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Sample records for included proteins collocated

  1. Collocations in Marine Engineering English

    Directory of Open Access Journals (Sweden)

    Mirjana Borucinsky

    2016-05-01

    Full Text Available Collocations are very frequent in the English language (Hill, 2000, and they are probably the most common and most representative of English multi-word expressions (Lewis, 2000. Furthermore, as a subset of formulaic sequences, collocations are considered to be a central aspect of communicative competence (Nation, 2001. Hence, the importance of teaching collocations in General English (GE as well as in English for Specific Purposes (ESP is undeniable. Understanding and determining the relevant collocations and their mastery are of “utmost importance to a ME instructor” (Cole et al., 2007, p. 137, and collocations are one of the most productive ways of enriching vocabulary and terminology in modern ME. Vişan & Georgescu (2011 have undertaken a relevant study on  collocations and “collocational competence” on board ships, including mostly nautical terminology. However, no substantial work on collocations in Marine Engineering English as a sub-register of ME has been carried out. Hence, this paper tries to determine the most important collocations in Marine Engineering English, based on a small corpus of collected e-mails. After determining the most relevant collocations, we suggest how to implement these in the language classroom and how to improve the collocational competence of marine engineering students.

  2. Teaching collocations

    DEFF Research Database (Denmark)

    Revier, Robert Lee; Henriksen, Birgit

    2006-01-01

    Very little pedadagoy has been made available to teachers interested in teaching collocations in foreign and/or second language classroom. This paper aims to contribute to and promote efforts in developing L2-based pedagogy for the teaching of phraseology. To this end, it presents pedagogical...

  3. A moving boundary problem and orthogonal collocation in solving a dynamic liquid surfactant membrane model including osmosis and breakage

    Directory of Open Access Journals (Sweden)

    E.C. Biscaia Junior

    2001-06-01

    Full Text Available A dynamic kinetic-diffusive model for the extraction of metallic ions from aqueous liquors using liquid surfactant membranes is proposed. The model incorporates undesirable intrinsic phenomena such as swelling and breakage of the emulsion globules that have to be controlled during process operation. These phenomena change the spatial location of the chemical reaction during the course of extraction, resulting in a transient moving boundary problem. The orthogonal collocation method was used to transform the partial differential equations into an ordinary differential equation set that was solved by an implicit numerical routine. The model was found to be numerically stable and reliable in predicting the behaviour of zinc extraction with acidic extractant for long residence times.

  4. Metagenome Analysis of Protein Domain Collocation within Cellulase Genes of Goat Rumen Microbes

    Directory of Open Access Journals (Sweden)

    SooYeon Lim

    2013-08-01

    Full Text Available In this study, protein domains with cellulase activity in goat rumen microbes were investigated using metagenomic and bioinformatic analyses. After the complete genome of goat rumen microbes was obtained using a shotgun sequencing method, 217,892,109 pair reads were filtered, including only those with 70% identity, 100-bp matches, and thresholds below E−10 using METAIDBA. These filtered contigs were assembled and annotated using blastN against the NCBI nucleotide database. As a result, a microbial community structure with 1431 species was analyzed, among which Prevotella ruminicola 23 bacteria and Butyrivibrio proteoclasticus B316 were the dominant groups. In parallel, 201 sequences related with cellulase activities (EC.3.2.1.4 were obtained through blast searches using the enzyme.dat file provided by the NCBI database. After translating the nucleotide sequence into a protein sequence using Interproscan, 28 protein domains with cellulase activity were identified using the HMMER package with threshold E values below 10−5. Cellulase activity protein domain profiling showed that the major protein domains such as lipase GDSL, cellulase, and Glyco hydro 10 were present in bacterial species with strong cellulase activities. Furthermore, correlation plots clearly displayed the strong positive correlation between some protein domain groups, which was indicative of microbial adaption in the goat rumen based on feeding habits. This is the first metagenomic analysis of cellulase activity protein domains using bioinformatics from the goat rumen.

  5. Collocated Interaction

    DEFF Research Database (Denmark)

    E. Fischer, Joel; Porcheron, Martin; Lucero, Andrés

    2016-01-01

    , and wearable technologies, spaces and spatial interaction, and those interested in the social aspects of interaction, such as conversation analysis and ethnomethodology. These communities have matured considerably, and produced significant exemplars of systems, methods, and studies concerned with collocated...... interactions. Yet, new challenges abound as people wear and carry more devices than ever, creating fragmented device ecologies at work, and changing the ways we socialise with each other. In this workshop we seek to start a dialogue to look back as well as forward, review best practices, discuss and design...

  6. Collocations and collocation types in ESP textbooks: Quantitative pedagogical analysis

    Directory of Open Access Journals (Sweden)

    Bogdanović Vesna Ž.

    2016-01-01

    Full Text Available The term collocation, even though it is rather common in the English language grammar, it is not a well known or commonly used term in the textbooks and scientific papers written in the Serbian language. Collocating is usually defined as a natural appearance of two (or more words, which are usually one next to another even though they can be separated in the text, while collocations are defined as words with natural semantic and/or syntactic relations being joined together in a sentence. Collocations are naturally used in all English written texts, including scientific texts and papers. Using two textbooks for English for Specific Purposes (ESP for intermediate students' courses, this paper presents the frequency of collocations and their typology. The paper tries to investigate the relationship between lexical and grammatical collocations written in the ESP texts and the reasons for their presence. There is an overview of the most used subtypes of lexical collocations as well. Furthermore, on applying the basic corpus analysis based on the quantitative analysis, the paper presents the number of open, restricted and bound collocations in ESP texts, trying to draw conclusions on their frequency and hence the modes for their learning. There is also a section related to the number and usage of scientific collocations, both common scientific and narrow-professional ones. The conclusion is that the number of present collocations in the selected two textbooks imposes a demand for further analysis of these lexical connections, as well as new modes for their teaching and presentations to the English learning students.

  7. Mobile Collocated Interactions

    DEFF Research Database (Denmark)

    Lucero, Andrés; Clawson, James; Lyons, Kent

    2015-01-01

    -smaller computers, ones that can be worn on our wrists or other parts of the body. The focus of this workshop is to bring together a community of researchers, designers and practitioners to explore the potential of extending mobile collocated interactions to the use of wearable devices.......Mobile devices such as smartphones and tablets were originally conceived and have traditionally been utilized for individual use. Research on mobile collocated interactions has been looking at situations in which collocated users engage in collaborative activities using their mobile devices, thus...

  8. Proxemic Mobile Collocated Interactions

    DEFF Research Database (Denmark)

    Porcheron, Martin; Lucero, Andrés; Quigley, Aaron

    2016-01-01

    would allow devices to not only react to presence and interaction, but also other indicators, such as the interpersonal distance people naturally use in everyday life. The aim of this one-day workshop is to bring together a community of researchers, designers and practitioners who are interested......Recent research on mobile collocated interactions has been looking at situations in which collocated users engage in collaborative activities using their mobile devices. However, existing practices fail to fully account for the culturally-dependent spatial relationships between people...... and their digital devices (i.e. the proxemic relationships). Building on the ideas of proxemic interactions, this workshop is motivated by the concept of ‘proxemic mobile collocated interactions’, to harness new or existing technologies to create engaging and interactionally relevant experiences. Such approaches...

  9. Semantic Analysis of Verbal Collocations with Lexical Functions

    CERN Document Server

    Gelbukh, Alexander

    2013-01-01

    This book is written for both linguists and computer scientists working in the field of artificial intelligence as well as to anyone interested in intelligent text processing. Lexical function is a concept that formalizes semantic and syntactic relations between lexical units. Collocational relation is a type of institutionalized lexical relations which holds between the base and its partner in a collocation. Knowledge of collocation is important for natural language processing because collocation comprises the restrictions on how words can be used together. The book shows how collocations can be annotated with lexical functions in a computer readable dictionary - allowing their precise semantic analysis in texts and their effective use in natural language applications including parsers, high quality machine translation, periphrasis system and computer-aided learning of lexica. The books shows how to extract collocations from corpora and annotate them with lexical functions automatically. To train algorithms,...

  10. Mobile Collocated Interactions With Wearables

    DEFF Research Database (Denmark)

    Lucero, Andrés; Wilde, Danielle; Robinson, Simon

    2015-01-01

    Research on mobile collocated interactions has been looking at situations in which collocated users engage in collaborative activities using their mobile devices, thus going from personal/individual toward shared/multiuser experiences and interactions. However, computers are getting smaller, more...... powerful, and closer to our bodies. Therefore, mobile collocated interactions research, which originally looked at smartphones and tablets, will inevitably move towards fully integrated wearable technologies. The focus of this workshop is to bring together a community of researchers, designers...

  11. Collocation Impact on Team Effectiveness

    Directory of Open Access Journals (Sweden)

    M Eccles

    2010-11-01

    Full Text Available The collocation of software development teams is common, specially in agile software development environments. However little is known about the impact of collocation on the team’s effectiveness. This paper explores the impact of collocating agile software development teams on a number of team effectiveness factors. The study focused on South African software development teams and gathered data through the use of questionnaires and interviews. The key finding was that collocation has a positive impact on a number of team effectiveness factors which can be categorised under team composition, team support, team management and structure and team communication. Some of the negative impact collocation had on team effectiveness relate to the fact that team members perceived that less emphasis was placed on roles, that morale of the group was influenced by individuals, and that collocation was invasive, reduced level of privacy and increased frequency of interruptions. Overall through it is proposed that companies should consider collocating their agile software development teams, as collocation might leverage overall team effectiveness.

  12. Rectangular spectral collocation

    KAUST Repository

    Driscoll, Tobin A.

    2015-02-06

    Boundary conditions in spectral collocation methods are typically imposed by removing some rows of the discretized differential operator and replacing them with others that enforce the required conditions at the boundary. A new approach based upon resampling differentiated polynomials into a lower-degree subspace makes differentiation matrices, and operators built from them, rectangular without any row deletions. Then, boundary and interface conditions can be adjoined to yield a square system. The resulting method is both flexible and robust, and avoids ambiguities that arise when applying the classical row deletion method outside of two-point scalar boundary-value problems. The new method is the basis for ordinary differential equation solutions in Chebfun software, and is demonstrated for a variety of boundary-value, eigenvalue and time-dependent problems.

  13. The Use of English Collocations in Reader's Digest

    OpenAIRE

    Sinaga, Yudita Putri Nurani; Sinaga, Lidiman Sahat Martua

    2014-01-01

    This descriptive qualitative study is aimed at identifying and describing the types of free collocations found in the articles of Reader's Digest. By taking a sample of ten articles from different months for each year since 2003 up to 2012, it was found all the four productive free collocations were in the data. Type 4 (Determiner + Adjective + Noun) was the dominant type (53.92 %). This was possible because the adjective in the pattern included the present participle and past participle of v...

  14. Measuring receptive collocational competence across proficiency ...

    African Journals Online (AJOL)

    Furthermore, EFL learners' collocational knowledge growth seems to be quantifiable, where both linguistic proficiency level and word frequency occupy crucial roles. While more collocational gains that EFL learners could potentially add as a result of change in proficiency are found at lower levels of proficiency, collocations ...

  15. Improving academic literacy by teaching collocations

    African Journals Online (AJOL)

    Kate H

    education students' use of collocations in writing are discussed. Keywords: teaching ... academic literacy in a South African context goes beyond language proficiency, the latter seems to be the only matter of ..... The results indicate that the explicit teaching of collocations results in significant gains in collocation growth, both ...

  16. Interlanguage Development and Collocational Clash

    Science.gov (United States)

    Shahheidaripour, Gholamabbass

    2000-01-01

    Background: Persian English learners committed mistakes and errors which were due to insufficient knowledge of different senses of the words and collocational structures they formed. Purpose: The study reported here was conducted for a thesis submitted in partial fulfillment of the requirements for The Master of Arts degree, School of Graduate…

  17. Collocation and finite difference-collocation methods for the solution of nonlinear Klein-Gordon equation

    Science.gov (United States)

    Lakestani, Mehrdad; Dehghan, Mehdi

    2010-08-01

    Two numerical techniques based on the finite difference and collocation methods are presented for the solution of nonlinear Klein-Gordon equation. The operational matrix of derivative for the cubic B-spline scaling functions is presented and is utilized to reduce the solution of nonlinear Klein-Gordon equation to the solution of algebraic equations. Illustrative examples are included to demonstrate the validity and applicability of the new techniques.

  18. Multi-Index Stochastic Collocation (MISC) for random elliptic PDEs

    KAUST Repository

    Haji Ali, Abdul Lateef

    2016-01-06

    In this work we introduce the Multi-Index Stochastic Collocation method (MISC) for computing statistics of the solution of a PDE with random data. MISC is a combination technique based on mixed differences of spatial approximations and quadratures over the space of random data. We propose an optimization procedure to select the most effective mixed differences to include in the MISC estimator: such optimization is a crucial step and allows us to build a method that, provided with sufficient solution regularity, is potentially more effective than other multi-level collocation methods already available in literature. We then provide a complexity analysis that assumes decay rates of product type for such mixed differences, showing that in the optimal case the convergence rate of MISC is only dictated by the convergence of the deterministic solver applied to a one dimensional problem. We show the effectiveness of MISC with some computational tests, comparing it with other related methods available in the literature, such as the Multi-Index and Multilevel Monte Carlo, Multilevel Stochastic Collocation, Quasi Optimal Stochastic Collocation and Sparse Composite Collocation methods.

  19. Multi-Index Stochastic Collocation for random PDEs

    KAUST Repository

    Haji Ali, Abdul Lateef

    2016-03-28

    In this work we introduce the Multi-Index Stochastic Collocation method (MISC) for computing statistics of the solution of a PDE with random data. MISC is a combination technique based on mixed differences of spatial approximations and quadratures over the space of random data. We propose an optimization procedure to select the most effective mixed differences to include in the MISC estimator: such optimization is a crucial step and allows us to build a method that, provided with sufficient solution regularity, is potentially more effective than other multi-level collocation methods already available in literature. We then provide a complexity analysis that assumes decay rates of product type for such mixed differences, showing that in the optimal case the convergence rate of MISC is only dictated by the convergence of the deterministic solver applied to a one dimensional problem. We show the effectiveness of MISC with some computational tests, comparing it with other related methods available in the literature, such as the Multi-Index and Multilevel Monte Carlo, Multilevel Stochastic Collocation, Quasi Optimal Stochastic Collocation and Sparse Composite Collocation methods.

  20. Chloroplast Protein Turnover: The Influence of Extraplastidic Processes, Including Autophagy

    Directory of Open Access Journals (Sweden)

    Masanori Izumi

    2018-03-01

    Full Text Available Most assimilated nutrients in the leaves of land plants are stored in chloroplasts as photosynthetic proteins, where they mediate CO2 assimilation during growth. During senescence or under suboptimal conditions, chloroplast proteins are degraded, and the amino acids released during this process are used to produce young tissues, seeds, or respiratory energy. Protein degradation machineries contribute to the quality control of chloroplasts by removing damaged proteins caused by excess energy from sunlight. Whereas previous studies revealed that chloroplasts contain several types of intraplastidic proteases that likely derived from an endosymbiosed prokaryotic ancestor of chloroplasts, recent reports have demonstrated that multiple extraplastidic pathways also contribute to chloroplast protein turnover in response to specific cues. One such pathway is autophagy, an evolutionarily conserved process that leads to the vacuolar or lysosomal degradation of cytoplasmic components in eukaryotic cells. Here, we describe and contrast the extraplastidic pathways that degrade chloroplasts. This review shows that diverse pathways participate in chloroplast turnover during sugar starvation, senescence, and oxidative stress. Elucidating the mechanisms that regulate these pathways will help decipher the relationship among the diverse pathways mediating chloroplast protein turnover.

  1. Measuring receptive collocational competence across proficiency levels

    Directory of Open Access Journals (Sweden)

    Déogratias Nizonkiza

    2015-12-01

    Full Text Available The present study investigates, (i English as Foreign Language (EFL learners’ receptive collocational knowledge growth in relation to their linguistic proficiency level; (ii how much receptive collocational knowledge is acquired as proficiency develops; and (iii the extent to which receptive knowledge of collocations of EFL learners varies across word frequency bands. A proficiency measure and a collocation test were administered to English majors at the University of Burundi. Results of the study suggest that receptive collocational competence develops alongside EFL learners’ linguistic proficiency; which lends empirical support to Gyllstad (2007, 2009 and Author (2011 among others, who reported similar findings. Furthermore, EFL learners’ collocations growth seems to be quantifiable wherein both linguistic proficiency level and word frequency occupy a crucial role. While more gains in terms of collocations that EFL learners could potentially add as a result of change in proficiency are found at lower levels of proficiency; collocations of words from more frequent word bands seem to be mastered first, and more gains are found at more frequent word bands. These results confirm earlier findings on the non-linearity nature of vocabulary growth (cf. Meara 1996 and the fundamental role played by frequency in word knowledge for vocabulary in general (Nation 1983, 1990, Nation and Beglar 2007, which are extended here to collocations knowledge.

  2. Supporting Collocation Learning with a Digital Library

    Science.gov (United States)

    Wu, Shaoqun; Franken, Margaret; Witten, Ian H.

    2010-01-01

    Extensive knowledge of collocations is a key factor that distinguishes learners from fluent native speakers. Such knowledge is difficult to acquire simply because there is so much of it. This paper describes a system that exploits the facilities offered by digital libraries to provide a rich collocation-learning environment. The design is based on…

  3. "Minimum input, maximum output, indeed!" Teaching Collocations ...

    African Journals Online (AJOL)

    Fifty-nine EFL college students participated in the study, and they received two 75-minute instructions between pre- and post-tests: one on the definition of colloca-tion and its importance, and the other on the skill of looking up collocational information in the Naver Dictionary — an English–Korean online dictionary. During ...

  4. Improving academic literacy by teaching collocations | Nizonkiza ...

    African Journals Online (AJOL)

    Stellenbosch Papers in Linguistics ... Abstract. This study explores the effect of teaching collocations on building academic vocabulary and hence improving academic writing abilities. ... They were presented with a completion task and an essay-writing task before and after being exposed to a collocation-based syllabus.

  5. Meshfree Local Radial Basis Function Collocation Method with Image Nodes

    Energy Technology Data Exchange (ETDEWEB)

    Baek, Seung Ki; Kim, Minjae [Pukyong National University, Busan (Korea, Republic of)

    2017-07-15

    We numerically solve two-dimensional heat diffusion problems by using a simple variant of the meshfree local radial-basis function (RBF) collocation method. The main idea is to include an additional set of sample nodes outside the problem domain, similarly to the method of images in electrostatics, to perform collocation on the domain boundaries. We can thereby take into account the temperature profile as well as its gradients specified by boundary conditions at the same time, which holds true even for a node where two or more boundaries meet with different boundary conditions. We argue that the image method is computationally efficient when combined with the local RBF collocation method, whereas the addition of image nodes becomes very costly in case of the global collocation. We apply our modified method to a benchmark test of a boundary value problem, and find that this simple modification reduces the maximum error from the analytic solution significantly. The reduction is small for an initial value problem with simpler boundary conditions. We observe increased numerical instability, which has to be compensated for by a sufficient number of sample nodes and/or more careful parameter choices for time integration.

  6. Measuring receptive collocational competence across proficiency ...

    African Journals Online (AJOL)

    Kate H

    146 doi: 10.5774/44-0-186. Measuring receptive collocational competence across proficiency levels. Déogratias Nizonkiza ..... structure and written expression, and vocabulary and reading comprehension. For accessibility and practical reasons ...

  7. The Effect of Input Enhancement of Collocations in Reading on Collocation Learning and Retention of EFL Learners

    Science.gov (United States)

    Goudarzi, Zahra; Moini, M. Raouf

    2012-01-01

    Collocation is one of the most problematic areas in second language learning and it seems that if one wants to improve his or her communication in another language should improve his or her collocation competence. This study attempts to determine the effect of applying three different kinds of collocation on collocation learning and retention of…

  8. Geostationary Collocation: Case Studies for Optimal Maneuvers

    Science.gov (United States)

    2016-03-01

    travel from edge to edge, and finish with two days in the last case. It is worth noting that we could not fit the whole longitude libration in the...DATES COVERED Master’s thesis 4. TITLE AND SUBTITLE GEOSTATIONARY COLLOCATION: CASE STUDIES FOR OPTIMAL MANEUVERS 5. FUNDING NUMBERS 6...distribution is unlimited 12b. DISTRIBUTION CODE 13. ABSTRACT (maximum 200 words) Satellite collocation is not a new topic in the space community

  9. Numerical simulation of GEW equation using RBF collocation method

    Directory of Open Access Journals (Sweden)

    Hamid Panahipour

    2012-08-01

    Full Text Available The generalized equal width (GEW equation is solved numerically by a meshless method based on a global collocation with standard types of radial basis functions (RBFs. Test problems including propagation of single solitons, interaction of two and three solitons, development of the Maxwellian initial condition pulses, wave undulation and wave generation are used to indicate the efficiency and accuracy of the method. Comparisons are made between the results of the proposed method and some other published numerical methods.

  10. Frequency of Input and L2 Collocational Processing: A Comparison of Congruent and Incongruent Collocations

    Science.gov (United States)

    Wolter, Brent; Gyllstad, Henrik

    2013-01-01

    This study investigated the influence of frequency effects on the processing of congruent (i.e., having an equivalent first language [L1] construction) collocations and incongruent (i.e., not having an equivalent L1 construction) collocations in a second language (L2). An acceptability judgment task was administered to native and advanced…

  11. guessing verb-adverb collocations: arab efl learners' use of ...

    African Journals Online (AJOL)

    user

    Alsakran (2011) involved 38 advanced Arab learners in an appropriate- ness judgment test and reported subject' incompetence in using collocations in all tests. They, however, performed better in the comprehension tasks with all types of collocations under scrutiny, verb–noun collocations being foremost. Satriawan (2009) ...

  12. The relationship between productive knowledge of collocations and ...

    African Journals Online (AJOL)

    This research explores tertiary level L2 students' mastery of the collocations pertaining to the Academic Word List (AWL) and the extent to which their knowledge of collocations grows alongside their academic literacy. A collocation test modelled on Laufer and Nation (1999), with target words selected from Coxhead's (2000) ...

  13. The Presentation and Treatment of Collocations as Secondary ...

    African Journals Online (AJOL)

    Although the discussion primarily focuses on printed dictionaries proposals are also made for the presentation of collocations in online dictionaries. Keywords: Article structure, collocation, complex collocation, cotext, example sentences, integrated microstructure, non-grouped ordering, search zone, semi-integrated ...

  14. Evaluating a new test of whole English collocations

    DEFF Research Database (Denmark)

    Revier, Robert Lee

    2009-01-01

    in their own right and, as such, feature formal, semantic, and usage properties similar to those borne by single words. Third, the semantic properties of the constituent words that combine to form collocations are likely to play a role in EFL learners' ability to 'produce' English collocations. Forth, testing...... of L2 collocation knowledge needs to focus on the recognition and production of whole collocations. It is this set of assumptions that the new collocation test presented in this chapter is desined to probe. More specifically, the test is designed to assess L2 learners' productive knowledge of whole...

  15. Schwarz and multilevel methods for quadratic spline collocation

    Energy Technology Data Exchange (ETDEWEB)

    Christara, C.C. [Univ. of Toronto, Ontario (Canada); Smith, B. [Univ. of California, Los Angeles, CA (United States)

    1994-12-31

    Smooth spline collocation methods offer an alternative to Galerkin finite element methods, as well as to Hermite spline collocation methods, for the solution of linear elliptic Partial Differential Equations (PDEs). Recently, optimal order of convergence spline collocation methods have been developed for certain degree splines. Convergence proofs for smooth spline collocation methods are generally more difficult than for Galerkin finite elements or Hermite spline collocation, and they require stronger assumptions and more restrictions. However, numerical tests indicate that spline collocation methods are applicable to a wider class of problems, than the analysis requires, and are very competitive to finite element methods, with respect to efficiency. The authors will discuss Schwarz and multilevel methods for the solution of elliptic PDEs using quadratic spline collocation, and compare these with domain decomposition methods using substructuring. Numerical tests on a variety of parallel machines will also be presented. In addition, preliminary convergence analysis using Schwarz and/or maximum principle techniques will be presented.

  16. Fully Consistent SIMPLE-Like Algorithms on Collocated Grids

    DEFF Research Database (Denmark)

    Kolmogorov, Dmitry; Shen, Wen Zhong; Sørensen, Niels N.

    2015-01-01

    To increase the convergence rate of SIMPLE-like algorithms on collocated grids, a compatibility condition between mass flux interpolation methods and SIMPLE-like algorithms is presented. Results of unsteady flow computations show that the SIMPLEC algorithm, when obeying the compatibility condition......, may obtain up to 35% higher convergence rate as compared to the standard SIMPLEC algorithm. Two new interpolation methods, fully compatible with the SIMPLEC algorithm, are presented and compared with some existing interpolation methods, including the standard methods of Choi [9] and Shen et al. [8...

  17. Relation work in collocated and distributed collaboration

    DEFF Research Database (Denmark)

    Christensen, Lars Rune; Jensen, Rasmus Eskild; Bjørn, Pernille

    2014-01-01

    Creating social ties are important for collaborative work; however, in geographically distributed organizations e.g. global software development, making social ties requires extra work: Relation work. We find that characteristics of relation work as based upon shared history and experiences......, emergent in personal and often humorous situations. Relation work is intertwined with other activities such as articulation work and it is rhythmic by following the work patterns of the participants. By comparing how relation work is conducted in collocated and geographically distributed settings we...... in this paper identify basic differences in relation work. Whereas collocated relation work is spontaneous, place-centric, and yet mobile, relation work in a distributed setting is semi-spontaneous, technology-mediated, and requires extra efforts....

  18. The Structure of an Afrikaans Collocation and Phrase Dictionary

    Directory of Open Access Journals (Sweden)

    Anna Nel Otto

    2012-09-01

    Full Text Available

    In this article an Afrikaans collocation and phrase dictionary for mother-tongue speakers (primary target group as well as advanced learners (secondary target group is discussed. The position which such a dictionary occupies among other dictionary types is pointed out. A motivation is also given for the inclusion of idioms and other fixed phrases in the proposed dictionary. The three key approaches with regard to the interpretation of the term collocation are examined, i.e. the text-oriented approach of Halliday and Hasan (1976, the statistically-oriented approach of Sinclair (Collins Cobuild and the significance-oriented approach of Hausmann (1984. The arguments in this article favour Benson et al.’s (1986 implementation of the significance-oriented approach. Statistical evidence could be used to examine the usage frequency of collocations and phrases. The advantages and/or disadvantages of these approaches are considered. Three types of words and their treatment in the dictionary are discussed: those which have a very wide range of combination, those which have selectional restrictions imposed by general semantic features, and those of which the range of combination is restricted by certain other words. It is argued that only the last two types should be included in this dictionary. As one of the target groups is unsophisticated learners with a limited grammatical background, the ideal would be to enter lexical collocations both at their bases and at the collocators. To save space however, more information such as examples could then be provided at the bases only. Grammatical collocations should be entered at the bases, i.e. nouns, verbs and adjectives. The division of the dictionary articles into two components to meet the needs of both intended target groups, is discussed.

     

     

    Die struktuur van 'n Afrikaanse kollokasie- en frasewoordeboek

    In hierdie artikel word 'n Afrikaanse kollokasie- en frasewoordeboek vir

  19. On Collocations and Their Interaction with Parsing and Translation

    Directory of Open Access Journals (Sweden)

    Violeta Seretan

    2013-10-01

    Full Text Available We address the problem of automatically processing collocations—a subclass of multi-word expressions characterized by a high degree of morphosyntactic flexibility—in the context of two major applications, namely, syntactic parsing and machine translation. We show that parsing and collocation identification are processes that are interrelated and that benefit from each other, inasmuch as syntactic information is crucial for acquiring collocations from corpora and, vice versa, collocational information can be used to improve parsing performance. Similarly, we focus on the interrelation between collocations and machine translation, highlighting the use of translation information for multilingual collocation identification, as well as the use of collocational knowledge for improving translation. We give a panorama of the existing relevant work, and we parallel the literature surveys with our own experiments involving a symbolic parser and a rule-based translation system. The results show a significant improvement over approaches in which the corresponding tasks are decoupled.

  20. The Study of the Students' Collocation Performance in Argumentative Writing

    OpenAIRE

    Oktavera, Haryati

    2014-01-01

    Collocation is used by most of the native speaker in both writing and speaking authentic English. This paper focused on knowing the students' collocation knowledge by examining their lexical and grammatical collocation performance in their argumentative writing. This research, therefore, conducted by analyzing deeply 10 argumentative writings of the third semester students of PBI STAIN JuraiSiwo Metro in academic year 2013/2014. The result of this research showed that there were 41 % errors f...

  1. Characterizing the Escherichia coli O157:H7 proteome including protein associations with higher order assemblies.

    Directory of Open Access Journals (Sweden)

    Rembert Pieper

    Full Text Available The recent outbreak of severe infections with Shiga toxin (Stx producing Escherichia coli (STEC serotype O104:H4 highlights the need to understand horizontal gene transfer among E. coli strains, identify novel virulence factors and elucidate their pathogenesis. Quantitative shotgun proteomics can contribute to such objectives, allowing insights into the part of the genome translated into proteins and the connectivity of biochemical pathways and higher order assemblies of proteins at the subcellular level.We examined protein profiles in cell lysate fractions of STEC strain 86-24 (serotype O157:H7, following growth in cell culture or bacterial isolation from intestines of infected piglets, in the context of functionally and structurally characterized biochemical pathways of E. coli. Protein solubilization in the presence of Triton X-100, EDTA and high salt was followed by size exclusion chromatography into the approximate M(r ranges greater than 280 kDa, 280-80 kDa and 80-10 kDa. Peptide mixtures resulting from these and the insoluble fraction were analyzed by quantitative 2D-LC-nESI-MS/MS. Of the 2521 proteins identified at a 1% false discovery rate, representing 47% of all predicted E. coli O157:H7 gene products, the majority of integral membrane proteins were enriched in the high M(r fraction. Hundreds of proteins were enriched in a M(r range higher than that predicted for a monomer supporting their participation in protein complexes. The insoluble STEC fraction revealed enrichment of aggregation-prone proteins, including many that are part of large structure/function entities such as the ribosome, cytoskeleton and O-antigen biosynthesis cluster.Nearly all E. coli O157:H7 proteins encoded by prophage regions were expressed at low abundance levels or not detected. Comparative quantitative analyses of proteins from distinct cell lysate fractions allowed us to associate uncharacterized proteins with membrane attachment, potential participation in

  2. Hinderin, a five-domains protein including coiled-coil motifs that binds to SMC3

    Directory of Open Access Journals (Sweden)

    Ghiselli Giancarlo

    2005-01-01

    Full Text Available Abstract Background The structural maintenance of chromosome proteins SMC1 and SMC3 play an important role in the maintenance of chromosomal integrity by preventing the premature separation of the sister chromatids at the onset of anaphase. The two proteins are constitutive components of the multimeric complex cohesin and form dimers by interacting at their central globular regions. Results In order to identify proteins that by binding to SMC3 may interfere with the protein dimerization process, a human cDNA library was screened by the yeast two-hybrid system by using the hinge region of SMC3 as bait. This has lead to the identification of Hinderin, a novel five domains protein including two coiled-coil motifs and sharing a strikingly structural similarity to the SMC family of proteins. Hinderin is ubiquitously expressed in human tissues. Orthologue forms of the protein are present in other vertebrates but not in lower organisms. A mapping of the interaction sites revealed that the N- and C-terminal globular domains mediate the binding of Hinderin to SMC3. Hinderin/SMC3 complexes could be recovered by immunoprecipitation from cell lysates using an anti-SMC3 antibody, thus demonstrating that the two proteins interact in vivo. On the contrary, Hinderin did not interact with SMC1. In vivo the rate of SMC1/SMC3 interaction was decreased by the ectopic expression of Hinderin. Conclusions Hinderin is a novel binding partner of SMC3. Based on its ability to modulate SMC1/SMC3 interaction we postulate that Hinderin affects the availability of SMC3 to engage in the formation of multimeric protein complexes.

  3. Producing high-accuracy lattice models from protein atomic coordinates including side chains.

    Science.gov (United States)

    Mann, Martin; Saunders, Rhodri; Smith, Cameron; Backofen, Rolf; Deane, Charlotte M

    2012-01-01

    Lattice models are a common abstraction used in the study of protein structure, folding, and refinement. They are advantageous because the discretisation of space can make extensive protein evaluations computationally feasible. Various approaches to the protein chain lattice fitting problem have been suggested but only a single backbone-only tool is available currently. We introduce LatFit, a new tool to produce high-accuracy lattice protein models. It generates both backbone-only and backbone-side-chain models in any user defined lattice. LatFit implements a new distance RMSD-optimisation fitting procedure in addition to the known coordinate RMSD method. We tested LatFit's accuracy and speed using a large nonredundant set of high resolution proteins (SCOP database) on three commonly used lattices: 3D cubic, face-centred cubic, and knight's walk. Fitting speed compared favourably to other methods and both backbone-only and backbone-side-chain models show low deviation from the original data (~1.5 Å RMSD in the FCC lattice). To our knowledge this represents the first comprehensive study of lattice quality for on-lattice protein models including side chains while LatFit is the only available tool for such models.

  4. Nephrin regulates lamellipodia formation by assembling a protein complex that includes Ship2, filamin and lamellipodin.

    Directory of Open Access Journals (Sweden)

    Madhusudan Venkatareddy

    Full Text Available Actin dynamics has emerged at the forefront of podocyte biology. Slit diaphragm junctional adhesion protein Nephrin is necessary for development of the podocyte morphology and transduces phosphorylation-dependent signals that regulate cytoskeletal dynamics. The present study extends our understanding of Nephrin function by showing in cultured podocytes that Nephrin activation induced actin dynamics is necessary for lamellipodia formation. Upon activation Nephrin recruits and regulates a protein complex that includes Ship2 (SH2 domain containing 5' inositol phosphatase, Filamin and Lamellipodin, proteins important in regulation of actin and focal adhesion dynamics, as well as lamellipodia formation. Using the previously described CD16-Nephrin clustering system, Nephrin ligation or activation resulted in phosphorylation of the actin crosslinking protein Filamin in a p21 activated kinase dependent manner. Nephrin activation in cell culture results in formation of lamellipodia, a process that requires specialized actin dynamics at the leading edge of the cell along with focal adhesion turnover. In the CD16-Nephrin clustering model, Nephrin ligation resulted in abnormal morphology of actin tails in human podocytes when Ship2, Filamin or Lamellipodin were individually knocked down. We also observed decreased lamellipodia formation and cell migration in these knock down cells. These data provide evidence that Nephrin not only initiates actin polymerization but also assembles a protein complex that is necessary to regulate the architecture of the generated actin filament network and focal adhesion dynamics.

  5. First-year University Students' Productive Knowledge of Collocations ...

    African Journals Online (AJOL)

    The present study examines productive knowledge of collocations of tertiary-level second language (L2) learners of English in an attempt to make estimates of the size of their knowledge. Participants involved first-year students at North-West University who sat a collocation test modelled on that developed by Laufer and ...

  6. Collocative meaning in the Igbo language | Okeke | Southern African ...

    African Journals Online (AJOL)

    The corpora comprise 20 randomly selected documents from different scholars published from 2013 to 2016 in the University of Nigeria, Nsukka; and a total of 405 tokens of collocates were used. Following Berkley's and Okoro's definitions of collocation, this paper engages on two major objectives of first, analysing the ...

  7. A Line-Tau Collocation Method for Partial Differential Equations ...

    African Journals Online (AJOL)

    The method of lines is used to convert the partial differential equation (PDE) to a sequence of ordinary differential equations (ODEs) which is then solved by the tau collocation method to obtain an approximate continuous solution in the spatial variable x at a fixed t-level. The choice of the tau collocation method over the tau ...

  8. A Study on the Phenomenon of Collocations: Methodology of Teaching English and German Collocations to Russian Students

    Science.gov (United States)

    Varlamova, Elena V.; Naciscione, Anita; Tulusina, Elena A.

    2016-01-01

    Relevance of the issue stated in the article is determined by the fact that there is a lack of research devoted to the methods of teaching English and German collocations. The aim of our work is to determine methods of teaching English and German collocations to Russian university students studying foreign languages through experimental testing.…

  9. A Stochastic Collocation Method for Elliptic Partial Differential Equations with Random Input Data

    KAUST Repository

    Babuška, Ivo

    2010-01-01

    This work proposes and analyzes a stochastic collocation method for solving elliptic partial differential equations with random coefficients and forcing terms. These input data are assumed to depend on a finite number of random variables. The method consists of a Galerkin approximation in space and a collocation in the zeros of suitable tensor product orthogonal polynomials (Gauss points) in the probability space, and naturally leads to the solution of uncoupled deterministic problems as in the Monte Carlo approach. It treats easily a wide range of situations, such as input data that depend nonlinearly on the random variables, diffusivity coefficients with unbounded second moments, and random variables that are correlated or even unbounded. We provide a rigorous convergence analysis and demonstrate exponential convergence of the “probability error” with respect to the number of Gauss points in each direction of the probability space, under some regularity assumptions on the random input data. Numerical examples show the effectiveness of the method. Finally, we include a section with developments posterior to the original publication of this work. There we review sparse grid stochastic collocation methods, which are effective collocation strategies for problems that depend on a moderately large number of random variables.

  10. Productive knowledge of collocations may predict academic literacy

    Directory of Open Access Journals (Sweden)

    Van Dyk, Tobie

    2016-12-01

    Full Text Available The present study examines the relationship between productive knowledge of collocations and academic literacy among first year students at North-West University. Participants were administered a collocation test, the items of which were selected from Nation’s (2006 word frequency bands, i.e. the 2000-word, 3000-word, 5000-word bands; and the Academic Word List (Coxhead, 2000. The scores from the collocation test were compared to those from the Test of Academic Literacy Levels (version administered in 2012. The results of this study indicate that, overall, knowledge of collocations is significantly correlated with academic literacy, which is also observed at each of the frequency bands from which the items were selected. These results support Nizonkiza’s (2014 findings that a significant correlation between mastery of collocations of words from the Academic Word List and academic literacy exists; which is extended here to words from other frequency bands. They also confirm previous findings that productive knowledge of collocations increases alongside overall proficiency (cf. Gitsaki, 1999; Bonk, 2001; Eyckmans et al., 2004; Boers et al., 2006; Nizonkiza, 2011; among others. This study therefore concludes that growth in productive knowledge of collocations may entail growth in academic literacy; suggesting that productive use of collocations is linked to academic literacy to a considerable extent. In light of these findings, teaching strategies aimed to assist first year students meet academic demands posed by higher education and avenues to explore for further research are discussed. Especially, we suggest adopting a productive oriented approach to teaching collocations, which we believe may prove useful.

  11. Bessel collocation approach for approximate solutions of Hantavirus infection model

    Directory of Open Access Journals (Sweden)

    Suayip Yuzbasi

    2017-11-01

    Full Text Available In this study, a collocation method is introduced to find the approximate solutions of Hantavirus infection model which is a system of nonlinear ordinary differential equations. The method is based on the Bessel functions of the first kind, matrix operations and collocation points. This method converts Hantavirus infection model into a matrix equation in terms of the Bessel functions of first kind, matrix operations and collocation points. The matrix equation corresponds to a system of nonlinear equations with the unknown Bessel coefficients. The reliability and efficiency of the suggested scheme are demonstrated by numerical applications and all numerical calculations have been done by using a program written in Maple.

  12. Modified Chebyshev Collocation Method for Solving Differential Equations

    Directory of Open Access Journals (Sweden)

    M Ziaul Arif

    2015-05-01

    Full Text Available This paper presents derivation of alternative numerical scheme for solving differential equations, which is modified Chebyshev (Vieta-Lucas Polynomial collocation differentiation matrices. The Scheme of modified Chebyshev (Vieta-Lucas Polynomial collocation method is applied to both Ordinary Differential Equations (ODEs and Partial Differential Equations (PDEs cases. Finally, the performance of the proposed method is compared with finite difference method and the exact solution of the example. It is shown that modified Chebyshev collocation method more effective and accurate than FDM for some example given.

  13. Developing and Evaluating a Web-Based Collocation Retrieval Tool for EFL Students and Teachers

    Science.gov (United States)

    Chen, Hao-Jan Howard

    2011-01-01

    The development of adequate collocational knowledge is important for foreign language learners; nonetheless, learners often have difficulties in producing proper collocations in the target language. Among the various ways of learning collocations, the DDL (data-driven learning) approach encourages independent learning of collocations and allows…

  14. Corpus-Aided Business English Collocation Pedagogy: An Empirical Study in Chinese EFL Learners

    Science.gov (United States)

    Chen, Lidan

    2017-01-01

    This study reports an empirical study of an explicit instruction of corpus-aided Business English collocations and verifies its effectiveness in improving learners' collocation awareness and learner autonomy, as a result of which is significant improvement of learners' collocation competence. An eight-week instruction in keywords' collocations,…

  15. Fibonacci collocation method with a residual error Function to solve linear Volterra integro differential equations

    Directory of Open Access Journals (Sweden)

    Salih Yalcinbas

    2016-01-01

    Full Text Available In this paper, a new collocation method based on the Fibonacci polynomials is introduced to solve the high-order linear Volterra integro-differential equations under the conditions. Numerical examples are included to demonstrate the applicability and validity of the proposed method and comparisons are made with the existing results. In addition, an error estimation based on the residual functions is presented for this method. The approximate solutions are improved by using this error estimation.

  16. An approach to including protein quality when assessing the net contribution of livestock to human food supply.

    Science.gov (United States)

    Ertl, P; Knaus, W; Zollitsch, W

    2016-11-01

    The production of protein from animal sources is often criticized because of the low efficiency of converting plant protein from feeds into protein in the animal products. However, this critique does not consider the fact that large portions of the plant-based proteins fed to animals may be human-inedible and that the quality of animal proteins is usually superior as compared with plant proteins. The aim of the present study was therefore to assess changes in protein quality in the course of the transformation of potentially human-edible plant proteins into animal products via livestock production; data from 30 Austrian dairy farms were used as a case study. A second aim was to develop an approach for combining these changes with quantitative aspects (e.g. with the human-edible feed conversion efficiency (heFCE), defined as kilogram protein in the animal product divided by kilogram potentially human-edible protein in the feeds). Protein quality of potentially human-edible inputs and outputs was assessed using the protein digestibility-corrected amino acid score and the digestible indispensable amino acid score, two methods proposed by the Food and Agriculture Organization of the United Nations to describe the nutritional value of proteins for humans. Depending on the method used, protein scores were between 1.40 and 1.87 times higher for the animal products than for the potentially human-edible plant protein input on a barn-gate level (=protein quality ratio (PQR)). Combining the PQR of 1.87 with the heFCE for the same farms resulted in heFCE×PQR of 2.15. Thus, considering both quantity and quality, the value of the proteins in the animal products for human consumption (in this case in milk and beef) is 2.15 times higher than that of proteins in the potentially human-edible plant protein inputs. The results of this study emphasize the necessity of including protein quality changes resulting from the transformation of plant proteins to animal proteins when

  17. Collocation mismatch uncertainties in satellite aerosol retrieval validation

    Science.gov (United States)

    Virtanen, Timo H.; Kolmonen, Pekka; Sogacheva, Larisa; Rodríguez, Edith; Saponaro, Giulia; de Leeuw, Gerrit

    2018-02-01

    Satellite-based aerosol products are routinely validated against ground-based reference data, usually obtained from sun photometer networks such as AERONET (AEROsol RObotic NETwork). In a typical validation exercise a spatial sample of the instantaneous satellite data is compared against a temporal sample of the point-like ground-based data. The observations do not correspond to exactly the same column of the atmosphere at the same time, and the representativeness of the reference data depends on the spatiotemporal variability of the aerosol properties in the samples. The associated uncertainty is known as the collocation mismatch uncertainty (CMU). The validation results depend on the sampling parameters. While small samples involve less variability, they are more sensitive to the inevitable noise in the measurement data. In this paper we study systematically the effect of the sampling parameters in the validation of AATSR (Advanced Along-Track Scanning Radiometer) aerosol optical depth (AOD) product against AERONET data and the associated collocation mismatch uncertainty. To this end, we study the spatial AOD variability in the satellite data, compare it against the corresponding values obtained from densely located AERONET sites, and assess the possible reasons for observed differences. We find that the spatial AOD variability in the satellite data is approximately 2 times larger than in the ground-based data, and the spatial variability correlates only weakly with that of AERONET for short distances. We interpreted that only half of the variability in the satellite data is due to the natural variability in the AOD, and the rest is noise due to retrieval errors. However, for larger distances (˜ 0.5°) the correlation is improved as the noise is averaged out, and the day-to-day changes in regional AOD variability are well captured. Furthermore, we assess the usefulness of the spatial variability of the satellite AOD data as an estimate of CMU by comparing the

  18. Collocation and Pattern Recognition Effects on System Failure Remediation

    Science.gov (United States)

    Trujillo, Anna C.; Press, Hayes N.

    2007-01-01

    Previous research found that operators prefer to have status, alerts, and controls located on the same screen. Unfortunately, that research was done with displays that were not designed specifically for collocation. In this experiment, twelve subjects evaluated two displays specifically designed for collocating system information against a baseline that consisted of dial status displays, a separate alert area, and a controls panel. These displays differed in the amount of collocation, pattern matching, and parameter movement compared to display size. During the data runs, subjects kept a randomly moving target centered on a display using a left-handed joystick and they scanned system displays to find a problem in order to correct it using the provided checklist. Results indicate that large parameter movement aided detection and then pattern recognition is needed for diagnosis but the collocated displays centralized all the information subjects needed, which reduced workload. Therefore, the collocated display with large parameter movement may be an acceptable display after familiarization because of the possible pattern recognition developed with training and its use.

  19. Transport survey calculations using the spectral collocation method

    International Nuclear Information System (INIS)

    Painter, S.L.; Lyon, J.F.

    1989-01-01

    A novel transport survey code has been developed and is being used to study the sensitivity of stellarator reactor performance to various transport assumptions. Instead of following one of the usual approaches, the steady-state transport equation are solved in integral form using the spectral collocation method. This approach effectively combine the computational efficiency of global models with the general nature of 1-D solutions. A compact torsatron reactor test case was used to study the convergence properties and flexibility of the new method. The heat transport model combined Shaing's model for ripple-induced neoclassical transport, the Chang-Hinton model for axisymmetric neoclassical transport, and neoalcator scaling for anomalous electron heat flux. Alpha particle heating, radiation losses, classical electron-ion heat flow, and external heating were included. For the test problem, the method exhibited some remarkable convergence properties. As the number of basis functions was increased, the maximum, pointwise error in the integrated power balance decayed exponentially until the numerical noise level as reached. Better than 10% accuracy in the globally-averaged quantities was achieved with only 5 basis functions; better than 1% accuracy was achieved with 10 basis functions. The numerical method was also found to be very general. Extreme temperature gradients at the plasma edge which sometimes arise from the neoclassical models and are difficult to resolve with finite-difference methods were easily resolved. 8 refs., 6 figs

  20. Health effects of an increased protein intake on kidney function and colorectal cancer risk factors, including the role of animal and plant protein sources – the PREVIEW project

    DEFF Research Database (Denmark)

    Møller, Grith

    data from three European population studies; NQplus, Lifelines and the Young Finns Study (paper I) as well as the large international RCT (paper II and paper III). In paper I, the aim of the study was to develop a protein diet score, based on both dietary protein quantity and source i.e. plant...... intake, including the role of animal and plant protein in pre-diabetic, overweight or obese individuals on health outcomes: markers of kidney function and putative risk factors for colorectal cancer as well as insulin sensitivity and kidney function in healthy individuals. The thesis is based on PREVIEW...... or animal protein. The score was used to investigate the relation to T2D-related adverse metabolic health events. A total of 76,777 healthy individuals were included in the analysis. We found that a higher total protein diet score (higher intake of total protein and plant to animal protein ratio...

  1. Air filter devices including nonwoven meshes of electrospun recombinant spider silk proteins.

    Science.gov (United States)

    Lang, Gregor; Jokisch, Stephan; Scheibel, Thomas

    2013-05-08

    Based on the natural sequence of Araneus diadematus Fibroin 4 (ADF4), the recombinant spider silk protein eADF4(C16) has been engineered. This highly repetitive protein has a molecular weight of 48kDa and is soluble in different solvents (hexafluoroisopropanol (HFIP), formic acid and aqueous buffers). eADF4(C16) provides a high potential for various technical applications when processed into morphologies such as films, capsules, particles, hydrogels, coatings, fibers and nonwoven meshes. Due to their chemical stability and controlled morphology, the latter can be used to improve filter materials. In this protocol, we present a procedure to enhance the efficiency of different air filter devices, by deposition of nonwoven meshes of electrospun recombinant spider silk proteins. Electrospinning of eADF4(C16) dissolved in HFIP results in smooth fibers. Variation of the protein concentration (5-25% w/v) results in different fiber diameters (80-1,100 nm) and thus pore sizes of the nonwoven mesh. Post-treatment of eADF4(C16) electrospun from HFIP is necessary since the protein displays a predominantly α-helical secondary structure in freshly spun fibers, and therefore the fibers are water soluble. Subsequent treatment with ethanol vapor induces formation of water resistant, stable β-sheet structures, preserving the morphology of the silk fibers and meshes. Secondary structure analysis was performed using Fourier transform infrared spectroscopy (FTIR) and subsequent Fourier self-deconvolution (FSD). The primary goal was to improve the filter efficiency of existing filter substrates by adding silk nonwoven layers on top. To evaluate the influence of electrospinning duration and thus nonwoven layer thickness on the filter efficiency, we performed air permeability tests in combination with particle deposition measurements. The experiments were carried out according to standard protocols.

  2. Air Filter Devices Including Nonwoven Meshes of Electrospun Recombinant Spider Silk Proteins

    Science.gov (United States)

    Lang, Gregor; Jokisch, Stephan; Scheibel, Thomas

    2013-01-01

    Based on the natural sequence of Araneus diadematus Fibroin 4 (ADF4), the recombinant spider silk protein eADF4(C16) has been engineered. This highly repetitive protein has a molecular weight of 48kDa and is soluble in different solvents (hexafluoroisopropanol (HFIP), formic acid and aqueous buffers). eADF4(C16) provides a high potential for various technical applications when processed into morphologies such as films, capsules, particles, hydrogels, coatings, fibers and nonwoven meshes. Due to their chemical stability and controlled morphology, the latter can be used to improve filter materials. In this protocol, we present a procedure to enhance the efficiency of different air filter devices, by deposition of nonwoven meshes of electrospun recombinant spider silk proteins. Electrospinning of eADF4(C16) dissolved in HFIP results in smooth fibers. Variation of the protein concentration (5-25% w/v) results in different fiber diameters (80-1,100 nm) and thus pore sizes of the nonwoven mesh. Post-treatment of eADF4(C16) electrospun from HFIP is necessary since the protein displays a predominantly α-helical secondary structure in freshly spun fibers, and therefore the fibers are water soluble. Subsequent treatment with ethanol vapor induces formation of water resistant, stable β-sheet structures, preserving the morphology of the silk fibers and meshes. Secondary structure analysis was performed using Fourier transform infrared spectroscopy (FTIR) and subsequent Fourier self-deconvolution (FSD). The primary goal was to improve the filter efficiency of existing filter substrates by adding silk nonwoven layers on top. To evaluate the influence of electrospinning duration and thus nonwoven layer thickness on the filter efficiency, we performed air permeability tests in combination with particle deposition measurements. The experiments were carried out according to standard protocols. PMID:23685883

  3. Testing knowledge of whole English collocations available for use in written production

    DEFF Research Database (Denmark)

    Revier, Robert Lee

    2014-01-01

    of English collocations. These are: (a) collocation knowledge can be conceptualized as an independent knowledge construct, (b) collocations are lexical items in their own right, (c) testing of collocation knowledge should also target knowledge of whole collocations, and (d) the learning burden of a whole......Testing knowledge of whole English collocations available for use in written production: Developing tests for use with intermediate and advanced Danish learners (dansk resume nedenfor) The present foreign language acquisition research derives its impetus from four assumptions regarding knowledge...... the development of Danish EFL learners’ productive knowledge of whole English collocations. Five empirical studies were designed to generate information that would shed light on the reliability and validity of the CONTRIX as a measure of collocation knowledge available for use in written production. Study 1...

  4. AIRS-CloudSat cloud mask and radar reflectivities collocation indexes V3.1

    Data.gov (United States)

    National Aeronautics and Space Administration — This is AIRS-AMSU-CloudSat collocation indexes, in ASCII format. These data map CloudSat profile indexes to the collocated AMSU field of views, and AIRS IR...

  5. A protein diet score, including plant and animal protein, investigating the association with HbA1c and eGFR - the PREVIEW project

    DEFF Research Database (Denmark)

    Møller, Grith; Sluik, Diewertje; Ritz, Christian

    2017-01-01

    Higher-protein diets have been advocated for body-weight regulation for the past few decades. However, the potential health risks of these diets are still uncertain. We aimed to develop a protein score based on the quantity and source of protein, and to examine the association of the score...... with glycated haemoglobin (HbA1c) and estimated glomerular filtration rate (eGFR). Analyses were based on three population studies included in the PREVIEW project (PREVention of diabetes through lifestyle Intervention and population studies in Europe and around the World): NQplus, Lifelines, and the Young Finns...... Study. Cross-sectional data from food-frequency questionnaires (n = 76,777 subjects) were used to develop a protein score consisting of two components: 1) percentage of energy from total protein, and 2) plant to animal protein ratio. An inverse association between protein score and HbA1c (slope -0...

  6. Novel drugs and vaccines based on the structure and function of HIV pathogenic proteins including Nef.

    Science.gov (United States)

    Azad, Ahmed A

    2005-11-01

    Evidence is presented to suggest that HIV-1 accessory protein Nef could be involved in AIDS pathogenesis. When present in extracellular medium, Nef causes the death of a wide variety of cells in vitro and may therefore be responsible for the depletion of bystander cells in lymphoid tissues during HIV infection. When present inside the cell, Nef could prevent the death of infected cells and thereby contribute to increased viral load. Intracellular Nef does this by preventing apoptosis of infected cells by either inhibiting proteins involved in apoptosis or preventing the infected cells from being recognized by CTLs. Neutralization of extracellular Nef could prevent the death of uninfected immune cells and thereby the destruction of the immune system. Neutralization of intracellular Nef could hasten the death of infected cells and help reduce the viral load. Nef is therefore a very important molecular target for developing therapeutics that slow progression to AIDS. The N-terminal region of Nef and the naturally occurring bee venom mellitin have very similar primary and tertiary structures, and they both act by destroying membranes. Chemical analogs of a mellitin inhibitor prevent Nef-mediated cell death and inhibit the interaction of Nef with cellular proteins involved in apoptosis. Naturally occurring bee propolis also contains substances that prevent Nef-mediated cell lysis and increases proliferation of CD4 cells in HIV-infected cultures. These chemical compounds and natural products are water soluble and nontoxic and are therefore potentially very useful candidate drugs.

  7. Effects of Input-based and Output-based Instructions on Iranian EFL Learners’ Productive Knowledge of Collocations

    Directory of Open Access Journals (Sweden)

    Nawal Gholami

    2017-03-01

    Full Text Available Few studies have investigated the effects of input-based and output-based instructions on collocational knowledge of EFL learners. Therefore, this study aimed to examine the effects of these instructional approaches on Iranian EFL learners’ productive knowledge of collocations. To this end, 80 senior high school students from three intact classes at Tali-e High School in Ahvaz, Iran, were selected. Each class was assigned to a control group (n = 28 and two experimental groups including the input group (n = 27 and the output group (n = 25. Twenty collocations were selected as the target collocations. Then, a pretest was administered to all groups. Two days after the last treatment session, an immediate posttest was given to the participants. A delayed posttest was also administered two weeks later. The results of Mixed-ANOVA, one-way ANOVA, and Tukey post hoc tests revealed that both input and output groups outperformed the control group on the immediate and delayed posttests. However, there were no significant differences between the input and output groups on the posttests. The implications and suggestions for future research are also presented.

  8. Collocations in Corpus-Based Language Learning Research: Identifying, Comparing, and Interpreting the Evidence

    Science.gov (United States)

    Gablasova, Dana; Brezina, Vaclav; McEnery, Tony

    2017-01-01

    This article focuses on the use of collocations in language learning research (LLR). Collocations, as units of formulaic language, are becoming prominent in our understanding of language learning and use; however, while the number of corpus-based LLR studies of collocations is growing, there is still a need for a deeper understanding of factors…

  9. ANTIFREEZE PROTEINS IN PLANTS: AN OVERVIEW WITH AN INSIGHT INTO THE DETECTION TECHNIQUES INCLUDING NANOBIOTECHNOLOGY

    Directory of Open Access Journals (Sweden)

    Bhavana Sharma

    2014-08-01

    Full Text Available Antifreeze proteins (AFPs are a class of polypeptides which enables various organisms to survive subzero temperatures and have been found in vertebrates, invertebrates, plants, fungi and lichens. AFPs possess the characteristic thermal hysteresis (TH and ice recrystallization inhibition (IRI properties which allow them to adsorb the surface of ice crystals and inhibit their growth and recrystallization. AFPs are also known as ice restructuring proteins due to their ability to modify ice crystal morphology which leads to formation of hexagonal shape ice crystals in the presence of AFPs and disc shape AFPs in its absence. AFPs have various applications in medical, agricultural, industrial and biotechnological field. This review provides an overview of the AFPs, their TH and IRI properties and potential biotechnological applications of AFPs. Various conventional detection methods like Capillary assay and Differential Scanning Calorimetry (DSC with their advantages and disadvantages are discussed in detail along with the commonly used Splat assay and Nanoliter osmometer. Moreover, a novel, high-throughput and efficient nanobiotechnological method for AFP detection is also discussed. The method is based on colorimetric detection of freeze-labile gold nanoparticles and can provide an alternative to overcome the limitations of conventional methods by providing quick and easy way to screen AFPs in multiple systems simultaneously

  10. Teachability of collocations: The role of word frequency counts ...

    African Journals Online (AJOL)

    Two collocation tests (modelled after Laufer and Nation 1999)1 with words selected from Nation's (2006)2 word list and Coxhead's (2000)3 Academic Word List were administered to two groups of English majors, at different stages of learning, from the University of Antwerp and the University of Burundi. Results showed that ...

  11. Testing controlled productive knowledge of adverb-verb collocations ...

    African Journals Online (AJOL)

    Testing controlled productive knowledge of adverb-verb collocations in junior researchers using English as a .... publication, until now, the AWL has been influential in testing, teaching and designing materials to teach for academic purposes ..... or less safely) in my memory. 1. Those items that seemed to me to have a full ...

  12. Collocability in Languages for Special Purposes (LSPs): some ...

    African Journals Online (AJOL)

    Analysis and systematisation of these textual "clusterings" is intended to separate them into two radically different types of entity: multiword segments possessing terminological status; and collocative material. The methods used to achieve the above objective are both qualitative, i.e. micro-environmental analysis, and ...

  13. Perturbed segmented domain collocation Tau-method for the ...

    African Journals Online (AJOL)

    This paper concerns the numerical solution of second order boundary value problems using a Perturbed segmented domain collocation-Tau method. The entire interval for which the problem is defined is partitioned into two segments and the solution technique is demonstrated on each of the segments. The Chebyshev ...

  14. Testing controlled productive knowledge of adverb-verb collocations ...

    African Journals Online (AJOL)

    Abstract. The present study examines English as a Foreign Language (EFL) junior researchers' use of adverbverb collocations of academic vocabulary in both free-written and controlled productions. A small corpus was compiled and analysed in order to identify verbs in adverb-verb combinations and examine which ones ...

  15. A new derivation of continuous collocation multistep methods using ...

    African Journals Online (AJOL)

    A new derivation of continuous collocation multistep methods using power series as basis function. ... Journal of the Nigerian Association of Mathematical Physics ... Rather than using Chebyshev polynomials as basis function as it was always done in the past, we introduced the use of direct form of power series as an ...

  16. The structure of an Afrikaans collocation and phrase dictionary | Otto ...

    African Journals Online (AJOL)

    In this article an Afrikaans collocation and phrase dictionary for mother-tongue speakers (primary target group) as well as advanced learners (secondary target group) is discussed. The position which such a dictionary occupies among other dictionary types is pointed out. A motivation is also given for the inclusion of idioms ...

  17. Collocations and grammatical patterns in a Multilingual Online Term ...

    African Journals Online (AJOL)

    user

    Collocations and Grammatical Patterns in a Multilingual Online Term Bank. 393 the design of a variety of terminology tools. The E-Advanced Learner's Dictionary of Verbs in Science (DicSci) project, reported on by Alonso et al. (2011), the. ARTES project of which one outcome is the compilation of an online bilingual.

