy these drawbacks, we propose a fast, open EEG classification framework centralized by EEG feature compression, low-dimensional representation, and convergent iterative channel ranking. First, to reduce the complexity, we use data clustering to compress the EEG features channel-wise, packing the high-dimensional EEG signal, and endowing them with numerical signatures. Second, to provide easy access to alternative superior methods, we structurally represent each EEG trial in a feature vector with its corresponding numerical signature. Thus, the recorded signals of many trials shrink to a low-dimensional structural matrix compatible with most pattern recognition methods. Third, a series of effective iterative feature selection approaches with theoretical convergence is introduced to rank the EEG channels and remove redundant ones, further accelerating the EEG classification process and ensuring its stability. Finally, a classical linear discriminant analysis (LDA model is employed to classify a single EEG trial with selected channels. Experimental results on two real world brain-computer interface (BCI competition datasets demonstrate the promising performance of the proposed framework over state-of-the-art methods.

Speech recognition using articulatory and excitation source features

CERN Document Server

Rao, K Sreenivasa

2017-01-01

This book discusses the contribution of articulatory and excitation source information in discriminating sound units. The authors focus on excitation source component of speech -- and the dynamics of various articulators during speech production -- for enhancement of speech recognition (SR) performance. Speech recognition is analyzed for read, extempore, and conversation modes of speech. Five groups of articulatory features (AFs) are explored for speech recognition, in addition to conventional spectral features. Each chapter provides the motivation for exploring the specific feature for SR task, discusses the methods to extract those features, and finally suggests appropriate models to capture the sound unit specific knowledge from the proposed features. The authors close by discussing various combinations of spectral, articulatory and source features, and the desired models to enhance the performance of SR systems.

Comparative sequence and structural analyses of G-protein-coupled receptor crystal structures and implications for molecular models.

Directory of Open Access Journals (Sweden)

Catherine L Worth

Full Text Available BACKGROUND: Up until recently the only available experimental (high resolution structure of a G-protein-coupled receptor (GPCR was that of bovine rhodopsin. In the past few years the determination of GPCR structures has accelerated with three new receptors, as well as squid rhodopsin, being successfully crystallized. All share a common molecular architecture of seven transmembrane helices and can therefore serve as templates for building molecular models of homologous GPCRs. However, despite the common general architecture of these structures key differences do exist between them. The choice of which experimental GPCR structure(s to use for building a comparative model of a particular GPCR is unclear and without detailed structural and sequence analyses, could be arbitrary. The aim of this study is therefore to perform a systematic and detailed analysis of sequence-structure relationships of known GPCR structures. METHODOLOGY: We analyzed in detail conserved and unique sequence motifs and structural features in experimentally-determined GPCR structures. Deeper insight into specific and important structural features of GPCRs as well as valuable information for template selection has been gained. Using key features a workflow has been formulated for identifying the most appropriate template(s for building homology models of GPCRs of unknown structure. This workflow was applied to a set of 14 human family A GPCRs suggesting for each the most appropriate template(s for building a comparative molecular model. CONCLUSIONS: The available crystal structures represent only a subset of all possible structural variation in family A GPCRs. Some GPCRs have structural features that are distributed over different crystal structures or which are not present in the templates suggesting that homology models should be built using multiple templates. This study provides a systematic analysis of GPCR crystal structures and a consistent method for identifying

Comparative sequence and structural analyses of G-protein-coupled receptor crystal structures and implications for molecular models.

Science.gov (United States)

Worth, Catherine L; Kleinau, Gunnar; Krause, Gerd

2009-09-16

Up until recently the only available experimental (high resolution) structure of a G-protein-coupled receptor (GPCR) was that of bovine rhodopsin. In the past few years the determination of GPCR structures has accelerated with three new receptors, as well as squid rhodopsin, being successfully crystallized. All share a common molecular architecture of seven transmembrane helices and can therefore serve as templates for building molecular models of homologous GPCRs. However, despite the common general architecture of these structures key differences do exist between them. The choice of which experimental GPCR structure(s) to use for building a comparative model of a particular GPCR is unclear and without detailed structural and sequence analyses, could be arbitrary. The aim of this study is therefore to perform a systematic and detailed analysis of sequence-structure relationships of known GPCR structures. We analyzed in detail conserved and unique sequence motifs and structural features in experimentally-determined GPCR structures. Deeper insight into specific and important structural features of GPCRs as well as valuable information for template selection has been gained. Using key features a workflow has been formulated for identifying the most appropriate template(s) for building homology models of GPCRs of unknown structure. This workflow was applied to a set of 14 human family A GPCRs suggesting for each the most appropriate template(s) for building a comparative molecular model. The available crystal structures represent only a subset of all possible structural variation in family A GPCRs. Some GPCRs have structural features that are distributed over different crystal structures or which are not present in the templates suggesting that homology models should be built using multiple templates. This study provides a systematic analysis of GPCR crystal structures and a consistent method for identifying suitable templates for GPCR homology modelling that will

MEVTV workshop on tectonic features on Mars

International Nuclear Information System (INIS)

Watters, T.R.; Golombek, M.P.

1989-01-01

The state of knowledge of tectonic features on Mars was determined and kinematic and mechanical models were assessed for their origin. Three sessions were held: wrinkle ridges and compressional structure; strike-slip faults; and extensional structures. Each session began with an overview of the features under discussion. In the case of wrinkle ridges and extensional structures, the overview was followed by keynote addresses by specialists working on similar structures on the Earth. The first session of the workshop focused on the controversy over the relative importance of folding, faulting, and intrusive volcanism in the origin of wrinkle ridges. The session ended with discussions of the origin of compressional flank structures associated with Martian volcanoes and the relationship between the volcanic complexes and the inferred regional stress field. The second day of the workshop began with the presentation and discussion of evidence for strike-slip faults on Mars at various scales. In the last session, the discussion of extensional structures ranged from the origin of grabens, tension cracks, and pit-crater chains to the origin of Valles Marineris canyons. Shear and tensile modes of brittle failure in the formation of extensional features and the role of these failure modes in the formation of pit-crater chains and the canyons of Valles Marineris were debated. The relationship of extensional features to other surface processes, such as carbonate dissolution (karst) were also discussed

Renal Epithelial Cell Injury Induced by Calcium Oxalate Monohydrate Depends on their Structural Features: Size, Surface, and Crystalline Structure.

Science.gov (United States)

Sun, Xin-Yuan; Ouyang, Jian-Ming; Gan, Qiong-Zhi; Liu, Ai-Jie

2016-11-01

Urinary crystals in normal and kidney stone patients often differ in crystal sizes and surface structures, but the effects of different crystal properties on renal tubular epithelial cells remain unclear. This study aimed to compare the cytotoxicity of micron/nano-calcium oxalate monohydrate (COM) crystals with sizes of 50 nm, 200 nm, 1 μm, 3 μm, and 10 μm to African green monkey renal epithelial (Vero) cells, to reveal the effect of crystal size and surface structure on cell injury, and to investigate the pathological mechanism of calcium oxalate kidney stones. Cell viability, cellular biochemical parameters, and internalized crystal amount in Vero cells were closely associated with the size of COM crystals. At the same concentration (200 μg/mL), COM-1 μm induced the most serious injury to Vero cells and caused the most significant change to cellular biochemical parameters, which were related to the specific porous structure and highest internalized amount in Vero cells. By contrast, COM-50 nm and COM-200 nm crystals lost their small size effect because of serious aggregation and weakened their toxicity to cells. COM-3 μm and COM-10 μm crystals were too large for cells to completely internalize; these crystals also exhibited a low specific surface area and thus weakened their toxicity. The excessive expression of intracellular ROS and reduction of the free-radical scavenger SOD were the main reasons for cell injury and eventually caused necrotic cell death. Crystal size, surface structure, aggregation, and internalization amount were closely related to the cytotoxicity of COM crystals.

Specific Features of Structural-Phase State and Properties of Reactor Pressure Vessel Steel at Elevated Irradiation Temperature

Directory of Open Access Journals (Sweden)

E. A. Kuleshova

2017-01-01

Full Text Available This paper considers influence of elevated irradiation temperature on structure and properties of 15Kh2NMFAA reactor pressure vessel (RPV steel. The steel is investigated after accelerated irradiation at 300°C (operating temperature of VVER-1000-type RPV and 400°C supposed to be the operating temperature of advanced RPVs. Irradiation at 300°C leads to formation of radiation-induced precipitates and radiation defects-dislocation loops, while no carbide phase transformation is observed. Irradiation at a higher temperature (400°C neither causes formation of radiation-induced precipitates nor provides formation of dislocation loops, but it does increase the number density of the main initial hardening phase—of the carbonitrides. Increase of phosphorus concentration in grain boundaries is more pronounced for irradiation at 400°C as compared to irradiation at 300°C due to influence of thermally enhanced diffusion at a higher temperature. The structural-phase changes determine the changes of mechanical properties: at both irradiation temperatures irradiation embrittlement is mainly due to the hardening mechanism with some contribution of the nonhardening one for irradiation at 400°C. Lack of formation of radiation-induced precipitates at T = 400°C provides a small ΔTK shift (17°C. The obtained results demonstrate that the investigated 15Kh2NMFAA steel may be a promising material for advanced reactors with an elevated operating temperature.

Verbal component specific features of creolized internet memes

Directory of Open Access Journals (Sweden)

Anikina T. V.

2017-09-01

Full Text Available the given article deals with Internet memes as a specific phenomenon of internet discourse. Creolized Internet memes serve to simplify and intensify communication among people. It is facilitated by such language means as language game, erratives and abbreviation

Graded territories: Towards the design, specification and simulation of materially graded bending active structures

DEFF Research Database (Denmark)

Nicholas, Paul; Tamke, Martin; Ramsgaard Thomsen, Mette

2012-01-01

these structures, the property of bending is activated and varied through bespoke material means so as to match a desired form. Within the architectural design process, formal control depends upon design approaches for material specification and simulation that consider behavior at the level of the material...... element as well as the structure. We describe an evolving approach to material specification and simulation, and highlight the digital and material considerations that frame the process.......The ability to make materials with bespoke behavior affords new perspectives on incorporating material properties within the design process not available through natural materials. This paper reports the design and assembly of two bending-active, fibre-reinforced composite structures. Within...

A composite method based on formal grammar and DNA structural features in detecting human polymerase II promoter region.

Directory of Open Access Journals (Sweden)

Sutapa Datta

Full Text Available An important step in understanding gene regulation is to identify the promoter regions where the transcription factor binding takes place. Predicting a promoter region de novo has been a theoretical goal for many researchers for a long time. There exists a number of in silico methods to predict the promoter region de novo but most of these methods are still suffering from various shortcomings, a major one being the selection of appropriate features of promoter region distinguishing them from non-promoters. In this communication, we have proposed a new composite method that predicts promoter sequences based on the interrelationship between structural profiles of DNA and primary sequence elements of the promoter regions. We have shown that a Context Free Grammar (CFG can formalize the relationships between different primary sequence features and by utilizing the CFG, we demonstrate that an efficient parser can be constructed for extracting these relationships from DNA sequences to distinguish the true promoter sequences from non-promoter sequences. Along with CFG, we have extracted the structural features of the promoter region to improve upon the efficiency of our prediction system. Extensive experiments performed on different datasets reveals that our method is effective in predicting promoter sequences on a genome-wide scale and performs satisfactorily as compared to other promoter prediction techniques.

