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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. Mobile Collocated Interactions

    DEFF Research Database (Denmark)

    Lucero, Andrés; Clawson, James; Lyons, Kent

    2015-01-01

    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...... 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 include ever......-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....

  3. 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...

  4. 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.

  5. 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.

  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. Proxemic Mobile Collocated Interactions

    DEFF Research Database (Denmark)

    Porcheron, Martin; Lucero, Andrés; Quigley, Aaron

    2016-01-01

    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......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...... in exploring proxemics and mobile collocated interactions....

  8. Rectangular spectral collocation

    KAUST Repository

    Driscoll, Tobin A.; Hale, Nicholas

    2015-01-01

    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

  9. Lexical and Grammatical Collocations in Writing Production of EFL Learners

    Directory of Open Access Journals (Sweden)

    Maryam Bahardoust

    2012-05-01

    Full Text Available Lewis (1993 recognized significance of word combinations including collocations by presenting lexical approach. Because of the crucial role of collocation in vocabulary acquisition, this research set out to evaluate the rate of collocations in Iranian EFL learners' writing production across L1 and L2. In addition, L1 interference with L2 collocational use in the learner' writing samples was studied. To achieve this goal, 200 Persian EFL learners at BA level were selected. These participants were taking paragraph writing and essay writing courses in two successive semesters. As for the data analysis, mid-term, final exam, and also the assignments of L2 learners were evaluated. Because of the nominal nature of the data, chi-square test was utilized for data analysis. Then, the rate of lexical and grammatical collocations was calculated. Results showed that the lexical collocations outnumbered the grammatical collocations. Different categories of lexical collocations were also compared with regard to their frequencies in EFL writing production. The rate of the verb-noun and adjective-noun collocations appeared to be the highest and noun-verb collocations the lowest. The results also showed that L1 had both positive and negative effect on the occurrence of both grammatical and lexical collocations.

  10. Geostationary satellites collocation

    CERN Document Server

    Li, Hengnian

    2014-01-01

    Geostationary Satellites Collocation aims to find solutions for deploying a safe and reliable collocation control. Focusing on the orbital perturbation analysis, the mathematical foundations for orbit and control of the geostationary satellite are summarized. The mathematical and physical principle of orbital maneuver and collocation strategies for multi geostationary satellites sharing with the same dead band is also stressed. Moreover, the book presents some applications using the above algorithms and mathematical models to help readers master the corrective method for planning station keeping maneuvers. Engineers and scientists in the fields of aerospace technology and space science can benefit from this book. Hengnian Li is the Deputy Director of State Key Laboratory of Astronautic Dynamics, China.

  11. 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,...

  12. Collocations and Grammatical Patterns in a Multilingual Online Term ...

    African Journals Online (AJOL)

    This article considers the importance of including various types of collocations in a terminological database, with the aim of making this information available to the user via the user interface. We refer specifically to the inclusion of empirical and phraseological collocations, and information on grammatical patterning.

  13. Verb-Noun Collocation Proficiency and Academic Years

    Directory of Open Access Journals (Sweden)

    Fatemeh Ebrahimi-Bazzaz

    2014-01-01

    Full Text Available Generally vocabulary and collocations in particular have significant roles in language proficiency. A collocation includes two words that are frequently joined concurrently in the memory of native speakers. There have been many linguistic studies trying to define, to describe, and to categorise English collocations. It contains grammatical collocations and lexical collocations which include nouns, adjectives, verbs, and adverb. In the context of a foreign language environment such as Iran, collocational proficiency can be useful because it helps the students improve their language proficiency. This paper investigates the possible relationship between verb-noun collocation proficiency among students from one academic year to the next. To reach this goal, a test of verb-noun collocations was administered to Iranian learners. The participants in the study were 212 Iranian students in an Iranian university. They were selected from the second term of freshman, sophomore, junior, and senior years. The students’ age ranged from 18 to 35.The results of ANOVA showed there was variability in the verb-noun collocations proficiency within each academic year and between the four academic years. The results of a post hoc multiple comparison tests demonstrated that the means are significantly different between the first year and the third and fourth years, and between the third and the fourth academic year; however, students require at least two years to show significant development in verb-noun collocation proficiency. These findings provided a vital implication that lexical collocations are learnt and developed through four academic years of university, but requires at least two years showing significant development in the language proficiency.

  14. 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...

  15. 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.

  16. 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.

  17. Translating English Idioms and Collocations

    Directory of Open Access Journals (Sweden)

    Rochayah Machali

    2004-01-01

    Full Text Available Learners of English should be made aware of the nature, types, and use of English idioms. This paper disensses the nature of idioms and collocations and translation issues related to them

  18. 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...

  19. Crosstalk statistics via collocation method

    NARCIS (Netherlands)

    Diouf, F.; Canavero, Flavio

    2009-01-01

    A probabilistic model for the evaluation of transmission lines crosstalk is proposed. The geometrical parameters are assumed to be unknown and the exact solution is decomposed into two functions, one depending solely on the random parameters and the other on the frequency. The stochastic collocation

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

    KAUST Repository

    Haji Ali, Abdul Lateef; Nobile, Fabio; Tamellini, Lorenzo; Tempone, Raul

    2016-01-01

    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.

  1. 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.

  2. 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.

  3. Multi-Index Stochastic Collocation for random PDEs

    KAUST Repository

    Haji Ali, Abdul Lateef; Nobile, Fabio; Tamellini, Lorenzo; Tempone, Raul

    2016-01-01

    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.

  4. 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.

  5. 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.

  6. 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…

  7. Measuring receptive collocational competence across proficiency ...

    African Journals Online (AJOL)

    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 linguistic proficiency develops; and (iii) the extent to which receptive knowledge of ...

  8. "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 ...

  9. 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.

  10. GUESSING VERB-ADVERB COLLOCATIONS: ARAB EFL ...

    African Journals Online (AJOL)

    user

    In the sections to follow, the concept and meaning of collocation is defined ... expressions (Alexander 1984); formulaic language or speech (Weinert 1995); multi- ... Two further studies reported Arab EFL learners' overall ignorance of col-.

  11. Slovene-English Contrastive Phraseology: Lexical Collocations

    Directory of Open Access Journals (Sweden)

    Primož Jurko

    2010-05-01

    Full Text Available Phraseology is seen as one of the key elements and arguably the most productive part of any language. %e paper is focused on collocations and separates them from other phraseological units, such as idioms or compounds. Highlighting the difference between a monolingual and a bilingual (i.e. contrastive approach to collocation, the article presents two distinct classes of collocations: grammatical and lexical. %e latter, treated contrastively, represent the focal point of the paper, since they are an unending source of translation errors to both students of translation and professional translators. %e author introduces a methodology of systematic classification of lexical collocations applied on the Slovene-English language pair and based on structural (lexical congruence and semantic (translational predictability criteria.

  12. 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…

  13. 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.

  14. Teaching vocabulary using collocations versus using definitions in EFL classes

    OpenAIRE

    Altınok, Şerife İper

    2000-01-01

    Ankara : Institute of Economics and Social Sciences of Bilkent Univ., 2000. Thesis (Master's) -- Bilkent University, 2000. Includes bibliographical references leaves 40-43 Teaching words in collocations is a comparatively new technique and it is accepted as an effective one in vocabulary teaching. The purpose of this study was to find out whether teaching vocabulary would result in better learning and remembering vocabulary items. This study investigated the differences betw...

  15. Pseudospectral collocation methods for fourth order differential equations

    Science.gov (United States)

    Malek, Alaeddin; Phillips, Timothy N.

    1994-01-01

    Collocation schemes are presented for solving linear fourth order differential equations in one and two dimensions. The variational formulation of the model fourth order problem is discretized by approximating the integrals by a Gaussian quadrature rule generalized to include the values of the derivative of the integrand at the boundary points. Collocation schemes are derived which are equivalent to this discrete variational problem. An efficient preconditioner based on a low-order finite difference approximation to the same differential operator is presented. The corresponding multidomain problem is also considered and interface conditions are derived. Pseudospectral approximations which are C1 continuous at the interfaces are used in each subdomain to approximate the solution. The approximations are also shown to be C3 continuous at the interfaces asymptotically. A complete analysis of the collocation scheme for the multidomain problem is provided. The extension of the method to the biharmonic equation in two dimensions is discussed and results are presented for a problem defined in a nonrectangular domain.

  16. An empirical understanding of triple collocation evaluation measure

    Science.gov (United States)

    Scipal, Klaus; Doubkova, Marcela; Hegyova, Alena; Dorigo, Wouter; Wagner, Wolfgang

    2013-04-01

    Triple collocation method is an advanced evaluation method that has been used in the soil moisture field for only about half a decade. The method requires three datasets with an independent error structure that represent an identical phenomenon. The main advantages of the method are that it a) doesn't require a reference dataset that has to be considered to represent the truth, b) limits the effect of random and systematic errors of other two datasets, and c) simultaneously assesses the error of three datasets. The objective of this presentation is to assess the triple collocation error (Tc) of the ASAR Global Mode Surface Soil Moisture (GM SSM 1) km dataset and highlight problems of the method related to its ability to cancel the effect of error of ancillary datasets. In particular, the goal is to a) investigate trends in Tc related to the change in spatial resolution from 5 to 25 km, b) to investigate trends in Tc related to the choice of a hydrological model, and c) to study the relationship between Tc and other absolute evaluation methods (namely RMSE and Error Propagation EP). The triple collocation method is implemented using ASAR GM, AMSR-E, and a model (either AWRA-L, GLDAS-NOAH, or ERA-Interim). First, the significance of the relationship between the three soil moisture datasets was tested that is a prerequisite for the triple collocation method. Second, the trends in Tc related to the choice of the third reference dataset and scale were assessed. For this purpose the triple collocation is repeated replacing AWRA-L with two different globally available model reanalysis dataset operating at different spatial resolution (ERA-Interim and GLDAS-NOAH). Finally, the retrieved results were compared to the results of the RMSE and EP evaluation measures. Our results demonstrate that the Tc method does not eliminate the random and time-variant systematic errors of the second and the third dataset used in the Tc. The possible reasons include the fact a) that the TC

  17. 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) ...

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

    African Journals Online (AJOL)

    A controlled productive test of adverb-verb collocations ..... The third approach to studying collocations, corpus analysis, ..... The collocation web model is thought to match Nation's (2001) psychological .... Theory, analysis, and applications. .... Canadian Modern ... Focus on vocabulary: Mastering the Academic Word List.

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

    African Journals Online (AJOL)

    The study also reveals that controlled productive knowledge of adverbverb collocations is less problematic. Based on these results, teaching strategies aimed at improving the use of adverb-verb collocations among EFL users are proposed. Keywords: academic writing, adverb-verb collocations, productive knowledge of ...

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

    African Journals Online (AJOL)

    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 ...

  1. 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 ...

  2. Measuring receptive collocational competence across proficiency ...

    African Journals Online (AJOL)

    Kate H

    frequency bands. A proficiency measure and a collocation test were administered to English ... battery may negatively impact the test-takers' performance. ..... examples. The major finding is that raising learners' awareness constitutes the best way forward ..... Amsterdam: John Benjamins Publishing Company. Green, R.

  3. Improving academic literacy by teaching collocations

    African Journals Online (AJOL)

    Kate H

    version of McCarthy and O'Dell's (2005) collocation web model were the techniques adopted ... both cued recall and essay writing, supporting earlier findings (cf. ..... from a 'holistic' representation of formulaic sequences in memory” (Boers et al. ... their study indicate that non-native speakers also retain words as they appear ...

  4. 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...

  5. 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.

  6. Extending Binary Collocations: (Lexicographical Implications of Going beyond the Prototypical a – b

    Directory of Open Access Journals (Sweden)

    Dušan Gabrovšek

    2014-05-01

    Full Text Available The paper focuses primarily on the Sinclairian concept of extended units of meaning in general and on extended collocations in particular, investigating their nature and types. Such extended units are extremely varied and diverse; they are regarded as instances of the functioning of the coselection principle. Some extended forms are used far more commonly that the corresponding prototypical (binary sequences. The final section delves into the ABCs of extended collocations in the context of lexicography, suggesting that dictionaries should make an effort to include a selection of such strings, especially for encoding tasks that are to be shown as examples of use. Most dictionaries incorporate very few such “loose” units, probably because of a powerful tradition to include as examples of use chiefly binary collocations and full sentences.

  7. 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....

  8. 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.

  9. 47 CFR 51.323 - Standards for physical collocation and virtual collocation.

    Science.gov (United States)

    2010-10-01

    ... standards or any other performance standards. An incumbent LEC that denies collocation of a competitor's equipment, citing safety standards, must provide to the competitive LEC within five business days of the... incumbent LEC contends the competitor's equipment fails to meet. This affidavit must set forth in detail...

  10. Determination of processed animal proteins, including meat and bone meal, in animal feed

    NARCIS (Netherlands)

    Gizzi, G.; Holst, von C.; Baeten, V.; Berben, G.; Raamsdonk, van L.W.D.

    2004-01-01

    The presence of processed animal proteins (PAP), including meat and bone meal (MBM) from various species, in animal feed was investigated. It was demonstrated that microscopy is the most reliable method for enforcing the current total MBM ban in the European Uion (EU). It was shown that near

  11. 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.

  12. COLLOCATION PHRASES IN RELATION TO OTHER LEXICAL PHRASES IN CROATIAN

    Directory of Open Access Journals (Sweden)

    Goranka Blagus Bartolec

    2012-01-01

    Full Text Available The paper analyzes the semantic and lexicological aspects of collocation phrases in Croatian with tendency to separate them from other lexical phrases in Croatian (terms, idioms, names. The collocation phrase is defined as a special lexical phrase on a syntagmatic level, based on the semantic correlation of the two individual lexical components in which their meanings are specified.

  13. Learning and Teaching L2 Collocations: Insights from Research

    Science.gov (United States)

    Szudarski, Pawel

    2017-01-01

    The aim of this article is to present and summarize the main research findings in the area of learning and teaching second language (L2) collocations. Being a large part of naturally occurring language, collocations and other types of multiword units (e.g., idioms, phrasal verbs, lexical bundles) have been identified as important aspects of L2…

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

    African Journals Online (AJOL)

    ... beginner/low-intermediate students and only exceed the 2 000-word band from the upper-intermediate learning stage onwards, a suggestion in line with Nation's (2006) discussion on how to teach vocabulary. Keywords: collocation size, controlled productive knowledge, teachability of collocations, word frequency counts, ...

  15. 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 ...

  16. Collocations of High Frequency Noun Keywords in Prescribed Science Textbooks

    Science.gov (United States)

    Menon, Sujatha; Mukundan, Jayakaran

    2012-01-01

    This paper analyses the discourse of science through the study of collocational patterns of high frequency noun keywords in science textbooks used by upper secondary students in Malaysia. Research has shown that one of the areas of difficulty in science discourse concerns lexis, especially that of collocations. This paper describes a corpus-based…

  17. 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.…

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

    KAUST Repository

    Babuška, Ivo; Nobile, Fabio; Tempone, Raul

    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.

  19. Stochastic Collocation Applications in Computational Electromagnetics

    Directory of Open Access Journals (Sweden)

    Dragan Poljak

    2018-01-01

    Full Text Available The paper reviews the application of deterministic-stochastic models in some areas of computational electromagnetics. Namely, in certain problems there is an uncertainty in the input data set as some properties of a system are partly or entirely unknown. Thus, a simple stochastic collocation (SC method is used to determine relevant statistics about given responses. The SC approach also provides the assessment of related confidence intervals in the set of calculated numerical results. The expansion of statistical output in terms of mean and variance over a polynomial basis, via SC method, is shown to be robust and efficient approach providing a satisfactory convergence rate. This review paper provides certain computational examples from the previous work by the authors illustrating successful application of SC technique in the areas of ground penetrating radar (GPR, human exposure to electromagnetic fields, and buried lines and grounding systems.

  20. Study of Anti-Fatigue Effect in Rats of Ferrous Chelates Including Hairtail Protein Hydrolysates

    Directory of Open Access Journals (Sweden)

    Saibo Huang

    2015-12-01

    Full Text Available The ability of ferrous chelates including hairtail protein hydrolysates to prevent and reduce fatigue was studied in rats. After hydrolysis of hairtail surimi with papain, the hairtail protein hydrolysates (HPH were separated into three groups by range of relative molecular weight using ultrafiltration membrane separation. Hairtail proteins were then chelated with ferrous ions, and the antioxidant activity, the amino acid composition and chelation rate of the three kinds of ferrous chelates including hairtail protein hydrolysates (Fe-HPH were determined. Among the three groups, the Fe-HPH chelate showing the best conditions was selected for the anti-fatigue animal experiment. For it, experimental rats were randomly divided into seven groups. Group A was designated as the negative control group given distilled water. Group B, the positive control group, was given glutathione. Groups C, D and E were designated as the Fe-HPH chelate treatment groups and given low, medium, and high doses, respectively. Group F was designated as HPH hydrolysate treatment group, and Group G was designated as FeCl2 treatment group. The different diets were orally administered to rats for 20 days. After that time, rats were subjected to forced swimming training after 1 h of gavage. Rats given Fe-FPH chelate had higher haemoglobin regeneration efficiency (HRE, longer exhaustive swimming time and higher SOD activity. Additionally, Fe-FPH chelate was found to significantly decrease the malondialdehyde content, visibly enhance the GSH-Px activity in liver and reduce blood lactic acid of rats. Fe-HPH chelate revealed an anti-fatigue effect, similar to or better than the positive control substance and superior to HPH or Fe when provided alone.

  1. 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.

  2. 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.

  3. 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.

  4. 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…

  5. 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,…

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

    KAUST Repository

    Farrell, Patricio; Wendland, Holger

    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

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

    African Journals Online (AJOL)

    user

    equivalents for key concepts in the African languages, but also additional con- ... for, inter alia, computational identification and extraction of collocations exist; .... sult' is to be followed by a prepositional phrase in which the preposition is.

  8. Recent advances in radial basis function collocation methods

    CERN Document Server

    Chen, Wen; Chen, C S

    2014-01-01

    This book surveys the latest advances in radial basis function (RBF) meshless collocation methods which emphasis on recent novel kernel RBFs and new numerical schemes for solving partial differential equations. The RBF collocation methods are inherently free of integration and mesh, and avoid tedious mesh generation involved in standard finite element and boundary element methods. This book focuses primarily on the numerical algorithms, engineering applications, and highlights a large class of novel boundary-type RBF meshless collocation methods. These methods have shown a clear edge over the traditional numerical techniques especially for problems involving infinite domain, moving boundary, thin-walled structures, and inverse problems. Due to the rapid development in RBF meshless collocation methods, there is a need to summarize all these new materials so that they are available to scientists, engineers, and graduate students who are interest to apply these newly developed methods for solving real world’s ...

  9. Protein folding includes oligomerization – examples from the endoplasmic reticulum and cytosol

    NARCIS (Netherlands)

    Christis, C.; Lubsen, N.H.; Braakman, I.

    2008-01-01

    A correct three-dimensional structure is a prerequisite for protein functionality, and therefore for life. Thus, it is not surprising that our cells are packed with proteins that assist protein folding, the process in which the native three-dimensional structure is formed. In general, plasma

  10. 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.

  11. Continuous Groundwater Monitoring Collocated at USGS Streamgages

    Science.gov (United States)

    Constantz, J. E.; Eddy-Miller, C.; Caldwell, R.; Wheeer, J.; Barlow, J.

    2012-12-01

    USGS Office of Groundwater funded a 2-year pilot study collocating groundwater wells for monitoring water level and temperature at several existing continuous streamgages in Montana and Wyoming, while U.S. Army Corps of Engineers funded enhancement to streamgages in Mississippi. To increase spatial relevance with in a given watershed, study sites were selected where near-stream groundwater was in connection with an appreciable aquifer, and where logistics and cost of well installations were considered representative. After each well installation and surveying, groundwater level and temperature were easily either radio-transmitted or hardwired to existing data acquisition system located in streamgaging shelter. Since USGS field personnel regularly visit streamgages during routine streamflow measurements and streamgage maintenance, the close proximity of observation wells resulted in minimum extra time to verify electronically transmitted measurements. After field protocol was tuned, stream and nearby groundwater information were concurrently acquired at streamgages and transmitted to satellite from seven pilot-study sites extending over nearly 2,000 miles (3,200 km) of the central US from October 2009 until October 2011, for evaluating the scientific and engineering add-on value of the enhanced streamgage design. Examination of the four-parameter transmission from the seven pilot study groundwater gaging stations reveals an internally consistent, dynamic data suite of continuous groundwater elevation and temperature in tandem with ongoing stream stage and temperature data. Qualitatively, the graphical information provides appreciation of seasonal trends in stream exchanges with shallow groundwater, as well as thermal issues of concern for topics ranging from ice hazards to suitability of fish refusia, while quantitatively this information provides a means for estimating flux exchanges through the streambed via heat-based inverse-type groundwater modeling. In June

  12. 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

  13. A collocation--Galerkin finite element model of cardiac action potential propagation.

    Science.gov (United States)

    Rogers, J M; McCulloch, A D

    1994-08-01

    A new computational method was developed for modeling the effects of the geometric complexity, nonuniform muscle fiber orientation, and material inhomogeneity of the ventricular wall on cardiac impulse propagation. The method was used to solve a modification to the FitzHugh-Nagumo system of equations. The geometry, local muscle fiber orientation, and material parameters of the domain were defined using linear Lagrange or cubic Hermite finite element interpolation. Spatial variations of time-dependent excitation and recovery variables were approximated using cubic Hermite finite element interpolation, and the governing finite element equations were assembled using the collocation method. To overcome the deficiencies of conventional collocation methods on irregular domains, Galerkin equations for the no-flux boundary conditions were used instead of collocation equations for the boundary degrees-of-freedom. The resulting system was evolved using an adaptive Runge-Kutta method. Converged two-dimensional simulations of normal propagation showed that this method requires less CPU time than a traditional finite difference discretization. The model also reproduced several other physiologic phenomena known to be important in arrhythmogenesis including: Wenckebach periodicity, slowed propagation and unidirectional block due to wavefront curvature, reentry around a fixed obstacle, and spiral wave reentry. In a new result, we observed wavespeed variations and block due to nonuniform muscle fiber orientation. The findings suggest that the finite element method is suitable for studying normal and pathological cardiac activation and has significant advantages over existing techniques.

  14. 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

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

    DEFF Research Database (Denmark)

    Revier, Robert Lee

    2014-01-01

    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...... 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...... 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...

  16. A Protein Diet Score, Including Plant and Animal Protein, Investigating the Association with HbA1c and eGFR—The PREVIEW Project

    Science.gov (United States)

    Mikkilä, Vera; Raitakari, Olli T.; Hutri-Kähönen, Nina; Dragsted, Lars O.; Poppitt, Sally D.; Silvestre, Marta P.; Feskens, Edith J.M.

    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 −0.02 ± 0.01 mmol/mol, p < 0.001) was seen in Lifelines. We found a positive association between the protein score and eGFR in Lifelines (slope 0.17 ± 0.02 mL/min/1.73 m2, p < 0.0001). Protein scoring might be a useful tool to assess both the effect of quantity and source of protein on health parameters. Further studies are needed to validate this newly developed protein score. PMID:28714926

  17. 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

    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...

  18. Examining Second Language Receptive Knowledge of Collocation and Factors That Affect Learning

    Science.gov (United States)

    Nguyen, Thi My Hang; Webb, Stuart

    2017-01-01

    This study investigated Vietnamese EFL learners' knowledge of verb-noun and adjective-noun collocations at the first three 1,000 word frequency levels, and the extent to which five factors (node word frequency, collocation frequency, mutual information score, congruency, and part of speech) predicted receptive knowledge of collocation. Knowledge…

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

    African Journals Online (AJOL)

    This paper deals with the numerical solution of second order linear partial differential equations with the use of the method of lines coupled with the tau collocation method. The method of lines is used to convert the partial differential equation (PDE) to a sequence of ordinary differential equations (ODEs) which is then ...

  20. Multimodal interaction design in collocated mobile phone use

    NARCIS (Netherlands)

    El-Ali, A.; Lucero, A.; Aaltonen, V.

    2011-01-01

    In the context of the Social and Spatial Interactions (SSI) platform, we explore how multimodal interaction design (input and output) can augment and improve the experience of collocated, collaborative activities using mobile phones. Based largely on our prototype evaluations, we reflect on and

  1. 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.

  2. 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

  3. 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

  4. 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

    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......, especially plant protein, on insulin sensitivity and kidney function. In paper II, the aim of the study was to assess the effect after one year of a higher protein intake on kidney function, measured by in creatinine clearance. This was investigated in pre-diabetic older adults based on a sub-group of 310...... pre-diabetic individuals included in the PREVIEW RCT. We found that a higher protein intake was associated with a significant increase in urea to creatinine ratio and serum urea after one year. There were no associations between increased protein intake and creatinine clearance, estimated glomerular...

  5. 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

  6. A unified pathogenesis for kidney diseases, including genetic diseases and cancers, by the protein-homeostasis-system hypothesis.

    Science.gov (United States)

    Lee, Kyung-Yil

    2017-06-01

    Every cell of an organism is separated and protected by a cell membrane. It is proposed that harmony between intercellular communication and the health of an organism is controlled by a system, designated the protein-homeostasis-system (PHS). Kidneys consist of a variety of types of renal cells, each with its own characteristic cell-receptor interactions and producing characteristic proteins. A functional union of these renal cells can be determined by various renal function tests, and harmonious intercellular communication is essential for the healthy state of the host. Injury to a kind of renal cells can impair renal function and induce an imbalance in total body health. Every acute or chronic renal disease has unknown etiologic substances that are responsible for renal cell injury at the molecular level. The immune/repair system of the host should control the etiologic substances acting against renal cells; if this system fails, the disease progresses to end stage renal disease. Each renal disease has its characteristic pathologic lesions where immune cells and immune proteins, such as immunoglobulins and complements, are infiltrated. These immune cells and immune proteins may control the etiologic substances involved in renal pathologic lesions. Also, genetic renal diseases and cancers may originate from a protein deficiency or malfunctioning protein under the PHS. A unified pathogenesis for renal diseases, including acute glomerulonephritis, idiopathic nephrotic syndrome, immunoglobulin A nephropathy, genetic renal diseases such as Alport syndrome, and malignancies such as Wilms tumor and renal cell carcinoma, is proposed using the PHS hypothesis.

  7. ZP Domain Proteins in the Abalone Egg Coat Include a Paralog of VERL under Positive Selection That Binds Lysin and 18-kDa Sperm Proteins

    Science.gov (United States)

    Aagaard, Jan E.; Vacquier, Victor D.; MacCoss, Michael J.; Swanson, Willie J.

    2010-01-01

    Identifying fertilization molecules is key to our understanding of reproductive biology, yet only a few examples of interacting sperm and egg proteins are known. One of the best characterized comes from the invertebrate archeogastropod abalone (Haliotis spp.), where sperm lysin mediates passage through the protective egg vitelline envelope (VE) by binding to the VE protein vitelline envelope receptor for lysin (VERL). Rapid adaptive divergence of abalone lysin and VERL are an example of positive selection on interacting fertilization proteins contributing to reproductive isolation. Previously, we characterized a subset of the abalone VE proteins that share a structural feature, the zona pellucida (ZP) domain, which is common to VERL and the egg envelopes of vertebrates. Here, we use additional expressed sequence tag sequencing and shotgun proteomics to characterize this family of proteins in the abalone egg VE. We expand 3-fold the number of known ZP domain proteins present within the VE (now 30 in total) and identify a paralog of VERL (vitelline envelope zona pellucida domain protein [VEZP] 14) that contains a putative lysin-binding motif. We find that, like VERL, the divergence of VEZP14 among abalone species is driven by positive selection on the lysin-binding motif alone and that these paralogous egg VE proteins bind a similar set of sperm proteins including a rapidly evolving 18-kDa paralog of lysin, which may mediate sperm–egg fusion. This work identifies an egg coat paralog of VERL under positive selection and the candidate sperm proteins with which it may interact during abalone fertilization. PMID:19767347

  8. 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.