  18. Lexical richness and collocational competence in second-language writing

    NARCIS (Netherlands)

    Vedder, I.; Benigno, V.

    2016-01-01

    In this article we report on an experiment set up to investigate lexical richness and collocational competence in the written production of 39 low-intermediate and intermediate learners of Italian L2. Lexical richness was assessed by means of a lexical profiling method inspired by Laufer and Nation

  19. Sinc-collocation method for solving the Blasius equation

    International Nuclear Information System (INIS)

    Parand, K.; Dehghan, Mehdi; Pirkhedri, A.

    2009-01-01

    Sinc-collocation method is applied for solving Blasius equation which comes from boundary layer equations. It is well known that sinc procedure converges to the solution at an exponential rate. Comparison with Howarth and Asaithambi's numerical solutions reveals that the proposed method is of high accuracy and reduces the solution of Blasius' equation to the solution of a system of algebraic equations.

  20. Temi firthiani di linguistica applicata: "Restricted Languages" e "Collocation" (Firthian Themes in Applied Linguistics: "Restricted Languages" and "Collocation")

    Science.gov (United States)

    Leonardi, Magda

    1977-01-01

    Discusses the importance of two Firthian themes for language teaching. The first theme, "Restricted Languages," concerns the "microlanguages" of every language (e.g., literary language, scientific, etc.). The second theme, "Collocation," shows that equivalent words in two languages rarely have the same position in…

  1. Presenting collocates in a dictionary of computing and the Internet according to user needs

    DEFF Research Database (Denmark)

    Leroyer, Patrick; L'Homme, Marie-Claude; Jousse, Anne-Laure

    2011-01-01

    implemented in the online version of the dictionary. Users are prompted with generic meanings associated with the classes we created and they can then select verb and noun collocates that express more specific meanings. The article describes the model for grouping collocations and its implementation. Finally......This paper presents a novel method for organizing and presenting collocations in a specialized dictionary of computing and the Internet. This work is undertaken in order to meet a specific user need, i.e. that of searching for a collocate (or a short list of collocates) that expresses a specific...

  2. Native SDS-PAGE: high resolution electrophoretic separation of proteins with retention of native properties including bound metal ions.

    Science.gov (United States)

    Nowakowski, Andrew B; Wobig, William J; Petering, David H

    2014-05-01

    Sodium dodecyl-sulfate polyacrylamide gel electrophoresis (SDS-PAGE) is commonly used to obtain high resolution separation of complex mixtures of proteins. The method initially denatures the proteins that will undergo electrophoresis. Although covalent structural features of resolved proteins can be determined with SDS-PAGE, functional properties are destroyed, including the presence of non-covalently bound metal ions. To address this shortcoming, blue-native (BN)-PAGE has been introduced. This method retains functional properties but at the cost of protein resolving power. To address the need for a high resolution PAGE method that results in the separation of native proteins, experiments tested the impact of changing the conditions of SDS-PAGE on the quality of protein separation and retention of functional properties. Removal of SDS and EDTA from the sample buffer together with omission of a heating step had no effect on the results of PAGE. Reduction of SDS in the running buffer from 0.1% to 0.0375% together with deletion of EDTA also made little impact on the quality of the electrophoretograms of fractions of pig kidney (LLC-PK1) cell proteome in comparison with that achieved with the SDS-PAGE method. The modified conditions were called native (N)SDS-PAGE. Retention of Zn(2+) bound in proteomic samples increased from 26 to 98% upon shifting from standard to modified conditions. Moreover, seven of nine model enzymes, including four Zn(2+) proteins that were subjected to NSDS-PAGE retained activity. All nine were active in BN-PAGE, whereas all underwent denaturation during SDS-PAGE. Metal retention after electrophoresis was additionally confirmed using laser ablation-inductively coupled plasma-mass spectrometry and in-gel Zn-protein staining using the fluorophore TSQ.

  3. The multi-element probabilistic collocation method (ME-PCM): Error analysis and applications

    International Nuclear Information System (INIS)

    Foo, Jasmine; Wan Xiaoliang; Karniadakis, George Em

    2008-01-01

    Stochastic spectral methods are numerical techniques for approximating solutions to partial differential equations with random parameters. In this work, we present and examine the multi-element probabilistic collocation method (ME-PCM), which is a generalized form of the probabilistic collocation method. In the ME-PCM, the parametric space is discretized and a collocation/cubature grid is prescribed on each element. Both full and sparse tensor product grids based on Gauss and Clenshaw-Curtis quadrature rules are considered. We prove analytically and observe in numerical tests that as the parameter space mesh is refined, the convergence rate of the solution depends on the quadrature rule of each element only through its degree of exactness. In addition, the L 2 error of the tensor product interpolant is examined and an adaptivity algorithm is provided. Numerical examples demonstrating adaptive ME-PCM are shown, including low-regularity problems and long-time integration. We test the ME-PCM on two-dimensional Navier-Stokes examples and a stochastic diffusion problem with various random input distributions and up to 50 dimensions. While the convergence rate of ME-PCM deteriorates in 50 dimensions, the error in the mean and variance is two orders of magnitude lower than the error obtained with the Monte Carlo method using only a small number of samples (e.g., 100). The computational cost of ME-PCM is found to be favorable when compared to the cost of other methods including stochastic Galerkin, Monte Carlo and quasi-random sequence methods

  4. Chemotherapy modulates intestinal immune gene expression including surfactant Protein-D and deleted in malignant brain tumors 1 in piglets

    DEFF Research Database (Denmark)

    Rathe, Mathias; Thomassen, Mads; Shen, René L.

    2016-01-01

    the BUCY and DOX piglets. Selected genes of potential biological significance with a similar change in expression across the treatments were controlled by real-time polymerase chain reaction. Key innate defense molecules, including surfactant protein-D and deleted in malignant brain tumors 1, were among...

  5. Computation of binding energies including their enthalpy and entropy components for protein-ligand complexes using support vector machines.

    Science.gov (United States)

    Koppisetty, Chaitanya A K; Frank, Martin; Kemp, Graham J L; Nyholm, Per-Georg

    2013-10-28

    Computing binding energies of protein-ligand complexes including their enthalpy and entropy terms by means of computational methods is an appealing approach for selecting initial hits and for further optimization in early stages of drug discovery. Despite the importance, computational predictions of thermodynamic components have evaded attention and reasonable solutions. In this study, support vector machines are used for developing scoring functions to compute binding energies and their enthalpy and entropy components of protein-ligand complexes. The binding energies computed from our newly derived scoring functions have better Pearson's correlation coefficients with experimental data than previously reported scoring functions in benchmarks for protein-ligand complexes from the PDBBind database. The protein-ligand complexes with binding energies dominated by enthalpy or entropy term could be qualitatively classified by the newly derived scoring functions with high accuracy. Furthermore, it is found that the inclusion of comprehensive descriptors based on ligand properties in the scoring functions improved the accuracy of classification as well as the prediction of binding energies including their thermodynamic components. The prediction of binding energies including the enthalpy and entropy components using the support vector machine based scoring functions should be of value in the drug discovery process.

  6. RBF Multiscale Collocation for Second Order Elliptic Boundary Value Problems

    KAUST Repository

    Farrell, Patricio

    2013-01-01

    In this paper, we discuss multiscale radial basis function collocation methods for solving elliptic partial differential equations on bounded domains. The approximate solution is constructed in a multilevel fashion, each level using compactly supported radial basis functions of smaller scale on an increasingly fine mesh. On each level, standard symmetric collocation is employed. A convergence theory is given, which builds on recent theoretical advances for multiscale approximation using compactly supported radial basis functions. We are able to show that the convergence is linear in the number of levels. We also discuss the condition numbers of the arising systems and the effect of simple, diagonal preconditioners, now proving rigorously previous numerical observations. © 2013 Society for Industrial and Applied Mathematics.

  7. Collocation-homotopy method to initial-boundary value problems

    Directory of Open Access Journals (Sweden)

    Ahmad Molabahrami

    2013-06-01

    Full Text Available In this paper, an algorithm based on the collocation and homotopy analysis methods, for solving initial-boundary value problems, is introduced. The application of this algorithm is based on the approximation and interpolation of the dependent variables by using suitable functions or polynomials according to their values in the collocation points corresponding to a suitable discretization of the space variable. Then the space derivatives are approximated using interpolation. Replacing them in the equation transforms the initial-boundary value problem into an initial value problem for ordinary differential equations. The obtained initial value problem is solved by homotopy analysis method. In the frame of the homotopy analysis method, the optimum value of convergence-parameter corresponding to each point is computed by a simple stochastic function minimizer, namely differential evolution method. Lagrange polynomials are usually adopted for the interpolation. In this framework, the Burgers model is considered as a prototype example.

  8. Locating CVBEM collocation points for steady state heat transfer problems

    Science.gov (United States)

    Hromadka, T.V.

    1985-01-01

    The Complex Variable Boundary Element Method or CVBEM provides a highly accurate means of developing numerical solutions to steady state two-dimensional heat transfer problems. The numerical approach exactly solves the Laplace equation and satisfies the boundary conditions at specified points on the boundary by means of collocation. The accuracy of the approximation depends upon the nodal point distribution specified by the numerical analyst. In order to develop subsequent, refined approximation functions, four techniques for selecting additional collocation points are presented. The techniques are compared as to the governing theory, representation of the error of approximation on the problem boundary, the computational costs, and the ease of use by the numerical analyst. ?? 1985.

  9. Part 6. Internationalization and collocation of FBR fuel cycle facilities

    International Nuclear Information System (INIS)

    Stevenson, M.G.; Abramson, P.B.; LeSage, L.G.

    1980-01-01

    This report examines some of the non-proliferation, technical, and institutional aspects of internationalization and/or collocation of major facilities of the Fast Breeder Reactor (FBR) fuel cycle. The national incentives and disincentives for establishment of FBR Fuel Cycle Centers are enumerated. The technical, legal, and administrative considerations in determining the feasibility of FBR Fuel Cycle Centers are addressed by making comparisons with Light Water Reactor (LWR) centers which have been studied in detail by the IAEA and UNSRC

  10. Metaphors in terminological collocations in English language and their equivalents in Serbian

    Directory of Open Access Journals (Sweden)

    Orčić Lidija S.

    2017-01-01

    Full Text Available The framework of this paper is the theory of conceptual metaphor where metaphor is the transfer of a more concrete source domain into a more abstract target domain. Metaphor is a fundamental human ability to speak about abstract concepts using specific terms where the meaning of a term is transferred to another, thus achieving semantic extensions. Although it was thought that in terminology polysemantic expressions are not desirable, in recent decades this traditional view has been abandoned. Metaphor is used not only as a linguistic decoration in language, but as a means of argumentation. It may be noted that the metaphor, as a universal phenomenon, is also common in business English discourse. The subject of our interest is to investigate collocations made up of those nouns and adjectives, which, according to the Oxford Business English Dictionary for Learners of English, are most frequently used in this field. The main objective of this work is to identify and analyze the source and target domains in metaphors in English collocations that contain these nouns and adjectives, and detect mechanisms applied in translating into Serbian. We categorised metaphors in collocations into four groups. The first group consists of metaphors in which the source domain is expressed with the living beings: inanimate entities are described as if they were alive. In these examples, the personification is used to explain abstract concepts, forces and processes in order to present them in a more understandable way. The second group consists of metaphors in which animals are the source domain and their behavior and characteristics serve as a starting point. In business discourse people and institutions are described with such metaphors. In the third group we included the metaphors based on objects that users are familiar with in everyday life. The fourth group consists of metaphors in which the source domain are natural phenomena. When translating a metaphor we

  11. The analysis of a sparse grid stochastic collocation method for partial differential equations with high-dimensional random input data.

    Energy Technology Data Exchange (ETDEWEB)

    Webster, Clayton; Tempone, Raul (Florida State University, Tallahassee, FL); Nobile, Fabio (Politecnico di Milano, Italy)

    2007-12-01

    This work describes the convergence analysis of a Smolyak-type sparse grid stochastic collocation method for the approximation of statistical quantities related to the solution of partial differential equations with random coefficients and forcing terms (input data of the model). To compute solution statistics, the sparse grid stochastic collocation method uses approximate solutions, produced here by finite elements, corresponding to a deterministic set of points in the random input space. This naturally requires solving uncoupled deterministic problems and, as such, the derived strong error estimates for the fully discrete solution are used to compare the computational efficiency of the proposed method with the Monte Carlo method. Numerical examples illustrate the theoretical results and are used to compare this approach with several others, including the standard Monte Carlo.

  12. Runge-Kutta and Hermite Collocation for a biological invasion problem modeled by a generalized Fisher equation

    International Nuclear Information System (INIS)

    Athanasakis, I E; Papadopoulou, E P; Saridakis, Y G

    2014-01-01

    Fisher's equation has been widely used to model the biological invasion of single-species communities in homogeneous one dimensional habitats. In this study we develop high order numerical methods to accurately capture the spatiotemporal dynamics of the generalized Fisher equation, a nonlinear reaction-diffusion equation characterized by density dependent non-linear diffusion. Working towards this direction we consider strong stability preserving Runge-Kutta (RK) temporal discretization schemes coupled with the Hermite cubic Collocation (HC) spatial discretization method. We investigate their convergence and stability properties to reveal efficient HC-RK pairs for the numerical treatment of the generalized Fisher equation. The Hadamard product is used to characterize the collocation discretized non linear equation terms as a first step for the treatment of generalized systems of relevant equations. Numerical experimentation is included to demonstrate the performance of the methods

  13. Integration of statistical collocation segmentations in a phrase-based statistical machine translation system

    OpenAIRE

    Ruiz Costa-Jussà, Marta; Daudaravicius, Vidas; Banchs, Rafael E.

    2010-01-01

    This study evaluates the impact of integrating two different collocation segmentations methods in a standard phrase-based statistical machine translation approach. The collocation segmentation techniques are implemented simultaneously in the source and target side. Each resulting collocation segmentation is used to extract translation units. Experiments are reported in the English-to-Spanish Bible task and promising results (an improvement over 0.7 BLEU absolute) are achieved in translation q...

  14. Corpus-Based Websites to Promote Learner Autonomy in Correcting Writing Collocation Errors

    Directory of Open Access Journals (Sweden)

    Pham Thuy Dung

    2016-12-01

    Full Text Available The recent yet powerful emergence of E-learning and using online resources in learning EFL (English as a Foreign Language has helped promote learner autonomy in language acquisition including self-correcting their mistakes. This pilot study despite conducted on a modest sample of 25 second year students majoring in Business English at Hanoi Foreign Trade University is an initial attempt to investigate the feasibility of using corpus-based websites to promote learner autonomy in correcting collocation errors in EFL writing. The data is collected using a pre-questionnaire and a post-interview aiming to find out the participants’ change in belief and attitude toward learner autonomy in collocation errors in writing, the extent of their success in using the corpus-based websites to self-correct the errors and the change in their confidence in self-correcting the errors using the websites. The findings show that a significant majority of students have shifted their belief and attitude toward a more autonomous mode of learning, enjoyed a fair success of using the websites to self-correct the errors and become more confident. The study also yields an implication that a face-to-face training of how to use these online tools is vital to the later confidence and success of the learners

  15. Fourier analysis of finite element preconditioned collocation schemes

    Science.gov (United States)

    Deville, Michel O.; Mund, Ernest H.

    1990-01-01

    The spectrum of the iteration operator of some finite element preconditioned Fourier collocation schemes is investigated. The first part of the paper analyses one-dimensional elliptic and hyperbolic model problems and the advection-diffusion equation. Analytical expressions of the eigenvalues are obtained with use of symbolic computation. The second part of the paper considers the set of one-dimensional differential equations resulting from Fourier analysis (in the tranverse direction) of the 2-D Stokes problem. All results agree with previous conclusions on the numerical efficiency of finite element preconditioning schemes.

  16. Collocating satellite-based radar and radiometer measurements – methodology and usage examples

    Directory of Open Access Journals (Sweden)

    G. Holl

    2010-06-01

    Full Text Available Collocations between two satellite sensors are occasions where both sensors observe the same place at roughly the same time. We study collocations between the Microwave Humidity Sounder (MHS on-board NOAA-18 and the Cloud Profiling Radar (CPR on-board CloudSat. First, a simple method is presented to obtain those collocations and this method is compared with a more complicated approach found in literature. We present the statistical properties of the collocations, with particular attention to the effects of the differences in footprint size. For 2007, we find approximately two and a half million MHS measurements with CPR pixels close to their centrepoints. Most of those collocations contain at least ten CloudSat pixels and image relatively homogeneous scenes. In the second part, we present three possible applications for the collocations. Firstly, we use the collocations to validate an operational Ice Water Path (IWP product from MHS measurements, produced by the National Environment Satellite, Data and Information System (NESDIS in the Microwave Surface and Precipitation Products System (MSPPS. IWP values from the CloudSat CPR are found to be significantly larger than those from the MSPPS. Secondly, we compare the relation between IWP and MHS channel 5 (190.311 GHz brightness temperature for two datasets: the collocated dataset, and an artificial dataset. We find a larger variability in the collocated dataset. Finally, we use the collocations to train an Artificial Neural Network and describe how we can use it to develop a new MHS-based IWP product. We also study the effect of adding measurements from the High Resolution Infrared Radiation Sounder (HIRS, channels 8 (11.11 μm and 11 (8.33 μm. This shows a small improvement in the retrieval quality. The collocations described in the article are available for public use.

  17. BS Methods: A New Class of Spline Collocation BVMs

    Science.gov (United States)

    Mazzia, Francesca; Sestini, Alessandra; Trigiante, Donato

    2008-09-01

    BS methods are a recently introduced class of Boundary Value Methods which is based on B-splines. They can also be interpreted as spline collocation methods. For uniform meshes, the coefficients defining the k-step BS method are just the values of the (k+1)-degree uniform B-spline and B-spline derivative at its integer active knots; for general nonuniform meshes they are computed by solving local linear systems whose dimension depends on k. An important specific feature of BS methods is the possibility to associate a spline of degree k+1 and smoothness Ck to the numerical solution produced by the k-step method of this class. Such spline collocates the differential equation at the knots, shares the convergence order with the numerical solution, and can be computed with negligible additional computational cost. Here a survey on such methods is given, presenting the general definition, the convergence and stability features, and introducing the strategy for the computation of the coefficients in the B-spline basis which define the associated spline. Finally, some related numerical results are also presented.

  18. Acoustic scattering by multiple elliptical cylinders using collocation multipole method

    International Nuclear Information System (INIS)

    Lee, Wei-Ming

    2012-01-01

    This paper presents the collocation multipole method for the acoustic scattering induced by multiple elliptical cylinders subjected to an incident plane sound wave. To satisfy the Helmholtz equation in the elliptical coordinate system, the scattered acoustic field is formulated in terms of angular and radial Mathieu functions which also satisfy the radiation condition at infinity. The sound-soft or sound-hard boundary condition is satisfied by uniformly collocating points on the boundaries. For the sound-hard or Neumann conditions, the normal derivative of the acoustic pressure is determined by using the appropriate directional derivative without requiring the addition theorem of Mathieu functions. By truncating the multipole expansion, a finite linear algebraic system is derived and the scattered field can then be determined according to the given incident acoustic wave. Once the total field is calculated as the sum of the incident field and the scattered field, the near field acoustic pressure along the scatterers and the far field scattering pattern can be determined. For the acoustic scattering of one elliptical cylinder, the proposed results match well with the analytical solutions. The proposed scattered fields induced by two and three elliptical–cylindrical scatterers are critically compared with those provided by the boundary element method to validate the present method. Finally, the effects of the convexity of an elliptical scatterer, the separation between scatterers and the incident wave number and angle on the acoustic scattering are investigated.

  19. Gimme Context – towards New Domain-Specific Collocational Dictionaries

    Directory of Open Access Journals (Sweden)

    Sylvana Krausse

    2011-04-01

    Full Text Available The days of traditional drudgery-filled lexicography are long gone. Fortunately today, computers help in the enormous task of storing and analysing language in order to condense and store the found information in the form of dictionaries. In this paper, the way from a corpus to a small domain-specific collocational dictionary will be described and thus exemplified based on the example of the domain-specific language of mining reclamation, which can be duplicated for other specific languages too. So far, domain-specific dictionaries are mostly rare as their creation is very labour- and thus cost-effective and all too often they are just a collection of terms plus translation without any information on how to use them in speech. Particular small domains which do not involve a lot of users have been disregarded by lexicographers as there is also always the question of how well it sells afterwards. Following this, I will describe the creation of a small collocational dictionary on mining reclamation language which is based on the consequent use of corpus information. It is relatively quick to realize in the design phase and is thought to provide the sort of linguistic information engineering experts need when they communicate in English or read specialist texts in the specific domain.

  20. English Collocation Learning through Corpus Data: On-Line Concordance and Statistical Information

    Science.gov (United States)

    Ohtake, Hiroshi; Fujita, Nobuyuki; Kawamoto, Takeshi; Morren, Brian; Ugawa, Yoshihiro; Kaneko, Shuji

    2012-01-01

    We developed an English Collocations On Demand system offering on-line corpus and concordance information to help Japanese researchers acquire a better command of English collocation patterns. The Life Science Dictionary Corpus consists of approximately 90,000,000 words collected from life science related research papers published in academic…

  1. The Structure of an Afrikaans Collocation and Phrase Dictionary·

    African Journals Online (AJOL)

    The dictionary article will be divided into two interactive components. The first component. In the first component combinations will be placed tinder the different polyse- mous senses of the lemma (i.e. the base of the combination) without examples. In the case of collocations no definitions will be provided since collocations ...

  2. Study on the Causes and Countermeasures of the Lexical Collocation Mistakes in College English

    Science.gov (United States)

    Yan, Hansheng

    2010-01-01

    The lexical collocation in English is an important content in the linguistics theory, and also a research topic which is more and more emphasized in English teaching practice of China. The collocation ability of English decides whether learners could masterly use real English in effective communication. In many years' English teaching practice,…

  3. Teaching and Learning Collocation in Adult Second and Foreign Language Learning

    Science.gov (United States)

    Boers, Frank; Webb, Stuart

    2018-01-01

    Perhaps the greatest challenge to creating a research timeline on teaching and learning collocation is deciding how wide to cast the net in the search for relevant publications. For one thing, the term "collocation" does not have the same meaning for all (applied) linguists and practitioners (Barfield & Gyllstad 2009) (see timeline).…

  4. Cross-Linguistic Influence: Its Impact on L2 English Collocation Production

    Science.gov (United States)

    Phoocharoensil, Supakorn

    2013-01-01

    This research study investigated the influence of learners' mother tongue on their acquisition of English collocations. Having drawn the linguistic data from two groups of Thai EFL learners differing in English proficiency level, the researcher found that the native language (L1) plays a significant role in the participants' collocation learning…

  5. Stochastic spectral Galerkin and collocation methods for PDEs with random coefficients: A numerical comparison

    KAUST Repository

    Bäck, Joakim

    2010-09-17

    Much attention has recently been devoted to the development of Stochastic Galerkin (SG) and Stochastic Collocation (SC) methods for uncertainty quantification. An open and relevant research topic is the comparison of these two methods. By introducing a suitable generalization of the classical sparse grid SC method, we are able to compare SG and SC on the same underlying multivariate polynomial space in terms of accuracy vs. computational work. The approximation spaces considered here include isotropic and anisotropic versions of Tensor Product (TP), Total Degree (TD), Hyperbolic Cross (HC) and Smolyak (SM) polynomials. Numerical results for linear elliptic SPDEs indicate a slight computational work advantage of isotropic SC over SG, with SC-SM and SG-TD being the best choices of approximation spaces for each method. Finally, numerical results corroborate the optimality of the theoretical estimate of anisotropy ratios introduced by the authors in a previous work for the construction of anisotropic approximation spaces. © 2011 Springer.

  6. Predicative instrumental in the light of collocational analysis

    Directory of Open Access Journals (Sweden)

    Hlebec Boris

    2008-01-01

    Full Text Available Primarily on the basis of the material provided in a monograph by Milka Ivić the author has aimed at highlighting the meanings of the so-called predicative instrumental and instrumental of basic characteristics (both used as predicative complements from a new perspective. To this purpose he has applied his developing collocational method, which leads to controlled lexical definitions. The conclusion is that both types of instrumental share the same 'u vidu' ('in manifested form', while the difference lies in the degree of subjectivity expressed by the verb. Namely, the former, being relatively subjective, is mainly in current usage, while the latter is obsolete due to its relative objectivity. Archaic usages of the former are midway between the two poles, i. e. semi-objective. The article reaffirms the results in Milka Ivić's famous study done half a century ago.

  7. Analysis of an upstream weighted collocation approximation to the transport equation

    International Nuclear Information System (INIS)

    Shapiro, A.; Pinder, G.F.

    1981-01-01

    The numerical behavior of a modified orthogonal collocation method, as applied to the transport equations, can be examined through the use of a Fourier series analysis. The necessity of such a study becomes apparent in the analysis of several techniques which emulate classical upstream weighting schemes. These techniques are employed in orthogonal collocation and other numerical methods as a means of handling parabolic partial differential equations with significant first-order terms. Divergent behavior can be shown to exist in one upstream weighting method applied to orthogonal collocation

  8. Responding to Research Challenges Related to Studying L2 Collocational Use in Professional Academic Discourse

    DEFF Research Database (Denmark)

    Henriksen, Birgit; Westbrook, Pete

    2017-01-01

    This study describes the English collocational use of non-native university teachers from two different disciplines lecturing in an English- medium instruction context at the University of Copenhagen (UCPH). The primary focus is on how we addressed the research challenges involved in identifying...... and classifying collocations used by L2 speakers in advanced, domain-specific oral academic discourse. The main findings seem to suggest that to map an informant’s complete collocational use and to get an understanding of disciplinary differences, we need to not only take account of general, academic and domain...

  9. Do we see what we should see? Describing non-covalent interactions in protein structures including precision

    Directory of Open Access Journals (Sweden)

    Manickam Gurusaran

    2014-01-01

    Full Text Available The power of X-ray crystal structure analysis as a technique is to `see where the atoms are'. The results are extensively used by a wide variety of research communities. However, this `seeing where the atoms are' can give a false sense of security unless the precision of the placement of the atoms has been taken into account. Indeed, the presentation of bond distances and angles to a false precision (i.e. to too many decimal places is commonplace. This article has three themes. Firstly, a basis for a proper representation of protein crystal structure results is detailed and demonstrated with respect to analyses of Protein Data Bank entries. The basis for establishing the precision of placement of each atom in a protein crystal structure is non-trivial. Secondly, a knowledge base harnessing such a descriptor of precision is presented. It is applied here to the case of salt bridges, i.e. ion pairs, in protein structures; this is the most fundamental place to start with such structure-precision representations since salt bridges are one of the tenets of protein structure stability. Ion pairs also play a central role in protein oligomerization, molecular recognition of ligands and substrates, allosteric regulation, domain motion and α-helix capping. A new knowledge base, SBPS (Salt Bridges in Protein Structures, takes these structural precisions into account and is the first of its kind. The third theme of the article is to indicate natural extensions of the need for such a description of precision, such as those involving metalloproteins and the determination of the protonation states of ionizable amino acids. Overall, it is also noted that this work and these examples are also relevant to protein three-dimensional structure molecular graphics software.

  10. Collocational Relations in Japanese Language Textbooks and Computer-Assisted Language Learning Resources

    Directory of Open Access Journals (Sweden)

    Irena SRDANOVIĆ

    2011-05-01

    Full Text Available In this paper, we explore presence of collocational relations in the computer-assisted language learning systems and other language resources for the Japanese language, on one side, and, in the Japanese language learning textbooks and wordlists, on the other side. After introducing how important it is to learn collocational relations in a foreign language, we examine their coverage in the various learners’ resources for the Japanese language. We particularly concentrate on a few collocations at the beginner’s level, where we demonstrate their treatment across various resources. A special attention is paid to what is referred to as unpredictable collocations, which have a bigger foreign language learning-burden than the predictable ones.

  11. Accumulation of small heat shock proteins, including mitochondrial HSP22, induced by oxidative stress and adaptive response in tomato cells

    International Nuclear Information System (INIS)

    Banzet, N.; Richaud, C.; Deveaux, Y.; Kazmaier, M.; Gagnon, J.; Triantaphylides, C.

    1998-01-01

    Changes in gene expression, by application of H2O2, O2.- generating agents (methyl viologen, digitonin) and gamma irradiation to tomato suspension cultures, were investigated and compared to the well-described heat shock response. Two-dimensional gel protein mapping analyses gave the first indication that at least small heat shock proteins (smHSP) accumulated in response to application of H2O2 and gamma irradiation, but not to O2.- generating agents. While some proteins seemed to be induced specifically by each treatment, only part of the heat shock response was observed. On the basis of Northern hybridization experiments performed with four heterologous cDNA, corresponding to classes I-IV of pea smHSP, it could be concluded that significant amounts of class I and II smHSP mRNA are induced by H2O2 and by irradiation. Taken together, these results demonstrate that in plants some HSP genes are inducible by oxidative stresses, as in micro-organisms and other eukaryotic cells. HSP22, the main stress protein that accumulates following H2O2 action or gamma irradiation, was also purified. Sequence homology of amino terminal and internal sequences, and immunoreactivity with Chenopodium rubrum mitochondrial smHSP antibody, indicated that the protein belongs to the recently discovered class of plant mitochondrial smHSP. Heat shock or a mild H2O2 pretreatment was also shown to lead to plant cell protection against oxidative injury. Therefore, the synthesis of these stress proteins can be considered as an adaptive mechanism in which mitochondrial protection could be essential

  12. Communication Collocations of the Lexeme Geld in General and Business German

    Directory of Open Access Journals (Sweden)

    Mirna Hocenski-Dreiseidl

    2010-07-01

    Full Text Available The authors aim to analyse and compare the lexeme Geld and its collocations on the grammatical and semantic levels in general and in business German. A special emphasis will be put on the importance of the communicative function that this lexeme and its collocations have in the language of banking. The paper also has a practical purpose. Its applicability in teaching is envisaged to improve the communicative competence of students of economics.

  13. Topology optimization considering material and geometric uncertainties using stochastic collocation methods

    DEFF Research Database (Denmark)

    Lazarov, Boyan Stefanov; Schevenels, Mattias; Sigmund, Ole

    2012-01-01

    The aim of this paper is to introduce the stochastic collocation methods in topology optimization for mechanical systems with material and geometric uncertainties. The random variations are modeled by a memory-less transformation of spatially varying Gaussian random fields which ensures...... their physical admissibility. The stochastic collocation method combined with the proposed material and geometry uncertainty models provides robust designs by utilizing already developed deterministic solvers. The computational cost is discussed in details and solutions to decrease it, like sparse grids...

  14. Entropy Stable Spectral Collocation Schemes for the Navier-Stokes Equations: Discontinuous Interfaces

    Science.gov (United States)

    Carpenter, Mark H.; Fisher, Travis C.; Nielsen, Eric J.; Frankel, Steven H.

    2013-01-01

    Nonlinear entropy stability and a summation-by-parts framework are used to derive provably stable, polynomial-based spectral collocation methods of arbitrary order. The new methods are closely related to discontinuous Galerkin spectral collocation methods commonly known as DGFEM, but exhibit a more general entropy stability property. Although the new schemes are applicable to a broad class of linear and nonlinear conservation laws, emphasis herein is placed on the entropy stability of the compressible Navier-Stokes equations.

  15. Age of Acquisition Effects in Chinese EFL learners’ Delexicalized Verb and Collocation Acquisition

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    Miao Haiyan

    2015-05-01

    Full Text Available This paper investigates age of acquisition (AoA effects and the acquisition of delexicalized verbs and collocations in Chinese EFL learners, and explores the underlying reasons from the connectionist model for these learners’ acquisition characteristics. The data were collected through a translation test consisted of delexialized verb information section and English-Chinese and Chinese-English collocation parts, aiming to focus on Chinese EFL learners’ receptive and productive abilities respectively. As Chinese EFL is a nationally classroom-based practice beginning from early primary school, the pedagogical value and different phases of acquisition are thus taken into consideration in designing the translation test. Research results show that the effects of AoA are significant not only in the learners’ acquisition of individual delexicalized verbs but also in delexicalized collocations. Although learners have long begun to learn delexicalized verbs, their production indicates that early learning does not guarantee total acquisition, because their grasp of delexicalized verbs still stay at the senior middle school level. AoA effects significantly affect the recognition but not the production of collocations. Furthermore, a plateau effect occurs in learners’ acquisition of college-level delexicalized collocations, as their recognition and production have no processing advantages over earlier learned collocations.

  16. Translating Legal Collocations in Contract Agreements by Iraqi EFL Students-Translators

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    Muntaha A. Abdulwahid

    2017-01-01

    Full Text Available Legal translation of contract agreements is a challenge to translators as it involves combining the literary translation with the technical terminological precision. In translating legal contract agreements, a legal translator must utilize the lexical or syntactic precision and, more importantly, the pragmatic awareness of the context. This will guarantee an overall communicative process and avoid inconsistency in legal translation. However, the inability of the translator to meet these two functions in translating the contract item not only affects the contractors’ comprehension of the contract item but also affects the parties’ contractual obligations. In light of this, the purpose of this study was to find out how legal collocations used in contract agreements are translated from Arabic into English by student-translators in terms of (1 purely technical, (2 semi-technical, and (3 everyday vocabulary collocations. For the data collection, a multiple-choice collocation test was used to be answered by 35 EFL Iraqi undergraduate translator-students to decide on the aspects of weaknesses and strengths of their translation, thus decide on the aspects of correction. The findings showed that these students had serious problems in translating legal collocations as they lack the linguistic knowledge and pragmatic awareness needed to achieve the legal meaning and effect. They were also unable to make a difference among the three categories of legal collocations, purely technical, semi-technical, and everyday vocabulary collocations. These students should be exposed to more legal translation practices to obtain the required experience needed for their future career.

  17. Evaluating the performance of collocated optical disdrometers: LPM and PARSIVEL

    Science.gov (United States)

    Angulo-Martinez, Marta; Begueria, Santiago; Latorre, Borja

    2017-04-01

    Optical disdrometers are present weather sensors with the ability of providing integrate information of precipitation like intensity and reflectivity together with discrete information of drop sizes and velocities distribution (DSVD) of the hydrometeors crossing the laser beam sampling area. These sensors constitute a step forward in comparison with pluviometers towards a more complete characterisation of precipitation. Their use is spreading in many research fields for several applications. Understanding the differences from one another helps in the election of the sensor and point out limitations to be fixed in future versions. Four collocated optical disdrometers, two Laser Precipitation Monitors (LPM-Thies Clima) and two PARSIVEL, 1-minute measurements of 800 natural rainfall events were compared. Results showed a general agreement in integrated variables, like intensity or liquid water content. Nevertheless, comparing raw data, as the number of particles and DSVD, great differences were found. LPM generally measures more and smaller drops than PARSIVEL and this difference increases with rainfall intensity. These results may affect especially the reflectivity value every disdrometer provide. A complete description of the measurements obtained, quantifiying the differences is provided, indicating their possible sources.

  18. Particle Choices and Collocation in Cameroon English Phrasal Verbs

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    Napoleon Epoge

    2016-02-01

    Full Text Available The meaning of some phrasal verbs can be guessed from the meanings of the parts (to sit down = sit + down, run after = run + after and the meaning of some others have to be learned (to put up (a visitor = accommodate, to hold up = cause delay or try to rob someone due to their syntactic and semantic complexities. In this regard, the syntactic and semantic properties are expected to be the same in every English speaking context. Thus, this paper aims to explore the input-oriented syntactic and semantic properties of phrasal verbs in Cameroon English. Findings reveal that the syntactic property of some phrasal verbs undergoes innovative processes such as particle substitution (to round up a point, omission (to bite more than you can chew, and redundancy (to meet up with the requirements; while the semantic property undergoes the process of semantic extension (to came out with a pathetic story to justify ones absence from office; to come out with a wonderful strategy to curb corruption, and semantic shift (to put up with someone for one semester. This reveals that, in the New English context such as Cameroon, users resort to the domestication of the alien language as a functional and dominant paradigm to combat cultural imperialism and express new identity. Keywords: Cameroon English, collocation, particle, phrasal verb, semantics, syntax

  19. Hepatic ALT isoenzymes are elevated in gluconeogenic conditions including diabetes and suppressed by insulin at the protein level.

    Science.gov (United States)

    Qian, Kun; Zhong, Shao; Xie, Keming; Yu, Daozhan; Yang, Rongze; Gong, Da-Wei

    2015-09-01

    Alanine transaminase (ALT) plays an important role in gluconeogenesis by converting alanine into pyruvate for glucose production. Early studies have shown that ALT activities are upregulated in gluconeogenic conditions and may be implicated in the development of diabetes. ALT consists of two isoforms, ALT1 and ALT2, with distinctive subcellular and tissue distributions. Whether and how they are regulated are largely unknown. By using Western blotting analysis, we measured hepatic ALT isoforms at the protein level in obese and diabetic animals and in Fao hepatoma cells treated with dexamethasone and insulin. In addition, we measured glucose output in Fao cells over-expressing ALT1 and ALT2. Both ALT isoforms in the liver were increased in diabetic Goto-Kakizaki rats and during fasting. However, in ob/ob mice, only ALT2, but not ALT1, protein levels were elevated, and the increase of ALT2 was correlated with that of ALT activity. We further demonstrated that, in vitro, both ALT1 and ALT2 were induced by glucocorticoid dexamethasone, but suppressed by insulin in Fao cells. Finally, we showed that the over-expression of ALT1 and ALT2 in Fao cells directly increased glucose output. We have shown the similarity and difference in the regulation of ALT isoforms in gluconeogenic conditions at the protein level, supporting that ALT isoenzymes play an important role in glucose metabolism and may be implicated the development of insulin resistance and diabetes. Copyright © 2015 John Wiley & Sons, Ltd.

  20. THE INVESTIGATION OF PRODUCTIVE AND RECEPTIVE COMPETENCE IN V+N AND ADJ+N COLLOCATIONS AMONG INDONESIAN EFL LEARNERS

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    Saudin Saudin

    2017-05-01

    Full Text Available The important role of collocation in learners’ language proficiency has been acknowledged widely. In Systemic Functional Linguistics (SFL, collocation is known as one prominent member of the super-ordinate lexical cohesion, which contributes significantly to the textual coherence, together with grammatical cohesion and structural cohesion (Halliday & Hasan, 1985. Collocation is also viewed as the hallmark of truly advanced English learners since the higher the learners’ proficiency is, the more they tend to use collocation (Bazzaz & Samad, 2011; Hsu, 2007; Zhang, 1993. Further, knowledge of collocation is regarded as part of the native speakers’ communicative competence (Bazzaz & Samad, 2011; and lack of the knowledge is the most important sign of foreignness among foreign language learners (McArthur, 1992; McCarthy, 1990. Taking the importance of collocation into account, this study is aimed to shed light on Indonesian EFL learners’ levels of collocational competence. In the study, the collocational competence is restricted to v+n and adj+n of collocation but broken down into productive and receptive competence, about which little work has been done (Henriksen, 2013. For this purpose, 49 second-year students of an English department in a state polytechnic were chosen as the subjects. Two sets of tests (filling in the blanks and multiple-choice were administered to obtain the data of the subjects’ levels of productive and receptive competence and to gain information of which type was more problematic for the learners. The test instruments were designed by referring to Brashi’s (2006 test model, and Koya’s (2003. In the analysis of the data, interpretive-qualitative method was used primarily to obtain broad explanatory information. The data analysis showed that the scores of productive competence were lower than those of receptive competence in both v+n and adj+n collocation. The analysis also revealed that the scores of productive

  1. Microparticles released from Mycobacterium tuberculosis-infected human macrophages contain increased levels of the type I interferon inducible proteins including ISG15.

    Science.gov (United States)

    Hare, Nathan J; Chan, Brian; Chan, Edwina; Kaufman, Kimberley L; Britton, Warwick J; Saunders, Bernadette M

    2015-09-01

    Microparticles (MPs) are small membranous particles (100-1000 nm) released under normal steady-state conditions and are thought to provide a communication network between host cells. Previous studies demonstrated that Mycobacterium tuberculosis (M. tb) infection of macrophages increased the release of MPs, and these MPs induced a proinflammatory response from uninfected macrophages in vitro and in vivo following their transfer into uninfected mice. To determine how M. tb infection modulates the protein composition of the MPs, and if this contributes to their proinflammatory properties, we compared the proteomes of MPs derived from M. tb-infected (TBinf-MP) and uninfected human THP-1 monocytic cells. MP proteins were analyzed by GeLC-MS/MS with spectral counting revealing 68 proteins with statistically significant differential abundances. The 42 proteins increased in abundance in TBinf-MPs included proteins associated with immune function (7), lysosomal/endosomal maturation (4), vesicular formation (12), nucleosome proteins (4), and antigen processing (9). Prominent among these were the type I interferon inducible proteins, ISG15, IFIT1, IFIT2, and IFIT3. Exposure of uninfected THP-1 cells to TBinf-MPs induced increased gene expression of isg15, ifit1, ifit2, and ifit3 and the release of proinflammatory cytokines. These proteins may regulate the proinflammatory potential of the MPs and provide candidate biomarkers for M. tb infection. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. Analysis of the key elements of FFAT-like motifs identifies new proteins that potentially bind VAP on the ER, including two AKAPs and FAPP2.

    Directory of Open Access Journals (Sweden)

    Veronika Mikitova

    Full Text Available BACKGROUND: Two phenylalanines (FF in an acidic tract (FFAT-motifs were originally described as having seven elements: an acidic flanking region followed by 6 residues (EFFDA-E. Such motifs are found in several lipid transfer protein (LTP families, and they interact with a protein on the cytosolic face of the ER called vesicle-associated membrane protein-associated protein (VAP. Mutation of which causes ER stress and motor neuron disease, making it important to determine which proteins bind VAP. Among other proteins that bind VAP, some contain FFAT-like motifs that are missing one or more of the seven elements. Defining how much variation is tolerated in FFAT-like motifs is a preliminary step prior to the identification of the full range of VAP interactors. RESULTS: We used a quantifiable in vivo system that measured ER targeting in a reporter yeast strain that over-expressed VAP to study the effect of substituting different elements of FFAT-like motifs in turn. By defining FFAT-like motifs more widely than before, we found them in novel proteins the functions of which had not previously been directly linked to the ER, including: two PKA anchoring proteins, AKAP220 and AKAP110; a family of plant LTPs; and the glycolipid LTP phosphatidylinositol-four-phosphate adaptor-protein-2 (FAPP-2. CONCLUSION: All of the seven essential elements of a FFAT motif tolerate variation, and weak targeting to the ER via VAP is still detected if two elements are substituted. In addition to the strong FFAT motifs already known, there are additional proteins with weaker FFAT-like motifs, which might be functionally important VAP interactors.

  3. Impact of WhatsApp on Learning and Retention of Collocation Knowledge among Iranian EFL Learners

    Directory of Open Access Journals (Sweden)

    Zahra Ashiyan

    2016-10-01

    Full Text Available During the recent technological years, language learning has been attempted to transform its path from the conventional methods to instrumental applications. Mobile phone provides people to reach and exchange information through chats (WhatsApp. It is a tool or mode that means the facilities are used for main purposes. The unique features of the application are its compatibility to exchange information, enhance communication and relationship. A mobile phone provides to download, upload and store learning materials and information files. The purpose of the current study was to investigate the use and effect of mobile applications such as WhatsApp on school work and out of school work. In this way, Oxford Placement Test (OPT was conducted among 80 learners in order to select intermediate EFL learners.  In total, 60 participants whose scores were 70 or higher were elected as the intermediate level and were divided into experimental and control groups. In order to control the reliability of the collocation pretest, the test was pilot studied on 15 learners. Then, the pretest was conducted to measure the learner’s collocation knowledge in both of the groups. The experimental group frequently installed WhatsApp application in order to learning and practicing new collocations in order to learning and practicing new collocations, while the control group did not use any tool for learning them. An immediate posttest after the treatment was administered. The results in each group were statistically evaluated and the findings manifested that the experimental group who used WhatsApp application in learning collocation significantly outperformed the control group in posttest. Thus usage of WhatsApp application to acquire collocations can reinforce and enhance the process of collocations acquisition and it can guarantee retention of collocations. This study also prepares pedagogical implications for utilizing mobile application as an influential instrument

  4. English collocations: A novel approach to teaching the language's last bastion

    Directory of Open Access Journals (Sweden)

    Rafe S. Zaabalawi

    2017-01-01

    Full Text Available Collocations are a class of idiomatic expressions comprised of a sequence of words which, for mostly arbitrary reasons, occur together in a prescribed order. Collocations are not necessarily grammatical and/or cannot be generated through knowledge of rules or formulae. Therefore, they are often not easily mastered by EFL learners and typically only dealt with during the latter phase of second language apprenticeship. Literature has mostly examined the phenomenon of collocations from one of two perspectives. First, there are studies focusing on error analysis and contingent pedagogical advice. Second, there is research concerned with theory development; a genre associated with a specific methodological limitations. This study reports on data pertaining to a novel approach to learning collocations; one based on a learner's incidental discovery of such structures in written texts. Our research question is: will students who have been introduced to and practiced specific collocations in reading texts be inclined to naturally use such exemplars appropriately in novel/unfamiliar subsequent contexts? Findings have implications for EFL teachers and those concerned with curriculum development.

  5. Least-squares collocation meshless approach for radiative heat transfer in absorbing and scattering media

    International Nuclear Information System (INIS)

    Liu, L.H.; Tan, J.Y.

    2007-01-01

    A least-squares collocation meshless method is employed for solving the radiative heat transfer in absorbing, emitting and scattering media. The least-squares collocation meshless method for radiative transfer is based on the discrete ordinates equation. A moving least-squares approximation is applied to construct the trial functions. Except for the collocation points which are used to construct the trial functions, a number of auxiliary points are also adopted to form the total residuals of the problem. The least-squares technique is used to obtain the solution of the problem by minimizing the summation of residuals of all collocation and auxiliary points. Three numerical examples are studied to illustrate the performance of this new solution method. The numerical results are compared with the other benchmark approximate solutions. By comparison, the results show that the least-squares collocation meshless method is efficient, accurate and stable, and can be used for solving the radiative heat transfer in absorbing, emitting and scattering media

  6. A two-level stochastic collocation method for semilinear elliptic equations with random coefficients

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Luoping; Zheng, Bin; Lin, Guang; Voulgarakis, Nikolaos

    2017-05-01

    In this work, we propose a novel two-level discretization for solving semilinear elliptic equations with random coefficients. Motivated by the two-grid method for deterministic partial differential equations (PDEs) introduced by Xu, our two-level stochastic collocation method utilizes a two-grid finite element discretization in the physical space and a two-level collocation method in the random domain. In particular, we solve semilinear equations on a coarse mesh $\\mathcal{T}_H$ with a low level stochastic collocation (corresponding to the polynomial space $\\mathcal{P}_{P}$) and solve linearized equations on a fine mesh $\\mathcal{T}_h$ using high level stochastic collocation (corresponding to the polynomial space $\\mathcal{P}_p$). We prove that the approximated solution obtained from this method achieves the same order of accuracy as that from solving the original semilinear problem directly by stochastic collocation method with $\\mathcal{T}_h$ and $\\mathcal{P}_p$. The two-level method is computationally more efficient, especially for nonlinear problems with high random dimensions. Numerical experiments are also provided to verify the theoretical results.

  7. The nuclear basket proteins Mlp1p and Mlp2p are part of a dynamic interactome including Esc1p and the proteasome

    Science.gov (United States)

    Niepel, Mario; Molloy, Kelly R.; Williams, Rosemary; Farr, Julia C.; Meinema, Anne C.; Vecchietti, Nicholas; Cristea, Ileana M.; Chait, Brian T.; Rout, Michael P.; Strambio-De-Castillia, Caterina

    2013-01-01

    The basket of the nuclear pore complex (NPC) is generally depicted as a discrete structure of eight protein filaments that protrude into the nucleoplasm and converge in a ring distal to the NPC. We show that the yeast proteins Mlp1p and Mlp2p are necessary components of the nuclear basket and that they also embed the NPC within a dynamic protein network, whose extended interactome includes the spindle organizer, silencing factors, the proteasome, and key components of messenger ribonucleoproteins (mRNPs). Ultrastructural observations indicate that the basket reduces chromatin crowding around the central transporter of the NPC and might function as a docking site for mRNP during nuclear export. In addition, we show that the Mlps contribute to NPC positioning, nuclear stability, and nuclear envelope morphology. Our results suggest that the Mlps are multifunctional proteins linking the nuclear transport channel to multiple macromolecular complexes involved in the regulation of gene expression and chromatin maintenance. PMID:24152732

  8. Spectral collocation for multiparameter eigenvalue problems arising from separable boundary value problems

    Science.gov (United States)

    Plestenjak, Bor; Gheorghiu, Călin I.; Hochstenbach, Michiel E.

    2015-10-01

    In numerous science and engineering applications a partial differential equation has to be solved on some fairly regular domain that allows the use of the method of separation of variables. In several orthogonal coordinate systems separation of variables applied to the Helmholtz, Laplace, or Schrödinger equation leads to a multiparameter eigenvalue problem (MEP); important cases include Mathieu's system, Lamé's system, and a system of spheroidal wave functions. Although multiparameter approaches are exploited occasionally to solve such equations numerically, MEPs remain less well known, and the variety of available numerical methods is not wide. The classical approach of discretizing the equations using standard finite differences leads to algebraic MEPs with large matrices, which are difficult to solve efficiently. The aim of this paper is to change this perspective. We show that by combining spectral collocation methods and new efficient numerical methods for algebraic MEPs it is possible to solve such problems both very efficiently and accurately. We improve on several previous results available in the literature, and also present a MATLAB toolbox for solving a wide range of problems.

  9. Stochastic collocation-based finite element of structural nonlinear dynamics with application in composite structures

    Directory of Open Access Journals (Sweden)

    Sepahvand K.

    2016-01-01

    Full Text Available Stochastic analysis of structures having nonlinearity by means of sampling methods leads to expensive cost in term of computational time. In contrast, non-sampling methods based on the spectral representation of uncertainty are very efficient with comparable accurate results. In this pa- per, the application of spectral methods to nonlinear dynamics of structures with random parameters is investigated. The impact of the parameter randomness on structural responses has been consid- ered. To this end, uncertain parameters and the structure responses are represented using the gPC expansions with unknown deterministic coefficients and random orthogonal polynomial basis. The deterministic finite element model of the structure is used as black-box and it is executed on a set of random collocation points. As the sample structure responses are estimated, a nonlinear optimization process is employed to calculate the unknown coefficients. The method has this main advantage that can be used for complicated nonlinear structural dynamic problems for which the deterministic FEM model has been already developed. Furthermore, it is very time efficient in comparison with sampling methods, as MC simulations. The application of the method is applied to the nonlinear transient analysis of composite beam structures including uncertain quadratic random damping. The results show that the proposed method can capture the large range of uncertainty in input parameters as well as in structural dynamic responses while it is too time-efficient.

  10. Trajectory Planning of Satellite Formation Flying using Nonlinear Programming and Collocation

    Science.gov (United States)

    Lim, Hyung-Chu; Bang, Hyochoong

    2008-12-01

    Recently, satellite formation flying has been a topic of significant research interest in aerospace society because it provides potential benefits compared to a large spacecraft. Some techniques have been proposed to design optimal formation trajectories minimizing fuel consumption in the process of formation configuration or reconfiguration. In this study, a method is introduced to build fuel-optimal trajectories minimizing a cost function that combines the total fuel consumption of all satellites and assignment of fuel consumption rate for each satellite. This approach is based on collocation and nonlinear programming to solve constraints for collision avoidance and the final configuration. New constraints of nonlinear equality or inequality are derived for final configuration, and nonlinear inequality constraints are established for collision avoidance. The final configuration constraints are that three or more satellites should form a projected circular orbit and make an equilateral polygon in the horizontal plane. Example scenarios, including these constraints and the cost function, are simulated by the method to generate optimal trajectories for the formation configuration and reconfiguration of multiple satellites.

  11. Trajectory Planning of Satellite Formation Flying using Nonlinear Programming and Collocation

    Directory of Open Access Journals (Sweden)

    Hyung-Chu Lim

    2008-12-01

    Full Text Available Recently, satellite formation flying has been a topic of significant research interest in aerospace society because it provides potential benefits compared to a large spacecraft. Some techniques have been proposed to design optimal formation trajectories minimizing fuel consumption in the process of formation configuration or reconfiguration. In this study, a method is introduced to build fuel-optimal trajectories minimizing a cost function that combines the total fuel consumption of all satellites and assignment of fuel consumption rate for each satellite. This approach is based on collocation and nonlinear programming to solve constraints for collision avoidance and the final configuration. New constraints of nonlinear equality or inequality are derived for final configuration, and nonlinear inequality constraints are established for collision avoidance. The final configuration constraints are that three or more satellites should form a projected circular orbit and make an equilateral polygon in the horizontal plane. Example scenarios, including these constraints and the cost function, are simulated by the method to generate optimal trajectories for the formation configuration and reconfiguration of multiple satellites.

  12. The Effect of Lexical Knowledge of Collocation on Student’s Reading Comprehension

    Directory of Open Access Journals (Sweden)

    Eva Yuni Rahmawati

    2017-06-01

    Full Text Available The aim of this research was to find out the effects of lexical collocation on Students’ Reading Comprehension. The method used is a survey method. Sample was taken as many as 60 people with simple random technique. Data was collected by test directly to the sample. Data analysis using descriptive statistics such as finding the mean, median, mode, standard deviation, and inferential statistics is to look for regression by using ANOVA and coefficient table. The results indicate that there is a significant effect of lexical knowledge of collocation on students reading comprehension. The result has shown the score of Sig = 0,043ttable.. Lexical knowledge of collocation can increase students reading comprehension abilities

  13. THE CASE FOR VERB-ADJECTIVE COLLOCATIONS: CORPUS-BASED ANALYSIS AND LEXICOGRAPHICAL TREATMENT

    Directory of Open Access Journals (Sweden)

    Moisés Almela

    2011-10-01

    Full Text Available This article explores a type of co-occurrence pattern which cannot be adequately described by existing models of collocation, and for which combinatory dictionaries have yet failed to provide sufficient information. The phenomenon of “oblique inter-collocation”, as I propose to call it, is characterised by a concatenation of syntagmatic preferences which partially contravenes the habitual grammatical order of semantic selection. In particular, I will examine some of the effects which the verb cause exerts on the distribution of attributive adjectives in the context of specific noun classes. The procedure for detecting and describing patterns of oblique inter-collocation is illustrated by means of SketchEngine corpus query tools. Based on the data extracted from a large-scale corpus, this paper carries out a critical analysis of the micro-structure in Oxford Collocations Dictionary.

  14. Preconditioning cubic spline collocation method by FEM and FDM for elliptic equations

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Sang Dong [KyungPook National Univ., Taegu (Korea, Republic of)

    1996-12-31

    In this talk we discuss the finite element and finite difference technique for the cubic spline collocation method. For this purpose, we consider the uniformly elliptic operator A defined by Au := -{Delta}u + a{sub 1}u{sub x} + a{sub 2}u{sub y} + a{sub 0}u in {Omega} (the unit square) with Dirichlet or Neumann boundary conditions and its discretization based on Hermite cubic spline spaces and collocation at the Gauss points. Using an interpolatory basis with support on the Gauss points one obtains the matrix A{sub N} (h = 1/N).

  15. Cubic Hermite Collocation Method for Solving Boundary Value Problems with Dirichlet, Neumann, and Robin Conditions

    Directory of Open Access Journals (Sweden)

    Ishfaq Ahmad Ganaie

    2014-01-01

    Full Text Available Cubic Hermite collocation method is proposed to solve two point linear and nonlinear boundary value problems subject to Dirichlet, Neumann, and Robin conditions. Using several examples, it is shown that the scheme achieves the order of convergence as four, which is superior to various well known methods like finite difference method, finite volume method, orthogonal collocation method, and polynomial and nonpolynomial splines and B-spline method. Numerical results for both linear and nonlinear cases are presented to demonstrate the effectiveness of the scheme.

  16. Collocation methods for the solution of eigenvalue problems for singular ordinary differential equations

    Directory of Open Access Journals (Sweden)

    Winfried Auzinger

    2006-01-01

    Full Text Available We demonstrate that eigenvalue problems for ordinary differential equations can be recast in a formulation suitable for the solution by polynomial collocation. It is shown that the well-posedness of the two formulations is equivalent in the regular as well as in the singular case. Thus, a collocation code equipped with asymptotically correct error estimation and adaptive mesh selection can be successfully applied to compute the eigenvalues and eigenfunctions efficiently and with reliable control of the accuracy. Numerical examples illustrate this claim.

  17. Solutions of First-Order Volterra Type Linear Integrodifferential Equations by Collocation Method

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    Olumuyiwa A. Agbolade

    2017-01-01

    Full Text Available The numerical solutions of linear integrodifferential equations of Volterra type have been considered. Power series is used as the basis polynomial to approximate the solution of the problem. Furthermore, standard and Chebyshev-Gauss-Lobatto collocation points were, respectively, chosen to collocate the approximate solution. Numerical experiments are performed on some sample problems already solved by homotopy analysis method and finite difference methods. Comparison of the absolute error is obtained from the present method and those from aforementioned methods. It is also observed that the absolute errors obtained are very low establishing convergence and computational efficiency.

  18. Formulaic Language and Collocations in German Essays: From Corpus-Driven Data to Corpus-Based Materials

    Science.gov (United States)

    Krummes, Cedric; Ensslin, Astrid

    2015-01-01

    Whereas there exists a plethora of research on collocations and formulaic language in English, this article contributes towards a somewhat less developed area: the understanding and teaching of formulaic language in German as a foreign language. It analyses formulaic sequences and collocations in German writing (corpus-driven) and provides modern…

  19. The Challenge of English Language Collocation Learning in an ES/FL Environment: PRC Students in Singapore

    Science.gov (United States)

    Ying, Yang

    2015-01-01

    This study aimed to seek an in-depth understanding about English collocation learning and the development of learner autonomy through investigating a group of English as a Second Language (ESL) learners' perspectives and practices in their learning of English collocations using an AWARE approach. A group of 20 PRC students learning English in…

  20. Identification and characterization of novel ERC-55 interacting proteins: evidence for the existence of several ERC-55 splicing variants; including the cytosolic ERC-55-C.

    Science.gov (United States)

    Ludvigsen, Maja; Jacobsen, Christian; Maunsbach, Arvid B; Honoré, Bent

    2009-12-01

    ERC-55, encoded from RCN2, is localized in the ER and belongs to the CREC protein family. ERC-55 is involved in various diseases and abnormal cell behavior, however, the function is not well defined and it has controversially been reported to interact with a cytosolic protein, the vitamin D receptor. We have used a number of proteomic techniques to further our functional understanding of ERC-55. By affinity purification, we observed interaction with a large variety of proteins, including those secreted and localized outside of the secretory pathway, in the cytosol and also in various organelles. We confirm the existence of several ERC-55 splicing variants including ERC-55-C localized in the cytosol in association with the cytoskeleton. Localization was verified by immunoelectron microscopy and sub-cellular fractionation. Interaction of lactoferrin, S100P, calcyclin (S100A6), peroxiredoxin-6, kininogen and lysozyme with ERC-55 was further studied in vitro by SPR experiments. Interaction of S100P requires [Ca(2+)] of approximately 10(-7) M or greater, while calcyclin interaction requires [Ca(2+)] of >10(-5) M. Interaction with peroxiredoxin-6 is independent of Ca(2+). Co-localization of lactoferrin, S100P and calcyclin with ERC-55 in the perinuclear area was analyzed by fluorescence confocal microscopy. The functional variety of the interacting proteins indicates a broad spectrum of ERC-55 activities such as immunity, redox homeostasis, cell cycle regulation and coagulation.