A Composite Method Based on Formal Grammar and DNA Structural Features in Detecting Human Polymerase II Promoter Region

Science.gov (United States)

Datta, Sutapa; Mukhopadhyay, Subhasis

2013-01-01

An important step in understanding gene regulation is to identify the promoter regions where the transcription factor binding takes place. Predicting a promoter region de novo has been a theoretical goal for many researchers for a long time. There exists a number of in silico methods to predict the promoter region de novo but most of these methods are still suffering from various shortcomings, a major one being the selection of appropriate features of promoter region distinguishing them from non-promoters. In this communication, we have proposed a new composite method that predicts promoter sequences based on the interrelationship between structural profiles of DNA and primary sequence elements of the promoter regions. We have shown that a Context Free Grammar (CFG) can formalize the relationships between different primary sequence features and by utilizing the CFG, we demonstrate that an efficient parser can be constructed for extracting these relationships from DNA sequences to distinguish the true promoter sequences from non-promoter sequences. Along with CFG, we have extracted the structural features of the promoter region to improve upon the efficiency of our prediction system. Extensive experiments performed on different datasets reveals that our method is effective in predicting promoter sequences on a genome-wide scale and performs satisfactorily as compared to other promoter prediction techniques. PMID:23437045

Predictive brain networks for major depression in a semi-multimodal fusion hierarchical feature reduction framework.

Science.gov (United States)

Yang, Jie; Yin, Yingying; Zhang, Zuping; Long, Jun; Dong, Jian; Zhang, Yuqun; Xu, Zhi; Li, Lei; Liu, Jie; Yuan, Yonggui

2018-02-05

Major depressive disorder (MDD) is characterized by dysregulation of distributed structural and functional networks. It is now recognized that structural and functional networks are related at multiple temporal scales. The recent emergence of multimodal fusion methods has made it possible to comprehensively and systematically investigate brain networks and thereby provide essential information for influencing disease diagnosis and prognosis. However, such investigations are hampered by the inconsistent dimensionality features between structural and functional networks. Thus, a semi-multimodal fusion hierarchical feature reduction framework is proposed. Feature reduction is a vital procedure in classification that can be used to eliminate irrelevant and redundant information and thereby improve the accuracy of disease diagnosis. Our proposed framework primarily consists of two steps. The first step considers the connection distances in both structural and functional networks between MDD and healthy control (HC) groups. By adding a constraint based on sparsity regularization, the second step fully utilizes the inter-relationship between the two modalities. However, in contrast to conventional multi-modality multi-task methods, the structural networks were considered to play only a subsidiary role in feature reduction and were not included in the following classification. The proposed method achieved a classification accuracy, specificity, sensitivity, and area under the curve of 84.91%, 88.6%, 81.29%, and 0.91, respectively. Moreover, the frontal-limbic system contributed the most to disease diagnosis. Importantly, by taking full advantage of the complementary information from multimodal neuroimaging data, the selected consensus connections may be highly reliable biomarkers of MDD. Copyright © 2017 Elsevier B.V. All rights reserved.

Efficient Feature Selection and Classification of Protein Sequence Data in Bioinformatics

Science.gov (United States)

Faye, Ibrahima; Samir, Brahim Belhaouari; Md Said, Abas

2014-01-01

Bioinformatics has been an emerging area of research for the last three decades. The ultimate aims of bioinformatics were to store and manage the biological data, and develop and analyze computational tools to enhance their understanding. The size of data accumulated under various sequencing projects is increasing exponentially, which presents difficulties for the experimental methods. To reduce the gap between newly sequenced protein and proteins with known functions, many computational techniques involving classification and clustering algorithms were proposed in the past. The classification of protein sequences into existing superfamilies is helpful in predicting the structure and function of large amount of newly discovered proteins. The existing classification results are unsatisfactory due to a huge size of features obtained through various feature encoding methods. In this work, a statistical metric-based feature selection technique has been proposed in order to reduce the size of the extracted feature vector. The proposed method of protein classification shows significant improvement in terms of performance measure metrics: accuracy, sensitivity, specificity, recall, F-measure, and so forth. PMID:25045727

[Production, specificity and structure of immunoglobulins].

Science.gov (United States)

Goujard, C; Delfraissy, J F

1991-03-21

Immunoglobulin is a key factor of the immune response resulting from B-cell activation and associated with T-cell stimulation. Because of its structure, this antibody has a dual function: it specifically recognizes the inducer antigen in the variable region and eliminates it by a constant portion which is responsible for effector properties. Surface immunoglobulin, therefore, is the B-cell antigen receptor; it differs from the T-cell receptor in that it recognizes the antigen unbound to the major istocompatibility complex; binding the antigen results in direct signal transduction first in the cytoplasm, then in the nucleus. This receptor can be secreted in the body: it is made up of circulating immunoglobulins. Human immunoglobulins are divided into 5 classes, each of them with its own response kinetics, distribution and functions. The variability of the antibody response accounts for a genetic organization involving numerous genes which may be associated with each other, or mutate, or recombine during maturation of the lymphocytes. Altogether, this system has a theoretical capacity of response to three hundred million different antigens.

Modeling specific phobias and posttraumatic stress disorder in rodents: the challenge to convey both cognitive and emotional features.

Science.gov (United States)

Berardi, Andrea; Trezza, Viviana; Campolongo, Campolongo

2012-01-01

Aberrant emotional memory processing is a core, disabling feature of both specific phobias and posttraumatic stress disorder (PTSD), two psychiatric diseases of significant prevalence and morbidity whose cognitive symptoms cannot be adequately treated by current psychopharmacological tools. Elucidating the neurobiological mechanisms involved in the etiology of these diseases is of great interest for the identification of new therapeutics that improve not only the symptomatology but also the full recovery from the pathology. To this aim, several animal models have been proposed based on substantial resemblance between the behavioral alterations seen in animals and the human pathology. The purpose of this review is to describe and comment on the most commonly used rodent models of specific phobias and PTSD. A particular focus will be reserved to the cued version of fear conditioning, as the highly specific stimulus-bound conditioned fear response seems to fit well with clinical descriptions of phobic fear.Moreover, animal models of PTSD will be evaluated by referring to three elements that are considered essential ina valid model of this disease: stressor exposure, memory for the stressor, and anxiety-related behaviors. Finally, current therapeutic directions, with a focus on cannabinoid and glucocorticoid compounds, will be briefly outlined.

Structured flowcharts for control logic specification in the Tritium Systems Test Assembly

International Nuclear Information System (INIS)

Nielson, C.W.; Claborn, G.W.

1983-01-01

The Tritium Systems Test Assembly (TSTA) contains several subsystems employing sophisticated chemical and physical processes to purify, transport, and capture the isotopes of hydrogen. The ultimate responsibility for the correct and safe operation of these subsystems lies with their designers. However, the logic is implemented in a computer system with program control. A means to insure unambiguous specification of the control logic in a form understandable to both the non-programming designers and the software staff was required. The computer programs are written in RATFOR, a language providing clear control structures and powerful symbol definition facilities. However, the actual code was considered unsatisfactory as a means of primary specification by the non-programming designers. On the other hand, simple English language descriptions of the desired behavior were not precise enough to insure correctness. Experimentation with traditional flowcharts proved that they were more difficult to follow than the RATFOR code. On the other hand, the use of structured flowcharts derived from those introduced by Nassi and Shneidermanl have proven to be very powerful. Using simple geometric forms for the basic control structures such as loops and conditional tests, and by using expansion rather than connection as the means of reducing any flowchart to a single page, a specification that is both understandable and precise has been obtained. A computer code automates the production and modification of these flowcharts. Combining these flowcharts with primitive subroutines which hide most of the details of control implementation has provided an effective medium for algorithm specification and validation. Examples of the flowcharts and the language used to specify them will be given

Prostatic adenocarcinoma with glomeruloid features.

Science.gov (United States)

Pacelli, A; Lopez-Beltran, A; Egan, A J; Bostwick, D G

1998-05-01

premalignant lesions, including hyperplasia and intraepithelial neoplasia. Glomeruloid structures in the prostate represent an uncommon but distinctive pattern of growth that is specific for malignancy. Glomeruloid features may be a useful diagnostic clue for malignancy, particularly in some challenging needle biopsy specimens. This pattern of growth is usually seen in high-grade adenocarcinoma, often with extraprostatic extension. Further investigations are required to determine its independent predictive value and correlation with stage and Gleason score.

Individual differences in personality traits reflect structural variance in specific brain regions.

Science.gov (United States)

Gardini, Simona; Cloninger, C Robert; Venneri, Annalena

2009-06-30

Personality dimensions such as novelty seeking (NS), harm avoidance (HA), reward dependence (RD) and persistence (PER) are said to be heritable, stable across time and dependent on genetic and neurobiological factors. Recently a better understanding of the relationship between personality traits and brain structures/systems has become possible due to advances in neuroimaging techniques. This Magnetic Resonance Imaging (MRI) study investigated if individual differences in these personality traits reflected structural variance in specific brain regions. A large sample of eighty five young adult participants completed the Three-dimensional Personality Questionnaire (TPQ) and had their brain imaged with MRI. A voxel-based correlation analysis was carried out between individuals' personality trait scores and grey matter volume values extracted from 3D brain scans. NS correlated positively with grey matter volume in frontal and posterior cingulate regions. HA showed a negative correlation with grey matter volume in orbito-frontal, occipital and parietal structures. RD was negatively correlated with grey matter volume in the caudate nucleus and in the rectal frontal gyrus. PER showed a positive correlation with grey matter volume in the precuneus, paracentral lobule and parahippocampal gyrus. These results indicate that individual differences in the main personality dimensions of NS, HA, RD and PER, may reflect structural variance in specific brain areas.

Structural studies of Pseudomonas and Chromobacterium ω-aminotransferases provide insights into their differing substrate specificity

International Nuclear Information System (INIS)

Sayer, Christopher; Isupov, Michail N.; Westlake, Aaron; Littlechild, Jennifer A.