  9. A collocation finite element method with prior matrix condensation

    International Nuclear Information System (INIS)

    Sutcliffe, W.J.

    1977-01-01

    For thin shells with general loading, sixteen degrees of freedom have been used for a previous finite element solution procedure using a Collocation method instead of the usual variational based procedures. Although the number of elements required was relatively small, nevertheless the final matrix for the simultaneous solution of all unknowns could become large for a complex compound structure. The purpose of the present paper is to demonstrate a method of reducing the final matrix size, so allowing solution for large structures with comparatively small computer storage requirements while retaining the accuracy given by high order displacement functions. Collocation points, a number are equilibrium conditions which must be satisfied independently of the overall compatibility of forces and deflections for a complete structure. (Auth.)

  10. 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

  11. Application of collocation meshless method to eigenvalue problem

    International Nuclear Information System (INIS)

    Saitoh, Ayumu; Matsui, Nobuyuki; Itoh, Taku; Kamitani, Atsushi; Nakamura, Hiroaki

    2012-01-01

    The numerical method for solving the nonlinear eigenvalue problem has been developed by using the collocation Element-Free Galerkin Method (EFGM) and its performance has been numerically investigated. The results of computations show that the approximate solution of the nonlinear eigenvalue problem can be obtained stably by using the developed method. Therefore, it can be concluded that the developed method is useful for solving the nonlinear eigenvalue problem. (author)

  12. Let's collocate: student generated worksheets as a motivational tool

    OpenAIRE

    Simpson, Adam John

    2006-01-01

    This article discusses the process of producing collocation worksheets and the values of these worksheets as a motivational tool within a tertiary level preparatory English program. Firstly, the method by which these worksheets were produced is described, followed by an analysis of their effectiveness as a resource in terms of student motivation, personalisation, involvement in the development of the curriculum and in raising awareness of corpus linguistics and its applications.

  13. CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins.

    Science.gov (United States)

    Couvin, David; Bernheim, Aude; Toffano-Nioche, Claire; Touchon, Marie; Michalik, Juraj; Néron, Bertrand; C Rocha, Eduardo P; Vergnaud, Gilles; Gautheret, Daniel; Pourcel, Christine

    2018-05-22

    CRISPR (clustered regularly interspaced short palindromic repeats) arrays and their associated (Cas) proteins confer bacteria and archaea adaptive immunity against exogenous mobile genetic elements, such as phages or plasmids. CRISPRCasFinder allows the identification of both CRISPR arrays and Cas proteins. The program includes: (i) an improved CRISPR array detection tool facilitating expert validation based on a rating system, (ii) prediction of CRISPR orientation and (iii) a Cas protein detection and typing tool updated to match the latest classification scheme of these systems. CRISPRCasFinder can either be used online or as a standalone tool compatible with Linux operating system. All third-party software packages employed by the program are freely available. CRISPRCasFinder is available at https://crisprcas.i2bc.paris-saclay.fr.

  14. B-spline Collocation with Domain Decomposition Method

    International Nuclear Information System (INIS)

    Hidayat, M I P; Parman, S; Ariwahjoedi, B

    2013-01-01

    A global B-spline collocation method has been previously developed and successfully implemented by the present authors for solving elliptic partial differential equations in arbitrary complex domains. However, the global B-spline approximation, which is simply reduced to Bezier approximation of any degree p with C 0 continuity, has led to the use of B-spline basis of high order in order to achieve high accuracy. The need for B-spline bases of high order in the global method would be more prominent in domains of large dimension. For the increased collocation points, it may also lead to the ill-conditioning problem. In this study, overlapping domain decomposition of multiplicative Schwarz algorithm is combined with the global method. Our objective is two-fold that improving the accuracy with the combination technique, and also investigating influence of the combination technique to the employed B-spline basis orders with respect to the obtained accuracy. It was shown that the combination method produced higher accuracy with the B-spline basis of much lower order than that needed in implementation of the initial method. Hence, the approximation stability of the B-spline collocation method was also increased.

  15. 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

  16. 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

  17. Vocabulary and Receptive Knowledge of English Collocations among Swedish Upper Secondary School Students

    OpenAIRE

    Bergström, Kerstin

    2008-01-01

    The aim of this study is to examine the vocabulary and receptive collocation knowledge in English among Swedish upper secondary school students. The primary material consists of two vocabulary tests, one collocation test, and a background questionnaire. The first research question concerns whether the students who receive a major part of their education in English have a higher level of vocabulary and receptive collocation knowledge in English than those who are taught primarily in Swedish. T...

  18. 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

  19. The treatment of lexical collocations in EFL coursebooks in the Estonian secondary school context

    Directory of Open Access Journals (Sweden)

    Liina Vassiljev

    2015-04-01

    Full Text Available The article investigates lexical collocations encountered in English as a Foreign Language (EFL instruction in Estonian upper secondary schools. This is achieved through a statistical analysis of collocations featuring in three coursebooks where the collocations found are analysed in terms of their type, frequency and usefulness index by studying them through an online language corpus (Collins Wordbanks Online. The coursebooks are systematically compared and contrasted relying upon the data gathered. The results of the study reveal that the frequency and range of lexical collocations in a language corpus have not been regarded as an essential criterion for their selection and practice by any of the coursebook authors under discussion.

  20. Simulation of electrically driven jet using Chebyshev collocation method

    Institute of Scientific and Technical Information of China (English)

    2011-01-01

    The model of electrically driven jet is governed by a series of quasi 1D dimensionless partial differential equations(PDEs).Following the method of lines,the Chebyshev collocation method is employed to discretize the PDEs and obtain a system of differential-algebraic equations(DAEs).By differentiating constrains in DAEs twice,the system is transformed into a set of ordinary differential equations(ODEs) with invariants.Then the implicit differential equations solver "ddaskr" is used to solve the ODEs and ...

  1. Benchmarking the Collocation Stand-Alone Library and Toolkit (CSALT)

    Science.gov (United States)

    Hughes, Steven; Knittel, Jeremy; Shoan, Wendy; Kim, Youngkwang; Conway, Claire; Conway, Darrel J.

    2017-01-01

    This paper describes the processes and results of Verification and Validation (VV) efforts for the Collocation Stand Alone Library and Toolkit (CSALT). We describe the test program and environments, the tools used for independent test data, and comparison results. The VV effort employs classical problems with known analytic solutions, solutions from other available software tools, and comparisons to benchmarking data available in the public literature. Presenting all test results are beyond the scope of a single paper. Here we present high-level test results for a broad range of problems, and detailed comparisons for selected problems.

  2. 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.

  3. BioInfra.Prot: A comprehensive proteomics workflow including data standardization, protein inference, expression analysis and data publication.

    Science.gov (United States)

    Turewicz, Michael; Kohl, Michael; Ahrens, Maike; Mayer, Gerhard; Uszkoreit, Julian; Naboulsi, Wael; Bracht, Thilo; Megger, Dominik A; Sitek, Barbara; Marcus, Katrin; Eisenacher, Martin

    2017-11-10

    The analysis of high-throughput mass spectrometry-based proteomics data must address the specific challenges of this technology. To this end, the comprehensive proteomics workflow offered by the de.NBI service center BioInfra.Prot provides indispensable components for the computational and statistical analysis of this kind of data. These components include tools and methods for spectrum identification and protein inference, protein quantification, expression analysis as well as data standardization and data publication. All particular methods of the workflow which address these tasks are state-of-the-art or cutting edge. As has been shown in previous publications, each of these methods is adequate to solve its specific task and gives competitive results. However, the methods included in the workflow are continuously reviewed, updated and improved to adapt to new scientific developments. All of these particular components and methods are available as stand-alone BioInfra.Prot services or as a complete workflow. Since BioInfra.Prot provides manifold fast communication channels to get access to all components of the workflow (e.g., via the BioInfra.Prot ticket system: bioinfraprot@rub.de) users can easily benefit from this service and get support by experts. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

  4. 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.

  5. Adaptive probabilistic collocation based Kalman filter for unsaturated flow problem

    Science.gov (United States)

    Man, J.; Li, W.; Zeng, L.; Wu, L.

    2015-12-01

    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 "cure of dimensionality". When the system nonlinearity is strong and number of parameters is large, PCKF is even more computationally expensive than EnKF. Motivated by recent developments in uncertainty quantification, we propose a restart adaptive probabilistic collocation based Kalman filter (RAPCKF) for data assimilation in unsaturated flow problem. During the implementation of RAPCKF, the important parameters are identified and active PCE basis functions are adaptively selected. The "restart" technology is used to alleviate the inconsistency between model parameters and states. The performance of RAPCKF is tested by unsaturated flow numerical cases. 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.

  6. 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.

  7. 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…

  8. Corpora and Collocations in Chinese-English Dictionaries for Chinese Users

    Science.gov (United States)

    Xia, Lixin

    2015-01-01

    The paper identifies the major problems of the Chinese-English dictionary in representing collocational information after an extensive survey of nine dictionaries popular among Chinese users. It is found that the Chinese-English dictionary only provides the collocation types of "v+n" and "v+n," but completely ignores those of…

  9. Not Just "Small Potatoes": Knowledge of the Idiomatic Meanings of Collocations

    Science.gov (United States)

    Macis, Marijana; Schmitt, Norbert

    2017-01-01

    This study investigated learner knowledge of the figurative meanings of 30 collocations that can be both literal and figurative. One hundred and seven Chilean Spanish-speaking university students of English were asked to complete a meaning-recall collocation test in which the target items were embedded in non-defining sentences. Results showed…

  10. 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

    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...

  11. Verb-Noun Collocations in Written Discourse of Iranian EFL Learners

    Directory of Open Access Journals (Sweden)

    Fatemeh Ebrahimi-Bazzaz

    2015-07-01

    Full Text Available When native speakers of English write, they employ both grammatical rules and collocations. Collocations are words that are present in the memory of native speakers as ready-made prefabricated chunks. Non-native speakers who wish to acquire native-like fluency should give appropriate attention to collocations in writing in order not to produce sentences that native speakers may consider odd. The present study tries to explore the use of verb-noun collocations in written discourse of English as foreign language (EFL among Iranian EFL learners from one academic year to the next in Iran. To measure the use of verb-noun collocations in written discourse, there was a 60-minute task of writing story  based on a series of six pictures whereby for each picture, three verb-noun collocations were measured, and nouns were provided to limit the choice of collocations. The results of the statistical analysis of ANOVA for the research question indicated that there was a significant difference in the use of lexical verb-noun collocations in written discourse both between and within the four academic years. The results of a post hoc multiple comparison tests confirmed that the means are significantly different between the first year and the third and fourth years, between the second and the fourth, and between the third and the fourth academic year which indicate substantial development in verb-noun collocation proficiency.  The vital implication is that the learners could use verb-noun collocations in productive skill of writing.

  12. 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.

  13. Optimization of Low-Thrust Spiral Trajectories by Collocation

    Science.gov (United States)

    Falck, Robert D.; Dankanich, John W.

    2012-01-01

    As NASA examines potential missions in the post space shuttle era, there has been a renewed interest in low-thrust electric propulsion for both crewed and uncrewed missions. While much progress has been made in the field of software for the optimization of low-thrust trajectories, many of the tools utilize higher-fidelity methods which, while excellent, result in extremely high run-times and poor convergence when dealing with planetocentric spiraling trajectories deep within a gravity well. Conversely, faster tools like SEPSPOT provide a reasonable solution but typically fail to account for other forces such as third-body gravitation, aerodynamic drag, solar radiation pressure. SEPSPOT is further constrained by its solution method, which may require a very good guess to yield a converged optimal solution. Here the authors have developed an approach using collocation intended to provide solution times comparable to those given by SEPSPOT while allowing for greater robustness and extensible force models.

  14. 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

  15. 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.

  16. Assigning Significance in Label-Free Quantitative Proteomics to Include Single-Peptide-Hit Proteins with Low Replicates

    OpenAIRE

    Li, Qingbo

    2010-01-01

    When sample replicates are limited in a label-free proteomics experiment, selecting differentially regulated proteins with an assignment of statistical significance remains difficult for proteins with a single-peptide hit or a small fold-change. This paper aims to address this issue. An important component of the approach employed here is to utilize the rule of Minimum number of Permuted Significant Pairings (MPSP) to reduce false positives. The MPSP rule generates permuted sample pairings fr...

  17. Application of a modified collocation method to the one dimensional, one group neutron transport equation

    International Nuclear Information System (INIS)

    Maschek, W.

    1976-07-01

    A modified collocation method is used for solving the one group criticality problem for a uniform multiplying slab. The critical parameters and the angular fluxes for a number of slabs are displayed and compared with previously published values. (orig.) [de

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

    KAUST Repository

    Yü cel, Abdulkadir C.; Bagci, Hakan; Michielssen, Eric

    2013-01-01

    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

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

    KAUST Repository

    Bä ck, Joakim; Nobile, Fabio; Tamellini, Lorenzo; Tempone, Raul

    2010-01-01

    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

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

    KAUST Repository

    Motamed, Mohammad; Nobile, Fabio; Tempone, Raul

    2012-01-01

    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

  1. High-frequency collocations of nouns in research articles across eight disciplines

    Directory of Open Access Journals (Sweden)

    Matthew Peacock

    2012-04-01

    Full Text Available This paper describes a corpus-based analysis of the distribution of the high-frequency collocates of abstract nouns in 320 research articles across eight disciplines: Chemistry, Computer Science, Materials Science, Neuroscience, Economics, Language and Linguistics, Management, and Psychology. Disciplinary variation was also examined – very little previous research seems to have investigated this. The corpus was analysed using WordSmith Tools. The 16 highest-frequency nouns across all eight disciplines were identified, followed by the highest-frequency collocates for each noun. Five disciplines showed over 50% variance from the overall results. Conclusions are that the differing patterns revealed are disciplinary norms and represent standard terminology within the disciplines arising from the topics discussed, research methods, and content of discussions. It is also concluded that the collocations are an important part of the meanings and functions of the nouns, and that this evidence of sharp discipline differences underlines the importance of discipline-specific collocation research.

  2. 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.

  3. Cold and Heat Stress Diversely Alter Both Cauliflower Respiration and Distinct Mitochondrial Proteins Including OXPHOS Components and Matrix Enzymes

    Science.gov (United States)

    Rurek, Michał; Czołpińska, Magdalena; Pawłowski, Tomasz Andrzej; Krzesiński, Włodzimierz; Spiżewski, Tomasz

    2018-01-01

    Complex proteomic and physiological approaches for studying cold and heat stress responses in plant mitochondria are still limited. Variations in the mitochondrial proteome of cauliflower (Brassica oleracea var. botrytis) curds after cold and heat and after stress recovery were assayed by two-dimensional polyacrylamide gel electrophoresis (2D PAGE) in relation to mRNA abundance and respiratory parameters. Quantitative analysis of the mitochondrial proteome revealed numerous stress-affected protein spots. In cold, major downregulations in the level of photorespiratory enzymes, porine isoforms, oxidative phosphorylation (OXPHOS) and some low-abundant proteins were observed. In contrast, carbohydrate metabolism enzymes, heat-shock proteins, translation, protein import, and OXPHOS components were involved in heat response and recovery. Several transcriptomic and metabolic regulation mechanisms are also suggested. Cauliflower plants appeared less susceptible to heat; closed stomata in heat stress resulted in moderate photosynthetic, but only minor respiratory impairments, however, photosystem II performance was unaffected. Decreased photorespiration corresponded with proteomic alterations in cold. Our results show that cold and heat stress not only operate in diverse modes (exemplified by cold-specific accumulation of some heat shock proteins), but exert some associations at molecular and physiological levels. This implies a more complex model of action of investigated stresses on plant mitochondria. PMID:29547512

  4. 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.

  5. Block Hybrid Collocation Method with Application to Fourth Order Differential Equations

    Directory of Open Access Journals (Sweden)

    Lee Ken Yap

    2015-01-01

    Full Text Available The block hybrid collocation method with three off-step points is proposed for the direct solution of fourth order ordinary differential equations. The interpolation and collocation techniques are applied on basic polynomial to generate the main and additional methods. These methods are implemented in block form to obtain the approximation at seven points simultaneously. Numerical experiments are conducted to illustrate the efficiency of the method. The method is also applied to solve the fourth order problem from ship dynamics.

  6. 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.

  7. 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

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

    Directory of Open Access Journals (Sweden)

    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.

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

    Directory of Open Access Journals (Sweden)

    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.

  10. 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.

  11. Multi-element probabilistic collocation method in high dimensions

    International Nuclear Information System (INIS)

    Foo, Jasmine; Karniadakis, George Em

    2010-01-01

    We combine multi-element polynomial chaos with analysis of variance (ANOVA) functional decomposition to enhance the convergence rate of polynomial chaos in high dimensions and in problems with low stochastic regularity. Specifically, we employ the multi-element probabilistic collocation method MEPCM and so we refer to the new method as MEPCM-A. We investigate the dependence of the convergence of MEPCM-A on two decomposition parameters, the polynomial order μ and the effective dimension ν, with ν<< N, and N the nominal dimension. Numerical tests for multi-dimensional integration and for stochastic elliptic problems suggest that ν≥μ for monotonic convergence of the method. We also employ MEPCM-A to obtain error bars for the piezometric head at the Hanford nuclear waste site under stochastic hydraulic conductivity conditions. Finally, we compare the cost of MEPCM-A against Monte Carlo in several hundred dimensions, and we find MEPCM-A to be more efficient for up to 600 dimensions for a specific multi-dimensional integration problem involving a discontinuous function.

  12. Collocated Dataglyphs for large-message storage and retrieval

    Science.gov (United States)

    Motwani, Rakhi C.; Breidenbach, Jeff A.; Black, John R.

    2004-06-01

    In contrast to the security and integrity of electronic files, printed documents are vulnerable to damage and forgery due to their physical nature. Researchers at Palo Alto Research Center utilize DataGlyph technology to render digital characteristics to printed documents, which provides them with the facility of tamper-proof authentication and damage resistance. This DataGlyph document is known as GlyphSeal. Limited DataGlyph carrying capacity per printed page restricted the application of this technology to a domain of graphically simple and small-sized single-paged documents. In this paper the authors design a protocol motivated by techniques from the networking domain and back-up strategies, which extends the GlyphSeal technology to larger-sized, graphically complex, multi-page documents. This protocol provides fragmentation, sequencing and data loss recovery. The Collocated DataGlyph Protocol renders large glyph messages onto multiple printed pages and recovers the glyph data from rescanned versions of the multi-page documents, even when pages are missing, reordered or damaged. The novelty of this protocol is the application of ideas from RAID to the domain of DataGlyphs. The current revision of this protocol is capable of generating at most 255 pages, if page recovery is desired and does not provide enough data density to store highly detailed images in a reasonable amount of page space.

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

    Directory of Open Access Journals (Sweden)

    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

  14. The HTLV-1 Tax protein binding domain of cyclin-dependent kinase 4 (CDK4 includes the regulatory PSTAIRE helix

    Directory of Open Access Journals (Sweden)

    Grassmann Ralph

    2005-09-01

    Full Text Available Abstract Background The Tax oncoprotein of human T-cell leukemia virus type 1 (HTLV-1 is leukemogenic in transgenic mice and induces permanent T-cell growth in vitro. It is found in active CDK holoenzyme complexes from adult T-cell leukemia-derived cultures and stimulates the G1- to-S phase transition by activating the cyclin-dependent kinase (CDK CDK4. The Tax protein directly and specifically interacts with CDK4 and cyclin D2 and binding is required for enhanced CDK4 kinase activity. The protein-protein contact between Tax and the components of the cyclin D/CDK complexes increases the association of CDK4 and its positive regulatory subunit cyclin D and renders the complex resistant to p21CIP inhibition. Tax mutants affecting the N-terminus cannot bind cyclin D and CDK4. Results To analyze, whether the N-terminus of Tax is capable of CDK4-binding, in vitro binding -, pull down -, and mammalian two-hybrid analyses were performed. These experiments revealed that a segment of 40 amino acids is sufficient to interact with CDK4 and cyclin D2. To define a Tax-binding domain and analyze how Tax influences the kinase activity, a series of CDK4 deletion mutants was tested. Different assays revealed two regions which upon deletion consistently result in reduced binding activity. These were isolated and subjected to mammalian two-hybrid analysis to test their potential to interact with the Tax N-terminus. These experiments concurrently revealed binding at the N- and C-terminus of CDK4. The N-terminal segment contains the PSTAIRE helix, which is known to control the access of substrate to the active cleft of CDK4 and thus the kinase activity. Conclusion Since the N- and C-terminus of CDK4 are neighboring in the predicted three-dimensional protein structure, it is conceivable that they comprise a single binding domain, which interacts with the Tax N-terminus.

  15. Proteomic identification of Drosophila melanogaster male accessory gland proteins, including a pro-cathepsin and a soluble γ-glutamyl transpeptidase

    Directory of Open Access Journals (Sweden)

    Sajid Mohammed

    2006-05-01

    Full Text Available Background In Drosophila melanogaster, the male seminal fluid contains proteins that are important for reproductive success. Many of these proteins are synthesised by the male accessory glands and are secreted into the accessory gland lumen, where they are stored until required. Previous studies on the identification of Drosophila accessory gland products have largely focused on characterisation of male-specific accessory gland cDNAs from D. melanogaster and, more recently, Drosophila simulans. In the present study, we have used a proteomics approach without any sex bias to identify proteins in D. melanogaster accessory gland secretions. Results Thirteen secreted accessory gland proteins, including seven new accessory gland proteins, were identified by 2D-gel electrophoresis combined with mass spectrometry of tryptic fragments. They included protein-folding and stress-response proteins, a hormone, a lipase, a serpin, a cysteine-rich protein and two peptidases, a pro-enzyme form of a cathepsin K-like cysteine peptidase and a γ-glutamyl transpeptidase. Enzymatic studies established that accessory gland secretions contain a cysteine peptidase zymogen that can be activated at low pH. This peptidase may have a role in the processing of female and other male-derived proteins, but is unlikely to be involved in the processing of the sex peptide. γ-Glutamyl transpeptidases are type II integral membrane proteins; however, the identified AG γ-glutamyl transpeptidase (GGT-1 is unusual in that it is predicted to be a soluble secreted protein, a prediction that is supported by biochemical evidence. GGT-1 is possibly involved in maintaining a protective redox environment for sperm. The strong γ-glutamyl transpeptidase activity found in the secretions provides an explanation for the observation that glutamic acid is the most abundant free amino acid in accessory gland secretions of D. melanogaster. Conclusion We have applied biochemical approaches, not used

  16. Proteomic identification of Drosophila melanogaster male accessory gland proteins, including a pro-cathepsin and a soluble gamma-glutamyl transpeptidase.

    Science.gov (United States)

    Walker, Michael J; Rylett, Caroline M; Keen, Jeff N; Audsley, Neil; Sajid, Mohammed; Shirras, Alan D; Isaac, R Elwyn

    2006-05-02

    In Drosophila melanogaster, the male seminal fluid contains proteins that are important for reproductive success. Many of these proteins are synthesised by the male accessory glands and are secreted into the accessory gland lumen, where they are stored until required. Previous studies on the identification of Drosophila accessory gland products have largely focused on characterisation of male-specific accessory gland cDNAs from D. melanogaster and, more recently, Drosophila simulans. In the present study, we have used a proteomics approach without any sex bias to identify proteins in D. melanogaster accessory gland secretions. Thirteen secreted accessory gland proteins, including seven new accessory gland proteins, were identified by 2D-gel electrophoresis combined with mass spectrometry of tryptic fragments. They included protein-folding and stress-response proteins, a hormone, a lipase, a serpin, a cysteine-rich protein and two peptidases, a pro-enzyme form of a cathepsin K-like cysteine peptidase and a gamma-glutamyl transpeptidase. Enzymatic studies established that accessory gland secretions contain a cysteine peptidase zymogen that can be activated at low pH. This peptidase may have a role in the processing of female and other male-derived proteins, but is unlikely to be involved in the processing of the sex peptide. gamma-Glutamyl transpeptidases are type II integral membrane proteins; however, the identified AG gamma-glutamyl transpeptidase (GGT-1) is unusual in that it is predicted to be a soluble secreted protein, a prediction that is supported by biochemical evidence. GGT-1 is possibly involved in maintaining a protective redox environment for sperm. The strong gamma-glutamyl transpeptidase activity found in the secretions provides an explanation for the observation that glutamic acid is the most abundant free amino acid in accessory gland secretions of D. melanogaster. We have applied biochemical approaches, not used previously, to characterise

  17. FTA Corpus: a parallel corpus of English and Spanish Free Trade Agreements for the study of specialized collocations

    Directory of Open Access Journals (Sweden)

    Pedro Patiño García

    2013-04-01

    Full Text Available This paper describes the Corpus of Free Trade Agreements (henceforth FTA, a specialized parallel corpus in English and Spanish from Europe and America and a smaller subcorpus in English-Norwegian and Spanish-Norwegian that was prepared and then aligned with Translation Corpus Aligner 2 (Hofland & Johansson, 1998. The data was taken from Free Trade Agreements. These agreements are specialized texts officially signed and ratified by several countries and blocks of countries in the last twenty years. Thus, FTAs are a rich repository for terminology and phraseology that is used in different fields of business activity throughout the world. The corpus contains around 1.37 million words in the English section and 1.48 million words in its Spanish counterpart, plus 60,000 words each in the Spanish-Norwegian and English-Norwegian subcorpus. The corpus is being used primarily to study the terms and specialized collocations that include these terms in this kind of specialized texts.Keywords: specialized collocation, specialized parallel corpus, corpus linguistics, Free Trade Agreement

  18. The TAL effector PthA4 interacts with nuclear factors involved in RNA-dependent processes including a HMG protein that selectively binds poly(U RNA.

    Directory of Open Access Journals (Sweden)

    Tiago Antonio de Souza

    Full Text Available Plant pathogenic bacteria utilize an array of effector proteins to cause disease. Among them, transcriptional activator-like (TAL effectors are unusual in the sense that they modulate transcription in the host. Although target genes and DNA specificity of TAL effectors have been elucidated, how TAL proteins control host transcription is poorly understood. Previously, we showed that the Xanthomonas citri TAL effectors, PthAs 2 and 3, preferentially targeted a citrus protein complex associated with transcription control and DNA repair. To extend our knowledge on the mode of action of PthAs, we have identified new protein targets of the PthA4 variant, required to elicit canker on citrus. Here we show that all the PthA4-interacting proteins are DNA and/or RNA-binding factors implicated in chromatin remodeling and repair, gene regulation and mRNA stabilization/modification. The majority of these proteins, including a structural maintenance of chromosomes protein (CsSMC, a translin-associated factor X (CsTRAX, a VirE2-interacting protein (CsVIP2, a high mobility group (CsHMG and two poly(A-binding proteins (CsPABP1 and 2, interacted with each other, suggesting that they assemble into a multiprotein complex. CsHMG was shown to bind DNA and to interact with the invariable leucine-rich repeat region of PthAs. Surprisingly, both CsHMG and PthA4 interacted with PABP1 and 2 and showed selective binding to poly(U RNA, a property that is novel among HMGs and TAL effectors. Given that homologs of CsHMG, CsPABP1, CsPABP2, CsSMC and CsTRAX in other organisms assemble into protein complexes to regulate mRNA stability and translation, we suggest a novel role of TAL effectors in mRNA processing and translational control.