  1. Lack of Detection of Bt Sugarcane Cry1Ab and NptII DNA and Proteins in Sugarcane Processing Products Including Raw Sugar

    Directory of Open Access Journals (Sweden)

    Adriana Cheavegatti-Gianotto

    2018-03-01

    Full Text Available Brazil is the largest sugarcane producer and the main sugar exporter in the world. The industrial processes applied by Brazilian mills are very efficient in producing highly purified sugar and ethanol. Literature presents evidence of lack of DNA/protein in these products, regardless of the nature of sugarcane used as raw material. Recently CTNBio, the Brazilian biosafety authority, has approved the first biotechnology-derived sugarcane variety for cultivation, event CTC175-A, which expresses the Cry1Ab protein to control the sugarcane borer (Diatraea saccharalis. The event also expresses neomycin-phosphotransferase type II (NptII protein used as selectable marker during the transformation process. Because of the high purity of sugar and ethanol produced from genetically modified sugarcane, these end-products should potentially be classified as “pure substances, chemically defined,” by Brazilian Biosafety Law No. 11.105. If this classification is to be adopted, these substances are not considered as “GMO derivatives” and fall out of the scope of Law No. 11.105. In order to assess sugar composition and quality, we evaluate Cry1Ab and NptII expression in several sugarcane tissues and in several fractions from laboratory-scale processing of event CTC175-A for the presence of these heterologous proteins as well as for the presence of traces of recombinant DNA. The results of these studies show that CTC175-A presents high expression of Cry1Ab in leaves and barely detectable expression of heterologous proteins in stalks. We also evaluated the presence of ribulose-1,5-bisphosphate carboxylase/oxygenase protein and DNA in the fractions of the industrial processing of conventional Brazilian sugarcane cultivars. Results from both laboratory and industrial processing were concordant, demonstrating that DNA and protein are not detected in the clarified juice and downstream processed fractions, including ethanol and raw sugar, indicating that protein

  2. Parallel algorithm of trigonometric collocation method in nonlinear dynamics of rotors

    Czech Academy of Sciences Publication Activity Database

    Musil, Tomáš; Jakl, Ondřej

    2007-01-01

    Roč. 1, č. 2 (2007), s. 555-564 ISSN 1802-680X. [Výpočtová mechanika 2007. Hrad Nečtiny, 05.11.2007-07.11.2007] Institutional research plan: CEZ:AV0Z20760514; CEZ:AV0Z30860518 Keywords : rotor system * trigonometric collocation * parallel computation Subject RIV: JR - Other Machinery

  3. Utilizing Lexical Data from a Web-Derived Corpus to Expand Productive Collocation Knowledge

    Science.gov (United States)

    Wu, Shaoqun; Witten, Ian H.; Franken, Margaret

    2010-01-01

    Collocations are of great importance for second language learners, and a learner's knowledge of them plays a key role in producing language fluently (Nation, 2001: 323). In this article we describe and evaluate an innovative system that uses a Web-derived corpus and digital library software to produce a vast concordance and present it in a way…

  4. Your Participation Is "Greatly/Highly" Appreciated: Amplifier Collocations in L2 English

    Science.gov (United States)

    Edmonds, Amanda; Gudmestad, Aarnes

    2014-01-01

    The current study sets out to investigate collocational knowledge for a set of 13 English amplifiers among native and nonnative speakers of English, by providing a partial replication of one of the projects reported on in Granger (1998). The project combines both phraseological and distributional approaches to research into formulaic language to…

  5. A stochastic collocation method for the second order wave equation with a discontinuous random speed

    KAUST Repository

    Motamed, Mohammad

    2012-08-31

    In this paper we propose and analyze a stochastic collocation method for solving the second order wave equation with a random wave speed and subjected to deterministic boundary and initial conditions. The speed is piecewise smooth in the physical space and depends on a finite number of random variables. The numerical scheme consists of a finite difference or finite element method in the physical space and a collocation in the zeros of suitable tensor product orthogonal polynomials (Gauss points) in the probability space. This approach leads to the solution of uncoupled deterministic problems as in the Monte Carlo method. We consider both full and sparse tensor product spaces of orthogonal polynomials. We provide a rigorous convergence analysis and demonstrate different types of convergence of the probability error with respect to the number of collocation points for full and sparse tensor product spaces and under some regularity assumptions on the data. In particular, we show that, unlike in elliptic and parabolic problems, the solution to hyperbolic problems is not in general analytic with respect to the random variables. Therefore, the rate of convergence may only be algebraic. An exponential/fast rate of convergence is still possible for some quantities of interest and for the wave solution with particular types of data. We present numerical examples, which confirm the analysis and show that the collocation method is a valid alternative to the more traditional Monte Carlo method for this class of problems. © 2012 Springer-Verlag.

  6. Symmetry-preserving discretization of Navier-Stokes equations on collocated unstructured grids

    NARCIS (Netherlands)

    Trias, F.X.; Lehmkuhl, O.; Oliva, A.; Pérez-Segarra, C.D.; Verstappen, R.W.C.P.

    2014-01-01

    A fully-conservative discretization is presented in this paper. The same principles followed earlier are generalized for unstructured meshes. Here, a collocated-mesh scheme is preferred over a staggered one due to its simpler form for such meshes. The basic idea behind this approach remains the

  7. Strategies in Translating Collocations in Religious Texts from Arabic into English

    Science.gov (United States)

    Dweik, Bader S.; Shakra, Mariam M. Abu

    2010-01-01

    The present study investigated the strategies adopted by students in translating specific lexical and semantic collocations in three religious texts namely, the Holy Quran, the Hadith and the Bible. For this purpose, the researchers selected a purposive sample of 35 MA translation students enrolled in three different public and private Jordanian…

  8. Action Research: Applying a Bilingual Parallel Corpus Collocational Concordancer to Taiwanese Medical School EFL Academic Writing

    Science.gov (United States)

    Reynolds, Barry Lee

    2016-01-01

    Lack of knowledge in the conventional usage of collocations in one's respective field of expertise cause Taiwanese students to produce academic writing that is markedly different than more competent writing. This is because Taiwanese students are first and foremost English as a Foreign language (EFL) readers and may have difficulties picking up on…

  9. The Effect of Corpus-Based Activities on Verb-Noun Collocations in EFL Classes

    Science.gov (United States)

    Ucar, Serpil; Yükselir, Ceyhun

    2015-01-01

    This current study sought to reveal the impacts of corpus-based activities on verb-noun collocation learning in EFL classes. This study was carried out on two groups--experimental and control groups- each of which consists of 15 students. The students were preparatory class students at School of Foreign Languages, Osmaniye Korkut Ata University.…

  10. A Comparison of the Performance Improvement by Collocated and Noncollocated Active Damping in Motion Systems

    NARCIS (Netherlands)

    Babakhani, B.; de Vries, Theodorus J.A.; van Amerongen, J.

    2012-01-01

    In this paper, both collocated and noncollocated active vibration control (AVC) of a the vibrations in a motion system are considered. Pole-zero plots of both the AVC loop and the motion-control (MC) loop are used to analyze the effect of the applied active damping on the system dynamics. Using

  11. Pattern recognition and lithological interpretation of collocated seismic and magnetotelluric models using self-organizing maps

    Science.gov (United States)

    Bauer, K.; Muñoz, G.; Moeck, I.

    2012-05-01

    Joint interpretation of models from seismic tomography and inversion of magnetotelluric (MT) data is an efficient approach to determine the lithology of the subsurface. Statistical methods are well established but were developed for only two types of models so far (seismic P velocity and electrical resistivity). We apply self-organizing maps (SOMs), which have no limitations in the number of parameters considered in the joint interpretation. Our SOM method includes (1) generation of data vectors from the seismic and MT images, (2) unsupervised learning, (3) definition of classes by algorithmic segmentation of the SOM using image processing techniques and (4) application of learned knowledge to classify all data vectors and assign a lithological interpretation for each data vector. We apply the workflow to collocated P velocity, vertical P-velocity gradient and resistivity models derived along a 40 km profile around the geothermal site Groß Schönebeck in the Northeast German Basin. The resulting lithological model consists of eight classes covering Cenozoic, Mesozoic and Palaeozoic sediments down to 5 km depth. There is a remarkable agreement between the litho-type distribution from the SOM analysis and regional marker horizons interpolated from sparse 2-D industrial reflection seismic data. The most interesting features include (1) characteristic properties of the Jurassic (low P-velocity gradients, low resistivity values) interpreted as the signature of shales, and (2) a pattern within the Upper Permian Zechstein layer with low resistivity and increased P-velocity values within the salt depressions and increased resistivity and decreased P velocities in the salt pillows. The latter is explained in our interpretation by flow of less dense salt matrix components to form the pillows while denser and more brittle evaporites such as anhydrite remain in place during the salt mobilization.

  12. Multi-Index Monte Carlo and stochastic collocation methods for random PDEs

    KAUST Repository

    Nobile, Fabio

    2016-01-09

    In this talk we consider the problem of computing statistics of the solution of a partial differential equation with random data, where the random coefficient is parametrized by means of a finite or countable sequence of terms in a suitable expansion. We describe and analyze a Multi-Index Monte Carlo (MIMC) and a Multi-Index Stochastic Collocation method (MISC). the former is both a stochastic version of the combination technique introduced by Zenger, Griebel and collaborators and an extension of the Multilevel Monte Carlo (MLMC) method first described by Heinrich and Giles. Instead of using firstorder differences as in MLMC, MIMC uses mixed differences to reduce the variance of the hierarchical differences dramatically. This in turn yields new and improved complexity results, which are natural generalizations of Giles s MLMC analysis, and which increase the domain of problem parameters for which we achieve the optimal convergence, O(TOL-2). On the same vein, MISC is a deterministic combination technique based on mixed differences of spatial approximations and quadratures over the space of random data. Provided enough mixed regularity, MISC can achieve better complexity than MIMC. Moreover, we show that in the optimal case the convergence rate of MISC is only dictated by the convergence of the deterministic solver applied to a one-dimensional spatial problem. We propose optimization procedures to select the most effective mixed differences to include in MIMC and MISC. Such optimization is a crucial step that allows us to make MIMC and MISC computationally effective. We finally show the effectiveness of MIMC and MISC with some computational tests, including tests with a infinite countable number of random parameters.

  13. Degradation of Redox-Sensitive Proteins including Peroxiredoxins and DJ-1 is Promoted by Oxidation-induced Conformational Changes and Ubiquitination

    Science.gov (United States)

    Song, In-Kang; Lee, Jae-Jin; Cho, Jin-Hwan; Jeong, Jihye; Shin, Dong-Hae; Lee, Kong-Joo

    2016-10-01

    Reactive oxygen species (ROS) are key molecules regulating various cellular processes. However, what the cellular targets of ROS are and how their functions are regulated is unclear. This study explored the cellular proteomic changes in response to oxidative stress using H2O2 in dose- and recovery time-dependent ways. We found discernible changes in 76 proteins appearing as 103 spots on 2D-PAGE. Of these, Prxs, DJ-1, UCH-L3 and Rla0 are readily oxidized in response to mild H2O2 stress, and then degraded and active proteins are newly synthesized during recovery. In studies designed to understand the degradation process, multiple cellular modifications of redox-sensitive proteins were identified by peptide sequencing with nanoUPLC-ESI-q-TOF tandem mass spectrometry and the oxidative structural changes of Prx2 explored employing hydrogen/deuterium exchange-mass spectrometry (HDX-MS). We found that hydrogen/deuterium exchange rate increased in C-terminal region of oxidized Prx2, suggesting the exposure of this region to solvent under oxidation. We also found that Lys191 residue in this exposed C-terminal region of oxidized Prx2 is polyubiquitinated and the ubiquitinated Prx2 is readily degraded in proteasome and autophagy. These findings suggest that oxidation-induced ubiquitination and degradation can be a quality control mechanism of oxidized redox-sensitive proteins including Prxs and DJ-1.

  14. batman Interacts with polycomb and trithorax group genes and encodes a BTB/POZ protein that is included in a complex containing GAGA factor.

    Science.gov (United States)

    Faucheux, M; Roignant, J-Y; Netter, S; Charollais, J; Antoniewski, C; Théodore, L

    2003-02-01

    Polycomb and trithorax group genes maintain the appropriate repressed or activated state of homeotic gene expression throughout Drosophila melanogaster development. We have previously identified the batman gene as a Polycomb group candidate since its function is necessary for the repression of Sex combs reduced. However, our present genetic analysis indicates functions of batman in both activation and repression of homeotic genes. The 127-amino-acid Batman protein is almost reduced to a BTB/POZ domain, an evolutionary conserved protein-protein interaction domain found in a large protein family. We show that this domain is involved in the interaction between Batman and the DNA binding GAGA factor encoded by the Trithorax-like gene. The GAGA factor and Batman codistribute on polytene chromosomes, coimmunoprecipitate from nuclear embryonic and larval extracts, and interact in the yeast two-hybrid assay. Batman, together with the GAGA factor, binds to MHS-70, a 70-bp fragment of the bithoraxoid Polycomb response element. This binding, like that of the GAGA factor, requires the presence of d(GA)n sequences. Together, our results suggest that batman belongs to a subset of the Polycomb/trithorax group of genes that includes Trithorax-like, whose products are involved in both activation and repression of homeotic genes.

  15. Synergistic multi-sensor and multi-frequency retrieval of cloud ice water path constrained by CloudSat collocations

    International Nuclear Information System (INIS)

    Islam, Tanvir; Srivastava, Prashant K.

    2015-01-01

    The cloud ice water path (IWP) is one of the major parameters that have a strong influence on earth's radiation budget. Onboard satellite sensors are recognized as valuable tools to measure the IWP in a global scale. Albeit, active sensors such as the Cloud Profiling Radar (CPR) onboard the CloudSat satellite has better capability to measure the ice water content profile, thus, its vertical integral, IWP, than any passive microwave (MW) or infrared (IR) sensors. In this study, we investigate the retrieval of IWP from MW and IR sensors, including AMSU-A, MHS, and HIRS instruments on-board the N19 satellite, such that the retrieval is consistent with the CloudSat IWP estimates. This is achieved through the collocations between the passive satellite measurements and CloudSat scenes. Potential benefit of synergistic multi-sensor multi-frequency retrieval is investigated. Two modeling approaches are explored for the IWP retrieval – generalized linear model (GLM) and neural network (NN). The investigation has been carried out over both ocean and land surface types. The MW/IR synergy is found to be retrieved more accurate IWP than the individual AMSU-A, MHS, or HIRS measurements. Both GLM and NN approaches have been able to exploit the synergistic retrievals. - Highlights: • MW/IR synergy is investigated for IWP retrieval. • The IWP retrieval is modeled using CloudSat collocations. • Two modeling approaches are explored – GLM and ANN. • MW/IR synergy performs better than the MW or IR only retrieval

  16. Language Proficiency, Collocational Knowledge and the Role of L1 Transfer: A Correlational Study of Iranian EFL Learners

    Directory of Open Access Journals (Sweden)

    Mustapha Hajebi

    2017-12-01

    Full Text Available The present study investigates the correlation between language proficiency, collocations and the role of L1 transfer with collocations. This is a quantitative research. The research places more emphases on collecting data in the form of numbers. It is also experimental research in the sense that it tests participants to measure their variables. The participants of the study were 57 Persian B.A students, both male and female from Islamic Azad University of Bandar Abbas, Iran. The results showed that there is a significant relationship between Iranian subjects’ language proficiency, as measured by the Michigan proficiency test and their knowledge of collocations, as measured by their performance on a collocation test designed for the current study. The results obtained from the research indicate that Iranian EFL learners are more likely to use the right collocation in cases of L1 transfer. This suggests that positive transfer plays a major role when it comes to EFL learners’ ability to produce the right collocations in their L2. The findings of this study have some implications for language teaching. Teachers can put emphasis on the inclusion of selected grammatical and lexical collocations in reading comprehension passages.

  17. [Spatio-Temporal Bioelectrical Brain Activity Organization during Reading Syntagmatic and Paradigmatic Collocations by Students with Different Foreign Language Proficiency].

    Science.gov (United States)

    Sokolova, L V; Cherkasova, A S

    2015-01-01

    Texts or words/pseudowords are often used as stimuli for human verbal activity research. Our study pays attention to decoding processes of grammatical constructions consisted of two-three words--collocations. Russian and English collocation sets without any narrative were presented to Russian-speaking students with different English language skill. Stimulus material had two types of collocations: paradigmatic and syntagmatic. 30 students (average age--20.4 ± 0.22) took part in the study, they were divided into two equal groups depending on their English language skill (linguists/nonlinguists). During reading brain bioelectrical activity of cortex has been registered from 12 electrodes in alfa-, beta-, theta-bands. Coherent function reflecting cooperation of different cortical areas during reading collocations has been analyzed. Increase of interhemispheric and diagonal connections while reading collocations in different languages in the group of students with low knowledge of foreign language testifies of importance of functional cooperation between the hemispheres. It has been found out that brain bioelectrical activity of students with good foreign language knowledge during reading of all collocation types in Russian and English is characterized by economization of nervous substrate resources compared to nonlinguists. Selective activation of certain cortical areas has also been observed (depending on the grammatical construction type) in nonlinguists group that is probably related to special decoding system which processes presented stimuli. Reading Russian paradigmatic constructions by nonlinguists entailed increase between left cortical areas, reading of English syntagmatic collocations--between right ones.

  18. Multi-index Stochastic Collocation Convergence Rates for Random PDEs with Parametric Regularity

    KAUST Repository

    Haji Ali, Abdul Lateef

    2016-08-26

    We analyze the recent Multi-index Stochastic Collocation (MISC) method for computing statistics of the solution of a partial differential equation (PDE) with random data, where the random coefficient is parametrized by means of a countable sequence of terms in a suitable expansion. MISC is a combination technique based on mixed differences of spatial approximations and quadratures over the space of random data, and naturally, the error analysis uses the joint regularity of the solution with respect to both the variables in the physical domain and parametric variables. In MISC, the number of problem solutions performed at each discretization level is not determined by balancing the spatial and stochastic components of the error, but rather by suitably extending the knapsack-problem approach employed in the construction of the quasi-optimal sparse-grids and Multi-index Monte Carlo methods, i.e., we use a greedy optimization procedure to select the most effective mixed differences to include in the MISC estimator. We apply our theoretical estimates to a linear elliptic PDE in which the log-diffusion coefficient is modeled as a random field, with a covariance similar to a Matérn model, whose realizations have spatial regularity determined by a scalar parameter. We conduct a complexity analysis based on a summability argument showing algebraic rates of convergence with respect to the overall computational work. The rate of convergence depends on the smoothness parameter, the physical dimensionality and the efficiency of the linear solver. Numerical experiments show the effectiveness of MISC in this infinite dimensional setting compared with the Multi-index Monte Carlo method and compare the convergence rate against the rates predicted in our theoretical analysis. © 2016 SFoCM

  19. Multiple Legionella pneumophila Type II secretion substrates, including a novel protein, contribute to differential infection of the amoebae Acanthamoeba castellanii, Hartmannella vermiformis, and Naegleria lovaniensis.

    Science.gov (United States)

    Tyson, Jessica Y; Pearce, Meghan M; Vargas, Paloma; Bagchi, Sreya; Mulhern, Brendan J; Cianciotto, Nicholas P

    2013-05-01

    Type II protein secretion (T2S) by Legionella pneumophila is required for intracellular infection of host cells, including macrophages and the amoebae Acanthamoeba castellanii and Hartmannella vermiformis. Previous proteomic analysis revealed that T2S by L. pneumophila 130b mediates the export of >25 proteins, including several that appeared to be novel. Following confirmation that they are unlike known proteins, T2S substrates NttA, NttB, and LegP were targeted for mutation. nttA mutants were impaired for intracellular multiplication in A. castellanii but not H. vermiformis or macrophages, suggesting that novel exoproteins which are specific to Legionella are especially important for infection. Because the importance of NttA was host cell dependent, we examined a panel of T2S substrate mutants that had not been tested before in more than one amoeba. As a result, RNase SrnA, acyltransferase PlaC, and metalloprotease ProA all proved to be required for optimal intracellular multiplication in H. vermiformis but not A. castellanii. Further examination of an lspF mutant lacking the T2S apparatus documented that T2S is also critical for infection of the amoeba Naegleria lovaniensis. Mutants lacking SrnA, PlaC, or ProA, but not those deficient for NttA, were defective in N. lovaniensis. Based upon analysis of a double mutant lacking PlaC and ProA, the role of ProA in H. vermiformis was connected to its ability to activate PlaC, whereas in N. lovaniensis, ProA appeared to have multiple functions. Together, these data document that the T2S system exports multiple effectors, including a novel one, which contribute in different ways to the broad host range of L. pneumophila.

  20. Multi-faceted proteomic characterization of host protein complement of Rift Valley fever virus virions and identification of specific heat shock proteins, including HSP90, as important viral host factors.

    Science.gov (United States)

    Nuss, Jonathan E; Kehn-Hall, Kylene; Benedict, Ashwini; Costantino, Julie; Ward, Michael; Peyser, Brian D; Retterer, Cary J; Tressler, Lyal E; Wanner, Laura M; McGovern, Hugh F; Zaidi, Anum; Anthony, Scott M; Kota, Krishna P; Bavari, Sina; Hakami, Ramin M

    2014-01-01

    Rift Valley fever is a potentially fatal disease of humans and domestic animals caused by Rift Valley fever virus (RVFV). Infection with RVFV in ruminants can cause near 100% abortion rates and recent outbreaks in naïve human populations have suggested case fatality rates of greater than thirty percent. To elucidate the roles that host proteins play during RVFV infection, proteomic analysis of RVFV virions was conducted using complementary analytical approaches, followed by functional validation studies of select identified host factors. Coupling the more traditional Gel LC/MS/MS approach (SDS PAGE followed by liquid chromatography tandem mass spectrometry) with an alternative technique that preserves protein complexes allowed the protein complement of these viral particles to be thoroughly examined. In addition to viral proteins present within the virions and virion-associated host proteins, multiple macromolecular complexes were identified. Bioinformatic analysis showed that host chaperones were among over-represented protein families associated with virions, and functional experiments using siRNA gene silencing and small molecule inhibitors identified several of these heat shock proteins, including heat shock protein 90 (HSP90), as important viral host factors. Further analysis indicated that HSP inhibition effects occur during the replication/transcription phase of the virus life cycle, leading to significant lowering of viral titers without compromising the functional capacity of released virions. Overall, these studies provide much needed further insight into interactions between RVFV and host cells, increasing our understanding of the infection process and suggesting novel strategies for anti-viral development. In particular, considering that several HSP90 inhibitors have been advancing through clinical trials for cancer treatment, these results also highlight the exciting potential of repurposing HSP90 inhibitors to treat RVF.

  1. Multi-faceted proteomic characterization of host protein complement of Rift Valley fever virus virions and identification of specific heat shock proteins, including HSP90, as important viral host factors.

    Directory of Open Access Journals (Sweden)

    Jonathan E Nuss

    Full Text Available Rift Valley fever is a potentially fatal disease of humans and domestic animals caused by Rift Valley fever virus (RVFV. Infection with RVFV in ruminants can cause near 100% abortion rates and recent outbreaks in naïve human populations have suggested case fatality rates of greater than thirty percent. To elucidate the roles that host proteins play during RVFV infection, proteomic analysis of RVFV virions was conducted using complementary analytical approaches, followed by functional validation studies of select identified host factors. Coupling the more traditional Gel LC/MS/MS approach (SDS PAGE followed by liquid chromatography tandem mass spectrometry with an alternative technique that preserves protein complexes allowed the protein complement of these viral particles to be thoroughly examined. In addition to viral proteins present within the virions and virion-associated host proteins, multiple macromolecular complexes were identified. Bioinformatic analysis showed that host chaperones were among over-represented protein families associated with virions, and functional experiments using siRNA gene silencing and small molecule inhibitors identified several of these heat shock proteins, including heat shock protein 90 (HSP90, as important viral host factors. Further analysis indicated that HSP inhibition effects occur during the replication/transcription phase of the virus life cycle, leading to significant lowering of viral titers without compromising the functional capacity of released virions. Overall, these studies provide much needed further insight into interactions between RVFV and host cells, increasing our understanding of the infection process and suggesting novel strategies for anti-viral development. In particular, considering that several HSP90 inhibitors have been advancing through clinical trials for cancer treatment, these results also highlight the exciting potential of repurposing HSP90 inhibitors to treat RVF.

  2. Parallel algorithm of trigonometric collocation method in nonlinear dynamics of rotors

    Directory of Open Access Journals (Sweden)

    Musil T.

    2007-11-01

    Full Text Available A parallel algorithm of a numeric procedure based on a method of trigonometric collocation is presented for investigating an unbalance response of a rotor supported by journal bearings. After a condensation process the trigonometric collocation method results in a set of nonlinear algebraic equations which is solved by the Newton-Raphson method. The order of the set is proportional to the number of nonlinear bearing coordinates and terms of the finite Fourier series. The algorithm, realized in the MATLAB parallel computing environment (DCT/DCE, uses message passing technique for interacting among processes on nodes of a parallel computer. This technique enables portability of the source code both on parallel computers with distributed and shared memory. Tests, made on a Beowulf cluster and a symmetric multiprocessor, have revealed very good speed-up and scalability of this algorithm.

  3. Robust Topology Optimization Based on Stochastic Collocation Methods under Loading Uncertainties

    Directory of Open Access Journals (Sweden)

    Qinghai Zhao

    2015-01-01

    Full Text Available A robust topology optimization (RTO approach with consideration of loading uncertainties is developed in this paper. The stochastic collocation method combined with full tensor product grid and Smolyak sparse grid transforms the robust formulation into a weighted multiple loading deterministic problem at the collocation points. The proposed approach is amenable to implementation in existing commercial topology optimization software package and thus feasible to practical engineering problems. Numerical examples of two- and three-dimensional topology optimization problems are provided to demonstrate the proposed RTO approach and its applications. The optimal topologies obtained from deterministic and robust topology optimization designs under tensor product grid and sparse grid with different levels are compared with one another to investigate the pros and cons of optimization algorithm on final topologies, and an extensive Monte Carlo simulation is also performed to verify the proposed approach.

  4. A Sparse Stochastic Collocation Technique for High-Frequency Wave Propagation with Uncertainty

    KAUST Repository

    Malenova, G.

    2016-09-08

    We consider the wave equation with highly oscillatory initial data, where there is uncertainty in the wave speed, initial phase, and/or initial amplitude. To estimate quantities of interest related to the solution and their statistics, we combine a high-frequency method based on Gaussian beams with sparse stochastic collocation. Although the wave solution, uϵ, is highly oscillatory in both physical and stochastic spaces, we provide theoretical arguments for simplified problems and numerical evidence that quantities of interest based on local averages of |uϵ|2 are smooth, with derivatives in the stochastic space uniformly bounded in ϵ, where ϵ denotes the short wavelength. This observable related regularity makes the sparse stochastic collocation approach more efficient than Monte Carlo methods. We present numerical tests that demonstrate this advantage.

  5. Numerical treatment of Hunter Saxton equation using cubic trigonometric B-spline collocation method

    Science.gov (United States)

    Hashmi, M. S.; Awais, Muhammad; Waheed, Ammarah; Ali, Qutab

    2017-09-01

    In this article, authors proposed a computational model based on cubic trigonometric B-spline collocation method to solve Hunter Saxton equation. The nonlinear second order partial differential equation arises in modeling of nematic liquid crystals and describes some aspects of orientation wave. The problem is decomposed into system of linear equations using cubic trigonometric B-spline collocation method with quasilinearization. To show the efficiency of the proposed method, two numerical examples have been tested for different values of t. The results are described using error tables and graphs and compared with the results existed in literature. It is evident that results are in good agreement with analytical solution and better than Arbabi, Nazari, and Davishi, Optik 127, 5255-5258 (2016). In current problem, it is also observed that the cubic trigonometric B-spline gives better results as compared to cubic B-spline.

  6. Domain decomposition methods for systems of conservation laws: Spectral collocation approximations

    Science.gov (United States)

    Quarteroni, Alfio

    1989-01-01

    Hyperbolic systems of conversation laws are considered which are discretized in space by spectral collocation methods and advanced in time by finite difference schemes. At any time-level a domain deposition method based on an iteration by subdomain procedure was introduced yielding at each step a sequence of independent subproblems (one for each subdomain) that can be solved simultaneously. The method is set for a general nonlinear problem in several space variables. The convergence analysis, however, is carried out only for a linear one-dimensional system with continuous solutions. A precise form of the error reduction factor at each iteration is derived. Although the method is applied here to the case of spectral collocation approximation only, the idea is fairly general and can be used in a different context as well. For instance, its application to space discretization by finite differences is straight forward.

  7. Application of Legendre spectral-collocation method to delay differential and stochastic delay differential equation

    Science.gov (United States)

    Khan, Sami Ullah; Ali, Ishtiaq

    2018-03-01

    Explicit solutions to delay differential equation (DDE) and stochastic delay differential equation (SDDE) can rarely be obtained, therefore numerical methods are adopted to solve these DDE and SDDE. While on the other hand due to unstable nature of both DDE and SDDE numerical solutions are also not straight forward and required more attention. In this study, we derive an efficient numerical scheme for DDE and SDDE based on Legendre spectral-collocation method, which proved to be numerical methods that can significantly speed up the computation. The method transforms the given differential equation into a matrix equation by means of Legendre collocation points which correspond to a system of algebraic equations with unknown Legendre coefficients. The efficiency of the proposed method is confirmed by some numerical examples. We found that our numerical technique has a very good agreement with other methods with less computational effort.

  8. Approximate solutions of the hyperchaotic Rössler system by using the Bessel collocation scheme

    Directory of Open Access Journals (Sweden)

    Şuayip Yüzbaşı

    2015-02-01

    Full Text Available The purpose of this study is to give a Bessel polynomial approximation for the solutions of the hyperchaotic Rössler system. For this purpose, the Bessel collocation method applied to different problems is developed for the mentioned system. This method is based on taking the truncated Bessel expansions of the functions in the hyperchaotic Rössler systems. The suggested secheme converts the problem into a system of nonlinear algebraic equations by means of the matrix operations and collocation points, The accuracy and efficiency of the proposed approach are demonstrated by numerical applications and performed with the help of a computer code written in Maple. Also, comparison between our method and the differential transformation method is made with the accuracy of solutions.

  9. On Using Collocation in Three Dimensions and Solving a Model Semiconductor Problem

    OpenAIRE

    Marchiando, J. F.

    1995-01-01

    A research code has been written to solve an elliptic system of coupled nonlinear partial differential equations of conservation form on a rectangularly shaped three-dimensional domain. The code uses the method of collocation of Gauss points with tricubic Hermite piecewise continuous polynomial basis functions. The system of equations is solved by iteration. The system of nonlinear equations is linearized, and the system of linear equations is solved by iterative methods. When the matrix of t...

  10. A Numerical Method for Lane-Emden Equations Using Hybrid Functions and the Collocation Method

    Directory of Open Access Journals (Sweden)

    Changqing Yang

    2012-01-01

    Full Text Available A numerical method to solve Lane-Emden equations as singular initial value problems is presented in this work. This method is based on the replacement of unknown functions through a truncated series of hybrid of block-pulse functions and Chebyshev polynomials. The collocation method transforms the differential equation into a system of algebraic equations. It also has application in a wide area of differential equations. Corresponding numerical examples are presented to demonstrate the accuracy of the proposed method.

  11. A high-order accurate, collocated boundary element method for wave propagation in layered media

    OpenAIRE

    Sundkvist, Elena

    2011-01-01

    The ultimate goal of this research is to construct a hybrid model for sound propagation in layered underwater environments with curved boundaries by employing a differential formulation for inhomogeneous layers and a boundary integral formulation for homogeneous layers. The discretization of the new hybrid model is a combination of a finite difference method for the Helmholtz equation for inhomogeneous media and a collocated boundary element method (BEM) for the integral equation for homogene...

  12. Cyclic reduction and FACR methods for piecewise hermite bicubic orthogonal spline collocation

    Science.gov (United States)

    Bialecki, Bernard

    1994-09-01

    Cyclic reduction and Fourier analysis-cyclic reduction (FACR) methods are presented for the solution of the linear systems which arise when orthogonal spline collocation with piecewise Hermite bicubics is applied to boundary value problems for certain separable partial differential equations on a rectangle. On anN×N uniform partition, the cyclic reduction and Fourier analysis-cyclic reduction methods requireO(N2log2N) andO(N2log2log2N) arithmetic operations, respectively.

  13. A fourth order spline collocation approach for a business cycle model

    Science.gov (United States)

    Sayfy, A.; Khoury, S.; Ibdah, H.

    2013-10-01

    A collocation approach, based on a fourth order cubic B-splines is presented for the numerical solution of a Kaleckian business cycle model formulated by a nonlinear delay differential equation. The equation is approximated and the nonlinearity is handled by employing an iterative scheme arising from Newton's method. It is shown that the model exhibits a conditionally dynamical stable cycle. The fourth-order rate of convergence of the scheme is verified numerically for different special cases.

  14. On the hybrid stability of the collocated virtual holonomic constraints basedwalking design

    Czech Academy of Sciences Publication Activity Database

    Anderle, Milan; Čelikovský, Sergej

    2017-01-01

    Roč. 6, č. 2 (2017), s. 47-56 ISSN 2223-7038 R&D Projects: GA ČR(CZ) GA17-04682S Institutional support: RVO:67985556 Keywords : Underactuated walking * Virtual holonomic constraints * Poincaré section method * collocated constraints Subject RIV: BC - Control Systems Theory OBOR OECD: Automation and control systems http://lib.physcon.ru/doc?id=60655c1961ed

  15. Isogeometric Collocation: Cost Comparison with Galerkin Methods and Extension to Adaptive Hierarchical NURBS Discretizations (Preprint)

    Science.gov (United States)

    2013-02-06

    the white collocation points have been truncated, although the basis functions remain 67 0.0 0.5 1.0 1.5 2.0 2.5 3.0 Fine-scale B-splines: Coarse...geometric design. Morgan Kaufmann Publishers, 2002. [75] Rhinoceros — NURBS modeling for Windows. http://www.rhino3d.com/, 2012. [76] B.A. Finlayson

  16. Least squares collocation applied to local gravimetric solutions from satellite gravity gradiometry data

    Science.gov (United States)

    Robbins, J. W.

    1985-01-01

    An autonomous spaceborne gravity gradiometer mission is being considered as a post Geopotential Research Mission project. The introduction of satellite diometry data to geodesy is expected to improve solid earth gravity models. The possibility of utilizing gradiometer data for the determination of pertinent gravimetric quantities on a local basis is explored. The analytical technique of least squares collocation is investigated for its usefulness in local solutions of this type. It is assumed, in the error analysis, that the vertical gravity gradient component of the gradient tensor is used as the raw data signal from which the corresponding reference gradients are removed to create the centered observations required in the collocation solution. The reference gradients are computed from a high degree and order geopotential model. The solution can be made in terms of mean or point gravity anomalies, height anomalies, or other useful gravimetric quantities depending on the choice of covariance types. Selected for this study were 30 x 30 foot mean gravity and height anomalies. Existing software and new software are utilized to implement the collocation technique. It was determined that satellite gradiometry data at an altitude of 200 km can be used successfully for the determination of 30 x 30 foot mean gravity anomalies to an accuracy of 9.2 mgal from this algorithm. It is shown that the resulting accuracy estimates are sensitive to gravity model coefficient uncertainties, data reduction assumptions and satellite mission parameters.

  17. An adaptive multi-element probabilistic collocation method for statistical EMC/EMI characterization

    KAUST Repository

    Yücel, Abdulkadir C.

    2013-12-01

    An adaptive multi-element probabilistic collocation (ME-PC) method for quantifying uncertainties in electromagnetic compatibility and interference phenomena involving electrically large, multi-scale, and complex platforms is presented. The method permits the efficient and accurate statistical characterization of observables (i.e., quantities of interest such as coupled voltages) that potentially vary rapidly and/or are discontinuous in the random variables (i.e., parameters that characterize uncertainty in a system\\'s geometry, configuration, or excitation). The method achieves its efficiency and accuracy by recursively and adaptively dividing the domain of the random variables into subdomains using as a guide the decay rate of relative error in a polynomial chaos expansion of the observables. While constructing local polynomial expansions on each subdomain, a fast integral-equation-based deterministic field-cable-circuit simulator is used to compute the observable values at the collocation/integration points determined by the adaptive ME-PC scheme. The adaptive ME-PC scheme requires far fewer (computationally costly) deterministic simulations than traditional polynomial chaos collocation and Monte Carlo methods for computing averages, standard deviations, and probability density functions of rapidly varying observables. The efficiency and accuracy of the method are demonstrated via its applications to the statistical characterization of voltages in shielded/unshielded microwave amplifiers and magnetic fields induced on car tire pressure sensors. © 2013 IEEE.

  18. The Effects of Input Flood and Consciousness-Raising Approach on Collocation Knowledge Development of Language Learners

    Directory of Open Access Journals (Sweden)

    Elaheh Hamed Mahvelati

    2012-11-01

    Full Text Available Many researchers stress the importance of lexical coherence and emphasize the need for teaching collocations at all levels of language proficiency. Thus, this study was conducted to measure the relative effectiveness of explicit (consciousness-raising approach versus implicit (input flood collocation instruction with regard to learners’ knowledge of both lexical and grammatical collocations. Ninety-five upper-intermediate learners, who were randomly assigned to the control and experimental groups, served as the participants of this study. While one of the experimental groups was provided with input flood treatment, the other group received explicit collocation instruction. In contrast, the participants in the control group did not receive any instruction on learning collocations. The results of the study, which were collected through pre-test, immediate post-test and delayed post-test, revealed that although both methods of teaching collocations proved effective, the explicit method of consciousness-raising approach was significantly superior to the implicit method of input flood treatment.

  19. Improved long-term expression from helper virus-free HSV-1 vectors packaged using combinations of mutated HSV-1 proteins that include the UL13 protein kinase and specific components of the VP16 transcriptional complex

    Directory of Open Access Journals (Sweden)

    Geller Alfred I

    2009-06-01

    Full Text Available Abstract Background Herpes Simplex Virus (HSV-1 gene expression is thought to shut off recombinant gene expression from HSV-1 vectors; however, in a helper virus-free HSV-1 vector system, a number of promoters support only short-term expression. These results raise the paradox that recombinant gene expression remains short-term even in the absence of almost all (~99% of the HSV-1 genome, HSV-1 genes, and HSV-1 gene expression. To resolve this paradox, we hypothesized that specific proteins in the HSV-1 virus particle shut off recombinant gene expression. In two earlier studies, we examined the effects on recombinant gene expression of packaging vectors using specific mutated HSV-1 proteins. We found that vectors packaged using mutated UL13 (a protein kinase, or VP16, or UL46 and/or UL47 (components of the VP16 transcriptional complex supported improved long-term expression, and vectors packaged using mutated UL46 and/or UL47 also supported improved gene transfer (numbers of cells at 4 days. These results suggested the hypothesis that specific proteins in the HSV-1 particle act by multiple pathways to reduce recombinant gene expression. To test this hypothesis, we examined combinations of mutated proteins that included both UL13 and specific components of the VP16 transcriptional complex. Results A HSV-1 vector containing a neuronal-specific promoter was packaged using specific combinations of mutated proteins, and the resulting vector stocks were tested in the rat striatum. For supporting long-term expression, the preferred combination of mutated HSV-1 proteins was mutated UL13, UL46, and UL47. Vectors packaged using this combination of mutated proteins supported a higher efficiency of gene transfer and high levels expression for 3 months, the longest time examined. Conclusion Vector particles containing this combination of mutated HSV-1 proteins improve recombinant gene expression. Implications of these results for strategies to further improve

  20. Improved long-term expression from helper virus-free HSV-1 vectors packaged using combinations of mutated HSV-1 proteins that include the UL13 protein kinase and specific components of the VP16 transcriptional complex.

    Science.gov (United States)

    Liu, Meng; Wang, Xiaodan; Geller, Alfred I

    2009-06-16

    Herpes Simplex Virus (HSV-1) gene expression is thought to shut off recombinant gene expression from HSV-1 vectors; however, in a helper virus-free HSV-1 vector system, a number of promoters support only short-term expression. These results raise the paradox that recombinant gene expression remains short-term even in the absence of almost all (approximately 99%) of the HSV-1 genome, HSV-1 genes, and HSV-1 gene expression. To resolve this paradox, we hypothesized that specific proteins in the HSV-1 virus particle shut off recombinant gene expression. In two earlier studies, we examined the effects on recombinant gene expression of packaging vectors using specific mutated HSV-1 proteins. We found that vectors packaged using mutated UL13 (a protein kinase), or VP16, or UL46 and/or UL47 (components of the VP16 transcriptional complex) supported improved long-term expression, and vectors packaged using mutated UL46 and/or UL47 also supported improved gene transfer (numbers of cells at 4 days). These results suggested the hypothesis that specific proteins in the HSV-1 particle act by multiple pathways to reduce recombinant gene expression. To test this hypothesis, we examined combinations of mutated proteins that included both UL13 and specific components of the VP16 transcriptional complex. A HSV-1 vector containing a neuronal-specific promoter was packaged using specific combinations of mutated proteins, and the resulting vector stocks were tested in the rat striatum. For supporting long-term expression, the preferred combination of mutated HSV-1 proteins was mutated UL13, UL46, and UL47. Vectors packaged using this combination of mutated proteins supported a higher efficiency of gene transfer and high levels expression for 3 months, the longest time examined. Vector particles containing this combination of mutated HSV-1 proteins improve recombinant gene expression. Implications of these results for strategies to further improve long-term expression are discussed

  1. Bioinformatic prediction of G protein-coupled receptor encoding sequences from the transcriptome of the foreleg, including the Haller's organ, of the cattle tick, Rhipicephalus australis.

    Directory of Open Access Journals (Sweden)

    Sergio Munoz

    Full Text Available The cattle tick of Australia, Rhipicephalus australis, is a vector for microbial parasites that cause serious bovine diseases. The Haller's organ, located in the tick's forelegs, is crucial for host detection and mating. To facilitate the development of new technologies for better control of this agricultural pest, we aimed to sequence and annotate the transcriptome of the R. australis forelegs and associated tissues, including the Haller's organ. As G protein-coupled receptors (GPCRs are an important family of eukaryotic proteins studied as pharmaceutical targets in humans, we prioritized the identification and classification of the GPCRs expressed in the foreleg tissues. The two forelegs from adult R. australis were excised, RNA extracted, and pyrosequenced with 454 technology. Reads were assembled into unigenes and annotated by sequence similarity. Python scripts were written to find open reading frames (ORFs from each unigene. These ORFs were analyzed by different GPCR prediction approaches based on sequence alignments, support vector machines, hidden Markov models, and principal component analysis. GPCRs consistently predicted by multiple methods were further studied by phylogenetic analysis and 3D homology modeling. From 4,782 assembled unigenes, 40,907 possible ORFs were predicted. Using Blastp, Pfam, GPCRpred, TMHMM, and PCA-GPCR, a basic set of 46 GPCR candidates were compiled and a phylogenetic tree was constructed. With further screening of tertiary structures predicted by RaptorX, 6 likely GPCRs emerged and the strongest candidate was classified by PCA-GPCR to be a GABAB receptor.

  2. Epigenetics targeted protein-vorinostat nanomedicine inducing apoptosis in heterogeneous population of primary acute myeloid leukemia cells including refractory and relapsed cases.

    Science.gov (United States)

    Chandran, Parwathy; Kavalakatt, Anu; Malarvizhi, Giridharan Loghanathan; Vasanthakumari, Divya Rani Vikraman Nair; Retnakumari, Archana Payickattu; Sidharthan, Neeraj; Pavithran, Keechilat; Nair, Shantikumar; Koyakutty, Manzoor

    2014-05-01

    Aberrant epigenetics play a key role in the onset and progression of acute myeloid leukemia (AML). Herein we report in silico modelling based development of a novel, protein-vorinostat nanomedicine exhibiting selective and superior anti-leukemic activity against heterogeneous population of AML patient samples (n=9), including refractory and relapsed cases, and three representative cell lines expressing CD34(+)/CD38(-) stem cell phenotype (KG-1a), promyelocytic phenotype (HL-60) and FLT3-ITD mutation (MV4-11). Nano-vorinostat having ~100nm size exhibited enhanced cellular uptake rendering significantly lower IC50 in AML cell lines and patient samples, and induced enhanced HDAC inhibition, oxidative injury, cell cycle arrest and apoptosis compared to free vorinostat. Most importantly, nanomedicine showed exceptional single-agent activity against the clonogenic proliferative capability of bone marrow derived leukemic progenitors, while remaining non-toxic to healthy bone marrow cells. Collectively, this epigenetics targeted nanomedicine appears to be a promising therapeutic strategy against various French-American-British (FAB) classes of AML. Through the use of a protein-vorinostat agent, exceptional single-agent activity was demonstrated against the clonogenic proliferative capability of bone marrow derived leukemic progenitors, while remaining non-toxic to healthy bone marrow cells. The studied epigenetics targeted nanomedicine approach is a promising therapeutic strategy against various French-American-British classes of acute myeloid leukemia. © 2014 Elsevier Inc. All rights reserved.

  3. Evaluation of multiple precipitation products across Mainland China using the triple collocation method without ground truth

    Science.gov (United States)

    Tang, G.; Li, C.; Hong, Y.; Long, D.

    2017-12-01

    Proliferation of satellite and reanalysis precipitation products underscores the need to evaluate their reliability, particularly over ungauged or poorly gauged regions. However, it is really challenging to perform such evaluations over regions lacking ground truth data. Here, using the triple collocation (TC) method that is capable of evaluating relative uncertainties in different products without ground truth, we evaluate five satellite-based precipitation products and comparatively assess uncertainties in three types of independent precipitation products, e.g., satellite-based, ground-observed, and model reanalysis over Mainland China, including a ground-based precipitation dataset (the gauge based daily precipitation analysis, CGDPA), the latest version of the European reanalysis agency reanalysis (ERA-interim) product, and five satellite-based products (i.e., 3B42V7, 3B42RT of TMPA, IMERG, CMORPH-CRT, PERSIANN-CDR) on a regular 0.25° grid at the daily timescale from 2013 to 2015. First, the effectiveness of the TC method is evaluated by comparison with traditional methods based on ground observations in a densely gauged region. Results show that the TC method is reliable because the correlation coefficient (CC) and root mean square error (RMSE) are close to those based on the traditional method with a maximum difference only up to 0.08 and 0.71 (mm/day) for CC and RMSE, respectively. Then, the TC method is applied to Mainland China and the Tibetan Plateau (TP). Results indicate that: (1) the overall performance of IMERG is better than the other satellite products over Mainland China; (2) over grid cells without rain gauges in the TP, IMERG and ERA show better performance than CGDPA, indicating the potential of remote sensing and reanalysis data over these regions and the inherent uncertainty of CGDPA due to interpolation using sparsely gauged data; (3) both TMPA-3B42 and CMORPH-CRT have some unexpected CC values over certain grid cells that contain water

  4. Gene expression profiling in the stress control brain region hypothalamic paraventricular nucleus reveals a novel gene network including Amyloid beta Precursor Protein

    Directory of Open Access Journals (Sweden)

    Deussing Jan M

    2010-10-01

    Full Text Available Abstract Background The pivotal role of stress in the precipitation of psychiatric diseases such as depression is generally accepted. This study aims at the identification of genes that are directly or indirectly responding to stress. Inbred mouse strains that had been evidenced to differ in their stress response as well as in their response to antidepressant treatment were chosen for RNA profiling after stress exposure. Gene expression and regulation was determined by microarray analyses and further evaluated by bioinformatics tools including pathway and cluster analyses. Results Forced swimming as acute stressor was applied to C57BL/6J and DBA/2J mice and resulted in sets of regulated genes in the paraventricular nucleus of the hypothalamus (PVN, 4 h or 8 h after stress. Although the expression changes between the mouse strains were quite different, they unfolded in phases over time in both strains. Our search for connections between the regulated genes resulted in potential novel signalling pathways in stress. In particular, Guanine nucleotide binding protein, alpha inhibiting 2 (GNAi2 and Amyloid β (A4 precursor protein (APP were detected as stress-regulated genes, and together with other genes, seem to be integrated into stress-responsive pathways and gene networks in the PVN. Conclusions This search for stress-regulated genes in the PVN revealed its impact on interesting genes (GNAi2 and APP and a novel gene network. In particular the expression of APP in the PVN that is governing stress hormone balance, is of great interest. The reported neuroprotective role of this molecule in the CNS supports the idea that a short acute stress can elicit positive adaptational effects in the brain.

  5. Spectral optical layer properties of cirrus from collocated airborne measurements and simulations

    Directory of Open Access Journals (Sweden)

    F. Finger

    2016-06-01

    Full Text Available Spectral upward and downward solar irradiances from vertically collocated measurements above and below a cirrus layer are used to derive cirrus optical layer properties such as spectral transmissivity, absorptivity, reflectivity, and cloud top albedo. The radiation measurements are complemented by in situ cirrus crystal size distribution measurements and radiative transfer simulations based on the microphysical data. The close collocation of the radiative and microphysical measurements, above, beneath, and inside the cirrus, is accomplished by using a research aircraft (Learjet 35A in tandem with the towed sensor platform AIRTOSS (AIRcraft TOwed Sensor Shuttle. AIRTOSS can be released from and retracted back to the research aircraft by means of a cable up to a distance of 4 km. Data were collected from two field campaigns over the North Sea and the Baltic Sea in spring and late summer 2013. One measurement flight over the North Sea proved to be exemplary, and as such the results are used to illustrate the benefits of collocated sampling. The radiative transfer simulations were applied to quantify the impact of cloud particle properties such as crystal shape, effective radius reff, and optical thickness τ on cirrus spectral optical layer properties. Furthermore, the radiative effects of low-level, liquid water (warm clouds as frequently observed beneath the cirrus are evaluated. They may cause changes in the radiative forcing of the cirrus by a factor of 2. When low-level clouds below the cirrus are not taken into account, the radiative cooling effect (caused by reflection of solar radiation due to the cirrus in the solar (shortwave spectral range is significantly overestimated.

  6. Fast and Accurate Collocation of the Visible Infrared Imaging Radiometer Suite Measurements with Cross-Track Infrared Sounder

    Directory of Open Access Journals (Sweden)

    Likun Wang

    2016-01-01

    Full Text Available Given the fact that Cross-track Infrared Sounder (CrIS and the Visible Infrared Imaging Radiometer Suite (VIIRS are currently onboard the Suomi National Polar-orbiting Partnership (Suomi NPP satellite and will continue to be carried on the same platform as future Joint Polar Satellite System (JPSS satellites for the next decade, it is desirable to develop a fast and accurate collocation scheme to collocate VIIRS products and measurements with CrIS for applications that rely on combining measurements from two sensors such as inter-calibration, geolocation assessment, and cloud detection. In this study, an accurate and fast collocation method to collocate VIIRS measurements within CrIS instantaneous field of view (IFOV directly based on line-of-sight (LOS pointing vectors is developed and discussed in detail. We demonstrate that this method is not only accurate and precise from a mathematical perspective, but also easy to implement computationally. More importantly, with optimization, this method is very fast and efficient and thus can meet operational requirements. Finally, this collocation method can be extended to a wide variety of sensors on different satellite platforms.

  7. Metaphors of the economy in the Dictionary of Brazilian Portuguese Collocations: A corpus-based multidimensional analysis

    Directory of Open Access Journals (Sweden)

    Tony Berber Sardinha

    2016-06-01

    Full Text Available This article presents the results from a corpus-based multidimensional analysis of the language of the Brazilian economy, building on a previous study that determined the major dimensions underlying the statistical collocations of the +8,000 most frequent words in Brazilian Portuguese (Berber Sardinha et al., submitted. The corpus used was the Corpus Brasileiro (Brazilian Corpus (LAEL, CEPRIL, PUCSP, Fapesp, CNPq, a multi-register corpus with 1 billion tokens. Dimensions of collocation are the communicative parameters that underlie collocational choice, and the method for identifying them is based on the Multidimensional Analysis framework developed by Biber (1988. This study focused on dimension 6, which reflects the language used to talk about the economy in Brazilian Portuguese; this dimension was broken down into five other (sub- dimensions, which further specify the nuances of the language of the economy. These five (sub-dimensions were then analyzed for metaphor by hand, and the analysis revealed that metaphors account for almost 30% of the collocations. Furthermore, metaphors are not distributed evenly across the (sub-dimensions of the language of the economy. This study is part of a larger project whose ultimate goal is to produce a corpus-based dictionary of Brazilian Portuguese collocations.

  8. A Comparative Study of the Use of Collocation in Iranian High School Textbooks and American English File Books

    Directory of Open Access Journals (Sweden)

    Mohsen Shahrokhi

    2014-05-01

    Full Text Available The present study investigates the extent to which lexical and grammatical collocations are used in Iranian high school English textbooks, compared with the American English File books. To achieve the purposes of this study, this study had to be carried out in two phases. In the first phase, the content of the instructional textbooks, that is, American English File book series, Book 2 and Iranian high school English Book 3, were analyzed to find the frequencies and proportions of the collocations used in the textbooks. Since the instructional textbooks used in the two teaching environments (i.e., Iranian high schools and language institutes were not equal with regard to the density of texts, from each textbook just the first 6000 words, content words as well as function words, were considered. Then, the frequencies of the collocations among the first 6000 words in high school English Book 3 and American English File Book 2 were determined.The results of the statistical analyses revealed that the two text book series differ marginally in terms of frequency and type of collocations. Major difference existed between them when it came to lexical collocations in American English File book 2.

  9. The triumph of dative experiencers: “entrar + state noun” collocations in diachrony

    Directory of Open Access Journals (Sweden)

    Josep Alba-Salas

    2016-06-01

    Full Text Available This study examines the historical evolution of three types of Spanish collocations formed with entrar and state nouns: with dative experiencers (e.g. le entró temor, with subject experiencers (e.g. el caballero entró en temor, and with locative experiencers (e.g. entró temor en él. The locative construction, which predominated initially, was eclipsed by the subject structure in the 1600s, but datives prevail since the 1800s. This evolution follows from other, more general changes in Spanish, particularly the victory of dative experiencers in constructions indicating involuntary physical or mental processes.

  10. An adaptive wavelet stochastic collocation method for irregular solutions of stochastic partial differential equations

    Energy Technology Data Exchange (ETDEWEB)

    Webster, Clayton G [ORNL; Zhang, Guannan [ORNL; Gunzburger, Max D [ORNL

    2012-10-01

    Accurate predictive simulations of complex real world applications require numerical approximations to first, oppose the curse of dimensionality and second, converge quickly in the presence of steep gradients, sharp transitions, bifurcations or finite discontinuities in high-dimensional parameter spaces. In this paper we present a novel multi-dimensional multi-resolution adaptive (MdMrA) sparse grid stochastic collocation method, that utilizes hierarchical multiscale piecewise Riesz basis functions constructed from interpolating wavelets. The basis for our non-intrusive method forms a stable multiscale splitting and thus, optimal adaptation is achieved. Error estimates and numerical examples will used to compare the efficiency of the method with several other techniques.

  11. Implementation of optimal Galerkin and Collocation approximations of PDEs with Random Coefficients

    KAUST Repository

    Beck, Joakim

    2011-12-22

    In this work we first focus on the Stochastic Galerkin approximation of the solution u of an elliptic stochastic PDE. We rely on sharp estimates for the decay of the coefficients of the spectral expansion of u on orthogonal polynomials to build a sequence of polynomial subspaces that features better convergence properties compared to standard polynomial subspaces such as Total Degree or Tensor Product. We consider then the Stochastic Collocation method, and use the previous estimates to introduce a new effective class of Sparse Grids, based on the idea of selecting a priori the most profitable hierarchical surpluses, that, again, features better convergence properties compared to standard Smolyak or tensor product grids.

  12. Numerical solution of sixth-order boundary-value problems using Legendre wavelet collocation method

    Science.gov (United States)

    Sohaib, Muhammad; Haq, Sirajul; Mukhtar, Safyan; Khan, Imad

    2018-03-01

    An efficient method is proposed to approximate sixth order boundary value problems. The proposed method is based on Legendre wavelet in which Legendre polynomial is used. The mechanism of the method is to use collocation points that converts the differential equation into a system of algebraic equations. For validation two test problems are discussed. The results obtained from proposed method are quite accurate, also close to exact solution, and other different methods. The proposed method is computationally more effective and leads to more accurate results as compared to other methods from literature.

  13. Application of collocated GPS and seismic sensors to earthquake monitoring and early warning.

    Science.gov (United States)

    Li, Xingxing; Zhang, Xiaohong; Guo, Bofeng

    2013-10-24

    We explore the use of collocated GPS and seismic sensors for earthquake monitoring and early warning. The GPS and seismic data collected during the 2011 Tohoku-Oki (Japan) and the 2010 El Mayor-Cucapah (Mexico) earthquakes are analyzed by using a tightly-coupled integration. The performance of the integrated results is validated by both time and frequency domain analysis. We detect the P-wave arrival and observe small-scale features of the movement from the integrated results and locate the epicenter. Meanwhile, permanent offsets are extracted from the integrated displacements highly accurately and used for reliable fault slip inversion and magnitude estimation.

  14. A nodal collocation method for the calculation of the lambda modes of the P L equations

    International Nuclear Information System (INIS)

    Capilla, M.; Talavera, C.F.; Ginestar, D.; Verdu, G.

    2005-01-01

    P L equations are classical approximations to the neutron transport equation admitting a diffusive form. Using this property, a nodal collocation method is developed for the P L approximations, which is based on the expansion of the flux in terms of orthonormal Legendre polynomials. This method approximates the differential lambda modes problem by an algebraic eigenvalue problem from which the fundamental and the subcritical modes of the system can be calculated. To test the performance of this method, two problems have been considered, a homogeneous slab, which admits an analytical solution, and a seven-region slab corresponding to a more realistic problem

  15. A Survey of Symplectic and Collocation Integration Methods for Orbit Propagation

    Science.gov (United States)

    Jones, Brandon A.; Anderson, Rodney L.

    2012-01-01

    Demands on numerical integration algorithms for astrodynamics applications continue to increase. Common methods, like explicit Runge-Kutta, meet the orbit propagation needs of most scenarios, but more specialized scenarios require new techniques to meet both computational efficiency and accuracy needs. This paper provides an extensive survey on the application of symplectic and collocation methods to astrodynamics. Both of these methods benefit from relatively recent theoretical developments, which improve their applicability to artificial satellite orbit propagation. This paper also details their implementation, with several tests demonstrating their advantages and disadvantages.

  16. Underground collocation of nuclear power plant reactors and repository to facilitate the post-renaissance expansion of nuclear power

    Energy Technology Data Exchange (ETDEWEB)

    Myers, Carl W [Los Alamos National Laboratory; Elkins, Ned Z [Los Alamos National Laboratory

    2008-01-01

    Underground collocation of nuclear power reactors and the nuclear waste management facilities supporting those reactors, termed an underground nuclear park (UNP), appears to have several advantages compared to the conventional approach to siting reactors and waste management facilities. These advantages include the potential to lower reactor capital and operating cost, lower nuclear waste management cost, and increase margins of physical security and safety. Envirorunental impacts related to worker health, facility accidents, waste transportation, and sabotage and terrorism appear to be lower for UNPs compared to the current approach. In-place decommissioning ofUNP reactors appears to have cost, safety, envirorunental and waste disposal advantages. The UNP approach has the potential to lead to greater public acceptance for the deployment of new power reactors. Use of the UNP during the post-nuclear renaissance time frame has the potential to enable a greater expansion of U.S. nuclear power generation than might otherwise result. Technical and economic aspects of the UNP concept need more study to determine the viability of the concept.

  17. L’ENSEIGNEMENT DES COLLOCATIONS EN CLASSE DE FLE / TEACHING COLLOCATIONS IN FRENCH AS A FOREIGN LANGUAGE (FFL CLASSES / PREDAREA COLOCAŢIILOR ÎN ORELE DE LIMBA FRANCEZĂ CA LIMBĂ STRĂINĂ

    Directory of Open Access Journals (Sweden)

    Ana-Marina Tomescu

    2014-12-01

    Full Text Available Dans le présent article nous voulons offrir quelques solutions qui aident à l’intégration des collocations en classe de FLE, vu leur présence incontournable dans la langue, à tous les niveaux et dans tous les registres de langue. Par conséquent, dans ce travail nous nous intéressons aux meilleures activités didactiques, adaptées à l’enseignement des collocations à des apprenants non francophones (sites Internet, recueils d’exercices, etc..

  18. Talk About Mouth Speculums: Collocational Competence and Spoken Fluency in Non-Native English-Speaking University Lecturers

    DEFF Research Database (Denmark)

    Westbrook, Pete

    might exist between overall language proficiency, collocational competence and spoken fluency in non-native English-speaking university lecturers. The data came from 15 20-minute mini-lectures recorded between 2009 and 2011 for an English oral proficiency test for lecturers employed at the University......Despite the large body of research into formulaic language and fluency, there seems to be a lack of empirical evidence for how collocations, often considered a subset of formulaic language, might impact on fluency. To address this problem, this dissertation examined to what extent correlations...... fluency measures calculated for each lecturer. Initial findings across all lecturers showed no correlation between collocational competence and either overall proficiency or fluency. However, further analysis of lecturers by department revealed that possible correlations were hidden by variations...

  19. A Highly Accurate Regular Domain Collocation Method for Solving Potential Problems in the Irregular Doubly Connected Domains

    Directory of Open Access Journals (Sweden)

    Zhao-Qing Wang

    2014-01-01

    Full Text Available Embedding the irregular doubly connected domain into an annular regular region, the unknown functions can be approximated by the barycentric Lagrange interpolation in the regular region. A highly accurate regular domain collocation method is proposed for solving potential problems on the irregular doubly connected domain in polar coordinate system. The formulations of regular domain collocation method are constructed by using barycentric Lagrange interpolation collocation method on the regular domain in polar coordinate system. The boundary conditions are discretized by barycentric Lagrange interpolation within the regular domain. An additional method is used to impose the boundary conditions. The least square method can be used to solve the overconstrained equations. The function values of points in the irregular doubly connected domain can be calculated by barycentric Lagrange interpolation within the regular domain. Some numerical examples demonstrate the effectiveness and accuracy of the presented method.