2013-01-01

The X-ray structures of two ω-aminotransferases from P. aeruginosa and C. violaceum in complex with an inhibitor offer the first detailed insight into the structural basis of the substrate specificity of these industrially important enzymes. The crystal structures and inhibitor complexes of two industrially important ω-aminotransferase enzymes from Pseudomonas aeruginosa and Chromobacterium violaceum have been determined in order to understand the differences in their substrate specificity. The two enzymes share 30% sequence identity and use the same amino acceptor, pyruvate; however, the Pseudomonas enzyme shows activity towards the amino donor β-alanine, whilst the Chromobacterium enzyme does not. Both enzymes show activity towards S-α-methylbenzylamine (MBA), with the Chromobacterium enzyme having a broader substrate range. The crystal structure of the P. aeruginosa enzyme has been solved in the holo form and with the inhibitor gabaculine bound. The C. violaceum enzyme has been solved in the apo and holo forms and with gabaculine bound. The structures of the holo forms of both enzymes are quite similar. There is little conformational difference observed between the inhibitor complex and the holoenzyme for the P. aeruginosa aminotransferase. In comparison, the crystal structure of the C. violaceum gabaculine complex shows significant structural rearrangements from the structures of both the apo and holo forms of the enzyme. It appears that the different rigidity of the protein scaffold contributes to the substrate specificity observed for the two ω-aminotransferases

Model-independent phenotyping of C. elegans locomotion using scale-invariant feature transform.

Directory of Open Access Journals (Sweden)

Yelena Koren

Full Text Available To uncover the genetic basis of behavioral traits in the model organism C. elegans, a common strategy is to study locomotion defects in mutants. Despite efforts to introduce (semi-automated phenotyping strategies, current methods overwhelmingly depend on worm-specific features that must be hand-crafted and as such are not generalizable for phenotyping motility in other animal models. Hence, there is an ongoing need for robust algorithms that can automatically analyze and classify motility phenotypes quantitatively. To this end, we have developed a fully-automated approach to characterize C. elegans' phenotypes that does not require the definition of nematode-specific features. Rather, we make use of the popular computer vision Scale-Invariant Feature Transform (SIFT from which we construct histograms of commonly-observed SIFT features to represent nematode motility. We first evaluated our method on a synthetic dataset simulating a range of nematode crawling gaits. Next, we evaluated our algorithm on two distinct datasets of crawling C. elegans with mutants affecting neuromuscular structure and function. Not only is our algorithm able to detect differences between strains, results capture similarities in locomotory phenotypes that lead to clustering that is consistent with expectations based on genetic relationships. Our proposed approach generalizes directly and should be applicable to other animal models. Such applicability holds promise for computational ethology as more groups collect high-resolution image data of animal behavior.

Memory-Based Specification of Verbal Features for Classifying Animals into Super-Ordinate and Sub-Ordinate Categories

OpenAIRE

Takahiro Soshi; Norio Fujimaki; Atsushi Matsumoto; Aya S. Ihara

2017-01-01

Accumulating evidence suggests that category representations are based on features. Distinguishing features are considered to define categories, because of all-or-none responses for objects in different categories; however, it is unclear how distinguishing features actually classify objects at various category levels. The present study included 75 animals within three classes (mammal, bird, and fish), along with 195 verbal features. Healthy adults participated in memory-based feature-animal m...

Sensing site-specific structural characteristics and chirality using vibrational circular dichroism of isotope labeled peptides.

Science.gov (United States)

Keiderling, Timothy A

2017-12-01

Isotope labeling has a long history in chemistry as a tool for probing structure, offering enhanced sensitivity, or enabling site selection with a wide range of spectroscopic tools. Chirality sensitive methods such as electronic circular dichroism are global structural tools and have intrinsically low resolution. Consequently, they are generally insensitive to modifications to enhance site selectivity. The use of isotope labeling to modify vibrational spectra with unique resolvable frequency shifts can provide useful site-specific sensitivity, and these methods have been recently more widely expanded in biopolymer studies. While the spectral shifts resulting from changes in isotopic mass can provide resolution of modes from specific parts of the molecule and can allow detection of local change in structure with perturbation, these shifts alone do not directly indicate structure or chirality. With vibrational circular dichroism (VCD), the shifted bands and their resultant sign patterns can be used to indicate local conformations in labeled biopolymers, particularly if multiple labels are used and if their coupling is theoretically modeled. This mini-review discusses selected examples of the use of labeling specific amides in peptides to develop local structural insight with VCD spectra. © 2017 Wiley Periodicals, Inc.

Guilt by Association: The 13 micron Dust Feature in Circumstellar Shells and Related Spectral Features

Science.gov (United States)

Sloan, G. C.; Kraemer, K. E.; Goebel, J. H.; Price, S. D.

A study of spectra from the SWS on ISO of optically thin oxygen-rich dust shells shows that the strength of the 13 micron dust emission feature is correlated with the CO2 bands (13--17 microns) and dust emission features at 19.8 and 28.1 microns. SRb variables tend to show stronger 13 micron features than Mira variables, suggesting that the presence of the 13 micron and related features depends on pulsation mode and mass-loss rate. The absence of any correlation to dust emission features at 16.8 and 32 microns makes spinel an unlikely carrier. The most plausible carrier of the 13 micron feature remains crystalline alumina, and we suggest that the related dust features may be crystalline silicates. When dust forms in regions of low density, it may condense into crystalline grain structures.

Segmenting Brain Tissues from Chinese Visible Human Dataset by Deep-Learned Features with Stacked Autoencoder

Directory of Open Access Journals (Sweden)

Guangjun Zhao

2016-01-01

Full Text Available Cryosection brain images in Chinese Visible Human (CVH dataset contain rich anatomical structure information of tissues because of its high resolution (e.g., 0.167 mm per pixel. Fast and accurate segmentation of these images into white matter, gray matter, and cerebrospinal fluid plays a critical role in analyzing and measuring the anatomical structures of human brain. However, most existing automated segmentation methods are designed for computed tomography or magnetic resonance imaging data, and they may not be applicable for cryosection images due to the imaging difference. In this paper, we propose a supervised learning-based CVH brain tissues segmentation method that uses stacked autoencoder (SAE to automatically learn the deep feature representations. Specifically, our model includes two successive parts where two three-layer SAEs take image patches as input to learn the complex anatomical feature representation, and then these features are sent to Softmax classifier for inferring the labels. Experimental results validated the effectiveness of our method and showed that it outperformed four other classical brain tissue detection strategies. Furthermore, we reconstructed three-dimensional surfaces of these tissues, which show their potential in exploring the high-resolution anatomical structures of human brain.

Gene expression in chicken reveals correlation with structural genomic features and conserved patterns of transcription in the terrestrial vertebrates.

Directory of Open Access Journals (Sweden)

Haisheng Nie

Full Text Available BACKGROUND: The chicken is an important agricultural and avian-model species. A survey of gene expression in a range of different tissues will provide a benchmark for understanding expression levels under normal physiological conditions in birds. With expression data for birds being very scant, this benchmark is of particular interest for comparative expression analysis among various terrestrial vertebrates. METHODOLOGY/PRINCIPAL FINDINGS: We carried out a gene expression survey in eight major chicken tissues using whole genome microarrays. A global picture of gene expression is presented for the eight tissues, and tissue specific as well as common gene expression were identified. A Gene Ontology (GO term enrichment analysis showed that tissue-specific genes are enriched with GO terms reflecting the physiological functions of the specific tissue, and housekeeping genes are enriched with GO terms related to essential biological functions. Comparisons of structural genomic features between tissue-specific genes and housekeeping genes show that housekeeping genes are more compact. Specifically, coding sequence and particularly introns are shorter than genes that display more variation in expression between tissues, and in addition intergenic space was also shorter. Meanwhile, housekeeping genes are more likely to co-localize with other abundantly or highly expressed genes on the same chromosomal regions. Furthermore, comparisons of gene expression in a panel of five common tissues between birds, mammals and amphibians showed that the expression patterns across tissues are highly similar for orthologous genes compared to random gene pairs within each pair-wise comparison, indicating a high degree of functional conservation in gene expression among terrestrial vertebrates. CONCLUSIONS: The housekeeping genes identified in this study have shorter gene length, shorter coding sequence length, shorter introns, and shorter intergenic regions, there seems

Sparse feature selection identifies H2A.Z as a novel, pattern-specific biomarker for asymmetrically self-renewing distributed stem cells

Directory of Open Access Journals (Sweden)

Yang Hoon Huh

2015-03-01

Full Text Available There is a long-standing unmet clinical need for biomarkers with high specificity for distributed stem cells (DSCs in tissues, or for use in diagnostic and therapeutic cell preparations (e.g., bone marrow. Although DSCs are essential for tissue maintenance and repair, accurate determination of their numbers for medical applications has been problematic. Previous searches for biomarkers expressed specifically in DSCs were hampered by difficulty obtaining pure DSCs and by the challenges in mining complex molecular expression data. To identify such useful and specific DSC biomarkers, we combined a novel sparse feature selection method with combinatorial molecular expression data focused on asymmetric self-renewal, a conspicuous property of DSCs. The analysis identified reduced expression of the histone H2A variant H2A.Z as a superior molecular discriminator for DSC asymmetric self-renewal. Subsequent molecular expression studies showed H2A.Z to be a novel “pattern-specific biomarker” for asymmetrically self-renewing cells, with sufficient specificity to count asymmetrically self-renewing DSCs in vitro and potentially in situ.

Features of morpho-anatomic structure of vegetative organs of Sedum antiquum Omelcz et Zaverucha (Crassulaceae DC.

Directory of Open Access Journals (Sweden)

Valentyna Berezkina

2015-05-01

Full Text Available The study results of biological features and morpho-anatomical structure of vegetative organs of Sedum antiquum Omelcz et Zaverucha (Crassulaceae DC. are given. S. antiquum is Eastern Carpathian-Opillia rare endemic species. It is listed in the Red Book of Ukraine and in the European Red List of Animals and Plants and is endangered in world scale. As a result of study of morpho-anatomic structure of leaves and stems of S. antiquum the anisocytic type of stomata and presence of cuticle have been determined. It was ascertained that structure of leaves is adapted to the accumulation of significant water reserves and its further gradual use. Ecological and phytocenotic conditions of growth are studied too. S. antiquum has been determined here as petrophyte, calcephyl, and succulent ephemer. This rare species need protection and control of population state in all natural habitats.

Specific features of Brodie’s tumors

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D. A. Denchik

2010-01-01

Full Text Available Brodie’s tumors are comparatively rare in oncological care and difficult-to-diagnose masses with an unpredictable course, predilection for recurrences, and a high probability of malignization. These tumors have a two-component structure with the predominant develop- ment of a connective tissue component that is absolute in sarcomas and, in a group of fibroepithelial tumors, combines with the parallel development of epithelial tissue.The etiology of Brodie’s tumor is unclear, so is its pathogenesis. Molecular genetic studies have shown that the carriers of germ line missence-mutation R1699W in the BRCA1 gene have an increased risk of developing malignant Brodie’s tumor, but allele losses at the D22S264 locus of the TP5 gene determine the progression of the disease. Deletion of the short-arm of chromosome 1 (1p and allelic imbalance are associated with the more aggressive course and recurrences of Brodie’s tumor.A complex clinicomorphological and molecular genetic study will help answer some questions concerning the diagnosis and treatment of Brodie’s tumors.