  19. 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

  20. 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.

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

    Science.gov (United States)

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

    2007-02-01

    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.

  2. 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

  3. 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.

  4. Nested sparse grid collocation method with delay and transformation for subsurface flow and transport problems

    Science.gov (United States)

    Liao, Qinzhuo; Zhang, Dongxiao; Tchelepi, Hamdi

    2017-06-01

    In numerical modeling of subsurface flow and transport problems, formation properties may not be deterministically characterized, which leads to uncertainty in simulation results. In this study, we propose a sparse grid collocation method, which adopts nested quadrature rules with delay and transformation to quantify the uncertainty of model solutions. We show that the nested Kronrod-Patterson-Hermite quadrature is more efficient than the unnested Gauss-Hermite quadrature. We compare the convergence rates of various quadrature rules including the domain truncation and domain mapping approaches. To further improve accuracy and efficiency, we present a delayed process in selecting quadrature nodes and a transformed process for approximating unsmooth or discontinuous solutions. The proposed method is tested by an analytical function and in one-dimensional single-phase and two-phase flow problems with different spatial variances and correlation lengths. An additional example is given to demonstrate its applicability to three-dimensional black-oil models. It is found from these examples that the proposed method provides a promising approach for obtaining satisfactory estimation of the solution statistics and is much more efficient than the Monte-Carlo simulations.

  5. 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.

  6. 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.

  7. Numerical simulation for fractional order stationary neutron transport equation using Haar wavelet collocation method

    Energy Technology Data Exchange (ETDEWEB)

    Saha Ray, S., E-mail: santanusaharay@yahoo.com; Patra, A.

    2014-10-15

    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: In this paper the numerical solution for the fractional order stationary neutron transport equation is presented using Haar wavelet Collocation Method (HWCM). Haar wavelet collocation method is efficient and powerful in solving wide class of linear and nonlinear differential equations. This paper intends to provide an application of Haar wavelets to nuclear science problems. This paper describes the application of Haar wavelets for the numerical solution of fractional order stationary neutron transport equation in homogeneous medium with isotropic scattering. The proposed method is mathematically very simple, easy and fast. To demonstrate about the efficiency and applicability of the method, two test problems are discussed.

  8. Molecular network including eIF1AX, RPS7, and 14-3-3γ regulates protein translation and cell proliferation in bovine mammary epithelial cells.

    Science.gov (United States)

    Yu, Cuiping; Luo, Chaochao; Qu, Bo; Khudhair, Nagam; Gu, Xinyu; Zang, Yanli; Wang, Chunmei; Zhang, Na; Li, Qingzhang; Gao, Xuejun

    2014-12-15

    14-3-3γ, an isoform of the 14-3-3 protein family, was proved to be a positive regulator of mTOR pathway. Here, we analyzed the function of 14-3-3γ in protein synthesis using bovine mammary epithelial cells (BMECs). We found that 14-3-3γ interacted with eIF1AX and RPS7 by 14-3-3γ coimmunoprecipitation (CoIP) and matrix-assisted laser desorption/ionization-time-of-flight/time-of-flight (MALDI-TOF/TOF) peptide mass fingerprinting analysis. These interactions of 14-3-3γ with eIF1AX and RPS7 were further confirmed by colocalization and fluorescence resonance energy transfer (FRET) analysis. We also found that methionine could promote protein synthesis and trigger the protein expression levels of 14-3-3γ, eIF1AX and RPS7. Analysis of overexpression and inhibition of 14-3-3γ confirmed that it positively affected the protein expression levels of eIF1AX, RPS7, Stat5 and mTOR pathway to promote protein synthesis and cell proliferation in BMECs. We further showed that overexpression of eIF1AX and RPS7 also triggered protein translation and cell proliferation. From these results, we conclude that molecular network including eIF1AX, RPS7, and 14-3-3γ regulates protein translation and cell proliferation in BMECs. Copyright © 2014 Elsevier Inc. All rights reserved.

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

    Directory of Open Access Journals (Sweden)

    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.

  10. Adaptive wavelet collocation methods for initial value boundary problems of nonlinear PDE's

    Science.gov (United States)

    Cai, Wei; Wang, Jian-Zhong

    1993-01-01

    We have designed a cubic spline wavelet decomposition for the Sobolev space H(sup 2)(sub 0)(I) where I is a bounded interval. Based on a special 'point-wise orthogonality' of the wavelet basis functions, a fast Discrete Wavelet Transform (DWT) is constructed. This DWT transform will map discrete samples of a function to its wavelet expansion coefficients in O(N log N) operations. Using this transform, we propose a collocation method for the initial value boundary problem of nonlinear PDE's. Then, we test the efficiency of the DWT transform and apply the collocation method to solve linear and nonlinear PDE's.

  11. Non-standard finite difference and Chebyshev collocation methods for solving fractional diffusion equation

    Science.gov (United States)

    Agarwal, P.; El-Sayed, A. A.

    2018-06-01

    In this paper, a new numerical technique for solving the fractional order diffusion equation is introduced. This technique basically depends on the Non-Standard finite difference method (NSFD) and Chebyshev collocation method, where the fractional derivatives are described in terms of the Caputo sense. The Chebyshev collocation method with the (NSFD) method is used to convert the problem into a system of algebraic equations. These equations solved numerically using Newton's iteration method. The applicability, reliability, and efficiency of the presented technique are demonstrated through some given numerical examples.

  12. 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.

  13. 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).

  14. 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…

  15. 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

    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.......02 ± 0.01 mmol/mol, p eGFR in Lifelines (slope 0.17 ± 0.02 mL/min/1.73 m², p

  16. 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.

  17. 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

  18. The Application of the Probabilistic Collocation Method to a Transonic Axial Flow Compressor

    NARCIS (Netherlands)

    Loeven, G.J.A.; Bijl, H.

    2010-01-01

    In this paper the Probabilistic Collocation method is used for uncertainty quantification of operational uncertainties in a transonic axial flow compressor (i.e. NASA Rotor 37). Compressor rotors are components of a gas turbine that are highly sensitive to operational and geometrical uncertainties.

  19. An improved triple collocation algorithm for decomposing autocorrelated and white soil moisture retrieval errors

    Science.gov (United States)

    If not properly account for, auto-correlated errors in observations can lead to inaccurate results in soil moisture data analysis and reanalysis. Here, we propose a more generalized form of the triple collocation algorithm (GTC) capable of decomposing the total error variance of remotely-sensed surf...

  20. 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…

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

    KAUST Repository

    Beck, Joakim; Nobile, F.; Tamellini, L.; Tempone, Raul

    2011-01-01

    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.

  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. 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

  4. 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.

  5. 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.

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

    KAUST Repository

    Nobile, Fabio; Haji Ali, Abdul Lateef; Tamellini, Lorenzo; Tempone, Raul

    2016-01-01

    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.

  7. 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.

  8. 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.

  9. 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

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

    KAUST Repository

    Haji Ali, Abdul Lateef; Nobile, Fabio; Tamellini, Lorenzo; Tempone, Raul

    2016-01-01

    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

  11. 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

  12. Members of the HCMV US12 family of predicted heptaspanning membrane proteins have unique intracellular distributions, including association with the cytoplasmic virion assembly complex

    International Nuclear Information System (INIS)

    Das, Subhendu; Pellett, Philip E.

    2007-01-01

    The human cytomegalovirus (HCMV) US12 gene family is a group of 10 predicted seven-transmembrane domain proteins that have some features in common with G-protein-coupled receptors. Little is known of their patterns of expression, localization, or functional interactions. Here, we studied the intracellular localization of three US12 family members, US14, US17, and US18, with respect to various intracellular markers and the cytoplasmic virion assembly compartment (AC). The three proteins have distinct patterns of expression, which include associations with the AC. US14 is often distributed in a uniform granular manner throughout the cytoplasm, concentrating in the AC in some cells. US17 is expressed in a segmented manner, with its N-terminal domain localizing to the periphery of what we show here to be the AC and the C-terminal domain localizing to nuclei and the cytoplasm [Das, S., Skomorovska-Prokvolit, Y., Wang, F. Z., Pellett, P.E., 2006. Infection-dependent nuclear localization of US17, a member of the US12 family of human cytomegalovirus-encoded seven-transmembrane proteins. J. Virol. 80, 1191-1203]. Here, we show that the C-terminal domain is present at the center of the AC, in close association with markers of early endosomes; the N-terminal staining corresponds to an area stained by markers for the Golgi and trans-Golgi. US18 is distributed throughout the cytoplasm, concentrating in the AC at later stages of infection; it is localized more to the periphery of the AC than are US14 and US17C, in association with markers of the trans-Golgi. Although not detected in virions, their structures and localization in various zones within the AC suggest possible roles for these proteins in the process of virion maturation and egress

  13. [Evaluation of ten fish species to be included as part of renal diet, due to their protein, phosphorus and fatty acids content].

    Science.gov (United States)

    Castro-González, Maria Isabel; Maafs-Rodríguez, Ana Gabriela; Pérez-Gil Romo, Fernando

    2012-06-01

    Because renal disease is highly complex, its nutritional treatment is complicated and many foods are restricted, including fish because its phosphorus content. The aim of the present study was to analyze ten fillet fish species, commonly consumed in Mexico (Cyprinus carpio carpio, Ophichthus rex, Symphurus elongatus, Eucinostomus entomelas, Chirostoma patzcuaro, Bairdiella chrysoura, Salmo salar Oreochromis urolepis hornorum, Sphyraena guachancho, Istiophorus albicans), to determine their phosphorus (P), protein (Pr), cholesterol, sodium, potassium, vitamins D3 and E, and n-3 PUFA (EPA+DHA) according to the AOAC techniques, in order to identify which species could be included in renal diet; particularly because of their risk:benefit relations (calculated with those results). Protein values ranged from 16.5 to 33.5g/100 g of fillet; the specie with the highest phosphorus contest was Salmo salar, and with the lowest, Symphurus elongatus. EPA+DHA quantity ranged from 79.64 mg/100 g to 1,381.53 mg/100 g. Considering de P/Pr relation recommended to renal patients, all analyzed species (except Salmo salar, Ophichthus rex and Istiophorus albicans) could be included in their diet. As for the P/EPA+DHA relation, the species most recommended to renal patients are Symphurus elongatus, Bairdiella chrysoura and Sphyraena guachancho.

  14. 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.

  15. 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.

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

    KAUST Repository

    Malenova, G.; Motamed, M.; Runborg, O.; Tempone, Raul

    2016-01-01

    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.

  17. 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.

  18. 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.

  19. A multi-dimensional Smolyak collocation method in curvilinear coordinates for computing vibrational spectra

    International Nuclear Information System (INIS)

    Avila, Gustavo; Carrington, Tucker

    2015-01-01

    In this paper, we improve the collocation method for computing vibrational spectra that was presented in Avila and Carrington, Jr. [J. Chem. Phys. 139, 134114 (2013)]. Using an iterative eigensolver, energy levels and wavefunctions are determined from values of the potential on a Smolyak grid. The kinetic energy matrix-vector product is evaluated by transforming a vector labelled with (nondirect product) grid indices to a vector labelled by (nondirect product) basis indices. Both the transformation and application of the kinetic energy operator (KEO) scale favorably. Collocation facilitates dealing with complicated KEOs because it obviates the need to calculate integrals of coordinate dependent coefficients of differential operators. The ideas are tested by computing energy levels of HONO using a KEO in bond coordinates

  20. 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.

  1. 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.

  2. 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

  3. Nodal collocation approximation for the multidimensional PL equations applied to transport source problems

    International Nuclear Information System (INIS)

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

    2012-01-01

    PL equations are classical high order approximations to the transport equations which are based on the expansion of the angular dependence of the angular neutron flux and the nuclear cross sections in terms of spherical harmonics. A nodal collocation method is used to discretize the PL equations associated with a neutron source transport problem. The performance of the method is tested solving two 1D problems with analytical solution for the transport equation and a classical 2D problem. (authors)

  4. Big Data and HPC collocation: Using HPC idle resources for Big Data Analytics

    OpenAIRE

    MERCIER , Michael; Glesser , David; Georgiou , Yiannis; Richard , Olivier

    2017-01-01

    International audience; Executing Big Data workloads upon High Performance Computing (HPC) infrastractures has become an attractive way to improve their performances. However, the collocation of HPC and Big Data workloads is not an easy task, mainly because of their core concepts' differences. This paper focuses on the challenges related to the scheduling of both Big Data and HPC workloads on the same computing platform. In classic HPC workloads, the rigidity of jobs tends to create holes in ...

  5. Nodal collocation approximation for the multidimensional PL equations applied to transport source problems

    Energy Technology Data Exchange (ETDEWEB)

    Verdu, G. [Departamento de Ingenieria Quimica Y Nuclear, Universitat Politecnica de Valencia, Cami de Vera, 14, 46022. Valencia (Spain); Capilla, M.; Talavera, C. F.; Ginestar, D. [Dept. of Nuclear Engineering, Departamento de Matematica Aplicada, Universitat Politecnica de Valencia, Cami de Vera, 14, 46022. Valencia (Spain)

    2012-07-01

    PL equations are classical high order approximations to the transport equations which are based on the expansion of the angular dependence of the angular neutron flux and the nuclear cross sections in terms of spherical harmonics. A nodal collocation method is used to discretize the PL equations associated with a neutron source transport problem. The performance of the method is tested solving two 1D problems with analytical solution for the transport equation and a classical 2D problem. (authors)

  6. 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.

  7. A Legendre Wavelet Spectral Collocation Method for Solving Oscillatory Initial Value Problems

    Directory of Open Access Journals (Sweden)

    A. Karimi Dizicheh

    2013-01-01

    wavelet suitable for large intervals, and then the Legendre-Guass collocation points of the Legendre wavelet are derived. Using this strategy, the iterative spectral method converts the differential equation to a set of algebraic equations. Solving these algebraic equations yields an approximate solution for the differential equation. The proposed method is illustrated by some numerical examples, and the result is compared with the exponentially fitted Runge-Kutta method. Our proposed method is simple and highly accurate.

  8. 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.

  9. Spline Collocation Method for Nonlinear Multi-Term Fractional Differential Equation

    OpenAIRE

    Choe, Hui-Chol; Kang, Yong-Suk

    2013-01-01

    We study an approximation method to solve nonlinear multi-term fractional differential equations with initial conditions or boundary conditions. First, we transform the nonlinear multi-term fractional differential equations with initial conditions and boundary conditions to nonlinear fractional integral equations and consider the relations between them. We present a Spline Collocation Method and prove the existence, uniqueness and convergence of approximate solution as well as error estimatio...

  10. Fermat collocation method for the solutions of nonlinear system of second order boundary value problems

    Directory of Open Access Journals (Sweden)

    Salih Yalcinbas

    2016-01-01

    Full Text Available In this study, a numerical approach is proposed to obtain approximate solutions of nonlinear system of second order boundary value problem. This technique is essentially based on the truncated Fermat series and its matrix representations with collocation points. Using the matrix method, we reduce the problem system of nonlinear algebraic equations. Numerical examples are also given to demonstrate the validity and applicability of the presented technique. The method is easy to implement and produces accurate results.

  11. 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.

  12. Application of adaptive hierarchical sparse grid collocation to the uncertainty quantification of nuclear reactor simulators

    Energy Technology Data Exchange (ETDEWEB)

    Yankov, A.; Downar, T. [University of Michigan, 2355 Bonisteel Blvd, Ann Arbor, MI 48109 (United States)

    2013-07-01

    Recent efforts in the application of uncertainty quantification to nuclear systems have utilized methods based on generalized perturbation theory and stochastic sampling. While these methods have proven to be effective they both have major drawbacks that may impede further progress. A relatively new approach based on spectral elements for uncertainty quantification is applied in this paper to several problems in reactor simulation. Spectral methods based on collocation attempt to couple the approximation free nature of stochastic sampling methods with the determinism of generalized perturbation theory. The specific spectral method used in this paper employs both the Smolyak algorithm and adaptivity by using Newton-Cotes collocation points along with linear hat basis functions. Using this approach, a surrogate model for the outputs of a computer code is constructed hierarchically by adaptively refining the collocation grid until the interpolant is converged to a user-defined threshold. The method inherently fits into the framework of parallel computing and allows for the extraction of meaningful statistics and data that are not within reach of stochastic sampling and generalized perturbation theory. This paper aims to demonstrate the advantages of spectral methods-especially when compared to current methods used in reactor physics for uncertainty quantification-and to illustrate their full potential. (authors)

  13. Using Small Parallel Corpora to Develop Collocation-Centred Activities in Specialized Translation Classes

    Directory of Open Access Journals (Sweden)

    Postolea Sorina

    2016-12-01

    Full Text Available The research devoted to special languages as well as the activities carried out in specialized translation classes tend to focus primarily on one-word or multi-word terminological units. However, a very important part in the making of specialist registers and texts is played by specialised collocations, i.e. relatively stable word combinations that do not designate concepts but are nevertheless of frequent use in a given field of activity. This is why helping students acquire competences relative to the identification and processing of collocations should become an important objective in specialised translation classes. An easily accessible and dependable resource that may be successfully used to this purpose is represented by corpora and corpus analysis tools, whose usefulness in translator training has been highlighted by numerous studies. This article proposes a series of practical, task-based activities-developed with the help of a small-size parallel corpus of specialised texts-that aim to raise the translation trainees′ awareness of the collocations present in specialised texts and to provide suggestions about their processing in translation.

  14. 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.

  15. 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.

  16. 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.

  17. Calibration laboratories as a regional repair center: consolidate or collocate

    OpenAIRE

    Mitchell, Marquita A; Pasch, John E.

    1996-01-01

    The purpose of this thesis is to examine the integration of AIMDs Miramar and North Island, and NADEP North Island calibration laboratories. The expected benefits and weaknesses or problems resulting from integration are examined. The benefits analyzed include those in the areas of manpower, training, standards reduction, inventory reduction, streamlining facilities, and increased productivity. The problems analyzed include increased transportation costs, facilities modification costs, reduce...

  18. 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.

  19. 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.

  20. A fractional spline collocation-Galerkin method for the time-fractional diffusion equation

    Directory of Open Access Journals (Sweden)

    Pezza L.

    2018-03-01

    Full Text Available The aim of this paper is to numerically solve a diffusion differential problem having time derivative of fractional order. To this end we propose a collocation-Galerkin method that uses the fractional splines as approximating functions. The main advantage is in that the derivatives of integer and fractional order of the fractional splines can be expressed in a closed form that involves just the generalized finite difference operator. This allows us to construct an accurate and efficient numerical method. Several numerical tests showing the effectiveness of the proposed method are presented.

  1. 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.

  2. 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.

  3. Collocational Networks Supporting Strategic Planning of Brand Communication: Analysis of Quarterly Reports of Telecommunication Companies

    Directory of Open Access Journals (Sweden)

    Pentti Järvi

    2004-10-01

    Full Text Available This study addresses analysing quarterly reports from a brandtheoretical viewpoint. The study addresses the issue through a method which introduces both a quantitative tool based on linguistic theory and qualitative decisions of the researchers. The research objects of this study are two quarterly reports each of three telecommunications companies: Ericsson, Motorola and Nokia. The method used is a collocational network. The analyses show that there are differences in communication and message strategies among investigated companies and also changes during a quite short period in each company

  4. 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.

  5. 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

  6. Modelling and Simulation of a Packed Bed of Pulp Fibers Using Mixed Collocation Method

    Directory of Open Access Journals (Sweden)

    Ishfaq Ahmad Ganaie

    2013-01-01

    Full Text Available A convenient computational approach for solving mathematical model related to diffusion dispersion during flow through packed bed is presented. The algorithm is based on the mixed collocation method. The method is particularly useful for solving stiff system arising in chemical and process engineering. The convergence of the method is found to be of order 2 using the roots of shifted Chebyshev polynomial. Model is verified using the literature data. This method has provided a convenient check on the accuracy of the results for wide range of parameters, namely, Peclet numbers. Breakthrough curves are plotted to check the effect of Peclet number on average and exit solute concentrations.

  7. 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.

  8. 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.

  9. Collocated Interaction

    DEFF Research Database (Denmark)

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

    2016-01-01

    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......In the 25 years since Ellis, Gibbs, and Rein proposed the time-space taxonomy, research in the ‘same time, same place’ quadrant has diversified, perhaps even fragmented. This one-day workshop will bring together researchers with diverse, yet convergent interests in tabletop, surface, mobile...

  10. 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.

  11. 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.

  12. Comparison of multiphase mixing simulations performed on a staggered and a collocated grid

    International Nuclear Information System (INIS)

    Leskovar, M.

    2000-01-01

    During a severe reactor accident following core meltdown when the molten fuel comes into contact with the coolant water a steam explosion may occur. The premixing phase of a steam explosion covers the interaction of the melt jet or droplets with the water prior to any steam explosion occurrence. To get a better insight of the hydrodynamic processes during the premixing phase beside hot premixing experiments, where the water evaporation is significant, also cold isothermal premixing experiments are performed. To analyze the cold premixing experiments the computer code ESE has been developed. The specialty of ESE is that it uses a combined single-multiphase flow model. Because of problems with the convergence of the momentum equation written in conservative form on a staggered grid, the development of a collocated grid version of ESE was planed. But since we obtained the commercial code CFX-4.3, which uses a collocated variable arrangement, we decided first to test the capabilities of CFX-4.3. With ESE and CFX-4.3 the cold premixing experiment Q08 has been simulated. In the paper the simulation results performed with both codes are presented and commented in comparison to experimental data. (author)

  13. 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.

  14. On multilevel RBF collocation to solve nonlinear PDEs arising from endogenous stochastic volatility models

    Science.gov (United States)

    Bastani, Ali Foroush; Dastgerdi, Maryam Vahid; Mighani, Abolfazl

    2018-06-01

    The main aim of this paper is the analytical and numerical study of a time-dependent second-order nonlinear partial differential equation (PDE) arising from the endogenous stochastic volatility model, introduced in [Bensoussan, A., Crouhy, M. and Galai, D., Stochastic equity volatility related to the leverage effect (I): equity volatility behavior. Applied Mathematical Finance, 1, 63-85, 1994]. As the first step, we derive a consistent set of initial and boundary conditions to complement the PDE, when the firm is financed by equity and debt. In the sequel, we propose a Newton-based iteration scheme for nonlinear parabolic PDEs which is an extension of a method for solving elliptic partial differential equations introduced in [Fasshauer, G. E., Newton iteration with multiquadrics for the solution of nonlinear PDEs. Computers and Mathematics with Applications, 43, 423-438, 2002]. The scheme is based on multilevel collocation using radial basis functions (RBFs) to solve the resulting locally linearized elliptic PDEs obtained at each level of the Newton iteration. We show the effectiveness of the resulting framework by solving a prototypical example from the field and compare the results with those obtained from three different techniques: (1) a finite difference discretization; (2) a naive RBF collocation and (3) a benchmark approximation, introduced for the first time in this paper. The numerical results confirm the robustness, higher convergence rate and good stability properties of the proposed scheme compared to other alternatives. We also comment on some possible research directions in this field.

  15. 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).

  16. 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.

  17. 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.

  18. Cranberry juice consumption lowers markers of cardiometabolic risk, including blood pressure and circulating C-reactive protein, triglyceride, and glucose concentrations in adults.

    Science.gov (United States)

    Novotny, Janet A; Baer, David J; Khoo, Christina; Gebauer, Sarah K; Charron, Craig S

    2015-06-01

    Cardiometabolic risk is the risk of cardiovascular disease (CVD), diabetes, or stroke, which are leading causes of mortality and morbidity worldwide. The objective of this study was to determine the potential of low-calorie cranberry juice (LCCJ) to lower cardiometabolic risk. A double-blind, placebo-controlled, parallel-arm study was conducted with controlled diets. Thirty women and 26 men (mean baseline characteristics: 50 y; weight, 79 kg; body mass index, 28 kg/m(2)) completed an 8-wk intervention with LCCJ or a flavor/color/energy-matched placebo beverage. Twice daily volunteers consumed 240 mL of LCCJ or the placebo beverage, containing 173 or 62 mg of phenolic compounds and 6.5 or 7.5 g of total sugar per 240-mL serving, respectively. Fasting serum triglycerides (TGs) were lower after consuming LCCJ and demonstrated a treatment × baseline interaction such that the participants with higher baseline TG concentrations were more likely to experience a larger treatment effect (1.15 ± 0.04 mmol/L vs. 1.25 ± 0.04 mmol/L, respectively; P = 0.027). Serum C-reactive protein (CRP) was lower for individuals consuming LCCJ than for individuals consuming the placebo beverage [ln transformed values of 0.522 ± 0.115 ln(mg/L) vs. 0.997 ± 0.120 ln(mg/L), P = 0.0054, respectively, and equivalent to 1.69 mg/L vs. 2.71 mg/L back-transformed]. LCCJ lowered diastolic blood pressure (BP) compared with the placebo beverage (69.2 ± 0.8 mm Hg for LCCJ vs. 71.6 ± 0.8 mm Hg for placebo; P = 0.048). Fasting plasma glucose was lower (P = 0.03) in the LCCJ group (5.32 ± 0.03 mmol/L) than in the placebo group (5.42 ± 0.03 mmol/L), and LCCJ had a beneficial effect on homeostasis model assessment of insulin resistance for participants with high baseline values (P = 0.035). LCCJ can improve several risk factors of CVD in adults, including circulating TGs, CRP, and glucose, insulin resistance, and diastolic BP. This trial was registered at clinicaltrials.gov as NCT01295684. © 2015

  19. 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

    Basement membranes contain several proteoglycans, and those bearing heparan sulfate glycosaminoglycans such as perlecan and agrin usually predominate. Most mammalian basement membranes also contain chondroitin sulfate, and a core protein, bamacan, has been partially characterized. We have now....... 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...

  20. 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...

  1. 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...