  20. Experimental validation of multi-epitope peptides including promising MHC class I- and class II-restricted epitopes of four known Leishmania infantum proteins

    Directory of Open Access Journals (Sweden)

    Maria eAgallou

    2014-06-01

    Full Text Available Leishmaniasis is a significant worldwide health problem for which no vaccine exists. Activation of CD4+ and CD8+ T cells is crucial for the generation of protective immunity against parasite. Recent trend in vaccine design has been shifted to epitope-based vaccines that are more specific, safe, and easy to produce. In the present study, four known antigenic Leishmania (L. infantum proteins, CPA, histone H1, KMP-11 and LeIF were analysed for the prediction of binding epitopes to H2d MHC class I and class II molecules, using online available algorithms. Based on in silico analysis, eight peptides including highly scored MHC class I- and class II-restricted epitopes were synthesized. Peptide immunogenicity was validated in MHC compatible BALB/c mice immunized with each synthetic peptide emulsified in CFA/IFA. CPA_p2, CPA_p3, H1_p1 and LeIF_p6 induced strong spleen cell proliferation upon in vitro peptide re-stimulation. In addition, the majority of the peptides, except of LeIF_p1 and KMP-11_p1, induced IFN-γ secretion, while KMP-11_p1 indicated a suppressive effect on IL-10 production. CPA_p2, CPA_p3, LeIF_p3 and LeIF_p6 induced IFN-γ-producing CD4+ T cells indicating a TH1 type response. In addition, CPA_p2, CPA_p3 and H1_p1 induced also the induction of CD8+ T cells. The induction of peptide-specific IgG in immunized mice designated also the existence of B cell epitopes in peptide sequences. Combining immunoinformatic tools and experimental validation, we demonstrated that CPA_p2, CPA_p3, H1_p1, H1_p3, CPA_p2, LeIF_p3 and LeIF_p6 are likely to include potential epitopes for the induction of protective cytotoxic and/or TH1-type immune responses supporting the feasibility of peptide-based vaccine development for leishmaniasis.

  1. Cost-effective and rapid lysis of Saccharomyces cerevisiae cells for quantitative western blot analysis of proteins, including phosphorylated eIF2α.

    Science.gov (United States)

    Lee, Su Jung; Ramesh, Rashmi; de Boor, Valerie; Gebler, Jan M; Silva, Richard C; Sattlegger, Evelyn

    2017-09-01

    The common method for liberating proteins from Saccharomyces cerevisiae cells involves mechanical cell disruption using glass beads and buffer containing inhibitors (protease, phosphatase and/or kinase inhibitors), followed by centrifugation to remove cell debris. This procedure requires the use of costly inhibitors and is laborious, in particular when many samples need to be processed. Also, enzymatic reactions can still occur during harvesting and cell breakage. As a result low-abundance and labile proteins may be degraded, and enzymes such as kinases and phosphatases may still modify proteins during and after cell lysis. We believe that our rapid sample preparation method helps overcome the above issues and offers the following advantages: (a) it is cost-effective, as no inhibitors and breaking buffer are needed; (b) cell breakage is fast (about 15 min) since it only involves a few steps; (c) the use of formaldehyde inactivates endogenous proteases prior to cell lysis, dramatically reducing the risk of protein degradation; (d) centrifugation steps only occur prior to cell lysis, circumventing the problem of losing protein complexes, in particular if cells were treated with formaldehyde intended to stabilize and capture large protein complexes; and (e) since formaldehyde has the potential to instantly terminate protein activity, this method also allows the study of enzymes in live cells, i.e. in their true physiological environment, such as the short-term effect of a drug on enzyme activity. Taken together, the rapid sample preparation procedure provides a more accurate snapshot of the cell's protein content at the time of harvesting. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

  2. Geographic analysis of the feasibility of collocating algal biomass production with wastewater treatment plants.

    Science.gov (United States)

    Fortier, Marie-Odile P; Sturm, Belinda S M

    2012-10-16

    Resource demand analyses indicate that algal biodiesel production would require unsustainable amounts of freshwater and fertilizer supplies. Alternatively, municipal wastewater effluent can be used, but this restricts production of algae to areas near wastewater treatment plants (WWTPs), and to date, there has been no geospatial analysis of the feasibility of collocating large algal ponds with WWTPs. The goals of this analysis were to determine the available areas by land cover type within radial extents (REs) up to 1.5 miles from WWTPs; to determine the limiting factor for algal production using wastewater; and to investigate the potential algal biomass production at urban, near-urban, and rural WWTPs in Kansas. Over 50% and 87% of the land around urban and rural WWTPs, respectively, was found to be potentially available for algal production. The analysis highlights a trade-off between urban WWTPs, which are generally land-limited but have excess wastewater effluent, and rural WWTPs, which are generally water-limited but have 96% of the total available land. Overall, commercial-scale algae production collocated with WWTPs is feasible; 29% of the Kansas liquid fuel demand could be met with implementation of ponds within 1 mile of all WWTPs and supplementation of water and nutrients when these are limited.

  3. An h-adaptive stochastic collocation method for stochastic EMC/EMI analysis

    KAUST Repository

    Yücel, Abdulkadir C.

    2010-07-01

    The analysis of electromagnetic compatibility and interference (EMC/EMI) phenomena is often fraught by randomness in a system\\'s excitation (e.g., the amplitude, phase, and location of internal noise sources) or configuration (e.g., the routing of cables, the placement of electronic systems, component specifications, etc.). To bound the probability of system malfunction, fast and accurate techniques to quantify the uncertainty in system observables (e.g., voltages across mission-critical circuit elements) are called for. Recently proposed stochastic frameworks [1-2] combine deterministic electromagnetic (EM) simulators with stochastic collocation (SC) methods that approximate system observables using generalized polynomial chaos expansion (gPC) [3] (viz. orthogonal polynomials spanning the entire random domain) to estimate their statistical moments and probability density functions (pdfs). When constructing gPC expansions, the EM simulator is used solely to evaluate system observables at collocation points prescribed by the SC-gPC scheme. The frameworks in [1-2] therefore are non-intrusive and straightforward to implement. That said, they become inefficient and inaccurate for system observables that vary rapidly or are discontinuous in the random variables (as their representations may require very high-order polynomials). © 2010 IEEE.

  4. In ‘other’ words: Some thoughts on the transferability of collocations

    Directory of Open Access Journals (Sweden)

    Terence Odlin

    2011-10-01

    Full Text Available In discussions of cross-linguistic influence (also known as language transfer, the focus is usually on the influence of a particular structure in a particular instance of language contact, for instance, the negative transfer of serial verbs by Vietnamese learners of English: She has managed to rise the kite fly over the tallest building (Helms-Park, 2003. Even so, as Helms-Park acknowledges, serial verb constructions can and do surface in contact situations besides the one she studied in Canada, and they can involve speakers of different languages. While serial verb constructions have unique syntactic traits, the same point about the transferability of multiword constructions in different contact settings is applicable in other instances and with collocations that can be viewed as unique in their lexical as well as syntactic characteristics. The following article considers such a case, based in part on my own teaching experience but also on transfer research from other settings as well. After a discussion of a collocation that I call the repeated other pattern found in different settings, I briefly consider other cases of transfer having lexical and syntactic peculiarities and appearing in more than one contact situation. There will also be some discussion of factors that transfer researchers and language teachers would do well to consider.

  5. Entropy Stable Staggered Grid Spectral Collocation for the Burgers' and Compressible Navier-Stokes Equations

    Science.gov (United States)

    Carpenter, Mark H.; Parsani, Matteo; Fisher, Travis C.; Nielsen, Eric J.

    2015-01-01

    Staggered grid, entropy stable discontinuous spectral collocation operators of any order are developed for Burgers' and the compressible Navier-Stokes equations on unstructured hexahedral elements. This generalization of previous entropy stable spectral collocation work [1, 2], extends the applicable set of points from tensor product, Legendre-Gauss-Lobatto (LGL) to a combination of tensor product Legendre-Gauss (LG) and LGL points. The new semi-discrete operators discretely conserve mass, momentum, energy and satisfy a mathematical entropy inequality for both Burgers' and the compressible Navier-Stokes equations in three spatial dimensions. They are valid for smooth as well as discontinuous flows. The staggered LG and conventional LGL point formulations are compared on several challenging test problems. The staggered LG operators are significantly more accurate, although more costly to implement. The LG and LGL operators exhibit similar robustness, as is demonstrated using test problems known to be problematic for operators that lack a nonlinearly stability proof for the compressible Navier-Stokes equations (e.g., discontinuous Galerkin, spectral difference, or flux reconstruction operators).

  6. Comparison of preconditioners for collocation Chebyshev approximation of 2D and 3D generalized Stokes problem

    International Nuclear Information System (INIS)

    Garba, Abdou; Haldenwang, Pierre

    2003-01-01

    The aim of the paper is concerned with the iterative resolution of the generalized Stokes problem in the framework of collocation Chebyshev approximation. More precisely, we analyze the performance of several preconditioners improving the classical Uzawa method. We first recall that the general Stokes problem (GSP) is an elementary substep of general interest for computing not only incompressible flows but also low Mach number flows. We then remark that performances of the classical Uzawa algorithm for solving the GSP are in fact closely related to the Reynolds number. In order to overcome this dependence, preconditioners are needed. The preconditioners we analyze here are recommended by Fourier analysis of the pressure operator. We additionally give interpretation of the preconditioners in terms of influence (or capacitance) techniques. We give a detailed analysis of the conditioning of the discrete collocation Chebyshev versions of the operators. Numerical comparison is conducted in 2D as well as in 3D rectangular geometry. Our comparative study shows that the fictitious wall permeability (FWP) method is the most efficient preconditioner. If complemented with a suitable pressure filtering, its efficiency still increases

  7. When Joy Matters: The Importance of Hedonic Stimulation in Collocated Collaboration with Large-Displays

    Science.gov (United States)

    Novak, Jasminko; Schmidt, Susanne

    Hedonic aspects are increasingly considered as an important factor in user acceptance of information systems, especially for activities with high self-fulfilling value for the users. In this paper we report on the results of an experiment investigating the hedonic qualities of an interactive large-display workspace for collocated collaboration in sales-oriented travel advisory. The results show a higher hedonic stimulation quality of a touch-based large-display travel advisory workspace than that of a traditional workspace with catalogues. Together with the feedback of both customers and travel agents this suggests the adequacy of using touch-based large-displays with visual workspaces for supporting the hedonic stimulation of user experience in collocated collaboration settings. The relation of high perception of hedonic quality to positive emotional attitudes towards the use of a large-display workspace indicates that even in utilitarian activities (e.g. reaching sales goals for travel agents) hedonic aspects can play an important role. This calls for reconsidering the traditional divide of hedonic vs. utilitarian systems in current literature, to a more balanced view towards systems which provide both utilitarian and hedonic sources of value to the user.

  8. Data assimilation for unsaturated flow models with restart adaptive probabilistic collocation based Kalman filter

    Energy Technology Data Exchange (ETDEWEB)

    Man, Jun; Li, Weixuan; Zeng, Lingzao; Wu, Laosheng

    2016-06-01

    The ensemble Kalman filter (EnKF) has gained popularity in hydrological data assimilation problems. As a Monte Carlo based method, a relatively large ensemble size is usually required to guarantee the accuracy. As an alternative approach, the probabilistic collocation based Kalman filter (PCKF) employs the polynomial chaos to approximate the original system. In this way, the sampling error can be reduced. However, PCKF suffers from the so-called "curse of dimensionality". When the system nonlinearity is strong and number of parameters is large, PCKF could be even more computationally expensive than EnKF. Motivated by most recent developments in uncertainty quantification, we propose a restart adaptive probabilistic collocation based Kalman filter (RAPCKF) for data assimilation in unsaturated flow problems. During the implementation of RAPCKF, the important parameters are identified and active PCE basis functions are adaptively selected. The "restart" technology is used to eliminate the inconsistency between model parameters and states. The performance of RAPCKF is tested with numerical cases of unsaturated flow models. It is shown that RAPCKF is more efficient than EnKF with the same computational cost. Compared with the traditional PCKF, the RAPCKF is more applicable in strongly nonlinear and high dimensional problems.

  9. ANALYSIS OF SPECIALISED COLLOCATIONS IN THE AREA OF REMOTE SENSING IN THE PERSPECTIVE OF PHRASEOLOGY

    Directory of Open Access Journals (Sweden)

    Diva Cardoso de CAMARGO

    2013-12-01

    Full Text Available The aim of this research is to build and analyze a parallel corpus in the field of remote sensing in order to identify, according to its frequency, specialized collocations in English and then search for their equivalents in Portuguese. The research is based on the interdisciplinary approach of Corpus-Based Translation Studies (BAKER, 1995; CAMARGO, 2007, Corpus Linguistics (BERBER SARDINHA, 2004; TOGNINI-BONELLI, 2001, Phraseology (ORENHA-OTTAIANO, 2009; PAVEL, 1993, and some principles of Terminology (BARROS, 2004. For manipulating the corpora, the program WordSmith Tools (SCOTT, 2012 version 6.0 is used. To support this study, two comparable corpora in English and Portuguese were also built from articles published in both national and international journals in remote sensing. The results show that the collocations in Portuguese seem to be still in the process of conventionalization, as the translators made use of greater variation in their translational options, which can be a way to make the text clearer for the reader.

  10. Haar Wavelet Collocation Method for Thermal Analysis of Porous Fin with Temperature-dependent Thermal Conductivity and Internal Heat Generation

    Directory of Open Access Journals (Sweden)

    George OGUNTALA

    2017-08-01

    Full Text Available In this study, the thermal performance analysis of porous fin with temperature-dependent thermal conductivity and internal heat generation is carried out using Haar wavelet collocation method. The effects of various parameters on the thermal characteristics of the porous fin are investigated. It is found that as the porosity increases, the rate of heat transfer from the fin increases and the thermal performance of the porous fin increases. The numerical solutions by the Haar wavelet collocation method are in good agreement with the standard numerical solutions.

  11. A Modified Generalized Laguerre-Gauss Collocation Method for Fractional Neutral Functional-Differential Equations on the Half-Line

    Directory of Open Access Journals (Sweden)

    Ali H. Bhrawy

    2014-01-01

    Full Text Available The modified generalized Laguerre-Gauss collocation (MGLC method is applied to obtain an approximate solution of fractional neutral functional-differential equations with proportional delays on the half-line. The proposed technique is based on modified generalized Laguerre polynomials and Gauss quadrature integration of such polynomials. The main advantage of the present method is to reduce the solution of fractional neutral functional-differential equations into a system of algebraic equations. Reasonable numerical results are achieved by choosing few modified generalized Laguerre-Gauss collocation points. Numerical results demonstrate the accuracy, efficiency, and versatility of the proposed method on the half-line.

  12. Soldier use of dietary supplements, including protein and body building supplements, in a combat zone is different than use in garrison.

    Science.gov (United States)

    Austin, Krista G; McLellan, Tom M; Farina, Emily K; McGraw, Susan M; Lieberman, Harris R

    2016-01-01

    United States Army personnel in garrison who are not deployed to combat theater report using dietary supplements (DSs) to promote health, increase physical and mental strength, and improve energy levels. Given the substantial physical and cognitive demands of combat, DS use may increase during deployment. This study compared DS use by garrison soldiers with DS use by personnel deployed to a combat theater in Afghanistan. Prevalence and patterns of DS use, demographic factors, and health behaviors were assessed by survey (deployed n = 221; garrison n = 1001). Eighty-two percent of deployed and 74% of garrison soldiers used DSs ≥ 1 time·week(-1). Logistic regression analyses, adjusted for significant demographic and health predictors of DS use, showed deployed personnel were more likely than garrison soldiers to use protein, amino acids, and combination products. Deployed females were more likely to use protein supplements and deployed males were more likely to use multivitamins, combination products, protein, and body building supplements than garrison respondents. Significantly more deployed (17%) than garrison (10%) personnel spent more than $50∙month(-1) on DSs. Higher protein supplement use among deployed personnel was associated with higher frequency of strength training and lower amounts of aerobic exercise for males but similar amounts of strength training and aerobic exercise for females. Protein supplements and combination products are used more frequently by deployed than garrison soldiers with the intent of enhancing strength and energy.

  13. cDNA cloning of the basement membrane chondroitin sulfate proteoglycan core protein, bamacan: a five domain structure including coiled-coil motifs

    DEFF Research Database (Denmark)

    Wu, R R; Couchman, J R

    1997-01-01

    obtained cDNA clones encoding the entire bamacan core protein of Mr = 138 kD, which reveal a five domain, head-rod-tail configuration. The head and tail are potentially globular, while the central large rod probably forms coiled-coil structures, with one large central and several very short interruptions....... The protein sequence has low overall homology, apart from very small NH2- and COOH-terminal motifs. At the junctions between the distal globular domains and the coiled-coil regions lie glycosylation sites, with up to three N-linked oligosaccharides and probably three chondroitin chains. Three other Ser...

  14. Expression of complement binding proteins (CD55 and CD59) on spermatozoa of patients included in the program for assisted reproduction

    Czech Academy of Sciences Publication Activity Database

    Djarkova, T.; Mollova, M.; Ivanova, M.; Pěknicová, Jana; Todorov, P.; Dimitrov, J.

    2001-01-01

    Roč. 10, - (2001), s. 5-9 ISSN 0303-4569 R&D Projects: GA MŠk EU1985 Keywords : assisted reproduction * spermatozoa * proteins CD55, CD59 Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 0.732, year: 2001

  15. Activation of AMP-activated protein kinase rapidly suppresses multiple pro-inflammatory pathways in adipocytes including IL-1 receptor-associated kinase-4 phosphorylation

    DEFF Research Database (Denmark)

    Mancini, Sarah J; White, Anna D; Bijland, Silvia

    2017-01-01

    Inflammation of adipose tissue in obesity is associated with increased IL-1β, IL-6 and TNF-α secretion and proposed to contribute to insulin resistance. AMP-activated protein kinase (AMPK) regulates nutrient metabolism and is reported to have anti-inflammatory actions in adipose tissue, yet the m...

  16. Identification of 17 HrpX-regulated proteins including two novel type III effectors, XOC_3956 and XOC_1550, in Xanthomonas oryzae pv. oryzicola.

    Science.gov (United States)

    Xue, Xiao-bo; Zou, Li-fang; Ma, Wen-xiu; Liu, Zhi-yang; Chen, Gong-you

    2014-01-01

    The function of some hypothetical proteins, possibly regulated by key hrp regulators, in the pathogenicity of phytopathogenic bacteria remains largely unknown. In the present study, in silicon microarray data demonstrated that the expression of 17 HrpX-regulated protein (Xrp) genes of X. oryzae pv. oryzicola (Xoc), which causes bacterial leaf streak in rice, were either positively or negatively regulated by HrpX or/and HrpG. Bioinformatics analysis demonstrated that five Xrps possess a putative type III secretion (T3S) signal in the first 50 N-terminal amino acids, six xrp genes contain a PIP-box-like sequence (TTCGB-NX-TTCGB, 9 ≤ X ≤ 25) in the promoter regions, and two Xrps have both motifs. Twelve Xrps are widely conserved in Xanthomonas spp., whereas four are specific for X. oryzae (Xrp6) or Xoc (Xrp8, Xrp14 and Xrp17). In addition to the regulation by HrpG/HrpX, some of the 17 genes were also modulated by another hrp regulator HrpD6. Mutagenesis of these 17 genes indicated that five Xrps (Xrp1, Xrp2, Xrp5, Xrp8 and Xrp14) were required for full virulence and bacterial growth in planta. Immunoblotting assays and fusion with N-terminally truncated AvrXa10 indicated that Xrp3 and Xrp5 were secreted and translocated into rice cells through the type-III secretion system (T3S), suggesting they are novel T3S effectors. Our results suggest that Xoc exploits an orchestra of proteins that are regulated by HrpG, HrpX and HrpD6, and these proteins facilitate both infection and metabolism.

  17. Posttranslational Control of ALA Synthesis Includes GluTR Degradation by Clp Protease and Stabilization by GluTR-Binding Protein.

    Science.gov (United States)

    Apitz, Janina; Nishimura, Kenji; Schmied, Judith; Wolf, Anja; Hedtke, Boris; van Wijk, Klaas J; Grimm, Bernhard

    2016-04-01

    5-Aminolevulinic acid (ALA) is the first committed substrate of tetrapyrrole biosynthesis and is formed from glutamyl-tRNA by two enzymatic steps. Glutamyl-tRNA reductase (GluTR) as the first enzyme of ALA synthesis is encoded by HEMA genes and tightly regulated at the transcriptional and posttranslational levels. Here, we show that the caseinolytic protease (Clp) substrate adaptor ClpS1 and the ClpC1 chaperone as well as the GluTR-binding protein (GBP) interact with the N terminus of GluTR Loss-of function mutants of ClpR2 and ClpC1 proteins show increased GluTR stability, whereas absence of GBP results in decreased GluTR stability. Thus, the Clp protease system and GBP contribute to GluTR accumulation levels, and thereby the rate-limiting ALA synthesis. These findings are supported with Arabidopsis (Arabidopsis thaliana) hema1 mutants expressing a truncated GluTR lacking the 29 N-terminal amino acid residues of the mature protein. Accumulation of this truncated GluTR is higher in dark periods, resulting in increased protochlorophyllide content. It is proposed that the proteolytic activity of Clp protease counteracts GBP binding to assure the appropriate content of GluTR and the adequate ALA synthesis for chlorophyll and heme in higher plants. © 2016 American Society of Plant Biologists. All Rights Reserved.

  18. Retention and Use of Lexical Collocations (Verb + Noun and Adjective + Noun) by Applying Lexical Approach in a Reading Course

    Science.gov (United States)

    Ördem, Eser; Paker, Turan

    2016-01-01

    The purpose of this study was to investigate whether teaching vocabulary via collocations would contribute to retention and use of foreign language, English. A quasi-experimental design was formed to see whether there would be a significant difference between the treatment and control groups. Three instruments developed were conducted to 60…

  19. Improvement of least-squares collocation error estimates using local GOCE Tzz signal standard deviations

    DEFF Research Database (Denmark)

    Tscherning, Carl Christian

    2015-01-01

    The method of Least-Squares Collocation (LSC) may be used for the modeling of the anomalous gravity potential (T) and for the computation (prediction) of quantities related to T by a linear functional. Errors may also be estimated. However, when using an isotropic covariance function or equivalen...

  20. A consistent method for finite volume discretization of body forces on collocated grids applied to flow through an actuator disk

    DEFF Research Database (Denmark)

    Troldborg, Niels; Sørensen, Niels N.; Réthoré, Pierre-Elouan

    2015-01-01

    This paper describes a consistent algorithm for eliminating the numerical wiggles appearing when solving the finite volume discretized Navier-Stokes equations with discrete body forces in a collocated grid arrangement. The proposed method is a modification of the Rhie-Chow algorithm where the for...

  1. The Impact of Length of Study Abroad on Collocational Knowledge: The Case of Saudi Students in Australia

    Directory of Open Access Journals (Sweden)

    Ibrahim R. Alqarni

    2017-04-01

    Full Text Available This study investigates the impact that study in Australia has on the lexical knowledge of Saudi Arabian students. It focuses on: 1 the effects that the length of study in Australia has on the acquisition of lexical collocations, as reflected by lexical knowledge tests, and 2 whether there is a significant gender difference in the acquisition of lexical collocation knowledge. The results indicate that there is a positive correlation between the length of stay in Australia and the knowledge of lexical collocation, since the overall mean scores of the entire sample increased with the number of the years spent in Australia. Participants who stayed for one year had the lowest mean score of 7.39, whereas those with the longest length of stay of four years had the highest mean score of 8.76. Participants staying for two or three years had minimal improvements, with mean scores of 7.64 and 7.68 respectively. The results indicate that there was only a slight difference between male and female participants in their knowledge of lexical collocations, with overall mean scores of 7.56 and 8.35 out of 12 respectively.

  2. FRBRization of a Library Catalog: Better Collocation of Records, Leading to Enhanced Search, Retrieval, and Display

    Directory of Open Access Journals (Sweden)

    Timothy J. Dickey

    2008-03-01

    Full Text Available The Functional Requirements for Bibliographic Records (FRBR’s hierarchical system defines families of bibliographic relationship between records and collocates them better than most extant bibliographic systems. Certain library materials (especially audio-visual formats pose notable challenges to search and retrieval; the first benefits of a FRBRized system would be felt in music libraries, but research already has proven its advantages for fine arts, theology, and literature—the bulk of the non-science, technology, and mathematics collections. This report will summarize the benefits of FRBR to nextgeneration library catalogs and OPACs, and will review the handful of ILS and catalog systems currently operating with its theoretical structure.

  3. Analytic regularity and collocation approximation for elliptic PDEs with random domain deformations

    KAUST Repository

    Castrillon, Julio

    2016-03-02

    In this work we consider the problem of approximating the statistics of a given Quantity of Interest (QoI) that depends on the solution of a linear elliptic PDE defined over a random domain parameterized by N random variables. The elliptic problem is remapped onto a corresponding PDE with a fixed deterministic domain. We show that the solution can be analytically extended to a well defined region in CN with respect to the random variables. A sparse grid stochastic collocation method is then used to compute the mean and variance of the QoI. Finally, convergence rates for the mean and variance of the QoI are derived and compared to those obtained in numerical experiments.

  4. SIMULASI NUMERIK PADA ALIRAN AIR TANAH MENGGUNAKAN COLLOCATION FINITE ELEMENT METHOD

    Directory of Open Access Journals (Sweden)

    UMMU SALAMAH

    2018-02-01

    Full Text Available This research presents a numerical simulation on groundwater flow using collocation finite element method (CFEM. Groundwater flow is known as the flow of water beneath the soil. Generally, groundwater flow is generated due to high hydraulic differences. The CFEM is an approximation solution of the differential equation by assuming the selected analytical function to fulfill the differential equation and setting the residual value turn out zero. Here, this research will discuss the case of groundwater flow on steady state and unsteady state. The results of numerical method CFEM is shown second order in terms of convergence by error. The numerical error in case of constant water flow is obtain 3.62E ? 23 using the grid size 6.1797e ? 07. Moreover, the flow of groundwater is simulated in various of hydraulic conductivity constants.

  5. PARALLEL SMAC ALGORITHMS TO SOLVE SHALLOW WATER EQUATION WITH UNSTRUCTURED COLLOCATED GRID SYSTEM

    Science.gov (United States)

    Yamashita, Haruka; Ushijima, Satoru

    A computational method to solve shallow water equations has been investigated with an SMAC method which is usually employed in the simulation for incompressible fluids. In particular, this numerical method is implemented in the unstructured collocated grid system with the distributed memory system to increase the parallel efficiency. The developed computational method was applied to the 1D dam-break problem and the free-surface flows in a meandering open channel. As a result of the 1D dam-break simulations, it was confirmed that this method improve the numerical stability. While, in the case of the meandering open channel, it was confirmed that the predicted water depth and depth-averaged velocity distributions are qualitatively in good agreement with the experimental results and that the reasonable parallel efficiencies are attained by parallel computations.

  6. A method for stochastic constrained optimization using derivative-free surrogate pattern search and collocation

    International Nuclear Information System (INIS)

    Sankaran, Sethuraman; Audet, Charles; Marsden, Alison L.

    2010-01-01

    Recent advances in coupling novel optimization methods to large-scale computing problems have opened the door to tackling a diverse set of physically realistic engineering design problems. A large computational overhead is associated with computing the cost function for most practical problems involving complex physical phenomena. Such problems are also plagued with uncertainties in a diverse set of parameters. We present a novel stochastic derivative-free optimization approach for tackling such problems. Our method extends the previously developed surrogate management framework (SMF) to allow for uncertainties in both simulation parameters and design variables. The stochastic collocation scheme is employed for stochastic variables whereas Kriging based surrogate functions are employed for the cost function. This approach is tested on four numerical optimization problems and is shown to have significant improvement in efficiency over traditional Monte-Carlo schemes. Problems with multiple probabilistic constraints are also discussed.

  7. On the a priori estimation of collocation error covariance functions: a feasibility study

    DEFF Research Database (Denmark)

    Arabelos, D.N.; Forsberg, René; Tscherning, C.C.

    2007-01-01

    Error covariance estimates are necessary information for the combination of solutions resulting from different kinds of data or methods, or for the assimilation of new results in already existing solutions. Such a combination or assimilation process demands proper weighting of the data, in order...... for the combination to be optimal and the error estimates of the results realistic. One flexible method for the gravity field approximation is least-squares collocation leading to optimal solutions for the predicted quantities and their error covariance estimates. The drawback of this method is related to the current...... ability of computers in handling very large systems of linear equations produced by an equally large amount of available input data. This problem becomes more serious when error covariance estimates have to be simultaneously computed. Using numerical experiments aiming at revealing dependencies between...

  8. Block preconditioners for linear systems arising from multiscale collocation with compactly supported RBFs

    KAUST Repository

    Farrell, Patricio

    2015-04-30

    © 2015John Wiley & Sons, Ltd. Symmetric collocation methods with RBFs allow approximation of the solution of a partial differential equation, even if the right-hand side is only known at scattered data points, without needing to generate a grid. However, the benefit of a guaranteed symmetric positive definite block system comes at a high computational cost. This cost can be alleviated somewhat by considering compactly supported RBFs and a multiscale technique. But the condition number and sparsity will still deteriorate with the number of data points. Therefore, we study certain block diagonal and triangular preconditioners. We investigate ideal preconditioners and determine the spectra of the preconditioned matrices before proposing more practical preconditioners based on a restricted additive Schwarz method with coarse grid correction. Numerical results verify the effectiveness of the preconditioners.

  9. Pseudo spectral collocation with Maxwell polynomials for kinetic equations with energy diffusion

    Science.gov (United States)

    Sánchez-Vizuet, Tonatiuh; Cerfon, Antoine J.

    2018-02-01

    We study the approximation and stability properties of a recently popularized discretization strategy for the speed variable in kinetic equations, based on pseudo-spectral collocation on a grid defined by the zeros of a non-standard family of orthogonal polynomials called Maxwell polynomials. Taking a one-dimensional equation describing energy diffusion due to Fokker–Planck collisions with a Maxwell–Boltzmann background distribution as the test bench for the performance of the scheme, we find that Maxwell based discretizations outperform other commonly used schemes in most situations, often by orders of magnitude. This provides a strong motivation for their use in high-dimensional gyrokinetic simulations. However, we also show that Maxwell based schemes are subject to a non-modal time stepping instability in their most straightforward implementation, so that special care must be given to the discrete representation of the linear operators in order to benefit from the advantages provided by Maxwell polynomials.

  10. Numerical solution of the Rosenau-KdV-RLW equation by using RBFs collocation method

    Science.gov (United States)

    Korkmaz, Bahar; Dereli, Yilmaz

    2016-04-01

    In this study, a meshfree method based on the collocation with radial basis functions (RBFs) is proposed to solve numerically an initial-boundary value problem of Rosenau-KdV-regularized long-wave (RLW) equation. Numerical values of invariants of the motion are computed to examine the fundamental conservative properties of the equation. Computational experiments for the simulation of solitary waves examine the accuracy of the scheme in terms of error norms L2 and L∞. Linear stability analysis is investigated to determine whether the present method is stable or unstable. The scheme gives unconditionally stable, and second-order convergent. The obtained results are compared with analytical solution and some other earlier works in the literature. The presented results indicate the accuracy and efficiency of the method.

  11. Solving Buckmaster equation using cubic B-spline and cubic trigonometric B-spline collocation methods

    Science.gov (United States)

    Chanthrasuwan, Maveeka; Asri, Nur Asreenawaty Mohd; Hamid, Nur Nadiah Abd; Majid, Ahmad Abd.; Azmi, Amirah

    2017-08-01

    The cubic B-spline and cubic trigonometric B-spline functions are used to set up the collocation in finding solutions for the Buckmaster equation. These splines are applied as interpolating functions in the spatial dimension while the finite difference method (FDM) is used to discretize the time derivative. The Buckmaster equation is linearized using Taylor's expansion and solved using two schemes, namely Crank-Nicolson and fully implicit. The von Neumann stability analysis is carried out on the two schemes and they are shown to be conditionally stable. In order to demonstrate the capability of the schemes, some problems are solved and compared with analytical and FDM solutions. The proposed methods are found to generate more accurate results than the FDM.

  12. Trajectory planning based on collocation methods for multiple aerial and ground autonomous vehicles

    OpenAIRE

    Vera Rendón, Santiago

    2015-01-01

    Esta tesis doctorar presenta una serie de contribuciones en los métodos de coordinación y generación de trayectorias de grupos de vehículos, concretamente de vehículos autónomos. Los métodos de colocación, más conocidos por su nombre en inglés “Collocation methods”, han despertado un creciente interés en los últimos años, entre los distintos métodos numéricos para resolver cualquier tipo de problema dentro del campo de la ingeniería. Esta tesis en concreto, presenta un nuevo punto de vista de...

  13. An iterative finite-element collocation method for parabolic problems using domain decomposition

    Energy Technology Data Exchange (ETDEWEB)

    Curran, M.C.

    1992-01-01

    Advection-dominated flows occur widely in the transport of groundwater contaminants, the movements of fluids in enhanced oil recovery projects, and many other contexts. In numerical models of such flows, adaptive local grid refinement is a conceptually attractive approach for resolving the sharp fronts or layers that tend to characterize the solutions. However, this approach can be difficult to implement in practice. A domain decomposition method developed by Bramble, Ewing, Pasciak, and Schatz, known as the BEPS method, overcomes many of the difficulties. We demonstrate the applicability of the iterative BEPS ideas to finite-element collocation on trial spaces of piecewise Hermite bicubics. The resulting scheme allows one to refine selected parts of a spatial grid without destroying algebraic efficiencies associated with the original coarse grid. We apply the method to two dimensional time-dependent advection-diffusion problems.

  14. An iterative finite-element collocation method for parabolic problems using domain decomposition

    Energy Technology Data Exchange (ETDEWEB)

    Curran, M.C.

    1992-11-01

    Advection-dominated flows occur widely in the transport of groundwater contaminants, the movements of fluids in enhanced oil recovery projects, and many other contexts. In numerical models of such flows, adaptive local grid refinement is a conceptually attractive approach for resolving the sharp fronts or layers that tend to characterize the solutions. However, this approach can be difficult to implement in practice. A domain decomposition method developed by Bramble, Ewing, Pasciak, and Schatz, known as the BEPS method, overcomes many of the difficulties. We demonstrate the applicability of the iterative BEPS ideas to finite-element collocation on trial spaces of piecewise Hermite bicubics. The resulting scheme allows one to refine selected parts of a spatial grid without destroying algebraic efficiencies associated with the original coarse grid. We apply the method to two dimensional time-dependent advection-diffusion problems.

  15. Absorption of Solar Radiation by the Cloudy Atmosphere Interpretations of Collocated Aircraft Measurements

    Science.gov (United States)

    Valero, Francisco P. J.; Cess, Robert D.; Zhang, Minghua; Pope, Shelly K.; Bucholtz, Anthony; Bush, Brett; Vitko, John, Jr.

    1997-01-01

    As part of the Atmospheric Radiation Measurement (ARM) Enhanced Shortwave Experiment (ARESE), we have obtained and analyzed measurements made from collocated aircraft of the absorption of solar radiation within the atmospheric column between the two aircraft. The measurements were taken during October 1995 at the ARM site in Oklahoma. Relative to a theoretical radiative transfer model, we find no evidence for excess solar absorption in the clear atmosphere and significant evidence for its existence in the cloudy atmosphere. This excess cloud solar absorption appears to occur in both visible (0.224-0.68 microns) and near-infrared (0.68-3.30 microns) spectral regions, although not at 0.5 microns for the visible contribution, and it is shown to be true absorption rather than an artifact of sampling errors caused by measuring three-dimensional clouds.

  16. A Bivariate Chebyshev Spectral Collocation Quasilinearization Method for Nonlinear Evolution Parabolic Equations

    Directory of Open Access Journals (Sweden)

    S. S. Motsa

    2014-01-01

    Full Text Available This paper presents a new method for solving higher order nonlinear evolution partial differential equations (NPDEs. The method combines quasilinearisation, the Chebyshev spectral collocation method, and bivariate Lagrange interpolation. In this paper, we use the method to solve several nonlinear evolution equations, such as the modified KdV-Burgers equation, highly nonlinear modified KdV equation, Fisher's equation, Burgers-Fisher equation, Burgers-Huxley equation, and the Fitzhugh-Nagumo equation. The results are compared with known exact analytical solutions from literature to confirm accuracy, convergence, and effectiveness of the method. There is congruence between the numerical results and the exact solutions to a high order of accuracy. Tables were generated to present the order of accuracy of the method; convergence graphs to verify convergence of the method and error graphs are presented to show the excellent agreement between the results from this study and the known results from literature.

  17. Solving Dym equation using quartic B-spline and quartic trigonometric B-spline collocation methods

    Science.gov (United States)

    Anuar, Hanis Safirah Saiful; Mafazi, Nur Hidayah; Hamid, Nur Nadiah Abd; Majid, Ahmad Abd.; Azmi, Amirah

    2017-08-01

    The nonlinear Dym equation is solved numerically using the quartic B-spline (QuBS) and quartic trigonometric B-spline (QuTBS) collocation methods. The QuBS and QuTBS are utilized as interpolating functions in the spatial dimension while the finite difference method (FDM) is applied to discretize the temporal space with the help of theta-weighted method. The nonlinear term in the Dym equation is linearized using Taylor's expansion. Two schemes are performed on both methods which are Crank-Nicolson and fully implicit. Applying the Von-Neumann stability analysis, these schemes are found to be conditionally stable. Several numerical examples of different forms are discussed and compared in term of errors with exact solutions and results from the FDM.

  18. Implementation of optimal Galerkin and Collocation approximations of PDEs with Random Coefficients⋆⋆⋆

    Directory of Open Access Journals (Sweden)

    Tempone R.

    2011-12-01

    Full Text Available In this work we first focus on the Stochastic Galerkin approximation of the solution u of an elliptic stochastic PDE. We rely on sharp estimates for the decay of the coefficients of the spectral expansion of u on orthogonal polynomials to build a sequence of polynomial subspaces that features better convergence properties compared to standard polynomial subspaces such as Total Degree or Tensor Product. We consider then the Stochastic Collocation method, and use the previous estimates to introduce a new effective class of Sparse Grids, based on the idea of selecting a priori the most profitable hierarchical surpluses, that, again, features better convergence properties compared to standard Smolyak or tensor product grids.

  19. Numerical solution of fractional differential equations using cubic B-spline wavelet collocation method

    Science.gov (United States)

    Li, Xinxiu

    2012-10-01

    Physical processes with memory and hereditary properties can be best described by fractional differential equations due to the memory effect of fractional derivatives. For that reason reliable and efficient techniques for the solution of fractional differential equations are needed. Our aim is to generalize the wavelet collocation method to fractional differential equations using cubic B-spline wavelet. Analytical expressions of fractional derivatives in Caputo sense for cubic B-spline functions are presented. The main characteristic of the approach is that it converts such problems into a system of algebraic equations which is suitable for computer programming. It not only simplifies the problem but also speeds up the computation. Numerical results demonstrate the validity and applicability of the method to solve fractional differential equation.

  20. Between initial familiarity and future use – a case of Collocated Collaborative Writing

    DEFF Research Database (Denmark)

    Bødker, Susanne; Polli, Anna Maria

    2014-01-01

    This paper reports on a design experiment in an art gallery, where we explored visitor practices of commenting on art, and how they were shaped in interaction with a newly designed collocated, collaborative writing technology. In particular we investigate what potentials previous practices carry...... with them that may affect early use and further development of use. We base our analyses on interviews in the art gallery and on socio-cultural theories of artefactmediated learning and collaboration. The analyses help identify three forms of collaborative writing, which are placed in the space between...... future use possibilities and initial familiarity based on everyday practices. These forms met and at times collided in a space where the actual use was shaped. We furthermore look back on initial assumptions made in design regarding a productive collaborative writing style, and confront...

  1. Application of the orthogonal collocation method to determination of temperature distribution in cylindrical conductors

    International Nuclear Information System (INIS)

    Fortini, Maria A.; Stamoulis, Michel N.; Ferreira, Angela F.M.; Pereira, Claubia; Costa, Antonella L.; Silva, Clarysson A.M.

    2008-01-01

    In this work, an analytical model for the determination of the temperature distribution in cylindrical heater components with characteristics of nuclear fuel rods, is presented. The heat conductor is characterized by an arbitrary number of solid walls and different types of materials, whose thermal properties are taken as function of temperature. The heat conduction fundamental equation is solved numerically with the method of weighted residuals (MWR) using a technique of orthogonal collocation. The results obtained with the proposed method are compared with the experimental data from tests performed in the TRIGA IPR-R1 research reactor localized at the CDTN/CNEN (Centro de Desenvolvimento da Tecnologia Nuclear/Comissao Nacional de Energia Nuclear) at Belo Horizonte in Brazil

  2. Relationships among properties of marine stratocumulus derived from collocated CALIPSO and MODIS observations

    Science.gov (United States)

    Hayes, C. R.; Coakley, J. A.; Tahnk, W. R.

    2010-01-01

    Collocated Moderate Resolution Imaging Spectroradiometer (MODIS) imagery and Cloud-Aerosol Lidar and Infrared Pathfinder Satellite Observation (CALIPSO) 532 nm total attenuated backscatter coefficients were used to identify 50 km scale segments for ocean regions that had only a single layer of marine stratocumulus. On the basis of whether the underlying ocean surface was detected in the backscatter coefficients, the segments were separated into those for which all of the 1 km MODIS pixels were identified as being overcast (no surface detected) and those for which there were breaks in the cloud layer (surface detected). Cloud properties for the collocated MODIS pixels were obtained from the MODIS MOD06 cloud product and from a retrieval scheme designed to account for broken clouds within imager pixels. For the 50 km overcast segments the variations in optical depth, τ, and droplet effective radius, Re, obtained from the MOD06 and partly cloudy pixel retrievals were in agreement, and the variations in layer temperature were consistent with those inferred from the CALIPSO backscatter coefficients. In addition, the droplet effective radii retrieved separately using the 1.6, 2.1, and 3.7 μm MODIS reflectances were consistent with droplets growing as clouds thickened and mean values of dlnRe/dlnτ were close to 0.2, as predicted by adiabatic cloud parcel models. When the segments contained broken clouds, however, the droplet effective radii for the three near-infrared wavelengths were inconsistent with droplets growing as clouds thickened and dlnRe/dlnτ departed from 0.2. This breakdown is thought to result from biases in the retrieved cloud properties caused by subpixel-scale variations in liquid water amount and droplet radius.

  3. Amino acid profiles of rumen undegradable protein: a comparison between forages including cereal straws and alfalfa and their respective total mixed rations.

    Science.gov (United States)

    Wang, B; Jiang, L S; Liu, J X

    2017-10-06

    Optimizing the amino acid (AA) profile of rumen undegradable protein (RUP) can positively affect the amount of milk protein. This study was conducted to improve knowledge regarding the AA profile of rumen undegradable protein from corn stover, rice straw and alfalfa hay as well as the total mixed ratio diets (TMR) based on one of them as forage source [forage-to-concentrate ratio of 45:55 (30% of corn stover (CS), 30% of rice straw (RS), 23% of alfalfa hay (AH) and dry matter basis)]. The other ingredients in the three TMR diets were similar. The RUP of all the forages and diets was estimated by incubation for 16 hr in the rumen of three ruminally cannulated lactating cows. All residues were corrected for microbial colonization, which was necessary in determining the AA composition of RUP from feed samples using in situ method. Compared with their original AA composition, the AA pattern of forages and forage-based diets changed drastically after rumen exposure. In addition, the extent of ruminal degradation of analysed AA was not constant among the forages. The greatest individual AA degradability of alfalfa hay and corn stover was Pro, but was His of rice straw. A remarkable difference was observed between microbial attachment corrected and uncorrected AA profiles of RUP, except for alfalfa hay and His in the three forages and TMR diets. The ruminal AA degradability of cereal straws was altered compared with alfalfa hay but not for the TMR diets. In summary, the AA composition of forages and TMR-based diets changed significantly after ruminal exposure, indicating that the original AA profiles of the feed cannot represent its AA composition of RUP. The AA profile of RUP and ruminal AA degradability for corn stover and rice straw contributed to missing information in the field. © 2017 Blackwell Verlag GmbH.

  4. EspC, an Autotransporter Protein Secreted by Enteropathogenic Escherichia coli, Causes Apoptosis and Necrosis through Caspase and Calpain Activation, Including Direct Procaspase-3 Cleavage

    Directory of Open Access Journals (Sweden)

    Antonio Serapio-Palacios

    2016-06-01

    Full Text Available Enteropathogenic Escherichia coli (EPEC has the ability to antagonize host apoptosis during infection through promotion and inhibition of effectors injected by the type III secretion system (T3SS, but the total number of these effectors and the overall functional relationships between these effectors during infection are poorly understood. EspC produced by EPEC cleaves fodrin, paxillin, and focal adhesion kinase (FAK, which are also cleaved by caspases and calpains during apoptosis. Here we show the role of EspC in cell death induced by EPEC. EspC is involved in EPEC-mediated cell death and induces both apoptosis and necrosis in epithelial cells. EspC induces apoptosis through the mitochondrial apoptotic pathway by provoking (i a decrease in the expression levels of antiapoptotic protein Bcl-2, (ii translocation of the proapoptotic protein Bax from cytosol to mitochondria, (iii cytochrome c release from mitochondria to the cytoplasm, (iv loss of mitochondrial membrane potential, (v caspase-9 activation, (vi cleavage of procaspase-3 and (vii an increase in caspase-3 activity, (viii PARP proteolysis, and (ix nuclear fragmentation and an increase in the sub-G1 population. Interestingly, EspC-induced apoptosis was triggered through a dual mechanism involving both independent and dependent functions of its EspC serine protease motif, the direct cleavage of procaspase-3 being dependent on this motif. This is the first report showing a shortcut for induction of apoptosis by the catalytic activity of an EPEC protein. Furthermore, this atypical intrinsic apoptosis appeared to induce necrosis through the activation of calpain and through the increase of intracellular calcium induced by EspC. Our data indicate that EspC plays a relevant role in cell death induced by EPEC.

  5. cDNA cloning of the basement membrane chondroitin sulfate proteoglycan core protein, bamacan: a five domain structure including coiled-coil motifs

    DEFF Research Database (Denmark)

    Wu, R R; Couchman, J R

    1997-01-01

    obtained cDNA clones encoding the entire bamacan core protein of Mr = 138 kD, which reveal a five domain, head-rod-tail configuration. The head and tail are potentially globular, while the central large rod probably forms coiled-coil structures, with one large central and several very short interruptions....../translation product from a full-length bamacan cDNA. The unusual structure of this proteoglycan is indicative of specific functional roles in basement membrane physiology, commensurate with its distinct expression in development and changes in disease models....

  6. Dynamic Regulation of a Cell Adhesion Protein Complex Including CADM1 by Combinatorial Analysis of FRAP with Exponential Curve-Fitting

    Science.gov (United States)

    Sakurai-Yageta, Mika; Maruyama, Tomoko; Suzuki, Takashi; Ichikawa, Kazuhisa; Murakami, Yoshinori

    2015-01-01

    Protein components of cell adhesion machinery show continuous renewal even in the static state of epithelial cells and participate in the formation and maintenance of normal epithelial architecture and tumor suppression. CADM1 is a tumor suppressor belonging to the immunoglobulin superfamily of cell adhesion molecule and forms a cell adhesion complex with an actin-binding protein, 4.1B, and a scaffold protein, MPP3, in the cytoplasm. Here, we investigate dynamic regulation of the CADM1-4.1B-MPP3 complex in mature cell adhesion by fluorescence recovery after photobleaching (FRAP) analysis. Traditional FRAP analysis were performed for relatively short period of around 10min. Here, thanks to recent advances in the sensitive laser detector systems, we examine FRAP of CADM1 complex for longer period of 60 min and analyze the recovery with exponential curve-fitting to distinguish the fractions with different diffusion constants. This approach reveals that the fluorescence recovery of CADM1 is fitted to a single exponential function with a time constant (τ) of approximately 16 min, whereas 4.1B and MPP3 are fitted to a double exponential function with two τs of approximately 40-60 sec and 16 min. The longer τ is similar to that of CADM1, suggesting that 4.1B and MPP3 have two distinct fractions, one forming a complex with CADM1 and the other present as a free pool. Fluorescence loss in photobleaching analysis supports the presence of a free pool of these proteins near the plasma membrane. Furthermore, double exponential fitting makes it possible to estimate the ratio of 4.1B and MPP3 present as a free pool and as a complex with CADM1 as approximately 3:2 and 3:1, respectively. Our analyses reveal a central role of CADM1 in stabilizing the complex with 4.1B and MPP3 and provide insight in the dynamics of adhesion complex formation. PMID:25780926

  7. Dynamic regulation of a cell adhesion protein complex including CADM1 by combinatorial analysis of FRAP with exponential curve-fitting.

    Science.gov (United States)

    Sakurai-Yageta, Mika; Maruyama, Tomoko; Suzuki, Takashi; Ichikawa, Kazuhisa; Murakami, Yoshinori

    2015-01-01

    Protein components of cell adhesion machinery show continuous renewal even in the static state of epithelial cells and participate in the formation and maintenance of normal epithelial architecture and tumor suppression. CADM1 is a tumor suppressor belonging to the immunoglobulin superfamily of cell adhesion molecule and forms a cell adhesion complex with an actin-binding protein, 4.1B, and a scaffold protein, MPP3, in the cytoplasm. Here, we investigate dynamic regulation of the CADM1-4.1B-MPP3 complex in mature cell adhesion by fluorescence recovery after photobleaching (FRAP) analysis. Traditional FRAP analysis were performed for relatively short period of around 10 min. Here, thanks to recent advances in the sensitive laser detector systems, we examine FRAP of CADM1 complex for longer period of 60 min and analyze the recovery with exponential curve-fitting to distinguish the fractions with different diffusion constants. This approach reveals that the fluorescence recovery of CADM1 is fitted to a single exponential function with a time constant (τ) of approximately 16 min, whereas 4.1B and MPP3 are fitted to a double exponential function with two τs of approximately 40-60 sec and 16 min. The longer τ is similar to that of CADM1, suggesting that 4.1B and MPP3 have two distinct fractions, one forming a complex with CADM1 and the other present as a free pool. Fluorescence loss in photobleaching analysis supports the presence of a free pool of these proteins near the plasma membrane. Furthermore, double exponential fitting makes it possible to estimate the ratio of 4.1B and MPP3 present as a free pool and as a complex with CADM1 as approximately 3:2 and 3:1, respectively. Our analyses reveal a central role of CADM1 in stabilizing the complex with 4.1B and MPP3 and provide insight in the dynamics of adhesion complex formation.

  8. Efficacy of humidity retention bags for the reduced adsorption and improved cleaning of tissue proteins including prion-associated amyloid to surgical stainless steel surfaces.

    Science.gov (United States)

    Secker, T J; Pinchin, H E; Hervé, R C; Keevil, C W

    2015-01-01

    Increasing drying time adversely affects attachment of tissue proteins and prion-associated amyloid to surgical stainless steel, and reduces the efficacy of commercial cleaning chemistries. This study tested the efficacy of commercial humidity retention bags to reduce biofouling on surgical stainless steel and to improve subsequent cleaning. Surgical stainless steel surfaces were contaminated with ME7-infected brain homogenates and left to dry for 15 to 1,440 min either in air, in dry polythene bags or within humidity retention bags. Residual contamination pre/post cleaning was analysed using Thioflavin T/SYPRO Ruby dual staining and microscope analysis. An increase in biofouling was observed with increased drying time in air or in sealed dry bags. Humidity retention bags kept both protein and prion-associated amyloid minimal across the drying times both pre- and post-cleaning. Therefore, humidity bags demonstrate a cheap, easy to implement solution to improve surgical instrument reprocessing and to potentially reduce associated hospital acquired infections.

  9. Full moment tensors with uncertainties for the 2017 North Korea declared nuclear test and for a collocated, subsequent event

    Science.gov (United States)

    Alvizuri, C. R.; Tape, C.

    2017-12-01

    A seismic moment tensor is a 3×3 symmetric matrix that characterizes the far-field seismic radiation from a source, whether it be an earthquake, volcanic event, explosion. We estimate full moment tensors and their uncertainties for the North Korea declared nuclear test and for a collocated event that occurred eight minutes later. The nuclear test and the subsequent event occurred on September 3, 2017 at around 03:30 and 03:38 UTC time. We perform a grid search over the six-dimensional space of moment tensors, generating synthetic waveforms at each moment tensor grid point and then evaluating a misfit function between the observed and synthetic waveforms. The synthetic waveforms are computed using a 1-D structure model for the region; this approximation requires careful assessment of time shifts between data and synthetics, as well as careful choice of the bandpass for filtering. For each moment tensor we characterize its uncertainty in terms of waveform misfit, a probability function, and a confidence curve for the probability that the true moment tensor lies within the neighborhood of the optimal moment tensor. For each event we estimate its moment tensor using observed waveforms from all available seismic stations within a 2000-km radius. We use as much of the waveform as possible, including surface waves for all stations, and body waves above 1 Hz for some of the closest stations. Our preliminary magnitude estimates are Mw 5.1-5.3 for the first event and Mw 4.7 for the second event. Our results show a dominantly positive isotropic moment tensor for the first event, and a dominantly negative isotropic moment tensor for the subsequent event. As expected, the details of the probability density, waveform fit, and confidence curves are influenced by the structural model, the choice of filter frequencies, and the selection of stations.

  10. Cloning and characterization of miRNAs and their targets, including a novel miRNA-targeted NBS-LRR protein class gene in apple (Golden Delicious).

    Science.gov (United States)

    Ma, Chao; Lu, You; Bai, Songlin; Zhang, Wennan; Duan, Xuwei; Meng, Dong; Wang, Zhigang; Wang, Aide; Zhou, Zongshan; Li, Tianzhong

    2014-01-01

    MicroRNA (miRNA) has emerged as an important regulator of gene expression in plants. 146 miRNAs were identified from apple (Malus domestica cv. Golden Delicious) by bioinformatic analysis and RNA library sequencing. From these, 135 were conserved and 11 were novel miRNAs. Target analysis predicted one of the novel miRNAs, Md-miRLn11 (Malus domestica microRNA Ln11), targeted an apple nucleotide-binding site (NBS)-leucine-rich repeat (LRR) class protein coding gene (Md-NBS). 5' RACE assay confirmed the ability of Md-miRLn11 to cleave Md-NBS at the 11-12-nt position. Analysis of the expression of Md-miRLn11 and Md-NBS during the optimum invasion period in 40 apple varieties showed that the expression of Md-NBS gene in resistant varieties is higher than in susceptible varieties, with an inverse pattern for Md-miRLn11. Seedlings from the resistant apple variety 'JiGuan' were used to carry out an Agrobacterium infiltration assay, and then inoculated with the apple leaf spot disease. The result showed a clear decline of disease resistance in JiGuan apples. In contrast, the susceptible variety 'FuJi' infiltrated with the Md-NBS gene showed a significant increase in disease resistance. Based on the above results, we propose that Md-miRLn11 regulates Md-NBS gene expression in particular under the condition of pathogen infection, and that the Md-miRLn11 targeting P-loop site may regulate many NBS-LRR protein class genes in woody plants.

  11. A dietary pattern including nopal, chia seed, soy protein, and oat reduces serum triglycerides and glucose intolerance in patients with metabolic syndrome.

    Science.gov (United States)

    Guevara-Cruz, Martha; Tovar, Armando R; Aguilar-Salinas, Carlos A; Medina-Vera, Isabel; Gil-Zenteno, Lidia; Hernández-Viveros, Isaac; López-Romero, Patricia; Ordaz-Nava, Guillermo; Canizales-Quinteros, Samuel; Guillen Pineda, Luz E; Torres, Nimbe

    2012-01-01

    Metabolic syndrome (MetS) is a health problem throughout the world and is associated with cardiovascular disease and diabetes. Thus, the purpose of the present work was to evaluate the effects of a dietary pattern (DP; soy protein, nopal, chia seed, and oat) on the biochemical variables of MetS, the AUC for glucose and insulin, glucose intolerance (GI), the relationship of the presence of certain polymorphisms related to MetS, and the response to the DP. In this randomized trial, the participants consumed their habitual diet but reduced by 500 kcal for 2 wk. They were then assigned to the placebo (P; n = 35) or DP (n = 32) group and consumed the reduced energy diet plus the P or DP beverage (235 kcal) minus the energy provided by these for 2 mo. All participants had decreases in body weight (BW), BMI, and waist circumference during the 2-mo treatment (P < 0.0001); however, only the DP group had decreases in serum TG, C-reactive protein (CRP), and AUC for insulin and GI after a glucose tolerance test. Interestingly, participants in the DP group with MetS and the ABCA1 R230C variant had a greater decrease in BW and an increase in serum adiponectin concentration after 2 mo of dietary treatment than those with the ABCA1 R230R variant. The results from this study suggest that lifestyle interventions involving specific DP for the treatment of MetS could be more effective if local foods and genetic variations of the population are considered.

  12. Absorption-enhancing effects of gemini surfactant on the intestinal absorption of poorly absorbed hydrophilic drugs including peptide and protein drugs in rats.

    Science.gov (United States)

    Alama, Tammam; Kusamori, Kosuke; Katsumi, Hidemasa; Sakane, Toshiyasu; Yamamoto, Akira

    2016-02-29

    In general, the intestinal absorption of small hydrophilic molecules and macromolecules like peptides, after oral administration is very poor. Absorption enhancers are considered to be one of the most promising agents to enhance the intestinal absorption of drugs. In this research, we focused on a gemini surfactant, a new type of absorption enhancer. The intestinal absorption of drugs, with or without sodium dilauramidoglutamide lysine (SLG-30), a gemini surfactant, was examined by an in situ closed-loop method in rats. The intestinal absorption of 5(6)-carboxyfluorescein (CF) and fluorescein isothiocyanate-dextrans (FDs) was significantly enhanced in the presence of SLG-30, such effect being reversible. Furthermore, the calcium levels in the plasma significantly decreased when calcitonin was co-administered with SLG-30, suggestive of the increased intestinal absorption of calcitonin. In addition, no significant increase in the of lactate dehydrogenase (LDH) activity or in protein release from the intestinal epithelium was observed in the presence of SLG-30, suggestive of the safety of this compound. These findings indicate that SLG-30 is an effective absorption-enhancer for improving the intestinal absorption of poorly absorbed drugs, without causing serious damage to the intestinal epithelium. Copyright © 2015 Elsevier B.V. All rights reserved.

  13. Planar optical waveguide based sandwich assay sensors and processes for the detection of biological targets including protein markers, pathogens and cellular debris

    Science.gov (United States)

    Martinez, Jennifer S [Santa Fe, NM; Swanson, Basil I [Los Alamos, NM; Grace, Karen M [Los Alamos, NM; Grace, Wynne K [Los Alamos, NM; Shreve, Andrew P [Santa Fe, NM

    2009-06-02

    An assay element is described including recognition ligands bound to a film on a single mode planar optical waveguide, the film from the group of a membrane, a polymerized bilayer membrane, and a self-assembled monolayer containing polyethylene glycol or polypropylene glycol groups therein and an assay process for detecting the presence of a biological target is described including injecting a biological target-containing sample into a sensor cell including the assay element, with the recognition ligands adapted for binding to selected biological targets, maintaining the sample within the sensor cell for time sufficient for binding to occur between selected biological targets within the sample and the recognition ligands, injecting a solution including a reporter ligand into the sensor cell; and, interrogating the sample within the sensor cell with excitation light from the waveguide, the excitation light provided by an evanescent field of the single mode penetrating into the biological target-containing sample to a distance of less than about 200 nanometers from the waveguide thereby exciting the fluorescent-label in any bound reporter ligand within a distance of less than about 200 nanometers from the waveguide and resulting in a detectable signal.

  14. An Analysis of Peak Wind Speed Data from Collocated Mechanical and Ultrasonic Anemometers

    Science.gov (United States)

    Short, David A.; Wells, Leonard; Merceret, Francis J.; Roeder, William P.