A Structure-Function Study of RecA: The Structural Basis for ATP Specificity in the Strand Exchange Reaction

Science.gov (United States)

Gegner, Julie; Spruill, Natalie; Plesniak, Leigh A.

1999-11-01

The terms "structure" and "function" can assume a variety of meanings. In biochemistry, the "structure" of a protein can refer to its sequence of amino acids, the three-dimensional arrangement of atoms within a subunit, or the arrangement of subunits into a larger oligomeric or filamentous state. Likewise, the function of biological macromolecules can be examined at many levels. The function of a protein can be described by its role in an organism's survival or by a chemical reaction that it promotes. We have designed a three-part biochemical laboratory experiment that characterizes the structure and function of the Escherichia coli RecA protein. The first part examines the importance of RecA in the survival of bacteria that have been exposed to UV light. This is the broadest view of function of the enzyme. Second, the students use an in vitro assay of RecA whereby the protein promotes homologous recombination. Because RecA functions not catalytically, but rather stoichiometrically, in this recombination reaction, the oligomeric state of RecA in complex with DNA must also be discussed. Finally, through molecular modeling of X-ray crystallographic structures, students identify functionally important features of the ATP cofactor binding site of RecA.

Area-specific temporal control of corticospinal motor neuron differentiation by COUP-TFI

Science.gov (United States)

Tomassy, Giulio Srubek; De Leonibus, Elvira; Jabaudon, Denis; Lodato, Simona; Alfano, Christian; Mele, Andrea; Macklis, Jeffrey D.; Studer, Michèle

2010-01-01

Transcription factors with gradients of expression in neocortical progenitors give rise to distinct motor and sensory cortical areas by controlling the area-specific differentiation of distinct neuronal subtypes. However, the molecular mechanisms underlying this area-restricted control are still unclear. Here, we show that COUP-TFI controls the timing of birth and specification of corticospinal motor neurons (CSMN) in somatosensory cortex via repression of a CSMN differentiation program. Loss of COUP-TFI function causes an area-specific premature generation of neurons with cardinal features of CSMN, which project to subcerebral structures, including the spinal cord. Concurrently, genuine CSMN differentiate imprecisely and do not project beyond the pons, together resulting in impaired skilled motor function in adult mice with cortical COUP-TFI loss-of-function. Our findings indicate that COUP-TFI exerts critical areal and temporal control over the precise differentiation of CSMN during corticogenesis, thereby enabling the area-specific functional features of motor and sensory areas to arise. PMID:20133588

Novel structural features drive DNA binding properties of Cmr, a CRP family protein in TB complex mycobacteria.

Science.gov (United States)

Ranganathan, Sridevi; Cheung, Jonah; Cassidy, Michael; Ginter, Christopher; Pata, Janice D; McDonough, Kathleen A

2018-01-09

Mycobacterium tuberculosis (Mtb) encodes two CRP/FNR family transcription factors (TF) that contribute to virulence, Cmr (Rv1675c) and CRPMt (Rv3676). Prior studies identified distinct chromosomal binding profiles for each TF despite their recognizing overlapping DNA motifs. The present study shows that Cmr binding specificity is determined by discriminator nucleotides at motif positions 4 and 13. X-ray crystallography and targeted mutational analyses identified an arginine-rich loop that expands Cmr's DNA interactions beyond the classical helix-turn-helix contacts common to all CRP/FNR family members and facilitates binding to imperfect DNA sequences. Cmr binding to DNA results in a pronounced asymmetric bending of the DNA and its high level of cooperativity is consistent with DNA-facilitated dimerization. A unique N-terminal extension inserts between the DNA binding and dimerization domains, partially occluding the site where the canonical cAMP binding pocket is found. However, an unstructured region of this N-terminus may help modulate Cmr activity in response to cellular signals. Cmr's multiple levels of DNA interaction likely enhance its ability to integrate diverse gene regulatory signals, while its novel structural features establish Cmr as an atypical CRP/FNR family member. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

The Semiotic Structure of Geometry Diagrams: How Textbook Diagrams Convey Meaning

Science.gov (United States)

Dimmel, Justin K.; Herbst, Patricio G.

2015-01-01

Geometry diagrams use the visual features of specific drawn objects to convey meaning about generic mathematical entities. We examine the semiotic structure of these visual features in two parts. One, we conduct a semiotic inquiry to conceptualize geometry diagrams as mathematical texts that comprise choices from different semiotic systems. Two,…

Features for Exploiting Black-Box Optimization Problem Structure

DEFF Research Database (Denmark)

Tierney, Kevin; Malitsky, Yuri; Abell, Tinus

2013-01-01

landscape of BBO problems and show how an algorithm portfolio approach can exploit these general, problem indepen- dent features and outperform the utilization of any single minimization search strategy. We test our methodology on data from the GECCO Workshop on BBO Benchmarking 2012, which contains 21...

Photoreflectance and contactless electroreflectance spectroscopy of GaAs-based structures: The below band gap oscillation features

International Nuclear Information System (INIS)

Kudrawiec, R.; Motyka, M.; Gladysiewicz, M.; Sitarek, P.; Misiewicz, J.

2006-01-01

GaAs-based structures characterized below band gap oscillation features (OFs) in photoreflectance (PR) are studied in both PR and contactless electro-reflectance (CER) spectroscopies. It has been shown that the OFs are usually very strong for structures grown on n-type GaAs substrate. The origin of the OFs is the modulation of the refractive index in the sample due to a generation of additional carriers by the modulated pump beam. The presence of OFs in PR spectra complicates the analysis of PR signal related to quantum well transitions. Therefore, PR spectroscopy is often limited to samples grown on semi-insolating (SI) type substrates. However, sometimes the OFs could be observed for structures grown on SI-type GaAs substrates. In this paper we show that the OFs could be successfully eliminated by applying the CER technique instead of PR one because during CER measurements any additional carriers are not generated and hence CER spectra are free of OFs. This advantage of CER spectroscopy is very important in investigations of all structures for which OFs are present in PR spectra

Hippocampal sleep features: relations to human memory function

Directory of Open Access Journals (Sweden)

Michele eFerrara

2012-04-01

Full Text Available The recent spread of intracranial EEG recordings techniques for presurgical evaluation of drug-resistant epileptic patients is providing new information on the activity of different brain structures during both wakefulness and sleep. The interest has been mainly focused on the medial temporal lobe, and in particular the hippocampal formation, whose peculiar local sleep features have been recently described, providing support to the idea that sleep is not a spatially global phenomenon. The study of the hippocampal sleep electrophysiology is particularly interesting because of its central role in the declarative memory formation. Recent data indicate that sleep contributes to memory formation. Therefore, it is relevant to understand whether specific pattern of activity taking place during sleep are related to memory consolidation processes. Fascinating similarities between different states of consciousness (wakefulness, REM sleep, NREM sleep in some electrophysiological mechanisms underlying cognitive processes have been reported. For instance, large-scale synchrony in gamma activity is important for waking memory and perception processes, and its changes during sleep may be the neurophysiological substrate of sleep-related deficits of declarative memory. Hippocampal activity seems to specifically support memory consolidation during sleep, through specific coordinated neurophysiological events (slow waves, spindles, ripples that would facilitate the integration of new information into the pre-existing cortical networks. A few studies indeed provided direct evidence that rhinal ripples as well as slow hippocampal oscillations are correlated with memory consolidation in humans. More detailed electrophysiological investigations assessing the specific relations between different types of memory consolidation and hippocampal EEG features are in order. These studies will add an important piece of knowledge to the elucidation of the ultimate sleep

Hippocampal Sleep Features: Relations to Human Memory Function

Science.gov (United States)

Ferrara, Michele; Moroni, Fabio; De Gennaro, Luigi; Nobili, Lino

2012-01-01

The recent spread of intracranial electroencephalographic (EEG) recording techniques for presurgical evaluation of drug-resistant epileptic patients is providing new information on the activity of different brain structures during both wakefulness and sleep. The interest has been mainly focused on the medial temporal lobe, and in particular the hippocampal formation, whose peculiar local sleep features have been recently described, providing support to the idea that sleep is not a spatially global phenomenon. The study of the hippocampal sleep electrophysiology is particularly interesting because of its central role in the declarative memory formation. Recent data indicate that sleep contributes to memory formation. Therefore, it is relevant to understand whether specific patterns of activity taking place during sleep are related to memory consolidation processes. Fascinating similarities between different states of consciousness (wakefulness, REM sleep, non-REM sleep) in some electrophysiological mechanisms underlying cognitive processes have been reported. For instance, large-scale synchrony in gamma activity is important for waking memory and perception processes, and its changes during sleep may be the neurophysiological substrate of sleep-related deficits of declarative memory. Hippocampal activity seems to specifically support memory consolidation during sleep, through specific coordinated neurophysiological events (slow waves, spindles, ripples) that would facilitate the integration of new information into the pre-existing cortical networks. A few studies indeed provided direct evidence that rhinal ripples as well as slow hippocampal oscillations are correlated with memory consolidation in humans. More detailed electrophysiological investigations assessing the specific relations between different types of memory consolidation and hippocampal EEG features are in order. These studies will add an important piece of knowledge to the elucidation of the ultimate

Structural analysis of polycrystalline (graphitized) materials

International Nuclear Information System (INIS)

Efremenko, M.M.; Kravchik, A.E.; Osmakov, A.S.

1993-01-01

Specific features of the structure of polycrystal carbon materials (CM), characterized by high enough degree of structural perfection and different genesis are analyzed. From the viewpoint of fine and supercrystallite structure analysis of the most characteristic groups of graphitized CM: artificial graphites, and natural graphites, as well, has been carried out. It is ascertained that in paracrystal CM a monolayer of hexagonally-bound carbon atoms is the basic element of the structure, and in graphitized CM - a microlayer. The importance of the evaluation of the degree of three-dimensional ordering of the microlayer is shown

Structural Characterization of the Hemagglutinin Receptor Specificity from the 2009 H1N1 Influenza Pandemic

Energy Technology Data Exchange (ETDEWEB)

Xu, Rui; McBride, Ryan; Nycholat, Corwin M.; Paulson, James C.; Wilson, Ian A. (Scripps)

2012-02-13

Influenza virus hemagglutinin (HA) is the viral envelope protein that mediates viral attachment to host cells and elicits membrane fusion. The HA receptor-binding specificity is a key determinant for the host range and transmissibility of influenza viruses. In human pandemics of the 20th century, the HA normally has acquired specificity for human-like receptors before widespread infection. Crystal structures of the H1 HA from the 2009 human pandemic (A/California/04/2009 [CA04]) in complex with human and avian receptor analogs reveal conserved recognition of the terminal sialic acid of the glycan ligands. However, favorable interactions beyond the sialic acid are found only for {alpha}2-6-linked glycans and are mediated by Asp190 and Asp225, which hydrogen bond with Gal-2 and GlcNAc-3. For {alpha}2-3-linked glycan receptors, no specific interactions beyond the terminal sialic acid are observed. Our structural and glycan microarray analyses, in the context of other high-resolution HA structures with {alpha}2-6- and {alpha}2-3-linked glycans, now elucidate the structural basis of receptor-binding specificity for H1 HAs in human and avian viruses and provide a structural explanation for the preference for {alpha}2-6 siaylated glycan receptors for the 2009 pandemic swine flu virus.