  2. Improvement of neutron kinetics module in TRAC-BF1code: one-dimensional nodal collocation method

    Energy Technology Data Exchange (ETDEWEB)

    Jambrina, Ana; Barrachina, Teresa; Miro, Rafael; Verdu, Gumersindo, E-mail: ajambrina@iqn.upv.es, E-mail: tbarrachina@iqn.upv.es, E-mail: rmiro@iqn.upv.es, E-mail: gverdu@iqn.upv.es [Universidade Politecnica de Valencia (UPV), Valencia (Spain); Soler, Amparo, E-mail: asoler@iberdrola.es [SEA Propulsion S.L., Madrid (Spain); Concejal, Alberto, E-mail: acbe@iberdrola.es [Iberdrola Ingenieria y Construcion S.A.U., Madrid (Spain)

    2013-07-01

    The TRAC-BF1 one-dimensional kinetic model is a formulation of the neutron diffusion equation in the two energy groups' approximation, based on the analytical nodal method (ANM). The advantage compared with a zero-dimensional kinetic model is that the axial power profile may vary with time due to thermal-hydraulic parameter changes and/or actions of the control systems but at has the disadvantages that in unusual situations it fails to converge. The nodal collocation method developed for the neutron diffusion equation and applied to the kinetics resolution of TRAC-BF1 thermal-hydraulics, is an adaptation of the traditional collocation methods for the discretization of partial differential equations, based on the development of the solution as a linear combination of analytical functions. It has chosen to use a nodal collocation method based on a development of Legendre polynomials of neutron fluxes in each cell. The qualification is carried out by the analysis of the turbine trip transient from the NEA benchmark in Peach Bottom NPP using both the original 1D kinetics implemented in TRAC-BF1 and the 1D nodal collocation method. (author)

  3. Application of a nodal collocation approximation for the multidimensional PL equations to the 3D Takeda benchmark problems

    International Nuclear Information System (INIS)

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

    2012-01-01

    Highlights: ► The multidimensional P L approximation to the nuclear transport equation is reviewed. ► A nodal collocation method is developed for the spatial discretization of P L equations. ► Advantages of the method are lower dimension and good characterists of the associated algebraic eigenvalue problem. ► The P L nodal collocation method is implemented into the computer code SHNC. ► The SHNC code is verified with 2D and 3D benchmark eigenvalue problems from Takeda and Ikeda, giving satisfactory results. - Abstract: P L equations are classical approximations to the neutron transport equations, which are obtained expanding the angular neutron flux in terms of spherical harmonics. These approximations are useful to study the behavior of reactor cores with complex fuel assemblies, for the homogenization of nuclear cross-sections, etc., and most of these applications are in three-dimensional (3D) geometries. In this work, we review the multi-dimensional P L equations and describe a nodal collocation method for the spatial discretization of these equations for arbitrary odd order L, which is based on the expansion of the spatial dependence of the fields in terms of orthonormal Legendre polynomials. The performance of the nodal collocation method is studied by means of obtaining the k eff and the stationary power distribution of several 3D benchmark problems. The solutions are obtained are compared with a finite element method and a Monte Carlo method.

  4. Monitoring of the spatial and temporal dynamics of BER/SSBR pathway proteins, including MYH, UNG2, MPG, NTH1 and NEIL1-3, during DNA replication.

    Science.gov (United States)

    Bj Rås, Karine Ø; Sousa, Mirta M L; Sharma, Animesh; Fonseca, Davi M; S Gaard, Caroline K; Bj Rås, Magnar; Otterlei, Marit

    2017-08-21

    Base lesions in DNA can stall the replication machinery or induce mutations if bypassed. Consequently, lesions must be repaired before replication or in a post-replicative process to maintain genomic stability. Base excision repair (BER) is the main pathway for repair of base lesions and is known to be associated with DNA replication, but how BER is organized during replication is unclear. Here we coupled the iPOND (isolation of proteins on nascent DNA) technique with targeted mass-spectrometry analysis, which enabled us to detect all proteins required for BER on nascent DNA and to monitor their spatiotemporal orchestration at replication forks. We demonstrate that XRCC1 and other BER/single-strand break repair (SSBR) proteins are enriched in replisomes in unstressed cells, supporting a cellular capacity of post-replicative BER/SSBR. Importantly, we identify for the first time the DNA glycosylases MYH, UNG2, MPG, NTH1, NEIL1, 2 and 3 on nascent DNA. Our findings suggest that a broad spectrum of DNA base lesions are recognized and repaired by BER in a post-replicative process. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  5. 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.

  6. 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.

  7. 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.

  8. Coefficient of restitution in fractional viscoelastic compliant impacts using fractional Chebyshev collocation

    Science.gov (United States)

    Dabiri, Arman; Butcher, Eric A.; Nazari, Morad

    2017-02-01

    Compliant impacts can be modeled using linear viscoelastic constitutive models. While such impact models for realistic viscoelastic materials using integer order derivatives of force and displacement usually require a large number of parameters, compliant impact models obtained using fractional calculus, however, can be advantageous since such models use fewer parameters and successfully capture the hereditary property. In this paper, we introduce the fractional Chebyshev collocation (FCC) method as an approximation tool for numerical simulation of several linear fractional viscoelastic compliant impact models in which the overall coefficient of restitution for the impact is studied as a function of the fractional model parameters for the first time. Other relevant impact characteristics such as hysteresis curves, impact force gradient, penetration and separation depths are also studied.

  9. Finite Volume Methods for Incompressible Navier-Stokes Equations on Collocated Grids with Nonconformal Interfaces

    DEFF Research Database (Denmark)

    Kolmogorov, Dmitry

    turbine computations, collocated grid-based SIMPLE-like algorithms are developed for computations on block-structured grids with nonconformal interfaces. A technique to enhance both the convergence speed and the solution accuracy of the SIMPLE-like algorithms is presented. The erroneous behavior, which...... versions of the SIMPLE algorithm. The new technique is implemented in an existing conservative 2nd order finite-volume scheme flow solver (EllipSys), which is extended to cope with grids with nonconformal interfaces. The behavior of the discrete Navier-Stokes equations is discussed in detail...... Block LU relaxation scheme is shown to possess several optimal conditions, which enables to preserve high efficiency of the multigrid solver on both conformal and nonconformal grids. The developments are done using a parallel MPI algorithm, which can handle multiple numbers of interfaces with multiple...

  10. 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.

  11. An embedded formula of the Chebyshev collocation method for stiff problems

    Science.gov (United States)

    Piao, Xiangfan; Bu, Sunyoung; Kim, Dojin; Kim, Philsu

    2017-12-01

    In this study, we have developed an embedded formula of the Chebyshev collocation method for stiff problems, based on the zeros of the generalized Chebyshev polynomials. A new strategy for the embedded formula, using a pair of methods to estimate the local truncation error, as performed in traditional embedded Runge-Kutta schemes, is proposed. The method is performed in such a way that not only the stability region of the embedded formula can be widened, but by allowing the usage of larger time step sizes, the total computational costs can also be reduced. In terms of concrete convergence and stability analysis, the constructed algorithm turns out to have an 8th order convergence and it exhibits A-stability. Through several numerical experimental results, we have demonstrated that the proposed method is numerically more efficient, compared to several existing implicit methods.

  12. 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.

  13. Collocated electrodynamic FDTD schemes using overlapping Yee grids and higher-order Hodge duals

    Science.gov (United States)

    Deimert, C.; Potter, M. E.; Okoniewski, M.

    2016-12-01

    The collocated Lebedev grid has previously been proposed as an alternative to the Yee grid for electromagnetic finite-difference time-domain (FDTD) simulations. While it performs better in anisotropic media, it performs poorly in isotropic media because it is equivalent to four overlapping, uncoupled Yee grids. We propose to couple the four Yee grids and fix the Lebedev method using discrete exterior calculus (DEC) with higher-order Hodge duals. We find that higher-order Hodge duals do improve the performance of the Lebedev grid, but they also improve the Yee grid by a similar amount. The effectiveness of coupling overlapping Yee grids with a higher-order Hodge dual is thus questionable. However, the theoretical foundations developed to derive these methods may be of interest in other problems.

  14. A bivariate Chebyshev spectral collocation quasilinearization method for nonlinear evolution parabolic equations.

    Science.gov (United States)

    Motsa, S S; Magagula, V M; Sibanda, P

    2014-01-01

    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.

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

    DEFF Research Database (Denmark)

    Bødker, Susanne; Polli, Anna Maria

    2014-01-01

    these with the three above forms of practice. The initial familiarity leads to two different early practices that get in the way of each other, and the collaborative writing idea. They point instead towards a discursive sharing of individual feelings, a different kind of past experiences than anticipated in design.......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...

  16. A nodal collocation approximation for the multi-dimensional PL equations - 2D applications

    International Nuclear Information System (INIS)

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

    2008-01-01

    A classical approach to solve the neutron transport equation is to apply the spherical harmonics method obtaining a finite approximation known as the P L equations. In this work, the derivation of the P L equations for multi-dimensional geometries is reviewed and a nodal collocation method is developed to discretize these equations on a rectangular mesh based on the expansion of the neutronic fluxes in terms of orthogonal Legendre polynomials. The performance of the method and the dominant transport Lambda Modes are obtained for a homogeneous 2D problem, a heterogeneous 2D anisotropic scattering problem, a heterogeneous 2D problem and a benchmark problem corresponding to a MOX fuel reactor core

  17. Adaptive collocation method for simultaneous heat and mass diffusion with phase change

    International Nuclear Information System (INIS)

    Chawla, T.C.; Leaf, G.; Minkowycz, W.J.; Pedersen, D.R.; Shouman, A.R.

    1983-01-01

    The present study is carried out to determine melting rates of a lead slab of various thicknesses by contact with sodium coolant and to evaluate the extent of penetration and the mixing rates of molten lead into liquid sodium by molecular diffusion alone. The study shows that these two calculations cannot be performed simultaneously without the use of adaptive coordinates which cause considerable stretching of the physical coordinates for mass diffusion. Because of the large difference in densities of these two liquid metals, the traditional constant density approximation for the calculation of mass diffusion cannot be used for studying their interdiffusion. The use of orthogonal collocation method along with adaptive coordinates produces extremely accurate results which are ascertained by comparing with the existing analytical solutions for concentration distribution for the case of constant density approximation and for melting rates for the case of infinite lead slab

  18. 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

  19. Demonstration of non-collocated vibration control of a flexible manipulator using electrical dynamic absorbers

    International Nuclear Information System (INIS)

    Kim, Sang-Myeong; Kim, Heungseob; Boo, Kwangsuck; Brennan, Michael J

    2013-01-01

    This paper describes an experimental study into the vibration control of a servo system comprising a servo motor and a flexible manipulator. Two modes of the system are controlled by using the servo motor and an accelerometer attached to the tip of the flexible manipulator. The control system is thus non-collocated. It consists of two electrical dynamic absorbers, each of which consists of a modal filter and, in case of an out-of-phase mode, a phase inverter. The experimental results show that each absorber acts as a mechanical dynamic vibration absorber attached to each mode and significantly reduces the settling time for the system response to a step input. (technical note)

  20. A fast collocation method for a variable-coefficient nonlocal diffusion model

    Science.gov (United States)

    Wang, Che; Wang, Hong

    2017-02-01

    We develop a fast collocation scheme for a variable-coefficient nonlocal diffusion model, for which a numerical discretization would yield a dense stiffness matrix. The development of the fast method is achieved by carefully handling the variable coefficients appearing inside the singular integral operator and exploiting the structure of the dense stiffness matrix. The resulting fast method reduces the computational work from O (N3) required by a commonly used direct solver to O (Nlog ⁡ N) per iteration and the memory requirement from O (N2) to O (N). Furthermore, the fast method reduces the computational work of assembling the stiffness matrix from O (N2) to O (N). Numerical results are presented to show the utility of the fast method.

  1. A Fourier Collocation Approach for Transit-Time Ultrasonic Flowmeter Under Multi-Phase Flow Conditions

    DEFF Research Database (Denmark)

    Simurda, Matej; Lassen, Benny; Duggen, Lars

    2017-01-01

    A numerical model for a clamp-on transit-time ultrasonic flowmeter (TTUF) under multi-phase flow conditions is presented. The method solves equations of linear elasticity for isotropic heterogeneous materials with background flow where acoustic media are modeled by setting shear modulus to zero....... Spatial derivatives are calculated by a Fourier collocation method allowing the use of the fast Fourier transform (FFT) and time derivatives are approximated by a finite difference (FD) scheme. This approach is sometimes referred to as a pseudospectral time-domain method. Perfectly matched layers (PML......) are used to avoid wave-wrapping and staggered grids are implemented to improve stability and efficiency. The method is verified against exact analytical solutions and the effect of the time-staggering and associated lowest number of points per minimum wavelengths value is discussed. The method...

  2. Improved statistical models for limited datasets in uncertainty quantification using stochastic collocation

    Energy Technology Data Exchange (ETDEWEB)

    Alwan, Aravind; Aluru, N.R.

    2013-12-15

    This paper presents a data-driven framework for performing uncertainty quantification (UQ) by choosing a stochastic model that accurately describes the sources of uncertainty in a system. This model is propagated through an appropriate response surface function that approximates the behavior of this system using stochastic collocation. Given a sample of data describing the uncertainty in the inputs, our goal is to estimate a probability density function (PDF) using the kernel moment matching (KMM) method so that this PDF can be used to accurately reproduce statistics like mean and variance of the response surface function. Instead of constraining the PDF to be optimal for a particular response function, we show that we can use the properties of stochastic collocation to make the estimated PDF optimal for a wide variety of response functions. We contrast this method with other traditional procedures that rely on the Maximum Likelihood approach, like kernel density estimation (KDE) and its adaptive modification (AKDE). We argue that this modified KMM method tries to preserve what is known from the given data and is the better approach when the available data is limited in quantity. We test the performance of these methods for both univariate and multivariate density estimation by sampling random datasets from known PDFs and then measuring the accuracy of the estimated PDFs, using the known PDF as a reference. Comparing the output mean and variance estimated with the empirical moments using the raw data sample as well as the actual moments using the known PDF, we show that the KMM method performs better than KDE and AKDE in predicting these moments with greater accuracy. This improvement in accuracy is also demonstrated for the case of UQ in electrostatic and electrothermomechanical microactuators. We show how our framework results in the accurate computation of statistics in micromechanical systems.

  3. Improved statistical models for limited datasets in uncertainty quantification using stochastic collocation

    International Nuclear Information System (INIS)

    Alwan, Aravind; Aluru, N.R.

    2013-01-01

    This paper presents a data-driven framework for performing uncertainty quantification (UQ) by choosing a stochastic model that accurately describes the sources of uncertainty in a system. This model is propagated through an appropriate response surface function that approximates the behavior of this system using stochastic collocation. Given a sample of data describing the uncertainty in the inputs, our goal is to estimate a probability density function (PDF) using the kernel moment matching (KMM) method so that this PDF can be used to accurately reproduce statistics like mean and variance of the response surface function. Instead of constraining the PDF to be optimal for a particular response function, we show that we can use the properties of stochastic collocation to make the estimated PDF optimal for a wide variety of response functions. We contrast this method with other traditional procedures that rely on the Maximum Likelihood approach, like kernel density estimation (KDE) and its adaptive modification (AKDE). We argue that this modified KMM method tries to preserve what is known from the given data and is the better approach when the available data is limited in quantity. We test the performance of these methods for both univariate and multivariate density estimation by sampling random datasets from known PDFs and then measuring the accuracy of the estimated PDFs, using the known PDF as a reference. Comparing the output mean and variance estimated with the empirical moments using the raw data sample as well as the actual moments using the known PDF, we show that the KMM method performs better than KDE and AKDE in predicting these moments with greater accuracy. This improvement in accuracy is also demonstrated for the case of UQ in electrostatic and electrothermomechanical microactuators. We show how our framework results in the accurate computation of statistics in micromechanical systems

  4. 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

    2018-06-01

    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.

  5. 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.

  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. Seismic Noise Analysis and Reduction through Utilization of Collocated Seismic and Atmospheric Sensors at the GRO Chile Seismic Network

    Science.gov (United States)

    Farrell, M. E.; Russo, R. M.

    2013-12-01

    The installation of Earthscope Transportable Array-style geophysical observatories in Chile expands open data seismic recording capabilities in the southern hemisphere by nearly 30%, and has nearly tripled the number of seismic stations providing freely-available data in southern South America. Through the use of collocated seismic and atmospheric sensors at these stations we are able to analyze how local atmospheric conditions generate seismic noise, which can degrade data in seismic frequency bands at stations in the ';roaring forties' (S latitudes). Seismic vaults that are climate-controlled and insulated from the local environment are now employed throughout the world in an attempt to isolate seismometers from as many noise sources as possible. However, this is an expensive solution that is neither practical nor possible for all seismic deployments; and also, the increasing number and scope of temporary seismic deployments has resulted in the collection and archiving of terabytes of seismic data that is affected to some degree by natural seismic noise sources such as wind and atmospheric pressure changes. Changing air pressure can result in a depression and subsequent rebound of Earth's surface - which generates low frequency noise in seismic frequency bands - and even moderate winds can apply enough force to ground-coupled structures or to the surface above the seismometers themselves, resulting in significant noise. The 10 stations of the permanent Geophysical Reporting Observatories (GRO Chile), jointly installed during 2011-12 by IRIS and the Chilean Servicio Sismológico, include instrumentation in addition to the standard three seismic components. These stations, spaced approximately 300 km apart along the length of the country, continuously record a variety of atmospheric data including infrasound, air pressure, wind speed, and wind direction. The collocated seismic and atmospheric sensors at each station allow us to analyze both datasets together, to

  8. Heterotrimeric G proteins-mediated resistance to necrotrophic pathogens includes mechanisms independent of salicylic acid-, jasmonic acid/ethylene- and abscisic acid-mediated defense signaling.

    Science.gov (United States)

    Trusov, Yuri; Sewelam, Nasser; Rookes, James Edward; Kunkel, Matt; Nowak, Ekaterina; Schenk, Peer Martin; Botella, José Ramón

    2009-04-01

    Heterotrimeric G proteins are involved in the defense response against necrotrophic fungi in Arabidopsis. In order to elucidate the resistance mechanisms involving heterotrimeric G proteins, we analyzed the effects of the Gβ (subunit deficiency in the mutant agb1-2 on pathogenesis-related gene expression, as well as the genetic interaction between agb1-2 and a number of mutants of established defense pathways. Gβ-mediated signaling suppresses the induction of salicylic acid (SA)-, jasmonic acid (JA)-, ethylene (ET)- and abscisic acid (ABA)-dependent genes during the initial phase of the infection with Fusarium oxysporum (up to 48 h after inoculation). However, at a later phase it enhances JA/ET-dependent genes such as PDF1.2 and PR4. Quantification of the Fusarium wilt symptoms revealed that Gβ- and SA-deficient mutants were more susceptible than wild-type plants, whereas JA- and ET-insensitive and ABA-deficient mutants demonstrated various levels of resistance. Analysis of the double mutants showed that the Gβ-mediated resistance to F. oxysporum and Alternaria brassicicola was mostly independent of all of the previously mentioned pathways. However, the progressive decay of agb1-2 mutants was compensated by coi1-21 and jin1-9 mutations, suggesting that at this stage of F. oxysporum infection Gβ acts upstream of COI1 and ATMYC2 in JA signaling. © 2008 The Authors. Journal compilation © 2008 Blackwell Publishing Ltd.

  9. 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.

  10. 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.

  11. Identification of quantitative trait loci underlying seed protein content of soybean including main, epistatic, and QTL × environment effects in different regions of Northeast China.

    Science.gov (United States)

    Teng, Weili; Li, Wen; Zhang, Qi; Wu, Depeng; Zhao, Xue; Li, Haiyan; Han, Yingpeng; Li, Wenbin

    2017-08-01

    The objective here was to identify QTL underlying soybean protein content (PC), and to evaluate the additive and epistatic effects of the QTLs. A mapping population, consisting of 129 recombinant inbred lines (RILs), was created by crossing 'Dongnong 46' and 'L-100'. Phenotypic data of the parents and RILs were collected for 4 years in three locations of Heilongjiang Province of China. A total of 213 SSR markers were used to construct a genetic linkage map. Eight QTLs, located on seven chromosomes (Chr), were identified to be associated with PC among the 10 tested environments. Of the seven QTLs, five QTLs, qPR-2 (Satt710, on Chr9), qPR-3 (Sat_122, on Chr12), qPR-5 (Satt543, on Chr17), qPR-7 (Satt163, on Chr18), and qPR-8 (Satt614, on Chr20), were detected in six, seven, seven, six, and seven environments, respectively, implying relatively stable QTLs. qPR-3 could explain 3.33%-11.26% of the phenotypic variation across eight tested environments. qPR-5 and qPR-8 explained 3.64%-10.1% and 11.86%-18.40% of the phenotypic variation, respectively, across seven tested environments. Eight QTLs associated with PC exhibited additive and (or) additive × environment interaction effects. The results showed that environment-independent QTLs often had higher additive effects. Moreover, five epistatic pairwise QTLs were identified in the 10 environments.

  12. 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.

  13. 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

  14. Generalized Lagrangian Jacobi Gauss collocation method for solving unsteady isothermal gas through a micro-nano porous medium

    Science.gov (United States)

    Parand, Kourosh; Latifi, Sobhan; Delkhosh, Mehdi; Moayeri, Mohammad M.

    2018-01-01

    In the present paper, a new method based on the Generalized Lagrangian Jacobi Gauss (GLJG) collocation method is proposed. The nonlinear Kidder equation, which explains unsteady isothermal gas through a micro-nano porous medium, is a second-order two-point boundary value ordinary differential equation on the unbounded interval [0, ∞). Firstly, using the quasilinearization method, the equation is converted to a sequence of linear ordinary differential equations. Then, by using the GLJG collocation method, the problem is reduced to solving a system of algebraic equations. It must be mentioned that this equation is solved without domain truncation and variable changing. A comparison with some numerical solutions made and the obtained results indicate that the presented solution is highly accurate. The important value of the initial slope, y'(0), is obtained as -1.191790649719421734122828603800159364 for η = 0.5. Comparing to the best result obtained so far, it is accurate up to 36 decimal places.

  15. 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.

  16. Classical solutions of two dimensional Stokes problems on non smooth domains. 2: Collocation method for the Radon equation

    International Nuclear Information System (INIS)

    Lubuma, M.S.

    1991-05-01

    The non uniquely solvable Radon boundary integral equation for the two-dimensional Stokes-Dirichlet problem on a non smooth domain is transformed into a well posed one by a suitable compact perturbation of the velocity double layer potential operator. The solution to the modified equation is decomposed into a regular part and a finite linear combination of intrinsic singular functions whose coefficients are computed from explicit formulae. Using these formulae, the classical collocation method, defined by continuous piecewise linear vector-valued basis functions, which converges slowly because of the lack of regularity of the solution, is improved into a collocation dual singular function method with optimal rates of convergence for the solution and for the coefficients of singularities. (author). 34 refs

  17. 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)

  18. 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

  19. Comparing multiple model-derived aerosol optical properties to spatially collocated ground-based and satellite measurements

    Science.gov (United States)

    Ocko, Ilissa B.; Ginoux, Paul A.

    2017-04-01

    Anthropogenic aerosols are a key factor governing Earth's climate and play a central role in human-caused climate change. However, because of aerosols' complex physical, optical, and dynamical properties, aerosols are one of the most uncertain aspects of climate modeling. Fortunately, aerosol measurement networks over the past few decades have led to the establishment of long-term observations for numerous locations worldwide. Further, the availability of datasets from several different measurement techniques (such as ground-based and satellite instruments) can help scientists increasingly improve modeling efforts. This study explores the value of evaluating several model-simulated aerosol properties with data from spatially collocated instruments. We compare aerosol optical depth (AOD; total, scattering, and absorption), single-scattering albedo (SSA), Ångström exponent (α), and extinction vertical profiles in two prominent global climate models (Geophysical Fluid Dynamics Laboratory, GFDL, CM2.1 and CM3) to seasonal observations from collocated instruments (AErosol RObotic NETwork, AERONET, and Cloud-Aerosol Lidar with Orthogonal Polarization, CALIOP) at seven polluted and biomass burning regions worldwide. We find that a multi-parameter evaluation provides key insights on model biases, data from collocated instruments can reveal underlying aerosol-governing physics, column properties wash out important vertical distinctions, and improved models does not mean all aspects are improved. We conclude that it is important to make use of all available data (parameters and instruments) when evaluating aerosol properties derived by models.

  20. 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.

  1. 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.

  2. A Least Squares Collocation Approach with GOCE gravity gradients for regional Moho-estimation

    Science.gov (United States)

    Rieser, Daniel; Mayer-Guerr, Torsten

    2014-05-01

    The depth of the Moho discontinuity is commonly derived by either seismic observations, gravity measurements or combinations of both. In this study, we aim to use the gravity gradient measurements of the GOCE satellite mission in a Least Squares Collocation (LSC) approach for the estimation of the Moho depth on regional scale. Due to its mission configuration and measurement setup, GOCE is able to contribute valuable information in particular in the medium wavelengths of the gravity field spectrum, which is also of special interest for the crust-mantle boundary. In contrast to other studies we use the full information of the gradient tensor in all three dimensions. The problem outline is formulated as isostatically compensated topography according to the Airy-Heiskanen model. By using a topography model in spherical harmonics representation the topographic influences can be reduced from the gradient observations. Under the assumption of constant mantle and crustal densities, surface densities are directly derived by LSC on regional scale, which in turn are converted in Moho depths. First investigations proofed the ability of this method to resolve the gravity inversion problem already with a small amount of GOCE data and comparisons with other seismic and gravitmetric Moho models for the European region show promising results. With the recently reprocessed GOCE gradients, an improved data set shall be used for the derivation of the Moho depth. In this contribution the processing strategy will be introduced and the most recent developments and results using the currently available GOCE data shall be presented.

  3. Structure soil structure interaction effects: Seismic analysis of safety related collocated concrete structures

    International Nuclear Information System (INIS)

    Joshi, J.R.

    2000-01-01

    The Process, Purification and Stack Buildings are collocated safety related concrete shear wall structures with plan dimensions in excess of 100 feet. An important aspect of their seismic analysis was the determination of structure soil structure interaction (SSSI) effects, if any. The SSSI analysis of the Process Building, with one other building at a time, was performed with the SASSI computer code for up to 50 frequencies. Each combined model had about 1500 interaction nodes. Results of the SSSI analysis were compared with those from soil structure interaction (SSI) analysis of the individual buildings, done with ABAQUS and SASSI codes, for three parameters: peak accelerations, seismic forces and the in-structure floor response spectra (FRS). The results may be of wider interest due to the model size and the potential applicability to other deep soil layered sites. Results obtained from the ABAQUS analysis were consistently higher, as expected, than those from the SSI and SSSI analyses using the SASSI. The SSSI effect between the Process and Purification Buildings was not significant. The Process and Stack Building results demonstrated that under certain conditions a massive structure can have an observable effect on the seismic response of a smaller and less stiff structure

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

    KAUST Repository

    Beck, Joakim; Tempone, Raul; Nobile, Fabio; Tamellini, Lorenzo

    2012-01-01

    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.

  5. 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.

  6. 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)

  7. 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.

  8. An efficient Bayesian inference approach to inverse problems based on an adaptive sparse grid collocation method

    International Nuclear Information System (INIS)

    Ma Xiang; Zabaras, Nicholas

    2009-01-01

    A new approach to modeling inverse problems using a Bayesian inference method is introduced. The Bayesian approach considers the unknown parameters as random variables and seeks the probabilistic distribution of the unknowns. By introducing the concept of the stochastic prior state space to the Bayesian formulation, we reformulate the deterministic forward problem as a stochastic one. The adaptive hierarchical sparse grid collocation (ASGC) method is used for constructing an interpolant to the solution of the forward model in this prior space which is large enough to capture all the variability/uncertainty in the posterior distribution of the unknown parameters. This solution can be considered as a function of the random unknowns and serves as a stochastic surrogate model for the likelihood calculation. Hierarchical Bayesian formulation is used to derive the posterior probability density function (PPDF). The spatial model is represented as a convolution of a smooth kernel and a Markov random field. The state space of the PPDF is explored using Markov chain Monte Carlo algorithms to obtain statistics of the unknowns. The likelihood calculation is performed by directly sampling the approximate stochastic solution obtained through the ASGC method. The technique is assessed on two nonlinear inverse problems: source inversion and permeability estimation in flow through porous media

  9. 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.

