Phosphatidylcholine Transfer Protein Interacts with Thioesterase Superfamily Member 2 to Attenuate Insulin Signaling

OpenAIRE

Ersoy, Baran A.; Tarun, Akansha; D’Aquino, Katharine; Hancer, Nancy J.; Ukomadu, Chinweike; White, Morris F.; Michel, Thomas; Manning, Brendan D.; Cohen, David E.

2013-01-01

Phosphatidylcholine transfer protein (PC-TP) is a phospholipid-binding protein that is enriched in liver and that interacts with thioesterase superfamily member 2 (THEM2). Mice lacking either protein exhibit improved hepatic glucose homeostasis and are resistant to diet-induced diabetes. Insulin receptor substrate 2 (IRS2) and mammalian target of rapamycin complex 1 (mTORC1) are key effectors of insulin signaling, which is attenuated in diabetes. We found that PC-TP inhibited IRS2, as evidenc...

Crystal structure and potential physiological role of zebra fish thioesterase superfamily member 2 (fTHEM2)

Energy Technology Data Exchange (ETDEWEB)

Yu, Shanshan; Li, Han; Gao, Feng; Zhou, Ying, E-mail: zhouying@moon.ibp.ac.cn

2015-08-07

Thioesterase superfamily member 2 (THEM2) is an essential protein for mammalian cell proliferation. It belongs to the hotdog-fold thioesterase superfamily and catalyzes hydrolysis of thioester bonds of acyl-CoA in vitro, while its in vivo function remains unrevealed. In this study, Zebra fish was selected as a model organism to facilitate the investigations on THEM2. First, we solved the crystal structure of recombinant fTHEM2 at the resolution of 1.80 Å, which displayed a similar scaffolding as hTHEM2. Second, functional studies demonstrated that fTHEM2 is capable of hydrolyzing palmitoyl-CoA in vitro. In addition, injection of morpholino against fTHEM2 at one-cell stage resulted in distorted early embryo development, including delayed cell division, retarded development and increased death rate. The above findings validated our hypothesis that fTHEM2 could serve as an ideal surrogate for studying the physiological functions of THEM2. - Highlights: • The crystal structure of recombinant fTHEM2 is presented. • fTHEM2 is capable of hydrolyzing palmitoyl-CoA. • The influence of fTHEM2 on early embryo development is demonstrated.

Structural basis for phosphopantetheinyl carrier domain interactions in the terminal module of nonribosomal peptide synthetases

Science.gov (United States)

Liu, Ye; Zheng, Tengfei; Bruner, Steven D.

2011-01-01

Summary Phosphopantetheine-modified carrier domains play a central role in the template-directed, biosynthesis of several classes of primary and secondary metabolites. Fatty acids, polyketides and nonribosomal peptides are constructed on multidomain enzyme assemblies using phosphopantetheinyl thioester-linked carrier domains to traffic and activate building blocks. The carrier domain is a dynamic component of the process, shuttling pathway intermediates to sequential enzyme active sites. Here we report an approach to structurally fix carrier domain/enzyme constructs suitable for X-ray crystallographic analysis. The structure of a two-domain construct of E. coli EntF was determined with a conjugated phosphopantetheinyl-based inhibitor. The didomain structure is locked in an active orientation relevant to the chemistry of nonribosomal peptide biosynthesis. This structure provides details into the interaction of phosphopantetheine arm with the carrier domain and the active site of the thioesterase domain. PMID:22118682

Thioesterase superfamily member 1 suppresses cold thermogenesis by limiting the oxidation of lipid droplet-derived fatty acids in brown adipose tissue

Directory of Open Access Journals (Sweden)

Kosuke Okada

2016-05-01

Full Text Available Objective: Non-shivering thermogenesis in brown adipose tissue (BAT plays a central role in energy homeostasis. Thioesterase superfamily member 1 (Them1, a BAT-enriched long chain fatty acyl-CoA thioesterase, is upregulated by cold and downregulated by warm ambient temperatures. Them1−/− mice exhibit increased energy expenditure and resistance to diet-induced obesity and diabetes, but the mechanistic contribution of Them1 to the regulation of cold thermogenesis remains unknown. Methods: Them1−/− and Them1+/+ mice were subjected to continuous metabolic monitoring to quantify the effects of ambient temperatures ranging from thermoneutrality (30 °C to cold (4 °C on energy expenditure, core body temperature, physical activity and food intake. The effects of Them1 expression on O2 consumption rates, thermogenic gene expression and lipolytic protein activation were determined ex vivo in BAT and in primary brown adipocytes. Results: Them1 suppressed thermogenesis in mice even in the setting of ongoing cold exposure. Without affecting thermogenic gene transcription, Them1 reduced O2 consumption rates in both isolated BAT and primary brown adipocytes. This was attributable to decreased mitochondrial oxidation of endogenous but not exogenous fatty acids. Conclusions: These results show that Them1 may act as a break on uncontrolled heat production and limit the extent of energy expenditure. Pharmacologic inhibition of Them1 could provide a targeted strategy for the management of metabolic disorders via activation of brown fat. Keywords: Energy expenditure, Fatty acyl-CoA, Acyl-CoA thioesterase, Mitochondria, Obesity

Biology as an Integrating Natural Science Domain

Indian Academy of Sciences (India)

Home; Journals; Resonance – Journal of Science Education; Volume 13; Issue 3. Biology as an Integrating Natural Science Domain: A Proposal for BSc (Hons) in Integrated Biology. Kambadur Muralidhar. Classroom Volume 13 Issue 3 March 2008 pp 272-276 ...

Multinuclear NMR resonance assignments and the secondary structure of Escherichia coli thioesterase/protease I: A member of a new subclass of lipolytic enzymes

International Nuclear Information System (INIS)

Lin Tahsien; Chen Chinpan; Huang Rongfong; Lee Yalin; Shaw Jeifu; Huang Taihuang

1998-01-01

Escherichia coli thioesterase/protease I is a 183 amino acid protein with a molecular mass of 20500. This protein belongs to a new subclass of lipolytic enzymes of the serine protease superfamily, but with a new GDSLS consensus motif, of which no structure has yet been determined. The protein forms a tetramer at pH values above 6.5 and exists as a monomer at lower pH values. Both monomer and tetramer are catalytically active. From analysis of a set of heteronuclear multidimensional NMR spectra with uniform and specific amino acid labeled protein samples, we have obtained near-complete resonance assignments of the backbone 1 H, 13 C and 15 N nuclei (BMRB databank accession number 4060). The secondary structure of E. coli thioesterase/protease I was further deduced from the consensus chemical shift indices, backbone short- and medium-range NOEs, and amide proton exchange rates. The protein was found to consist of four β-strands and seven α-helices, arranged in alternate order. The four β-strands were shown to form a parallel β-sheet. The topological arrangement of the β-strands of -1x, +2x, +1x appears to resemble that of the core region of the αβ hydrolase superfamily, typically found in common lipases and esterases. However, substantial differences, such as the number of β-strands and the location of the catalytic triad residues, make it difficult to give a definitive classification of the structure of E. coli thioesterase/protease I at present

Acyl-ACP thioesterases from castor (Ricinus communis L.): an enzymatic system appropriate for high rates of oil synthesis and accumulation.

Science.gov (United States)

Sánchez-García, Alicia; Moreno-Pérez, Antonio J; Muro-Pastor, Alicia M; Salas, Joaquín J; Garcés, Rafael; Martínez-Force, Enrique

2010-06-01

Acyl-acyl carrier protein (ACP) thioesterases are enzymes that terminate the intraplastidial fatty acid synthesis in plants by hydrolyzing the acyl-ACP intermediates and releasing free fatty acids to be incorporated into glycerolipids. These enzymes are classified in two families, FatA and FatB, which differ in amino acid sequence and substrate specificity. In the present work, both FatA and FatB thioesterases were cloned, sequenced and characterized from castor (Ricinus communis) seeds, a crop of high interest in oleochemistry. Single copies of FatA and FatB were found in castor resulting to be closely related with those of Jatropha curcas. The corresponding mature proteins were heterologously expressed in Escherichia coli for biochemical characterization after purification, resulting in high catalytic efficiency of RcFatA on oleoyl-ACP and palmitoleoyl-ACP and high efficiencies of RcFatB for oleoyl-ACP and palmitoyl-ACP. The expression profile of these genes displayed the highest levels in expanding tissues that typically are very active in lipid biosynthesis such as developing seed endosperm and young expanding leaves. The contribution of these two enzymes to the synthesis of castor oil is discussed. Copyright 2010 Elsevier Ltd. All rights reserved.

Mechanisms for integration of information models across related domains

Science.gov (United States)

Atkinson, Rob

2010-05-01

It is well recognised that there are opportunities and challenges in cross-disciplinary data integration. A significant barrier, however, is creating a conceptual model of the combined domains and the area of integration. For example, a groundwater domain application may require information from several related domains: geology, hydrology, water policy, etc. Each domain may have its own data holdings and conceptual models, but these will share various common concepts (eg. The concept of an aquifer). These areas of semantic overlap present significant challenges, firstly to choose a single representation (model) of a concept that appears in multiple disparate models,, then to harmonise these other models with the single representation. In addition, models may exist at different levels of abstraction depending on how closely aligned they are with a particular implementation. This makes it hard for modellers in one domain to introduce elements from another domain without either introducing a specific style of implementation, or conversely dealing with a set of abstract patterns that are hard to integrate with existing implementations. Models are easier to integrate if they are broken down into small units, with common concepts implemented using common models from well-known, and predictably managed shared libraries. This vision however requires development of a set of mechanisms (tools and procedures) for implementing and exploiting libraries of model components. These mechanisms need to handle publication, discovery, subscription, versioning and implementation of models in different forms. In this presentation a coherent suite of such mechanisms is proposed, using a scenario based on re-use of geosciences models. This approach forms the basis of a comprehensive strategy to empower domain modellers to create more interoperable systems. The strategy address a range of concerns and practice, and includes methodologies, an accessible toolkit, improvements to available

Xanthomonas campestris RpfB is a Fatty Acyl-CoA Ligase Required to Counteract the Thioesterase Activity of the RpfF Diffusible Signal Factor (DSF) Synthase

Science.gov (United States)

Bi, Hongkai; Yu, Yonghong; Dong, Huijuan; Wang, Haihong; Cronan, John E.

2014-01-01

SUMMARY In Xanthomonas campestris pv. campestris (Xcc), the proteins encoded by the rpf (regulator of pathogenicity factor) gene cluster produce and sense a fatty acid signal molecule called diffusible signaling factor (DSF, 2(Z)-11-methyldodecenoic acid). RpfB was reported to be involved in DSF processing and was predicted to encode an acyl-CoA ligase. We report that RpfB activates a wide range of fatty acids to their CoA esters in vitro. Moreover, RpfB can functionally replace the paradigm bacterial acyl-CoA ligase, Escherichia coli FadD, in the E. coli β-oxidation pathway and deletion of RpfB from the Xcc genome results in a strain unable to utilize fatty acids as carbon sources. An essential RpfB function in the pathogenicity factor pathway was demonstrated by the properties of a strain deleted for both the rpfB and rpfC genes. The ΔrpfB ΔrpfC strain grew poorly and lysed upon entering stationary phase. Deletion of rpfF, the gene encoding the DSF synthetic enzyme, restored normal growth to this strain. RpfF is a dual function enzyme that synthesizes DSF by dehydration of a 3-hydroxyacyl-acyl carrier protein (ACP) fatty acid synthetic intermediate and also cleaves the thioester bond linking DSF to ACP. However, the RpfF thioesterase activity is of broad specificity and upon elimination of its RpfC inhibitor RpfF attains maximal activity and its thioesterase activity proceeds to block membrane lipid synthesis by cleavage of acyl-ACP intermediates. This resulted in release of the nascent acyl chains to the medium as free fatty acids. This lack of acyl chains for phospholipid synthesis results in cell lysis unless RpfB is present to counteract the RpfF thioesterase activity by catalyzing uptake and activation of the free fatty acids to give acyl-CoAs that can be utilized to restore membrane lipid synthesis. Heterologous expression of a different fatty acid activating enzyme, the Vibrio harveyi acyl-ACP synthetase, replaced RpfB in counteracting the effects of

An Integrated Framework to Specify Domain-Specific Modeling Languages

DEFF Research Database (Denmark)

Zarrin, Bahram; Baumeister, Hubert

2018-01-01

, a logic-based specification language. The drawback of MS DSL Tools is it does not provide a formal and rigorous approach for semantics specifications. In this framework, we use Microsoft DSL Tools to define the metamodel and graphical notations of DSLs, and an extended version of ForSpec as a formal......In this paper, we propose an integrated framework that can be used by DSL designers to implement their desired graphical domain-specific languages. This framework relies on Microsoft DSL Tools, a meta-modeling framework to build graphical domain-specific languages, and an extension of ForSpec...... language to define their semantics. Integrating these technologies under the umbrella of Microsoft Visual Studio IDE allows DSL designers to utilize a single development environment for developing their desired domain-specific languages....

Semistar-Krull and Valuative Dimension of Integral Domains

OpenAIRE

Sahandi, Parviz

2008-01-01

Given a stable semistar operation of finite type $\\star$ on an integral domain $D$, we show that it is possible to define in a canonical way a stable semistar operation of finite type $\\star[X]$ on the polynomial ring $D[X]$, such that, if $n:=\\star$-$\\dim(D)$, then $n+1\\leq \\star[X]\\text{-}\\dim(D[X])\\leq 2n+1$. We also establish that if $D$ is a $\\star$-Noetherian domain or is a Pr\\"{u}fer $\\star$-multiplication domain, then $\\star[X]\\text{-}\\dim(D[X])=\\star\\text{-}\\dim(D)+1$. Moreover we de...

Policing starter unit selection of the enterocin type II polyketide synthase by the type II thioesterase EncL.

Science.gov (United States)

Kalaitzis, John A; Cheng, Qian; Meluzzi, Dario; Xiang, Longkuan; Izumikawa, Miho; Dorrestein, Pieter C; Moore, Bradley S

2011-11-15

Enterocin is an atypical type II polyketide synthase (PKS) product from the marine actinomycete 'Streptomyces maritimus'. The enterocin biosynthesis gene cluster (enc) codes for proteins involved in the assembly and attachment of the rare benzoate primer that initiates polyketide assembly with the addition of seven malonate molecules and culminates in a Favorskii-like rearrangement of the linear poly-β-ketone to give its distinctive non-aromatic, caged core structure. Fundamental to enterocin biosynthesis, which utilizes a single acyl carrier protein (ACP), EncC, for both priming with benzoate and elongating with malonate, involves maintaining the correct balance of acyl-EncC substrates for efficient polyketide assembly. Here, we report the characterization of EncL as a type II thioesterase that functions to edit starter unit (mis)priming of EncC. We performed a series of in vivo mutational studies, heterologous expression experiments, in vitro reconstitution studies, and Fourier-transform mass spectrometry-monitored competitive enzyme assays that together support the proposed selective hydrolase activity of EncL toward misprimed acetyl-ACP over benzoyl-ACP to facilitate benzoyl priming of the enterocin PKS complex. While this system resembles the R1128 PKS that also utilizes an editing thioesterase (ZhuC) to purge acetate molecules from its initiation module ACP in favor of alkylacyl groups, the enterocin system is distinct in its usage of a single ACP for both priming and elongating reactions with different substrates. Copyright © 2011 Elsevier Ltd. All rights reserved.

Structural and Biochemical Studies of a Fluoroacetyl-CoA-Specific Thioesterase Reveal a Molecular Basis for Fluorine Selectivity†,‡

OpenAIRE

Weeks, Amy M.; Coyle, Scott M.; Jinek, Martin; Doudna, Jennifer A.; Chang, Michelle C. Y.

2010-01-01

We have initiated a broad-based program aimed at understanding the molecular basis of fluorine specificity in enzymatic systems, and in this context, we report crystallographic and biochemical studies on a fluoroacetyl-coenzyme A (CoA) specific thioesterase (FlK) from Streptomyces cattleya. Our data establish that FlK is competent to protect its host from fluoroacetate toxicity in vivo and demonstrate a 106-fold discrimination between fluoroacetyl-CoA(kcat/KM=5×107M−1 s−1) and acetyl-CoA(kcat...

Domain decomposition and multilevel integration for fermions

International Nuclear Information System (INIS)

Ce, Marco; Giusti, Leonardo; Schaefer, Stefan

2016-01-01

The numerical computation of many hadronic correlation functions is exceedingly difficult due to the exponentially decreasing signal-to-noise ratio with the distance between source and sink. Multilevel integration methods, using independent updates of separate regions in space-time, are known to be able to solve such problems but have so far been available only for pure gauge theory. We present first steps into the direction of making such integration schemes amenable to theories with fermions, by factorizing a given observable via an approximated domain decomposition of the quark propagator. This allows for multilevel integration of the (large) factorized contribution to the observable, while its (small) correction can be computed in the standard way.

Explicit solution of Calderon preconditioned time domain integral equations

KAUST Repository

Ulku, Huseyin Arda

2013-07-01

An explicit marching on-in-time (MOT) scheme for solving Calderon-preconditioned time domain integral equations is proposed. The scheme uses Rao-Wilton-Glisson and Buffa-Christiansen functions to discretize the domain and range of the integral operators and a PE(CE)m type linear multistep to march on in time. Unlike its implicit counterpart, the proposed explicit solver requires the solution of an MOT system with a Gram matrix that is sparse and well-conditioned independent of the time step size. Numerical results demonstrate that the explicit solver maintains its accuracy and stability even when the time step size is chosen as large as that typically used by an implicit solver. © 2013 IEEE.

Dominant integration locus drives continuous diversification of plant immune receptors with exogenous domain fusions.

Science.gov (United States)

Bailey, Paul C; Schudoma, Christian; Jackson, William; Baggs, Erin; Dagdas, Gulay; Haerty, Wilfried; Moscou, Matthew; Krasileva, Ksenia V

2018-02-19

The plant immune system is innate and encoded in the germline. Using it efficiently, plants are capable of recognizing a diverse range of rapidly evolving pathogens. A recently described phenomenon shows that plant immune receptors are able to recognize pathogen effectors through the acquisition of exogenous protein domains from other plant genes. We show that plant immune receptors with integrated domains are distributed unevenly across their phylogeny in grasses. Using phylogenetic analysis, we uncover a major integration clade, whose members underwent repeated independent integration events producing diverse fusions. This clade is ancestral in grasses with members often found on syntenic chromosomes. Analyses of these fusion events reveals that homologous receptors can be fused to diverse domains. Furthermore, we discover a 43 amino acid long motif associated with this dominant integration clade which is located immediately upstream of the fusion site. Sequence analysis reveals that DNA transposition and/or ectopic recombination are the most likely mechanisms of formation for nucleotide binding leucine rich repeat proteins with integrated domains. The identification of this subclass of plant immune receptors that is naturally adapted to new domain integration will inform biotechnological approaches for generating synthetic receptors with novel pathogen "baits."

Acyl coenzyme A thioesterase 7 regulates neuronal fatty acid metabolism to prevent neurotoxicity.

Science.gov (United States)

Ellis, Jessica M; Wong, G William; Wolfgang, Michael J

2013-05-01

Numerous neurological diseases are associated with dysregulated lipid metabolism; however, the basic metabolic control of fatty acid metabolism in neurons remains enigmatic. Here we have shown that neurons have abundant expression and activity of the long-chain cytoplasmic acyl coenzyme A (acyl-CoA) thioesterase 7 (ACOT7) to regulate lipid retention and metabolism. Unbiased and targeted metabolomic analysis of fasted mice with a conditional knockout of ACOT7 in the nervous system, Acot7(N-/-), revealed increased fatty acid flux into multiple long-chain acyl-CoA-dependent pathways. The alterations in brain fatty acid metabolism were concomitant with a loss of lean mass, hypermetabolism, hepatic steatosis, dyslipidemia, and behavioral hyperexcitability in Acot7(N-/-) mice. These failures in adaptive energy metabolism are common in neurodegenerative diseases. In agreement, Acot7(N-/-) mice exhibit neurological dysfunction and neurodegeneration. These data show that ACOT7 counterregulates fatty acid metabolism in neurons and protects against neurotoxicity.

Integrative curriculum reform, domain dependent knowing, and teachers` epistemological theories: Implications for middle-level teaching

Energy Technology Data Exchange (ETDEWEB)

Powell, R.R. [Texas Tech Univ., Lubbock, TX (United States). College of Education

1998-12-01

Integrative curriculum as both a theoretical construct and a practical reality, and as a theme-based, problem-centered, democratic way of schooling, is becoming more widely considered as a feasible alternative to traditional middle-level curricula. Importantly for teaching and learning, domain dependence requires teachers to view one area of knowledge as fully interdependent with other areas of knowledge during the learning process. This requires teachers to adopt personal epistemological theories that reflect integrative, domain dependent knowing. This study explored what happened when teachers from highly traditional domain independent school settings encountered an ambitious college-level curriculum project that was designed to help the teachers understand the potential that integrative, domain dependent teaching holds for precollege settings. This study asked: What influence does an integrative, domain dependent curriculum project have on teachers` domain independent, epistemological theories for teaching and learning? Finding an answer to this question is essential if we, as an educational community, are to understand how integrative curriculum theory is transformed by teachers into systemic curriculum reform. The results suggest that the integrative curriculum project that teachers participated in did not explicitly alter their classroom practices in a wholesale manner. Personal epistemological theories of teachers collectively precluded teachers from making any wholesale changes in their individual classroom teaching. However, teachers became aware of integrative curriculum as an alternative, and they expressed interest in infusing integrative practices into their classrooms as opportunities arise.

Heterologous co-expression of accA, fabD, and thioesterase genes for improving long-chain fatty acid production in Pseudomonas aeruginosa and Escherichia coli.

Science.gov (United States)

Lee, Sunhee; Jeon, Eunyoung; Jung, Yeontae; Lee, Jinwon

2012-05-01

The goal of the present study was to increase the content of intracellular long-chain fatty acids in two bacterial strains, Pseudomonas aeruginosa PA14 and Escherichia coli K-12 MG1655, by co-overexpressing essential enzymes that are involved in the fatty acid synthesis metabolic pathway. Recently, microbial fatty acids and their derivatives have been receiving increasing attention as an alternative source of fuel. By introducing two genes (accA and fabD) of P. aeruginosa into the two bacterial strains and by co-expressing with them the fatty acyl-acyl carrier protein thioesterase gene of Streptococcus pyogenes (strain MGAS10270), we have engineered recombinant strains that are efficient producers of long-chain fatty acids (C16 and C18). The recombinant strains exhibit a 1.3-1.7-fold increase in the production of long-chain fatty acids over the wild-type strains. To enhance the production of total long-chain fatty acids, we researched the carbon sources for optimized culture conditions and results were used for post-culture incubation period. E. coli SGJS17 (containing the accA, fabD, and thioesterase genes) produced the highest content of intracellular total fatty acids; in particular, the unsaturated fatty acid content was about 20-fold higher than that in the wild-type E. coli.

AERIS: An Integrated Domain Information System for Aerospace Science and Technology

Science.gov (United States)

Hatua, Sudip Ranjan; Madalli, Devika P.

2011-01-01

Purpose: The purpose of this paper is to discuss the methodology in building an integrated domain information system with illustrations that provide proof of concept. Design/methodology/approach: The present work studies the usual search engine approach to information and its pitfalls. A methodology was adopted for construction of a domain-based…

Second-order domain derivative of normal-dependent boundary integrals

KAUST Repository

Balzer, Jonathan

2010-03-17

Numerous reconstruction tasks in (optical) surface metrology allow for a variational formulation. The occurring boundary integrals may be interpreted as shape functions. The paper is concerned with the second-order analysis of such functions. Shape Hessians of boundary integrals are considered difficult to find analytically because they correspond to third-order derivatives of an, in a sense equivalent, domain integral. We complement previous results by considering cost functions depending explicitly on the surface normal. The correctness and practicability of our calculations are verified in the context of a Newton-type shape reconstruction method. © 2010 Birkhäuser / Springer Basel AG.

On the initial condition problem of the time domain PMCHWT surface integral equation

KAUST Repository

Uysal, Ismail Enes

2017-05-13

Non-physical, linearly increasing and constant current components are induced in marching on-in-time solution of time domain surface integral equations when initial conditions on time derivatives of (unknown) equivalent currents are not enforced properly. This problem can be remedied by solving the time integral of the surface integral for auxiliary currents that are defined to be the time derivatives of the equivalent currents. Then the equivalent currents are obtained by numerically differentiating the auxiliary ones. In this work, this approach is applied to the marching on-in-time solution of the time domain Poggio-Miller-Chan-Harrington-Wu-Tsai surface integral equation enforced on dispersive/plasmonic scatterers. Accuracy of the proposed method is demonstrated by a numerical example.

A note on domains of discourse. Logical know-how for integrated environmental modelling

Energy Technology Data Exchange (ETDEWEB)

Gerstengarbe, F.W. (ed.); Jaeger, C.C.

2003-10-01

Building computer models means implementing a mathematical structure on a piece of hardware in such a way that insights about some other phenomenon can be gained, remembered and communicated. For meaningful computer modelling, the phenomenon to be modelled must be described in a logically coherent way. This can be quite difficult, especially when a combination of highly heterogeneous scientific disciplines is needed, as is often the case in environmental research. The paper shows how the notion of a domain of discourse as developed by logicians can be used to map out the cognitive landscape of integrated modelling. This landscape is not a fixed universe, but a multiverse resonating with an evolving pluralism of domains of discourse. Integrated modelling involves a never-ending activity of translation between such domains, an activity that often goes hand in hand with major efforts to overcome conceptual confusions within given domains. For these purposes, a careful use of mathematics, including tools of formal logic presented in the paper, can be helpful. The concept of vulnerability as currently used in global change research is discussed as an example of the challenges to be met in integrated environmental modelling. (orig.)

Analysis of the Sequences, Structures, and Functions of Product-Releasing Enzyme Domains in Fungal Polyketide Synthases

Directory of Open Access Journals (Sweden)

Lu Liu

2017-09-01

Full Text Available Product-releasing enzyme (PRE domains in fungal non-reducing polyketide synthases (NR-PKSs play a crucial role in catalysis and editing during polyketide biosynthesis, especially accelerating final biosynthetic reactions accompanied with product offloading. However, up to date, the systematic knowledge about PRE domains is deficient. In the present study, the relationships between sequences, structures, and functions of PRE domains were analyzed with 574 NR-PKSs of eight groups (I–VIII. It was found that the PRE domains in NR-PKSs could be mainly classified into three types, thioesterase (TE, reductase (R, and metallo-β-lactamase-type TE (MβL-TE. The widely distributed TE or TE-like domains were involved in NR-PKSs of groups I–IV, VI, and VIII. The R domains appeared in NR-PKSs of groups IV and VII, while the physically discrete MβL-TE domains were employed by most NR-PKSs of group V. The changes of catalytic sites and structural characteristics resulted in PRE functional differentiations. The phylogeny revealed that the evolution of TE domains was accompanied by complex functional divergence. The diverse sequence lengths of TE lid-loops affected substrate specificity with different chain lengths. The volume diversification of TE catalytic pockets contributed to catalytic mechanisms with functional differentiations. The above findings may help to understand the crucial catalysis of fungal aromatic polyketide biosyntheses and govern recombination of NR-PKSs to obtain unnatural target products.

RNA-protein binding motifs mining with a new hybrid deep learning based cross-domain knowledge integration approach

DEFF Research Database (Denmark)

Pan, Xiaoyong; Shen, Hong Bin

2017-01-01

, their domain specific features and formats have posed significant computational challenges. One of current difficulties is that the cross-source shared common knowledge is at a higher abstraction level beyond the observed data, resulting in a low efficiency of direct integration of observed data across domains...... space using multiple layers of learning blocks, where the shared representations across different domains are integrated. To validate our iDeep method, we performed experiments on 31 large-scale CLIP-seq datasets, and our results show that by integrating multiple sources of data, the average AUC can...... be improved by 8% compared to the best single-source-based predictor; and through cross-domain knowledge integration at an abstraction level, it outperforms the state-of-the-art predictors by 6%. Besides the overall enhanced prediction performance, the convolutional neural network module embedded in i...

A higher order space-time Galerkin scheme for time domain integral equations

KAUST Repository

Pray, Andrew J.

2014-12-01

Stability of time domain integral equation (TDIE) solvers has remained an elusive goal formany years. Advancement of this research has largely progressed on four fronts: 1) Exact integration, 2) Lubich quadrature, 3) smooth temporal basis functions, and 4) space-time separation of convolutions with the retarded potential. The latter method\\'s efficacy in stabilizing solutions to the time domain electric field integral equation (TD-EFIE) was previously reported for first-order surface descriptions (flat elements) and zeroth-order functions as the temporal basis. In this work, we develop the methodology necessary to extend the scheme to higher order surface descriptions as well as to enable its use with higher order basis functions in both space and time. These basis functions are then used in a space-time Galerkin framework. A number of results are presented that demonstrate convergence in time. The viability of the space-time separation method in producing stable results is demonstrated experimentally for these examples.

A higher order space-time Galerkin scheme for time domain integral equations

KAUST Repository

Pray, Andrew J.; Beghein, Yves; Nair, Naveen V.; Cools, Kristof; Bagci, Hakan; Shanker, Balasubramaniam

2014-01-01

Stability of time domain integral equation (TDIE) solvers has remained an elusive goal formany years. Advancement of this research has largely progressed on four fronts: 1) Exact integration, 2) Lubich quadrature, 3) smooth temporal basis functions, and 4) space-time separation of convolutions with the retarded potential. The latter method's efficacy in stabilizing solutions to the time domain electric field integral equation (TD-EFIE) was previously reported for first-order surface descriptions (flat elements) and zeroth-order functions as the temporal basis. In this work, we develop the methodology necessary to extend the scheme to higher order surface descriptions as well as to enable its use with higher order basis functions in both space and time. These basis functions are then used in a space-time Galerkin framework. A number of results are presented that demonstrate convergence in time. The viability of the space-time separation method in producing stable results is demonstrated experimentally for these examples.

Divergence of substrate specificity and function in the Escherichia coli hotdog-fold thioesterase paralogs YdiI and YbdB.

Science.gov (United States)

Latham, John A; Chen, Danqi; Allen, Karen N; Dunaway-Mariano, Debra

2014-07-29

The work described in this paper, and its companion paper (Wu, R., Latham, J. A., Chen, D., Farelli, J., Zhao, H., Matthews, K. Allen, K. N., and Dunaway-Mariano, D. (2014) Structure and Catalysis in the Escherichia coli Hotdog-fold Thioesterase Paralogs YdiI and YbdB. Biochemistry, DOI: 10.1021/bi500334v), focuses on the evolution of a pair of paralogous hotdog-fold superfamily thioesterases of E. coli, YbdB and YdiI, which share a high level of sequence identity but perform different biological functions (viz., proofreader of 2,3-dihydroxybenzoyl-holoEntB in the enterobactin biosynthetic pathway and catalyst of the 1,4-dihydoxynapthoyl-CoA hydrolysis step in the menaquinone biosynthetic pathway, respectively). In vitro substrate activity screening of a library of thioester metabolites showed that YbdB displays high activity with benzoyl-holoEntB and benzoyl-CoA substrates, marginal activity with acyl-CoA thioesters, and no activity with 1,4-dihydoxynapthoyl-CoA. YdiI, on the other hand, showed a high level of activity with its physiological substrate, significant activity toward a wide range of acyl-CoA thioesters, and minimal activity toward benzoyl-holoEntB. These results were interpreted as evidence for substrate promiscuity that facilitates YbdB and YdiI evolvability, and divergence in substrate preference, which correlates with their assumed biological function. YdiI support of the menaquinone biosynthetic pathway was confirmed by demonstrating reduced anaerobic growth of the E. coli ydiI-knockout mutant (vs wild-type E. coli) on glucose in the presence of the electron acceptor fumarate. Bioinformatic analysis revealed that a small biological range exists for YbdB orthologs (i.e., limited to Enterobacteriales) relative to that of YdiI orthologs. The divergence in YbdB and YdiI substrate specificity detailed in this paper set the stage for their structural analyses reported in the companion paper.

High-Order Calderón Preconditioned Time Domain Integral Equation Solvers

KAUST Repository

Valdes, Felipe; Ghaffari-Miab, Mohsen; Andriulli, Francesco P.; Cools, Kristof; Michielssen,

2013-01-01

Two high-order accurate Calderón preconditioned time domain electric field integral equation (TDEFIE) solvers are presented. In contrast to existing Calderón preconditioned time domain solvers, the proposed preconditioner allows for high-order surface representations and current expansions by using a novel set of fully-localized high-order div-and quasi curl-conforming (DQCC) basis functions. Numerical results demonstrate that the linear systems of equations obtained using the proposed basis functions converge rapidly, regardless of the mesh density and of the order of the current expansion. © 1963-2012 IEEE.

High-Order Calderón Preconditioned Time Domain Integral Equation Solvers

KAUST Repository

Valdes, Felipe

2013-05-01

Two high-order accurate Calderón preconditioned time domain electric field integral equation (TDEFIE) solvers are presented. In contrast to existing Calderón preconditioned time domain solvers, the proposed preconditioner allows for high-order surface representations and current expansions by using a novel set of fully-localized high-order div-and quasi curl-conforming (DQCC) basis functions. Numerical results demonstrate that the linear systems of equations obtained using the proposed basis functions converge rapidly, regardless of the mesh density and of the order of the current expansion. © 1963-2012 IEEE.

On the mixed discretization of the time domain magnetic field integral equation

KAUST Repository

Ulku, Huseyin Arda; Bogaert, Ignace; Cools, Kristof; Andriulli, Francesco P.; Bagci, Hakan

2012-01-01

Time domain magnetic field integral equation (MFIE) is discretized using divergence-conforming Rao-Wilton-Glisson (RWG) and curl-conforming Buffa-Christiansen (BC) functions as spatial basis and testing functions, respectively. The resulting mixed

Transactivation domain of p53 regulates DNA repair and integrity in human iPS cells.

Science.gov (United States)

Kannappan, Ramaswamy; Mattapally, Saidulu; Wagle, Pooja A; Zhang, Jianyi

2018-05-18

The role of p53 transactivation domain (p53-TAD), a multifunctional and dynamic domain, on DNA repair and retaining DNA integrity in human iPS cells has never been studied. p53-TAD was knocked out in iPS cells using CRISPR/Cas9 and was confirmed by DNA sequencing. p53-TAD KO cells were characterized by: accelerated proliferation, decreased population doubling time, and unaltered Bcl2, BBC3, IGF1R, Bax and altered Mdm2, p21, and PIDD transcripts expression. In p53-TAD KO cells p53 regulated DNA repair proteins XPA, DNA polH and DDB2 expression were found to be reduced compared to p53-WT cells. Exposure to low dose of doxorubicin (Doxo) induced similar DNA damage and DNA damage response (DDR) measured by RAD50 and MRE11 expression, Checkpoint kinase 2 activation and γH2A.X recruitment at DNA strand breaks in both the cell groups indicating silencing p53-TAD do not affect DDR mechanism upstream of p53. Following removal of Doxo p53-WT hiPS cells underwent DNA repair, corrected their damaged DNA and restored DNA integrity. Conversely, p53-TAD KO hiPS cells did not undergo complete DNA repair and failed to restore DNA integrity. More importantly continuous culture of p53-TAD KO hiPS cells underwent G2/M cell cycle arrest and expressed cellular senescent marker p16 INK4a . Our data clearly shows that silencing transactivation domain of p53 did not affect DDR but affected the DNA repair process implying the crucial role of p53 transactivation domain in maintaining DNA integrity. Therefore, activating p53-TAD domain using small molecules may promote DNA repair and integrity of cells and prevent senescence.

Time-domain single-source integral equations for analyzing scattering from homogeneous penetrable objects

KAUST Repository

Valdés, Felipe

2013-03-01

Single-source time-domain electric-and magnetic-field integral equations for analyzing scattering from homogeneous penetrable objects are presented. Their temporal discretization is effected by using shifted piecewise polynomial temporal basis functions and a collocation testing procedure, thus allowing for a marching-on-in-time (MOT) solution scheme. Unlike dual-source formulations, single-source equations involve space-time domain operator products, for which spatial discretization techniques developed for standalone operators do not apply. Here, the spatial discretization of the single-source time-domain integral equations is achieved by using the high-order divergence-conforming basis functions developed by Graglia alongside the high-order divergence-and quasi curl-conforming (DQCC) basis functions of Valdés The combination of these two sets allows for a well-conditioned mapping from div-to curl-conforming function spaces that fully respects the space-mapping properties of the space-time operators involved. Numerical results corroborate the fact that the proposed procedure guarantees accuracy and stability of the MOT scheme. © 2012 IEEE.

A hybrid time-domain discontinuous galerkin-boundary integral method for electromagnetic scattering analysis

KAUST Repository

Li, Ping; Shi, Yifei; Jiang, Lijun; Bagci, Hakan

2014-01-01

A scheme hybridizing discontinuous Galerkin time-domain (DGTD) and time-domain boundary integral (TDBI) methods for accurately analyzing transient electromagnetic scattering is proposed. Radiation condition is enforced using the numerical flux on the truncation boundary. The fields required by the flux are computed using the TDBI from equivalent currents introduced on a Huygens' surface enclosing the scatterer. The hybrid DGTDBI ensures that the radiation condition is mathematically exact and the resulting computation domain is as small as possible since the truncation boundary conforms to scatterer's shape and is located very close to its surface. Locally truncated domains can also be defined around each disconnected scatterer additionally reducing the size of the overall computation domain. Numerical examples demonstrating the accuracy and versatility of the proposed method are presented. © 2014 IEEE.

A hybrid time-domain discontinuous galerkin-boundary integral method for electromagnetic scattering analysis

KAUST Repository

Li, Ping

2014-05-01

A scheme hybridizing discontinuous Galerkin time-domain (DGTD) and time-domain boundary integral (TDBI) methods for accurately analyzing transient electromagnetic scattering is proposed. Radiation condition is enforced using the numerical flux on the truncation boundary. The fields required by the flux are computed using the TDBI from equivalent currents introduced on a Huygens\\' surface enclosing the scatterer. The hybrid DGTDBI ensures that the radiation condition is mathematically exact and the resulting computation domain is as small as possible since the truncation boundary conforms to scatterer\\'s shape and is located very close to its surface. Locally truncated domains can also be defined around each disconnected scatterer additionally reducing the size of the overall computation domain. Numerical examples demonstrating the accuracy and versatility of the proposed method are presented. © 2014 IEEE.

Acyl carrier proteins from sunflower (Helianthus annuus L.) seeds and their influence on FatA and FatB acyl-ACP thioesterase activities.

Science.gov (United States)

Aznar-Moreno, Jose A; Venegas-Calerón, Mónica; Martínez-Force, Enrique; Garcés, Rafael; Salas, Joaquín J

2016-08-01

The kinetics of acyl-ACP thioesterases from sunflower importantly changed when endogenous ACPs were used. Sunflower FatB was much more specific towards saturated acyl-ACPs when assayed with them. Acyl carrier proteins (ACPs) are small (~9 kDa), soluble, acidic proteins involved in fatty acid synthesis in plants and bacteria. ACPs bind to fatty acids through a thioester bond, generating the acyl-ACP lipoproteins that are substrates for fatty acid synthase (FAS) complexes, and that are required for fatty acid chain elongation, acting as important intermediates in de novo fatty acid synthesis in plants. Plants, usually express several ACP isoforms with distinct functionalities. We report here the cloning of three ACPs from developing sunflower seeds: HaACP1, HaACP2, and HaACP3. These proteins were plastidial ACPs expressed strongly in seeds, and as such they are probably involved in the synthesis of sunflower oil. The recombinant sunflower ACPs were expressed in bacteria but they were lethal to the prokaryote host. Thus, they were finally produced using the GST gene fusion system, which allowed the apo-enzyme to be produced and later activated to the holo form. Radiolabelled acyl-ACPs from the newly cloned holo-ACP forms were also synthesized and used to characterize the activity of recombinant sunflower FatA and FatB thioesterases, important enzymes in plant fatty acids synthesis. The activity of these enzymes changed significantly when the endogenous ACPs were used. Thus, FatA importantly increased its activity levels, whereas FatB displayed a different specificity profile, with much high activity levels towards saturated acyl-CoA derivatives. All these data pointed to an important influence of the ACP moieties on the activity of enzymes involved in lipid synthesis.

INTRASURGICAL MICROSCOPE-INTEGRATED SPECTRAL DOMAIN OPTICAL COHERENCE TOMOGRAPHY-ASSISTED MEMBRANE PEELING.

Science.gov (United States)

Falkner-Radler, Christiane I; Glittenberg, Carl; Gabriel, Max; Binder, Susanne

2015-10-01

To evaluate microscope-integrated intrasurgical spectral domain optical coherence tomography during macular surgery in a prospective monocenter study. Before pars plana vitrectomy and before, during, and after membrane peeling, 512 × 128 macular cube scans were performed using a Carl Zeiss Meditec Cirrus high-definition OCT system adapted to the optical pathway of a Zeiss OPMI VISU 200 surgical microscope and compared with retinal staining. The study included 51 patients with epiretinal membranes, with 8 of those having additional lamellar macular holes, 11 patients with vitreomacular traction, and 8 patients with full-thickness macular holes. Intraoperative spectral domain optical coherence tomography allowed performing membrane peeling without using retinal dyes in 40% of cases (28 of 70 patients). No residual membranes were found in 94.3% of patients (66 of 70 patients) in intrasurgical spectral domain optical coherence tomography and subsequent (re)staining. In patients with vitreomacular traction, intrasurgical spectral domain optical coherence tomography scans facilitated decisions on the need for an intraocular tamponade after membrane peeling. Intraoperative spectral domain optical coherence tomography was comparable with retinal dyes in confirming success after membrane peeling. However, the visualization of flat membranes was better after staining.

Quantum-corrected plasmonic field analysis using a time domain PMCHWT integral equation

KAUST Repository

Uysal, Ismail E.

2016-03-13

When two structures are within sub-nanometer distance of each other, quantum tunneling, i.e., electrons "jumping" from one structure to another, becomes relevant. Classical electromagnetic solvers do not directly account for this additional path of current. In this work, an auxiliary tunnel made of Drude material is used to "connect" the structures as a support for this current path (R. Esteban et al., Nat. Commun., 2012). The plasmonic fields on the resulting connected structure are analyzed using a time domain surface integral equation solver. Time domain samples of the dispersive medium Green function and the dielectric permittivities are computed from the analytical inverse Fourier transform applied to the rational function representation of their frequency domain samples.

Time-domain single-source integral equations for analyzing scattering from homogeneous penetrable objects

KAUST Repository

Valdé s, Felipe; Andriulli, Francesco P.; Bagci, Hakan; Michielssen, Eric

2013-01-01

Single-source time-domain electric-and magnetic-field integral equations for analyzing scattering from homogeneous penetrable objects are presented. Their temporal discretization is effected by using shifted piecewise polynomial temporal basis

Integral equation approach to time-dependent kinematic dynamos in finite domains

International Nuclear Information System (INIS)

Xu Mingtian; Stefani, Frank; Gerbeth, Gunter

2004-01-01

The homogeneous dynamo effect is at the root of cosmic magnetic field generation. With only a very few exceptions, the numerical treatment of homogeneous dynamos is carried out in the framework of the differential equation approach. The present paper tries to facilitate the use of integral equations in dynamo research. Apart from the pedagogical value to illustrate dynamo action within the well-known picture of the Biot-Savart law, the integral equation approach has a number of practical advantages. The first advantage is its proven numerical robustness and stability. The second and perhaps most important advantage is its applicability to dynamos in arbitrary geometries. The third advantage is its intimate connection to inverse problems relevant not only for dynamos but also for technical applications of magnetohydrodynamics. The paper provides the first general formulation and application of the integral equation approach to time-dependent kinematic dynamos, with stationary dynamo sources, in finite domains. The time dependence is restricted to the magnetic field, whereas the velocity or corresponding mean-field sources of dynamo action are supposed to be stationary. For the spherically symmetric α 2 dynamo model it is shown how the general formulation is reduced to a coupled system of two radial integral equations for the defining scalars of the poloidal and toroidal field components. The integral equation formulation for spherical dynamos with general stationary velocity fields is also derived. Two numerical examples - the α 2 dynamo model with radially varying α and the Bullard-Gellman model - illustrate the equivalence of the approach with the usual differential equation method. The main advantage of the method is exemplified by the treatment of an α 2 dynamo in rectangular domains

MiDas: automatic extraction of a common domain of discourse in sleep medicine for multi-center data integration.

Science.gov (United States)

Sahoo, Satya S; Ogbuji, Chimezie; Luo, Lingyun; Dong, Xiao; Cui, Licong; Redline, Susan S; Zhang, Guo-Qiang

2011-01-01

Clinical studies often use data dictionaries with controlled sets of terms to facilitate data collection, limited interoperability and sharing at a local site. Multi-center retrospective clinical studies require that these data dictionaries, originating from individual participating centers, be harmonized in preparation for the integration of the corresponding clinical research data. Domain ontologies are often used to facilitate multi-center data integration by modeling terms from data dictionaries in a logic-based language, but interoperability among domain ontologies (using automated techniques) is an unresolved issue. Although many upper-level reference ontologies have been proposed to address this challenge, our experience in integrating multi-center sleep medicine data highlights the need for an upper level ontology that models a common set of terms at multiple-levels of abstraction, which is not covered by the existing upper-level ontologies. We introduce a methodology underpinned by a Minimal Domain of Discourse (MiDas) algorithm to automatically extract a minimal common domain of discourse (upper-domain ontology) from an existing domain ontology. Using the Multi-Modality, Multi-Resource Environment for Physiological and Clinical Research (Physio-MIMI) multi-center project in sleep medicine as a use case, we demonstrate the use of MiDas in extracting a minimal domain of discourse for sleep medicine, from Physio-MIMI's Sleep Domain Ontology (SDO). We then extend the resulting domain of discourse with terms from the data dictionary of the Sleep Heart and Health Study (SHHS) to validate MiDas. To illustrate the wider applicability of MiDas, we automatically extract the respective domains of discourse from 6 sample domain ontologies from the National Center for Biomedical Ontologies (NCBO) and the OBO Foundry.

On the initial condition problem of the time domain PMCHWT surface integral equation

KAUST Repository

Uysal, Ismail Enes; Bagci, Hakan; Ergin, A. Arif; Ulku, H. Arda

2017-01-01

Non-physical, linearly increasing and constant current components are induced in marching on-in-time solution of time domain surface integral equations when initial conditions on time derivatives of (unknown) equivalent currents are not enforced

The Bone Dysplasia Ontology: integrating genotype and phenotype information in the skeletal dysplasia domain

Directory of Open Access Journals (Sweden)

Groza Tudor

2012-03-01

Full Text Available Abstract Background Skeletal dysplasias are a rare and heterogeneous group of genetic disorders affecting skeletal development. Patients with skeletal dysplasias suffer from many complex medical issues including degenerative joint disease and neurological complications. Because the data and expertise associated with this field is both sparse and disparate, significant benefits will potentially accrue from the availability of an ontology that provides a shared conceptualisation of the domain knowledge and enables data integration, cross-referencing and advanced reasoning across the relevant but distributed data sources. Results We introduce the design considerations and implementation details of the Bone Dysplasia Ontology. We also describe the different components of the ontology, including a comprehensive and formal representation of the skeletal dysplasia domain as well as the related genotypes and phenotypes. We then briefly describe SKELETOME, a community-driven knowledge curation platform that is underpinned by the Bone Dysplasia Ontology. SKELETOME enables domain experts to use, refine and extend and apply the ontology without any prior ontology engineering experience--to advance the body of knowledge in the skeletal dysplasia field. Conclusions The Bone Dysplasia Ontology represents the most comprehensive structured knowledge source for the skeletal dysplasias domain. It provides the means for integrating and annotating clinical and research data, not only at the generic domain knowledge level, but also at the level of individual patient case studies. It enables links between individual cases and publicly available genotype and phenotype resources based on a community-driven curation process that ensures a shared conceptualisation of the domain knowledge and its continuous incremental evolution.

Structure and Functional Analysis of ClbQ, an Unusual Intermediate-Releasing Thioesterase from the Colibactin Biosynthetic Pathway.

Science.gov (United States)

Guntaka, Naga Sandhya; Healy, Alan R; Crawford, Jason M; Herzon, Seth B; Bruner, Steven D

2017-10-20

Colibactin is a genotoxic hybrid nonribosomal peptide/polyketide secondary metabolite produced by various pathogenic and probiotic bacteria residing in the human gut. The presence of colibactin metabolites has been correlated to colorectal cancer formation in several studies. The specific function of many gene products in the colibactin gene cluster can be predicted. However, the role of ClbQ, a type II editing thioesterase, has not been established. The importance of ClbQ has been demonstrated by genetic deletions that abolish colibactin cytotoxic activity, and recent studies suggest an atypical role in releasing pathway intermediates from the assembly line. Here we report the 2.0 Å crystal structure and biochemical characterization of ClbQ. Our data reveal that ClbQ exhibits greater catalytic efficiency toward acyl-thioester substrates as compared to precolibactin intermediates and does not discriminate among carrier proteins. Cyclized pyridone-containing colibactins, which are off-pathway derivatives, are not viable substrates for ClbQ, while linear precursors are, supporting a role of ClbQ in facilitating the promiscuous off-loading of premature precolibactin metabolites and novel insights into colibactin biosynthesis.

Structure and Functional Analysis of ClbQ, an Unusual Intermediate-Releasing Thioesterase from the Colibactin Biosynthetic Pathway

Energy Technology Data Exchange (ETDEWEB)

Guntaka, Naga Sandhya; Healy, Alan R.; Crawford, Jason M.; Herzon, Seth B.; Bruner, Steven D. (Yale); (Florida); (Yale-MED)

2017-09-08

Colibactin is a genotoxic hybrid nonribosomal peptide/polyketide secondary metabolite produced by various pathogenic and probiotic bacteria residing in the human gut. The presence of colibactin metabolites has been correlated to colorectal cancer formation in several studies. The specific function of many gene products in the colibactin gene cluster can be predicted. However, the role of ClbQ, a type II editing thioesterase, has not been established. The importance of ClbQ has been demonstrated by genetic deletions that abolish colibactin cytotoxic activity, and recent studies suggest an atypical role in releasing pathway intermediates from the assembly line. Here we report the 2.0 Å crystal structure and biochemical characterization of ClbQ. Our data reveal that ClbQ exhibits greater catalytic efficiency toward acyl-thioester substrates as compared to precolibactin intermediates and does not discriminate among carrier proteins. Cyclized pyridone-containing colibactins, which are off-pathway derivatives, are not viable substrates for ClbQ, while linear precursors are, supporting a role of ClbQ in facilitating the promiscuous off-loading of premature precolibactin metabolites and novel insights into colibactin biosynthesis.

A discontinuous galerkin time domain-boundary integral method for analyzing transient electromagnetic scattering

KAUST Repository

Li, Ping

2014-07-01

This paper presents an algorithm hybridizing discontinuous Galerkin time domain (DGTD) method and time domain boundary integral (BI) algorithm for 3-D open region electromagnetic scattering analysis. The computational domain of DGTD is rigorously truncated by analytically evaluating the incoming numerical flux from the outside of the truncation boundary through BI method based on the Huygens\\' principle. The advantages of the proposed method are that it allows the truncation boundary to be conformal to arbitrary (convex/ concave) scattering objects, well-separated scatters can be truncated by their local meshes without losing the physics (such as coupling/multiple scattering) of the problem, thus reducing the total mesh elements. Furthermore, low frequency waves can be efficiently absorbed, and the field outside the truncation domain can be conveniently calculated using the same BI formulation. Numerical examples are benchmarked to demonstrate the accuracy and versatility of the proposed method.

Preclinical evaluation and intraoperative human retinal imaging with a high-resolution microscope-integrated spectral domain optical coherence tomography device.

Science.gov (United States)

Hahn, Paul; Migacz, Justin; O'Donnell, Rachelle; Day, Shelley; Lee, Annie; Lin, Phoebe; Vann, Robin; Kuo, Anthony; Fekrat, Sharon; Mruthyunjaya, Prithvi; Postel, Eric A; Izatt, Joseph A; Toth, Cynthia A

2013-01-01

The authors have recently developed a high-resolution microscope-integrated spectral domain optical coherence tomography (MIOCT) device designed to enable OCT acquisition simultaneous with surgical maneuvers. The purpose of this report is to describe translation of this device from preclinical testing into human intraoperative imaging. Before human imaging, surgical conditions were fully simulated for extensive preclinical MIOCT evaluation in a custom model eye system. Microscope-integrated spectral domain OCT images were then acquired in normal human volunteers and during vitreoretinal surgery in patients who consented to participate in a prospective institutional review board-approved study. Microscope-integrated spectral domain OCT images were obtained before and at pauses in surgical maneuvers and were compared based on predetermined diagnostic criteria to images obtained with a high-resolution spectral domain research handheld OCT system (HHOCT; Bioptigen, Inc) at the same time point. Cohorts of five consecutive patients were imaged. Successful end points were predefined, including ≥80% correlation in identification of pathology between MIOCT and HHOCT in ≥80% of the patients. Microscope-integrated spectral domain OCT was favorably evaluated by study surgeons and scrub nurses, all of whom responded that they would consider participating in human intraoperative imaging trials. The preclinical evaluation identified significant improvements that were made before MIOCT use during human surgery. The MIOCT transition into clinical human research was smooth. Microscope-integrated spectral domain OCT imaging in normal human volunteers demonstrated high resolution comparable to tabletop scanners. In the operating room, after an initial learning curve, surgeons successfully acquired human macular MIOCT images before and after surgical maneuvers. Microscope-integrated spectral domain OCT imaging confirmed preoperative diagnoses, such as full-thickness macular hole

Domain XML semantic integration based on extraction rules and ontology mapping

Directory of Open Access Journals (Sweden)

Huayu LI

2016-08-01

Full Text Available A plenty of XML documents exist in petroleum engineering field, but traditional XML integration solution can’t provide semantic query, which leads to low data use efficiency. In light of WeXML(oil&gas well XML data semantic integration and query requirement, this paper proposes a semantic integration method based on extraction rules and ontology mapping. The method firstly defines a series of extraction rules with which elements and properties of WeXML Schema are mapped to classes and properties in WeOWL ontology, respectively; secondly, an algorithm is used to transform WeXML documents into WeOWL instances. Because WeOWL provides limited semantics, ontology mappings between two ontologies are then built to explain class and property of global ontology with terms of WeOWL, and semantic query based on global domain concepts model is provided. By constructing a WeXML data semantic integration prototype system, the proposed transformational rule, the transfer algorithm and the mapping rule are tested.

Phosphatidylcholine transfer protein interacts with thioesterase superfamily member 2 to attenuate insulin signaling.

Science.gov (United States)

Ersoy, Baran A; Tarun, Akansha; D'Aquino, Katharine; Hancer, Nancy J; Ukomadu, Chinweike; White, Morris F; Michel, Thomas; Manning, Brendan D; Cohen, David E

2013-07-30

Phosphatidylcholine transfer protein (PC-TP) is a phospholipid-binding protein that is enriched in liver and that interacts with thioesterase superfamily member 2 (THEM2). Mice lacking either protein exhibit improved hepatic glucose homeostasis and are resistant to diet-induced diabetes. Insulin receptor substrate 2 (IRS2) and mammalian target of rapamycin complex 1 (mTORC1) are key effectors of insulin signaling, which is attenuated in diabetes. We found that PC-TP inhibited IRS2, as evidenced by insulin-independent IRS2 activation after knockdown, genetic ablation, or chemical inhibition of PC-TP. In addition, IRS2 was activated after knockdown of THEM2, providing support for a role for the interaction of PC-TP with THEM2 in suppressing insulin signaling. Additionally, we showed that PC-TP bound to tuberous sclerosis complex 2 (TSC2) and stabilized the components of the TSC1-TSC2 complex, which functions to inhibit mTORC1. Preventing phosphatidylcholine from binding to PC-TP disrupted interactions of PC-TP with THEM2 and TSC2, and disruption of the PC-TP-THEM2 complex was associated with increased activation of both IRS2 and mTORC1. In livers of mice with genetic ablation of PC-TP or that had been treated with a PC-TP inhibitor, steady-state amounts of IRS2 were increased, whereas those of TSC2 were decreased. These findings reveal a phospholipid-dependent mechanism that suppresses insulin signaling downstream of its receptor.