    2007-01-01

    This study compared peak wind speeds reported by mechanical and ultrasonic anemometers at Cape Canaveral Air Force Station and Kennedy Space Center (CCAFS/KSC) on the east central coast of Florida and Vandenberg Air Force Base (VAFB) on the central coast of California. Launch Weather Officers, forecasters, and Range Safety analysts need to understand the performance of wind sensors at CCAFS/KSC and VAFB for weather warnings, watches, advisories, special ground processing operations, launch pad exposure forecasts, user Launch Commit Criteria (LCC) forecasts and evaluations, and toxic dispersion support. The legacy CCAFS/KSC and VAFB weather tower wind instruments are being changed from propeller-and-vane (CCAFS/KSC) and cup-and-vane (VAFB) sensors to ultrasonic sensors under the Range Standardization and Automation (RSA) program. Mechanical and ultrasonic wind measuring techniques are known to cause differences in the statistics of peak wind speed as shown in previous studies. The 45th Weather Squadron (45 WS) and the 30th Weather Squadron (30 WS) requested the Applied Meteorology Unit (AMU) to compare data between the RSA ultrasonic and legacy mechanical sensors to determine if there are significant differences. Note that the instruments were sited outdoors under naturally varying conditions and that this comparison was not designed to verify either technology. Approximately 3 weeks of mechanical and ultrasonic wind data from each range from May and June 2005 were used in this study. The CCAFS/KSC data spanned the full diurnal cycle, while the VAFB data were confined to 1000-1600 local time. The sample of 1-minute data from numerous levels on five different towers on each range totaled more than 500,000 minutes of data (482,979 minutes of data after quality control). The ten towers were instrumented at several levels, ranging from 12 ft to 492 ft above ground level. The ultrasonic sensors were collocated at the same vertical levels as the mechanical sensors and

  15. Assessment of 3D cloud radiative transfer effects applied to collocated A-Train data

    Science.gov (United States)

    Okata, M.; Nakajima, T.; Suzuki, K.; Toshiro, I.; Nakajima, T. Y.; Okamoto, H.

    2017-12-01

    This study investigates broadband radiative fluxes in the 3D cloud-laden atmospheres using a 3D radiative transfer (RT) model, MCstar, and the collocated A-Train cloud data. The 3D extinction coefficients are constructed by a newly devised Minimum cloud Information Deviation Profiling Method (MIDPM) that extrapolates CPR radar profiles at nadir into off-nadir regions within MODIS swath based on collocated information of MODIS-derived cloud properties and radar reflectivity profiles. The method is applied to low level maritime water clouds, for which the 3D-RT simulations are performed. The radiative fluxes thus simulated are compared to those obtained from CERES as a way to validate the MIDPM-constructed clouds and our 3D-RT simulations. The results show that the simulated SW flux agrees with CERES values within 8 - 50 Wm-2. One of the large biases occurred by cyclic boundary condition that was required to pose into our computational domain limited to 20km by 20km with 1km resolution. Another source of the bias also arises from the 1D assumption for cloud property retrievals particularly for thin clouds, which tend to be affected by spatial heterogeneity leading to overestimate of the cloud optical thickness. These 3D-RT simulations also serve to address another objective of this study, i.e. to characterize the "observed" specific 3D-RT effects by the cloud morphology. We extend the computational domain to 100km by 100km for this purpose. The 3D-RT effects are characterized by errors of existing 1D approximations to 3D radiation field. The errors are investigated in terms of their dependence on solar zenith angle (SZA) for the satellite-constructed real cloud cases, and we define two indices from the error tendencies. According to the indices, the 3D-RT effects are classified into three types which correspond to different simple three morphologies types, i.e. isolated cloud type, upper cloud-roughened type and lower cloud-roughened type. These 3D-RT effects linked

  16. The current strain distribution in the North China Basin of eastern China by least-squares collocation

    Science.gov (United States)

    Wu, J. C.; Tang, H. W.; Chen, Y. Q.; Li, Y. X.

    2006-07-01

    In this paper, the velocities of 154 stations obtained in 2001 and 2003 GPS survey campaigns are applied to formulate a continuous velocity field by the least-squares collocation method. The strain rate field obtained by the least-squares collocation method shows more clear deformation patterns than that of the conventional discrete triangle method. The significant deformation zones obtained are mainly located in three places, to the north of Tangshan, between Tianjing and Shijiazhuang, and to the north of Datong, which agree with the places of the Holocene active deformation zones obtained by geological investigations. The maximum shear strain rate is located at latitude 38.6°N and longitude 116.8°E, with a magnitude of 0.13 ppm/a. The strain rate field obtained can be used for earthquake prediction research in the North China Basin.

  17. Puncture black hole initial data: A single domain Galerkin-collocation method for trumpet and wormhole data sets

    Science.gov (United States)

    Clemente, P. C. M.; de Oliveira, H. P.

    2017-07-01

    We present a single-domain Galerkin-collocation method to calculate puncture initial data sets for single and binary black holes, either in the trumpet or wormhole geometries. The combination of aspects belonging to the Galerkin and the collocation methods together with the adoption of spherical coordinates in all cases are shown to be very effective. We propose a unified expression for the conformal factor to describe trumpet and spinning black holes. In particular, for the spinning trumpet black holes, we exhibit the deformation of the limit surface due to the spin from a sphere to an oblate spheroid. We also revisit the energy content in the trumpet and wormhole puncture data sets. The algorithm can be extended to describe binary black holes.

  18. Composite multi-modal vibration control for a stiffened plate using non-collocated acceleration sensor and piezoelectric actuator

    International Nuclear Information System (INIS)

    Li, Shengquan; Li, Juan; Mo, Yueping; Zhao, Rong

    2014-01-01

    A novel active method for multi-mode vibration control of an all-clamped stiffened plate (ACSP) is proposed in this paper, using the extended-state-observer (ESO) approach based on non-collocated acceleration sensors and piezoelectric actuators. Considering the estimated capacity of ESO for system state variables, output superposition and control coupling of other modes, external excitation, and model uncertainties simultaneously, a composite control method, i.e., the ESO based vibration control scheme, is employed to ensure the lumped disturbances and uncertainty rejection of the closed-loop system. The phenomenon of phase hysteresis and time delay, caused by non-collocated sensor/actuator pairs, degrades the performance of the control system, even inducing instability. To solve this problem, a simple proportional differential (PD) controller and acceleration feed-forward with an output predictor design produce the control law for each vibration mode. The modal frequencies, phase hysteresis loops and phase lag values due to non-collocated placement of the acceleration sensor and piezoelectric patch actuator are experimentally obtained, and the phase lag is compensated by using the Smith Predictor technology. In order to improve the vibration control performance, the chaos optimization method based on logistic mapping is employed to auto-tune the parameters of the feedback channel. The experimental control system for the ACSP is tested using the dSPACE real-time simulation platform. Experimental results demonstrate that the proposed composite active control algorithm is an effective approach for suppressing multi-modal vibrations. (paper)

  19. Geometric Collocation Method on SO(3 with Application to Optimal Attitude Control of a 3D Rotating Rigid Body

    Directory of Open Access Journals (Sweden)

    Xiaojia Xiang

    2015-01-01

    Full Text Available The collocation method is extended to the special orthogonal group SO(3 with application to optimal attitude control (OAC of a rigid body. A left-invariant rigid-body attitude dynamical model on SO(3 is established. For the left invariance of the attitude configuration equation in body-fixed frame, a geometrically exact numerical method on SO(3, referred to as the geometric collocation method, is proposed by deriving the equivalent Lie algebra equation in so(3 of the left-invariant configuration equation. When compared with the general Gauss pseudo-spectral method, the explicit RKMK, and Lie group variational integrator having the same order and stepsize in numerical tests for evolving a free-floating rigid-body attitude dynamics, the proposed method is higher in accuracy, time performance, and structural conservativeness. In addition, the numerical method is applied to solve a constrained OAC problem on SO(3. The optimal control problem is transcribed into a nonlinear programming problem, in which the equivalent Lie algebra equation is being considered as the defect constraints instead of the configuration equation. The transcription method is coordinate-free and does not need chart switching or special handling of singularities. More importantly, with the numerical advantage of the geometric collocation method, the proposed OAC method may generate satisfying convergence rate.

  20. Two-dimensional Haar wavelet Collocation Method for the solution of Stationary Neutron Transport Equation in a homogeneous isotropic medium

    International Nuclear Information System (INIS)

    Patra, A.; Saha Ray, S.

    2014-01-01

    Highlights: • A stationary transport equation has been solved using the technique of Haar wavelet Collocation Method. • This paper intends to provide the great utility of Haar wavelets to nuclear science problem. • In the present paper, two-dimensional Haar wavelets are applied. • The proposed method is mathematically very simple, easy and fast. - Abstract: This paper emphasizes on finding the solution for a stationary transport equation using the technique of Haar wavelet Collocation Method (HWCM). Haar wavelet Collocation Method is efficient and powerful in solving wide class of linear and nonlinear differential equations. Recently Haar wavelet transform has gained the reputation of being a very effective tool for many practical applications. This paper intends to provide the great utility of Haar wavelets to nuclear science problem. In the present paper, two-dimensional Haar wavelets are applied for solution of the stationary Neutron Transport Equation in homogeneous isotropic medium. The proposed method is mathematically very simple, easy and fast. To demonstrate about the efficiency of the method, one test problem is discussed. It can be observed from the computational simulation that the numerical approximate solution is much closer to the exact solution

  1. Prediction of Navigation Satellite Clock Bias Considering Clock's Stochastic Variation Behavior with Robust Least Square Collocation

    Directory of Open Access Journals (Sweden)

    WANG Yupu

    2016-06-01

    Full Text Available In order to better express the characteristic of satellite clock bias (SCB and further improve its prediction precision, a new SCB prediction model is proposed, which can take the physical feature, cyclic variation and stochastic variation behaviors of the space-borne atomic clock into consideration by using a robust least square collocation (LSC method. The proposed model firstly uses a quadratic polynomial model with periodic terms to fit and abstract the trend term and cyclic terms of SCB. Then for the residual stochastic variation part and possible gross errors hidden in SCB data, the model employs a robust LSC method to process them. The covariance function of the LSC is determined by selecting an empirical function and combining SCB prediction tests. Using the final precise IGS SCB products to conduct prediction tests, the results show that the proposed model can get better prediction performance. Specifically, the results' prediction accuracy can enhance 0.457 ns and 0.948 ns respectively, and the corresponding prediction stability can improve 0.445 ns and 1.233 ns, compared with the results of quadratic polynomial model and grey model. In addition, the results also show that the proposed covariance function corresponding to the new model is reasonable.

  2. A probabilistic collocation based iterative Kalman filter for landfill data assimilation

    Science.gov (United States)

    Zheng, Qiang; Xu, Wenjie; Man, Jun; Zeng, Lingzao; Wu, Laosheng

    2017-11-01

    Accurate forecast of landfill gas (LFG) transport has remained as an active research area, due to the safety and environmental concerns, as well as the green energy potential. The iterative ensemble Kalman filter (IEnKF) has been used to characterize the heterogeneous permeability field of landfills. As a Monte Carlo-based method, IEnKF requires a sufficiently large ensemble size to guarantee its accuracy, which may result in a huge computational cost, especially for large-scale problems. In this study, an efficient probabilistic collocation based iterative Kalman filter (PCIKF) is developed. The polynomial chaos expansion (PCE) is employed to represent and propagate the uncertainties, and an iterative form of Kalman filter is used to assimilate the measurements. To further reduce the computational cost, only the zeroth and first-order ANOVA (analysis of variance) components are kept in the PCE approximation. As demonstrated by two numerical case studies, PCIKF shows significant superiority over IEnKF in terms of accuracy and efficiency. The developed method has the potential to reliably predict and develop best management practices for landfill gas production.

  3. Hybrid motion sensing and experimental modal analysis using collocated smartphone camera and accelerometers

    International Nuclear Information System (INIS)

    Ozer, Ekin; Feng, Dongming; Feng, Maria Q

    2017-01-01

    State-of-the-art multisensory technologies and heterogeneous sensor networks propose a wide range of response measurement opportunities for structural health monitoring (SHM). Measuring and fusing different physical quantities in terms of structural vibrations can provide alternative acquisition methods and improve the quality of the modal testing results. In this study, a recently introduced SHM concept, SHM with smartphones, is focused to utilize multisensory smartphone features for a hybridized structural vibration response measurement framework. Based on vibration testing of a small-scale multistory laboratory model, displacement and acceleration responses are monitored using two different smartphone sensors, an embedded camera and accelerometer, respectively. Double-integration or differentiation among different measurement types is performed to combine multisensory measurements on a comparative basis. In addition, distributed sensor signals from collocated devices are processed for modal identification, and performance of smartphone-based sensing platforms are tested under different configuration scenarios and heterogeneity levels. The results of these tests show a novel and successful implementation of a hybrid motion sensing platform through multiple sensor type and device integration. Despite the heterogeneity of motion data obtained from different smartphone devices and technologies, it is shown that multisensory response measurements can be blended for experimental modal analysis. Getting benefit from the accessibility of smartphone technology, similar smartphone-based dynamic testing methodologies can provide innovative SHM solutions with mobile, programmable, and cost-free interfaces. (paper)

  4. Hybrid motion sensing and experimental modal analysis using collocated smartphone camera and accelerometers

    Science.gov (United States)

    Ozer, Ekin; Feng, Dongming; Feng, Maria Q.

    2017-10-01

    State-of-the-art multisensory technologies and heterogeneous sensor networks propose a wide range of response measurement opportunities for structural health monitoring (SHM). Measuring and fusing different physical quantities in terms of structural vibrations can provide alternative acquisition methods and improve the quality of the modal testing results. In this study, a recently introduced SHM concept, SHM with smartphones, is focused to utilize multisensory smartphone features for a hybridized structural vibration response measurement framework. Based on vibration testing of a small-scale multistory laboratory model, displacement and acceleration responses are monitored using two different smartphone sensors, an embedded camera and accelerometer, respectively. Double-integration or differentiation among different measurement types is performed to combine multisensory measurements on a comparative basis. In addition, distributed sensor signals from collocated devices are processed for modal identification, and performance of smartphone-based sensing platforms are tested under different configuration scenarios and heterogeneity levels. The results of these tests show a novel and successful implementation of a hybrid motion sensing platform through multiple sensor type and device integration. Despite the heterogeneity of motion data obtained from different smartphone devices and technologies, it is shown that multisensory response measurements can be blended for experimental modal analysis. Getting benefit from the accessibility of smartphone technology, similar smartphone-based dynamic testing methodologies can provide innovative SHM solutions with mobile, programmable, and cost-free interfaces.

  5. Parametric study on a collocated PZT beam vibration absorber and power harvester

    Energy Technology Data Exchange (ETDEWEB)

    Huang, Shyh Chin [Mechanical Engineering, Ming Chi University of Technology, New Taipei (China); Tsai, Chao Yang [Mechanical Engineering Army Academy, R.O.C., Taoyuan (China); Liao, Hsiao Hui [LNG Construction and Project Division, CPC Corp., Taipei (China)

    2016-11-15

    The parametric effects of a PZT beam that is simultaneously used as a vibration absorber and a power harvester were investigated in this study. A cantilever beam paved with PZT layers and with added tip mass has been widely used as a harvester or sometimes as a Dynamic vibration absorber (DVA). However, the beam is rarely considered a collocated device. In this study, the first step was theoretical derivation of a distributed beam covered with bimorph PZT layers. Then, the beam was attached to a 1DOF vibratory main system. Two indicators for vibration absorption and power harvesting were defined. Numerical results demonstrated that the lumped mass ratio favored both of the abilities, but that the DVA mass ratio influenced these two abilities in exactly the opposite way. The conjunction of a harvester circuit into a DVA shifted its resonance frequency up to 5 % (an extreme case of open circuit R→∞). Simultaneous power harvesting diminished the absorption capability up to 35 % for each set of mass ratios. To achieve the maximum degree of power harvesting, a corresponding load resistance that somewhat increases with the lumped mass ratio is applied. Experimental results verified the existence of the best load resistance, but the measured harvested curve was lower than the theoretical calculation because of structure damping and deviations of PZT material properties.

  6. Membrane covered duct lining for high-frequency noise attenuation: prediction using a Chebyshev collocation method.

    Science.gov (United States)

    Huang, Lixi

    2008-11-01

    A spectral method of Chebyshev collocation with domain decomposition is introduced for linear interaction between sound and structure in a duct lined with flexible walls backed by cavities with or without a porous material. The spectral convergence is validated by a one-dimensional problem with a closed-form analytical solution, and is then extended to the two-dimensional configuration and compared favorably against a previous method based on the Fourier-Galerkin procedure and a finite element modeling. The nonlocal, exact Dirichlet-to-Neumann boundary condition is embedded in the domain decomposition scheme without imposing extra computational burden. The scheme is applied to the problem of high-frequency sound absorption by duct lining, which is normally ineffective when the wavelength is comparable with or shorter than the duct height. When a tensioned membrane covers the lining, however, it scatters the incident plane wave into higher-order modes, which then penetrate the duct lining more easily and get dissipated. For the frequency range of f=0.3-3 studied here, f=0.5 being the first cut-on frequency of the central duct, the membrane cover is found to offer an additional 0.9 dB attenuation per unit axial distance equal to half of the duct height.

  7. A Least Squares Collocation Method for Accuracy Improvement of Mobile LiDAR Systems

    Directory of Open Access Journals (Sweden)

    Qingzhou Mao

    2015-06-01

    Full Text Available In environments that are hostile to Global Navigation Satellites Systems (GNSS, the precision achieved by a mobile light detection and ranging (LiDAR system (MLS can deteriorate into the sub-meter or even the meter range due to errors in the positioning and orientation system (POS. This paper proposes a novel least squares collocation (LSC-based method to improve the accuracy of the MLS in these hostile environments. Through a thorough consideration of the characteristics of POS errors, the proposed LSC-based method effectively corrects these errors using LiDAR control points, thereby improving the accuracy of the MLS. This method is also applied to the calibration of misalignment between the laser scanner and the POS. Several datasets from different scenarios have been adopted in order to evaluate the effectiveness of the proposed method. The results from experiments indicate that this method would represent a significant improvement in terms of the accuracy of the MLS in environments that are essentially hostile to GNSS and is also effective regarding the calibration of misalignment.

  8. On the optimal polynomial approximation of stochastic PDEs by galerkin and collocation methods

    KAUST Repository

    Beck, Joakim

    2012-09-01

    In this work we focus on the numerical approximation of the solution u of a linear elliptic PDE with stochastic coefficients. The problem is rewritten as a parametric PDE and the functional dependence of the solution on the parameters is approximated by multivariate polynomials. We first consider the stochastic Galerkin method, and rely on sharp estimates for the decay of the Fourier coefficients of the spectral expansion of u on an orthogonal polynomial basis to build a sequence of polynomial subspaces that features better convergence properties, in terms of error versus number of degrees of freedom, than standard choices such as Total Degree or Tensor Product subspaces. We consider then the Stochastic Collocation method, and use the previous estimates to introduce a new class of Sparse Grids, based on the idea of selecting a priori the most profitable hierarchical surpluses, that, again, features better convergence properties compared to standard Smolyak or tensor product grids. Numerical results show the effectiveness of the newly introduced polynomial spaces and sparse grids. © 2012 World Scientific Publishing Company.

  9. Non-stationary covariance function modelling in 2D least-squares collocation

    Science.gov (United States)

    Darbeheshti, N.; Featherstone, W. E.

    2009-06-01

    Standard least-squares collocation (LSC) assumes 2D stationarity and 3D isotropy, and relies on a covariance function to account for spatial dependence in the observed data. However, the assumption that the spatial dependence is constant throughout the region of interest may sometimes be violated. Assuming a stationary covariance structure can result in over-smoothing of, e.g., the gravity field in mountains and under-smoothing in great plains. We introduce the kernel convolution method from spatial statistics for non-stationary covariance structures, and demonstrate its advantage for dealing with non-stationarity in geodetic data. We then compared stationary and non- stationary covariance functions in 2D LSC to the empirical example of gravity anomaly interpolation near the Darling Fault, Western Australia, where the field is anisotropic and non-stationary. The results with non-stationary covariance functions are better than standard LSC in terms of formal errors and cross-validation against data not used in the interpolation, demonstrating that the use of non-stationary covariance functions can improve upon standard (stationary) LSC.

  10. Parallel iterative solution of the Hermite Collocation equations on GPUs II

    International Nuclear Information System (INIS)

    Vilanakis, N; Mathioudakis, E

    2014-01-01

    Hermite Collocation is a high order finite element method for Boundary Value Problems modelling applications in several fields of science and engineering. Application of this integration free numerical solver for the solution of linear BVPs results in a large and sparse general system of algebraic equations, suggesting the usage of an efficient iterative solver especially for realistic simulations. In part I of this work an efficient parallel algorithm of the Schur complement method coupled with Bi-Conjugate Gradient Stabilized (BiCGSTAB) iterative solver has been designed for multicore computing architectures with a Graphics Processing Unit (GPU). In the present work the proposed algorithm has been extended for high performance computing environments consisting of multiprocessor machines with multiple GPUs. Since this is a distributed GPU and shared CPU memory parallel architecture, a hybrid memory treatment is needed for the development of the parallel algorithm. The realization of the algorithm took place on a multiprocessor machine HP SL390 with Tesla M2070 GPUs using the OpenMP and OpenACC standards. Execution time measurements reveal the efficiency of the parallel implementation

  11. Vibration suppression in cutting tools using collocated piezoelectric sensors/actuators with an adaptive control algorithm

    Energy Technology Data Exchange (ETDEWEB)

    Radecki, Peter P [Los Alamos National Laboratory; Farinholt, Kevin M [Los Alamos National Laboratory; Park, Gyuhae [Los Alamos National Laboratory; Bement, Matthew T [Los Alamos National Laboratory

    2008-01-01

    The machining process is very important in many engineering applications. In high precision machining, surface finish is strongly correlated with vibrations and the dynamic interactions between the part and the cutting tool. Parameters affecting these vibrations and dynamic interactions, such as spindle speed, cut depth, feed rate, and the part's material properties can vary in real-time, resulting in unexpected or undesirable effects on the surface finish of the machining product. The focus of this research is the development of an improved machining process through the use of active vibration damping. The tool holder employs a high bandwidth piezoelectric actuator with an adaptive positive position feedback control algorithm for vibration and chatter suppression. In addition, instead of using external sensors, the proposed approach investigates the use of a collocated piezoelectric sensor for measuring the dynamic responses from machining processes. The performance of this method is evaluated by comparing the surface finishes obtained with active vibration control versus baseline uncontrolled cuts. Considerable improvement in surface finish (up to 50%) was observed for applications in modern day machining.

  12. Studying the influence of a secondary variable in Collocated Cokriging estimates

    Directory of Open Access Journals (Sweden)

    Marcelo M. Rocha

    2012-06-01

    Full Text Available Neste artigo examina-se a influência da variável secundária como função da correlação com a variável primária na cokrigagem colocalizada. Para este estudo cinco bases de dados completas foram geradas no computador a partir das quais amostras com 60 e 104 pontos de dados foram retirados através do método de amostragem aleatória estratificada. Estas bases de dados completas foram geradas partindo-se de um par de variáveis, primária e secundária, que apresentam boa correlação. Então sucessivos conjuntos foram gerados adicionando-se uma quantidade de ruído branco de modo que a correlação se tornasse menor. Utilizando-se estas amostras foi possível encontrar o quanto as informações primária e secundária são utilizadas na estimativa de um ponto não amostrado conforme o nível de correlação.In this paper the influence of a secondary variable as a function of the correlation with the primary variable for collocated cokriging is examined. For this study five exhaustive data sets were generated in computer, from which samples with 60 and 104 data points were drawn using the stratified random sampling method. These exhaustive data sets were generated departing from a pair of primary and secondary variables showing a good correlation. Then successive sets were generated by adding an amount of white noise in such a way that the correlation gets poorer. Using these samples, it was possible to find out how primary and secondary information is used to estimate an unsampled location according to the correlation level.

  13. Collocation methods for uncertainty quanti cation in PDE models with random data

    KAUST Repository

    Nobile, Fabio

    2014-01-06

    In this talk we consider Partial Differential Equations (PDEs) whose input data are modeled as random fields to account for their intrinsic variability or our lack of knowledge. After parametrizing the input random fields by finitely many independent random variables, we exploit the high regularity of the solution of the PDE as a function of the input random variables and consider sparse polynomial approximations in probability (Polynomial Chaos expansion) by collocation methods. We first address interpolatory approximations where the PDE is solved on a sparse grid of Gauss points in the probability space and the solutions thus obtained interpolated by multivariate polynomials. We present recent results on optimized sparse grids in which the selection of points is based on a knapsack approach and relies on sharp estimates of the decay of the coefficients of the polynomial chaos expansion of the solution. Secondly, we consider regression approaches where the PDE is evaluated on randomly chosen points in the probability space and a polynomial approximation constructed by the least square method. We present recent theoretical results on the stability and optimality of the approximation under suitable conditions between the number of sampling points and the dimension of the polynomial space. In particular, we show that for uniform random variables, the number of sampling point has to scale quadratically with the dimension of the polynomial space to maintain the stability and optimality of the approximation. Numerical results show that such condition is sharp in the monovariate case but seems to be over-constraining in higher dimensions. The regression technique seems therefore to be attractive in higher dimensions.

  14. Inverse Modeling Using Markov Chain Monte Carlo Aided by Adaptive Stochastic Collocation Method with Transformation

    Science.gov (United States)

    Zhang, D.; Liao, Q.

    2016-12-01

    The Bayesian inference provides a convenient framework to solve statistical inverse problems. In this method, the parameters to be identified are treated as random variables. The prior knowledge, the system nonlinearity, and the measurement errors can be directly incorporated in the posterior probability density function (PDF) of the parameters. The Markov chain Monte Carlo (MCMC) method is a powerful tool to generate samples from the posterior PDF. However, since the MCMC usually requires thousands or even millions of forward simulations, it can be a computationally intensive endeavor, particularly when faced with large-scale flow and transport models. To address this issue, we construct a surrogate system for the model responses in the form of polynomials by the stochastic collocation method. In addition, we employ interpolation based on the nested sparse grids and takes into account the different importance of the parameters, under the condition of high random dimensions in the stochastic space. Furthermore, in case of low regularity such as discontinuous or unsmooth relation between the input parameters and the output responses, we introduce an additional transform process to improve the accuracy of the surrogate model. Once we build the surrogate system, we may evaluate the likelihood with very little computational cost. We analyzed the convergence rate of the forward solution and the surrogate posterior by Kullback-Leibler divergence, which quantifies the difference between probability distributions. The fast convergence of the forward solution implies fast convergence of the surrogate posterior to the true posterior. We also tested the proposed algorithm on water-flooding two-phase flow reservoir examples. The posterior PDF calculated from a very long chain with direct forward simulation is assumed to be accurate. The posterior PDF calculated using the surrogate model is in reasonable agreement with the reference, revealing a great improvement in terms of

  15. Stress intensity factors and weight functions for the edge cracked plate calculated by the boundary collocation method

    International Nuclear Information System (INIS)

    Fett, T.

    1990-09-01

    The determination of stress intensity factors for cracks exposed to arbitrary stress distribution according to the weight function method calls for knowledge of the crack opening displacements and stress intensity factor for a reference load case. The determination of these variables by means of the Boundary Collocation Method (BCM) is discussed by the example of the drawn plate with an edge crack. After derivation of the formulas for evaluation the influence is studied of the relative crack depth and the plate length on the stress intensity factor, and the results are compared with data from the literature. The crack opening displacement field is determined from the stress function established by the Boundary Collocation Method and the fracture mechanical weight function is calculated from it. The results are compared with an analytical weight function obtained on the basis of approximative crack opening displacement fields. A formula is indicated for the weight function which covers the total range from a/W=0 to a/W=1. This formula is the result of BCM computations made up to a/W=0.8 for a relative plate length of a/H > 1.5 and applies to the limit case a/W=1 known from the analysis. Finally the Boundary Collocation Method is used to calculate the mode II stress intensity factors for shear loaded plates with an edge crack. The results of the computations are compared with solutions proposed in the literature. For the edge crack loaded with constant shear stresses, which act on the crack surfaces, a numerical formula is given of the geometric function. Values applicable to the weight function are determined from the crack opening displacements. (orig.) [de

  16. Convulxin induces platelet activation by a tyrosine-kinase-dependent pathway and stimulates tyrosine phosphorylation of platelet proteins, including PLC gamma 2, independently of integrin alpha IIb beta 3.

    Science.gov (United States)

    Francischetti, I M; Ghazaleh, F A; Reis, R A; Carlini, C R; Guimarães, J A

    1998-05-15

    1Convulxin (Cvx) is a well-characterized platelet aggregating glycoprotein isolated from Crotalus durissus terrificus and C. d. cascavella venoms. In the present report we show that Cvx induces tyrosine phosphorylation of human platelet proteins, including phospholipase C-gamma 2 (PLC gamma 2), and also stimulates [3H]arachidonic acid ([3H]AA) mobilization, pleckstrin phosphorylation, and an increase in the cytosolic Ca2+ concentration ([Ca2+]in) due to both Ca2+ entry and internal Ca2+ mobilization. Staurosporine, a potent protein kinase inhibitor, and genistein, a specific inhibitor of protein tyrosine kinases (PTK), were used to evaluate the role of protein tyrosine phosphorylation (PTP) in the signal transduction evoked by Cvx. Staurosporine and genistein inhibited in a dose-dependent manner platelet aggregation induced by Cvx. Both inhibitors significantly blocked to near basal levels breakdown of phosphatidylinositol 4,5-bisphosphate from [myo-2-3H]inositol-labeled platelets and the production of [3H]AA metabolites from [3H]AA-labeled platelets after challenge with Cvx. Cvx provokes an increase in [Ca2+]in in Fura-2-loaded platelets that was abolished by concentrations of staurosporine which also inhibited Cvx-induced platelet aggregation. In addition, Cvx stimulates a rapid increase in tyrosine phosphorylation of human platelets proteins with molecular masses of 40, 72/74, 78/80, 105, 120, and 145 kDa, followed by dephosphorylation. Furthermore, Cvx stimulates a rapid tyrosyl phosphorylation of a 145-kDa molecular mass protein that was identified as PLC gamma 2. PTP induced by Cvx was not inhibited when platelets were stimulated in the presence of indomethacin, apyrase, EDTA, or RGDS peptide. These results indicate that PTP is chronologically proximal to Cvx binding to platelets, and is independent of aggregation or fibrinogen binding to the integrin alpha IIb beta 3. On the other hand, the dephosphorylation step is inhibited by RGDS peptide or EDTA

  17. Hybrid B-Spline Collocation Method for Solving the Generalized Burgers-Fisher and Burgers-Huxley Equations

    Directory of Open Access Journals (Sweden)

    Imtiaz Wasim

    2018-01-01

    Full Text Available In this study, we introduce a new numerical technique for solving nonlinear generalized Burgers-Fisher and Burgers-Huxley equations using hybrid B-spline collocation method. This technique is based on usual finite difference scheme and Crank-Nicolson method which are used to discretize the time derivative and spatial derivatives, respectively. Furthermore, hybrid B-spline function is utilized as interpolating functions in spatial dimension. The scheme is verified unconditionally stable using the Von Neumann (Fourier method. Several test problems are considered to check the accuracy of the proposed scheme. The numerical results are in good agreement with known exact solutions and the existing schemes in literature.

  18. An efficient approach to numerical study of the coupled-BBM system with B-spline collocation method

    Directory of Open Access Journals (Sweden)

    khalid ali

    2016-11-01

    Full Text Available In the present paper, a numerical method is proposed for the numerical solution of a coupled-BBM system with appropriate initial and boundary conditions by using collocation method with cubic trigonometric B-spline on the uniform mesh points. The method is shown to be unconditionally stable using von-Neumann technique. To test accuracy the error norms2L, ?L are computed. Furthermore, interaction of two and three solitary waves are used to discuss the effect of the behavior of the solitary waves after the interaction. These results show that the technique introduced here is easy to apply. We make linearization for the nonlinear term.

  19. Kalman filter parameter estimation for a nonlinear diffusion model of epithelial cell migration using stochastic collocation and the Karhunen-Loeve expansion.

    Science.gov (United States)

    Barber, Jared; Tanase, Roxana; Yotov, Ivan

    2016-06-01

    Several Kalman filter algorithms are presented for data assimilation and parameter estimation for a nonlinear diffusion model of epithelial cell migration. These include the ensemble Kalman filter with Monte Carlo sampling and a stochastic collocation (SC) Kalman filter with structured sampling. Further, two types of noise are considered -uncorrelated noise resulting in one stochastic dimension for each element of the spatial grid and correlated noise parameterized by the Karhunen-Loeve (KL) expansion resulting in one stochastic dimension for each KL term. The efficiency and accuracy of the four methods are investigated for two cases with synthetic data with and without noise, as well as data from a laboratory experiment. While it is observed that all algorithms perform reasonably well in matching the target solution and estimating the diffusion coefficient and the growth rate, it is illustrated that the algorithms that employ SC and KL expansion are computationally more efficient, as they require fewer ensemble members for comparable accuracy. In the case of SC methods, this is due to improved approximation in stochastic space compared to Monte Carlo sampling. In the case of KL methods, the parameterization of the noise results in a stochastic space of smaller dimension. The most efficient method is the one combining SC and KL expansion. Copyright © 2016 Elsevier Inc. All rights reserved.

  20. Glass-Cockpit Pilot Subjective Ratings of Predictive Information, Collocation, and Mission Status Graphics: An Analysis and Summary of the Future Focus of Flight Deck Research Survey

    Science.gov (United States)

    Bartolone, Anthony; Trujillo, Anna

    2002-01-01

    NASA Langley Research Center has been researching ways to improve flight crew decision aiding for systems management. Our current investigation is how to display a wide variety of aircraft parameters in ways that will improve the flight crew's situation awareness. To accomplish this, new means are being explored that will monitor the overall health of a flight and report the current status of the aircraft and forecast impending problems to the pilots. The initial step in this research was to conduct a survey addressing how current glass-cockpit commercial pilots would value a prediction of the status of critical aircraft systems. We also addressed how this new type of data ought to be conveyed and utilized. Therefore, two other items associated with predictive information were also included in the survey. The first addressed the need for system status, alerts and procedures, and system controls to be more logically grouped together, or collocated, on the flight deck. The second idea called for the survey respondents opinions on the functionality of mission status graphics; a display methodology that groups a variety of parameters onto a single display that can instantaneously convey a complete overview of both an aircraft's system and mission health.

  1. A tandem approach for collocated measurements of microphysical and radiative cirrus properties

    Directory of Open Access Journals (Sweden)

    M. Klingebiel

    2017-09-01

    -platform measurements at different altitudes or by making use of the collocated irradiance measurements at different altitudes of the tandem platform. Due to unavoidable biases of the measurements between the individual flight legs, the single-platform approach failed to provide a realistic solar heating rate profile, while the uncertainties of the tandem approach are reduced. Here, the solar heating rates range up to 6 K day−1 at top of the cirrus layer.

  2. A tandem approach for collocated measurements of microphysical and radiative cirrus properties

    Science.gov (United States)

    Klingebiel, Marcus; Ehrlich, André; Finger, Fanny; Röschenthaler, Timo; Jakirlić, Suad; Voigt, Matthias; Müller, Stefan; Maser, Rolf; Wendisch, Manfred; Hoor, Peter; Spichtinger, Peter; Borrmann, Stephan

    2017-09-01

    altitudes or by making use of the collocated irradiance measurements at different altitudes of the tandem platform. Due to unavoidable biases of the measurements between the individual flight legs, the single-platform approach failed to provide a realistic solar heating rate profile, while the uncertainties of the tandem approach are reduced. Here, the solar heating rates range up to 6 K day-1 at top of the cirrus layer.

  3. Glucose control and medication adherence among veterans with diabetes and serious mental illness: does collocation of primary care and mental health care matter?

    Science.gov (United States)

    Long, Judith A; Wang, Andrew; Medvedeva, Elina L; Eisen, Susan V; Gordon, Adam J; Kreyenbuhl, Julie; Marcus, Steven C

    2014-08-01

    Persons with serious mental illness (SMI) may benefit from collocation of medical and mental health healthcare professionals and services in attending to their chronic comorbid medical conditions. We evaluated and compared glucose control and diabetes medication adherence among patients with SMI who received collocated care to those not receiving collocated care (which we call usual care). We performed a cross-sectional, observational cohort study of 363 veteran patients with type 2 diabetes and SMI who received care from one of three Veterans Affairs medical facilities: two sites that provided both collocated and usual care and one site that provided only usual care. Through a survey, laboratory tests, and medical records, we assessed patient characteristics, glucose control as measured by a current HbA1c, and adherence to diabetes medication as measured by the medication possession ration (MPR) and self-report. In the sample, the mean HbA1c was 7.4% (57 mmol/mol), the mean MPR was 80%, and 51% reported perfect adherence to their diabetes medications. In both unadjusted and adjusted analyses, there were no differences in glucose control and medication adherence by collocation of care. Patients seen in collocated care tended to have better HbA1c levels (β = -0.149; P = 0.393) and MPR values (β = 0.34; P = 0.132) and worse self-reported adherence (odds ratio 0.71; P = 0.143), but these were not statistically significant. In a population of veterans with comorbid diabetes and SMI, patients on average had good glucose control and medication adherence regardless of where they received primary care. © 2014 by the American Diabetes Association. Readers may use this article as long as the work is properly cited, the use is educational and not for profit, and the work is not altered.

  4. An analytical investigation on unsteady motion of vertically falling spherical particles in non-Newtonian fluid by Collocation Method

    Directory of Open Access Journals (Sweden)

    M. Rahimi-Gorji

    2015-06-01

    Full Text Available An analytical investigation is applied for unsteady motion of a rigid spherical particle in a quiescent shear-thinning power-law fluid. The results were compared with those obtained from Collocation Method (CM and the established Numerical Method (Fourth order Runge–Kutta scheme. It was shown that CM gave accurate results. Collocation Method (CM and Numerical Method are used to solve the present problem. We obtained that the CM which was used to solve such nonlinear differential equation with fractional power is simpler and more accurate than series method such as HPM which was used in some previous works by others but the new method named Akbari-Ganji’s Method (AGM is an accurate and simple method which is slower than CM for solving such problems. The terminal settling velocity—that is the velocity at which the net forces on a falling particle eliminate—for three different spherical particles (made of plastic, glass and steel and three flow behavior index n, in three sets of power-law non-Newtonian fluids was investigated, based on polynomial solution (CM. Analytical results obtained indicated that the time of reaching the terminal velocity in a falling procedure is significantly increased with growing of the particle size that validated with Numerical Method. Further, with approaching flow behavior to Newtonian behavior from shear-thinning properties of flow (n → 1, the transient time to achieving the terminal settling velocity is decreased.

  5. Boundary element computations in the forward and inverse problems of electrocardiography: comparison of collocation and Galerkin weightings.

    Science.gov (United States)

    Stenroos, Matti; Haueisen, Jens

    2008-09-01

    In electrocardiographic imaging, epicardial potentials are reconstructed computationally from electrocardiographic measurements. The reconstruction is typically done with the help of the boundary element method (BEM), using the point collocation weighting and constant or linear basis functions. In this paper, we evaluated the performance of constant and linear point collocation and Galerkin BEMs in the epicardial potential problem. The integral equations and discretizations were formulated in terms of the single- and double-layer operators. All inner element integrals were calculated analytically. The computational methods were validated against analytical solutions in a simplified geometry. On the basis of the validation, no method was optimal in all testing scenarios. In the forward computation of the epicardial potential, the linear Galerkin (LG) method produced the smallest errors. The LG method also produced the smallest discretization error on the epicardial surface. In the inverse computation of epicardial potential, the electrode-specific transfer matrix performed better than the full transfer matrix. The Tikhonov 2 regularization outperformed the Tikhonov 0. In the optimal modeling conditions, the best BEM technique depended on electrode positions and chosen error measure. When large modeling errors such as omission of the lungs were present, the choice of the basis and weighting functions was not significant.

  6. Entropy Stable Staggered Grid Discontinuous Spectral Collocation Methods of any Order for the Compressible Navier--Stokes Equations

    KAUST Repository

    Parsani, Matteo

    2016-10-04

    Staggered grid, entropy stable discontinuous spectral collocation operators of any order are developed for the compressible Euler and Navier--Stokes equations on unstructured hexahedral elements. This generalization of previous entropy stable spectral collocation work [M. H. Carpenter, T. C. Fisher, E. J. Nielsen, and S. H. Frankel, SIAM J. Sci. Comput., 36 (2014), pp. B835--B867, M. Parsani, M. H. Carpenter, and E. J. Nielsen, J. Comput. Phys., 292 (2015), pp. 88--113], extends the applicable set of points from tensor product, Legendre--Gauss--Lobatto (LGL), to a combination of tensor product Legendre--Gauss (LG) and LGL points. The new semidiscrete operators discretely conserve mass, momentum, energy, and satisfy a mathematical entropy inequality for the compressible Navier--Stokes equations in three spatial dimensions. They are valid for smooth as well as discontinuous flows. The staggered LG and conventional LGL point formulations are compared on several challenging test problems. The staggered LG operators are significantly more accurate, although more costly from a theoretical point of view. The LG and LGL operators exhibit similar robustness, as is demonstrated using test problems known to be problematic for operators that lack a nonlinear stability proof for the compressible Navier--Stokes equations (e.g., discontinuous Galerkin, spectral difference, or flux reconstruction operators).

  7. Non-collocated fuzzy logic and input shaping control strategy for elastic joint manipulator: vibration suppression and time response analysis

    International Nuclear Information System (INIS)

    Rashidifar, Mohammed Amin; Rashidifar, Ali Amin

    2014-01-01

    Conventional model-based control strategies are very complex and difficult to synthesize due to high complexity of the dynamics of robots manipulator considering joint elasticity. This paper presents investigations into the development of hybrid control schemes for trajectory tracking and vibration control of a flexible joint manipulator. To study the effectiveness of the controllers, initially a collocated proportional-derivative (P D)-type Fuzzy Logic Controller (FLC) is developed for tip angular position control of a flexible joint manipulator. This is then extended to incorporate a non-collocated Fuzzy Logic Controller and input shaping scheme for vibration reduction of the flexible joint system. The positive zero-vibration-derivative-derivative (ZVDD) shaper is designed based on the properties of the system. Simulation results of the response of the flexible joint manipulator with the controllers are presented in time and frequency domains. The performances of the hybrid control schemes are examined in terms of input tracking capability, level of vibration reduction and time response specifications. Finally, a comparative assessment of the control techniques is presented and discussed. (Author)

  8. The Significance of Immunohistochemical Staining, Including that for Glucose Transporter Protein Isoform 1, as Related to the Clinical and Angiographic Features of Adult Soft-Tissue Hemangioma and Arteriovenous Malformation in the Head and Neck

    International Nuclear Information System (INIS)

    Lee, Ha Young; Kim, Seon Mi; Choi, Jin Woo

    2009-01-01

    Glucose transporter protein isoform 1 (GLUT1) has been introduced to diagnose the hemangiomas of infancy. We investigated the usefulness of several immunohistochemical markers, including GLUT1, as related with the clinical and radiologic findings for making the diagnosis of adult subcutaneous vascular lesions in the head and neck. Materials and Methods: The 24 patients who underwent operations for soft tissue vascular lesion during the previous 7 years were included in this study. We analyzed the angiographic data, the clinical data and the immunohistochemical study results, including the GLUT1, S-100 protein and Movat pentichrome staining. Results: Twenty-two patients were confirmed to have arteriovenous malformation (AVM) and two hemangiomas, respectively. The number of lesions with positive Movat pentichrome, S-100 and GLUT1 staining in the patients with AVM and those patients with hemangioma were 22/22, 20/22 and 0/22, and 0/2, 0/2 and 0/2, respectively. For the 22 patients with AVMs, eight had a soft tissue vascular lesion at birth, 13 had cutaneous change and 15 had a change of the size of the lesion. For the 2 patients with one hemangioma each, neither patient had a soft tissue vascular lesion at birth, and both patients had cutaneous change and a change of the size of the lesion. The angiograms revealed a focal hypervascular mass (19/24) or diffuse staining (5/24) without showing significant features for making the definitive differential diagnosis. Our study revealed that none of the patients with AVM or hemangioma had GLUT1 positivity, and an arteriovenous malformation was more common than the adult-type hemangioma

  9. Synchronous and Asynchronous Multimedia and Iranian EFL Learners’ Learning of Collocations

    Directory of Open Access Journals (Sweden)

    Goudarz Alibakhshi

    2016-07-01

    Full Text Available The use of effective multimedia instructions such as mobiles, computers, and the internet in language learning has turned out to be useful since the last decades. The impact of multimedia and synchronous approaches of computer-assisted language learning (CALL on English as a foreign language (EFL learners' learning of language skills and components has been studied to some extent. However, the impact of computerized mediated instruction through multimedia (text and graphics on learning collocations requires further investigations. This study aimed at investigating whether synchronous and asynchronous multimedia components: text and text with added graphics had any effects on EFL learners' learning of collocations. In doing so, 150 male EFL learners at pre-intermediate proficiency level were selected through convenience sampling. They were divided into six groups. The results of the study showed that computerized mediated instruction was more effective than non-computerized instruction. Also, synchronous computerized instruction was more effective than asynchronous computerized instruction. The results also showed that presentation through text with added graphics was more effective than presentation through simple text. The results are discussed and some pedagogical implications are presented.   Persian Abstract: استفاده ازآموزش های چند رسانه ای مؤثر مانند موبایل، کامپیوتر، و اینترنت در آموزش زبان  از چند دهه قبل مرسوم شده است. تأثیر چند رسانه ای و روش های همزمان یادگیری  زبان به کمک کامپیوتر (CALL  بر  یادگیری مؤلفه ها و مهارتهای زبان انگلیسی به عنوان یک زبان خارجی (EFL توسط زبان آموزان  تا حدی مورد  مطالعه قرار گرفته است. بااین حال، تأثیر آموزش با کامپیوتر از طریق

  10. Intralesional immunotherapy with tuberculin purified protein derivative (PPD) in recalcitrant wart: A randomized, placebo-controlled, double-blind clinical trial including an extra group of candidates for cryotherapy.

    Science.gov (United States)

    Amirnia, Mehdi; Khodaeiani, Effat; Fouladi, Daniel F; Masoudnia, Sima

    2016-01-01

    Due to paucity of randomized clinical trials, intralesional immunotherapy has not been yet accepted as a standard therapeutic method. To examine the efficacy and safety of intralesional immunotherapy with tuberculin purified protein derivative (PPD) for treating recalcitrant wart. In this randomized, placebo-controlled, double-blind clinical trial, a total of 69 patients with recalcitrant warts received either intralesional PPD antigen (n = 35) or intralesional saline (n = 34) for six times at 2-week intervals. A third group of candidates for cryotherapy (n = 33) was also included. The decrease in lesion size (good: complete response, intermediate: 50-99% improvement, poor: cryotherapy patients, respectively (PPD versus placebo: p cryotherapy: p cryotherapy groups, respectively (p > 0.05). Intralesional immunotherapy with PPD antigen is highly effective and safe for treating recalcitrant warts. IRCT201407089844N3 in the Iranian Registry of Clinical Trials (IRCT).

  11. An estimation of the height system bias parameter N (0) using least squares collocation from observed gravity and GPS-levelling data

    DEFF Research Database (Denmark)

    Sadiq, Muhammad; Tscherning, Carl C.; Ahmad, Zulfiqar

    2009-01-01

    This paper deals with the analysis of gravity anomaly and precise levelling in conjunction with GPS-Levelling data for the computation of a gravimetric geoid and an estimate of the height system bias parameter N-o for the vertical datum in Pakistan by means of least squares collocation technique....

  12. The Effects of Utilizing Corpus Resources to Correct Collocation Errors in L2 Writing--Students' Performance, Corpus Use and Perceptions

    Science.gov (United States)

    Wu, Yi-ju

    2016-01-01

    Data-Driven Learning (DDL), in which learners "confront [themselves] directly with the corpus data" (Johns, 2002, p. 108), has shown to be effective in collocation learning in L2 writing. Nevertheless, there have been only few research studies of this type examining the relationship between English proficiency and corpus consultation.…

  13. Solving nonlinear Benjamin-Bona-Mahony equation using cubic B-spline and cubic trigonometric B-spline collocation methods

    Science.gov (United States)

    Rahan, Nur Nadiah Mohd; Ishak, Siti Noor Shahira; Hamid, Nur Nadiah Abd; Majid, Ahmad Abd.; Azmi, Amirah

    2017-04-01

    In this research, the nonlinear Benjamin-Bona-Mahony (BBM) equation is solved numerically using the cubic B-spline (CuBS) and cubic trigonometric B-spline (CuTBS) collocation methods. The CuBS and CuTBS are utilized as interpolating functions in the spatial dimension while the standard finite difference method (FDM) is applied to discretize the temporal space. In order to solve the nonlinear problem, the BBM equation is linearized using Taylor's expansion. Applying the von-Neumann stability analysis, the proposed techniques are shown to be unconditionally stable under the Crank-Nicolson scheme. Several numerical examples are discussed and compared with exact solutions and results from the FDM.

  14. Fracture analysis of one-dimensional hexagonal quasicrystals: Researches of a finite dimension rectangular plate by boundary collocation method

    Energy Technology Data Exchange (ETDEWEB)

    Jiaxing, Cheng; Dongfa, Sheng [Southwest Forestry University, Yunnan (China)

    2017-05-15

    As an important supplement and development to crystallography, the applications about quasicrystal materials have played a core role in many fields, such as manufacturing and the space industry. Due to the sensitivity of quasicrystals to defects, the research on the fracture problem of quasicrystals has attracted a great deal of attention. We present a boundary collocation method to research fracture problems for a finite dimension rectangular one-dimensional hexagonal quasicrystal plate. Because mode I and mode II problems for one- dimensional hexagonal quasicrystals are like that for the classical elastic materials, only the anti-plane problem is discussed in this paper. The correctness of the present numerical method is verified through a comparison of the present results and the existing results. And then, the size effects on stress field, stress intensity factor and energy release rate are discussed in detail. The obtained results can provide valuable references for the fracture behavior of quasicrystals.

  15. A Multi-Point, Boundary-Value Problem, Collocation Toolbox for the Continuation of sets of Constrained Orbit Segments

    DEFF Research Database (Denmark)

    Dankowicz, Harry; Schilder, Frank

    This paper presents a collocation toolbox for multi-point, boundary-value problems. This toolbox has been recently developed by the authors to support general-purpose parameter continuation of sets of constrained orbit segments, such as i) segmented trajectories in hybrid dynamical systems......, for example, mechanical systems with impacts, friction, and switching control, ii) homoclinic orbits represented by an equilibrium point and a finite-time trajectory that starts and ends near this equilibrium point, and iii) collections of trajectories that represent quasi-periodic invariant tori...... the continuation of families of periodic orbits in a hybrid dynamical system with impacts and friction as well as detection and constrained continuation of selected degeneracies characteristic of such systems, such as grazing and switching-sliding bifurcations....

  16. A Simple Time Domain Collocation Method to Precisely Search for the Periodic Orbits of Satellite Relative Motion

    Directory of Open Access Journals (Sweden)

    Xiaokui Yue

    2014-01-01

    Full Text Available A numerical approach for obtaining periodic orbits of satellite relative motion is proposed, based on using the time domain collocation (TDC method to search for the periodic solutions of an exact J2 nonlinear relative model. The initial conditions for periodic relative orbits of the Clohessy-Wiltshire (C-W equations or Tschauner-Hempel (T-H equations can be refined with this approach to generate nearly bounded orbits. With these orbits, a method based on the least-squares principle is then proposed to generate projected closed orbit (PCO, which is a reference for the relative motion control. Numerical simulations reveal that the presented TDC searching scheme is effective and simple, and the projected closed orbit is very fuel saving.

  17. Outbreak epidemiologically linked with a composite product of beef, mechanically separated chicken and textured vegetable protein contaminated with multiple serotypes of Salmonella enterica including multidrug-resistant Infantis, California 2016.

    Science.gov (United States)

    Hutchinson, J A; Wheeler, C; Mohle-Boetani, J C

    2018-03-01

    A salmonellosis outbreak occurred at a California prison in April and May 2016. In a cohort study of 371 inmates, persons who consumed dishes from the prison kitchen made from ground meat had a higher attack rate (15%) than those who did not (4%) (risk ratio 3.4, 95% CI 1.1-10.6). The ground meat product was composed exclusively of beef, mechanically separated chicken (MSC) and textured vegetable protein; eight of eight lots of the product collected from the prison and processing facility were contaminated with Salmonella enterica of eight serotypes and 17 distinct PFGE patterns, including multidrug-resistant S. Infantis. Either the MSC or the beef could have been the source of the particular strains of S. enterica isolated from patients or the product. The microbiological evidence is most consistent with MSC as the source of the high levels of S. enterica in the epidemiologically linked meat product. Our findings contribute to the growing body of evidence about the hazard posed by the use of products containing raw mechanically separated poultry in kitchens in institutions.

  18. The Escherichia coli O157:H7 cattle immunoproteome includes outer membrane protein A (OmpA), a modulator of adherence to bovine rectoanal junction squamous epithelial (RSE) cells

    Science.gov (United States)

    Building on previous studies, we defined the repertoire of proteins comprising the antigenome of Escherichia coli (E. coli) O157 cultured in Dulbecco's Modified Eagles Medium (DMEM) supplemented with norepinephrine (NE; O157 protein-antigenome), a beta-adrenergic hormone that regulates E. coli O157 ...

  19. Versions of the Collocation and Least Residuals Method for Solving Problems of Mathematical Physics in the Convex Quadrangular Domains

    Directory of Open Access Journals (Sweden)

    Vasily A. Belyaev

    2017-01-01

    Full Text Available The new versions of the collocations and least residuals (CLR method of high-order accuracy are proposed and implemented for the numerical solution of the boundary value problems for PDE in the convex quadrangular domains. Their implementation and numerical experiments are performed by the examples of solving the biharmonic and Poisson equations. The solution of the biharmonic equation is used for simulation of the stress-strain state of an isotropic plate under the action of the transverse load. Differential problems are projected into the space of fourth-degree polynomials by the CLR method. The boundary conditions for the approximate solution are put down exactly on the boundary of the computational domain. The versions of the CLR method are implemented on the grids, which are constructed by two different ways. In the first version, a “quasiregular” grid is constructed in the domain, the extreme lines of this grid coincide with the boundaries of the domain. In the second version, the domain is initially covered by a regular grid with rectangular cells. Herewith, the collocation and matching points that are situated outside the domain are used for approximation of the differential equations in the boundary cells that had been crossed by the boundary. In addition the “small” irregular triangular cells that had been cut off by the domain boundary from rectangular cells of the initial regular grid are joined to adjacent quadrangular cells. This technique allowed to essentially reduce the conditionality of the system of linear algebraic equations of the approximate problem in comparison with the case when small irregular cells together with other cells were used as independent ones for constructing an approximate solution of the problem. It is shown that the approximate solution of problems converges with high order and matches with high accuracy with the analytical solution of the test problems in the case of the known solution in

  20. A nonclassical Radau collocation method for solving the Lane-Emden equations of the polytropic index 4.75 ≤ α < 5

    Science.gov (United States)

    Tirani, M. D.; Maleki, M.; Kajani, M. T.

    2014-11-01

    A numerical method for solving the Lane-Emden equations of the polytropic index α when 4.75 ≤ α ≤ 5 is introduced. The method is based upon nonclassical Gauss-Radau collocation points and Freud type weights. Nonclassical orthogonal polynomials, nonclassical Radau points and weighted interpolation are introduced and are utilized in the interval [0,1]. A smooth, strictly monotonic transformation is used to map the infinite domain x ∈ [0,∞) onto a half-open interval t ∈ [0,1). The resulting problem on the finite interval is then transcribed to a system of nonlinear algebraic equations using collocation. The method is easy to implement and yields very accurate results.

  1. Full-Wave Analysis of the Shielding Effectiveness of Thin Graphene Sheets with the 3D Unidirectionally Collocated HIE-FDTD Method

    Directory of Open Access Journals (Sweden)

    Arne Van Londersele

    2017-01-01

    Full Text Available Graphene-based electrical components are inherently multiscale, which poses a real challenge for finite-difference time-domain (FDTD solvers due to the stringent time step upper bound. Here, a unidirectionally collocated hybrid implicit-explicit (UCHIE FDTD method is put forward that exploits the planar structure of graphene to increase the time step by implicitizing the critical dimension. The method replaces the traditional Yee discretization by a partially collocated scheme that allows a more accurate numerical description of the material boundaries. Moreover, the UCHIE-FDTD method preserves second-order accuracy even for nonuniform discretization in the direction of collocation. The auxiliary differential equation (ADE approach is used to implement the graphene sheet as a dispersive Drude medium. The finite grid is terminated by a uniaxial perfectly matched layer (UPML to permit open-space simulations. Special care is taken to elaborate on the efficient implementation of the implicit update equations. The UCHIE-FDTD method is validated by computing the shielding effectiveness of a typical graphene sheet.

  2. TEACHING COLLOCATION USING LEXICAL APPROACH AS USED IN MADE FRIDA YULIA’S VOCABULARY: LEXICALLY-BASED SECOND THOUSANDS WORDS OF GENERAL SERVICE LIST BOOK

    Directory of Open Access Journals (Sweden)

    Petrus Chandra

    2014-11-01

    Full Text Available This research was to give insight to English teachers and practitioners who had the same problem faced by the writer and his students especially dealing with the lack of collocation. Moreover, this research inspired particularly those who involved in teaching practices for how to improve their professionalism by implementing Lexical-Based Approach in class activities and to find the solution and hindrances for a better teaching technique in the future. For students who had problems in collocation, this Lexical-Based Approach as used in Made Frida Yulia’s Vocabulary: Lexically-Based Second Thousand Words of General Service List book might improve the awareness toward lexical phrases, chunks and collocations. For teachers and practitioners who want to use this Lexical-Based Approach in the future could use bilingual explanation that is needed for Indonesian students rather than monolingual explanation in English, try to create a good note taking habit for lexical phrases as soon as possible, and use vivid pictures or audio visuals to kill the boredom of the students

  3. Pump apparatus including deconsolidator

    Energy Technology Data Exchange (ETDEWEB)

    Sonwane, Chandrashekhar; Saunders, Timothy; Fitzsimmons, Mark Andrew

    2014-10-07

    A pump apparatus includes a particulate pump that defines a passage that extends from an inlet to an outlet. A duct is in flow communication with the outlet. The duct includes a deconsolidator configured to fragment particle agglomerates received from the passage.

  4. A finite-volume/Newton method for a two-phase heat flow problem using primitive variables and collocated grids

    International Nuclear Information System (INIS)

    Liang, M.C.; Lan, C.W.

    1996-01-01

    A finite-volume/Newton's method is presented for solving the incompressible heat flow problem in an inclined enclosure with an unknown melt/solid interface using primitive variables and collocated grids. The unknown melt/solid interface is solved simultaneously with all of the field variables by imposing the weighted melting-point isotherm. In the finite-volume formulation of the continuity equation, a modified momentum interpolation scheme is adopted to enhance velocity/pressure coupling. During Newton's iterations, the ILU (0) preconditioned GMRES matrix solver is applied to solve the linear system, where the sparse Jacobian matrix is estimated by finite differences. Nearly quadratic convergence of the method is observed. The robustness of the method is further enhanced with the implementation of the pseudo-arclength continuation. The effects of the Rayleigh number and gravity orientation on flow patterns and the interface are demonstrated. Bifurcation diagrams are also constructed to illustrate flow transition and multiple steady states. 42 refs., 13 figs., 5 tabs

  5. POD for Real-Time Simulation of Hyperelastic Soft Biological Tissue Using the Point Collocation Method of Finite Spheres

    Directory of Open Access Journals (Sweden)

    Suleiman Banihani

    2013-01-01

    Full Text Available The point collocation method of finite spheres (PCMFS is used to model the hyperelastic response of soft biological tissue in real time within the framework of virtual surgery simulation. The proper orthogonal decomposition (POD model order reduction (MOR technique was used to achieve reduced-order model of the problem, minimizing computational cost. The PCMFS is a physics-based meshfree numerical technique for real-time simulation of surgical procedures where the approximation functions are applied directly on the strong form of the boundary value problem without the need for integration, increasing computational efficiency. Since computational speed has a significant role in simulation of surgical procedures, the proposed technique was able to model realistic nonlinear behavior of organs in real time. Numerical results are shown to demonstrate the effectiveness of the new methodology through a comparison between full and reduced analyses for several nonlinear problems. It is shown that the proposed technique was able to achieve good agreement with the full model; moreover, the computational and data storage costs were significantly reduced.