  10. Evolutionary optimization with data collocation for reverse engineering of biological networks.

    Science.gov (United States)

    Tsai, Kuan-Yao; Wang, Feng-Sheng

    2005-04-01

    Modern experimental biology is moving away from analyses of single elements to whole-organism measurements. Such measured time-course data contain a wealth of information about the structure and dynamic of the pathway or network. The dynamic modeling of the whole systems is formulated as a reverse problem that requires a well-suited mathematical model and a very efficient computational method to identify the model structure and parameters. Numerical integration for differential equations and finding global parameter values are still two major challenges in this field of the parameter estimation of nonlinear dynamic biological systems. We compare three techniques of parameter estimation for nonlinear dynamic biological systems. In the proposed scheme, the modified collocation method is applied to convert the differential equations to the system of algebraic equations. The observed time-course data are then substituted into the algebraic system equations to decouple system interactions in order to obtain the approximate model profiles. Hybrid differential evolution (HDE) with population size of five is able to find a global solution. The method is not only suited for parameter estimation but also can be applied for structure identification. The solution obtained by HDE is then used as the starting point for a local search method to yield the refined estimates.

  11. 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.

  12. 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

  13. Feedback control of acoustic musical instruments: collocated control using physical analogs.

    Science.gov (United States)

    Berdahl, Edgar; Smith, Julius O; Niemeyer, Günter

    2012-01-01

    Traditionally, the average professional musician has owned numerous acoustic musical instruments, many of them having distinctive acoustic qualities. However, a modern musician could prefer to have a single musical instrument whose acoustics are programmable by feedback control, where acoustic variables are estimated from sensor measurements in real time and then fed back in order to influence the controlled variables. In this paper, theory is presented that describes stable feedback control of an acoustic musical instrument. The presentation should be accessible to members of the musical acoustics community who may have limited or no experience with feedback control. First, the only control strategy guaranteed to be stable subject to any musical instrument mobility is described: the sensors and actuators must be collocated, and the controller must emulate a physical analog system. Next, the most fundamental feedback controllers and the corresponding physical analog systems are presented. The effects that these controllers have on acoustic musical instruments are described. Finally, practical design challenges are discussed. A proof explains why changing the resonance frequency of a musical resonance requires much more control power than changing the decay time of the resonance. © 2012 Acoustical Society of America.

  14. 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.

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

    International Nuclear Information System (INIS)

    Huang, Shyh Chin; Tsai, Chao Yang; Liao, Hsiao Hui

    2016-01-01

    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

  16. Orbiting Carbon Observatory-2 (OCO-2) cloud screening algorithms; validation against collocated MODIS and CALIOP data

    Science.gov (United States)

    Taylor, T. E.; O'Dell, C. W.; Frankenberg, C.; Partain, P.; Cronk, H. Q.; Savtchenko, A.; Nelson, R. R.; Rosenthal, E. J.; Chang, A. Y.; Fisher, B.; Osterman, G.; Pollock, R. H.; Crisp, D.; Eldering, A.; Gunson, M. R.

    2015-12-01

    The objective of the National Aeronautics and Space Administration's (NASA) Orbiting Carbon Observatory-2 (OCO-2) mission is to retrieve the column-averaged carbon dioxide (CO2) dry air mole fraction (XCO2) from satellite measurements of reflected sunlight in the near-infrared. These estimates can be biased by clouds and aerosols within the instrument's field of view (FOV). Screening of the most contaminated soundings minimizes unnecessary calls to the computationally expensive Level 2 (L2) XCO2 retrieval algorithm. Hence, robust cloud screening methods have been an important focus of the OCO-2 algorithm development team. Two distinct, computationally inexpensive cloud screening algorithms have been developed for this application. The A-Band Preprocessor (ABP) retrieves the surface pressure using measurements in the 0.76 μm O2 A-band, neglecting scattering by clouds and aerosols, which introduce photon path-length (PPL) differences that can cause large deviations between the expected and retrieved surface pressure. The Iterative Maximum A-Posteriori (IMAP) Differential Optical Absorption Spectroscopy (DOAS) Preprocessor (IDP) retrieves independent estimates of the CO2 and H2O column abundances using observations taken at 1.61 μm (weak CO2 band) and 2.06 μm (strong CO2 band), while neglecting atmospheric scattering. The CO2 and H2O column abundances retrieved in these two spectral regions differ significantly in the presence of cloud and scattering aerosols. The combination of these two algorithms, which key off of different features in the spectra, provides the basis for cloud screening of the OCO-2 data set. To validate the OCO-2 cloud screening approach, collocated measurements from NASA's Moderate Resolution Imaging Spectrometer (MODIS), aboard the Aqua platform, were compared to results from the two OCO-2 cloud screening algorithms. With tuning to allow throughputs of ≃ 30 %, agreement between the OCO-2 and MODIS cloud screening methods is found to be

  17. Orbiting Carbon Observatory-2 (OCO-2) cloud screening algorithms: validation against collocated MODIS and CALIOP data

    Science.gov (United States)

    Taylor, Thomas E.; O'Dell, Christopher W.; Frankenberg, Christian; Partain, Philip T.; Cronk, Heather Q.; Savtchenko, Andrey; Nelson, Robert R.; Rosenthal, Emily J.; Chang, Albert Y.; Fisher, Brenden; Osterman, Gregory B.; Pollock, Randy H.; Crisp, David; Eldering, Annmarie; Gunson, Michael R.

    2016-03-01

    The objective of the National Aeronautics and Space Administration's (NASA) Orbiting Carbon Observatory-2 (OCO-2) mission is to retrieve the column-averaged carbon dioxide (CO2) dry air mole fraction (XCO2) from satellite measurements of reflected sunlight in the near-infrared. These estimates can be biased by clouds and aerosols, i.e., contamination, within the instrument's field of view. Screening of the most contaminated soundings minimizes unnecessary calls to the computationally expensive Level 2 (L2) XCO2 retrieval algorithm. Hence, robust cloud screening methods have been an important focus of the OCO-2 algorithm development team. Two distinct, computationally inexpensive cloud screening algorithms have been developed for this application. The A-Band Preprocessor (ABP) retrieves the surface pressure using measurements in the 0.76 µm O2 A band, neglecting scattering by clouds and aerosols, which introduce photon path-length differences that can cause large deviations between the expected and retrieved surface pressure. The Iterative Maximum A Posteriori (IMAP) Differential Optical Absorption Spectroscopy (DOAS) Preprocessor (IDP) retrieves independent estimates of the CO2 and H2O column abundances using observations taken at 1.61 µm (weak CO2 band) and 2.06 µm (strong CO2 band), while neglecting atmospheric scattering. The CO2 and H2O column abundances retrieved in these two spectral regions differ significantly in the presence of cloud and scattering aerosols. The combination of these two algorithms, which are sensitive to different features in the spectra, provides the basis for cloud screening of the OCO-2 data set.To validate the OCO-2 cloud screening approach, collocated measurements from NASA's Moderate Resolution Imaging Spectrometer (MODIS), aboard the Aqua platform, were compared to results from the two OCO-2 cloud screening algorithms. With tuning of algorithmic threshold parameters that allows for processing of ≃ 20-25 % of all OCO-2 soundings

  18. Temporal gravity field modeling based on least square collocation with short-arc approach

    Science.gov (United States)

    ran, jiangjun; Zhong, Min; Xu, Houze; Liu, Chengshu; Tangdamrongsub, Natthachet

    2014-05-01

    After the launch of the Gravity Recovery And Climate Experiment (GRACE) in 2002, several research centers have attempted to produce the finest gravity model based on different approaches. In this study, we present an alternative approach to derive the Earth's gravity field, and two main objectives are discussed. Firstly, we seek the optimal method to estimate the accelerometer parameters, and secondly, we intend to recover the monthly gravity model based on least square collocation method. The method has been paid less attention compared to the least square adjustment method because of the massive computational resource's requirement. The positions of twin satellites are treated as pseudo-observations and unknown parameters at the same time. The variance covariance matrices of the pseudo-observations and the unknown parameters are valuable information to improve the accuracy of the estimated gravity solutions. Our analyses showed that introducing a drift parameter as an additional accelerometer parameter, compared to using only a bias parameter, leads to a significant improvement of our estimated monthly gravity field. The gravity errors outside the continents are significantly reduced based on the selected set of the accelerometer parameters. We introduced the improved gravity model namely the second version of Institute of Geodesy and Geophysics, Chinese Academy of Sciences (IGG-CAS 02). The accuracy of IGG-CAS 02 model is comparable to the gravity solutions computed from the Geoforschungszentrum (GFZ), the Center for Space Research (CSR) and the NASA Jet Propulsion Laboratory (JPL). In term of the equivalent water height, the correlation coefficients over the study regions (the Yangtze River valley, the Sahara desert, and the Amazon) among four gravity models are greater than 0.80.

  19. 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

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. Investigating electro-mechanical signals from collocated piezoelectric wafers for the reference-free damage diagnosis of a plate

    International Nuclear Information System (INIS)

    Kim, Eun Jin; Park, Hyun Woo; Kim, Min Koo; Sohn, Hoon

    2011-01-01

    The electro-mechanical (EM) signals from piezoelectric (PZT) wafers are investigated for reference-free damage diagnosis so that a notch in a plate can be detected without requiring direct comparison with a baseline EM signal. Two identical PZT wafers collocated on both surfaces of a plate are utilized for extracting the mode-converted Lamb wave signals created by a notch. As harmonic input voltage signals are exerted on the collocated PZT wafers, the corresponding mode-converted Lamb wave signals become steady-state in the presence of damage. Applying fast Fourier transform to these mode-converted Lamb wave signals followed by a proper normalization, the EM signals associated with the mode conversion can be obtained. The theoretical finding of this paper is validated through spectral element simulations of a cantilever beam with a notch. The effects of the size and the location of the notch on the mode-converted EM signals are investigated as well. Finally, the applicability of the decomposed EM signals to reference-free damage diagnosis is discussed

  5. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

    Rashidifar, Mohammed Amin [Faculty of Mechanical Engineering, Islamic Azad University, SHADEGAN (Iran, Islamic Republic of); Rashidifar, Ali Amin, E-mail: rashidifar_58@yahoo.com [Computer Science, Islamic Azad University, SHADEGAN (Iran, Islamic Republic of)

    2014-07-01

    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)

  7. 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).

  8. 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

  9. Discretisation of the non-linear heat transfer equation for food freezing processes using orthogonal collocation on finite elements

    Directory of Open Access Journals (Sweden)

    E. D. Resende

    2007-09-01

    Full Text Available The freezing process is considered as a propagation problem and mathematically classified as an "initial value problem." The mathematical formulation involves a complex situation of heat transfer with simultaneous changes of phase and abrupt variation in thermal properties. The objective of the present work is to solve the non-linear heat transfer equation for food freezing processes using orthogonal collocation on finite elements. This technique has not yet been applied to freezing processes and represents an alternative numerical approach in this area. The results obtained confirmed the good capability of the numerical method, which allows the simulation of the freezing process in approximately one minute of computer time, qualifying its application in a mathematical optimising procedure. The influence of the latent heat released during the crystallisation phenomena was identified by the significant increase in heat load in the early stages of the freezing process.

  10. 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.

  11. Fourier Collocation Approach With Mesh Refinement Method for Simulating Transit-Time Ultrasonic Flowmeters Under Multiphase Flow Conditions.

    Science.gov (United States)

    Simurda, Matej; Duggen, Lars; Basse, Nils T; Lassen, Benny

    2018-02-01

    A numerical model for transit-time ultrasonic flowmeters operating under multiphase flow conditions previously presented by us is extended by mesh refinement and grid point redistribution. The method solves modified first-order stress-velocity equations of elastodynamics with additional terms to account for the effect of the background flow. Spatial derivatives are calculated by a Fourier collocation scheme allowing the use of the fast Fourier transform, while the time integration is realized by the explicit third-order Runge-Kutta finite-difference scheme. The method is compared against analytical solutions and experimental measurements to verify the benefit of using mapped grids. Additionally, a study of clamp-on and in-line ultrasonic flowmeters operating under multiphase flow conditions is carried out.

  12. 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.

  13. Reference frame access under the effects of great earthquakes: a least squares collocation approach for non-secular post-seismic evolution

    Science.gov (United States)

    Gómez, D. D.; Piñón, D. A.; Smalley, R.; Bevis, M.; Cimbaro, S. R.; Lenzano, L. E.; Barón, J.

    2016-03-01

    The 2010, (Mw 8.8) Maule, Chile, earthquake produced large co-seismic displacements and non-secular, post-seismic deformation, within latitudes 28°S-40°S extending from the Pacific to the Atlantic oceans. Although these effects are easily resolvable by fitting geodetic extended trajectory models (ETM) to continuous GPS (CGPS) time series, the co- and post-seismic deformation cannot be determined at locations without CGPS (e.g., on passive geodetic benchmarks). To estimate the trajectories of passive geodetic benchmarks, we used CGPS time series to fit an ETM that includes the secular South American plate motion and plate boundary deformation, the co-seismic discontinuity, and the non-secular, logarithmic post-seismic transient produced by the earthquake in the Posiciones Geodésicas Argentinas 2007 (POSGAR07) reference frame (RF). We then used least squares collocation (LSC) to model both the background secular inter-seismic and the non-secular post-seismic components of the ETM at the locations without CGPS. We tested the LSC modeled trajectories using campaign and CGPS data that was not used to generate the model and found standard deviations (95 % confidence level) for position estimates for the north and east components of 3.8 and 5.5 mm, respectively, indicating that the model predicts the post-seismic deformation field very well. Finally, we added the co-seismic displacement field, estimated using an elastic finite element model. The final, trajectory model allows accessing the POSGAR07 RF using post-Maule earthquake coordinates within 5 cm for ˜ 91 % of the passive test benchmarks.

  14. 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: PPD patients; 0%, 14.7% and 85.3% of the placebo patients and 18.2%, 33.3% and 48.5% of the cryotherapy patients, respectively (PPD versus placebo: p PPD versus cryotherapy: p PPD group. The recurrence rate was 8.6%, 5.9% and 24.2% in the PPD, placebo and 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).

  15. 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

  16. 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.

  17. 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...... covariance parameters has facilitated to achieve gravimetric height anomalies in a global geocentric datum. Residual terrain modeling (RTM) technique has been used in combination with the EGM96 for the reduction and smoothing of the gravity data. A value for the bias parameter N-o has been estimated...... with reference to the local GPS-Levelling datum that appears to be 0.705 m with 0.07 m mean square error. The gravimetric height anomalies were compared with height anomalies obtained from GPS-Levelling stations using least square collocation with and without bias adjustment. The bias adjustment minimizes...

  18. 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.

  19. 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.

  20. Towards Improving the Efficiency of Bayesian Model Averaging Analysis for Flow in Porous Media via the Probabilistic Collocation Method

    Directory of Open Access Journals (Sweden)

    Liang Xue

    2018-04-01

    Full Text Available The characterization of flow in subsurface porous media is associated with high uncertainty. To better quantify the uncertainty of groundwater systems, it is necessary to consider the model uncertainty. Multi-model uncertainty analysis can be performed in the Bayesian model averaging (BMA framework. However, the BMA analysis via Monte Carlo method is time consuming because it requires many forward model evaluations. A computationally efficient BMA analysis framework is proposed by using the probabilistic collocation method to construct a response surface model, where the log hydraulic conductivity field and hydraulic head are expanded into polynomials through Karhunen–Loeve and polynomial chaos methods. A synthetic test is designed to validate the proposed response surface analysis method. The results show that the posterior model weight and the key statistics in BMA framework can be accurately estimated. The relative errors of mean and total variance in the BMA analysis results are just approximately 0.013% and 1.18%, but the proposed method can be 16 times more computationally efficient than the traditional BMA method.

  1. 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.

  2. 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.

  3. A fractional factorial probabilistic collocation method for uncertainty propagation of hydrologic model parameters in a reduced dimensional space

    Science.gov (United States)

    Wang, S.; Huang, G. H.; Huang, W.; Fan, Y. R.; Li, Z.

    2015-10-01

    In this study, a fractional factorial probabilistic collocation method is proposed to reveal statistical significance of hydrologic model parameters and their multi-level interactions affecting model outputs, facilitating uncertainty propagation in a reduced dimensional space. The proposed methodology is applied to the Xiangxi River watershed in China to demonstrate its validity and applicability, as well as its capability of revealing complex and dynamic parameter interactions. A set of reduced polynomial chaos expansions (PCEs) only with statistically significant terms can be obtained based on the results of factorial analysis of variance (ANOVA), achieving a reduction of uncertainty in hydrologic predictions. The predictive performance of reduced PCEs is verified by comparing against standard PCEs and the Monte Carlo with Latin hypercube sampling (MC-LHS) method in terms of reliability, sharpness, and Nash-Sutcliffe efficiency (NSE). Results reveal that the reduced PCEs are able to capture hydrologic behaviors of the Xiangxi River watershed, and they are efficient functional representations for propagating uncertainties in hydrologic predictions.

  4. Triple collocation-based estimation of spatially correlated observation error covariance in remote sensing soil moisture data assimilation

    Science.gov (United States)

    Wu, Kai; Shu, Hong; Nie, Lei; Jiao, Zhenhang

    2018-01-01

    Spatially correlated errors are typically ignored in data assimilation, thus degenerating the observation error covariance R to a diagonal matrix. We argue that a nondiagonal R carries more observation information making assimilation results more accurate. A method, denoted TC_Cov, was proposed for soil moisture data assimilation to estimate spatially correlated observation error covariance based on triple collocation (TC). Assimilation experiments were carried out to test the performance of TC_Cov. AMSR-E soil moisture was assimilated with a diagonal R matrix computed using the TC and assimilated using a nondiagonal R matrix, as estimated by proposed TC_Cov. The ensemble Kalman filter was considered as the assimilation method. Our assimilation results were validated against climate change initiative data and ground-based soil moisture measurements using the Pearson correlation coefficient and unbiased root mean square difference metrics. These experiments confirmed that deterioration of diagonal R assimilation results occurred when model simulation is more accurate than observation data. Furthermore, nondiagonal R achieved higher correlation coefficient and lower ubRMSD values over diagonal R in experiments and demonstrated the effectiveness of TC_Cov to estimate richly structuralized R in data assimilation. In sum, compared with diagonal R, nondiagonal R may relieve the detrimental effects of assimilation when simulated model results outperform observation data.

  5. 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.

  6. Using a biomimetic membrane surface experiment to investigate the activity of the magnetite biomineralisation protein Mms6† †Electronic supplementary information (ESI) available: Including Mms6 protein and peptide sequences, additional QCM-D and SEM data and protein modelling. See DOI: 10.1039/c5ra16469a Click here for additional data file.

    Science.gov (United States)

    Bird, Scott M.; Rawlings, Andrea E.; Galloway, Johanna M.

    2016-01-01

    Magnetotactic bacteria are able to synthesise precise nanoparticles of the iron oxide magnetite within their cells. These particles are formed in dedicated organelles termed magnetosomes. These lipid membrane compartments use a range of biomineralisation proteins to nucleate and regulate the magnetite crystallisation process. A key component is the membrane protein Mms6, which binds to iron ions and helps to control the formation of the inorganic core. We have previously used Mms6 on gold surfaces patterned with a self-assembled monolayer to successfully produce arrays of magnetic nanoparticles. Here we use this surface system as a mimic of the interior face of the magnetosome membrane to study differences between intact Mms6 and the acid-rich C-terminal peptide subregion of the Mms6 protein. When immobilised on surfaces, the peptide is unable to reproduce the particle size or homogeneity control exhibited by the full Mms6 protein in our experimental setup. Moreover, the peptide is unable to support anchoring of a dense array of nanoparticles to the surface. This system also allows us to deconvolute particle binding from particle nucleation, and shows that Mms6 particle binding is less efficient when supplied with preformed magnetite nanoparticles when compared to particles precipitated from solution in the presence of the surface immobilised Mms6. This suggests that Mms6 binds to iron ions rather than to magnetite surfaces in our system, and is perhaps a nucleating agent rather than a controller of magnetite crystal growth. The comparison between the peptide and the protein under identical experimental conditions indicates that the full length sequence is required to support the full function of Mms6 on surfaces. PMID:27019707

  7. 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

    2012-01-01

    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

  8. 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

  9. 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...

  10. 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 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.

  11. 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.

  12. New seismograph includes filters

    Energy Technology Data Exchange (ETDEWEB)

    1979-11-02

    The new Nimbus ES-1210 multichannel signal enhancement seismograph from EG and G geometrics has recently been redesigned to include multimode signal fillers on each amplifier. The ES-1210F is a shallow exploration seismograph for near subsurface exploration such as in depth-to-bedrock, geological hazard location, mineral exploration, and landslide investigations.

  13. Polynomial Collocation for Handling an Inaccurately Known Measurement Configuration in Electrical Impedance Tomography

    DEFF Research Database (Denmark)

    Hyvönen, Niina; Kaarnioja, V.; Mustonen, L.

    2017-01-01

    The objective of electrical impedance tomography is to reconstruct the internal conductivity of a physical body based on measurements of current and potential at a finite number of electrodes attached to its boundary. Although the conductivity is the quantity of main interest in impedance...... tomography, a real-world measurement configuration includes other unknown parameters as well: The information on the contact resistances, electrode positions, and body shape is almost always incomplete. In this work, the dependence of the electrode measurements on all aforementioned model properties...

  14. Prediction of binding modes between protein L-isoaspartyl (D-aspartyl) O-methyltransferase and peptide substrates including isomerized aspartic acid residues using in silico analytic methods for the substrate screening.

    Science.gov (United States)

    Oda, Akifumi; Noji, Ikuhiko; Fukuyoshi, Shuichi; Takahashi, Ohgi

    2015-12-10

    Because the aspartic acid (Asp) residues in proteins are occasionally isomerized in the human body, not only l-α-Asp but also l-β-Asp, D-α-Asp and D-β-Asp are found in human proteins. In these isomerized aspartic acids, the proportion of D-β-Asp is the largest and the proportions of l-β-Asp and D-α-Asp found in human proteins are comparatively small. To explain the proportions of aspartic acid isomers, the possibility of an enzyme able to repair l-β-Asp and D-α-Asp is frequently considered. The protein L-isoaspartyl (D-aspartyl) O-methyltransferase (PIMT) is considered one of the possible repair enzymes for l-β-Asp and D-α-Asp. Human PIMT is an enzyme that recognizes both l-β-Asp and D-α-Asp, and catalyzes the methylation of their side chains. In this study, the binding modes between PIMT and peptide substrates containing l-β-Asp or D-α-Asp residues were investigated using computational protein-ligand docking and molecular dynamics simulations. The results indicate that carboxyl groups of both l-β-Asp and D-α-Asp were recognized in similar modes by PIMT and that the C-terminal regions of substrate peptides were located in similar positions on PIMT for both the l-β-Asp and D-α-Asp peptides. In contrast, for peptides containing l-α-Asp or D-β-Asp residues, which are not substrates of PIMT, the computationally constructed binding modes between PIMT and peptides greatly differed from those between PIMT and substrates. In the nonsubstrate peptides, not inter- but intra-molecular hydrogen bonds were observed, and the conformations of peptides were more rigid than those of substrates. Thus, the in silico analytical methods were able to distinguish substrates from nonsubstrates and the computational methods are expected to complement experimental analytical methods. Copyright © 2015 Elsevier B.V. All rights reserved.

  15. Analytic device including nanostructures

    KAUST Repository

    Di Fabrizio, Enzo M.; Fratalocchi, Andrea; Totero Gongora, Juan Sebastian; Coluccio, Maria Laura; Candeloro, Patrizio; Cuda, Gianni

    2015-01-01

    A device for detecting an analyte in a sample comprising: an array including a plurality of pixels, each pixel including a nanochain comprising: a first nanostructure, a second nanostructure, and a third nanostructure, wherein size of the first nanostructure is larger than that of the second nanostructure, and size of the second nanostructure is larger than that of the third nanostructure, and wherein the first nanostructure, the second nanostructure, and the third nanostructure are positioned on a substrate such that when the nanochain is excited by an energy, an optical field between the second nanostructure and the third nanostructure is stronger than an optical field between the first nanostructure and the second nanostructure, wherein the array is configured to receive a sample; and a detector arranged to collect spectral data from a plurality of pixels of the array.

  16. Saskatchewan resources. [including uranium

    Energy Technology Data Exchange (ETDEWEB)

    1979-09-01

    The production of chemicals and minerals for the chemical industry in Saskatchewan are featured, with some discussion of resource taxation. The commodities mentioned include potash, fatty amines, uranium, heavy oil, sodium sulfate, chlorine, sodium hydroxide, sodium chlorate and bentonite. Following the successful outcome of the Cluff Lake inquiry, the uranium industry is booming. Some developments and production figures for Gulf Minerals, Amok, Cenex and Eldorado are mentioned.

  17. Serum protein concentrations, including acute phase proteins, in calves with hepatogenous photosensitization Teores séricos de proteínas, inclusive proteínas de fase aguda, em bovinos com fotossensibilização hepatógena

    Directory of Open Access Journals (Sweden)

    J.J. Fagliari

    2007-12-01

    Full Text Available One hundred 6- to 12-month-old Nelore calves were allotted into control group (G1; 50 healthy calves and photosensitization group (G2; n= 50. Blood samples were collected 12 to 24 hours after the onset of dermatitis (M1, and 15 to 30 days after that (M2, at time of resolution of clinical signs. Serum protein electrophoresis was performed by means of sodium dodecyl sulphate-polyacrylamide gel electrophoresis. Eighteen serum proteins with molecular weights ranging from 16,000 to 189,000 daltons (Da were identified in all calves. In M1 and M2 serum concentrations of proteins with molecular weights of 115,000Da (ceruloplasmin, 61,000Da (a1-antitrypsin, 45,000Da (haptoglobin, and 40,000Da (acid glycoprotein were significantly increased in calves. In conclusion, measurement of serum acute phase protein concentrations may be useful in monitoring the progression of bovine hepatogenous photosensitization, including guide probable alteration on therapeutic procedures.Foram examinados 100 bezerros da raça Nelore com 6 a 12 meses de idade, distribuídos em: grupo controle (G1; 50 bezerros sadios e grupo fotossensibilização (G2; n= 50. As amostras de sangue foram coletadas 12 a 24 horas após o início da dermatite (M1 e 15 a 30 dias após (M2, época da cura das lesões cutâneas. O proteinograma sérico foi obtido por eletroforese em gel de acrilamida. Em todos os bezerros foram identificadas 18 proteínas com pesos moleculares (PM entre 16.000 a 189.000 dáltons (Da. Em M1 e M2, as concentrações séricas das proteínas de PM 115.000Da (ceruloplasmina, 61.000Da (1-antitripsina, 45.000Da (haptoglobina e 40.000Da (glicoproteína ácida foram significativamente maiores em bezerros com fotossensibilização hepatógena em comparação com aquelas dos animais do grupo-controle. A determinação dos teores séricos de proteínas de fase aguda pode ser útil no monitoramento da progressão da fotossensibilização hepatógena em bovinos, inclusive orientando

  18. Being Included and Excluded

    DEFF Research Database (Denmark)

    Korzenevica, Marina

    2016-01-01

    Following the civil war of 1996–2006, there was a dramatic increase in the labor mobility of young men and the inclusion of young women in formal education, which led to the transformation of the political landscape of rural Nepal. Mobility and schooling represent a level of prestige that rural...... politics. It analyzes how formal education and mobility either challenge or reinforce traditional gendered norms which dictate a lowly position for young married women in the household and their absence from community politics. The article concludes that women are simultaneously excluded and included from...... community politics. On the one hand, their mobility and decision-making powers decrease with the increase in the labor mobility of men and their newly gained education is politically devalued when compared to the informal education that men gain through mobility, but on the other hand, schooling strengthens...