UPCaD: A Methodology of Integration Between Ontology-Based Context-Awareness Modeling and Relational Domain Data

Directory of Open Access Journals (Sweden)

Vinícius Maran

2018-01-01

Full Text Available Context-awareness is a key feature for ubiquitous computing scenarios applications. Currently, technologies and methodologies have been proposed for the integration of context-awareness concepts in intelligent information systems to adapt them to the execution of services, user interfaces and data retrieval. Recent research proposed conceptual modeling alternatives to the integration of the domain modeling in RDBMS and context-awareness modeling. The research described using highly expressiveness ontologies. The present work describes the UPCaD (Unified Process for Integration between Context-Awareness and Domain methodology, which is composed of formalisms and processes to guide the data integration considering RDBMS and context modeling. The methodology was evaluated in a virtual learning environment application. The evaluation shows the possibility to use a highly expressive context ontology to filter the relational data query and discusses the main contributions of the methodology compared with recent approaches.

Peripartum depression and anxiety as an integrative cross domain target for psychiatric preventative measures.

Science.gov (United States)

Babb, Jessica A; Deligiannidis, Kristina M; Murgatroyd, Christopher A; Nephew, Benjamin C

2015-01-01

Exposure to high levels of early life stress has been identified as a potent risk factor for neurodevelopmental delays in infants, behavioral problems and autism in children, but also for several psychiatric illnesses in adulthood, such as depression, anxiety, autism, and posttraumatic stress disorder. Despite having robust adverse effects on both mother and infant, the pathophysiology of peripartum depression and anxiety are poorly understood. The objective of this review is to highlight the advantages of using an integrated approach addressing several behavioral domains in both animal and clinical studies of peripartum depression and anxiety. It is postulated that a greater focus on integrated cross domain studies will lead to advances in treatments and preventative measures for several disorders associated with peripartum depression and anxiety. Copyright © 2014 Elsevier B.V. All rights reserved.

Analysis of electromagnetic wave interactions on nonlinear scatterers using time domain volume integral equations

KAUST Repository

Ulku, Huseyin Arda

2014-07-06

Effects of material nonlinearities on electromagnetic field interactions become dominant as field amplitudes increase. A typical example is observed in plasmonics, where highly localized fields “activate” Kerr nonlinearities. Naturally, time domain solvers are the method of choice when it comes simulating these nonlinear effects. Oftentimes, finite difference time domain (FDTD) method is used for this purpose. This is simply due to the fact that explicitness of the FDTD renders the implementation easier and the material nonlinearity can be easily accounted for using an auxiliary differential equation (J.H. Green and A. Taflove, Opt. Express, 14(18), 8305-8310, 2006). On the other hand, explicit marching on-in-time (MOT)-based time domain integral equation (TDIE) solvers have never been used for the same purpose even though they offer several advantages over FDTD (E. Michielssen, et al., ECCOMAS CFD, The Netherlands, Sep. 5-8, 2006). This is because explicit MOT solvers have never been stabilized until not so long ago. Recently an explicit but stable MOT scheme has been proposed for solving the time domain surface magnetic field integral equation (H.A. Ulku, et al., IEEE Trans. Antennas Propag., 61(8), 4120-4131, 2013) and later it has been extended for the time domain volume electric field integral equation (TDVEFIE) (S. B. Sayed, et al., Pr. Electromagn. Res. S., 378, Stockholm, 2013). This explicit MOT scheme uses predictor-corrector updates together with successive over relaxation during time marching to stabilize the solution even when time step is as large as in the implicit counterpart. In this work, an explicit MOT-TDVEFIE solver is proposed for analyzing electromagnetic wave interactions on scatterers exhibiting Kerr nonlinearity. Nonlinearity is accounted for using the constitutive relation between the electric field intensity and flux density. Then, this relation and the TDVEFIE are discretized together by expanding the intensity and flux - sing half

Attentional selection in visual perception, memory and action: a quest for cross-domain integration.

Science.gov (United States)

Schneider, Werner X; Einhäuser, Wolfgang; Horstmann, Gernot

2013-10-19

For decades, the cognitive and neural sciences have benefitted greatly from a separation of mind and brain into distinct functional domains. The tremendous success of this approach notwithstanding, it is self-evident that such a view is incomplete. Goal-directed behaviour of an organism requires the joint functioning of perception, memory and sensorimotor control. A prime candidate for achieving integration across these functional domains are attentional processes. Consequently, this Theme Issue brings together studies of attentional selection from many fields, both experimental and theoretical, that are united in their quest to find overreaching integrative principles of attention between perception, memory and action. In all domains, attention is understood as combination of competition and priority control ('bias'), with the task as a decisive driving factor to ensure coherent goal-directed behaviour and cognition. Using vision as the predominant model system for attentional selection, many studies of this Theme Issue focus special emphasis on eye movements as a selection process that is both a fundamental action and serves a key function in perception. The Theme Issue spans a wide range of methods, from measuring human behaviour in the real word to recordings of single neurons in the non-human primate brain. We firmly believe that combining such a breadth in approaches is necessary not only for attentional selection, but also to take the next decisive step in all of the cognitive and neural sciences: to understand cognition and behaviour beyond isolated domains.

Attentional selection in visual perception, memory and action: a quest for cross-domain integration

Science.gov (United States)

Schneider, Werner X.; Einhäuser, Wolfgang; Horstmann, Gernot

2013-01-01

For decades, the cognitive and neural sciences have benefitted greatly from a separation of mind and brain into distinct functional domains. The tremendous success of this approach notwithstanding, it is self-evident that such a view is incomplete. Goal-directed behaviour of an organism requires the joint functioning of perception, memory and sensorimotor control. A prime candidate for achieving integration across these functional domains are attentional processes. Consequently, this Theme Issue brings together studies of attentional selection from many fields, both experimental and theoretical, that are united in their quest to find overreaching integrative principles of attention between perception, memory and action. In all domains, attention is understood as combination of competition and priority control (‘bias’), with the task as a decisive driving factor to ensure coherent goal-directed behaviour and cognition. Using vision as the predominant model system for attentional selection, many studies of this Theme Issue focus special emphasis on eye movements as a selection process that is both a fundamental action and serves a key function in perception. The Theme Issue spans a wide range of methods, from measuring human behaviour in the real word to recordings of single neurons in the non-human primate brain. We firmly believe that combining such a breadth in approaches is necessary not only for attentional selection, but also to take the next decisive step in all of the cognitive and neural sciences: to understand cognition and behaviour beyond isolated domains. PMID:24018715

A web-based system architecture for ontology-based data integration in the domain of IT benchmarking

Science.gov (United States)

Pfaff, Matthias; Krcmar, Helmut

2018-03-01

In the domain of IT benchmarking (ITBM), a variety of data and information are collected. Although these data serve as the basis for business analyses, no unified semantic representation of such data yet exists. Consequently, data analysis across different distributed data sets and different benchmarks is almost impossible. This paper presents a system architecture and prototypical implementation for an integrated data management of distributed databases based on a domain-specific ontology. To preserve the semantic meaning of the data, the ITBM ontology is linked to data sources and functions as the central concept for database access. Thus, additional databases can be integrated by linking them to this domain-specific ontology and are directly available for further business analyses. Moreover, the web-based system supports the process of mapping ontology concepts to external databases by introducing a semi-automatic mapping recommender and by visualizing possible mapping candidates. The system also provides a natural language interface to easily query linked databases. The expected result of this ontology-based approach of knowledge representation and data access is an increase in knowledge and data sharing in this domain, which will enhance existing business analysis methods.

The effectivenes of science domain-based science learning integrated with local potency

Science.gov (United States)

Kurniawati, Arifah Putri; Prasetyo, Zuhdan Kun; Wilujeng, Insih; Suryadarma, I. Gusti Putu

2017-08-01

This research aimed to determine the significant effect of science domain-based science learning integrated with local potency toward science process skills. The research method used was a quasi-experimental design with nonequivalent control group design. The population of this research was all students of class VII SMP Negeri 1 Muntilan. The sample of this research was selected through cluster random sampling, namely class VII B as an experiment class (24 students) and class VII C as a control class (24 students). This research used a test instrument that was adapted from Agus Dwianto's research. The aspect of science process skills in this research was observation, classification, interpretation and communication. The analysis of data used the one factor anova at 0,05 significance level and normalized gain score. The significance level result of science process skills with one factor anova is 0,000. It shows that the significance level < alpha (0,05). It means that there was significant effect of science domain-based science learning integrated with local potency toward science learning process skills. The results of analysis show that the normalized gain score are 0,29 (low category) in control class and 0,67 (medium category) in experiment class.

Towards a Conceptual Design of a Cross-Domain Integrative Information System for the Geosciences

Science.gov (United States)

Zaslavsky, I.; Richard, S. M.; Valentine, D. W.; Malik, T.; Gupta, A.

2013-12-01

As geoscientists increasingly focus on studying processes that span multiple research domains, there is an increased need for cross-domain interoperability solutions that can scale to the entire geosciences, bridging information and knowledge systems, models, software tools, as well as connecting researchers and organization. Creating a community-driven cyberinfrastructure (CI) to address the grand challenges of integrative Earth science research and education is the focus of EarthCube, a new research initiative of the U.S. National Science Foundation. We are approaching EarthCube design as a complex socio-technical system of systems, in which communication between various domain subsystems, people and organizations enables more comprehensive, data-intensive research designs and knowledge sharing. In particular, we focus on integrating 'traditional' layered CI components - including information sources, catalogs, vocabularies, services, analysis and modeling tools - with CI components supporting scholarly communication, self-organization and social networking (e.g. research profiles, Q&A systems, annotations), in a manner that follows and enhances existing patterns of data, information and knowledge exchange within and across geoscience domains. We describe an initial architecture design focused on enabling the CI to (a) provide an environment for scientifically sound information and software discovery and reuse; (b) evolve by factoring in the impact of maturing movements like linked data, 'big data', and social collaborations, as well as experience from work on large information systems in other domains; (c) handle the ever increasing volume, complexity and diversity of geoscience information; (d) incorporate new information and analytical requirements, tools, and techniques, and emerging types of earth observations and models; (e) accommodate different ideas and approaches to research and data stewardship; (f) be responsive to the existing and anticipated needs

Integrating Moral and Social Development within Middle School Social Studies: A Social Cognitive Domain Approach

Science.gov (United States)

Nucci, Larry; Creane, Michael W.; Powers, Deborah W.

2015-01-01

Eleven teachers and 254 urban middle-school students comprised the sample of this study examining the social and moral development outcomes of the integration of social cognitive domain theory within regular classroom instruction. Participating teachers were trained to construct and implement history lessons that stimulated students' moral…

Retarded potentials and time domain boundary integral equations a road map

CERN Document Server

Sayas, Francisco-Javier

2016-01-01

This book offers a thorough and self-contained exposition of the mathematics of time-domain boundary integral equations associated to the wave equation, including applications to scattering of acoustic and elastic waves. The book offers two different approaches for the analysis of these integral equations, including a systematic treatment of their numerical discretization using Galerkin (Boundary Element) methods in the space variables and Convolution Quadrature in the time variable. The first approach follows classical work started in the late eighties, based on Laplace transforms estimates. This approach has been refined and made more accessible by tailoring the necessary mathematical tools, avoiding an excess of generality. A second approach contains a novel point of view that the author and some of his collaborators have been developing in recent years, using the semigroup theory of evolution equations to obtain improved results. The extension to electromagnetic waves is explained in one of the appendices...

Domain decomposition method for solving elliptic problems in unbounded domains

International Nuclear Information System (INIS)

Khoromskij, B.N.; Mazurkevich, G.E.; Zhidkov, E.P.

1991-01-01

Computational aspects of the box domain decomposition (DD) method for solving boundary value problems in an unbounded domain are discussed. A new variant of the DD-method for elliptic problems in unbounded domains is suggested. It is based on the partitioning of an unbounded domain adapted to the given asymptotic decay of an unknown function at infinity. The comparison of computational expenditures is given for boundary integral method and the suggested DD-algorithm. 29 refs.; 2 figs.; 2 tabs

Mutational analyses of the core domain of Avian Leukemia and Sarcoma Viruses integrase: critical residues for concerted integration and multimerization

International Nuclear Information System (INIS)

Moreau, Karen; Faure, Claudine; Violot, Sebastien; Gouet, Patrice; Verdier, Gerard; Ronfort, Corinne

2004-01-01

During replicative cycle of retroviruses, the reverse-transcribed viral DNA is integrated into the cell DNA by the viral integrase (IN) enzyme. The central core domain of IN contains the catalytic site of the enzyme and is involved in binding viral ends and cell DNA as well as dimerization. We previously performed single amino acid substitutions in the core domain of an Avian Leukemia and Sarcoma Virus (ALSV) IN [Arch. Virol. 147 (2002) 1761]. Here, we modeled the resulting IN mutants and analyzed the ability of these mutants to mediate concerted DNA integration in an in vitro assay, and to form dimers by protein-protein cross-linking and size exclusion chromatography. The N197C mutation resulted in the inability of the mutant to perform concerted integration that was concomitant with a loss of IN dimerization. Surprisingly, mutations Q102G and A106V at the dimer interface resulted in mutants with higher efficiencies than the wild-type IN in performing two-ended concerted integration of viral DNA ends. The G139D and A195V mutants had a trend to perform one-ended DNA integration of viral ends instead of two-ended integration. More drastically, the I88L and L135G mutants preferentially mediated nonconcerted DNA integration although the proteins form dimers. Therefore, these mutations may alter the formation of IN complexes of higher molecular size than a dimer that would be required for concerted integration. This study points to the important role of core domain residues in the concerted integration of viral DNA ends as well as in the oligomerization of the enzyme

Integral formula for elliptic SOS models with domain walls and a reflecting end

Energy Technology Data Exchange (ETDEWEB)

Lamers, Jules, E-mail: j.lamers@uu.nl

2015-12-15

In this paper we extend previous work of Galleas and the author to elliptic SOS models. We demonstrate that the dynamical reflection algebra can be exploited to obtain a functional equation characterizing the partition function of an elliptic SOS model with domain-wall boundaries and one reflecting end. Special attention is paid to the structure of the functional equation. Through this approach we find a novel multiple-integral formula for that partition function.

Vertically Integrated Models for Carbon Storage Modeling in Heterogeneous Domains

Science.gov (United States)

Bandilla, K.; Celia, M. A.

2017-12-01

Numerical modeling is an essential tool for studying the impacts of geologic carbon storage (GCS). Injection of carbon dioxide (CO2) into deep saline aquifers leads to multi-phase flow (injected CO2 and resident brine), which can be described by a set of three-dimensional governing equations, including mass-balance equation, volumetric flux equations (modified Darcy), and constitutive equations. This is the modeling approach on which commonly used reservoir simulators such as TOUGH2 are based. Due to the large density difference between CO2 and brine, GCS models can often be simplified by assuming buoyant segregation and integrating the three-dimensional governing equations in the vertical direction. The integration leads to a set of two-dimensional equations coupled with reconstruction operators for vertical profiles of saturation and pressure. Vertically-integrated approaches have been shown to give results of comparable quality as three-dimensional reservoir simulators when applied to realistic CO2 injection sites such as the upper sand wedge at the Sleipner site. However, vertically-integrated approaches usually rely on homogeneous properties over the thickness of a geologic layer. Here, we investigate the impact of general (vertical and horizontal) heterogeneity in intrinsic permeability, relative permeability functions, and capillary pressure functions. We consider formations involving complex fluvial deposition environments and compare the performance of vertically-integrated models to full three-dimensional models for a set of hypothetical test cases consisting of high permeability channels (streams) embedded in a low permeability background (floodplains). The domains are randomly generated assuming that stream channels can be represented by sinusoidal waves in the plan-view and by parabolas for the streams' cross-sections. Stream parameters such as width, thickness and wavelength are based on values found at the Ketzin site in Germany. Results from the

On the mixed discretization of the time domain magnetic field integral equation

KAUST Repository

Ulku, Huseyin Arda

2012-09-01

Time domain magnetic field integral equation (MFIE) is discretized using divergence-conforming Rao-Wilton-Glisson (RWG) and curl-conforming Buffa-Christiansen (BC) functions as spatial basis and testing functions, respectively. The resulting mixed discretization scheme, unlike the classical scheme which uses RWG functions as both basis and testing functions, is proper: Testing functions belong to dual space of the basis functions. Numerical results demonstrate that the marching on-in-time (MOT) solution of the mixed discretized MFIE yields more accurate results than that of classically discretized MFIE. © 2012 IEEE.

Time Domain Surface Integral Equation Solvers for Quantum Corrected Electromagnetic Analysis of Plasmonic Nanostructures

KAUST Repository

Uysal, Ismail Enes

2016-10-01

Plasmonic structures are utilized in many applications ranging from bio-medicine to solar energy generation and transfer. Numerical schemes capable of solving equations of classical electrodynamics have been the method of choice for characterizing scattering properties of such structures. However, as dimensions of these plasmonic structures reduce to nanometer scale, quantum mechanical effects start to appear. These effects cannot be accurately modeled by available classical numerical methods. One of these quantum effects is the tunneling, which is observed when two structures are located within a sub-nanometer distance of each other. At these small distances electrons “jump" from one structure to another and introduce a path for electric current to flow. Classical equations of electrodynamics and the schemes used for solving them do not account for this additional current path. This limitation can be lifted by introducing an auxiliary tunnel with material properties obtained using quantum models and applying a classical solver to the structures connected by this auxiliary tunnel. Early work on this topic focused on quantum models that are generated using a simple one-dimensional wave function to find the tunneling probability and assume a simple Drude model for the permittivity of the tunnel. These tunnel models are then used together with a classical frequency domain solver. In this thesis, a time domain surface integral equation solver for quantum corrected analysis of transient plasmonic interactions is proposed. This solver has several advantages: (i) As opposed to frequency domain solvers, it provides results at a broad band of frequencies with a single simulation. (ii) As opposed to differential equation solvers, it only discretizes surfaces (reducing number of unknowns), enforces the radiation condition implicitly (increasing the accuracy), and allows for time step selection independent of spatial discretization (increasing efficiency). The quantum model

Integrated cross-domain object storage in working memory: evidence from a verbal-spatial memory task.

Science.gov (United States)

Morey, Candice C

2009-11-01

Working-memory theories often include domain-specific verbal and visual stores (e.g., the phonological and visuospatial buffers of Baddeley, 1986), and some also posit more general stores thought to be capable of holding verbal or visuospatial materials (Baddeley, 2000; Cowan, 2005). However, it is currently unclear which type of store is primarily responsible for maintaining objects that include components from multiple domains. In these studies, a spatial array of letters was followed by a single probe identical to an item in the array or differing systematically in spatial location, letter identity, or their combination. Concurrent verbal rehearsal suppression impaired memory in each of these trial types in a task that required participants to remember verbal-spatial binding, but did not impair memory for spatial locations if the task did not require verbal-spatial binding for a correct response. Thus, spatial information might be stored differently when it must be bound to verbal information. This suggests that a cross-domain store such as the episodic buffer of Baddeley (2000) or the focus of attention of Cowan (2001) might be used for integrated object storage, rather than the maintenance of associations between features stored in separate domain-specific buffers.

Analytical solutions of linear diffusion and wave equations in semi-infinite domains by using a new integral transform

Directory of Open Access Journals (Sweden)

Gao Lin

2017-01-01

Full Text Available Recently, a new integral transform similar to Sumudu transform has been proposed by Yang [1]. Some of the properties of the integral transform are expanded in the present article. Meanwhile, new applications to the linear wave and diffusion equations in semi-infinite domains are discussed in detail. The proposed method provides an alternative approach to solve the partial differential equations in mathematical physics.

Integral ceramic superstructure evaluation using time domain optical coherence tomography

Science.gov (United States)

Sinescu, Cosmin; Bradu, Adrian; Topala, Florin I.; Negrutiu, Meda Lavinia; Duma, Virgil-Florin; Podoleanu, Adrian G.

2014-02-01

Optical Coherence Tomography (OCT) is a non-invasive low coherence interferometry technique that includes several technologies (and the corresponding devices and components), such as illumination and detection, interferometry, scanning, adaptive optics, microscopy and endoscopy. From its large area of applications, we consider in this paper a critical aspect in dentistry - to be investigated with a Time Domain (TD) OCT system. The clinical situation of an edentulous mandible is considered; it can be solved by inserting 2 to 6 implants. On these implants a mesostructure will be manufactured and on it a superstructure is needed. This superstructure can be integral ceramic; in this case materials defects could be trapped inside the ceramic layers and those defects could lead to fractures of the entire superstructure. In this paper we demonstrate that a TD-OCT imaging system has the potential to properly evaluate the presence of the defects inside the ceramic layers and those defects can be fixed before inserting the prosthesis inside the oral cavity. Three integral ceramic superstructures were developed by using a CAD/CAM technology. After the milling, the ceramic layers were applied on the core. All the three samples were evaluated by a TD-OCT system working at 1300 nm. For two of the superstructures evaluated, no defects were found in the most stressed areas. The third superstructure presented four ceramic defects in the mentioned areas. Because of those defects the superstructure may fracture. The integral ceramic prosthesis was send back to the dental laboratory to fix the problems related to the material defects found. Thus, TD-OCT proved to be a valuable method for diagnosing the ceramic defects inside the integral ceramic superstructures in order to prevent fractures at this level.

An Operator-Integration-Factor Splitting (OIFS) method for Incompressible Flows in Moving Domains

Energy Technology Data Exchange (ETDEWEB)

Patel, Saumil S. [Argonne National Lab. (ANL), Argonne, IL (United States); Fischer, Paul F. [Argonne National Lab. (ANL), Argonne, IL (United States); Univ. of Illinois, Urbana-Champaign, IL (United States); Min, Misun [Argonne National Lab. (ANL), Argonne, IL (United States); Tomboulides, Ananias G [Argonne National Lab. (ANL), Argonne, IL (United States); Aristotle Univ., Thessaloniki (Greece)

2017-10-21

In this paper, we present a characteristic-based numerical procedure for simulating incompressible flows in domains with moving boundaries. Our approach utilizes an operator-integration-factor splitting technique to help produce an effcient and stable numerical scheme. Using the spectral element method and an arbitrary Lagrangian-Eulerian formulation, we investigate flows where the convective acceleration effects are non-negligible. Several examples, ranging from laminar to turbulent flows, are considered. Comparisons with a standard, semi-implicit time-stepping procedure illustrate the improved performance of the scheme.

Cardiomyocyte specific expression of Acyl-coA thioesterase 1 attenuates sepsis induced cardiac dysfunction and mortality

Energy Technology Data Exchange (ETDEWEB)

Xia, Congying [Departments of Internal Medicine and Institute of Hypertension, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan (China); Dong, Ruolan [Department of Geriatric Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030 (China); Chen, Chen [Departments of Internal Medicine and Institute of Hypertension, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan (China); Wang, Hong, E-mail: hong.wang1988@yahoo.com [Departments of Internal Medicine and Institute of Hypertension, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan (China); Wang, Dao Wen, E-mail: dwwang@tjh.tjmu.edu.cn [Departments of Internal Medicine and Institute of Hypertension, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan (China)

2015-12-25

Compromised cardiac fatty acid oxidation (FAO) induced energy deprivation is a critical cause of cardiac dysfunction in sepsis. Acyl-CoA thioesterase 1 (ACOT1) is involved in regulating cardiac energy production via altering substrate metabolism. This study aims to clarify whether ACOT1 has a potency to ameliorate septic myocardial dysfunction via enhancing cardiac FAO. Transgenic mice with cardiomyocyte specific expression of ACOT1 (αMHC-ACOT1) and their wild type (WT) littermates were challenged with Escherichia coli lipopolysaccharide (LPS; 5 mg/kg i.p.) and myocardial function was assessed 6 h later using echocardiography and hemodynamics. Deteriorated cardiac function evidenced by reduction of the percentage of left ventricular ejection fraction and fractional shortening after LPS administration was significantly attenuated by cardiomyocyte specific expression of ACOT1. αMHC-ACOT1 mice exhibited a markedly increase in glucose utilization and cardiac FAO compared with LPS-treated WT mice. Suppression of cardiac peroxisome proliferator activated receptor alpha (PPARa) and PPARγ-coactivator-1α (PGC1a) signaling observed in LPS-challenged WT mice was activated by the presence of ACOT1. These results suggest that ACOT1 has potential therapeutic values to protect heart from sepsis mediated dysfunction, possibly through activating PPARa/PGC1a signaling. - Highlights: • ACOT1 has potential therapeutic values to protect heart from sepsis mediated dysfunction. • ACOT1 can regulate PPARa/PGC1a signaling pathway. • We first generate the transgenic mice with cardiomyocyte specific expression of ACOT1.

Cardiomyocyte specific expression of Acyl-coA thioesterase 1 attenuates sepsis induced cardiac dysfunction and mortality

International Nuclear Information System (INIS)

Xia, Congying; Dong, Ruolan; Chen, Chen; Wang, Hong; Wang, Dao Wen

2015-01-01

Compromised cardiac fatty acid oxidation (FAO) induced energy deprivation is a critical cause of cardiac dysfunction in sepsis. Acyl-CoA thioesterase 1 (ACOT1) is involved in regulating cardiac energy production via altering substrate metabolism. This study aims to clarify whether ACOT1 has a potency to ameliorate septic myocardial dysfunction via enhancing cardiac FAO. Transgenic mice with cardiomyocyte specific expression of ACOT1 (αMHC-ACOT1) and their wild type (WT) littermates were challenged with Escherichia coli lipopolysaccharide (LPS; 5 mg/kg i.p.) and myocardial function was assessed 6 h later using echocardiography and hemodynamics. Deteriorated cardiac function evidenced by reduction of the percentage of left ventricular ejection fraction and fractional shortening after LPS administration was significantly attenuated by cardiomyocyte specific expression of ACOT1. αMHC-ACOT1 mice exhibited a markedly increase in glucose utilization and cardiac FAO compared with LPS-treated WT mice. Suppression of cardiac peroxisome proliferator activated receptor alpha (PPARa) and PPARγ-coactivator-1α (PGC1a) signaling observed in LPS-challenged WT mice was activated by the presence of ACOT1. These results suggest that ACOT1 has potential therapeutic values to protect heart from sepsis mediated dysfunction, possibly through activating PPARa/PGC1a signaling. - Highlights: • ACOT1 has potential therapeutic values to protect heart from sepsis mediated dysfunction. • ACOT1 can regulate PPARa/PGC1a signaling pathway. • We first generate the transgenic mice with cardiomyocyte specific expression of ACOT1.

RNA-protein binding motifs mining with a new hybrid deep learning based cross-domain knowledge integration approach.

Science.gov (United States)

Pan, Xiaoyong; Shen, Hong-Bin

2017-02-28

RNAs play key roles in cells through the interactions with proteins known as the RNA-binding proteins (RBP) and their binding motifs enable crucial understanding of the post-transcriptional regulation of RNAs. How the RBPs correctly recognize the target RNAs and why they bind specific positions is still far from clear. Machine learning-based algorithms are widely acknowledged to be capable of speeding up this process. Although many automatic tools have been developed to predict the RNA-protein binding sites from the rapidly growing multi-resource data, e.g. sequence, structure, their domain specific features and formats have posed significant computational challenges. One of current difficulties is that the cross-source shared common knowledge is at a higher abstraction level beyond the observed data, resulting in a low efficiency of direct integration of observed data across domains. The other difficulty is how to interpret the prediction results. Existing approaches tend to terminate after outputting the potential discrete binding sites on the sequences, but how to assemble them into the meaningful binding motifs is a topic worth of further investigation. In viewing of these challenges, we propose a deep learning-based framework (iDeep) by using a novel hybrid convolutional neural network and deep belief network to predict the RBP interaction sites and motifs on RNAs. This new protocol is featured by transforming the original observed data into a high-level abstraction feature space using multiple layers of learning blocks, where the shared representations across different domains are integrated. To validate our iDeep method, we performed experiments on 31 large-scale CLIP-seq datasets, and our results show that by integrating multiple sources of data, the average AUC can be improved by 8% compared to the best single-source-based predictor; and through cross-domain knowledge integration at an abstraction level, it outperforms the state-of-the-art predictors by 6

Domain Decomposition Solvers for Frequency-Domain Finite Element Equations

KAUST Repository

Copeland, Dylan

2010-10-05

The paper is devoted to fast iterative solvers for frequency-domain finite element equations approximating linear and nonlinear parabolic initial boundary value problems with time-harmonic excitations. Switching from the time domain to the frequency domain allows us to replace the expensive time-integration procedure by the solution of a simple linear elliptic system for the amplitudes belonging to the sine- and to the cosine-excitation or a large nonlinear elliptic system for the Fourier coefficients in the linear and nonlinear case, respectively. The fast solution of the corresponding linear and nonlinear system of finite element equations is crucial for the competitiveness of this method. © 2011 Springer-Verlag Berlin Heidelberg.

Domain Decomposition Solvers for Frequency-Domain Finite Element Equations

KAUST Repository

Copeland, Dylan; Kolmbauer, Michael; Langer, Ulrich

2010-01-01

The paper is devoted to fast iterative solvers for frequency-domain finite element equations approximating linear and nonlinear parabolic initial boundary value problems with time-harmonic excitations. Switching from the time domain to the frequency domain allows us to replace the expensive time-integration procedure by the solution of a simple linear elliptic system for the amplitudes belonging to the sine- and to the cosine-excitation or a large nonlinear elliptic system for the Fourier coefficients in the linear and nonlinear case, respectively. The fast solution of the corresponding linear and nonlinear system of finite element equations is crucial for the competitiveness of this method. © 2011 Springer-Verlag Berlin Heidelberg.

Explicit solution of the time domain magnetic field integral equation using a predictor-corrector scheme

KAUST Repository

Ulku, Huseyin Arda; Bagci, Hakan; Michielssen, Eric

2012-01-01

An explicit yet stable marching-on-in-time (MOT) scheme for solving the time domain magnetic field integral equation (TD-MFIE) is presented. The stability of the explicit scheme is achieved via (i) accurate evaluation of the MOT matrix elements using closed form expressions and (ii) a PE(CE) m type linear multistep method for time marching. Numerical results demonstrate the accuracy and stability of the proposed explicit MOT-TD-MFIE solver. © 2012 IEEE.

Explicit solution of the time domain magnetic field integral equation using a predictor-corrector scheme

KAUST Repository

Ulku, Huseyin Arda

2012-09-01

An explicit yet stable marching-on-in-time (MOT) scheme for solving the time domain magnetic field integral equation (TD-MFIE) is presented. The stability of the explicit scheme is achieved via (i) accurate evaluation of the MOT matrix elements using closed form expressions and (ii) a PE(CE) m type linear multistep method for time marching. Numerical results demonstrate the accuracy and stability of the proposed explicit MOT-TD-MFIE solver. © 2012 IEEE.

AcEST: BP921787 [AcEST

Lifescience Database Archive (English)

Full Text Available ... 37 0.49 tr|O04793|O04793_9ROSI Acyl-ACP thioesterase OS=Garcinia mangost... ...cyl-ACP thioesterase OS=Garcinia mangost... 36 0.84 tr|B8BDB0|B8BDB0_ORYSI Putative uncharacterized protein ...LRFAGAGDEINRGRTVWR 285 >tr|O04793|O04793_9ROSI Acyl-ACP thioesterase OS=Garcinia mango... LR A EINRGRTVW+ Sbjct: 248 QRQFLHCLRFAGNGNEINRGRTVWR 272 >tr|O04792|O04792_9ROSI Acyl-ACP thioesterase OS=Garcinia mango

analysis of large electromagnetic pulse simulators using the electric field integral equation method in time domain

International Nuclear Information System (INIS)

Jamali, J.; Aghajafari, R.; Moini, R.; Sadeghi, H.

2002-01-01

A time-domain approach is presented to calculate electromagnetic fields inside a large Electromagnetic Pulse (EMP) simulator. This type of EMP simulator is used for studying the effect of electromagnetic pulses on electrical apparatus in various structures such as vehicles, a reoplanes, etc. The simulator consists of three planar transmission lines. To solve the problem, we first model the metallic structure of the simulator as a grid of conducting wires. The numerical solution of the governing electric field integral equation is then obtained using the method of moments in time domain. To demonstrate the accuracy of the model, we consider a typical EMP simulator. The comparison of our results with those obtained experimentally in the literature validates the model introduced in this paper

Constructive-Developmental Theory and the Integrated Domains of Wisdom: Are Post-Conventional Leaders Really Wiser?

Directory of Open Access Journals (Sweden)

Sharon L. Spano

2015-03-01

Full Text Available How leaders experience wisdom is important to our understanding of leadership behavior as well as to our overall understanding of leadership. The article explores qualitative findings that may advance academic discourse and research at the intersection between leadership, wisdom, and constructive-developmental theory. The present study examined how 12 executive leaders who assessed at the conventional and post-conventional stages of adult development experience wisdom. It is significant in that it addresses a gap in the literature between wisdom and constructive-developmental theory. Semi-structured interviews were conducted to determine how executive leaders understand their leadership role in terms of the cognitive, reflective, and affective domains of wisdom. Contrary to research that defines and operationalizes wisdom as the integration of these domains, findings indicate that participants experience wisdom in one or more of the domains of wisdom. Participants were also assessed for their meaning-making capacity to determine their stage of development using the SCTi-Map instrument. Contrary to research in constructive-developmental theory that suggests that post-conventional levels of development may equate to higher levels of wisdom, findings also indicate that there was no significant difference between how leaders describe their propensity for wisdom and their measured adult stage of development. Leaders who assessed at both the conventional and post-conventional stages of development described a propensity for wisdom. Analysis of participant responses suggests that the wisdom, in all its complexity, has its own trajectory and therefore necessitates inquiry into the lines of human development to include integral perspectives associated with spiritual, emotional, and psychosocial measures. The results of this study indicate the potential for additional research that explores wisdom in the context of both adult lines and adult stages of

SAS-1 Is a C2 Domain Protein Critical for Centriole Integrity in C. elegans

Science.gov (United States)

Delattre, Marie; Balestra, Fernando R.; Blanchoud, Simon; Finger, Susanne; Knott, Graham; Müller-Reichert, Thomas; Gönczy, Pierre

2014-01-01

Centrioles are microtubule-based organelles important for the formation of cilia, flagella and centrosomes. Despite progress in understanding the underlying assembly mechanisms, how centriole integrity is ensured is incompletely understood, including in sperm cells, where such integrity is particularly critical. We identified C. elegans sas-1 in a genetic screen as a locus required for bipolar spindle assembly in the early embryo. Our analysis reveals that sperm-derived sas-1 mutant centrioles lose their integrity shortly after fertilization, and that a related defect occurs when maternal sas-1 function is lacking. We establish that sas-1 encodes a C2 domain containing protein that localizes to centrioles in C. elegans, and which can bind and stabilize microtubules when expressed in human cells. Moreover, we uncover that SAS-1 is related to C2CD3, a protein required for complete centriole formation in human cells and affected in a type of oral-facial-digital (OFD) syndrome. PMID:25412110

SAS-1 is a C2 domain protein critical for centriole integrity in C. elegans.

Directory of Open Access Journals (Sweden)

Lukas von Tobel

2014-11-01

Full Text Available Centrioles are microtubule-based organelles important for the formation of cilia, flagella and centrosomes. Despite progress in understanding the underlying assembly mechanisms, how centriole integrity is ensured is incompletely understood, including in sperm cells, where such integrity is particularly critical. We identified C. elegans sas-1 in a genetic screen as a locus required for bipolar spindle assembly in the early embryo. Our analysis reveals that sperm-derived sas-1 mutant centrioles lose their integrity shortly after fertilization, and that a related defect occurs when maternal sas-1 function is lacking. We establish that sas-1 encodes a C2 domain containing protein that localizes to centrioles in C. elegans, and which can bind and stabilize microtubules when expressed in human cells. Moreover, we uncover that SAS-1 is related to C2CD3, a protein required for complete centriole formation in human cells and affected in a type of oral-facial-digital (OFD syndrome.

A time-domain finite element boundary integral approach for elastic wave scattering

Science.gov (United States)

Shi, F.; Lowe, M. J. S.; Skelton, E. A.; Craster, R. V.

2018-04-01

The response of complex scatterers, such as rough or branched cracks, to incident elastic waves is required in many areas of industrial importance such as those in non-destructive evaluation and related fields; we develop an approach to generate accurate and rapid simulations. To achieve this we develop, in the time domain, an implementation to efficiently couple the finite element (FE) method within a small local region, and the boundary integral (BI) globally. The FE explicit scheme is run in a local box to compute the surface displacement of the scatterer, by giving forcing signals to excitation nodes, which can lie on the scatterer itself. The required input forces on the excitation nodes are obtained with a reformulated FE equation, according to the incident displacement field. The surface displacements computed by the local FE are then projected, through time-domain BI formulae, to calculate the scattering signals with different modes. This new method yields huge improvements in the efficiency of FE simulations for scattering from complex scatterers. We present results using different shapes and boundary conditions, all simulated using this approach in both 2D and 3D, and then compare with full FE models and theoretical solutions to demonstrate the efficiency and accuracy of this numerical approach.

DIMA 3.0: Domain Interaction Map.

Science.gov (United States)

Luo, Qibin; Pagel, Philipp; Vilne, Baiba; Frishman, Dmitrij

2011-01-01

Domain Interaction MAp (DIMA, available at http://webclu.bio.wzw.tum.de/dima) is a database of predicted and known interactions between protein domains. It integrates 5807 structurally known interactions imported from the iPfam and 3did databases and 46,900 domain interactions predicted by four computational methods: domain phylogenetic profiling, domain pair exclusion algorithm correlated mutations and domain interaction prediction in a discriminative way. Additionally predictions are filtered to exclude those domain pairs that are reported as non-interacting by the Negatome database. The DIMA Web site allows to calculate domain interaction networks either for a domain of interest or for entire organisms, and to explore them interactively using the Flash-based Cytoscape Web software.

Final Technical Report - Integrated Hydrogeophysical and Hydrogeologic Driven Parameter Upscaling for Dual-Domain Transport Modeling

Energy Technology Data Exchange (ETDEWEB)

Shafer, John M

2012-11-05

The three major components of this research were: 1. Application of minimally invasive, cost effective hydrogeophysical techniques (surface and borehole), to generate fine scale (~1m or less) 3D estimates of subsurface heterogeneity. Heterogeneity is defined as spatial variability in hydraulic conductivity and/or hydrolithologic zones. 2. Integration of the fine scale characterization of hydrogeologic parameters with the hydrogeologic facies to upscale the finer scale assessment of heterogeneity to field scale. 3. Determination of the relationship between dual-domain parameters and practical characterization data.

Parallel, explicit, and PWTD-enhanced time domain volume integral equation solver

KAUST Repository

Liu, Yang

2013-07-01

Time domain volume integral equations (TDVIEs) are useful for analyzing transient scattering from inhomogeneous dielectric objects in applications as varied as photonics, optoelectronics, and bioelectromagnetics. TDVIEs typically are solved by implicit marching-on-in-time (MOT) schemes [N. T. Gres et al., Radio Sci., 36, 379-386, 2001], requiring the solution of a system of equations at each and every time step. To reduce the computational cost associated with such schemes, [A. Al-Jarro et al., IEEE Trans. Antennas Propagat., 60, 5203-5215, 2012] introduced an explicit MOT-TDVIE method that uses a predictor-corrector technique to stably update field values throughout the scatterer. By leveraging memory-efficient nodal spatial discretization and scalable parallelization schemes [A. Al-Jarro et al., in 28th Int. Rev. Progress Appl. Computat. Electromagn., 2012], this solver has been successfully applied to the analysis of scattering phenomena involving 0.5 million spatial unknowns. © 2013 IEEE.

Generalized vector calculus on convex domain

Science.gov (United States)

Agrawal, Om P.; Xu, Yufeng

2015-06-01

In this paper, we apply recently proposed generalized integral and differential operators to develop generalized vector calculus and generalized variational calculus for problems defined over a convex domain. In particular, we present some generalization of Green's and Gauss divergence theorems involving some new operators, and apply these theorems to generalized variational calculus. For fractional power kernels, the formulation leads to fractional vector calculus and fractional variational calculus for problems defined over a convex domain. In special cases, when certain parameters take integer values, we obtain formulations for integer order problems. Two examples are presented to demonstrate applications of the generalized variational calculus which utilize the generalized vector calculus developed in the paper. The first example leads to a generalized partial differential equation and the second example leads to a generalized eigenvalue problem, both in two dimensional convex domains. We solve the generalized partial differential equation by using polynomial approximation. A special case of the second example is a generalized isoperimetric problem. We find an approximate solution to this problem. Many physical problems containing integer order integrals and derivatives are defined over arbitrary domains. We speculate that future problems containing fractional and generalized integrals and derivatives in fractional mechanics will be defined over arbitrary domains, and therefore, a general variational calculus incorporating a general vector calculus will be needed for these problems. This research is our first attempt in that direction.

A Domain Specific Embedded Language in C++ for Automatic Differentiation, Projection, Integration and Variational Formulations

Directory of Open Access Journals (Sweden)

Christophe Prud'homme

2006-01-01

Full Text Available In this article, we present a domain specific embedded language in C++ that can be used in various contexts such as numerical projection onto a functional space, numerical integration, variational formulations and automatic differentiation. Albeit these tools operate in different ways, the language overcomes this difficulty by decoupling expression constructions from evaluation. The language is implemented using expression templates and meta-programming techniques and uses various Boost libraries. The language is exercised on a number of non-trivial examples and a benchmark presents the performance behavior on a few test problems.

Memory and Comprehension for Health Information among Older Adults: Distinguishing the Effects of Domain-General and Domain-Specific Knowledge

Science.gov (United States)

Chin, Jessie; Payne, Brennan; Gao, Xuefei; Conner-Garcia, Thembi; Graumlich, James F.; Murray, Michael D.; Morrow, Daniel G.; Stine-Morrow, Elizabeth A.L.

2014-01-01

While there is evidence that knowledge influences understanding of health information, less is known about the processing mechanisms underlying this effect and its impact on memory. We used the moving window paradigm to examine how older adults varying in domain-general crystallized ability (verbal ability) and health knowledge allocate attention to understand health and domain-general texts. Participants (n=107, aged 60 to 88 yrs) read and recalled single sentences about hypertension and about non-health topics. Mixed-effects modeling of word-by-word reading times suggested that domain-general crystallized ability increased conceptual integration regardless of text domain, while health knowledge selectively increased resource allocation to conceptual integration at clause boundaries in health texts. These patterns of attentional allocation were related to subsequent recall performance. Although older adults with lower levels of crystallized ability were less likely to engage in integrative processing, when they did, this strategy had a compensatory effect in improving recall. These findings suggest that semantic integration during reading is an important comprehension process that supports the construction of the memory representation and is engendered by knowledge. Implications of the findings for theories of text processing and memory as well as for designing patient education materials are discussed. PMID:24787361

Memory and comprehension for health information among older adults: distinguishing the effects of domain-general and domain-specific knowledge.

Science.gov (United States)

Chin, Jessie; Payne, Brennan; Gao, Xuefei; Conner-Garcia, Thembi; Graumlich, James F; Murray, Michael D; Morrow, Daniel G; Stine-Morrow, Elizabeth A L

2015-01-01

While there is evidence that knowledge influences understanding of health information, less is known about the processing mechanisms underlying this effect and its impact on memory. We used the moving window paradigm to examine how older adults varying in domain-general crystallised ability (verbal ability) and health knowledge allocate attention to understand health and domain-general texts. Participants (n = 107, age: 60-88 years) read and recalled single sentences about hypertension and about non-health topics. Mixed-effects modelling of word-by-word reading times suggested that domain-general crystallised ability increased conceptual integration regardless of text domain, while health knowledge selectively increased resource allocation to conceptual integration at clause boundaries in health texts. These patterns of attentional allocation were related to subsequent recall performance. Although older adults with lower levels of crystallised ability were less likely to engage in integrative processing, when they did, this strategy had a compensatory effect in improving recall. These findings suggest that semantic integration during reading is an important comprehension process that supports the construction of the memory representation and is engendered by knowledge. Implications of the findings for theories of text processing and memory as well as for designing patient education materials are discussed.

Structural and biochemical studies of a fluoroacetyl-CoA-specific thioesterase reveal a molecular basis for fluorine selectivity.

Science.gov (United States)

Weeks, Amy M; Coyle, Scott M; Jinek, Martin; Doudna, Jennifer A; Chang, Michelle C Y

2010-11-02

We have initiated a broad-based program aimed at understanding the molecular basis of fluorine specificity in enzymatic systems, and in this context, we report crystallographic and biochemical studies on a fluoroacetyl-coenzyme A (CoA) specific thioesterase (FlK) from Streptomyces cattleya. Our data establish that FlK is competent to protect its host from fluoroacetate toxicity in vivo and demonstrate a 10(6)-fold discrimination between fluoroacetyl-CoA (k(cat)/K(M) = 5 × 10⁷ M⁻¹ s⁻¹) and acetyl-CoA (k(cat)/K(M) = 30 M⁻¹ s⁻¹) based on a single fluorine substitution that originates from differences in both substrate reactivity and binding. We show that Thr 42, Glu 50, and His 76 are key catalytic residues and identify several factors that influence substrate selectivity. We propose that FlK minimizes interaction with the thioester carbonyl, leading to selection against acetyl-CoA binding that can be recovered in part by new C═O interactions in the T42S and T42C mutants. We hypothesize that the loss of these interactions is compensated by the entropic driving force for fluorinated substrate binding in a hydrophobic binding pocket created by a lid structure, containing Val 23, Leu 26, Phe 33, and Phe 36, that is not found in other structurally characterized members of this superfamily. We further suggest that water plays a critical role in fluorine specificity based on biochemical and structural studies focused on the unique Phe 36 "gate" residue, which functions to exclude water from the active site. Taken together, the findings from these studies offer molecular insights into organofluorine recognition and design of fluorine-specific enzymes.

Apoplastic domains and sub-domains in the shoots of etiolated corn seedlings

Science.gov (United States)

Epel, B. L.; Bandurski, R. S.

1990-01-01

Light Green, an apoplastic probe, was applied to the cut mesocotyl base or to the cut coleoptile apex of etiolated seedlings of Zea mays L. cv. Silver Queen. Probe transport was measured and its tissue distribution determined. In the mesocotyl, there is an apoplastic barrier between cortex and stele. This barrier creates two apoplastic domains which are non-communicating. A kinetic barrier exists between the apoplast of the mesocotyl stele and that of the coleoptile. This kinetic barrier is not absolute and there is limited communication between the apoplasts of the two regions. This kinetic barrier effectively creates two sub-domains. In the coleoptile, there is communication between the apoplast of the vascular strands and that of the surrounding cortical tissue. No apoplastic communication was observed between the coleoptile cortex and the mesocotyl cortex. Thus, the apoplastic space of the coleoptile cortex is a sub-domain of the integrated coleoptile domain and is separate from that of the apoplastic domain of the mesocotyl cortex.

Integral UBL domain proteins: a family of proteasome interacting proteins

DEFF Research Database (Denmark)

Hartmann-Petersen, Rasmus; Gordon, Colin

2004-01-01

The family of ubiquitin-like (UBL) domain proteins (UDPs) comprises a conserved group of proteins involved in a multitude of different cellular activities. However, recent studies on UBL-domain proteins indicate that these proteins appear to share a common property in their ability to interact...

The ICOS Experience: Integration of Multi-disciplinary Data and Beyond Its Domains Into a Network of Networks

Science.gov (United States)

Vermeulen, A. T.; Hellström, M.; Mirzov, O.; Juurola, E.; Lavric, J. V.; Kutsch, W. L.

2016-12-01

ICOS as long-term observational system for the carbon cycle has a long history in Europe, but has only recently been established formally as one of the first European Research Infrastructure Consortia (ERIC). ICOS data will be provided through the ICOS Carbon Portal and data usage will be absolutely unrestricted under the Creative Commons Attribution 4.0 International (CC4.0BY) license. ICOS strives to further integrate its data streams internally across the domains and externally, building on scalable open access tools and open data technologies. Through the ENVRIplus project, led by ICOS, and the EUDAT2020 project, the work on interoperability and scalability is now progressing quickly in the European environmental Research Infrastructures domain. In this presentation we will demonstrate the recent progress in ICOS in implementing the Carbon Portal as the one stop shop for ICOS data.

Explicit solution of the time domain volume integral equation using a stable predictor-corrector scheme

KAUST Repository

Al Jarro, Ahmed

2012-11-01

An explicit marching-on-in-time (MOT) scheme for solving the time domain volume integral equation is presented. The proposed method achieves its stability by employing, at each time step, a corrector scheme, which updates/corrects fields computed by the explicit predictor scheme. The proposedmethod is computationally more efficient when compared to the existing filtering techniques used for the stabilization of explicit MOT schemes. Numerical results presented in this paper demonstrate that the proposed method maintains its stability even when applied to the analysis of electromagnetic wave interactions with electrically large structures meshed using approximately half a million discretization elements.

Explicit solution of the time domain volume integral equation using a stable predictor-corrector scheme

KAUST Repository

Al Jarro, Ahmed; Salem, Mohamed; Bagci, Hakan; Benson, Trevor; Sewell, Phillip D.; Vuković, Ana

2012-01-01

An explicit marching-on-in-time (MOT) scheme for solving the time domain volume integral equation is presented. The proposed method achieves its stability by employing, at each time step, a corrector scheme, which updates/corrects fields computed by the explicit predictor scheme. The proposedmethod is computationally more efficient when compared to the existing filtering techniques used for the stabilization of explicit MOT schemes. Numerical results presented in this paper demonstrate that the proposed method maintains its stability even when applied to the analysis of electromagnetic wave interactions with electrically large structures meshed using approximately half a million discretization elements.

Frequency domain analysis of piping systems under short duration loading

International Nuclear Information System (INIS)

Sachs, K.; Sand, H.; Lockau, J.

1981-01-01

In piping analysis two procedures are used almost exclusively: the modal superposition method for relatively long input time histories (e.g., earthquake) and direct integration of the equations of motion for short input time histories. A third possibility, frequency domain analysis, has only rarely been applied to piping systems to date. This paper suggests the use of frequency domain analysis for specific piping problems for which only direct integration could be used in the past. Direct integration and frequency domain analysis are compared, and it is shown that the frequency domain method is less costly if more than four or five load cases are considered. In addition, this method offers technical advantages, such as more accurate representation of modal damping and greater insight into the structural behavior of the system. (orig.)

A space-time mixed galerkin marching-on-in-time scheme for the time-domain combined field integral equation

KAUST Repository

Beghein, Yves

2013-03-01

The time domain combined field integral equation (TD-CFIE), which is constructed from a weighted sum of the time domain electric and magnetic field integral equations (TD-EFIE and TD-MFIE) for analyzing transient scattering from closed perfect electrically conducting bodies, is free from spurious resonances. The standard marching-on-in-time technique for discretizing the TD-CFIE uses Galerkin and collocation schemes in space and time, respectively. Unfortunately, the standard scheme is theoretically not well understood: stability and convergence have been proven for only one class of space-time Galerkin discretizations. Moreover, existing discretization schemes are nonconforming, i.e., the TD-MFIE contribution is tested with divergence conforming functions instead of curl conforming functions. We therefore introduce a novel space-time mixed Galerkin discretization for the TD-CFIE. A family of temporal basis and testing functions with arbitrary order is introduced. It is explained how the corresponding interactions can be computed efficiently by existing collocation-in-time codes. The spatial mixed discretization is made fully conforming and consistent by leveraging both Rao-Wilton-Glisson and Buffa-Christiansen basis functions and by applying the appropriate bi-orthogonalization procedures. The combination of both techniques is essential when high accuracy over a broad frequency band is required. © 2012 IEEE.

Time-Domain Simulation of RF Couplers

International Nuclear Information System (INIS)

Smithe, David; Carlsson, Johan; Austin, Travis

2009-01-01

We have developed a finite-difference time-domain (FDTD) fluid-like approach to integrated plasma-and-coupler simulation [1], and show how it can be used to model LH and ICRF couplers in the MST and larger tokamaks.[2] This approach permits very accurate 3-D representation of coupler geometry, and easily includes non-axi-symmetry in vessel wall, magnetic equilibrium, and plasma density. The plasma is integrated with the FDTD Maxwell solver in an implicit solve that steps over electron time-scales, and permits tenuous plasma in the coupler itself, without any need to distinguish or interface between different regions of vacuum and/or plasma. The FDTD algorithm is also generalized to incorporate a time-domain sheath potential [3] on metal structures within the simulation, to look for situations where the sheath potential might generate local sputtering opportunities. Benchmarking of the time-domain sheath algorithm has been reported in the references. Finally, the time-domain software [4] permits the use of particles, either as field diagnostic (test particles) or to self-consistently compute plasma current from the applied RF power.

Parallel PWTD-Accelerated Explicit Solution of the Time Domain Electric Field Volume Integral Equation

KAUST Repository

Liu, Yang

2016-03-25

A parallel plane-wave time-domain (PWTD)-accelerated explicit marching-on-in-time (MOT) scheme for solving the time domain electric field volume integral equation (TD-EFVIE) is presented. The proposed scheme leverages pulse functions and Lagrange polynomials to spatially and temporally discretize the electric flux density induced throughout the scatterers, and a finite difference scheme to compute the electric fields from the Hertz electric vector potentials radiated by the flux density. The flux density is explicitly updated during time marching by a predictor-corrector (PC) scheme and the vector potentials are efficiently computed by a scalar PWTD scheme. The memory requirement and computational complexity of the resulting explicit PWTD-PC-EFVIE solver scale as ( log ) s s O N N and ( ) s t O N N , respectively. Here, s N is the number of spatial basis functions and t N is the number of time steps. A scalable parallelization of the proposed MOT scheme on distributed- memory CPU clusters is described. The efficiency, accuracy, and applicability of the resulting (parallelized) PWTD-PC-EFVIE solver are demonstrated via its application to the analysis of transient electromagnetic wave interactions on canonical and real-life scatterers represented with up to 25 million spatial discretization elements.

Parallel PWTD-Accelerated Explicit Solution of the Time Domain Electric Field Volume Integral Equation

KAUST Repository

Liu, Yang; Al-Jarro, Ahmed; Bagci, Hakan; Michielssen, Eric

2016-01-01

A parallel plane-wave time-domain (PWTD)-accelerated explicit marching-on-in-time (MOT) scheme for solving the time domain electric field volume integral equation (TD-EFVIE) is presented. The proposed scheme leverages pulse functions and Lagrange polynomials to spatially and temporally discretize the electric flux density induced throughout the scatterers, and a finite difference scheme to compute the electric fields from the Hertz electric vector potentials radiated by the flux density. The flux density is explicitly updated during time marching by a predictor-corrector (PC) scheme and the vector potentials are efficiently computed by a scalar PWTD scheme. The memory requirement and computational complexity of the resulting explicit PWTD-PC-EFVIE solver scale as ( log ) s s O N N and ( ) s t O N N , respectively. Here, s N is the number of spatial basis functions and t N is the number of time steps. A scalable parallelization of the proposed MOT scheme on distributed- memory CPU clusters is described. The efficiency, accuracy, and applicability of the resulting (parallelized) PWTD-PC-EFVIE solver are demonstrated via its application to the analysis of transient electromagnetic wave interactions on canonical and real-life scatterers represented with up to 25 million spatial discretization elements.