Structural features of anodic oxide films formed on aluminum substrate coated with self-assembled microspheres

International Nuclear Information System (INIS)

Asoh, Hidetaka; Uchibori, Kota; Ono, Sachiko

2009-01-01

The structural features of anodic oxide films formed on an aluminum substrate coated with self-assembled microspheres were investigated by scanning electron microscopy and atomic force microscopy. In the first anodization in neutral solution, the growth of a barrier-type film was partially suppressed in the contact area between the spheres and the underlying aluminum substrate, resulting in the formation of ordered dimple arrays in an anodic oxide film. After the subsequent second anodization in acid solution at a voltage lower than that of the first anodization, nanopores were generated only within each dimple. The nanoporous region could be removed selectively by post-chemical etching using the difference in structural dimensions between the porous region and the surrounding barrier region. The mechanism of anodic oxide growth on the aluminum substrate coated with microspheres through multistep anodization is discussed.

Structural features of anodic oxide films formed on aluminum substrate coated with self-assembled microspheres

Energy Technology Data Exchange (ETDEWEB)

Asoh, Hidetaka [Department of Applied Chemistry, Faculty of Engineering, Kogakuin University, 2665-1 Nakano, Hachioji, Tokyo 192-0015 (Japan)], E-mail: asoh@cc.kogakuin.ac.jp; Uchibori, Kota; Ono, Sachiko [Department of Applied Chemistry, Faculty of Engineering, Kogakuin University, 2665-1 Nakano, Hachioji, Tokyo 192-0015 (Japan)

2009-07-15

The structural features of anodic oxide films formed on an aluminum substrate coated with self-assembled microspheres were investigated by scanning electron microscopy and atomic force microscopy. In the first anodization in neutral solution, the growth of a barrier-type film was partially suppressed in the contact area between the spheres and the underlying aluminum substrate, resulting in the formation of ordered dimple arrays in an anodic oxide film. After the subsequent second anodization in acid solution at a voltage lower than that of the first anodization, nanopores were generated only within each dimple. The nanoporous region could be removed selectively by post-chemical etching using the difference in structural dimensions between the porous region and the surrounding barrier region. The mechanism of anodic oxide growth on the aluminum substrate coated with microspheres through multistep anodization is discussed.

An integrated in silico approach to design specific inhibitors targeting human poly(a-specific ribonuclease.

Directory of Open Access Journals (Sweden)

Dimitrios Vlachakis

Full Text Available Poly(A-specific ribonuclease (PARN is an exoribonuclease/deadenylase that degrades 3'-end poly(A tails in almost all eukaryotic organisms. Much of the biochemical and structural information on PARN comes from the human enzyme. However, the existence of PARN all along the eukaryotic evolutionary ladder requires further and thorough investigation. Although the complete structure of the full-length human PARN, as well as several aspects of the catalytic mechanism still remain elusive, many previous studies indicate that PARN can be used as potent and promising anti-cancer target. In the present study, we attempt to complement the existing structural information on PARN with in-depth bioinformatics analyses, in order to get a hologram of the molecular evolution of PARNs active site. In an effort to draw an outline, which allows specific drug design targeting PARN, an unequivocally specific platform was designed for the development of selective modulators focusing on the unique structural and catalytic features of the enzyme. Extensive phylogenetic analysis based on all the publicly available genomes indicated a broad distribution for PARN across eukaryotic species and revealed structurally important amino acids which could be assigned as potentially strong contributors to the regulation of the catalytic mechanism of PARN. Based on the above, we propose a comprehensive in silico model for the PARN's catalytic mechanism and moreover, we developed a 3D pharmacophore model, which was subsequently used for the introduction of DNP-poly(A amphipathic substrate analog as a potential inhibitor of PARN. Indeed, biochemical analysis revealed that DNP-poly(A inhibits PARN competitively. Our approach provides an efficient integrated platform for the rational design of pharmacophore models as well as novel modulators of PARN with therapeutic potential.

Capturing structured, pulmonary disease-specific data elements in electronic health records.

Science.gov (United States)

Gronkiewicz, Cynthia; Diamond, Edward J; French, Kim D; Christodouleas, John; Gabriel, Peter E

2015-04-01

Electronic health records (EHRs) have the potential to improve health-care quality by allowing providers to make better decisions at the point of care based on electronically aggregated data and by facilitating clinical research. These goals are easier to achieve when key, disease-specific clinical information is documented as structured data elements (SDEs) that computers can understand and process, rather than as free-text/natural-language narrative. This article reviews the benefits of capturing disease-specific SDEs. It highlights several design and implementation considerations, including the impact on efficiency and expressivity of clinical documentation and the importance of adhering to data standards when available. Pulmonary disease-specific examples of collection instruments are provided from two commonly used commercial EHRs. Future developments that can leverage SDEs to improve clinical quality and research are discussed.

Temporal Feature Integration for Music Organisation

DEFF Research Database (Denmark)

Meng, Anders

2006-01-01

This Ph.D. thesis focuses on temporal feature integration for music organisation. Temporal feature integration is the process of combining all the feature vectors of a given time-frame into a single new feature vector in order to capture relevant information in the frame. Several existing methods...... for handling sequences of features are formulated in the temporal feature integration framework. Two datasets for music genre classification have been considered as valid test-beds for music organisation. Human evaluations of these, have been obtained to access the subjectivity on the datasets. Temporal...... ranking' approach is proposed for ranking the short-time features at larger time-scales according to their discriminative power in a music genre classification task. The multivariate AR (MAR) model has been proposed for temporal feature integration. It effectively models local dynamical structure...

Structure And Specificity of a Quorum-Quenching Lactonase (AiiB) From Agrobacterium Tumefaciens

Energy Technology Data Exchange (ETDEWEB)

Liu, D.; Thomas, P.W.; Momb, J.; Hoang, Q.Q.; Petsko, G.A.; Ringe, D.; Fast, W.

2009-06-03

N-Acyl-l-homoserine lactone (AHL) mediated quorum-sensing regulates virulence factor production in a variety of Gram-negative bacteria. Proteins capable of degrading these autoinducers have been called 'quorum-quenching' enzymes, can block many quorum-sensing dependent phenotypes, and represent potentially useful reagents for clinical, agricultural, and industrial applications. The most characterized quorum-quenching enzymes to date are the AHL lactonases, which are metalloproteins that belong to the metallo-beta-lactamase superfamily. Here, we report the cloning, heterologous expression, purification, metal content, substrate specificity, and three-dimensional structure of AiiB, an AHL lactonase from Agrobacterium tumefaciens. Much like a homologous AHL lactonase from Bacillus thuringiensis, AiiB appears to be a metal-dependent AHL lactonase with broad specificity. A phosphate dianion is bound to the dinuclear zinc site and the active-site structure suggests specific mechanistic roles for an active site tyrosine and aspartate. To our knowledge, this is the second representative structure of an AHL lactonase and the first of an AHL lactonase from a microorganism that also produces AHL autoinducers. This work should help elucidate the hydrolytic ring-opening mechanism of this family of enzymes and also facilitate the design of more effective quorum-quenching catalysts.

Low temperature features of the local structure of Sm1-xYxS

International Nuclear Information System (INIS)

Menushenkov, A. P.; Chernikov, R. V.; Sidorov, V. V.; Klementiev, K. V.; Alekseev, P. A.; Rybina, A. V.

2007-01-01

The particular features of the local electronic and local crystal structures of the mixed-valence compound Sm 1-x Y x S are studied by the XAFS spectroscopy methods in the temperature range 20-300 K for the yttrium concentration x = 0.17, 0.25, 0.33, and 0.45. The temperature behavior of the valence of Sm, as well as of the lengths and the Debye-Waller factors of the bonds Sm-S, Sm-Sm(Y), Y-S, and Y-Sm(Y), has been determined. The violation of the Vegard law has been observed. A model for the estimation of the energy width of the 4f level and of its position with respect to the Fermi level is proposed

GeneViTo: Visualizing gene-product functional and structural features in genomic datasets

Directory of Open Access Journals (Sweden)

Promponas Vasilis J

2003-10-01

Full Text Available Abstract Background The availability of increasing amounts of sequence data from completely sequenced genomes boosts the development of new computational methods for automated genome annotation and comparative genomics. Therefore, there is a need for tools that facilitate the visualization of raw data and results produced by bioinformatics analysis, providing new means for interactive genome exploration. Visual inspection can be used as a basis to assess the quality of various analysis algorithms and to aid in-depth genomic studies. Results GeneViTo is a JAVA-based computer application that serves as a workbench for genome-wide analysis through visual interaction. The application deals with various experimental information concerning both DNA and protein sequences (derived from public sequence databases or proprietary data sources and meta-data obtained by various prediction algorithms, classification schemes or user-defined features. Interaction with a Graphical User Interface (GUI allows easy extraction of genomic and proteomic data referring to the sequence itself, sequence features, or general structural and functional features. Emphasis is laid on the potential comparison between annotation and prediction data in order to offer a supplement to the provided information, especially in cases of "poor" annotation, or an evaluation of available predictions. Moreover, desired information can be output in high quality JPEG image files for further elaboration and scientific use. A compilation of properly formatted GeneViTo input data for demonstration is available to interested readers for two completely sequenced prokaryotes, Chlamydia trachomatis and Methanococcus jannaschii. Conclusions GeneViTo offers an inspectional view of genomic functional elements, concerning data stemming both from database annotation and analysis tools for an overall analysis of existing genomes. The application is compatible with Linux or Windows ME-2000-XP operating

Comprehensive structural and substrate specificity classification of the Saccharomyces cerevisiae methyltransferome.