  19. Phenolic promiscuity in the cell nucleus--epigallocatechingallate (EGCG) and theaflavin-3,3'-digallate from green and black tea bind to model cell nuclear structures including histone proteins, double stranded DNA and telomeric quadruplex DNA.

    Science.gov (United States)

    Mikutis, Gediminas; Karaköse, Hande; Jaiswal, Rakesh; LeGresley, Adam; Islam, Tuhidul; Fernandez-Lahore, Marcelo; Kuhnert, Nikolai

    2013-02-01

    Flavanols from tea have been reported to accumulate in the cell nucleus in considerable concentrations. The nature of this phenomenon, which could provide novel approaches in understanding the well-known beneficial health effects of tea phenols, is investigated in this contribution. The interaction between epigallocatechin gallate (EGCG) from green tea and a selection of theaflavins from black tea with selected cell nuclear structures such as model histone proteins, double stranded DNA and quadruplex DNA was investigated using mass spectrometry, Circular Dichroism spectroscopy and fluorescent assays. The selected polyphenols were shown to display affinity to all of the selected cell nuclear structures, thereby demonstrating a degree of unexpected molecular promiscuity. Most interestingly theaflavin-digallate was shown to display the highest affinity to quadruplex DNA reported for any naturally occurring molecule reported so far. This finding has immediate implications in rationalising the chemopreventive effect of the tea beverage against cancer and possibly the role of tea phenolics as "life span essentials".

  20. The collocated station Košetice - Kešín u Pacova, Czech Republic: an important research infrastructure in central Europe

    Science.gov (United States)

    Dvorska, Alice; Milan, Váňa; Vlastimil, Hanuš; Marian, Pavelka

    2013-04-01

    The collocated station Košetice - Křešín u Pacova, central Czech Republic, is a major research and monitoring infrastructure in the Czech Republic and central Europe. It consists of two basic components: the observatory Košetice run since 1988 by the Czech Hydrometeorological Institute and the atmospheric station (AS) Křešín u Pacova starting operation in 2013. The AS is built and run by CzechGlobe - Global Change Research Centre, Academy of Sciences of the Czech Republic and is situated 100 m far from the observatory. There are three research and monitoring activities at the collocated station providing data necessary for the research on climate and related changes. The AS Křešín u Pacova consists of a 250 m tall tower serving for ground-based and vertical gradient measurements of (i) concentrations of CO2, CO, CH4, total gaseous mercury and tropospheric ozone (continuously), (ii) elemental and organic carbon (semicontinuously), (iii) carbon and oxygen isotopes, radon, N2O, SF6 and other species (episodically), (iv) optical properties of atmospheric aerosols and (v) meteorological parameters and the boundary layer height. Further, eddy covariance measurements in the nearby agroecosystem provide data on CO2 and H2O fluxes between the atmosphere and the ecosystem. Finally, monitoring activities at the nearby small hydrological catchment Anenské povodí run under the GEOMON network enables studying local hydrological and biogeochemical cycles. These measurements are supported by the long-term monitoring of meteorological and air quality parameters at the observatory Košetice, that are representative for the central European background. The collocated station provides a big research opportunity and challenge due to (i) a broad spectra of monitored chemical species, meteorological, hydrological and other parameters, (ii) measurements in various environmental compartments and especially the atmosphere, (iii) provision of data suitable for conducting

  1. 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

  2. Radiation budget studies using collocated observations from advanced Very High Resolution Radiometer, High-Resolution Infrared Sounder/2, and Earth Radiation Budget Experiment instruments

    Science.gov (United States)

    Ackerman, Steven A.; Frey, Richard A.; Smith, William L.

    1992-01-01

    Collocated observations from the Advanced Very High Resolution Radiometer (AVHRR), High-Resolution Infrared Sounder/2 (HIRS/2), and Earth Radiation Budget Experiment (ERBE) instruments onboard the NOAA 9 satellite are combined to describe the broadband and spectral radiative properties of the earth-atmosphere system. Broadband radiative properties are determined from the ERBE observations, while spectral properties are determined from the HIRS/2 and AVHRR observations. The presence of clouds, their areal coverage, and cloud top pressure are determined from a combination of the HIRS/2 and the AVHRR observations. The CO2 slicing method is applied to the HIRS/2 to determine the presence of upper level clouds and their effective emissivity. The AVHRR data collocated within the HIRS/2 field of view are utilized to determine the uniformity of the scene and retrieve sea surface temperature. Changes in the top of the atmosphere longwave and shortwave radiative energy budgets, and the spectral distribution of longwave radiation are presented as a function of cloud amount and cloud top pressure. The radiative characteristics of clear sky conditions over oceans are presented as a function of sea surface temperature and atmospheric water vapor structure.

  3. 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.

  4. 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.

  5. An Improved Collocation Meshless Method Based on the Variable Shaped Radial Basis Function for the Solution of the Interior Acoustic Problems

    Directory of Open Access Journals (Sweden)

    Shuang Wang

    2012-01-01

    Full Text Available As an efficient tool, radial basis function (RBF has been widely used for the multivariate approximation, interpolating continuous, and the solution of the particle differential equations. However, ill-conditioned interpolation matrix may be encountered when the interpolation points are very dense or irregularly arranged. To avert this problem, RBFs with variable shape parameters are introduced, and several new variation strategies are proposed. Comparison with the RBF with constant shape parameters are made, and the results show that the condition number of the interpolation matrix grows much slower with our strategies. As an application, an improved collocation meshless method is formulated by employing the new RBF. In addition, the Hermite-type interpolation is implemented to handle the Neumann boundary conditions and an additional sine/cosine basis is introduced for the Helmlholtz equation. Then, two interior acoustic problems are solved with the presented method; the results demonstrate the robustness and effectiveness of the method.

  6. 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.

  7. Thermoluminescence of SrAl_2O_4:Eu"2"+, Dy"3"+: dosimetric characteristics and evidence of glow-peak collocation

    International Nuclear Information System (INIS)

    Chithambo, M.L.

    2016-01-01

    The thermoluminescence of SrAl_2O_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_2O_4:Eu"2"+, Dy"3"+ is reported. Measurements using X-ray excited optical luminescence show that stimulated luminescence from SrAl_2O_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_s_t_o_p 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_2O_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)

  8. 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

  9. 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

  10. Study on the plasma proteins of A-bomb survived patients including those suffered by the remained radioactivities. Report 2. Quantitative observation of the plasma protein fractions by electrophoretic test and to solve the problems for physiological clinical significance of its patterns

    Energy Technology Data Exchange (ETDEWEB)

    Makidono, J; Takanashi, S; Yoshimoto, T; Kai, T; Yoshimoto, K; Matsutani, M; Miura, M

    1963-10-01

    The plasma proteins of A-bombed survivors, healthy persons, long term x-ray equipment handling people (for instance the radiologists and x-ray technicians), cancer patients, and tumor irradiated cancer patients were examined by the electrophoretic test. It was found that the electrophoretic patterns of plasma proteins could be divided into normal (N-pattern) and abnormal (..beta.. and ..gamma.. patterns) patterns, when they were classified according to the accents of each fraction. The patterns of the healthy persons and the long term x-ray handling people showed normal (N) pattern, however, it showed 43% abnormal patterns in A-bombed survivors and 48% in cancer patients. Furthermore, the patterns could be changed by radiotherapy to cancer, ie., from N to ..beta.. or vice versa. As a result of the quantitative observation about individual pattern, the accents of ..beta..-globulins in ..beta..-patterns and ..gamma..-globulins in ..gamma..-patterns were found. The globulins increased in the A bomb survivors and the long term x-ray handling people, and this increase was also seen in the cases of cancer patients which showed 85% of them were effected with uclers (self disintegrated) by clinical examinations. A physiological clinical significance of these abnormal patterns (..beta.. and ..gamma..) in the plasma proteins indicates the disorders in its body and an important immunological meaning. Abnormal patterns in those who suffered by the remained radioactivities caused by the A-bomb showed 70%, whose average was much higher than those of direct A-bombed survivors. It is pointed out that, in recent days, there is a trend of more and gradual increase in the malignant neoplamsm than the disorders of direct A-bombed survivors.

  11. 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...

  12. Collocation lists as instruments for metaphor detection in corpora Listas de colocações como instrumentos para detecção de metáforas em corpora

    Directory of Open Access Journals (Sweden)

    Tony Berber Sardinha

    2006-01-01

    Full Text Available This paper reports a study on the use of collocation lists as instruments for detecting metaphors in corpora. A collocation list contains the collocations for selected words in corpora together with concordances for those words. As corpora become more available to metaphor researchers, there is a growing need for developing ways to gain access to as much data as the corpus can offer. The research described here has hopefully come some way toward meeting the challenges of developing tools for metaphor corpus research. Results suggest that the collocation lists seem to be a good pre-processing instrument for corpus research of metaphor, despite accuracy problems.Este trabalho apresenta uma pesquisa sobre o uso de listas de colocações como instrumentos para detecção de metáforas em corpora. Uma lista de colocação contém as colocações de palavras selecionadas de corpora juntamente com as concordâncias dessas palavras. Na medida que os corpora se tornam mais acessíveis aos pesquisadores de metáfora, começa a surgir uma necessidade de desenvolver maneiras de acessar a maior quantidade possível de dados que um corpus oferece. A pesquisa descrita aqui tentou enfrentar esse desafio, criando e testando ferramentas para pesquisa de metáfora baseada em corpus. Os resultados sugerem que as listas de colocações podem ser um instrumento eficaz de pré-processamento de corpus com vistas à análise humana de metáforas, a despeito de alguns problemas de precisão.

  13. 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

  14. [Renal patient's diet: Can fish be included?].

    Science.gov (United States)

    Castro González, M I; Maafs Rodríguez, A G; Galindo Gómez, C

    2012-01-01

    Medical and nutritional treatment for renal disease, now a major public health issue, is highly complicated. Nutritional therapy must seek to retard renal dysfunction, maintain an optimal nutritional status and prevent the development of underlying pathologies. To analyze ten fish species to identify those that, because of their low phosphorus content, high biological value protein and elevated n-3 fatty acids EPA and DHA, could be included in renal patient's diet. The following fish species (Litte tunny, Red drum, Spotted eagleray, Escolar, Swordfish, Big-scale pomfret, Cortez flounder, Largemouth blackbass, Periche mojarra, Florida Pompano) were analyzed according to the AOAC and Keller techniques to determine their protein, phosphorus, sodium, potassium, cholesterol, vitamins D(3) and E, and n-3 EPA+DHA content. These results were used to calculate relations between nutrients. The protein in the analyzed species ranged from 16.5 g/100 g of fillet (Largemouth black bass) to 27.2 g/100 g (Red drum); the lowest phosphorus value was 28.6 mg/100 g (Periche mojarra) and the highest 216.3 mg/100 g (Spotted eagle ray). 80% of the fish presented > 100 mg EPA + DHA in 100 g of fillet. By its Phosphorus/gProtein ratio, Escolar and Swordfish could not be included in the renal diet; Little tunny, Escolar, Big-scale pomfret, Largemouth black-bass, Periche mojarra and Florida Pompano presented a lower Phosphorus/EPA + DHA ratio. Florida pompano is the most recommended specie for renal patients, due to its optimal nutrient relations. However, all analyzed species, except Escolar and Swordfish, could be included in renal diets.

  15. 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.

  16. A Hydrological Tomography Collocated with Time-varying Gravimetry for Hydrogeology -An Example in Yun-Lin Alluvial Plain and Ming-Ju Basin in Taiwan

    Science.gov (United States)

    Chen, K. H.; Cheng, C. C.; Hwang, C.

    2016-12-01

    A new inversion technique featured by the collocation of hydrological modeling and gravimetry observation is presented in this report. Initially this study started from a project attempting to build a sequence of hydrodynamic models of ground water system, which was applied to identify the supplement areas of alluvial plains and basins along the west coast of Taiwan. To calibrate the decent hydro-geological parameters for the modeling, geological evolution were carefully investigated and absolute gravity observations, along with other on-site hydrological monitoring data were specially introduced. It was discovered in the data processing that the time-varying gravimetrical data are highly sensitive to certain boundary conditions in the hydrodynamic model, which are correspondent with respective geological features. A new inversion technique coined by the term "hydrological tomography" is therefore developed by reversing the boundary condition into the unknowns to be solved. An example of accurate estimate for water storage and precipitation infiltration of a costal alluvial plain Yun-Lin is presented. In the mean time, the study of an anticline structure of the upstream basin Ming-Ju is also presented to demonstrate how a geological formation is outlined when the gravimetrical data and hydrodynamic model are re-directed into an inversion.

  17. Study on the Single Scattering of Elastic Waves by a Cylindrical Fiber with a Partially Imperfect Bonding Using the Collocation Point Method

    Directory of Open Access Journals (Sweden)

    Jun Zhang

    2018-01-01

    Full Text Available The single scattering of P- and SV-waves by a cylindrical fiber with a partially imperfect bonding to the surrounding matrix is investigated, which benefits the characterization of the behavior of elastic waves in composite materials. The imperfect interface is modelled by the spring model. To solve the corresponding single scattering problem, a collocation point (CP method is introduced. Based on this method, influence of various aspects of the imperfect interface on the scattering of P- and SV-waves is studied. Results indicate that (i the total scattering cross section (SCS is almost symmetric about the axis α=π/2 with respect to the location (α of the imperfect interface, (ii imperfect interfaces located at α=0 and α=π highly reduce the total SCS under a P-wave incidence and imperfect interfaces located at α=π/2 reduce the total SCS most significantly under SV-incidence, and (iii under a P-wave incidence the SCS has a high sensitivity to the bonding level of imperfect interfaces when α is small, while it becomes more sensitive to the bonding level when α is larger under SV-wave incidence.

  18. 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

  19. 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.

  20. (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.

  1. 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

  2. Theory including future not excluded

    DEFF Research Database (Denmark)

    Nagao, K.; Nielsen, H.B.

    2013-01-01

    We study a complex action theory (CAT) whose path runs over not only past but also future. We show that, if we regard a matrix element defined in terms of the future state at time T and the past state at time TA as an expectation value in the CAT, then we are allowed to have the Heisenberg equation......, Ehrenfest's theorem, and the conserved probability current density. In addition,we showthat the expectation value at the present time t of a future-included theory for large T - t and large t - T corresponds to that of a future-not-included theory with a proper inner product for large t - T. Hence, the CAT...

  3. 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...

  4. Polarizable protein packing

    KAUST Repository

    Ng, Albert H.; Snow, Christopher D.

    2011-01-01

    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

  5. Macrophysical and optical properties of midlatitude cirrus clouds from four ground-based lidars and collocated CALIOP observations

    Energy Technology Data Exchange (ETDEWEB)

    Dupont, Jean-Charles; Haeffelin, M.; Morille, Y.; Noel, V.; Keckhut, P.; Winker, D.; Comstock, Jennifer M.; Chervet, P.; Roblin, A.

    2010-05-27

    Ground-based lidar and CALIOP datasets gathered over four mid-latitude sites, two US and two French sites, are used to evaluate the consistency of cloud macrophysical and optical property climatologies that can be derived by such datasets. The consistency in average cloud height (both base and top height) between the CALIOP and ground datasets ranges from -0.4km to +0.5km. The cloud geometrical thickness distributions vary significantly between the different datasets, due in part to the original vertical resolutions of the lidar profiles. Average cloud geometrical thicknesses vary from 1.2 to 1.9km, i.e. by more than 50%. Cloud optical thickness distributions in subvisible, semi-transparent and moderate intervals differ by more than 50% between ground and space-based datasets. The cirrus clouds with 2 optical thickness below 0.1 (not included in historical cloud climatologies) represent 30-50% of the non-opaque cirrus class. The differences in average cloud base altitude between ground and CALIOP datasets of 0.0-0.1 km, 0.0-0.2 km and 0.0-0.2 km can be attributed to irregular sampling of seasonal variations in the ground-based data, to day-night differences in detection capabilities by CALIOP, and to the restriction to situations without low-level clouds in ground-based data, respectively. The cloud geometrical thicknesses are not affected by irregular sampling of seasonal variations in the ground-based data, while up to 0.0-0.2 km and 0.1-0.3 km differences can be attributed to day-night differences in detection capabilities by CALIOP, and to the restriction to situations without lowlevel clouds in ground-based data, respectively.

  6. Device including a contact detector

    DEFF Research Database (Denmark)

    2011-01-01

    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......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 the test sample by movement of the probe relative to the surface of the test sample into the specific orientation.; The probe may further comprise a contact detector (14) extending from the supporting body arranged so as to contact the surface of the test sample prior to any one of the plurality...

  7. Neoclassical transport including collisional nonlinearity.

    Science.gov (United States)

    Candy, J; Belli, E A

    2011-06-10

    In the standard δf theory of neoclassical transport, the zeroth-order (Maxwellian) solution is obtained analytically via the solution of a nonlinear equation. The first-order correction δf is subsequently computed as the solution of a linear, inhomogeneous equation that includes the linearized Fokker-Planck collision operator. This equation admits analytic solutions only in extreme asymptotic limits (banana, plateau, Pfirsch-Schlüter), and so must be solved numerically for realistic plasma parameters. Recently, numerical codes have appeared which attempt to compute the total distribution f more accurately than in the standard ordering by retaining some nonlinear terms related to finite-orbit width, while simultaneously reusing some form of the linearized collision operator. In this work we show that higher-order corrections to the distribution function may be unphysical if collisional nonlinearities are ignored.

  8. Towards ligand docking including explicit interface water molecules.

    Directory of Open Access Journals (Sweden)

    Gordon Lemmon

    Full Text Available Small molecule docking predicts the interaction of a small molecule ligand with a protein at atomic-detail accuracy including position and conformation the ligand but also conformational changes of the protein upon ligand binding. While successful in the majority of cases, docking algorithms including RosettaLigand fail in some cases to predict the correct protein/ligand complex structure. In this study we show that simultaneous docking of explicit interface water molecules greatly improves Rosetta's ability to distinguish correct from incorrect ligand poses. This result holds true for both protein-centric water docking wherein waters are located relative to the protein binding site and ligand-centric water docking wherein waters move with the ligand during docking. Protein-centric docking is used to model 99 HIV-1 protease/protease inhibitor structures. We find protease inhibitor placement improving at a ratio of 9:1 when one critical interface water molecule is included in the docking simulation. Ligand-centric docking is applied to 341 structures from the CSAR benchmark of diverse protein/ligand complexes [1]. Across this diverse dataset we see up to 56% recovery of failed docking studies, when waters are included in the docking simulation.

  9. 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

  10. 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

  11. 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,...

  12. 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

  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. 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.

  15. Protein docking prediction using predicted protein-protein interface.

    Science.gov (United States)

    Li, Bin; Kihara, Daisuke

    2012-01-10

    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. 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. 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.

  16. Protein-Protein Docking in Drug Design and Discovery.

    Science.gov (United States)

    Kaczor, Agnieszka A; Bartuzi, Damian; Stępniewski, Tomasz Maciej; Matosiuk, Dariusz; Selent, Jana

    2018-01-01

    Protein-protein interactions (PPIs) are responsible for a number of key physiological processes in the living cells and underlie the pathomechanism of many diseases. Nowadays, along with the concept of so-called "hot spots" in protein-protein interactions, which are well-defined interface regions responsible for most of the binding energy, these interfaces can be targeted with modulators. In order to apply structure-based design techniques to design PPIs modulators, a three-dimensional structure of protein complex has to be available. In this context in silico approaches, in particular protein-protein docking, are a valuable complement to experimental methods for elucidating 3D structure of protein complexes. Protein-protein docking is easy to use and does not require significant computer resources and time (in contrast to molecular dynamics) and it results in 3D structure of a protein complex (in contrast to sequence-based methods of predicting binding interfaces). However, protein-protein docking cannot address all the aspects of protein dynamics, in particular the global conformational changes during protein complex formation. In spite of this fact, protein-protein docking is widely used to model complexes of water-soluble proteins and less commonly to predict structures of transmembrane protein assemblies, including dimers and oligomers of G protein-coupled receptors (GPCRs). In this chapter we review the principles of protein-protein docking, available algorithms and software and discuss the recent examples, benefits, and drawbacks of protein-protein docking application to water-soluble proteins, membrane anchoring and transmembrane proteins, including GPCRs.

  17. Bacterial Ice Crystal Controlling Proteins

    Science.gov (United States)

    Lorv, Janet S. H.; Rose, David R.; Glick, Bernard R.

    2014-01-01

    Across the world, many ice active bacteria utilize ice crystal controlling proteins for aid in freezing tolerance at subzero temperatures. Ice crystal controlling proteins include both antifreeze and ice nucleation proteins. Antifreeze proteins minimize freezing damage by inhibiting growth of large ice crystals, while ice nucleation proteins induce formation of embryonic ice crystals. Although both protein classes have differing functions, these proteins use the same ice binding mechanisms. Rather than direct binding, it is probable that these protein classes create an ice surface prior to ice crystal surface adsorption. Function is differentiated by molecular size of the protein. This paper reviews the similar and different aspects of bacterial antifreeze and ice nucleation proteins, the role of these proteins in freezing tolerance, prevalence of these proteins in psychrophiles, and current mechanisms of protein-ice interactions. PMID:24579057

  18. 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.

  19. 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

    resulting from displaced brine. Quantifying risk on the basis of numerical simulations requires consideration of different kinds of uncertainties and this study considers both, scenario uncertainty and statistical uncertainty. Addressing scenario uncertainty involves expert opinion on relevant geological......Comprehensive risk assessment is a major task for large-scale projects such as geological storage of CO2. Basic hazards are damage to the integrity of caprocks, leakage of CO2, or reduction of groundwater quality due to intrusion of fluids. This study focuses on salinization of freshwater aquifers...... 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...

  20. Asymmetric free vibrations of laminated annular cross-ply circular plates including the effects of shear deformation and rotary inertia. Spline method

    Energy Technology Data Exchange (ETDEWEB)

    Viswanathan, K.K.; Kim, Kyung Su; Lee, Jang Hyun [Inha Univ., Incheon (Korea). Dept. of Naval Architecture and Ocean Engineering

    2009-12-15

    Asymmetric free vibrations of annular cross-ply circular plates are studied using spline function approximation. The governing equations are formulated including the effects of shear deformation and rotary inertia. Assumptions are made to study the cross-ply layered plates. A system of coupled differential equations are obtained in terms of displacement functions and rotational functions. These functions are approximated using Bickley- type spline functions of suitable order. Then the system is converted into the eigenvalue problem by applying the point collocation technique and suitable boundary conditions. Parametric studies have been made to investigate the effect of transverse shear deformation and rotary inertia on frequency parameter with respect to the circumferential node number, radii ratio and thickness to radius ratio for both symmetric and anti-symmetric cross-ply plates using various types of material properties. (orig.)

  1. With Protein Foods, Variety Is Key: 10 Tips for Choosing Protein

    Science.gov (United States)

    ... Dietary Guidelines Communicator’s Guide 10 Tips: Vary Your Protein Routine You are here Home 10 Tips: Vary ... Protein Routine Print Share 10 Tips: Vary Your Protein Routine Protein foods include both animal (meat, poultry, ...

  2. Designing proteins for therapeutic applications.

    Science.gov (United States)

    Lazar, Greg A; Marshall, Shannon A; Plecs, Joseph J; Mayo, Stephen L; Desjarlais, John R

    2003-08-01

    Protein design is becoming an increasingly useful tool for optimizing protein drugs and creating novel biotherapeutics. Recent progress includes the engineering of monoclonal antibodies, cytokines, enzymes and viral fusion inhibitors.

  3. 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

  4. 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.

  5. 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 ...

  6. 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.)

  7. Whey Protein

    Science.gov (United States)

    ... reliable information about the safety of taking whey protein if you are pregnant or breast feeding. Stay on the safe side and avoid use. Milk allergy: If you are allergic to cow's milk, avoid using whey protein.

  8. Cellular strategies to cope with protein aggregation

    NARCIS (Netherlands)

    Scior, Annika; Juenemann, Katrin; Kirstein, Janine

    2016-01-01

    Nature has evolved several mechanisms to detoxify intracellular protein aggregates that arise upon proteotoxic challenges. These include the controlled deposition of misfolded proteins at distinct cellular sites, the protein disaggregation and refolding by molecular chaperones and/or degradation of

  9. 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.

  10. 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

  11. 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

  12. 42 CFR 410.100 - Included services.

    Science.gov (United States)

    2010-10-01

    ... service; however, maintenance therapy itself is not covered as part of these services. (c) Occupational... increase respiratory function, such as graded activity services; these services include physiologic... rehabilitation plan of treatment, including physical therapy services, occupational therapy services, speech...

  13. 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

  14. 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.

  15. 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,

  16. 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,

  17. 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.

  18. 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.

  19. cDNA encoding a polypeptide including a hevein sequence

    Energy Technology Data Exchange (ETDEWEB)

    Raikhel, N.V.; Broekaert, W.F.; Chua, N.H.; Kush, A.

    1999-05-04

    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. 12 figs.

  20. cDNA encoding a polypeptide including a hevein sequence

    Energy Technology Data Exchange (ETDEWEB)

    Raikhel, Natasha V. (Okemos, MI); Broekaert, Willem F. (Dilbeek, BE); Chua, Nam-Hai (Scarsdale, NY); Kush, Anil (New York, NY)

    1999-05-04

    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.

  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.

    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 1,018 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. 11 figures.

  2. Ultrafiltration of pegylated proteins

    Science.gov (United States)

    Molek, Jessica R.

    There is considerable clinical interest in the use of "second-generation" therapeutics produced by conjugation of a native protein with various polymers including polyethylene glycol (PEG). PEG--protein conjugates, so-called PEGylated proteins, can exhibit enhanced stability, half-life, and bioavailability. One of the challenges in the commercial production of PEGylated proteins is the purification required to remove unreacted polymer, native protein, and in many cases PEGylated proteins with nonoptimal degrees of conjugation. The overall objective of this thesis was to examine the use of ultrafiltration for the purification of PEGylated proteins. This included: (1) analysis of size-based separation of PEGylated proteins using conventional ultrafiltration membranes, (2) use of electrically-charged membranes to exploit differences in electrostatic interactions, and (3) examination of the effects of PEGylation on protein fouling. The experimental results were analyzed using appropriate theoretical models, with the underlying physical properties of the PEGylated proteins evaluated using size exclusion chromatography, capillary electrophoresis, dynamic light scattering, and reverse phase chromatography. PEGylated proteins were produced by covalent attachment of activated PEG to a protein via primary amines on the lysine residues. A simple model was developed for the reaction kinetics, which was used to explore the effect of reaction conditions and mode of operation on the distribution of PEGylated products. The effective size of the PEGylated proteins was evaluated using size exclusion chromatography, with appropriate correlations developed for the size in terms of the molecular weight of the native protein and attached PEG. The electrophoretic mobility of the PEGylated proteins were evaluated by capillary electrophoresis with the data in good agreement with a simple model accounting for the increase in protein size and the reduction in the number of protonated amine

  3. Detecting annual and seasonal variations of CO2, CO and N2O from a multi-year collocated satellite-radiosonde data-set using the new Rapid Radiance Reconstruction (3R-N) model

    International Nuclear Information System (INIS)

    Chedin, A.; Serrar, S.; Hollingsworth, A.; Armante, R.; Scott, N.A.