Perspective taking in language: Integrating the spatial and action domains.

Directory of Open Access Journals (Sweden)

Madeleine Edith Louisa Beveridge

2013-09-01

Full Text Available Language is an inherently social behaviour. In this paper, we bring together two research areas that typically occupy distinct sections of the literature: perspective taking in spatial language (whether people represent a scene from their own or a different spatial perspective, and perspective taking in action language (the extent to which they simulate an action as though they were performing that action. First, we note that vocabulary is used inconsistently across the spatial and action domains, and propose a more transparent vocabulary that will allow researchers to integrate action- and spatial-perspective taking. Second, we note that embodied theories of language comprehension often make the narrow assumption that understanding action descriptions involves adopting the perspective of an agent carrying out that action. We argue that comprehenders can adopt embodied action-perspectives other than that of the agent, including those of the patient or an observer. Third, we review evidence showing that perspective taking in spatial language is a flexible process. We argue that the flexibility of spatial-perspective taking provides a means for conversation partners engaged in dialogue to maximise similarity between their situation models. These situation models can then be used as the basis for action language simulations, in which language users adopt a particular action-perspective.

Nonequilibrium spin transport in integrable spin chains: Persistent currents and emergence of magnetic domains

Science.gov (United States)

De Luca, Andrea; Collura, Mario; De Nardis, Jacopo

2017-07-01

We construct exact steady states of unitary nonequilibrium time evolution in the gapless XXZ spin-1/2 chain where integrability preserves ballistic spin transport at long times. We characterize the quasilocal conserved quantities responsible for this feature and introduce a computationally effective way to evaluate their expectation values on generic matrix product initial states. We employ this approach to reproduce the long-time limit of local observables in all quantum quenches which explicitly break particle-hole or time-reversal symmetry. We focus on a class of initial states supporting persistent spin currents and our predictions remarkably agree with numerical simulations at long times. Furthermore, we propose a protocol for this model where interactions, even when antiferromagnetic, are responsible for the unbounded growth of a macroscopic magnetic domain.

Facilitating Inter-Domain Synergies in Ambient Assisted Living Environments.

Science.gov (United States)

Schwartze, Jonas; Schrom, Harald; Wolf, Klaus-Hendrik; Marschollek, Michael

2016-01-01

Current Ambient Assisted Living (AAL) environments lack integration of sensors and actuators of other sub-domains. Creating technical and organizational integration is addressed by the BASIS project (Build Automation by a Scalable and Intelligent System), which aims to build a cross-domain home bus system. The main objective of this paper is to present an overview of design, architecture and state of realization of BASIS by describing the requirements development process, underlying hardware design and software architecture. We built a distributed system of one independent building manager with several redundantly meshed segment controllers, each controlling a bus segment with any number of bus nodes. The software system layer is divided into logical partitions representing each sub-domain. Structured data storage is possible with a special FHIR based home centered data warehouse. The system has been implemented in six apartments running under daily living conditions. BASIS integrates a broad range of sub-domains, which poses challenges to all project partners in terms of a common terminology, and project management methods, but enables development of inter-domain synergies like using the same sensor and actuator hardware for a broad range of services and use cases.

Integral particle reflection coefficient for oblique incidence of photons as universal function in the domain of initial energies up to 300 keV

Directory of Open Access Journals (Sweden)

Ljubenov Vladan L.

2014-01-01

Full Text Available In this paper we present the results of calculations and analyses of the integral particle reflection coefficient of photons for oblique photon incidence on planar targets, in the domain of initial photon energies from 100 keV to 300 keV. The results are based on the Monte Carlo simulations of the photon reflection from water, concrete, aluminum, iron, and copper materials, performed by the MCNP code. It has been observed that the integral particle reflection coefficient as a function of the ratio of total cross-section of photons and effective atomic number of target material shows universal behavior for all the analyzed shielding materials in the selected energy domain. Analytical formulas for different angles of photon incidence have been proposed, which describe the reflection of photons for all the materials and energies analyzed.

A Wavelet-Enhanced PWTD-Accelerated Time-Domain Integral Equation Solver for Analysis of Transient Scattering from Electrically Large Conducting Objects

KAUST Repository

Liu, Yang

2018-02-26

A wavelet-enhanced plane-wave time-domain (PWTD) algorithm for efficiently and accurately solving time-domain surface integral equations (TD-SIEs) on electrically large conducting objects is presented. The proposed scheme reduces the memory requirement and computational cost of the PWTD algorithm by representing the PWTD ray data using local cosine wavelet bases (LCBs) and performing PWTD operations in the wavelet domain. The memory requirement and computational cost of the LCB-enhanced PWTD-accelerated TD-SIE solver, when applied to the analysis of transient scattering from smooth quasi-planar objects with near-normal incident pulses, scale nearly as O(Ns log Ns) and O(Ns 1.5 ), respectively. Here, Ns denotes the number of spatial unknowns. The efficiency and accuracy of the proposed scheme are demonstrated through its applications to the analysis of transient scattering from a 185 wave-length-long NASA almond and a 123-wavelength long Air-bus-A320 model.

AcEST: BP915195 [AcEST

Lifescience Database Archive (English)

Full Text Available -25 tr|O04792|O04792_9ROSI Acyl-ACP thioesterase OS=Garcinia mangost... 119 1e-25 tr|B8BDB0|B8BDB0_ORYSI Put...04793_9ROSI Acyl-ACP thioesterase OS=Garcinia mangost... 117 3e-25 tr|B8LS31|B8LS31_PICSI Putative uncharact...tr|O04792|O04792_9ROSI Acyl-ACP thioesterase OS=Garcinia mangostana GN=FatA1 PE=2 SV=1 Length = 352 Score =

A multi-domain spectral method for time-fractional differential equations

Science.gov (United States)

Chen, Feng; Xu, Qinwu; Hesthaven, Jan S.

2015-07-01

This paper proposes an approach for high-order time integration within a multi-domain setting for time-fractional differential equations. Since the kernel is singular or nearly singular, two main difficulties arise after the domain decomposition: how to properly account for the history/memory part and how to perform the integration accurately. To address these issues, we propose a novel hybrid approach for the numerical integration based on the combination of three-term-recurrence relations of Jacobi polynomials and high-order Gauss quadrature. The different approximations used in the hybrid approach are justified theoretically and through numerical examples. Based on this, we propose a new multi-domain spectral method for high-order accurate time integrations and study its stability properties by identifying the method as a generalized linear method. Numerical experiments confirm hp-convergence for both time-fractional differential equations and time-fractional partial differential equations.

Regional climate model sensitivity to domain size

Science.gov (United States)

Leduc, Martin; Laprise, René

2009-05-01

Regional climate models are increasingly used to add small-scale features that are not present in their lateral boundary conditions (LBC). It is well known that the limited area over which a model is integrated must be large enough to allow the full development of small-scale features. On the other hand, integrations on very large domains have shown important departures from the driving data, unless large scale nudging is applied. The issue of domain size is studied here by using the “perfect model” approach. This method consists first of generating a high-resolution climatic simulation, nicknamed big brother (BB), over a large domain of integration. The next step is to degrade this dataset with a low-pass filter emulating the usual coarse-resolution LBC. The filtered nesting data (FBB) are hence used to drive a set of four simulations (LBs for Little Brothers), with the same model, but on progressively smaller domain sizes. The LB statistics for a climate sample of four winter months are compared with BB over a common region. The time average (stationary) and transient-eddy standard deviation patterns of the LB atmospheric fields generally improve in terms of spatial correlation with the reference (BB) when domain gets smaller. The extraction of the small-scale features by using a spectral filter allows detecting important underestimations of the transient-eddy variability in the vicinity of the inflow boundary, which can penalize the use of small domains (less than 100 × 100 grid points). The permanent “spatial spin-up” corresponds to the characteristic distance that the large-scale flow needs to travel before developing small-scale features. The spin-up distance tends to grow in size at higher levels in the atmosphere.

Regional climate model sensitivity to domain size

Energy Technology Data Exchange (ETDEWEB)

Leduc, Martin [Universite du Quebec a Montreal, Canadian Regional Climate Modelling and Diagnostics (CRCMD) Network, ESCER Centre, Montreal (Canada); UQAM/Ouranos, Montreal, QC (Canada); Laprise, Rene [Universite du Quebec a Montreal, Canadian Regional Climate Modelling and Diagnostics (CRCMD) Network, ESCER Centre, Montreal (Canada)

2009-05-15

Regional climate models are increasingly used to add small-scale features that are not present in their lateral boundary conditions (LBC). It is well known that the limited area over which a model is integrated must be large enough to allow the full development of small-scale features. On the other hand, integrations on very large domains have shown important departures from the driving data, unless large scale nudging is applied. The issue of domain size is studied here by using the ''perfect model'' approach. This method consists first of generating a high-resolution climatic simulation, nicknamed big brother (BB), over a large domain of integration. The next step is to degrade this dataset with a low-pass filter emulating the usual coarse-resolution LBC. The filtered nesting data (FBB) are hence used to drive a set of four simulations (LBs for Little Brothers), with the same model, but on progressively smaller domain sizes. The LB statistics for a climate sample of four winter months are compared with BB over a common region. The time average (stationary) and transient-eddy standard deviation patterns of the LB atmospheric fields generally improve in terms of spatial correlation with the reference (BB) when domain gets smaller. The extraction of the small-scale features by using a spectral filter allows detecting important underestimations of the transient-eddy variability in the vicinity of the inflow boundary, which can penalize the use of small domains (less than 100 x 100 grid points). The permanent ''spatial spin-up'' corresponds to the characteristic distance that the large-scale flow needs to travel before developing small-scale features. The spin-up distance tends to grow in size at higher levels in the atmosphere. (orig.)

Non-destructive evaluation of the hidden voids in integrated circuit packages using terahertz time-domain spectroscopy

International Nuclear Information System (INIS)

Park, Sung-Hyeon; Kim, Hak-Sung; Jang, Jin-Wook

2015-01-01

In this work, a terahertz time-domain spectroscopy (THz-TDS) imaging technique was used as a non-destructive inspection method for detecting voids in integrated circuit (IC) packages. Transmission and reflection modes, with an angle of incidence of 30°, were used to detect voids in IC packages. The locations of the detected voids in the IC packages could be calculated by analyzing THz waveforms. Finally, voids that are positioned at the different interfaces in the IC package samples could be successfully detected and imaged. Therefore, this THz-TDS imaging technique is expected to be a promising technique for non-destructive evaluation of IC packages. (paper)

A difference-equation formalism for the nodal domains of separable billiards

Energy Technology Data Exchange (ETDEWEB)

Manjunath, Naren; Samajdar, Rhine [Indian Institute of Science, Bangalore 560012 (India); Jain, Sudhir R., E-mail: srjain@barc.gov.in [Nuclear Physics Division, Bhabha Atomic Research Centre, Mumbai 400085 (India)

2016-09-15

Recently, the nodal domain counts of planar, integrable billiards with Dirichlet boundary conditions were shown to satisfy certain difference equations in Samajdar and Jain (2014). The exact solutions of these equations give the number of domains explicitly. For complete generality, we demonstrate this novel formulation for three additional separable systems and thus extend the statement to all integrable billiards.

On the internal resonant modes in marching-on-in-time solution of the time domain electric field integral equation

KAUST Repository

Shi, Yifei; Bagci, Hakan; Lu, Mingyu

2013-01-01

Internal resonant modes are always observed in the marching-on-in-time (MOT) solution of the time domain electric field integral equation (EFIE), although 'relaxed initial conditions,' which are enforced at the beginning of time marching, should in theory prevent these spurious modes from appearing. It has been conjectured that, numerical errors built up during time marching establish the necessary initial conditions and induce the internal resonant modes. However, this conjecture has never been proved by systematic numerical experiments. Our numerical results in this communication demonstrate that, the internal resonant modes' amplitudes are indeed dictated by the numerical errors. Additionally, it is shown that in a few cases, the internal resonant modes can be made 'invisible' by significantly suppressing the numerical errors. These tests prove the conjecture that the internal resonant modes are induced by numerical errors when the time domain EFIE is solved by the MOT method. © 2013 IEEE.

On the internal resonant modes in marching-on-in-time solution of the time domain electric field integral equation

KAUST Repository

Shi, Yifei

2013-08-01

Internal resonant modes are always observed in the marching-on-in-time (MOT) solution of the time domain electric field integral equation (EFIE), although \\'relaxed initial conditions,\\' which are enforced at the beginning of time marching, should in theory prevent these spurious modes from appearing. It has been conjectured that, numerical errors built up during time marching establish the necessary initial conditions and induce the internal resonant modes. However, this conjecture has never been proved by systematic numerical experiments. Our numerical results in this communication demonstrate that, the internal resonant modes\\' amplitudes are indeed dictated by the numerical errors. Additionally, it is shown that in a few cases, the internal resonant modes can be made \\'invisible\\' by significantly suppressing the numerical errors. These tests prove the conjecture that the internal resonant modes are induced by numerical errors when the time domain EFIE is solved by the MOT method. © 2013 IEEE.

Integration of domain and resource-based reasoning for real-time control in dynamic environments

Science.gov (United States)

Morgan, Keith; Whitebread, Kenneth R.; Kendus, Michael; Cromarty, Andrew S.

1993-01-01

A real-time software controller that successfully integrates domain-based and resource-based control reasoning to perform task execution in a dynamically changing environment is described. The design of the controller is based on the concept of partitioning the process to be controlled into a set of tasks, each of which achieves some process goal. It is assumed that, in general, there are multiple ways (tasks) to achieve a goal. The controller dynamically determines current goals and their current criticality, choosing and scheduling tasks to achieve those goals in the time available. It incorporates rule-based goal reasoning, a TMS-based criticality propagation mechanism, and a real-time scheduler. The controller has been used to build a knowledge-based situation assessment system that formed a major component of a real-time, distributed, cooperative problem solving system built under DARPA contract. It is also being employed in other applications now in progress.

The SH2 Domain Interaction Landscape

Directory of Open Access Journals (Sweden)

Michele Tinti

2013-04-01

Full Text Available Members of the SH2 domain family modulate signal transduction by binding to short peptides containing phosphorylated tyrosines. Each domain displays a distinct preference for the sequence context of the phosphorylated residue. We have developed a high-density peptide chip technology that allows for probing of the affinity of most SH2 domains for a large fraction of the entire complement of tyrosine phosphopeptides in the human proteome. Using this technique, we have experimentally identified thousands of putative SH2-peptide interactions for more than 70 different SH2 domains. By integrating this rich data set with orthogonal context-specific information, we have assembled an SH2-mediated probabilistic interaction network, which we make available as a community resource in the PepspotDB database. A predicted dynamic interaction between the SH2 domains of the tyrosine phosphatase SHP2 and the phosphorylated tyrosine in the extracellular signal-regulated kinase activation loop was validated by experiments in living cells.

Design Considerations for Integration of Terahertz Time-Domain Spectroscopy in Microfluidic Platforms

Directory of Open Access Journals (Sweden)

Rasha Al-Hujazy

2018-03-01

Full Text Available Microfluidic platforms have received much attention in recent years. In particular, there is interest in combining spectroscopy with microfluidic platforms. This work investigates the integration of microfluidic platforms and terahertz time-domain spectroscopy (THz-TDS systems. A semiclassical computational model is used to simulate the emission of THz radiation from a GaAs photoconductive THz emitter. This model incorporates white noise with increasing noise amplitude (corresponding to decreasing dynamic range values. White noise is selected over other noise due to its contributions in THz-TDS systems. The results from this semiclassical computational model, in combination with defined sample thicknesses, can provide the maximum measurable absorption coefficient for a microfluidic-based THz-TDS system. The maximum measurable frequencies for such systems can be extracted through the relationship between the maximum measurable absorption coefficient and the absorption coefficient for representative biofluids. The sample thickness of the microfluidic platform and the dynamic range of the THz-TDS system play a role in defining the maximum measurable frequency for microfluidic-based THz-TDS systems. The results of this work serve as a design tool for the development of such systems.

Intrasurgical Human Retinal Imaging With Manual Instrument Tracking Using a Microscope-Integrated Spectral-Domain Optical Coherence Tomography Device.

Science.gov (United States)

Hahn, Paul; Carrasco-Zevallos, Oscar; Cunefare, David; Migacz, Justin; Farsiu, Sina; Izatt, Joseph A; Toth, Cynthia A

2015-07-01

To characterize the first in-human intraoperative imaging using a custom prototype spectral-domain microscope-integrated optical coherence tomography (MIOCT) device during vitreoretinal surgery with instruments in the eye. Under institutional review board approval for a prospective intraoperative study, MIOCT images were obtained at surgical pauses with instruments held static in the vitreous cavity and then concurrently with surgical maneuvers. Postoperatively, MIOCT images obtained at surgical pauses were compared with images obtained with a high-resolution handheld spectral-domain OCT (HHOCT) system with objective endpoints, including acquisition of images acceptable for analysis and identification of predefined macular morphologic or pathologic features. Human MIOCT images were successfully obtained before incision and during pauses in surgical maneuvers. MIOCT imaging confirmed preoperative diagnoses, such as epiretinal membrane, full-thickness macular hole, and vitreomacular traction and demonstrated successful achievement of surgical goals. MIOCT and HHOCT images obtained at surgical pauses in two cohorts of five patients were comparable with greater than or equal to 80% correlation in 80% of patients. Real-time video-imaging concurrent with surgical manipulations enabled, for the first time using this device, visualization of dynamic instrument-retina interaction with targeted OCT tracking. MIOCT is successful for imaging at surgical pauses and for real-time image guidance with implementation of targeted OCT tracking. Even faster acquisition speeds are currently being developed with incorporation of a swept-source MIOCT engine. Further refinements and investigations will be directed toward continued integration for real-time volumetric imaging of surgical maneuvers. Ongoing development of seamless MIOCT systems will likely transform surgical visualization, approaches, and decision-making.

Interoperable cross-domain semantic and geospatial framework for automatic change detection

Science.gov (United States)

Kuo, Chiao-Ling; Hong, Jung-Hong

2016-01-01

With the increasingly diverse types of geospatial data established over the last few decades, semantic interoperability in integrated applications has attracted much interest in the field of Geographic Information System (GIS). This paper proposes a new strategy and framework to process cross-domain geodata at the semantic level. This framework leverages the semantic equivalence of concepts between domains through bridge ontology and facilitates the integrated use of different domain data, which has been long considered as an essential superiority of GIS, but is impeded by the lack of understanding about the semantics implicitly hidden in the data. We choose the task of change detection to demonstrate how the introduction of ontology concept can effectively make the integration possible. We analyze the common properties of geodata and change detection factors, then construct rules and summarize possible change scenario for making final decisions. The use of topographic map data to detect changes in land use shows promising success, as far as the improvement of efficiency and level of automation is concerned. We believe the ontology-oriented approach will enable a new way for data integration across different domains from the perspective of semantic interoperability, and even open a new dimensionality for the future GIS.

A Stable Marching on-in-time Scheme for Solving the Time Domain Electric Field Volume Integral Equation on High-contrast Scatterers

KAUST Repository

Sayed, Sadeed Bin

2015-05-05

A time domain electric field volume integral equation (TD-EFVIE) solver is proposed for characterizing transient electromagnetic wave interactions on high-contrast dielectric scatterers. The TD-EFVIE is discretized using the Schaubert- Wilton-Glisson (SWG) and approximate prolate spherical wave (APSW) functions in space and time, respectively. The resulting system of equations can not be solved by a straightforward application of the marching on-in-time (MOT) scheme since the two-sided APSW interpolation functions require the knowledge of unknown “future” field samples during time marching. Causality of the MOT scheme is restored using an extrapolation technique that predicts the future samples from known “past” ones. Unlike the extrapolation techniques developed for MOT schemes that are used in solving time domain surface integral equations, this scheme trains the extrapolation coefficients using samples of exponentials with exponents on the complex frequency plane. This increases the stability of the MOT-TD-EFVIE solver significantly, since the temporal behavior of decaying and oscillating electromagnetic modes induced inside the scatterers is very accurately taken into account by this new extrapolation scheme. Numerical results demonstrate that the proposed MOT solver maintains its stability even when applied to analyzing wave interactions on high-contrast scatterers.

A Stable Marching on-in-time Scheme for Solving the Time Domain Electric Field Volume Integral Equation on High-contrast Scatterers

KAUST Repository

Sayed, Sadeed Bin; Ulku, Huseyin; Bagci, Hakan

2015-01-01

A time domain electric field volume integral equation (TD-EFVIE) solver is proposed for characterizing transient electromagnetic wave interactions on high-contrast dielectric scatterers. The TD-EFVIE is discretized using the Schaubert- Wilton-Glisson (SWG) and approximate prolate spherical wave (APSW) functions in space and time, respectively. The resulting system of equations can not be solved by a straightforward application of the marching on-in-time (MOT) scheme since the two-sided APSW interpolation functions require the knowledge of unknown “future” field samples during time marching. Causality of the MOT scheme is restored using an extrapolation technique that predicts the future samples from known “past” ones. Unlike the extrapolation techniques developed for MOT schemes that are used in solving time domain surface integral equations, this scheme trains the extrapolation coefficients using samples of exponentials with exponents on the complex frequency plane. This increases the stability of the MOT-TD-EFVIE solver significantly, since the temporal behavior of decaying and oscillating electromagnetic modes induced inside the scatterers is very accurately taken into account by this new extrapolation scheme. Numerical results demonstrate that the proposed MOT solver maintains its stability even when applied to analyzing wave interactions on high-contrast scatterers.

Integral consideration of integrated management systems

International Nuclear Information System (INIS)

Frauenknecht, Stefan; Schmitz, Hans

2010-01-01

Aim of the project for the NPPs Kruemmel and Brunsbuettel (Vattenfall) is the integral view of the business process as basis for the implementation and operation of management systems in the domains quality, safety and environment. The authors describe the integral view of the business processes in the frame of integrated management systems with the focus nuclear safety, lessons learned in the past, the concept of a process-based controlling system and experiences from the practical realization.

Prediction of Cancer Proteins by Integrating Protein Interaction, Domain Frequency, and Domain Interaction Data Using Machine Learning Algorithms

Directory of Open Access Journals (Sweden)

Chien-Hung Huang

2015-01-01

Full Text Available Many proteins are known to be associated with cancer diseases. It is quite often that their precise functional role in disease pathogenesis remains unclear. A strategy to gain a better understanding of the function of these proteins is to make use of a combination of different aspects of proteomics data types. In this study, we extended Aragues’s method by employing the protein-protein interaction (PPI data, domain-domain interaction (DDI data, weighted domain frequency score (DFS, and cancer linker degree (CLD data to predict cancer proteins. Performances were benchmarked based on three kinds of experiments as follows: (I using individual algorithm, (II combining algorithms, and (III combining the same classification types of algorithms. When compared with Aragues’s method, our proposed methods, that is, machine learning algorithm and voting with the majority, are significantly superior in all seven performance measures. We demonstrated the accuracy of the proposed method on two independent datasets. The best algorithm can achieve a hit ratio of 89.4% and 72.8% for lung cancer dataset and lung cancer microarray study, respectively. It is anticipated that the current research could help understand disease mechanisms and diagnosis.

An integrated domain specific language for post-processing and visualizing electrophysiological signals in Java.

Science.gov (United States)

Strasser, T; Peters, T; Jagle, H; Zrenner, E; Wilke, R

2010-01-01

Electrophysiology of vision - especially the electroretinogram (ERG) - is used as a non-invasive way for functional testing of the visual system. The ERG is a combined electrical response generated by neural and non-neuronal cells in the retina in response to light stimulation. This response can be recorded and used for diagnosis of numerous disorders. For both clinical practice and clinical trials it is important to process those signals in an accurate and fast way and to provide the results as structured, consistent reports. Therefore, we developed a freely available and open-source framework in Java (http://www.eye.uni-tuebingen.de/project/idsI4sigproc). The framework is focused on an easy integration with existing applications. By leveraging well-established software patterns like pipes-and-filters and fluent interfaces as well as by designing the application programming interfaces (API) as an integrated domain specific language (DSL) the overall framework provides a smooth learning curve. Additionally, it already contains several processing methods and visualization features and can be extended easily by implementing the provided interfaces. In this way, not only can new processing methods be added but the framework can also be adopted for other areas of signal processing. This article describes in detail the structure and implementation of the framework and demonstrate its application through the software package used in clinical practice and clinical trials at the University Eye Hospital Tuebingen one of the largest departments in the field of visual electrophysiology in Europe.

The SH2 domain interaction landscape.

Science.gov (United States)

Tinti, Michele; Kiemer, Lars; Costa, Stefano; Miller, Martin L; Sacco, Francesca; Olsen, Jesper V; Carducci, Martina; Paoluzi, Serena; Langone, Francesca; Workman, Christopher T; Blom, Nikolaj; Machida, Kazuya; Thompson, Christopher M; Schutkowski, Mike; Brunak, Søren; Mann, Matthias; Mayer, Bruce J; Castagnoli, Luisa; Cesareni, Gianni

2013-04-25

Members of the SH2 domain family modulate signal transduction by binding to short peptides containing phosphorylated tyrosines. Each domain displays a distinct preference for the sequence context of the phosphorylated residue. We have developed a high-density peptide chip technology that allows for probing of the affinity of most SH2 domains for a large fraction of the entire complement of tyrosine phosphopeptides in the human proteome. Using this technique, we have experimentally identified thousands of putative SH2-peptide interactions for more than 70 different SH2 domains. By integrating this rich data set with orthogonal context-specific information, we have assembled an SH2-mediated probabilistic interaction network, which we make available as a community resource in the PepspotDB database. A predicted dynamic interaction between the SH2 domains of the tyrosine phosphatase SHP2 and the phosphorylated tyrosine in the extracellular signal-regulated kinase activation loop was validated by experiments in living cells. Copyright © 2013 The Authors. Published by Elsevier Inc. All rights reserved.

Marching on-in-time solution of the time domain magnetic field integral equation using a predictor-corrector scheme

KAUST Repository

Ulku, Huseyin Arda; Bagci, Hakan; Michielssen, Eric

2013-01-01

An explicit marching on-in-time (MOT) scheme for solving the time-domain magnetic field integral equation (TD-MFIE) is presented. The proposed MOT-TD-MFIE solver uses Rao-Wilton-Glisson basis functions for spatial discretization and a PE(CE)m-type linear multistep method for time marching. Unlike previous explicit MOT-TD-MFIE solvers, the time step size can be chosen as large as that of the implicit MOT-TD-MFIE solvers without adversely affecting accuracy or stability. An algebraic stability analysis demonstrates the stability of the proposed explicit solver; its accuracy and efficiency are established via numerical examples. © 1963-2012 IEEE.

Marching on-in-time solution of the time domain magnetic field integral equation using a predictor-corrector scheme

KAUST Repository

Ulku, Huseyin Arda

2013-08-01

An explicit marching on-in-time (MOT) scheme for solving the time-domain magnetic field integral equation (TD-MFIE) is presented. The proposed MOT-TD-MFIE solver uses Rao-Wilton-Glisson basis functions for spatial discretization and a PE(CE)m-type linear multistep method for time marching. Unlike previous explicit MOT-TD-MFIE solvers, the time step size can be chosen as large as that of the implicit MOT-TD-MFIE solvers without adversely affecting accuracy or stability. An algebraic stability analysis demonstrates the stability of the proposed explicit solver; its accuracy and efficiency are established via numerical examples. © 1963-2012 IEEE.

The DIMA web resource--exploring the protein domain network.

Science.gov (United States)

Pagel, Philipp; Oesterheld, Matthias; Stümpflen, Volker; Frishman, Dmitrij

2006-04-15

Conserved domains represent essential building blocks of most known proteins. Owing to their role as modular components carrying out specific functions they form a network based both on functional relations and direct physical interactions. We have previously shown that domain interaction networks provide substantially novel information with respect to networks built on full-length protein chains. In this work we present a comprehensive web resource for exploring the Domain Interaction MAp (DIMA), interactively. The tool aims at integration of multiple data sources and prediction techniques, two of which have been implemented so far: domain phylogenetic profiling and experimentally demonstrated domain contacts from known three-dimensional structures. A powerful yet simple user interface enables the user to compute, visualize, navigate and download domain networks based on specific search criteria. http://mips.gsf.de/genre/proj/dima

Rascal: A domain specific language for source code analysis and manipulation

NARCIS (Netherlands)

P. Klint (Paul); T. van der Storm (Tijs); J.J. Vinju (Jurgen); A. Walenstein; S. Schuppe

2009-01-01

htmlabstractMany automated software engineering tools require tight integration of techniques for source code analysis and manipulation. State-of-the-art tools exist for both, but the domains have remained notoriously separate because different computational paradigms fit each domain best. This

RASCAL : a domain specific language for source code analysis and manipulationa

NARCIS (Netherlands)

Klint, P.; Storm, van der T.; Vinju, J.J.

2009-01-01

Many automated software engineering tools require tight integration of techniques for source code analysis and manipulation. State-of-the-art tools exist for both, but the domains have remained notoriously separate because different computational paradigms fit each domain best. This impedance

CARDS: A blueprint and environment for domain-specific software reuse

Science.gov (United States)

Wallnau, Kurt C.; Solderitsch, Anne Costa; Smotherman, Catherine

1992-01-01

CARDS (Central Archive for Reusable Defense Software) exploits advances in domain analysis and domain modeling to identify, specify, develop, archive, retrieve, understand, and reuse domain-specific software components. An important element of CARDS is to provide visibility into the domain model artifacts produced by, and services provided by, commercial computer-aided software engineering (CASE) technology. The use of commercial CASE technology is important to provide rich, robust support for the varied roles involved in a reuse process. We refer to this kind of use of knowledge representation systems as supporting 'knowledge-based integration.'

Ontology for Semantic Data Integration in the Domain of IT Benchmarking.

Science.gov (United States)

Pfaff, Matthias; Neubig, Stefan; Krcmar, Helmut

2018-01-01

A domain-specific ontology for IT benchmarking has been developed to bridge the gap between a systematic characterization of IT services and their data-based valuation. Since information is generally collected during a benchmark exercise using questionnaires on a broad range of topics, such as employee costs, software licensing costs, and quantities of hardware, it is commonly stored as natural language text; thus, this information is stored in an intrinsically unstructured form. Although these data form the basis for identifying potentials for IT cost reductions, neither a uniform description of any measured parameters nor the relationship between such parameters exists. Hence, this work proposes an ontology for the domain of IT benchmarking, available at https://w3id.org/bmontology. The design of this ontology is based on requirements mainly elicited from a domain analysis, which considers analyzing documents and interviews with representatives from Small- and Medium-Sized Enterprises and Information and Communications Technology companies over the last eight years. The development of the ontology and its main concepts is described in detail (i.e., the conceptualization of benchmarking events, questionnaires, IT services, indicators and their values) together with its alignment with the DOLCE-UltraLite foundational ontology.

Nuclear trafficking of the HIV-1 pre-integration complex depends on the ADAM10 intracellular domain

International Nuclear Information System (INIS)

Endsley, Mark A.; Somasunderam, Anoma D.; Li, Guangyu; Oezguen, Numan; Thiviyanathan, Varatharasa; Murray, James L.; Rubin, Donald H.; Hodge, Thomas W.

2014-01-01

Previously, we showed that ADAM10 is necessary for HIV-1 replication in primary human macrophages and immortalized cell lines. Silencing ADAM10 expression interrupted the HIV-1 life cycle prior to nuclear translocation of viral cDNA. Furthermore, our data indicated that HIV-1 replication depends on the expression of ADAM15 and γ-secretase, which proteolytically processes ADAM10. Silencing ADAM15 or γ-secretase expression inhibits HIV-1 replication between reverse transcription and nuclear entry. Here, we show that ADAM10 expression also supports replication in CD4 + T lymphocytes. The intracellular domain (ICD) of ADAM10 associates with the HIV-1 pre-integration complex (PIC) in the cytoplasm and immunoprecipitates and co-localizes with HIV-1 integrase, a key component of PIC. Taken together, our data support a model whereby ADAM15/γ-secretase processing of ADAM10 releases the ICD, which then incorporates into HIV-1 PIC to facilitate nuclear trafficking. Thus, these studies suggest ADAM10 as a novel therapeutic target for inhibiting HIV-1 prior to nuclear entry. - Highlights: • Nuclear trafficking of the HIV-1 pre-integration complex depends on ADAM10. • ADAM10 associates with HIV-1 integrase in the pre-integration complex. • HIV-1 replication depends on the expression of ADAM15 and γ-secretase. • Silencing ADAM15 or γ-secretase expression inhibits nuclear import of viral cDNA. • ADAM10 is important for HIV-1 replication in human macrophages and CD4 + T lymphocytes

Nuclear trafficking of the HIV-1 pre-integration complex depends on the ADAM10 intracellular domain

Energy Technology Data Exchange (ETDEWEB)

Endsley, Mark A., E-mail: maendsle@utmb.edu [Department Internal Medicine, Division of Infectious Diseases, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555 (United States); Somasunderam, Anoma D., E-mail: asomasun@utmb.edu [Department Internal Medicine, Division of Infectious Diseases, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555 (United States); Li, Guangyu, E-mail: LIG001@mail.etsu.edu [Department of Internal Medicine, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614 (United States); Oezguen, Numan, E-mail: numan.oezguen@bcm.edu [Department of Pathology and Immunology, Microbiome Center, Texas Children' s Hospital, Houston, TX 77030 (United States); Thiviyanathan, Varatharasa, E-mail: Varatharasa.Thiviyanathan@uth.tmc.edu [Institute of Molecular Medicine, University of Texas Health Science Center, Houston, TX 77030 (United States); Murray, James L., E-mail: jmurray100@yahoo.com [GeneTAG Technology, Inc., 3155 Northwoods Place, Norcross, GA 30071 (United States); Rubin, Donald H., E-mail: don.h.rubin@vanderbilt.edu [Research Medicine, VA Tennessee Valley Healthcare System, 1310 24th Ave. South, Nashville, TN 37212 (United States); Departments of Medicine, Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, 1161 21st Ave South, Nashville, TN 37232 (United States); Hodge, Thomas W., E-mail: twhodge3@gmail.com [Pre-clinical and Antiviral Research, Tamir Biotechnology, Inc., 12625 High Bluff Dr., Suite 113, San Diego, CA 92130 (United States); and others

2014-04-15

Previously, we showed that ADAM10 is necessary for HIV-1 replication in primary human macrophages and immortalized cell lines. Silencing ADAM10 expression interrupted the HIV-1 life cycle prior to nuclear translocation of viral cDNA. Furthermore, our data indicated that HIV-1 replication depends on the expression of ADAM15 and γ-secretase, which proteolytically processes ADAM10. Silencing ADAM15 or γ-secretase expression inhibits HIV-1 replication between reverse transcription and nuclear entry. Here, we show that ADAM10 expression also supports replication in CD4{sup +} T lymphocytes. The intracellular domain (ICD) of ADAM10 associates with the HIV-1 pre-integration complex (PIC) in the cytoplasm and immunoprecipitates and co-localizes with HIV-1 integrase, a key component of PIC. Taken together, our data support a model whereby ADAM15/γ-secretase processing of ADAM10 releases the ICD, which then incorporates into HIV-1 PIC to facilitate nuclear trafficking. Thus, these studies suggest ADAM10 as a novel therapeutic target for inhibiting HIV-1 prior to nuclear entry. - Highlights: • Nuclear trafficking of the HIV-1 pre-integration complex depends on ADAM10. • ADAM10 associates with HIV-1 integrase in the pre-integration complex. • HIV-1 replication depends on the expression of ADAM15 and γ-secretase. • Silencing ADAM15 or γ-secretase expression inhibits nuclear import of viral cDNA. • ADAM10 is important for HIV-1 replication in human macrophages and CD4{sup +} T lymphocytes.

Indicators and Measurement Tools for Health Systems Integration: A Knowledge Synthesis

Directory of Open Access Journals (Sweden)

Esther Suter

2017-11-01

Full Text Available Background: Despite far reaching support for integrated care, conceptualizing and measuring integrated care remains challenging. This knowledge synthesis aimed to identify indicator domains and tools to measure progress towards integrated care. Methods: We used an established framework and a Delphi survey with integration experts to identify relevant measurement domains. For each domain, we searched and reviewed the literature for relevant tools. Findings: From 7,133 abstracts, we retrieved 114 unique tools. We found many quality tools to measure care coordination, patient engagement and team effectiveness/performance. In contrast, there were few tools in the domains of performance measurement and information systems, alignment of organizational goals and resource allocation. The search yielded 12 tools that measure overall integration or three or more indicator domains. Discussion: Our findings highlight a continued gap in tools to measure foundational components that support integrated care. In the absence of such targeted tools, “overall integration” tools may be useful for a broad assessment of the overall state of a system. Conclusions: Continued progress towards integrated care depends on our ability to evaluate the success of strategies across different levels and context. This study has identified 114 tools that measure integrated care across 16 domains, supporting efforts towards a unified measurement framework.

Indicators and Measurement Tools for Health Systems Integration: A Knowledge Synthesis

Science.gov (United States)

Oelke, Nelly D.; da Silva Lima, Maria Alice Dias; Stiphout, Michelle; Janke, Robert; Witt, Regina Rigatto; Van Vliet-Brown, Cheryl; Schill, Kaela; Rostami, Mahnoush; Hepp, Shelanne; Birney, Arden; Al-Roubaiai, Fatima; Marques, Giselda Quintana

2017-01-01

Background: Despite far reaching support for integrated care, conceptualizing and measuring integrated care remains challenging. This knowledge synthesis aimed to identify indicator domains and tools to measure progress towards integrated care. Methods: We used an established framework and a Delphi survey with integration experts to identify relevant measurement domains. For each domain, we searched and reviewed the literature for relevant tools. Findings: From 7,133 abstracts, we retrieved 114 unique tools. We found many quality tools to measure care coordination, patient engagement and team effectiveness/performance. In contrast, there were few tools in the domains of performance measurement and information systems, alignment of organizational goals and resource allocation. The search yielded 12 tools that measure overall integration or three or more indicator domains. Discussion: Our findings highlight a continued gap in tools to measure foundational components that support integrated care. In the absence of such targeted tools, “overall integration” tools may be useful for a broad assessment of the overall state of a system. Conclusions: Continued progress towards integrated care depends on our ability to evaluate the success of strategies across different levels and context. This study has identified 114 tools that measure integrated care across 16 domains, supporting efforts towards a unified measurement framework. PMID:29588637

Domains I and IV of annexin A2 affect the formation and integrity of in vitro capillary-like networks.

Directory of Open Access Journals (Sweden)

Aase M Raddum

Full Text Available Annexin A2 (AnxA2 is a widely expressed multifunctional protein found in different cellular compartments. In spite of lacking a hydrophobic signal peptide, AnxA2 is found at the cell surface of endothelial cells, indicative of a role in angiogenesis. Increased extracellular levels of AnxA2 in tumours correlate with neoangiogenesis, metastasis and poor prognosis. We hypothesised that extracellular AnxA2 may contribute to angiogenesis by affecting endothelial cell-cell interactions and motility. To address this question, we studied the effect of heterotetrameric and monomeric forms of AnxA2, as well as its two soluble domains on the formation and maintenance of capillary-like structures by using an in vitro co-culture system consisting of endothelial and smooth muscle cells. In particular, addition of purified domains I and IV of AnxA2 potently inhibited the vascular endothelial growth factor (VEGF-dependent formation of the capillary-like networks in a dose-dependent manner. In addition, these AnxA2 domains disrupted endothelial cell-cell contacts in preformed capillary-like networks, resulting in the internalisation of vascular endothelial (VE-cadherin and the formation of VE-cadherin-containing filopodia-like structures between the endothelial cells, suggesting increased cell motility. Addition of monoclonal AnxA2 antibodies, in particular against Tyr23 phosphorylated AnxA2, also strongly inhibited network formation in the co-culture system. These results suggest that extracellular AnxA2, most likely in its Tyr phosphorylated form, plays a pivotal role in angiogenesis. The exogenously added AnxA2 domains most likely mediate their effects by competing with endogenous AnxA2 for extracellular factors necessary for the initiation and maintenance of angiogenesis, such as those involved in the formation/integrity of cell-cell contacts.

Dynamics of domain wall driven by spin-transfer torque

International Nuclear Information System (INIS)

Chureemart, P.; Evans, R. F. L.; Chantrell, R. W.

2011-01-01

Spin-torque switching of magnetic devices offers new technological possibilities for data storage and integrated circuits. We have investigated domain-wall motion in a ferromagnetic thin film driven by a spin-polarized current using an atomistic spin model with a modified Landau-Lifshitz-Gilbert equation including the effect of the spin-transfer torque. The presence of the spin-transfer torque is shown to create an out-of-plane domain wall, in contrast to the external-field-driven case where an in-plane wall is found. We have investigated the effect of the spin torque on domain-wall displacement, domain-wall velocity, and domain-wall width, as well as the equilibration time in the presence of the spin-transfer torque. We have shown that the minimum spin-current density, regarded as the critical value for domain-wall motion, decreases with increasing temperature.

Loop integration results using numerical extrapolation for a non-scalar integral

International Nuclear Information System (INIS)

Doncker, E. de; Shimizu, Y.; Fujimoto, J.; Yuasa, F.; Kaugars, K.; Cucos, L.; Van Voorst, J.

2004-01-01

Loop integration results have been obtained using numerical integration and extrapolation. An extrapolation to the limit is performed with respect to a parameter in the integrand which tends to zero. Results are given for a non-scalar four-point diagram. Extensions to accommodate loop integration by existing integration packages are also discussed. These include: using previously generated partitions of the domain and roundoff error guards

ViSlang: A system for interpreted domain-specific languages for scientific visualization

KAUST Repository

Rautek, Peter; Bruckner, Stefan; Grö ller, Meister Eduard; Hadwiger, Markus

2014-01-01

-level interface). In this paper we present a system that integrates domain-specific languages (DSLs) and facilitates the creation of new DSLs. DSLs provide an effective interface for domain scientists avoiding the difficulties involved with low-level interfaces

Finding Commonalities: Social Information Processing and Domain Theory in the Study of Aggression

Science.gov (United States)

Nucci, Larry

2004-01-01

The Arsenio and Lemerise (this issue) proposal integrating social information processing (SIP) and domain theory to study children's aggression is evaluated from a domain theory perspective. Basic tenets of domain theory rendering it compatible with SIP are discussed as well as points of divergence. Focus is directed to the proposition that…

DRK methods for time-domain oscillator simulation

NARCIS (Netherlands)

Sevat, M.F.; Houben, S.H.M.J.; Maten, ter E.J.W.; Di Bucchianico, A.; Mattheij, R.M.M.; Peletier, M.A.

2006-01-01

This paper presents a new Runge-Kutta type integration method that is well-suited for time-domain simulation of oscillators. A unique property of the new method is that its damping characteristics can be controlled by a continuous parameter.

Is there a domain-general cognitive structuring system? Evidence from structural priming across music, math, action descriptions, and language.

Science.gov (United States)

Van de Cavey, Joris; Hartsuiker, Robert J

2016-01-01

Cognitive processing in many domains (e.g., sentence comprehension, music listening, and math solving) requires sequential information to be organized into an integrational structure. There appears to be some overlap in integrational processing across domains, as shown by cross-domain interference effects when for example linguistic and musical stimuli are jointly presented (Koelsch, Gunter, Wittfoth, & Sammler, 2005; Slevc, Rosenberg, & Patel, 2009). These findings support theories of overlapping resources for integrational processing across domains (cfr. SSIRH Patel, 2003; SWM, Kljajevic, 2010). However, there are some limitations to the studies mentioned above, such as the frequent use of unnaturalistic integrational difficulties. In recent years, the idea has risen that evidence for domain-generality in structural processing might also be yielded though priming paradigms (cfr. Scheepers, 2003). The rationale behind this is that integrational processing across domains regularly requires the processing of dependencies across short or long distances in the sequence, involving respectively less or more syntactic working memory resources (cfr. SWM, Kljajevic, 2010), and such processing decisions might persist over time. However, whereas recent studies have shown suggestive priming of integrational structure between language and arithmetics (though often dependent on arithmetic performance, cfr. Scheepers et al., 2011; Scheepers & Sturt, 2014), it remains to be investigated to what extent we can also find evidence for priming in other domains, such as music and action (cfr. SWM, Kljajevic, 2010). Experiment 1a showed structural priming from the processing of musical sequences onto the position in the sentence structure (early or late) to which a relative clause was attached in subsequent sentence completion. Importantly, Experiment 1b showed that a similar structural manipulation based on non-hierarchically ordered color sequences did not yield any priming effect

In a model of Batten disease, palmitoyl protein thioesterase-1 deficiency is associated with brown adipose tissue and thermoregulation abnormalities.

Directory of Open Access Journals (Sweden)

Alfia Khaibullina

Full Text Available Infantile neuronal ceroid lipofuscinosis (INCL is a fatal neurodegenerative disorder caused by a deficiency of palmitoyl-protein thioesterase-1 (PPT1. We have previously shown that children with INCL have increased risk of hypothermia during anesthesia and that PPT1-deficiency in mice is associated with disruption of adaptive energy metabolism, downregulation of peroxisome proliferator-activated receptor γ coactivator 1α (PGC-1α, and mitochondrial dysfunction. Here we hypothesized that Ppt1-knockout mice, a well-studied model of INCL that shows many of the neurologic manifestations of the disease, would recapitulate the thermoregulation impairment observed in children with INCL. We also hypothesized that when exposed to cold, Ppt1-knockout mice would be unable to maintain body temperature as in mice thermogenesis requires upregulation of Pgc-1α and uncoupling protein 1 (Ucp-1 in brown adipose tissue. We found that the Ppt1-KO mice had lower basal body temperature as they aged and developed hypothermia during cold exposure. Surprisingly, this inability to maintain body temperature during cold exposure in Ppt1-KO mice was associated with an adequate upregulation of Pgc-1α and Ucp-1 but with lower levels of sympathetic neurotransmitters in brown adipose tissue. In addition, during baseline conditions, brown adipose tissue of Ppt1-KO mice had less vacuolization (lipid droplets compared to wild-type animals. After cold stress, wild-type animals had significant decreases whereas Ppt1-KO had insignificant changes in lipid droplets compared with baseline measurements, thus suggesting that Ppt1-KO had less lipolysis in response to cold stress. These results uncover a previously unknown phenotype associated with PPT1 deficiency, that of altered thermoregulation, which is associated with impaired lipolysis and neurotransmitter release to brown adipose tissue during cold exposure. These findings suggest that INCL should be added to the list of

Integrated optical sensors for the chemical domain

NARCIS (Netherlands)

Lambeck, Paul

2006-01-01

During the last decade there has been a rapidly growing interest in integrated optical (IO) sensors, expecially because many of them principally allow for sensitive, real time, label-free-on-site measurements of the concentration of (bio-)chemical species. This review aims at giving an overview of

A wavelet-based PWTD algorithm-accelerated time domain surface integral equation solver

KAUST Repository

Liu, Yang

2015-10-26

© 2015 IEEE. The multilevel plane-wave time-domain (PWTD) algorithm allows for fast and accurate analysis of transient scattering from, and radiation by, electrically large and complex structures. When used in tandem with marching-on-in-time (MOT)-based surface integral equation (SIE) solvers, it reduces the computational and memory costs of transient analysis from equation and equation to equation and equation, respectively, where Nt and Ns denote the number of temporal and spatial unknowns (Ergin et al., IEEE Trans. Antennas Mag., 41, 39-52, 1999). In the past, PWTD-accelerated MOT-SIE solvers have been applied to transient problems involving half million spatial unknowns (Shanker et al., IEEE Trans. Antennas Propag., 51, 628-641, 2003). Recently, a scalable parallel PWTD-accelerated MOT-SIE solver that leverages a hiearchical parallelization strategy has been developed and successfully applied to the transient problems involving ten million spatial unknowns (Liu et. al., in URSI Digest, 2013). We further enhanced the capabilities of this solver by implementing a compression scheme based on local cosine wavelet bases (LCBs) that exploits the sparsity in the temporal dimension (Liu et. al., in URSI Digest, 2014). Specifically, the LCB compression scheme was used to reduce the memory requirement of the PWTD ray data and computational cost of operations in the PWTD translation stage.

Joining RDC data from flexible protein domains

International Nuclear Information System (INIS)

Sgheri, Luca

2010-01-01

We study the inverse problem of determining the conformational freedom of two protein domains from residual dipolar coupling (RDC) measurements. For each paramagnetic ion attached to one of the domains we obtain a magnetic susceptibility tensor χ from the RDC of couples of atoms of that domain, and a mean paramagnetic susceptibility tensor χ-bar from the RDC of couples of atoms of the other domain. The latter is an integral average of rotations of χ which depends on the conformational freedom of the two domains. In this paper we consider the case when we have data from paramagnetic ions attached separately to each of the domains. We prove that in this case not all the elements of χ and χ-bar are independent. We derive the mathematical equations for the compatibility of the measurements and show how these relations can be used in the presence of noisy data to determine a compatible set of χ and χ-bar with an unconstrained minimization. If available, information about the shape of the noise can be included in the target function. We show that in this case the compatible set obtained has a reduced error with respect to the noisy data

Domain Specific Language for Modeling Waste Management Systems

DEFF Research Database (Denmark)

Zarrin, Bahram

environmental technologies i.e. solid waste management systems. Flow-based programming is used to support concurrent execution of the processes, and provides a model-integration language for composing processes from homogeneous or heterogeneous domains. And a domain-specific language is used to define atomic......In order to develop sustainable waste management systems with considering life cycle perspective, scientists and domain experts in environmental science require readily applicable tools for modeling and evaluating the life cycle impacts of the waste management systems. Practice has proved...... a domain specific language for modeling of waste-management systems on the basis of our framework. We evaluate the language by providing a set of case studies. The contributions of this thesis are; addressing separation of concerns in Flow-based programming and providing the formal specification of its...

Kinematic evolution of the Mbakop Pan-African granitoids (western Cameroon domain): An integrated AMS and EBSD approach

Science.gov (United States)

Bella Nké, B. E.; Njanko, T.; Mamtani, M. A.; Njonfang, E.; Rochette, P.

2018-06-01

This study integrates anisotropy of magnetic susceptibility, microstructural and crystallographic preferred orientation (CPO) data from the Mbakop granitic pluton (MGP; Pan-African age) in order to decipher its kinematic evolution. The MGP lies close to NE-SW branch of Central Cameroon Shear Zone (CCSZ) and is emplaced in gneissic basement. High mean magnetic susceptibility and presence of multi-domain magnetite are recorded. Quartz CPO measured using Electron Backscatter diffraction reveals dominance of rhomb , prism and prism slip in different samples, which is consistent with microstructures developed under upper greenschist/amphibolite facies conditions. Quartz CPO along with other kinematic indicators (feldspar porphyroclasts/mineral fish) indicate non-coaxial deformation was important during tectonic evolution of the MGP. Contrasting sense of shear is recorded implying multi-stage mylonitization in the Western Cameroon Domain. Top-towards-south sense of shear is related to regional D2 deformation (613-585 Ma), while top-towards-north is related to D3 (585-540 Ma). The magnetic fabric in MGP records D3. The obliquity between mean orientation of magnetic foliation (N12°E) and the NE-SW CCSZ branch (N48°E) gives kinematic vorticity number of 0.95. This indicates dominantly simple shear with a minor pure shear component. It is concluded that regional transpression was important during MGP emplacement.

Drug-domain interaction networks in myocardial infarction.

Science.gov (United States)

Wang, Haiying; Zheng, Huiru; Azuaje, Francisco; Zhao, Xing-Ming

2013-09-01

It has been well recognized that the pace of the development of new drugs and therapeutic interventions lags far behind biological knowledge discovery. Network-based approaches have emerged as a promising alternative to accelerate the discovery of new safe and effective drugs. Based on the integration of several biological resources including two recently published datasets i.e., Drug-target interactions in myocardial infarction (My-DTome) and drug-domain interaction network, this paper reports the association between drugs and protein domains in the context of myocardial infarction (MI). A MI drug-domain interaction network, My-DDome, was firstly constructed, followed by topological analysis and functional characterization of the network. The results show that My-DDome has a very clear modular structure, where drugs interacting with the same domain(s) within each module tend to have similar therapeutic effects. Moreover it has been found that drugs acting on blood and blood forming organs (ATC code B) and sensory organs (ATC code S) are significantly enriched in My-DDome (p drugs, their known targets, and seemingly unrelated proteins can be revealed.

Spring integration essentials

CERN Document Server

Pandey, Chandan

2015-01-01

This book is intended for developers who are either already involved with enterprise integration or planning to venture into the domain. Basic knowledge of Java and Spring is expected. For newer users, this book can be used to understand an integration scenario, what the challenges are, and how Spring Integration can be used to solve it. Prior experience of Spring Integration is not expected as this book will walk you through all the code examples.

Parallel time domain solvers for electrically large transient scattering problems

KAUST Repository

Liu, Yang

2014-09-26

Marching on in time (MOT)-based integral equation solvers represent an increasingly appealing avenue for analyzing transient electromagnetic interactions with large and complex structures. MOT integral equation solvers for analyzing electromagnetic scattering from perfect electrically conducting objects are obtained by enforcing electric field boundary conditions and implicitly time advance electric surface current densities by iteratively solving sparse systems of equations at all time steps. Contrary to finite difference and element competitors, these solvers apply to nonlinear and multi-scale structures comprising geometrically intricate and deep sub-wavelength features residing atop electrically large platforms. Moreover, they are high-order accurate, stable in the low- and high-frequency limits, and applicable to conducting and penetrable structures represented by highly irregular meshes. This presentation reviews some recent advances in the parallel implementations of time domain integral equation solvers, specifically those that leverage multilevel plane-wave time-domain algorithm (PWTD) on modern manycore computer architectures including graphics processing units (GPUs) and distributed memory supercomputers. The GPU-based implementation achieves at least one order of magnitude speedups compared to serial implementations while the distributed parallel implementation are highly scalable to thousands of compute-nodes. A distributed parallel PWTD kernel has been adopted to solve time domain surface/volume integral equations (TDSIE/TDVIE) for analyzing transient scattering from large and complex-shaped perfectly electrically conducting (PEC)/dielectric objects involving ten million/tens of millions of spatial unknowns.

Comparative structural analysis of lipid binding START domains.

Directory of Open Access Journals (Sweden)

Ann-Gerd Thorsell

Full Text Available Steroidogenic acute regulatory (StAR protein related lipid transfer (START domains are small globular modules that form a cavity where lipids and lipid hormones bind. These domains can transport ligands to facilitate lipid exchange between biological membranes, and they have been postulated to modulate the activity of other domains of the protein in response to ligand binding. More than a dozen human genes encode START domains, and several of them are implicated in a disease.We report crystal structures of the human STARD1, STARD5, STARD13 and STARD14 lipid transfer domains. These represent four of the six functional classes of START domains.Sequence alignments based on these and previously reported crystal structures define the structural determinants of human START domains, both those related to structural framework and those involved in ligand specificity.This article can also be viewed as an enhanced version in which the text of the article is integrated with interactive 3D representations and animated transitions. Please note that a web plugin is required to access this enhanced functionality. Instructions for the installation and use of the web plugin are available in Text S1.

Domain structure in soft ferrites by the longitudinal Kerr effect

International Nuclear Information System (INIS)

Kaczmarek, R.; Dautain, M.; Barradi-Ismail, T.

1992-01-01

For the first time, the longitudinal Kerr effect has been used in order to observe magnetic domains and their development in power ferrites. Image subtraction and processing leads to a magnetic contrast being a quasi derivative of the domains. A kind of integration procedure applied to them permits a reconstruction of a local hysteresis which parameters closely approach the global hysteresis data. (orig.)

Europlexus: a domain decomposition method in explicit dynamics

International Nuclear Information System (INIS)

Faucher, V.; Hariddh, Bung; Combescure, A.