Science.gov (United States)

Wlodarski, Tomasz; Kutner, Jan; Towpik, Joanna; Knizewski, Lukasz; Rychlewski, Leszek; Kudlicki, Andrzej; Rowicka, Maga; Dziembowski, Andrzej; Ginalski, Krzysztof

2011-01-01

Methylation is one of the most common chemical modifications of biologically active molecules and it occurs in all life forms. Its functional role is very diverse and involves many essential cellular processes, such as signal transduction, transcriptional control, biosynthesis, and metabolism. Here, we provide further insight into the enzymatic methylation in S. cerevisiae by conducting a comprehensive structural and functional survey of all the methyltransferases encoded in its genome. Using distant homology detection and fold recognition, we found that the S. cerevisiae methyltransferome comprises 86 MTases (53 well-known and 33 putative with unknown substrate specificity). Structural classification of their catalytic domains shows that these enzymes may adopt nine different folds, the most common being the Rossmann-like. We also analyzed the domain architecture of these proteins and identified several new domain contexts. Interestingly, we found that the majority of MTase genes are periodically expressed during yeast metabolic cycle. This finding, together with calculated isoelectric point, fold assignment and cellular localization, was used to develop a novel approach for predicting substrate specificity. Using this approach, we predicted the general substrates for 24 of 33 putative MTases and confirmed these predictions experimentally in both cases tested. Finally, we show that, in S. cerevisiae, methylation is carried out by 34 RNA MTases, 32 protein MTases, eight small molecule MTases, three lipid MTases, and nine MTases with still unknown substrate specificity.

Comprehensive structural and substrate specificity classification of the Saccharomyces cerevisiae methyltransferome.

Directory of Open Access Journals (Sweden)

Tomasz Wlodarski

Full Text Available Methylation is one of the most common chemical modifications of biologically active molecules and it occurs in all life forms. Its functional role is very diverse and involves many essential cellular processes, such as signal transduction, transcriptional control, biosynthesis, and metabolism. Here, we provide further insight into the enzymatic methylation in S. cerevisiae by conducting a comprehensive structural and functional survey of all the methyltransferases encoded in its genome. Using distant homology detection and fold recognition, we found that the S. cerevisiae methyltransferome comprises 86 MTases (53 well-known and 33 putative with unknown substrate specificity. Structural classification of their catalytic domains shows that these enzymes may adopt nine different folds, the most common being the Rossmann-like. We also analyzed the domain architecture of these proteins and identified several new domain contexts. Interestingly, we found that the majority of MTase genes are periodically expressed during yeast metabolic cycle. This finding, together with calculated isoelectric point, fold assignment and cellular localization, was used to develop a novel approach for predicting substrate specificity. Using this approach, we predicted the general substrates for 24 of 33 putative MTases and confirmed these predictions experimentally in both cases tested. Finally, we show that, in S. cerevisiae, methylation is carried out by 34 RNA MTases, 32 protein MTases, eight small molecule MTases, three lipid MTases, and nine MTases with still unknown substrate specificity.

Time-Contrastive Learning Based DNN Bottleneck Features for Text-Dependent Speaker Verification

DEFF Research Database (Denmark)

Sarkar, Achintya Kumar; Tan, Zheng-Hua

2017-01-01

In this paper, we present a time-contrastive learning (TCL) based bottleneck (BN) feature extraction method for speech signals with an application to text-dependent (TD) speaker verification (SV). It is well-known that speech signals exhibit quasi-stationary behavior in and only in a short interval......, and the TCL method aims to exploit this temporal structure. More specifically, it trains deep neural networks (DNNs) to discriminate temporal events obtained by uniformly segmenting speech signals, in contrast to existing DNN based BN feature extraction methods that train DNNs using labeled data...... to discriminate speakers or pass-phrases or phones or a combination of them. In the context of speaker verification, speech data of fixed pass-phrases are used for TCL-BN training, while the pass-phrases used for TCL-BN training are excluded from being used for SV, so that the learned features can be considered...

Specific features of steam turbine design at LMZ

International Nuclear Information System (INIS)

Pichugin, I.I.; Tsvetkov, A.M.; Simkin, M.S.

1993-01-01

General structural layouts of the condensation steam turbines produced by the Leningrad metalworks (LM) are considered. Currently LM produced 50 types and modifications of steam turbines with the capacity from 30 up to 1200 MW. Problems of turbine efficiency and ways of the flow section improvement are discussed

Visualization of protein sequence features using JavaScript and SVG with pViz.js.

Science.gov (United States)

Mukhyala, Kiran; Masselot, Alexandre

2014-12-01

pViz.js is a visualization library for displaying protein sequence features in a Web browser. By simply providing a sequence and the locations of its features, this lightweight, yet versatile, JavaScript library renders an interactive view of the protein features. Interactive exploration of protein sequence features over the Web is a common need in Bioinformatics. Although many Web sites have developed viewers to display these features, their implementations are usually focused on data from a specific source or use case. Some of these viewers can be adapted to fit other use cases but are not designed to be reusable. pViz makes it easy to display features as boxes aligned to a protein sequence with zooming functionality but also includes predefined renderings for secondary structure and post-translational modifications. The library is designed to further customize this view. We demonstrate such applications of pViz using two examples: a proteomic data visualization tool with an embedded viewer for displaying features on protein structure, and a tool to visualize the results of the variant_effect_predictor tool from Ensembl. pViz.js is a JavaScript library, available on github at https://github.com/Genentech/pviz. This site includes examples and functional applications, installation instructions and usage documentation. A Readme file, which explains how to use pViz with examples, is available as Supplementary Material A. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Research of features and structure of electoral space of Ukraine in 2014 with the use of synthetic approach

Directory of Open Access Journals (Sweden)

M. M. Shelemba

2015-02-01

Full Text Available The article is aimed at the ground of expediency of the use of synthetic authorial model for research of features and structure of electoral space of Ukraine in 2014 year. Methodological principles of the use of synthetic model are expounded with the use of quality and quantitative methods researches of electoral space, among that methods of factor and cross­correlation analysis. A synthetic model (approach that is built on the basis of the use of the best scientific approaches takes into account features and progress of electoral space of Ukraine trends. The analysis of features and structure of electoral space of Ukraine is conducted in 2014 with the use of an offer model. The application author synthetic model allows the study of the use of association factor and correlation analysis to justify support to political parties during election campaigns, respectively, depending on the factors and the most important correlates. It was found that electoral choice depends on the actions of those factors in the highest degree the expectations of the region. This article has shown that the use of Ukraine at this stage of the investigated during election campaigns as the most significant social correlates of «Human Development Index» is reasonable and one that makes it possible to obtain reliable results. It is proved that a high level of correlation holds at a high level of support the party and, consequently, high sense of social correlates all variants of expert research.

O'nyong nyong virus molecular determinants of unique vector specificity reside in non-structural protein 3.

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Kali D Saxton-Shaw

Full Text Available O'nyong nyong virus (ONNV and Chikungunya virus (CHIKV are two closely related alphaviruses with very different infection patterns in the mosquito, Anopheles gambiae. ONNV is the only alphavirus transmitted by anopheline mosquitoes, but specific molecular determinants of infection of this unique vector specificity remain unidentified. Fifteen distinct chimeric viruses were constructed to evaluate both structural and non-structural regions of the genome and infection patterns were determined through artificial infectious feeds in An. gambiae with each of these chimeras. Only one region, non-structural protein 3 (nsP3, was sufficient to up-regulate infection to rates similar to those seen with parental ONNV. When ONNV non-structural protein 3 (nsP3 replaced nsP3 from CHIKV virus in one of the chimeric viruses, infection rates in An. gambiae went from 0% to 63.5%. No other single gene or viral region addition was able to restore infection rates. Thus, we have shown that a non-structural genome element involved in viral replication is a major element involved in ONNV's unique vector specificity.

FEATURES BASED ON NEIGHBORHOOD PIXELS DENSITY - A STUDY AND COMPARISON

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Satish Kumar

2016-02-01

Full Text Available In optical character recognition applications, the feature extraction method(s used to recognize document images play an important role. The features are the properties of the pattern that can be statistical, structural and/or transforms or series expansion. The structural features are difficult to compute particularly from hand-printed images. The structure of the strokes present inside the hand-printed images can be estimated using statistical means. In this paper three features have been purposed, those are based on the distribution of B/W pixels on the neighborhood of a pixel in an image. We name these features as Spiral Neighbor Density, Layer Pixel Density and Ray Density. The recognition performance of these features has been compared with two more features Neighborhood Pixels Weight and Total Distances in Four Directions already studied in our work. We have used more than 20000 Devanagari handwritten character images for conducting experiments. The experiments are conducted with two classifiers i.e. PNN and k-NN.

Comparison of segmentation techniques to determine the geometric parameters of structured surfaces

International Nuclear Information System (INIS)

MacAulay, Gavin D; Giusca, Claudiu L; Leach, Richard K; Senin, Nicola

2014-01-01

Structured surfaces, defined as surfaces characterized by topography features whose shape is defined by design specifications, are increasingly being used in industry for a variety of applications, including improving the tribological properties of surfaces. However, characterization of such surfaces still remains an issue. Techniques have been recently proposed, based on identifying and extracting the relevant features from a structured surface so they can be verified individually, using methods derived from those commonly applied to standard-sized parts. Such emerging approaches show promise but are generally complex and characterized by multiple data processing steps making performance difficult to assess. This paper focuses on the segmentation step, i.e. partitioning the topography so that the relevant features can be separated from the background. Segmentation is key for defining the geometric boundaries of the individual feature, which in turn affects any computation of feature size, shape and localization. This paper investigates the effect of varying the segmentation algorithm and its controlling parameters by considering a test case: a structured surface for bearing applications, the relevant features being micro-dimples designed for friction reduction. In particular, the mechanisms through which segmentation leads to identification of the dimple boundary and influences dimensional properties, such as dimple diameter and depth, are illustrated. It is shown that, by using different methods and control parameters, a significant range of measurement results can be achieved, which may not necessarily agree. Indications on how to investigate the influence of each specific choice are given; in particular, stability of the algorithms with respect to control parameters is analyzed as a means to investigate ease of calibration and flexibility to adapt to specific, application-dependent characterization requirements. (paper)

Phrase-Final Words in Greek Storytelling Speech: A Study on the Effect of a Culturally-Specific Prosodic Feature on Short-Term Memory.

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Loutrari, Ariadne; Tselekidou, Freideriki; Proios, Hariklia

2018-02-27

Prosodic patterns of speech appear to make a critical contribution to memory-related processing. We considered the case of a previously unexplored prosodic feature of Greek storytelling and its effect on free recall in thirty typically developing children between the ages of 10 and 12 years, using short ecologically valid auditory stimuli. The combination of a falling pitch contour and, more notably, extensive final-syllable vowel lengthening, which gives rise to the prosodic feature in question, led to statistically significantly higher performance in comparison to neutral phrase-final prosody. Number of syllables in target words did not reveal substantial difference in performance. The current study presents a previously undocumented culturally-specific prosodic pattern and its effect on short-term memory.

Face recognition algorithm using extended vector quantization histogram features.

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Yan, Yan; Lee, Feifei; Wu, Xueqian; Chen, Qiu

2018-01-01

In this paper, we propose a face recognition algorithm based on a combination of vector quantization (VQ) and Markov stationary features (MSF). The VQ algorithm has been shown to be an effective method for generating features; it extracts a codevector histogram as a facial feature representation for face recognition. Still, the VQ histogram features are unable to convey spatial structural information, which to some extent limits their usefulness in discrimination. To alleviate this limitation of VQ histograms, we utilize Markov stationary features (MSF) to extend the VQ histogram-based features so as to add spatial structural information. We demonstrate the effectiveness of our proposed algorithm by achieving recognition results superior to those of several state-of-the-art methods on publicly available face databases.