  6. Modeling diffusion in random heterogeneous media: Data-driven models, stochastic collocation and the variational multiscale method

    International Nuclear Information System (INIS)

    Ganapathysubramanian, Baskar; Zabaras, Nicholas

    2007-01-01

    In recent years, there has been intense interest in understanding various physical phenomena in random heterogeneous media. Any accurate description/simulation of a process in such media has to satisfactorily account for the twin issues of randomness as well as the multilength scale variations in the material properties. An accurate model of the material property variation in the system is an important prerequisite towards complete characterization of the system response. We propose a general methodology to construct a data-driven, reduced-order model to describe property variations in realistic heterogeneous media. This reduced-order model then serves as the input to the stochastic partial differential equation describing thermal diffusion through random heterogeneous media. A decoupled scheme is used to tackle the problems of stochasticity and multilength scale variations in properties. A sparse-grid collocation strategy is utilized to reduce the solution of the stochastic partial differential equation to a set of deterministic problems. A variational multiscale method with explicit subgrid modeling is used to solve these deterministic problems. An illustrative example using experimental data is provided to showcase the effectiveness of the proposed methodology

  7. Spectral collocation method with a flexible angular discretization scheme for radiative transfer in multi-layer graded index medium

    Science.gov (United States)

    Wei, Linyang; Qi, Hong; Sun, Jianping; Ren, Yatao; Ruan, Liming

    2017-05-01

    The spectral collocation method (SCM) is employed to solve the radiative transfer in multi-layer semitransparent medium with graded index. A new flexible angular discretization scheme is employed to discretize the solid angle domain freely to overcome the limit of the number of discrete radiative direction when adopting traditional SN discrete ordinate scheme. Three radial basis function interpolation approaches, named as multi-quadric (MQ), inverse multi-quadric (IMQ) and inverse quadratic (IQ) interpolation, are employed to couple the radiative intensity at the interface between two adjacent layers and numerical experiments show that MQ interpolation has the highest accuracy and best stability. Variable radiative transfer problems in double-layer semitransparent media with different thermophysical properties are investigated and the influence of these thermophysical properties on the radiative transfer procedure in double-layer semitransparent media is also analyzed. All the simulated results show that the present SCM with the new angular discretization scheme can predict the radiative transfer in multi-layer semitransparent medium with graded index efficiently and accurately.

  8. "They never realized that, you know": linguistic collocation and interactional functions of you know in contemporary academin spoken english

    Directory of Open Access Journals (Sweden)

    Rodrigo Borba

    2012-12-01

    Full Text Available Discourse markers are a collection of one-word or multiword terms that help language users organize their utterances on the grammar, semantic, pragmatic and interactional levels. Researchers have characterized some of their roles in written and spoken discourse (Halliday & Hasan, 1976, Schffrin, 1988, 2001. Following this trend, this paper advances a discussion of discourse markers in contemporary academic spoken English. Through quantitative and qualitative analyses of the use of the discourse marker ‘you know’ in the Michigan Corpus of Academic Spoken English (MICASE we describe its frequency in this corpus, its collocation on the sentence level and its interactional functions. Grammatically, a concordance analysis shows that you know (as other discourse markers is linguistically fl exible as it seems to be placed in any grammatical slot of an utterance. Interactionally, a qualitative analysis indicates that its use in contemporary English goes beyond the uses described in the literature. We defend that besides serving as a hedging strategy (Lakoff, 1975, you know also serves as a powerful face-saving (Goffman, 1955 technique which constructs students’ identities vis-à-vis their professors’ and vice-versa.

  9. Ice particle production in mid-level stratiform mixed-phase clouds observed with collocated A-Train measurements

    Directory of Open Access Journals (Sweden)

    D. Zhang

    2018-03-01

    Full Text Available Collocated A-Train CloudSat radar and CALIPSO lidar measurements between 2006 and 2010 are analyzed to study primary ice particle production characteristics in mid-level stratiform mixed-phase clouds on a global scale. For similar clouds in terms of cloud top temperature and liquid water path, Northern Hemisphere latitude bands have layer-maximum radar reflectivity (ZL that is  ∼  1 to 8 dBZ larger than their counterparts in the Southern Hemisphere. The systematically larger ZL under similar cloud conditions suggests larger ice number concentrations in mid-level stratiform mixed-phase clouds over the Northern Hemisphere, which is possibly related to higher background aerosol loadings. Furthermore, we show that springtime northern mid- and high latitudes have ZL that is larger by up to 6 dBZ (a factor of 4 higher ice number concentration than other seasons, which might be related to more dust events that provide effective ice nucleating particles. Our study suggests that aerosol-dependent ice number concentration parameterizations are required in climate models to improve mixed-phase cloud simulations, especially over the Northern Hemisphere.

  10. On the equivalence of spherical splines with least-squares collocation and Stokes's formula for regional geoid computation

    Science.gov (United States)

    Ophaug, Vegard; Gerlach, Christian

    2017-11-01

    This work is an investigation of three methods for regional geoid computation: Stokes's formula, least-squares collocation (LSC), and spherical radial base functions (RBFs) using the spline kernel (SK). It is a first attempt to compare the three methods theoretically and numerically in a unified framework. While Stokes integration and LSC may be regarded as classic methods for regional geoid computation, RBFs may still be regarded as a modern approach. All methods are theoretically equal when applied globally, and we therefore expect them to give comparable results in regional applications. However, it has been shown by de Min (Bull Géod 69:223-232, 1995. doi: 10.1007/BF00806734) that the equivalence of Stokes's formula and LSC does not hold in regional applications without modifying the cross-covariance function. In order to make all methods comparable in regional applications, the corresponding modification has been introduced also in the SK. Ultimately, we present numerical examples comparing Stokes's formula, LSC, and SKs in a closed-loop environment using synthetic noise-free data, to verify their equivalence. All agree on the millimeter level.

  11. Ice particle production in mid-level stratiform mixed-phase clouds observed with collocated A-Train measurements

    Science.gov (United States)

    Zhang, Damao; Wang, Zhien; Kollias, Pavlos; Vogelmann, Andrew M.; Yang, Kang; Luo, Tao

    2018-03-01

    Collocated A-Train CloudSat radar and CALIPSO lidar measurements between 2006 and 2010 are analyzed to study primary ice particle production characteristics in mid-level stratiform mixed-phase clouds on a global scale. For similar clouds in terms of cloud top temperature and liquid water path, Northern Hemisphere latitude bands have layer-maximum radar reflectivity (ZL) that is ˜ 1 to 8 dBZ larger than their counterparts in the Southern Hemisphere. The systematically larger ZL under similar cloud conditions suggests larger ice number concentrations in mid-level stratiform mixed-phase clouds over the Northern Hemisphere, which is possibly related to higher background aerosol loadings. Furthermore, we show that springtime northern mid- and high latitudes have ZL that is larger by up to 6 dBZ (a factor of 4 higher ice number concentration) than other seasons, which might be related to more dust events that provide effective ice nucleating particles. Our study suggests that aerosol-dependent ice number concentration parameterizations are required in climate models to improve mixed-phase cloud simulations, especially over the Northern Hemisphere.

  12. Colorectal laterally spreading tumors show characteristic expression of cell polarity factors, including atypical protein kinase C λ/ι, E-cadherin, β-catenin and basement membrane component.

    Science.gov (United States)

    Ichikawa, Yasushi; Nagashima, Yoji; Morioka, Kaori; Akimoto, Kazunori; Kojima, Yasuyuki; Ishikawa, Takashi; Goto, Ayumu; Kobayashi, Noritoshi; Watanabe, Kazuteru; Ota, Mitsuyoshi; Fujii, Shoichi; Kawamata, Mayumi; Takagawa, Ryo; Kunizaki, Chikara; Takahashi, Hirokazu; Nakajima, Atsushi; Maeda, Shin; Shimada, Hiroshi; Inayama, Yoshiaki; Ohno, Shigeo; Endo, Itaru

    2014-09-01

    Colorectal flat-type tumors include laterally spreading tumors (LSTs) and flat depressed-type tumors. The former of which shows a predominant lateral spreading growth rather than an invasive growth. The present study examined the morphological characteristics of LSTs, in comparison with polypoid- or flat depressed-type tumors, along with the expression of atypical protein kinase C (aPKC) λ/ι, a pivotal cell polarity regulator, and the hallmarks of cell polarity, as well as with type IV collagen, β-catenin and E-cadherin. In total, 37 flat-type (24 LSTs and 13 flat depressed-type tumors) and 20 polypoid-type colorectal tumors were examined. The LSTs were classified as 15 LST adenoma (LST-A) and nine LST cancer in adenoma (LST-CA). An immunohistochemical examination was performed on aPKC λ/ι, type IV collagen, β-catenin and E-cadherin. The LST-A and -CA showed a superficial replacing growth pattern, with expression of β-catenin and E-cadherin in the basolateral membrane and type IV collagen along the basement membrane. In addition, 86.6% of LST-A and 55.6% of LST-CA showed aPKC λ/ι expression of 1+ (weak to normal intensity staining in the cytoplasm compared with the normal epithelium). Furthermore, ~45% of the polypoid-type adenomas showed 2+ (moderate intensity staining in the cytoplasm and/or nucleus) and 66.7% of the polypoid-type cancer in adenoma were 3+ (strong intensity staining in the cytoplasm and nucleus). A statistically significant positive correlation was observed between the expression of aPKC λ/ι and β-catenin (r=0.842; P<0.001), or type IV collagen (r=0.823; P<0.001). The LSTs showed a unique growth pattern, different from the expanding growth pattern presented by a polypoid tumor and invasive cancer. The growth characteristics of LST appear to be caused by adequate coexpression of β-catenin, type IV collagen and aPKC λ/ι.

  13. Optical modulator including grapene

    Science.gov (United States)

    Liu, Ming; Yin, Xiaobo; Zhang, Xiang

    2016-06-07

    The present invention provides for a one or more layer graphene optical modulator. In a first exemplary embodiment the optical modulator includes an optical waveguide, a nanoscale oxide spacer adjacent to a working region of the waveguide, and a monolayer graphene sheet adjacent to the spacer. In a second exemplary embodiment, the optical modulator includes at least one pair of active media, where the pair includes an oxide spacer, a first monolayer graphene sheet adjacent to a first side of the spacer, and a second monolayer graphene sheet adjacent to a second side of the spacer, and at least one optical waveguide adjacent to the pair.

  14. GPM GMI Level 1C Common Calibrated Brightness Temperatures Collocated V03

    Data.gov (United States)

    National Aeronautics and Space Administration — All 1C products have a common L1C data structure, simple and generic. Each L1C swath includes scan time, latitude and longitude, scan status, quality, incidence...

  15. GPM GMI Level 1C Common Calibrated Brightness Temperatures Collocated VV03A

    Data.gov (United States)

    National Aeronautics and Space Administration — All 1C products have a common L1C data structure, simple and generic. Each L1C swath includes scan time, latitude and longitude, scan status, quality, incidence...

  16. GPM Level 1C R Common Calibrated Brightness Temperatures Collocated VV03B

    Data.gov (United States)

    National Aeronautics and Space Administration — All 1C products have a common L1C data structure, simple and generic. Each L1C swath includes scan time, latitude and longitude, scan status, quality, incidence...

  17. GPM Level 1C R Common Calibrated Brightness Temperatures Collocated VV03A

    Data.gov (United States)

    National Aeronautics and Space Administration — All 1C products have a common L1C data structure, simple and generic. Each L1C swath includes scan time, latitude and longitude, scan status, quality, incidence...

  18. GPM GMI Level 1C Common Calibrated Brightness Temperatures Collocated VV03B

    Data.gov (United States)

    National Aeronautics and Space Administration — All 1C products have a common L1C data structure, simple and generic. Each L1C swath includes scan time, latitude and longitude, scan status, quality, incidence...

  19. GPM Level 1C R Common Calibrated Brightness Temperatures Collocated V03

    Data.gov (United States)

    National Aeronautics and Space Administration — All 1C products have a common L1C data structure, simple and generic. Each L1C swath includes scan time, latitude and longitude, scan status, quality, incidence...

  20. Anatomy of the pectoral and forelimb muscles of wildtype and green fluorescent protein-transgenic axolotls and comparison with other tetrapods including humans: a basis for regenerative, evolutionary and developmental studies.

    Science.gov (United States)

    Diogo, R; Tanaka, E M

    2012-12-01

    The axolotl Ambystoma mexicanum is one of the most used model organisms in evolutionary, developmental and regenerative studies, particularly because it can reconstitute a fully functional and complete forelimb/hindlimb. Surprisingly, there is no publication that describes all the pectoral and forelimb muscles of this species or provides a comparative framework between these muscles and those of other model organisms and of modern humans. In the present paper we describe and illustrate all these muscles in A. mexicanum and provide the first report about the myology of adults of a model organism that is based on analyses and dissections of both wildtype animals and transgenic animals that express green fluorescent protein (GFP) in muscle fibers. On the one hand, the inclusion of GFP-transgenic animals allows us to show the muscles as more commonly seen, and thus easier to understand, by current developmental and regenerative biologists. On the other hand, by including wildtype and GFP-transgenic animals and by visualizing these latter animals with and without a simultaneous transmission laser light, we were able to obtain a more complete and clearer understanding of the exact limit of the fleshy and tendinous parts of the muscles and their specific connections with the skeletal elements. This in turn allowed us to settle some controversies in previous anatomical and comparative studies. As most developmental, regenerative and evolutionary biologists are interested in comparing their observations of A. mexicanum with observations in other model organisms, and ultimately in using this information to increase the understanding of human evolution and medicine, we also provide tables showing the homologies between the pectoral and forelimb muscles of axolotls, of model organisms such as mice, frogs and chicken, and of Homo sapiens. An example illustrating the outcomes of using our methodology and of our observations is that they revealed that, contrary to what is often

  1. Brine migration resulting from CO2 injection into saline aquifers – An approach to risk estimation including various levels of uncertainty

    DEFF Research Database (Denmark)

    Walter, Lena; Binning, Philip John; Oladyshkin, Sergey

    2012-01-01

    for large-scale 3D models including complex physics. Therefore, we apply a model reduction based on arbitrary polynomial chaos expansion combined with probabilistic collocation method. It is shown that, dependent on data availability, both types of uncertainty can be equally significant. The presented study...... provides estimates of the risk of brine discharge into freshwater aquifers due to CO2 injection into geological formations and resultant salt concentrations in the overlying drinking water aquifers....

  2. Including whey protein and whey permeate in ready-to-use supplementary food improves recovery rates in children with moderate acute malnutrition: A randomized, double-blind clinical trial

    Science.gov (United States)

    The utility of dairy ingredients in the supplementary foods used in the treatment of childhood moderate acute malnutrition (MAM) remains unsettled. We evaluated the effectiveness of a peanut-based ready-to-use supplementary food (RUSF) with soy protein compared with a novel RUSF containing dairy in...

  3. Including whey protein and whey permeate in ready-to-use supplementary food improves recovery rates in children with moderate acute malnutrition: a randomized, double-blind clinical trial.

    Science.gov (United States)

    Stobaugh, Heather C; Ryan, Kelsey N; Kennedy, Julie A; Grise, Jennifer B; Crocker, Audrey H; Thakwalakwa, Chrissie; Litkowski, Patricia E; Maleta, Kenneth M; Manary, Mark J; Trehan, Indi

    2016-03-01

    The utility of dairy ingredients in the supplementary foods used in the treatment of childhood moderate acute malnutrition (MAM) remains unsettled. We evaluated the effectiveness of a peanut-based ready-to-use supplementary food (RUSF) with soy protein compared with a novel RUSF containing dairy ingredients in the form of whey permeate and whey protein concentrate in the treatment of children with MAM. We conducted a randomized, double-blind clinical effectiveness trial involving rural Malawian and Mozambican children 6-59 mo of age with MAM treated with either soy RUSF or a novel whey RUSF treatment of ~75 kcal · kg(-1) · d(-1) for up to 12 wk. The proportion of children that recovered from MAM was significantly higher in the group that received whey RUSF (960 of 1144; 83.9%) than in the group that received soy RUSF (874 of 1086; 80.5%; P whey RUSF also demonstrated better growth markers, with a higher mean midupper arm circumference (MUAC) at the time of discharge (P protein in the treatment of MAM, because the use of a novel whey RUSF resulted in higher recovery rates and improved growth than did soy RUSF, although the whey RUSF supplement provided less total protein and energy than the soy RUSF. This study was registered at clinicaltrials.gov as NCT01790048. © 2016 American Society for Nutrition.

  4. Recombinant protein production technology

    Science.gov (United States)

    Recombinant protein production is an important technology for antibody production, biochemical activity study, and structural determination during the post-genomic era. Limiting factors in recombinant protein production include low-level protein expression, protein precipitation, and loss of protein...

  5. Comparison between two meshless methods based on collocation technique for the numerical solution of four-species tumor growth model

    Science.gov (United States)

    Dehghan, Mehdi; Mohammadi, Vahid

    2017-03-01

    As is said in [27], the tumor-growth model is the incorporation of nutrient within the mixture as opposed to being modeled with an auxiliary reaction-diffusion equation. The formulation involves systems of highly nonlinear partial differential equations of surface effects through diffuse-interface models [27]. Simulations of this practical model using numerical methods can be applied for evaluating it. The present paper investigates the solution of the tumor growth model with meshless techniques. Meshless methods are applied based on the collocation technique which employ multiquadrics (MQ) radial basis function (RBFs) and generalized moving least squares (GMLS) procedures. The main advantages of these choices come back to the natural behavior of meshless approaches. As well as, a method based on meshless approach can be applied easily for finding the solution of partial differential equations in high-dimension using any distributions of points on regular and irregular domains. The present paper involves a time-dependent system of partial differential equations that describes four-species tumor growth model. To overcome the time variable, two procedures will be used. One of them is a semi-implicit finite difference method based on Crank-Nicolson scheme and another one is based on explicit Runge-Kutta time integration. The first case gives a linear system of algebraic equations which will be solved at each time-step. The second case will be efficient but conditionally stable. The obtained numerical results are reported to confirm the ability of these techniques for solving the two and three-dimensional tumor-growth equations.

  6. The Collocation of Elves and OH Meinel Band Nightglow: The Visible Upper Boundry of the VLF Waveguide

    Science.gov (United States)

    Wu, Y. J.; Williams, E. R.; Chang, S. C.; Chou, J. K.; Friedrich, M.; Peng, K. M.; Hsu, R. R.; Chen, A. B. C.; Su, H. T.; Frey, H. U.; Takahashi, Y.; Lee, L. C.

    2016-12-01

    The elve is the dominant type of Transient Luminous Event (TLE) at the base of the E-region ionosphere and the OH* Meinel band nightglow (OH* nightglow hereafter) has been reported at a similar altitude. However, a physical basis for this collocation has long been doubted because the OH* nightglow is the result of photochemical reactions, while for elves an electromagnetic process is involved. By virtue of the time resolution on the order of 29 millisecond and the specific filter of the imager for the 1PN2 and the OH* Meinel (8,3) and (9,3) in the wavelength range 620 nm to 750 nm, the Imager of Sprite and Upper Atmospheric Lightning (ISUAL) onboard Formosat 2 is the only space-borne instrument equipped for simultaneous observation of elves and OH* nightglow. Major ISUAL re-calibration of both OH* nightglow and elve imaging with star-finding methods has led to major improvements in the height accuracy in limb viewing. The most frequent height is 87 km with a HMFW of 7 km based on a total 130,000 sample images. 90% of the 168 limb elves at the center of the image are located within +/- 4 km of the altitude of the brightest OH* nightglow emission. Both elves and OH* nightglow show the semiannual oscillation (SAO) at low latitude. An environment-based and sounding-verified electron density profile is used as an input to the conventional elve model to know the brightest height. The inputs are the neutral gas profiles from the MSISE-90 model, the meteoric dust particle profile in Plane et al. (2015), as well as the loss of Lyman-α by O2 above the target height. Atomic oxygen, product of uv dissociation, is a necessary reactant to produce ozone, then go on to achieve the key reaction of OH* nightglow and the quenching process [Xu et al., 2010]. Both models show that the brightest layer is higher when the ledge of the atomic oxygen profile is higher, and vice versa. Finally, the incident lightning radiation electric field at VLF decreases exponentially by the height

  7. Extreme Mutation Tolerance: Nearly Half of the Archaeal Fusellovirus Sulfolobus Spindle-Shaped Virus 1 Genes Are Not Required for Virus Function, Including the Minor Capsid Protein Gene vp3.

    Science.gov (United States)

    Iverson, Eric A; Goodman, David A; Gorchels, Madeline E; Stedman, Kenneth M

    2017-05-15

    Viruses infecting the Archaea harbor a tremendous amount of genetic diversity. This is especially true for the spindle-shaped viruses of the family Fuselloviridae , where >90% of the viral genes do not have detectable homologs in public databases. This significantly limits our ability to elucidate the role of viral proteins in the infection cycle. To address this, we have developed genetic techniques to study the well-characterized fusellovirus Sulfolobus spindle-shaped virus 1 (SSV1), which infects Sulfolobus solfataricus in volcanic hot springs at 80°C and pH 3. Here, we present a new comparative genome analysis and a thorough genetic analysis of SSV1 using both specific and random mutagenesis and thereby generate mutations in all open reading frames. We demonstrate that almost half of the SSV1 genes are not essential for infectivity, and the requirement for a particular gene correlates well with its degree of conservation within the Fuselloviridae The major capsid gene vp1 is essential for SSV1 infectivity. However, the universally conserved minor capsid gene vp3 could be deleted without a loss in infectivity and results in virions with abnormal morphology. IMPORTANCE Most of the putative genes in the spindle-shaped archaeal hyperthermophile fuselloviruses have no sequences that are clearly similar to characterized genes. In order to determine which of these SSV genes are important for function, we disrupted all of the putative genes in the prototypical fusellovirus, SSV1. Surprisingly, about half of the genes could be disrupted without destroying virus function. Even deletions of one of the known structural protein genes that is present in all known fuselloviruses, vp3 , allows the production of infectious viruses. However, viruses lacking vp3 have abnormal shapes, indicating that the vp3 gene is important for virus structure. Identification of essential genes will allow focused research on minimal SSV genomes and further understanding of the structure of

  8. Orbiting Carbon Observatory-2 (OCO-2) Cloud Screening; Validation Against Collocated MODIS and Initial Comparison to CALIOP Data

    Science.gov (United States)

    Taylor, Thomas E.; O'Dell, Christopher W.; Frankenberg, Christian; Partain, Philip; Cronk, Heather W.; Savtchenko, Andrey; Nelson, Robert R.; Rosenthal, Emily J.; Chang, Albert; Crisp, David; hide

    2015-01-01

    The retrieval of the column-averaged carbon dioxide (CO2) dry air mole fraction (XCO2 ) from satellite measurements of reflected sunlight in the near-infrared can be biased due to contamination by clouds and aerosols within the instrument's field of view (FOV). Therefore, accurate aerosol and cloud screening of soundings is required prior to their use in the computationally expensive XCO2 retrieval algorithm. Robust cloud screening methods have been an important focus of the retrieval algorithm team for the National Aeronautics and Space Administration (NASA) Orbiting Carbon Observatory-2 (OCO-2), which was successfully launched into orbit on July 2, 2014. Two distinct spectrally-based algorithms have been developed for the purpose of cloud clearing OCO-2 soundings. The A-Band Preprocessor (ABP) performs a retrieval of surface pressure using measurements in the 0.76 micron O2 A-band to distinguish changes in the expected photon path length. The Iterative Maximum A-Posteriori (IMAP) Differential Optical Absorption Spectroscopy (DOAS) (IDP) algorithm is a non- scattering routine that operates on the O2 A-band as well as two CO2 absorption bands at 1.6 m (weak CO2 band) and 2.0 m (strong CO2 band) to provide band-dependent estimates of CO2 and H2O. Spectral ratios of retrieved CO2 and H2O identify measurements contaminated with cloud and scattering aerosols. Information from the two preprocessors is feed into a sounding selection tool to strategically down select from the order one million daily soundings collected by OCO-2 to a manageable number (order 10 to 20%) to be processed by the OCO-2 L2 XCO2 retrieval algorithm. Regional biases or errors in the selection of clear-sky soundings will introduce errors in the final retrieved XCO2 values, ultimately yielding errors in the flux inversion models used to determine global sources and sinks of CO2. In this work collocated measurements from NASA's Moderate Resolution Imaging Spectrometer (MODIS), aboard the Aqua

  9. Protein nanoparticles for therapeutic protein delivery.

    Science.gov (United States)

    Herrera Estrada, L P; Champion, J A

    2015-06-01

    Therapeutic proteins can face substantial challenges to their activity, requiring protein modification or use of a delivery vehicle. Nanoparticles can significantly enhance delivery of encapsulated cargo, but traditional small molecule carriers have some limitations in their use for protein delivery. Nanoparticles made from protein have been proposed as alternative carriers and have benefits specific to therapeutic protein delivery. This review describes protein nanoparticles made by self-assembly, including protein cages, protein polymers, and charged or amphipathic peptides, and by desolvation. It presents particle fabrication and delivery characterization for a variety of therapeutic and model proteins, as well as comparison of the features of different protein nanoparticles.

  10. OMI/Aura Level 2 Ozone (O3) Total Column 1-Orbit Subset and Collocated Swath along CloudSat track 200-km wide at 13x24 km2 resolution

    Data.gov (United States)

    National Aeronautics and Space Administration — This is a CloudSat-collocated subset of the original product OMTO3, for the purposes of the A-Train mission. The goal of the subset is to select and return OMI data...

  11. OMI/Aura Level 2 Sulphur Dioxide (SO2) Trace Gas Column Data 1-Orbit Subset and Collocated Swath along CloudSat V003 (OMSO2_CPR) at GES DISC

    Data.gov (United States)

    National Aeronautics and Space Administration — This is a CloudSat-collocated subset of the original product OMSO2, for the purposes of the A-Train mission. The goal of the subset is to select and return OMI data...

  12. Well-posedness and exact controllability of a fourth order Schrodinger equation with variable coefficients and Neumann boundary control and collocated observation

    Directory of Open Access Journals (Sweden)

    Ruili Wen

    2016-08-01

    Full Text Available We consider an open-loop system of a fourth order Schrodinger equation with variable coefficients and Neumann boundary control and collocated observation. Using the multiplier method on Riemannian manifold we show that that the system is well-posed in the sense of Salamon. This implies that the exponential stability of the closed-loop system under the direct proportional output feedback control and the exact controllability of open-loop system are equivalent. So in order to conclude feedback stabilization from well-posedness, we study the exact controllability under a uniqueness assumption by presenting the observability inequality for the dual system. In addition, we show that the system is regular in the sense of Weiss, and that the feedthrough operator is zero.

  13. Thermoluminescence of SrAl2O4:Eu2+, Dy3+: dosimetric characteristics and evidence of glow-peak collocation

    International Nuclear Information System (INIS)

    Chithambo, M.L.

    2016-01-01

    The thermoluminescence of SrAl 2 O 4 :Eu 2+ , Dy 3+ consists of collocated peaks whereby a dominant component subsumes subsidiary ones to such an extent that they appear as one; Qualitative and quantitative analysis of such cases will be described with suitable illustrative examples. The general features and qualitative kinetics properties of thermoluminescence from SrAl 2 O 4 :Eu 2+ , Dy 3+ is reported. Measurements using X-ray excited optical luminescence show that stimulated luminescence from SrAl 2 O 4 :Eu 2+ , Dy 3+ has two prominent emission bands, one at 475 nm and a more intense one near 575 nm, studied in this work. There are also weaker intensity emissions at 405, 510, 600 and 660 nm. The natural thermoluminescence measured at 1°C s -1 shows three peaks at 74, 170 and 340°C whereas 20 Gy beta-irradiation produces TL dominated by a single peak at 34°C. Analysis of this peak for its order of kinetics produces somewhat inconclusive results. The results of the partial heating procedure T m - T stop are consistent with both first and second-order kinetics. On the other hand, the position of the peak is independent of dose for several ranges of doses implying that the apparently single peak consists of multiple first-order peaks. Complementary investigations using the fractional glow technique, resolution by isothermal heating and the effect of fading on the peak show that the glow-curve of SrAl 2 O 4 :Eu 2+ , Dy 3+ comprises closely collocated thermoluminescence peaks. The implication of such complexity on kinetic analysis on this material and others that share this feature will be discussed. (author)

  14. Vs30 and spectral response from collocated shallow, active- and passive-source Vs data at 27 sites in Puerto Rico

    Science.gov (United States)

    Odum, Jack K.; Stephenson, William J.; Williams, Robert A.; von Hillebrandt-Andrade, Christa

    2013-01-01

    Shear‐wave velocity (VS) and time‐averaged shear‐wave velocity to 30 m depth (VS30) are the key parameters used in seismic site response modeling and earthquake engineering design. Where VS data are limited, available data are often used to develop and refine map‐based proxy models of VS30 for predicting ground‐motion intensities. In this paper, we present shallow VS data from 27 sites in Puerto Rico. These data were acquired using a multimethod acquisition approach consisting of noninvasive, collocated, active‐source body‐wave (refraction/reflection), active‐source surface wave at nine sites, and passive‐source surface‐wave refraction microtremor (ReMi) techniques. VS‐versus‐depth models are constructed and used to calculate spectral response plots for each site. Factors affecting method reliability are analyzed with respect to site‐specific differences in bedrock VS and spectral response. At many but not all sites, body‐ and surface‐wave methods generally determine similar depths to bedrock, and it is the difference in bedrock VS that influences site amplification. The predicted resonant frequencies for the majority of the sites are observed to be within a relatively narrow bandwidth of 1–3.5 Hz. For a first‐order comparison of peak frequency position, predictive spectral response plots from eight sites are plotted along with seismograph instrument spectra derived from the time series of the 16 May 2010 Puerto Rico earthquake. We show how a multimethod acquisition approach using collocated arrays compliments and corroborates VS results, thus adding confidence that reliable site characterization information has been obtained.

  15. Prediction of flexible/rigid regions from protein sequences using k-spaced amino acid pairs

    Directory of Open Access Journals (Sweden)

    Ruan Jishou

    2007-04-01

    Full Text Available Abstract Background Traditionally, it is believed that the native structure of a protein corresponds to a global minimum of its free energy. However, with the growing number of known tertiary (3D protein structures, researchers have discovered that some proteins can alter their structures in response to a change in their surroundings or with the help of other proteins or ligands. Such structural shifts play a crucial role with respect to the protein function. To this end, we propose a machine learning method for the prediction of the flexible/rigid regions of proteins (referred to as FlexRP; the method is based on a novel sequence representation and feature selection. Knowledge of the flexible/rigid regions may provide insights into the protein folding process and the 3D structure prediction. Results The flexible/rigid regions were defined based on a dataset, which includes protein sequences that have multiple experimental structures, and which was previously used to study the structural conservation of proteins. Sequences drawn from this dataset were represented based on feature sets that were proposed in prior research, such as PSI-BLAST profiles, composition vector and binary sequence encoding, and a newly proposed representation based on frequencies of k-spaced amino acid pairs. These representations were processed by feature selection to reduce the dimensionality. Several machine learning methods for the prediction of flexible/rigid regions and two recently proposed methods for the prediction of conformational changes and unstructured regions were compared with the proposed method. The FlexRP method, which applies Logistic Regression and collocation-based representation with 95 features, obtained 79.5% accuracy. The two runner-up methods, which apply the same sequence representation and Support Vector Machines (SVM and Naïve Bayes classifiers, obtained 79.2% and 78.4% accuracy, respectively. The remaining considered methods are

  16. Solid-state nuclear magnetic resonance (NMR) spectroscopy of human immunodeficiency virus gp41 protein that includes the fusion peptide: NMR detection of recombinant Fgp41 in inclusion bodies in whole bacterial cells and structural characterization of purified and membrane-associated Fgp41.

    Science.gov (United States)

    Vogel, Erica P; Curtis-Fisk, Jaime; Young, Kaitlin M; Weliky, David P

    2011-11-22

    Human immunodeficiency virus (HIV) infection of a host cell begins with fusion of the HIV and host cell membranes and is mediated by the gp41 protein, a single-pass integral membrane protein of HIV. The 175 N-terminal residues make up the ectodomain that lies outside the virus. This work describes the production and characterization of an ectodomain construct containing the 154 N-terminal gp41 residues, including the fusion peptide (FP) that binds to target cell membranes. The Fgp41 sequence was derived from one of the African clade A strains of HIV-1 that have been less studied than European/North American clade B strains. Fgp41 expression at a level of ~100 mg/L of culture was evidenced by an approach that included amino acid type (13)CO and (15)N labeling of recombinant protein and solid-state NMR (SSNMR) spectroscopy of lyophilized whole cells. The approach did not require any protein solubilization or purification and may be a general approach for detection of recombinant protein. The purified Fgp41 yield was ~5 mg/L of culture. SSNMR spectra of membrane-associated Fgp41 showed high helicity for the residues C-terminal of the FP. This was consistent with a "six-helix bundle" (SHB) structure that is the final gp41 state during membrane fusion. This observation and negligible Fgp41-induced vesicle fusion supported a function for SHB gp41 of membrane stabilization and fusion arrest. SSNMR spectra of residues in the membrane-associated FP provided evidence of a mixture of molecular populations with either helical or β-sheet FP conformation. These and earlier SSNMR data strongly support the existence of these populations in the SHB state of membrane-associated gp41. © 2011 American Chemical Society

  17. Tau protein

    DEFF Research Database (Denmark)

    Frederiksen, Jette Lautrup Battistini; Kristensen, Kim; Bahl, Jmc

    2011-01-01

    Background: Tau protein has been proposed as biomarker of axonal damage leading to irreversible neurological impairment in MS. CSF concentrations may be useful when determining risk of progression from ON to MS. Objective: To investigate the association between tau protein concentration and 14......-3-3 protein in the cerebrospinal fluid (CSF) of patients with monosymptomatic optic neuritis (ON) versus patients with monosymptomatic onset who progressed to multiple sclerosis (MS). To evaluate results against data found in a complete literature review. Methods: A total of 66 patients with MS and/or ON from...... the Department of Neurology of Glostrup Hospital, University of Copenhagen, Denmark, were included. CSF samples were analysed for tau protein and 14-3-3 protein, and clinical and paraclinical information was obtained from medical records. Results: The study shows a significantly increased concentration of tau...

  18. ENGLISH COLLOCATIONS OF THE VERBS “TO BE”, “TO HAVE” AND “TO TAKE” AND THEIR EQUIVALENTS IN GERMAN, FRENCH AND ITALIAN LANGUAGES: LINGUISTIC–CULTURAL ASPECT

    Directory of Open Access Journals (Sweden)

    Anna Nikolaevna Panamaryova

    2013-10-01

    Full Text Available The aim of this research is to find out conceptual characteristics of English, German, French, Italian languages world image. The subject of this paper is English collocations with the verbs “to be”, “to have” and “to take” and their equivalents in German, French and Italian languages. The task of this paper is to compare English collocations of the verbs “to be”, “to have” and “to take” and their equivalents in German, French and Italian languages in linguistic–cultural aspect. In Russian language studies such word groups are called “synlexis”. This term was coined by G. I. Klimovskaya, the professor ofTomskStateUniversity. The main method of the research is a comparative study of linguistic units. The conclusions made in the research are essential in the further study of European linguistic world image and can be used in textbooks on Cultural Linguistics.The practical result of the research can be a cross-cultural collocation dictionary of some languages. Such a dictionary is important for linguists, translators and people studying foreign languages.DOI: http://dx.doi.org/10.12731/2218-7405-2013-8-32

  19. Application of Computer Algebra Systems to the Construction of the Collocations and Least Residuals Method for Solving the 3D Navier–Stokes Equations

    Directory of Open Access Journals (Sweden)

    V. P. Shapeev

    2014-01-01

    Full Text Available The method of collocations and least residuals (CLR, which was proposed previously for the numerical solution of two-dimensional Navier–Stokes equations governing the stationary flows of a viscous incompressible fluid, is extended here for the three-dimensional case. The solution is sought in the implemented version of the method in the form of an expansion in the basis solenoidal functions. At all stages of the CLR method construction, a computer algebra system (CAS is applied for the derivation and verification of the formulas of the method and for their translation into arithmetic operators of the Fortran language. For accelerating the convergence of iterations a sufficiently universal algorithm is proposed, which is simple in its implementation and is based on the use of the Krylov’s subspaces. The obtained computational formulas of the CLR method were verified on the exact analytic solution of a test problem. Comparisons with the published numerical results of solving the benchmark problem of the 3D driven cubic cavity flow show that the accuracy of the results obtained by the CLR method corresponds to the known high-accuracy solutions.

  20. QTL for phytosterol and sinapate ester content in Brassica napus L. collocate with the two erucic acid genes

    Science.gov (United States)

    Amar, Samija; Ecke, Wolfgang; Becker, Heiko C.

    2008-01-01

    Improving oil and protein quality for food and feed purposes is an important goal in rapeseed (Brassica napus L.) breeding programs. Rapeseed contains phytosterols, used to enrich food products, and sinapate esters, which are limiting the utilization of rapeseed proteins in the feed industry. Increasing the phytosterol content of oil and lowering sinapate ester content of meal could increase the value of the oilseed rape crop. The objective of the present study was to identify quantitative trait loci (QTL) for phytosterol and sinapate ester content in a winter rapeseed population of 148 doubled haploid lines, previously found to have a large variation for these two traits. This population also segregated for the two erucic acid genes. A close negative correlation was found between erucic acid and phytosterol content (Spearman’s rank correlation, rs = −0.80**). For total phytosterol content, three QTL were detected, explaining 60% of the genetic variance. The two QTL with the strongest additive effects were mapped on linkage groups N8 and N13 within the confidence intervals of the two erucic acid genes. For sinapate ester content four QTL were detected, explaining 53% of the genetic variance. Again, a close negative correlation was found between erucic acid and sinapate ester content (rs = −0.66**) and the QTL with the strongest additive effects mapped on linkage groups N8 and N13 within the confidence intervals of the two erucic acid genes. The results suggests, that there is a pleiotropic effect of the two erucic acid genes on phytosterol and sinapate ester content; the effect of the alleles for low erucic acid content is to increase phytosterol and sinapate ester content. Possible reasons for this are discussed based on known biosynthetic pathways. Electronic supplementary material The online version of this article (doi:10.1007/s00122-008-0734-2) contains supplementary material, which is available to authorized users. PMID:18335203

  1. Closed-form solutions for linear regulator-design of mechanical systems including optimal weighting matrix selection

    Science.gov (United States)

    Hanks, Brantley R.; Skelton, Robert E.

    1991-01-01

    This paper addresses the restriction of Linear Quadratic Regulator (LQR) solutions to the algebraic Riccati Equation to design spaces which can be implemented as passive structural members and/or dampers. A general closed-form solution to the optimal free-decay control problem is presented which is tailored for structural-mechanical systems. The solution includes, as subsets, special cases such as the Rayleigh Dissipation Function and total energy. Weighting matrix selection is a constrained choice among several parameters to obtain desired physical relationships. The closed-form solution is also applicable to active control design for systems where perfect, collocated actuator-sensor pairs exist. Some examples of simple spring mass systems are shown to illustrate key points.

  2. (including travel dates) Proposed itinerary

    Indian Academy of Sciences (India)

    Ashok

    31 July to 22 August 2012 (including travel dates). Proposed itinerary: Arrival in Bangalore on 1 August. 1-5 August: Bangalore, Karnataka. Suggested institutions: Indian Institute of Science, Bangalore. St Johns Medical College & Hospital, Bangalore. Jawaharlal Nehru Centre, Bangalore. 6-8 August: Chennai, TN.

  3. Malignant lymphomas (including myeloproliferative disorders)

    International Nuclear Information System (INIS)

    Todd, I.D.H.

    1985-01-01

    This chapter deals with the radiotherapy and cytotoxic chemotherapy of the malignant lymphomas. Included within this group are Hodgkin's disease, non-Hodgkin's lymphoma, mycosis fungoides, and chronic lymphatic leukaemia. A further section deals with the myeloproliferative disorders, including granulocytic leukaemia, polycythaemia vera, and primary thrombocythaemia. Excluded are myeloma and reticulum cell sarcoma of bone and acute leukaemia. With regard to Hodgkin's disease, the past 25 years have seen general recognition of the curative potential of radiotherapy, at least in the local stages, and, more recently, awareness of the ability to achieve long-term survival after combination chemotherapy in generalised or in recurrent disease. At the same time the importance of staging has become appreciated and the introduction of procedures such as lymphography, staging laparotomy, and computer tomography (CT) has enormously increased its reliability. Advances have not been so dramatic in the complex group of non-Hodgkins's lymphomas, but are still very real

  4. cAMP does not inhibit convulxin-induced tyrosyl-phosphorylation of human platelet proteins, including PLCgamma2, but completely blocks the integrin alphaIIb beta3-dependent dephosphorylation step: comparisons with RGDS peptide, cytochalasin D, and phenylarsine oxide.

    Science.gov (United States)

    Francischetti, I M; Carlini, C R; Guimarães, J A

    1998-06-15

    Convulxin (Cvx) isolated from Crotalus durissus terrificus venom, induces platelet aggregation, phospholipase C (PLC) activation, and tyrosyl-phosphorylation (PTP) of multiple proteins, including PLCgamma2 by a mechanism independent of integrin alphaIIb beta3. However, PTP induced by Cvx is followed by a dephosphorylation step in a platelet aggregation-dependent manner. Here we show that increasing intraplatelet content of cAMP with forskolin is associated with the inhibition of Cvx-induced platelet aggregation, ATP secretion, and inositol-phosphates production. However, the early onset of Cvx-induced PTP is not sensitive to cAMP (including PLCgamma2), and it also occurs in the presence of integrin alphaIIb beta3-antagonist (RGDS peptide, RGDS) or inhibitors of actin polymerization (cytochalasin D, CD) and tyrosine-phosphatases (phenylarsine oxide, PAO). However, forskolin, RGDS, and CD prevented the dephosphorylation step together with inhibition of platelet aggregation, whereas in the presence of phenylarsine oxide (PAO) the dephosphorylation step was replaced by an increase in the number and intensity of tyrosyl-phosphorylated proteins. Our data provide evidence to conclude that (i) cAMP inhibits platelet aggregation at a downstream site to PLCgamma2 tyrosyl-phosphorylation; (ii) Cvx-induced PTP is independent on integrin alphaIIb beta3 engagement, actin polymerization, and tyrosine-phosphatases activation; (iii) integrin alphaIIb beta3 mediates the dephosphorylation step in a platelet aggregation-dependent manner; and (iv) Cvx and collagen stimulate platelets by a similar signal transduction pathway. Copyright 1998 Academic Press.

  5. Protein Foods

    Science.gov (United States)

    ... Text Size: A A A Listen En Español Protein Foods Foods high in protein such as fish, ... for the vegetarian proteins, whether they have carbohydrate. Protein Choices Plant-Based Proteins Plant-based protein foods ...

  6. Accounting for the water-leaving radiance in the simultaneous retrieval of atmosphere and ocean properties from collocated polarimeters and lidar measurements: results for the SABOR campaign

    Science.gov (United States)

    Chowdhary, J.; Brian, C.; Stamnes, S.; Hostetler, C. A.; Cetinic, I.; Slade, W. H.; Hu, Y.

    2017-12-01

    Ocean spectra typically contribute less than 10% to top-of-atmosphere (TOA) radiance observations in the visible (VIS). The remaining 90% of TOA radiance originates from scattering in the atmosphere which needs to be removed (i.e. corrected) but varies substantially with the aerosol present at the time of observation. The traditional approach for atmospheric correction (AC), used for ocean color sensors such as SeaWiFS, MODIS, and VIIRS, estimates aerosol scattering properties from TOA radiance observations in the near-infrared/short-wave infrared (NIR/SWIR) where the ocean becomes dark. The aerosol model is subsequently used to compute the atmospheric scattering contribution to the TOA radiance in the VIS. The final step is to subtract this computed scattering contribution from the real (i.e. observed) TOA radiance. As an alternative to the traditional approach for AC, we retrieve the atmosphere (i.e., aerosol) and ocean (i.e., color) properties simultaneously from measurements in the VIS. To separate the information content for the atmosphere and ocean, we use lidar measurements and multi-angle polarization measurements. Lidar and polarimeter measurements are powerful tools to enhance the ocean product retrievals from conventional ocean color sensors, and are under consideration to accompany future generation ocean color sensors. Here, we present results of simultaneous atmosphere-ocean retrievals using collocated airborne lidar and polarimeter data that were acquired during the Ship-Aircraft Bio-Optical Research (SABOR) campaign. We discuss 2 hydrosol models (which differ in number of free parameters) that were used for these inversions. We then compare our ocean retrievals with measurements obtained from the accompanying cruise ship. Finally, we touch upon a next generation of hydrosol models that accommodates the unique sensitivity of ocean lidar profiles to plankton morphology.

  7. Dryland Agrivoltaics: A novel approach to collocating food production and solar renewable energy to maximize food production, water savings, and energy generation

    Science.gov (United States)

    Barron-Gafford, G.; Escobedo, E. B.; Smith, J.; Raub, H.; Jimenez, J. R.; Sutter, L., Jr.; Barnett-Moreno, I.; Blackett, D. T.; Thompson, M. S.; Minor, R. L.; Pavao-Zuckerman, M.

    2017-12-01

    Conventional understanding of land use asserts an inherent "zero-sum-game" of competition between renewable energy and agricultural food production. This discourse is so fundamentally entrenched that it drives most current policy around conservation practices, land and water allotments for agriculture, and permitting for large-scale renewable energy installations. We are investigating a novel approach to solve a problem key to our environment and economy in drylands by creating a hybrid of collocated "green" agriculture and "grey" solar photovoltaic (PV) infrastructure to maximize agricultural production while improving renewable energy production. We are monitoring atmospheric microclimatic conditions, soil moisture, plant ecophysiological function, and biomass production within both this novel "agrivoltaics" ecosystem and in traditional PV installations and agricultural settings (control plot) to quantify tradeoffs associated with this approach. We have found that levels of soil moisture remained higher after each irrigation event within the soils under the agrivoltaics installation than the traditional agricultural setting due to the shading provided by the PV panels overhead. We initiated a drought treatment, which underscored the water-savings under the agrivoltaics installation and increased water use efficiency in this system. We hypothesized that we will see more temperature and drought stresses on photosynthetic capacity and water use efficiency in the control plants relative to the agrivoltaic installation, and we found that several food crops either experienced significantly more production within the agrivoltaics area, whereas others resulted in nearly equal production but at significant water savings. Combined with localized cooling of the PV panels resulting from the transpiration from the vegetative "understory", we are finding a win-win-win at the food-water-energy nexus. photo credit: Bob Demers/UANews

  8. Analysis of pCERC7, a small antibiotic resistance plasmid from a commensal ST131 Escherichia coli, defines a diverse group of plasmids that include various segments adjacent to a multimer resolution site and encode the same NikA relaxase accessory protein enabling mobilisation.

    Science.gov (United States)

    Moran, Robert A; Hall, Ruth M

    2017-01-01

    The ampicillin resistance plasmid pCERC7, carrying transposon Tn2 with an IS4 insertion, was detected in the draft genome of a commensal Escherichia coli isolate. The genome data also revealed that this isolate belongs to ST131, clade B. pCERC7 is 9712bp comprised of a 3319bp backbone, Tn2::IS4 (6388bp) and 5bp of target site duplication, and was present at a copy number of 40. pCERC7 is related to several plasmids composed of only the backbone, or the backbone with the Tn2 insertion in the same position. These plasmids have been found previously in Escherichia coli or Salmonella enterica recovered in several different countries from as early as the 1970s. This group was named the NTP16 group after the best studied example. pCERC7 was annotated using available information about plasmids in this group and additional analyses. The backbone includes genes for RNA I and RNA II to initiate replication and the Tn2 interrupts a gene found here to encode a protein 66% identical to the Rom regulatory protein of ColE1. NTP16 family plasmids include a gene, previously designated mobA, that was found to encode a homologue (53% identical) of the NikA relaxase accessory protein of the conjugative IncI1 plasmid R64, which is known to bind to the R64 oriT. However, a nikB relaxase gene is not present, indicating that a relaxase must be supplied in trans for mobilisation by R64 to occur, as demonstrated previously for NTP16. Hence, MobA of NTP16 and relatives was renamed NikA. Upstream of nikA, we found a region closely related to the oriT of R64. pCERC7 and all members of the NTP16 family also include a multimer resolution site, nmr, similar to the cer site of ColE1. The backbone of the NTP16 family also includes genes for a demonstrated toxin-antitoxin system, LsoAB. Several more distantly related groups of plasmids that include a very closely related nmr-nikA-oriT segment (99.4-93.7% DNA identity) were identified in the GenBank non-redundant DNA database. All use an RNA I/RNA II

  9. Device including a contact detector

    DEFF Research Database (Denmark)

    2011-01-01

    The present invention relates to a probe for determining an electrical property of an area of a surface of a test sample, the probe is intended to be in a specific orientation relative to the test sample. The probe may comprise a supporting body defining a first surface. A plurality of cantilever...... of cantilever arms (12) contacting the surface of the test sample when performing the movement....... arms (12) may extend from the supporting body in co-planar relationship with the first surface. The plurality of cantilever arms (12) may extend substantially parallel to each other and each of the plurality of cantilever arms (12) may include an electrical conductive tip for contacting the area...

  10. Protein Data Bank (PDB)

    Data.gov (United States)

    U.S. Department of Health & Human Services — The Protein Data Bank (PDB) archive is the single worldwide repository of information about the 3D structures of large biological molecules, including proteins and...

  11. An Integrated Biochemistry Laboratory, Including Molecular Modeling

    Science.gov (United States)

    Hall, Adele J. Wolfson Mona L.; Branham, Thomas R.

    1996-11-01

    The dilemma of designing an advanced undergraduate laboratory lies in the desire to teach and reinforce basic principles and techniques while at the same time exposing students to the excitement of research. We report here on a one-semester, project-based biochemistry laboratory that combines the best features of a cookbook approach (high success rate, achievement of defined goals) with those of an investigative, discovery-based approach (student involvement in the experimental design, excitement of real research). Individual modules may be selected and combined to meet the needs of different courses and different institutions. The central theme of this lab is protein purification and design. This laboratory accompanies the first semester of biochemistry (Structure and Function of Macromolecules, a course taken mainly by junior and senior chemistry and biological chemistry majors). The protein chosen as the object of study is the enzyme lysozyme, which is utilized in all projects. It is suitable for a student lab because it is easily and inexpensively obtained from egg white and is extremely stable, and its high isoelectric point (pI = 11) allows for efficient separation from other proteins by ion-exchange chromatography. Furthermore, a literature search conducted by the resourceful student reveals a wealth of information, since lysozyme has been the subject of numerous studies. It was the first enzyme whose structure was determined by crystallography (1). Hendrickson et al. (2) have previously described an intensive one-month laboratory course centered around lysozyme, although their emphasis is on protein stability rather than purification and engineering. Lysozyme continues to be the focus of much exciting new work on protein folding and dynamics, structure and activity (3 - 5). This lab course includes the following features: (i) reinforcement of basic techniques, such as preparation of buffers, simple enzyme kinetics, and absorption spectroscopy; (ii

  12. Membrane bending by protein-protein crowding.

    Science.gov (United States)

    Stachowiak, Jeanne C; Schmid, Eva M; Ryan, Christopher J; Ann, Hyoung Sook; Sasaki, Darryl Y; Sherman, Michael B; Geissler, Phillip L; Fletcher, Daniel A; Hayden, Carl C

    2012-09-01

    Curved membranes are an essential feature of dynamic cellular structures, including endocytic pits, filopodia protrusions and most organelles. It has been proposed that specialized proteins induce curvature by binding to membranes through two primary mechanisms: membrane scaffolding by curved proteins or complexes; and insertion of wedge-like amphipathic helices into the membrane. Recent computational studies have raised questions about the efficiency of the helix-insertion mechanism, predicting that proteins must cover nearly 100% of the membrane surface to generate high curvature, an improbable physiological situation. Thus, at present, we lack a sufficient physical explanation of how protein attachment bends membranes efficiently. On the basis of studies of epsin1 and AP180, proteins involved in clathrin-mediated endocytosis, we propose a third general mechanism for bending fluid cellular membranes: protein-protein crowding. By correlating membrane tubulation with measurements of protein densities on membrane surfaces, we demonstrate that lateral pressure generated by collisions between bound proteins drives bending. Whether proteins attach by inserting a helix or by binding lipid heads with an engineered tag, protein coverage above ~20% is sufficient to bend membranes. Consistent with this crowding mechanism, we find that even proteins unrelated to membrane curvature, such as green fluorescent protein (GFP), can bend membranes when sufficiently concentrated. These findings demonstrate a highly efficient mechanism by which the crowded protein environment on the surface of cellular membranes can contribute to membrane shape change.

  13. Closed-form solutions for linear regulator design of mechanical systems including optimal weighting matrix selection

    Science.gov (United States)

    Hanks, Brantley R.; Skelton, Robert E.

    1991-01-01

    Vibration in modern structural and mechanical systems can be reduced in amplitude by increasing stiffness, redistributing stiffness and mass, and/or adding damping if design techniques are available to do so. Linear Quadratic Regulator (LQR) theory in modern multivariable control design, attacks the general dissipative elastic system design problem in a global formulation. The optimal design, however, allows electronic connections and phase relations which are not physically practical or possible in passive structural-mechanical devices. The restriction of LQR solutions (to the Algebraic Riccati Equation) to design spaces which can be implemented as passive structural members and/or dampers is addressed. A general closed-form solution to the optimal free-decay control problem is presented which is tailored for structural-mechanical system. The solution includes, as subsets, special cases such as the Rayleigh Dissipation Function and total energy. Weighting matrix selection is a constrained choice among several parameters to obtain desired physical relationships. The closed-form solution is also applicable to active control design for systems where perfect, collocated actuator-sensor pairs exist.

  14. Simultaneous estimation of cross-validation errors in least squares collocation applied for statistical testing and evaluation of the noise variance components

    Science.gov (United States)

    Behnabian, Behzad; Mashhadi Hossainali, Masoud; Malekzadeh, Ahad

    2018-02-01

    The cross-validation technique is a popular method to assess and improve the quality of prediction by least squares collocation (LSC). We present a formula for direct estimation of the vector of cross-validation errors (CVEs) in LSC which is much faster than element-wise CVE computation. We show that a quadratic form of CVEs follows Chi-squared distribution. Furthermore, a posteriori noise variance factor is derived by the quadratic form of CVEs. In order to detect blunders in the observations, estimated standardized CVE is proposed as the test statistic which can be applied when noise variances are known or unknown. We use LSC together with the methods proposed in this research for interpolation of crustal subsidence in the northern coast of the Gulf of Mexico. The results show that after detection and removing outliers, the root mean square (RMS) of CVEs and estimated noise standard deviation are reduced about 51 and 59%, respectively. In addition, RMS of LSC prediction error at data points and RMS of estimated noise of observations are decreased by 39 and 67%, respectively. However, RMS of LSC prediction error on a regular grid of interpolation points covering the area is only reduced about 4% which is a consequence of sparse distribution of data points for this case study. The influence of gross errors on LSC prediction results is also investigated by lower cutoff CVEs. It is indicated that after elimination of outliers, RMS of this type of errors is also reduced by 19.5% for a 5 km radius of vicinity. We propose a method using standardized CVEs for classification of dataset into three groups with presumed different noise variances. The noise variance components for each of the groups are estimated using restricted maximum-likelihood method via Fisher scoring technique. Finally, LSC assessment measures were computed for the estimated heterogeneous noise variance model and compared with those of the homogeneous model. The advantage of the proposed method is the

  15. Similarity measures for protein ensembles

    DEFF Research Database (Denmark)

    Lindorff-Larsen, Kresten; Ferkinghoff-Borg, Jesper

    2009-01-01

    Analyses of similarities and changes in protein conformation can provide important information regarding protein function and evolution. Many scores, including the commonly used root mean square deviation, have therefore been developed to quantify the similarities of different protein conformatio...

  16. Similarity measures for protein ensembles

    DEFF Research Database (Denmark)

    Lindorff-Larsen, Kresten; Ferkinghoff-Borg, Jesper

    2009-01-01

    Analyses of similarities and changes in protein conformation can provide important information regarding protein function and evolution. Many scores, including the commonly used root mean square deviation, have therefore been developed to quantify the similarities of different protein conformations...

  17. Variational collocation on finite intervals

    International Nuclear Information System (INIS)

    Amore, Paolo; Cervantes, Mayra; Fernandez, Francisco M

    2007-01-01

    In this paper, we study a set of functions, defined on an interval of finite width, which are orthogonal and which reduce to the sinc functions when the appropriate limit is taken. We show that these functions can be used within a variational approach to obtain accurate results for a variety of problems. We have applied them to the interpolation of functions on finite domains and to the solution of the Schroedinger equation, and we have compared the performance of the present approach with others

  18. Ubiquitous media for collocated interaction

    DEFF Research Database (Denmark)

    Morrison, Ann; Jacucci, Giulio; Peltonen, Peter

    2010-01-01

    Has ubiquitous computing entered our lives as anticipated in the early 90s or at the turn of the millennium? In this last decade, the processing of media combined with sensing and communication capabilities has been slowly entering our lives through powerful smartphones, multimodal game consoles,......, instrumented cars, and large displays pervading public spaces. However, the visionary formulations (Weiser 1991) and updated scenarios (Abowd and Mynatt 2000) have not been realized, despite the fact that the technology has become increasingly accessible....

  19. Protein-protein interactions

    DEFF Research Database (Denmark)

    Byron, Olwyn; Vestergaard, Bente

    2015-01-01

    Responsive formation of protein:protein interaction (PPI) upon diverse stimuli is a fundament of cellular function. As a consequence, PPIs are complex, adaptive entities, and exist in structurally heterogeneous interplays defined by the energetic states of the free and complexed protomers......, are reported. The aim is to depict how the elucidation of the interplay of structures requires the interplay of methods....

  20. Ontological visualization of protein-protein interactions

    Directory of Open Access Journals (Sweden)

    Hill David P

    2005-02-01

    Full Text Available Abstract Background Cellular processes require the interaction of many proteins across several cellular compartments. Determining the collective network of such interactions is an important aspect of understanding the role and regulation of individual proteins. The Gene Ontology (GO is used by model organism databases and other bioinformatics resources to provide functional annotation of proteins. The annotation process provides a mechanism to document the binding of one protein with another. We have constructed protein interaction networks for mouse proteins utilizing the information encoded in the GO annotations. The work reported here presents a methodology for integrating and visualizing information on protein-protein interactions. Results GO annotation at Mouse Genome Informatics (MGI captures 1318 curated, documented interactions. These include 129 binary interactions and 125 interaction involving three or more gene products. Three networks involve over 30 partners, the largest involving 109 proteins. Several tools are available at MGI to visualize and analyze these data. Conclusions Curators at the MGI database annotate protein-protein interaction data from experimental reports from the literature. Integration of these data with the other types of data curated at MGI places protein binding data into the larger context of mouse biology and facilitates the generation of new biological hypotheses based on physical interactions among gene products.

  1. Protein docking prediction using predicted protein-protein interface

    Directory of Open Access Journals (Sweden)

    Li Bin

    2012-01-01

    Full Text Available Abstract Background Many important cellular processes are carried out by protein complexes. To provide physical pictures of interacting proteins, many computational protein-protein prediction methods have been developed in the past. However, it is still difficult to identify the correct docking complex structure within top ranks among alternative conformations. Results We present a novel protein docking algorithm that utilizes imperfect protein-protein binding interface prediction for guiding protein docking. Since the accuracy of protein binding site prediction varies depending on cases, the challenge is to develop a method which does not deteriorate but improves docking results by using a binding site prediction which may not be 100% accurate. The algorithm, named PI-LZerD (using Predicted Interface with Local 3D Zernike descriptor-based Docking algorithm, is based on a pair wise protein docking prediction algorithm, LZerD, which we have developed earlier. PI-LZerD starts from performing docking prediction using the provided protein-protein binding interface prediction as constraints, which is followed by the second round of docking with updated docking interface information to further improve docking conformation. Benchmark results on bound and unbound cases show that PI-LZerD consistently improves the docking prediction accuracy as compared with docking without using binding site prediction or using the binding site prediction as post-filtering. Conclusion We have developed PI-LZerD, a pairwise docking algorithm, which uses imperfect protein-protein binding interface prediction to improve docking accuracy. PI-LZerD consistently showed better prediction accuracy over alternative methods in the series of benchmark experiments including docking using actual docking interface site predictions as well as unbound docking cases.

  2. Highly thermostable fluorescent proteins

    Science.gov (United States)

    Bradbury, Andrew M [Santa Fe, NM; Waldo, Geoffrey S [Santa Fe, NM; Kiss, Csaba [Los Alamos, NM

    2011-03-22

    Thermostable fluorescent proteins (TSFPs), methods for generating these and other stability-enhanced proteins, polynucleotides encoding such proteins, and assays and method for using the TSFPs and TSFP-encoding nucleic acid molecules are provided. The TSFPs of the invention show extremely enhanced levels of stability and thermotolerance. In one case, for example, a TSFP of the invention is so stable it can be heated to 99.degree. C. for short periods of time without denaturing, and retains 85% of its fluorescence when heated to 80.degree. C. for several minutes. The invention also provides a method for generating stability-enhanced variants of a protein, including but not limited to fluorescent proteins.