2003-01-01

Explicit time integration methods are used in structural dynamics to simulate fast transient phenomena, such as impacts or explosions. A very fine analysis is required in the vicinity of the loading areas but extending the same method, and especially the same small time-step, to the whole structure frequently yields excessive calculation times. We thus perform a dual Schur domain decomposition, to divide the global problem into several independent ones, to which is added a reduced size interface problem, to ensure connections between sub-domains. Each sub-domain is given its own time-step and its own mesh fineness. Non-matching meshes at the interfaces are handled. An industrial example demonstrates the interest of our approach. (authors)

A hybrid method combining the FDTD and a time domain boundary-integral equation marching-on-in-time algorithm

Directory of Open Access Journals (Sweden)

A. Becker

2003-01-01

Full Text Available In this paper a hybrid method combining the FDTD/FIT with a Time Domain Boundary-Integral Marching-on-in-Time Algorithm (TD-BIM is presented. Inhomogeneous regions are modelled with the FIT-method, an alternative formulation of the FDTD. Homogeneous regions (which is in the presented numerical example the open space are modelled using a TD-BIM with equivalent electric and magnetic currents flowing on the boundary between the inhomogeneous and the homogeneous regions. The regions are coupled by the tangential magnetic fields just outside the inhomogeneous regions. These fields are calculated by making use of a Mixed Potential Integral Formulation for the magnetic field. The latter consists of equivalent electric and magnetic currents on the boundary plane between the homogeneous and the inhomogeneous region. The magnetic currents result directly from the electric fields of the Yee lattice. Electric currents in the same plane are calculated by making use of the TD-BIM and using the electric field of the Yee lattice as boundary condition. The presented hybrid method only needs the interpolations inherent in FIT and no additional interpolation. A numerical result is compared to a calculation that models both regions with FDTD.

A Methodology For The Development Of Complex Domain Specific Languages

CERN Document Server

Risoldi, Matteo; Falquet, Gilles

2010-01-01

The term Domain-Specific Modeling Language is used in software development to indicate a modeling (and sometimes programming) language dedicated to a particular problem domain, a particular problem representation technique and/or a particular solution technique. The concept is not new -- special-purpose programming language and all kinds of modeling/specification languages have always existed, but the term DSML has become more popular due to the rise of domain-specific modeling. Domain-specific languages are considered 4GL programming languages. Domain-specific modeling techniques have been adopted for a number of years now. However, the techniques and frameworks used still suffer from problems of complexity of use and fragmentation. Although in recent times some integrated environments are seeing the light, it is not common to see many concrete use cases in which domain-specific modeling has been put to use. The main goal of this thesis is tackling the domain of interactive systems and applying a DSML-based...

Time Domain Partitioning of Electricity Production Cost Simulations

Energy Technology Data Exchange (ETDEWEB)

Barrows, C. [National Renewable Energy Lab. (NREL), Golden, CO (United States); Hummon, M. [National Renewable Energy Lab. (NREL), Golden, CO (United States); Jones, W. [National Renewable Energy Lab. (NREL), Golden, CO (United States); Hale, E. [National Renewable Energy Lab. (NREL), Golden, CO (United States)

2014-01-01

Production cost models are often used for planning by simulating power system operations over long time horizons. The simulation of a day-ahead energy market can take several weeks to compute. Tractability improvements are often made through model simplifications, such as: reductions in transmission modeling detail, relaxation of commitment variable integrality, reductions in cost modeling detail, etc. One common simplification is to partition the simulation horizon so that weekly or monthly horizons can be simulated in parallel. However, horizon partitions are often executed with overlap periods of arbitrary and sometimes zero length. We calculate the time domain persistence of historical unit commitment decisions to inform time domain partitioning of production cost models. The results are implemented using PLEXOS production cost modeling software in an HPC environment to improve the computation time of simulations while maintaining solution integrity.

A methodology for extending domain coverage in SemRep.

Science.gov (United States)

Rosemblat, Graciela; Shin, Dongwook; Kilicoglu, Halil; Sneiderman, Charles; Rindflesch, Thomas C

2013-12-01

We describe a domain-independent methodology to extend SemRep coverage beyond the biomedical domain. SemRep, a natural language processing application originally designed for biomedical texts, uses the knowledge sources provided by the Unified Medical Language System (UMLS©). Ontological and terminological extensions to the system are needed in order to support other areas of knowledge. We extended SemRep's application by developing a semantic representation of a previously unsupported domain. This was achieved by adapting well-known ontology engineering phases and integrating them with the UMLS knowledge sources on which SemRep crucially depends. While the process to extend SemRep coverage has been successfully applied in earlier projects, this paper presents in detail the step-wise approach we followed and the mechanisms implemented. A case study in the field of medical informatics illustrates how the ontology engineering phases have been adapted for optimal integration with the UMLS. We provide qualitative and quantitative results, which indicate the validity and usefulness of our methodology. Published by Elsevier Inc.

Biotechnological applications of halophilic lipases and thioesterases.

Science.gov (United States)

Schreck, Steven D; Grunden, Amy M

2014-02-01

Lipases and esterases are enzymes which hydrolyze ester bonds between a fatty acid moiety and an esterified conjugate, such as a glycerol or phosphate. These enzymes have a wide spectrum of use in industrial applications where their high activity, broad substrate specificity, and stability under harsh conditions have made them integral in biofuel production, textile processing, waste treatment, and as detergent additives. To date, these industrial applications have mainly leveraged enzymes from mesophilic and thermophilic organisms. However, increasingly, attention has turned to halophilic enzymes as catalysts in environments where high salt stability is desired. This review provides a brief overview of lipases and esterases and examines specific structural motifs and evolutionary adaptations of halophilic lipases. Finally, we examine the state of research involving these enzymes and provide an in-depth look at an exciting algal-based biofuel production system. This system uses a recombinant halophilic lipase to increase oil production efficiency by cleaving algal fatty acids from the acyl carrier protein, which eliminates feedback inhibition of fatty acid synthesis.

Angle-domain inverse scattering migration/inversion in isotropic media

Science.gov (United States)

Li, Wuqun; Mao, Weijian; Li, Xuelei; Ouyang, Wei; Liang, Quan

2018-07-01

The classical seismic asymptotic inversion can be transformed into a problem of inversion of generalized Radon transform (GRT). In such methods, the combined parameters are linearly attached to the scattered wave-field by Born approximation and recovered by applying an inverse GRT operator to the scattered wave-field data. Typical GRT-style true-amplitude inversion procedure contains an amplitude compensation process after the weighted migration via dividing an illumination associated matrix whose elements are integrals of scattering angles. It is intuitional to some extent that performs the generalized linear inversion and the inversion of GRT together by this process for direct inversion. However, it is imprecise to carry out such operation when the illumination at the image point is limited, which easily leads to the inaccuracy and instability of the matrix. This paper formulates the GRT true-amplitude inversion framework in an angle-domain version, which naturally degrades the external integral term related to the illumination in the conventional case. We solve the linearized integral equation for combined parameters of different fixed scattering angle values. With this step, we obtain high-quality angle-domain common-image gathers (CIGs) in the migration loop which provide correct amplitude-versus-angle (AVA) behavior and reasonable illumination range for subsurface image points. Then we deal with the over-determined problem to solve each parameter in the combination by a standard optimization operation. The angle-domain GRT inversion method keeps away from calculating the inaccurate and unstable illumination matrix. Compared with the conventional method, the angle-domain method can obtain more accurate amplitude information and wider amplitude-preserved range. Several model tests demonstrate the effectiveness and practicability.

An explicit marching on-in-time solver for the time domain volume magnetic field integral equation

KAUST Repository

Sayed, Sadeed Bin

2014-07-01

Transient scattering from inhomogeneous dielectric objects can be modeled using time domain volume integral equations (TDVIEs). TDVIEs are oftentimes solved using marching on-in-time (MOT) techniques. Classical MOT-TDVIE solvers expand the field induced on the scatterer using local spatio-temporal basis functions. Inserting this expansion into the TDVIE and testing the resulting equation in space and time yields a system of equations that is solved by time marching. Depending on the type of the basis and testing functions and the time step, the time marching scheme can be implicit (N. T. Gres, et al., Radio Sci., 36(3), 379-386, 2001) or explicit (A. Al-Jarro, et al., IEEE Trans. Antennas Propag., 60(11), 5203-5214, 2012). Implicit MOT schemes are known to be more stable and accurate. However, under low-frequency excitation, i.e., when the time step size is large, they call for inversion of a full matrix system at very time step.

An explicit marching on-in-time solver for the time domain volume magnetic field integral equation

KAUST Repository

Sayed, Sadeed Bin; Ulku, Huseyin Arda; Bagci, Hakan

2014-01-01

Transient scattering from inhomogeneous dielectric objects can be modeled using time domain volume integral equations (TDVIEs). TDVIEs are oftentimes solved using marching on-in-time (MOT) techniques. Classical MOT-TDVIE solvers expand the field induced on the scatterer using local spatio-temporal basis functions. Inserting this expansion into the TDVIE and testing the resulting equation in space and time yields a system of equations that is solved by time marching. Depending on the type of the basis and testing functions and the time step, the time marching scheme can be implicit (N. T. Gres, et al., Radio Sci., 36(3), 379-386, 2001) or explicit (A. Al-Jarro, et al., IEEE Trans. Antennas Propag., 60(11), 5203-5214, 2012). Implicit MOT schemes are known to be more stable and accurate. However, under low-frequency excitation, i.e., when the time step size is large, they call for inversion of a full matrix system at very time step.

Conceptual view of Cyberloafing and Non-Work Domain

Directory of Open Access Journals (Sweden)

Soh Patrick Chin-Hooi

2017-01-01

Full Text Available In an attempt to understand the reasons for employees’ personal Internet use at work, known as cyberloafing, this paper attempts a new perspective to look at the phenomenon. As the barrier between the previously separate work and home domains reduces, employees are increasingly integrating their working and private world. This phenomenon has resulted in employees using their personal time for work-related tasks through technology in the privacy of their homes and private domain. Conversely, employees could be carrying out non-work related Internet use during office hours. This paper aims to explore the possibility of non-work domain as a factor for employees to cyberloaf. This paper proposed a conceptual model based on border theory and theory of interpersonal behaviour. The resultant augmented theory offers a richer explanation of how non-work domain affects employees’ decision making process on cyberloafing.

Smart systems integration and simulation

CERN Document Server

Poncino, Massimo; Pravadelli, Graziano

2016-01-01

This book-presents new methods and tools for the integration and simulation of smart devices. The design approach described in this book explicitly accounts for integration of Smart Systems components and subsystems as a specific constraint. It includes methodologies and EDA tools to enable multi-disciplinary and multi-scale modeling and design, simulation of multi-domain systems, subsystems and components at all levels of abstraction, system integration and exploration for optimization of functional and non-functional metrics. By covering theoretical and practical aspects of smart device design, this book targets people who are working and studying on hardware/software modelling, component integration and simulation under different positions (system integrators, designers, developers, researchers, teachers, students etc.). In particular, it is a good introduction to people who have interest in managing heterogeneous components in an efficient and effective way on different domains and different abstraction l...

Beyond cross-domain learning: Multiple-domain nonnegative matrix factorization

KAUST Repository

Wang, Jim Jing-Yan; Gao, Xin

2014-01-01

Traditional cross-domain learning methods transfer learning from a source domain to a target domain. In this paper, we propose the multiple-domain learning problem for several equally treated domains. The multiple-domain learning problem assumes that samples from different domains have different distributions, but share the same feature and class label spaces. Each domain could be a target domain, while also be a source domain for other domains. A novel multiple-domain representation method is proposed for the multiple-domain learning problem. This method is based on nonnegative matrix factorization (NMF), and tries to learn a basis matrix and coding vectors for samples, so that the domain distribution mismatch among different domains will be reduced under an extended variation of the maximum mean discrepancy (MMD) criterion. The novel algorithm - multiple-domain NMF (MDNMF) - was evaluated on two challenging multiple-domain learning problems - multiple user spam email detection and multiple-domain glioma diagnosis. The effectiveness of the proposed algorithm is experimentally verified. © 2013 Elsevier Ltd. All rights reserved.

Beyond cross-domain learning: Multiple-domain nonnegative matrix factorization

KAUST Repository

Wang, Jim Jing-Yan

2014-02-01

Traditional cross-domain learning methods transfer learning from a source domain to a target domain. In this paper, we propose the multiple-domain learning problem for several equally treated domains. The multiple-domain learning problem assumes that samples from different domains have different distributions, but share the same feature and class label spaces. Each domain could be a target domain, while also be a source domain for other domains. A novel multiple-domain representation method is proposed for the multiple-domain learning problem. This method is based on nonnegative matrix factorization (NMF), and tries to learn a basis matrix and coding vectors for samples, so that the domain distribution mismatch among different domains will be reduced under an extended variation of the maximum mean discrepancy (MMD) criterion. The novel algorithm - multiple-domain NMF (MDNMF) - was evaluated on two challenging multiple-domain learning problems - multiple user spam email detection and multiple-domain glioma diagnosis. The effectiveness of the proposed algorithm is experimentally verified. © 2013 Elsevier Ltd. All rights reserved.

Classification and Lineage Tracing of SH2 Domains Throughout Eukaryotes.

Science.gov (United States)

Liu, Bernard A

2017-01-01

Today there exists a rapidly expanding number of sequenced genomes. Cataloging protein interaction domains such as the Src Homology 2 (SH2) domain across these various genomes can be accomplished with ease due to existing algorithms and predictions models. An evolutionary analysis of SH2 domains provides a step towards understanding how SH2 proteins integrated with existing signaling networks to position phosphotyrosine signaling as a crucial driver of robust cellular communication networks in metazoans. However organizing and tracing SH2 domain across organisms and understanding their evolutionary trajectory remains a challenge. This chapter describes several methodologies towards analyzing the evolutionary trajectory of SH2 domains including a global SH2 domain classification system, which facilitates annotation of new SH2 sequences essential for tracing the lineage of SH2 domains throughout eukaryote evolution. This classification utilizes a combination of sequence homology, protein domain architecture and the boundary positions between introns and exons within the SH2 domain or genes encoding these domains. Discrete SH2 families can then be traced across various genomes to provide insight into its origins. Furthermore, additional methods for examining potential mechanisms for divergence of SH2 domains from structural changes to alterations in the protein domain content and genome duplication will be discussed. Therefore a better understanding of SH2 domain evolution may enhance our insight into the emergence of phosphotyrosine signaling and the expansion of protein interaction domains.

Time- and Frequency-domain Comparisons of the Wavepiston Wave Energy Converter

DEFF Research Database (Denmark)

Read, Robert; Bingham, Harry

Analysis of wave-energy converters is most frequently undertaken in the time-domain. This formulation allows the direct inclusion of nonlinear time-varying loads such as power take-off (PTO) reactions, mooring forces, and viscous drag. However, integrating the governing equations of motion...... forces arising from both the PTO reactions and the non-negligible viscous drag acting on the plate. Equivalent linear damping coeffcients are used to model these forces in the frequency domain, while they are included explicitly in the time domain. The main idea of this paper is to quantify...

Java-Based Coupling for Parallel Predictive-Adaptive Domain Decomposition

Directory of Open Access Journals (Sweden)

Cécile Germain‐Renaud

1999-01-01

Full Text Available Adaptive domain decomposition exemplifies the problem of integrating heterogeneous software components with intermediate coupling granularity. This paper describes an experiment where a data‐parallel (HPF client interfaces with a sequential computation server through Java. We show that seamless integration of data‐parallelism is possible, but requires most of the tools from the Java palette: Java Native Interface (JNI, Remote Method Invocation (RMI, callbacks and threads.

Wavefield Extrapolation in Pseudo-depth Domain

KAUST Repository

Ma, Xuxin

2011-12-11

Wave-equation based seismic migration and inversion tools are widely used by the energy industry to explore hydrocarbon and mineral resources. By design, most of these techniques simulate wave propagation in a space domain with the vertical axis being depth measured from the surface. Vertical depth is popular because it is a straightforward mapping of the subsurface space. It is, however, not computationally cost-effective because the wavelength changes with local elastic wave velocity, which in general increases with depth in the Earth. As a result, the sampling per wavelength also increases with depth. To avoid spatial aliasing in deep fast media, the seismic wave is oversampled in shallow slow media and therefore increase the total computation cost. This issue is effectively tackled by using the vertical time axis instead of vertical depth. This is because in a vertical time representation, the "wavelength" is essentially time period for vertical rays. This thesis extends the vertical time axis to the pseudo-depth axis, which features distance unit while preserving the properties of the vertical time representation. To explore the potentials of doing wave-equation based imaging in the pseudo-depth domain, a Partial Differential Equation (PDE) is derived to describe acoustic wave in this new domain. This new PDE is inherently anisotropic because the use of a constant vertical velocity to convert between depth and vertical time. Such anisotropy results in lower reflection coefficients compared with conventional space domain modeling results. This feature is helpful to suppress the low wavenumber artifacts in reverse-time migration images, which are caused by the widely used cross-correlation imaging condition. This thesis illustrates modeling acoustic waves in both conventional space domain and pseudo-depth domain. The numerical tool used to model acoustic waves is built based on the lowrank approximation of Fourier integral operators. To investigate the potential

Domain switching in single-phase multiferroics

Science.gov (United States)

Jia, Tingting; Cheng, Zhenxiang; Zhao, Hongyang; Kimura, Hideo

2018-06-01

Multiferroics are a time-honoured research subject by reason for their tremendous application potential in the information industry, such as in multi-state information storage devices and new types of sensors. An outburst of studies on multiferroicity has been witnessed in the 21st century, although this field has a long research history since the 19th century. Multiferroicity has now become one of the hottest research topics in condensed matter physics and materials science. Numerous efforts have been made to investigate the cross-coupling phenomena among ferroic orders such as ferroelectricity, (anti-)ferromagnetism, and ferroelasticity, especially the coupling between electric and magnetic orderings that would account for the magnetoelectric (ME) effect in multiferroic materials. The magnetoelectric properties and coupling behavior of single phase multiferroics are dominated by their domain structures. It was also noted that, however, the multiferroic materials exhibit very complicated domain structures. Studies on domain structure characterization and domain switching are a crucial step in the exploration of approaches to the control and manipulation of magnetic (electric) properties using an electric (magnetic) field or other means. In this review, following a concise outline of our current basic knowledge on the magnetoelectric (ME) effect, we summarize some important research activities on domain switching in single-phase multiferroic materials in the form of single crystals and thin films, especially domain switching behavior involving strain and the related physics in the last decade. We also introduce recent developments in characterization techniques for domain structures of ferroelectric or multiferroic materials, which have significantly advanced our understanding of domain switching dynamics and interactions. The effects of a series of issues such as electric field, magnetic field, and stress effects on domain switching are been discussed as well. It

INTEGRATED MARKETING COMMUNICATION IN POLITICS?

Directory of Open Access Journals (Sweden)

Ovidiu-Aurel GHIUŢĂ

2009-06-01

Full Text Available The current study has practical applicability in politic al domain and theoretical involvement at politicalmarketing communication level. The type of the research is a qualitative one, using as survey methods scientificobservation and documentary search. The aim of the research is to prove the applicability of marketing communicationconcept integrated in political marketing and global marketing communication. There are also exceptions, justanalyzing the industry – politics, in which integrated communication can’t be considered global communication.The subject of integrated marketing communication is relatively a new one in marketing (two decades, but itsapplicability in political domain and the specifications that assumes this application represents o new vision atEuropean and worldwide level. This study clearly presents the differences between the integrated marketingcommunication and global marketing communication.In documentary research, the author used studies belonging to Anglo – Saxons theoreticians and practitioners(Americans, Canadians, British but also Europeans (French, Belgians, Romanians. The main reason is the fact that inmarketing domain on extremely narrow scientific sections the visions belonging to these two main orientations aren’talways equable. Also, in scientific observation, t he research analyses political events from United States of America,France and Romania. Due to this reason, we can affirm that the current study has not only a regional applicability butalso a global one.

Recent advances in marching-on-in-time schemes for solving time domain volume integral equations

KAUST Repository

Sayed, Sadeed Bin; Ulku, Huseyin Arda; Bagci, Hakan

2015-01-01

Transient electromagnetic field interactions on inhomogeneous penetrable scatterers can be analyzed by solving time domain volume integral equations (TDVIEs). TDVIEs are constructed by setting the summation of the incident and scattered field intensities to the total field intensity on the volumetric support of the scatterer. The unknown can be the field intensity or flux/current density. Representing the total field intensity in terms of the unknown using the relevant constitutive relation and the scattered field intensity in terms of the spatiotemporal convolution of the unknown with the Green function yield the final form of the TDVIE. The unknown is expanded in terms of local spatial and temporal basis functions. Inserting this expansion into the TDVIE and testing the resulting equation at discrete times yield a system of equations that is solved by the marching on-in-time (MOT) scheme. At each time step, a smaller system of equations, termed MOT system is solved for the coefficients of the expansion. The right-hand side of this system consists of the tested incident field and discretized spatio-temporal convolution of the unknown samples computed at the previous time steps with the Green function.

Recent advances in marching-on-in-time schemes for solving time domain volume integral equations

KAUST Repository

Sayed, Sadeed Bin

2015-05-16

Transient electromagnetic field interactions on inhomogeneous penetrable scatterers can be analyzed by solving time domain volume integral equations (TDVIEs). TDVIEs are constructed by setting the summation of the incident and scattered field intensities to the total field intensity on the volumetric support of the scatterer. The unknown can be the field intensity or flux/current density. Representing the total field intensity in terms of the unknown using the relevant constitutive relation and the scattered field intensity in terms of the spatiotemporal convolution of the unknown with the Green function yield the final form of the TDVIE. The unknown is expanded in terms of local spatial and temporal basis functions. Inserting this expansion into the TDVIE and testing the resulting equation at discrete times yield a system of equations that is solved by the marching on-in-time (MOT) scheme. At each time step, a smaller system of equations, termed MOT system is solved for the coefficients of the expansion. The right-hand side of this system consists of the tested incident field and discretized spatio-temporal convolution of the unknown samples computed at the previous time steps with the Green function.

FDTD-SPICE for Characterizing Metamaterials Integrated with Electronic Circuits

Directory of Open Access Journals (Sweden)

Zhengwei Hao

2012-01-01

Full Text Available A powerful time-domain FDTD-SPICE simulator is implemented and applied to the broadband analysis of metamaterials integrated with active and tunable circuit elements. First, the FDTD-SPICE modeling theory is studied and details of interprocess communication and hybridization of the two techniques are discussed. To verify the model, some simple cases are simulated with results in both time domain and frequency domain. Then, simulation of a metamaterial structure constructed from periodic resonant loops integrated with lumped capacitor elements is studied, which demonstrates tuning resonance frequency of medium by changing the capacitance of the integrated elements. To increase the bandwidth of the metamaterial, non-Foster transistor configurations are integrated with the loops and FDTD-SPICE is applied to successfully bridge the physics of electromagnetic and circuit topologies and to model the whole composite structure. Our model is also applied to the design and simulation of a metasurface integrated with nonlinear varactors featuring tunable reflection phase characteristic.

Integrating angle-frequency domain synchronous averaging technique with feature extraction for gear fault diagnosis

Science.gov (United States)

Zhang, Shengli; Tang, J.

2018-01-01

Gear fault diagnosis relies heavily on the scrutiny of vibration responses measured. In reality, gear vibration signals are noisy and dominated by meshing frequencies as well as their harmonics, which oftentimes overlay the fault related components. Moreover, many gear transmission systems, e.g., those in wind turbines, constantly operate under non-stationary conditions. To reduce the influences of non-synchronous components and noise, a fault signature enhancement method that is built upon angle-frequency domain synchronous averaging is developed in this paper. Instead of being averaged in the time domain, the signals are processed in the angle-frequency domain to solve the issue of phase shifts between signal segments due to uncertainties caused by clearances, input disturbances, and sampling errors, etc. The enhanced results are then analyzed through feature extraction algorithms to identify the most distinct features for fault classification and identification. Specifically, Kernel Principal Component Analysis (KPCA) targeting at nonlinearity, Multilinear Principal Component Analysis (MPCA) targeting at high dimensionality, and Locally Linear Embedding (LLE) targeting at local similarity among the enhanced data are employed and compared to yield insights. Numerical and experimental investigations are performed, and the results reveal the effectiveness of angle-frequency domain synchronous averaging in enabling feature extraction and classification.

A Fast, Efficient Domain Adaptation Technique for Cross-Domain Electroencephalography(EEG-Based Emotion Recognition

Directory of Open Access Journals (Sweden)

Xin Chai

2017-05-01

Full Text Available Electroencephalography (EEG-based emotion recognition is an important element in psychiatric health diagnosis for patients. However, the underlying EEG sensor signals are always non-stationary if they are sampled from different experimental sessions or subjects. This results in the deterioration of the classification performance. Domain adaptation methods offer an effective way to reduce the discrepancy of marginal distribution. However, for EEG sensor signals, both marginal and conditional distributions may be mismatched. In addition, the existing domain adaptation strategies always require a high level of additional computation. To address this problem, a novel strategy named adaptive subspace feature matching (ASFM is proposed in this paper in order to integrate both the marginal and conditional distributions within a unified framework (without any labeled samples from target subjects. Specifically, we develop a linear transformation function which matches the marginal distributions of the source and target subspaces without a regularization term. This significantly decreases the time complexity of our domain adaptation procedure. As a result, both marginal and conditional distribution discrepancies between the source domain and unlabeled target domain can be reduced, and logistic regression (LR can be applied to the new source domain in order to train a classifier for use in the target domain, since the aligned source domain follows a distribution which is similar to that of the target domain. We compare our ASFM method with six typical approaches using a public EEG dataset with three affective states: positive, neutral, and negative. Both offline and online evaluations were performed. The subject-to-subject offline experimental results demonstrate that our component achieves a mean accuracy and standard deviation of 80.46% and 6.84%, respectively, as compared with a state-of-the-art method, the subspace alignment auto-encoder (SAAE, which

Domains and domain loss

DEFF Research Database (Denmark)

Haberland, Hartmut

2005-01-01

politicians and in the media, especially in the discussion whether some languages undergo ‘domain loss’ vis-à-vis powerful international languages like English. An objection that has been raised here is that domains, as originally conceived, are parameters of language choice and not properties of languages...

Simulating propagation of decoupled elastic waves using low-rank approximate mixed-domain integral operators for anisotropic media

KAUST Repository

Cheng, Jiubing; Alkhalifah, Tariq Ali; Wu, Zedong; Zou, Peng; Wang, Chenlong

2016-01-01

In elastic imaging, the extrapolated vector fields are decoupled into pure wave modes, such that the imaging condition produces interpretable images. Conventionally, mode decoupling in anisotropic media is costly because the operators involved are dependent on the velocity, and thus they are not stationary. We have developed an efficient pseudospectral approach to directly extrapolate the decoupled elastic waves using low-rank approximate mixed-domain integral operators on the basis of the elastic displacement wave equation. We have applied k-space adjustment to the pseudospectral solution to allow for a relatively large extrapolation time step. The low-rank approximation was, thus, applied to the spectral operators that simultaneously extrapolate and decompose the elastic wavefields. Synthetic examples on transversely isotropic and orthorhombic models showed that our approach has the potential to efficiently and accurately simulate the propagations of the decoupled quasi-P and quasi-S modes as well as the total wavefields for elastic wave modeling, imaging, and inversion.

Simulating propagation of decoupled elastic waves using low-rank approximate mixed-domain integral operators for anisotropic media

KAUST Repository

Cheng, Jiubing

2016-03-15

In elastic imaging, the extrapolated vector fields are decoupled into pure wave modes, such that the imaging condition produces interpretable images. Conventionally, mode decoupling in anisotropic media is costly because the operators involved are dependent on the velocity, and thus they are not stationary. We have developed an efficient pseudospectral approach to directly extrapolate the decoupled elastic waves using low-rank approximate mixed-domain integral operators on the basis of the elastic displacement wave equation. We have applied k-space adjustment to the pseudospectral solution to allow for a relatively large extrapolation time step. The low-rank approximation was, thus, applied to the spectral operators that simultaneously extrapolate and decompose the elastic wavefields. Synthetic examples on transversely isotropic and orthorhombic models showed that our approach has the potential to efficiently and accurately simulate the propagations of the decoupled quasi-P and quasi-S modes as well as the total wavefields for elastic wave modeling, imaging, and inversion.

Improving the performance of DomainDiscovery of protein domain boundary assignment using inter-domain linker index

Directory of Open Access Journals (Sweden)

Zomaya Albert Y

2006-12-01

Full Text Available Abstract Background Knowledge of protein domain boundaries is critical for the characterisation and understanding of protein function. The ability to identify domains without the knowledge of the structure – by using sequence information only – is an essential step in many types of protein analyses. In this present study, we demonstrate that the performance of DomainDiscovery is improved significantly by including the inter-domain linker index value for domain identification from sequence-based information. Improved DomainDiscovery uses a Support Vector Machine (SVM approach and a unique training dataset built on the principle of consensus among experts in defining domains in protein structure. The SVM was trained using a PSSM (Position Specific Scoring Matrix, secondary structure, solvent accessibility information and inter-domain linker index to detect possible domain boundaries for a target sequence. Results Improved DomainDiscovery is compared with other methods by benchmarking against a structurally non-redundant dataset and also CASP5 targets. Improved DomainDiscovery achieves 70% accuracy for domain boundary identification in multi-domains proteins. Conclusion Improved DomainDiscovery compares favourably to the performance of other methods and excels in the identification of domain boundaries for multi-domain proteins as a result of introducing support vector machine with benchmark_2 dataset.

Structure of synaptophysin: a hexameric MARVEL-domain channel protein.

Science.gov (United States)

Arthur, Christopher P; Stowell, Michael H B

2007-06-01

Synaptophysin I (SypI) is an archetypal member of the MARVEL-domain family of integral membrane proteins and one of the first synaptic vesicle proteins to be identified and cloned. Most all MARVEL-domain proteins are involved in membrane apposition and vesicle-trafficking events, but their precise role in these processes is unclear. We have purified mammalian SypI and determined its three-dimensional (3D) structure by using electron microscopy and single-particle 3D reconstruction. The hexameric structure resembles an open basket with a large pore and tenuous interactions within the cytosolic domain. The structure suggests a model for Synaptophysin's role in fusion and recycling that is regulated by known interactions with the SNARE machinery. This 3D structure of a MARVEL-domain protein provides a structural foundation for understanding the role of these important proteins in a variety of biological processes.

A fast-multipole domain decomposition integral equation solver for characterizing electromagnetic wave propagation in mine environments

KAUST Repository

Yücel, Abdulkadir C.

2013-07-01

Reliable and effective wireless communication and tracking systems in mine environments are key to ensure miners\\' productivity and safety during routine operations and catastrophic events. The design of such systems greatly benefits from simulation tools capable of analyzing electromagnetic (EM) wave propagation in long mine tunnels and large mine galleries. Existing simulation tools for analyzing EM wave propagation in such environments employ modal decompositions (Emslie et. al., IEEE Trans. Antennas Propag., 23, 192-205, 1975), ray-tracing techniques (Zhang, IEEE Tran. Vehic. Tech., 5, 1308-1314, 2003), and full wave methods. Modal approaches and ray-tracing techniques cannot accurately account for the presence of miners and their equipments, as well as wall roughness (especially when the latter is comparable to the wavelength). Full-wave methods do not suffer from such restrictions but require prohibitively large computational resources. To partially alleviate this computational burden, a 2D integral equation-based domain decomposition technique has recently been proposed (Bakir et. al., in Proc. IEEE Int. Symp. APS, 1-2, 8-14 July 2012). © 2013 IEEE.

Equivalence of linear canonical transform domains to fractional Fourier domains and the bicanonical width product: a generalization of the space-bandwidth product.

Science.gov (United States)

Oktem, Figen S; Ozaktas, Haldun M

2010-08-01

Linear canonical transforms (LCTs) form a three-parameter family of integral transforms with wide application in optics. We show that LCT domains correspond to scaled fractional Fourier domains and thus to scaled oblique axes in the space-frequency plane. This allows LCT domains to be labeled and ordered by the corresponding fractional order parameter and provides insight into the evolution of light through an optical system modeled by LCTs. If a set of signals is highly confined to finite intervals in two arbitrary LCT domains, the space-frequency (phase space) support is a parallelogram. The number of degrees of freedom of this set of signals is given by the area of this parallelogram, which is equal to the bicanonical width product but usually smaller than the conventional space-bandwidth product. The bicanonical width product, which is a generalization of the space-bandwidth product, can provide a tighter measure of the actual number of degrees of freedom, and allows us to represent and process signals with fewer samples.

Structure of Concatenated HAMP Domains Provides a Mechanism for Signal Transduction

Energy Technology Data Exchange (ETDEWEB)

Airola, Michael V.; Watts, Kylie J.; Bilwes, Alexandrine M.; Crane, Brian R. (Cornell); (Lorma Linda U)

2010-08-23

HAMP domains are widespread prokaryotic signaling modules found as single domains or poly-HAMP chains in both transmembrane and soluble proteins. The crystal structure of a three-unit poly-HAMP chain from the Pseudomonas aeruginosa soluble receptor Aer2 defines a universal parallel four-helix bundle architecture for diverse HAMP domains. Two contiguous domains integrate to form a concatenated di-HAMP structure. The three HAMP domains display two distinct conformations that differ by changes in helical register, crossing angle, and rotation. These conformations are stabilized by different subsets of conserved residues. Known signals delivered to HAMP would be expected to switch the relative stability of the two conformations and the position of a coiled-coil phase stutter at the junction with downstream helices. We propose that the two conformations represent opposing HAMP signaling states and suggest a signaling mechanism whereby HAMP domains interconvert between the two states, which alternate down a poly-HAMP chain.

A wavelet-based PWTD algorithm-accelerated time domain surface integral equation solver

KAUST Repository

Liu, Yang; Yucel, Abdulkadir C.; Gilbert, Anna C.; Bagci, Hakan; Michielssen, Eric

2015-01-01

© 2015 IEEE. The multilevel plane-wave time-domain (PWTD) algorithm allows for fast and accurate analysis of transient scattering from, and radiation by, electrically large and complex structures. When used in tandem with marching-on-in-time (MOT

Cholesterol Bilayer Domains in the Eye Lens Health: A Review.

Science.gov (United States)

Widomska, Justyna; Subczynski, Witold K; Mainali, Laxman; Raguz, Marija

2017-12-01

The most unique biochemical characteristic of the eye lens fiber cell plasma membrane is its extremely high cholesterol content, the need for which is still unclear. It is evident, however, that the disturbance of Chol homeostasis may result in damages associated with cataracts. Electron paramagnetic resonance methods allow discrimination of two types of lipid domains in model membranes overloaded with Chol, namely, phospholipid-cholesterol domains and pure Chol bilayer domains. These domains are also detected in human lens lipid membranes prepared from the total lipids extracted from lens cortices and nuclei of donors from different age groups. Independent of the age-related changes in phospholipid composition, the physical properties of phospholipid-Chol domains remain the same for all age groups and are practically identical for cortical and nuclear membranes. The presence of Chol bilayer domains in these membranes provides a buffering capacity for cholesterol concentration in the surrounding phospholipid-Chol domains, keeping it at a constant saturating level and thus keeping the physical properties of the membrane consistent with and independent of changes in phospholipid composition. It seems that the presence of Chol bilayer domains plays an integral role in the regulation of cholesterol-dependent processes in fiber cell plasm membranes and in the maintenance of fiber cell membrane homeostasis.

Integrating art into science education: a survey of science teachers' practices

Science.gov (United States)

Turkka, Jaakko; Haatainen, Outi; Aksela, Maija

2017-07-01

Numerous case studies suggest that integrating art and science education could engage students with creative projects and encourage students to express science in multitude of ways. However, little is known about art integration practices in everyday science teaching. With a qualitative e-survey, this study explores the art integration of science teachers (n = 66). A pedagogical model for science teachers' art integration emerged from a qualitative content analysis conducted on examples of art integration. In the model, art integration is characterised as integration through content and activities. Whilst the links in the content were facilitated either directly between concepts and ideas or indirectly through themes or artefacts, the integration through activity often connected an activity in one domain and a concept, idea or artefact in the other domain with the exception of some activities that could belong to both domains. Moreover, the examples of art integration in everyday classroom did not include expression of emotions often associated with art. In addition, quantitative part of the survey confirmed that integration is infrequent in all mapped areas. The findings of this study have implications for science teacher education that should offer opportunities for more consistent art integration.

Phospho-Ser/Thr-binding domains: navigating the cell cycle and DNA damage response.

Science.gov (United States)

Reinhardt, H Christian; Yaffe, Michael B

2013-09-01

Coordinated progression through the cell cycle is a complex challenge for eukaryotic cells. Following genotoxic stress, diverse molecular signals must be integrated to establish checkpoints specific for each cell cycle stage, allowing time for various types of DNA repair. Phospho-Ser/Thr-binding domains have emerged as crucial regulators of cell cycle progression and DNA damage signalling. Such domains include 14-3-3 proteins, WW domains, Polo-box domains (in PLK1), WD40 repeats (including those in the E3 ligase SCF(βTrCP)), BRCT domains (including those in BRCA1) and FHA domains (such as in CHK2 and MDC1). Progress has been made in our understanding of the motif (or motifs) that these phospho-Ser/Thr-binding domains connect with on their targets and how these interactions influence the cell cycle and DNA damage response.

Domain decomposition for the computation of radiosity in lighting simulation; Decomposition de domaines pour le calcul de la radiosite en simulation d'eclairage

Energy Technology Data Exchange (ETDEWEB)

Salque, B

1998-07-01

This work deals with the equation of radiosity, this equation describes the transport of light energy through a diffuse medium, its resolution enables us to simulate the presence of light sources. The equation of radiosity is an integral equation who admits a unique solution in realistic cases. The different methods of solving are reviewed. The equation of radiosity can not be formulated as the integral form of a classical partial differential equation, but this work shows that the technique of domain decomposition can be successfully applied to the equation of radiosity if this approach is framed by considerations of physics. This method provides a system of independent equations valid for each sub-domain and whose main parameter is luminance. Some numerical examples give an idea of the convergence of the algorithm. This method is applied to the optimization of the shape of a light reflector.

Quasi-exact evaluation of time domain MFIE MOT matrix elements

KAUST Repository

Shi, Yifei; Bagci, Hakan; Shanker, Balasubramaniam; Lu, Mingyu; Michielssen, Eric

2013-01-01

A previously proposed quasi-exact scheme for evaluating matrix elements resulting from the marching-on-in-time (MOT) discretization of the time domain electric field integral equation (EFIE) is extended to matrix entries resulting from the discretization of its magnetic field integral equation (MFIE) counterpart. Numerical results demonstrate the accuracy of the scheme as well as the late-time stability of the resulting MOT-MFIE solver. © 2013 IEEE.

Quasi-exact evaluation of time domain MFIE MOT matrix elements

KAUST Repository

Shi, Yifei

2013-07-01

A previously proposed quasi-exact scheme for evaluating matrix elements resulting from the marching-on-in-time (MOT) discretization of the time domain electric field integral equation (EFIE) is extended to matrix entries resulting from the discretization of its magnetic field integral equation (MFIE) counterpart. Numerical results demonstrate the accuracy of the scheme as well as the late-time stability of the resulting MOT-MFIE solver. © 2013 IEEE.

The stress-reward-mentalizing model of depression: An integrative developmental cascade approach to child and adolescent depressive disorder based on the research domain criteria (RDoC) approach.

Science.gov (United States)

Luyten, Patrick; Fonagy, Peter

2017-10-09

The Research Domain Criteria (RDoC) propose a much-needed change in approach to the study of vulnerability factors implicated in mental disorders, shifting away from a categorical, disease-oriented model to a dimensional approach that focuses on underlying systems implicated in psychopathology. In this paper we illustrate this approach with a focus on the emergence of depression in childhood and adolescence. Based on evolutionary biological and developmental psychopathology considerations, we present an integrative developmental cascade model of depression that essentially suggests that depression emerges out of a three-pronged series of interacting impairments in the domains of stress regulation, reward, and mentalizing. We discuss the relation of these impairments to the five domains proposed by RDoC. We also focus on how this model may explain in large part the marked comorbidity of depression with other psychiatric disorders, as well as with functional somatic and somatic disorders. Limitations of this theoretical approach are discussed, as well as implications for the development, evaluation, and dissemination of interventions aimed at preventing or treating depression. Copyright © 2017 Elsevier Ltd. All rights reserved.

3DSwap: Curated knowledgebase of proteins involved in 3D domain swapping

KAUST Repository

Shameer, Khader

2011-09-29

Three-dimensional domain swapping is a unique protein structural phenomenon where two or more protein chains in a protein oligomer share a common structural segment between individual chains. This phenomenon is observed in an array of protein structures in oligomeric conformation. Protein structures in swapped conformations perform diverse functional roles and are also associated with deposition diseases in humans. We have performed in-depth literature curation and structural bioinformatics analyses to develop an integrated knowledgebase of proteins involved in 3D domain swapping. The hallmark of 3D domain swapping is the presence of distinct structural segments such as the hinge and swapped regions. We have curated the literature to delineate the boundaries of these regions. In addition, we have defined several new concepts like \\'secondary major interface\\' to represent the interface properties arising as a result of 3D domain swapping, and a new quantitative measure for the \\'extent of swapping\\' in structures. The catalog of proteins reported in 3DSwap knowledgebase has been generated using an integrated structural bioinformatics workflow of database searches, literature curation, by structure visualization and sequence-structure-function analyses. The current version of the 3DSwap knowledgebase reports 293 protein structures, the analysis of such a compendium of protein structures will further the understanding molecular factors driving 3D domain swapping. The Author(s) 2011.

Integrated Rudder/Fin Concise Control Based on Frequency Domain Analysis

OpenAIRE

W. Guan; Z. J. Su; G. Q. Zhang

2013-01-01

This paper describes a concise robust controller design of integrated rudder and fin control system in use of the closed loop gain shaping algorithm (CGSA) strategy. Compared with the arbitrary selection of weighting function in integrated rudder and fin H∞ mixed sensitivity control design procedures, the CGSA methods provided a relatively more straightforward and concise design method. Simulations were described that the overall performance of each CGSA rudder and fin control loop and the in...

Physiomodel - an integrative physiology in Modelica.

Science.gov (United States)

Matejak, Marek; Kofranek, Jiri

2015-08-01

Physiomodel (http://www.physiomodel.org) is our reimplementation and extension of an integrative physiological model called HumMod 1.6 (http://www.hummod.org) using our Physiolibrary (http://www.physiolibrary.org). The computer language Modelica is well-suited to exactly formalize integrative physiology. Modelica is an equation-based, and object-oriented language for hybrid ordinary differential equations (http:// www.modelica.org). Almost every physiological term can be defined as a class in this language and can be instantiated as many times as it occurs in the body. Each class has a graphical icon for use in diagrams. These diagrams are self-describing; the Modelica code generated from them is the full representation of the underlying mathematical model. Special Modelica constructs of physical connectors from Physiolibrary allow us to create diagrams that are analogies of electrical circuits with Kirchhoff's laws. As electric currents and electric potentials are connected in electrical domain, so are molar flows and concentrations in the chemical domain; volumetric flows and pressures in the hydraulic domain; flows of heat energy and temperatures in the thermal domain; and changes and amounts of members in the population domain.

Integrated Visualisation and Description of Complex Systems

National Research Council Canada - National Science Library

Goodburn, D

1999-01-01

... on system topographies and feature overlays. System information from the domain's information space is filtered and integrated into a Composite Systems Model that provides a basis for consistency and integration between all system views...

Aggression and Moral Development: Integrating Social Information Processing and Moral Domain Models

Science.gov (United States)

Arsenio, William F.; Lemerise, Elizabeth A.

2004-01-01

Social information processing and moral domain theories have developed in relative isolation from each other despite their common focus on intentional harm and victimization, and mutual emphasis on social cognitive processes in explaining aggressive, morally relevant behaviors. This article presents a selective summary of these literatures with…

Integrating cross-scale analysis in the spatial and temporal domains for classification of behavioral movement

Directory of Open Access Journals (Sweden)

Ali Soleymani

2014-06-01

Full Text Available Since various behavioral movement patterns are likely to be valid within different, unique ranges of spatial and temporal scales (e.g., instantaneous, diurnal, or seasonal with the corresponding spatial extents, a cross-scale approach is needed for accurate classification of behaviors expressed in movement. Here, we introduce a methodology for the characterization and classification of behavioral movement data that relies on computing and analyzing movement features jointly in both the spatial and temporal domains. The proposed methodology consists of three stages. In the first stage, focusing on the spatial domain, the underlying movement space is partitioned into several zonings that correspond to different spatial scales, and features related to movement are computed for each partitioning level. In the second stage, concentrating on the temporal domain, several movement parameters are computed from trajectories across a series of temporal windows of increasing sizes, yielding another set of input features for the classification. For both the spatial and the temporal domains, the ``reliable scale'' is determined by an automated procedure. This is the scale at which the best classification accuracy is achieved, using only spatial or temporal input features, respectively. The third stage takes the measures from the spatial and temporal domains of movement, computed at the corresponding reliable scales, as input features for behavioral classification. With a feature selection procedure, the most relevant features contributing to known behavioral states are extracted and used to learn a classification model. The potential of the proposed approach is demonstrated on a dataset of adult zebrafish (Danio rerio swimming movements in testing tanks, following exposure to different drug treatments. Our results show that behavioral classification accuracy greatly increases when firstly cross-scale analysis is used to determine the best analysis scale, and

Second-order domain derivative of normal-dependent boundary integrals

KAUST Repository

Balzer, Jonathan

2010-01-01

Numerous reconstruction tasks in (optical) surface metrology allow for a variational formulation. The occurring boundary integrals may be interpreted as shape functions. The paper is concerned with the second-order analysis of such functions. Shape

Intercloud Architecture Framework for Interoperability and Integration

NARCIS (Netherlands)

Demchenko, Y.; Ngo, C.; Makkes, M.X.; Strijkers, R.J.

2013-01-01

This report presents on-going research to develop the Intercloud Architecture Framework (ICAF) that addresses interoperability and integration issues in multi-provider multi-domain heterogeneous Cloud based infrastructure services and applications provisioning, including integration and

The Four Domains Model: Connecting Spirituality, Health and Well-Being

Directory of Open Access Journals (Sweden)

John Fisher

2011-01-01

Full Text Available At our core, or coeur, we humans are spiritual beings. Spirituality can be viewed in a variety of ways from a traditional understanding of spirituality as an expression of religiosity, in search of the sacred, through to a humanistic view of spirituality devoid of religion. Health is also multi-faceted, with increasing evidence reporting the relationship of spirituality with physical, mental, emotional, social and vocational well-being. This paper presents spiritual health as a, if not THE, fundamental dimension of people’s overall health and well-being, permeating and integrating all the other dimensions of health. Spiritual health is a dynamic state of being, reflected in the quality of relationships that people have in up to four domains of spiritual well-being: Personal domain where a person intra-relates with self; Communal domain, with in-depth inter-personal relationships; Environmental domain, connecting with nature; Transcendental domain, relating to some-thing or some‑One beyond the human level. The Four Domains Model of Spiritual Health and Well‑Being embraces all extant world-views from the ardently religious to the atheistic rationalist.

Ground Operations Autonomous Control and Integrated Health Management

Science.gov (United States)

Daniels, James

2014-01-01

The Ground Operations Autonomous Control and Integrated Health Management plays a key role for future ground operations at NASA. The software that is integrated into this system is called G2 2011 Gensym. The purpose of this report is to describe the Ground Operations Autonomous Control and Integrated Health Management with the use of the G2 Gensym software and the G2 NASA toolkit for Integrated System Health Management (ISHM) which is a Computer Software Configuration Item (CSCI). The decision rationale for the use of the G2 platform is to develop a modular capability for ISHM and AC. Toolkit modules include knowledge bases that are generic and can be applied in any application domain module. That way, there's a maximization of reusability, maintainability, and systematic evolution, portability, and scalability. Engine modules are generic, while application modules represent the domain model of a specific application. Furthermore, the NASA toolkit, developed since 2006 (a set of modules), makes it possible to create application domain models quickly, using pre-defined objects that include sensors and components libraries for typical fluid, electrical, and mechanical systems.

Integral equations for free-molecule ow in MEMS: recent advancements

Directory of Open Access Journals (Sweden)

Fedeli Patrick

2017-03-01

Full Text Available We address a Boundary Integral Equation (BIE approach for the analysis of gas dissipation in near-vacuum for Micro Electro Mechanical Systems (MEMS. Inspired by an analogy with the radiosity equation in computer graphics, we discuss an efficient way to compute the visible domain of integration. Moreover, we tackle the issue of near singular integrals by developing a set of analytical formulas for planar polyhedral domains. Finally a validation with experimental results taken from the literature is presented.

Proof of Concept Integration of a Single-Level Service-Oriented Architecture into a Multi-Domain Secure Environment

National Research Council Canada - National Science Library

Gilkey, Craig M

2008-01-01

.... Such web services operating across multiple security domains would provide additional advantages, including improved intelligence aggregation, and real-time collaboration between users in different security domains...

Unfolding of a Temperature-Sensitive Domain Controls Voltage-Gated Channel Activation.

Science.gov (United States)

Arrigoni, Cristina; Rohaim, Ahmed; Shaya, David; Findeisen, Felix; Stein, Richard A; Nurva, Shailika Reddy; Mishra, Smriti; Mchaourab, Hassane S; Minor, Daniel L

2016-02-25

Voltage-gated ion channels (VGICs) are outfitted with diverse cytoplasmic domains that impact function. To examine how such elements may affect VGIC behavior, we addressed how the bacterial voltage-gated sodium channel (BacNa(V)) C-terminal cytoplasmic domain (CTD) affects function. Our studies show that the BacNa(V) CTD exerts a profound influence on gating through a temperature-dependent unfolding transition in a discrete cytoplasmic domain, the neck domain, proximal to the pore. Structural and functional studies establish that the BacNa(V) CTD comprises a bi-partite four-helix bundle that bears an unusual hydrophilic core whose integrity is central to the unfolding mechanism and that couples directly to the channel activation gate. Together, our findings define a general principle for how the widespread four-helix bundle cytoplasmic domain architecture can control VGIC responses, uncover a mechanism underlying the diverse BacNa(V) voltage dependencies, and demonstrate that a discrete domain can encode the temperature-dependent response of a channel. Copyright © 2016 Elsevier Inc. All rights reserved.

Assessing readiness of cyberinfrastructure resources for cross-domain interoperability: a view from an NSF EarthCube roadmap

Science.gov (United States)

Zaslavsky, Ilya; Couch, Alva; Richard, Stephen; Valentine, David; Lehnert, Kerstin; Stocks, Karen; Murphy, Philip

2013-04-01

EarthCube is a new research initiative of the U.S. National Science Foundation, with the mission to develop community-guided cyberinfrastructure integrating data, models and other resources across geoscience disciplines. Analysis and modeling of physical processes that are not confined to disciplinary or jurisdictional boundaries, requires that data and models can be re-used outside the original context in which they are collected or developed. Infrastructure readiness for cross-domain interoperability encompasses the capabilities that need to be in place to enable such information re-use and ensure that it is both scientifically sound and technically feasible. In an ideal cross-domain information integration scenario, resources can be discovered via federated catalogs and linked nomenclatures from neighboring domains, while standard data services can be used to transparently compile composite data products and to integrate information using commonality in key data characteristics related to shared models of spatial features, time measurements, and observations. The main premise of the cross-domain readiness assessment is that when accessing domain resources from another domain, a user expects to be able to discover these resources, interpret them, retrieve the information, and integrate it with other data. Documentation of the resource must be sufficient for a user in a different context to determine fitness for use, and establish trust in scientific soundness. As part of an EarthCube roadmap focused on cross-domain interoperability, we explored a number of approaches to cyberinfrastructure readiness assessment, addressing both readiness of existing resources, and readiness of processes that enable cross-domain communication and information exchange across disciplinary boundaries. Our initial assessment considers basic infrastructure components required to enable cross-domain interoperability in the geosciences. These components, and the evaluation metrics

Multi-GPU-based acceleration of the explicit time domain volume integral equation solver using MPI-OpenACC

KAUST Repository

Feki, Saber

2013-07-01

An explicit marching-on-in-time (MOT)-based time-domain volume integral equation (TDVIE) solver has recently been developed for characterizing transient electromagnetic wave interactions on arbitrarily shaped dielectric bodies (A. Al-Jarro et al., IEEE Trans. Antennas Propag., vol. 60, no. 11, 2012). The solver discretizes the spatio-temporal convolutions of the source fields with the background medium\\'s Green function using nodal discretization in space and linear interpolation in time. The Green tensor, which involves second order spatial and temporal derivatives, is computed using finite differences on the temporal and spatial grid. A predictor-corrector algorithm is used to maintain the stability of the MOT scheme. The simplicity of the discretization scheme permits the computation of the discretized spatio-temporal convolutions on the fly during time marching; no \\'interaction\\' matrices are pre-computed or stored resulting in a memory efficient scheme. As a result, most often the applicability of this solver to the characterization of wave interactions on electrically large structures is limited by the computation time but not the memory. © 2013 IEEE.

CONNJUR Workflow Builder: a software integration environment for spectral reconstruction.

Science.gov (United States)

Fenwick, Matthew; Weatherby, Gerard; Vyas, Jay; Sesanker, Colbert; Martyn, Timothy O; Ellis, Heidi J C; Gryk, Michael R

2015-07-01

CONNJUR Workflow Builder (WB) is an open-source software integration environment that leverages existing spectral reconstruction tools to create a synergistic, coherent platform for converting biomolecular NMR data from the time domain to the frequency domain. WB provides data integration of primary data and metadata using a relational database, and includes a library of pre-built workflows for processing time domain data. WB simplifies maximum entropy reconstruction, facilitating the processing of non-uniformly sampled time domain data. As will be shown in the paper, the unique features of WB provide it with novel abilities to enhance the quality, accuracy, and fidelity of the spectral reconstruction process. WB also provides features which promote collaboration, education, parameterization, and non-uniform data sets along with processing integrated with the Rowland NMR Toolkit (RNMRTK) and NMRPipe software packages. WB is available free of charge in perpetuity, dual-licensed under the MIT and GPL open source licenses.

CONNJUR Workflow Builder: a software integration environment for spectral reconstruction

Energy Technology Data Exchange (ETDEWEB)

Fenwick, Matthew; Weatherby, Gerard; Vyas, Jay; Sesanker, Colbert [UConn Health, Department of Molecular Biology and Biophysics (United States); Martyn, Timothy O. [Rensselaer at Hartford, Department of Engineering and Science (United States); Ellis, Heidi J. C. [Western New England College, Department of Computer Science and Information Technology (United States); Gryk, Michael R., E-mail: gryk@uchc.edu [UConn Health, Department of Molecular Biology and Biophysics (United States)

2015-07-15

CONNJUR Workflow Builder (WB) is an open-source software integration environment that leverages existing spectral reconstruction tools to create a synergistic, coherent platform for converting biomolecular NMR data from the time domain to the frequency domain. WB provides data integration of primary data and metadata using a relational database, and includes a library of pre-built workflows for processing time domain data. WB simplifies maximum entropy reconstruction, facilitating the processing of non-uniformly sampled time domain data. As will be shown in the paper, the unique features of WB provide it with novel abilities to enhance the quality, accuracy, and fidelity of the spectral reconstruction process. WB also provides features which promote collaboration, education, parameterization, and non-uniform data sets along with processing integrated with the Rowland NMR Toolkit (RNMRTK) and NMRPipe software packages. WB is available free of charge in perpetuity, dual-licensed under the MIT and GPL open source licenses.