    2003-01-01

    The NOAA polar meteorological satellites have embarked the TIROS-N operational vertical sounder (TOVS) since 1979. Using radiosondes and NOAA-10 TOVS measurements which are collocated within a narrow space and time window, we have studied the differences between the TOVS measurements and simulated measurements from a new fast, Rapid Radiance Reconstruction Network (3R-N), non-linear radiative transfer model with up to date spectroscopy. Simulations use radiosonde temperature and humidity measurements as the prime input. The radiative transfer model also uses fixed greenhouse gas absorber amounts (CO 2 ,CO,N 2 O) and reasonable estimates of O 3 and of surface temperature. The 3R-N model is first presented and validated. Then, a study of the differences between the simulated and measured radiances shows annual trends and seasonal variations consistent with independent measurements of variations in CO 2 and other greenhouse gases atmospheric concentrations. The improved accuracy of 3R-N and a better handling of its deviations with respect to observations allow most of difficulties met in a previous study (J. Climate 15 (2002) 95) to be resolved

  4. Detecting annual and seasonal variations of CO{sub 2}, CO and N{sub 2}O from a multi-year collocated satellite-radiosonde data-set using the new Rapid Radiance Reconstruction (3R-N) model

    Energy Technology Data Exchange (ETDEWEB)

    Chedin, A.; Serrar, S.; Hollingsworth, A.; Armante, R.; Scott, N.A

    2003-03-15

    The NOAA polar meteorological satellites have embarked the TIROS-N operational vertical sounder (TOVS) since 1979. Using radiosondes and NOAA-10 TOVS measurements which are collocated within a narrow space and time window, we have studied the differences between the TOVS measurements and simulated measurements from a new fast, Rapid Radiance Reconstruction Network (3R-N), non-linear radiative transfer model with up to date spectroscopy. Simulations use radiosonde temperature and humidity measurements as the prime input. The radiative transfer model also uses fixed greenhouse gas absorber amounts (CO{sub 2},CO,N{sub 2}O) and reasonable estimates of O{sub 3} and of surface temperature. The 3R-N model is first presented and validated. Then, a study of the differences between the simulated and measured radiances shows annual trends and seasonal variations consistent with independent measurements of variations in CO{sub 2} and other greenhouse gases atmospheric concentrations. The improved accuracy of 3R-N and a better handling of its deviations with respect to observations allow most of difficulties met in a previous study (J. Climate 15 (2002) 95) to be resolved.

  5. HIV protein sequence hotspots for crosstalk with host hub proteins.

    Directory of Open Access Journals (Sweden)

    Mahdi Sarmady

    Full Text Available HIV proteins target host hub proteins for transient binding interactions. The presence of viral proteins in the infected cell results in out-competition of host proteins in their interaction with hub proteins, drastically affecting cell physiology. Functional genomics and interactome datasets can be used to quantify the sequence hotspots on the HIV proteome mediating interactions with host hub proteins. In this study, we used the HIV and human interactome databases to identify HIV targeted host hub proteins and their host binding partners (H2. We developed a high throughput computational procedure utilizing motif discovery algorithms on sets of protein sequences, including sequences of HIV and H2 proteins. We identified as HIV sequence hotspots those linear motifs that are highly conserved on HIV sequences and at the same time have a statistically enriched presence on the sequences of H2 proteins. The HIV protein motifs discovered in this study are expressed by subsets of H2 host proteins potentially outcompeted by HIV proteins. A large subset of these motifs is involved in cleavage, nuclear localization, phosphorylation, and transcription factor binding events. Many such motifs are clustered on an HIV sequence in the form of hotspots. The sequential positions of these hotspots are consistent with the curated literature on phenotype altering residue mutations, as well as with existing binding site data. The hotspot map produced in this study is the first global portrayal of HIV motifs involved in altering the host protein network at highly connected hub nodes.

  6. 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......, is a general hallmark. They also include the α1-antitrypsin deficiency, where disease-causing mutations in the serine protease inhibitor, α1-antitrypsin (α1AT), leads to accumulation of the aberrant protein in the liver of these patients. The native metastable structure of α1AT constitutes a molecular trap...... 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...

  7. Synthesis of Lipidated Proteins.

    Science.gov (United States)

    Mejuch, Tom; Waldmann, Herbert

    2016-08-17

    Protein lipidation is one of the major post-translational modifications (PTM) of proteins. The attachment of the lipid moiety frequently determines the localization and the function of the lipoproteins. Lipidated proteins participate in many essential biological processes in eukaryotic cells, including vesicular trafficking, signal transduction, and regulation of the immune response. Malfunction of these cellular processes usually leads to various diseases such as cancer. Understanding the mechanism of cellular signaling and identifying the protein-protein and protein-lipid interactions in which the lipoproteins are involved is a crucial task. To achieve these goals, fully functional lipidated proteins are required. However, access to lipoproteins by means of standard expression is often rather limited. Therefore, semisynthetic methods, involving the synthesis of lipidated peptides and their subsequent chemoselective ligation to yield full-length lipoproteins, were developed. In this Review we summarize the commonly used methods for lipoprotein synthesis and the development of the corresponding chemoselective ligation techniques. Several key studies involving full-length semisynthetic lipidated Ras, Rheb, and LC3 proteins are presented.

  8. 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

  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. The tubby family proteins

    OpenAIRE

    Mukhopadhyay, Saikat; Jackson, Peter K

    2011-01-01

    The tubby mouse shows a tripartite syndrome characterized by maturity-onset obesity, blindness and deafness. The causative gene Tub is the founding member of a family of related proteins present throughout the animal and plant kingdoms, each characterized by a signature carboxy-terminal tubby domain. This domain consists of a β barrel enclosing a central α helix and binds selectively to specific membrane phosphoinositides. The vertebrate family of tubby-like proteins (TULPs) includes the foun...

  11. The caveolin proteins

    OpenAIRE

    Williams, Terence M; Lisanti, Michael P

    2004-01-01

    The caveolin gene family has three members in vertebrates: caveolin-1, caveolin-2, and caveolin-3. So far, most caveolin-related research has been conducted in mammals, but the proteins have also been found in other animals, including Xenopus laevis, Fugu rubripes, and Caenorhabditis elegans. Caveolins can serve as protein markers of caveolae ('little caves'), invaginations in the plasma membrane 50-100 nanometers in diameter. Caveolins are found predominantly at the plasma membrane but also ...

  12. 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,...

  13. 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......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...

  14. Gas storage materials, including hydrogen storage materials

    Science.gov (United States)

    Mohtadi, Rana F; Wicks, George G; Heung, Leung K; Nakamura, Kenji

    2013-02-19

    A material for the storage and release of gases comprises a plurality of hollow elements, each hollow element comprising a porous wall enclosing an interior cavity, the interior cavity including structures of a solid-state storage material. In particular examples, the storage material is a hydrogen storage material such as a solid state hydride. An improved method for forming such materials includes the solution diffusion of a storage material solution through a porous wall of a hollow element into an interior cavity.

  15. Scoring functions for protein-protein interactions.

    Science.gov (United States)

    Moal, Iain H; Moretti, Rocco; Baker, David; Fernández-Recio, Juan

    2013-12-01

    The computational evaluation of protein-protein interactions will play an important role in organising the wealth of data being generated by high-throughput initiatives. Here we discuss future applications, report recent developments and identify areas requiring further investigation. Many functions have been developed to quantify the structural and energetic properties of interacting proteins, finding use in interrelated challenges revolving around the relationship between sequence, structure and binding free energy. These include loop modelling, side-chain refinement, docking, multimer assembly, affinity prediction, affinity change upon mutation, hotspots location and interface design. Information derived from models optimised for one of these challenges can be used to benefit the others, and can be unified within the theoretical frameworks of multi-task learning and Pareto-optimal multi-objective learning. Copyright © 2013 Elsevier Ltd. All rights reserved.

  16. A gene encoding an abscisic acid biosynthetic enzyme (LsNCED4) collocates with the high temperature germination locus Htg6.1 in lettuce (Lactuca sp.).

    Science.gov (United States)

    Argyris, Jason; Truco, María José; Ochoa, Oswaldo; McHale, Leah; Dahal, Peetambar; Van Deynze, Allen; Michelmore, Richard W; Bradford, Kent J

    2011-01-01

    Thermoinhibition, or failure of seeds to germinate when imbibed at warm temperatures, can be a significant problem in lettuce (Lactuca sativa L.) production. The reliability of stand establishment would be improved by increasing the ability of lettuce seeds to germinate at high temperatures. Genes encoding germination- or dormancy-related proteins were mapped in a recombinant inbred line population derived from a cross between L. sativa cv. Salinas and L. serriola accession UC96US23. This revealed several candidate genes that are located in the genomic regions containing quantitative trait loci (QTLs) associated with temperature and light requirements for germination. In particular, LsNCED4, a temperature-regulated gene in the biosynthetic pathway for abscisic acid (ABA), a germination inhibitor, mapped to the center of a previously detected QTL for high temperature germination (Htg6.1) from UC96US23. Three sets of sister BC(3)S(2) near-isogenic lines (NILs) that were homozygous for the UC96US23 allele of LsNCED4 at Htg6.1 were developed by backcrossing to cv. Salinas and marker-assisted selection followed by selfing. The maximum temperature for germination of NIL seed lots with the UC96US23 allele at LsNCED4 was increased by 2-3°C when compared with sister NIL seed lots lacking the introgression. In addition, the expression of LsNCED4 was two- to threefold lower in the former NIL lines as compared to expression in the latter. Together, these data strongly implicate LsNCED4 as the candidate gene responsible for the Htg6.1 phenotype and indicate that decreased ABA biosynthesis at high imbibition temperatures is a major factor responsible for the increased germination thermotolerance of UC96US23 seeds.

  17. 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

  18. 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.

  19. 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.

  20. 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.

  1. 28 CFR 20.32 - Includable offenses.

    Science.gov (United States)

    2010-07-01

    ... Exchange of Criminal History Record Information § 20.32 Includable offenses. (a) Criminal history record... vehicular manslaughter, driving under the influence of drugs or liquor, and hit and run), when unaccompanied by a § 20.32(a) offense. These exclusions may not be applicable to criminal history records...

  2. 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…

  3. 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 ...

  4. 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 ...

  5. 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…

  6. Electron transfer in proteins

    DEFF Research Database (Denmark)

    Farver, O; Pecht, I

    1991-01-01

    Electron migration between and within proteins is one of the most prevalent forms of biological energy conversion processes. Electron transfer reactions take place between active centers such as transition metal ions or organic cofactors over considerable distances at fast rates and with remarkable...... specificity. The electron transfer is attained through weak electronic interaction between the active sites, so that considerable research efforts are centered on resolving the factors that control the rates of long-distance electron transfer reactions in proteins. These factors include (in addition......-containing proteins. These proteins serve almost exclusively in electron transfer reactions, and as it turns out, their metal coordination sites are endowed with properties uniquely optimized for their function....

  7. 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

  8. The interface of protein structure, protein biophysics, and molecular evolution

    Science.gov (United States)

    Liberles, David A; Teichmann, Sarah A; Bahar, Ivet; Bastolla, Ugo; Bloom, Jesse; Bornberg-Bauer, Erich; Colwell, Lucy J; de Koning, A P Jason; Dokholyan, Nikolay V; Echave, Julian; Elofsson, Arne; Gerloff, Dietlind L; Goldstein, Richard A; Grahnen, Johan A; Holder, Mark T; Lakner, Clemens; Lartillot, Nicholas; Lovell, Simon C; Naylor, Gavin; Perica, Tina; Pollock, David D; Pupko, Tal; Regan, Lynne; Roger, Andrew; Rubinstein, Nimrod; Shakhnovich, Eugene; Sjölander, Kimmen; Sunyaev, Shamil; Teufel, Ashley I; Thorne, Jeffrey L; Thornton, Joseph W; Weinreich, Daniel M; Whelan, Simon

    2012-01-01

    Abstract The interface of protein structural biology, protein biophysics, molecular evolution, and molecular population genetics forms the foundations for a mechanistic understanding of many aspects of protein biochemistry. Current efforts in interdisciplinary protein modeling are in their infancy and the state-of-the art of such models is described. Beyond the relationship between amino acid substitution and static protein structure, protein function, and corresponding organismal fitness, other considerations are also discussed. More complex mutational processes such as insertion and deletion and domain rearrangements and even circular permutations should be evaluated. The role of intrinsically disordered proteins is still controversial, but may be increasingly important to consider. Protein geometry and protein dynamics as a deviation from static considerations of protein structure are also important. Protein expression level is known to be a major determinant of evolutionary rate and several considerations including selection at the mRNA level and the role of interaction specificity are discussed. Lastly, the relationship between modeling and needed high-throughput experimental data as well as experimental examination of protein evolution using ancestral sequence resurrection and in vitro biochemistry are presented, towards an aim of ultimately generating better models for biological inference and prediction. PMID:22528593

  9. 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.

  10. 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)

  11. Nuclear reactor shield including magnesium oxide

    International Nuclear Information System (INIS)

    Rouse, C.A.; Simnad, M.T.

    1981-01-01

    An improvement is described for nuclear reactor shielding of a type used in reactor applications involving significant amounts of fast neutron flux. The reactor shielding includes means providing structural support, neutron moderator material, neutron absorber material and other components, wherein at least a portion of the neutron moderator material is magnesium in the form of magnesium oxide either alone or in combination with other moderator materials such as graphite and iron

  12. Model for safety reports including descriptive examples

    International Nuclear Information System (INIS)

    1995-12-01

    Several safety reports will be produced in the process of planning and constructing the system for disposal of high-level radioactive waste in Sweden. The present report gives a model, with detailed examples, of how these reports should be organized and what steps they should include. In the near future safety reports will deal with the encapsulation plant and the repository. Later reports will treat operation of the handling systems and the repository

  13. 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

  14. MOS modeling hierarchy including radiation effects

    International Nuclear Information System (INIS)

    Alexander, D.R.; Turfler, R.M.

    1975-01-01

    A hierarchy of modeling procedures has been developed for MOS transistors, circuit blocks, and integrated circuits which include the effects of total dose radiation and photocurrent response. The models were developed for use with the SCEPTRE circuit analysis program, but the techniques are suitable for other modern computer aided analysis programs. The modeling hierarchy permits the designer or analyst to select the level of modeling complexity consistent with circuit size, parametric information, and accuracy requirements. Improvements have been made in the implementation of important second order effects in the transistor MOS model, in the definition of MOS building block models, and in the development of composite terminal models for MOS integrated circuits

  15. Drug delivery device including electrolytic pump

    KAUST Repository

    Foulds, Ian G.; Buttner, Ulrich; Yi, Ying

    2016-01-01

    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.

  16. 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.

  17. Energy principle with included boundary conditions

    International Nuclear Information System (INIS)

    Lehnert, B.

    1994-01-01

    Earlier comments by the author on the limitations of the classical form of the extended energy principle are supported by a complementary analysis on the potential energy change arising from free-boundary displacements of a magnetically confined plasma. In the final formulation of the extended principle, restricted displacements, satisfying pressure continuity by means of plasma volume currents in a thin boundary layer, are replaced by unrestricted (arbitrary) displacements which can give rise to induced surface currents. It is found that these currents contribute to the change in potential energy, and that their contribution is not taken into account by such a formulation. A general expression is further given for surface currents induced by arbitrary displacements. The expression is used to reformulate the energy principle for the class of displacements which satisfy all necessary boundary conditions, including that of the pressure balance. This makes a minimization procedure of the potential energy possible, for the class of all physically relevant test functions which include the constraints imposed by the boundary conditions. Such a procedure is also consistent with a corresponding variational calculus. (Author)

  18. 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

  19. Addressing Stillbirth in India Must Include Men.

    Science.gov (United States)

    Roberts, Lisa; Montgomery, Susanne; Ganesh, Gayatri; Kaur, Harinder Pal; Singh, Ratan

    2017-07-01

    Millennium Development Goal 4, to reduce child mortality, can only be achieved by reducing stillbirths globally. A confluence of medical and sociocultural factors contribute to the high stillbirth rates in India. The psychosocial aftermath of stillbirth is a well-documented public health problem, though less is known of the experience for men, particularly outside of the Western context. Therefore, men's perceptions and knowledge regarding reproductive health, as well as maternal-child health are important. Key informant interviews (n = 5) were analyzed and 28 structured interviews were conducted using a survey based on qualitative themes. Qualitative themes included men's dual burden and right to medical and reproductive decision making power. Wives were discouraged from expressing grief and pushed to conceive again. If not successful, particularly if a son was not conceived, a second wife was considered a solution. Quantitative data revealed that men with a history of stillbirths had greater anxiety and depression, perceived less social support, but had more egalitarian views towards women than men without stillbirth experience. At the same time fathers of stillbirths were more likely to be emotionally or physically abusive. Predictors of mental health, attitudes towards women, and perceived support are discussed. Patriarchal societal values, son preference, deficient women's autonomy, and sex-selective abortion perpetuate the risk for future poor infant outcomes, including stillbirth, and compounds the already higher risk of stillbirth for males. Grief interventions should explore and take into account men's perceptions, attitudes, and behaviors towards reproductive decision making.

  20. Identifying Key Attributes for Protein Beverages.

    Science.gov (United States)

    Oltman, A E; Lopetcharat, K; Bastian, E; Drake, M A

    2015-06-01

    This study identified key attributes of protein beverages and evaluated effects of priming on liking of protein beverages. An adaptive choice-based conjoint study was conducted along with Kano analysis to gain insight on protein beverage consumers (n = 432). Attributes evaluated included label claim, protein type, amount of protein, carbohydrates, sweeteners, and metabolic benefits. Utility scores for levels and importance scores for attributes were determined. Subsequently, two pairs of clear acidic whey protein beverages were manufactured that differed by age of protein source or the amount of whey protein per serving. Beverages were evaluated by 151 consumers on two occasions with or without priming statements. One priming statement declared "great flavor," the other priming statement declared 20 g protein per serving. A two way analysis of variance was applied to discern the role of each priming statement. The most important attribute for protein beverages was sweetener type, followed by amount of protein, followed by type of protein followed by label claim. Beverages with whey protein, naturally sweetened, reduced sugar and ≥15 g protein per serving were most desired. Three consumer clusters were identified, differentiated by their preferences for protein type, sweetener and amount of protein. Priming statements positively impacted concept liking (P 0.05). Consistent with trained panel profiles of increased cardboard flavor with higher protein content, consumers liked beverages with 10 g protein more than beverages with 20 g protein (6.8 compared with 5.7, P appeal. © 2015 Institute of Food Technologists®

  1. 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

  2. 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.

  3. Including gauge corrections to thermal leptogenesis

    Energy Technology Data Exchange (ETDEWEB)

    Huetig, Janine

    2013-05-17

    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

  4. 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

  5. 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

  6. 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...... surgical techniques and better outcome after peripheral nerve injury. Decision making in peripheral nerve surgery continues to be a complex challenge, where the mechanism of injury, repeated clinical evaluation, neuroradiological and neurophysiological examination, and detailed knowledge of the peripheral...... nervous system response to injury are prerequisite to obtain the best possible outcome. Surgery continues to be the primary treatment modality for peripheral nerve tumors and advances in adjuvant oncological treatment has improved outcome after malignant peripheral nerve tumors. The present chapter...

  7. 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

    1994-12-31

    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.

  8. 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.

  9. 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...

  10. 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...

  11. 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...

  12. Critical point anomalies include expansion shock waves

    Energy Technology Data Exchange (ETDEWEB)

    Nannan, N. R., E-mail: ryan.nannan@uvs.edu [Mechanical Engineering Discipline, Anton de Kom University of Suriname, Leysweg 86, PO Box 9212, Paramaribo, Suriname and Process and Energy Department, Delft University of Technology, Leeghwaterstraat 44, 2628 CA Delft (Netherlands); Guardone, A., E-mail: alberto.guardone@polimi.it [Department of Aerospace Science and Technology, Politecnico di Milano, Via La Masa 34, 20156 Milano (Italy); Colonna, P., E-mail: p.colonna@tudelft.nl [Propulsion and Power, Delft University of Technology, Kluyverweg 1, 2629 HS Delft (Netherlands)

    2014-02-15

    From first-principle fluid dynamics, complemented by a rigorous state equation accounting for critical anomalies, we discovered that expansion shock waves may occur in the vicinity of the liquid-vapor critical point in the two-phase region. Due to universality of near-critical thermodynamics, the result is valid for any common pure fluid in which molecular interactions are only short-range, namely, for so-called 3-dimensional Ising-like systems, and under the assumption of thermodynamic equilibrium. In addition to rarefaction shock waves, diverse non-classical effects are admissible, including composite compressive shock-fan-shock waves, due to the change of sign of the fundamental derivative of gasdynamics.

  13. 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...

  14. 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.

  15. 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....

  16. 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

  17. Including climate change in energy investment decisions

    International Nuclear Information System (INIS)

    Ybema, J.R.; Boonekamp, P.G.M.; Smit, J.T.J.

    1995-08-01

    To properly take climate change into account in the analysis of energy investment decisions, it is required to apply decision analysis methods that are capable of considering the specific characteristics of climate change (large uncertainties, long term horizon). Such decision analysis methods do exist. They can explicitly include evolving uncertainties, multi-stage decisions, cumulative effects and risk averse attitudes. Various methods are considered in this report and two of these methods have been selected: hedging calculations and sensitivity analysis. These methods are applied to illustrative examples, and its limitations are discussed. The examples are (1a) space heating and hot water for new houses from a private investor perspective and (1b) as example (1a) but from a government perspective, (2) electricity production with an integrated coal gasification combined cycle (ICGCC) with or without CO 2 removal, and (3) national energy strategy to hedge for climate change. 9 figs., 21 tabs., 42 refs., 1 appendix

  18. 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.

  19. Cellulose binding domain proteins

    Science.gov (United States)

    Shoseyov, Oded; Shpiegl, Itai; Goldstein, Marc; Doi, Roy

    1998-01-01

    A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production thereof. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques.

  20. Analysis of Smart Composite Structures Including Debonding

    Science.gov (United States)

    Chattopadhyay, Aditi; Seeley, Charles E.

    1997-01-01

    Smart composite structures with distributed sensors and actuators have the capability to actively respond to a changing environment while offering significant weight savings and additional passive controllability through ply tailoring. Piezoelectric sensing and actuation of composite laminates is the most promising concept due to the static and dynamic control capabilities. Essential to the implementation of these smart composites are the development of accurate and efficient modeling techniques and experimental validation. This research addresses each of these important topics. A refined higher order theory is developed to model composite structures with surface bonded or embedded piezoelectric transducers. These transducers are used as both sensors and actuators for closed loop control. The theory accurately captures the transverse shear deformation through the thickness of the smart composite laminate while satisfying stress free boundary conditions on the free surfaces. The theory is extended to include the effect of debonding at the actuator-laminate interface. The developed analytical model is implemented using the finite element method utilizing an induced strain approach for computational efficiency. This allows general laminate geometries and boundary conditions to be analyzed. The state space control equations are developed to allow flexibility in the design of the control system. Circuit concepts are also discussed. Static and dynamic results of smart composite structures, obtained using the higher order theory, are correlated with available analytical data. Comparisons, including debonded laminates, are also made with a general purpose finite element code and available experimental data. Overall, very good agreement is observed. Convergence of the finite element implementation of the higher order theory is shown with exact solutions. Additional results demonstrate the utility of the developed theory to study piezoelectric actuation of composite

  1. Kinetic models of gene expression including non-coding RNAs

    Energy Technology Data Exchange (ETDEWEB)

    Zhdanov, Vladimir P., E-mail: zhdanov@catalysis.r

    2011-03-15

    In cells, genes are transcribed into mRNAs, and the latter are translated into proteins. Due to the feedbacks between these processes, the kinetics of gene expression may be complex even in the simplest genetic networks. The corresponding models have already been reviewed in the literature. A new avenue in this field is related to the recognition that the conventional scenario of gene expression is fully applicable only to prokaryotes whose genomes consist of tightly packed protein-coding sequences. In eukaryotic cells, in contrast, such sequences are relatively rare, and the rest of the genome includes numerous transcript units representing non-coding RNAs (ncRNAs). During the past decade, it has become clear that such RNAs play a crucial role in gene expression and accordingly influence a multitude of cellular processes both in the normal state and during diseases. The numerous biological functions of ncRNAs are based primarily on their abilities to silence genes via pairing with a target mRNA and subsequently preventing its translation or facilitating degradation of the mRNA-ncRNA complex. Many other abilities of ncRNAs have been discovered as well. Our review is focused on the available kinetic models describing the mRNA, ncRNA and protein interplay. In particular, we systematically present the simplest models without kinetic feedbacks, models containing feedbacks and predicting bistability and oscillations in simple genetic networks, and models describing the effect of ncRNAs on complex genetic networks. Mathematically, the presentation is based primarily on temporal mean-field kinetic equations. The stochastic and spatio-temporal effects are also briefly discussed.

  2. Zγ production at NNLO including anomalous couplings

    Science.gov (United States)

    Campbell, John M.; Neumann, Tobias; Williams, Ciaran

    2017-11-01

    In this paper we present a next-to-next-to-leading order (NNLO) QCD calculation of the processes pp → l + l -γ and pp\\to ν \\overline{ν}γ that we have implemented in MCFM. Our calculation includes QCD corrections at NNLO both for the Standard Model (SM) and additionally in the presence of Zγγ and ZZγ anomalous couplings. We compare our implementation, obtained using the jettiness slicing approach, with a previous SM calculation and find broad agreement. Focusing on the sensitivity of our results to the slicing parameter, we show that using our setup we are able to compute NNLO cross sections with numerical uncertainties of about 0.1%, which is small compared to residual scale uncertainties of a few percent. We study potential improvements using two different jettiness definitions and the inclusion of power corrections. At √{s}=13 TeV we present phenomenological results and consider Zγ as a background to H → Zγ production. We find that, with typical cuts, the inclusion of NNLO corrections represents a small effect and loosens the extraction of limits on anomalous couplings by about 10%.

  3. Alternating phase focussing including space charge

    International Nuclear Information System (INIS)

    Cheng, W.H.; Gluckstern, R.L.

    1992-01-01

    Longitudinal stability can be obtained in a non-relativistic drift tube accelerator by traversing each gap as the rf accelerating field rises. However, the rising accelerating field leads to a transverse defocusing force which is usually overcome by magnetic focussing inside the drift tubes. The radio frequency quadrupole is one way of providing simultaneous longitudinal and transverse focusing without the use of magnets. One can also avoid the use of magnets by traversing alternate gaps between drift tubes as the field is rising and falling, thus providing an alternation of focussing and defocusing forces in both the longitudinal and transverse directions. The stable longitudinal phase space area is quite small, but recent efforts suggest that alternating phase focussing (APF) may permit low velocity acceleration of currents in the 100-300 ma range. This paper presents a study of the parameter space and a test of crude analytic predictions by adapting the code PARMILA, which includes space charge, to APF. 6 refs., 3 figs

  4. Probabilistic production simulation including CHP plants

    Energy Technology Data Exchange (ETDEWEB)

    Larsen, H.V.; Palsson, H.; Ravn, H.F.