Cathodoluminescence studies of chevron features in semi-polar (11 2 ¯ 2 ) InGaN/GaN multiple quantum well structures

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Brasser, C.; Bruckbauer, J.; Gong, Y.; Jiu, L.; Bai, J.; Warzecha, M.; Edwards, P. R.; Wang, T.; Martin, R. W.

2018-05-01

Epitaxial overgrowth of semi-polar III-nitride layers and devices often leads to arrowhead-shaped surface features, referred to as chevrons. We report on a study into the optical, structural, and electrical properties of these features occurring in two very different semi-polar structures, a blue-emitting multiple quantum well structure, and an amber-emitting light-emitting diode. Cathodoluminescence (CL) hyperspectral imaging has highlighted shifts in their emission energy, occurring in the region of the chevron. These variations are due to different semi-polar planes introduced in the chevron arms resulting in a lack of uniformity in the InN incorporation across samples, and the disruption of the structure which could cause a narrowing of the quantum wells (QWs) in this region. Atomic force microscopy has revealed that chevrons can penetrate over 150 nm into the sample and quench light emission from the active layers. The dominance of non-radiative recombination in the chevron region was exposed by simultaneous measurement of CL and the electron beam-induced current. Overall, these results provide an overview of the nature and impact of chevrons on the luminescence of semi-polar devices.

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

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

2013-06-01

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

Sensitivity of radiographic features and specificity of scintigraphic imaging in hand osteoarthritis

International Nuclear Information System (INIS)

Buckland-Wright, J.C.; MacFarlane, D.G.; Lynch, J.A.

1995-01-01

We undertook to determine which of the radiographic features most reliably detected the presence and disease progression in osteoarthritis in the hand; and which of the radiographic features corresponded with the radionuclide bone scan images. 32 patients with osteoarthritis had X5 macroradiographs taken of their wrists and hands at 6 monthly intervals over an 18 month period. The high magnification and resolution of microfocal radiography permitted quantitative detection of the extent and change in joint space width, subchondral sclerosis, osteophytosis and juxtaarticular radiolucencies. 4-hour technetium 99 m methylene bisphophonate bone scans were taken at 0 and 12 months and the activity of the tracer uptake at each joint scored. The latter was compared with the radiographic features at each visit and the changes between visits analysed. In hand OA the most sensitive radiographic parameters for detecting disease were osteophytes, subchondral sclerosis and justaarticular radiolucencies, with radionuclide imaging demonstrating the increased activity in bone formation associated with the growth and remodelling of osteophytes. Changes in the number and size of osteophytes and joint space narrowing were the only reliable and sensitive parameters for assessing disease progression. We conclude that in osteoarthritis, the bony changes progress significantly before the occurrence of radiographically evident joint space narrowing indicative of cartilage thinning. (authors). 48 refs., 2 tabs., 11 figs

Standard technical specifications for Westinghouse pressurized water reactors

International Nuclear Information System (INIS)

Wagner, P.C.

1979-07-01

This Standard Technical Specification (STS) has been structured for the broadest possible use on Westinghouse plants currently being reviewed for an Operating License. Accordingly, the document contains specifications applicable to plants with (1) either 3 or 4 loops and (2) with and without loop stop valves. In addition, four separate and discrete containment specification sections are provided for each of the following containment types: Atmospheric, Ice Condenser, Sub-Atmospheric, and Dual. Optional specifications are provided for those features and systems which may be included in individual plant designs but are not generic in their scope of application. Alternate specifications are provided in a limited number of cases to cover situations where alternate specification requirements are necessary on a generic basis because of design differences. This revision of the STS does not typically include requirements which may be added or revised as a result of the NRC staff's further review of the Three Mile Island incident

Exposure to Hycanthone alters chromatin structure around specific gene functions and specific repeats in Schistosoma mansoni

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David eRoquis

2014-07-01

Full Text Available Schistosoma mansoni is a parasitic plathyhelminth responsible for intestinal schistosomiasis (or bilharziasis, a disease affecting 67 million people worldwide and causing an important economic burden. The schistosomicides hycanthone, and its later proxy oxamniquine, were widely used for treatments in endemic areas during the 20th century. Recently, the mechanism of action, as well as the genetic origin of a stably and Mendelian inherited resistance for both drugs was elucidated in two strains. However, several observations suggested early on that alternative mechanisms might exist, by which resistance could be induced for these two drugs in sensitive lines of schistosomes. This induced resistance appeared rapidly, within the first generation, but was metastable (not stably inherited. Epigenetic inheritance could explain such a phenomenon and we therefore re-analyzed the historical data with our current knowledge of epigenetics. In addition, we performed new experiments such as ChIP-seq on hycanthone treated worms. We found distinct chromatin structure changes between sensitive worms and induced resistant worms from the same strain. No specific pathway was discovered, but genes in which chromatin structure modification were observed are mostly associated with transport and catabolism, which makes sense in the context of the elimination of the drug. Specific differences were observed in the repetitive compartment of the genome. We finally describe what types of experiments are needed to understand the complexity of heritability that can be based on genetic and/or epigenetic mechanisms for drug resistance in schistosomes.

Individually specific call feature is not used to neighbour-stranger discrimination: the corncrake case.

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Michał Budka

Full Text Available In various contexts, animals rely on acoustic signals to differentiate between conspecifics. Currently, studies examining vocal signatures use two main approaches. In the first approach, researchers search for acoustic characteristics that have the potential to be individual specific. This approach yields information on variation in signal parameters both within and between individuals and generates practical tools that can be used in population monitoring. In the second approach, playback experiments with natural calls are conducted to discern whether animals are capable of discriminating among the vocal signatures of different individuals. However, both approaches do not reveal the exact signal characteristics that are being used in the discrimination process. In this study, we tested whether an individual-specific call characteristic--namely the length of the intervals between successive maximal amplitude peaks within syllables (PPD--is crucial in neighbour-stranger discrimination by males of the nocturnal and highly secretive bird species, the corncrake (Crex crex. We conducted paired playback experiments in which corncrakes (n = 47 were exposed to artificial calls with PPD characteristics of neighbour and stranger birds. These artificial calls differed only in PPD structure. The calls were broadcast from a speaker, and we recorded the birds' behavioural responses. Although corncrakes have previously been experimentally shown to discriminate between neighbours and strangers, we found no difference in the responses to the artificial calls representing neighbours versus strangers. This finding demonstrates that even if vocal signatures are individual specific within a species, it does not automatically mean that said signatures are being crucial in discrimination among individuals. At the same time, the birds' aggressive responses to the artificial calls indicated that the information transmitted by PPDs is important in species-specific

Nucleon structure functions

International Nuclear Information System (INIS)

Virchaux, M.

1992-11-01

The present status of experimental measurements of the nucleon structure functions is reviewed. The results from nearly all deep inelastic experiments are in good mutual agreement. Principles of the analysis of these structure function data in the framework of QCD are described. The specific features of the perturbative QCD predictions are observed in the data. This provides quantitative tests of the validity of QCD as well as determinations of the various parton distributions in the nucleon and some of the most precise measurements of the strong coupling constant αs. The future of this field of experimental physics is sketched

Automated detection of qualitative spatio-temporal features in electrocardiac activation maps.

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Ironi, Liliana; Tentoni, Stefania

2007-02-01

This paper describes a piece of work aiming at the realization of a tool for the automated interpretation of electrocardiac maps. Such maps can capture a number of electrical conduction pathologies, such as arrhytmia, that can be missed by the analysis of traditional electrocardiograms. But, their introduction into the clinical practice is still far away as their interpretation requires skills that belongs to very few experts. Then, an automated interpretation tool would bridge the gap between the established research outcome and clinical practice with a consequent great impact on health care. Qualitative spatial reasoning can play a crucial role in the identification of spatio-temporal patterns and salient features that characterize the heart electrical activity. We adopted the spatial aggregation (SA) conceptual framework and an interplay of numerical and qualitative information to extract features from epicardial maps, and to make them available for reasoning tasks. Our focus is on epicardial activation isochrone maps as they are a synthetic representation of spatio-temporal aspects of the propagation of the electrical excitation. We provide a computational SA-based methodology to extract, from 3D epicardial data gathered over time, (1) the excitation wavefront structure, and (2) the salient features that characterize wavefront propagation and visually correspond to specific geometric objects. The proposed methodology provides a robust and efficient way to identify salient pieces of information in activation time maps. The hierarchical structure of the abstracted geometric objects, crucial in capturing the prominent information, facilitates the definition of general rules necessary to infer the correlation between pathophysiological patterns and wavefront structure and propagation.

Structural safety features for superconducting magnets

International Nuclear Information System (INIS)

Lehner, J.; Reich, M.; Powell, J.; Bezler, P.; Gardner, D.; Yu, W.; Chang, T.Y.

1975-01-01

A survey has been carried out for various potential structural safety problems of superconducting fusion magnets. These areas include: (1) Stresses due to inhomogeneous temperature distributions in magnets where normal regions have been initiated. (2) Stress distributions and yield forces due to cracks and failed regions. (3) Superconducting magnet response due to seismic excitation. These analyses have been carried out using a variety of large capacity finite element computer codes that allow for the evaluation of stresses in elastic or elastic-plastic zones and around singularities in the magnet structure. Thus far, these analyses have been carried out on UWMAK-I type magnet systems

Passive Safety Features for Small Modular Reactors

International Nuclear Information System (INIS)

Ingersoll, Daniel T.

2010-01-01

The rapid growth in the size and complexity of commercial nuclear power plants in the 1970s spawned an interest in smaller, simpler designs that are inherently or intrinsically safe through the use of passive design features. Several designs were developed, but none were ever built, although some of their passive safety features were incorporated into large commercial plant designs that are being planned or built today. In recent years, several reactor vendors are actively redeveloping small modular reactor (SMR) designs with even greater use of passive features. Several designs incorporate the ultimate in passive safety they completely eliminate specific accident initiators from the design. Other design features help to reduce the likelihood of an accident or help to mitigate the accidents consequences, should one occur. While some passive safety features are common to most SMR designs, irrespective of the coolant technology, other features are specific to water, gas, or liquid-metal cooled SMR designs. The extensive use of passive safety features in SMRs promise to make these plants highly robust, protecting both the general public and the owner/investor. Once demonstrated, these plants should allow nuclear power to be used confidently for a broader range of customers and applications than will be possible with large plants alone.

Joint Feature Selection and Classification for Multilabel Learning.