CONNJUR Workflow Builder: a software integration environment for spectral reconstruction

International Nuclear Information System (INIS)

Fenwick, Matthew; Weatherby, Gerard; Vyas, Jay; Sesanker, Colbert; Martyn, Timothy O.; Ellis, Heidi J. C.; Gryk, Michael R.

2015-01-01

CONNJUR Workflow Builder (WB) is an open-source software integration environment that leverages existing spectral reconstruction tools to create a synergistic, coherent platform for converting biomolecular NMR data from the time domain to the frequency domain. WB provides data integration of primary data and metadata using a relational database, and includes a library of pre-built workflows for processing time domain data. WB simplifies maximum entropy reconstruction, facilitating the processing of non-uniformly sampled time domain data. As will be shown in the paper, the unique features of WB provide it with novel abilities to enhance the quality, accuracy, and fidelity of the spectral reconstruction process. WB also provides features which promote collaboration, education, parameterization, and non-uniform data sets along with processing integrated with the Rowland NMR Toolkit (RNMRTK) and NMRPipe software packages. WB is available free of charge in perpetuity, dual-licensed under the MIT and GPL open source licenses

ViSlang: A system for interpreted domain-specific languages for scientific visualization

KAUST Repository

Rautek, Peter

2014-12-31

Researchers from many domains use scientific visualization in their daily practice. Existing implementations of algorithms usually come with a graphical user interface (high-level interface), or as software library or source code (low-level interface). In this paper we present a system that integrates domain-specific languages (DSLs) and facilitates the creation of new DSLs. DSLs provide an effective interface for domain scientists avoiding the difficulties involved with low-level interfaces and at the same time offering more flexibility than high-level interfaces. We describe the design and implementation of ViSlang, an interpreted language specifically tailored for scientific visualization. A major contribution of our design is the extensibility of the ViSlang language. Novel DSLs that are tailored to the problems of the domain can be created and integrated into ViSlang. We show that our approach can be added to existing user interfaces to increase the flexibility for expert users on demand, but at the same time does not interfere with the user experience of novice users. To demonstrate the flexibility of our approach we present new DSLs for volume processing, querying and visualization. We report the implementation effort for new DSLs and compare our approach with Matlab and Python implementations in terms of run-time performance.

The BRCT domain is a phospho-protein binding domain.

Science.gov (United States)

Yu, Xiaochun; Chini, Claudia Christiano Silva; He, Miao; Mer, Georges; Chen, Junjie

2003-10-24

The carboxyl-terminal domain (BRCT) of the Breast Cancer Gene 1 (BRCA1) protein is an evolutionarily conserved module that exists in a large number of proteins from prokaryotes to eukaryotes. Although most BRCT domain-containing proteins participate in DNA-damage checkpoint or DNA-repair pathways, or both, the function of the BRCT domain is not fully understood. We show that the BRCA1 BRCT domain directly interacts with phosphorylated BRCA1-Associated Carboxyl-terminal Helicase (BACH1). This specific interaction between BRCA1 and phosphorylated BACH1 is cell cycle regulated and is required for DNA damage-induced checkpoint control during the transition from G2 to M phase of the cell cycle. Further, we show that two other BRCT domains interact with their respective physiological partners in a phosphorylation-dependent manner. Thirteen additional BRCT domains also preferentially bind phospho-peptides rather than nonphosphorylated control peptides. These data imply that the BRCT domain is a phospho-protein binding domain involved in cell cycle control.

Simulating propagation of decomposed elastic waves using low-rank approximate mixed-domain integral operators for heterogeneous transversely isotropic media

KAUST Repository

Cheng, Jiubing

2014-08-05

In elastic imaging, the extrapolated vector fields are decomposed into pure wave modes, such that the imaging condition produces interpretable images, which characterize reflectivity of different reflection types. Conventionally, wavefield decomposition in anisotropic media is costly as the operators involved is dependent on the velocity, and thus not stationary. In this abstract, we propose an efficient approach to directly extrapolate the decomposed elastic waves using lowrank approximate mixed space/wavenumber domain integral operators for heterogeneous transverse isotropic (TI) media. The low-rank approximation is, thus, applied to the pseudospectral extrapolation and decomposition at the same time. The pseudo-spectral implementation also allows for relatively large time steps in which the low-rank approximation is applied. Synthetic examples show that it can yield dispersionfree extrapolation of the decomposed quasi-P (qP) and quasi- SV (qSV) modes, which can be used for imaging, as well as the total elastic wavefields.

Late replication domains are evolutionary conserved in the Drosophila genome.

Science.gov (United States)

Andreyenkova, Natalya G; Kolesnikova, Tatyana D; Makunin, Igor V; Pokholkova, Galina V; Boldyreva, Lidiya V; Zykova, Tatyana Yu; Zhimulev, Igor F; Belyaeva, Elena S

2013-01-01

Drosophila chromosomes are organized into distinct domains differing in their predominant chromatin composition, replication timing and evolutionary conservation. We show on a genome-wide level that genes whose order has remained unaltered across 9 Drosophila species display late replication timing and frequently map to the regions of repressive chromatin. This observation is consistent with the existence of extensive domains of repressive chromatin that replicate extremely late and have conserved gene order in the Drosophila genome. We suggest that such repressive chromatin domains correspond to a handful of regions that complete replication at the very end of S phase. We further demonstrate that the order of genes in these regions is rarely altered in evolution. Substantial proportion of such regions significantly coincide with large synteny blocks. This indicates that there are evolutionary mechanisms maintaining the integrity of these late-replicating chromatin domains. The synteny blocks corresponding to the extremely late-replicating regions in the D. melanogaster genome consistently display two-fold lower gene density across different Drosophila species.

Homogenization of the evolution Stokes equation in a perforated domain with a stochastic Fourier boundary condition

KAUST Repository

Bessaih, Hakima

2015-04-01

The evolution Stokes equation in a domain containing periodically distributed obstacles subject to Fourier boundary condition on the boundaries is considered. We assume that the dynamic is driven by a stochastic perturbation on the interior of the domain and another stochastic perturbation on the boundaries of the obstacles. We represent the solid obstacles by holes in the fluid domain. The macroscopic (homogenized) equation is derived as another stochastic partial differential equation, defined in the whole non perforated domain. Here, the initial stochastic perturbation on the boundary becomes part of the homogenized equation as another stochastic force. We use the twoscale convergence method after extending the solution with 0 in the holes to pass to the limit. By Itô stochastic calculus, we get uniform estimates on the solution in appropriate spaces. In order to pass to the limit on the boundary integrals, we rewrite them in terms of integrals in the whole domain. In particular, for the stochastic integral on the boundary, we combine the previous idea of rewriting it on the whole domain with the assumption that the Brownian motion is of trace class. Due to the particular boundary condition dealt with, we get that the solution of the stochastic homogenized equation is not divergence free. However, it is coupled with the cell problem that has a divergence free solution. This paper represents an extension of the results of Duan and Wang (Comm. Math. Phys. 275:1508-1527, 2007), where a reaction diffusion equation with a dynamical boundary condition with a noise source term on both the interior of the domain and on the boundary was studied, and through a tightness argument and a pointwise two scale convergence method the homogenized equation was derived. © American Institute of Mathematical Sciences.

A parallel algorithm for solving the multidimensional within-group discrete ordinates equations with spatial domain decomposition - 104

International Nuclear Information System (INIS)

Zerr, R.J.; Azmy, Y.Y.

2010-01-01

A spatial domain decomposition with a parallel block Jacobi solution algorithm has been developed based on the integral transport matrix formulation of the discrete ordinates approximation for solving the within-group transport equation. The new methodology abandons the typical source iteration scheme and solves directly for the fully converged scalar flux. Four matrix operators are constructed based upon the integral form of the discrete ordinates equations. A single differential mesh sweep is performed to construct these operators. The method is parallelized by decomposing the problem domain into several smaller sub-domains, each treated as an independent problem. The scalar flux of each sub-domain is solved exactly given incoming angular flux boundary conditions. Sub-domain boundary conditions are updated iteratively, and convergence is achieved when the scalar flux error in all cells meets a pre-specified convergence criterion. The method has been implemented in a computer code that was then employed for strong scaling studies of the algorithm's parallel performance via a fixed-size problem in tests ranging from one domain up to one cell per sub-domain. Results indicate that the best parallel performance compared to source iterations occurs for optically thick, highly scattering problems, the variety that is most difficult for the traditional SI scheme to solve. Moreover, the minimum execution time occurs when each sub-domain contains a total of four cells. (authors)

Varieties of Cognitive Integration

Science.gov (United States)

Scott, William A.

1974-01-01

The author examines how students in three countries use four styles of cognitive integration (affective balance, affective-evaluative consistency, centralization, and image comparability) within the cognitive domains of nations, acquaintances, self-roles, and family relations. (DE)

Domain analysis

DEFF Research Database (Denmark)

Hjørland, Birger

2017-01-01

The domain-analytic approach to knowledge organization (KO) (and to the broader field of library and information science, LIS) is outlined. The article reviews the discussions and proposals on the definition of domains, and provides an example of a domain-analytic study in the field of art studies....... Varieties of domain analysis as well as criticism and controversies are presented and discussed....

Spectral analysis of point-vortex dynamics: first application to vortex polygons in a circular domain

International Nuclear Information System (INIS)

Speetjens, M F M; Meleshko, V V; Van Heijst, G J F

2014-01-01

The present study addresses the classical problem of the dynamics and stability of a cluster of N-point vortices of equal strength arranged in a polygonal configuration (‘N-vortex polygons’). In unbounded domains, such N-vortex polygons are unconditionally stable for N⩽7. Confinement in a circular domain tightens the stability conditions to N⩽6 and a maximum polygon size relative to the domain radius. This work expands on existing studies on stability and integrability by a first giving an exploratory spectral analysis of the dynamics of N vortex polygons in circular domains. Key to this is that the spectral signature of the time evolution of vortex positions reflects their qualitative behaviour. Expressing vortex motion by a generic evolution operator (the so-called Koopman operator) provides a rigorous framework for such spectral analyses. This paves the way to further differentiation and classification of point-vortex behaviour beyond stability and integrability. The concept of Koopman-based spectral analysis is demonstrated for N-vortex polygons. This reveals that conditional stability can be seen as a local form of integrability and confirms an important generic link between spectrum and dynamics: discrete spectra imply regular (quasi-periodic) motion; continuous (sub-)spectra imply chaotic motion. Moreover, this exposes rich nonlinear dynamics as intermittency between regular and chaotic motion and quasi-coherent structures formed by chaotic vortices. (ss 1)

Inferring domain-domain interactions from protein-protein interactions with formal concept analysis.

Directory of Open Access Journals (Sweden)

Susan Khor

Full Text Available Identifying reliable domain-domain interactions will increase our ability to predict novel protein-protein interactions, to unravel interactions in protein complexes, and thus gain more information about the function and behavior of genes. One of the challenges of identifying reliable domain-domain interactions is domain promiscuity. Promiscuous domains are domains that can occur in many domain architectures and are therefore found in many proteins. This becomes a problem for a method where the score of a domain-pair is the ratio between observed and expected frequencies because the protein-protein interaction network is sparse. As such, many protein-pairs will be non-interacting and domain-pairs with promiscuous domains will be penalized. This domain promiscuity challenge to the problem of inferring reliable domain-domain interactions from protein-protein interactions has been recognized, and a number of work-arounds have been proposed. This paper reports on an application of Formal Concept Analysis to this problem. It is found that the relationship between formal concepts provides a natural way for rare domains to elevate the rank of promiscuous domain-pairs and enrich highly ranked domain-pairs with reliable domain-domain interactions. This piggybacking of promiscuous domain-pairs onto less promiscuous domain-pairs is possible only with concept lattices whose attribute-labels are not reduced and is enhanced by the presence of proteins that comprise both promiscuous and rare domains.

Inferring Domain-Domain Interactions from Protein-Protein Interactions with Formal Concept Analysis

Science.gov (United States)

Khor, Susan

2014-01-01

Identifying reliable domain-domain interactions will increase our ability to predict novel protein-protein interactions, to unravel interactions in protein complexes, and thus gain more information about the function and behavior of genes. One of the challenges of identifying reliable domain-domain interactions is domain promiscuity. Promiscuous domains are domains that can occur in many domain architectures and are therefore found in many proteins. This becomes a problem for a method where the score of a domain-pair is the ratio between observed and expected frequencies because the protein-protein interaction network is sparse. As such, many protein-pairs will be non-interacting and domain-pairs with promiscuous domains will be penalized. This domain promiscuity challenge to the problem of inferring reliable domain-domain interactions from protein-protein interactions has been recognized, and a number of work-arounds have been proposed. This paper reports on an application of Formal Concept Analysis to this problem. It is found that the relationship between formal concepts provides a natural way for rare domains to elevate the rank of promiscuous domain-pairs and enrich highly ranked domain-pairs with reliable domain-domain interactions. This piggybacking of promiscuous domain-pairs onto less promiscuous domain-pairs is possible only with concept lattices whose attribute-labels are not reduced and is enhanced by the presence of proteins that comprise both promiscuous and rare domains. PMID:24586450

PHIDIAS- Pathogen Host Interaction Data Integration and Analysis

Indian Academy of Sciences (India)

PHIDIAS- Pathogen Host Interaction Data Integration and Analysis- allows searching of integrated genome sequences, conserved domains and gene expressions data related to pathogen host interactions in high priority agents for public health and security ...

Improving pairwise comparison of protein sequences with domain co-occurrence

Science.gov (United States)

Gascuel, Olivier

2018-01-01

Comparing and aligning protein sequences is an essential task in bioinformatics. More specifically, local alignment tools like BLAST are widely used for identifying conserved protein sub-sequences, which likely correspond to protein domains or functional motifs. However, to limit the number of false positives, these tools are used with stringent sequence-similarity thresholds and hence can miss several hits, especially for species that are phylogenetically distant from reference organisms. A solution to this problem is then to integrate additional contextual information to the procedure. Here, we propose to use domain co-occurrence to increase the sensitivity of pairwise sequence comparisons. Domain co-occurrence is a strong feature of proteins, since most protein domains tend to appear with a limited number of other domains on the same protein. We propose a method to take this information into account in a typical BLAST analysis and to construct new domain families on the basis of these results. We used Plasmodium falciparum as a case study to evaluate our method. The experimental findings showed an increase of 14% of the number of significant BLAST hits and an increase of 25% of the proteome area that can be covered with a domain. Our method identified 2240 new domains for which, in most cases, no model of the Pfam database could be linked. Moreover, our study of the quality of the new domains in terms of alignment and physicochemical properties show that they are close to that of standard Pfam domains. Source code of the proposed approach and supplementary data are available at: https://gite.lirmm.fr/menichelli/pairwise-comparison-with-cooccurrence PMID:29293498

Exceptionally High Piezoelectric Coefficient and Low Strain Hysteresis in Grain-Oriented (Ba, Ca)(Ti, Zr)O3 through Integrating Crystallographic Texture and Domain Engineering.

Science.gov (United States)

Liu, Yingchun; Chang, Yunfei; Li, Fei; Yang, Bin; Sun, Yuan; Wu, Jie; Zhang, Shantao; Wang, Ruixue; Cao, Wenwu

2017-09-06

Both low strain hysteresis and high piezoelectric performance are required for practical applications in precisely controlled piezoelectric devices and systems. Unfortunately, enhanced piezoelectric properties were usually obtained with the presence of a large strain hysteresis in BaTiO 3 (BT)-based piezoceramics. In this work, we propose to integrate crystallographic texturing and domain engineering strategies into BT-based ceramics to resolve this challenge. [001] c grain-oriented (Ba 0.94 Ca 0.06 )(Ti 0.95 Zr 0.05 )O 3 (BCTZ) ceramics with a texture degree as high as 98.6% were synthesized by templated grain growth. A very high piezoelectric coefficient (d 33 ) of 755 pC/N, and an extremely large piezoelectric strain coefficient (d 33 * = 2027 pm/V) along with an ultralow strain hysteresis (H s ) of 4.1% were simultaneously achieved in BT-based systems for the first time, which are among the best values ever reported on both lead-free and lead-based piezoceramics. The exceptionally high piezoelectric response is mainly from the reversible contribution, and can be ascribed to the piezoelectric anisotropy, the favorable domain configuration, and the formation of smaller sized domains in the BCTZ textured ceramics. This study paves a new pathway to develop lead-free piezoelectrics with both low strain hysteresis and high piezoelectric coefficient. More importantly, it represents a very exciting discovery with potential application of BT-based ceramics in high-precision piezoelectric actuators.

Domain decomposition solvers for nonlinear multiharmonic finite element equations

KAUST Repository

Copeland, D. M.

2010-01-01

In many practical applications, for instance, in computational electromagnetics, the excitation is time-harmonic. Switching from the time domain to the frequency domain allows us to replace the expensive time-integration procedure by the solution of a simple elliptic equation for the amplitude. This is true for linear problems, but not for nonlinear problems. However, due to the periodicity of the solution, we can expand the solution in a Fourier series. Truncating this Fourier series and approximating the Fourier coefficients by finite elements, we arrive at a large-scale coupled nonlinear system for determining the finite element approximation to the Fourier coefficients. The construction of fast solvers for such systems is very crucial for the efficiency of this multiharmonic approach. In this paper we look at nonlinear, time-harmonic potential problems as simple model problems. We construct and analyze almost optimal solvers for the Jacobi systems arising from the Newton linearization of the large-scale coupled nonlinear system that one has to solve instead of performing the expensive time-integration procedure. © 2010 de Gruyter.

The OXL format for the exchange of integrated datasets

Directory of Open Access Journals (Sweden)

Taubert Jan

2007-12-01

Full Text Available A prerequisite for systems biology is the integration and analysis of heterogeneous experimental data stored in hundreds of life-science databases and millions of scientific publications. Several standardised formats for the exchange of specific kinds of biological information exist. Such exchange languages facilitate the integration process; however they are not designed to transport integrated datasets. A format for exchanging integrated datasets needs to i cover data from a broad range of application domains, ii be flexible and extensible to combine many different complex data structures, iii include metadata and semantic definitions, iv include inferred information, v identify the original data source for integrated entities and vi transport large integrated datasets. Unfortunately, none of the exchange formats from the biological domain (e.g. BioPAX, MAGE-ML, PSI-MI, SBML or the generic approaches (RDF, OWL fulfil these requirements in a systematic way.

iPfam: a database of protein family and domain interactions found in the Protein Data Bank.

Science.gov (United States)

Finn, Robert D; Miller, Benjamin L; Clements, Jody; Bateman, Alex

2014-01-01

The database iPfam, available at http://ipfam.org, catalogues Pfam domain interactions based on known 3D structures that are found in the Protein Data Bank, providing interaction data at the molecular level. Previously, the iPfam domain-domain interaction data was integrated within the Pfam database and website, but it has now been migrated to a separate database. This allows for independent development, improving data access and giving clearer separation between the protein family and interactions datasets. In addition to domain-domain interactions, iPfam has been expanded to include interaction data for domain bound small molecule ligands. Functional annotations are provided from source databases, supplemented by the incorporation of Wikipedia articles where available. iPfam (version 1.0) contains >9500 domain-domain and 15 500 domain-ligand interactions. The new website provides access to this data in a variety of ways, including interactive visualizations of the interaction data.

An Integrated Virtual Environment System

National Research Council Canada - National Science Library

Hahn, James K; Gritz, Larry; Darken, Rudolph; Geigel, Joseph; Lee, Jong W

1993-01-01

.... A joint research at the George Washington University and the Naval Research Laboratory is bringing together issues from these domains to study the factors that contribute to an integrated virtual environment...

Defining inter-cloud architecture for interoperability and integration

NARCIS (Netherlands)

Demchenko, Y.; Ngo, C.; Makkes, M.X.; Strijkers, R.; de Laat, C.; Zimmermann, W.; Lee, Y.W.; Demchenko, Y.

2012-01-01

This paper presents an on-going research to develop the Inter-Cloud Architecture, which addresses the architectural problems in multi-provider multi-domain heterogeneous cloud based applications integration and interoperability, including integration and interoperability with legacy infrastructure

Defining Inter-Cloud Architecture for Interoperability and Integration

NARCIS (Netherlands)

Demchenko, Y.; Ngo, C.; Makkes, M.X.; Strijkers, R.J.; Laat, C. de

2012-01-01

This paper presents on-going research to develop the Inter-Cloud Architecture that should address problems in multi-provider multi-domain heterogeneous Cloud based applications integration and interoperability, including integration and interoperability with legacy infrastructure services. Cloud

3-D electromagnetic modeling for very early time sounding of shallow targets using integral equations

International Nuclear Information System (INIS)

Xiong, Z.; Tripp, A.C.

1994-01-01

This paper presents an integral equation algorithm for 3D EM modeling at high frequencies for applications in engineering an environmental studies. The integral equation method remains the same for low and high frequencies, but the dominant roles of the displacements currents complicate both numerical treatments and interpretations. With singularity extraction technique they successively extended the application of the Hankel filtering technique to the computation of Hankel integrals occurring in high frequency EM modeling. Time domain results are calculated from frequency domain results via Fourier transforms. While frequency domain data are not obvious for interpretations, time domain data show wave-like pictures that resemble seismograms. Both 1D and 3D numerical results show clearly the layer interfaces

Business Level Service-Oriented Enterprise Application Integration

NARCIS (Netherlands)

Pokraev, S.; Quartel, Dick; Steen, Maarten W.A.; Wombacher, Andreas; Reichert, M.U.

2007-01-01

In this paper we propose a new approach for service-oriented enterprise application integration (EAI). Unlike current EAI solutions, which mainly focus on technological aspects, our approach allows business domain experts to get more involved in the integration process. First, we provide a technique

Precise Aperture-Dependent Motion Compensation with Frequency Domain Fast Back-Projection Algorithm

Directory of Open Access Journals (Sweden)

Man Zhang

2017-10-01

Full Text Available Precise azimuth-variant motion compensation (MOCO is an essential and difficult task for high-resolution synthetic aperture radar (SAR imagery. In conventional post-filtering approaches, residual azimuth-variant motion errors are generally compensated through a set of spatial post-filters, where the coarse-focused image is segmented into overlapped blocks concerning the azimuth-dependent residual errors. However, image domain post-filtering approaches, such as precise topography- and aperture-dependent motion compensation algorithm (PTA, have difficulty of robustness in declining, when strong motion errors are involved in the coarse-focused image. In this case, in order to capture the complete motion blurring function within each image block, both the block size and the overlapped part need necessary extension leading to degeneration of efficiency and robustness inevitably. Herein, a frequency domain fast back-projection algorithm (FDFBPA is introduced to deal with strong azimuth-variant motion errors. FDFBPA disposes of the azimuth-variant motion errors based on a precise azimuth spectrum expression in the azimuth wavenumber domain. First, a wavenumber domain sub-aperture processing strategy is introduced to accelerate computation. After that, the azimuth wavenumber spectrum is partitioned into a set of wavenumber blocks, and each block is formed into a sub-aperture coarse resolution image via the back-projection integral. Then, the sub-aperture images are straightforwardly fused together in azimuth wavenumber domain to obtain a full resolution image. Moreover, chirp-Z transform (CZT is also introduced to implement the sub-aperture back-projection integral, increasing the efficiency of the algorithm. By disusing the image domain post-filtering strategy, robustness of the proposed algorithm is improved. Both simulation and real-measured data experiments demonstrate the effectiveness and superiority of the proposal.

Strain-controlled magnetic domain wall propagation in hybrid piezoelectric/ferromagnetic structures.

Science.gov (United States)

Lei, Na; Devolder, Thibaut; Agnus, Guillaume; Aubert, Pascal; Daniel, Laurent; Kim, Joo-Von; Zhao, Weisheng; Trypiniotis, Theodossis; Cowburn, Russell P; Chappert, Claude; Ravelosona, Dafiné; Lecoeur, Philippe

2013-01-01

The control of magnetic order in nanoscale devices underpins many proposals for integrating spintronics concepts into conventional electronics. A key challenge lies in finding an energy-efficient means of control, as power dissipation remains an important factor limiting future miniaturization of integrated circuits. One promising approach involves magnetoelectric coupling in magnetostrictive/piezoelectric systems, where induced strains can bear directly on the magnetic anisotropy. While such processes have been demonstrated in several multiferroic heterostructures, the incorporation of such complex materials into practical geometries has been lacking. Here we demonstrate the possibility of generating sizeable anisotropy changes, through induced strains driven by applied electric fields, in hybrid piezoelectric/spin-valve nanowires. By combining magneto-optical Kerr effect and magnetoresistance measurements, we show that domain wall propagation fields can be doubled under locally applied strains. These results highlight the prospect of constructing low-power domain wall gates for magnetic logic devices.

Application of the Integrated Safety Assessment methodology to safety margins. Dynamic Event Trees, Damage Domains and Risk Assessment

International Nuclear Information System (INIS)

Ibánez, L.; Hortal, J.; Queral, C.; Gómez-Magán, J.; Sánchez-Perea, M.; Fernández, I.; Meléndez, E.; Expósito, A.; Izquierdo, J.M.; Gil, J.; Marrao, H.; Villalba-Jabonero, E.

2016-01-01

The Integrated Safety Assessment (ISA) methodology, developed by the Consejo de Seguridad Nuclear, has been applied to an analysis of Zion NPP for sequences with Loss of the Component Cooling Water System (CCWS). The ISA methodology proposal starts from the unfolding of the Dynamic Event Tree (DET). Results from this first step allow assessing the sequence delineation of standard Probabilistic Safety Analysis results. For some sequences of interest of the outlined DET, ISA then identifies the Damage Domain (DD). This is the region of uncertain times and/or parameters where a safety limit is exceeded, which indicates the occurrence of certain damage situation. This paper illustrates application of this concept obtained simulating sequences with MAAP and with TRACE. From information of simulation results of sequence transients belonging to the DD and the time-density probability distributions of the manual actions and of occurrence of stochastic phenomena, ISA integrates the dynamic reliability equations proposed to obtain the sequence contribution to the global Damage Exceedance Frequency (DEF). Reported results show a slight increase in the DEF for sequences investigated following a power uprate from 100% to 110%. This demonstrates the potential use of the method to help in the assessment of design modifications. - Highlights: • This paper illustrates an application of the ISA methodology to safety margins. • Dynamic Event Trees are useful tool for verifying the standard PSA Event Trees. • The ISA methodology takes into account the uncertainties in human action times. • The ISA methodology shows the Damage Exceedance Frequency increase in power uprates.

The YARHG domain: an extracellular domain in search of a function.

Directory of Open Access Journals (Sweden)

Penny Coggill

Full Text Available We have identified a new bacterial protein domain that we hypothesise binds to peptidoglycan. This domain is called the YARHG domain after the most highly conserved sequence-segment. The domain is found in the extracellular space and is likely to be composed of four alpha-helices. The domain is found associated with protein kinase domains, suggesting it is associated with signalling in some bacteria. The domain is also found associated with three different families of peptidases. The large number of different domains that are found associated with YARHG suggests that it is a useful functional module that nature has recombined multiple times.

Fatty acid-producing hosts

Science.gov (United States)

Pfleger, Brian F; Lennen, Rebecca M

2013-12-31

Described are hosts for overproducing a fatty acid product such as a fatty acid. The hosts include an exogenous nucleic acid encoding a thioesterase and, optionally, an exogenous nucleic acid encoding an acetyl-CoA carboxylase, wherein an acyl-CoA synthetase in the hosts are functionally delected. The hosts prefereably include the nucleic acid encoding the thioesterase at an intermediate copy number. The hosts are preferably recominantly stable and growth-competent at 37.degree. C. Methods of producing a fatty acid product comprising culturing such hosts at 37.degree. C. are also described.

Confluent education: an integrative method for nursing (continuing) education.

NARCIS (Netherlands)

Francke, A.L.; Erkens, T.

1994-01-01

Confluent education is presented as a method to bridge the gap between cognitive and affective learning. Attention is focused on three main characteristics of confluent education: (a) the integration of four overlapping domains in a learning process (readiness, the cognitive domain, the affective

.Gov Domains API

Data.gov (United States)

General Services Administration — This dataset offers the list of all .gov domains, including state, local, and tribal .gov domains. It does not include .mil domains, or other federal domains outside...

A boundary value problem for a third order hyperbolic equation with degeneration of order inside the domain

Directory of Open Access Journals (Sweden)

Ruzanna Kh. Makaova

2017-12-01

Full Text Available In this paper we study the boundary value problem for a degenerating third order equation of hyperbolic type in a mixed domain. The equation under consideration in the positive part of the domain coincides with the Hallaire equation, which is a pseudoparabolic type equation. Moreover, in the negative part of the domain it coincides with a degenerating hyperbolic equation of the first kind, the particular case of the Bitsadze–Lykov equation. The existence and uniqueness theorem for the solution is proved. The uniqueness of the solution to the problem is proved with the Tricomi method. Using the functional relationships of the positive and negative parts of the domain on the degeneration line, we arrive at the convolution type Volterra integral equation of the 2nd kind with respect to the desired solution by a derivative trace. With the Laplace transform method, we obtain the solution of the integral equation in its explicit form. At last, the solution to the problem under study is written out explicitly as the solution of the second boundary-value problem in the positive part of the domain for the Hallaire equation and as the solution to the Cauchy problem in the negative part of the domain for a degenerate hyperbolic equation of the first kind.

Pattern deformation and annihilation in two-dimensional excitable media in oscillatory domains

International Nuclear Information System (INIS)

Ramos, J.I.

2008-01-01

The effects of oscillatory domains on the dynamics of the FitzHugh-Nagumo equation in two dimensions is investigated as a function of the amplitude and frequency of the boundary motion. It is shown that the moving-boundary problem introduces anisotropy through the diffusion terms and an advection-like term in the direction of the boundary motion. If the advection-like term is neglected, it is shown that spiral wave solutions of the FitzHugh-Nagumo equation are robust and do not lose their integrity under the anisotropic effects induced by the moving domain, albeit undergo stretching and compression in the direction of the boundary motion. However, when the advection-like terms are accounted for, the anisotropy and stretching/compression of the initial spiral wave result in a homogeneous state at high frequencies, and the time required to achieve such a uniformity is mainly a function of the amplitude of the boundary motion. For frequencies comparable to that of the spiral wave in a fixed domain, it is shown that the spiral wave preserves its integrity for low amplitudes of the boundary motion and is annihilated at high amplitudes

Investigation into the efficacy of generating synthetic pathological oscillations for domain adaptation

Science.gov (United States)

Lewis, Rory; Ellenberger, James; Williams, Colton; White, Andrew M.

2013-11-01

In the ongoing investigation of integrating Knowledge Discovery in Databases (KDD) into neuroscience, we present a paper that facilitates overcoming the two challenges preventing this integration. Pathological oscillations found in the human brain are difficult to evaluate because 1) there is often no time to learn and train off of the same distribution in the fatally sick, and 2) sinusoidal signals found in the human brain are complex and transient in nature requiring large data sets to work with which are costly and often very expensive or impossible to acquire. Overcoming these challenges in today's neuro-intensive-care unit (ICU) requires insurmountable resources. For these reasons, optimizing KDD for pathological oscillations so machine learning systems can predict neuropathological states would be of immense value. Domain adaptation, which allows a way of predicting on a separate set of data than the training data, can theoretically overcome the first challenge. However, the challenge of acquiring large data sets that show whether domain adaptation is a good candidate to test in a live neuro ICU remains a challenge. To solve this conundrum, we present a methodology for generating synthesized neuropathological oscillations for domain adaptation.

Minimum-domain impulse theory for unsteady aerodynamic force

Science.gov (United States)

Kang, L. L.; Liu, L. Q.; Su, W. D.; Wu, J. Z.

2018-01-01

We extend the impulse theory for unsteady aerodynamics from its classic global form to finite-domain formulation then to minimum-domain form and from incompressible to compressible flows. For incompressible flow, the minimum-domain impulse theory raises the finding of Li and Lu ["Force and power of flapping plates in a fluid," J. Fluid Mech. 712, 598-613 (2012)] to a theorem: The entire force with discrete wake is completely determined by only the time rate of impulse of those vortical structures still connecting to the body, along with the Lamb-vector integral thereof that captures the contribution of all the rest disconnected vortical structures. For compressible flows, we find that the global form in terms of the curl of momentum ∇ × (ρu), obtained by Huang [Unsteady Vortical Aerodynamics (Shanghai Jiaotong University Press, 1994)], can be generalized to having an arbitrary finite domain, but the formula is cumbersome and in general ∇ × (ρu) no longer has discrete structures and hence no minimum-domain theory exists. Nevertheless, as the measure of transverse process only, the unsteady field of vorticity ω or ρω may still have a discrete wake. This leads to a minimum-domain compressible vorticity-moment theory in terms of ρω (but it is beyond the classic concept of impulse). These new findings and applications have been confirmed by our numerical experiments. The results not only open an avenue to combine the theory with computation-experiment in wide applications but also reveal a physical truth that it is no longer necessary to account for all wake vortical structures in computing the force and moment.

Instruments Measuring Integrated Care: A Systematic Review of Measurement Properties.

Science.gov (United States)

Bautista, Mary Ann C; Nurjono, Milawaty; Lim, Yee Wei; Dessers, Ezra; Vrijhoef, Hubertus Jm

2016-12-01

-centered care (49%); fewer studies measured care continuity/comprehensive care (15%) and care coordination/case management (3%). We mapped 84% of the measured constructs to the clinical integration domain of the RMIC, with fewer constructs related to the domains of professional (3.7%), organizational (3.4%), and functional (0.5%) integration. Only 8% of the instruments were mapped to a combination of domains; none were mapped exclusively to the system or normative integration domains. The majority of instruments were administered to either patients (60%) or health care providers (20%). Of the measurement properties, responsiveness (4%), measurement error (7%), and criterion (12%) and cross-cultural validity (14%) were less commonly reported. We found measurement properties. Only a minority of index instruments showed strong evidence of positive findings for internal consistency (15%), content validity (19%), and structural validity (7%); with moderate evidence of positive findings for internal consistency (14%) and construct validity (14%). Our results suggest that the quality of measurement properties of instruments measuring integrated care is in need of improvement with the less-studied constructs and domains to become part of newly developed instruments. © 2016 Milbank Memorial Fund.

Instruments Measuring Integrated Care: A Systematic Review of Measurement Properties

Science.gov (United States)

BAUTISTA, MARY ANN C.; NURJONO, MILAWATY; DESSERS, EZRA; VRIJHOEF, HUBERTUS JM

2016-01-01

integration (33%) and patient‐centered care (49%); fewer studies measured care continuity/comprehensive care (15%) and care coordination/case management (3%). We mapped 84% of the measured constructs to the clinical integration domain of the RMIC, with fewer constructs related to the domains of professional (3.7%), organizational (3.4%), and functional (0.5%) integration. Only 8% of the instruments were mapped to a combination of domains; none were mapped exclusively to the system or normative integration domains. The majority of instruments were administered to either patients (60%) or health care providers (20%). Of the measurement properties, responsiveness (4%), measurement error (7%), and criterion (12%) and cross‐cultural validity (14%) were less commonly reported. We found measurement properties. Only a minority of index instruments showed strong evidence of positive findings for internal consistency (15%), content validity (19%), and structural validity (7%); with moderate evidence of positive findings for internal consistency (14%) and construct validity (14%). Conclusions Our results suggest that the quality of measurement properties of instruments measuring integrated care is in need of improvement with the less‐studied constructs and domains to become part of newly developed instruments. PMID:27995711

Same but not alike: Structure, flexibility and energetics of domains in multi-domain proteins are influenced by the presence of other domains.

Science.gov (United States)

Vishwanath, Sneha; de Brevern, Alexandre G; Srinivasan, Narayanaswamy

2018-02-01

The majority of the proteins encoded in the genomes of eukaryotes contain more than one domain. Reasons for high prevalence of multi-domain proteins in various organisms have been attributed to higher stability and functional and folding advantages over single-domain proteins. Despite these advantages, many proteins are composed of only one domain while their homologous domains are part of multi-domain proteins. In the study presented here, differences in the properties of protein domains in single-domain and multi-domain systems and their influence on functions are discussed. We studied 20 pairs of identical protein domains, which were crystallized in two forms (a) tethered to other proteins domains and (b) tethered to fewer protein domains than (a) or not tethered to any protein domain. Results suggest that tethering of domains in multi-domain proteins influences the structural, dynamic and energetic properties of the constituent protein domains. 50% of the protein domain pairs show significant structural deviations while 90% of the protein domain pairs show differences in dynamics and 12% of the residues show differences in the energetics. To gain further insights on the influence of tethering on the function of the domains, 4 pairs of homologous protein domains, where one of them is a full-length single-domain protein and the other protein domain is a part of a multi-domain protein, were studied. Analyses showed that identical and structurally equivalent functional residues show differential dynamics in homologous protein domains; though comparable dynamics between in-silico generated chimera protein and multi-domain proteins were observed. From these observations, the differences observed in the functions of homologous proteins could be attributed to the presence of tethered domain. Overall, we conclude that tethered domains in multi-domain proteins not only provide stability or folding advantages but also influence pathways resulting in differences in

On spurious resonant modes in the MOT solution of time domain EFIE

KAUST Repository

Shi, Yifei; Bagci, Hakan; Lu, Mingyu

2013-01-01

Theoretically, internal resonant modes should not be induced in the marching-on-in-time (MOT) solution of the time domain electric field integral equation since zero initial conditions are enforced at the beginning of time marching and the internal

Photoreceptor inner segment ellipsoid band integrity on spectral domain optical coherence tomography

Directory of Open Access Journals (Sweden)

Saxena S

2014-12-01

Full Text Available Sandeep Saxena,1 Khushboo Srivastav,1 Chui M Cheung,2 Joanne YW Ng,3 Timothy YY Lai3 1Retina Service, Department of Ophthalmology, King George’s Medical University Lucknow, India; 2Singapore National Eye Centre, Singapore; 3Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Kowloon, Hong Kong Abstract: Spectral domain optical coherence tomography cross-sectional imaging of the macula has conventionally been resolved into four bands. However, some doubts were raised regarding authentication of the existence of these bands. Recently, a number of studies have suggested that the second band appeared to originate from the inner segment ellipsoids of the foveal cone photoreceptors, and therefore the previously called inner segment-outer segment junction is now referred to as inner segment ellipsoidband. Photoreceptor dysfunction may be a significant predictor of visual acuity in a spectrum of surgical and medical retinal diseases. This review aims to provide an overview and summarizes the role of the photoreceptor inner segment ellipsoid band in the management and prognostication of various vitreoretinal diseases. Keywords: spectral domain optical coherence tomography, inner segment-outer segment junction, external limiting membrane, macular hole, diabetic macular edema, age relate macular degeneration

Research Progress of Global Land Domain Service Computing:Take GlobeLand 30 as an Example

Directory of Open Access Journals (Sweden)

CHEN Jun

2017-10-01

Full Text Available Combining service-computing technology with domain requirements is one of the important development directions of geographic information under Internet+, which provides highly efficient technical means for information sharing and collaborative services. Using GlobeLand 30 as an example, this paper analyzes the basic problems of integrating land cover information processing and service computing, introduces the latest research progress in domain service modeling, online computing method and dynamic service technology, and the GlobeLand 30 information service platform. The paper also discusses the further development directions of GlobeLand 30 domain service computing.

Robust Visual Knowledge Transfer via Extreme Learning Machine Based Domain Adaptation.

Science.gov (United States)

Zhang, Lei; Zhang, David

2016-08-10

We address the problem of visual knowledge adaptation by leveraging labeled patterns from source domain and a very limited number of labeled instances in target domain to learn a robust classifier for visual categorization. This paper proposes a new extreme learning machine based cross-domain network learning framework, that is called Extreme Learning Machine (ELM) based Domain Adaptation (EDA). It allows us to learn a category transformation and an ELM classifier with random projection by minimizing the -norm of the network output weights and the learning error simultaneously. The unlabeled target data, as useful knowledge, is also integrated as a fidelity term to guarantee the stability during cross domain learning. It minimizes the matching error between the learned classifier and a base classifier, such that many existing classifiers can be readily incorporated as base classifiers. The network output weights cannot only be analytically determined, but also transferrable. Additionally, a manifold regularization with Laplacian graph is incorporated, such that it is beneficial to semi-supervised learning. Extensively, we also propose a model of multiple views, referred as MvEDA. Experiments on benchmark visual datasets for video event recognition and object recognition, demonstrate that our EDA methods outperform existing cross-domain learning methods.

Not all risks are created equal: A twin study and meta-analyses of risk taking across seven domains.

Science.gov (United States)

Wang, X T Xiao-Tian; Zheng, Rui; Xuan, Yan-Hua; Chen, Jie; Li, Shu

2016-11-01

Humans routinely deal with both traditional and novel risks. Different kinds of risks have been a driving force for both evolutionary adaptations and personal development. This study explored the genetic and environmental influences on human risk taking in different task domains. Our approach was threefold. First, we integrated several scales of domain-specific risk-taking propensity and developed a synthetic scale, including both evolutionarily typical and modern risks in the following 7 domains: cooperation/competition, safety, reproduction, natural/physical risk, moral risk, financial risk, and gambling. Second, we conducted a twin study using the scale to estimate the contributions of genes and environment to risk taking in each of these 7 domains. Third, we conducted a series of meta-analyses of extant twin studies across the 7 risk domains. The results showed that individual differences in risk-taking propensity and its consistency across domains were mainly regulated by additive genetic influences and individually unique environmental experiences. The heritability estimates from the meta-analyses ranged from 29% in financial risk taking to 55% in safety. Supporting the notion of risk-domain specificity, both the behavioral and genetic correlations among the 7 domains were generally low. Among the relatively few correlations between pairs of risk domains, our analysis revealed a common genetic factor that regulates moral, financial, and natural/physical risk taking. This is the first effort to separate genetic and environmental influences on risk taking across multiple domains in a single study and integrate the findings of extant twin studies via a series of meta-analyses conducted in different task domains. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

A PROPOSED TAXONOMY OF THE PERCEPTUAL DOMAIN AND SOME SUGGESTED APPLICATIONS.

Science.gov (United States)

MOORE, MAXINE R.

THIS PROPOSAL FOR A PRELIMINARY TAXONOMY OF THE PERCEPTUAL DOMAIN, ORGANIZED ON THE PRINCIPLE OF INTEGRATION, DREW ON GUILFORD'S THEORETICAL AND FACTOR-ANALYTICAL WORK, ON WITKIN'S FIGURE-GROUND STUDIES, AND ON THE "TAXONOMY OF EDUCATIONAL OBJECTIVES" MODELS. THE TAXONOMY CATEGORIES ARE SENSATION, FIGURE PERCEPTION, SYMBOL PERCEPTION, PERCEPTION…

Open-geometry Fourier modal method: modeling nanophotonic structures in infinite domains

DEFF Research Database (Denmark)

Häyrynen, Teppo; de Lasson, Jakob Rosenkrantz; Gregersen, Niels

2016-01-01

We present an open-geometry Fourier modal method based on a new combination of open boundary conditions and an efficient k-space discretization. The open boundary of the computational domain is obtained using basis functions that expand the whole space, and the integrals subsequently appearing due...

Global integrability of cosmological scalar fields

Science.gov (United States)

Maciejewski, Andrzej J.; Przybylska, Maria; Stachowiak, Tomasz; Szydłowski, Marek

2008-11-01

We investigate the Liouvillian integrability of Hamiltonian systems describing a universe filled with a scalar field (possibly complex). The tool used is the differential Galois group approach, as introduced by Morales-Ruiz and Ramis. The main result is that the generic systems with minimal coupling are non-integrable, although there still exist some values of parameters for which integrability remains undecided; the conformally coupled systems are only integrable in four known cases. We also draw a connection with the chaos present in such cosmological models, and the issues of the integrability restricted to the real domain.

Global integrability of cosmological scalar fields

International Nuclear Information System (INIS)

Maciejewski, Andrzej J; Przybylska, Maria; Stachowiak, Tomasz; Szydlowski, Marek

2008-01-01

We investigate the Liouvillian integrability of Hamiltonian systems describing a universe filled with a scalar field (possibly complex). The tool used is the differential Galois group approach, as introduced by Morales-Ruiz and Ramis. The main result is that the generic systems with minimal coupling are non-integrable, although there still exist some values of parameters for which integrability remains undecided; the conformally coupled systems are only integrable in four known cases. We also draw a connection with the chaos present in such cosmological models, and the issues of the integrability restricted to the real domain

A study on group decision-making based fault multi-symptom-domain consensus diagnosis

International Nuclear Information System (INIS)

He Yongyong; Chu Fulei; Zhong Binglin

2001-01-01

In the field of fault diagnosis for rotating machines, the conventional methods or the neural network based methods are mainly single symptom domain based methods, and the diagnosis accuracy of which is not always satisfactory. In this paper, in order to utilize multiple symptom domains to improve the diagnosis accuracy, an idea of fault multi-symptom-domain consensus diagnosis is developed. From the point of view of the group decision-making, two particular multi-symptom-domain diagnosis strategies are proposed. The proposed strategies use BP (Back-Propagation) neural networks as diagnosis models in various symptom domains, and then combine the outputs of these networks by two combination schemes, which are based on Dempster-Shafer evidence theory and fuzzy integral theory, respectively. Finally, a case study pertaining to the fault diagnosis for rotor-bearing systems is given in detail, and the results show that the proposed diagnosis strategies are feasible and more efficient than conventional stacked-vector methods

PANDA: Protein function prediction using domain architecture and affinity propagation.

Science.gov (United States)

Wang, Zheng; Zhao, Chenguang; Wang, Yiheng; Sun, Zheng; Wang, Nan

2018-02-22

We developed PANDA (Propagation of Affinity and Domain Architecture) to predict protein functions in the format of Gene Ontology (GO) terms. PANDA at first executes profile-profile alignment algorithm to search against PfamA, KOG, COG, and SwissProt databases, and then launches PSI-BLAST against UniProt for homologue search. PANDA integrates a domain architecture inference algorithm based on the Bayesian statistics that calculates the probability of having a GO term. All the candidate GO terms are pooled and filtered based on Z-score. After that, the remaining GO terms are clustered using an affinity propagation algorithm based on the GO directed acyclic graph, followed by a second round of filtering on the clusters of GO terms. We benchmarked the performance of all the baseline predictors PANDA integrates and also for every pooling and filtering step of PANDA. It can be found that PANDA achieves better performances in terms of area under the curve for precision and recall compared to the baseline predictors. PANDA can be accessed from http://dna.cs.miami.edu/PANDA/ .

Broad Substrate Specificity of the Loading Didomain of the Lipomycin Polyketide Synthase

Energy Technology Data Exchange (ETDEWEB)

Yuzawa, S; Eng, CH; Katz, L; Keasling, JD

2013-06-04

LipPks1, a polyketide synthase subunit of the lipomycin synthase, is believed to catalyze the polyketide chain initiation reaction using isobutyryl-CoA as a substrate, followed by an elongation reaction with methylmalonyl-CoA to start the biosynthesis of antibiotic alpha-lipomycin in Streptomyces aureofaciens Tu117. Recombinant LipPks1, containing the thioesterase domain from the 6-deoxyerythronolide B synthase, was produced in Escherichia coli, and its substrate specificity was investigated in vitro. Surprisingly, several different acyl-CoAs, including isobutyryl-CoA, were accepted as the starter substrates, while no product was observed with acetyl-CoA. These results demonstrate the broad substrate specificity of LipPks1 and may be applied to producing new antibiotics.

Facile construction of a random protein domain insertion library using an engineered transposon.

Science.gov (United States)

Shah, Vandan; Pierre, Brennal; Kim, Jin Ryoun

2013-01-15

Insertional fusion between multiple protein domains represents a novel means of creating integrated functionalities. Currently, there is no robust guideline for selection of insertion sites ensuring the desired functional outcome of insertional fusion. Therefore, construction and testing of random domain insertion libraries, in which a host protein domain is randomly inserted into a guest protein domain, significantly benefit extensive exploration of sequence spaces for insertion sites. Short peptide residues are usually introduced between protein domains to alleviate structural conflicts, and the interdomain linker residues may affect the functional outcome of protein insertion complexes. Unfortunately, optimal control of interdomain linker residues is not always available in conventional methods used to construct random domain insertion libraries. Moreover, most conventional methods employ blunt-end rather than sticky-end ligation between host and guest DNA fragments, thus lowering library construction efficiency. Here, we report the facile construction of random domain insertion libraries using an engineered transposon. We show that random domain insertion with optimal control of interdomain linker residues was possible with our engineered transposon-based method. In addition, our method employs sticky-end rather than blunt-end ligation between host and guest DNA fragments, thus allowing for facile construction of relatively large sized libraries. Copyright © 2012 Elsevier Inc. All rights reserved.

Specificity and autoregulation of Notch binding by tandem WW domains in suppressor of Deltex.

Science.gov (United States)

Jennings, Martin D; Blankley, Richard T; Baron, Martin; Golovanov, Alexander P; Avis, Johanna M

2007-09-28

WW domains target proline-tyrosine (PY) motifs and frequently function as tandem pairs. When studied in isolation, single WW domains are notably promiscuous and regulatory mechanisms are undoubtedly required to ensure selective interactions. Here, we show that the fourth WW domain (WW4) of Suppressor of Deltex, a modular Nedd4-like protein that down-regulates the Notch receptor, is the primary mediator of a direct interaction with a Notch-PY motif. A natural Trp to Phe substitution in WW4 reduces its affinity for general PY sequences and enhances selective interaction with the Notch-PY motif via compensatory specificity-determining interactions with PY-flanking residues. When WW4 is paired with WW3, domain-domain association, impeding proper folding, competes with Notch-PY binding to WW4. This novel mode of autoinhibition is relieved by binding of another ligand to WW3. Such cooperativity may facilitate the transient regulatory interactions observed in vivo between Su(dx) and Notch in the endocytic pathway. The highly conserved tandem arrangement of WW domains in Nedd4 proteins, and similar arrangements in more diverse proteins, suggests domain-domain communication may be integral to regulation of their associated cellular activities.

Assessing healthcare professionals' experiences of integrated care: do surveys tell the full story?

Science.gov (United States)

Stephenson, Matthew D; Campbell, Jared M; Lisy, Karolina; Aromataris, Edoardo C

2017-09-01

Integrated care is the combination of different healthcare services with the goal to provide comprehensive, seamless, effective and efficient patient care. Assessing the experiences of healthcare professionals (HCPs) is an important aspect when evaluating integrated care strategies. The aim of this rapid review was to investigate if quantitative surveys used to assess HCPs' experiences with integrated care capture all the aspects highlighted as being important in qualitative research, with a view to informing future survey development. The review considered all types of health professionals in primary care, and hospital and specialist services, with a specific focus on the provision of integrated care aimed at improving the patient journey. PubMed, CINAHL and grey literature sources were searched for relevant surveys/program evaluations and qualitative research studies. Full text articles deemed to be of relevance to the review were appraised for methodological quality using abridged critical appraisal instruments from the Joanna Briggs Institute. Data were extracted from included studies using standardized data extraction templates. Findings from included studies were grouped into domains based on similarity of meaning. Similarities and differences in the domains covered in quantitative surveys and those identified as being important in qualitative research were explored. A total of 37 studies (19 quantitative surveys, 14 qualitative studies and four mixed-method studies) were included in the review. A range of healthcare professions participated in the included studies, the majority being primary care providers. Common domains identified from quantitative surveys and qualitative studies included Communication, Agreement on Clear Roles and Responsibilities, Facilities, Information Systems, and Coordination of Care and Access. Qualitative research highlighted domains identified by HCPs as being relevant to their experiences with integrated care that have not

Domain Engineering

Science.gov (United States)

Bjørner, Dines

Before software can be designed we must know its requirements. Before requirements can be expressed we must understand the domain. So it follows, from our dogma, that we must first establish precise descriptions of domains; then, from such descriptions, “derive” at least domain and interface requirements; and from those and machine requirements design the software, or, more generally, the computing systems.

Time-domain hybrid method for simulating large amplitude motions of ships advancing in waves

Directory of Open Access Journals (Sweden)

Shukui Liu

2011-03-01

Full Text Available Typical results obtained by a newly developed, nonlinear time domain hybrid method for simulating large amplitude motions of ships advancing with constant forward speed in waves are presented. The method is hybrid in the way of combining a time-domain transient Green function method and a Rankine source method. The present approach employs a simple double integration algorithm with respect to time to simulate the free-surface boundary condition. During the simulation, the diffraction and radiation forces are computed by pressure integration over the mean wetted surface, whereas the incident wave and hydrostatic restoring forces/moments are calculated on the instantaneously wetted surface of the hull. Typical numerical results of application of the method to the seakeeping performance of a standard containership, namely the ITTC S175, are herein presented. Comparisons have been made between the results from the present method, the frequency domain 3D panel method (NEWDRIFT of NTUA-SDL and available experimental data and good agreement has been observed for all studied cases between the results of the present method and comparable other data.

Evolution of Chemical Diversity in a Group of Non-Reduced Polyketide Gene Clusters: Using Phylogenetics to Inform the Search for Novel Fungal Natural Products

Directory of Open Access Journals (Sweden)

Kurt Throckmorton

2015-09-01

Full Text Available Fungal polyketides are a diverse class of natural products, or secondary metabolites (SMs, with a wide range of bioactivities often associated with toxicity. Here, we focus on a group of non-reducing polyketide synthases (NR-PKSs in the fungal phylum Ascomycota that lack a thioesterase domain for product release, group V. Although widespread in ascomycete taxa, this group of NR-PKSs is notably absent in the mycotoxigenic genus Fusarium and, surprisingly, found in genera not known for their secondary metabolite production (e.g., the mycorrhizal genus Oidiodendron, the powdery mildew genus Blumeria, and the causative agent of white-nose syndrome in bats, Pseudogymnoascus destructans. This group of NR-PKSs, in association with the other enzymes encoded by their gene clusters, produces a variety of different chemical classes including naphthacenediones, anthraquinones, benzophenones, grisandienes, and diphenyl ethers. We discuss the modification of and transitions between these chemical classes, the requisite enzymes, and the evolution of the SM gene clusters that encode them. Integrating this information, we predict the likely products of related but uncharacterized SM clusters, and we speculate upon the utility of these classes of SMs as virulence factors or chemical defenses to various plant, animal, and insect pathogens, as well as mutualistic fungi.

Using Semantic Web technologies for the generation of domain-specific templates to support clinical study metadata standards.

Science.gov (United States)

Jiang, Guoqian; Evans, Julie; Endle, Cory M; Solbrig, Harold R; Chute, Christopher G

2016-01-01

The Biomedical Research Integrated Domain Group (BRIDG) model is a formal domain analysis model for protocol-driven biomedical research, and serves as a semantic foundation for application and message development in the standards developing organizations (SDOs). The increasing sophistication and complexity of the BRIDG model requires new approaches to the management and utilization of the underlying semantics to harmonize domain-specific standards. The objective of this study is to develop and evaluate a Semantic Web-based approach that integrates the BRIDG model with ISO 21090 data types to generate domain-specific templates to support clinical study metadata standards development. We developed a template generation and visualization system based on an open source Resource Description Framework (RDF) store backend, a SmartGWT-based web user interface, and a "mind map" based tool for the visualization of generated domain-specific templates. We also developed a RESTful Web Service informed by the Clinical Information Modeling Initiative (CIMI) reference model for access to the generated domain-specific templates. A preliminary usability study is performed and all reviewers (n = 3) had very positive responses for the evaluation questions in terms of the usability and the capability of meeting the system requirements (with the average score of 4.6). Semantic Web technologies provide a scalable infrastructure and have great potential to enable computable semantic interoperability of models in the intersection of health care and clinical research.