  3. Interfacial Protein-Protein Associations

    OpenAIRE

    Langdon, Blake B.; Kastantin, Mark; Walder, Robert; Schwartz, Daniel K.

    2013-01-01

    While traditional models of protein adsorption focus primarily on direct protein-surface interactions, recent findings suggest that protein-protein interactions may play a central role. Using high-throughput intermolecular resonance energy transfer (RET) tracking, we directly observed dynamic, protein-protein associations of bovine serum albumin on poly(ethylene glycol) modified surfaces. The associations were heterogeneous and reversible, and associating molecules resided on the surface for ...

  4. Photoswitchable cyan fluorescent protein for protein tracking.

    Science.gov (United States)

    Chudakov, Dmitriy M; Verkhusha, Vladislav V; Staroverov, Dmitry B; Souslova, Ekaterina A; Lukyanov, Sergey; Lukyanov, Konstantin A

    2004-11-01

    In recent years diverse photolabeling techniques using green fluorescent protein (GFP)-like proteins have been reported, including photoactivatable PA-GFP, photoactivatable protein Kaede, the DsRed 'greening' technique and kindling fluorescent proteins. So far, only PA-GFP, which is monomeric and gives 100-fold fluorescence contrast, could be applied for protein tracking. Here we describe a dual-color monomeric protein, photoswitchable cyan fluorescent protein (PS-CFP). PS-CFP is capable of efficient photoconversion from cyan to green, changing both its excitation and emission spectra in response to 405-nm light irradiation. Complete photoactivation of PS-CFP results in a 1,500-fold increase in the green-to-cyan fluorescence ratio, making it the highest-contrast monomeric photoactivatable fluorescent protein described to date. We used PS-CFP as a photoswitchable tag to study trafficking of human dopamine transporter in living cells. At moderate excitation intensities, PS-CFP can be used as a pH-stable cyan label for protein tagging and fluorescence resonance energy transfer applications.

  5. Protein supplementation with aging.

    Science.gov (United States)

    Bauer, Juergen M; Diekmann, Rebecca

    2015-01-01

    To highlight the recent evicence for optimal protein intake and protein supplementation in older adults. A special focus has been placed on the effects on muscle protein synthesis, strength and overall performance in this population. Although for older adults, some additional evidence on the benefits of a higher protein intake than 0.8 g/kg body weight per day has been provided, the results of studies focusing on the timing of protein intake over the day have been contradictory. Supplementation with so-called 'fast' proteins, which are also rich in leucine, for example whey protein, proved superior with regard to muscle protein synthesis. First studies in frail older persons showed increased strength after supplementation with milk protein, whereas the combination with physical exercise increased muscle mass without additional benefit for strength or functionality. Recent evidence suggests positive effects of protein supplementation on muscle protein synthesis, muscle mass and muscle strength. However, as most studies included only small numbers of participants for short treatment periods, larger studies with longer duration are necessary to support the clinical relevance of these observations.

  6. Allosteric Regulation of Proteins

    Indian Academy of Sciences (India)

    For example, the structural changes that allowed for allosteric regulation of haemoglobin were re- vealed through structural elucidation of the protein in free and oxygen-bound forms by X-ray crystallography. Following this,. X-ray crystallography has been utilized to study a variety of al- losteric proteins including ATCase. 2.

  7. Amino acids and proteins

    NARCIS (Netherlands)

    van Goudoever, Johannes B.; Vlaardingerbroek, Hester; van den Akker, Chris H.; de Groof, Femke; van der Schoor, Sophie R. D.

    2014-01-01

    Amino acids and protein are key factors for growth. The neonatal period requires the highest intake in life to meet the demands. Those demands include amino acids for growth, but proteins and amino acids also function as signalling molecules and function as neurotransmitters. Often the nutritional

  8. The COG database: an updated version includes eukaryotes

    Directory of Open Access Journals (Sweden)

    Sverdlov Alexander V

    2003-09-01

    Full Text Available Abstract Background The availability of multiple, essentially complete genome sequences of prokaryotes and eukaryotes spurred both the demand and the opportunity for the construction of an evolutionary classification of genes from these genomes. Such a classification system based on orthologous relationships between genes appears to be a natural framework for comparative genomics and should facilitate both functional annotation of genomes and large-scale evolutionary studies. Results We describe here a major update of the previously developed system for delineation of Clusters of Orthologous Groups of proteins (COGs from the sequenced genomes of prokaryotes and unicellular eukaryotes and the construction of clusters of predicted orthologs for 7 eukaryotic genomes, which we named KOGs after eukaryotic orthologous groups. The COG collection currently consists of 138,458 proteins, which form 4873 COGs and comprise 75% of the 185,505 (predicted proteins encoded in 66 genomes of unicellular organisms. The eukaryotic orthologous groups (KOGs include proteins from 7 eukaryotic genomes: three animals (the nematode Caenorhabditis elegans, the fruit fly Drosophila melanogaster and Homo sapiens, one plant, Arabidopsis thaliana, two fungi (Saccharomyces cerevisiae and Schizosaccharomyces pombe, and the intracellular microsporidian parasite Encephalitozoon cuniculi. The current KOG set consists of 4852 clusters of orthologs, which include 59,838 proteins, or ~54% of the analyzed eukaryotic 110,655 gene products. Compared to the coverage of the prokaryotic genomes with COGs, a considerably smaller fraction of eukaryotic genes could be included into the KOGs; addition of new eukaryotic genomes is expected to result in substantial increase in the coverage of eukaryotic genomes with KOGs. Examination of the phyletic patterns of KOGs reveals a conserved core represented in all analyzed species and consisting of ~20% of the KOG set. This conserved portion of the

  9. Protein Colloidal Aggregation Project

    Science.gov (United States)

    Oliva-Buisson, Yvette J. (Compiler)

    2014-01-01

    To investigate the pathways and kinetics of protein aggregation to allow accurate predictive modeling of the process and evaluation of potential inhibitors to prevalent diseases including cataract formation, chronic traumatic encephalopathy, Alzheimer's Disease, Parkinson's Disease and others.

  10. Protein Misfolding Diseases.

    Science.gov (United States)

    Hartl, F Ulrich

    2017-06-20

    The majority of protein molecules must fold into defined three-dimensional structures to acquire functional activity. However, protein chains can adopt a multitude of conformational states, and their biologically active conformation is often only marginally stable. Metastable proteins tend to populate misfolded species that are prone to forming toxic aggregates, including soluble oligomers and fibrillar amyloid deposits, which are linked with neurodegeneration in Alzheimer and Parkinson disease, and many other pathologies. To prevent or regulate protein aggregation, all cells contain an extensive protein homeostasis (or proteostasis) network comprising molecular chaperones and other factors. These defense systems tend to decline during aging, facilitating the manifestation of aggregate deposition diseases. This volume of the Annual Review of Biochemistry contains a set of three articles addressing our current understanding of the structures of pathological protein aggregates and their associated disease mechanisms. These articles also discuss recent insights into the strategies cells have evolved to neutralize toxic aggregates by sequestering them in specific cellular locations.

  11. Static, Lightweight Includes Resolution for PHP

    NARCIS (Netherlands)

    M.A. Hills (Mark); P. Klint (Paul); J.J. Vinju (Jurgen)

    2014-01-01

    htmlabstractDynamic languages include a number of features that are challenging to model properly in static analysis tools. In PHP, one of these features is the include expression, where an arbitrary expression provides the path of the file to include at runtime. In this paper we present two

  12. Article Including Environmental Barrier Coating System

    Science.gov (United States)

    Lee, Kang N. (Inventor)

    2015-01-01

    An enhanced environmental barrier coating for a silicon containing substrate. The enhanced barrier coating may include a bond coat doped with at least one of an alkali metal oxide and an alkali earth metal oxide. The enhanced barrier coating may include a composite mullite bond coat including BSAS and another distinct second phase oxide applied over said surface.

  13. Rare thoracic cancers, including peritoneum mesothelioma

    NARCIS (Netherlands)

    Siesling, Sabine; van der Zwan, Jan Maarten; Izarzugaza, Isabel; Jaal, Jana; Treasure, Tom; Foschi, Roberto; Ricardi, Umberto; Groen, Harry; Tavilla, Andrea; Ardanaz, Eva

    Rare thoracic cancers include those of the trachea, thymus and mesothelioma (including peritoneum mesothelioma). The aim of this study was to describe the incidence, prevalence and survival of rare thoracic tumours using a large database, which includes cancer patients diagnosed from 1978 to 2002,

  14. Rare thoracic cancers, including peritoneum mesothelioma

    NARCIS (Netherlands)

    Siesling, Sabine; Zwan, J.M.V.D.; Izarzugaza, I.; Jaal, J.; Treasure, T.; Foschi, R.; Ricardi, U.; Groen, H.; Tavilla, A.; Ardanaz, E.

    2012-01-01

    Rare thoracic cancers include those of the trachea, thymus and mesothelioma (including peritoneum mesothelioma). The aim of this study was to describe the incidence, prevalence and survival of rare thoracic tumours using a large database, which includes cancer patients diagnosed from 1978 to 2002,

  15. Proteins engineering

    International Nuclear Information System (INIS)

    2000-01-01

    At the - Departement d'Ingenierie et d'etudes de proteines (Deip) of the CEA more than seventy researchers are working hard to understand the function of proteins. For that they use the molecular labelling technique (F.M.)

  16. Total protein

    Science.gov (United States)

    ... page: //medlineplus.gov/ency/article/003483.htm Total protein To use the sharing features on this page, please enable JavaScript. The total protein test measures the total amount of two classes ...

  17. Expression of multiple proteins in transgenic plants

    Science.gov (United States)

    Vierstra, Richard D.; Walker, Joseph M.

    2002-01-01

    A method is disclosed for the production of multiple proteins in transgenic plants. A DNA construct for introduction into plants includes a provision to express a fusion protein of two proteins of interest joined by a linking domain including plant ubiquitin. When the fusion protein is produced in the cells of a transgenic plant transformed with the DNA construction, native enzymes present in plant cells cleave the fusion protein to release both proteins of interest into the cells of the transgenic plant. Since the proteins are produced from the same fusion protein, the initial quantities of the proteins in the cells of the plant are approximately equal.

  18. Protein Correlation Profiles Identify Lipid Droplet Proteins with High Confidence*

    Science.gov (United States)

    Krahmer, Natalie; Hilger, Maximiliane; Kory, Nora; Wilfling, Florian; Stoehr, Gabriele; Mann, Matthias; Farese, Robert V.; Walther, Tobias C.

    2013-01-01

    Lipid droplets (LDs) are important organelles in energy metabolism and lipid storage. Their cores are composed of neutral lipids that form a hydrophobic phase and are surrounded by a phospholipid monolayer that harbors specific proteins. Most well-established LD proteins perform important functions, particularly in cellular lipid metabolism. Morphological studies show LDs in close proximity to and interacting with membrane-bound cellular organelles, including the endoplasmic reticulum, mitochondria, peroxisomes, and endosomes. Because of these close associations, it is difficult to purify LDs to homogeneity. Consequently, the confident identification of bona fide LD proteins via proteomics has been challenging. Here, we report a methodology for LD protein identification based on mass spectrometry and protein correlation profiles. Using LD purification and quantitative, high-resolution mass spectrometry, we identified LD proteins by correlating their purification profiles to those of known LD proteins. Application of the protein correlation profile strategy to LDs isolated from Drosophila S2 cells led to the identification of 111 LD proteins in a cellular LD fraction in which 1481 proteins were detected. LD localization was confirmed in a subset of identified proteins via microscopy of the expressed proteins, thereby validating the approach. Among the identified LD proteins were both well-characterized LD proteins and proteins not previously known to be localized to LDs. Our method provides a high-confidence LD proteome of Drosophila cells and a novel approach that can be applied to identify LD proteins of other cell types and tissues. PMID:23319140

  19. A simple dependence between protein evolution rate and the number of protein-protein interactions

    Directory of Open Access Journals (Sweden)

    Hirsh Aaron E

    2003-05-01

    Full Text Available Abstract Background It has been shown for an evolutionarily distant genomic comparison that the number of protein-protein interactions a protein has correlates negatively with their rates of evolution. However, the generality of this observation has recently been challenged. Here we examine the problem using protein-protein interaction data from the yeast Saccharomyces cerevisiae and genome sequences from two other yeast species. Results In contrast to a previous study that used an incomplete set of protein-protein interactions, we observed a highly significant correlation between number of interactions and evolutionary distance to either Candida albicans or Schizosaccharomyces pombe. This study differs from the previous one in that it includes all known protein interactions from S. cerevisiae, and a larger set of protein evolutionary rates. In both evolutionary comparisons, a simple monotonic relationship was found across the entire range of the number of protein-protein interactions. In agreement with our earlier findings, this relationship cannot be explained by the fact that proteins with many interactions tend to be important to yeast. The generality of these correlations in other kingdoms of life unfortunately cannot be addressed at this time, due to the incompleteness of protein-protein interaction data from organisms other than S. cerevisiae. Conclusions Protein-protein interactions tend to slow the rate at which proteins evolve. This may be due to structural constraints that must be met to maintain interactions, but more work is needed to definitively establish the mechanism(s behind the correlations we have observed.

  20. CDNA encoding a polypeptide including a hevein sequence

    Science.gov (United States)

    Raikhel, Natasha V.; Broekaert, Willem F.; Chua, Nam-Hai; Kush, Anil

    1995-03-21

    A cDNA clone (HEV1) encoding hevein was isolated via polymerase chain reaction (PCR) using mixed oligonucleotides corresponding to two regions of hevein as primers and a Hevea brasiliensis latex cDNA library as a template. HEV1 is 1018 nucleotides long and includes an open reading frame of 204 amino acids. The deduced amino acid sequence contains a putative signal sequence of 17 amino acid residues followed by a 187 amino acid polypeptide. The amino-terminal region (43 amino acids) is identical to hevein and shows homology to several chitin-binding proteins and to the amino-termini of wound-induced genes in potato and poplar. The carboxyl-terminal portion of the polypeptide (144 amino acids) is 74-79% homologous to the carboxyl-terminal region of wound-inducible genes of potato. Wounding, as well as application of the plant hormones abscisic acid and ethylene, resulted in accumulation of hevein transcripts in leaves, stems and latex, but not in roots, as shown by using the cDNA as a probe. A fusion protein was produced in E. coli from the protein of the present invention and maltose binding protein produced by the E. coli.

  1. cDNA encoding a polypeptide including a hevein sequence

    Energy Technology Data Exchange (ETDEWEB)

    Raikhel, N.V.; Broekaert, W.F.; Chua, N.H.; Kush, A.

    2000-07-04

    A cDNA clone (HEV1) encoding hevein was isolated via polymerase chain reaction (PCR) using mixed oligonucleotides corresponding to two regions of hevein as primers and a Hevea brasiliensis latex cDNA library as a template. HEV1 is 1018 nucleotides long and includes an open reading frame of 204 amino acids. The deduced amino acid sequence contains a putative signal sequence of 17 amino acid residues followed by a 187 amino acid polypeptide. The amino-terminal region (43 amino acids) is identical to hevein and shows homology to several chitin-binding proteins and to the amino-termini of wound-induced genes in potato and poplar. The carboxyl-terminal portion of the polypeptide (144 amino acids) is 74--79% homologous to the carboxyl-terminal region of wound-inducible genes of potato. Wounding, as well as application of the plant hormones abscisic acid and ethylene, resulted in accumulation of hevein transcripts in leaves, stems and latex, but not in roots, as shown by using the cDNA as a probe. A fusion protein was produced in E. coli from the protein of the present invention and maltose binding protein produced by the E. coli.

  2. Composite Pressure Vessel Including Crack Arresting Barrier

    Science.gov (United States)

    DeLay, Thomas K. (Inventor)

    2013-01-01

    A pressure vessel includes a ported fitting having an annular flange formed on an end thereof and a tank that envelopes the annular flange. A crack arresting barrier is bonded to and forming a lining of the tank within the outer surface thereof. The crack arresting barrier includes a cured resin having a post-curing ductility rating of at least approximately 60% through the cured resin, and further includes randomly-oriented fibers positioned in and throughout the cured resin.

  3. Including Organizational Cultural Parameters in Work Processes

    National Research Council Canada - National Science Library

    Handley, Holly A; Heacox, Nancy J

    2004-01-01

    .... In order to represent the organizational impact on the work process, five organizational cultural parameters were identified and included in an algorithm for modeling and simulation of cultural...

  4. Haemophilus influenzae Disease (Including Hib) Symptoms

    Science.gov (United States)

    ... Links Global Hib Vaccination Hib Vaccination Meningitis Pneumonia Sepsis ... Haemophilus influenzae , including H. influenzae type b or Hib, can cause many different kinds of infections . Symptoms depend on ...

  5. Collocated cokriging and neural-network multi-attribute transform in the prediction of effective porosity: A comparative case study for the Second Wall Creek Sand of the Teapot Dome field, Wyoming, USA

    Science.gov (United States)

    Moon, Seonghoon; Lee, Gwang H.; Kim, Hyeonju; Choi, Yosoon; Kim, Han-Joon

    2016-08-01

    Collocated cokriging (CCK) and neural-network multi-attribute transform (NN-MAT) are widely used in the prediction of reservoir properties because they can integrate sparsely-distributed, high-resolution well-log data and densely-sampled, low-resolution seismic data. CCK is a linear-weighted averaging method based on spatial covariance model. NN-MAT, based on a nonlinear relationship between seismic attributes and log values, treats data as spatially independent observations. In this study, we analyzed 3-D seismic and well-log data from the Second Wall Creek Sand of the Teapot Dome field, Wyoming, USA to investigate: (1) how CCK and NN-MAT perform in the prediction of porosity and (2) how the number of wells affects the results. Among a total of 64 wells, 25 wells were selected for CCK and NN-MAT and 39 wells were withheld for validation. We examined four cases: 25, 20, 15, and 10 wells. CCK overpredicted the porosity in the validation wells for all cases likely due to the strong influence of high values, but failed to predict very large porosities. Overprediction of CCK porosity becomes more pronounced with decreasing number of wells. NN-MAT largely underpredicted the porosity for all cases probably due to the band-limited nature of seismic data. The performance of CCK appears to be not affected significantly by the number of wells. Overall, NN-MAT performed better than CCK although its performance decreases continuously with decreasing number of wells.

  6. Acanthamoeba castellanii STAT protein.

    Science.gov (United States)

    Kicinska, Anna; Leluk, Jacek; Jarmuszkiewicz, Wieslawa

    2014-01-01

    STAT (signal transducers and activators of transcription) proteins are one of the important mediators of phosphotyrosine-regulated signaling in metazoan cells. We described the presence of STAT protein in a unicellular, free-living amoebae with a simple life cycle, Acanthamoeba castellanii. A. castellanii is the only, studied to date, Amoebozoan that does not belong to Mycetozoa but possesses STATs. A sequence of the A. castellanii STAT protein includes domains similar to those of the Dictyostelium STAT proteins: a coiled coil (characteristic for Dictyostelium STAT coiled coil), a STAT DNA-binding domain and a Src-homology domain. The search for protein sequences homologous to A. castellanii STAT revealed 17 additional sequences from lower eukaryotes. Interestingly, all of these sequences come from Amoebozoa organisms that belong to either Mycetozoa (slime molds) or Centramoebida. We showed that there are four separated clades within the slime mold STAT proteins. The A. castellanii STAT protein branches next to a group of STATc proteins from Mycetozoa. We also demonstrate that Amoebozoa form a distinct monophyletic lineage within the STAT protein world that is well separated from the other groups.

  7. Acanthamoeba castellanii STAT protein.

    Directory of Open Access Journals (Sweden)

    Anna Kicinska

    Full Text Available STAT (signal transducers and activators of transcription proteins are one of the important mediators of phosphotyrosine-regulated signaling in metazoan cells. We described the presence of STAT protein in a unicellular, free-living amoebae with a simple life cycle, Acanthamoeba castellanii. A. castellanii is the only, studied to date, Amoebozoan that does not belong to Mycetozoa but possesses STATs. A sequence of the A. castellanii STAT protein includes domains similar to those of the Dictyostelium STAT proteins: a coiled coil (characteristic for Dictyostelium STAT coiled coil, a STAT DNA-binding domain and a Src-homology domain. The search for protein sequences homologous to A. castellanii STAT revealed 17 additional sequences from lower eukaryotes. Interestingly, all of these sequences come from Amoebozoa organisms that belong to either Mycetozoa (slime molds or Centramoebida. We showed that there are four separated clades within the slime mold STAT proteins. The A. castellanii STAT protein branches next to a group of STATc proteins from Mycetozoa. We also demonstrate that Amoebozoa form a distinct monophyletic lineage within the STAT protein world that is well separated from the other groups.

  8. The surgery of peripheral nerves (including tumors)

    DEFF Research Database (Denmark)

    Fugleholm, Kåre

    2013-01-01

    Surgical pathology of the peripheral nervous system includes traumatic injury, entrapment syndromes, and tumors. The recent significant advances in the understanding of the pathophysiology and cellular biology of peripheral nerve degeneration and regeneration has yet to be translated into improved...

  9. Including Indigenous Minorities in Decision-Making

    DEFF Research Database (Denmark)

    Pristed Nielsen, Helene

    Based on theories of public sphere participation and deliberative democracy, this book presents empirical results from a study of experiences with including Aboriginal and Maori groups in political decision-making in respectively Western Australia and New Zealand...

  10. Lung Disease Including Asthma and Adult Vaccination

    Science.gov (United States)

    ... Diseases Resources Lung Disease including Asthma and Adult Vaccination Language: English (US) Español (Spanish) Recommend on Facebook ... more about health insurance options. Learn about adult vaccination and other health conditions Asplenia Diabetes Heart Disease, ...

  11. Births and deaths including fetal deaths

    Data.gov (United States)

    U.S. Department of Health & Human Services — Access to a variety of United States birth and death files including fetal deaths: Birth Files, 1968-2009; 1995-2005; Fetal death file, 1982-2005; Mortality files,...

  12. Protein Extractability

    African Journals Online (AJOL)

    Results showed that protein extractability was dependent on pH, type of salt, salt concentrations and extraction time. Salts extracted more proteins from the moringa seed flour than water. Maximum extraction of protein was. 85.06% and 84.72% with 0.5 M CaCl and 0.75 M NaCl respectively. On varying the pH, maximum ...

  13. Isolators Including Main Spring Linear Guide Systems

    Science.gov (United States)

    Goold, Ryan (Inventor); Buchele, Paul (Inventor); Hindle, Timothy (Inventor); Ruebsamen, Dale Thomas (Inventor)

    2017-01-01

    Embodiments of isolators, such as three parameter isolators, including a main spring linear guide system are provided. In one embodiment, the isolator includes first and second opposing end portions, a main spring mechanically coupled between the first and second end portions, and a linear guide system extending from the first end portion, across the main spring, and toward the second end portion. The linear guide system expands and contracts in conjunction with deflection of the main spring along the working axis, while restricting displacement and rotation of the main spring along first and second axes orthogonal to the working axis.

  14. Electrochemical cell structure including an ionomeric barrier

    Science.gov (United States)

    Lambert, Timothy N.; Hibbs, Michael

    2017-06-20

    An apparatus includes an electrochemical half-cell comprising: an electrolyte, an anode; and an ionomeric barrier positioned between the electrolyte and the anode. The anode may comprise a multi-electron vanadium phosphorous alloy, such as VP.sub.x, wherein x is 1-5. The electrochemical half-cell is configured to oxidize the vanadium and phosphorous alloy to release electrons. A method of mitigating corrosion in an electrochemical cell includes disposing an ionomeric barrier in a path of electrolyte or ion flow to an anode and mitigating anion accumulation on the surface of the anode.

  15. Electric Power Monthly, August 1990. [Glossary included

    Energy Technology Data Exchange (ETDEWEB)

    1990-11-29

    The Electric Power Monthly (EPM) presents monthly summaries of electric utility statistics at the national, Census division, and State level. The purpose of this publication is to provide energy decisionmakers with accurate and timely information that may be used in forming various perspectives on electric issues that lie ahead. Data includes generation by energy source (coal, oil, gas, hydroelectric, and nuclear); generation by region; consumption of fossil fuels for power generation; sales of electric power, cost data; and unusual occurrences. A glossary is included.

  16. English collocations extracted from a corpus of university learners and its contribution to a language teaching pedagogy=Colocações em inglês extraídas de um corpus de aprendizes universitários e sua contribuição para uma pedagogia no ensino de línguas

    Directory of Open Access Journals (Sweden)

    Adriane Orenha-Ottaiano

    2012-07-01

    Full Text Available Taking into consideration the relevance of foreign language teaching and the learning of collocations (ALTENBERG; EEG-OLOFSSON, 1990; FONTENELLE, 1994; MEUNIER; GRANGER, 2008, this paper aims at showing results of an investigation on whether the teaching of collocations should be implicit or explicit to the Brazilian university students. Furthermore, the research has the purpose of presenting some collocational aspects from a corpus of the written language learners made up of intermediate, upper intermediate and advanced university students’ argumentative essays at a public university in Brazil. With the help of WordSmith Tools (SCOTT, 2007, it was possible to raise students’ most frequent collocational choices and patterns, the most/least used type of collocations, the influence of the mother tongue on their choices, among other aspects. With the purpose of motivating and involving students in classroom research, it was also introduced The Corpus of Contemporary American English (COCA, created by Mark Davies. By doing so, students could compare their collocational choices with the patterns found in the online corpus, extract more collocational patterns and, consequently, be aware of the potential of corpora for the foreign learning process, specifically for raising language awareness, with focus on prefabricated chunks.Considerando a relevância das colocações para o ensino-aprendizagem de língua estrangeira (ALTENBERG; EEG-OLOFSSON, 1990; FONTENELLE, 1994; MEUNIER; GRANGER, 2008, este artigo tem como propósito mostrar os resultados de uma investigação a respeito do ensino implícito ou explícito de colocações para alunos universitários brasileiros. Além disso, a pesquisa visa apresentar alguns aspectos colocacionais, levantados a partir de um corpus de aprendizes de língua escrita, composto por textos argumentativos de alunos de nível intermediário, intermediário avançado e avançado, de uma universidade pública, no Brasil

  17. Diversification of Smallholder Tobacco Systems to include ...

    International Development Research Centre (IDRC) Digital Library (Canada)

    Tobacco is the mainstay of the economy of Malawi, accounting for over 70% of export earnings. Of the 100 000 members of the National Smallholder Farmers' Association of Malawi (NASFAM), 60% rely on tobacco for their sole source of income. Like their counterparts elsewhere, they face many difficulties, including: ...

  18. BIOLOGIC AND ECONOMIC EFFECTS OF INCLUDING DIFFERENT ...

    African Journals Online (AJOL)

    The biologic and economic effects of including three agro-industrial by-products as ingredients in turkey poult diets were investigated using 48 turkey poults in a completely randomised design experiment. Diets were formulated to contain the three by-products – wheat offal, rice husk and palm kernel meal, each at 20% level ...

  19. Extending flood damage assessment methodology to include ...

    African Journals Online (AJOL)

    Optimal and sustainable flood plain management, including flood control, can only be achieved when the impacts of flood control measures are considered for both the man-made and natural environments, and the sociological aspects are fully considered. Until now, methods/models developed to determine the influences ...

  20. Including Children Dependent on Ventilators in School.

    Science.gov (United States)

    Levine, Jack M.

    1996-01-01

    Guidelines for including ventilator-dependent children in school are offered, based on experience with six such students at a New York State school. Guidelines stress adherence to the medical management plan, the school-family partnership, roles of the social worker and psychologist, orientation, transportation, classroom issues, and steps toward…

  1. Musculoskeletal ultrasound including definitions for ultrasonographic pathology

    DEFF Research Database (Denmark)

    Wakefield, RJ; Balint, PV; Szkudlarek, Marcin

    2005-01-01

    Ultrasound (US) has great potential as an outcome in rheumatoid arthritis trials for detecting bone erosions, synovitis, tendon disease, and enthesopathy. It has a number of distinct advantages over magnetic resonance imaging, including good patient tolerability and ability to scan multiple joint...

  2. Modernizing Agrifood Markets : Including Small Producers in ...

    International Development Research Centre (IDRC) Digital Library (Canada)

    Against this baseline data, they will endeavor to identify success stories or examples of interventions that ensure small farmers' access to modernizing agrifood markets. The research will inform a set of policy recommendations to be promoted through policy platforms in a large number of developing countries, including but ...

  3. Including Students with Visual Impairments: Softball

    Science.gov (United States)

    Brian, Ali; Haegele, Justin A.

    2014-01-01

    Research has shown that while students with visual impairments are likely to be included in general physical education programs, they may not be as active as their typically developing peers. This article provides ideas for equipment modifications and game-like progressions for one popular physical education unit, softball. The purpose of these…

  4. Numerical simulation of spark ignition including ionization

    NARCIS (Netherlands)

    Thiele, M; Selle, S; Riedel, U; Warnatz, J; Maas, U

    2000-01-01

    A detailed understanding of the processes associated Midi spark ignition, as a first step during combustion, is of great importance fur clean operation of spark ignition engines. In the past 10 years. a growing concern for environmental protection, including low emission of pollutants, has increased

  5. Protein crystallography prescreen kit

    Science.gov (United States)

    Segelke, Brent W.; Krupka, Heike I.; Rupp, Bernhard

    2005-07-12

    A kit for prescreening protein concentration for crystallization includes a multiplicity of vials, a multiplicity of pre-selected reagents, and a multiplicity of sample plates. The reagents and a corresponding multiplicity of samples of the protein in solutions of varying concentrations are placed on sample plates. The sample plates containing the reagents and samples are incubated. After incubation the sample plates are examined to determine which of the sample concentrations are too low and which the sample concentrations are too high. The sample concentrations that are optimal for protein crystallization are selected and used.

  6. Green fluorescent protein.

    Science.gov (United States)

    Chalfie, M

    1995-10-01

    Several bioluminescent coelenterates use a secondary fluorescent protein, the green fluorescent protein (GFP), in an energy transfer reaction to produce green light. The most studied of these proteins have been the GFPs from the jellyfish Aequorea victoria and the sea pansy Renilla reniformis. Although the proteins from these organisms are not identical, they are thought to have the same chromophore, which is derived from the primary amino acid sequence of GFP. The differences are thought to be due to changes in the protein environment of the chromophore. Recent interest in these molecules has arisen from the cloning of the Aequorea gfp cDNA and the demonstration that its expression in the absence of other Aequorea proteins results in a fluorescent product. This demonstration indicated that GFP could be used as a marker of gene expression and protein localization in living and fixed tissues. Bacterial, plant and animal (including mammalian) cells all express GFP. The heterologous expression of the gfp cDNA has also meant that it could be mutated to produce proteins with different fluorescent properties. Variants with more intense fluorescence or alterations in the excitation and emission spectra have been produced.

  7. Protein politics

    NARCIS (Netherlands)

    Vijver, Marike

    2005-01-01

    This study is part of the program of the interdisciplinary research group Profetas (protein foods, environment, technology and society). Profetas consists of technological, environmental and socio-economic research projects on protein food systems which result in the development of scenarios and

  8. Whey Protein

    Science.gov (United States)

    ... Fraction de Lactosérum, Fraction de Petit-Lait, Goat Milk Whey, Goat Whey, Isolat de Protéine de Lactosérum, Isolat de Protéine de Petit-Lait, Lactosérum de Lait de Chèvre, MBP, Milk Protein, Milk Protein Isolate, Mineral Whey Concentrate, Proteínas ...

  9. Protein adhesives

    Science.gov (United States)

    Charles R. Frihart; Linda F. Lorenz

    2018-01-01

    Nature uses a wide variety of chemicals for providing adhesion internally (e.g., cell to cell) and externally (e.g., mussels to ships and piers). This adhesive bonding is chemically and mechanically complex, involving a variety of proteins, carbohydrates, and other compounds.Consequently,the effect of protein structures on adhesive properties is only partially...

  10. Protein-protein interactions: impact of solvent and effects of fluorination

    OpenAIRE

    Samsonov, Sergey

    2009-01-01

    Proteins have an indispensable role in the cell. They carry out a wide variety of structural, catalytic and signaling functions in all known biological systems. To perform their biological functions, proteins establish interactions with other bioorganic molecules including other proteins. Therefore, protein-protein interactions is one of the central topics in molecular biology. My thesis is devoted to three different topics in the field of protein-protein interactions. The first one focuses o...

  11. Photoactive devices including porphyrinoids with coordinating additives

    Science.gov (United States)

    Forrest, Stephen R; Zimmerman, Jeramy; Yu, Eric K; Thompson, Mark E; Trinh, Cong; Whited, Matthew; Diev, Vlacheslav

    2015-05-12

    Coordinating additives are included in porphyrinoid-based materials to promote intermolecular organization and improve one or more photoelectric characteristics of the materials. The coordinating additives are selected from fullerene compounds and organic compounds having free electron pairs. Combinations of different coordinating additives can be used to tailor the characteristic properties of such porphyrinoid-based materials, including porphyrin oligomers. Bidentate ligands are one type of coordinating additive that can form coordination bonds with a central metal ion of two different porphyrinoid compounds to promote porphyrinoid alignment and/or pi-stacking. The coordinating additives can shift the absorption spectrum of a photoactive material toward higher wavelengths, increase the external quantum efficiency of the material, or both.

  12. Electric power monthly, September 1990. [Glossary included

    Energy Technology Data Exchange (ETDEWEB)

    1990-12-17

    The purpose of this report is to provide energy decision makers with accurate and timely information that may be used in forming various perspectives on electric issues. The power plants considered include coal, petroleum, natural gas, hydroelectric, and nuclear power plants. Data are presented for power generation, fuel consumption, fuel receipts and cost, sales of electricity, and unusual occurrences at power plants. Data are compared at the national, Census division, and state levels. 4 figs., 52 tabs. (CK)

  13. Power generation method including membrane separation

    Science.gov (United States)

    Lokhandwala, Kaaeid A.

    2000-01-01

    A method for generating electric power, such as at, or close to, natural gas fields. The method includes conditioning natural gas containing C.sub.3+ hydrocarbons and/or acid gas by means of a membrane separation step. This step creates a leaner, sweeter, drier gas, which is then used as combustion fuel to run a turbine, which is in turn used for power generation.

  14. Should Trade Agreements Include Environmental Policy?

    OpenAIRE

    Josh Ederington

    2010-01-01

    This article examines the extent to which environmental and trade policies should be treated equally, or symmetrically, in international negotiations. It reviews the recent economics literature on trade and the environment to address two questions. First, should trade negotiations include negotiations over environmental policies and the setting of binding environmental standards? Second, if there are grounds for international environmental negotiations, should environmental agreements b...

  15. Jet-calculus approach including coherence effects

    International Nuclear Information System (INIS)

    Jones, L.M.; Migneron, R.; Narayanan, K.S.S.

    1987-01-01

    We show how integrodifferential equations typical of jet calculus can be combined with an averaging procedure to obtain jet-calculus-based results including the Mueller interference graphs. Results in longitudinal-momentum fraction x for physical quantities are higher at intermediate x and lower at large x than with the conventional ''incoherent'' jet calculus. These results resemble those of Marchesini and Webber, who used a Monte Carlo approach based on the same dynamics

  16. Revisiting Hansen Solubility Parameters by Including Thermodynamics.

    Science.gov (United States)

    Louwerse, Manuel J; Maldonado, Ana; Rousseau, Simon; Moreau-Masselon, Chloe; Roux, Bernard; Rothenberg, Gadi

    2017-11-03

    The Hansen solubility parameter approach is revisited by implementing the thermodynamics of dissolution and mixing. Hansen's pragmatic approach has earned its spurs in predicting solvents for polymer solutions, but for molecular solutes improvements are needed. By going into the details of entropy and enthalpy, several corrections are suggested that make the methodology thermodynamically sound without losing its ease of use. The most important corrections include accounting for the solvent molecules' size, the destruction of the solid's crystal structure, and the specificity of hydrogen-bonding interactions, as well as opportunities to predict the solubility at extrapolated temperatures. Testing the original and the improved methods on a large industrial dataset including solvent blends, fit qualities improved from 0.89 to 0.97 and the percentage of correct predictions rose from 54 % to 78 %. Full Matlab scripts are included in the Supporting Information, allowing readers to implement these improvements on their own datasets. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  17. Regulation of protein turnover by heat shock proteins.

    Science.gov (United States)

    Bozaykut, Perinur; Ozer, Nesrin Kartal; Karademir, Betul

    2014-12-01

    Protein turnover reflects the balance between synthesis and degradation of proteins, and it is a crucial process for the maintenance of the cellular protein pool. The folding of proteins, refolding of misfolded proteins, and also degradation of misfolded and damaged proteins are involved in the protein quality control (PQC) system. Correct protein folding and degradation are controlled by many different factors, one of the most important of which is the heat shock protein family. Heat shock proteins (HSPs) are in the class of molecular chaperones, which may prevent the inappropriate interaction of proteins and induce correct folding. On the other hand, these proteins play significant roles in the degradation pathways, including endoplasmic reticulum-associated degradation (ERAD), the ubiquitin-proteasome system, and autophagy. This review focuses on the emerging role of HSPs in the regulation of protein turnover; the effects of HSPs on the degradation machineries ERAD, autophagy, and proteasome; as well as the role of posttranslational modifications in the PQC system. Copyright © 2014 Elsevier Inc. All rights reserved.

  18. Protein-Protein Interaction Databases

    DEFF Research Database (Denmark)

    Szklarczyk, Damian; Jensen, Lars Juhl

    2015-01-01

    of research are explored. Here we present an overview of the most widely used protein-protein interaction databases and the methods they employ to gather, combine, and predict interactions. We also point out the trade-off between comprehensiveness and accuracy and the main pitfall scientists have to be aware...

  19. Drug delivery device including electrolytic pump

    KAUST Repository

    Foulds, Ian G.

    2016-03-31

    Systems and methods are provided for a drug delivery device and use of the device for drug delivery. In various aspects, the drug delivery device combines a “solid drug in reservoir” (SDR) system with an electrolytic pump. In various aspects an improved electrolytic pump is provided including, in particular, an improved electrolytic pump for use with a drug delivery device, for example an implantable drug delivery device. A catalytic reformer can be incorporated in a periodically pulsed electrolytic pump to provide stable pumping performance and reduced actuation cycle.

  20. Chemical Protein Modification through Cysteine.

    Science.gov (United States)

    Gunnoo, Smita B; Madder, Annemieke

    2016-04-01

    The modification of proteins with non-protein entities is important for a wealth of applications, and methods for chemically modifying proteins attract considerable attention. Generally, modification is desired at a single site to maintain homogeneity and to minimise loss of function. Though protein modification can be achieved by targeting some natural amino acid side chains, this often leads to ill-defined and randomly modified proteins. Amongst the natural amino acids, cysteine combines advantageous properties contributing to its suitability for site-selective modification, including a unique nucleophilicity, and a low natural abundance--both allowing chemo- and regioselectivity. Native cysteine residues can be targeted, or Cys can be introduced at a desired site in a protein by means of reliable genetic engineering techniques. This review on chemical protein modification through cysteine should appeal to those interested in modifying proteins for a range of applications. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  1. Constraining aerosol optical models using ground-based, collocated particle size and mass measurements in variable air mass regimes during the 7-SEAS/Dongsha experiment

    Science.gov (United States)

    Bell, Shaun W.; Hansell, Richard A.; Chow, Judith C.; Tsay, Si-Chee; Hsu, N. Christina; Lin, Neng-Huei; Wang, Sheng-Hsiang; Ji, Qiang; Li, Can; Watson, John G.; Khlystov, Andrey

    2013-10-01

    During the spring of 2010, NASA Goddard's COMMIT ground-based mobile laboratory was stationed on Dongsha Island off the southwest coast of Taiwan, in preparation for the upcoming 2012 7-SEAS field campaign. The measurement period offered a unique opportunity for conducting detailed investigations of the optical properties of aerosols associated with different air mass regimes including background maritime and those contaminated by anthropogenic air pollution and mineral dust. What appears to be the first time for this region, a shortwave optical closure experiment (λ = 550 nm) for both scattering and absorption was attempted over a 12-day period during which aerosols exhibited the most change. Constraints to the optical model included combined SMPS and APS number concentration data for a continuum of fine and coarse-mode particle sizes up to PM2.5. We also take advantage of an IMPROVE chemical sampler to help constrain aerosol composition and mass partitioning of key elemental species including sea-salt, particulate organic matter, soil, non sea-salt sulfate, nitrate, and elemental carbon. Achieving full optical closure is hampered by limitations in accounting for the role of water vapor in the system, uncertainties in the instruments and the need for further knowledge in the source apportionment of the model's major chemical components. Nonetheless, our results demonstrate that the observed aerosol scattering and absorption for these diverse air masses are reasonably captured by the model, where peak aerosol events and transitions between key aerosols types are evident. Signatures of heavy polluted aerosol composed mostly of ammonium and non sea-salt sulfate mixed with some dust with transitions to background sea-salt conditions are apparent in the absorption data, which is particularly reassuring owing to the large variability in the imaginary component of the refractive indices. Consistency between the measured and modeled optical parameters serves as an

  2. Constraining Aerosol Optical Models Using Ground-Based, Collocated Particle Size and Mass Measurements in Variable Air Mass Regimes During the 7-SEAS/Dongsha Experiment

    Science.gov (United States)

    Bell, Shaun W.; Hansell, Richard A.; Chow, Judith C.; Tsay, Si-Chee; Wang, Sheng-Hsiang; Ji, Qiang; Li, Can; Watson, John G.; Khlystov, Andrey

    2012-01-01

    During the spring of 2010, NASA Goddard's COMMIT ground-based mobile laboratory was stationed on Dongsha Island off the southwest coast of Taiwan, in preparation for the upcoming 2012 7-SEAS field campaign. The measurement period offered a unique opportunity for conducting detailed investigations of the optical properties of aerosols associated with different air mass regimes including background maritime and those contaminated by anthropogenic air pollution and mineral dust. What appears to be the first time for this region, a shortwave optical closure experiment for both scattering and absorption was attempted over a 12-day period during which aerosols exhibited the most change. Constraints to the optical model included combined SMPS and APS number concentration data for a continuum of fine and coarse-mode particle sizes up to PM2.5. We also take advantage of an IMPROVE chemical sampler to help constrain aerosol composition and mass partitioning of key elemental species including sea-salt, particulate organic matter, soil, non sea-salt sulphate, nitrate, and elemental carbon. Our results demonstrate that the observed aerosol scattering and absorption for these diverse air masses are reasonably captured by the model, where peak aerosol events and transitions between key aerosols types are evident. Signatures of heavy polluted aerosol composed mostly of ammonium and non sea-salt sulphate mixed with some dust with transitions to background sea-salt conditions are apparent in the absorption data, which is particularly reassuring owing to the large variability in the imaginary component of the refractive indices. Extinctive features at significantly smaller time scales than the one-day sample period of IMPROVE are more difficult to reproduce, as this requires further knowledge concerning the source apportionment of major chemical components in the model. Consistency between the measured and modeled optical parameters serves as an important link for advancing remote

  3. Aerosol simulation including chemical and nuclear reactions

    International Nuclear Information System (INIS)

    Marwil, E.S.; Lemmon, E.C.

    1985-01-01

    The numerical simulation of aerosol transport, including the effects of chemical and nuclear reactions presents a challenging dynamic accounting problem. Particles of different sizes agglomerate and settle out due to various mechanisms, such as diffusion, diffusiophoresis, thermophoresis, gravitational settling, turbulent acceleration, and centrifugal acceleration. Particles also change size, due to the condensation and evaporation of materials on the particle. Heterogeneous chemical reactions occur at the interface between a particle and the suspending medium, or a surface and the gas in the aerosol. Homogeneous chemical reactions occur within the aersol suspending medium, within a particle, and on a surface. These reactions may include a phase change. Nuclear reactions occur in all locations. These spontaneous transmutations from one element form to another occur at greatly varying rates and may result in phase or chemical changes which complicate the accounting process. This paper presents an approach for inclusion of these effects on the transport of aerosols. The accounting system is very complex and results in a large set of stiff ordinary differential equations (ODEs). The techniques for numerical solution of these ODEs require special attention to achieve their solution in an efficient and affordable manner. 4 refs

  4. EDITORIAL: Precision proteins Precision proteins

    Science.gov (United States)

    Demming, Anna

    2010-06-01

    Since the birth of modern day medicine, during the times of Hippocrates in ancient Greece, the profession has developed from the rudimentary classification of disease into a rigorous science with an inspiring capability to treat and cure. Scientific methodology has distilled clinical diagnostic tools from the early arts of prognosis, which used to rely as much on revelation and prophecy, as intuition and judgement [1]. Over the past decade, research into the interactions between proteins and nanosystems has provided some ingenious and apt techniques for delving into the intricacies of anatomical systems. In vivo biosensing has emerged as a vibrant field of research, as much of medical diagnosis relies on the detection of substances or an imbalance in the chemicals in the body. The inherent properties of nanoscale structures, such as cantilevers, make them well suited to biosensing applications that demand the detection of molecules at very low concentrations. Measurable deflections in cantilevers functionalised with antibodies provide quantitative indicators of the presence of specific antigens when the two react. Such developments have roused mounting interest in the interactions of proteins with nanostructures, such as carbon nanotubes [3], which have demonstrated great potential as generic biomarkers. Plasmonic properties are also being exploited in sensing applications, such as the molecular sentinel recently devised by researchers in the US. The device uses the plasmonic properties of a silver nanoparticle linked to a Raman labelled hairpin DNA probe to signal changes in the probe geometry resulting from interactions with substances in the environment. Success stories so far include the detection of two specific genes associated with breast cancer [4]. A greater understanding of how RNA interference regulates gene expression has highlighted the potential of using this natural process as another agent for combating disease in personalized medicine. However, the

  5. Including gauge corrections to thermal leptogenesis

    International Nuclear Information System (INIS)

    Huetig, Janine

    2013-01-01

    This thesis provides the first approach of a systematic inclusion of gauge corrections to leading order to the ansatz of thermal leptogenesis. We have derived a complete expression for the integrated lepton number matrix including all resummations needed. For this purpose, a new class of diagram has been invented, namely the cylindrical diagram, which allows diverse investigations into the topic of leptogenesis such as the case of resonant leptogenesis. After a brief introduction of the topic of the baryon asymmetry in the universe and a discussion of its most promising solutions as well as their advantages and disadvantages, we have presented our framework of thermal leptogenesis. An effective model was described as well as the associated Feynman rules. The basis for using nonequilibrium quantum field theory has been built in chapter 3. At first, the main definitions have been presented for equilibrium thermal field theory, afterwards we have discussed the Kadanoff-Baym equations for systems out of equilibrium using the example of the Majorana neutrino. The equations have also been solved in the context of leptogenesis in chapter 4. Since gauge corrections play a crucial role throughout this thesis, we have also repeated the naive ansatz by replacing the free equilibrium propagator by propagators including thermal damping rates due to the Standard Model damping widths for lepton and Higgs fields. It is shown that this leads to a comparable result to the solutions of the Boltzmann equations for thermal leptogenesis. Thus it becomes obvious that Standard Model corrections are not negligible for thermal leptogenesis and therefore need to be included systematically from first principles. In order to achieve this we have started discussing the calculation of ladder rung diagrams for Majorana neutrinos using the HTL and the CTL approach in chapter 5. All gauge corrections are included in this framework and thus it has become the basis for the following considerations

  6. Immunomodulation in human and experimental arthritis: including vitamin D, helminths and heat-shock proteins.

    Science.gov (United States)

    Ishikawa, L L W; Shoenfeld, Y; Sartori, A

    2014-05-01

    Rheumatoid arthritis (RA) is a chronic inflammatory autoimmune disease that is mainly directed to the joints, affecting the synovial membrane, the cartilage and also the bone. This disease affects 1% to 2% of the world population and is associated with significant morbidity and increased mortality. RA experimental models have allowed a great deal of information to be translated to the corresponding human disease. This review summarizes some of the most relevant findings targeting immunomodulation in arthritis. Some general guidelines to choose an adequate experimental model and also our experience with arthritis are supplied.

  7. The Arabidopsis SOMATIC EMBRYOGENESIS RECEPTOR-LIKE KINASE1 protein complex includes BRASSINOSTEROID-INSENSITIVE1.

    NARCIS (Netherlands)

    Karlova, R.B.; Boeren, J.A.; Russinova, E.T.; Aker, J.C.M.; Vervoort, J.J.M.; Vries, de S.C.

    2006-01-01

    Arabidopsis thaliana SOMATIC EMBRYOGENESIS RECEPTOR-LIKE KINASE1 (SERK1) is a leucine-rich repeat receptor-like kinase (LRR-RLK) involved in the acquisition of embryogenic competence and in male sporogenesis. To determine the composition of the SERK1 signaling complex in vivo, we generated plants

  8. Grand unified models including extra Z bosons

    International Nuclear Information System (INIS)

    Li Tiezhong

    1989-01-01

    The grand unified theories (GUT) of the simple Lie groups including extra Z bosons are discussed. Under authors's hypothesis there are only SU 5+m SO 6+4n and E 6 groups. The general discussion of SU 5+m is given, then the SU 6 and SU 7 are considered. In SU 6 the 15+6 * +6 * fermion representations are used, which are not same as others in fermion content, Yukawa coupling and broken scales. A conception of clans of particles, which are not families, is suggested. These clans consist of extra Z bosons and the corresponding fermions of the scale. The all of fermions in the clans are down quarks except for the standard model which consists of Z bosons and 15 fermions, therefore, the spectrum of the hadrons which are composed of these down quarks are different from hadrons at present

  9. CLIC expands to include the Southern Hemisphere

    CERN Multimedia

    Roberto Cantoni

    2010-01-01

    Australia has recently joined the CLIC collaboration: the enlargement will bring new expertise and resources to the project, and is especially welcome in the wake of CERN budget redistributions following the recent adoption of the Medium Term Plan.   The countries involved in CLIC collaboration With the signing of a Memorandum of Understanding on 26 August 2010, the ACAS network (Australian Collaboration for Accelerator Science) became the 40th member of in the multilateral CLIC collaboration making Australia the 22nd country to join the collaboration. “The new MoU was signed by the ACAS network, which includes the Australian Synchrotron and the University of Melbourne”, explains Jean-Pierre Delahaye, CLIC Study Leader. “Thanks to their expertise, the Australian institutes will contribute greatly to the CLIC damping rings and the two-beam test modules." Institutes from any country wishing to join the CLIC collaboration are invited to assume responsibility o...

  10. Musculoskeletal ultrasound including definitions for ultrasonographic pathology

    DEFF Research Database (Denmark)

    Wakefield, RJ; Balint, PV; Szkudlarek, Marcin

    2005-01-01

    Ultrasound (US) has great potential as an outcome in rheumatoid arthritis trials for detecting bone erosions, synovitis, tendon disease, and enthesopathy. It has a number of distinct advantages over magnetic resonance imaging, including good patient tolerability and ability to scan multiple joints...... in a short period of time. However, there are scarce data regarding its validity, reproducibility, and responsiveness to change, making interpretation and comparison of studies difficult. In particular, there are limited data describing standardized scanning methodology and standardized definitions of US...... pathologies. This article presents the first report from the OMERACT ultrasound special interest group, which has compared US against the criteria of the OMERACT filter. Also proposed for the first time are consensus US definitions for common pathological lesions seen in patients with inflammatory arthritis....

  11. Education Program on Fossil Resources Including Coal

    Science.gov (United States)

    Usami, Masahiro

    Fossil fuels including coal play a key role as crucial energies in contributing to economic development in Asia. On the other hand, its limited quantity and the environmental problems causing from its usage have become a serious global issue and a countermeasure to solve such problems is very much demanded. Along with the pursuit of sustainable development, environmentally-friendly use of highly efficient fossil resources should be therefore, accompanied. Kyushu-university‧s sophisticated research through long years of accumulated experience on the fossil resources and environmental sectors together with the advanced large-scale commercial and empirical equipments will enable us to foster cooperative research and provide internship program for the future researchers. Then, this program is executed as a consignment business from the Ministry of Economy, Trade and Industry from 2007 fiscal year to 2009 fiscal year. The lecture that uses the textbooks developed by this program is scheduled to be started a course in fiscal year 2010.

  12. Should Broca's area include Brodmann area 47?

    Science.gov (United States)

    Ardila, Alfredo; Bernal, Byron; Rosselli, Monica

    2017-02-01

    Understanding brain organization of speech production has been a principal goal of neuroscience. Historically, brain speech production has been associated with so-called Broca’s area (Brodmann area –BA- 44 and 45), however, modern neuroimaging developments suggest speech production is associated with networks rather than with areas. The purpose of this paper was to analyze the connectivity of BA47 ( pars orbitalis) in relation to language . A meta-analysis was conducted to assess the language network in which BA47 is involved. The Brainmap database was used. Twenty papers corresponding to 29 experimental conditions with a total of 373 subjects were included. Our results suggest that BA47 participates in a “frontal language production system” (or extended Broca’s system). The BA47  connectivity found is also concordant with a minor role in language semantics. BA47 plays a central role in the language production system.

  13. Pulmonary disorders, including vocal cord dysfunction.

    Science.gov (United States)

    Greenberger, Paul A; Grammer, Leslie C

    2010-02-01

    The lung is a very complex immunologic organ and responds in a variety of ways to inhaled antigens, organic or inorganic materials, infectious or saprophytic agents, fumes, and irritants. There might be airways obstruction, restriction, neither, or both accompanied by inflammatory destruction of the pulmonary interstitium, alveoli, or bronchioles. This review focuses on diseases organized by their predominant immunologic responses, either innate or acquired. Pulmonary innate immune conditions include transfusion-related acute lung injury, World Trade Center cough, and acute respiratory distress syndrome. Adaptive immunity responses involve the systemic and mucosal immune systems, activated lymphocytes, cytokines, and antibodies that produce CD4(+) T(H)1 phenotypes, such as for tuberculosis or acute forms of hypersensitivity pneumonitis, and CD4(+) T(H)2 phenotypes, such as for asthma, Churg-Strauss syndrome, and allergic bronchopulmonary aspergillosis. Copyright 2010 American Academy of Allergy, Asthma & Immunology. Published by Mosby, Inc. All rights reserved.

  14. CERN Technical Training: LABVIEW courses include RADE

    CERN Multimedia

    HR Department

    2009-01-01

    The contents of the "LabView Basic I" and "LabView Intermediate II" courses have recently been changed to include, respectively, an introduction to and expert training in the Rapid Application Development Environment (RADE). RADE is a LabView-based application developed at CERN to integrate LabView in the accelerator and experiment control infrastructure. It is a suitable solution to developing expert tools, machine development analysis and independent test facilities. The course names have also been changed to "LabVIEW Basics I with RADE Introduction" and "LabVIEW Intermediate II with Advanced RADE Application". " LabVIEW Basics I with RADE Introduction" is designed for: Users preparing to develop applications using LabVIEW, or NI Developer Suite; users and technical managers evaluating LabVIEW or NI Developer Suite in purchasing decisions; users pursuing the Certified LabVIEW Developer certification. The course pr...

  15. CERN Technical Training: LABVIEW courses include RADE

    CERN Multimedia

    HR Department

    2009-01-01

    The contents of "LabView Basic I" and "LabView Intermediate II" trainings have been recently changed to include, respectively, an introduction and an expert training on the Rapid Application Development Environment (RADE). RADE is a LabView-based application developed at CERN to integrate LabView in the accelerator and experiment control infrastructure. It is a suitable solution to develop expert tools, machine development analysis and independent test facilities. The course names have also been changed to "LabVIEW Basics I with RADE Introduction" and "LabVIEW Intermediate II with Advanced RADE Application". " LabVIEW Basics I with RADE Introduction" is designed for: Users preparing to develop applications using LabVIEW, or NI Developer Suite; users and technical managers evaluating LabVIEW or NI Developer Suite in purchasing decisions; users pursuing the Certified LabVIEW Developer certification. The course prepare...

  16. CERN Technical Training: LABVIEW courses include RADE

    CERN Multimedia

    HR Department

    2009-01-01

    The contents of the "LabView Basic I" and "LabView Intermediate II" courses have recently been changed to include, respectively, an introduction to and expert training in the Rapid Application Development Environment (RADE). RADE is a LabView-based application developed at CERN to integrate LabView in the accelerator and experiment control infrastructure. It is a suitable solution to developing expert tools, machine development analysis and independent test facilities. The course names have also been changed to "LabVIEW Basics I with RADE Introduction" and "LabVIEW Intermediate II with Advanced RADE Application". " LabVIEW Basics I with RADE Introduction" is designed for: Users preparing to develop applications using LabVIEW, or NI Developer Suite; users and technical managers evaluating LabVIEW or NI Developer Suite in purchasing decisions; users pursuing the Certified LabVIEW Developer certification. The course prepares participants to develop test and measurement, da...

  17. AMS at the ANU including biomedical applications

    International Nuclear Information System (INIS)

    Fifield, L.K.; Allan, G.L.; Cresswell, R.G.; Ophel, T.R.; King, S.J.; Day, J.P.

    1993-01-01

    An extensive accelerator mass spectrometry program has been conducted on the 14UD accelerator at the Australian National University since 1986. In the two years since the previous conference, the research program has expanded significantly to include biomedical applications of 26 Al and studies of landform evolution using isotopes produced in situ in surface rocks by cosmic ray bombardment. The system is now used for the measurement of 10 Be, 14 C, 26 Al, 36 Cl, 59 Ni and 129 I, and research is being undertaken in hydrology, environmental geochemistry, archaeology and biomedicine. On the technical side, a new test system has permitted the successful off-line development of a high-intensity ion source. A new injection line to the 14UD has been established and the new source is now in position and providing beams to the accelerator. 4 refs

  18. AMS at the ANU including biomedical applications

    Energy Technology Data Exchange (ETDEWEB)

    Fifield, L.K.; Allan, G.L.; Cresswell, R.G.; Ophel, T.R. [Australian National Univ., Canberra, ACT (Australia); King, S.J.; Day, J.P. [Manchester Univ. (United Kingdom). Dept. of Chemistry

    1993-12-31

    An extensive accelerator mass spectrometry program has been conducted on the 14UD accelerator at the Australian National University since 1986. In the two years since the previous conference, the research program has expanded significantly to include biomedical applications of {sup 26}Al and studies of landform evolution using isotopes produced in situ in surface rocks by cosmic ray bombardment. The system is now used for the measurement of {sup 10}Be, {sup 14}C, {sup 26}Al, {sup 36}Cl, {sup 59}Ni and {sup 129}I, and research is being undertaken in hydrology, environmental geochemistry, archaeology and biomedicine. On the technical side, a new test system has permitted the successful off-line development of a high-intensity ion source. A new injection line to the 14UD has been established and the new source is now in position and providing beams to the accelerator. 4 refs.

  19. Protein deamidation

    OpenAIRE

    Robinson, Noah E.

    2002-01-01

    A completely automatic computerized technique for the quantitative estimation of the deamidation rates of any protein for which the three-dimensional structure is known has been developed. Calculations of the specific deamidation rates of 170,014 asparaginyl residues in 13,335 proteins have been carried out. The calculated values have good quantitative reliability when compared with experimental measurements. These rates demonstrate that deamidation may be a biologically ...

  20. A micromanipulation cell including a tool changer

    Science.gov (United States)

    Clévy, Cédric; Hubert, Arnaud; Agnus, Joël; Chaillet, Nicolas

    2005-10-01

    This paper deals with the design, fabrication and characterization of a tool changer for micromanipulation cells. This tool changer is part of a manipulation cell including a three linear axes robot and a piezoelectric microgripper. All these parts are designed to perform micromanipulation tasks in confined spaces such as a microfactory or in the chamber of a scanning electron microscope (SEM). The tool changer principle is to fix a pair of tools (i.e. the gripper tips) either on the tips of the microgripper actuator (piezoceramic bulk) or on a tool magazine. The temperature control of a thermal glue enables one to fix or release this pair of tools. Liquefaction and solidification are generated by surface mounted device (SMD) resistances fixed on the surface of the actuator or magazine. Based on this principle, the tool changer can be adapted to other kinds of micromanipulation cells. Hundreds of automatic tool exchanges were performed with a maximum positioning error between two consecutive tool exchanges of 3.2 µm, 2.3 µm and 2.8 µm on the X, Y and Z axes respectively (Z refers to the vertical axis). Finally, temperature measurements achieved under atmospheric pressure and in a vacuum environment and pressure measurements confirm the possibility of using this device in the air as well as in a SEM.

  1. Robust Unit Commitment Including Frequency Stability Constraints

    Directory of Open Access Journals (Sweden)

    Felipe Pérez-Illanes

    2016-11-01

    Full Text Available An increased use of variable generation technologies such as wind power and photovoltaic generation can have important effects on system frequency performance during normal operation as well as contingencies. The main reasons are the operational principles and inherent characteristics of these power plants like operation at maximum power point and no inertial response during power system imbalances. This has led to new challenges for Transmission System Operators in terms of ensuring system security during contingencies. In this context, this paper proposes a Robust Unit Commitment including a set of additional frequency stability constraints. To do this, a simplified dynamic model of the initial system frequency response is used in combination with historical frequency nadir data during contingencies. The proposed approach is especially suitable for power systems with cost-based economic dispatch like those in most Latin American countries. The study is done considering the Northern Interconnected System of Chile, a 50-Hz medium size isolated power system. The results obtained were validated by means of dynamic simulations of different system contingencies.