Science.gov (United States)

Huang, Jun; Li, Guorong; Huang, Qingming; Wu, Xindong

2018-03-01

Multilabel learning deals with examples having multiple class labels simultaneously. It has been applied to a variety of applications, such as text categorization and image annotation. A large number of algorithms have been proposed for multilabel learning, most of which concentrate on multilabel classification problems and only a few of them are feature selection algorithms. Current multilabel classification models are mainly built on a single data representation composed of all the features which are shared by all the class labels. Since each class label might be decided by some specific features of its own, and the problems of classification and feature selection are often addressed independently, in this paper, we propose a novel method which can perform joint feature selection and classification for multilabel learning, named JFSC. Different from many existing methods, JFSC learns both shared features and label-specific features by considering pairwise label correlations, and builds the multilabel classifier on the learned low-dimensional data representations simultaneously. A comparative study with state-of-the-art approaches manifests a competitive performance of our proposed method both in classification and feature selection for multilabel learning.

Modification of electronic structure, magnetic structure, and topological phase of bismuthene by point defects

Science.gov (United States)

Kadioglu, Yelda; Kilic, Sevket Berkay; Demirci, Salih; Aktürk, O. Üzengi; Aktürk, Ethem; Ciraci, Salim

2017-12-01

This paper reveals how the electronic structure, magnetic structure, and topological phase of two-dimensional (2D), single-layer structures of bismuth are modified by point defects. We first showed that a free-standing, single-layer, hexagonal structure of bismuth, named h-bismuthene, exhibits nontrivial band topology. We then investigated interactions between single foreign adatoms and bismuthene structures, which comprise stability, bonding, electronic structure, and magnetic structures. Localized states in diverse locations of the band gap and resonant states in band continua of bismuthene are induced upon the adsorption of different adatoms, which modify electronic and magnetic properties. Specific adatoms result in reconstruction around the adsorption site. Single vacancies and divacancies can form readily in bismuthene structures and remain stable at high temperatures. Through rebondings, Stone-Whales-type defects are constructed by divacancies, which transform into a large hole at high temperature. Like adsorbed adatoms, vacancies induce also localized gap states, which can be eliminated through rebondings in divacancies. We also showed that not only the optical and magnetic properties, but also the topological features of pristine h-bismuthene can be modified by point defects. The modification of the topological features depends on the energies of localized states and also on the strength of coupling between point defects.

Magnetic susceptibility, specific heat and magnetic structure of CuNi2(PO4)2

International Nuclear Information System (INIS)

Escobal, Jaione; Pizarro, Jose L.; Mesa, Jose L.; Larranaga, Aitor; Fernandez, Jesus Rodriguez; Arriortua, Maria I.; Rojo, Teofilo

2006-01-01

The CuNi 2 (PO 4 ) 2 phosphate has been synthesized by the ceramic method at 800 deg. C in air. The crystal structure consists of a three-dimensional skeleton constructed from MO 4 (M II =Cu and Ni) planar squares and M 2 O 8 dimers with square pyramidal geometry, which are interconnected by (PO 4 ) 3- oxoanions with tetrahedral geometry. The magnetic behavior has been studied on powdered sample by using susceptibility, specific heat and neutron diffraction data. The bimetallic copper(II)-nickel(II) orthophosphate exhibits a three-dimensional magnetic ordering at, approximately, 29.8 K. However, its complex crystal structure hampers any parametrization of the J-exchange parameter. The specific heat measurements exhibit a three-dimensional magnetic ordering (λ-type) peak at 29.5 K. The magnetic structure of this phosphate shows ferromagnetic interactions inside the Ni 2 O 8 dimers, whereas the sublattice of Cu(II) ions presents antiferromagnetic couplings along the y-axis. The change of the sign in the magnetic unit-cell, due to the [1/2, 0, 1/2] propagation vector determines a purely antiferromagnetic structure. - Graphical abstract: Magnetic structure of CuNi2(PO4)2

Temperature and Magnetic Field Driven Modifications in the I-V Features of Gold-DNA-Gold Structure

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Nadia Mahmoudi Khatir

2014-10-01

Full Text Available The fabrication of Metal-DNA-Metal (MDM structure-based high sensitivity sensors from DNA micro-and nanoarray strands is a key issue in their development. The tunable semiconducting response of DNA in the presence of external electromagnetic and thermal fields is a gift for molecular electronics. The impact of temperatures (25–55 °C and magnetic fields (0–1200 mT on the current-voltage (I-V features of Au-DNA-Au (GDG structures with an optimum gap of 10 μm is reported. The I-V characteristics acquired in the presence and absence of magnetic fields demonstrated the semiconducting diode nature of DNA in GDG structures with high temperature sensitivity. The saturation current in the absence of magnetic field was found to increase sharply with the increase of temperature up to 45 °C and decrease rapidly thereafter. This increase was attributed to the temperature-assisted conversion of double bonds into single bond in DNA structures. Furthermore, the potential barrier height and Richardson constant for all the structures increased steadily with the increase of external magnetic field irrespective of temperature variations. Our observation on magnetic field and temperature sensitivity of I-V response in GDG sandwiches may contribute towards the development of DNA-based magnetic sensors.

Specific "scientific" data structures, and their processing

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Jerzy Karczmarczuk

2011-09-01

Full Text Available Programming physicists use, as all programmers, arrays, lists, tuples, records, etc., and this requires some change in their thought patterns while converting their formulae into some code, since the "data structures" operated upon, while elaborating some theory and its consequences, are rather: power series and Padé approximants, differential forms and other instances of differential algebras, functionals (for the variational calculus, trajectories (solutions of differential equations, Young diagrams and Feynman graphs, etc. Such data is often used in a [semi-]numerical setting, not necessarily "symbolic", appropriate for the computer algebra packages. Modules adapted to such data may be "just libraries", but often they become specific, embedded sub-languages, typically mapped into object-oriented frameworks, with overloaded mathematical operations. Here we present a functional approach to this philosophy. We show how the usage of Haskell datatypes and - fundamental for our tutorial - the application of lazy evaluation makes it possible to operate upon such data (in particular: the "infinite" sequences in a natural and comfortable manner.

Treatment recommendations for DSM-5-defined mixed features.

Science.gov (United States)

Rosenblat, Joshua D; McIntyre, Roger S

2017-04-01

The Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition (DSM-5) mixed features specifier provides a less restrictive definition of mixed mood states, compared to the Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition, Text Revision (DSM-IV-TR), including mood episodes that manifest with subthreshold symptoms of the opposite mood state. A limited number of studies have assessed the efficacy of treatments specifically for DSM-5-defined mixed features in mood disorders. As such, there is currently an inadequate amount of data to appropriately inform evidence-based treatment guidelines of DSM-5 defined mixed features. However, given the high prevalence and morbidity of mixed features, treatment recommendations based on the currently available evidence along with expert opinion may be of benefit. This article serves to provide these interim treatment recommendations while humbly acknowledging the limited amount of evidence currently available. Second-generation antipsychotics (SGAs) appear to have the greatest promise in the treatment of bipolar disorder (BD) with mixed features. Conventional mood stabilizing agents (ie, lithium and divalproex) may also be of benefit; however, they have been inadequately studied. In the treatment of major depressive disorder (MDD) with mixed features, the comparable efficacy of antidepressants versus other treatments, such as SGAs, remains unknown. As such, antidepressants remain first-line treatment of MDD with or without mixed features; however, there are significant safety concerns associated with antidepressant monotherapy when mixed features are present, which merits increased monitoring. Lurasidone is the only SGA monotherapy that has been shown to be efficacious specifically in the treatment of MDD with mixed features. Further research is needed to accurately determine the efficacy, safety, and tolerability of treatments specifically for mood episodes with mixed features to adequately inform

The specific features of gold ore provinces of the south of Siberia in a magnetic field at ground height and heights of flight of satellite Champ.

Science.gov (United States)

Litvinova, Tamara; Petrova, Alevtina

2010-05-01

The specific features of gold ore provinces of the south of Siberia in a magnetic field at ground height and heights of flight of satellite Champ. T.Litvinova -All-Russian Geological Research Institute (VSEGEI) A. Petrova - St. Petersburg, SPbF IZMIRAN, Russian Academy of Sciences, St. Petersburg For allocation of specific features known gold ore objects (Olimpiadninskoje, Suchoi Log, etc.) is executed the morphological analysis of the magnetic field received on materials of aeromagnetic data and satellite measurements at heights of 100 and 400 km. On the ground data on a map of magnetic anomalies of Russia of scale 1:2 500000 of 50 km on the extended structures crossing known gold ore deposits and promising ore units have been constructed geomagnetic and densitys sections up to depth. On geomagnetic and densitys sections to known large gold ore to deposits are dated deep synvertical the permeable zones described by a synlenticular -layered structure. Extended horizons of not magnetic formations are located on depths about 10, 12, 15-18, 30 and 40 km. On deep densitys sections reference sites ¬ the Suchoi Log, Olimpiadninskoje and Vodorazdelnoje ¬ is characterized by zones of inversion of density. Areas of the loosened breeds are dated to synvertical to deep zones of hydrothermal and fluid study of breeds inside which the loosened lenses in intervals of depths from 2 up to 5 km are formed, 8-13 km, 18-20 and 25-30 km of 35-40 km within the limits of the bottom bark. The analysis of a magnetic field has shown, that gold mineralization in researched region is dated for zones of long-living regional explosive infringements, to permeable terrigenous to thicknesses of depressions, to adjournment depression structures in units of crossing of tectonofluid zones of diagonal orientation. Terrigenous adjournment depression structures are shown on a geomagnetic section as the powerful deflections filled with low-magnetic thicknesses. These deflections are dated to

Contrasting effects of landscape features on genetic structure in different geographic regions in the ornate dragon lizard, Ctenophorus ornatus.

Science.gov (United States)

Levy, Esther; Tomkins, Joseph L; Lebas, Natasha R; Kennington, W Jason

2013-08-01

Habitat fragmentation can have profound effects on the distribution of genetic variation within and between populations. Previously, we showed that in the ornate dragon lizard, Ctenophorus ornatus, lizards residing on outcrops that are separated by cleared agricultural land are significantly more isolated and hold less genetic variation than lizards residing on neighbouring outcrops connected by undisturbed native vegetation. Here, we extend the fine-scale study to examine the pattern of genetic variation and population structure across the species' range. Using a landscape genetics approach, we test whether land clearing for agricultural purposes has affected the population structure of the ornate dragon lizard. We found significant genetic differentiation between outcrop populations (FST  = 0.12), as well as isolation by distance within each geographic region. In support of our previous study, land clearing was associated with higher genetic divergences between outcrops and lower genetic variation within outcrops, but only in the region that had been exposed to intense agriculture for the longest period of time. No other landscape features influenced population structure in any geographic region. These results show that the effects of landscape features can vary across species' ranges and suggest there may be a temporal lag in response to contemporary changes in land use. These findings therefore highlight the need for caution when assessing the impact of contemporary land use practices on genetic variation and population structure. © 2013 John Wiley & Sons Ltd.

Synthesis, structure and luminescence properties of lanthanide complex with a new tetrapodal ligand featuring salicylamide arms