Analysis of electromagnetic wave interactions on nonlinear scatterers using time domain volume integral equations

KAUST Repository

Ulku, Huseyin Arda; Sayed, Sadeed Bin; Bagci, Hakan

2014-01-01

solvers are the method of choice when it comes simulating these nonlinear effects. Oftentimes, finite difference time domain (FDTD) method is used for this purpose. This is simply due to the fact that explicitness of the FDTD renders the implementation

Analysis of noise in energy-dispersive spectrometers using time-domain methods

CERN Document Server

Goulding, F S

2002-01-01

This paper presents an integrated time domain approach to the optimization of the signal-to-noise ratio in all spectrometer systems that contain a detector that converts incoming quanta of radiation into electrical pulse signals that are amplified and shaped by an electronic pulse shaper. It allows analysis of normal passive pulse shapers as well as time-variant systems where switching of shaping elements occurs in synchronism with the signal. It also deals comfortably with microcalorimeters (sometimes referred to as bolometers), where noise-determining elements, such as the temperature-sensing element's resistance and temperature, change with time in the presence of a signal. As part of the purely time-domain approach, a new method of calculating the Johnson noise in resistors using only the statistics of electron motion is presented. The result is a time-domain analog of the Nyquist formula.

Model-based Engineering for the Integration of Manufacturing Systems with Advanced Analytics

OpenAIRE

Lechevalier , David; Narayanan , Anantha; Rachuri , Sudarsan; Foufou , Sebti; Lee , Y Tina

2016-01-01

Part 3: Interoperability and Systems Integration; International audience; To employ data analytics effectively and efficiently on manufacturing systems, engineers and data scientists need to collaborate closely to bring their domain knowledge together. In this paper, we introduce a domain-specific modeling approach to integrate a manufacturing system model with advanced analytics, in particular neural networks, to model predictions. Our approach combines a set of meta-models and transformatio...

Domain dynamics of the Bacillus subtilis peripheral preprotein translocase subunit SecA

NARCIS (Netherlands)

Driessen, A.J.M.; Ladbury, JE; Chowdhry, BZ

1998-01-01

The homodimeric SecA protein is the peripheral subunit of the preprotein translocase in bacteria. It promotes the preprotein translocation across the cytoplasmic membrane by nucleotide-modulated co-insertion and de-insertion into the integral domain of the translocase. SecA has two essential

Quality control and authentication of packaged integrated circuits using enhanced-spatial-resolution terahertz time-domain spectroscopy and imaging

Science.gov (United States)

Ahi, Kiarash; Shahbazmohamadi, Sina; Asadizanjani, Navid

2018-05-01

In this paper, a comprehensive set of techniques for quality control and authentication of packaged integrated circuits (IC) using terahertz (THz) time-domain spectroscopy (TDS) is developed. By material characterization, the presence of unexpected materials in counterfeit components is revealed. Blacktopping layers are detected using THz time-of-flight tomography, and thickness of hidden layers is measured. Sanded and contaminated components are detected by THz reflection-mode imaging. Differences between inside structures of counterfeit and authentic components are revealed through developing THz transmission imaging. For enabling accurate measurement of features by THz transmission imaging, a novel resolution enhancement technique (RET) has been developed. This RET is based on deconvolution of the THz image and the THz point spread function (PSF). The THz PSF is mathematically modeled through incorporating the spectrum of the THz imaging system, the axis of propagation of the beam, and the intensity extinction coefficient of the object into a Gaussian beam distribution. As a result of implementing this RET, the accuracy of the measurements on THz images has been improved from 2.4 mm to 0.1 mm and bond wires as small as 550 μm inside the packaging of the ICs are imaged.

Fourier transforms in the complex domain

CERN Document Server

Wiener, N

1934-01-01

With the aid of Fourier-Mellin transforms as a tool in analysis, the authors were able to attack such diverse analytic questions as those of quasi-analytic functions, Mercer's theorem on summability, Milne's integral equation of radiative equilibrium, the theorems of Münz and Szász concerning the closure of sets of powers of an argument, Titchmarsh's theory of entire functions of semi-exponential type with real negative zeros, trigonometric interpolation and developments in polynomials of the form \\sum^N_1A_ne^{i\\lambda_nx}, lacunary series, generalized harmonic analysis in the complex domain,

NovelFam3000 – Uncharacterized human protein domains conserved across model organisms

Science.gov (United States)

Kemmer, Danielle; Podowski, Raf M; Arenillas, David; Lim, Jonathan; Hodges, Emily; Roth, Peggy; Sonnhammer, Erik LL; Höög, Christer; Wasserman, Wyeth W

2006-01-01

Background Despite significant efforts from the research community, an extensive portion of the proteins encoded by human genes lack an assigned cellular function. Most metazoan proteins are composed of structural and/or functional domains, of which many appear in multiple proteins. Once a domain is characterized in one protein, the presence of a similar sequence in an uncharacterized protein serves as a basis for inference of function. Thus knowledge of a domain's function, or the protein within which it arises, can facilitate the analysis of an entire set of proteins. Description From the Pfam domain database, we extracted uncharacterized protein domains represented in proteins from humans, worms, and flies. A data centre was created to facilitate the analysis of the uncharacterized domain-containing proteins. The centre both provides researchers with links to dispersed internet resources containing gene-specific experimental data and enables them to post relevant experimental results or comments. For each human gene in the system, a characterization score is posted, allowing users to track the progress of characterization over time or to identify for study uncharacterized domains in well-characterized genes. As a test of the system, a subset of 39 domains was selected for analysis and the experimental results posted to the NovelFam3000 system. For 25 human protein members of these 39 domain families, detailed sub-cellular localizations were determined. Specific observations are presented based on the analysis of the integrated information provided through the online NovelFam3000 system. Conclusion Consistent experimental results between multiple members of a domain family allow for inferences of the domain's functional role. We unite bioinformatics resources and experimental data in order to accelerate the functional characterization of scarcely annotated domain families. PMID:16533400

NovelFam3000 – Uncharacterized human protein domains conserved across model organisms

Directory of Open Access Journals (Sweden)

Sonnhammer Erik LL

2006-03-01

Full Text Available Abstract Background Despite significant efforts from the research community, an extensive portion of the proteins encoded by human genes lack an assigned cellular function. Most metazoan proteins are composed of structural and/or functional domains, of which many appear in multiple proteins. Once a domain is characterized in one protein, the presence of a similar sequence in an uncharacterized protein serves as a basis for inference of function. Thus knowledge of a domain's function, or the protein within which it arises, can facilitate the analysis of an entire set of proteins. Description From the Pfam domain database, we extracted uncharacterized protein domains represented in proteins from humans, worms, and flies. A data centre was created to facilitate the analysis of the uncharacterized domain-containing proteins. The centre both provides researchers with links to dispersed internet resources containing gene-specific experimental data and enables them to post relevant experimental results or comments. For each human gene in the system, a characterization score is posted, allowing users to track the progress of characterization over time or to identify for study uncharacterized domains in well-characterized genes. As a test of the system, a subset of 39 domains was selected for analysis and the experimental results posted to the NovelFam3000 system. For 25 human protein members of these 39 domain families, detailed sub-cellular localizations were determined. Specific observations are presented based on the analysis of the integrated information provided through the online NovelFam3000 system. Conclusion Consistent experimental results between multiple members of a domain family allow for inferences of the domain's functional role. We unite bioinformatics resources and experimental data in order to accelerate the functional characterization of scarcely annotated domain families.

The SHOCT domain: a widespread domain under-represented in model organisms.

Directory of Open Access Journals (Sweden)

Ruth Y Eberhardt

Full Text Available We have identified a new protein domain, which we have named the SHOCT domain (Short C-terminal domain. This domain is widespread in bacteria with over a thousand examples. But we found it is missing from the most commonly studied model organisms, despite being present in closely related species. It's predominantly C-terminal location, co-occurrence with numerous other domains and short size is reminiscent of the Gram-positive anchor motif, however it is present in a much wider range of species. We suggest several hypotheses about the function of SHOCT, including oligomerisation and nucleic acid binding. Our initial experiments do not support its role as an oligomerisation domain.

BIOMedical Search Engine Framework: Lightweight and customized implementation of domain-specific biomedical search engines.

Science.gov (United States)

Jácome, Alberto G; Fdez-Riverola, Florentino; Lourenço, Anália

2016-07-01

Text mining and semantic analysis approaches can be applied to the construction of biomedical domain-specific search engines and provide an attractive alternative to create personalized and enhanced search experiences. Therefore, this work introduces the new open-source BIOMedical Search Engine Framework for the fast and lightweight development of domain-specific search engines. The rationale behind this framework is to incorporate core features typically available in search engine frameworks with flexible and extensible technologies to retrieve biomedical documents, annotate meaningful domain concepts, and develop highly customized Web search interfaces. The BIOMedical Search Engine Framework integrates taggers for major biomedical concepts, such as diseases, drugs, genes, proteins, compounds and organisms, and enables the use of domain-specific controlled vocabulary. Technologies from the Typesafe Reactive Platform, the AngularJS JavaScript framework and the Bootstrap HTML/CSS framework support the customization of the domain-oriented search application. Moreover, the RESTful API of the BIOMedical Search Engine Framework allows the integration of the search engine into existing systems or a complete web interface personalization. The construction of the Smart Drug Search is described as proof-of-concept of the BIOMedical Search Engine Framework. This public search engine catalogs scientific literature about antimicrobial resistance, microbial virulence and topics alike. The keyword-based queries of the users are transformed into concepts and search results are presented and ranked accordingly. The semantic graph view portraits all the concepts found in the results, and the researcher may look into the relevance of different concepts, the strength of direct relations, and non-trivial, indirect relations. The number of occurrences of the concept shows its importance to the query, and the frequency of concept co-occurrence is indicative of biological relations

Different functional modes of BAR domain proteins in formation and plasticity of mammalian postsynapses.

Science.gov (United States)

Kessels, Michael M; Qualmann, Britta

2015-09-01

A plethora of cell biological processes involve modulations of cellular membranes. By using extended lipid-binding interfaces, some proteins have the power to shape membranes by attaching to them. Among such membrane shapers, the superfamily of Bin-Amphiphysin-Rvs (BAR) domain proteins has recently taken center stage. Extensive structural work on BAR domains has revealed a common curved fold that can serve as an extended membrane-binding interface to modulate membrane topologies and has allowed the grouping of the BAR domain superfamily into subfamilies with structurally slightly distinct BAR domain subtypes (N-BAR, BAR, F-BAR and I-BAR). Most BAR superfamily members are expressed in the mammalian nervous system. Neurons are elaborately shaped and highly compartmentalized cells. Therefore, analyses of synapse formation and of postsynaptic reorganization processes (synaptic plasticity) - a basis for learning and memory formation - has unveiled important physiological functions of BAR domain superfamily members. These recent advances, furthermore, have revealed that the functions of BAR domain proteins include different aspects. These functions are influenced by the often complex domain organization of BAR domain proteins. In this Commentary, we review these recent insights and propose to classify BAR domain protein functions into (1) membrane shaping, (2) physical integration, (3) action through signaling components, and (4) suppression of other BAR domain functions. © 2015. Published by The Company of Biologists Ltd.

Hydrolysis of ibuprofenoyl-CoA and other 2-APA-CoA esters by human acyl-CoA thioesterases-1 and -2 and their possible role in the chiral inversion of profens.

Science.gov (United States)

Qu, Xiao; Allan, Amanda; Chui, Grace; Hutchings, Thomas J; Jiao, Ping; Johnson, Lawrence; Leung, Wai Y; Li, Portia K; Steel, Georgina R; Thompson, Andrew S; Threadgill, Michael D; Woodman, Timothy J; Lloyd, Matthew D

2013-12-01

Ibuprofen and related 2-arylpropanoic acid (2-APA) drugs are often given as a racemic mixture and the R-enantiomers undergo activation in vivo by metabolic chiral inversion. The chiral inversion pathway consists of conversion of the drug to the coenzyme A ester (by an acyl-CoA synthetase) followed by chiral inversion by α-methylacyl-CoA racemase (AMACR; P504S). The enzymes responsible for hydrolysis of the product S-2-APA-CoA ester to the active S-2-APA drug have not been identified. In this study, conversion of a variety of 2-APA-CoA esters by human acyl-CoA thioesterase-1 and -2 (ACOT-1 and -2) was investigated. Human recombinant ACOT-1 and -2 (ACOT-1 and -2) were both able to efficiently hydrolyse a variety of 2-APA-CoA substrates. Studies with the model substrates R- and S-2-methylmyristoyl-CoA showed that both enzymes were able to efficiently hydrolyse both of the epimeric substrates with (2R)- and (2S)- methyl groups. ACOT-1 is located in the cytosol and is able to hydrolyse 2-APA-CoA esters exported from the mitochondria and peroxisomes for inhibition of cyclo-oxygenase-1 and -2 in the endoplasmic reticulum. It is a prime candidate to be the enzyme responsible for the pharmacological action of chiral inverted drugs. ACOT-2 activity may be important in 2-APA toxicity effects and for the regulation of mitochondrial free coenzyme A levels. These results support the idea that 2-APA drugs undergo chiral inversion via a common pathway. Copyright © 2013 Elsevier Inc. All rights reserved.

Domain-to-domain coupling in voltage-sensing phosphatase.

Science.gov (United States)

Sakata, Souhei; Matsuda, Makoto; Kawanabe, Akira; Okamura, Yasushi

2017-01-01

Voltage-sensing phosphatase (VSP) consists of a transmembrane voltage sensor and a cytoplasmic enzyme region. The enzyme region contains the phosphatase and C2 domains, is structurally similar to the tumor suppressor phosphatase PTEN, and catalyzes the dephosphorylation of phosphoinositides. The transmembrane voltage sensor is connected to the phosphatase through a short linker region, and phosphatase activity is induced upon membrane depolarization. Although the detailed molecular characteristics of the voltage sensor domain and the enzyme region have been revealed, little is known how these two regions are coupled. In addition, it is important to know whether mechanism for coupling between the voltage sensor domain and downstream effector function is shared among other voltage sensor domain-containing proteins. Recent studies in which specific amino acid sites were genetically labeled using a fluorescent unnatural amino acid have enabled detection of the local structural changes in the cytoplasmic region of Ciona intestinalis VSP that occur with a change in membrane potential. The results of those studies provide novel insight into how the enzyme activity of the cytoplasmic region of VSP is regulated by the voltage sensor domain.

Protein domain evolution is associated with reproductive diversification and adaptive radiation in the genus Eucalyptus.

Science.gov (United States)

Kersting, Anna R; Mizrachi, Eshchar; Bornberg-Bauer, Erich; Myburg, Alexander A

2015-06-01

Eucalyptus is a pivotal genus within the rosid order Myrtales with distinct geographic history and adaptations. Comparative analysis of protein domain evolution in the newly sequenced Eucalyptus grandis genome and other rosid lineages sheds light on the adaptive mechanisms integral to the success of this genus of woody perennials. We reconstructed the ancestral domain content to elucidate the gain, loss and expansion of protein domains and domain arrangements in Eucalyptus in the context of rosid phylogeny. We used functional gene ontology (GO) annotation of genes to investigate the possible biological and evolutionary consequences of protein domain expansion. We found that protein modulation within the angiosperms occurred primarily on the level of expansion of certain domains and arrangements. Using RNA-Seq data from E. grandis, we showed that domain expansions have contributed to tissue-specific expression of tandemly duplicated genes. Our results indicate that tandem duplication of genes, a key feature of the Eucalyptus genome, has played an important role in the expansion of domains, particularly in proteins related to the specialization of reproduction and biotic and abiotic interactions affecting root and floral biology, and that tissue-specific expression of proteins with expanded domains has facilitated subfunctionalization in domain families. © 2014 University of Pretoria New Phytologist © 2014 New Phytologist Trust.

Memory integration in amnesia: prior knowledge supports verbal short-term memory.

Science.gov (United States)

Race, Elizabeth; Palombo, Daniela J; Cadden, Margaret; Burke, Keely; Verfaellie, Mieke

2015-04-01

Short-term memory (STM) and long-term memory (LTM) have traditionally been considered cognitively distinct. However, it is known that STM can improve when to-be-remembered information appears in contexts that make contact with prior knowledge, suggesting a more interactive relationship between STM and LTM. The current study investigated whether the ability to leverage LTM in support of STM critically depends on the integrity of the hippocampus. Specifically, we investigated whether the hippocampus differentially supports between-domain versus within-domain STM-LTM integration given prior evidence that the representational domain of the elements being integrated in memory is a critical determinant of whether memory performance depends on the hippocampus. In Experiment 1, we investigated hippocampal contributions to within-domain STM-LTM integration by testing whether immediate verbal recall of words improves in MTL amnesic patients when words are presented in familiar verbal contexts (meaningful sentences) compared to unfamiliar verbal contexts (random word lists). Patients demonstrated a robust sentence superiority effect, whereby verbal STM performance improved in familiar compared to unfamiliar verbal contexts, and the magnitude of this effect did not differ from that in controls. In Experiment 2, we investigated hippocampal contributions to between-domain STM-LTM integration by testing whether immediate verbal recall of digits improves in MTL amnesic patients when digits are presented in a familiar visuospatial context (a typical keypad layout) compared to an unfamiliar visuospatial context (a random keypad layout). Immediate verbal recall improved in both patients and controls when digits were presented in the familiar compared to the unfamiliar keypad array, indicating a preserved ability to integrate activated verbal information with stored visuospatial knowledge. Together, these results demonstrate that immediate verbal recall in amnesia can benefit from two

Fully integrated modelling for sustainability assessment of resource recovery from waste.

Science.gov (United States)

Millward-Hopkins, Joel; Busch, Jonathan; Purnell, Phil; Zwirner, Oliver; Velis, Costas A; Brown, Andrew; Hahladakis, John; Iacovidou, Eleni

2018-01-15

This paper presents an integrated modelling approach for value assessments, focusing on resource recovery from waste. The method tracks and forecasts a range of values across environmental, social, economic and technical domains by attaching these to material-flows, thus building upon and integrating unidimensional models such as material flow analysis (MFA) and lifecycle assessment (LCA). We argue that the usual classification of metrics into these separate domains is useful for interpreting the outputs of multidimensional assessments, but unnecessary for modelling. We thus suggest that multidimensional assessments can be better performed by integrating the calculation methods of unidimensional models rather than their outputs. To achieve this, we propose a new metric typology that forms the foundation of a multidimensional model. This enables dynamic simulations to be performed with material-flows (or values in any domain) driven by changes in value in other domains. We then apply the model in an illustrative case highlighting links between the UK coal-based electricity-production and concrete/cement industries, investigating potential impacts that may follow the increased use of low-carbon fuels (biomass and solid recovered fuels; SRF) in the former. We explore synergies and trade-offs in value across domains and regions, e.g. how changes in carbon emissions in one part of the system may affect mortality elsewhere. This highlights the advantages of recognising complex system dynamics and making high-level inferences of their effects, even when rigorous analysis is not possible. We also indicate how changes in social, environmental and economic 'values' can be understood as being driven by changes in the technical value of resources. Our work thus emphasises the advantages of building fully integrated models to inform conventional sustainability assessments, rather than applying hybrid approaches that integrate outputs from parallel models. The approach we

Hydrology Domain Cyberinfrastructures: Successes, Challenges, and Opportunities

Science.gov (United States)

Horsburgh, J. S.

2015-12-01

Anticipated changes to climate, human population, land use, and urban form will alter the hydrology and availability of water within the water systems on which the world's population relies. Understanding the effects of these changes will be paramount in sustainably managing water resources, as well as maintaining associated capacity to provide ecosystem services (e.g., regulating flooding, maintaining instream flow during dry periods, cycling nutrients, and maintaining water quality). It will require better information characterizing both natural and human mediated hydrologic systems and enhanced ability to generate, manage, store, analyze, and share growing volumes of observational data. Over the past several years, a number of hydrology domain cyberinfrastructures have emerged or are currently under development that are focused on providing integrated access to and analysis of data for cross-domain synthesis studies. These include the Consortium of Universities for the Advancement of Hydrologic Science, Inc. (CUAHSI) Hydrologic Information System (HIS), the Critical Zone Observatory Information System (CZOData), HyroShare, the BiG CZ software system, and others. These systems have focused on sharing, integrating, and analyzing hydrologic observations data. This presentation will describe commonalities and differences in the cyberinfrastructure approaches used by these projects and will highlight successes and lessons learned in addressing the challenges of big and complex data. It will also identify new challenges and opportunities for next generation cyberinfrastructure and a next generation of cyber-savvy scientists and engineers as developers and users.

Estimating Creativity with a Multiple-Measurement Approach within Scientific and Artistic Domains

Science.gov (United States)

Agnoli, Sergio; Corazza, Giovanni E.; Runco, Mark A.

2016-01-01

This article presents the structure and the composition of a newly developed multifaceted test battery for the measurement of creativity within scientific and artistic domains. By integrating existing procedures for the evaluation of creativity, the new battery promises to become a comprehensive assessment of creativity, encompassing both…

MIT domain of Vps4 is a Ca2+-dependent phosphoinositide-binding domain.

Science.gov (United States)

Iwaya, Naoko; Takasu, Hirotoshi; Goda, Natsuko; Shirakawa, Masahiro; Tanaka, Toshiki; Hamada, Daizo; Hiroaki, Hidekazu

2013-05-01

The microtubule interacting and trafficking (MIT) domain is a small protein module that is conserved in proteins of diverged function, such as Vps4, spastin and sorting nexin 15 (SNX15). The molecular function of the MIT domain is protein-protein interaction, in which the domain recognizes peptides containing MIT-interacting motifs. Recently, we identified an evolutionarily related domain, 'variant' MIT domain at the N-terminal region of the microtubule severing enzyme katanin p60. We found that the domain was responsible for binding to microtubules and Ca(2+). Here, we have examined whether the authentic MIT domains also bind Ca(2+). We found that the loop between the first and second α-helices of the MIT domain binds a Ca(2+) ion. Furthermore, the MIT domains derived from Vps4b and SNX15a showed phosphoinositide-binding activities in a Ca(2+)-dependent manner. We propose that the MIT domain is a novel membrane-associating domain involved in endosomal trafficking.

Effective elements of school health promotion across behavioral domains: a systematic review of reviews

Directory of Open Access Journals (Sweden)

Peters Louk WH

2009-06-01

Full Text Available Abstract Background Most school health education programs focus on a single behavioral domain. Integrative programs that address multiple behaviors may be more efficient, but only if the elements of change are similar for these behaviors. The objective of this study was to examine which effective elements of school health education are similar across three particular behavioral domains. Methods A systematic review of reviews of the effectiveness of school-based health promotion programs was conducted for the domains of substance abuse, sexual behavior, and nutrition. The literature search spanned the time period between 1995 and October 2006 and included three databases, websites of review centers and backward search. Fifty-five reviews and meta-analyses met predetermined relevance and publication criteria and were included. Data was extracted by one reviewer and checked by a second reviewer. A standardized data extraction form was used, with detailed attention to effective elements pertaining to program goals, development, content, methods, facilitator, components and intensity. Two assessors rated the quality of reviews as strong, moderate or weak. We included only strong and moderate reviews in two types of analysis: one based on interpretation of conflicting results, the other on a specific vote-counting rule. Results Thirty six reviews were rated strong, 6 moderate, and 13 weak. A multitude of effective elements was identified in the included reviews and many elements were similar for two or more domains. In both types of analysis, five elements with evidence from strong reviews were found to be similar for all three domains: use of theory; addressing social influences, especially social norms; addressing cognitive-behavioral skills; training of facilitators; and multiple components. Two additional elements had positive results in all domains with the rule-based method of analysis, but had inconclusive results in at least one domain with

Processes of fungal proteome evolution and gain of function: gene duplication and domain rearrangement

International Nuclear Information System (INIS)

Cohen-Gihon, Inbar; Nussinov, Ruth; Sharan, Roded

2011-01-01

During evolution, organisms have gained functional complexity mainly by modifying and improving existing functioning systems rather than creating new ones ab initio. Here we explore the interplay between two processes which during evolution have had major roles in the acquisition of new functions: gene duplication and protein domain rearrangements. We consider four possible evolutionary scenarios: gene families that have undergone none of these event types; only gene duplication; only domain rearrangement, or both events. We characterize each of the four evolutionary scenarios by functional attributes. Our analysis of ten fungal genomes indicates that at least for the fungi clade, species significantly appear to gain complexity by gene duplication accompanied by the expansion of existing domain architectures via rearrangements. We show that paralogs gaining new domain architectures via duplication tend to adopt new functions compared to paralogs that preserve their domain architectures. We conclude that evolution of protein families through gene duplication and domain rearrangement is correlated with their functional properties. We suggest that in general, new functions are acquired via the integration of gene duplication and domain rearrangements rather than each process acting independently

White matter correlates of cognitive domains in normal aging with diffusion tensor imaging

Directory of Open Access Journals (Sweden)

Efrat eSasson

2013-03-01

Full Text Available The ability to perform complex as well as simple cognitive tasks engages a network of brain regions that is mediated by the white matter fiber bundles connecting them. Different cognitive tasks employ distinctive white matter fiber bundles. The temporal lobe and its projections subserve a variety of key functions known to deteriorate during aging. In a cohort of 52 healthy subjects (ages 25-82 years, we performed voxel-wise regression analysis correlating performance in higher-order cognitive domains (executive function, information processing speed, and memory with white matter integrity, as measured by diffusion tensor imaging (DTI fiber tracking in the temporal lobe projections (uncinate fasciculus (UF, fornix, cingulum, inferior longitudinal fasciculus (ILF, and superior longitudinal fasciculus (SLF. The fiber tracts were spatially registered and statistical parametric maps were produced to spatially localize the significant correlations. Results showed that performance in the executive function domain is correlated with DTI parameters in the left SLF and right UF; performance in the information processing speed domain is correlated with fractional anisotropy (FA in the left cingulum, left fornix, right and left ILF and SLF; and the memory domain shows significant correlations with DTI parameters in the right fornix, right cingulum, left ILF, left SLF and right UF. These findings suggest that DTI tractography enables anatomical definition of region of interest for correlation of behavioral parameters with diffusion indices, and functionality can be correlated with white matter integrity.

A structural role for the PHP domain in E. coli DNA polymerase III.

Science.gov (United States)

Barros, Tiago; Guenther, Joel; Kelch, Brian; Anaya, Jordan; Prabhakar, Arjun; O'Donnell, Mike; Kuriyan, John; Lamers, Meindert H

2013-05-14

In addition to the core catalytic machinery, bacterial replicative DNA polymerases contain a Polymerase and Histidinol Phosphatase (PHP) domain whose function is not entirely understood. The PHP domains of some bacterial replicases are active metal-dependent nucleases that may play a role in proofreading. In E. coli DNA polymerase III, however, the PHP domain has lost several metal-coordinating residues and is likely to be catalytically inactive. Genomic searches show that the loss of metal-coordinating residues in polymerase PHP domains is likely to have coevolved with the presence of a separate proofreading exonuclease that works with the polymerase. Although the E. coli Pol III PHP domain has lost metal-coordinating residues, the structure of the domain has been conserved to a remarkable degree when compared to that of metal-binding PHP domains. This is demonstrated by our ability to restore metal binding with only three point mutations, as confirmed by the metal-bound crystal structure of this mutant determined at 2.9 Å resolution. We also show that Pol III, a large multi-domain protein, unfolds cooperatively and that mutations in the degenerate metal-binding site of the PHP domain decrease the overall stability of Pol III and reduce its activity. While the presence of a PHP domain in replicative bacterial polymerases is strictly conserved, its ability to coordinate metals and to perform proofreading exonuclease activity is not, suggesting additional non-enzymatic roles for the domain. Our results show that the PHP domain is a major structural element in Pol III and its integrity modulates both the stability and activity of the polymerase.

Planning for Integrating Teaching Technologies

Directory of Open Access Journals (Sweden)

Mandie Aaron

2004-06-01

Full Text Available Teaching technologies offer pedagogical advantages which vary with specific contexts. Successfully integrating them hinges on clearly identifying pedagogical goals, then planning for the many decisions that technological change demands. In examining different ways of organizing this process, we have applied planning tools from other domains - Fault Tree Analysis and Capability Maturity Modeling- at the school and college levels. In another approach, we have examined attempts to broadly model the integration process at the university level. Our studies demonstrate that the use of a variety of tools and techniques can render the integration of teaching technologies more systematic.

Conversion of Dielectric Data from the Time Domain to the Frequency Domain

Directory of Open Access Journals (Sweden)

Vladimir Durman

2005-01-01

Full Text Available Polarisation and conduction processes in dielectric systems can be identified by the time domain or the frequency domain measurements. If the systems is a linear one, the results of the time domain measurements can be transformed into the frequency domain, and vice versa. Commonly, the time domain data of the absorption conductivity are transformed into the frequency domain data of the dielectric susceptibility. In practice, the relaxation are mainly evaluated by the frequency domain data. In the time domain, the absorption current measurement were prefered up to now. Recent methods are based on the recovery voltage measurements. In this paper a new method of the recovery data conversion from the time the frequency domain is proposed. The method is based on the analysis of the recovery voltage transient based on the Maxwell equation for the current density in a dielectric. Unlike the previous published solutions, the Laplace fransform was used to derive a formula suitable for practical purposes. the proposed procedure allows also calculating of the insulation resistance and separating the polarisation and conduction losses.

Predicting detection performance with model observers: Fourier domain or spatial domain?

Science.gov (United States)

Chen, Baiyu; Yu, Lifeng; Leng, Shuai; Kofler, James; Favazza, Christopher; Vrieze, Thomas; McCollough, Cynthia

2016-02-27

The use of Fourier domain model observer is challenged by iterative reconstruction (IR), because IR algorithms are nonlinear and IR images have noise texture different from that of FBP. A modified Fourier domain model observer, which incorporates nonlinear noise and resolution properties, has been proposed for IR and needs to be validated with human detection performance. On the other hand, the spatial domain model observer is theoretically applicable to IR, but more computationally intensive than the Fourier domain method. The purpose of this study is to compare the modified Fourier domain model observer to the spatial domain model observer with both FBP and IR images, using human detection performance as the gold standard. A phantom with inserts of various low contrast levels and sizes was repeatedly scanned 100 times on a third-generation, dual-source CT scanner at 5 dose levels and reconstructed using FBP and IR algorithms. The human detection performance of the inserts was measured via a 2-alternative-forced-choice (2AFC) test. In addition, two model observer performances were calculated, including a Fourier domain non-prewhitening model observer and a spatial domain channelized Hotelling observer. The performance of these two mode observers was compared in terms of how well they correlated with human observer performance. Our results demonstrated that the spatial domain model observer correlated well with human observers across various dose levels, object contrast levels, and object sizes. The Fourier domain observer correlated well with human observers using FBP images, but overestimated the detection performance using IR images.

A dual role of the extracellular domain of Drosophila Crumbs for morphogenesis of the embryonic neuroectoderm

Directory of Open Access Journals (Sweden)

Shradha Das

2018-01-01

Full Text Available Epithelia are highly polarised tissues and several highly conserved polarity protein complexes serve to establish and maintain polarity. The transmembrane protein Crumbs (Crb, the central component of the Crb protein complex, is required, among others, for the maintenance of polarity in most epithelia in the Drosophila embryo. However, different epithelia exhibit different phenotypic severity upon loss of crb. Using a transgenomic approach allowed us to more accurately define the role of crb in different epithelia. In particular, we provide evidence that the loss of epithelial tissue integrity in the ventral epidermis of crb mutant embryos is due to impaired actomyosin activity and an excess number of neuroblasts. We demonstrate that the intracellular domain of Crb could only partially rescue this phenotype, while it is able to completely restore tissue integrity in other epithelia. Based on these results we suggest a dual role of the extracellular domain of Crb in the ventral neuroectoderm. First, it is required for apical enrichment of the Crb protein, which in turn regulates actomyosin activity and thereby ensures tissue integrity; and second, the extracellular domain of Crb stabilises the Notch receptor and thereby ensures proper Notch signalling and specification of the correct number of neuroblasts.

Temporal abstraction and temporal Bayesian networks in clinical domains: a survey.

Science.gov (United States)

Orphanou, Kalia; Stassopoulou, Athena; Keravnou, Elpida

2014-03-01

Temporal abstraction (TA) of clinical data aims to abstract and interpret clinical data into meaningful higher-level interval concepts. Abstracted concepts are used for diagnostic, prediction and therapy planning purposes. On the other hand, temporal Bayesian networks (TBNs) are temporal extensions of the known probabilistic graphical models, Bayesian networks. TBNs can represent temporal relationships between events and their state changes, or the evolution of a process, through time. This paper offers a survey on techniques/methods from these two areas that were used independently in many clinical domains (e.g. diabetes, hepatitis, cancer) for various clinical tasks (e.g. diagnosis, prognosis). A main objective of this survey, in addition to presenting the key aspects of TA and TBNs, is to point out important benefits from a potential integration of TA and TBNs in medical domains and tasks. The motivation for integrating these two areas is their complementary function: TA provides clinicians with high level views of data while TBNs serve as a knowledge representation and reasoning tool under uncertainty, which is inherent in all clinical tasks. Key publications from these two areas of relevance to clinical systems, mainly circumscribed to the latest two decades, are reviewed and classified. TA techniques are compared on the basis of: (a) knowledge acquisition and representation for deriving TA concepts and (b) methodology for deriving basic and complex temporal abstractions. TBNs are compared on the basis of: (a) representation of time, (b) knowledge representation and acquisition, (c) inference methods and the computational demands of the network, and (d) their applications in medicine. The survey performs an extensive comparative analysis to illustrate the separate merits and limitations of various TA and TBN techniques used in clinical systems with the purpose of anticipating potential gains through an integration of the two techniques, thus leading to a

Intelligent Electric Vehicle Integration - Domain Interfaces and Supporting Informatics

DEFF Research Database (Denmark)

Andersen, Peter Bach

This thesis seeks to apply the field of informatics to the intelligent integration of electric vehicles into the power system. The main goal is to release the potential of electric vehicles in relation to a reliable, economically efficient power system based on renewables. To make intelligent EV...... and services in which the electric vehicle may be best suited to participate. The next stakeholder investigated is the distribution system operator representing the low voltage grid. The challenge is assessed by considering a number of grid impacts studies. Next, a set of grid congestion mitigation strategies...

A class of Fourier integrals based on the electric potential of an elongated dipole.

Science.gov (United States)

Skianis, Georgios Aim

2014-01-01

In the present paper the closed expressions of a class of non tabulated Fourier integrals are derived. These integrals are associated with a group of functions at space domain, which represent the electric potential of a distribution of elongated dipoles which are perpendicular to a flat surface. It is shown that the Fourier integrals are produced by the Fourier transform of the Green's function of the potential of the dipole distribution, times a definite integral in which the distribution of the polarization is involved. Therefore the form of this distribution controls the expression of the Fourier integral. Introducing various dipole distributions, the respective Fourier integrals are derived. These integrals may be useful in the quantitative interpretation of electric potential anomalies produced by elongated dipole distributions, at spatial frequency domain.

Integrated Modular Avionics for Spacecraft: Earth Observation Use Case Demonstrator

Science.gov (United States)

Deredempt, Marie-Helene; Rossignol, Alain; Hyounet, Philippe

2013-08-01

Integrated Modular Avionics (IMA) for Space, as European Space Agency initiative, aimed to make applicable to space domain the time and space partitioning concepts and particularly the ARINC 653 standard [1][2]. Expected benefits of such an approach are development flexibility, capability to provide differential V&V for different criticality level functionalities and to integrate late or In-Orbit delivery. This development flexibility could improve software subcontracting, industrial organization and software reuse. Time and space partitioning technique facilitates integration of software functions as black boxes and integration of decentralized function such as star tracker in On Board Computer to save mass and power by limiting electronics resources. In aeronautical domain, Integrated Modular Avionics architecture is based on a network of LRU (Line Replaceable Unit) interconnected by AFDX (Avionic Full DupleX). Time and Space partitioning concept is applicable to LRU and provides independent partitions which inter communicate using ARINC 653 communication ports. Using End System (LRU component) intercommunication between LRU is managed in the same way than intercommunication between partitions in LRU. In such architecture an application developed using only communication port can be integrated in an LRU or another one without impacting the global architecture. In space domain, a redundant On Board Computer controls (ground monitoring TM) and manages the platform (ground command TC) in terms of power, solar array deployment, attitude, orbit, thermal, maintenance, failure detection and recovery isolation. In addition, Payload units and platform units such as RIU, PCDU, AOCS units (Star tracker, Reaction wheels) are considered in this architecture. Interfaces are mainly realized through MIL-STD-1553B busses and SpaceWire and this could be considered as the main constraint for IMA implementation in space domain. During the first phase of IMA SP project, ARINC653

Connecting the dots within: creative performance and identity integration.

Science.gov (United States)

Cheng, Chi-Ying; Sanchez-Burks, Jeffrey; Lee, Fiona

2008-11-01

In two studies drawing from social identity theory and the creative-cognition approach, we found that higher levels of identity integration--perceived compatibility between two social identities--predict higher levels of creative performance in tasks that draw on both identity-relevant knowledge domains. Study 1 showed that Asian Americans with higher identity integration were more creative in developing new dishes using a given set of ingredients, but only when both Asian and American ingredients were available. Study 2 showed that female engineers with higher identity integration were more creative in designing a product, but only when the product was targeted to female users. These findings suggest that the psychological management of multiple social identities may be related to accessibility of multiple knowledge domains, which in turn influences creativity.

Employing finite-state machines in data integrity problems

Directory of Open Access Journals (Sweden)

Malikov Andrey

2016-01-01

Full Text Available This paper explores the issue of group integrity of tuple subsets regarding corporate integrity constraints in relational databases. A solution may be found by applying the finite-state machine theory to guarantee group integrity of data. We present a practical guide to coding such an automaton. After creating SQL queries to manipulate data and control its integrity for real data domains, we study the issue of query performance, determine the level of transaction isolation, and generate query plans.

Bayesian modeling of the yeast SH3 domain interactome predicts spatiotemporal dynamics of endocytosis proteins.

Directory of Open Access Journals (Sweden)

Raffi Tonikian

2009-10-01

Full Text Available SH3 domains are peptide recognition modules that mediate the assembly of diverse biological complexes. We scanned billions of phage-displayed peptides to map the binding specificities of the SH3 domain family in the budding yeast, Saccharomyces cerevisiae. Although most of the SH3 domains fall into the canonical classes I and II, each domain utilizes distinct features of its cognate ligands to achieve binding selectivity. Furthermore, we uncovered several SH3 domains with specificity profiles that clearly deviate from the two canonical classes. In conjunction with phage display, we used yeast two-hybrid and peptide array screening to independently identify SH3 domain binding partners. The results from the three complementary techniques were integrated using a Bayesian algorithm to generate a high-confidence yeast SH3 domain interaction map. The interaction map was enriched for proteins involved in endocytosis, revealing a set of SH3-mediated interactions that underlie formation of protein complexes essential to this biological pathway. We used the SH3 domain interaction network to predict the dynamic localization of several previously uncharacterized endocytic proteins, and our analysis suggests a novel role for the SH3 domains of Lsb3p and Lsb4p as hubs that recruit and assemble several endocytic complexes.

Integration and interpolation of sampled waveforms

International Nuclear Information System (INIS)

Stearns, S.D.

1978-01-01

Methods for integrating, interpolating, and improving the signal-to-noise ratio of digitized waveforms are discussed with regard to seismic data from underground tests. The frequency-domain integration method and the digital interpolation method of Schafer and Rabiner are described and demonstrated using test data. The use of bandpass filtering for noise reduction is also demonstrated. With these methods, a backlog of seismic test data has been successfully processed

Concrete domains

OpenAIRE

Kahn, G.; Plotkin, G.D.

1993-01-01

This paper introduces the theory of a particular kind of computation domains called concrete domains. The purpose of this theory is to find a satisfactory framework for the notions of coroutine computation and sequentiality of evaluation.

A Logic for Inclusion of Administrative Domains and Administrators in Multi-domain Authorization

Science.gov (United States)

Iranmanesh, Zeinab; Amini, Morteza; Jalili, Rasool

Authorization policies for an administrative domain or a composition of multiple domains in multi-domain environments are determined by either one administrator or multiple administrators' cooperation. Several logic-based models for multi-domain environments' authorization have been proposed; however, they have not considered administrators and administrative domains in policies' representation. In this paper, we propose the syntax, proof theory, and semantics of a logic for multi-domain authorization policies including administrators and administrative domains. Considering administrators in policies provides the possibility of presenting composite administration having applicability in many collaborative applications. Indeed, administrators and administrative domains stated in policies can be used in authorization. The presented logic is based on modal logic and utilizes two calculi named the calculus of administrative domains and the calculus of administrators. It is also proved that the logic is sound. A case study is presented signifying the logic application in practical projects.

Interferometrically enhanced sub-terahertz picosecond imaging utilizing a miniature collapsing-field-domain source

Science.gov (United States)

Vainshtein, Sergey N.; Duan, Guoyong; Mikhnev, Valeri A.; Zemlyakov, Valery E.; Egorkin, Vladimir I.; Kalyuzhnyy, Nikolay A.; Maleev, Nikolai A.; Näpänkangas, Juha; Sequeiros, Roberto Blanco; Kostamovaara, Juha T.

2018-05-01

Progress in terahertz spectroscopy and imaging is mostly associated with femtosecond laser-driven systems, while solid-state sources, mainly sub-millimetre integrated circuits, are still in an early development phase. As simple and cost-efficient an emitter as a Gunn oscillator could cause a breakthrough in the field, provided its frequency limitations could be overcome. Proposed here is an application of the recently discovered collapsing field domains effect that permits sub-THz oscillations in sub-micron semiconductor layers thanks to nanometer-scale powerfully ionizing domains arising due to negative differential mobility in extreme fields. This shifts the frequency limit by an order of magnitude relative to the conventional Gunn effect. Our first miniature picosecond pulsed sources cover the 100-200 GHz band and promise milliwatts up to ˜500 GHz. Thanks to the method of interferometrically enhanced time-domain imaging proposed here and the low single-shot jitter of ˜1 ps, our simple imaging system provides sufficient time-domain imaging contrast for fresh-tissue terahertz histology.

Rerepresenting and Restructuring Domain Theories: A Constructive Induction Approach

OpenAIRE

Donoho, S. K.; Rendell, L. A.

1995-01-01

Theory revision integrates inductive learning and background knowledge by combining training examples with a coarse domain theory to produce a more accurate theory. There are two challenges that theory revision and other theory-guided systems face. First, a representation language appropriate for the initial theory may be inappropriate for an improved theory. While the original representation may concisely express the initial theory, a more accurate theory forced to use that same representati...

A database of immunoglobulins with integrated tools: DIGIT.

KAUST Repository

Chailyan, Anna; Tramontano, Anna; Marcatili, Paolo

2011-01-01

The DIGIT (Database of ImmunoGlobulins with Integrated Tools) database (http://biocomputing.it/digit) is an integrated resource storing sequences of annotated immunoglobulin variable domains and enriched with tools for searching and analyzing them. The annotations in the database include information on the type of antigen, the respective germline sequences and on pairing information between light and heavy chains. Other annotations, such as the identification of the complementarity determining regions, assignment of their structural class and identification of mutations with respect to the germline, are computed on the fly and can also be obtained for user-submitted sequences. The system allows customized BLAST searches and automatic building of 3D models of the domains to be performed.

A database of immunoglobulins with integrated tools: DIGIT.

KAUST Repository

Chailyan, Anna

2011-11-10

The DIGIT (Database of ImmunoGlobulins with Integrated Tools) database (http://biocomputing.it/digit) is an integrated resource storing sequences of annotated immunoglobulin variable domains and enriched with tools for searching and analyzing them. The annotations in the database include information on the type of antigen, the respective germline sequences and on pairing information between light and heavy chains. Other annotations, such as the identification of the complementarity determining regions, assignment of their structural class and identification of mutations with respect to the germline, are computed on the fly and can also be obtained for user-submitted sequences. The system allows customized BLAST searches and automatic building of 3D models of the domains to be performed.

Cyberspace at the Operational Level: Warfighting in All Five Domains

Science.gov (United States)

2016-05-13

Sean Hall 5e. TASK NUMBER Paper Advisor: Prof John Sappenfield 5f. WORK UNIT NUMBER 7. PERFORMING ORGANIZATION NAME(S) AND ADDRESS...decisive, operational objective, center of gravity , planner, commander. 16. SECURITY CLASSIFICATION OF: 17. LIMITATION OF ABSTRACT 18. NUMBER OF...requires much more than doctrinal definitions. History shows how well or poorly nations integrated the sea, air, and space domains in their infancy

Feature-level domain adaptation

DEFF Research Database (Denmark)

Kouw, Wouter M.; Van Der Maaten, Laurens J P; Krijthe, Jesse H.

2016-01-01

-level domain adaptation (flda), that models the dependence between the two domains by means of a feature-level transfer model that is trained to describe the transfer from source to target domain. Subsequently, we train a domain-adapted classifier by minimizing the expected loss under the resulting transfer...... modeled via a dropout distribution, which allows the classiffier to adapt to differences in the marginal probability of features in the source and the target domain. Our experiments on several real-world problems show that flda performs on par with state-of-the-art domainadaptation techniques.......Domain adaptation is the supervised learning setting in which the training and test data are sampled from different distributions: training data is sampled from a source domain, whilst test data is sampled from a target domain. This paper proposes and studies an approach, called feature...

Intelligent Integrated System Health Management

Science.gov (United States)

Figueroa, Fernando

2012-01-01

Intelligent Integrated System Health Management (ISHM) is the management of data, information, and knowledge (DIaK) with the purposeful objective of determining the health of a system (Management: storage, distribution, sharing, maintenance, processing, reasoning, and presentation). Presentation discusses: (1) ISHM Capability Development. (1a) ISHM Knowledge Model. (1b) Standards for ISHM Implementation. (1c) ISHM Domain Models (ISHM-DM's). (1d) Intelligent Sensors and Components. (2) ISHM in Systems Design, Engineering, and Integration. (3) Intelligent Control for ISHM-Enabled Systems

Enhanced feature integration in musicians

DEFF Research Database (Denmark)

Hansen, Niels Christian; Højlund, Andreas; Møller, Cecilie

the classical oddball control paradigm which used identical sounds. This novel finding supports the dependent processing hypothesis suggesting that musicians recruit overlapping neural resources facilitating more holistic representations of domain-relevant stimuli. These specialised refinements in predictive......Distinguishing and integrating features of sensory input is essential to human survival and no less paramount in music perception and cognition. Yet, little is known about training-induced plasticity of neural mechanisms for auditory feature integration. This study aimed to contrast the two...

Intercloud Architecture for interoperability and integration

NARCIS (Netherlands)

Demchenko, Y.; Makkes, M.X.; Strijkers, R.J.; Laat, C. de

2012-01-01

This paper presents on-going research to develop the Intercloud Architecture Framework (ICAF) that addresses problems in multi-provider multi-domain heterogeneous cloud based infrastructure services and applications integration and interoperability. The paper refers to existing standards in Cloud

Intercloud architecture for interoperability and integration

NARCIS (Netherlands)

Demchenko, Y.; Makkes, M.X.; Strijkers, R.; de Laat, C.

2012-01-01

This paper presents on-going research to develop the Intercloud Architecture Framework (ICAF) that addresses problems in multi-provider multi-domain heterogeneous cloud based infrastructure services and applications integration and interoperability. The paper refers to existing standards in Cloud

On the static loop modes in the marching-on-in-time solution of the time-domain electric field integral equation

KAUST Repository

Shi, Yifei; Bagci, Hakan; Lu, Mingyu

2014-01-01

When marching-on-in-time (MOT) method is applied to solve the time-domain electric field integral equation, spurious internal resonant and static loop modes are always observed in the solution. The internal resonant modes have recently been studied by the authors; this letter investigates the static loop modes. Like internal resonant modes, static loop modes, in theory, should not be observed in the MOT solution since they do not satisfy the zero initial conditions; their appearance is attributed to numerical errors. It is discussed in this letter that the dependence of spurious static loop modes on numerical errors is substantially different from that of spurious internal resonant modes. More specifically, when Rao-Wilton-Glisson functions and Lagrange interpolation functions are used as spatial and temporal basis functions, respectively, errors due to space-time discretization have no discernible impact on spurious static loop modes. Numerical experiments indeed support this discussion and demonstrate that the numerical errors due to the approximate solution of the MOT matrix system have dominant impact on spurious static loop modes in the MOT solution. © 2014 IEEE.

PREFACE: Domain wall dynamics in nanostructures Domain wall dynamics in nanostructures

Science.gov (United States)

Marrows, C. H.; Meier, G.

2012-01-01

Domain structures in magnetic materials are ubiquitous and have been studied for decades. The walls that separate them are topological defects in the magnetic order parameter and have a wide variety of complex forms. In general, their investigation is difficult in bulk materials since only the domain structure on the surface of a specimen is visible. Cutting the sample to reveal the interior causes a rearrangement of the domains into a new form. As with many other areas of magnetism, the study of domain wall physics has been revitalised by the advent of nanotechnology. The ability to fabricate nanoscale structures has permitted the formation of simplified and controlled domain patterns; the development of advanced microscopy methods has permitted them to be imaged and then modelled; subjecting them to ultrashort field and current pulses has permitted their dynamics to be explored. The latest results from all of these advances are described in this special issue. Not only has this led to results of great scientific beauty, but also to concepts of great applicability to future information technologies. In this issue the reader will find the latest results for these domain wall dynamics and the high-speed processes of topological structures such as domain walls and magnetic vortices. These dynamics can be driven by the application of magnetic fields, or by flowing currents through spintronic devices using the novel physics of spin-transfer torque. This complexity has been studied using a wide variety of experimental techniques at the edge of the spatial and temporal resolution currently available, and can be described using sophisticated analytical theory and computational modelling. As a result, the dynamics can be engineered to give rise to finely controlled memory and logic devices with new functionality. Moreover, the field is moving to study not only the conventional transition metal ferromagnets, but also complex heterostructures, novel magnets and even other

Time-domain modeling of electromagnetic diffusion with a frequency-domain code

NARCIS (Netherlands)

Mulder, W.A.; Wirianto, M.; Slob, E.C.

2007-01-01

We modeled time-domain EM measurements of induction currents for marine and land applications with a frequency-domain code. An analysis of the computational complexity of a number of numerical methods shows that frequency-domain modeling followed by a Fourier transform is an attractive choice if a

Structure determination and analysis of a haemolytic gingipain adhesin domain from Porphyromonas gingivalis

Energy Technology Data Exchange (ETDEWEB)

Li, N.; Yun, P.; Nadkarni, M.A.; Ghadikolaee, N.B.; Nguyen, K.A.; Lee, M.; Hunter, N.; Collyer, C.A. (Sydney)

2010-08-27

Porphyromonas gingivalis is an obligately anaerobic bacterium recognized as an aetiological agent of adult periodontitis. P. gingivalis produces cysteine proteinases, the gingipains. The crystal structure of a domain within the haemagglutinin region of the lysine gingipain (Kgp) is reported here. The domain was named K2 as it is the second of three homologous structural modules in Kgp. The K2 domain structure is a 'jelly-roll' fold with two anti-parallel {beta}-sheets. This fold topology is shared with adhesive domains from functionally diverse receptors such as MAM domains, ephrin receptor ligand binding domains and a number of carbohydrate binding modules. Possible functions of K2 were investigated. K2 induced haemolysis of erythrocytes in a dose-dependent manner that was augmented by the blocking of anion transport. Further, cysteine-activated arginine gingipain RgpB, which degrades glycophorin A, sensitized erythrocytes to the haemolytic effect of K2. Cleaved K2, similar to that found in extracted Kgp, lacks the haemolytic activity indicating that autolysis of Kgp may be a staged process which is artificially enhanced by extraction of the protein. The data indicate a functional role for K2 in the integrated capacity conferred by Kgp to enable the porphyrin auxotroph P. gingivalis to capture essential haem from erythrocytes.

Mental retardation-related protease, motopsin (prss12), binds to the BRICHOS domain of the integral membrane protein 2a.

Science.gov (United States)

Mitsui, Shinichi; Osako, Yoji; Yuri, Kazunari

2014-01-01

Motopsin (prss12), a mosaic serine protease secreted by neuronal cells, is believed to be important for cognitive function, as the loss of its function causes severe nonsyndromic mental retardation. To understand the molecular role of motopsin, we identified the integral membrane protein 2a (Itm2a) as a motopsin-interacting protein using a yeast two-hybrid system. A pull-down assay showed that the BRICHOS domain of Itm2a was essential for this interaction. Motopsin and Itm2a co-localized in COS cells and in cultured neurons when transiently expressed in these cells. Both proteins were co-immunoprecipitated from lysates of these transfected COS cells. Itm2a was strongly detected in a brain lysate prepared between postnatal day 0 and 10, during which period motopsin protein was also enriched in the brain. Immunohistochemistry detected Itm2a as patchy spots along endothelial cells of brain capillaries (which also expressed myosin II regulatory light chain [RLC]), and on glial fibrillary acidic protein (GFAP)-positive processes in the developing cerebral cortex. The data raise the possibility that secreted motopsin interacts with endothelial cells in the developing brain. © 2013 International Federation for Cell Biology.

Separated matter and antimatter domains with vanishing domain walls

Energy Technology Data Exchange (ETDEWEB)

Dolgov, A.D.; Godunov, S.I.; Rudenko, A.S.; Tkachev, I.I., E-mail: dolgov@fe.infn.it, E-mail: sgodunov@itep.ru, E-mail: a.s.rudenko@inp.nsk.su, E-mail: tkachev@ms2.inr.ac.ru [Physics Department and Laboratory of Cosmology and Elementary Particle Physics, Novosibirsk State University, Pirogova st. 2, Novosibirsk, 630090 (Russian Federation)

2015-10-01

We present a model of spontaneous (or dynamical) C and CP violation where it is possible to generate domains of matter and antimatter separated by cosmologically large distances. Such C(CP) violation existed only in the early universe and later it disappeared with the only trace of generated baryonic and/or antibaryonic domains. So the problem of domain walls in this model does not exist. These features are achieved through a postulated form of interaction between inflaton and a new scalar field, realizing short time C(CP) violation.

Robust Reliability or reliable robustness? - Integrated consideration of robustness and reliability aspects

DEFF Research Database (Denmark)

Kemmler, S.; Eifler, Tobias; Bertsche, B.

2015-01-01

products are and vice versa. For a comprehensive understanding and to use existing synergies between both domains, this paper discusses the basic principles of Reliability- and Robust Design theory. The development of a comprehensive model will enable an integrated consideration of both domains...

Full Wave Analysis of Passive Microwave Monolithic Integrated Circuit Devices Using a Generalized Finite Difference Time Domain (GFDTD) Algorithm

Science.gov (United States)

Lansing, Faiza S.; Rascoe, Daniel L.

1993-01-01

This paper presents a modified Finite-Difference Time-Domain (FDTD) technique using a generalized conformed orthogonal grid. The use of the Conformed Orthogonal Grid, Finite Difference Time Domain (GFDTD) enables the designer to match all the circuit dimensions, hence eliminating a major source o error in the analysis.

Computation of integral bases

NARCIS (Netherlands)

Bauch, J.H.P.

2015-01-01

Let $A$ be a Dedekind domain, $K$ the fraction field of $A$, and $f\\in A[x]$ a monic irreducible separable polynomial. For a given non-zero prime ideal $\\mathfrak{p}$ of $A$ we present in this paper a new method to compute a $\\mathfrak{p}$-integral basis of the extension of $K$ determined by $f$.

Computation of integral bases

NARCIS (Netherlands)

Bauch, J.D.

2016-01-01

Let A be a Dedekind domain, K the fraction field of A, and f∈. A[. x] a monic irreducible separable polynomial. For a given non-zero prime ideal p of A we present in this paper a new characterization of a p-integral basis of the extension of K determined by f. This characterization yields in an

Integrating CFD and building simulation

DEFF Research Database (Denmark)

Bartak, M.; Beausoleil-Morrison, I.; Clarke, J.A.

2002-01-01

Commission, which furthered the CFD modelling aspects of the ESP-r system. The paper summarises the form of the CFD model, describes the method used to integrate the thermal and 3ow domains and reports the outcome from an empirical validation exercise. © 2002 Published by Elsevier Science Ltd....