    1997-04-01

    A probabilistic production simulation method is presented for an energy system containing combined heat and power plants. The method permits incorporation of stochastic failures (forced outages) of the plants and is well suited for analysis of the dimensioning of the system, that is, for finding the appropriate types and capacities of production plants in relation to expansion planning. The method is in the tradition of similar approaches for the analysis of power systems, based on the load duration curve. The present method extends on this by considering a two-dimensional load duration curve where the two dimensions represent heat and power. The method permits the analysis of a combined heat and power system which includes all the basic relevant types of plants, viz., condensing plants, back pressure plants, extraction plants and heat plants. The focus of the method is on the situation where the heat side has priority. This implies that on the power side there may be imbalances between demand and production. The method permits quantification of the expected power overflow, the expected unserviced power demand, and the expected unserviced heat demand. It is shown that a discretization method as well as double Fourier series may be applied in algorithms based on the method. (au) 1 tab., 28 ills., 21 refs.

  5. Langevin simulations of QCD, including fermions

    International Nuclear Information System (INIS)

    Kronfeld, A.S.

    1986-02-01

    We encounter critical slow down in updating when xi/a -> infinite and in matrix inversion (needed to include fermions) when msub(q)a -> 0. A simulation that purports to solve QCD numerically will encounter these limits, so to face the challenge in the title of this workshop, we must cure the disease of critical slow down. Physically, this critical slow down is due to the reluctance of changes at short distances to propagate to large distances. Numerically, the stability of an algorithm at short wavelengths requires a (moderately) small step size; critical slow down occurs when the effective long wavelength step size becomes tiny. The remedy for this disease is an algorithm that propagates signals quickly throughout the system; i.e. one whose effective step size is not reduced for the long wavelength conponents of the fields. (Here the effective ''step size'' is essentially an inverse decorrelation time.) To do so one must resolve various wavelengths of the system and modify the dynamics (in CPU time) of the simulation so that all modes evolve at roughly the same rate. This can be achieved by introducing Fourier transforms. I show how to implement Fourier acceleration for Langevin updating and for conjugate gradient matrix inversion. The crucial feature of these algorithms that lends them to Fourier acceleration is that they update the lattice globally; hence the Fourier transforms are computed once per sweep rather than once per hit. (orig./HSI)

  6. 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

  7. 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

  8. Vegetarian Choices in the Protein Foods Group

    Science.gov (United States)

    ... foods selected are adequate. Protein sources from the Protein Foods Group for vegetarians include eggs (for ovo-vegetarians), beans and peas, nuts, nut butters, and soy products (tofu, tempeh, ...

  9. 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)

  10. Protein stress and stress proteins: implications in aging and disease

    Indian Academy of Sciences (India)

    Madhu Sudhan

    2007-04-02

    Apr 2, 2007 ... (iii) modulating protein activity via stabilization and/or maturation to ... Resistance to any physical stress is correlated with longevity in many, if not all .... range of pathologies including cancer, diabetes, immune- problems and ...

  11. Mapping Protein-Protein Interactions by Quantitative Proteomics

    DEFF Research Database (Denmark)

    Dengjel, Joern; Kratchmarova, Irina; Blagoev, Blagoy

    2010-01-01

    spectrometry (MS)-based proteomics in combination with affinity purification protocols has become the method of choice to map and track the dynamic changes in protein-protein interactions, including the ones occurring during cellular signaling events. Different quantitative MS strategies have been used...... to characterize protein interaction networks. In this chapter we describe in detail the use of stable isotope labeling by amino acids in cell culture (SILAC) for the quantitative analysis of stimulus-dependent dynamic protein interactions.......Proteins exert their function inside a cell generally in multiprotein complexes. These complexes are highly dynamic structures changing their composition over time and cell state. The same protein may thereby fulfill different functions depending on its binding partners. Quantitative mass...

  12. Protein-Protein Interaction Databases

    DEFF Research Database (Denmark)

    Szklarczyk, Damian; Jensen, Lars Juhl

    2015-01-01

    Years of meticulous curation of scientific literature and increasingly reliable computational predictions have resulted in creation of vast databases of protein interaction data. Over the years, these repositories have become a basic framework in which experiments are analyzed and new directions...

  13. 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.

  14. 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

  15. 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.

  16. Protein supplementation with sports protein bars in renal patients.

    Science.gov (United States)

    Meade, Anthony

    2007-05-01

    Malnutrition prevalence in patients on dialysis is well established. The protein requirements for both hemodialysis and peritoneal dialysis have been documented elsewhere, including the Kidney Disease Outcomes Quality Initiative Clinical Practice Guidelines for Nutrition in Chronic Renal Failure. The clinical challenge is to assist patients in meeting these targets, especially in those with anorexia. Traditional supplements have included fluid, which is an issue for patients who are fluid restricted. The study objectives were to (1) investigate the range of sports protein supplements that may be suitable for patients on hemodialysis to use and (2) trial nonfluid protein supplements in patients on hemodialysis. Known manufacturers of sports protein bars and other sports supplements available in Australia were contacted for the nutrient breakdown of high-protein products, specifically potassium, protein, and phosphorus contents. As a result, selected high-protein sports bars (Protein FX, Aussie Bodies, Port Melbourne, Victoria, Australia) were used as an alternative to the more commonly used renal-specific fluid supplements (Nepro, Abbott Laboratories, Abbott Park, IL; Novasource Renal, Novartis Nutrition Corporation, Fremont, MI; and Renilon, Nutricia, Wiltshire, UK) in patients with poor nutritional status requiring supplementation. Patient satisfaction and clinical nutrition markers were investigated. The study took place at inpatient, in-center, and satellite hemodialysis settings in Adelaide, South Australia. A total of 32 patients (16 females and 16 males) with an average age of 62.9 years (range 32-86 years) undergoing hemodialysis (acute and maintenance) were included. Subjects were selected by the author as part of routine clinical nutrition care. Patients trialed sports protein bars as a protein supplement alone or in conjunction with other supplementary products. All patients were in favor of the trial, with 22 of 32 patients continuing with the protein

  17. Encoding Collocations in DiCoInfo

    DEFF Research Database (Denmark)

    Leroyer, Patrick; L'Homme, Marie-Claude; Robichaud, Benoît

    2012-01-01

    This contribution presents an online lexical database and shows how some of its data categories were converted to make them more accessible to users. The database is called DiCoInfo and contains English, French, and Spanish terms related to the fields of computing and the Internet. Entries...

  18. Active damping based on decoupled collocated control

    NARCIS (Netherlands)

    Holterman, J.; de Vries, Theodorus J.A.; Auer, Frank; Gardonio, P.; Rafaely, B.

    2002-01-01

    High-precision machines typically suffer from small but persistent vibrations. As it is difficult to damp these vibrations by passive means, research at the Drebbel Institute at the University of Twente is aimed at the development of an active structural element that can be used for vibration

  19. Geostationary Collocation: Case Studies for Optimal Maneuvers

    Science.gov (United States)

    2016-03-01

    Microcosm Inc., 1994, pp. 123. Soop [13] adds that larger satellites, with large solar panels , will have bigger probabilities of a collision...10 2. The Solar and Lunar Perturbations ................................................ 13 3. The Solar Radiation Perturbation...16 Figure 9. Solar radiation pressure effect

  20. Maintaining protein composition in cilia.

    Science.gov (United States)

    Stephen, Louise A; Elmaghloob, Yasmin; Ismail, Shehab

    2017-12-20

    The primary cilium is a sensory organelle that is vital in regulating several signalling pathways. Unlike most organelles cilia are open to the rest of the cell, not enclosed by membranes. The distinct protein composition is crucial to the function of cilia and many signalling proteins and receptors are specifically concentrated within distinct compartments. To maintain this composition, a mechanism is required to deliver proteins to the cilium whilst another must counter the entropic tendency of proteins to distribute throughout the cell. The combination of the two mechanisms should result in the concentration of ciliary proteins to the cilium. In this review we will look at different cellular mechanisms that play a role in maintaining the distinct composition of cilia, including regulation of ciliary access and trafficking of ciliary proteins to, from and within the cilium.

  1. Proteins aggregation and human diseases

    Science.gov (United States)

    Hu, Chin-Kun

    2015-04-01

    Many human diseases and the death of most supercentenarians are related to protein aggregation. Neurodegenerative diseases include Alzheimer's disease (AD), Huntington's disease (HD), Parkinson's disease (PD), frontotemporallobar degeneration, etc. Such diseases are due to progressive loss of structure or function of neurons caused by protein aggregation. For example, AD is considered to be related to aggregation of Aβ40 (peptide with 40 amino acids) and Aβ42 (peptide with 42 amino acids) and HD is considered to be related to aggregation of polyQ (polyglutamine) peptides. In this paper, we briefly review our recent discovery of key factors for protein aggregation. We used a lattice model to study the aggregation rates of proteins and found that the probability for a protein sequence to appear in the conformation of the aggregated state can be used to determine the temperature at which proteins can aggregate most quickly. We used molecular dynamics and simple models of polymer chains to study relaxation and aggregation of proteins under various conditions and found that when the bending-angle dependent and torsion-angle dependent interactions are zero or very small, then protein chains tend to aggregate at lower temperatures. All atom models were used to identify a key peptide chain for the aggregation of insulin chains and to find that two polyQ chains prefer anti-parallel conformation. It is pointed out that in many cases, protein aggregation does not result from protein mis-folding. A potential drug from Chinese medicine was found for Alzheimer's disease.

  2. 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)

  3. 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

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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

  9. Kabuki syndrome: expanding the phenotype to include microphthalmia and anophthalmia.

    Science.gov (United States)

    McVeigh, Terri P; Banka, Siddharth; Reardon, William

    2015-10-01

    Kabuki syndrome is a rare genetic malformation syndrome that is characterized by distinct facies, structural defects and intellectual disability. Kabuki syndrome may be caused by mutations in one of two histone methyltransferase genes: KMT2D and KDM6A. We describe a male child of nonconsanguineous Irish parents presenting with multiple malformations, including bilateral extreme microphthalmia; cleft palate; congenital diaphragmatic hernia; duplex kidney; as well as facial features of Kabuki syndrome, including interrupted eyebrows and lower lid ectropion. A de-novo germline mutation in KMT2D was identified. Whole-exome sequencing failed to reveal mutations in any of the known microphthalmia/anopthalmia genes. We also identified four other patients with Kabuki syndrome and microphthalmia. We postulate that Kabuki syndrome may produce this type of ocular phenotype as a result of extensive interaction between KMT2D, WAR complex proteins and PAXIP1. Children presenting with microphthalmia/anophthalmia should be examined closely for other signs of Kabuki syndrome, especially at an age where the facial gestalt might be less readily appreciable.

  10. 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

  11. 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.

  12. 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.

  13. 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.

  14. Safety of protein hydrolysates, fractions thereof and

    NARCIS (Netherlands)

    Gertjan Schaafsma

    2009-01-01

    This paper evaluates the safety for humans with regard to consumption of protein hydrolysates and fractions thereof, including bioactive peptides. The available literature on the safety of protein, protein hydrolysates, fractions thereof and free amino acids on relevant food legislation is reviewed

  15. 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...

  16. 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

  17. Protein oxidation in muscle foods: A review

    DEFF Research Database (Denmark)

    Lund, Marianne; Heinonen, Marina; Baron, Caroline P.

    2011-01-01

    insight into the reactions involved in the oxidative modifications undergone by muscle proteins. Moreover, a variety of products derived from oxidized muscle proteins, including cross-links and carbonyls, have been identified. The impact of oxidation on protein functionality and on specific meat quality...... and consequences of Pox in muscle foods. The efficiency of different anti-oxidant strategies against the oxidation of muscle proteins is also reported.......Protein oxidation in living tissues is known to play an essential role in the pathogenesis of relevant degenerative diseases, whereas the occurrence and impact of protein oxidation (Pox) in food systems have been ignored for decades. Currently, the increasing interest among food scientists...

  18. 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.

  19. Heterochiral Knottin Protein: Folding and Solution Structure.

    Science.gov (United States)

    Mong, Surin K; Cochran, Frank V; Yu, Hongtao; Graziano, Zachary; Lin, Yu-Shan; Cochran, Jennifer R; Pentelute, Bradley L

    2017-10-31

    Homochirality is a general feature of biological macromolecules, and Nature includes few examples of heterochiral proteins. Herein, we report on the design, chemical synthesis, and structural characterization of heterochiral proteins possessing loops of amino acids of chirality opposite to that of the rest of a protein scaffold. Using the protein Ecballium elaterium trypsin inhibitor II, we discover that selective β-alanine substitution favors the efficient folding of our heterochiral constructs. Solution nuclear magnetic resonance spectroscopy of one such heterochiral protein reveals a homogeneous global fold. Additionally, steered molecular dynamics simulation indicate β-alanine reduces the free energy required to fold the protein. We also find these heterochiral proteins to be more resistant to proteolysis than homochiral l-proteins. This work informs the design of heterochiral protein architectures containing stretches of both d- and l-amino acids.

  20. 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.

  1. Measurements of Protein Crystal Face Growth Rates

    Science.gov (United States)

    Gorti, S.

    2014-01-01

    Protein crystal growth rates will be determined for several hyperthermophile proteins.; The growth rates will be assessed using available theoretical models, including kinetic roughening.; If/when kinetic roughening supersaturations are established, determinations of protein crystal quality over a range of supersaturations will also be assessed.; The results of our ground based effort may well address the existence of a correlation between fundamental growth mechanisms and protein crystal quality.

  2. FERM proteins in animal morphogenesis.

    Science.gov (United States)

    Tepass, Ulrich

    2009-08-01

    Proteins containing a FERM domain are ubiquitous components of the cytocortex of animal cells where they are engaged in structural, transport, and signaling functions. Recent years have seen a wealth of genetic studies in model organisms that explore FERM protein function in development and tissue organization. In addition, mutations in several FERM protein-encoding genes have been associated with human diseases. This review will provide a brief overview of the FERM domain structure and the FERM protein superfamily and then discuss recent advances in our understanding of the mechanism of function and developmental requirement of several FERM proteins including Moesin, Myosin-VIIA, Myosin-XV, Coracle/Band4.1 as well as Yurt and its vertebrate homologs Mosaic Eyes and EPB41L5/YMO1/Limulus.

  3. Microdomain forming proteins in oncogenesis

    Directory of Open Access Journals (Sweden)

    I. B. Zborovskaya

    2016-01-01

    Full Text Available Lipid rafts are lateral assembles of cholesterol, sphingomyelin, glicosphingolipids and specific proteins within cell plasma membrane. These microdomains are involved into a number of important cellular processes including membrane rearrangement, protein internalization, signal transduction, entry of viruses into the cell. Some of lipid rafts are stabilized by special microdomain-forming proteins such as caveolins, SPFH domain containing superfamily, tetraspanins, galectins, which maintain integrity of rafts and regulate signal transduction via forming of “signalosomes”. Involvement of the different lipid rafts is necessary in many situations such as binding of growth factors with their receptors, integrin regulation, cytoskeleton and extracellular matrix rearrangements, vesicular transport, etc. However, such classes of microdomain-forming proteins are still considered separately from each other. In this review we tried to perform complex analysis of microdomain-forming proteins in regulation of cancer assotiated processes.

  4. 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.

  5. 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.

  6. 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

  7. 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.

  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. 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

  10. The E5 Proteins

    OpenAIRE

    DiMaio, Daniel; Petti, Lisa

    2013-01-01

    The E5 proteins are short transmembrane proteins encoded by many animal and human papillomaviruses. These proteins display transforming activity in cultured cells and animals, and they presumably also play a role in the productive virus life cycle. The E5 proteins are thought to act by modulating the activity of cellular proteins. Here, we describe the biological activities of the best-studied E5 proteins and discuss the evidence implicating specific protein targets and pathways in mediating ...

  11. Shotgun protein sequencing.

    Energy Technology Data Exchange (ETDEWEB)

    Faulon, Jean-Loup Michel; Heffelfinger, Grant S.

    2009-06-01

    A novel experimental and computational technique based on multiple enzymatic digestion of a protein or protein mixture that reconstructs protein sequences from sequences of overlapping peptides is described in this SAND report. This approach, analogous to shotgun sequencing of DNA, is to be used to sequence alternative spliced proteins, to identify post-translational modifications, and to sequence genetically engineered proteins.

  12. Introduction to protein blotting.

    Science.gov (United States)

    Kurien, Biji T; Scofield, R Hal

    2009-01-01

    Protein blotting is a powerful and important procedure for the immunodetection of proteins following electrophoresis, particularly proteins that are of low abundance. Since the inception of the protocol for protein transfer from an electrophoresed gel to a membrane in 1979, protein blotting has evolved greatly. The scientific community is now confronted with a variety of ways and means to carry out this transfer.

  13. Proteins aggregation and human diseases

    International Nuclear Information System (INIS)

    Hu, Chin-Kun

    2015-01-01

    Many human diseases and the death of most supercentenarians are related to protein aggregation. Neurodegenerative diseases include Alzheimer's disease (AD), Huntington's disease (HD), Parkinson's disease (PD), frontotemporallobar degeneration, etc. Such diseases are due to progressive loss of structure or function of neurons caused by protein aggregation. For example, AD is considered to be related to aggregation of Aβ40 (peptide with 40 amino acids) and Aβ42 (peptide with 42 amino acids) and HD is considered to be related to aggregation of polyQ (polyglutamine) peptides. In this paper, we briefly review our recent discovery of key factors for protein aggregation. We used a lattice model to study the aggregation rates of proteins and found that the probability for a protein sequence to appear in the conformation of the aggregated state can be used to determine the temperature at which proteins can aggregate most quickly. We used molecular dynamics and simple models of polymer chains to study relaxation and aggregation of proteins under various conditions and found that when the bending-angle dependent and torsion-angle dependent interactions are zero or very small, then protein chains tend to aggregate at lower temperatures. All atom models were used to identify a key peptide chain for the aggregation of insulin chains and to find that two polyQ chains prefer anti-parallel conformation. It is pointed out that in many cases, protein aggregation does not result from protein mis-folding. A potential drug from Chinese medicine was found for Alzheimer's disease. (paper)

  14. Protein improvement in crop plants

    Energy Technology Data Exchange (ETDEWEB)

    Rabson, R

    1974-07-01

    There are compelling reasons for attempting to increase the quality and quantity of protein available in crop plants through plant breeding, despite the fact that some critics have argued that no worldwide protein shortage exists. What used to be thought of as a 'protein gap' has now come to be considered in terms of protein-calorie malnutrition. This is only right since protein and calorie nutrition are inextricable. t the moment there are still unanswered questions as to the precise protein requirements of humans as a function of age, health and ambient conditions. There are, in addition, some indications that the incidence of Kwashiorkor (protein deficiency disease) is increasing in different parts of the world. At a recent meeting of the Protein Advisory Group of the United Nations System, Dr. Jean Mayer, an eminent human nutritionist of Harvard University, U.S.A., indicated the reasons for concern for the current food situation generally, and the protein food supply in particular. These factors include: - Immoderate continuing human population increases, most pronounced in some poor developing countries. - The highly accelerated consumption of animal foods associated with increasing affluence in the richer countries of the world. The production of such foods as meat demands great expenditures of grain, which is an inefficient mode of obtaining the required calories and protein for human consumption. - The over-exploitation of many of the world's fishery resources resulting in reduced yields, perhaps irreversibly, of some fishes. - Recent price increases in petroleum and fertilizer products which have imposed a major obstacle to increasing crop production. - The apparent alteration of climates in places like Africa, Asia and other parts of the Northern hemisphere which may put significant restrictions on crop production. hey are cogent reasons to be seriously concerned about these matters. (author)

  15. Protein improvement in crop plants

    International Nuclear Information System (INIS)

    Rabson, R.

    1974-01-01

    There are compelling reasons for attempting to increase the quality and quantity of protein available in crop plants through plant breeding, despite the fact that some critics have argued that no worldwide protein shortage exists. What used to be thought of as a 'protein gap' has now come to be considered in terms of protein-calorie malnutrition. This is only right since protein and calorie nutrition are inextricable. t the moment there are still unanswered questions as to the precise protein requirements of humans as a function of age, health and ambient conditions. There are, in addition, some indications that the incidence of Kwashiorkor (protein deficiency disease) is increasing in different parts of the world. At a recent meeting of the Protein Advisory Group of the United Nations System, Dr. Jean Mayer, an eminent human nutritionist of Harvard University, U.S.A., indicated the reasons for concern for the current food situation generally, and the protein food supply in particular. These factors include: - Immoderate continuing human population increases, most pronounced in some poor developing countries. - The highly accelerated consumption of animal foods associated with increasing affluence in the richer countries of the world. The production of such foods as meat demands great expenditures of grain, which is an inefficient mode of obtaining the required calories and protein for human consumption. - The over-exploitation of many of the world's fishery resources resulting in reduced yields, perhaps irreversibly, of some fishes. - Recent price increases in petroleum and fertilizer products which have imposed a major obstacle to increasing crop production. - The apparent alteration of climates in places like Africa, Asia and other parts of the Northern hemisphere which may put significant restrictions on crop production. hey are cogent reasons to be seriously concerned about these matters. (author)

  16. Identification of astrocytoma associated genes including cell surface markers

    International Nuclear Information System (INIS)

    Boon, Kathy; Edwards, Jennifer B; Eberhart, Charles G; Riggins, Gregory J

    2004-01-01

    Despite intense effort the treatment options for the invasive astrocytic tumors are still limited to surgery and radiation therapy, with chemotherapy showing little or no increase in survival. The generation of Serial Analysis of Gene Expression (SAGE) profiles is expected to aid in the identification of astrocytoma-associated genes and highly expressed cell surface genes as molecular therapeutic targets. SAGE tag counts can be easily added to public expression databases and quickly disseminated to research efforts worldwide. We generated and analyzed the SAGE transcription profiles of 25 primary grade II, III and IV astrocytomas [1]. These profiles were produced as part of the Cancer Genome Anatomy Project's SAGE Genie [2], and were used in an in silico search for candidate therapeutic targets by comparing astrocytoma to normal brain transcription. Real-time PCR and immunohistochemistry were used for the validation of selected candidate target genes in 2 independent sets of primary tumors. A restricted set of tumor-associated genes was identified for each grade that included genes not previously associated with astrocytomas (e.g. VCAM1, SMOC1, and thymidylate synthetase), with a high percentage of cell surface genes. Two genes with available antibodies, Aquaporin 1 and Topoisomerase 2A, showed protein expression consistent with transcript level predictions. This survey of transcription in malignant and normal brain tissues reveals a small subset of human genes that are activated in malignant astrocytomas. In addition to providing insights into pathway biology, we have revealed and quantified expression for a significant portion of cell surface and extra-cellular astrocytoma genes

  17. Our interests in protein-protein interactions

    Indian Academy of Sciences (India)

    protein interactions. Evolution of P-P partnerships. Evolution of P-P structures. Evolutionary dynamics of P-P interactions. Dynamics of P-P interaction network. Host-pathogen interactions. CryoEM mapping of gigantic protein assemblies.

  18. Canola/rapeseed protein-functionality and nutrition

    Directory of Open Access Journals (Sweden)

    Wanasundara Janitha P.D.

    2016-07-01

    Full Text Available Protein rich meal is a valuable co-product of canola/rapeseed oil extraction. Seed storage proteins that include cruciferin (11S and napin (2S dominate the protein complement of canola while oleosins, lipid transfer proteins and other minor proteins of non-storage nature are also found. Although oil-free canola meal contains 36–40% protein on a dry weight basis, non-protein components including fibre, polymeric phenolics, phytates and sinapine, etc. of the seed coat and cellular components make protein less suitable for food use. Separation of canola protein from non-protein components is a technical challenge but necessary to obtain full nutritional and functional potential of protein. Process conditions of raw material and protein preparation are critical of nutritional and functional value of the final protein product. The storage proteins of canola can satisfy many nutritional and functional requirements for food applications. Protein macromolecules of canola also provide functionalities required in applications beyond edible uses; there exists substantial potential as a source of plant protein and a renewable biopolymer. Available information at present is mostly based on the protein products that can be obtained as mixtures of storage protein types and other chemical constituents of the seed; therefore, full potential of canola storage proteins is yet to be revealed.

  19. A method for investigating protein-protein interactions related to Salmonella typhimurium pathogenesis

    Energy Technology Data Exchange (ETDEWEB)

    Chowdhury, Saiful M. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Shi, Liang [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Yoon, Hyunjin [Dartmouth College, Hanover, NH (United States); Ansong, Charles [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Rommereim, Leah M. [Dartmouth College, Hanover, NH (United States); Norbeck, Angela D. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Auberry, Kenneth J. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Moore, R. J. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Adkins, Joshua N. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Heffron, Fred [Oregon Health and Science Univ., Portland, OR (United States); Smith, Richard D. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

    2009-02-10

    We successfully modified an existing method to investigate protein-protein interactions in the pathogenic bacterium Salmonella typhimurium (STM). This method includes i) addition of a histidine-biotin-histidine tag to the bait proteins via recombinant DNA techniques; ii) in vivo cross-linking with formaldehyde; iii) tandem affinity purification of bait proteins under fully denaturing conditions; and iv) identification of the proteins cross-linked to the bait proteins by liquid-chromatography in conjunction with tandem mass-spectrometry. In vivo cross-linking stabilized protein interactions permitted the subsequent two-step purification step conducted under denaturing conditions. The two-step purification greatly reduced nonspecific binding of non-cross-linked proteins to bait proteins. Two different negative controls were employed to reduce false-positive identification. In an initial demonstration of this approach, we tagged three selected STM proteins- HimD, PduB and PhoP- with known binding partners that ranged from stable (e.g., HimD) to transient (i.e., PhoP). Distinct sets of interacting proteins were identified with each bait protein, including the known binding partners such as HimA for HimD, as well as anticipated and unexpected binding partners. Our results suggest that novel protein-protein interactions may be critical to pathogenesis by Salmonella typhimurium. .

  20. PDZ Protein Regulation of G Protein-Coupled Receptor Trafficking and Signaling Pathways.

    Science.gov (United States)

    Dunn, Henry A; Ferguson, Stephen S G

    2015-10-01

    G protein-coupled receptors (GPCRs) contribute to the regulation of every aspect of human physiology and are therapeutic targets for the treatment of numerous diseases. As a consequence, understanding the myriad of mechanisms controlling GPCR signaling and trafficking is essential for the development of new pharmacological strategies for the treatment of human pathologies. Of the many GPCR-interacting proteins, postsynaptic density protein of 95 kilodaltons, disc large, zona occludens-1 (PDZ) domain-containing proteins appear most abundant and have similarly been implicated in disease mechanisms. PDZ proteins play an important role in regulating receptor and channel protein localization within synapses and tight junctions and function to scaffold intracellular signaling protein complexes. In the current study, we review the known functional interactions between PDZ domain-containing proteins and GPCRs and provide insight into the potential mechanisms of action. These PDZ domain-containing proteins include the membrane-associated guanylate-like kinases [postsynaptic density protein of 95 kilodaltons; synapse-associated protein of 97 kilodaltons; postsynaptic density protein of 93 kilodaltons; synapse-associated protein of 102 kilodaltons; discs, large homolog 5; caspase activation and recruitment domain and membrane-associated guanylate-like kinase domain-containing protein 3; membrane protein, palmitoylated 3; calcium/calmodulin-dependent serine protein kinase; membrane-associated guanylate kinase protein (MAGI)-1, MAGI-2, and MAGI-3], Na(+)/H(+) exchanger regulatory factor proteins (NHERFs) (NHERF1, NHERF2, PDZ domain-containing kidney protein 1, and PDZ domain-containing kidney protein 2), Golgi-associated PDZ proteins (Gα-binding protein interacting protein, C-terminus and CFTR-associated ligand), PDZ domain-containing guanine nucleotide exchange factors (GEFs) 1 and 2, regulator of G protein signaling (RGS)-homology-RhoGEFs (PDZ domain-containing RhoGEF and