  2. Unifying all elementary particle forces including gravity

    International Nuclear Information System (INIS)

    Terazawa, H.

    1979-01-01

    It is a final goal in physics to unify all four basic forces, strong, weak, electromagnetic and gravitational. First, the unified gauge theories of strong, weak and electromagnetic interactions are discussed. There are two standard models, the model of Pati and Salam in which leptons have the fourth color, and the model of Georgi and Glashow in which a simple group SU (5) is assumed for grand unification. Two mass relations for leptons and quarks were derived, and the extension of the Georgi-Glashow model to a grand unified model of SU (6) gauge group has been made. The quantization of the electric charge of elementary particles is one of the most satisfactory features in grand unified gauge theories. The constraint relations between the gauge couplings, the weak mixing angle and the mass scale of symmetry breaking owing to the renormalization effect are not so severe as those in the grand unified models. However, the mass scale becomes far above the Planck mass in some cases. The baryon number non-conservation is one of the most intriguing features common to grand unified gauge theories. The unified models of all elementary particle forces including gravity are discussed. The discovery of weak vector bosons and the production of subquark pairs are anticipated. (Kako, I.)

  3. SEEPAGE MODEL FOR PA INCLUDING DRIFT COLLAPSE

    International Nuclear Information System (INIS)

    C. Tsang

    2004-01-01

    The purpose of this report is to document the predictions and analyses performed using the seepage model for performance assessment (SMPA) for both the Topopah Spring middle nonlithophysal (Tptpmn) and lower lithophysal (Tptpll) lithostratigraphic units at Yucca Mountain, Nevada. Look-up tables of seepage flow rates into a drift (and their uncertainty) are generated by performing numerical simulations with the seepage model for many combinations of the three most important seepage-relevant parameters: the fracture permeability, the capillary-strength parameter 1/a, and the percolation flux. The percolation flux values chosen take into account flow focusing effects, which are evaluated based on a flow-focusing model. Moreover, multiple realizations of the underlying stochastic permeability field are conducted. Selected sensitivity studies are performed, including the effects of an alternative drift geometry representing a partially collapsed drift from an independent drift-degradation analysis (BSC 2004 [DIRS 166107]). The intended purpose of the seepage model is to provide results of drift-scale seepage rates under a series of parameters and scenarios in support of the Total System Performance Assessment for License Application (TSPA-LA). The SMPA is intended for the evaluation of drift-scale seepage rates under the full range of parameter values for three parameters found to be key (fracture permeability, the van Genuchten 1/a parameter, and percolation flux) and drift degradation shape scenarios in support of the TSPA-LA during the period of compliance for postclosure performance [Technical Work Plan for: Performance Assessment Unsaturated Zone (BSC 2002 [DIRS 160819], Section I-4-2-1)]. The flow-focusing model in the Topopah Spring welded (TSw) unit is intended to provide an estimate of flow focusing factors (FFFs) that (1) bridge the gap between the mountain-scale and drift-scale models, and (2) account for variability in local percolation flux due to

  4. [Contracts including performance and management of uncertainty].

    Science.gov (United States)

    Duru, G; Garassus, P; Auray, J-P

    2013-09-01

    Since many decades in France, the most important part of ambulatory health care expenditure is represented by drug consumption. By the fact, French patient is indeed the greatest world consumer of pharmaceuticals treatments. Therefore, the regulation authorities by successive strategies, attempt to limit or even restrict market access for new drugs in the health care sector secured by public social insurance coverage. Common objectives are to assess the reimbursement to scientific studies and to fix the price of therapeutics at an acceptable level for both industries and government. New trends try then to determine recently the drug price in a dual approach, as a component of global and effective contract, including performance and outcome. The first diffusion authorization is diffusion concerned, but this concept takes into account the eventual success of new produces in long-term survey. Signed for a fixed period as reciprocal partnership between regulation authorities and pharmaceutics industries, the contract integrates two dimensions of incertitude. The first one is represented by the strategy of new treatments development according to efficacy and adapted price, and the second one is linked to the result of diffusion and determines adapted rules if eventual non-respects of the previous engagement are registered. This paper discusses problems related to this new dimension of incertitude affected by conditional drug prices in market access strategy and the adapted follow-up of new treatment diffusion fixed by "outcome" contract between French regulation administration and pharmaceutics industries in our recent economic context. Copyright © 2013 Elsevier Masson SAS. All rights reserved.

  5. Resection of thymoma should include nodal sampling.

    Science.gov (United States)

    Weksler, Benny; Pennathur, Arjun; Sullivan, Jennifer L; Nason, Katie S

    2015-03-01

    Thymoma is best treated by surgical resection; however, no clear guidelines have been created regarding lymph node sampling at the time of resection. Additionally, the prognostic implications of nodal metastases are unclear. The aim of this study was to analyze the prognostic implications of nodal metastases in thymoma. The Surveillance, Epidemiology, and End Results database was queried for patients who underwent surgical resection of thymoma with documented pathologic examination of lymph nodes. The impact of nodal status on survival and thymoma staging was examined. We identified 442 patients who underwent thymoma resection with pathologic evaluation of 1 or more lymph nodes. A median of 2 nodes were sampled per patient. Fifty-nine patients (59 of 442, 13.3%) had ≥ 1 positive node. Patients with positive nodes were younger and had smaller tumors than node-negative patients. Median survival in the node-positive patients was 98 months, compared with 144 months in node-negative patients (P = .013). In multivariable analysis, the presence of positive nodes had a significant, independent, adverse impact on survival (hazard ratio 1.945, 95% confidence interval 1.296-2.919, P = .001). The presence of nodal metastases resulted in a change in classification to a higher stage in 80% of patients, the majority from Masaoka-Koga stage III to stage IV. Nodal status seems to be an important prognostic factor in patients with thymoma. Until the prognostic significance of nodal metastases is better understood, surgical therapy for thymoma should include sampling of regional lymph nodes. Copyright © 2015 The American Association for Thoracic Surgery. Published by Elsevier Inc. All rights reserved.

  6. Protein Crystallizability.

    Science.gov (United States)

    Smialowski, Pawel; Wong, Philip

    2016-01-01

    Obtaining diffracting quality crystals remains a major challenge in protein structure research. We summarize and compare methods for selecting the best protein targets for crystallization, construct optimization and crystallization condition design. Target selection methods are divided into algorithms predicting the chance of successful progression through all stages of structural determination (from cloning to solving the structure) and those focusing only on the crystallization step. We tried to highlight pros and cons of different approaches examining the following aspects: data size, redundancy and representativeness, overfitting during model construction, and results evaluation. In summary, although in recent years progress was made and several sequence properties were reported to be relevant for crystallization, the successful prediction of protein crystallization behavior and selection of corresponding crystallization conditions continue to challenge structural researchers.

  7. Metagenomics and the protein universe

    Science.gov (United States)

    Godzik, Adam

    2011-01-01

    Metagenomics sequencing projects have dramatically increased our knowledge of the protein universe and provided over one-half of currently known protein sequences; they have also introduced a much broader phylogenetic diversity into the protein databases. The full analysis of metagenomic datasets is only beginning, but it has already led to the discovery of thousands of new protein families, likely representing novel functions specific to given environments. At the same time, a deeper analysis of such novel families, including experimental structure determination of some representatives, suggests that most of them represent distant homologs of already characterized protein families, and thus most of the protein diversity present in the new environments are due to functional divergence of the known protein families rather than the emergence of new ones. PMID:21497084

  8. Bioinformatic Prediction of WSSV-Host Protein-Protein Interaction

    Directory of Open Access Journals (Sweden)

    Zheng Sun

    2014-01-01

    Full Text Available WSSV is one of the most dangerous pathogens in shrimp aquaculture. However, the molecular mechanism of how WSSV interacts with shrimp is still not very clear. In the present study, bioinformatic approaches were used to predict interactions between proteins from WSSV and shrimp. The genome data of WSSV (NC_003225.1 and the constructed transcriptome data of F. chinensis were used to screen potentially interacting proteins by searching in protein interaction databases, including STRING, Reactome, and DIP. Forty-four pairs of proteins were suggested to have interactions between WSSV and the shrimp. Gene ontology analysis revealed that 6 pairs of these interacting proteins were classified into “extracellular region” or “receptor complex” GO-terms. KEGG pathway analysis showed that they were involved in the “ECM-receptor interaction pathway.” In the 6 pairs of interacting proteins, an envelope protein called “collagen-like protein” (WSSV-CLP encoded by an early virus gene “wsv001” in WSSV interacted with 6 deduced proteins from the shrimp, including three integrin alpha (ITGA, two integrin beta (ITGB, and one syndecan (SDC. Sequence analysis on WSSV-CLP, ITGA, ITGB, and SDC revealed that they possessed the sequence features for protein-protein interactions. This study might provide new insights into the interaction mechanisms between WSSV and shrimp.

  9. Combinable protein crop production

    OpenAIRE

    Wright, Isobel

    2008-01-01

    This research topic review aims to summarise research knowledge and observational experience of combinable protein crop production in organic farming systems for the UK. European research on peas, faba beans and lupins is included; considering their role in the rotation, nitrogen fixation, varieties, establishment, weed control, yields, problems experienced and intercropping with cereals.

  10. Protein kinase substrate identification on functional protein arrays

    Directory of Open Access Journals (Sweden)

    Zhou Fang

    2008-02-01

    Full Text Available Abstract Background Over the last decade, kinases have emerged as attractive therapeutic targets for a number of different diseases, and numerous high throughput screening efforts in the pharmaceutical community are directed towards discovery of compounds that regulate kinase function. The emerging utility of systems biology approaches has necessitated the development of multiplex tools suitable for proteomic-scale experiments to replace lower throughput technologies such as mass spectroscopy for the study of protein phosphorylation. Recently, a new approach for identifying substrates of protein kinases has applied the miniaturized format of functional protein arrays to characterize phosphorylation for thousands of candidate protein substrates in a single experiment. This method involves the addition of protein kinases in solution to arrays of immobilized proteins to identify substrates using highly sensitive radioactive detection and hit identification algorithms. Results To date, the factors required for optimal performance of protein array-based kinase substrate identification have not been described. In the current study, we have carried out a detailed characterization of the protein array-based method for kinase substrate identification, including an examination of the effects of time, buffer compositions, and protein concentration on the results. The protein array approach was compared to standard solution-based assays for assessing substrate phosphorylation, and a correlation of greater than 80% was observed. The results presented here demonstrate how novel substrates for protein kinases can be quickly identified from arrays containing thousands of human proteins to provide new clues to protein kinase function. In addition, a pooling-deconvolution strategy was developed and applied that enhances characterization of specific kinase-substrate relationships and decreases reagent consumption. Conclusion Functional protein microarrays are an

  11. Essential Protein Detection by Random Walk on Weighted Protein-Protein Interaction Networks.

    Science.gov (United States)

    Xu, Bin; Guan, Jihong; Wang, Yang; Wang, Zewei

    2017-05-12

    Essential proteins are critical to the development and survival of cells. Identification of essential proteins is helpful for understanding the minimal set of required genes in a living cell and for designing new drugs. To detect essential proteins, various computational methods have been proposed based on protein-protein interaction (PPI) networks. However, protein interaction data obtained by highthroughput experiments usually contain high false positives, which negatively impacts the accuracy of essential protein detection. Moreover, most existing studies focused on the local information of proteins in PPI networks, while ignoring the influence of indirect protein interactions on essentiality. In this paper, we propose a novel method, called Essentiality Ranking (EssRank in short), to boost the accuracy of essential protein detection. To deal with the inaccuracy of PPI data, confidence scores of interactions are evaluated by integrating various biological information. Weighted edge clustering coefficient (WECC), considering both interaction confidence scores and network topology, is proposed to calculate edge weights in PPI networks. The weight of each node is evaluated by the sum of WECC values of its linking edges. A random walk method, making use of both direct and indirect protein interactions, is then employed to calculate protein essentiality iteratively. Experimental results on the yeast PPI network show that EssRank outperforms most existing methods, including the most commonly-used centrality measures (SC, DC, BC, CC, IC, EC), topology based methods (DMNC and NC) and the data integrating method IEW.

  12. Website on Protein Interaction and Protein Structure Related Work

    Science.gov (United States)

    Samanta, Manoj; Liang, Shoudan; Biegel, Bryan (Technical Monitor)

    2003-01-01

    In today's world, three seemingly diverse fields - computer information technology, nanotechnology and biotechnology are joining forces to enlarge our scientific knowledge and solve complex technological problems. Our group is dedicated to conduct theoretical research exploring the challenges in this area. The major areas of research include: 1) Yeast Protein Interactions; 2) Protein Structures; and 3) Current Transport through Small Molecules.

  13. Uncertainty Analysis of Power Systems Using Collocation

    Science.gov (United States)

    2008-05-01

    sensitivity can be inferred and to construct surrogate models with which interpolation can be used to propagate PDF ?s. These techniques are applied to...with time and use. There is significant environmental interaction in the form of wind and waves; a large wave can partially of fully expose the...Power System We analyze uncertainty in a Simulink model describing the operation of a large pulse load reflecting the power consumption of a rail gun [8

  14. Improving academic literacy by teaching collocations

    African Journals Online (AJOL)

    Kate H

    dimensions: a social (exchange information), cognitive (understand, organise and reason about information) as well as a linguistic (language) dimension” (cf. also Nizonkiza and Van Dyk. (2015:152). More specifically, the linguistic dimension of academic literacy and writing skills in particular are relevant for this study.

  15. Protein folding on a chip

    CERN Multimedia

    2004-01-01

    "Scientists at the U.S. Department of Energy's Brookhaven National Laboratory are proposing to use a super- computer originally developed to simulate elementary particles in high- energy physics to help determine the structures and functions of proteins, including, for example, the 30,000 or so proteins encoded by the human genome" (1 page)

  16. Ionic liquids, electrolyte solutions including the ionic liquids, and energy storage devices including the ionic liquids

    Science.gov (United States)

    Gering, Kevin L.; Harrup, Mason K.; Rollins, Harry W.

    2015-12-08

    An ionic liquid including a phosphazene compound that has a plurality of phosphorus-nitrogen units and at least one pendant group bonded to each phosphorus atom of the plurality of phosphorus-nitrogen units. One pendant group of the at least one pendant group comprises a positively charged pendant group. Additional embodiments of ionic liquids are disclosed, as are electrolyte solutions and energy storage devices including the embodiments of the ionic liquid.

  17. Exploiting amino acid composition for predicting protein-protein interactions.

    Directory of Open Access Journals (Sweden)

    Sushmita Roy

    2009-11-01

    Full Text Available Computational prediction of protein interactions typically use protein domains as classifier features because they capture conserved information of interaction surfaces. However, approaches relying on domains as features cannot be applied to proteins without any domain information. In this paper, we explore the contribution of pure amino acid composition (AAC for protein interaction prediction. This simple feature, which is based on normalized counts of single or pairs of amino acids, is applicable to proteins from any sequenced organism and can be used to compensate for the lack of domain information.AAC performed at par with protein interaction prediction based on domains on three yeast protein interaction datasets. Similar behavior was obtained using different classifiers, indicating that our results are a function of features and not of classifiers. In addition to yeast datasets, AAC performed comparably on worm and fly datasets. Prediction of interactions for the entire yeast proteome identified a large number of novel interactions, the majority of which co-localized or participated in the same processes. Our high confidence interaction network included both well-studied and uncharacterized proteins. Proteins with known function were involved in actin assembly and cell budding. Uncharacterized proteins interacted with proteins involved in reproduction and cell budding, thus providing putative biological roles for the uncharacterized proteins.AAC is a simple, yet powerful feature for predicting protein interactions, and can be used alone or in conjunction with protein domains to predict new and validate existing interactions. More importantly, AAC alone performs at par with existing, but more complex, features indicating the presence of sequence-level information that is predictive of interaction, but which is not necessarily restricted to domains.

  18. Intracellular Protein Delivery for Treating Breast Cancer

    Science.gov (United States)

    2014-08-01

    Intracellular delivery of such proteins, including human tumor suppressors (such as p53) (Brown et al., 2009) and exogenous tumor-killing proteins...vivo systems. Nature materials 11, 1038-1043. Chorny, M., Hood, E., Levy, R.J., and Muzykantov, V.R. (2010). Endothelial delivery of antioxidant ...for the ntracellular delivery of such proteins, including human umor suppressors [7] and exogenous tumor-killing proteins 8—10]), is attractive as a

  19. High throughput protein production screening

    Science.gov (United States)

    Beernink, Peter T [Walnut Creek, CA; Coleman, Matthew A [Oakland, CA; Segelke, Brent W [San Ramon, CA

    2009-09-08

    Methods, compositions, and kits for the cell-free production and analysis of proteins are provided. The invention allows for the production of proteins from prokaryotic sequences or eukaryotic sequences, including human cDNAs using PCR and IVT methods and detecting the proteins through fluorescence or immunoblot techniques. This invention can be used to identify optimized PCR and WT conditions, codon usages and mutations. The methods are readily automated and can be used for high throughput analysis of protein expression levels, interactions, and functional states.

  20. NMR Studies of Protein Hydration and Protein-Ligand Interactions

    Science.gov (United States)

    Chong, Yuan

    Water on the surface of a protein is called hydration water. Hydration water is known to play a crucial role in a variety of biological processes including protein folding, enzymatic activation, and drug binding. Although the significance of hydration water has been recognized, the underlying mechanism remains far from being understood. This dissertation employs a unique in-situ nuclear magnetic resonance (NMR) technique to study the mechanism of protein hydration and the role of hydration in alcohol-protein interactions. Water isotherms in proteins are measured at different temperatures via the in-situ NMR technique. Water is found to interact differently with hydrophilic and hydrophobic groups on the protein. Water adsorption on hydrophilic groups is hardly affected by the temperature, while water adsorption on hydrophobic groups strongly depends on the temperature around 10 C, below which the adsorption is substantially reduced. This effect is induced by the dramatic decrease in the protein flexibility below 10 C. Furthermore, nanosecond to microsecond protein dynamics and the free energy, enthalpy, and entropy of protein hydration are studied as a function of hydration level and temperature. A crossover at 10 C in protein dynamics and thermodynamics is revealed. The effect of water at hydrophilic groups on protein dynamics and thermodynamics shows little temperature dependence, whereas water at hydrophobic groups has stronger effect above 10 C. In addition, I investigate the role of water in alcohol binding to the protein using the in-situ NMR detection. The isotherms of alcohols are first measured on dry proteins, then on proteins with a series of controlled hydration levels. The free energy, enthalpy, and entropy of alcohol binding are also determined. Two distinct types of alcohol binding are identified. On the one hand, alcohols can directly bind to a few specific sites on the protein. This type of binding is independent of temperature and can be

  1. Protein Polymers and Amyloids

    DEFF Research Database (Denmark)

    Risør, Michael Wulff

    2014-01-01

    Several human disorders are caused by a common general disease mechanism arising from abnormal folding and aggregation of the underlying protein. These include the prevalent dementias like Alzheimer’s and Parkinson’s, where accumulation of protein fibrillar structures, known as amyloid fibrils...... that inhibits its target protease through a large conformational change but mutations compromise this function and cause premature structural collapse into hyperstable polymers. Understanding the conformational disorders at a molecular level is not only important for our general knowledge on protein folding......, underlining the importance of understanding this relationship. The monomeric C-36 peptide was investigated by liquid-state NMR spectroscopy and found to be intrinsically disordered with minor propensities towards β-sheet structure. The plasticity of such a peptide makes it suitable for a whole range...

  2. Polarizable protein packing

    KAUST Repository

    Ng, Albert H.

    2011-01-24

    To incorporate protein polarization effects within a protein combinatorial optimization framework, we decompose the polarizable force field AMOEBA into low order terms. Including terms up to the third-order provides a fair approximation to the full energy while maintaining tractability. We represent the polarizable packing problem for protein G as a hypergraph and solve for optimal rotamers with the FASTER combinatorial optimization algorithm. These approximate energy models can be improved to high accuracy [root mean square deviation (rmsd) < 1 kJ mol -1] via ridge regression. The resulting trained approximations are used to efficiently identify new, low-energy solutions. The approach is general and should allow combinatorial optimization of other many-body problems. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011 Copyright © 2011 Wiley Periodicals, Inc.

  3. Interactions between soy protein hydrolyzates and wheat proteins in noodle making dough.

    Science.gov (United States)

    Guo, Xingfeng; Sun, Xiaohong; Zhang, Yingying; Wang, Ruihong; Yan, Xin

    2018-04-15

    Soy protein hydrolyzate has been used as supplements in wheat flour to enhance the nutritional value of its products, but it may negatively affect the gluten properties simultaneously. In order to explore the mechanism of this effect, protein characteristics including disulfide bond, protein composition, intermolecular force of dough proteins, and atomic force microscope images of gluten were obtained. Results showed that disulfide bonds in dough increased when soy protein hydrolyzate was added, but glutenin macropolymer decreased. Atomic force microscope images showed that gluten were weakened by soy protein hydrolyzate. Based on these results, a model was developed to describe the interaction between soy protein hydrolyzates and wheat proteins: soy protein hydrolyzates linked with wheat proteins through disulfide bond, disrupted the glutenins polymerization, thus hindered gluten networks formation. The interaction between wheat proteins and soy protein hydrolyzates in noodle making dough could be described with this model reasonably. Copyright © 2017 Elsevier Ltd. All rights reserved.

  4. Catalyst support structure, catalyst including the structure, reactor including a catalyst, and methods of forming same

    Science.gov (United States)

    Van Norman, Staci A.; Aston, Victoria J.; Weimer, Alan W.

    2017-05-09

    Structures, catalysts, and reactors suitable for use for a variety of applications, including gas-to-liquid and coal-to-liquid processes and methods of forming the structures, catalysts, and reactors are disclosed. The catalyst material can be deposited onto an inner wall of a microtubular reactor and/or onto porous tungsten support structures using atomic layer deposition techniques.

  5. The Protein 4.1 family: hub proteins in animals for organizing membrane proteins.

    Science.gov (United States)

    Baines, Anthony J; Lu, Hui-Chun; Bennett, Pauline M

    2014-02-01

    Proteins of the 4.1 family are characteristic of eumetazoan organisms. Invertebrates contain single 4.1 genes and the Drosophila model suggests that 4.1 is essential for animal life. Vertebrates have four paralogues, known as 4.1R, 4.1N, 4.1G and 4.1B, which are additionally duplicated in the ray-finned fish. Protein 4.1R was the first to be discovered: it is a major mammalian erythrocyte cytoskeletal protein, essential to the mechanochemical properties of red cell membranes because it promotes the interaction between spectrin and actin in the membrane cytoskeleton. 4.1R also binds certain phospholipids and is required for the stable cell surface accumulation of a number of erythrocyte transmembrane proteins that span multiple functional classes; these include cell adhesion molecules, transporters and a chemokine receptor. The vertebrate 4.1 proteins are expressed in most tissues, and they are required for the correct cell surface accumulation of a very wide variety of membrane proteins including G-Protein coupled receptors, voltage-gated and ligand-gated channels, as well as the classes identified in erythrocytes. Indeed, such large numbers of protein interactions have been mapped for mammalian 4.1 proteins, most especially 4.1R, that it appears that they can act as hubs for membrane protein organization. The range of critical interactions of 4.1 proteins is reflected in disease relationships that include hereditary anaemias, tumour suppression, control of heartbeat and nervous system function. The 4.1 proteins are defined by their domain structure: apart from the spectrin/actin-binding domain they have FERM and FERM-adjacent domains and a unique C-terminal domain. Both the FERM and C-terminal domains can bind transmembrane proteins, thus they have the potential to be cross-linkers for membrane proteins. The activity of the FERM domain is subject to multiple modes of regulation via binding of regulatory ligands, phosphorylation of the FERM associated domain and

  6. Introduction: G Protein-coupled Receptors and RGS Proteins.

    Science.gov (United States)

    Stewart, Adele; Fisher, Rory A

    2015-01-01

    Here, we provide an overview of the role of regulator of G protein-signaling (RGS) proteins in signaling by G protein-coupled receptors (GPCRs), the latter of which represent the largest class of cell surface receptors in humans responsible for transducing diverse extracellular signals into the intracellular environment. Given that GPCRs regulate virtually every known physiological process, it is unsurprising that their dysregulation plays a causative role in many human diseases and they are targets of 40-50% of currently marketed pharmaceuticals. Activated GPCRs function as GTPase exchange factors for Gα subunits of heterotrimeric G proteins, promoting the formation of Gα-GTP and dissociated Gβγ subunits that regulate diverse effectors including enzymes, ion channels, and protein kinases. Termination of signaling is mediated by the intrinsic GTPase activity of Gα subunits leading to reformation of the inactive Gαβγ heterotrimer. RGS proteins determine the magnitude and duration of cellular responses initiated by many GPCRs by functioning as GTPase-accelerating proteins (GAPs) for specific Gα subunits. Twenty canonical mammalian RGS proteins, divided into four subfamilies, act as functional GAPs while almost 20 additional proteins contain nonfunctional RGS homology domains that often mediate interaction with GPCRs or Gα subunits. RGS protein biochemistry has been well elucidated in vitro, but the physiological functions of each RGS family member remain largely unexplored. This book summarizes recent advances employing modified model organisms that reveal RGS protein functions in vivo, providing evidence that RGS protein modulation of G protein signaling and GPCRs can be as important as initiation of signaling by GPCRs. © 2015 Elsevier Inc. All rights reserved.

  7. Spin-label EPR approaches to protein interactions

    NARCIS (Netherlands)

    Son, Martin van

    2014-01-01

    Protein-protein interactions are essential for various biological processes including cell metabolism, muscle contraction, and signal transduction. The dissertation describes a study of the interaction between the proteins cytochrome c and cytochrome c peroxidase by electron paramagnetic resonance

  8. Kinetics of protein unfolding at interfaces

    International Nuclear Information System (INIS)

    Yano, Yohko F

    2012-01-01

    The conformation of protein molecules is determined by a balance of various forces, including van der Waals attraction, electrostatic interaction, hydrogen bonding, and conformational entropy. When protein molecules encounter an interface, they are often adsorbed on the interface. The conformation of an adsorbed protein molecule strongly depends on the interaction between the protein and the interface. Recent time-resolved investigations have revealed that protein conformation changes during the adsorption process due to the protein-protein interaction increasing with increasing interface coverage. External conditions also affect the protein conformation. This review considers recent dynamic observations of protein adsorption at various interfaces and their implications for the kinetics of protein unfolding at interfaces. (topical review)

  9. Protein Adsorption in Three Dimensions

    Science.gov (United States)

    Vogler, Erwin A.

    2011-01-01

    Recent experimental and theoretical work clarifying the physical chemistry of blood-protein adsorption from aqueous-buffer solution to various kinds of surfaces is reviewed and interpreted within the context of biomaterial applications, especially toward development of cardiovascular biomaterials. The importance of this subject in biomaterials surface science is emphasized by reducing the “protein-adsorption problem” to three core questions that require quantitative answer. An overview of the protein-adsorption literature identifies some of the sources of inconsistency among many investigators participating in more than five decades of focused research. A tutorial on the fundamental biophysical chemistry of protein adsorption sets the stage for a detailed discussion of the kinetics and thermodynamics of protein adsorption, including adsorption competition between two proteins for the same adsorbent immersed in a binary-protein mixture. Both kinetics and steady-state adsorption can be rationalized using a single interpretive paradigm asserting that protein molecules partition from solution into a three-dimensional (3D) interphase separating bulk solution from the physical-adsorbent surface. Adsorbed protein collects in one-or-more adsorbed layers, depending on protein size, solution concentration, and adsorbent surface energy (water wettability). The adsorption process begins with the hydration of an adsorbent surface brought into contact with an aqueous-protein solution. Surface hydration reactions instantaneously form a thin, pseudo-2D interface between the adsorbent and protein solution. Protein molecules rapidly diffuse into this newly-formed interface, creating a truly 3D interphase that inflates with arriving proteins and fills to capacity within milliseconds at mg/mL bulk-solution concentrations CB. This inflated interphase subsequently undergoes time-dependent (minutes-to-hours) decrease in volume VI by expulsion of either-or-both interphase water and

  10. Human cancer protein-protein interaction network: a structural perspective.

    Directory of Open Access Journals (Sweden)

    Gozde Kar

    2009-12-01

    Full Text Available Protein-protein interaction networks provide a global picture of cellular function and biological processes. Some proteins act as hub proteins, highly connected to others, whereas some others have few interactions. The dysfunction of some interactions causes many diseases, including cancer. Proteins interact through their interfaces. Therefore, studying the interface properties of cancer-related proteins will help explain their role in the interaction networks. Similar or overlapping binding sites should be used repeatedly in single interface hub proteins, making them promiscuous. Alternatively, multi-interface hub proteins make use of several distinct binding sites to bind to different partners. We propose a methodology to integrate protein interfaces into cancer interaction networks (ciSPIN, cancer structural protein interface network. The interactions in the human protein interaction network are replaced by interfaces, coming from either known or predicted complexes. We provide a detailed analysis of cancer related human protein-protein interfaces and the topological properties of the cancer network. The results reveal that cancer-related proteins have smaller, more planar, more charged and less hydrophobic binding sites than non-cancer proteins, which may indicate low affinity and high specificity of the cancer-related interactions. We also classified the genes in ciSPIN according to phenotypes. Within phenotypes, for breast cancer, colorectal cancer and leukemia, interface properties were found to be discriminating from non-cancer interfaces with an accuracy of 71%, 67%, 61%, respectively. In addition, cancer-related proteins tend to interact with their partners through distinct interfaces, corresponding mostly to multi-interface hubs, which comprise 56% of cancer-related proteins, and constituting the nodes with higher essentiality in the network (76%. We illustrate the interface related affinity properties of two cancer-related hub

  11. Launch Lock Assemblies Including Axial Gap Amplification Devices and Spacecraft Isolation Systems Including the Same

    Science.gov (United States)

    Barber, Tim Daniel (Inventor); Hindle, Timothy (Inventor); Young, Ken (Inventor); Davis, Torey (Inventor)

    2014-01-01

    Embodiments of a launch lock assembly are provided, as are embodiments of a spacecraft isolation system including one or more launch lock assemblies. In one embodiment, the launch lock assembly includes first and second mount pieces, a releasable clamp device, and an axial gap amplification device. The releasable clamp device normally maintains the first and second mount pieces in clamped engagement; and, when actuated, releases the first and second mount pieces from clamped engagement to allow relative axial motion there between. The axial gap amplification device normally residing in a blocking position wherein the gap amplification device obstructs relative axial motion between the first and second mount pieces. The axial gap amplification device moves into a non-blocking position when the first and second mount pieces are released from clamped engagement to increase the range of axial motion between the first and second mount pieces.

  12. Adhesives from modified soy protein

    Science.gov (United States)

    Sun, Susan [Manhattan, KS; Wang, Donghai [Manhattan, KS; Zhong, Zhikai [Manhattan, KS; Yang, Guang [Shanghai, CN

    2008-08-26

    The present invention provides useful adhesive compositions having similar adhesive properties to conventional UF and PPF resins. The compositions generally include a protein portion and modifying ingredient portion selected from the group consisting of carboxyl-containing compounds, aldehyde-containing compounds, epoxy group-containing compounds, and mixtures thereof. The composition is preferably prepared at a pH level at or near the isoelectric point of the protein. In other preferred forms, the adhesive composition includes a protein portion and a carboxyl-containing group portion.

  13. Aquaporin Protein-Protein Interactions

    Directory of Open Access Journals (Sweden)

    Jennifer Virginia Roche

    2017-10-01

    Full Text Available Aquaporins are tetrameric membrane-bound channels that facilitate transport of water and other small solutes across cell membranes. In eukaryotes, they are frequently regulated by gating or trafficking, allowing for the cell to control membrane permeability in a specific manner. Protein–protein interactions play crucial roles in both regulatory processes and also mediate alternative functions such as cell adhesion. In this review, we summarize recent knowledge about aquaporin protein–protein interactions; dividing the interactions into three types: (1 interactions between aquaporin tetramers; (2 interactions between aquaporin monomers within a tetramer (hetero-tetramerization; and (3 transient interactions with regulatory proteins. We particularly focus on the structural aspects of the interactions, discussing the small differences within a conserved overall fold that allow for aquaporins to be differentially regulated in an organism-, tissue- and trigger-specific manner. A deep knowledge about these differences is needed to fully understand aquaporin function and regulation in many physiological processes, and may enable design of compounds targeting specific aquaporins for treatment of human disease.

  14. Protein function prediction using neighbor relativity in protein-protein interaction network.

    Science.gov (United States)

    Moosavi, Sobhan; Rahgozar, Masoud; Rahimi, Amir

    2013-04-01

    There is a large gap between the number of discovered proteins and the number of functionally annotated ones. Due to the high cost of determining protein function by wet-lab research, function prediction has become a major task for computational biology and bioinformatics. Some researches utilize the proteins interaction information to predict function for un-annotated proteins. In this paper, we propose a novel approach called "Neighbor Relativity Coefficient" (NRC) based on interaction network topology which estimates the functional similarity between two proteins. NRC is calculated for each pair of proteins based on their graph-based features including distance, common neighbors and the number of paths between them. In order to ascribe function to an un-annotated protein, NRC estimates a weight for each neighbor to transfer its annotation to the unknown protein. Finally, the unknown protein will be annotated by the top score transferred functions. We also investigate the effect of using different coefficients for various types of functions. The proposed method has been evaluated on Saccharomyces cerevisiae and Homo sapiens interaction networks. The performance analysis demonstrates that NRC yields better results in comparison with previous protein function prediction approaches that utilize interaction network. Copyright © 2012 Elsevier Ltd. All rights reserved.

  15. Protein immobilization strategies for protein biochips

    NARCIS (Netherlands)

    Rusmini, F.; Rusmini, Federica; Zhong, Zhiyuan; Feijen, Jan

    2007-01-01

    In the past few years, protein biochips have emerged as promising proteomic and diagnostic tools for obtaining information about protein functions and interactions. Important technological innovations have been made. However, considerable development is still required, especially regarding protein

  16. Multiple protonation equilibria in electrostatics of protein-protein binding.

    Science.gov (United States)

    Piłat, Zofia; Antosiewicz, Jan M

    2008-11-27

    All proteins contain groups capable of exchanging protons with their environment. We present here an approach, based on a rigorous thermodynamic cycle and the partition functions for energy levels characterizing protonation states of the associating proteins and their complex, to compute the electrostatic pH-dependent contribution to the free energy of protein-protein binding. The computed electrostatic binding free energies include the pH of the solution as the variable of state, mutual "polarization" of associating proteins reflected as changes in the distribution of their protonation states upon binding and fluctuations between available protonation states. The only fixed property of both proteins is the conformation; the structure of the monomers is kept in the same conformation as they have in the complex structure. As a reference, we use the electrostatic binding free energies obtained from the traditional Poisson-Boltzmann model, computed for a single macromolecular conformation fixed in a given protonation state, appropriate for given solution conditions. The new approach was tested for 12 protein-protein complexes. It is shown that explicit inclusion of protonation degrees of freedom might lead to a substantially different estimation of the electrostatic contribution to the binding free energy than that based on the traditional Poisson-Boltzmann model. This has important implications for the balancing of different contributions to the energetics of protein-protein binding and other related problems, for example, the choice of protein models for Brownian dynamics simulations of their association. Our procedure can be generalized to include conformational degrees of freedom by combining it with molecular dynamics simulations at constant pH. Unfortunately, in practice, a prohibitive factor is an enormous requirement for computer time and power. However, there may be some hope for solving this problem by combining existing constant pH molecular dynamics

  17. Cry protein crystals: a novel platform for protein delivery.

    Science.gov (United States)

    Nair, Manoj S; Lee, Marianne M; Bonnegarde-Bernard, Astrid; Wallace, Julie A; Dean, Donald H; Ostrowski, Michael C; Burry, Richard W; Boyaka, Prosper N; Chan, Michael K

    2015-01-01

    Protein delivery platforms are important tools in the development of novel protein therapeutics and biotechnologies. We have developed a new class of protein delivery agent based on sub-micrometer-sized Cry3Aa protein crystals that naturally form within the bacterium Bacillus thuringiensis. We demonstrate that fusion of the cry3Aa gene to that of various reporter proteins allows for the facile production of Cry3Aa fusion protein crystals for use in subsequent applications. These Cry3Aa fusion protein crystals are efficiently taken up and retained by macrophages and other cell lines in vitro, and can be delivered to mice in vivo via multiple modes of administration. Oral delivery of Cry3Aa fusion protein crystals to C57BL/6 mice leads to their uptake by MHC class II cells, including macrophages in the Peyer's patches, supporting the notion that the Cry3Aa framework can be used to stabilize cargo protein against degradation for delivery to gastrointestinal lymphoid tissues.

  18. Cry protein crystals: a novel platform for protein delivery.

    Directory of Open Access Journals (Sweden)

    Manoj S Nair

    Full Text Available Protein delivery platforms are important tools in the development of novel protein therapeutics and biotechnologies. We have developed a new class of protein delivery agent based on sub-micrometer-sized Cry3Aa protein crystals that naturally form within the bacterium Bacillus thuringiensis. We demonstrate that fusion of the cry3Aa gene to that of various reporter proteins allows for the facile production of Cry3Aa fusion protein crystals for use in subsequent applications. These Cry3Aa fusion protein crystals are efficiently taken up and retained by macrophages and other cell lines in vitro, and can be delivered to mice in vivo via multiple modes of administration. Oral delivery of Cry3Aa fusion protein crystals to C57BL/6 mice leads to their uptake by MHC class II cells, including macrophages in the Peyer's patches, supporting the notion that the Cry3Aa framework can be used to stabilize cargo protein against degradation for delivery to gastrointestinal lymphoid tissues.

  19. Cry Protein Crystals: A Novel Platform for Protein Delivery

    Science.gov (United States)

    Bonnegarde-Bernard, Astrid; Wallace, Julie A.; Dean, Donald H.; Ostrowski, Michael C.; Burry, Richard W.; Boyaka, Prosper N.; Chan, Michael K.

    2015-01-01

    Protein delivery platforms are important tools in the development of novel protein therapeutics and biotechnologies. We have developed a new class of protein delivery agent based on sub-micrometer-sized Cry3Aa protein crystals that naturally form within the bacterium Bacillus thuringiensis. We demonstrate that fusion of the cry3Aa gene to that of various reporter proteins allows for the facile production of Cry3Aa fusion protein crystals for use in subsequent applications. These Cry3Aa fusion protein crystals are efficiently taken up and retained by macrophages and other cell lines in vitro, and can be delivered to mice in vivo via multiple modes of administration. Oral delivery of Cry3Aa fusion protein crystals to C57BL/6 mice leads to their uptake by MHC class II cells, including macrophages in the Peyer’s patches, supporting the notion that the Cry3Aa framework can be used to stabilize cargo protein against degradation for delivery to gastrointestinal lymphoid tissues. PMID:26030844

  20. Electrolyte solutions including a phosphoranimine compound, and energy storage devices including same

    Science.gov (United States)

    Klaehn, John R.; Dufek, Eric J.; Rollins, Harry W.; Harrup, Mason K.; Gering, Kevin L.

    2017-09-12

    An electrolyte solution comprising at least one phosphoranimine compound and a metal salt. The at least one phosphoranimine compound comprises a compound of the chemical structure ##STR00001## where X is an organosilyl group or a tert-butyl group and each of R.sup.1, R.sup.2, and R.sup.3 is independently selected from the group consisting of an alkyl group, an aryl group, an alkoxy group, or an aryloxy group. An energy storage device including the electrolyte solution is also disclosed.

  1. Detection and quantification of protein-protein interactions by far-western blotting.

    Science.gov (United States)

    Jadwin, Joshua A; Mayer, Bruce J; Machida, Kazuya

    2015-01-01

    Far-western blotting is a convenient method to characterize protein-protein interactions, in which protein samples of interest are immobilized on a membrane and then probed with a non-antibody protein. In contrast to western blotting, which uses specific antibodies to detect target proteins, far-western blotting detects proteins on the basis of the presence or absence of binding sites for the protein probe. When specific modular protein binding domains are used as probes, this approach allows characterization of protein-protein interactions involved in biological processes such as signal transduction, including interactions regulated by posttranslational modification. We here describe a rapid and simple protocol for far-western blotting, in which GST-tagged Src homology 2 (SH2) domains are used to probe cellular proteins in a phosphorylation-dependent manner. We also present a batch quantification method that allows for the direct comparison of probe binding patterns.

  2. Protein intrinsic disorder in plants.

    Science.gov (United States)

    Pazos, Florencio; Pietrosemoli, Natalia; García-Martín, Juan A; Solano, Roberto

    2013-09-12

    To some extent contradicting the classical paradigm of the relationship between protein 3D structure and function, now it is clear that large portions of the proteomes, especially in higher organisms, lack a fixed structure and still perform very important functions. Proteins completely or partially unstructured in their native (functional) form are involved in key cellular processes underlain by complex networks of protein interactions. The intrinsic conformational flexibility of these disordered proteins allows them to bind multiple partners in transient interactions of high specificity and low affinity. In concordance, in plants this type of proteins has been found in processes requiring these complex and versatile interaction networks. These include transcription factor networks, where disordered proteins act as integrators of different signals or link different transcription factor subnetworks due to their ability to interact (in many cases simultaneously) with different partners. Similarly, they also serve as signal integrators in signaling cascades, such as those related to response to external stimuli. Disordered proteins have also been found in plants in many stress-response processes, acting as protein chaperones or protecting other cellular components and structures. In plants, it is especially important to have complex and versatile networks able to quickly and efficiently respond to changing environmental conditions since these organisms cannot escape and have no other choice than adapting to them. Consequently, protein disorder can play an especially important role in plants, providing them with a fast mechanism to obtain complex, interconnected and versatile molecular networks.

  3. Protein intrinsic disorder in plants

    Directory of Open Access Journals (Sweden)

    Florencio ePazos

    2013-09-01

    Full Text Available To some extent contradicting the classical paradigm of the relationship between protein 3D structure and function, now it is clear that large portions of the proteomes, especially in higher organisms, lack a fixed structure and still perform very important functions. Proteins completely or partially unstructured in their native (functional form are involved in key cellular processes underlain by complex networks of protein interactions. The intrinsic conformational flexibility of these disordered proteins allows them to bind multiple partners in transient interactions of high specificity and low affinity. In concordance, in plants this type of proteins has been found in processes requiring these complex and versatile interaction networks. These include transcription factor networks, where disordered proteins act as integrators of different signals or link different transcription factor subnetworks due to their ability to interact (in many cases simultaneously with different partners. Similarly, they also serve as signal integrators in signalling cascades, such as those related to response to external stimuli. Disordered proteins have also been found in plants in many stress-response processes, acting as protein chaperones or protecting other cellular components and structures. In plants, it is especially important to have complex and versatile networks able to quickly and efficiently respond to changing environmental conditions since these organisms can not escape and have no other choice than adapting to them. Consequently, protein disorder can play an especially important role in plants, providing them with a fast mechanism to obtain complex, interconnected and versatile molecular networks.

  4. Membrane fission by protein crowding.

    Science.gov (United States)

    Snead, Wilton T; Hayden, Carl C; Gadok, Avinash K; Zhao, Chi; Lafer, Eileen M; Rangamani, Padmini; Stachowiak, Jeanne C

    2017-04-18

    Membrane fission, which facilitates compartmentalization of biological processes into discrete, membrane-bound volumes, is essential for cellular life. Proteins with specific structural features including constricting rings, helical scaffolds, and hydrophobic membrane insertions are thought to be the primary drivers of fission. In contrast, here we report a mechanism of fission that is independent of protein structure-steric pressure among membrane-bound proteins. In particular, random collisions among crowded proteins generate substantial pressure, which if unbalanced on the opposite membrane surface can dramatically increase membrane curvature, leading to fission. Using the endocytic protein epsin1 N-terminal homology domain (ENTH), previously thought to drive fission by hydrophobic insertion, our results show that membrane coverage correlates equally with fission regardless of the hydrophobicity of insertions. Specifically, combining FRET-based measurements of membrane coverage with multiple, independent measurements of membrane vesiculation revealed that fission became spontaneous as steric pressure increased. Further, fission efficiency remained equally potent when helices were replaced by synthetic membrane-binding motifs. These data challenge the view that hydrophobic insertions drive membrane fission, suggesting instead that the role of insertions is to anchor proteins strongly to membrane surfaces, amplifying steric pressure. In line with these conclusions, even green fluorescent protein (GFP) was able to drive fission efficiently when bound to the membrane at high coverage. Our conclusions are further strengthened by the finding that intrinsically disordered proteins, which have large hydrodynamic radii yet lack a defined structure, drove fission with substantially greater potency than smaller, structured proteins.

  5. Topological characteristics of helical repeat proteins

    NARCIS (Netherlands)

    Groves, M R; Barford, D

    The recent elucidation of protein structures based upon repeating amino acid motifs, including the armadillo motif, the HEAT motif and tetratricopeptide repeats, reveals that they belong to the class of helical repeat proteins. These proteins share the common property of being assembled from tandem

  6. Extracting knowledge from protein structure geometry

    DEFF Research Database (Denmark)

    Røgen, Peter; Koehl, Patrice

    2013-01-01

    potential from geometric knowledge extracted from native and misfolded conformers of protein structures. This new potential, Metric Protein Potential (MPP), has two main features that are key to its success. Firstly, it is composite in that it includes local and nonlocal geometric information on proteins...

  7. Proteome of monocyte priming by lipopolysaccharide, including changes in interleukin-1beta and leukocyte elastase inhibitor

    Directory of Open Access Journals (Sweden)

    Beranova-Giorgianni Sarka

    2008-05-01

    Full Text Available Abstract Background Monocytes can be primed in vitro by lipopolysaccharide (LPS for release of cytokines, for enhanced killing of cancer cells, and for enhanced release of microbicidal oxygen radicals like superoxide and peroxide. We investigated the proteins involved in regulating priming, using 2D gel proteomics. Results Monocytes from 4 normal donors were cultured for 16 h in chemically defined medium in Teflon bags ± LPS and ± 4-(2-aminoethyl-benzenesulfonyl fluoride (AEBSF, a serine protease inhibitor. LPS-primed monocytes released inflammatory cytokines, and produced increased amounts of superoxide. AEBSF blocked priming for enhanced superoxide, but did not affect cytokine release, showing that AEBSF was not toxic. After staining large-format 2D gels with Sypro ruby, we compared the monocyte proteome under the four conditions for each donor. We found 30 protein spots that differed significantly in response to LPS or AEBSF, and these proteins were identified by ion trap mass spectrometry. Conclusion We identified 19 separate proteins that changed in response to LPS or AEBSF, including ATP synthase, coagulation factor XIII, ferritin, coronin, HN ribonuclear proteins, integrin alpha IIb, pyruvate kinase, ras suppressor protein, superoxide dismutase, transketolase, tropomyosin, vimentin, and others. Interestingly, in response to LPS, precursor proteins for interleukin-1β appeared; and in response to AEBSF, there was an increase in elastase inhibitor. The increase in elastase inhibitor provides support for our hypothesis that priming requires an endogenous serine protease.

  8. Subcellular localization of secondary lipid metabolites including fragrance volatiles in carnation petals

    International Nuclear Information System (INIS)

    Hudak, K.A.; Thompson, J.E.

    1997-01-01

    Pulse-chase labeling of carnation (Dianthus caryophyllus L. cv Improved White Sim) petals with [14C]acetate has provided evidence for a hydrophobic subcompartment of lipid-protein particles within the cytosol that resemble oil bodies, are formed by blebbing from membranes, and are enriched in lipid metabolites (including fragrance volatiles) derived from membrane fatty acids. Fractionation of the petals during pulse-chase labeling revealed that radiolabeled fatty acids appear first in microsomal membranes and subsequently in cytosolic lipid-protein particles, indicating that the particles originate from membranes. This interpretation is supported by the finding that the cytosolic lipid-protein particles contain phospholipid as well as the same fatty acids found in microsomal membranes. Radiolabeled polar lipid metabolites (methanol/ water-soluble) were detectable in both in situ lipid-protein particles isolated from the cytosol and those generated in vitro from isolated radiolabeled microsomal membranes. The lipid-protein particles were also enriched in hexanal, trans-2-hexenal, 1-hexanol, 3-hexen-1-ol, and 2-hexanol, volatiles of carnation flower fragrance that are derived from membrane fatty acids through the lipoxygenase pathway. Therefore, secondary lipid metabolites, including components of fragrance, appear to be formed within membranes of petal tissue and are subsequently released from the membrane bilayers into the cytosol by blebbing of lipid-protein particles

  9. Learning about Proteins

    Science.gov (United States)

    ... Videos for Educators Search English Español Learning About Proteins KidsHealth / For Kids / Learning About Proteins What's in ... from the foods you eat. Different Kinds of Protein Protein from animal sources, such as meat and ...

  10. Annotating the protein-RNA interaction sites in proteins using evolutionary information and protein backbone structure.

    Science.gov (United States)

    Li, Tao; Li, Qian-Zhong

    2012-11-07

    RNA-protein interactions play important roles in various biological processes. The precise detection of RNA-protein interaction sites is very important for understanding essential biological processes and annotating the function of the proteins. In this study, based on various features from amino acid sequence and structure, including evolutionary information, solvent accessible surface area and torsion angles (φ, ψ) in the backbone structure of the polypeptide chain, a computational method for predicting RNA-binding sites in proteins is proposed. When the method is applied to predict RNA-binding sites in three datasets: RBP86 containing 86 protein chains, RBP107 containing 107 proteins chains and RBP109 containing 109 proteins chains, better sensitivities and specificities are obtained compared to previously published methods in five-fold cross-validation tests. In order to make further examination for the efficiency of our method, the RBP107 dataset is used as training set, RBP86 and RBP109 datasets are used as the independent test sets. In addition, as examples of our prediction, RNA-binding sites in a few proteins are presented. The annotated results are consistent with the PDB annotation. These results show that our method is useful for annotating RNA binding sites of novel proteins.

  11. IGF binding proteins.

    Science.gov (United States)

    Bach, Leon A

    2017-12-18

    Insulin-like growth factor binding proteins (IGFBPs) 1-6 bind IGFs but not insulin with high affinity. They were initially identified as serum carriers and passive inhibitors of IGF actions. However, subsequent studies showed that, although IGFBPs inhibit IGF actions in many circumstances, they may also potentiate these actions. IGFBPs are widely expressed in most tissues, and they are flexible endocrine and autocrine/paracrine regulators of IGF activity, which is essential for this important physiological system. More recently, individual IGFBPs have been shown to have IGF-independent actions. Mechanisms underlying these actions include (i) interaction with non-IGF proteins in compartments including the extracellular space and matrix, the cell surface and intracellularly; (ii) interaction with and modulation of other growth factor pathways including EGF, TGF- and VEGF; and (iii) direct or indirect transcriptional effects following nuclear entry of IGFBPs. Through these IGF-dependent and IGF-independent actions, IGFBPs modulate essential cellular processes including proliferation, survival, migration, senescence, autophagy and angiogenesis. They have been implicated in a range of disorders including malignant, metabolic, neurological and immune diseases. A more complete understanding of their cellular roles may lead to the development of novel IGFBP-based therapeutic opportunities.

  12. Random copolymers that protect proteins

    Science.gov (United States)

    Alexander-Katz, Alfredo; Van Lehn, Reid C.

    2018-03-01

    Scientists have tried and in some limited cases succeeded to harness proteins to do chemistry (1) or use them in functional materials. However, most proteins only function correctly if they fold into specific conformations, which typically occurs with the assistance of other proteins (such as chaperones, translocons, or transporters) that mediate structure formation, membrane insertion, and intracellular trafficking (2, 3). Several methods have been used to improve protein stability in nonbiological environments—including micelle encapsulation, polymer conjugation, and sol-gel trapping (4)—but for most intended applications, they suffer from low levels of functionality, difficult chemical postfunctionalization, or the requirement of very specific solvent environments. On page 1239 of this issue, Panganiban et al. (5) introduce an approach for stabilizing proteins in disparate solvent environments that does not suffer from these drawbacks.

  13. Activation of repair and checkpoints by double-strand breaks of DNA. Activational cascade of protein phosphorylation

    International Nuclear Information System (INIS)

    Koltovaya, N.A.

    2007-01-01

    Molecular mechanisms of double-strand breaks repair and checkpoints include phosphorylations of repair and checkpoint-proteins by protein kinases. Chemical modification of proteins has different consequences including activation, changing of affinity to proteins and localization

  14. ProteinHistorian: tools for the comparative analysis of eukaryote protein origin.

    Directory of Open Access Journals (Sweden)

    John A Capra

    Full Text Available The evolutionary history of a protein reflects the functional history of its ancestors. Recent phylogenetic studies identified distinct evolutionary signatures that characterize proteins involved in cancer, Mendelian disease, and different ontogenic stages. Despite the potential to yield insight into the cellular functions and interactions of proteins, such comparative phylogenetic analyses are rarely performed, because they require custom algorithms. We developed ProteinHistorian to make tools for performing analyses of protein origins widely available. Given a list of proteins of interest, ProteinHistorian estimates the phylogenetic age of each protein, quantifies enrichment for proteins of specific ages, and compares variation in protein age with other protein attributes. ProteinHistorian allows flexibility in the definition of protein age by including several algorithms for estimating ages from different databases of evolutionary relationships. We illustrate the use of ProteinHistorian with three example analyses. First, we demonstrate that proteins with high expression in human, compared to chimpanzee and rhesus macaque, are significantly younger than those with human-specific low expression. Next, we show that human proteins with annotated regulatory functions are significantly younger than proteins with catalytic functions. Finally, we compare protein length and age in many eukaryotic species and, as expected from previous studies, find a positive, though often weak, correlation between protein age and length. ProteinHistorian is available through a web server with an intuitive interface and as a set of command line tools; this allows biologists and bioinformaticians alike to integrate these approaches into their analysis pipelines. ProteinHistorian's modular, extensible design facilitates the integration of new datasets and algorithms. The ProteinHistorian web server, source code, and pre-computed ages for 32 eukaryotic genomes are

  15. The Geobiochemistry of Methanogen Proteins

    Science.gov (United States)

    Prasad, A.; Shock, E.

    2013-12-01

    A principle of geobiochemistry is that adaptation over evolutionary time includes a thermodynamic drive to minimize costs of making biomolecules like proteins and lipids. If so, then biomolecule abundances will reflect, at least in part, their relative stabilities at the conditions imposed by external environments. We tested this hypothesis by comparing relative stabilities of 138 orthologous proteins between a representative lake-sediment methanogen (Methanoculleus marisnigri) and a representative rumen methanogen (Methanospirillum hungatei) at the compositional constraints of their respective environments. Chemical affinities of the proteins were calculated based on pH, temperature, and concentrations of dissolved hydrogen, bicarbonate, ammonia, and hydrogen sulfide, together with standard Gibbs energies of formation of proteins from the elements predicted with a group additivity algorithm for unfolded proteins [1]. Methanogens were chosen as they are chemoautotrophs and their metabolism proceeds at relatively small affinities. Also, they are found in a variety of compositionally varying habitats like rumen, sediments, hydrothermal systems and sewage. The methanogens selected belong to the same order of taxonomy and are closely related. Preliminary results show that a majority of the proteins belonging to the rumen methanogen (66%) are more stable in the rumen environment, while a majority of the proteins belonging to the lake-sediment methanogen (58%) are more stable at sediment conditions. In a separate observation, it was noted that while the complete protein ';proteasome subunit alpha' of another rumen methanogen (Methanobrevibacter smithii) was less stable in its more reducing habitat as compared to a sewage methanogen (Methanothermobacter thermoautotophicus), its first 26 amino acid residues (N terminal) were in fact more stable in its own environment. These 26 residues are reported to be unique as compared to other proteasome proteins and are suggested to

  16. Protein binding of psychotropic agents

    International Nuclear Information System (INIS)

    Hassan, H.A.

    1990-01-01

    Based upon fluorescence measurements, protein binding of some psychotropic agents (chlorpromazine, promethazine, and trifluoperazine) to human IgG and HSA was studied in aqueous cacodylate buffer, PH7. The interaction parameters determined from emission quenching of the proteins. The interaction parameters determined include the equilibrium constant (K), calculated from equations derived by Borazan and coworkers, the number of binding sites (n) available to the monomer molecules on a single protein molecule. The results revealed a high level of affinity, as reflected by high values of K, and the existence of specific binding sites, since a limited number of n values are obtained. 39 tabs.; 37 figs.; 83 refs

  17. Nonlinear dynamics of globular proteins

    Energy Technology Data Exchange (ETDEWEB)

    Lomdahl, P.S.

    1983-01-01

    Some ongoing work aimed at generalizing DAVYDOV's ideas to a real globular protein is described. So far, a computer code, GLOP, which calculates amide-I bond energy evolution on a globular protein has been developed and tested. The code is quite versatile and takes as input the coordinates of a protein. The full geometry of the molecule is then taken into account when the dipole-dipole interaction between peptide groups is calculated. The amide-I energy is coupled to one intramolecular excitation, but can without difficulty be extended to more or to include intermolecular excitations.

  18. Roles of accessory proteins for heterotrimeric G-protein in the development of cardiovascular diseases.

    Science.gov (United States)

    Sato, Motohiko

    2013-01-01

    Signal processing via heterotrimeric G-proteins is one of the most widely used systems for signal transfer across the cell membrane. This signaling system regulates most physiological and pathophysiological processes in mammals and is therefore the primary target of many pharmaceutical agents. The heterotrimeric G-protein signaling system includes the G-protein-coupled receptor (GPCR), heterotrimeric G-proteins, and effectors. The G-proteins are activated by the GPCR to mediate a signal to effector molecules. However, other players in this system that regulate the activation status of heterotrimeric G-proteins independently of GPCR have been identified. Such accessory proteins for heterotrimeric G-protein can provide additional signal input to the G-protein signaling system, or may act as alternative binding partners of G-protein subunits serving as yet unknown roles in cells. It has been reported that this class of proteins is expressed in the cardiovascular system and contributes to signal integration involved in the various diseases. This review provides an overview of the current understanding of accessory proteins for heterotrimeric G-proteins in their 4 functional subsets, including guanine nucleotide exchange factors (GEFs), guanine nucleotide dissociation inhibitors (GDIs), GTPase-activating proteins (GAPs), and Gβγ-interacting proteins, and discusses their roles in the development of cardiovascular diseases. Better understanding of these components may contribute new insight into the complex network of molecules governing GPCR signaling in the cardiovascular system. 

  19. Fusion-protein-assisted protein crystallization.

    Science.gov (United States)

    Kobe, Bostjan; Ve, Thomas; Williams, Simon J

    2015-07-01

    Fusion proteins can be used directly in protein crystallization to assist crystallization in at least two different ways. In one approach, the `heterologous fusion-protein approach', the fusion partner can provide additional surface area to promote crystal contact formation. In another approach, the `fusion of interacting proteins approach', protein assemblies can be stabilized by covalently linking the interacting partners. The linker connecting the proteins plays different roles in the two applications: in the first approach a rigid linker is required to reduce conformational heterogeneity; in the second, conversely, a flexible linker is required that allows the native interaction between the fused proteins. The two approaches can also be combined. The recent applications of fusion-protein technology in protein crystallization from the work of our own and other laboratories are briefly reviewed.

  20. Modeling and analysis of the affinity filtration process, including broth feeding, washing, and elution steps.

    Science.gov (United States)

    He, L Z; Dong, X Y; Sun, Y

    1998-01-01

    Affinity filtration is a developing protein purification technique that combines the high selectivity of affinity chromatography and the high processing speed of membrane filtration. In this work a lumped kinetic model was developed to describe the whole affinity filtration process, including broth feeding, contaminant washing, and elution steps. Affinity filtration experiments were conducted to evaluate the model using bovine serum albumin as a model protein and a highly substituted Blue Sepharose as an affinity adsorbent. The model with nonadjustable parameters agreed fairly to the experimental results. Thus, the performance of the affinity filtration in processing a crude broth containing contaminant proteins was analyzed by computer simulations using the lumped model. The simulation results show that there is an optimal protein loading for obtaining the maximum recovery yield of the desired protein with a constant purity at each operating condition. The concentration of a crude broth is beneficial in increasing the recovery yield of the desired protein. Using a constant amount of the affinity adsorbent, the recovery yield can be enhanced by decreasing the solution volume in the stirred tank due to the increase of the adsorbent weight fraction. It was found that the lumped kinetic model was simple and useful in analyzing the whole affinity filtration process.