Free vibration analysis of elastic structures submerged in an infinite or semi-infinite fluid domain by means of a coupled FE-BE solver

Science.gov (United States)

Zheng, Chang-Jun; Bi, Chuan-Xing; Zhang, Chuanzeng; Gao, Hai-Feng; Chen, Hai-Bo

2018-04-01

The vibration behavior of thin elastic structures can be noticeably influenced by the surrounding water, which represents a kind of heavy fluid. Since the feedback of the acoustic pressure onto the structure cannot be neglected in this case, a strong coupled scheme between the structural and fluid domains is usually required. In this work, a coupled finite element and boundary element (FE-BE) solver is developed for the free vibration analysis of structures submerged in an infinite fluid domain or a semi-infinite fluid domain with a free water surface. The structure is modeled by the finite element method (FEM). The compressibility of the fluid is taken into account, and hence the Helmholtz equation serves as the governing equation of the fluid domain. The boundary element method (BEM) is employed to model the fluid domain, and a boundary integral formulation with a half-space fundamental solution is used to satisfy the Dirichlet boundary condition on the free water surface exactly. The resulting nonlinear eigenvalue problem (NEVP) is converted into a small linear one by using a contour integral method. Adequate modifications are suggested to improve the efficiency of the contour integral method and avoid missing the eigenfrequencies of interest. The Burton-Miller method is used to filter out the fictitious eigenfrequencies of the boundary integral formulations. Numerical examples are given to demonstrate the accuracy and applicability of the developed eigensolver, and also show that the fluid-loading effect strongly depends on both the water depth and the mode shapes.

A graph kernel approach for alignment-free domain-peptide interaction prediction with an application to human SH3 domains.

Science.gov (United States)

Kundu, Kousik; Costa, Fabrizio; Backofen, Rolf

2013-07-01

State-of-the-art experimental data for determining binding specificities of peptide recognition modules (PRMs) is obtained by high-throughput approaches like peptide arrays. Most prediction tools applicable to this kind of data are based on an initial multiple alignment of the peptide ligands. Building an initial alignment can be error-prone, especially in the case of the proline-rich peptides bound by the SH3 domains. Here, we present a machine-learning approach based on an efficient graph-kernel technique to predict the specificity of a large set of 70 human SH3 domains, which are an important class of PRMs. The graph-kernel strategy allows us to (i) integrate several types of physico-chemical information for each amino acid, (ii) consider high-order correlations between these features and (iii) eliminate the need for an initial peptide alignment. We build specialized models for each human SH3 domain and achieve competitive predictive performance of 0.73 area under precision-recall curve, compared with 0.27 area under precision-recall curve for state-of-the-art methods based on position weight matrices. We show that better models can be obtained when we use information on the noninteracting peptides (negative examples), which is currently not used by the state-of-the art approaches based on position weight matrices. To this end, we analyze two strategies to identify subsets of high confidence negative data. The techniques introduced here are more general and hence can also be used for any other protein domains, which interact with short peptides (i.e. other PRMs). The program with the predictive models can be found at http://www.bioinf.uni-freiburg.de/Software/SH3PepInt/SH3PepInt.tar.gz. We also provide a genome-wide prediction for all 70 human SH3 domains, which can be found under http://www.bioinf.uni-freiburg.de/Software/SH3PepInt/Genome-Wide-Predictions.tar.gz. Supplementary data are available at Bioinformatics online.

Diffusion phenomenon for linear dissipative wave equations in an exterior domain

Science.gov (United States)

Ikehata, Ryo

Under the general condition of the initial data, we will derive the crucial estimates which imply the diffusion phenomenon for the dissipative linear wave equations in an exterior domain. In order to derive the diffusion phenomenon for dissipative wave equations, the time integral method which was developed by Ikehata and Matsuyama (Sci. Math. Japon. 55 (2002) 33) plays an effective role.

Integrating Intelligent Systems Domain Knowledge Into the Earth Science Curricula

Science.gov (United States)

Güereque, M.; Pennington, D. D.; Pierce, S. A.

2017-12-01

High-volume heterogeneous datasets are becoming ubiquitous, migrating to center stage over the last ten years and transcending the boundaries of computationally intensive disciplines into the mainstream, becoming a fundamental part of every science discipline. Despite the fact that large datasets are now pervasive across industries and academic disciplines, the array of skills is generally absent from earth science programs. This has left the bulk of the student population without access to curricula that systematically teach appropriate intelligent-systems skills, creating a void for skill sets that should be universal given their need and marketability. While some guidance regarding appropriate computational thinking and pedagogy is appearing, there exist few examples where these have been specifically designed and tested within the earth science domain. Furthermore, best practices from learning science have not yet been widely tested for developing intelligent systems-thinking skills. This research developed and tested evidence based computational skill modules that target this deficit with the intention of informing the earth science community as it continues to incorporate intelligent systems techniques and reasoning into its research and classrooms.

A new multi-domain method based on an analytical control surface for linear and second-order mean drift wave loads on floating bodies

Science.gov (United States)

Liang, Hui; Chen, Xiaobo

2017-10-01

A novel multi-domain method based on an analytical control surface is proposed by combining the use of free-surface Green function and Rankine source function. A cylindrical control surface is introduced to subdivide the fluid domain into external and internal domains. Unlike the traditional domain decomposition strategy or multi-block method, the control surface here is not panelized, on which the velocity potential and normal velocity components are analytically expressed as a series of base functions composed of Laguerre function in vertical coordinate and Fourier series in the circumference. Free-surface Green function is applied in the external domain, and the boundary integral equation is constructed on the control surface in the sense of Galerkin collocation via integrating test functions orthogonal to base functions over the control surface. The external solution gives rise to the so-called Dirichlet-to-Neumann [DN2] and Neumann-to-Dirichlet [ND2] relations on the control surface. Irregular frequencies, which are only dependent on the radius of the control surface, are present in the external solution, and they are removed by extending the boundary integral equation to the interior free surface (circular disc) on which the null normal derivative of potential is imposed, and the dipole distribution is expressed as Fourier-Bessel expansion on the disc. In the internal domain, where the Rankine source function is adopted, new boundary integral equations are formulated. The point collocation is imposed over the body surface and free surface, while the collocation of the Galerkin type is applied on the control surface. The present method is valid in the computation of both linear and second-order mean drift wave loads. Furthermore, the second-order mean drift force based on the middle-field formulation can be calculated analytically by using the coefficients of the Fourier-Laguerre expansion.

A numerical method for resonance integral calculations

International Nuclear Information System (INIS)

Tanbay, Tayfun; Ozgener, Bilge

2013-01-01

A numerical method has been proposed for resonance integral calculations and a cubic fit based on least squares approximation to compute the optimum Bell factor is given. The numerical method is based on the discretization of the neutron slowing down equation. The scattering integral is approximated by taking into account the location of the upper limit in energy domain. The accuracy of the method has been tested by performing computations of resonance integrals for uranium dioxide isolated rods and comparing the results with empirical values. (orig.)

Multi-material micro-electromechanical fibers with bendable functional domains

Science.gov (United States)

Nguyen-Dang, Tung; Page, Alexis G.; Qu, Yunpeng; Volpi, Marco; Yan, Wei; Sorin, Fabien

2017-04-01

The integration of increasingly complex functionalities within thermally drawn multi-material fibers is heralding a novel path towards advanced soft electronics and smart fabrics. Fibers capable of electronic, optoelectronic, piezoelectric or energy harvesting functions are created by assembling new materials in intimate contact within increasingly complex architectures. Thus far, however, the opportunities associated with the integration of cantilever-like structures with freely moving functional domains within multi-material fibers have not been explored. Used extensively in the micro-electromechanical system (MEMS) technology, electro-mechanical transductance from moving and bendable domains is used in a myriad of applications. In this article we demonstrate the thermal drawing of micro-electromechanical fibers (MEMF) that can detect and localize pressure with high accuracy along their entire length. This ability results from an original cantilever-like design where a freestanding electrically conductive polymer composite film bends under an applied pressure. As it comes into contact with another conducting domain, placed at a prescribed position in the fiber cross-section, an electrical signal is generated. We show that by a judicious choice of materials and electrical connectivity, this signal can be uniquely related to a position along the fiber axis. We establish a model that predicts the position of a local touch from the measurement of currents generated in the 1D MEMF device, and demonstrate an excellent agreement with the experimental data. This ability to detect and localize touch over large areas, curved surfaces and textiles holds significant opportunities in robotics and prosthetics, flexible electronic interfaces, and medical textiles. , which features invited work from the best early-career researchers working within the scope of J. Phys. D. This project is part of the Journal of Physics series’ 50th anniversary celebrations in 2017. Fabien Sorin

Domain Walls and Matter-Antimatter Domains in the Early Universe

Directory of Open Access Journals (Sweden)

Dolgov A.D.

2017-01-01

Full Text Available We suggest a scenario of spontaneous (or dynamical C and CP violation according to which it is possible to generate domains of matter and antimatter separated by cosmologically large distances. Such C(CP violation existed only in the early universe and later it disappeared with the only trace of generated matter and antimatter domains. So this scenario does not suffer from the problem of domain walls. According to this scenario the width of the domain wall should grow exponentially to prevent annihilation at the domain boundaries. Though there is a classical result obtained by Basu and Vilenkin that the width of the wall tends to the one of the stationary solution (constant physical width. That is why we considered thick domain walls in a de Sitter universe following paper by Basu and Vilenkin. However, we were interested not only in stationary solutions found therein, but also investigated the general case of domain wall evolution with time. When the wall thickness parameter, δ0 , is smaller than H−1/2 where H is the Hubble parameter in de Sitter space-time, then the stationary solutions exist, and initial field configurations tend with time to the stationary ones. However, there are no stationary solutions for δ0>H−1/2 We have calculated numerically the rate of the wall expansion in this case and have found that the width of the wall grows exponentially fast for δ0≫H−1 An explanation for the critical value δ0c=H−1/2 is also proposed.

Designing Domain-Specific Heterogeneous Architectures from Dataflow Programs

Directory of Open Access Journals (Sweden)

Süleyman Savas

2018-04-01

Full Text Available The last ten years have seen performance and power requirements pushing computer architectures using only a single core towards so-called manycore systems with hundreds of cores on a single chip. To further increase performance and energy efficiency, we are now seeing the development of heterogeneous architectures with specialized and accelerated cores. However, designing these heterogeneous systems is a challenging task due to their inherent complexity. We proposed an approach for designing domain-specific heterogeneous architectures based on instruction augmentation through the integration of hardware accelerators into simple cores. These hardware accelerators were determined based on their common use among applications within a certain domain.The objective was to generate heterogeneous architectures by integrating many of these accelerated cores and connecting them with a network-on-chip. The proposed approach aimed to ease the design of heterogeneous manycore architectures—and, consequently, exploration of the design space—by automating the design steps. To evaluate our approach, we enhanced our software tool chain with a tool that can generate accelerated cores from dataflow programs. This new tool chain was evaluated with the aid of two use cases: radar signal processing and mobile baseband processing. We could achieve an approximately 4 × improvement in performance, while executing complete applications on the augmented cores with a small impact (2.5–13% on area usage. The generated accelerators are competitive, achieving more than 90% of the performance of hand-written implementations.

ASIC3 Channels Integrate Agmatine and Multiple Inflammatory Signals through the Nonproton Ligand Sensing Domain

Directory of Open Access Journals (Sweden)

Cao Hui

2010-12-01

Full Text Available Abstract Background Acid-sensing ion channels (ASICs have long been known to sense extracellular protons and contribute to sensory perception. Peripheral ASIC3 channels represent natural sensors of acidic and inflammatory pain. We recently reported the use of a synthetic compound, 2-guanidine-4-methylquinazoline (GMQ, to identify a novel nonproton sensing domain in the ASIC3 channel, and proposed that, based on its structural similarity with GMQ, the arginine metabolite agmatine (AGM may be an endogenous nonproton ligand for ASIC3 channels. Results Here, we present further evidence for the physiological correlation between AGM and ASIC3. Among arginine metabolites, only AGM and its analog arcaine (ARC activated ASIC3 channels at neutral pH in a sustained manner similar to GMQ. In addition to the homomeric ASIC3 channels, AGM also activated heteromeric ASIC3 plus ASIC1b channels, extending its potential physiological relevance. Importantly, the process of activation by AGM was highly sensitive to mild acidosis, hyperosmolarity, arachidonic acid (AA, lactic acid and reduced extracellular Ca2+. AGM-induced ASIC3 channel activation was not through the chelation of extracellular Ca2+ as occurs with increased lactate, but rather through a direct interaction with the newly identified nonproton ligand sensing domain. Finally, AGM cooperated with the multiple inflammatory signals to cause pain-related behaviors in an ASIC3-dependent manner. Conclusions Nonproton ligand sensing domain might represent a novel mechanism for activation or sensitization of ASIC3 channels underlying inflammatory pain-sensing under in vivo conditions.

The IntFOLD server: an integrated web resource for protein fold recognition, 3D model quality assessment, intrinsic disorder prediction, domain prediction and ligand binding site prediction.

Science.gov (United States)

Roche, Daniel B; Buenavista, Maria T; Tetchner, Stuart J; McGuffin, Liam J

2011-07-01

The IntFOLD server is a novel independent server that integrates several cutting edge methods for the prediction of structure and function from sequence. Our guiding principles behind the server development were as follows: (i) to provide a simple unified resource that makes our prediction software accessible to all and (ii) to produce integrated output for predictions that can be easily interpreted. The output for predictions is presented as a simple table that summarizes all results graphically via plots and annotated 3D models. The raw machine readable data files for each set of predictions are also provided for developers, which comply with the Critical Assessment of Methods for Protein Structure Prediction (CASP) data standards. The server comprises an integrated suite of five novel methods: nFOLD4, for tertiary structure prediction; ModFOLD 3.0, for model quality assessment; DISOclust 2.0, for disorder prediction; DomFOLD 2.0 for domain prediction; and FunFOLD 1.0, for ligand binding site prediction. Predictions from the IntFOLD server were found to be competitive in several categories in the recent CASP9 experiment. The IntFOLD server is available at the following web site: http://www.reading.ac.uk/bioinf/IntFOLD/.

Low-cost access to development and manufacturing of photonic integrated circuits

NARCIS (Netherlands)

Smit, M.K.

2014-01-01

Generic photonic integration technology is rapidly gaining popularity. It applies the methodology that is so successful in microelectronics (CMOS technology) to the domain of photonics: providing lowcost access to highly standardized high-performance processes that support integration in a single

Education, implementation, and policy barriers to greater integration of palliative care: A literature review.

Science.gov (United States)

Aldridge, Melissa D; Hasselaar, Jeroen; Garralda, Eduardo; van der Eerden, Marlieke; Stevenson, David; McKendrick, Karen; Centeno, Carlos; Meier, Diane E

2016-03-01

Early integration of palliative care into the management of patients with serious disease has the potential to both improve quality of life of patients and families and reduce healthcare costs. Despite these benefits, significant barriers exist in the United States to the early integration of palliative care in the disease trajectory of individuals with serious illness. To provide an overview of the barriers to more widespread palliative care integration in the United States. A literature review using PubMed from 2005 to March 2015 augmented by primary data collected from 405 hospitals included in the Center to Advance Palliative Care's National Palliative Care Registry for years 2012 and 2013. We use the World Health Organization's Public Health Strategy for Palliative Care as a framework for analyzing barriers to palliative care integration. We identified key barriers to palliative care integration across three World Health Organization domains: (1) education domain: lack of adequate education/training and perception of palliative care as end-of-life care; (2) implementation domain: inadequate size of palliative medicine-trained workforce, challenge of identifying patients appropriate for palliative care referral, and need for culture change across settings; (3) policy domain: fragmented healthcare system, need for greater funding for research, lack of adequate reimbursement for palliative care, and regulatory barriers. We describe the key policy and educational opportunities in the United States to address and potentially overcome the barriers to greater integration of palliative care into the healthcare of Americans with serious illness. © The Author(s) 2015.

Integrated cross-domain object storage in working memory : Evidence from a verbal-spatial memory task

NARCIS (Netherlands)

Morey, C.C.

2009-01-01

Working-memory theories often include domain-specific verbal and visual stores (e.g., the phonological and visuospatial buffers of Baddeley, 1986), and some also posit more general stores thought to be capable of holding verbal or visuospatial materials (Baddeley, 2000; Cowan, 2005). However, it is

The Integrated Microbial Genomes (IMG) System: An Expanding Comparative Analysis Resource

Energy Technology Data Exchange (ETDEWEB)

Markowitz, Victor M.; Chen, I-Min A.; Palaniappan, Krishna; Chu, Ken; Szeto, Ernest; Grechkin, Yuri; Ratner, Anna; Anderson, Iain; Lykidis, Athanasios; Mavromatis, Konstantinos; Ivanova, Natalia N.; Kyrpides, Nikos C.

2009-09-13

The integrated microbial genomes (IMG) system serves as a community resource for comparative analysis of publicly available genomes in a comprehensive integrated context. IMG contains both draft and complete microbial genomes integrated with other publicly available genomes from all three domains of life, together with a large number of plasmids and viruses. IMG provides tools and viewers for analyzing and reviewing the annotations of genes and genomes in a comparative context. Since its first release in 2005, IMG's data content and analytical capabilities have been constantly expanded through regular releases. Several companion IMG systems have been set up in order to serve domain specific needs, such as expert review of genome annotations. IMG is available at .

Design of energy efficient optical networks with software enabled integrated control plane

DEFF Research Database (Denmark)

Wang, Jiayuan; Yan, Ying; Dittmann, Lars

2015-01-01

energy consumption by proposing a new integrated control plane structure utilising Software Defined Networking technologies. The integrated control plane increases the efficiencies of exchanging control information across different network domains, while introducing new possibilities to the routing...... methods and the control over quality of service (QoS). The structure is defined as an overlay generalised multi-protocol label switching (GMPLS) control model. With the defined structure, the integrated control plane is able to gather information from different domains (i.e. optical core network......'s) routing behaviours. With the flexibility of the routing structure, results show that the energy efficiency of the network can be improved without compromising the QoS for delay/blocking sensitive services....

Adaptive control in multi-threaded iterated integration

International Nuclear Information System (INIS)

Doncker, Elise de; Yuasa, Fukuko

2013-01-01

In recent years we have developed a technique for the direct computation of Feynman loop-integrals, which are notorious for the occurrence of integrand singularities. Especially for handling singularities in the interior of the domain, we approximate the iterated integral using an adaptive algorithm in the coordinate directions. We present a novel multi-core parallelization scheme for adaptive multivariate integration, by assigning threads to the rule evaluations in the outer dimensions of the iterated integral. The method ensures a large parallel granularity as each function evaluation by itself comprises an integral over the lower dimensions, while the application of the threads is governed by the adaptive control in the outer level. We give computational results for a test set of 3- to 6-dimensional integrals, where several problems exhibit a loop integral behavior.

Work and personal life boundary management: boundary strength, work/personal life balance, and the segmentation-integration continuum.

Science.gov (United States)

Bulger, Carrie A; Matthews, Russell A; Hoffman, Mark E

2007-10-01

While researchers are increasingly interested in understanding the boundaries surrounding the work and personal life domains, few have tested the propositions set forth by theory. Boundary theory proposes that individuals manage the boundaries between work and personal life through processes of segmenting and/or integrating the domains. The authors investigated boundary management profiles of 332 workers in an investigation of the segmentation-integration continuum. Cluster analysis indicated consistent clusters of boundary management practices related to varying segmentation and integration of the work and personal life domains. But, the authors suggest that the segmentation-integration continuum may be more complicated. Results also indicated relationships between boundary management practices and work-personal life interference and work-personal life enhancement. Less flexible and more permeable boundaries were related to more interference, while more flexible and more permeable boundaries were related to more enhancement.

Model-Based Integration and Interpretation of Data

DEFF Research Database (Denmark)

Petersen, Johannes

2004-01-01

Data integration and interpretation plays a crucial role in supervisory control. The paper defines a set of generic inference steps for the data integration and interpretation process based on a three-layer model of system representations. The three-layer model is used to clarify the combination...... of constraint and object-centered representations of the work domain throwing new light on the basic principles underlying the data integration and interpretation process of Rasmussen's abstraction hierarchy as well as other model-based approaches combining constraint and object-centered representations. Based...

Seven domains for leadership mentoring and executive coaching A reflective paper

Directory of Open Access Journals (Sweden)

Paul O. Olson

2014-07-01

Full Text Available This article discusses how coaching and mentoring can be integrated and work together as systematic tools for leadership development. The author draws on psychotherapy as a parallel for practitioner research and posits five validation hypotheses for coaching and mentoring. Arguably coaching is not sufficient to develop leaders, but a useful toolbox within mentoring. Internal mentors in particular have cultural and industry knowledge of direct relevance to the adept. Seven domains are identified for an integrated framework: Insight from reflection and meta-learning; Working with the whole person; Competence modelling; Deep listening, beyond words; Emotional intelligence; Coaching for results; and Systemic thinking and team development.

Structural coupling of SH2-kinase domains links Fes and Abl substrate recognition and kinase activation.

Science.gov (United States)

Filippakopoulos, Panagis; Kofler, Michael; Hantschel, Oliver; Gish, Gerald D; Grebien, Florian; Salah, Eidarus; Neudecker, Philipp; Kay, Lewis E; Turk, Benjamin E; Superti-Furga, Giulio; Pawson, Tony; Knapp, Stefan

2008-09-05

The SH2 domain of cytoplasmic tyrosine kinases can enhance catalytic activity and substrate recognition, but the molecular mechanisms by which this is achieved are poorly understood. We have solved the structure of the prototypic SH2-kinase unit of the human Fes tyrosine kinase, which appears specialized for positive signaling. In its active conformation, the SH2 domain tightly interacts with the kinase N-terminal lobe and positions the kinase alphaC helix in an active configuration through essential packing and electrostatic interactions. This interaction is stabilized by ligand binding to the SH2 domain. Our data indicate that Fes kinase activation is closely coupled to substrate recognition through cooperative SH2-kinase-substrate interactions. Similarly, we find that the SH2 domain of the active Abl kinase stimulates catalytic activity and substrate phosphorylation through a distinct SH2-kinase interface. Thus, the SH2 and catalytic domains of active Fes and Abl pro-oncogenic kinases form integrated structures essential for effective tyrosine kinase signaling.

High-speed extended-term time-domain simulation for online cascading analysis of power system

Science.gov (United States)

Fu, Chuan

A high-speed extended-term (HSET) time domain simulator (TDS), intended to become a part of an energy management system (EMS), has been newly developed for use in online extended-term dynamic cascading analysis of power systems. HSET-TDS includes the following attributes for providing situational awareness of high-consequence events: (i) online analysis, including n-1 and n-k events, (ii) ability to simulate both fast and slow dynamics for 1-3 hours in advance, (iii) inclusion of rigorous protection-system modeling, (iv) intelligence for corrective action ID, storage, and fast retrieval, and (v) high-speed execution. Very fast on-line computational capability is the most desired attribute of this simulator. Based on the process of solving algebraic differential equations describing the dynamics of power system, HSET-TDS seeks to develop computational efficiency at each of the following hierarchical levels, (i) hardware, (ii) strategies, (iii) integration methods, (iv) nonlinear solvers, and (v) linear solver libraries. This thesis first describes the Hammer-Hollingsworth 4 (HH4) implicit integration method. Like the trapezoidal rule, HH4 is symmetrically A-Stable but it possesses greater high-order precision (h4 ) than the trapezoidal rule. Such precision enables larger integration steps and therefore improves simulation efficiency for variable step size implementations. This thesis provides the underlying theory on which we advocate use of HH4 over other numerical integration methods for power system time-domain simulation. Second, motivated by the need to perform high speed extended-term time domain simulation (HSET-TDS) for on-line purposes, this thesis presents principles for designing numerical solvers of differential algebraic systems associated with power system time-domain simulation, including DAE construction strategies (Direct Solution Method), integration methods(HH4), nonlinear solvers(Very Dishonest Newton), and linear solvers(SuperLU). We have

A service integration platform for collaborative networks

NARCIS (Netherlands)

Osorio, A. L.; Afsarmanesh, H.; Camarinha-Matos, L.M.

2011-01-01

Integrated manufacturing constitutes a complex system made of heterogeneous information and control subsystems. Those subsystems are not designed to the cooperation. Typically each subsystem automates specific processes, and establishes closed application domains, therefore it is very difficult to

Domain shape instabilities and dendrite domain growth in uniaxial ferroelectrics

Science.gov (United States)

Shur, Vladimir Ya.; Akhmatkhanov, Andrey R.

2018-01-01

The effects of domain wall shape instabilities and the formation of nanodomains in front of moving walls obtained in various uniaxial ferroelectrics are discussed. Special attention is paid to the formation of self-assembled nanoscale and dendrite domain structures under highly non-equilibrium switching conditions. All obtained results are considered in the framework of the unified kinetic approach to domain structure evolution based on the analogy with first-order phase transformation. This article is part of the theme issue `From atomistic interfaces to dendritic patterns'.

III-nitride integration on ferroelectric materials of lithium niobate by molecular beam epitaxy

International Nuclear Information System (INIS)

Namkoong, Gon; Lee, Kyoung-Keun; Madison, Shannon M.; Henderson, Walter; Ralph, Stephen E.; Doolittle, W. Alan

2005-01-01

Integration of III-nitride electrical devices on the ferroelectric material lithium niobate (LiNbO 3 ) has been demonstrated. As a ferroelectric material, lithium niobate has a polarization which may provide excellent control of the polarity of III-nitrides. However, while high temperature, 1000 deg. C, thermal treatments produce atomically smooth surfaces, improving adhesion of GaN epitaxial layers on lithium niobate, repolarization of the substrate in local domains occurs. These effects result in multi domains of mixed polarization in LiNbO 3 , producing inversion domains in subsequent GaN epilayers. However, it is found that AlN buffer layers suppress inversion domains of III-nitrides. Therefore, two-dimensional electron gases in AlGaN/GaN heterojunction structures are obtained. Herein, the demonstration of the monolithic integration of high power devices with ferroelectric materials presents possibilities to control LiNbO 3 modulators on compact optoelectronic/electronic chips

Integrative Scenario Development

Directory of Open Access Journals (Sweden)

Joerg A. Priess

2014-03-01

Full Text Available Scenarios are employed to address a large number of future environmental and socioeconomic challenges. We present a conceptual framework for the development of scenarios to integrate the objectives of different stakeholder groups. Based on the framework, land-use scenarios were developed to provide a common base for further research. At the same time, these scenarios assisted regional stakeholders to bring forward their concerns and arrive at a shared understanding of challenges between scientific and regional stakeholders, which allowed them to eventually support regional decision making. The focus on the integration of views and knowledge domains of different stakeholder groups, such as scientists and practitioners, required rigorous and repeated measures of quality control. The application of the integrative concept provided products for both stakeholder groups, and the process of scenario development facilitated cooperation and learning within both the scientist and practitioner groups as well as between the two groups.

Jahn-teller domains and magnetic domains in Mn2FeO4

NARCIS (Netherlands)

Kub, J.; Brabers, V.A.M.; Novák, P.; Gemperle, R.; Simsova, J.

2000-01-01

Elastic (Jahn–Teller) domains and magnetic domains in the tetragonal spinel Mn2FeO4 were studied using X-ray double-crystal topography, X-ray diffractometry and the colloid-SEM method. The Jahn–Teller domains of the measured samples are tetragonal with the [0 0 1] c-axis alternating perpendicularly

The extended-domain-eigenfunction method for solving elliptic boundary value problems with annular domains

Energy Technology Data Exchange (ETDEWEB)

Aarao, J; Bradshaw-Hajek, B H; Miklavcic, S J; Ward, D A, E-mail: Stan.Miklavcic@unisa.edu.a [School of Mathematics and Statistics, University of South Australia, Mawson Lakes, SA 5095 (Australia)

2010-05-07

Standard analytical solutions to elliptic boundary value problems on asymmetric domains are rarely, if ever, obtainable. In this paper, we propose a solution technique wherein we embed the original domain into one with simple boundaries where the classical eigenfunction solution approach can be used. The solution in the larger domain, when restricted to the original domain, is then the solution of the original boundary value problem. We call this the extended-domain-eigenfunction method. To illustrate the method's strength and scope, we apply it to Laplace's equation on an annular-like domain.

A meta-analysis of self-reported achievement goals and nonself-report performance across three achievement domains (work, sports, and education.

Directory of Open Access Journals (Sweden)

Nico W Van Yperen

Full Text Available During the past three decades, the achievement goal approach to achievement motivation has emerged as an influential area of research, and is dedicated to understanding the reasons behind the individual's drive to achieve competence and performance. However, the current literature on achievement goals is segmented rather than integrated. That is, citations across the three major and distinct achievement domains (work, education, and sports are more the exception than the rule and similarities and differences between findings for the different achievement domains have yet to be tested. The purpose of the present study was to examine the relationships between self-reported achievement goals and nonself-report performance through meta-analysis, and the moderating potential of achievement domain. Identifying achievement domain as moderator improves our understanding to which contexts we can (not generalize conclusions to, it helps to understand seemingly inconsistent findings, and opens avenues for future research on the underlying processes. Because the achievement goal (AG measure used in a study is partially confounded with achievement domain, we examined the moderating role of this variable as well. Our findings suggest that - overall - approach goals (either mastery or performance were associated positively with performance attainment, whereas avoidance goals (either mastery or performance were associated negatively with performance attainment. These relationships were moderated by achievement domain. For example, relative to the education or work domain, in the sports domain, we did not observe negative correlations between avoidance goals and performance. The absence of statistical moderation due to AG measure suggests that the observed moderation of achievement domain cannot be explained by the AG measure utilized. We suggest further steps to integrate the achievement goal literature, and accordingly, to broaden and deepen understanding of

A meta-analysis of self-reported achievement goals and nonself-report performance across three achievement domains (work, sports, and education).

Science.gov (United States)

Van Yperen, Nico W; Blaga, Monica; Postmes, Tom

2014-01-01

During the past three decades, the achievement goal approach to achievement motivation has emerged as an influential area of research, and is dedicated to understanding the reasons behind the individual's drive to achieve competence and performance. However, the current literature on achievement goals is segmented rather than integrated. That is, citations across the three major and distinct achievement domains (work, education, and sports) are more the exception than the rule and similarities and differences between findings for the different achievement domains have yet to be tested. The purpose of the present study was to examine the relationships between self-reported achievement goals and nonself-report performance through meta-analysis, and the moderating potential of achievement domain. Identifying achievement domain as moderator improves our understanding to which contexts we can (not) generalize conclusions to, it helps to understand seemingly inconsistent findings, and opens avenues for future research on the underlying processes. Because the achievement goal (AG) measure used in a study is partially confounded with achievement domain, we examined the moderating role of this variable as well. Our findings suggest that - overall - approach goals (either mastery or performance) were associated positively with performance attainment, whereas avoidance goals (either mastery or performance) were associated negatively with performance attainment. These relationships were moderated by achievement domain. For example, relative to the education or work domain, in the sports domain, we did not observe negative correlations between avoidance goals and performance. The absence of statistical moderation due to AG measure suggests that the observed moderation of achievement domain cannot be explained by the AG measure utilized. We suggest further steps to integrate the achievement goal literature, and accordingly, to broaden and deepen understanding of performance

Between-Domain Relations of Students’ Academic Emotions and Their Judgments of School Domain Similarity

Directory of Open Access Journals (Sweden)

Thomas eGoetz

2014-10-01

Full Text Available With the aim to deepen our understanding of the between-domain relations of academic emotions, a series of three studies was conducted. We theorized that between-domain relations of trait (i.e., habitual emotions reflected students’ judgments of domain similarities, whereas between-domain relations of state (i.e., momentary emotions did not. This supposition was based on the accessibility model of emotional self-report, according to which individuals’ beliefs tend to strongly impact trait, but not state emotions. The aim of Study 1 (interviews; N = 40; 8th and 11th graders was to gather salient characteristics of academic domains from students’ perspective. In Study 2 (N=1709; 8th and 11th graders the 13 characteristics identified in Study 1 were assessed along with academic emotions in four different domains (mathematics, physics, German, and English using a questionnaire-based trait assessment. With respect to the same domains, state emotions were assessed in Study 3 (N = 121; 8th and 11th graders by employing an experience sampling approach. In line with our initial assumptions, between-domain relations of trait but not state academic emotions reflected between-domain relations of domain characteristics. Implications for research and practice are discussed.

Between-domain relations of students' academic emotions and their judgments of school domain similarity

Science.gov (United States)

Goetz, Thomas; Haag, Ludwig; Lipnevich, Anastasiya A.; Keller, Melanie M.; Frenzel, Anne C.; Collier, Antonie P. M.

2014-01-01

With the aim to deepen our understanding of the between-domain relations of academic emotions, a series of three studies was conducted. We theorized that between-domain relations of trait (i.e., habitual) emotions reflected students' judgments of domain similarities, whereas between-domain relations of state (i.e., momentary) emotions did not. This supposition was based on the accessibility model of emotional self-report, according to which individuals' beliefs tend to strongly impact trait, but not state emotions. The aim of Study 1 (interviews; N = 40; 8th and 11th graders) was to gather salient characteristics of academic domains from students' perspective. In Study 2 (N = 1709; 8th and 11th graders) the 13 characteristics identified in Study 1 were assessed along with academic emotions in four different domains (mathematics, physics, German, and English) using a questionnaire-based trait assessment. With respect to the same domains, state emotions were assessed in Study 3 (N = 121; 8th and 11th graders) by employing an experience sampling approach. In line with our initial assumptions, between-domain relations of trait but not state academic emotions reflected between-domain relations of domain characteristics. Implications for research and practice are discussed. PMID:25374547

Integrating the context-appropriate balanced attention model and reinforcement sensitivity theory: Towards a domain-general personality process model.

Science.gov (United States)

Collins, Michael D; Jackson, Chris J; Walker, Benjamin R; O'Connor, Peter J; Gardiner, Elliroma

2017-01-01

Over the last 40 years or more the personality literature has been dominated by trait models based on the Big Five (B5). Trait-based models describe personality at the between-person level but cannot explain the within-person mental mechanisms responsible for personality. Nor can they adequately account for variations in emotion and behavior experienced by individuals across different situations and over time. An alternative, yet understated, approach to personality architecture can be found in neurobiological theories of personality, most notably reinforcement sensitivity theory (RST). In contrast to static trait-based personality models like the B5, RST provides a more plausible basis for a personality process model, namely, one that explains how emotions and behavior arise from the dynamic interaction between contextual factors and within-person mental mechanisms. In this article, the authors review the evolution of a neurobiologically based personality process model based on RST, the response modulation model and the context-appropriate balanced attention model. They argue that by integrating this complex literature, and by incorporating evidence from personality neuroscience, one can meaningfully explain personality at both the within- and between-person levels. This approach achieves a domain-general architecture based on RST and self-regulation that can be used to align within-person mental mechanisms, neurobiological systems and between-person measurement models. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

Integrated Microwave Photonics

OpenAIRE

Marpaung, David; Roeloffzen, Chris; Heideman, René; Leinse, Arne; Sales Maicas, Salvador; Capmany Francoy, José

2013-01-01

Microwave photonics (MWP) is an emerging field in which radio frequency (RF) signals are generated, distributed, processed and analyzed using the strength of photonic techniques. It is a technology that enables various functionalities which are not feasible to achieve only in the microwave domain. A particular aspect that recently gains significant interests is the use of photonic integrated circuit (PIC) technology in the MWP field for enhanced functionalities and robustness as well as the r...

Expansion of protein domain repeats.

Directory of Open Access Journals (Sweden)

Asa K Björklund

2006-08-01

Full Text Available Many proteins, especially in eukaryotes, contain tandem repeats of several domains from the same family. These repeats have a variety of binding properties and are involved in protein-protein interactions as well as binding to other ligands such as DNA and RNA. The rapid expansion of protein domain repeats is assumed to have evolved through internal tandem duplications. However, the exact mechanisms behind these tandem duplications are not well-understood. Here, we have studied the evolution, function, protein structure, gene structure, and phylogenetic distribution of domain repeats. For this purpose we have assigned Pfam-A domain families to 24 proteomes with more sensitive domain assignments in the repeat regions. These assignments confirmed previous findings that eukaryotes, and in particular vertebrates, contain a much higher fraction of proteins with repeats compared with prokaryotes. The internal sequence similarity in each protein revealed that the domain repeats are often expanded through duplications of several domains at a time, while the duplication of one domain is less common. Many of the repeats appear to have been duplicated in the middle of the repeat region. This is in strong contrast to the evolution of other proteins that mainly works through additions of single domains at either terminus. Further, we found that some domain families show distinct duplication patterns, e.g., nebulin domains have mainly been expanded with a unit of seven domains at a time, while duplications of other domain families involve varying numbers of domains. Finally, no common mechanism for the expansion of all repeats could be detected. We found that the duplication patterns show no dependence on the size of the domains. Further, repeat expansion in some families can possibly be explained by shuffling of exons. However, exon shuffling could not have created all repeats.

[Sex and gender: Two different scientific domains to be clarified].

Science.gov (United States)

Fernández, Juan

2010-05-01

Nowadays, the word sex and its related terms (sexual differences, sexual roles and stereotypes), so common not long ago, seems to have been replaced by gender and its related terms (gender differences, gender roles and stereotypes). We can sometimes find both sex and gender sharing the same space in scientific articles, although referring to different domains. In this paper, I try to explain the need for a model that can integrate both of these complex domains of sex and gender, leading to two independent, although complementary, disciplines: Sexology and Genderology. In both cases, I start from a functional standpoint, which will give meaning to both disciplines' specificities, as it is meant to link contributions from different fields of knowledge. This approach can have consequences for research, education, the experience of women, men, and ambiguous individuals, and therapy.

On domain modelling of the service system with its application to enterprise information systems

Science.gov (United States)

Wang, J. W.; Wang, H. F.; Ding, J. L.; Furuta, K.; Kanno, T.; Ip, W. H.; Zhang, W. J.

2016-01-01

Information systems are a kind of service systems and they are throughout every element of a modern industrial and business system, much like blood in our body. Types of information systems are heterogeneous because of extreme uncertainty in changes in modern industrial and business systems. To effectively manage information systems, modelling of the work domain (or domain) of information systems is necessary. In this paper, a domain modelling framework for the service system is proposed and its application to the enterprise information system is outlined. The framework is defined based on application of a general domain modelling tool called function-context-behaviour-principle-state-structure (FCBPSS). The FCBPSS is based on a set of core concepts, namely: function, context, behaviour, principle, state and structure and system decomposition. Different from many other applications of FCBPSS in systems engineering, the FCBPSS is applied to both infrastructure and substance systems, which is novel and effective to modelling of service systems including enterprise information systems. It is to be noted that domain modelling of systems (e.g. enterprise information systems) is a key to integration of heterogeneous systems and to coping with unanticipated situations facing to systems.

Recent progress on lipid lateral heterogeneity in plasma membranes: from rafts to submicrometric domains

Science.gov (United States)

Carquin, Mélanie; D'Auria, Ludovic; Pollet, Hélène; Bongarzone, Ernesto R.; Tyteca, Donatienne

2016-01-01

The concept of transient nanometric domains known as lipid rafts has brought interest to reassess the validity of the Singer-Nicholson model of a fluid bilayer for cell membranes. However, this new view is still insufficient to explain the cellular control of surface lipid diversity or membrane deformability. During the past decade, the hypothesis that some lipids form large (submicrometric/mesoscale vs nanometric rafts) and stable (> min vs sec) membrane domains has emerged, largely based on indirect methods. Morphological evidence for stable submicrometric lipid domains, well-accepted for artificial and highly specialized biological membranes, was further reported for a variety of living cells from prokaryotes to yeast and mammalian cells. However, results remained questioned based on limitations of available fluorescent tools, use of poor lipid fixatives, and imaging artifacts due to non-resolved membrane projections. In this review, we will discuss recent evidence generated using powerful and innovative approaches such as lipid-specific toxin fragments that support the existence of submicrometric domains. We will integrate documented mechanisms involved in the formation and maintenance of these domains, and provide a perspective on their relevance on membrane deformability and regulation of membrane protein distribution. PMID:26738447

The multi-domain protein Np95 connects DNA methylation and histone modification.

Science.gov (United States)

Rottach, Andrea; Frauer, Carina; Pichler, Garwin; Bonapace, Ian Marc; Spada, Fabio; Leonhardt, Heinrich

2010-04-01

DNA methylation and histone modifications play a central role in the epigenetic regulation of gene expression and cell differentiation. Recently, Np95 (also known as UHRF1 or ICBP90) has been found to interact with Dnmt1 and to bind hemimethylated DNA, indicating together with genetic studies a central role in the maintenance of DNA methylation. Using in vitro binding assays we observed a weak preference of Np95 and its SRA (SET- and Ring-associated) domain for hemimethylated CpG sites. However, the binding kinetics of Np95 in living cells was not affected by the complete loss of genomic methylation. Investigating further links with heterochromatin, we could show that Np95 preferentially binds histone H3 N-terminal tails with trimethylated (H3K9me3) but not acetylated lysine 9 via a tandem Tudor domain. This domain contains three highly conserved aromatic amino acids that form an aromatic cage similar to the one binding H3K9me3 in the chromodomain of HP1ss. Mutations targeting the aromatic cage of the Np95 tandem Tudor domain (Y188A and Y191A) abolished specific H3 histone tail binding. These multiple interactions of the multi-domain protein Np95 with hemimethylated DNA and repressive histone marks as well as with DNA and histone methyltransferases integrate the two major epigenetic silencing pathways.

Property Integration: Componentless Design Techniques and Visualization Tools

DEFF Research Database (Denmark)

El-Halwagi, Mahmoud M; Glasgow, I.M.; Eden, Mario Richard

2004-01-01

integration is defined as a functionality-based, holistic approach to the allocation and manipulation of streams and processing units, which is based on tracking, adjusting, assigning, and matching functionalities throughout the process. Revised lever arm rules are devised to allow optimal allocation while...... maintaining intra- and interstream conservation of the property-based clusters. The property integration problem is mapped into the cluster domain. This dual problem is solved in terms of clusters and then mapped to the primal problem in the property domain. Several new rules are derived for graphical...... techniques. Particularly, systematic rules and visualization techniques for the identification of optimal mixing of streams and their allocation to units. Furthermore, a derivation of the correspondence between clustering arms and fractional contribution of streams is presented. This correspondence...

An Accurate Integral Method for Vibration Signal Based on Feature Information Extraction

Directory of Open Access Journals (Sweden)

Yong Zhu

2015-01-01

Full Text Available After summarizing the advantages and disadvantages of current integral methods, a novel vibration signal integral method based on feature information extraction was proposed. This method took full advantage of the self-adaptive filter characteristic and waveform correction feature of ensemble empirical mode decomposition in dealing with nonlinear and nonstationary signals. This research merged the superiorities of kurtosis, mean square error, energy, and singular value decomposition on signal feature extraction. The values of the four indexes aforementioned were combined into a feature vector. Then, the connotative characteristic components in vibration signal were accurately extracted by Euclidean distance search, and the desired integral signals were precisely reconstructed. With this method, the interference problem of invalid signal such as trend item and noise which plague traditional methods is commendably solved. The great cumulative error from the traditional time-domain integral is effectively overcome. Moreover, the large low-frequency error from the traditional frequency-domain integral is successfully avoided. Comparing with the traditional integral methods, this method is outstanding at removing noise and retaining useful feature information and shows higher accuracy and superiority.

Interoperable domain models : The ISO land administration domain model LADM and its external classes

NARCIS (Netherlands)

Lemmen, C.H.J.; Van Oosterom, P.J.M.; Uitermark, H.T.; Zevenbergen, J.A.; Cooper, A.K.

2011-01-01

This paper provides a brief overview of one of the first spatial domain standards: a standard for the domain of Land Administration (LA). This standard is in the draft stage of development now (May 2011). The development of domain standards is a logical follow up after domain-independent standards,

Identification of hidden relationships from the coupling of hydrophobic cluster analysis and domain architecture information.

Science.gov (United States)

Faure, Guilhem; Callebaut, Isabelle

2013-07-15

Describing domain architecture is a critical step in the functional characterization of proteins. However, some orphan domains do not match any profile stored in dedicated domain databases and are thereby difficult to analyze. We present here an original novel approach, called TREMOLO-HCA, for the analysis of orphan domain sequences and inspired from our experience in the use of Hydrophobic Cluster Analysis (HCA). Hidden relationships between protein sequences can be more easily identified from the PSI-BLAST results, using information on domain architecture, HCA plots and the conservation degree of amino acids that may participate in the protein core. This can lead to reveal remote relationships with known families of domains, as illustrated here with the identification of a hidden Tudor tandem in the human BAHCC1 protein and a hidden ET domain in the Saccharomyces cerevisiae Taf14p and human AF9 proteins. The results obtained in such a way are consistent with those provided by HHPRED, based on pairwise comparisons of HHMs. Our approach can, however, be applied even in absence of domain profiles or known 3D structures for the identification of novel families of domains. It can also be used in a reverse way for refining domain profiles, by starting from known protein domain families and identifying highly divergent members, hitherto considered as orphan. We provide a possible integration of this approach in an open TREMOLO-HCA package, which is fully implemented in python v2.7 and is available on request. Instructions are available at http://www.impmc.upmc.fr/∼callebau/tremolohca.html. isabelle.callebaut@impmc.upmc.fr Supplementary Data are available at Bioinformatics online.

Leveraging the Domain of Work to Improve Migrant Health.

Science.gov (United States)

Flynn, Michael A; Wickramage, Kolitha

2017-10-19

Work is a principal driver of current international migration, a primary social determinant of health, and a fundamental point of articulation between migrants and their host society. Efforts by international organizations to promote migrant health have traditionally focused on infectious diseases and access to healthcare, while international labor organizations have largely focused on issues of occupational health. The underutilization of the domain of work in addressing the health of migrants is truly a missed opportunity for influencing worker well-being and reducing societal economic burden. Understanding of the relationships among migration, work, and health would facilitate further integration of migrant health concerns into the policy agenda of governments and international agencies that work at the nexus of labor, health and development. The domain of work offers an opportunity to capitalize on the existing health and development infrastructure and leverage technical resources, programs and research to promote migrant health. It also provides the opportunity to advance migrant health through new and innovative approaches and partnerships.

Extended HSR/CARD domain mediates AIRE binding to DNA

Energy Technology Data Exchange (ETDEWEB)

Maslovskaja, Julia, E-mail: julia.maslovskaja@ut.ee; Saare, Mario; Liiv, Ingrid; Rebane, Ana; Peterson, Pärt

2015-12-25

Autoimmune regulator (AIRE) activates the transcription of many genes in an unusual promiscuous and stochastic manner. The mechanism by which AIRE binds to the chromatin and DNA is not fully understood, and the regulatory elements that AIRE target genes possess are not delineated. In the current study, we demonstrate that AIRE activates the expression of transiently transfected luciferase reporters that lack defined promoter regions, as well as intron and poly(A) signal sequences. Our protein-DNA interaction experiments with mutated AIRE reveal that the intact homogeneously staining region/caspase recruitment domain (HSR/CARD) and amino acids R113 and K114 are key elements involved in AIRE binding to DNA. - Highlights: • Promoter and mRNA processing elements are not important for AIRE to activate gene expression from reporter plasmids. • AIRE protein fragment aa 1–138 mediates direct binding to DNA. • Integrity of the HSR/CARD domain is needed for AIRE binding to DNA.

Extended HSR/CARD domain mediates AIRE binding to DNA

International Nuclear Information System (INIS)

Maslovskaja, Julia; Saare, Mario; Liiv, Ingrid; Rebane, Ana; Peterson, Pärt

2015-01-01

Autoimmune regulator (AIRE) activates the transcription of many genes in an unusual promiscuous and stochastic manner. The mechanism by which AIRE binds to the chromatin and DNA is not fully understood, and the regulatory elements that AIRE target genes possess are not delineated. In the current study, we demonstrate that AIRE activates the expression of transiently transfected luciferase reporters that lack defined promoter regions, as well as intron and poly(A) signal sequences. Our protein-DNA interaction experiments with mutated AIRE reveal that the intact homogeneously staining region/caspase recruitment domain (HSR/CARD) and amino acids R113 and K114 are key elements involved in AIRE binding to DNA. - Highlights: • Promoter and mRNA processing elements are not important for AIRE to activate gene expression from reporter plasmids. • AIRE protein fragment aa 1–138 mediates direct binding to DNA. • Integrity of the HSR/CARD domain is needed for AIRE binding to DNA.

Domain architecture conservation in orthologs

Science.gov (United States)

2011-01-01

Background As orthologous proteins are expected to retain function more often than other homologs, they are often used for functional annotation transfer between species. However, ortholog identification methods do not take into account changes in domain architecture, which are likely to modify a protein's function. By domain architecture we refer to the sequential arrangement of domains along a protein sequence. To assess the level of domain architecture conservation among orthologs, we carried out a large-scale study of such events between human and 40 other species spanning the entire evolutionary range. We designed a score to measure domain architecture similarity and used it to analyze differences in domain architecture conservation between orthologs and paralogs relative to the conservation of primary sequence. We also statistically characterized the extents of different types of domain swapping events across pairs of orthologs and paralogs. Results The analysis shows that orthologs exhibit greater domain architecture conservation than paralogous homologs, even when differences in average sequence divergence are compensated for, for homologs that have diverged beyond a certain threshold. We interpret this as an indication of a stronger selective pressure on orthologs than paralogs to retain the domain architecture required for the proteins to perform a specific function. In general, orthologs as well as the closest paralogous homologs have very similar domain architectures, even at large evolutionary separation. The most common domain architecture changes observed in both ortholog and paralog pairs involved insertion/deletion of new domains, while domain shuffling and segment duplication/deletion were very infrequent. Conclusions On the whole, our results support the hypothesis that function conservation between orthologs demands higher domain architecture conservation than other types of homologs, relative to primary sequence conservation. This supports the

Effects of sub-domain structure on initial magnetization curve and domain size distribution of stacked media

International Nuclear Information System (INIS)

Sato, S.; Kumagai, S.; Sugita, R.

2015-01-01

In this paper, in order to confirm the sub-domain structure in stacked media demagnetized with in-plane field, initial magnetization curves and magnetic domain size distribution were investigated. Both experimental and simulation results showed that an initial magnetization curve for the medium demagnetized with in-plane field (MDI) initially rose faster than that for the medium demagnetized with perpendicular field (MDP). It is inferred that this is because the MDI has a larger number of domain walls than the MDP due to the existence of the sub-domains, resulting in an increase in the probability of domain wall motion. Dispersion of domain size for the MDI was larger than that for the MDP. This is because sub-domains are formed not only inside the domain but also at the domain boundary region, and they change the position of the domain boundary to affect the domain size. - Highlights: • An initial magnetization curve for MDI initially rose faster than that for MDP. • Dispersion of domain size for the MDI was larger than that for the MDP. • Experimental and simulation results can be explained by existence of sub-domains

Crystal Structure of the Human, FIC-Domain Containing Protein HYPE and Implications for Its Functions

Science.gov (United States)

Bunney, Tom D.; Cole, Ambrose R.; Broncel, Malgorzata; Esposito, Diego; Tate, Edward W.; Katan, Matilda

2014-01-01

Summary Protein AMPylation, the transfer of AMP from ATP to protein targets, has been recognized as a new mechanism of host-cell disruption by some bacterial effectors that typically contain a FIC-domain. Eukaryotic genomes also encode one FIC-domain protein, HYPE, which has remained poorly characterized. Here we describe the structure of human HYPE, solved by X-ray crystallography, representing the first structure of a eukaryotic FIC-domain protein. We demonstrate that HYPE forms stable dimers with structurally and functionally integrated FIC-domains and with TPR-motifs exposed for protein-protein interactions. As HYPE also uniquely possesses a transmembrane helix, dimerization is likely to affect its positioning and function in the membrane vicinity. The low rate of autoAMPylation of the wild-type HYPE could be due to autoinhibition, consistent with the mechanism proposed for a number of putative FIC AMPylators. Our findings also provide a basis to further consider possible alternative cofactors of HYPE and distinct modes of target-recognition. PMID:25435325

A Review of Domain Modelling and Domain Imaging Techniques in Ferroelectric Crystals

Directory of Open Access Journals (Sweden)

John E. Huber

2011-02-01

Full Text Available The present paper reviews models of domain structure in ferroelectric crystals, thin films and bulk materials. Common crystal structures in ferroelectric materials are described and the theory of compatible domain patterns is introduced. Applications to multi-rank laminates are presented. Alternative models employing phase-field and related techniques are reviewed. The paper then presents methods of observing ferroelectric domain structure, including optical, polarized light, scanning electron microscopy, X-ray and neutron diffraction, atomic force microscopy and piezo-force microscopy. Use of more than one technique for unambiguous identification of the domain structure is also described.

Multiple-image hiding using super resolution reconstruction in high-frequency domains

Science.gov (United States)

Li, Xiao-Wei; Zhao, Wu-Xiang; Wang, Jun; Wang, Qiong-Hua

2017-12-01

In this paper, a robust multiple-image hiding method using the computer-generated integral imaging and the modified super-resolution reconstruction algorithm is proposed. In our work, the host image is first transformed into frequency domains by cellular automata (CA), to assure the quality of the stego-image, the secret images are embedded into the CA high-frequency domains. The proposed method has the following advantages: (1) robustness to geometric attacks because of the memory-distributed property of elemental images, (2) increasing quality of the reconstructed secret images as the scheme utilizes the modified super-resolution reconstruction algorithm. The simulation results show that the proposed multiple-image hiding method outperforms other similar hiding methods and is robust to some geometric attacks, e.g., Gaussian noise and JPEG compression attacks.

Chemical Shift Assignments of the C-terminal Eps15 Homology Domain-3 EH Domain*

Science.gov (United States)

Caplan, Steve; Sorgen, Paul L.

2013-01-01

The C-terminal Eps15 homology (EH) domain 3 (EHD3) belongs to a eukaryotic family of endocytic regulatory proteins and is involved in the recycling of various receptors from the early endosome to the endocytic recycling compartment or in retrograde transport from the endosomes to the Golgi. EH domains are highly conserved in the EHD family and function as protein-protein interaction units that bind to Asn-Pro-Phe (NPF) motif-containing proteins. The EH domain of EHD1 was the first C-terminal EH domain from the EHD family to be solved by NMR. The differences observed between this domain and proteins with N-terminal EH domains helped describe a mechanism for the differential binding of NPF-containing proteins. Here, structural studies were expanded to include the EHD3 EH domain. While the EHD1 and EHD3 EH domains are highly homologous, they have different protein partners. A comparison of these structures will help determine the selectivity in protein binding between the EHD family members and lead to a better understanding of their unique roles in endocytic regulation. PMID:23754701

An Approach to Formalizing Ontology Driven Semantic Integration: Concepts, Dimensions and Framework

Science.gov (United States)

Gao, Wenlong

2012-01-01

The ontology approach has been accepted as a very promising approach to semantic integration today. However, because of the diversity of focuses and its various connections to other research domains, the core concepts, theoretical and technical approaches, and research areas of this domain still remain unclear. Such ambiguity makes it difficult to…

Simplicity and Specificity in Language: Domain-General Biases Have Domain-Specific Effects

Science.gov (United States)

Culbertson, Jennifer; Kirby, Simon

2016-01-01

The extent to which the linguistic system—its architecture, the representations it operates on, the constraints it is subject to—is specific to language has broad implications for cognitive science and its relation to evolutionary biology. Importantly, a given property of the linguistic system can be “specific” to the domain of language in several ways. For example, if the property evolved by natural selection under the pressure of the linguistic function it serves then the property is domain-specific in the sense that its design is tailored for language. Equally though, if that property evolved to serve a different function or if that property is domain-general, it may nevertheless interact with the linguistic system in a way that is unique. This gives a second sense in which a property can be thought of as specific to language. An evolutionary approach to the language faculty might at first blush appear to favor domain-specificity in the first sense, with individual properties of the language faculty being specifically linguistic adaptations. However, we argue that interactions between learning, culture, and biological evolution mean any domain-specific adaptations that evolve will take the form of weak biases rather than hard constraints. Turning to the latter sense of domain-specificity, we highlight a very general bias, simplicity, which operates widely in cognition and yet interacts with linguistic representations in domain-specific ways. PMID:26793132

The Tiam1 PDZ Domain Couples to Syndecan1 and Promotes Cell-Matrix Adhesion

Energy Technology Data Exchange (ETDEWEB)

Shepherd, Tyson R; Klaus, Suzi M; Liu, Xu; Ramaswamy, S; DeMali, Kris A; Fuentes, Ernesto J [Iowa

2010-08-12

The T-cell lymphoma invasion and metastasis gene 1 (Tiam1) is a guanine exchange factor (GEF) for the Rho-family GTPase Rac1 that is crucial for the integrity of adherens junctions, tight junctions, and cell-matrix interactions. This GEF contains several protein-protein interaction domains, including a PDZ domain. Earlier studies identified a consensus PDZ-binding motif and a synthetic peptide capable of binding to the Tiam1 PDZ domain, but little is known about its ligand specificity and physiological role in cells. Here, we investigated the structure, specificity, and function of the Tiam1 PDZ domain. We determined the crystal structures of the Tiam1 PDZ domain free and in complex with a 'model' peptide, which revealed the structural basis for ligand specificity. Protein database searches using the consensus PDZ-binding motif identified two eukaryotic cell adhesion proteins, Syndecan1 and Caspr4, as potential Tiam1 PDZ domain binding proteins. Equilibrium binding experiments confirmed that C-terminal peptides derived from Syndecan1 and Caspr4 bound the Tiam1 PDZ domain. NMR chemical shift perturbation experiments indicated that the Tiam1 PDZ/Syndecan1 and PDZ/Caspr4 complexes were structurally distinct and identified key residues likely to be responsible for ligand selectivity. Moreover, cell biological analysis established that Syndecan1 is a physiological binding partner of Tiam1 and that the PDZ domain has a function in cell-matrix adhesion and cell migration. Collectively, our data provide insight into the structure, specificity, and function of the Tiam1 PDZ domain. Importantly, our data report on a physiological role for the Tiam1 PDZ domain and establish a novel link between two previously unrelated signal transduction pathways, both of which are implicated in cancer.

Integration into Big Data: First Steps to Support Reuse of Comprehensive Toxicity Model Modules (SOT)

Science.gov (United States)

Data surrounding the needs of human disease and toxicity modeling are largely siloed limiting the ability to extend and reuse modules across knowledge domains. Using an infrastructure that supports integration across knowledge domains (animal toxicology, high-throughput screening...

Integrated Semantics Service Platform for the Internet of Things: A Case Study of a Smart Office

Science.gov (United States)

Ryu, Minwoo; Kim, Jaeho; Yun, Jaeseok

2015-01-01

The Internet of Things (IoT) allows machines and devices in the world to connect with each other and generate a huge amount of data, which has a great potential to provide useful knowledge across service domains. Combining the context of IoT with semantic technologies, we can build integrated semantic systems to support semantic interoperability. In this paper, we propose an integrated semantic service platform (ISSP) to support ontological models in various IoT-based service domains of a smart city. In particular, we address three main problems for providing integrated semantic services together with IoT systems: semantic discovery, dynamic semantic representation, and semantic data repository for IoT resources. To show the feasibility of the ISSP, we develop a prototype service for a smart office using the ISSP, which can provide a preset, personalized office environment by interpreting user text input via a smartphone. We also discuss a scenario to show how the ISSP-based method would help build a smart city, where services in each service domain can discover and exploit IoT resources that are wanted across domains. We expect that our method could eventually contribute to providing people in a smart city with more integrated, comprehensive services based on semantic interoperability. PMID:25608216

Integrated Semantics Service Platform for the Internet of Things: A Case Study of a Smart Office

Directory of Open Access Journals (Sweden)

Minwoo Ryu

2015-01-01

Full Text Available The Internet of Things (IoT allows machines and devices in the world to connect with each other and generate a huge amount of data, which has a great potential to provide useful knowledge across service domains. Combining the context of IoT with semantic technologies, we can build integrated semantic systems to support semantic interoperability. In this paper, we propose an integrated semantic service platform (ISSP to support ontological models in various IoT-based service domains of a smart city. In particular, we address three main problems for providing integrated semantic services together with IoT systems: semantic discovery, dynamic semantic representation, and semantic data repository for IoT resources. To show the feasibility of the ISSP, we develop a prototype service for a smart office using the ISSP, which can provide a preset, personalized office environment by interpreting user text input via a smartphone. We also discuss a scenario to show how the ISSP-based method would help build a smart city, where services in each service domain can discover and exploit IoT resources that are wanted across domains. We expect that our method could eventually contribute to providing people in a smart city with more integrated, comprehensive services based on semantic interoperability.

Integrated semantics service platform for the Internet of Things: a case study of a smart office.

Science.gov (United States)

Ryu, Minwoo; Kim, Jaeho; Yun, Jaeseok

2015-01-19

The Internet of Things (IoT) allows machines and devices in the world to connect with each other and generate a huge amount of data, which has a great potential to provide useful knowledge across service domains. Combining the context of IoT with semantic technologies, we can build integrated semantic systems to support semantic interoperability. In this paper, we propose an integrated semantic service platform (ISSP) to support ontological models in various IoT-based service domains of a smart city. In particular, we address three main problems for providing integrated semantic services together with IoT systems: semantic discovery, dynamic semantic representation, and semantic data repository for IoT resources. To show the feasibility of the ISSP, we develop a prototype service for a smart office using the ISSP, which can provide a preset, personalized office environment by interpreting user text input via a smartphone. We also discuss a scenario to show how the ISSP-based method would help build a smart city, where services in each service domain can discover and exploit IoT resources that are wanted across domains. We expect that our method could eventually contribute to providing people in a smart city with more integrated, comprehensive services based on semantic interoperability.

The framing of scientific domains

DEFF Research Database (Denmark)

Dam Christensen, Hans

2014-01-01

domains, and UNISIST helps understanding this navigation. Design/methodology/approach The UNISIST models are tentatively applied to the domain of art history at three stages, respectively two modern, partially overlapping domains, as well as an outline of an art historical domain anno c1820...

Feynman maps without improper integrals

International Nuclear Information System (INIS)

Exner, P.; Kolerov, G.I.

1980-01-01

The Feynman maps introduced first by Truman are examined. The domain considered here consists of the Fresnel-inteo-rable functions in the sense of Albeverio and Hoegh-Krohn. The original definition of the F-maps is slightly modified: it is started from the underlying measures on the Hilbert space of paths in order to avoid use of improper integrals. Some new properties of the F-maps are derived. In particular, the dominated convergence theorem is shown to be not valid for the F 1 -map (or Feynman integral); this fact is of a certain importance for classical limit of quantum mechanics

Protein domain organisation: adding order.

Science.gov (United States)

Kummerfeld, Sarah K; Teichmann, Sarah A

2009-01-29

Domains are the building blocks of proteins. During evolution, they have been duplicated, fused and recombined, to produce proteins with novel structures and functions. Structural and genome-scale studies have shown that pairs or groups of domains observed together in a protein are almost always found in only one N to C terminal order and are the result of a single recombination event that has been propagated by duplication of the multi-domain unit. Previous studies of domain organisation have used graph theory to represent the co-occurrence of domains within proteins. We build on this approach by adding directionality to the graphs and connecting nodes based on their relative order in the protein. Most of the time, the linear order of domains is conserved. However, using the directed graph representation we have identified non-linear features of domain organization that are over-represented in genomes. Recognising these patterns and unravelling how they have arisen may allow us to understand the functional relationships between domains and understand how the protein repertoire has evolved. We identify groups of domains that are not linearly conserved, but instead have been shuffled during evolution so that they occur in multiple different orders. We consider 192 genomes across all three kingdoms of life and use domain and protein annotation to understand their functional significance. To identify these features and assess their statistical significance, we represent the linear order of domains in proteins as a directed graph and apply graph theoretical methods. We describe two higher-order patterns of domain organisation: clusters and bi-directionally associated domain pairs and explore their functional importance and phylogenetic conservation. Taking into account the order of domains, we have derived a novel picture of global protein organization. We found that all genomes have a higher than expected degree of clustering and more domain pairs in forward and

Protein domain organisation: adding order

Directory of Open Access Journals (Sweden)

Kummerfeld Sarah K

2009-01-01

Full Text Available Abstract Background Domains are the building blocks of proteins. During evolution, they have been duplicated, fused and recombined, to produce proteins with novel structures and functions. Structural and genome-scale studies have shown that pairs or groups of domains observed together in a protein are almost always found in only one N to C terminal order and are the result of a single recombination event that has been propagated by duplication of the multi-domain unit. Previous studies of domain organisation have used graph theory to represent the co-occurrence of domains within proteins. We build on this approach by adding directionality to the graphs and connecting nodes based on their relative order in the protein. Most of the time, the linear order of domains is conserved. However, using the directed graph representation we have identified non-linear features of domain organization that are over-represented in genomes. Recognising these patterns and unravelling how they have arisen may allow us to understand the functional relationships between domains and understand how the protein repertoire has evolved. Results We identify groups of domains that are not linearly conserved, but instead have been shuffled during evolution so that they occur in multiple different orders. We consider 192 genomes across all three kingdoms of life and use domain and protein annotation to understand their functional significance. To identify these features and assess their statistical significance, we represent the linear order of domains in proteins as a directed graph and apply graph theoretical methods. We describe two higher-order patterns of domain organisation: clusters and bi-directionally associated domain pairs and explore their functional importance and phylogenetic conservation. Conclusion Taking into account the order of domains, we have derived a novel picture of global protein organization. We found that all genomes have a higher than expected

Semantic Observation Integration

Directory of Open Access Journals (Sweden)

Werner Kuhn

2012-09-01

Full Text Available Although the integration of sensor-based information into analysis and decision making has been a research topic for many years, semantic interoperability has not yet been reached. The advent of user-generated content for the geospatial domain, Volunteered Geographic Information (VGI, makes it even more difficult to establish semantic integration. This paper proposes a novel approach to integrating conventional sensor information and VGI, which is exploited in the context of detecting forest fires. In contrast to common logic-based semantic descriptions, we present a formal system using algebraic specifications to unambiguously describe the processing steps from natural phenomena to value-added information. A generic ontology of observations is extended and profiled for forest fire detection in order to illustrate how the sensing process, and transformations between heterogeneous sensing systems, can be represented as mathematical functions and grouped into abstract data types. We discuss the required ontological commitments and a possible generalization.

Integrated care: a comprehensive bibliometric analysis and literature review

Directory of Open Access Journals (Sweden)

Xiaowei Sun

2014-06-01

Full Text Available Introduction: Integrated care could not only fix up fragmented health care but also improve the continuity of care and the quality of life. Despite the volume and variety of publications, little is known about how ‘integrated care’ has developed. There is a need for a systematic bibliometric analysis on studying the important features of the integrated care literature.Aim: To investigate the growth pattern, core journals and jurisdictions and identify the key research domains of integrated care.Methods: We searched Medline/PubMed using the search strategy ‘(delivery of health care, integrated [MeSH Terms] OR integrated care [Title/Abstract]’ without time and language limits. Second, we extracted the publishing year, journals, jurisdictions and keywords of the retrieved articles. Finally, descriptive statistical analysis by the Bibliographic Item Co-occurrence Matrix Builder and hierarchical clustering by SPSS were used.Results: As many as 9090 articles were retrieved. Results included: (1 the cumulative numbers of the publications on integrated care rose perpendicularly after 1993; (2 all documents were recorded by 1646 kinds of journals. There were 28 core journals; (3 the USA is the predominant publishing country; and (4 there are six key domains including: the definition/models of integrated care, interdisciplinary patient care team, disease management for chronically ill patients, types of health care organizations and policy, information system integration and legislation/jurisprudence.Discussion and conclusion: Integrated care literature has been most evident in developed countries. International Journal of Integrated Care is highly recommended in this research area. The bibliometric analysis and identification of publication hotspots provides researchers and practitioners with core target journals, as well as an overview of the field for further research in integrated care.

Insights into function of PSI domains from structure of the Met receptor PSI domain

International Nuclear Information System (INIS)

Kozlov, Guennadi; Perreault, Audrey; Schrag, Joseph D.; Park, Morag; Cygler, Miroslaw; Gehring, Kalle; Ekiel, Irena

2004-01-01

PSI domains are cysteine-rich modules found in extracellular fragments of hundreds of signaling proteins, including plexins, semaphorins, integrins, and attractins. Here, we report the solution structure of the PSI domain from the human Met receptor, a receptor tyrosine kinase critical for proliferation, motility, and differentiation. The structure represents a cysteine knot with short regions of secondary structure including a three-stranded antiparallel β-sheet and two α-helices. All eight cysteines are involved in disulfide bonds with the pattern consistent with that for the PSI domain from Sema4D. Comparison with the Sema4D structure identifies a structurally conserved core comprising the N-terminal half of the PSI domain. Interestingly, this part links adjacent SEMA and immunoglobulin domains in the Sema4D structure, suggesting that the PSI domain serves as a wedge between propeller and immunoglobulin domains and is responsible for the correct positioning of the ligand-binding site of the receptor

Resource Unavailability (RU) Per Domain Behavior

NARCIS (Netherlands)

Karagiannis, Georgios; Westberg, L.; Bader, A.; Tschofenig, Hannes; Tschofenig, H.

2006-01-01

This draft specifies a Per Domain Behavior that provides the ability to Diffserv nodes located outside Diffserv domain(s), e.g., receiver or other Diffserv enabled router to detect when the resources provided by the Diffserv domain(s) are not available. The unavailability of resources in the domain

Multi-functional roles for the polypeptide transport associated domains of Toc75 in chloroplast protein import

Science.gov (United States)

Paila, Yamuna D; Richardson, Lynn GL; Inoue, Hitoshi; Parks, Elizabeth S; McMahon, James; Inoue, Kentaro; Schnell, Danny J

2016-01-01

Toc75 plays a central role in chloroplast biogenesis in plants as the membrane channel of the protein import translocon at the outer envelope of chloroplasts (TOC). Toc75 is a member of the Omp85 family of bacterial and organellar membrane insertases, characterized by N-terminal POTRA (polypeptide-transport associated) domains and C-terminal membrane-integrated β-barrels. We demonstrate that the Toc75 POTRA domains are essential for protein import and contribute to interactions with TOC receptors, thereby coupling preprotein recognition at the chloroplast surface with membrane translocation. The POTRA domains also interact with preproteins and mediate the recruitment of molecular chaperones in the intermembrane space to facilitate membrane transport. Our studies are consistent with the multi-functional roles of POTRA domains observed in other Omp85 family members and demonstrate that the domains of Toc75 have evolved unique properties specific to the acquisition of protein import during endosymbiotic evolution of the TOC system in plastids. DOI: http://dx.doi.org/10.7554/eLife.12631.001 PMID:26999824

Mesh adaptation technique for Fourier-domain fluorescence lifetime imaging

International Nuclear Information System (INIS)

Soloviev, Vadim Y.

2006-01-01

A novel adaptive mesh technique in the Fourier domain is introduced for problems in fluorescence lifetime imaging. A dynamical adaptation of the three-dimensional scheme based on the finite volume formulation reduces computational time and balances the ill-posed nature of the inverse problem. Light propagation in the medium is modeled by the telegraph equation, while the lifetime reconstruction algorithm is derived from the Fredholm integral equation of the first kind. Stability and computational efficiency of the method are demonstrated by image reconstruction of two spherical fluorescent objects embedded in a tissue phantom

Baikov-Lee representations of cut Feynman integrals

International Nuclear Information System (INIS)

Harley, Mark; Moriello, Francesco; Schabinger, Robert M.

2017-01-01

We develop a general framework for the evaluation of d-dimensional cut Feynman integrals based on the Baikov-Lee representation of purely-virtual Feynman integrals. We implement the generalized Cutkosky cutting rule using Cauchy’s residue theorem and identify a set of constraints which determine the integration domain. The method applies equally well to Feynman integrals with a unitarity cut in a single kinematic channel and to maximally-cut Feynman integrals. Our cut Baikov-Lee representation reproduces the expected relation between cuts and discontinuities in a given kinematic channel and furthermore makes the dependence on the kinematic variables manifest from the beginning. By combining the Baikov-Lee representation of maximally-cut Feynman integrals and the properties of periods of algebraic curves, we are able to obtain complete solution sets for the homogeneous differential equations satisfied by Feynman integrals which go beyond multiple polylogarithms. We apply our formalism to the direct evaluation of a number of interesting cut Feynman integrals.

Algebraic non-integrability of magnetic billiards

International Nuclear Information System (INIS)

Bialy, Misha; Mironov, Andrey E

2016-01-01

We consider billiard ball motion in a convex domain of the Euclidean plane bounded by a piece-wise smooth curve under the action of a constant magnetic field. We show that if there exists a first integral polynomial in the velocities of the magnetic billiard flow, then every smooth piece γ of the boundary must be algebraic, and either is a circle or satisfies very strong restrictions. In particular, it follows that any non-circular magnetic Birkhoff billiard is not algebraically integrable for all but finitely many values of the magnitude of the magnetic field. Moreover, a magnetic billiard in ellipse is not algebraically integrable for all values of the magnitude of the magnetic field. We conjecture that the circle is the only integrable magnetic billiard, not only in the algebraic sense, but also for a broader meaning of integrability. We also introduce what we call outer magnetic billiards. As an application of our method, we prove analogous results on algebraically integrable outer magnetic billiards. (paper)

Bifurcation Observation of Combining Spiral Gear Transmission Based on Parameter Domain Structure Analysis

Directory of Open Access Journals (Sweden)

He Lin

2016-01-01

Full Text Available This study considers the bifurcation evolutions for a combining spiral gear transmission through parameter domain structure analysis. The system nonlinear vibration equations are created with piecewise backlash and general errors. Gill’s numerical integration algorithm is implemented in calculating the vibration equation sets. Based on cell-mapping method (CMM, two-dimensional dynamic domain planes have been developed and primarily focused on the parameters of backlash, transmission error, mesh frequency and damping ratio, and so forth. Solution demonstrates that Period-doubling bifurcation happens as the mesh frequency increases; moreover nonlinear discontinuous jump breaks the periodic orbit and also turns the periodic state into chaos suddenly. In transmission error planes, three cell groups which are Period-1, Period-4, and Chaos have been observed, and the boundary cells are the sensitive areas to dynamic response. Considering the parameter planes which consist of damping ratio associated with backlash, transmission error, mesh stiffness, and external load, the solution domain structure reveals that the system step into chaos undergoes Period-doubling cascade with Period-2m (m: integer periodic regions. Direct simulations to obtain the bifurcation diagram and largest Lyapunov exponent (LE match satisfactorily with the parameter domain solutions.

Chemical Approach to Biological Safety: Molecular-Level Control of an Integrated Zinc Finger Nuclease

DEFF Research Database (Denmark)

Németh, Eszter; Asaka, Masamitsu N; Kato, Kohsuke

2018-01-01

circular dichroism spectroscopy, and nano-electrospray ionisation mass spectrometry. In situ intramolecular activation of the nuclease domain was observed, resulting in specific cleavage of DNA with moderate activity. This study represents a new approach to AN design through integrated nucleases consisting......Application of artificial nucleases (ANs) in genome editing is still hindered by their cytotoxicity related to off-target cleavages. This problem can be targeted by regulation of the nuclease domain. Here, we provide an experimental survey of computationally designed integrated zinc finger...... nucleases, constructed by linking the inactivated catalytic centre and the allosteric activator sequence of the colicin E7 nuclease domain to the two opposite termini of a zinc finger array. DNA specificity and metal binding were confirmed by electrophoretic mobility shift assays, synchrotron radiation...

Vector tomography for reconstructing electric fields with non-zero divergence in bounded domains

Science.gov (United States)

Koulouri, Alexandra; Brookes, Mike; Rimpiläinen, Ville

2017-01-01

In vector tomography (VT), the aim is to reconstruct an unknown multi-dimensional vector field using line integral data. In the case of a 2-dimensional VT, two types of line integral data are usually required. These data correspond to integration of the parallel and perpendicular projection of the vector field along the integration lines and are called the longitudinal and transverse measurements, respectively. In most cases, however, the transverse measurements cannot be physically acquired. Therefore, the VT methods are typically used to reconstruct divergence-free (or source-free) velocity and flow fields that can be reconstructed solely from the longitudinal measurements. In this paper, we show how vector fields with non-zero divergence in a bounded domain can also be reconstructed from the longitudinal measurements without the need of explicitly evaluating the transverse measurements. To the best of our knowledge, VT has not previously been used for this purpose. In particular, we study low-frequency, time-harmonic electric fields generated by dipole sources in convex bounded domains which arise, for example, in electroencephalography (EEG) source imaging. We explain in detail the theoretical background, the derivation of the electric field inverse problem and the numerical approximation of the line integrals. We show that fields with non-zero divergence can be reconstructed from the longitudinal measurements with the help of two sparsity constraints that are constructed from the transverse measurements and the vector Laplace operator. As a comparison to EEG source imaging, we note that VT does not require mathematical modeling of the sources. By numerical simulations, we show that the pattern of the electric field can be correctly estimated using VT and the location of the source activity can be determined accurately from the reconstructed magnitudes of the field.

Recovering protein-protein and domain-domain interactions from aggregation of IP-MS proteomics of coregulator complexes.

Directory of Open Access Journals (Sweden)

Amin R Mazloom

2011-12-01

Full Text Available Coregulator proteins (CoRegs are part of multi-protein complexes that transiently assemble with transcription factors and chromatin modifiers to regulate gene expression. In this study we analyzed data from 3,290 immuno-precipitations (IP followed by mass spectrometry (MS applied to human cell lines aimed at identifying CoRegs complexes. Using the semi-quantitative spectral counts, we scored binary protein-protein and domain-domain associations with several equations. Unlike previous applications, our methods scored prey-prey protein-protein interactions regardless of the baits used. We also predicted domain-domain interactions underlying predicted protein-protein interactions. The quality of predicted protein-protein and domain-domain interactions was evaluated using known binary interactions from the literature, whereas one protein-protein interaction, between STRN and CTTNBP2NL, was validated experimentally; and one domain-domain interaction, between the HEAT domain of PPP2R1A and the Pkinase domain of STK25, was validated using molecular docking simulations. The scoring schemes presented here recovered known, and predicted many new, complexes, protein-protein, and domain-domain interactions. The networks that resulted from the predictions are provided as a web-based interactive application at http://maayanlab.net/HT-IP-MS-2-PPI-DDI/.

Seven domains for leadership mentoring and executive coaching A reflective paper

OpenAIRE

Paul O. Olson

2014-01-01

This article discusses how coaching and mentoring can be integrated and work together as systematic tools for leadership development. The author draws on psychotherapy as a parallel for practitioner research and posits five validation hypotheses for coaching and mentoring. Arguably coaching is not sufficient to develop leaders, but a useful toolbox within mentoring. Internal mentors in particular have cultural and industry knowledge of direct relevance to the adept. Seven domains are iden...

Full waveform inversion in the frequency domain using classified time-domain residual wavefields

Science.gov (United States)

Son, Woohyun; Koo, Nam-Hyung; Kim, Byoung-Yeop; Lee, Ho-Young; Joo, Yonghwan

2017-04-01

We perform the acoustic full waveform inversion in the frequency domain using residual wavefields that have been separated in the time domain. We sort the residual wavefields in the time domain according to the order of absolute amplitudes. Then, the residual wavefields are separated into several groups in the time domain. To analyze the characteristics of the residual wavefields, we compare the residual wavefields of conventional method with those of our residual separation method. From the residual analysis, the amplitude spectrum obtained from the trace before separation appears to have little energy at the lower frequency bands. However, the amplitude spectrum obtained from our strategy is regularized by the separation process, which means that the low-frequency components are emphasized. Therefore, our method helps to emphasize low-frequency components of residual wavefields. Then, we generate the frequency-domain residual wavefields by taking the Fourier transform of the separated time-domain residual wavefields. With these wavefields, we perform the gradient-based full waveform inversion in the frequency domain using back-propagation technique. Through a comparison of gradient directions, we confirm that our separation method can better describe the sub-salt image than the conventional approach. The proposed method is tested on the SEG/EAGE salt-dome model. The inversion results show that our algorithm is better than the conventional gradient based waveform inversion in the frequency domain, especially for deeper parts of the velocity model.

Micropore extrusion-induced alignment transition from perpendicular to parallel of cylindrical domains in block copolymers.

Science.gov (United States)

Qu, Ting; Zhao, Yongbin; Li, Zongbo; Wang, Pingping; Cao, Shubo; Xu, Yawei; Li, Yayuan; Chen, Aihua

2016-02-14

The orientation transition from perpendicular to parallel alignment of PEO cylindrical domains of PEO-b-PMA(Az) films has been demonstrated by extruding the block copolymer (BCP) solutions through a micropore of a plastic gastight syringe. The parallelized orientation of PEO domains induced by this micropore extrusion can be recovered to perpendicular alignment via ultrasonication of the extruded BCP solutions and subsequent annealing. A plausible mechanism is proposed in this study. The BCP films can be used as templates to prepare nanowire arrays with controlled layers, which has enormous potential application in the field of integrated circuits.

The multi-domain protein Np95 connects DNA methylation and histone modification

Science.gov (United States)

Rottach, Andrea; Frauer, Carina; Pichler, Garwin; Bonapace, Ian Marc; Spada, Fabio; Leonhardt, Heinrich

2010-01-01

DNA methylation and histone modifications play a central role in the epigenetic regulation of gene expression and cell differentiation. Recently, Np95 (also known as UHRF1 or ICBP90) has been found to interact with Dnmt1 and to bind hemimethylated DNA, indicating together with genetic studies a central role in the maintenance of DNA methylation. Using in vitro binding assays we observed a weak preference of Np95 and its SRA (SET- and Ring-associated) domain for hemimethylated CpG sites. However, the binding kinetics of Np95 in living cells was not affected by the complete loss of genomic methylation. Investigating further links with heterochromatin, we could show that Np95 preferentially binds histone H3 N-terminal tails with trimethylated (H3K9me3) but not acetylated lysine 9 via a tandem Tudor domain. This domain contains three highly conserved aromatic amino acids that form an aromatic cage similar to the one binding H3K9me3 in the chromodomain of HP1ß. Mutations targeting the aromatic cage of the Np95 tandem Tudor domain (Y188A and Y191A) abolished specific H3 histone tail binding. These multiple interactions of the multi-domain protein Np95 with hemimethylated DNA and repressive histone marks as well as with DNA and histone methyltransferases integrate the two major epigenetic silencing pathways. PMID:20026581

Domain fusion analysis by applying relational algebra to protein sequence and domain databases.

Science.gov (United States)

Truong, Kevin; Ikura, Mitsuhiko

2003-05-06

Domain fusion analysis is a useful method to predict functionally linked proteins that may be involved in direct protein-protein interactions or in the same metabolic or signaling pathway. As separate domain databases like BLOCKS, PROSITE, Pfam, SMART, PRINTS-S, ProDom, TIGRFAMs, and amalgamated domain databases like InterPro continue to grow in size and quality, a computational method to perform domain fusion analysis that leverages on these efforts will become increasingly powerful. This paper proposes a computational method employing relational algebra to find domain fusions in protein sequence databases. The feasibility of this method was illustrated on the SWISS-PROT+TrEMBL sequence database using domain predictions from the Pfam HMM (hidden Markov model) database. We identified 235 and 189 putative functionally linked protein partners in H. sapiens and S. cerevisiae, respectively. From scientific literature, we were able to confirm many of these functional linkages, while the remainder offer testable experimental hypothesis. Results can be viewed at http://calcium.uhnres.utoronto.ca/pi. As the analysis can be computed quickly on any relational database that supports standard SQL (structured query language), it can be dynamically updated along with the sequence and domain databases, thereby improving the quality of predictions over time.

Vector tomography for reconstructing electric fields with non-zero divergence in bounded domains

Energy Technology Data Exchange (ETDEWEB)

Koulouri, Alexandra, E-mail: koulouri@uni-muenster.de [Institute for Computational and Applied Mathematics, University of Münster, Einsteinstrasse 62, D-48149 Münster (Germany); Department of Electrical and Electronic Engineering, Imperial College London, Exhibition Road, London SW7 2BT (United Kingdom); Brookes, Mike [Department of Electrical and Electronic Engineering, Imperial College London, Exhibition Road, London SW7 2BT (United Kingdom); Rimpiläinen, Ville [Institute for Biomagnetism and Biosignalanalysis, University of Münster, Malmedyweg 15, D-48149 Münster (Germany); Department of Mathematics, University of Auckland, Private bag 92019, Auckland 1142 (New Zealand)

2017-01-15

In vector tomography (VT), the aim is to reconstruct an unknown multi-dimensional vector field using line integral data. In the case of a 2-dimensional VT, two types of line integral data are usually required. These data correspond to integration of the parallel and perpendicular projection of the vector field along the integration lines and are called the longitudinal and transverse measurements, respectively. In most cases, however, the transverse measurements cannot be physically acquired. Therefore, the VT methods are typically used to reconstruct divergence-free (or source-free) velocity and flow fields that can be reconstructed solely from the longitudinal measurements. In this paper, we show how vector fields with non-zero divergence in a bounded domain can also be reconstructed from the longitudinal measurements without the need of explicitly evaluating the transverse measurements. To the best of our knowledge, VT has not previously been used for this purpose. In particular, we study low-frequency, time-harmonic electric fields generated by dipole sources in convex bounded domains which arise, for example, in electroencephalography (EEG) source imaging. We explain in detail the theoretical background, the derivation of the electric field inverse problem and the numerical approximation of the line integrals. We show that fields with non-zero divergence can be reconstructed from the longitudinal measurements with the help of two sparsity constraints that are constructed from the transverse measurements and the vector Laplace operator. As a comparison to EEG source imaging, we note that VT does not require mathematical modeling of the sources. By numerical simulations, we show that the pattern of the electric field can be correctly estimated using VT and the location of the source activity can be determined accurately from the reconstructed magnitudes of the field. - Highlights: • Vector tomography is used to reconstruct electric fields generated by dipole

Domain management OSSs: bridging the gap between legacy and standards-based network management systems

Science.gov (United States)

Lemley, Todd A.

1996-11-01

The rapid change in the telecommunications environment is forcing carriers to re-assess not only their service offering, but also their network management philosophy. The competitive carrier environment has taken away the luxury of throwing technology at a problem by using legacy and proprietary systems and architectures. A more flexible management environment is necessary to effectively gain, and maintain operating margins in the new market era. Competitive forces are driving change which gives carriers more choices than those that are available in legacy and standards-based solutions alone. However, creating an operational support system (OSS) with this gap between legacy and standards has become as dynamic as the services which it supports. A philosophy which helps to integrate the legacy and standards systems is domain management. Domain management relates to a specific service or market 'domain,'and its associated operational support requirements. It supports a companies definition of its business model, which drives the definition of each domain. It also attempts to maximize current investment while injecting new technology available in a practical approach. The following paragraphs offer an overview of legacy systems, standards-based philosophy, and the potential of domain management to help bridge the gap between the two types of systems.

A service platform architecture design towards a light integration of heterogeneous systems in the wellbeing domain.

Science.gov (United States)

Yang, Yaojin; Ahtinen, Aino; Lahteenmaki, Jaakko; Nyman, Petri; Paajanen, Henrik; Peltoniemi, Teijo; Quiroz, Carlos

2007-01-01

System integration is one of the major challenges for building wellbeing or healthcare related information systems. In this paper, we are going to share our experiences on how to design a service platform called Nuadu service platform, for providing integrated services in occupational health promotion and health risk management through two heterogeneous systems. Our design aims for a light integration covering the layers, from data through service up to presentation, while maintaining the integrity of the underlying systems.

Single-domain versus two-domain configuration in thin ferromagnetic prisms

International Nuclear Information System (INIS)

Pini, Maria Gloria; Politi, Paolo

2007-01-01

Thin ferromagnetic elements in the form of rectangular prisms are theoretically investigated in order to study the transition from single-domain to two-domain state, with changing the in-plane aspect ratio p. We address two main questions: first, how general is the transition; second, how the critical value p c depends on the physical parameters. We use two complementary methods: discrete-lattice calculations and a micromagnetic continuum approach. Ultrathin films do not appear to split in two domains. Instead, thicker films may undergo the above transition. We have used the continuum approach to analyze recent magnetic force microscopy observations in 30nm-thick patterned permalloy elements, finding a good agreement for p c

Topological domain walls in helimagnets

Science.gov (United States)

Schoenherr, P.; Müller, J.; Köhler, L.; Rosch, A.; Kanazawa, N.; Tokura, Y.; Garst, M.; Meier, D.

2018-05-01

Domain walls naturally arise whenever a symmetry is spontaneously broken. They interconnect regions with different realizations of the broken symmetry, promoting structure formation from cosmological length scales to the atomic level1,2. In ferroelectric and ferromagnetic materials, domain walls with unique functionalities emerge, holding great promise for nanoelectronics and spintronics applications3-5. These walls are usually of Ising, Bloch or Néel type and separate homogeneously ordered domains. Here we demonstrate that a wide variety of new domain walls occurs in the presence of spatially modulated domain states. Using magnetic force microscopy and micromagnetic simulations, we show three fundamental classes of domain walls to arise in the near-room-temperature helimagnet iron germanium. In contrast to conventional ferroics, the domain walls exhibit a well-defined inner structure, which—analogous to cholesteric liquid crystals—consists of topological disclination and dislocation defects. Similar to the magnetic skyrmions that form in the same material6,7, the domain walls can carry a finite topological charge, permitting an efficient coupling to spin currents and contributions to a topological Hall effect. Our study establishes a new family of magnetic nano-objects with non-trivial topology, opening the door to innovative device concepts based on helimagnetic domain walls.

Prediction Reweighting for Domain Adaptation.

Science.gov (United States)

Shuang Li; Shiji Song; Gao Huang

2017-07-01

There are plenty of classification methods that perform well when training and testing data are drawn from the same distribution. However, in real applications, this condition may be violated, which causes degradation of classification accuracy. Domain adaptation is an effective approach to address this problem. In this paper, we propose a general domain adaptation framework from the perspective of prediction reweighting, from which a novel approach is derived. Different from the major domain adaptation methods, our idea is to reweight predictions of the training classifier on testing data according to their signed distance to the domain separator, which is a classifier that distinguishes training data (from source domain) and testing data (from target domain). We then propagate the labels of target instances with larger weights to ones with smaller weights by introducing a manifold regularization method. It can be proved that our reweighting scheme effectively brings the source and target domains closer to each other in an appropriate sense, such that classification in target domain becomes easier. The proposed method can be implemented efficiently by a simple two-stage algorithm, and the target classifier has a closed-form solution. The effectiveness of our approach is verified by the experiments on artificial datasets and two standard benchmarks, a visual object recognition task and a cross-domain sentiment analysis of text. Experimental results demonstrate that our method is competitive with the state-of-the-art domain adaptation algorithms.

Temporal integration of consecutive tones into synthetic vowels demonstrates perceptual assembly in audition

NARCIS (Netherlands)

Saija, Jefta D.; Andringa, Tjeerd C.; Başkent, Deniz; Akyürek, Elkan G.

Temporal integration is the perceptual process combining sensory stimulation over time into longer percepts that can span over 10 times the duration of a minimally detectable stimulus. Particularly in the auditory domain, such "long-term" temporal integration has been characterized as a relatively

A localized interaction surface for voltage-sensing domains on the pore domain of a K+ channel.

Science.gov (United States)

Li-Smerin, Y; Hackos, D H; Swartz, K J

2000-02-01

Voltage-gated K+ channels contain a central pore domain and four surrounding voltage-sensing domains. How and where changes in the structure of the voltage-sensing domains couple to the pore domain so as to gate ion conduction is not understood. The crystal structure of KcsA, a bacterial K+ channel homologous to the pore domain of voltage-gated K+ channels, provides a starting point for addressing this question. Guided by this structure, we used tryptophan-scanning mutagenesis on the transmembrane shell of the pore domain in the Shaker voltage-gated K+ channel to localize potential protein-protein and protein-lipid interfaces. Some mutants cause only minor changes in gating and when mapped onto the KcsA structure cluster away from the interface between pore domain subunits. In contrast, mutants producing large changes in gating tend to cluster near this interface. These results imply that voltage-sensing domains interact with localized regions near the interface between adjacent pore domain subunits.

Numerical integration of the Teukolsky equation in the time domain

International Nuclear Information System (INIS)

Pazos-Avalos, Enrique; Lousto, Carlos O.

2005-01-01

We present a fourth-order convergent (2+1)-dimensional, numerical formalism to solve the Teukolsky equation in the time domain. Our approach is first to rewrite the Teukolsky equation as a system of first-order differential equations. In this way we get a system that has the form of an advection equation. This is then used in combination with a series expansion of the solution in powers of time. To obtain a fourth-order scheme we kept terms up to fourth derivative in time and use the advectionlike system of differential equations to substitute the temporal derivatives by spatial derivatives. This scheme is applied to evolve gravitational perturbations in the Schwarzschild and Kerr backgrounds. Our numerical method proved to be stable and fourth-order convergent in r* and θ directions. The correct power-law tail, ∼1/t 2l+3 , for general initial data, and ∼1/t 2l+4 , for time-symmetric data, was found in our runs. We noted that it is crucial to resolve accurately the angular dependence of the mode at late times in order to obtain these values of the exponents in the power-law decay. In other cases, when the decay was too fast and round-off error was reached before a tail was developed, then the quasinormal modes frequencies provided a test to determine the validity of our code

Supersymmetric domain walls

NARCIS (Netherlands)

Bergshoeff, Eric A.; Kleinschmidt, Axel; Riccioni, Fabio

2012-01-01

We classify the half-supersymmetric "domain walls," i.e., branes of codimension one, in toroidally compactified IIA/IIB string theory and show to which gauged supergravity theory each of these domain walls belong. We use as input the requirement of supersymmetric Wess-Zumino terms, the properties of

Frequency domain kinetic of positron-electron annihilation in the MgO-Al2O3 spinel-type ceramics

Science.gov (United States)

Fl'unt, Orest; Klym, Halyna; Ingram, Adam

2018-03-01

In this work, the kinetic of positron-electron annihilation in the MgO-Al2O3 spinel-type ceramics sintered at different temperatures (1100, 1200 and 1400 °C) has been calculated and analyzed in a frequency domain. The spectra of real (in-phase) and imaginary (quadrature) components of positron-electron annihilation kinetic have been obtained numerically from usual temporal characteristics using integral Fourier transform. The numerical calculations were carried out using cubic spline interpolation of the pulse characteristics of MgO-Al2O3 ceramics in time domain with following analytical calculations of integrals. The obtained spectra as real so imaginary part of MgO-Al2O3 ceramics in frequency domain almost good obey a Debye law denying correlation between elementary positron annihilation processes. Complex diagrams of frequency domain responses of as-prepared samples have a shape of semicircles with close characteristic frequencies. Some deviation on low-frequency side of the semicircles is observed confirming an availability of longer time kinetic processes. Sintering temperature dependencies of the relaxation times and characteristic frequencies of positron-electron annihilation processes have been obtained. It is shown that position of large maxima on the frequency dependencies of imaginary part corresponds to fast average relaxation lifetime representing the most intensive interaction process of positrons with small cavity traps in solids.

Spacer capture and integration by a type I-F Cas1-Cas2-3 CRISPR adaptation complex.

Science.gov (United States)

Fagerlund, Robert D; Wilkinson, Max E; Klykov, Oleg; Barendregt, Arjan; Pearce, F Grant; Kieper, Sebastian N; Maxwell, Howard W R; Capolupo, Angela; Heck, Albert J R; Krause, Kurt L; Bostina, Mihnea; Scheltema, Richard A; Staals, Raymond H J; Fineran, Peter C

2017-06-27

CRISPR-Cas adaptive immune systems capture DNA fragments from invading bacteriophages and plasmids and integrate them as spacers into bacterial CRISPR arrays. In type I-E and II-A CRISPR-Cas systems, this adaptation process is driven by Cas1-Cas2 complexes. Type I-F systems, however, contain a unique fusion of Cas2, with the type I effector helicase and nuclease for invader destruction, Cas3. By using biochemical, structural, and biophysical methods, we present a structural model of the 400-kDa Cas1 4 -Cas2-3 2 complex from Pectobacterium atrosepticum with bound protospacer substrate DNA. Two Cas1 dimers assemble on a Cas2 domain dimeric core, which is flanked by two Cas3 domains forming a groove where the protospacer binds to Cas1-Cas2. We developed a sensitive in vitro assay and demonstrated that Cas1-Cas2-3 catalyzed spacer integration into CRISPR arrays. The integrase domain of Cas1 was necessary, whereas integration was independent of the helicase or nuclease activities of Cas3. Integration required at least partially duplex protospacers with free 3'-OH groups, and leader-proximal integration was stimulated by integration host factor. In a coupled capture and integration assay, Cas1-Cas2-3 processed and integrated protospacers independent of Cas3 activity. These results provide insight into the structure of protospacer-bound type I Cas1-Cas2-3 adaptation complexes and their integration mechanism.

Integrated all optical transmodulator circuits with non-linear gain elements and tunable optical fibers

NARCIS (Netherlands)

Kuindersma, P.I.; Leijtens, X.J.M.; Zantvoort, van J.H.C.; Waardt, de H.

2012-01-01

We characterize integrated InP circuits for high speed ‘all-optical’ signal processing. Single chip circuits act as optical transistors. Transmodulation is performed by non-linear gain sections. Integrated tunable filters give signal equalization in time domain.

Frequency domain analysis of lightning protection using four lightning protection rods

Directory of Open Access Journals (Sweden)

Javor Vesna

2008-01-01

Full Text Available In this paper the lightning discharge channel is modeled as a vertical monopole antenna excited by a pulse generator at its base. The lightning electromagnetic field of a nearby lightning discharge in the case of lightning protection using four vertical lightning protection rods was determined in the frequency domain. Unknown current distributions were determined by numerical solving of a system of integral equations of two potentials using the Point Matching Method and polynomial approximation of the current distributions. The influence of the real ground, treated as homogeneous loss half-space of known electrical parameters, expressed through a Sommerfeld integral kernel, was modeled using a new Two-image approximation which gives good results in both near and far fields.

A Systems Approach to Biometrics in the Military Domain.

Science.gov (United States)

Wilson, Lauren; Gahan, Michelle; Lennard, Chris; Robertson, James

2018-02-21

Forensic biometrics is the application of forensic science principles to physical and behavioral characteristics. Forensic biometrics is a secondary sub-system in the forensic science "system of systems," which describes forensic science as a sub-system in the larger criminal justice, law enforcement, intelligence, and military system. The purpose of this paper is to discuss biometrics in the military domain and integration into the wider forensic science system of systems. The holistic system thinking methodology was applied to the U.S. biometric system to map it to the system of systems framework. The U.S. biometric system is used as a case study to help guide other countries to develop military biometric systems that are integrated and interoperable at the whole-of-government level. The aim is to provide the system of systems framework for agencies to consider for proactive design of biometric systems. © 2018 American Academy of Forensic Sciences.

Methods for enhancing numerical integration

International Nuclear Information System (INIS)

Doncker, Elise de

2003-01-01

We give a survey of common strategies for numerical integration (adaptive, Monte-Carlo, Quasi-Monte Carlo), and attempt to delineate their realm of applicability. The inherent accuracy and error bounds for basic integration methods are given via such measures as the degree of precision of cubature rules, the index of a family of lattice rules, and the discrepancy of uniformly distributed point sets. Strategies incorporating these basic methods often use paradigms to reduce the error by, e.g., increasing the number of points in the domain or decreasing the mesh size, locally or uniformly. For these processes the order of convergence of the strategy is determined by the asymptotic behavior of the error, and may be too slow in practice for the type of problem at hand. For certain problem classes we may be able to improve the effectiveness of the method or strategy by such techniques as transformations, absorbing a difficult part of the integrand into a weight function, suitable partitioning of the domain, transformations and extrapolation or convergence acceleration. Situations warranting the use of these techniques (possibly in an 'automated' way) are described and illustrated by sample applications

Interoperable domain models: the ISO land administration domain model LADM and its external classes

CSIR Research Space (South Africa)

Lemmen, CHJ

2011-09-01

Full Text Available This paper provides a brief overview of one of the first spatial domain standards: a standard for the domain of Land Administration (LA). This standard is in the draft stage of development now (May 2011). The development of domain standards is a...

Development of a three dimensional elastic plastic analysis system for the integrity evaluation of nuclear power plant components

International Nuclear Information System (INIS)

Huh, Nam Su; Im, Chang Ju; Kim, Young Jin; Pyo, Chang Ryul; Park, Chi Yong

2000-01-01

In order to evaluate the integrity of nuclear power plant components, the analysis based on fracture mechanics is crucial. For this purpose, finite element method is popularly used to obtain J-integral. However, it is time consuming to design the finite element model of a cracked structure. Also, the J-integral should by verified by alternative methods since it may differ depending on the calculation method. The objective of this paper is to develop a three-dimensional elastic-plastic J-integral analysis system which is named as EPAS program. The EPAS program consists of an automatic mesh generator for a through-wall crack and a surface crack, a solver based on ABAQUS program, and a J-integral calculation program which provides DI (Domain Integral) and EDI (Equivalent Domain Integral) based J-integral calculation. Using the EPAS program, an optimized finite element model for a cracked structure can be generated and corresponding J-integral can be obtained subsequently

Testing an integral conceptual model of frailty.

Science.gov (United States)

Gobbens, Robbert J; van Assen, Marcel A; Luijkx, Katrien G; Schols, Jos M

2012-09-01

This paper is a report of a study conducted to test three hypotheses derived from an integral conceptual model of frailty.   The integral model of frailty describes the pathway from life-course determinants to frailty to adverse outcomes. The model assumes that life-course determinants and the three domains of frailty (physical, psychological, social) affect adverse outcomes, the effect of disease(s) on adverse outcomes is mediated by frailty, and the effect of frailty on adverse outcomes depends on the life-course determinants. In June 2008 a questionnaire was sent to a sample of community-dwelling people, aged 75 years and older (n = 213). Life-course determinants and frailty were assessed using the Tilburg frailty indicator. Adverse outcomes were measured using the Groningen activity restriction scale, the WHOQOL-BREF and questions regarding healthcare utilization. The effect of seven self-reported chronic diseases was examined. Life-course determinants, chronic disease(s), and frailty together explain a moderate to large part of the variance of the seven continuous adverse outcomes (26-57%). All these predictors together explained a significant part of each of the five dichotomous adverse outcomes. The effect of chronic disease(s) on all 12 adverse outcomes was mediated at least partly by frailty. The effect of frailty domains on adverse outcomes did not depend on life-course determinants. Our finding that the adverse outcomes are differently and uniquely affected by the three domains of frailty (physical, psychological, social), and life-course determinants and disease(s), emphasizes the importance of an integral conceptual model of frailty. © 2011 Blackwell Publishing Ltd.

Multifunctionalities driven by ferroic domains

Science.gov (United States)

Yang, J. C.; Huang, Y. L.; He, Q.; Chu, Y. H.

2014-08-01

Considerable attention has been paid to ferroic systems in pursuit of advanced applications in past decades. Most recently, the emergence and development of multiferroics, which exhibit the coexistence of different ferroic natures, has offered a new route to create functionalities in the system. In this manuscript, we step from domain engineering to explore a roadmap for discovering intriguing phenomena and multifunctionalities driven by periodic domain patters. As-grown periodic domains, offering exotic order parameters, periodic local perturbations and the capability of tailoring local spin, charge, orbital and lattice degrees of freedom, are introduced as modeling templates for fundamental studies and novel applications. We discuss related significant findings on ferroic domain, nanoscopic domain walls, and conjunct heterostructures based on the well-organized domain patterns, and end with future prospects and challenges in the field.

Text Processing of Domain-Related Information for Individuals with High and Low Domain Knowledge.

Science.gov (United States)

Spilich, George J.; And Others

1979-01-01

The way in which previously acquired knowledge affects the processing on new domain-related information was investigated. Text processing was studied in two groups differing in knowledge of the domain of baseball. A knowledge structure for the domain was constructed, and text propositions were classified. (SW)

Engineering planetary exploration systems : Integrating novel technologies and the human element using work domain analysis

NARCIS (Netherlands)

Baker, C.; Naikar, N.; Neerincx, M.

2008-01-01

The realisation of sustainable space exploration and utilisation requires not only the development of novel concepts and technologies, but also their successful integration. Hardware, software, and the human element must be integrated effectively to make the dream for which these technologies were

Functional interchangeability of late domains, late domain cofactors and ubiquitin in viral budding.

Directory of Open Access Journals (Sweden)

Maria Zhadina

2010-10-01

Full Text Available The membrane scission event that separates nascent enveloped virions from host cell membranes often requires the ESCRT pathway, which can be engaged through the action of peptide motifs, termed late (L- domains, in viral proteins. Viral PTAP and YPDL-like L-domains bind directly to the ESCRT-I and ALIX components of the ESCRT pathway, while PPxY motifs bind Nedd4-like, HECT-domain containing, ubiquitin ligases (e.g. WWP1. It has been unclear precisely how ubiquitin ligase recruitment ultimately leads to particle release. Here, using a lysine-free viral Gag protein derived from the prototypic foamy virus (PFV, where attachment of ubiquitin to Gag can be controlled, we show that several different HECT domains can replace the WWP1 HECT domain in chimeric ubiquitin ligases and drive budding. Moreover, artificial recruitment of isolated HECT domains to Gag is sufficient to stimulate budding. Conversely, the HECT domain becomes dispensable if the other domains of WWP1 are directly fused to an ESCRT-1 protein. In each case where budding is driven by a HECT domain, its catalytic activity is essential, but Gag ubiquitination is dispensable, suggesting that ubiquitin ligation to trans-acting proteins drives budding. Paradoxically, however, we also demonstrate that direct fusion of a ubiquitin moiety to the C-terminus of PFV Gag can also promote budding, suggesting that ubiquitination of Gag can substitute for ubiquitination of trans-acting proteins. Depletion of Tsg101 and ALIX inhibits budding that is dependent on ubiquitin that is fused to Gag, or ligated to trans-acting proteins through the action of a PPxY motif. These studies underscore the flexibility in the ways that the ESCRT pathway can be engaged, and suggest a model in which the identity of the protein to which ubiquitin is attached is not critical for subsequent recruitment of ubiquitin-binding components of the ESCRT pathway and viral budding to proceed.

THE IMPORTANCE OF THE IMPLEMENTATION OF INTEGRATED INFORMATION SYSTEMS IN THE RESTRUCTURING AND EUROPEAN INTEGRATION PROCESS OF ORGANIZATIONS

Directory of Open Access Journals (Sweden)

Steliac Nela

2010-12-01

Full Text Available Many of the organizations that are part of the public and private domain in Romania have reached the stage in which the existing information systems can no longer comply with the requests of users. Therefore, we are compelled by necessity to use integrated information systems which should be able to control all kinds of data and to allow access to them, to ensure the coherence and consistency of the stored information. Managers must be aware of the importance of the implementation of integrated information systems in the background restructuring of the organization, which can thus become consistent and competitive with the European Union one, so the integration process becomes a real and possible one.

Translation, adaptation and validation of "Community Integration Questionnaire"

Directory of Open Access Journals (Sweden)

Helena Maria Silveira Fraga-Maia

2015-05-01

Full Text Available Objective: To translate, adapt, and validate the "Community Integration Questionnaire (CIQ," a tool that evaluates community integration after traumatic brain injury (TBI.Methods: A study of 61 TBI survivors was carried out. The appraisal of the measurement equivalence was based on a reliability assessment by estimating inter-rater agreement, item-scale correlation and internal consistency of CIQ scales, concurrent validity, and construct validity.Results: Inter-rater agreement ranged from substantial to almost perfect. The item-scale correlations were generally higher between the items and their respective domains, whereas the intra-class correlation coefficients were high for both the overall scale and the CIQ domains. The correlation between the CIQ and Disability Rating Scale (DRS, the Extended Glasgow Outcome Scale (GOSE, and the Rancho Los Amigos Level of Cognitive Functioning Scale (RLA reached values considered satisfactory. However, the factor analysis generated four factors (dimensions that did not correspond with the dimensional structure of the original tool.Conclusion: The resulting tool herein may be useful in globally assessing community integration after TBI in the Brazilian context, at least until new CIQ psychometric assessment studies are developed with larger samples.

Efficient odd straight medium chain free fatty acid production by metabolically engineered Escherichia coli.

Science.gov (United States)

Wu, Hui; San, Ka-Yiu

2014-11-01

Free fatty acids (FFAs) can be used as precursors for the production of biofuels or chemicals. Different composition of FFAs will be useful for further modification of the biofuel/biochemical quality. Microbial biosynthesis of even chain FFAs can be achieved by introducing an acyl-acyl carrier protein thioesterase gene into E. coli. In this study, odd straight medium chain FFAs production was investigated by using metabolic engineered E. coli carrying acyl-ACP thioesterase (TE, Ricinus communis), propionyl-CoA synthase (Salmonella enterica), and β-ketoacyl-acyl carrier protein synthase III (four different sources) with supplement of extracellular propionate. By using these metabolically engineered E. coli, significant quantity of C13 and C15 odd straight-chain FFAs could be produced from glucose and propionate. The highest concentration of total odd straight chain FFAs attained was 1205 mg/L by the strain HWK201 (pXZ18, pBHE2), and 85% of the odd straight chain FFAs was C15. However, the highest percentage of odd straight chain FFAs was achieved by the strain HWK201 (pXZ18, pBHE3) of 83.2% at 48 h. This strategy was also applied successfully in strains carrying different TE, such as the medium length acyl-ACP thioesterase gene from Umbellularia californica. C11 and C13 became the major odd straight-chain FFAs. © 2014 Wiley Periodicals, Inc.

S3QL: A distributed domain specific language for controlled semantic integration of life sciences data

Directory of Open Access Journals (Sweden)

de Lencastre Hermínia

2011-07-01

Full Text Available Abstract Background The value and usefulness of data increases when it is explicitly interlinked with related data. This is the core principle of Linked Data. For life sciences researchers, harnessing the power of Linked Data to improve biological discovery is still challenged by a need to keep pace with rapidly evolving domains and requirements for collaboration and control as well as with the reference semantic web ontologies and standards. Knowledge organization systems (KOSs can provide an abstraction for publishing biological discoveries as Linked Data without complicating transactions with contextual minutia such as provenance and access control. We have previously described the Simple Sloppy Semantic Database (S3DB as an efficient model for creating knowledge organization systems using Linked Data best practices with explicit distinction between domain and instantiation and support for a permission control mechanism that automatically migrates between the two. In this report we present a domain specific language, the S3DB query language (S3QL, to operate on its underlying core model and facilitate management of Linked Data. Results Reflecting the data driven nature of our approach, S3QL has been implemented as an application programming interface for S3DB systems hosting biomedical data, and its syntax was subsequently generalized beyond the S3DB core model. This achievement is illustrated with the assembly of an S3QL query to manage entities from the Simple Knowledge Organization System. The illustrative use cases include gastrointestinal clinical trials, genomic characterization of cancer by The Cancer Genome Atlas (TCGA and molecular epidemiology of infectious diseases. Conclusions S3QL was found to provide a convenient mechanism to represent context for interoperation between public and private datasets hosted at biomedical research institutions and linked data formalisms.

Mechanical performances of lead-free solder joint connections with applications in the aerospace domain